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source: palm/trunk/SCRIPTS/palmrun @ 2605

Last change on this file since 2605 was 2605, checked in by raasch, 7 years ago
input files are not sent with remote batch job file any more
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 87.2 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
	6	# This file is part of PALM.
	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	#
	19	# Copyright 2017 Leibniz Universitaet Hannover
	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
	28	# $Id: palmrun 2605 2017-11-09 15:31:46Z raasch $
[2605]	29	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	30	# will not be sent with the job file any more, but copied into the
	31	# SOURCES_FOR_RUN... folder on the remote host, before he job is submitted
	32	#
	33	# 2600 2017-11-01 14:11:20Z raasch
[2600]	34	# cycle numbers are made three digits wide
	35	#
	36	# 2566 2017-10-20 08:50:47Z raasch
[2566]	37	# execute command for combine_plot_fields added
	38	# "TEMPDIR" renamed "tempdir"
	39	# temporary working directory for local batch jobs is created immediately within
	40	# the user's palmrun call, due to a requirement of the "grid engine" batch
	41	# system, where the working directory is given with batch directive -wd and must
	42	# already exist when the job is submitted,
	43	# informative messages in non-trace mode reduced and partly reformatted
	44	#
	45	# 2551 2017-10-18 07:25:11Z raasch
[2551]	46	# TEMPDIR added as replacement string to be used in batch directives
	47	#
	48	# 2512 2017-10-04 08:26:59Z raasch
[2507]	49	# bugfix for determining cycle numbers of NetCDF input files
	50	#
	51	# 2506 2017-09-29 08:30:37Z raasch
[2506]	52	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	53	# host configuration added to SOURCES_FOR_RUN_... folder name
	54	# host_identifier renamed host_configuration
	55	# option -W added to allow for job dependencies
	56	#
	57	# 2501 2017-09-26 11:41:55Z raasch
[2501]	58	# default value for number of cores (option -X) set to 1
	59	# bugfix for mechanism which overwrites configuration file settings with values
	60	# provided by palmrun options
	61	#
	62	# 2499 2017-09-22 16:47:58Z kanani
[2499]	63	# option -h named configuration identifier
	64	#
	65	# 2480 2017-09-19 06:24:14Z maronga
[2480]	66	# bugfix for last revision
	67	#
	68	# 2479 2017-09-19 06:12:16Z raasch
[2479]	69	# option -A (project account number) added
	70	#
	71	# 2422 2017-09-08 08:25:41Z raasch
[2410]	72	# initial revision
[2380]	73	#
	74	#--------------------------------------------------------------------------------#
	75	# palmrun - script for running PALM jobs on local and remote hosts
	76	#--------------------------------------------------------------------------------#
	77
	78
	79
	80	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	81
	82	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	83	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	84	# (TOO MANY ARGUMENTS - PROBLEM)
	85	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	86
	87	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	88	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	89	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	90	# SCRIPT-OPTION ARGUMENTS
	91	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	92	typeset -i icycle inode ival maxcycle mpi_tasks
	93	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	94
	95	activation_string_list=""
	96	AddFilenames=""
	97	combine_plot_fields=true
	98	compiler_name=""
	99	compiler_name_ser=""
	100	compiler_options=""
[2501]	101	cores=1
[2380]	102	cores_atmos=0
	103	cores_ocean=0
	104	coupled_dist=""
	105	cpp_options=""
	106	cpumax=0
[2506]	107	create_batch_job=false
[2380]	108	create_jobfile_only=false
	109	create_remote_batch_job=false
	110	dashes=" ----------------------------------------------------------------------------"
	111	defaultqueue=""
[2506]	112	delete_temporary_catalog=true
[2380]	113	do_compile=true
	114	do_trace=false
	115	executable=""
	116	execute_command=""
	117	execution_error=false
	118	fileconnection_file=.palm.iofiles
	119	fname=test
	120	global_revision=""
[2506]	121	host_configuration="default"
[2380]	122	hostfile=""
	123	hp=""
	124	keep_data_from_previous_run=false
	125	link_local_input=false
	126	link_local_output=false
[2388]	127	linker_options=""
[2385]	128	local_jobcatalog=""
[2380]	129	locat=normal
	130	makefile=""
	131	max_par_io_str=""
	132	prc=$0
	133	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	134	do
	135	prc=`echo $prc \| cut -f2- -d"/"`
	136	done
	137	module_calls=""
[2506]	138	palmrun_memory=""
[2380]	139	palmrun_script_name=$prc
	140	openmp=false
[2506]	141	previous_job=""
[2479]	142	project_account=""
[2380]	143	queue=none
	144	restart_run=false
	145	return_address=""
[2385]	146	remote_jobcatalog=""
[2380]	147	remote_username=""
	148	running_in_batch_mode=false
	149	run_coupled_model=false
	150	run_id=""
	151	silent=false
	152	source_list=""
	153	source_path=""
[2501]	154	tasks_per_node=0
[2380]	155	threads_per_task=1
	156	transfer_problems=false
[2384]	157	user_source_path=""
[2506]	158	use_existing_sources_folder=""
[2380]	159	use_openmp=false
[2422]	160	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	161	working_directory=`pwd`
	162	write_binary=""
	163	TOPT=""
	164
	165
	166	# ERROR HANDLING IN CASE OF EXIT
[2404]	167	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	168	then
	169
	170	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	171	(( i = 0 ))
	172	while (( i < iec ))
	173	do
	174	(( i = i + 1 ))
	175	printf "\n *** Execution of ERROR-command:\n"
	176	printf " >>> ${err_command[$i]}\n"
	177	eval ${err_command[$i]}
	178	done
[2566]	179	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	180	printf "\n\n+++ palmrun killed \n\n"
	181	elif [[ $locat != control_c ]]
	182	then
[2566]	183	printf "\n --> palmrun finished\n\n"
[2380]	184	fi' exit
	185
	186
	187	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	188	trap 'cd; rm -rf $tempdir
[2380]	189	printf "\n+++ palmrun killed by \"^C\" \n\n"
	190	locat=control_c
	191	exit
	192	' 2
	193
	194
	195	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	196	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	197	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	198	do
	199	case $option in
	200	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	201	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	202	(b) create_batch_job=true; prc="$prc -b";;
	203	(B) delete_temporary_catalog=false; prc="$prc -B";;
	204	(C) restart_run=true; prc="$prc -C";;
	205	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	206	(F) create_jobfile_only=true;;
	207	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	208	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	209	(j) running_in_batch_mode=true;;
	210	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	211	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	212	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	213	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	214	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	215	(r) run_id=$OPTARG;;
	216	(R) return_address=$OPTARG;;
	217	(s) source_list=$OPTARG;;
[2501]	218	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	219	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	220	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	221	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	222	(v) silent=true; prc="$prc -v";;
[2506]	223	(V) use_existing_sources_folder="-V";;
[2380]	224	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	225	(W) previous_job=$OPTARG;;
[2380]	226	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	227	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	228	(y) ocean_file_appendix=true; prc="$prc -y";;
	229	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	230	(Z) combine_plot_fields=false; prc="$prc -Z";;
	231	(\?) printf "\n +++ unknown option $OPTARG \n"
	232	printf "\n --> type \"$0 ?\" for available options \n"
	233	locat=parameter;exit;;
	234	esac
	235	done
	236
	237
	238	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	239	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	240	(( to_shift = $OPTIND - 1 ))
	241	shift $to_shift
	242
	243	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	244	if [[ "$1" = "?" ]]
	245	then
	246	(printf "\n *** Description of available palmrun options:\n"
	247	printf "\n Option Description Default-Value"
	248	printf "\n -a activation string list \"\" "
[2479]	249	printf "\n -A project account number ---"
[2380]	250	printf "\n -b batch-job on local machine ---"
	251	printf "\n -B do not delete temporary directory at end ---"
	252	printf "\n -d base name of files attached to program test"
	253	printf "\n -F create batch job file only ---"
[2506]	254	printf "\n -h host configuration \"default\" "
[2380]	255	printf "\n -k keep data from previous run"
	256	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	257	printf "\n -M Makefile name Makefile"
	258	printf "\n -O threads per openMP task ---"
	259	printf "\n -q queue \"$queue\" "
	260	printf "\n -s filenames of routines to be compiled \"\" "
	261	printf "\n must end with .f, .f90, .F, or .c !"
