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source: palm/trunk/SCRIPTS/palmrun @ 3573

Last change on this file since 3573 was 3573, checked in by raasch, 6 years ago
bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command, r3570 reverted
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.8 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 3573 2018-11-28 13:03:44Z raasch $
[3573]	29	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	30	# removed,
	31	# r3570 reverted
	32	#
	33	# 3570 2018-11-27 17:44:21Z kanani
[3570]	34	# Rename job-id by run_id
	35	#
	36	# 3555 2018-11-22 13:50:37Z raasch
[3555]	37	# sed-command to remove repeated space-characters replaced by tr-command, to
	38	# guarantee mac compatible
	39	#
	40	# 3549 2018-11-21 15:44:44Z raasch
[3549]	41	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	42	# of login messages on specific systems
	43	#
	44	# 3534 2018-11-19 15:35:16Z raasch
[3534]	45	# batch_scp for sending back the job protocol file is called via login-node if
	46	# a login-node has been set in the config-file
	47	# ssh-calls rearranged to avoid output of system/user-profile messages
	48	#
	49	# 3505 2018-11-08 09:14:30Z raasch
[3505]	50	# job folders are created in case that they do not exist
	51	#
	52	# 3455 2018-10-30 14:12:31Z raasch
[3455]	53	# options -h and -d renamed -c and -r, respectively
	54	#
	55	# 3402 2018-10-23 11:49:24Z knoop
[3346]	56	# job_id is set for compatibility reasons with older versions of config files
	57	#
	58	# 3313 2018-10-06 15:22:48Z knoop
[3294]	59	# more detailed error message for outdated fileconnection file
	60	#
	61	# 3236 2018-09-10 09:07:06Z raasch
[3236]	62	# warning issued in case of file connection file version mismatch,
	63	# host_configuration renamed configuration_identifier,
	64	# "host identifier" in header output renamed "config. identifier",
	65	# jobname renamed run_identifier,
	66	# run_id renamed run_id_number
	67	# job_id renamed run_id
	68	# option -r renamed -i
	69	#
	70	# 3151 2018-07-19 08:45:38Z raasch
[3151]	71	# removed additional listing of files to be compiled, print PALM code revision
	72	# in header
	73	#
	74	# 3132 2018-07-16 11:44:58Z raasch
[3132]	75	# create consistent error messages in case of failed restarts,
	76	# check existence of remote job catalog
	77	#
	78	# 3043 2018-05-25 10:47:54Z raasch
[3043]	79	# check for setting of fast_io_catalog
	80	#
	81	# 3033 2018-05-23 15:26:19Z raasch
[3025]	82	# -T option not required for interactive runs (tasks per node =
	83	# total number of cores is assumed as default, if option is not given),
	84	# reformatting of a few messages,
	85	# bugfix: destination output directory is created if attribute "pe" is set in
	86	# .palm.iofiles
	87	#
	88	# 2718 2018-01-02 08:49:38Z maronga
[2993]	89	# bugfix of r2990
	90	#
	91	# 2718 2018-01-02 08:49:38Z maronga
[2990]	92	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	93	# not in the working directory from where palmrun is called
	94	#
	95	# 2718 2018-01-02 08:49:38Z maronga
[2957]	96	# svfout in the activation string will be replaced now by svfin in case of
	97	# automatic restarts
	98	#
	99	# 2718 2018-01-02 08:49:38Z maronga
[2906]	100	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	101	# the possible output or input of sky view factors
	102	#
	103	# 2718 2018-01-02 08:49:38Z maronga
[2834]	104	# "fname" renamed to "jobname"
	105	#
	106	# 2718 2018-01-02 08:49:38Z maronga
[2799]	107	# parameters are allowed in output commands (OC:)
	108	#
	109	# 2718 2018-01-02 08:49:38Z maronga
[2789]	110	# bugfix: exit if no queue has been given neither with option -q nor in the
	111	# configuration file
	112	#
	113	# 2718 2018-01-02 08:49:38Z maronga
[2762]	114	# file connection file from trunk/SCRIPTS is taken by default
	115	#
	116	# 2718 2018-01-02 08:49:38Z maronga
[2716]	117	# Corrected "Former revisions" section
	118	#
	119	# 2696 2017-12-14 17:12:51Z kanani
	120	# Change in file header (GPL part)
	121	#
	122	# 2693 2017-12-13 12:33:49Z raasch
[2693]	123	# replacement of variables given by {{<variable>}} in configuration file is now
	124	# done in a more general way, variable names are written in small letters
	125	#
	126	# 2670 2017-12-06 16:32:19Z raasch
[2670]	127	# test printouts removed
	128	#
	129	# 2669 2017-12-06 16:03:27Z raasch
[2669]	130	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	131	# removed,
	132	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	133	# files,
	134	# informative messages in case of missing optional input files shortened
	135	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	136	#
	137	# 2638 2017-11-23 12:44:23Z raasch
[2610]	138	# use of wildcards in file connection statements enabled
	139	#
	140	# 2605 2017-11-09 15:31:46Z raasch
[2605]	141	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	142	# will not be sent with the job file any more, but copied into the
[2610]	143	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	144	#
	145	# 2600 2017-11-01 14:11:20Z raasch
[2600]	146	# cycle numbers are made three digits wide
	147	#
	148	# 2566 2017-10-20 08:50:47Z raasch
[2566]	149	# execute command for combine_plot_fields added
	150	# "TEMPDIR" renamed "tempdir"
	151	# temporary working directory for local batch jobs is created immediately within
	152	# the user's palmrun call, due to a requirement of the "grid engine" batch
	153	# system, where the working directory is given with batch directive -wd and must
	154	# already exist when the job is submitted,
	155	# informative messages in non-trace mode reduced and partly reformatted
	156	#
	157	# 2551 2017-10-18 07:25:11Z raasch
[2551]	158	# TEMPDIR added as replacement string to be used in batch directives
	159	#
	160	# 2512 2017-10-04 08:26:59Z raasch
[2507]	161	# bugfix for determining cycle numbers of NetCDF input files
	162	#
	163	# 2506 2017-09-29 08:30:37Z raasch
[2506]	164	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	165	# host configuration added to SOURCES_FOR_RUN_... folder name
	166	# host_identifier renamed host_configuration
	167	# option -W added to allow for job dependencies
	168	#
	169	# 2501 2017-09-26 11:41:55Z raasch
[2501]	170	# default value for number of cores (option -X) set to 1
	171	# bugfix for mechanism which overwrites configuration file settings with values
	172	# provided by palmrun options
	173	#
	174	# 2499 2017-09-22 16:47:58Z kanani
[2499]	175	# option -h named configuration identifier
	176	#
	177	# 2480 2017-09-19 06:24:14Z maronga
[2480]	178	# bugfix for last revision
	179	#
	180	# 2479 2017-09-19 06:12:16Z raasch
[2479]	181	# option -A (project account number) added
	182	#
	183	# 2422 2017-09-08 08:25:41Z raasch
[2410]	184	# initial revision
[2380]	185	#
	186	#--------------------------------------------------------------------------------#
	187	# palmrun - script for running PALM jobs on local and remote hosts
	188	#--------------------------------------------------------------------------------#
	189
	190
	191
	192	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	193
	194	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	195	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	196	# (TOO MANY ARGUMENTS - PROBLEM)
	197	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	198
[2610]	199	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	200	typeset -i nr_of_output_files=0
[2380]	201	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	202	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	203	# SCRIPT-OPTION ARGUMENTS
	204	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	205	typeset -i icycle inode ival maxcycle mpi_tasks
	206	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	207
	208	activation_string_list=""
	209	AddFilenames=""
	210	combine_plot_fields=true
	211	compiler_name=""
	212	compiler_name_ser=""
	213	compiler_options=""
[3236]	214	configuration_identifier="default"
[2501]	215	cores=1
[2380]	216	cores_atmos=0
	217	cores_ocean=0
	218	coupled_dist=""
	219	cpp_options=""
	220	cpumax=0
[2506]	221	create_batch_job=false
[2380]	222	create_jobfile_only=false
	223	create_remote_batch_job=false
	224	dashes=" ----------------------------------------------------------------------------"
	225	defaultqueue=""
[2506]	226	delete_temporary_catalog=true
[2380]	227	do_compile=true
	228	do_trace=false
	229	executable=""
	230	execute_command=""
	231	execution_error=false
[2762]	232	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	233	global_revision=""
	234	hostfile=""
	235	hp=""
	236	keep_data_from_previous_run=false
	237	link_local_input=false
	238	link_local_output=false
[2388]	239	linker_options=""
[2385]	240	local_jobcatalog=""
[2380]	241	locat=normal
	242	makefile=""
	243	max_par_io_str=""
	244	prc=$0
	245	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	246	do
	247	prc=`echo $prc \| cut -f2- -d"/"`
	248	done
	249	module_calls=""
[2506]	250	palmrun_memory=""
[2380]	251	palmrun_script_name=$prc
	252	openmp=false
[2506]	253	previous_job=""
[2479]	254	project_account=""
[2380]	255	queue=none
[2906]	256	read_svf=""
[2380]	257	restart_run=false
	258	return_address=""
[2385]	259	remote_jobcatalog=""
[2380]	260	remote_username=""
	261	running_in_batch_mode=false
[3313]	262	running_in_test_mode=false
[2380]	263	run_coupled_model=false
	264	run_id=""
[3236]	265	run_id_number=""
	266	run_identifier=test
[2380]	267	silent=false
	268	source_list=""
	269	source_path=""
[2501]	270	tasks_per_node=0
[2380]	271	threads_per_task=1
	272	transfer_problems=false
[2384]	273	user_source_path=""
[2506]	274	use_existing_sources_folder=""
[2380]	275	use_openmp=false
[3033]	276	version="palmrun 1.0 Rev$Rev: 3573 $"
[2380]	277	working_directory=`pwd`
	278	write_binary=""
[2906]	279	write_svf=""
[2380]	280
	281
	282	# ERROR HANDLING IN CASE OF EXIT
[2404]	283	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	284	then
	285
	286	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	287	(( i = 0 ))
	288	while (( i < iec ))
	289	do
	290	(( i = i + 1 ))
	291	printf "\n *** Execution of ERROR-command:\n"
	292	printf " >>> ${err_command[$i]}\n"
	293	eval ${err_command[$i]}
	294	done
[2566]	295	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	296	printf "\n\n+++ palmrun crashed \n\n"
	297	exit 1
	298	elif [[ $locat != normal ]]
[2380]	299	then
[3312]	300	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	301	printf "\n+++ palmrun killed by \"^C\" \n\n"
	302	exit 2
	303	else
[2566]	304	printf "\n --> palmrun finished\n\n"
[3312]	305	exit 0
[2380]	306	fi' exit
	307
	308
	309	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	310	trap 'locat=control_c
	311	exit 1
[2380]	312	' 2
	313
	314
	315	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	316	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	317	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]	318	do
	319	case $option in
	320	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	321	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	322	(b) create_batch_job=true; prc="$prc -b";;
	323	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	324	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	325	(C) restart_run=true; prc="$prc -C";;
	326	(F) create_jobfile_only=true;;
	327	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	328	(i) run_id_number=$OPTARG;;
[2380]	329	(j) running_in_batch_mode=true;;
	330	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	331	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	332	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	333	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	334	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	335	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	336	(R) return_address=$OPTARG;;
	337	(s) source_list=$OPTARG;;
[2501]	338	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	339	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	340	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	341	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	342	(v) silent=true; prc="$prc -v";;
[2506]	343	(V) use_existing_sources_folder="-V";;
[2380]	344	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	345	(W) previous_job=$OPTARG;;
[2380]	346	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	347	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	348	(y) ocean_file_appendix=true; prc="$prc -y";;
	349	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	350	(z) running_in_test_mode=true;;
[2380]	351	(Z) combine_plot_fields=false; prc="$prc -Z";;
	352	(\?) printf "\n +++ unknown option $OPTARG \n"
	353	printf "\n --> type \"$0 ?\" for available options \n"
	354	locat=parameter;exit;;
	355	esac
	356	done
	357
	358
	359	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	360	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	361	(( to_shift = $OPTIND - 1 ))
	362	shift $to_shift
	363
	364	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	365	if [[ "$1" = "?" ]]
	366	then
	367	(printf "\n *** Description of available palmrun options:\n"
	368	printf "\n Option Description Default-Value"
	369	printf "\n -a activation string list \"\" "
[2479]	370	printf "\n -A project account number ---"
[2380]	371	printf "\n -b batch-job on local machine ---"
	372	printf "\n -B do not delete temporary directory at end ---"
[3455]	373	printf "\n -c configuration identifier \"default\" "
[2380]	374	printf "\n -F create batch job file only ---"
	375	printf "\n -k keep data from previous run"
	376	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	377	printf "\n -M Makefile name Makefile"
	378	printf "\n -O threads per openMP task ---"
	379	printf "\n -q queue \"$queue\" "
[3455]	380	printf "\n -r run identifier test"
[2380]	381	printf "\n -s filenames of routines to be compiled \"\" "
	382	printf "\n must end with .f, .f90, .F, or .c !"
