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source: palm/trunk/SCRIPTS/palmrun @ 3668

Last change on this file since 3668 was 3665, checked in by raasch, 6 years ago
dummy statements added to avoid compiler warnings about unused variables, unused variables removed, ssh-call for submitting batch jobs on remote systems modified again to avoid output of login messages on specific systems
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.0 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 3665 2019-01-10 08:28:24Z maronga $
[3665]	29	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	30	# of login messages on specific systems
	31	#
	32	# 3574 2018-11-28 13:14:39Z raasch
[3574]	33	# syntax-error in last commit fixed
	34	#
	35	# 3573 2018-11-28 13:03:44Z raasch
[3573]	36	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	37	# removed,
	38	# r3570 reverted
	39	#
	40	# 3570 2018-11-27 17:44:21Z kanani
[3570]	41	# Rename job-id by run_id
	42	#
	43	# 3555 2018-11-22 13:50:37Z raasch
[3555]	44	# sed-command to remove repeated space-characters replaced by tr-command, to
	45	# guarantee mac compatible
	46	#
	47	# 3549 2018-11-21 15:44:44Z raasch
[3549]	48	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	49	# of login messages on specific systems
	50	#
	51	# 3534 2018-11-19 15:35:16Z raasch
[3534]	52	# batch_scp for sending back the job protocol file is called via login-node if
	53	# a login-node has been set in the config-file
	54	# ssh-calls rearranged to avoid output of system/user-profile messages
	55	#
	56	# 3505 2018-11-08 09:14:30Z raasch
[3505]	57	# job folders are created in case that they do not exist
	58	#
	59	# 3455 2018-10-30 14:12:31Z raasch
[3455]	60	# options -h and -d renamed -c and -r, respectively
	61	#
	62	# 3402 2018-10-23 11:49:24Z knoop
[3346]	63	# job_id is set for compatibility reasons with older versions of config files
	64	#
	65	# 3313 2018-10-06 15:22:48Z knoop
[3294]	66	# more detailed error message for outdated fileconnection file
	67	#
	68	# 3236 2018-09-10 09:07:06Z raasch
[3236]	69	# warning issued in case of file connection file version mismatch,
	70	# host_configuration renamed configuration_identifier,
	71	# "host identifier" in header output renamed "config. identifier",
	72	# jobname renamed run_identifier,
	73	# run_id renamed run_id_number
	74	# job_id renamed run_id
	75	# option -r renamed -i
	76	#
	77	# 3151 2018-07-19 08:45:38Z raasch
[3151]	78	# removed additional listing of files to be compiled, print PALM code revision
	79	# in header
	80	#
	81	# 3132 2018-07-16 11:44:58Z raasch
[3132]	82	# create consistent error messages in case of failed restarts,
	83	# check existence of remote job catalog
	84	#
	85	# 3043 2018-05-25 10:47:54Z raasch
[3043]	86	# check for setting of fast_io_catalog
	87	#
	88	# 3033 2018-05-23 15:26:19Z raasch
[3025]	89	# -T option not required for interactive runs (tasks per node =
	90	# total number of cores is assumed as default, if option is not given),
	91	# reformatting of a few messages,
	92	# bugfix: destination output directory is created if attribute "pe" is set in
	93	# .palm.iofiles
	94	#
	95	# 2718 2018-01-02 08:49:38Z maronga
[2993]	96	# bugfix of r2990
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2990]	99	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	100	# not in the working directory from where palmrun is called
	101	#
	102	# 2718 2018-01-02 08:49:38Z maronga
[2957]	103	# svfout in the activation string will be replaced now by svfin in case of
	104	# automatic restarts
	105	#
	106	# 2718 2018-01-02 08:49:38Z maronga
[2906]	107	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	108	# the possible output or input of sky view factors
	109	#
	110	# 2718 2018-01-02 08:49:38Z maronga
[2834]	111	# "fname" renamed to "jobname"
	112	#
	113	# 2718 2018-01-02 08:49:38Z maronga
[2799]	114	# parameters are allowed in output commands (OC:)
	115	#
	116	# 2718 2018-01-02 08:49:38Z maronga
[2789]	117	# bugfix: exit if no queue has been given neither with option -q nor in the
	118	# configuration file
	119	#
	120	# 2718 2018-01-02 08:49:38Z maronga
[2762]	121	# file connection file from trunk/SCRIPTS is taken by default
	122	#
	123	# 2718 2018-01-02 08:49:38Z maronga
[2716]	124	# Corrected "Former revisions" section
	125	#
	126	# 2696 2017-12-14 17:12:51Z kanani
	127	# Change in file header (GPL part)
	128	#
	129	# 2693 2017-12-13 12:33:49Z raasch
[2693]	130	# replacement of variables given by {{<variable>}} in configuration file is now
	131	# done in a more general way, variable names are written in small letters
	132	#
	133	# 2670 2017-12-06 16:32:19Z raasch
[2670]	134	# test printouts removed
	135	#
	136	# 2669 2017-12-06 16:03:27Z raasch
[2669]	137	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	138	# removed,
	139	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	140	# files,
	141	# informative messages in case of missing optional input files shortened
	142	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	143	#
	144	# 2638 2017-11-23 12:44:23Z raasch
[2610]	145	# use of wildcards in file connection statements enabled
	146	#
	147	# 2605 2017-11-09 15:31:46Z raasch
[2605]	148	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	149	# will not be sent with the job file any more, but copied into the
[2610]	150	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	151	#
	152	# 2600 2017-11-01 14:11:20Z raasch
[2600]	153	# cycle numbers are made three digits wide
	154	#
	155	# 2566 2017-10-20 08:50:47Z raasch
[2566]	156	# execute command for combine_plot_fields added
	157	# "TEMPDIR" renamed "tempdir"
	158	# temporary working directory for local batch jobs is created immediately within
	159	# the user's palmrun call, due to a requirement of the "grid engine" batch
	160	# system, where the working directory is given with batch directive -wd and must
	161	# already exist when the job is submitted,
	162	# informative messages in non-trace mode reduced and partly reformatted
	163	#
	164	# 2551 2017-10-18 07:25:11Z raasch
[2551]	165	# TEMPDIR added as replacement string to be used in batch directives
	166	#
	167	# 2512 2017-10-04 08:26:59Z raasch
[2507]	168	# bugfix for determining cycle numbers of NetCDF input files
	169	#
	170	# 2506 2017-09-29 08:30:37Z raasch
[2506]	171	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	172	# host configuration added to SOURCES_FOR_RUN_... folder name
	173	# host_identifier renamed host_configuration
	174	# option -W added to allow for job dependencies
	175	#
	176	# 2501 2017-09-26 11:41:55Z raasch
[2501]	177	# default value for number of cores (option -X) set to 1
	178	# bugfix for mechanism which overwrites configuration file settings with values
	179	# provided by palmrun options
	180	#
	181	# 2499 2017-09-22 16:47:58Z kanani
[2499]	182	# option -h named configuration identifier
	183	#
	184	# 2480 2017-09-19 06:24:14Z maronga
[2480]	185	# bugfix for last revision
	186	#
	187	# 2479 2017-09-19 06:12:16Z raasch
[2479]	188	# option -A (project account number) added
	189	#
	190	# 2422 2017-09-08 08:25:41Z raasch
[2410]	191	# initial revision
[2380]	192	#
	193	#--------------------------------------------------------------------------------#
	194	# palmrun - script for running PALM jobs on local and remote hosts
	195	#--------------------------------------------------------------------------------#
	196
	197
	198
	199	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	200
	201	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	202	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	203	# (TOO MANY ARGUMENTS - PROBLEM)
	204	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	205
[2610]	206	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	207	typeset -i nr_of_output_files=0
[2380]	208	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	209	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	210	# SCRIPT-OPTION ARGUMENTS
	211	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	212	typeset -i icycle inode ival maxcycle mpi_tasks
	213	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	214
	215	activation_string_list=""
	216	AddFilenames=""
	217	combine_plot_fields=true
	218	compiler_name=""
	219	compiler_name_ser=""
	220	compiler_options=""
[3236]	221	configuration_identifier="default"
[2501]	222	cores=1
[2380]	223	cores_atmos=0
	224	cores_ocean=0
	225	coupled_dist=""
	226	cpp_options=""
	227	cpumax=0
[2506]	228	create_batch_job=false
[2380]	229	create_jobfile_only=false
	230	create_remote_batch_job=false
	231	dashes=" ----------------------------------------------------------------------------"
	232	defaultqueue=""
[2506]	233	delete_temporary_catalog=true
[2380]	234	do_compile=true
	235	do_trace=false
	236	executable=""
	237	execute_command=""
	238	execution_error=false
[2762]	239	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	240	global_revision=""
	241	hostfile=""
	242	hp=""
	243	keep_data_from_previous_run=false
	244	link_local_input=false
	245	link_local_output=false
[2388]	246	linker_options=""
[2385]	247	local_jobcatalog=""
[2380]	248	locat=normal
	249	makefile=""
	250	max_par_io_str=""
	251	prc=$0
	252	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	253	do
	254	prc=`echo $prc \| cut -f2- -d"/"`
	255	done
	256	module_calls=""
[2506]	257	palmrun_memory=""
[2380]	258	palmrun_script_name=$prc
	259	openmp=false
[2506]	260	previous_job=""
[2479]	261	project_account=""
[2380]	262	queue=none
[2906]	263	read_svf=""
[2380]	264	restart_run=false
	265	return_address=""
[2385]	266	remote_jobcatalog=""
[2380]	267	remote_username=""
	268	running_in_batch_mode=false
[3313]	269	running_in_test_mode=false
[2380]	270	run_coupled_model=false
	271	run_id=""
[3236]	272	run_id_number=""
	273	run_identifier=test
[2380]	274	silent=false
	275	source_list=""
	276	source_path=""
[2501]	277	tasks_per_node=0
[2380]	278	threads_per_task=1
	279	transfer_problems=false
[2384]	280	user_source_path=""
[2506]	281	use_existing_sources_folder=""
[2380]	282	use_openmp=false
[3033]	283	version="palmrun 1.0 Rev$Rev: 3665 $"
[2380]	284	working_directory=`pwd`
	285	write_binary=""
[2906]	286	write_svf=""
[2380]	287
	288
	289	# ERROR HANDLING IN CASE OF EXIT
[2404]	290	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	291	then
	292
	293	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	294	(( i = 0 ))
	295	while (( i < iec ))
	296	do
	297	(( i = i + 1 ))
	298	printf "\n *** Execution of ERROR-command:\n"
	299	printf " >>> ${err_command[$i]}\n"
	300	eval ${err_command[$i]}
	301	done
[2566]	302	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	303	printf "\n\n+++ palmrun crashed \n\n"
	304	exit 1
	305	elif [[ $locat != normal ]]
[2380]	306	then
[3312]	307	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	308	printf "\n+++ palmrun killed by \"^C\" \n\n"
	309	exit 2
	310	else
[2566]	311	printf "\n --> palmrun finished\n\n"
[3312]	312	exit 0
[2380]	313	fi' exit
	314
	315
	316	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	317	trap 'locat=control_c
	318	exit 1
[2380]	319	' 2
	320
	321
	322	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	323	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	324	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]	325	do
	326	case $option in
	327	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	328	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	329	(b) create_batch_job=true; prc="$prc -b";;
	330	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	331	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	332	(C) restart_run=true; prc="$prc -C";;
	333	(F) create_jobfile_only=true;;
	334	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	335	(i) run_id_number=$OPTARG;;
[2380]	336	(j) running_in_batch_mode=true;;
	337	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	338	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	339	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	340	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	341	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	342	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	343	(R) return_address=$OPTARG;;
	344	(s) source_list=$OPTARG;;
[2501]	345	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	346	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	347	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	348	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	349	(v) silent=true; prc="$prc -v";;
[2506]	350	(V) use_existing_sources_folder="-V";;
[2380]	351	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	352	(W) previous_job=$OPTARG;;
[2380]	353	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	354	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	355	(y) ocean_file_appendix=true; prc="$prc -y";;
	356	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	357	(z) running_in_test_mode=true;;
[2380]	358	(Z) combine_plot_fields=false; prc="$prc -Z";;
	359	(\?) printf "\n +++ unknown option $OPTARG \n"
	360	printf "\n --> type \"$0 ?\" for available options \n"
	361	locat=parameter;exit;;
	362	esac
	363	done
	364
	365
	366	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	367	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	368	(( to_shift = $OPTIND - 1 ))
	369	shift $to_shift
	370
	371	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	372	if [[ "$1" = "?" ]]
	373	then
	374	(printf "\n *** Description of available palmrun options:\n"
	375	printf "\n Option Description Default-Value"
	376	printf "\n -a activation string list \"\" "
[2479]	377	printf "\n -A project account number ---"
[2380]	378	printf "\n -b batch-job on local machine ---"
	379	printf "\n -B do not delete temporary directory at end ---"
[3455]	380	printf "\n -c configuration identifier \"default\" "
[2380]	381	printf "\n -F create batch job file only ---"
	382	printf "\n -k keep data from previous run"
	383	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	384	printf "\n -M Makefile name Makefile"
	385	printf "\n -O threads per openMP task ---"
	386	printf "\n -q queue \"$queue\" "
[3455]	387	printf "\n -r run identifier test"
[2380]	388	printf "\n -s filenames of routines to be compiled \"\" "
	389	printf "\n must end with .f, .f90, .F, or .c !"