	262	printf "\n use \"..\" for more than one file and wildcards"
	263	printf "\n -s LM compiles all locally modified files"
	264	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	265	printf "\n -T tasks per node ---"
[2380]	266	printf "\n -u username on remote machine \"\" "
	267	printf "\n -v no prompt for confirmation ---"
[2506]	268	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	269	printf "\n -w maximum parallel io streams as given by -X"
[2506]	270	printf "\n -W name of job to wait for ---"
[2380]	271	printf "\n -x tracing of palmrun for debug purposes ---"
	272	printf "\n -X # of processors (on parallel machines) 1"
	273	printf "\n -y add appendix \"_O\" to all local output"
	274	printf "\n files (ocean precursor runs followed by"
	275	printf "\n coupled atmosphere-ocean runs) ---"
	276	printf "\n -Y run coupled model, \"#1 #2\" with"
	277	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	278	printf "\n -Z skip combine_plot_fields at the end of "
	279	printf "\n the simulation ---"
	280	printf "\n "
	281	printf "\n Possible values of positional parameter <modus>:"
	282	printf "\n \"?\" - this outline \n\n") \| more
	283	exit
	284	elif [[ "$1" != "" ]]
	285	then
	286	printf "\n +++ positional parameter $1 unknown \n"
	287	locat=parameter; exit
	288	fi
	289
	290
	291
	292	# SHORT STARTING MESSAGE
	293	printf "\n*** $version "
	294	printf "\n will be executed. Please wait ..."
	295
	296
[2506]	297	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	298	config_file=.palm.config.$host_configuration
	299	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	300
	301
	302	# CHECK, IF CONFIGURATION FILE EXISTS
	303	if [[ ! -f $config_file ]]
	304	then
	305	printf "\n\n +++ configuration file: "
	306	printf "\n $config_file"
	307	printf "\n does not exist"
	308	locat=connect; exit
	309	fi
	310
	311
	312	# CHECK, IF FILE CONNECTION FILE EXISTS
	313	if [[ ! -f $fileconnection_file ]]
	314	then
	315	printf "\n\n +++ file connection file: "
	316	printf "\n $fileconnection_file"
	317	printf "\n does not exist"
	318	locat=connect; exit
	319	fi
	320
	321
[2404]	322	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	323	if [[ "$activation_string_list" = "" ]]
	324	then
	325	printf "\n\n +++ no activation string list given: "
	326	printf "\n please set palmrun option \"-a\" "
	327	locat=palmrun_option; exit
	328	fi
	329
	330
	331	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	332	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	333	then
	334	write_binary=true
	335	else
	336	write_binary=false
	337	fi
	338
	339
[2380]	340	# READ AND EVALUATE THE CONFIGURATION-FILE
	341	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	342
	343	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	344	while read line
	345	do
	346
	347	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	348	eval line=\"$line\"
	349
	350
	351	# INTERPRET THE LINE
	352	if [[ "$(echo $line)" = "" ]]
	353	then
	354
	355	# EMPTY LINE, NO ACTION
	356	continue
	357
	358	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	359	then
	360
	361	# LINE IS A COMMENT LINE
	362	continue
	363
	364	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	365	then
	366
	367	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	368	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	369	value=`echo $line \| cut -d" " -s -f2-`
	370
	371
	372	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	373	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	374	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	375	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	376	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	377	# CONFIGURATION-FILE.
	378	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	379	then
	380	eval export $var="\$value"
	381
	382	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	383	if [[ $do_trace = true ]]
	384	then
	385	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	386	fi
	387	fi
	388
	389	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	390	then
	391
	392	# LINE DEFINES BATCH-DIRECTIVE
	393	(( ibd = ibd + 1 ))
	394	line=$(echo $line \| cut -c4-)
	395	batch_directive[$ibd]="$line"
	396
	397	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	398	then
	399
	400	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	401	# REMOTE TO A LOCAL HOST
	402	(( ibdt = ibdt + 1 ))
	403	line=$(echo $line \| cut -c5-)
	404	batch_directive_transfer[$ibdt]="$line"
	405
	406	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	407	then
	408
	409	# LINE DEFINES ERROR-COMMAND
	410	(( iec = iec + 1 ))
	411	line=$(echo $line \| cut -c4-)
	412	err_command[$iec]="$line"
	413
	414	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	415	then
	416
	417	# LINE DEFINES INPUT-COMMAND
	418	(( iic = iic + 1 ))
	419	line=$(echo $line \| cut -c4-)
	420	in_command[$iic]="$line"
	421
	422	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	423	then
	424
	425	# LINE DEFINES OUTPUT-COMMAND
	426	(( ioc = ioc + 1 ))
	427	line=$(echo $line \| cut -c4-)
	428	out_command[$ioc]="$line"
	429
	430	else
	431
	432	# SKIP ALL OTHER LINES
	433	continue
	434
	435	fi
	436
	437	done < $config_file
	438
	439
	440	# CHECK SETTING OF REQUIRED PARAMETERS
	441	if [[ "$compiler_name" = "" ]]
	442	then
	443	printf "\n +++ no compiler name found in $config_file"
	444	printf "\n Please add line \"compiler_name ...\" to that file."
	445	locat=config_file; exit
	446	fi
	447	if [[ "$compiler_name_ser" = "" ]]
	448	then
	449	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	450	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	451	locat=config_file; exit
	452	fi
	453	if [[ "$compiler_options" = "" ]]
	454	then
	455	printf "\n +++ no compiler options found in $config_file"
	456	printf "\n Please add line \"compiler_options ...\" to that file."
	457	locat=config_file; exit
	458	fi
[2388]	459	if [[ "$linker_options" = "" ]]
[2380]	460	then
[2388]	461	printf "\n +++ no linker options found in $config_file"
	462	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	463	locat=config_file; exit
	464	fi
	465	if [[ "$execute_command" = "" ]]
	466	then
	467	printf "\n +++ no execute command found in $config_file"
	468	printf "\n Please add line \"execute_command ...\" to that file."
	469	locat=config_file; exit
	470	fi
	471
	472	if [[ "$hostfile" != "" ]]
	473	then
	474	if [[ $hostfile != auto && ! -f $hostfile ]]
	475	then
	476	printf "\n +++ no hostfile \"$hostfile\" found"
	477	printf "\n Please check line \"hostfile ...\" in $config_file"
	478	locat=config_file; exit
	479	fi
	480	fi
	481
	482
	483	# DETERMINE THE CALL STATUS
	484	if [[ "$return_address" != "" ]]
	485	then
	486
	487	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	488	# BATCH MODE AND ...
	489	running_on_remote=true
	490
	491	else
	492
	493	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	494	if [[ "$remote_ip" != "" ]]
	495	then
	496
	497	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	498	create_remote_batch_job=true
	499
	500	fi
	501	running_on_remote=false
	502	fi
	503
	504
	505
	506	# READ AND EVALUATE THE I/O-FILE LIST
	507	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	508
	509	# READ THE FILE CONNECTION FILE LINE BY LINE
	510	while read line
	511	do
	512
	513	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	514	eval line=\"$line\"
	515
	516
	517	# INTERPRET THE LINE
	518	if [[ "$(echo $line)" = "" ]]
	519	then
	520	# EMPTY LINE, NO ACTION
	521	continue
	522
	523	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	524	then
	525
	526	# LINE IS A COMMENT LINE
	527	true
	528
	529	else
	530
	531	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	532	# s2a: in/out - field
	533	# s2b: loc - field (optional)
	534	# s2c: tr/ar - field (optional)
	535	s1=`echo $line \| cut -d" " -f1`
	536	s2=`echo $line \| cut -d" " -s -f2`
	537	s2a=$(echo $s2 \| cut -d":" -f1)
	538	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	539	then
	540	s2b=""
	541	s2c=""
	542	else
	543	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	544	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	545	fi
	546	s3=`echo $line \| cut -d" " -f3`
	547	s4=`echo $line \| cut -d" " -s -f4`
	548	s5=`echo $line \| cut -d" " -s -f5`
	549	s6=`echo $line \| cut -d" " -s -f6`
	550
	551
	552	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	553	# INPUT- OR OUTPUT-LIST.
	554	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	555	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	556	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	557	# IS NOT CHECKED AND STORED.