	383	printf "\n use \"..\" for more than one file and wildcards"
	384	printf "\n -s LM compiles all locally modified files"
	385	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	386	printf "\n -T tasks per node ---"
[2380]	387	printf "\n -u username on remote machine \"\" "
	388	printf "\n -v no prompt for confirmation ---"
[2506]	389	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	390	printf "\n -w maximum parallel io streams as given by -X"
[2506]	391	printf "\n -W name of job to wait for ---"
[2380]	392	printf "\n -x tracing of palmrun for debug purposes ---"
	393	printf "\n -X # of processors (on parallel machines) 1"
	394	printf "\n -y add appendix \"_O\" to all local output"
	395	printf "\n files (ocean precursor runs followed by"
	396	printf "\n coupled atmosphere-ocean runs) ---"
	397	printf "\n -Y run coupled model, \"#1 #2\" with"
	398	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	399	printf "\n -Z skip combine_plot_fields at the end of "
	400	printf "\n the simulation ---"
	401	printf "\n "
	402	printf "\n Possible values of positional parameter <modus>:"
	403	printf "\n \"?\" - this outline \n\n") \| more
	404	exit
	405	elif [[ "$1" != "" ]]
	406	then
	407	printf "\n +++ positional parameter $1 unknown \n"
	408	locat=parameter; exit
	409	fi
	410
	411
	412
	413	# SHORT STARTING MESSAGE
	414	printf "\n*** $version "
	415	printf "\n will be executed. Please wait ..."
	416
	417
[2506]	418	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	419	config_file=.palm.config.$configuration_identifier
	420	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	421
	422
	423	# CHECK, IF CONFIGURATION FILE EXISTS
	424	if [[ ! -f $config_file ]]
	425	then
	426	printf "\n\n +++ configuration file: "
	427	printf "\n $config_file"
	428	printf "\n does not exist"
	429	locat=connect; exit
	430	fi
	431
	432
[2762]	433	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	434	if [[ -f .palm.iofiles ]]
	435	then
[3236]	436
	437	# CHECK VERSION MISMATCH
[3573]	438	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	439	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	440	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	441	then
	442	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	443	then
	444	printf "\n\n +++ WARNING: A file connection file has been found in your"
	445	printf "\n working directory, but its revision does not match"
	446	printf "\n the revision of the default (trunk) version."
[3294]	447	printf "\n You may need to update your connection file"
	448	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	449	fi
	450	fi
	451
[2762]	452	fileconnection_file=.palm.iofiles
[3236]	453
[2762]	454	fi
	455
	456
[2380]	457	# CHECK, IF FILE CONNECTION FILE EXISTS
	458	if [[ ! -f $fileconnection_file ]]
	459	then
	460	printf "\n\n +++ file connection file: "
	461	printf "\n $fileconnection_file"
	462	printf "\n does not exist"
	463	locat=connect; exit
	464	fi
	465
	466
[2404]	467	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	468	if [[ "$activation_string_list" = "" ]]
	469	then
	470	printf "\n\n +++ no activation string list given: "
	471	printf "\n please set palmrun option \"-a\" "
	472	locat=palmrun_option; exit
	473	fi
	474
	475
	476	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	477	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	478	then
	479	write_binary=true
	480	else
	481	write_binary=false
	482	fi
	483
[2906]	484	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	485	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	486	then
	487	write_svf=true
	488	else
	489	write_svf=false
	490	fi
[2404]	491
[2906]	492	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	493	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	494	then
	495	read_svf=true
	496	else
	497	read_svf=false
	498	fi
	499
	500
[2380]	501	# READ AND EVALUATE THE CONFIGURATION-FILE
	502	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	503
	504	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	505	while read line
	506	do
	507
	508	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	509	eval line=\"$line\"
	510
	511
	512	# INTERPRET THE LINE
	513	if [[ "$(echo $line)" = "" ]]
	514	then
	515
	516	# EMPTY LINE, NO ACTION
	517	continue
	518
	519	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	520	then
	521
	522	# LINE IS A COMMENT LINE
	523	continue
	524
	525	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	526	then
	527
	528	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	529	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	530	value=`echo $line \| cut -d" " -s -f2-`
	531
	532
	533	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	534	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	535	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	536	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	537	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	538	# CONFIGURATION-FILE.
	539	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	540	then
	541	eval export $var="\$value"
	542
	543	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	544	if [[ $do_trace = true ]]
	545	then
	546	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	547	fi
	548	fi
	549
	550	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	551	then
	552
	553	# LINE DEFINES BATCH-DIRECTIVE
	554	(( ibd = ibd + 1 ))
	555	line=$(echo $line \| cut -c4-)
	556	batch_directive[$ibd]="$line"
	557
	558	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	559	then
	560
	561	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	562	# REMOTE TO A LOCAL HOST
	563	(( ibdt = ibdt + 1 ))
	564	line=$(echo $line \| cut -c5-)
	565	batch_directive_transfer[$ibdt]="$line"
	566
	567	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	568	then
	569
	570	# LINE DEFINES ERROR-COMMAND
	571	(( iec = iec + 1 ))
	572	line=$(echo $line \| cut -c4-)
	573	err_command[$iec]="$line"
	574
	575	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	576	then
	577
	578	# LINE DEFINES INPUT-COMMAND
	579	(( iic = iic + 1 ))
	580	line=$(echo $line \| cut -c4-)
	581	in_command[$iic]="$line"
	582
	583	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	584	then
	585
	586	# LINE DEFINES OUTPUT-COMMAND
	587	(( ioc = ioc + 1 ))
	588	line=$(echo $line \| cut -c4-)
	589	out_command[$ioc]="$line"
	590
	591	else
	592
	593	# SKIP ALL OTHER LINES
	594	continue
	595
	596	fi
	597
	598	done < $config_file
	599
	600
	601	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	602	if [[ "$fast_io_catalog" = "" ]]
	603	then
	604	printf "\n +++ no fast_io_catalog found in $config_file"
	605	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	606	locat=config_file; exit
	607	fi
[2380]	608	if [[ "$compiler_name" = "" ]]
	609	then
	610	printf "\n +++ no compiler name found in $config_file"
	611	printf "\n Please add line \"compiler_name ...\" to that file."
	612	locat=config_file; exit
	613	fi
	614	if [[ "$compiler_name_ser" = "" ]]
	615	then
	616	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	617	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	618	locat=config_file; exit
	619	fi
	620	if [[ "$compiler_options" = "" ]]
	621	then
	622	printf "\n +++ no compiler options found in $config_file"
	623	printf "\n Please add line \"compiler_options ...\" to that file."
	624	locat=config_file; exit
	625	fi
[2388]	626	if [[ "$linker_options" = "" ]]
[2380]	627	then
[2388]	628	printf "\n +++ no linker options found in $config_file"
	629	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	630	locat=config_file; exit
	631	fi
	632	if [[ "$execute_command" = "" ]]
	633	then
	634	printf "\n +++ no execute command found in $config_file"
	635	printf "\n Please add line \"execute_command ...\" to that file."
	636	locat=config_file; exit
	637	fi
	638
	639	if [[ "$hostfile" != "" ]]
	640	then
	641	if [[ $hostfile != auto && ! -f $hostfile ]]
	642	then
	643	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	644	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	645	locat=config_file; exit
	646	fi
	647	fi
	648
	649
	650	# DETERMINE THE CALL STATUS
	651	if [[ "$return_address" != "" ]]
	652	then
	653
	654	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	655	# BATCH MODE AND ...