	390	printf "\n use \"..\" for more than one file and wildcards"
	391	printf "\n -s LM compiles all locally modified files"
	392	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	393	printf "\n -T tasks per node ---"
[2380]	394	printf "\n -u username on remote machine \"\" "
	395	printf "\n -v no prompt for confirmation ---"
[2506]	396	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	397	printf "\n -w maximum parallel io streams as given by -X"
[2506]	398	printf "\n -W name of job to wait for ---"
[2380]	399	printf "\n -x tracing of palmrun for debug purposes ---"
	400	printf "\n -X # of processors (on parallel machines) 1"
	401	printf "\n -y add appendix \"_O\" to all local output"
	402	printf "\n files (ocean precursor runs followed by"
	403	printf "\n coupled atmosphere-ocean runs) ---"
	404	printf "\n -Y run coupled model, \"#1 #2\" with"
	405	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	406	printf "\n -Z skip combine_plot_fields at the end of "
	407	printf "\n the simulation ---"
	408	printf "\n "
	409	printf "\n Possible values of positional parameter <modus>:"
	410	printf "\n \"?\" - this outline \n\n") \| more
	411	exit
	412	elif [[ "$1" != "" ]]
	413	then
	414	printf "\n +++ positional parameter $1 unknown \n"
	415	locat=parameter; exit
	416	fi
	417
	418
	419
	420	# SHORT STARTING MESSAGE
	421	printf "\n*** $version "
	422	printf "\n will be executed. Please wait ..."
	423
	424
[2506]	425	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	426	config_file=.palm.config.$configuration_identifier
	427	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	428
	429
	430	# CHECK, IF CONFIGURATION FILE EXISTS
	431	if [[ ! -f $config_file ]]
	432	then
	433	printf "\n\n +++ configuration file: "
	434	printf "\n $config_file"
	435	printf "\n does not exist"
	436	locat=connect; exit
	437	fi
	438
	439
[2762]	440	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	441	if [[ -f .palm.iofiles ]]
	442	then
[3236]	443
	444	# CHECK VERSION MISMATCH
[3573]	445	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	446	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	447	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	448	then
	449	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	450	then
	451	printf "\n\n +++ WARNING: A file connection file has been found in your"
	452	printf "\n working directory, but its revision does not match"
	453	printf "\n the revision of the default (trunk) version."
[3294]	454	printf "\n You may need to update your connection file"
	455	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	456	fi
	457	fi
	458
[2762]	459	fileconnection_file=.palm.iofiles
[3236]	460
[2762]	461	fi
	462
	463
[2380]	464	# CHECK, IF FILE CONNECTION FILE EXISTS
	465	if [[ ! -f $fileconnection_file ]]
	466	then
	467	printf "\n\n +++ file connection file: "
	468	printf "\n $fileconnection_file"
	469	printf "\n does not exist"
	470	locat=connect; exit
	471	fi
	472
	473
[2404]	474	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	475	if [[ "$activation_string_list" = "" ]]
	476	then
	477	printf "\n\n +++ no activation string list given: "
	478	printf "\n please set palmrun option \"-a\" "
	479	locat=palmrun_option; exit
	480	fi
	481
	482
	483	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	484	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	485	then
	486	write_binary=true
	487	else
	488	write_binary=false
	489	fi
	490
[2906]	491	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	492	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	493	then
	494	write_svf=true
	495	else
	496	write_svf=false
	497	fi
[2404]	498
[2906]	499	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	500	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	501	then
	502	read_svf=true
	503	else
	504	read_svf=false
	505	fi
	506
	507
[2380]	508	# READ AND EVALUATE THE CONFIGURATION-FILE
	509	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	510
	511	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	512	while read line
	513	do
	514
	515	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	516	eval line=\"$line\"
	517
	518
	519	# INTERPRET THE LINE
	520	if [[ "$(echo $line)" = "" ]]
	521	then
	522
	523	# EMPTY LINE, NO ACTION
	524	continue
	525
	526	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	527	then
	528
	529	# LINE IS A COMMENT LINE
	530	continue
	531
	532	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	533	then
	534
	535	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	536	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	537	value=`echo $line \| cut -d" " -s -f2-`
	538
	539
	540	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	541	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	542	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	543	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	544	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	545	# CONFIGURATION-FILE.
	546	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	547	then
	548	eval export $var="\$value"
	549
	550	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	551	if [[ $do_trace = true ]]
	552	then
	553	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	554	fi
	555	fi
	556
	557	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	558	then
	559
	560	# LINE DEFINES BATCH-DIRECTIVE
	561	(( ibd = ibd + 1 ))
	562	line=$(echo $line \| cut -c4-)
	563	batch_directive[$ibd]="$line"
	564
	565	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	566	then
	567
	568	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	569	# REMOTE TO A LOCAL HOST
	570	(( ibdt = ibdt + 1 ))
	571	line=$(echo $line \| cut -c5-)
	572	batch_directive_transfer[$ibdt]="$line"
	573
	574	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	575	then
	576
	577	# LINE DEFINES ERROR-COMMAND
	578	(( iec = iec + 1 ))
	579	line=$(echo $line \| cut -c4-)
	580	err_command[$iec]="$line"
	581
	582	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	583	then
	584
	585	# LINE DEFINES INPUT-COMMAND
	586	(( iic = iic + 1 ))
	587	line=$(echo $line \| cut -c4-)
	588	in_command[$iic]="$line"
	589
	590	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	591	then
	592
	593	# LINE DEFINES OUTPUT-COMMAND
	594	(( ioc = ioc + 1 ))
	595	line=$(echo $line \| cut -c4-)
	596	out_command[$ioc]="$line"
	597
	598	else
	599
	600	# SKIP ALL OTHER LINES
	601	continue
	602
	603	fi
	604
	605	done < $config_file
	606
	607
	608	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	609	if [[ "$fast_io_catalog" = "" ]]
	610	then
	611	printf "\n +++ no fast_io_catalog found in $config_file"
	612	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	613	locat=config_file; exit
	614	fi
[2380]	615	if [[ "$compiler_name" = "" ]]
	616	then
	617	printf "\n +++ no compiler name found in $config_file"
	618	printf "\n Please add line \"compiler_name ...\" to that file."
	619	locat=config_file; exit
	620	fi
	621	if [[ "$compiler_name_ser" = "" ]]
	622	then
	623	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	624	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	625	locat=config_file; exit
	626	fi
	627	if [[ "$compiler_options" = "" ]]
	628	then
	629	printf "\n +++ no compiler options found in $config_file"
	630	printf "\n Please add line \"compiler_options ...\" to that file."
	631	locat=config_file; exit
	632	fi
[2388]	633	if [[ "$linker_options" = "" ]]
[2380]	634	then
[2388]	635	printf "\n +++ no linker options found in $config_file"
	636	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	637	locat=config_file; exit
	638	fi
	639	if [[ "$execute_command" = "" ]]
	640	then
	641	printf "\n +++ no execute command found in $config_file"
	642	printf "\n Please add line \"execute_command ...\" to that file."
	643	locat=config_file; exit
	644	fi
	645
	646	if [[ "$hostfile" != "" ]]
	647	then
	648	if [[ $hostfile != auto && ! -f $hostfile ]]
	649	then
	650	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	651	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	652	locat=config_file; exit
	653	fi
	654	fi
	655
	656
	657	# DETERMINE THE CALL STATUS
	658	if [[ "$return_address" != "" ]]
	659	then
	660
	661	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	662	# BATCH MODE AND ...