	558	IFSALT="$IFS"; IFS="$IFS:"
	559	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	560	then
	561	found=false
	562	for actual in $activation_string_list
	563	do
	564	for formal in $s3
	565	do
	566	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	567	done
	568	done
	569	if [[ $found = true ]]
	570	then
	571	(( iin = iin + 1 ))
	572	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	573	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	574	extin[$iin]=$s6
[2605]	575
	576	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	577	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
	578	if [[ $running_on_remote = true && ( "$s2b" = job \|\| "$s2b" = jobopt ) ]]
	579	then
	580	pathin[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
	581	fi
	582
[2380]	583	fi
	584	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	585	then
	586	found=false
	587	for actual in $activation_string_list
	588	do
	589	for formal in $s3
	590	do
	591	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	592	done
	593	done
	594	if [[ $found = true ]]
	595	then
	596	(( iout = iout + 1 ))
	597	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	598	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	599	fi
	600	elif [[ "$s2a" != in && "$s2a" != out ]]
	601	then
	602	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	603	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	604	locat=connect; exit
	605	fi
	606	IFS="$IFSALT"
	607	fi
	608
	609	done < $fileconnection_file
	610
	611
	612
[2501]	613	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	614	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	615	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	616	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	617	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	618	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	619
	620
	621
[2380]	622	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	623	if [[ $run_coupled_model = true ]]
	624	then
	625
	626	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	627	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	628
	629	if (( $cores_ocean + $cores_atmos != $cores ))
	630	then
	631
	632	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	633	printf "\n PEs (total) : $cores"
	634	printf "\n PEs (atmosphere): $cores_atmos"
	635	printf "\n PEs (ocean) : $cores_ocean"
	636	locat=coupling; exit
	637
	638	fi
	639
	640	fi
	641
	642
	643	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	644	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	645	# FOLDER
	646	if [[ $running_in_batch_mode = true ]]
	647	then
	648
[2506]	649	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	650	then
[2506]	651	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	652	printf "\n Please check the output of the palmrun-call"
	653	printf "\n that you did on your local host."
	654	locat=SOURCES_FOR_RUN; exit
	655	fi
	656
	657	else
	658
	659	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	660	# AUTOMATIC RESTART RUN
	661	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	662	if [[ $restart_run = false ]]
	663	then
	664
	665	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	666	# THE LOCAL HOST
	667	if [[ ! -d $source_path ]]
	668	then
	669	printf "\n\n +++ source path \"$source_path\" on local host"
	670	printf "\n \"$(hostname)\" does not exist"
	671	locat=source_path; exit
	672	fi
	673
[2506]	674	rm -rf $sources_for_run_catalog
	675	mkdir -p $sources_for_run_catalog
[2380]	676
	677	if [[ "$source_list" = LM ]]
	678	then
	679
	680	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	681	source_list=""
	682	cd $source_path
	683
	684
[2512]	685	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	686	if [[ ! -d ../.svn ]]
[2380]	687	then
	688	printf "\n\n +++ source directory"
	689	printf "\n \"$source_path\" "
	690	printf "\n is not under control of \"subversion\"."
[2512]	691	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	692	fi
	693
	694
	695	# LIST ALL MODIFIED SOURCE CODE FILES
	696	Filenames=""
[2404]	697	svn status > tmp_svnstatus
[2380]	698	while read line
	699	do
	700	firstc=`echo $line \| cut -c1`
	701	if [[ $firstc = M \|\| $firstc = "?" ]]
	702	then
	703	Name=`echo "$line" \| cut -c8-`
	704	extension=`echo $Name \| cut -d. -f2`
	705	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	706	then
	707	Filenames="$Filenames "$Name
	708	fi
	709	fi
[2404]	710	done < tmp_svnstatus
	711	rm -rf tmp_svnstatus
[2380]	712
	713
	714	# COPY FILES TO SOURCES_FOR_RUN_...
	715	for filename in $Filenames
	716	do
[2506]	717	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	718	source_list=$source_list"$filename "
	719	done
	720
	721	cd - > /dev/null
	722
	723
	724	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	725	elif [[ "$source_list" != "" ]]
	726	then
	727
	728	cd $source_path
	729
	730	for filename in $source_list
	731	do
	732
	733	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	734	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	735	then
	736	printf "\n +++ source code file: $filename"
	737	printf "\n must not contain (\"/\") "
	738	locat=source; exit
	739	fi
	740
	741	if [[ ! -f $filename ]]
	742	then
	743	printf "\n +++ source code file: $filename"
	744	printf "\n does not exist"
	745	locat=source; exit
	746	else
[2506]	747	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	748	fi
	749
	750	done
	751
	752	cd - > /dev/null
	753
	754	fi
	755
	756	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	757	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	758	if [[ ! -f $makefile ]]
	759	then
	760	printf "\n +++ file \"$makefile\" does not exist"
	761	locat=make; exit
	762	else
[2506]	763	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	764	fi
	765
	766
	767	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	768	if [[ "$user_source_path" != "" ]]
[2380]	769	then
	770
	771	# DOES THE DIRECTORY EXIST?
[2384]	772	if [[ ! -d $user_source_path ]]
[2380]	773	then
	774
	775	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	776	printf "\n \"$user_source_path\" "
[2380]	777	printf "\n does not exist or is not a directory."
	778	printf "\n No source code will be used from this directory!\n"
[2384]	779	user_source_path=""
[2380]	780	if [[ $silent == false ]]
	781	then
	782	sleep 2
	783	fi
	784
	785	else
	786
[2384]	787	cd $user_source_path
[2380]	788	found=false
	789
	790	Names=$(ls -1 *.f90 2>&1)
	791	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	792	Names=$(ls -1 *.F90 2>&1)
	793	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	794	Names=$(ls -1 *.F 2>&1)
	795	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	796	Names=$(ls -1 *.f 2>&1)
	797	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	798	Names=$(ls -1 *.c 2>&1)
	799	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	800
	801	cd - > /dev/null
[2506]	802	cd $sources_for_run_catalog
[2380]	803
	804	# COPY MAKEFILE IF EXISTING
[2384]	805	if [[ -f $user_source_path/Makefile ]]
[2380]	806	then
	807	printf "\n\n *** user Makefile from directory"
[2384]	808	printf "\n \"$user_source_path\" is used \n"
[2380]	809	if [[ $silent == false ]]
	810	then
	811	sleep 1
	812	fi
[2384]	813	cp $user_source_path/Makefile .
[2380]	814	fi
	815
	816	for filename in $AddFilenames
	817	do
	818	if [[ -f $filename ]]
	819	then
	820	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	821	printf "\n source code directory \"$user_source_path\" "
[2380]	822	printf "\n but was also given with option \"-s\" which means that it should be taken"
	823	printf "\n from directory \"$source_path\"."
	824	locat=source; exit
	825	fi
	826
[2384]	827	cp $user_source_path/$filename .