	656	running_on_remote=true
	657
	658	else
	659
	660	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	661	if [[ "$remote_ip" != "" ]]
	662	then
	663
	664	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	665	create_remote_batch_job=true
	666
[3132]	667	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	668	if [[ "$remote_jobcatalog" = "" ]]
	669	then
	670	printf "\n +++ no remote jobcatalog found in $config_file"
	671	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	672	locat=config_file; exit
	673	fi
	674
	675
[2380]	676	fi
	677	running_on_remote=false
	678	fi
	679
	680
	681
	682	# READ AND EVALUATE THE I/O-FILE LIST
	683	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	684
	685	# READ THE FILE CONNECTION FILE LINE BY LINE
	686	while read line
	687	do
	688
[2669]	689	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	690	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	691	line=`echo "$line" \| tr -s " "`
[2380]	692
	693	# INTERPRET THE LINE
	694	if [[ "$(echo $line)" = "" ]]
	695	then
	696	# EMPTY LINE, NO ACTION
	697	continue
	698
	699	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	700	then
	701
	702	# LINE IS A COMMENT LINE
	703	true
	704
	705	else
	706
	707	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	708	# s2a: in/out - field
[2669]	709	# s2b: action - field (optional)
	710	s1=`echo "$line" \| cut -d" " -f1`
	711	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	712	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	713	then
[2669]	714	s2a=$s2
[2380]	715	s2b=""
	716	else
[2669]	717	s2a=`echo $s2 \| cut -d":" -f1`
	718	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	719	fi
[2669]	720	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	721	s4=`echo "$line" \| cut -d" " -s -f4`
	722	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	723	s5=`echo "$line" \| cut -d" " -s -f5`
	724	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	725
	726
	727	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	728	# INPUT- OR OUTPUT-LIST.
	729	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	730	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	731	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	732	# IS NOT CHECKED AND STORED.
[2610]	733	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	734	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	735	then
	736	found=false
	737	for actual in $activation_string_list
	738	do
	739	for formal in $s3
	740	do
	741	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	742	done
	743	done
	744	if [[ $found = true ]]
	745	then
	746	(( iin = iin + 1 ))
[2669]	747	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	748	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	749	if [[ "$s2a" = inopt ]]
	750	then
	751	optin_pre[$iin]=yes
	752	else
	753	optin_pre[$iin]=no
	754	fi
[2605]	755
	756	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	757	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	758	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	759	then
[2610]	760	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	761	fi
	762
[2610]	763	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	764	# THE WILDCARD FROM THE ENDING
	765	if [[ "${s5: -1}" = "*" ]]
	766	then
[2669]	767	if [[ "$s2b" = "di" ]]
[2610]	768	then
	769	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	770	printf "\n see file \"$fileconnection_file\", line"
	771	printf "\n$line"
	772	locat=iofiles_file; exit
	773	fi
	774	multin[$iin]=true
	775	string=${endin_pre[$iin]}
	776	endin_pre[$iin]="${string%?}"
	777	else
	778	multin[$iin]=false
	779	fi
[2380]	780	fi
[2669]	781	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	782	then
	783	found=false
	784	for actual in $activation_string_list
	785	do
	786	for formal in $s3
	787	do
[2670]	788	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	789	done
	790	done
	791	if [[ $found = true ]]
	792	then
	793	(( iout = iout + 1 ))
[2669]	794	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	795	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	796
[2669]	797	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	798	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	799	if [[ $formal = wildcard ]]
	800	then
	801	warnout_pre[$iout]=false
	802	else
	803	warnout_pre[$iout]=true
	804	fi
	805
[2610]	806	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	807	# THE WILDCARD FROM THE LOCAL FILENAME
	808	if [[ "${s1: -1}" = "*" ]]
	809	then
[2669]	810	if [[ "$s2b" = "di" ]]
[2610]	811	then
	812	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	813	printf "\n see file \"$fileconnection_file\", line"
	814	printf "\n$line"
	815	locat=iofiles_file; exit
	816	fi
	817	multout[$iout]=true
	818	string=${localout_pre[$iout]}
	819	localout_pre[$iout]="${string%?}"
	820	else
	821	multout[$iout]=false
	822	fi
[2380]	823	fi
[2669]	824	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	825	then
[2669]	826	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	827	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	828	locat=connect; exit
	829	fi
	830	IFS="$IFSALT"
	831	fi
	832
	833	done < $fileconnection_file
	834
	835
	836
[2501]	837	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	838	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	839	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	840	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	841	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	842	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	843
	844
	845
[2380]	846	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	847	if [[ $run_coupled_model = true ]]
	848	then
	849
	850	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	851	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	852
	853	if (( $cores_ocean + $cores_atmos != $cores ))
	854	then
	855
	856	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	857	printf "\n PEs (total) : $cores"
	858	printf "\n PEs (atmosphere): $cores_atmos"
	859	printf "\n PEs (ocean) : $cores_ocean"
	860	locat=coupling; exit
	861
	862	fi
	863
	864	fi
	865
	866
	867	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	868	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	869	# FOLDER
	870	if [[ $running_in_batch_mode = true ]]
	871	then
	872
[2506]	873	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	874	then
[2506]	875	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	876	printf "\n Please check the output of the palmrun-call"
	877	printf "\n that you did on your local host."
	878	locat=SOURCES_FOR_RUN; exit
	879	fi
	880
	881	else
	882
	883	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	884	# AUTOMATIC RESTART RUN
	885	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	886	if [[ $restart_run = false ]]
	887	then
	888
	889	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	890	# THE LOCAL HOST
	891	if [[ ! -d $source_path ]]
	892	then
	893	printf "\n\n +++ source path \"$source_path\" on local host"
	894	printf "\n \"$(hostname)\" does not exist"
	895	locat=source_path; exit
	896	fi
	897
[2990]	898	rm -rf ${base_directory}/${sources_for_run_catalog}
	899	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	900
	901	if [[ "$source_list" = LM ]]
	902	then
	903
	904	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	905	source_list=""
	906	cd $source_path
	907
	908
[2512]	909	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	910	if [[ ! -d ../.svn ]]
[2380]	911	then
	912	printf "\n\n +++ source directory"
	913	printf "\n \"$source_path\" "
	914	printf "\n is not under control of \"subversion\"."
[2512]	915	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	916	fi
	917
	918
	919	# LIST ALL MODIFIED SOURCE CODE FILES
	920	Filenames=""
[2404]	921	svn status > tmp_svnstatus
[2380]	922	while read line
	923	do
	924	firstc=`echo $line \| cut -c1`
	925	if [[ $firstc = M \|\| $firstc = "?" ]]
	926	then
	927	Name=`echo "$line" \| cut -c8-`
	928	extension=`echo $Name \| cut -d. -f2`
	929	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	930	then
	931	Filenames="$Filenames "$Name
	932	fi
	933	fi
[2404]	934	done < tmp_svnstatus
	935	rm -rf tmp_svnstatus
[2380]	936
	937
	938	# COPY FILES TO SOURCES_FOR_RUN_...
	939	for filename in $Filenames
	940	do
[2990]	941	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	942	source_list=$source_list"$filename "
	943	done
	944
	945	cd - > /dev/null
	946
	947
	948	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	949	elif [[ "$source_list" != "" ]]
	950	then
	951
	952	cd $source_path
	953
	954	for filename in $source_list
	955	do
	956
	957	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	958	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	959	then
	960	printf "\n +++ source code file: $filename"
	961	printf "\n must not contain (\"/\") "
	962	locat=source; exit
	963	fi
	964
	965	if [[ ! -f $filename ]]
	966	then
	967	printf "\n +++ source code file: $filename"
	968	printf "\n does not exist"
	969	locat=source; exit
	970	else
[2990]	971	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	972	fi
	973
	974	done
	975
	976	cd - > /dev/null
	977
	978	fi
	979
	980	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	981	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	982	if [[ ! -f $makefile ]]
	983	then
	984	printf "\n +++ file \"$makefile\" does not exist"
	985	locat=make; exit
	986	else
[2990]	987	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	988	fi
	989
	990
	991	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	992	if [[ "$user_source_path" != "" ]]
[2380]	993	then
	994
	995	# DOES THE DIRECTORY EXIST?
[2384]	996	if [[ ! -d $user_source_path ]]
[2380]	997	then
	998
	999	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1000	printf "\n \"$user_source_path\" "
[2380]	1001	printf "\n does not exist or is not a directory."
	1002	printf "\n No source code will be used from this directory!\n"
[2384]	1003	user_source_path=""
[2380]	1004	if [[ $silent == false ]]
	1005	then
	1006	sleep 2
	1007	fi
	1008
	1009	else
	1010
[2384]	1011	cd $user_source_path
[2380]	1012
	1013	Names=$(ls -1 *.f90 2>&1)
	1014	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1015	Names=$(ls -1 *.F90 2>&1)
	1016	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1017	Names=$(ls -1 *.F 2>&1)
	1018	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1019	Names=$(ls -1 *.f 2>&1)
	1020	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1021	Names=$(ls -1 *.c 2>&1)
	1022	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1023
	1024	cd - > /dev/null
[2990]	1025	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1026
	1027	# COPY MAKEFILE IF EXISTING
[2384]	1028	if [[ -f $user_source_path/Makefile ]]
[2380]	1029	then
	1030	printf "\n\n *** user Makefile from directory"
[2384]	1031	printf "\n \"$user_source_path\" is used \n"
[2380]	1032	if [[ $silent == false ]]
	1033	then
	1034	sleep 1
	1035	fi
[2384]	1036	cp $user_source_path/Makefile .
[2380]	1037	fi
	1038
	1039	for filename in $AddFilenames
	1040	do
	1041	if [[ -f $filename ]]
	1042	then
	1043	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1044	printf "\n source code directory \"$user_source_path\" "
[2380]	1045	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1046	printf "\n from directory \"$source_path\"."
	1047	locat=source; exit
	1048	fi
	1049
[2384]	1050	cp $user_source_path/$filename .