	663	running_on_remote=true
	664
	665	else
	666
	667	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	668	if [[ "$remote_ip" != "" ]]
	669	then
	670
	671	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	672	create_remote_batch_job=true
	673
[3132]	674	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	675	if [[ "$remote_jobcatalog" = "" ]]
	676	then
	677	printf "\n +++ no remote jobcatalog found in $config_file"
	678	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	679	locat=config_file; exit
	680	fi
	681
	682
[2380]	683	fi
	684	running_on_remote=false
	685	fi
	686
	687
	688
	689	# READ AND EVALUATE THE I/O-FILE LIST
	690	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	691
	692	# READ THE FILE CONNECTION FILE LINE BY LINE
	693	while read line
	694	do
	695
[2669]	696	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	697	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	698	line=`echo "$line" \| tr -s " "`
[2380]	699
	700	# INTERPRET THE LINE
	701	if [[ "$(echo $line)" = "" ]]
	702	then
	703	# EMPTY LINE, NO ACTION
	704	continue
	705
	706	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	707	then
	708
	709	# LINE IS A COMMENT LINE
	710	true
	711
	712	else
	713
	714	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	715	# s2a: in/out - field
[2669]	716	# s2b: action - field (optional)
	717	s1=`echo "$line" \| cut -d" " -f1`
	718	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	719	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	720	then
[2669]	721	s2a=$s2
[2380]	722	s2b=""
	723	else
[2669]	724	s2a=`echo $s2 \| cut -d":" -f1`
	725	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	726	fi
[2669]	727	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	728	s4=`echo "$line" \| cut -d" " -s -f4`
	729	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	730	s5=`echo "$line" \| cut -d" " -s -f5`
	731	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	732
	733
	734	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	735	# INPUT- OR OUTPUT-LIST.
	736	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	737	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	738	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	739	# IS NOT CHECKED AND STORED.
[2610]	740	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	741	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	742	then
	743	found=false
	744	for actual in $activation_string_list
	745	do
	746	for formal in $s3
	747	do
	748	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	749	done
	750	done
	751	if [[ $found = true ]]
	752	then
	753	(( iin = iin + 1 ))
[2669]	754	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	755	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	756	if [[ "$s2a" = inopt ]]
	757	then
	758	optin_pre[$iin]=yes
	759	else
	760	optin_pre[$iin]=no
	761	fi
[2605]	762
	763	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	764	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	765	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	766	then
[2610]	767	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	768	fi
	769
[2610]	770	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	771	# THE WILDCARD FROM THE ENDING
	772	if [[ "${s5: -1}" = "*" ]]
	773	then
[2669]	774	if [[ "$s2b" = "di" ]]
[2610]	775	then
	776	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	777	printf "\n see file \"$fileconnection_file\", line"
	778	printf "\n$line"
	779	locat=iofiles_file; exit
	780	fi
	781	multin[$iin]=true
	782	string=${endin_pre[$iin]}
	783	endin_pre[$iin]="${string%?}"
	784	else
	785	multin[$iin]=false
	786	fi
[2380]	787	fi
[2669]	788	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	789	then
	790	found=false
	791	for actual in $activation_string_list
	792	do
	793	for formal in $s3
	794	do
[2670]	795	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	796	done
	797	done
	798	if [[ $found = true ]]
	799	then
	800	(( iout = iout + 1 ))
[2669]	801	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	802	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	803
[2669]	804	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	805	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	806	if [[ $formal = wildcard ]]
	807	then
	808	warnout_pre[$iout]=false
	809	else
	810	warnout_pre[$iout]=true
	811	fi
	812
[2610]	813	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	814	# THE WILDCARD FROM THE LOCAL FILENAME
	815	if [[ "${s1: -1}" = "*" ]]
	816	then
[2669]	817	if [[ "$s2b" = "di" ]]
[2610]	818	then
	819	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	820	printf "\n see file \"$fileconnection_file\", line"
	821	printf "\n$line"
	822	locat=iofiles_file; exit
	823	fi
	824	multout[$iout]=true
	825	string=${localout_pre[$iout]}
	826	localout_pre[$iout]="${string%?}"
	827	else
	828	multout[$iout]=false
	829	fi
[2380]	830	fi
[2669]	831	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	832	then
[2669]	833	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	834	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	835	locat=connect; exit
	836	fi
	837	IFS="$IFSALT"
	838	fi
	839
	840	done < $fileconnection_file
	841
	842
	843
[2501]	844	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	845	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	846	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	847	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	848	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	849	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	850
	851
	852
[2380]	853	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	854	if [[ $run_coupled_model = true ]]
	855	then
	856
	857	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	858	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	859
	860	if (( $cores_ocean + $cores_atmos != $cores ))
	861	then
	862
	863	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	864	printf "\n PEs (total) : $cores"
	865	printf "\n PEs (atmosphere): $cores_atmos"
	866	printf "\n PEs (ocean) : $cores_ocean"
	867	locat=coupling; exit
	868
	869	fi
	870
	871	fi
	872
	873
	874	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	875	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	876	# FOLDER
	877	if [[ $running_in_batch_mode = true ]]
	878	then
	879
[2506]	880	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	881	then
[2506]	882	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	883	printf "\n Please check the output of the palmrun-call"
	884	printf "\n that you did on your local host."
	885	locat=SOURCES_FOR_RUN; exit
	886	fi
	887
	888	else
	889
	890	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	891	# AUTOMATIC RESTART RUN
	892	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	893	if [[ $restart_run = false ]]
	894	then
	895
	896	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	897	# THE LOCAL HOST
	898	if [[ ! -d $source_path ]]
	899	then
	900	printf "\n\n +++ source path \"$source_path\" on local host"
	901	printf "\n \"$(hostname)\" does not exist"
	902	locat=source_path; exit
	903	fi
	904
[2990]	905	rm -rf ${base_directory}/${sources_for_run_catalog}
	906	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	907
	908	if [[ "$source_list" = LM ]]
	909	then
	910
	911	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	912	source_list=""
	913	cd $source_path
	914
	915
[2512]	916	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	917	if [[ ! -d ../.svn ]]
[2380]	918	then
	919	printf "\n\n +++ source directory"
	920	printf "\n \"$source_path\" "
	921	printf "\n is not under control of \"subversion\"."
[2512]	922	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	923	fi
	924
	925
	926	# LIST ALL MODIFIED SOURCE CODE FILES
	927	Filenames=""
[2404]	928	svn status > tmp_svnstatus
[2380]	929	while read line
	930	do
	931	firstc=`echo $line \| cut -c1`
	932	if [[ $firstc = M \|\| $firstc = "?" ]]
	933	then
	934	Name=`echo "$line" \| cut -c8-`
	935	extension=`echo $Name \| cut -d. -f2`
	936	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	937	then
	938	Filenames="$Filenames "$Name
	939	fi
	940	fi
[2404]	941	done < tmp_svnstatus
	942	rm -rf tmp_svnstatus
[2380]	943
	944
	945	# COPY FILES TO SOURCES_FOR_RUN_...
	946	for filename in $Filenames
	947	do
[2990]	948	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	949	source_list=$source_list"$filename "
	950	done
	951
	952	cd - > /dev/null
	953
	954
	955	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	956	elif [[ "$source_list" != "" ]]
	957	then
	958
	959	cd $source_path
	960
	961	for filename in $source_list
	962	do
	963
	964	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	965	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	966	then
	967	printf "\n +++ source code file: $filename"
	968	printf "\n must not contain (\"/\") "
	969	locat=source; exit
	970	fi
	971
	972	if [[ ! -f $filename ]]
	973	then
	974	printf "\n +++ source code file: $filename"
	975	printf "\n does not exist"
	976	locat=source; exit
	977	else
[2990]	978	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	979	fi
	980
	981	done
	982
	983	cd - > /dev/null
	984
	985	fi
	986
	987	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	988	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	989	if [[ ! -f $makefile ]]
	990	then
	991	printf "\n +++ file \"$makefile\" does not exist"
	992	locat=make; exit
	993	else
[2990]	994	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	995	fi
	996
	997
	998	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	999	if [[ "$user_source_path" != "" ]]
[2380]	1000	then
	1001
	1002	# DOES THE DIRECTORY EXIST?
[2384]	1003	if [[ ! -d $user_source_path ]]
[2380]	1004	then
	1005
	1006	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1007	printf "\n \"$user_source_path\" "
[2380]	1008	printf "\n does not exist or is not a directory."
	1009	printf "\n No source code will be used from this directory!\n"
[2384]	1010	user_source_path=""
[2380]	1011	if [[ $silent == false ]]
	1012	then
	1013	sleep 2
	1014	fi
	1015
	1016	else
	1017
[2384]	1018	cd $user_source_path
[2380]	1019
	1020	Names=$(ls -1 *.f90 2>&1)
	1021	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1022	Names=$(ls -1 *.F90 2>&1)
	1023	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1024	Names=$(ls -1 *.F 2>&1)
	1025	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1026	Names=$(ls -1 *.f 2>&1)
	1027	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1028	Names=$(ls -1 *.c 2>&1)
	1029	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1030
	1031	cd - > /dev/null
[2990]	1032	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1033
	1034	# COPY MAKEFILE IF EXISTING
[2384]	1035	if [[ -f $user_source_path/Makefile ]]
[2380]	1036	then
	1037	printf "\n\n *** user Makefile from directory"
[2384]	1038	printf "\n \"$user_source_path\" is used \n"
[2380]	1039	if [[ $silent == false ]]
	1040	then
	1041	sleep 1
	1042	fi
[2384]	1043	cp $user_source_path/Makefile .
[2380]	1044	fi
	1045
	1046	for filename in $AddFilenames
	1047	do
	1048	if [[ -f $filename ]]
	1049	then
	1050	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1051	printf "\n source code directory \"$user_source_path\" "
[2380]	1052	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1053	printf "\n from directory \"$source_path\"."
	1054	locat=source; exit
	1055	fi
	1056
[2384]	1057	cp $user_source_path/$filename .