[2380]	828	source_list="$source_list $filename"
	829
	830	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	831	if [[ $(grep -c $filename Makefile) = 0 ]]
	832	then
	833	printf "\n\n +++ user file \"$filename\" "
	834	printf "\n is not listed in Makefile \n"
	835	locat=source; exit
	836	else
	837
	838	if [[ $found = false ]]
	839	then
	840	found=true
	841	printf "\n\n *** following user file(s) added to the"
	842	printf " files to be translated:\n "
	843	fi
	844	printf "$filename "
	845	if [[ $silent == false ]]
	846	then
	847	sleep 0.5
	848	fi
	849
	850	fi
	851	done
	852	[[ $found = true ]] && printf "\n"
	853	cd - > /dev/null
	854	fi
	855	fi
	856
	857	# COPY CONFIGURATION FILES
[2506]	858	cp $config_file $sources_for_run_catalog
	859	cp $fileconnection_file $sources_for_run_catalog
[2380]	860
	861	# COPY SHELLSCRIPTS
[2506]	862	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	863	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	864
	865	fi
	866
	867	fi
	868
[2605]	869
[2380]	870	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	871	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	872	if [[ "$global_revision" = "" ]]
	873	then
	874	global_revision=`svnversion $source_path 2>/dev/null`
	875	global_revision="Rev: $global_revision"
	876	fi
	877
	878
	879	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	880	if [[ -n $cores ]]
	881	then
	882
	883	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	884	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	885	if [[ $tasks_per_node = 0 ]]
[2380]	886	then
	887	printf "\n"
	888	printf "\n +++ option \"-T\" (tasks per node) is missing"
	889	printf "\n set -T option or define tasks_per_node in the config file"
	890	locat=tasks_per_node; (( iec = 0 )); exit
	891	fi
	892
	893	if (( cores < tasks_per_node ))
	894	then
	895	printf "\n"
	896	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	897	printf "\n given values: -T $tasks_per_node -X $cores"
	898	locat=tasks_per_node; (( iec = 0 )); exit
	899	fi
	900
	901	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	902	(( mpi_tasks = cores / threads_per_task ))
	903	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	904	(( ii = cores / tasks_per_node ))
	905	(( remaining_cores = cores - ii * tasks_per_node ))
	906	if (( remaining_cores > 0 ))
	907	then
	908	printf "\n"
	909	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	910	printf "\n divisor of the total number of cores (option \"-X\")"
	911	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	912	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	913	(( nodes = nodes + 1 ))
	914	fi
	915
	916	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	917	if [[ "$tasks_per_node" != "" ]]
	918	then
	919	TOPT="-T $tasks_per_node"
	920	fi
	921
	922	fi
	923
	924
	925	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	926	if [[ "$maximum_parallel_io_streams" = "" ]]
	927	then
	928	maximum_parallel_io_streams=$cores
	929	fi
	930
	931
	932	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	933	if [[ "$scp_port" != "" ]]
	934	then
	935	PORTOPT="-P $scp_port"
	936	SSH_PORTOPT="-p $scp_port"
	937	fi
	938
	939
	940	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	941	# CONFIG-FILE
	942	if [[ "$ssh_key" != "" ]]
	943	then
	944	ssh_key="-i $HOME/.ssh/$ssh_key"
	945	fi
	946
	947
	948	# SET QUEUE, IF NOT GIVEN
	949	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	950	then
	951
	952	if [[ $queue = none && "$defaultqueue" = "" ]]
	953	then
	954	printf "\n"
	955	printf "\n +++ no default queue given in configuration file and no queue"
	956	printf "\n given with option -q"
	957	fi
	958	if [[ $queue = none ]]
	959	then
	960	queue=$defaultqueue
	961	fi
	962
	963	fi
	964
	965
	966	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	967	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	968	(( i = 0 ))
	969	while (( i < iin ))
	970	do
	971	(( i = i + 1 ))
	972	(( maxcycle = 0 ))
	973
	974	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	975	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	976	if [[ "${actionin[$i]}" = di ]]
	977	then
	978	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	979	# HOST ONLY
	980	eval filename=${pathin[$i]}/${endin[$i]}
	981	else
	982	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	983	# HOST ONLY
	984	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	985	fi
	986	eval pathname=${pathin[$i]}
	987
	988	# CHECK IF FILE EXISTS
	989	if ! ls $filename* 1>/dev/null 2>&1
	990	then
	991
	992	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[2605]	993	if [[ "${transin[$i]}" != "locopt" && "${transin[$i]}" != "jobopt" ]]
[2380]	994	then
	995	printf "\n\n +++ INPUT-file: "
	996	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	997	then
	998	printf "\n $filename"
	999	else
	1000	printf "\n $filename.${extin[$i]}"
	1001	fi
	1002	printf "\n does not exist\n"
	1003	locat=input; exit
	1004	else
	1005	transin[$i]="unavailable"
	1006	fi
[2605]	1007
[2380]	1008	else
	1009
	1010	# DETERMINE THE FILE'S CYCLE NUMBER
	1011	ls -1 -d $filename > filelist 2>/dev/null
	1012	ls -1 -d $filename.* >> filelist 2>/dev/null
	1013	while read line
	1014	do
	1015	# filename without path (i.e. after the last "/")
	1016	basefilename=$(basename ${line})
	1017
	1018	# check if there is an extension
	1019	extension=${basefilename##*.}
[2507]	1020	if [[ "$extension" = "${extin[$i]}" ]]
[2380]	1021	then
[2507]	1022	basefilename=${basefilename%.*}
[2380]	1023	fi
	1024
	1025	# check for an existing cycle number
	1026	cycle=${basefilename##*.}
	1027	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1028	then
	1029	(( icycle = $cycle ))
	1030	else
	1031	(( icycle = 0 ))
	1032	fi
	1033
	1034	if (( icycle > maxcycle ))
	1035	then
	1036	(( maxcycle = icycle ))
[2600]	1037
	1038	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1039	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1040	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1041	then
	1042	leading_zero=true
	1043	else
	1044	leading_zero=false
	1045	fi
[2380]	1046	fi
	1047
	1048	done <filelist
	1049	rm filelist
	1050
[2600]	1051	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1052	if [[ $leading_zero = true ]]
	1053	then
	1054	cyclestring=`printf "%03d" $maxcycle`
	1055	else
	1056	cyclestring=$maxcycle
	1057	fi
	1058
[2380]	1059	# APPEND CYCLE NUMBER TO FILENAME
	1060	if (( maxcycle > 0 ))
	1061	then
	1062	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1063	then
[2600]	1064	filename=${filename}.$cyclestring.${extin[$i]}
[2380]	1065	else
[2600]	1066	filename=${filename}.$cyclestring
[2380]	1067	fi
	1068	else
	1069	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1070	then
	1071	filename=${filename}.${extin[$i]}
	1072	fi
	1073	fi
	1074
	1075	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1076	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1077	absnamein[$i]=$filename
	1078	if (( maxcycle > 0 ))
	1079	then
	1080	if [[ "${actionin[$i]}" = di ]]
	1081	then
[2600]	1082	frelin[$i]=${endin[$i]}.$cyclestring
[2380]	1083	else
[2600]	1084	frelin[$i]=${fname}${endin[$i]}.$cyclestring
[2380]	1085	fi
	1086	else
	1087	if [[ "${actionin[$i]}" = di ]]
	1088	then
	1089	frelin[$i]=${endin[$i]}
	1090	else
	1091	frelin[$i]=${fname}${endin[$i]}
	1092	fi
	1093	fi
	1094
	1095	fi
	1096	done
	1097
	1098
	1099	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1100	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1101	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1102	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1103	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1104	# REMOTE HOST)
	1105	(( i = 0 ))
	1106	while (( i < iout ))
	1107	do
	1108	(( i = i + 1 ))
	1109	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1110	then
	1111	if [[ "${actionout[$i]}" = tr ]]
	1112	then
	1113	actionout[$i]=""
	1114	elif [[ "${actionout[$i]}" = trpe ]]
	1115	then
	1116	actionout[$i]=pe
	1117	elif [[ "${actionout[$i]}" = tra ]]
	1118	then
	1119	actionout[$i]=a
	1120	fi
	1121	(( maxcycle = 0 ))
	1122	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1123	eval catalogname=${pathout[$i]}
	1124	if ! ls $filename* 1>/dev/null 2>&1
	1125	then
	1126
	1127	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1128	if cat /dev/null > $filename
	1129	then
	1130	rm $filename
	1131	else
	1132
	1133	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1134	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1135	if [[ ! -d $catalogname ]]
	1136	then
	1137	if mkdir -p $catalogname
	1138	then