[2380]	1051	source_list="$source_list $filename"
	1052
	1053	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1054	if [[ $(grep -c $filename Makefile) = 0 ]]
	1055	then
	1056	printf "\n\n +++ user file \"$filename\" "
	1057	printf "\n is not listed in Makefile \n"
	1058	locat=source; exit
	1059	fi
	1060	done
	1061	cd - > /dev/null
	1062	fi
	1063	fi
	1064
	1065	# COPY CONFIGURATION FILES
[2990]	1066	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1067	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1068
	1069	# COPY SHELLSCRIPTS
[2990]	1070	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1071	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1072
	1073	fi
	1074
	1075	fi
	1076
[2605]	1077
[2380]	1078	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1079	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1080	if [[ "$global_revision" = "" ]]
	1081	then
	1082	global_revision=`svnversion $source_path 2>/dev/null`
	1083	global_revision="Rev: $global_revision"
	1084	fi
	1085
	1086
	1087	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1088	if [[ -n $cores ]]
	1089	then
	1090
	1091	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1092	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1093	if [[ $tasks_per_node = 0 ]]
[2380]	1094	then
[3025]	1095	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1096	then
	1097	printf "\n"
	1098	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1099	printf "\n set -T option or define tasks_per_node in the config file"
	1100	locat=tasks_per_node; (( iec = 0 )); exit
	1101	else
	1102	# DEFAULT FOR INTERACTIVE RUN
	1103	tasks_per_node=$cores
	1104	fi
[2380]	1105	fi
	1106
	1107	if (( cores < tasks_per_node ))
	1108	then
	1109	printf "\n"
	1110	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1111	printf "\n given values: -T $tasks_per_node -X $cores"
	1112	locat=tasks_per_node; (( iec = 0 )); exit
	1113	fi
	1114
	1115	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1116	(( mpi_tasks = cores / threads_per_task ))
	1117	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1118	(( ii = cores / tasks_per_node ))
	1119	(( remaining_cores = cores - ii * tasks_per_node ))
	1120	if (( remaining_cores > 0 ))
	1121	then
	1122	printf "\n"
	1123	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1124	printf "\n divisor of the total number of cores (option \"-X\")"
	1125	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1126	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1127	(( nodes = nodes + 1 ))
	1128	fi
	1129
	1130	fi
	1131
	1132
	1133	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1134	if [[ "$maximum_parallel_io_streams" = "" ]]
	1135	then
	1136	maximum_parallel_io_streams=$cores
	1137	fi
	1138
	1139
	1140	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1141	if [[ "$scp_port" != "" ]]
	1142	then
	1143	PORTOPT="-P $scp_port"
	1144	SSH_PORTOPT="-p $scp_port"
	1145	fi
	1146
	1147
	1148	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1149	# CONFIG-FILE
	1150	if [[ "$ssh_key" != "" ]]
	1151	then
	1152	ssh_key="-i $HOME/.ssh/$ssh_key"
	1153	fi
	1154
	1155
	1156	# SET QUEUE, IF NOT GIVEN
	1157	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1158	then
	1159
	1160	if [[ $queue = none && "$defaultqueue" = "" ]]
	1161	then
	1162	printf "\n"
	1163	printf "\n +++ no default queue given in configuration file and no queue"
	1164	printf "\n given with option -q"
[2789]	1165	locat=queue; exit
[2380]	1166	fi
	1167	if [[ $queue = none ]]
	1168	then
	1169	queue=$defaultqueue
	1170	fi
	1171
	1172	fi
	1173
	1174
	1175	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1176	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1177	(( i = 0 ))
[2610]	1178	(( nr_of_input_files = 0 ))
[2380]	1179	while (( i < iin ))
	1180	do
	1181	(( i = i + 1 ))
	1182
	1183	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1184	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1185	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1186	then
[2610]	1187	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1188	else
[3236]	1189	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1190	fi
	1191
[2610]	1192
[2380]	1193	# CHECK IF FILE EXISTS
	1194	if ! ls $filename* 1>/dev/null 2>&1
	1195	then
	1196
[2669]	1197	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1198	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1199	then
	1200	printf "\n\n +++ INPUT-file: "
[2610]	1201	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1202	then
	1203	printf "\n $filename"
	1204	else
[2610]	1205	printf "\n $filename.${extin_pre[$i]}"
[2380]	1206	fi
	1207	printf "\n does not exist\n"
	1208	locat=input; exit
	1209	else
[2610]	1210	(( nr_of_input_files = nr_of_input_files + 1 ))
	1211	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1212	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1213	actionin[$nr_of_input_files]="unavailable"
[2610]	1214	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1215	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1216	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1217	fi
[2605]	1218
[2380]	1219	else
	1220
[3236]	1221	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1222	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1223	# ENDINGS
[2610]	1224	if [[ "${multin[$i]}" = true ]]
	1225	then
	1226	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1227	ls -1 -d ${filename} > filelist 2>/dev/null
	1228	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1229	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1230
[2610]	1231	endings=""
	1232	while read line
	1233	do
	1234	# filename without path (i.e. after the last "/")
	1235	basefilename=$(basename ${line})
[2380]	1236
[2610]	1237	# check if there is an extension and remove it
	1238	ext=${basefilename##*.}
	1239	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1240	then
	1241	basefilename=${basefilename%.*}
	1242	fi
[2380]	1243
[2610]	1244	# check for an existing cycle number and remove it
	1245	cycle=${basefilename##*.}
	1246	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1247	then
	1248	basefilename=${basefilename%.*}
	1249	fi
[2600]	1250
[3236]	1251	# remove the run_identifier from the beginning
	1252	length_run_identifier=${#run_identifier}
	1253	ending=${basefilename:${length_run_identifier}}
[2610]	1254
	1255	# remove the ending given in the .iofiles from the beginning
	1256	endingstring="${endin_pre[$i]}"
	1257	length_ending=${#endingstring}
	1258	ending=${ending:${length_ending}}
	1259
	1260	if [[ "$ending" = "" ]]
[2600]	1261	then
[2610]	1262	# standard ending as given in the .iofiles
	1263	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1264	then
	1265	endings="$endings DEFAULT"
	1266	fi
[2600]	1267	else
[2610]	1268	# ending must start with "_", otherwise its a different file
	1269	if [[ "${ending:0:1}" = "_" ]]
	1270	then
	1271	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1272	then
	1273	endings="$endings $ending"
	1274	fi
	1275	fi
[2600]	1276	fi
[2610]	1277
	1278	done <filelist
[2380]	1279
[2610]	1280	rm filelist
[2380]	1281
[2600]	1282	else
[2610]	1283
	1284	# SINGLE NAME
	1285	endings=DEFAULT
	1286
[2600]	1287	fi
	1288
[2610]	1289	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1290	for ending in $endings
	1291	do
	1292
	1293	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1294	if [[ $ending = DEFAULT ]]
[2380]	1295	then
[2610]	1296	ending=""
	1297	fi
	1298
	1299	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1300	(( nr_of_input_files = nr_of_input_files + 1 ))
	1301	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1302	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1303	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1304	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1305	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1306	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1307
	1308
	1309	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1310	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1311	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1312	then
	1313	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1314	else
[3236]	1315	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1316	fi
[2610]	1317
	1318	# DETERMINE THE FILE'S CYCLE NUMBER
	1319	(( maxcycle = 0 ))
	1320	ls -1 -d $filename > filelist 2>/dev/null
	1321	ls -1 -d $filename.* >> filelist 2>/dev/null
	1322	while read line
	1323	do
	1324	# filename without path (i.e. after the last "/")
	1325	basefilename=$(basename ${line})
	1326
	1327	# check if there is an extension
	1328	extension=${basefilename##*.}
	1329	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1330	then
	1331	basefilename=${basefilename%.*}
	1332	fi
	1333
	1334	# check for an existing cycle number
	1335	cycle=${basefilename##*.}
	1336	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1337	then
[2669]	1338	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1339	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1340	(( icycle = $((10#$cycle)) ))
[2610]	1341	else
	1342	(( icycle = 0 ))
	1343	fi
	1344
	1345	if (( icycle > maxcycle ))
	1346	then
	1347	(( maxcycle = icycle ))
	1348
	1349	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1350	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1351	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1352	then
	1353	leading_zero=true
	1354	else
	1355	leading_zero=false
	1356	fi
	1357	fi
	1358
	1359	done <filelist
	1360	rm filelist
	1361
	1362	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1363	if [[ $leading_zero = true ]]
[2380]	1364	then
[2610]	1365	cyclestring=`printf "%03d" $maxcycle`
	1366	else
	1367	cyclestring=$maxcycle
[2380]	1368	fi
[2610]	1369
	1370	# APPEND CYCLE NUMBER TO FILENAME
	1371	if (( maxcycle > 0 ))
[2380]	1372	then
[2610]	1373	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1374	then
	1375	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1376	else
	1377	filename=${filename}.$cyclestring
	1378	fi
[2380]	1379	else
[2610]	1380	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1381	then
	1382	filename=${filename}.${extin[$nr_of_input_files]}
	1383	fi
[2380]	1384	fi
[2610]	1385
	1386	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1387	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1388	absnamein[$nr_of_input_files]=$filename
	1389	if (( maxcycle > 0 ))
[2380]	1390	then
[2610]	1391	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1392	then
	1393	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1394	else
[3236]	1395	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1396	fi
[2380]	1397	else
[2610]	1398	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1399	then
	1400	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1401	else
[3236]	1402	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1403	fi
[2380]	1404	fi
	1405
[2610]	1406	done
	1407
[2380]	1408	fi
[2610]	1409
[2380]	1410	done
	1411
[2610]	1412
[2380]	1413	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1414	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1415	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1416	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1417	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1418	# REMOTE HOST)
	1419	(( i = 0 ))
	1420	while (( i < iout ))
	1421	do
	1422	(( i = i + 1 ))
[2610]	1423	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1424	then
[2610]	1425	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1426	then
[2610]	1427	actionout_pre[$i]=""
	1428	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1429	then
[2610]	1430	actionout_pre[$i]=pe
	1431	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1432	then
[2610]	1433	actionout_pre[$i]=a
[2380]	1434	fi
	1435	(( maxcycle = 0 ))
[3236]	1436	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1437	eval catalogname=${pathout_pre[$i]}
[2380]	1438	if ! ls $filename* 1>/dev/null 2>&1
	1439	then
	1440
	1441	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1442	if cat /dev/null > $filename