[2380]	1058	source_list="$source_list $filename"
	1059
	1060	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1061	if [[ $(grep -c $filename Makefile) = 0 ]]
	1062	then
	1063	printf "\n\n +++ user file \"$filename\" "
	1064	printf "\n is not listed in Makefile \n"
	1065	locat=source; exit
	1066	fi
	1067	done
	1068	cd - > /dev/null
	1069	fi
	1070	fi
	1071
	1072	# COPY CONFIGURATION FILES
[2990]	1073	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1074	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1075
	1076	# COPY SHELLSCRIPTS
[2990]	1077	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1078	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1079
	1080	fi
	1081
	1082	fi
	1083
[2605]	1084
[2380]	1085	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1086	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1087	if [[ "$global_revision" = "" ]]
	1088	then
	1089	global_revision=`svnversion $source_path 2>/dev/null`
	1090	global_revision="Rev: $global_revision"
	1091	fi
	1092
	1093
	1094	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1095	if [[ -n $cores ]]
	1096	then
	1097
	1098	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1099	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1100	if [[ $tasks_per_node = 0 ]]
[2380]	1101	then
[3025]	1102	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1103	then
	1104	printf "\n"
	1105	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1106	printf "\n set -T option or define tasks_per_node in the config file"
	1107	locat=tasks_per_node; (( iec = 0 )); exit
	1108	else
	1109	# DEFAULT FOR INTERACTIVE RUN
	1110	tasks_per_node=$cores
	1111	fi
[2380]	1112	fi
	1113
	1114	if (( cores < tasks_per_node ))
	1115	then
	1116	printf "\n"
	1117	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1118	printf "\n given values: -T $tasks_per_node -X $cores"
	1119	locat=tasks_per_node; (( iec = 0 )); exit
	1120	fi
	1121
	1122	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1123	(( mpi_tasks = cores / threads_per_task ))
	1124	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1125	(( ii = cores / tasks_per_node ))
	1126	(( remaining_cores = cores - ii * tasks_per_node ))
	1127	if (( remaining_cores > 0 ))
	1128	then
	1129	printf "\n"
	1130	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1131	printf "\n divisor of the total number of cores (option \"-X\")"
	1132	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1133	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1134	(( nodes = nodes + 1 ))
	1135	fi
	1136
	1137	fi
	1138
	1139
	1140	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1141	if [[ "$maximum_parallel_io_streams" = "" ]]
	1142	then
	1143	maximum_parallel_io_streams=$cores
	1144	fi
	1145
	1146
	1147	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1148	if [[ "$scp_port" != "" ]]
	1149	then
	1150	PORTOPT="-P $scp_port"
	1151	SSH_PORTOPT="-p $scp_port"
	1152	fi
	1153
	1154
	1155	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1156	# CONFIG-FILE
	1157	if [[ "$ssh_key" != "" ]]
	1158	then
	1159	ssh_key="-i $HOME/.ssh/$ssh_key"
	1160	fi
	1161
	1162
	1163	# SET QUEUE, IF NOT GIVEN
	1164	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1165	then
	1166
	1167	if [[ $queue = none && "$defaultqueue" = "" ]]
	1168	then
	1169	printf "\n"
	1170	printf "\n +++ no default queue given in configuration file and no queue"
	1171	printf "\n given with option -q"
[2789]	1172	locat=queue; exit
[2380]	1173	fi
	1174	if [[ $queue = none ]]
	1175	then
	1176	queue=$defaultqueue
	1177	fi
	1178
	1179	fi
	1180
	1181
	1182	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1183	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1184	(( i = 0 ))
[2610]	1185	(( nr_of_input_files = 0 ))
[2380]	1186	while (( i < iin ))
	1187	do
	1188	(( i = i + 1 ))
	1189
	1190	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1191	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1192	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1193	then
[2610]	1194	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1195	else
[3236]	1196	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1197	fi
	1198
[2610]	1199
[2380]	1200	# CHECK IF FILE EXISTS
	1201	if ! ls $filename* 1>/dev/null 2>&1
	1202	then
	1203
[2669]	1204	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1205	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1206	then
	1207	printf "\n\n +++ INPUT-file: "
[2610]	1208	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1209	then
	1210	printf "\n $filename"
	1211	else
[2610]	1212	printf "\n $filename.${extin_pre[$i]}"
[2380]	1213	fi
	1214	printf "\n does not exist\n"
	1215	locat=input; exit
	1216	else
[2610]	1217	(( nr_of_input_files = nr_of_input_files + 1 ))
	1218	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1219	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1220	actionin[$nr_of_input_files]="unavailable"
[2610]	1221	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1222	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1223	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1224	fi
[2605]	1225
[2380]	1226	else
	1227
[3236]	1228	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1229	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1230	# ENDINGS
[2610]	1231	if [[ "${multin[$i]}" = true ]]
	1232	then
	1233	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1234	ls -1 -d ${filename} > filelist 2>/dev/null
	1235	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1236	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1237
[2610]	1238	endings=""
	1239	while read line
	1240	do
	1241	# filename without path (i.e. after the last "/")
	1242	basefilename=$(basename ${line})
[2380]	1243
[2610]	1244	# check if there is an extension and remove it
	1245	ext=${basefilename##*.}
	1246	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1247	then
	1248	basefilename=${basefilename%.*}
	1249	fi
[2380]	1250
[2610]	1251	# check for an existing cycle number and remove it
	1252	cycle=${basefilename##*.}
	1253	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1254	then
	1255	basefilename=${basefilename%.*}
	1256	fi
[2600]	1257
[3236]	1258	# remove the run_identifier from the beginning
	1259	length_run_identifier=${#run_identifier}
	1260	ending=${basefilename:${length_run_identifier}}
[2610]	1261
	1262	# remove the ending given in the .iofiles from the beginning
	1263	endingstring="${endin_pre[$i]}"
	1264	length_ending=${#endingstring}
	1265	ending=${ending:${length_ending}}
	1266
	1267	if [[ "$ending" = "" ]]
[2600]	1268	then
[2610]	1269	# standard ending as given in the .iofiles
	1270	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1271	then
	1272	endings="$endings DEFAULT"
	1273	fi
[2600]	1274	else
[2610]	1275	# ending must start with "_", otherwise its a different file
	1276	if [[ "${ending:0:1}" = "_" ]]
	1277	then
	1278	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1279	then
	1280	endings="$endings $ending"
	1281	fi
	1282	fi
[2600]	1283	fi
[2610]	1284
	1285	done <filelist
[2380]	1286
[2610]	1287	rm filelist
[2380]	1288
[2600]	1289	else
[2610]	1290
	1291	# SINGLE NAME
	1292	endings=DEFAULT
	1293
[2600]	1294	fi
	1295
[2610]	1296	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1297	for ending in $endings
	1298	do
	1299
	1300	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1301	if [[ $ending = DEFAULT ]]
[2380]	1302	then
[2610]	1303	ending=""
	1304	fi
	1305
	1306	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1307	(( nr_of_input_files = nr_of_input_files + 1 ))
	1308	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1309	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1310	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1311	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1312	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1313	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1314
	1315
	1316	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1317	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1318	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1319	then
	1320	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1321	else
[3236]	1322	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1323	fi
[2610]	1324
	1325	# DETERMINE THE FILE'S CYCLE NUMBER
	1326	(( maxcycle = 0 ))
	1327	ls -1 -d $filename > filelist 2>/dev/null
	1328	ls -1 -d $filename.* >> filelist 2>/dev/null
	1329	while read line
	1330	do
	1331	# filename without path (i.e. after the last "/")
	1332	basefilename=$(basename ${line})
	1333
	1334	# check if there is an extension
	1335	extension=${basefilename##*.}
	1336	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1337	then
	1338	basefilename=${basefilename%.*}
	1339	fi
	1340
	1341	# check for an existing cycle number
	1342	cycle=${basefilename##*.}
	1343	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1344	then
[2669]	1345	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1346	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1347	(( icycle = $((10#$cycle)) ))
[2610]	1348	else
	1349	(( icycle = 0 ))
	1350	fi
	1351
	1352	if (( icycle > maxcycle ))
	1353	then
	1354	(( maxcycle = icycle ))
	1355
	1356	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1357	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1358	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1359	then
	1360	leading_zero=true
	1361	else
	1362	leading_zero=false
	1363	fi
	1364	fi
	1365
	1366	done <filelist
	1367	rm filelist
	1368
	1369	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1370	if [[ $leading_zero = true ]]
[2380]	1371	then
[2610]	1372	cyclestring=`printf "%03d" $maxcycle`
	1373	else
	1374	cyclestring=$maxcycle
[2380]	1375	fi
[2610]	1376
	1377	# APPEND CYCLE NUMBER TO FILENAME
	1378	if (( maxcycle > 0 ))
[2380]	1379	then
[2610]	1380	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1381	then
	1382	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1383	else
	1384	filename=${filename}.$cyclestring
	1385	fi
[2380]	1386	else
[2610]	1387	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1388	then
	1389	filename=${filename}.${extin[$nr_of_input_files]}
	1390	fi
[2380]	1391	fi
[2610]	1392
	1393	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1394	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1395	absnamein[$nr_of_input_files]=$filename
	1396	if (( maxcycle > 0 ))
[2380]	1397	then
[2610]	1398	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1399	then
	1400	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1401	else
[3236]	1402	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1403	fi
[2380]	1404	else
[2610]	1405	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1406	then
	1407	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1408	else
[3236]	1409	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1410	fi
[2380]	1411	fi
	1412
[2610]	1413	done
	1414
[2380]	1415	fi
[2610]	1416
[2380]	1417	done
	1418
[2610]	1419
[2380]	1420	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1421	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1422	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1423	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1424	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1425	# REMOTE HOST)
	1426	(( i = 0 ))
	1427	while (( i < iout ))
	1428	do
	1429	(( i = i + 1 ))
[2610]	1430	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1431	then
[2610]	1432	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1433	then
[2610]	1434	actionout_pre[$i]=""
	1435	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1436	then
[2610]	1437	actionout_pre[$i]=pe
	1438	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1439	then
[2610]	1440	actionout_pre[$i]=a
[2380]	1441	fi
	1442	(( maxcycle = 0 ))
[3236]	1443	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1444	eval catalogname=${pathout_pre[$i]}
[2380]	1445	if ! ls $filename* 1>/dev/null 2>&1
	1446	then
	1447
	1448	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1449	if cat /dev/null > $filename
	1450	then