	1139	printf "\n\n *** directory:"
	1140	printf "\n $catalogname"
	1141	printf "\n was created\n"
	1142	else
	1143	printf "\n\n +++ OUTPUT-file:"
	1144	printf "\n $filename"
	1145	printf "\n cannot be created, because directory does not exist"
	1146	printf "\n and cannot be created either"
	1147	printf "\n"
	1148	locat=output ; exit
	1149	fi 2>/dev/null
	1150	else
	1151	printf "\n\n +++ OUTPUT-file:"
	1152	printf "\n $filename"
	1153	printf "\n cannot be created, although directory exists"
	1154	printf "\n"
	1155	locat=output ; exit
	1156	fi
	1157	fi 2>/dev/null
	1158	else
	1159
	1160	# DETERMINE THE CYCLE NUMBER
	1161	ls -1 -d $filename > filelist 2>/dev/null
	1162	ls -1 -d $filename.* >> filelist 2>/dev/null
	1163	while read line
	1164	do
	1165
	1166	# filename without path (i.e. after the last "/")
	1167	basefilename=$(basename ${line})
	1168
	1169	# check if there is an extension
	1170	extension=${basefilename##*.}
	1171	if [[ "$extension" = "${extout[$i]}" ]]
	1172	then
	1173	basefilename=${basefilename%.*}
	1174	fi
	1175
	1176	# check for an existing cycle number
	1177	cycle=${basefilename##*.}
	1178	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1179	then
	1180	(( icycle = $cycle + 1 ))
	1181	else
	1182	(( icycle = 1 ))
	1183	fi
	1184
	1185	if (( icycle > maxcycle ))
	1186	then
	1187	(( maxcycle = icycle ))
	1188	fi
	1189
	1190	done <filelist
	1191	rm filelist
	1192	fi
	1193
	1194	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1195	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1196	if [[ "${actionout[$i]}" != a ]]
	1197	then
[2600]	1198	cyclestring=`printf "%03d" $maxcycle`
[2380]	1199	if (( maxcycle > 0 ))
	1200	then
[2600]	1201	filename_tmp=${filename}.$cyclestring
[2380]	1202	if cat /dev/null > $filename_tmp
	1203	then
	1204	rm $filename_tmp
	1205	else
	1206	printf "\n +++ OUTPUT-file:"
	1207	printf "\n $filename_tmp"
	1208	printf "\n cannot be created"
	1209	locat=output ; exit
	1210	fi
	1211	fi
	1212	else
	1213	(( maxcycle = maxcycle - 1 ))
	1214	fi
	1215
	1216	(( cycnum[$i] = maxcycle ))
	1217	pathout[$i]=$filename
	1218
	1219	fi
	1220	done
	1221
	1222
	1223	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1224	if [[ $running_in_batch_mode = false ]]
	1225	then
	1226	run_id=$RANDOM
	1227	job_id=${fname}.$run_id
	1228
[2566]	1229	tempdir=$fast_io_catalog/$job_id
[2380]	1230	fi
	1231
	1232
	1233	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1234	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1235	then
	1236
	1237	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1238	if [[ $ibd = 0 ]]
	1239	then
	1240	printf "\n"
	1241	printf "\n +++ no batch directives found in configuration file"
	1242	locat=config_file_batch_directives; (( iec = 0 )); exit
	1243	fi
	1244
	1245	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1246	done=false
[2384]	1247	cputime=$cpumax
[2380]	1248	while [[ $done = false ]]
	1249	do
[2384]	1250	if (( cputime == 0 ))
[2380]	1251	then
	1252	printf "\n +++ cpu-time is undefined"
	1253	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1254	printf "\n >>> "
[2384]	1255	read cputime 1>/dev/null 2>&1
[2380]	1256	else
	1257	done=true
	1258	fi
	1259	done
[2420]	1260	cpumax=$cputime
[2380]	1261
	1262	# CHECK THE MEMORY DEMAND
	1263	done=false
	1264	while [[ $done = false ]]
	1265	do
	1266	if (( memory == 0 ))
	1267	then
	1268	printf "\n +++ memory demand is undefined"
	1269	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1270	printf "\n >>> "
	1271	read memory 1>/dev/null 2>&1
	1272	else
	1273	done=true
	1274	fi
	1275	done
	1276
	1277	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1278	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1279	then
	1280	while [[ -z $remote_username ]]
	1281	do
[2420]	1282	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1283	printf "\n >>> Please type username:"
	1284	printf "\n >>> "
	1285	read remote_username
	1286	done
	1287	fi
	1288
	1289	else
	1290
[2420]	1291	if [[ $running_in_batch_mode = false ]]
	1292	then
	1293	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1294	cpumax=$cputime
	1295	else
	1296	cputime=$cpumax
	1297	fi
[2380]	1298
	1299	fi
	1300
	1301
	1302	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1303	(( cpu_hours = cputime / 3600 ))
	1304	(( resttime = cputime - cpu_hours * 3600 ))
	1305	(( cpu_minutes = resttime / 60 ))
	1306	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1307	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1308
	1309
	1310	# OUTPUT OF THE PALMRUN-HEADER
	1311	calltime=$(date)
	1312	printf "\n"
	1313	printf "#------------------------------------------------------------------------# \n"
	1314	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1315	printf "\| \| \n"
	1316	column1="called on:"; column2=$(hostname)
	1317	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1318	if [[ $create_remote_batch_job = true ]]
	1319	then
[2506]	1320	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1321	else
	1322	if [[ $running_on_remote = true ]]
	1323	then
[2506]	1324	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1325	else
[2506]	1326	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1327	fi
	1328	fi
	1329	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1330
	1331	column1="running in:"
	1332	if [[ $running_in_batch_mode = true ]]
	1333	then
	1334	column2="batch job mode"
	1335	else
	1336	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1337	then
	1338	column2="job creation mode"
	1339	else
	1340	column2="interactive run mode"
	1341	fi
	1342	fi
	1343	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1344
[2479]	1345	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1346	then
[2480]	1347	if [[ "$project_account" != "" ]]
[2479]	1348	then
	1349	column1="project account number:"
	1350	column2="$project_account"
	1351	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1352	fi
	1353	fi
	1354
[2380]	1355	if [[ -n $cores ]]
	1356	then
	1357	if [[ $run_coupled_model = false ]]
	1358	then
	1359	column1="number of cores:"; column2=$cores
	1360	else
	1361	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1362	fi
	1363	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1364	fi
	1365	if [[ -n $tasks_per_node ]]
	1366	then
	1367	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1368	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1369	if (( remaining_cores > 0 ))
	1370	then
	1371	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1372	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1373	fi
	1374	fi
	1375	if [[ $maximum_parallel_io_streams != $cores ]]
	1376	then
	1377	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1378	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1379	fi
	1380	if [[ $use_openmp = true ]]
	1381	then
	1382	column1="threads per task:"; column2="$threads_per_task"
	1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1384	fi
[2384]	1385	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1386	then
[2506]	1387	column1="memory demand / PE":; column2="$memory MB"
	1388	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1389	column1="job cpu time (h:m:s):"; column2="$timestring"
	1390	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1391	fi
[2380]	1392	printf "\| \| \n"
	1393	if [[ "$source_list" != "" ]]
	1394	then
	1395	if [[ "$make_options" != "" ]]
	1396	then
	1397	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1398	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1399	line=$(echo "$make_options" \| cut -c46-)
	1400	while [[ "$line" != "" ]]
	1401	do
	1402	column1=""
	1403	column2=$(echo "$line" \| cut -c-45)
	1404	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1405	line=$(echo "$line" \| cut -c46-)
	1406	done
	1407	fi
	1408	fi
	1409
	1410	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1412	line=$(echo "$cpp_options" \| cut -c46-)
	1413	while [[ "$line" != "" ]]
	1414	do
	1415	column1=""
	1416	column2=$(echo "$line" \| cut -c-45)
	1417	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1418	line=$(echo "$line" \| cut -c46-)
	1419	done
	1420
	1421	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1422	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1423	line=$(echo "$compiler_options" \| cut -c46-)
	1424	while [[ "$line" != "" ]]
	1425	do
	1426	column1=""
	1427	column2=$(echo "$line" \| cut -c-45)
	1428	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1429	line=$(echo "$line" \| cut -c46-)
	1430	done
	1431
[2388]	1432	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1434	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1435	while [[ "$line" != "" ]]