	1443	then
	1444	rm $filename
	1445	else
	1446
	1447	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1448	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1449	if [[ ! -d $catalogname ]]
	1450	then
	1451	if mkdir -p $catalogname
	1452	then
	1453	printf "\n\n *** directory:"
	1454	printf "\n $catalogname"
	1455	printf "\n was created\n"
	1456	else
	1457	printf "\n\n +++ OUTPUT-file:"
	1458	printf "\n $filename"
	1459	printf "\n cannot be created, because directory does not exist"
	1460	printf "\n and cannot be created either"
	1461	printf "\n"
	1462	locat=output ; exit
	1463	fi 2>/dev/null
	1464	else
	1465	printf "\n\n +++ OUTPUT-file:"
	1466	printf "\n $filename"
	1467	printf "\n cannot be created, although directory exists"
	1468	printf "\n"
	1469	locat=output ; exit
	1470	fi
	1471	fi 2>/dev/null
	1472
	1473	fi
	1474
	1475	fi
	1476	done
	1477
	1478
	1479	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1480	if [[ $running_in_batch_mode = false ]]
	1481	then
[3236]	1482	run_id_number=$RANDOM
	1483	run_id=${run_identifier}.$run_id_number
[2380]	1484
[3236]	1485	tempdir=$fast_io_catalog/$run_id
[3346]	1486
	1487	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1488	export job_id=$run_id
	1489
[2380]	1490	fi
	1491
	1492
	1493	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1494	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1495	then
	1496
	1497	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1498	if [[ $ibd = 0 ]]
	1499	then
	1500	printf "\n"
	1501	printf "\n +++ no batch directives found in configuration file"
	1502	locat=config_file_batch_directives; (( iec = 0 )); exit
	1503	fi
	1504
	1505	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1506	done=false
[2384]	1507	cputime=$cpumax
[2380]	1508	while [[ $done = false ]]
	1509	do
[2384]	1510	if (( cputime == 0 ))
[2380]	1511	then
	1512	printf "\n +++ cpu-time is undefined"
	1513	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1514	printf "\n >>> "
[2384]	1515	read cputime 1>/dev/null 2>&1
[2380]	1516	else
	1517	done=true
	1518	fi
	1519	done
[2420]	1520	cpumax=$cputime
[2380]	1521
	1522	# CHECK THE MEMORY DEMAND
	1523	done=false
	1524	while [[ $done = false ]]
	1525	do
	1526	if (( memory == 0 ))
	1527	then
	1528	printf "\n +++ memory demand is undefined"
	1529	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1530	printf "\n >>> "
	1531	read memory 1>/dev/null 2>&1
	1532	else
	1533	done=true
	1534	fi
	1535	done
	1536
	1537	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1538	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1539	then
	1540	while [[ -z $remote_username ]]
	1541	do
[2420]	1542	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1543	printf "\n >>> Please type username:"
	1544	printf "\n >>> "
	1545	read remote_username
	1546	done
	1547	fi
	1548
	1549	else
	1550
[2420]	1551	if [[ $running_in_batch_mode = false ]]
	1552	then
	1553	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1554	cpumax=$cputime
	1555	else
	1556	cputime=$cpumax
	1557	fi
[2380]	1558
	1559	fi
	1560
	1561
	1562	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1563	(( cpu_hours = cputime / 3600 ))
	1564	(( resttime = cputime - cpu_hours * 3600 ))
	1565	(( cpu_minutes = resttime / 60 ))
	1566	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1567	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1568
	1569
	1570	# OUTPUT OF THE PALMRUN-HEADER
	1571	calltime=$(date)
	1572	printf "\n"
	1573	printf "#------------------------------------------------------------------------# \n"
	1574	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1575	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1576	printf "\| \| \n"
	1577	column1="called on:"; column2=$(hostname)
	1578	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1579	if [[ $create_remote_batch_job = true ]]
	1580	then
[3236]	1581	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1582	else
	1583	if [[ $running_on_remote = true ]]
	1584	then
[3236]	1585	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1586	else
[3236]	1587	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1588	fi
	1589	fi
	1590	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1591
	1592	column1="running in:"
	1593	if [[ $running_in_batch_mode = true ]]
	1594	then
	1595	column2="batch job mode"
	1596	else
	1597	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1598	then
	1599	column2="job creation mode"
	1600	else
	1601	column2="interactive run mode"
	1602	fi
	1603	fi
	1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1605
[2479]	1606	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1607	then
[2480]	1608	if [[ "$project_account" != "" ]]
[2479]	1609	then
	1610	column1="project account number:"
	1611	column2="$project_account"
	1612	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1613	fi
	1614	fi
	1615
[2380]	1616	if [[ -n $cores ]]
	1617	then
	1618	if [[ $run_coupled_model = false ]]
	1619	then
	1620	column1="number of cores:"; column2=$cores
	1621	else
	1622	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1623	fi
	1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1625	fi
	1626	if [[ -n $tasks_per_node ]]
	1627	then
	1628	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1630	if (( remaining_cores > 0 ))
	1631	then
	1632	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1634	fi
	1635	fi
	1636	if [[ $maximum_parallel_io_streams != $cores ]]
	1637	then
	1638	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1640	fi
	1641	if [[ $use_openmp = true ]]
	1642	then
	1643	column1="threads per task:"; column2="$threads_per_task"
	1644	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1645	fi
[2384]	1646	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1647	then
[2506]	1648	column1="memory demand / PE":; column2="$memory MB"
	1649	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1650	column1="job cpu time (h:m:s):"; column2="$timestring"
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	fi
[2380]	1653	printf "\| \| \n"
	1654	if [[ "$source_list" != "" ]]
	1655	then
	1656	if [[ "$make_options" != "" ]]
	1657	then
	1658	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1659	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1660	line=$(echo "$make_options" \| cut -c46-)
	1661	while [[ "$line" != "" ]]
	1662	do
	1663	column1=""
	1664	column2=$(echo "$line" \| cut -c-45)
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1666	line=$(echo "$line" \| cut -c46-)
	1667	done
	1668	fi
	1669	fi
	1670
	1671	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1672	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1673	line=$(echo "$cpp_options" \| cut -c46-)
	1674	while [[ "$line" != "" ]]
	1675	do
	1676	column1=""
	1677	column2=$(echo "$line" \| cut -c-45)
	1678	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1679	line=$(echo "$line" \| cut -c46-)
	1680	done
	1681
	1682	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1683	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1684	line=$(echo "$compiler_options" \| cut -c46-)
	1685	while [[ "$line" != "" ]]
	1686	do
	1687	column1=""
	1688	column2=$(echo "$line" \| cut -c-45)
	1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1690	line=$(echo "$line" \| cut -c46-)
	1691	done
	1692
[2388]	1693	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1695	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1696	while [[ "$line" != "" ]]
	1697	do
	1698	column1=""
	1699	column2=$(echo "$line" \| cut -c-45)
	1700	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1701	line=$(echo "$line" \| cut -c46-)
	1702	done
	1703
	1704	if [[ "$login_init_cmd" != "" ]]
	1705	then
	1706	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1707	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1708	line=$(echo "$login_init_cmd" \| cut -c46-)
	1709	while [[ "$line" != "" ]]
	1710	do
	1711	column1=""
	1712	column2=$(echo "$line" \| cut -c-45)
	1713	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1714	line=$(echo "$line" \| cut -c46-)
	1715	done
	1716	fi
	1717
	1718	if [[ "$module_commands" != "" ]]
	1719	then
	1720	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1721	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1722	line=$(echo "$module_commands" \| cut -c46-)
	1723	while [[ "$line" != "" ]]
	1724	do
	1725	column1=""
	1726	column2=$(echo "$line" \| cut -c-45)
	1727	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1728	line=$(echo "$line" \| cut -c46-)
	1729	done
	1730	fi
	1731	printf "\| \| \n"
[3236]	1732	column1="run identifier:"; column2=$run_identifier
[2380]	1733	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1734	column1="activation string list:"; column2=$(echo $activation_string_list)
	1735	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1736
	1737	if [[ "$ocean_file_appendix" = true ]]
	1738	then
	1739	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1740	fi
	1741
	1742	if [[ "$source_list" != "" ]]
	1743	then
	1744	printf "\| \| \n"
	1745	printf "\| Files to be compiled: \| \n"
	1746	line=$source_list
	1747	while [[ "$line" != "" ]]
	1748	do
	1749	linestart=$(echo $line \| cut -c-70)
	1750	printf "\| %-70s \| \n" "$linestart"
	1751	line=$(echo "$line" \| cut -c71-)
	1752	done
	1753	fi
	1754	printf "#------------------------------------------------------------------------#"
	1755
	1756
	1757
	1758	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1759	if [[ $do_trace = true ]]
	1760	then
	1761	(( i = 0 ))
[2610]	1762	while (( i < nr_of_input_files ))
[2380]	1763	do
	1764	(( i = i + 1 ))
	1765	if (( i == 1 ))
	1766	then
	1767	printf "\n\n >>> INPUT-file assignments:\n"
	1768	fi
	1769	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1770	done
	1771	(( i = 0 ))
	1772	while (( i < iout ))
	1773	do
	1774	(( i = i + 1 ))
	1775	if (( i == 1 ))
	1776	then
	1777	printf "\n\n >>> OUTPUT-file assignments:\n"
	1778	fi
	1779	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1780	done
	1781	(( i = 0 ))
	1782	while (( i < iic ))
	1783	do
	1784	(( i = i + 1 ))
	1785	if (( i == 1 ))
	1786	then
	1787	printf "\n\n >>> INPUT-commands:\n"
	1788	fi
	1789	printf "\n ${in_command[$i]}"
	1790	done
	1791	(( i = 0 ))
	1792	while (( i < ioc ))
	1793	do
	1794	(( i = i + 1 ))
	1795	if (( i == 1 ))
	1796	then
	1797	printf "\n\n >>> OUTPUT-commands:\n"
	1798	fi
	1799	printf "\n ${out_command[$i]}"
	1800	done
	1801	fi
	1802
	1803	# QUERY FOR CONTINUE
	1804	if [[ $silent = false && $running_in_batch_mode = false ]]
	1805	then
	1806	antwort=dummy
	1807	printf "\n\n"
	1808	printf " >>> everything o.k. (y/n) ? "
	1809	while read antwort
	1810	do
	1811	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1812	then
	1813	printf " >>> everything o.k. (y/n) ? "
	1814	else
	1815	break
	1816	fi
	1817	done
	1818	if [[ $antwort = n \|\| $antwort = N ]]
	1819	then
	1820	locat=user_abort; (( iec = 0 )); exit
	1821	fi
	1822	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1823	then
[2566]	1824	printf "\n *** batch-job will be created and submitted"
[2380]	1825	else
[2566]	1826	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1827	fi
	1828	fi
	1829
	1830
	1831
	1832	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1833	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1834	then
	1835
	1836	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1837	then
[2566]	1838	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1839	else
[2566]	1840	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1841	fi
	1842
[2422]	1843	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1844	# IT SHALL BE CREATED
	1845	ask_for_make_depository=false
	1846	if [[ $create_remote_batch_job = true ]]
	1847	then
	1848
	1849	line=`grep %base_directory $config_file`
[3236]	1850	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1851	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1852
[3236]	1853	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1854	then
	1855	printf "\n\n +++ make depository \"${make_depository}\""
	1856	printf "\n on remote host not found!"