	1451	rm $filename
	1452	else
	1453
	1454	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1455	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1456	if [[ ! -d $catalogname ]]
	1457	then
	1458	if mkdir -p $catalogname
	1459	then
	1460	printf "\n\n *** directory:"
	1461	printf "\n $catalogname"
	1462	printf "\n was created\n"
	1463	else
	1464	printf "\n\n +++ OUTPUT-file:"
	1465	printf "\n $filename"
	1466	printf "\n cannot be created, because directory does not exist"
	1467	printf "\n and cannot be created either"
	1468	printf "\n"
	1469	locat=output ; exit
	1470	fi 2>/dev/null
	1471	else
	1472	printf "\n\n +++ OUTPUT-file:"
	1473	printf "\n $filename"
	1474	printf "\n cannot be created, although directory exists"
	1475	printf "\n"
	1476	locat=output ; exit
	1477	fi
	1478	fi 2>/dev/null
	1479
	1480	fi
	1481
	1482	fi
	1483	done
	1484
	1485
	1486	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1487	if [[ $running_in_batch_mode = false ]]
	1488	then
[3236]	1489	run_id_number=$RANDOM
	1490	run_id=${run_identifier}.$run_id_number
[2380]	1491
[3236]	1492	tempdir=$fast_io_catalog/$run_id
[3346]	1493
	1494	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1495	export job_id=$run_id
	1496
[2380]	1497	fi
	1498
	1499
	1500	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1501	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1502	then
	1503
	1504	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1505	if [[ $ibd = 0 ]]
	1506	then
	1507	printf "\n"
	1508	printf "\n +++ no batch directives found in configuration file"
	1509	locat=config_file_batch_directives; (( iec = 0 )); exit
	1510	fi
	1511
	1512	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1513	done=false
[2384]	1514	cputime=$cpumax
[2380]	1515	while [[ $done = false ]]
	1516	do
[2384]	1517	if (( cputime == 0 ))
[2380]	1518	then
	1519	printf "\n +++ cpu-time is undefined"
	1520	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1521	printf "\n >>> "
[2384]	1522	read cputime 1>/dev/null 2>&1
[2380]	1523	else
	1524	done=true
	1525	fi
	1526	done
[2420]	1527	cpumax=$cputime
[2380]	1528
	1529	# CHECK THE MEMORY DEMAND
	1530	done=false
	1531	while [[ $done = false ]]
	1532	do
	1533	if (( memory == 0 ))
	1534	then
	1535	printf "\n +++ memory demand is undefined"
	1536	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1537	printf "\n >>> "
	1538	read memory 1>/dev/null 2>&1
	1539	else
	1540	done=true
	1541	fi
	1542	done
	1543
	1544	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1545	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1546	then
	1547	while [[ -z $remote_username ]]
	1548	do
[2420]	1549	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1550	printf "\n >>> Please type username:"
	1551	printf "\n >>> "
	1552	read remote_username
	1553	done
	1554	fi
	1555
	1556	else
	1557
[2420]	1558	if [[ $running_in_batch_mode = false ]]
	1559	then
	1560	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1561	cpumax=$cputime
	1562	else
	1563	cputime=$cpumax
	1564	fi
[2380]	1565
	1566	fi
	1567
	1568
	1569	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1570	(( cpu_hours = cputime / 3600 ))
	1571	(( resttime = cputime - cpu_hours * 3600 ))
	1572	(( cpu_minutes = resttime / 60 ))
	1573	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1574	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1575
	1576
	1577	# OUTPUT OF THE PALMRUN-HEADER
	1578	calltime=$(date)
	1579	printf "\n"
	1580	printf "#------------------------------------------------------------------------# \n"
	1581	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1582	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1583	printf "\| \| \n"
	1584	column1="called on:"; column2=$(hostname)
	1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1586	if [[ $create_remote_batch_job = true ]]
	1587	then
[3236]	1588	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1589	else
	1590	if [[ $running_on_remote = true ]]
	1591	then
[3236]	1592	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1593	else
[3236]	1594	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1595	fi
	1596	fi
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598
	1599	column1="running in:"
	1600	if [[ $running_in_batch_mode = true ]]
	1601	then
	1602	column2="batch job mode"
	1603	else
	1604	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1605	then
	1606	column2="job creation mode"
	1607	else
	1608	column2="interactive run mode"
	1609	fi
	1610	fi
	1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1612
[2479]	1613	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1614	then
[2480]	1615	if [[ "$project_account" != "" ]]
[2479]	1616	then
	1617	column1="project account number:"
	1618	column2="$project_account"
	1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1620	fi
	1621	fi
	1622
[2380]	1623	if [[ -n $cores ]]
	1624	then
	1625	if [[ $run_coupled_model = false ]]
	1626	then
	1627	column1="number of cores:"; column2=$cores
	1628	else
	1629	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1630	fi
	1631	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1632	fi
	1633	if [[ -n $tasks_per_node ]]
	1634	then
	1635	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1637	if (( remaining_cores > 0 ))
	1638	then
	1639	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	fi
	1642	fi
	1643	if [[ $maximum_parallel_io_streams != $cores ]]
	1644	then
	1645	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1646	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1647	fi
	1648	if [[ $use_openmp = true ]]
	1649	then
	1650	column1="threads per task:"; column2="$threads_per_task"
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	fi
[2384]	1653	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1654	then
[2506]	1655	column1="memory demand / PE":; column2="$memory MB"
	1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1657	column1="job cpu time (h:m:s):"; column2="$timestring"
	1658	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1659	fi
[2380]	1660	printf "\| \| \n"
	1661	if [[ "$source_list" != "" ]]
	1662	then
	1663	if [[ "$make_options" != "" ]]
	1664	then
	1665	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1666	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1667	line=$(echo "$make_options" \| cut -c46-)
	1668	while [[ "$line" != "" ]]
	1669	do
	1670	column1=""
	1671	column2=$(echo "$line" \| cut -c-45)
	1672	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1673	line=$(echo "$line" \| cut -c46-)
	1674	done
	1675	fi
	1676	fi
	1677
	1678	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1680	line=$(echo "$cpp_options" \| cut -c46-)
	1681	while [[ "$line" != "" ]]
	1682	do
	1683	column1=""
	1684	column2=$(echo "$line" \| cut -c-45)
	1685	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1686	line=$(echo "$line" \| cut -c46-)
	1687	done
	1688
	1689	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1690	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1691	line=$(echo "$compiler_options" \| cut -c46-)
	1692	while [[ "$line" != "" ]]
	1693	do
	1694	column1=""
	1695	column2=$(echo "$line" \| cut -c-45)
	1696	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1697	line=$(echo "$line" \| cut -c46-)
	1698	done
	1699
[2388]	1700	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1701	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1702	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1703	while [[ "$line" != "" ]]
	1704	do
	1705	column1=""
	1706	column2=$(echo "$line" \| cut -c-45)
	1707	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1708	line=$(echo "$line" \| cut -c46-)
	1709	done
	1710
	1711	if [[ "$login_init_cmd" != "" ]]
	1712	then
	1713	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1714	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1715	line=$(echo "$login_init_cmd" \| cut -c46-)
	1716	while [[ "$line" != "" ]]
	1717	do
	1718	column1=""
	1719	column2=$(echo "$line" \| cut -c-45)
	1720	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1721	line=$(echo "$line" \| cut -c46-)
	1722	done
	1723	fi
	1724
	1725	if [[ "$module_commands" != "" ]]
	1726	then
	1727	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1728	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1729	line=$(echo "$module_commands" \| cut -c46-)
	1730	while [[ "$line" != "" ]]
	1731	do
	1732	column1=""
	1733	column2=$(echo "$line" \| cut -c-45)
	1734	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1735	line=$(echo "$line" \| cut -c46-)
	1736	done
	1737	fi
	1738	printf "\| \| \n"
[3236]	1739	column1="run identifier:"; column2=$run_identifier
[2380]	1740	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1741	column1="activation string list:"; column2=$(echo $activation_string_list)
	1742	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1743
	1744	if [[ "$ocean_file_appendix" = true ]]
	1745	then
	1746	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1747	fi
	1748
	1749	if [[ "$source_list" != "" ]]
	1750	then
	1751	printf "\| \| \n"
	1752	printf "\| Files to be compiled: \| \n"
	1753	line=$source_list
	1754	while [[ "$line" != "" ]]
	1755	do
	1756	linestart=$(echo $line \| cut -c-70)
	1757	printf "\| %-70s \| \n" "$linestart"
	1758	line=$(echo "$line" \| cut -c71-)
	1759	done
	1760	fi
	1761	printf "#------------------------------------------------------------------------#"
	1762
	1763
	1764
	1765	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1766	if [[ $do_trace = true ]]
	1767	then
	1768	(( i = 0 ))
[2610]	1769	while (( i < nr_of_input_files ))
[2380]	1770	do
	1771	(( i = i + 1 ))
	1772	if (( i == 1 ))
	1773	then
	1774	printf "\n\n >>> INPUT-file assignments:\n"
	1775	fi
	1776	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1777	done
	1778	(( i = 0 ))
	1779	while (( i < iout ))
	1780	do
	1781	(( i = i + 1 ))
	1782	if (( i == 1 ))
	1783	then
	1784	printf "\n\n >>> OUTPUT-file assignments:\n"
	1785	fi
	1786	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1787	done
	1788	(( i = 0 ))
	1789	while (( i < iic ))
	1790	do
	1791	(( i = i + 1 ))
	1792	if (( i == 1 ))
	1793	then
	1794	printf "\n\n >>> INPUT-commands:\n"
	1795	fi
	1796	printf "\n ${in_command[$i]}"
	1797	done
	1798	(( i = 0 ))
	1799	while (( i < ioc ))
	1800	do
	1801	(( i = i + 1 ))
	1802	if (( i == 1 ))
	1803	then
	1804	printf "\n\n >>> OUTPUT-commands:\n"
	1805	fi
	1806	printf "\n ${out_command[$i]}"
	1807	done
	1808	fi
	1809
	1810	# QUERY FOR CONTINUE
	1811	if [[ $silent = false && $running_in_batch_mode = false ]]
	1812	then
	1813	antwort=dummy
	1814	printf "\n\n"
	1815	printf " >>> everything o.k. (y/n) ? "
	1816	while read antwort
	1817	do
	1818	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1819	then
	1820	printf " >>> everything o.k. (y/n) ? "
	1821	else
	1822	break
	1823	fi
	1824	done
	1825	if [[ $antwort = n \|\| $antwort = N ]]
	1826	then
	1827	locat=user_abort; (( iec = 0 )); exit
	1828	fi
	1829	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1830	then
[2566]	1831	printf "\n *** batch-job will be created and submitted"
[2380]	1832	else
[2566]	1833	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1834	fi
	1835	fi
	1836
	1837
	1838
	1839	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1840	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1841	then
	1842
	1843	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1844	then
[2566]	1845	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1846	else
[2566]	1847	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1848	fi
	1849
[2422]	1850	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1851	# IT SHALL BE CREATED
	1852	ask_for_make_depository=false
	1853	if [[ $create_remote_batch_job = true ]]
	1854	then
	1855
	1856	line=`grep %base_directory $config_file`
[3236]	1857	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1858	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1859
[3236]	1860	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1861	then
	1862	printf "\n\n +++ make depository \"${make_depository}\""
	1863	printf "\n on remote host not found!"