	1436	do
	1437	column1=""
	1438	column2=$(echo "$line" \| cut -c-45)
	1439	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1440	line=$(echo "$line" \| cut -c46-)
	1441	done
	1442
	1443	if [[ "$login_init_cmd" != "" ]]
	1444	then
	1445	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1446	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1447	line=$(echo "$login_init_cmd" \| cut -c46-)
	1448	while [[ "$line" != "" ]]
	1449	do
	1450	column1=""
	1451	column2=$(echo "$line" \| cut -c-45)
	1452	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1453	line=$(echo "$line" \| cut -c46-)
	1454	done
	1455	fi
	1456
	1457	if [[ "$module_commands" != "" ]]
	1458	then
	1459	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1461	line=$(echo "$module_commands" \| cut -c46-)
	1462	while [[ "$line" != "" ]]
	1463	do
	1464	column1=""
	1465	column2=$(echo "$line" \| cut -c-45)
	1466	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1467	line=$(echo "$line" \| cut -c46-)
	1468	done
	1469	fi
	1470	printf "\| \| \n"
	1471	column1="base name of files:"; column2=$fname
	1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1473	column1="activation string list:"; column2=$(echo $activation_string_list)
	1474	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1475
	1476	if [[ "$ocean_file_appendix" = true ]]
	1477	then
	1478	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1479	fi
	1480
	1481	if [[ "$source_list" != "" ]]
	1482	then
	1483	printf "\| \| \n"
	1484	printf "\| Files to be compiled: \| \n"
	1485	line=$source_list
	1486	while [[ "$line" != "" ]]
	1487	do
	1488	linestart=$(echo $line \| cut -c-70)
	1489	printf "\| %-70s \| \n" "$linestart"
	1490	line=$(echo "$line" \| cut -c71-)
	1491	done
	1492	fi
	1493	printf "#------------------------------------------------------------------------#"
	1494
	1495
	1496
	1497	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1498	if [[ $do_trace = true ]]
	1499	then
	1500	(( i = 0 ))
	1501	while (( i < iin ))
	1502	do
	1503	(( i = i + 1 ))
	1504	if (( i == 1 ))
	1505	then
	1506	printf "\n\n >>> INPUT-file assignments:\n"
	1507	fi
	1508	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1509	done
	1510	(( i = 0 ))
	1511	while (( i < iout ))
	1512	do
	1513	(( i = i + 1 ))
	1514	if (( i == 1 ))
	1515	then
	1516	printf "\n\n >>> OUTPUT-file assignments:\n"
	1517	fi
	1518	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1519	done
	1520	(( i = 0 ))
	1521	while (( i < iic ))
	1522	do
	1523	(( i = i + 1 ))
	1524	if (( i == 1 ))
	1525	then
	1526	printf "\n\n >>> INPUT-commands:\n"
	1527	fi
	1528	printf "\n ${in_command[$i]}"
	1529	done
	1530	(( i = 0 ))
	1531	while (( i < ioc ))
	1532	do
	1533	(( i = i + 1 ))
	1534	if (( i == 1 ))
	1535	then
	1536	printf "\n\n >>> OUTPUT-commands:\n"
	1537	fi
	1538	printf "\n ${out_command[$i]}"
	1539	done
	1540	fi
	1541
	1542	# QUERY FOR CONTINUE
	1543	if [[ $silent = false && $running_in_batch_mode = false ]]
	1544	then
	1545	antwort=dummy
	1546	printf "\n\n"
	1547	printf " >>> everything o.k. (y/n) ? "
	1548	while read antwort
	1549	do
	1550	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1551	then
	1552	printf " >>> everything o.k. (y/n) ? "
	1553	else
	1554	break
	1555	fi
	1556	done
	1557	if [[ $antwort = n \|\| $antwort = N ]]
	1558	then
	1559	locat=user_abort; (( iec = 0 )); exit
	1560	fi
	1561	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1562	then
[2566]	1563	printf "\n *** batch-job will be created and submitted"
[2380]	1564	else
[2566]	1565	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1566	fi
	1567	fi
	1568
	1569
	1570
	1571	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1572	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1573	then
	1574
	1575	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1576	then
[2566]	1577	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1578	else
[2566]	1579	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1580	fi
	1581
[2422]	1582	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1583	# IT SHALL BE CREATED
	1584	ask_for_make_depository=false
	1585	if [[ $create_remote_batch_job = true ]]
	1586	then
	1587
	1588	line=`grep %base_directory $config_file`
[2506]	1589	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1590	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
[2422]	1591
[2506]	1592	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1593	then
	1594	printf "\n\n +++ make depository \"${make_depository}\""
	1595	printf "\n on remote host not found!"
	1596	ask_for_make_depository=true
	1597	fi
[2506]	1598	rm ${host_configuration}_last_make_protokoll
[2422]	1599
	1600	else
	1601
	1602	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1603	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1604	if [[ ! -d ${make_depository} ]]
	1605	then
	1606	printf "\n\n +++ make depository \"${make_depository}\""
	1607	printf "\n on local host not found!"
	1608	ask_for_make_depository=true
	1609	fi
	1610
	1611	fi
	1612
	1613	if [[ $ask_for_make_depository = true ]]
	1614	then
	1615
	1616	antwort=dummy
	1617	printf "\n\n"
	1618	printf " >>> Create a new one (y/n) ? "
	1619	while read antwort
	1620	do
	1621	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1622	then
	1623	printf " >>> Create a new one (y/n) ? "
	1624	else
	1625	break
	1626	fi
	1627	done
	1628	if [[ $antwort = n \|\| $antwort = N ]]
	1629	then
	1630	locat=user_abort; (( iec = 0 )); exit
	1631	fi
	1632
[2566]	1633	if [[ $do_trace = true ]]
	1634	then
	1635	palmbuild -h $host_configuration
	1636	else
	1637	palmbuild -v -h $host_configuration
	1638	fi
[2422]	1639
	1640	if [[ $? != 0 ]]
	1641	then
	1642
	1643	# ABORT IN CASE OF COMPILATION PROBLEMS
	1644	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1645	locat=make_depository
	1646	exit
	1647	else
	1648	echo " *** now continue with creating executable and other sources"
	1649	fi
	1650
	1651	fi
	1652
[2566]	1653	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1654	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1655
	1656	if [[ $? != 0 ]]
	1657	then
	1658
	1659	# ABORT IN CASE OF COMPILATION PROBLEMS
	1660	printf "\n +++ error while creating executable and/or other sources"
	1661	locat=execution
[2506]	1662	rm -rf $sources_for_run_catalog
[2380]	1663	exit
	1664
	1665	else
	1666
[2566]	1667	printf " *** executable and other sources created\n"
[2506]	1668	rm -rf $sources_for_run_catalog
[2380]	1669
	1670	fi
	1671
	1672	fi
	1673
	1674
[2605]	1675	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH JOB-ATTRIBUT WILL
	1676	# BE COPIED TO THE REMOTE HOST
	1677	if [[ $create_remote_batch_job = true ]]
	1678	then
	1679	(( i = 0 ))
	1680	while (( i < iin ))
	1681	do
	1682	(( i = i + 1 ))
	1683	if [[ "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ]]
	1684	then
	1685	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1686	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1687	fi
	1688	done
	1689	if (( i > 0 ))
	1690	then
	1691	printf " *** input files have been copied to the remote host\n"
	1692	fi
	1693	fi
	1694
	1695
[2380]	1696	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1697	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1698	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1699	then
	1700
	1701	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1702	if [[ $running_in_batch_mode = false ]]
	1703	then
	1704	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1705	# FOLDER
[2566]	1706	mkdir -p $tempdir
	1707	chmod go+rx $tempdir
	1708	cd $tempdir
	1709	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1710	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1711
	1712	else
	1713
	1714	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1715	printf "\n *** running in temporary directory: $tempdir"
[2380]	1716
	1717	fi
	1718
	1719
	1720	# PROVIDE THE INPUT FILES
	1721	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1722	(( i = 0 ))
	1723	while (( i < iin ))
	1724	do
	1725	(( i = i + 1 ))
	1726	if (( i == 1 ))
	1727	then
	1728	printf "\n\n *** providing INPUT-files:\n$dashes"
	1729	fi
	1730
	1731
	1732	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1733	if [[ "${transin[$i]}" = unavailable ]]
	1734	then
	1735	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1736	then
	1737	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1738	printf "\n is not available!"
	1739	else
	1740	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1741	printf "\n is not available!"