	1857	ask_for_make_depository=true
	1858	fi
[3236]	1859	rm ${configuration_identifier}_last_make_protokoll
[2422]	1860
	1861	else
	1862
	1863	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1864	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1865	if [[ ! -d ${make_depository} ]]
	1866	then
	1867	printf "\n\n +++ make depository \"${make_depository}\""
	1868	printf "\n on local host not found!"
	1869	ask_for_make_depository=true
	1870	fi
	1871
	1872	fi
	1873
	1874	if [[ $ask_for_make_depository = true ]]
	1875	then
	1876
	1877	antwort=dummy
	1878	printf "\n\n"
	1879	printf " >>> Create a new one (y/n) ? "
	1880	while read antwort
	1881	do
	1882	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1883	then
	1884	printf " >>> Create a new one (y/n) ? "
	1885	else
	1886	break
	1887	fi
	1888	done
	1889	if [[ $antwort = n \|\| $antwort = N ]]
	1890	then
	1891	locat=user_abort; (( iec = 0 )); exit
	1892	fi
	1893
[2566]	1894	if [[ $do_trace = true ]]
	1895	then
[3455]	1896	palmbuild -c $configuration_identifier
[2566]	1897	else
[3455]	1898	palmbuild -v -c $configuration_identifier
[2566]	1899	fi
[2422]	1900
[3312]	1901	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1902	then
	1903
	1904	# ABORT IN CASE OF COMPILATION PROBLEMS
	1905	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1906	locat=make_depository
	1907	exit
	1908	else
	1909	echo " *** now continue with creating executable and other sources"
	1910	fi
	1911
	1912	fi
	1913
[2566]	1914	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1915	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1916
[3312]	1917	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1918	then
	1919
	1920	# ABORT IN CASE OF COMPILATION PROBLEMS
	1921	printf "\n +++ error while creating executable and/or other sources"
	1922	locat=execution
[2990]	1923	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1924	exit
	1925
	1926	else
	1927
[2566]	1928	printf " *** executable and other sources created\n"
[2990]	1929	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1930
	1931	fi
	1932
	1933	fi
	1934
	1935
[2669]	1936	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1937	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1938	if [[ $create_remote_batch_job = true ]]
	1939	then
	1940	(( i = 0 ))
[2610]	1941	while (( i < nr_of_input_files ))
[2605]	1942	do
	1943	(( i = i + 1 ))
[2669]	1944	if [[ "${actionin[$i]}" = tr ]]
[2605]	1945	then
	1946	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1947	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1948	fi
	1949	done
	1950	if (( i > 0 ))
	1951	then
[3025]	1952	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1953	fi
	1954	fi
	1955
	1956
[2380]	1957	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1958	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1959	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1960	then
	1961
	1962	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1963	if [[ $running_in_batch_mode = false ]]
	1964	then
	1965	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1966	# FOLDER
[2566]	1967	mkdir -p $tempdir
	1968	chmod go+rx $tempdir
	1969	cd $tempdir
	1970	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1971	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1972
	1973	else
	1974
	1975	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1976	printf "\n *** running in temporary directory: $tempdir"
[2380]	1977
	1978	fi
	1979
	1980
	1981	# PROVIDE THE INPUT FILES
	1982	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1983	optional_files_missing=false
[2380]	1984	(( i = 0 ))
[2610]	1985	while (( i < nr_of_input_files ))
[2380]	1986	do
	1987	(( i = i + 1 ))
	1988	if (( i == 1 ))
	1989	then
	1990	printf "\n\n *** providing INPUT-files:\n$dashes"
	1991	fi
	1992
	1993
	1994	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1995	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1996	then
[2669]	1997	optional_files_missing=true
[2380]	1998	continue
	1999	fi
	2000
	2001	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2002	files_for_cores=false; filetype=file
	2003	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2004	then
	2005	files_for_cores=true; filetype=files
	2006	actionin[$i]=""
	2007	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2008	then
	2009	actionin[$i]=""
	2010	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2011	then
	2012	files_for_cores=true; filetype=files
	2013	actionin[$i]="ln"
	2014	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2015	then
	2016	actionin[$i]="ln"
	2017	fi
	2018
	2019	if [[ $files_for_cores = true ]]
	2020	then
	2021	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2022	else
	2023	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2024	fi
	2025
	2026	# INPUT-FILES TO BE LINKED
	2027	if [[ "${actionin[$i]}" = ln ]]
	2028	then
	2029
	2030	printf "\n $filetype will be linked"
	2031	if [[ $files_for_cores = false ]]
	2032	then
	2033	if [[ -f "${absnamein[$i]}" ]]
	2034	then
	2035	ln ${absnamein[$i]} ${localin[$i]}
	2036	got_tmp[$i]=true
	2037	fi
	2038	else
	2039	if [[ -d "${absnamein[$i]}" ]]
	2040	then
[2396]	2041	mkdir -p ${localin[$i]}
[2380]	2042	cd ${absnamein[$i]}
	2043	for file in $(ls *)
	2044	do
[2566]	2045	ln $file $tempdir/${localin[$i]}
[2380]	2046	done >\|/dev/null 2>&1
[2566]	2047	cd $tempdir
[2380]	2048	fi
	2049
	2050	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2051	if [[ ! -f "${localin[$i]}/_000000" ]]
	2052	then
	2053	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2054	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2055	fi
	2056
	2057	got_tmp[$i]=true
	2058	fi
	2059	fi
	2060
	2061	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2062	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2063	then
	2064
	2065	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2066	then
	2067
	2068	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2069	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2070	printf "\n file will be provided for $cores processors"
[2396]	2071	mkdir -p ${localin[$i]}
[2380]	2072	ival=$cores
	2073	(( ii = 0 ))
	2074	while (( ii <= ival-1 ))
	2075	do
	2076	if (( ii < 10 ))
	2077	then
	2078	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2079	elif (( ii < 100 ))
	2080	then
	2081	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2082	elif (( ii < 1000 ))
	2083	then
	2084	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2085	else
	2086	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2087	fi
	2088	(( ii = ii + 1 ))
	2089	done
	2090
	2091	else
	2092
	2093	if [[ $files_for_cores = true ]]
	2094	then
	2095
	2096	# PROVIDE FILES FOR EACH CORE
	2097	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2098	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2099	printf "\n providing $cores files for the respective cores"
[2396]	2100	mkdir -p ${localin[$i]}
[2380]	2101	if [[ $link_local_input = true ]]
	2102	then
	2103	printf " files will be linked\n"
	2104	cd ${absnamein[$i]}
	2105	for file in $(ls *)
	2106	do
	2107	ln -f $file ${localin[$i]}
	2108	done
[2566]	2109	cd $tempdir
[2380]	2110	fi
	2111
	2112	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2113	if [[ ! -f "${localin[$i]}/_000000" ]]
	2114	then
	2115	if [[ $link_local_input = true ]]
	2116	then
	2117	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2118	fi
	2119	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2120	fi
	2121
	2122	else
	2123
	2124	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2125	if [[ $link_local_input = true ]]
	2126	then
	2127	printf " file will be linked\n"
	2128	ln -f ${absnamein[$i]} ${localin[$i]}
	2129	fi
[2605]	2130	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2131	if [[ ! -f "${localin[$i]}" ]]
	2132	then
	2133	if [[ $link_local_input = true ]]
	2134	then
	2135	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2136	fi
[2669]	2137	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2138	then
	2139	mv ${absnamein[$i]} ${localin[$i]}
	2140	else
	2141	cp ${absnamein[$i]} ${localin[$i]}
	2142	fi
[2380]	2143	fi
	2144	fi
	2145	fi
	2146	fi
	2147
	2148	done
	2149	if (( i != 0 ))
	2150	then
[2669]	2151	if [[ $optional_files_missing = true ]]
	2152	then
	2153	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2154	fi
[2380]	2155	printf "\n$dashes\n *** all INPUT-files provided \n"
	2156	fi
	2157
	2158
	2159	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2160	(( i = 0 ))
	2161	while (( i < iic ))
	2162	do
	2163	(( i = i + 1 ))
	2164	if (( i == 1 ))
	2165	then
	2166	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2167	fi
	2168	printf "\n >>> ${in_command[$i]}"
	2169	eval ${in_command[$i]}
	2170	if (( i == iic ))
	2171	then
	2172	printf "\n$dashes\n"
	2173	fi
	2174	done
	2175
	2176
[3313]	2177	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2178	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2179	then
	2180	progress_bar_disabled=true
	2181	else
	2182	progress_bar_disabled=false
	2183	fi
	2184
	2185
[2380]	2186	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2187	# (FILE ENVPAR WILL BE READ BY PALM)
	2188	cat > ENVPAR << EOF
[3236]	2189	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2190	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2191	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2192	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2193	maximum_cpu_time_allowed = ${cpumax}.,
	2194	revision = '$global_revision',
[3313]	2195	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2196
	2197	EOF
	2198
	2199
	2200	# STARTING THE EXECUTABLE
	2201	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2202	PATH=$PATH:$tempdir
[2380]	2203
	2204
	2205	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2206	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2207	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2208	eval line=\"$line\"
	2209	execute_command="$line"
	2210
	2211
	2212	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2213	if [[ "$execute_command_for_combine" = "" ]]
	2214	then
	2215	eval line2=\"$line2\"
	2216	execute_command_for_combine="$line2"
	2217	fi
	2218
[2380]	2219
	2220
	2221	# PROVIDE A HOSTFILE, IF REQUIRED
	2222	if [[ "$hostfile" != "" ]]
	2223	then
	2224
	2225	if [[ $hostfile = auto ]]
	2226	then
	2227	# CREATE A NEW HOSTFILE
	2228	(( ii = 1 ))
	2229	while (( ii <= cores / threads_per_task ))
	2230	do
	2231	echo $(hostname) >> hostfile
	2232	(( ii = ii + 1 ))
	2233	done
	2234	if (( cores / threads_per_task == 0 ))
	2235	then
	2236	echo $(hostname) >> hostfile
	2237	fi
	2238
	2239	else
	2240	cp $hostfile hostfile
	2241	fi
	2242	eval line=\"`head -n $ii hostfile`\"
	2243	printf "\n *** running on: $line"
	2244	fi
	2245
	2246
	2247
	2248	# SET THE NUMBER OF OPENMP-THREADS
	2249	if [[ $use_openmp = true ]]
	2250	then
	2251	export OMP_NUM_THREADS=$threads_per_task
	2252	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2253	else
	2254	export OMP_NUM_THREADS=1
	2255	fi
	2256
	2257
[2610]	2258	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2259	if [[ $run_coupled_model = false ]]
	2260	then
	2261	if [[ "$ocean_file_appendix" = true ]]
	2262	then
	2263	echo "precursor_ocean" > coupling_steering
	2264	else
	2265	echo "precursor_atmos" > coupling_steering
	2266	fi
	2267	else
	2268	(( iia = $cores_atmos / $threads_per_task ))
	2269	(( iio = $cores_ocean / $threads_per_task ))
	2270	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2271	printf "\n\n"
	2272	echo "coupled_run $iia $iio" > coupling_steering
	2273	fi
	2274
	2275	printf "\n *** execute command:"
	2276	printf "\n \"$execute_command\" \n\n"
	2277
	2278
[3393]	2279	if [[ $progress_bar_disabled = true ]]
[2380]	2280	then
[3402]	2281	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2282	exit_code=${PIPESTATUS[0]}
	2283	else
	2284	$execute_command < coupling_steering &> >(tee STDOUT)
	2285	exit_code=${PIPESTATUS[0]}
	2286	fi
[2380]	2287
[3393]	2288	if [[ ${exit_code} != 0 ]]
	2289	then
	2290
[2380]	2291	# ABORT IN CASE OF RUNTIME ERRORS
	2292	printf "\n +++ runtime error occured"
	2293	locat=execution
	2294	exit
	2295
	2296	else
	2297
	2298	printf "\n$dashes\n *** execution finished \n"
	2299
	2300	fi
	2301
	2302
	2303	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2304	# BY EACH CORE INTO ONE FILE
	2305	if [[ ! -f combine_plot_fields.x ]]
	2306	then
	2307
	2308	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2309	printf "\n 2d- and/or 3d-data may be incomplete!"