	1864	ask_for_make_depository=true
	1865	fi
[3236]	1866	rm ${configuration_identifier}_last_make_protokoll
[2422]	1867
	1868	else
	1869
	1870	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1871	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1872	if [[ ! -d ${make_depository} ]]
	1873	then
	1874	printf "\n\n +++ make depository \"${make_depository}\""
	1875	printf "\n on local host not found!"
	1876	ask_for_make_depository=true
	1877	fi
	1878
	1879	fi
	1880
	1881	if [[ $ask_for_make_depository = true ]]
	1882	then
	1883
	1884	antwort=dummy
	1885	printf "\n\n"
	1886	printf " >>> Create a new one (y/n) ? "
	1887	while read antwort
	1888	do
	1889	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1890	then
	1891	printf " >>> Create a new one (y/n) ? "
	1892	else
	1893	break
	1894	fi
	1895	done
	1896	if [[ $antwort = n \|\| $antwort = N ]]
	1897	then
	1898	locat=user_abort; (( iec = 0 )); exit
	1899	fi
	1900
[2566]	1901	if [[ $do_trace = true ]]
	1902	then
[3455]	1903	palmbuild -c $configuration_identifier
[2566]	1904	else
[3455]	1905	palmbuild -v -c $configuration_identifier
[2566]	1906	fi
[2422]	1907
[3312]	1908	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1909	then
	1910
	1911	# ABORT IN CASE OF COMPILATION PROBLEMS
	1912	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1913	locat=make_depository
	1914	exit
	1915	else
	1916	echo " *** now continue with creating executable and other sources"
	1917	fi
	1918
	1919	fi
	1920
[2566]	1921	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1922	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1923
[3312]	1924	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1925	then
	1926
	1927	# ABORT IN CASE OF COMPILATION PROBLEMS
	1928	printf "\n +++ error while creating executable and/or other sources"
	1929	locat=execution
[2990]	1930	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1931	exit
	1932
	1933	else
	1934
[2566]	1935	printf " *** executable and other sources created\n"
[2990]	1936	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1937
	1938	fi
	1939
	1940	fi
	1941
	1942
[2669]	1943	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1944	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1945	if [[ $create_remote_batch_job = true ]]
	1946	then
	1947	(( i = 0 ))
[2610]	1948	while (( i < nr_of_input_files ))
[2605]	1949	do
	1950	(( i = i + 1 ))
[2669]	1951	if [[ "${actionin[$i]}" = tr ]]
[2605]	1952	then
	1953	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1954	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1955	fi
	1956	done
	1957	if (( i > 0 ))
	1958	then
[3025]	1959	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1960	fi
	1961	fi
	1962
	1963
[2380]	1964	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1965	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1966	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1967	then
	1968
	1969	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1970	if [[ $running_in_batch_mode = false ]]
	1971	then
	1972	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1973	# FOLDER
[2566]	1974	mkdir -p $tempdir
	1975	chmod go+rx $tempdir
	1976	cd $tempdir
	1977	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1978	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1979
	1980	else
	1981
	1982	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1983	printf "\n *** running in temporary directory: $tempdir"
[2380]	1984
	1985	fi
	1986
	1987
	1988	# PROVIDE THE INPUT FILES
	1989	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1990	optional_files_missing=false
[2380]	1991	(( i = 0 ))
[2610]	1992	while (( i < nr_of_input_files ))
[2380]	1993	do
	1994	(( i = i + 1 ))
	1995	if (( i == 1 ))
	1996	then
	1997	printf "\n\n *** providing INPUT-files:\n$dashes"
	1998	fi
	1999
	2000
	2001	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	2002	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2003	then
[2669]	2004	optional_files_missing=true
[2380]	2005	continue
	2006	fi
	2007
	2008	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2009	files_for_cores=false; filetype=file
	2010	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2011	then
	2012	files_for_cores=true; filetype=files
	2013	actionin[$i]=""
	2014	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2015	then
	2016	actionin[$i]=""
	2017	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2018	then
	2019	files_for_cores=true; filetype=files
	2020	actionin[$i]="ln"
	2021	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2022	then
	2023	actionin[$i]="ln"
	2024	fi
	2025
	2026	if [[ $files_for_cores = true ]]
	2027	then
	2028	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2029	else
	2030	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2031	fi
	2032
	2033	# INPUT-FILES TO BE LINKED
	2034	if [[ "${actionin[$i]}" = ln ]]
	2035	then
	2036
	2037	printf "\n $filetype will be linked"
	2038	if [[ $files_for_cores = false ]]
	2039	then
	2040	if [[ -f "${absnamein[$i]}" ]]
	2041	then
	2042	ln ${absnamein[$i]} ${localin[$i]}
	2043	got_tmp[$i]=true
	2044	fi
	2045	else
	2046	if [[ -d "${absnamein[$i]}" ]]
	2047	then
[2396]	2048	mkdir -p ${localin[$i]}
[2380]	2049	cd ${absnamein[$i]}
	2050	for file in $(ls *)
	2051	do
[2566]	2052	ln $file $tempdir/${localin[$i]}
[2380]	2053	done >\|/dev/null 2>&1
[2566]	2054	cd $tempdir
[2380]	2055	fi
	2056
	2057	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2058	if [[ ! -f "${localin[$i]}/_000000" ]]
	2059	then
	2060	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2061	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2062	fi
	2063
	2064	got_tmp[$i]=true
	2065	fi
	2066	fi
	2067
	2068	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2069	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2070	then
	2071
	2072	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2073	then
	2074
	2075	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2076	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2077	printf "\n file will be provided for $cores processors"
[2396]	2078	mkdir -p ${localin[$i]}
[2380]	2079	ival=$cores
	2080	(( ii = 0 ))
	2081	while (( ii <= ival-1 ))
	2082	do
	2083	if (( ii < 10 ))
	2084	then
	2085	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2086	elif (( ii < 100 ))
	2087	then
	2088	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2089	elif (( ii < 1000 ))
	2090	then
	2091	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2092	else
	2093	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2094	fi
	2095	(( ii = ii + 1 ))
	2096	done
	2097
	2098	else
	2099
	2100	if [[ $files_for_cores = true ]]
	2101	then
	2102
	2103	# PROVIDE FILES FOR EACH CORE
	2104	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2105	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2106	printf "\n providing $cores files for the respective cores"
[2396]	2107	mkdir -p ${localin[$i]}
[2380]	2108	if [[ $link_local_input = true ]]
	2109	then
	2110	printf " files will be linked\n"
	2111	cd ${absnamein[$i]}
	2112	for file in $(ls *)
	2113	do
	2114	ln -f $file ${localin[$i]}
	2115	done
[2566]	2116	cd $tempdir
[2380]	2117	fi
	2118
	2119	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2120	if [[ ! -f "${localin[$i]}/_000000" ]]
	2121	then
	2122	if [[ $link_local_input = true ]]
	2123	then
	2124	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2125	fi
	2126	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2127	fi
	2128
	2129	else
	2130
	2131	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2132	if [[ $link_local_input = true ]]
	2133	then
	2134	printf " file will be linked\n"
	2135	ln -f ${absnamein[$i]} ${localin[$i]}
	2136	fi
[2605]	2137	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2138	if [[ ! -f "${localin[$i]}" ]]
	2139	then
	2140	if [[ $link_local_input = true ]]
	2141	then
	2142	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2143	fi
[2669]	2144	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2145	then
	2146	mv ${absnamein[$i]} ${localin[$i]}
	2147	else
	2148	cp ${absnamein[$i]} ${localin[$i]}
	2149	fi
[2380]	2150	fi
	2151	fi
	2152	fi
	2153	fi
	2154
	2155	done
	2156	if (( i != 0 ))
	2157	then
[2669]	2158	if [[ $optional_files_missing = true ]]
	2159	then
	2160	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2161	fi
[2380]	2162	printf "\n$dashes\n *** all INPUT-files provided \n"
	2163	fi
	2164
	2165
	2166	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2167	(( i = 0 ))
	2168	while (( i < iic ))
	2169	do
	2170	(( i = i + 1 ))
	2171	if (( i == 1 ))
	2172	then
	2173	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2174	fi
	2175	printf "\n >>> ${in_command[$i]}"
	2176	eval ${in_command[$i]}
	2177	if (( i == iic ))
	2178	then
	2179	printf "\n$dashes\n"
	2180	fi
	2181	done
	2182
	2183
[3313]	2184	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2185	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2186	then
	2187	progress_bar_disabled=true
	2188	else
	2189	progress_bar_disabled=false
	2190	fi
	2191
	2192
[2380]	2193	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2194	# (FILE ENVPAR WILL BE READ BY PALM)
	2195	cat > ENVPAR << EOF
[3236]	2196	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2197	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2198	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2199	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2200	maximum_cpu_time_allowed = ${cpumax}.,
	2201	revision = '$global_revision',
[3313]	2202	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2203
	2204	EOF
	2205
	2206
	2207	# STARTING THE EXECUTABLE
	2208	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2209	PATH=$PATH:$tempdir
[2380]	2210
	2211
	2212	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2213	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2214	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2215	eval line=\"$line\"
	2216	execute_command="$line"
	2217
	2218
	2219	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2220	if [[ "$execute_command_for_combine" = "" ]]
	2221	then
	2222	eval line2=\"$line2\"
	2223	execute_command_for_combine="$line2"
	2224	fi
	2225
[2380]	2226
	2227
	2228	# PROVIDE A HOSTFILE, IF REQUIRED
	2229	if [[ "$hostfile" != "" ]]
	2230	then
	2231
	2232	if [[ $hostfile = auto ]]
	2233	then
	2234	# CREATE A NEW HOSTFILE
	2235	(( ii = 1 ))
	2236	while (( ii <= cores / threads_per_task ))
	2237	do
	2238	echo $(hostname) >> hostfile
	2239	(( ii = ii + 1 ))
	2240	done
	2241	if (( cores / threads_per_task == 0 ))
	2242	then
	2243	echo $(hostname) >> hostfile
	2244	fi
	2245
	2246	else
	2247	cp $hostfile hostfile
	2248	fi
	2249	eval line=\"`head -n $ii hostfile`\"
	2250	printf "\n *** running on: $line"
	2251	fi
	2252
	2253
	2254
	2255	# SET THE NUMBER OF OPENMP-THREADS
	2256	if [[ $use_openmp = true ]]
	2257	then
	2258	export OMP_NUM_THREADS=$threads_per_task
	2259	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2260	else
	2261	export OMP_NUM_THREADS=1
	2262	fi
	2263
	2264
[2610]	2265	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2266	if [[ $run_coupled_model = false ]]
	2267	then
	2268	if [[ "$ocean_file_appendix" = true ]]
	2269	then
	2270	echo "precursor_ocean" > coupling_steering
	2271	else
	2272	echo "precursor_atmos" > coupling_steering
	2273	fi
	2274	else
	2275	(( iia = $cores_atmos / $threads_per_task ))
	2276	(( iio = $cores_ocean / $threads_per_task ))
	2277	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2278	printf "\n\n"
	2279	echo "coupled_run $iia $iio" > coupling_steering
	2280	fi
	2281
	2282	printf "\n *** execute command:"
	2283	printf "\n \"$execute_command\" \n\n"
	2284
	2285
[3393]	2286	if [[ $progress_bar_disabled = true ]]
[2380]	2287	then
[3402]	2288	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2289	exit_code=${PIPESTATUS[0]}
	2290	else
	2291	$execute_command < coupling_steering &> >(tee STDOUT)
	2292	exit_code=${PIPESTATUS[0]}
	2293	fi
[2380]	2294
[3393]	2295	if [[ ${exit_code} != 0 ]]
	2296	then
	2297
[2380]	2298	# ABORT IN CASE OF RUNTIME ERRORS
	2299	printf "\n +++ runtime error occured"
	2300	locat=execution
	2301	exit
	2302
	2303	else
	2304
	2305	printf "\n$dashes\n *** execution finished \n"
	2306
	2307	fi
	2308
	2309
	2310	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2311	# BY EACH CORE INTO ONE FILE
	2312	if [[ ! -f combine_plot_fields.x ]]
	2313	then
	2314
	2315	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2316	printf "\n 2d- and/or 3d-data may be incomplete!"