	1742	fi
	1743	continue
	1744	fi
	1745
	1746	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1747	files_for_cores=false; filetype=file
	1748	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1749	then
	1750	files_for_cores=true; filetype=files
	1751	actionin[$i]=""
	1752	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1753	then
	1754	actionin[$i]=""
	1755	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1756	then
	1757	files_for_cores=true; filetype=files
	1758	actionin[$i]="ln"
	1759	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1760	then
	1761	actionin[$i]="ln"
	1762	fi
	1763
	1764	if [[ $files_for_cores = true ]]
	1765	then
	1766	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1767	else
	1768	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1769	fi
	1770
	1771	# INPUT-FILES TO BE LINKED
	1772	if [[ "${actionin[$i]}" = ln ]]
	1773	then
	1774
	1775	printf "\n $filetype will be linked"
	1776	if [[ $files_for_cores = false ]]
	1777	then
	1778	if [[ -f "${absnamein[$i]}" ]]
	1779	then
	1780	ln ${absnamein[$i]} ${localin[$i]}
	1781	got_tmp[$i]=true
	1782	fi
	1783	else
	1784	if [[ -d "${absnamein[$i]}" ]]
	1785	then
[2396]	1786	mkdir -p ${localin[$i]}
[2380]	1787	cd ${absnamein[$i]}
	1788	for file in $(ls *)
	1789	do
[2566]	1790	ln $file $tempdir/${localin[$i]}
[2380]	1791	done >\|/dev/null 2>&1
[2566]	1792	cd $tempdir
[2380]	1793	fi
	1794
	1795	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1796	if [[ ! -f "${localin[$i]}/_000000" ]]
	1797	then
	1798	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1799	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1800	fi
	1801
	1802	got_tmp[$i]=true
	1803	fi
	1804	fi
	1805
	1806	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1807	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1808	then
	1809
	1810	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1811	then
	1812
	1813	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1814	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1815	printf "\n file will be provided for $cores processors"
[2396]	1816	mkdir -p ${localin[$i]}
[2380]	1817	ival=$cores
	1818	(( ii = 0 ))
	1819	while (( ii <= ival-1 ))
	1820	do
	1821	if (( ii < 10 ))
	1822	then
	1823	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1824	elif (( ii < 100 ))
	1825	then
	1826	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1827	elif (( ii < 1000 ))
	1828	then
	1829	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1830	else
	1831	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1832	fi
	1833	(( ii = ii + 1 ))
	1834	done
	1835
	1836	else
	1837
	1838	if [[ $files_for_cores = true ]]
	1839	then
	1840
	1841	# PROVIDE FILES FOR EACH CORE
	1842	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1843	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1844	printf "\n providing $cores files for the respective cores"
[2396]	1845	mkdir -p ${localin[$i]}
[2380]	1846	if [[ $link_local_input = true ]]
	1847	then
	1848	printf " files will be linked\n"
	1849	cd ${absnamein[$i]}
	1850	for file in $(ls *)
	1851	do
	1852	ln -f $file ${localin[$i]}
	1853	done
[2566]	1854	cd $tempdir
[2380]	1855	fi
	1856
	1857	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1858	if [[ ! -f "${localin[$i]}/_000000" ]]
	1859	then
	1860	if [[ $link_local_input = true ]]
	1861	then
	1862	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1863	fi
	1864	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1865	fi
	1866
	1867	else
	1868
	1869	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1870	if [[ $link_local_input = true ]]
	1871	then
	1872	printf " file will be linked\n"
	1873	ln -f ${absnamein[$i]} ${localin[$i]}
	1874	fi
[2605]	1875	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	1876	if [[ ! -f "${localin[$i]}" ]]
	1877	then
	1878	if [[ $link_local_input = true ]]
	1879	then
	1880	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1881	fi
[2605]	1882	if [[ $running_on_remote = true && ( "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ) ]]
	1883	then
	1884	mv ${absnamein[$i]} ${localin[$i]}
	1885	else
	1886	cp ${absnamein[$i]} ${localin[$i]}
	1887	fi
[2380]	1888	fi
	1889	fi
	1890	fi
	1891	fi
	1892
	1893	done
	1894	if (( i != 0 ))
	1895	then
	1896	printf "\n$dashes\n *** all INPUT-files provided \n"
	1897	fi
	1898
	1899
	1900	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1901	(( i = 0 ))
	1902	while (( i < iic ))
	1903	do
	1904	(( i = i + 1 ))
	1905	if (( i == 1 ))
	1906	then
	1907	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1908	fi
	1909	printf "\n >>> ${in_command[$i]}"
	1910	eval ${in_command[$i]}
	1911	if (( i == iic ))
	1912	then
	1913	printf "\n$dashes\n"
	1914	fi
	1915	done
	1916
	1917
	1918	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1919	# (FILE ENVPAR WILL BE READ BY PALM)
	1920	cat > ENVPAR << EOF
[2506]	1921	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	1922	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1923	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1924	maximum_cpu_time_allowed = ${cpumax}.,
	1925	revision = '$global_revision',
	1926	batch_job = .${running_in_batch_mode}. /
	1927
	1928	EOF
	1929
	1930
	1931	# STARTING THE EXECUTABLE
	1932	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	1933	PATH=$PATH:$tempdir
[2380]	1934
	1935
	1936	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1937	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1938	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1939	eval line=\"$line\"
	1940	execute_command="$line"
	1941
	1942
	1943	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	1944	if [[ "$execute_command_for_combine" = "" ]]
	1945	then
	1946	eval line2=\"$line2\"
	1947	execute_command_for_combine="$line2"
	1948	fi
	1949
[2380]	1950
	1951
	1952	# PROVIDE A HOSTFILE, IF REQUIRED
	1953	if [[ "$hostfile" != "" ]]
	1954	then
	1955
	1956	if [[ $hostfile = auto ]]
	1957	then
	1958	# CREATE A NEW HOSTFILE
	1959	(( ii = 1 ))
	1960	while (( ii <= cores / threads_per_task ))
	1961	do
	1962	echo $(hostname) >> hostfile
	1963	(( ii = ii + 1 ))
	1964	done
	1965	if (( cores / threads_per_task == 0 ))
	1966	then
	1967	echo $(hostname) >> hostfile
	1968	fi
	1969
	1970	else
	1971	cp $hostfile hostfile
	1972	fi
	1973	eval line=\"`head -n $ii hostfile`\"
	1974	printf "\n *** running on: $line"
	1975	fi
	1976
	1977
	1978
	1979	# SET THE NUMBER OF OPENMP-THREADS
	1980	if [[ $use_openmp = true ]]
	1981	then
	1982	export OMP_NUM_THREADS=$threads_per_task
	1983	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1984	else
	1985	export OMP_NUM_THREADS=1
	1986	fi
	1987
	1988
	1989	# PROVIDE DATA FOR
	1990	if [[ $run_coupled_model = false ]]
	1991	then
	1992	if [[ "$ocean_file_appendix" = true ]]
	1993	then
	1994	echo "precursor_ocean" > coupling_steering
	1995	else
	1996	echo "precursor_atmos" > coupling_steering
	1997	fi
	1998	else
	1999	(( iia = $cores_atmos / $threads_per_task ))
	2000	(( iio = $cores_ocean / $threads_per_task ))
	2001	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2002	printf "\n\n"
	2003	echo "coupled_run $iia $iio" > coupling_steering
	2004	fi
	2005
	2006	printf "\n *** execute command:"
	2007	printf "\n \"$execute_command\" \n\n"
	2008
	2009	$execute_command < coupling_steering
	2010
	2011	if [[ $? != 0 ]]
	2012	then
	2013
	2014	# ABORT IN CASE OF RUNTIME ERRORS
	2015	printf "\n +++ runtime error occured"
	2016	locat=execution
	2017	exit
	2018
	2019	else
	2020
	2021	printf "\n$dashes\n *** execution finished \n"
	2022
	2023	fi
	2024
	2025
	2026	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2027	# BY EACH CORE INTO ONE FILE
	2028	if [[ ! -f combine_plot_fields.x ]]
	2029	then
	2030
	2031	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2032	printf "\n 2d- and/or 3d-data may be incomplete!"