	2310	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2311
	2312	elif [[ "$combine_plot_fields" == true ]]
	2313	then
	2314
	2315	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2316	$execute_command_for_combine
	2317
	2318	else
	2319
	2320	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2321	# DATA OUTPUT
[2380]	2322	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2323	fi
	2324
	2325
	2326
	2327	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2328	(( i = 0 ))
	2329	while (( i < ioc ))
	2330	do
	2331	(( i = i + 1 ))
	2332	if (( i == 1 ))
	2333	then
	2334	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2335	fi
[2799]	2336
	2337	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2338	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2339
[2380]	2340	printf "\n >>> ${out_command[$i]}"
	2341	eval ${out_command[$i]}
	2342	if (( i == ioc ))
	2343	then
	2344	printf "\n$dashes\n"
	2345	fi
	2346	done
	2347
	2348
[2610]	2349	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2350	# WILDCARDS
[2380]	2351	(( i = 0 ))
[2610]	2352	(( nr_of_output_files = 0 ))
	2353
[2380]	2354	while (( i < iout ))
	2355	do
[2610]	2356
[2380]	2357	(( i = i + 1 ))
[2610]	2358
	2359	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2360	# CREATE A LIST FOR THE DETECTED ENDINGS
	2361	if [[ "${multout[$i]}" = true ]]
	2362	then
	2363	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2364	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2365	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2366
	2367	endings="DEFAULT"
	2368	while read line
	2369	do
	2370	# remove the local name from the beginning
	2371	localnamestring="${localout_pre[$i]}"
	2372	length_localname=${#localnamestring}
	2373	ending=${line:${length_localname}}
	2374
	2375	if [[ "$ending" != "" ]]
	2376	then
	2377	endings="$endings $ending"
	2378	fi
	2379
	2380	done <filelist
	2381
	2382	rm filelist
	2383
	2384	else
	2385
	2386	# SINGLE NAME
	2387	endings=DEFAULT
	2388
	2389	fi
	2390
	2391	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2392	for ending in $endings
	2393	do
	2394
	2395	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2396	if [[ $ending = DEFAULT ]]
	2397	then
	2398	ending=""
	2399	fi
	2400
	2401	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2402	(( nr_of_output_files = nr_of_output_files + 1 ))
	2403	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2404	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2405	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2406	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2407	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2408	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2409	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2410
	2411	done
	2412
	2413	done
	2414
	2415
	2416
	2417
	2418	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2419	(( i = 0 ))
	2420	while (( i < nr_of_output_files ))
	2421	do
	2422	(( i = i + 1 ))
[2380]	2423	if (( i == 1 ))
	2424	then
	2425	printf "\n\n *** saving OUTPUT-files:"
	2426
	2427	# GET RUN NUMBER ASSIGNED BY PALM
	2428	if [[ -f RUN_NUMBER ]]
	2429	then
	2430	read run_number < RUN_NUMBER
	2431	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2432	usecycle_option="-U $run_number"
	2433	else
	2434	run_number=0
	2435	usecycle_option=""
	2436	fi
	2437	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2438	then
[2404]	2439	printf "\n *** in case of SCP transfers to local host"
	2440	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2441	fi
	2442	printf "\n$dashes"
	2443	fi
	2444
	2445	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2446	then
	2447
[3236]	2448	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2449
	2450	# DETERMINE THE CYCLE NUMBER
	2451	ls -1 -d $filename > filelist 2>/dev/null
	2452	ls -1 -d $filename.* >> filelist 2>/dev/null
	2453	while read line
	2454	do
	2455
	2456	# filename without path (i.e. after the last "/")
	2457	basefilename=$(basename ${line})
	2458
	2459	# check if there is an extension
	2460	extension=${basefilename##*.}
	2461	if [[ "$extension" = "${extout[$i]}" ]]
	2462	then
	2463	basefilename=${basefilename%.*}
	2464	fi
	2465
	2466	# check for an existing cycle number
	2467	cycle=${basefilename##*.}
	2468	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2469	then
[2669]	2470	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2471	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2472	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2473	else
	2474	(( icycle = 1 ))
	2475	fi
	2476
	2477	if (( icycle > maxcycle ))
	2478	then
	2479	(( maxcycle = icycle ))
	2480	fi
	2481
	2482	done <filelist
	2483	rm filelist
	2484
	2485
	2486	# SET THE CYCLE NUMBER
	2487	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2488	if [[ "${actionout[$i]}" = a ]]
	2489	then
	2490	(( maxcycle = maxcycle - 1 ))
	2491	fi
	2492
	2493	(( cycnum[$i] = maxcycle ))
	2494	pathout[$i]=$filename
	2495
	2496
	2497	# ADD CYCLE NUMBER TO FILENAME
	2498	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2499	if [[ "${actionout[$i]}" != "a" ]]
	2500	then
	2501	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2502	# WITH AN EXISTING CYCLE NUMBER
	2503	if (( run_number >= cycnum[$i] ))
	2504	then
	2505	(( cycnum[$i] = run_number ))
	2506	else
	2507	if (( run_number > 0 ))
	2508	then
	2509	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2510	fi
	2511	fi
	2512	fi
	2513	if (( cycnum[$i] > 0 ))
	2514	then
[2600]	2515	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2516	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2517	fi
	2518	fi
	2519
	2520	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2521	files_for_cores=false; filetype=file
	2522	link_local_output=false
	2523	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2524	then
	2525	files_for_cores=true; filetype=directory
	2526	actionout[$i]=""
	2527	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2528	then
	2529	actionout[$i]=""
	2530	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2531	then
	2532	files_for_cores=true; filetype=directory
	2533	link_local_output=true
	2534	actionout[$i]=""
	2535	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2536	then
	2537	link_local_output
	2538	actionout[$i]=""
	2539	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2540	then
	2541	files_for_cores=true; filetype=directory
	2542	actionout[$i]="tr"
	2543	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2544	then
	2545	actionout[$i]="tr"
	2546	fi
	2547
	2548	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2549	then
[2669]	2550	if [[ ${warnout[$i]} = true ]]
	2551	then
	2552	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2553	fi
[2380]	2554	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2555	then
[2669]	2556	if [[ ${warnout[$i]} = true ]]
	2557	then
	2558	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2559	fi
[2380]	2560	else
	2561
	2562
	2563	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2564	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2565	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2566	then
	2567	if [[ $running_on_remote = true ]]
	2568	then
	2569
	2570	# SET OPTIONS FOR TRANSFER
	2571	if [[ "${actionout[$i]}" = tr ]]
	2572	then
	2573	if [[ $files_for_cores = false ]]
	2574	then
	2575	catalog_option=""
	2576	catalog_string=""
	2577	else
	2578	catalog_option="-c"
	2579	catalog_string="/"
	2580	fi
	2581	append_option=""
	2582	append_string=""
	2583	else
	2584	append_option="-A"
	2585	append_string="append"
	2586	fi
	2587
	2588	transfer_failed=false
	2589	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2590	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2591
	2592	# TRANSFER VIA SCP
	2593	if [[ "$remote_loginnode" != "" ]]
	2594	then
[3534]	2595	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]	2596	else
[3236]	2597	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]	2598	fi
[3312]	2599	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2600
	2601
	2602	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2603	if [[ $transfer_failed = true ]]
	2604	then
	2605	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2606	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2607
	2608	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2609	eval local_catalog=${pathout[$i]}
	2610	if [[ ! -d $local_catalog ]]
	2611	then
	2612	printf " *** local directory does not exist. Trying to create:\n"
	2613	printf " $local_catalog \n"
	2614	mkdir -p $local_catalog
	2615	fi
[3236]	2616	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2617	transfer_problems=true
	2618	fi
	2619
	2620	else
	2621
	2622	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2623	# BE COPIED OR APPENDED ON THIS MACHINE
	2624	if [[ "${actionout[$i]}" = tr ]]
	2625	then
	2626	actionout[$i]=""
	2627	else
	2628	actionout[$i]="a"
	2629	fi
	2630	fi
	2631	fi
	2632
	2633
	2634	# APPEND ON THIS MACHINE
	2635	if [[ "${actionout[$i]}" = "a" ]]
	2636	then
	2637	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2638	then
	2639	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2640	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2641	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2642	else
	2643	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2644	printf "\n ${pathout[$i]}\n"
	2645	cat ${localout[$i]} >> ${pathout[$i]}
	2646	fi
	2647	fi
	2648
	2649	# COPY ON THIS MACHINE
	2650	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2651	# ON DIFFERENT FILE-SYSTEMS
	2652	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2653	then
	2654
	2655	# COPY IN CASE OF RUNS ON SINGLE CORES
	2656	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2657	then
	2658	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2659	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2660	if [[ $link_local_output = true ]]
	2661	then
	2662	printf " file will be linked\n"
	2663	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2664	fi
	2665	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2666	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2667	then
	2668	if [[ $link_local_output = true ]]
	2669	then
	2670	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2671	fi
	2672	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2673	else
	2674	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2675	fi
	2676	else
	2677	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2678	printf "\n ${pathout[$i]}\n"
	2679	if [[ $link_local_output = true ]]
	2680	then
	2681	printf " file will be linked\n"
	2682	ln -f ${localout[$i]} ${pathout[$i]}
	2683	fi
	2684	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2685	if [[ ! -f "${pathout[$i]}" ]]
	2686	then
	2687	if [[ $link_local_output = true ]]
	2688	then
	2689	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2690	fi
	2691	cp ${localout[$i]} ${pathout[$i]}
	2692	else
	2693	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2694	fi
	2695	fi
	2696
	2697	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2698	then
	2699
	2700	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2701	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2702	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2703	printf "\n ${pathout[$i]}\n"
	2704	if [[ $link_local_output = true ]]
	2705	then
	2706	printf " files will be linked\n"
[2396]	2707	mkdir -p ${pathout[$i]}
[2380]	2708	cd ${localout[$i]}
	2709	for file in $(ls *)
	2710	do
	2711	ln -f $file ${pathout[$i]}
	2712	done >\|/dev/null 2>&1
[2566]	2713	cd $tempdir
[2380]	2714	fi
	2715
	2716	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2717	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2718	then
	2719	if [[ $link_local_output = true ]]
	2720	then
	2721	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2722	fi
[3025]	2723	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2724	cp -r ${localout[$i]}/* ${pathout[$i]}
	2725	fi
	2726
	2727	fi
	2728	fi
	2729	done
	2730
	2731	if (( i != 0 ))
	2732	then
	2733	if [[ $transfer_problems = true ]]
	2734	then
	2735	printf "\n$dashes\n *** OUTPUT-files saved"
	2736	printf "\n +++ WARNING: some data transfers failed! \n"
	2737	else
	2738	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2739	fi
	2740	fi
	2741
	2742
	2743	# IF REQUIRED, START A RESTART-JOB
	2744	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2745	if [[ -f CONTINUE_RUN ]]
	2746	then
	2747
	2748	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2749	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2750	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2751	# -b START A BATCH JOB
	2752	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2753	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2754	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2755
[2957]	2756	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2757	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2758	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2759	then
	2760	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2761	fi
[2380]	2762
	2763	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2764	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2765	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2766	then
[2381]	2767	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2768	fi
	2769
	2770
	2771	# START THE RESTART-JOB
	2772	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2773	echo " $prc"
	2774	printf "\n$dashes\n"
	2775	if [[ $running_on_remote = true ]]
	2776	then
	2777
	2778	echo "*** ssh will be used to initiate restart-runs!"