	2317	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2318
	2319	elif [[ "$combine_plot_fields" == true ]]
	2320	then
	2321
	2322	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2323	$execute_command_for_combine
	2324
	2325	else
	2326
	2327	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2328	# DATA OUTPUT
[2380]	2329	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2330	fi
	2331
	2332
	2333
	2334	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2335	(( i = 0 ))
	2336	while (( i < ioc ))
	2337	do
	2338	(( i = i + 1 ))
	2339	if (( i == 1 ))
	2340	then
	2341	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2342	fi
[2799]	2343
	2344	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2345	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2346
[2380]	2347	printf "\n >>> ${out_command[$i]}"
	2348	eval ${out_command[$i]}
	2349	if (( i == ioc ))
	2350	then
	2351	printf "\n$dashes\n"
	2352	fi
	2353	done
	2354
	2355
[2610]	2356	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2357	# WILDCARDS
[2380]	2358	(( i = 0 ))
[2610]	2359	(( nr_of_output_files = 0 ))
	2360
[2380]	2361	while (( i < iout ))
	2362	do
[2610]	2363
[2380]	2364	(( i = i + 1 ))
[2610]	2365
	2366	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2367	# CREATE A LIST FOR THE DETECTED ENDINGS
	2368	if [[ "${multout[$i]}" = true ]]
	2369	then
	2370	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2371	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2372	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2373
	2374	endings="DEFAULT"
	2375	while read line
	2376	do
	2377	# remove the local name from the beginning
	2378	localnamestring="${localout_pre[$i]}"
	2379	length_localname=${#localnamestring}
	2380	ending=${line:${length_localname}}
	2381
	2382	if [[ "$ending" != "" ]]
	2383	then
	2384	endings="$endings $ending"
	2385	fi
	2386
	2387	done <filelist
	2388
	2389	rm filelist
	2390
	2391	else
	2392
	2393	# SINGLE NAME
	2394	endings=DEFAULT
	2395
	2396	fi
	2397
	2398	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2399	for ending in $endings
	2400	do
	2401
	2402	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2403	if [[ $ending = DEFAULT ]]
	2404	then
	2405	ending=""
	2406	fi
	2407
	2408	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2409	(( nr_of_output_files = nr_of_output_files + 1 ))
	2410	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2411	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2412	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2413	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2414	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2415	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2416	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2417
	2418	done
	2419
	2420	done
	2421
	2422
	2423
	2424
	2425	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2426	(( i = 0 ))
	2427	while (( i < nr_of_output_files ))
	2428	do
	2429	(( i = i + 1 ))
[2380]	2430	if (( i == 1 ))
	2431	then
	2432	printf "\n\n *** saving OUTPUT-files:"
	2433
	2434	# GET RUN NUMBER ASSIGNED BY PALM
	2435	if [[ -f RUN_NUMBER ]]
	2436	then
	2437	read run_number < RUN_NUMBER
	2438	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2439	usecycle_option="-U $run_number"
	2440	else
	2441	run_number=0
	2442	usecycle_option=""
	2443	fi
	2444	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2445	then
[2404]	2446	printf "\n *** in case of SCP transfers to local host"
	2447	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2448	fi
	2449	printf "\n$dashes"
	2450	fi
	2451
	2452	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2453	then
	2454
[3236]	2455	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2456
	2457	# DETERMINE THE CYCLE NUMBER
	2458	ls -1 -d $filename > filelist 2>/dev/null
	2459	ls -1 -d $filename.* >> filelist 2>/dev/null
	2460	while read line
	2461	do
	2462
	2463	# filename without path (i.e. after the last "/")
	2464	basefilename=$(basename ${line})
	2465
	2466	# check if there is an extension
	2467	extension=${basefilename##*.}
	2468	if [[ "$extension" = "${extout[$i]}" ]]
	2469	then
	2470	basefilename=${basefilename%.*}
	2471	fi
	2472
	2473	# check for an existing cycle number
	2474	cycle=${basefilename##*.}
	2475	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2476	then
[2669]	2477	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2478	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2479	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2480	else
	2481	(( icycle = 1 ))
	2482	fi
	2483
	2484	if (( icycle > maxcycle ))
	2485	then
	2486	(( maxcycle = icycle ))
	2487	fi
	2488
	2489	done <filelist
	2490	rm filelist
	2491
	2492
	2493	# SET THE CYCLE NUMBER
	2494	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2495	if [[ "${actionout[$i]}" = a ]]
	2496	then
	2497	(( maxcycle = maxcycle - 1 ))
	2498	fi
	2499
	2500	(( cycnum[$i] = maxcycle ))
	2501	pathout[$i]=$filename
	2502
	2503
	2504	# ADD CYCLE NUMBER TO FILENAME
	2505	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2506	if [[ "${actionout[$i]}" != "a" ]]
	2507	then
	2508	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2509	# WITH AN EXISTING CYCLE NUMBER
	2510	if (( run_number >= cycnum[$i] ))
	2511	then
	2512	(( cycnum[$i] = run_number ))
	2513	else
	2514	if (( run_number > 0 ))
	2515	then
	2516	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2517	fi
	2518	fi
	2519	fi
	2520	if (( cycnum[$i] > 0 ))
	2521	then
[2600]	2522	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2523	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2524	fi
	2525	fi
	2526
	2527	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2528	files_for_cores=false; filetype=file
	2529	link_local_output=false
	2530	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2531	then
	2532	files_for_cores=true; filetype=directory
	2533	actionout[$i]=""
	2534	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2535	then
	2536	actionout[$i]=""
	2537	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2538	then
	2539	files_for_cores=true; filetype=directory
	2540	link_local_output=true
	2541	actionout[$i]=""
	2542	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2543	then
	2544	link_local_output
	2545	actionout[$i]=""
	2546	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2547	then
	2548	files_for_cores=true; filetype=directory
	2549	actionout[$i]="tr"
	2550	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2551	then
	2552	actionout[$i]="tr"
	2553	fi
	2554
	2555	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2556	then
[2669]	2557	if [[ ${warnout[$i]} = true ]]
	2558	then
	2559	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2560	fi
[2380]	2561	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2562	then
[2669]	2563	if [[ ${warnout[$i]} = true ]]
	2564	then
	2565	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2566	fi
[2380]	2567	else
	2568
	2569
	2570	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2571	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2572	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2573	then
	2574	if [[ $running_on_remote = true ]]
	2575	then
	2576
	2577	# SET OPTIONS FOR TRANSFER
	2578	if [[ "${actionout[$i]}" = tr ]]
	2579	then
	2580	if [[ $files_for_cores = false ]]
	2581	then
	2582	catalog_option=""
	2583	catalog_string=""
	2584	else
	2585	catalog_option="-c"
	2586	catalog_string="/"
	2587	fi
	2588	append_option=""
	2589	append_string=""
	2590	else
	2591	append_option="-A"
	2592	append_string="append"
	2593	fi
	2594
	2595	transfer_failed=false
	2596	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2597	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2598
	2599	# TRANSFER VIA SCP
	2600	if [[ "$remote_loginnode" != "" ]]
	2601	then
[3534]	2602	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]	2603	else
[3236]	2604	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]	2605	fi
[3312]	2606	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2607
	2608
	2609	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2610	if [[ $transfer_failed = true ]]
	2611	then
	2612	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2613	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2614
	2615	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2616	eval local_catalog=${pathout[$i]}
	2617	if [[ ! -d $local_catalog ]]
	2618	then
	2619	printf " *** local directory does not exist. Trying to create:\n"
	2620	printf " $local_catalog \n"
	2621	mkdir -p $local_catalog
	2622	fi
[3236]	2623	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2624	transfer_problems=true
	2625	fi
	2626
	2627	else
	2628
	2629	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2630	# BE COPIED OR APPENDED ON THIS MACHINE
	2631	if [[ "${actionout[$i]}" = tr ]]
	2632	then
	2633	actionout[$i]=""
	2634	else
	2635	actionout[$i]="a"
	2636	fi
	2637	fi
	2638	fi
	2639
	2640
	2641	# APPEND ON THIS MACHINE
	2642	if [[ "${actionout[$i]}" = "a" ]]
	2643	then
	2644	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2645	then
	2646	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2647	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2648	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2649	else
	2650	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2651	printf "\n ${pathout[$i]}\n"
	2652	cat ${localout[$i]} >> ${pathout[$i]}
	2653	fi
	2654	fi
	2655
	2656	# COPY ON THIS MACHINE
	2657	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2658	# ON DIFFERENT FILE-SYSTEMS
	2659	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2660	then
	2661
	2662	# COPY IN CASE OF RUNS ON SINGLE CORES
	2663	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2664	then
	2665	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2666	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2667	if [[ $link_local_output = true ]]
	2668	then
	2669	printf " file will be linked\n"
	2670	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2671	fi
	2672	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2673	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2674	then
	2675	if [[ $link_local_output = true ]]
	2676	then
	2677	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2678	fi
	2679	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2680	else
	2681	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2682	fi
	2683	else
	2684	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2685	printf "\n ${pathout[$i]}\n"
	2686	if [[ $link_local_output = true ]]
	2687	then
	2688	printf " file will be linked\n"
	2689	ln -f ${localout[$i]} ${pathout[$i]}
	2690	fi
	2691	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2692	if [[ ! -f "${pathout[$i]}" ]]
	2693	then
	2694	if [[ $link_local_output = true ]]
	2695	then
	2696	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2697	fi
	2698	cp ${localout[$i]} ${pathout[$i]}
	2699	else
	2700	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2701	fi
	2702	fi
	2703
	2704	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2705	then
	2706
	2707	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2708	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2709	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2710	printf "\n ${pathout[$i]}\n"
	2711	if [[ $link_local_output = true ]]
	2712	then
	2713	printf " files will be linked\n"
[2396]	2714	mkdir -p ${pathout[$i]}
[2380]	2715	cd ${localout[$i]}
	2716	for file in $(ls *)
	2717	do
	2718	ln -f $file ${pathout[$i]}
	2719	done >\|/dev/null 2>&1
[2566]	2720	cd $tempdir
[2380]	2721	fi
	2722
	2723	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2724	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2725	then
	2726	if [[ $link_local_output = true ]]
	2727	then
	2728	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2729	fi
[3025]	2730	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2731	cp -r ${localout[$i]}/* ${pathout[$i]}
	2732	fi
	2733
	2734	fi
	2735	fi
	2736	done
	2737
	2738	if (( i != 0 ))
	2739	then
	2740	if [[ $transfer_problems = true ]]
	2741	then
	2742	printf "\n$dashes\n *** OUTPUT-files saved"
	2743	printf "\n +++ WARNING: some data transfers failed! \n"
	2744	else
	2745	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2746	fi
	2747	fi
	2748
	2749
	2750	# IF REQUIRED, START A RESTART-JOB
	2751	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2752	if [[ -f CONTINUE_RUN ]]
	2753	then
	2754
	2755	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2756	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2757	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2758	# -b START A BATCH JOB
	2759	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2760	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2761	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2762
[2957]	2763	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2764	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2765	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2766	then
	2767	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2768	fi
[2380]	2769
	2770	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2771	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2772	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2773	then
[2381]	2774	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2775	fi
	2776
	2777
	2778	# START THE RESTART-JOB
	2779	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2780	echo " $prc"
	2781	printf "\n$dashes\n"
	2782	if [[ $running_on_remote = true ]]
	2783	then
	2784
	2785	echo "*** ssh will be used to initiate restart-runs!"