	2779	echo " return_address=\"$return_address\" "
	2780	echo " return_username=\"$local_username\" "
	2781
	2782	if [[ "$remote_loginnode" != "" ]]
	2783	then
[3534]	2784	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]	2785	else
[3534]	2786	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2787	fi
	2788
	2789	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2790	sleep 30
	2791
	2792	else
	2793
	2794	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2795	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2796
	2797	fi
	2798
[3132]	2799	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2800	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2801	then
	2802	printf "\n$dashes\n +++ creating restart run failed \n"
	2803	locat=create_restart
[3455]	2804	rm palmrun_restart.log
[3132]	2805	exit
	2806	else
	2807	printf "\n$dashes\n *** restart run initiated \n"
	2808	rm palmrun_restart.log
	2809	fi
[2380]	2810
[3132]	2811
[2380]	2812	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2813	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2814	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2815	# MAY BE VERY HUGE)
	2816	(( i = 0 ))
[2610]	2817	while (( i < nr_of_input_files ))
[2380]	2818	do
	2819	(( i = i + 1 ))
	2820	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2821	then
	2822	rm -r ${absnamein[$i]}
	2823	fi
	2824	done
	2825
	2826	fi
	2827
	2828
	2829	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2830	cd $HOME
[2566]	2831	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2832
	2833
	2834	else
	2835
	2836
	2837	# PREPARING ACTIONS,
	2838	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2839
	2840	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2841	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2842	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2843	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2844	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2845	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2846	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2847	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2848	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2849	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2850	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2851	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2852	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2853	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2854	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2855	if [[ $create_remote_batch_job = true ]]
	2856	then
	2857	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2858	if [[ $do_trace = true ]]
	2859	then
	2860	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2861	fi
[2380]	2862	elif [[ $create_batch_job = true ]]
	2863	then
	2864	palmrun_com=${palmrun_com}" -j"
[2420]	2865	if [[ $do_trace = true ]]
	2866	then
	2867	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2868	fi
[2380]	2869	fi
	2870
	2871
	2872	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2873	# REMOTE HOST
[3236]	2874	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2875	job_protocol_file=$job_protocol_file_local
	2876	if [[ $create_remote_batch_job = true ]]
	2877	then
[3236]	2878	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2879	job_protocol_file=$job_protocol_file_remote
	2880	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2881	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2882	fi
	2883
	2884
	2885	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2886	jobfile=jobfile.$run_id_number
[2380]	2887
	2888
	2889	# FIRST CREATE THE BATCH DIRECTIVES
	2890	(( i = 0 ))
	2891	while (( i < ibd ))
	2892	do
	2893	(( i = i + 1 ))
[2693]	2894	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2895	eval line=\"$line\"
	2896	echo "$line" >> $jobfile
	2897	done
	2898	echo " " >> $jobfile
	2899
	2900
	2901	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2902	# PROTOCOL
	2903	if [[ $create_remote_batch_job = true ]]
	2904	then
[3236]	2905	echo "set +vx" >> $jobfile
	2906	echo "trap '" >> $jobfile
	2907	echo "set +vx" >> $jobfile
	2908	echo "cd ${remote_jobcatalog}" >> $jobfile
	2909	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2910
	2911	# ADD THE BATCH DIRECTIVES
	2912	(( i = 0 ))
	2913	while (( i < ibdt ))
	2914	do
	2915	(( i = i + 1 ))
[2693]	2916	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2917	eval line=\"$line\"
	2918	echo "$line" >> $jobfile
	2919	done
	2920	echo " " >> $jobfile
	2921
	2922	echo "set -x" >> $jobfile
[3534]	2923	if [[ "$remote_loginnode" != "" ]]
	2924	then
	2925	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}\" " >> $jobfile
	2926	else
	2927	echo "${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
	2928	fi
[2380]	2929	echo "%%END%%" >> $jobfile
	2930	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2931	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2932	echo "rm $scpjob_file" >> $jobfile
[2404]	2933	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2934	echo "set -x" >> $jobfile
	2935	echo " ' exit" >> $jobfile
	2936	fi
	2937
	2938
	2939	# ACTIVATE ERROR-TRACEBACK
	2940	if [[ $do_trace = true ]]
	2941	then
	2942	echo "set -x" >> $jobfile
	2943	else
	2944	echo "set +vx" >> $jobfile
	2945	fi
	2946
	2947
	2948	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2949	if [[ "$login_init_cmd" != "" ]]
	2950	then
	2951	echo "$login_init_cmd" >> $jobfile
	2952	fi
	2953	if [[ "$module_commands" != "" ]]
	2954	then
	2955	echo "$module_commands" >> $jobfile
	2956	fi
	2957
	2958
	2959	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2960	if [[ $create_remote_batch_job = true ]]
	2961	then
	2962	echo "mkdir $tempdir" >> $jobfile
	2963	echo "chmod go+rx $tempdir" >> $jobfile
	2964	else
	2965	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2966	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2967	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2968	mkdir $tempdir
	2969	chmod go+rx $tempdir
	2970	fi
	2971	echo "cd $tempdir" >> $jobfile
	2972	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2973	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2974	echo "export PATH=.:\$PATH" >> $jobfile
	2975	echo "export execute_palmrun=true" >> $jobfile
	2976
	2977
	2978	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2979	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2980	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2981	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2982	echo "export LOCAL_PWD" >> $jobfile
	2983
	2984
	2985	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2986	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2987	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2988
	2989
	2990	# CALL PALMRUN WITHIN THE JOB
	2991	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2992	echo "set -x" >> $jobfile
	2993	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2994
	2995
	2996	# TRANSFER JOBFILE TO THE TARGET HOST
	2997	if [[ $create_jobfile_only = false ]]
	2998	then
	2999
[3505]	3000	# CREATE LOCAL JOB FOLDER
	3001	eval local_jobcatalog=$local_jobcatalog
	3002	if [[ ! -d $local_jobcatalog ]]
	3003	then
	3004	echo " "
	3005	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3006	mkdir $local_jobcatalog
	3007	fi
	3008
[2380]	3009	if [[ $create_remote_batch_job = true ]]
	3010	then
	3011
[2420]	3012	echo " "
[2566]	3013	echo " *** transfer of job to remote host via scp"
[3505]	3014
	3015	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3016	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3017
	3018	# COPY THE JOB FILE
[2420]	3019	if [[ $do_trace = true ]]
	3020	then
[3236]	3021	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3022	fi
[3236]	3023	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3024
[3505]	3025	# SUBMIT THE JOB
[3573]	3026	printf " *** submit the job (output of submit command, \"
	3027	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3028	if [[ $do_trace = true ]]
	3029	then
[3549]	3030	echo " echo \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null"
[2420]	3031	fi
[3549]	3032	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null
[2380]	3033
	3034	elif [[ $create_batch_job = true ]]
	3035	then
	3036
[2385]	3037	eval local_jobcatalog=$local_jobcatalog
[3236]	3038	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3039	cd $local_jobcatalog
[2380]	3040	echo " "
[2420]	3041	echo " *** submit the job"
	3042	if [[ $do_trace = true ]]
	3043	then
[3236]	3044	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3045	fi
[3236]	3046	$submit_command ${configuration_identifier}_${run_id}
	3047	rm ${configuration_identifier}_${run_id}
[2380]	3048	cd - > /dev/null
	3049
	3050	fi
	3051
	3052	rm -rf $jobfile
	3053
	3054	else
	3055
	3056	printf "\n *** jobfile created under name \"$jobfile\" "
	3057	printf "\n no batch-job has been sent!"
	3058
	3059	fi
	3060
	3061	fi # END OF REMOTE-PART

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