	2786	echo " return_address=\"$return_address\" "
	2787	echo " return_username=\"$local_username\" "
	2788
	2789	if [[ "$remote_loginnode" != "" ]]
	2790	then
[3534]	2791	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]	2792	else
[3534]	2793	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2794	fi
	2795
	2796	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2797	sleep 30
	2798
	2799	else
	2800
	2801	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2802	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2803
	2804	fi
	2805
[3132]	2806	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2807	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2808	then
	2809	printf "\n$dashes\n +++ creating restart run failed \n"
	2810	locat=create_restart
[3455]	2811	rm palmrun_restart.log
[3132]	2812	exit
	2813	else
	2814	printf "\n$dashes\n *** restart run initiated \n"
	2815	rm palmrun_restart.log
	2816	fi
[2380]	2817
[3132]	2818
[2380]	2819	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2820	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2821	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2822	# MAY BE VERY HUGE)
	2823	(( i = 0 ))
[2610]	2824	while (( i < nr_of_input_files ))
[2380]	2825	do
	2826	(( i = i + 1 ))
	2827	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2828	then
	2829	rm -r ${absnamein[$i]}
	2830	fi
	2831	done
	2832
	2833	fi
	2834
	2835
	2836	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2837	cd $HOME
[2566]	2838	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2839
	2840
	2841	else
	2842
	2843
	2844	# PREPARING ACTIONS,
	2845	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2846
	2847	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2848	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2849	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2850	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2851	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2852	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2853	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2854	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2855	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2856	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2857	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2858	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2859	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2860	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2861	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2862	if [[ $create_remote_batch_job = true ]]
	2863	then
	2864	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2865	if [[ $do_trace = true ]]
	2866	then
	2867	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2868	fi
[2380]	2869	elif [[ $create_batch_job = true ]]
	2870	then
	2871	palmrun_com=${palmrun_com}" -j"
[2420]	2872	if [[ $do_trace = true ]]
	2873	then
	2874	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2875	fi
[2380]	2876	fi
	2877
	2878
	2879	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2880	# REMOTE HOST
[3236]	2881	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2882	job_protocol_file=$job_protocol_file_local
	2883	if [[ $create_remote_batch_job = true ]]
	2884	then
[3236]	2885	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2886	job_protocol_file=$job_protocol_file_remote
	2887	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2888	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2889	fi
	2890
	2891
	2892	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2893	jobfile=jobfile.$run_id_number
[2380]	2894
	2895
	2896	# FIRST CREATE THE BATCH DIRECTIVES
	2897	(( i = 0 ))
	2898	while (( i < ibd ))
	2899	do
	2900	(( i = i + 1 ))
[2693]	2901	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2902	eval line=\"$line\"
	2903	echo "$line" >> $jobfile
	2904	done
	2905	echo " " >> $jobfile
	2906
	2907
	2908	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2909	# PROTOCOL
	2910	if [[ $create_remote_batch_job = true ]]
	2911	then
[3236]	2912	echo "set +vx" >> $jobfile
	2913	echo "trap '" >> $jobfile
	2914	echo "set +vx" >> $jobfile
	2915	echo "cd ${remote_jobcatalog}" >> $jobfile
	2916	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2917
	2918	# ADD THE BATCH DIRECTIVES
	2919	(( i = 0 ))
	2920	while (( i < ibdt ))
	2921	do
	2922	(( i = i + 1 ))
[2693]	2923	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2924	eval line=\"$line\"
	2925	echo "$line" >> $jobfile
	2926	done
	2927	echo " " >> $jobfile
	2928
	2929	echo "set -x" >> $jobfile
[3534]	2930	if [[ "$remote_loginnode" != "" ]]
	2931	then
	2932	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}\" " >> $jobfile
	2933	else
	2934	echo "${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
	2935	fi
[2380]	2936	echo "%%END%%" >> $jobfile
	2937	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2938	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2939	echo "rm $scpjob_file" >> $jobfile
[2404]	2940	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2941	echo "set -x" >> $jobfile
	2942	echo " ' exit" >> $jobfile
	2943	fi
	2944
	2945
	2946	# ACTIVATE ERROR-TRACEBACK
	2947	if [[ $do_trace = true ]]
	2948	then
	2949	echo "set -x" >> $jobfile
	2950	else
	2951	echo "set +vx" >> $jobfile
	2952	fi
	2953
	2954
	2955	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2956	if [[ "$login_init_cmd" != "" ]]
	2957	then
	2958	echo "$login_init_cmd" >> $jobfile
	2959	fi
	2960	if [[ "$module_commands" != "" ]]
	2961	then
	2962	echo "$module_commands" >> $jobfile
	2963	fi
	2964
	2965
	2966	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2967	if [[ $create_remote_batch_job = true ]]
	2968	then
	2969	echo "mkdir $tempdir" >> $jobfile
	2970	echo "chmod go+rx $tempdir" >> $jobfile
	2971	else
	2972	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2973	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2974	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2975	mkdir $tempdir
	2976	chmod go+rx $tempdir
	2977	fi
	2978	echo "cd $tempdir" >> $jobfile
	2979	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2980	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2981	echo "export PATH=.:\$PATH" >> $jobfile
	2982	echo "export execute_palmrun=true" >> $jobfile
	2983
	2984
	2985	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2986	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2987	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2988	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2989	echo "export LOCAL_PWD" >> $jobfile
	2990
	2991
	2992	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2993	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2994	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2995
	2996
	2997	# CALL PALMRUN WITHIN THE JOB
	2998	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2999	echo "set -x" >> $jobfile
	3000	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3001
	3002
	3003	# TRANSFER JOBFILE TO THE TARGET HOST
	3004	if [[ $create_jobfile_only = false ]]
	3005	then
	3006
[3505]	3007	# CREATE LOCAL JOB FOLDER
	3008	eval local_jobcatalog=$local_jobcatalog
	3009	if [[ ! -d $local_jobcatalog ]]
	3010	then
	3011	echo " "
	3012	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3013	mkdir $local_jobcatalog
	3014	fi
	3015
[2380]	3016	if [[ $create_remote_batch_job = true ]]
	3017	then
	3018
[2420]	3019	echo " "
[2566]	3020	echo " *** transfer of job to remote host via scp"
[3505]	3021
	3022	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3023	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3024
	3025	# COPY THE JOB FILE
[2420]	3026	if [[ $do_trace = true ]]
	3027	then
[3236]	3028	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3029	fi
[3236]	3030	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3031
[3505]	3032	# SUBMIT THE JOB
[3574]	3033	printf " *** submit the job (output of submit command, \n"
[3573]	3034	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3035	if [[ $do_trace = true ]]
	3036	then
[3665]	3037	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}\" "
[2420]	3038	fi
[3665]	3039	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
[2380]	3040
	3041	elif [[ $create_batch_job = true ]]
	3042	then
	3043
[2385]	3044	eval local_jobcatalog=$local_jobcatalog
[3236]	3045	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3046	cd $local_jobcatalog
[2380]	3047	echo " "
[2420]	3048	echo " *** submit the job"
	3049	if [[ $do_trace = true ]]
	3050	then
[3236]	3051	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3052	fi
[3236]	3053	$submit_command ${configuration_identifier}_${run_id}
	3054	rm ${configuration_identifier}_${run_id}
[2380]	3055	cd - > /dev/null
	3056
	3057	fi
	3058
	3059	rm -rf $jobfile
	3060
	3061	else
	3062
	3063	printf "\n *** jobfile created under name \"$jobfile\" "
	3064	printf "\n no batch-job has been sent!"
	3065
	3066	fi
	3067
	3068	fi # END OF REMOTE-PART

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