	2033	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2034
	2035	elif [[ "$combine_plot_fields" == true ]]
	2036	then
	2037
	2038	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2039	$execute_command_for_combine
	2040
	2041	else
	2042
	2043	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2044	# DATA OUTPUT
[2380]	2045	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2046	fi
	2047
	2048
	2049
	2050	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2051	(( i = 0 ))
	2052	while (( i < ioc ))
	2053	do
	2054	(( i = i + 1 ))
	2055	if (( i == 1 ))
	2056	then
	2057	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2058	fi
	2059	printf "\n >>> ${out_command[$i]}"
	2060	eval ${out_command[$i]}
	2061	if (( i == ioc ))
	2062	then
	2063	printf "\n$dashes\n"
	2064	fi
	2065	done
	2066
	2067
	2068	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2069	(( i = 0 ))
	2070	while (( i < iout ))
	2071	do
	2072	(( i = i + 1 ))
	2073	if (( i == 1 ))
	2074	then
	2075	printf "\n\n *** saving OUTPUT-files:"
	2076
	2077	# GET RUN NUMBER ASSIGNED BY PALM
	2078	if [[ -f RUN_NUMBER ]]
	2079	then
	2080	read run_number < RUN_NUMBER
	2081	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2082	usecycle_option="-U $run_number"
	2083	else
	2084	run_number=0
	2085	usecycle_option=""
	2086	fi
	2087	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2088	then
[2404]	2089	printf "\n *** in case of SCP transfers to local host"
	2090	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2091	fi
	2092	printf "\n$dashes"
	2093	fi
	2094
	2095	# ADD CYCLE NUMBER TO FILENAME
	2096	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2097	then
	2098
	2099	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2100	if [[ "${actionout[$i]}" != "a" ]]
	2101	then
	2102	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2103	# WITH AN EXISTING CYCLE NUMBER
	2104	if (( run_number >= cycnum[$i] ))
	2105	then
	2106	(( cycnum[$i] = run_number ))
	2107	else
	2108	if (( run_number > 0 ))
	2109	then
	2110	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2111	fi
	2112	fi
	2113	fi
	2114	if (( cycnum[$i] > 0 ))
	2115	then
[2600]	2116	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2117	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2118	fi
	2119	fi
	2120
	2121	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2122	files_for_cores=false; filetype=file
	2123	link_local_output=false
	2124	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2125	then
	2126	files_for_cores=true; filetype=directory
	2127	actionout[$i]=""
	2128	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2129	then
	2130	actionout[$i]=""
	2131	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2132	then
	2133	files_for_cores=true; filetype=directory
	2134	link_local_output=true
	2135	actionout[$i]=""
	2136	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2137	then
	2138	link_local_output
	2139	actionout[$i]=""
	2140	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2141	then
	2142	files_for_cores=true; filetype=directory
	2143	actionout[$i]="tr"
	2144	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2145	then
	2146	actionout[$i]="tr"
	2147	fi
	2148
	2149	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2150	then
	2151	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2152	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2153	then
	2154	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2155	else
	2156
	2157
	2158	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2159	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2160	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2161	then
	2162	if [[ $running_on_remote = true ]]
	2163	then
	2164
	2165	# SET OPTIONS FOR TRANSFER
	2166	if [[ "${actionout[$i]}" = tr ]]
	2167	then
	2168	if [[ $files_for_cores = false ]]
	2169	then
	2170	catalog_option=""
	2171	catalog_string=""
	2172	else
	2173	catalog_option="-c"
	2174	catalog_string="/"
	2175	fi
	2176	append_option=""
	2177	append_string=""
	2178	else
	2179	append_option="-A"
	2180	append_string="append"
	2181	fi
	2182
	2183	transfer_failed=false
	2184	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2185	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2186
	2187	# TRANSFER VIA SCP
	2188	if [[ "$remote_loginnode" != "" ]]
	2189	then
[2566]	2190	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2191	else
[2506]	2192	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2193	fi
	2194	[[ $? != 0 ]] && transfer_failed=true
	2195
	2196
	2197	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2198	if [[ $transfer_failed = true ]]
	2199	then
	2200	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2201	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2202
	2203	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2204	eval local_catalog=${pathout[$i]}
	2205	if [[ ! -d $local_catalog ]]
	2206	then
	2207	printf " *** local directory does not exist. Trying to create:\n"
	2208	printf " $local_catalog \n"
	2209	mkdir -p $local_catalog
	2210	fi
[2506]	2211	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2212	transfer_problems=true
	2213	fi
	2214
	2215	else
	2216
	2217	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2218	# BE COPIED OR APPENDED ON THIS MACHINE
	2219	if [[ "${actionout[$i]}" = tr ]]
	2220	then
	2221	actionout[$i]=""
	2222	else
	2223	actionout[$i]="a"
	2224	fi
	2225	fi
	2226	fi
	2227
	2228
	2229	# APPEND ON THIS MACHINE
	2230	if [[ "${actionout[$i]}" = "a" ]]
	2231	then
	2232	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2233	then
	2234	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2235	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2236	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2237	else
	2238	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2239	printf "\n ${pathout[$i]}\n"
	2240	cat ${localout[$i]} >> ${pathout[$i]}
	2241	fi
	2242	fi
	2243
	2244	# COPY ON THIS MACHINE
	2245	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2246	# ON DIFFERENT FILE-SYSTEMS
	2247	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2248	then
	2249
	2250	# COPY IN CASE OF RUNS ON SINGLE CORES
	2251	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2252	then
	2253	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2254	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2255	if [[ $link_local_output = true ]]
	2256	then
	2257	printf " file will be linked\n"
	2258	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2259	fi
	2260	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2261	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2262	then
	2263	if [[ $link_local_output = true ]]
	2264	then
	2265	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2266	fi
	2267	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2268	else
	2269	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2270	fi
	2271	else
	2272	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2273	printf "\n ${pathout[$i]}\n"
	2274	if [[ $link_local_output = true ]]
	2275	then
	2276	printf " file will be linked\n"
	2277	ln -f ${localout[$i]} ${pathout[$i]}
	2278	fi
	2279	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2280	if [[ ! -f "${pathout[$i]}" ]]
	2281	then
	2282	if [[ $link_local_output = true ]]
	2283	then
	2284	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2285	fi
	2286	cp ${localout[$i]} ${pathout[$i]}
	2287	else
	2288	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2289	fi
	2290	fi
	2291
	2292	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2293	then
	2294
	2295	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2296	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2297	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2298	printf "\n ${pathout[$i]}\n"
	2299	if [[ $link_local_output = true ]]
	2300	then
	2301	printf " files will be linked\n"
[2396]	2302	mkdir -p ${pathout[$i]}
[2380]	2303	cd ${localout[$i]}
	2304	for file in $(ls *)
	2305	do
	2306	ln -f $file ${pathout[$i]}
	2307	done >\|/dev/null 2>&1
[2566]	2308	cd $tempdir
[2380]	2309	fi
	2310
	2311	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2312	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2313	then
	2314	if [[ $link_local_output = true ]]
	2315	then
	2316	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2317	fi
	2318	cp -r ${localout[$i]}/* ${pathout[$i]}
	2319	fi
	2320
	2321	fi
	2322	fi
	2323	done
	2324
	2325	if (( i != 0 ))
	2326	then
	2327	if [[ $transfer_problems = true ]]
	2328	then
	2329	printf "\n$dashes\n *** OUTPUT-files saved"
	2330	printf "\n +++ WARNING: some data transfers failed! \n"
	2331	else
	2332	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2333	fi
	2334	fi
	2335
	2336
	2337	# IF REQUIRED, START A RESTART-JOB
	2338	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2339	if [[ -f CONTINUE_RUN ]]
	2340	then
	2341
	2342	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2343	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2344	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2345	# -b START A BATCH JOB
	2346	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2347	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2348	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2349
	2350
	2351	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2352	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2353	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2354	then
[2381]	2355	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2356	fi
	2357
	2358
	2359	# START THE RESTART-JOB
	2360	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2361	echo " $prc"
	2362	printf "\n$dashes\n"
	2363	if [[ $running_on_remote = true ]]
	2364	then
	2365
	2366	echo "*** ssh will be used to initiate restart-runs!"
	2367	echo " return_address=\"$return_address\" "
	2368	echo " return_username=\"$local_username\" "
	2369
	2370	if [[ "$remote_loginnode" != "" ]]
	2371	then
[2420]	2372	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
[2380]	2373	else
[2420]	2374	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2375	fi
	2376
	2377	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2378	sleep 30
	2379
	2380	else
	2381
	2382	# START THE RESTART JOB ON THE LOCAL HOST
	2383	eval $prc # THE ' MUST BE EVALUATED
	2384	cd - > /dev/null
	2385
	2386	fi
	2387	printf "\n$dashes\n *** restart-run initiated \n"
	2388
	2389
	2390	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2391	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2392	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2393	# MAY BE VERY HUGE)
	2394	(( i = 0 ))
	2395	while (( i < iin ))
	2396	do
	2397	(( i = i + 1 ))
	2398	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2399	then
	2400	rm -r ${absnamein[$i]}
	2401	fi
	2402	done
	2403
	2404	fi
	2405
	2406
	2407	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2408	cd $HOME
[2566]	2409	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2410
	2411
	2412	else
	2413
	2414
	2415	# PREPARING ACTIONS,
	2416	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2417
	2418	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2419	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2420	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2421	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2422	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2423	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2424	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2425	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2426	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2427	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2428	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2429	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2430	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2431	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2432	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2433	if [[ $create_remote_batch_job = true ]]
	2434	then
	2435	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2436	if [[ $do_trace = true ]]
	2437	then
	2438	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2439	fi
[2380]	2440	elif [[ $create_batch_job = true ]]
	2441	then
	2442	palmrun_com=${palmrun_com}" -j"
[2420]	2443	if [[ $do_trace = true ]]
	2444	then
	2445	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2446	fi
[2380]	2447	fi
	2448
	2449
	2450	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2451	# REMOTE HOST
[2506]	2452	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2453	job_protocol_file=$job_protocol_file_local
	2454	if [[ $create_remote_batch_job = true ]]
	2455	then
[2506]	2456	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2457	job_protocol_file=$job_protocol_file_remote
	2458	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2459	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2460	fi
	2461
	2462
	2463	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2464	jobfile=jobfile.$run_id
	2465
	2466
	2467	# FIRST CREATE THE BATCH DIRECTIVES
	2468	(( i = 0 ))
	2469	while (( i < ibd ))
	2470	do
	2471	(( i = i + 1 ))
[2566]	2472	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' \| sed 's/{{PREVIOUS_JOB}}/$previous_job/g' \| sed 's/{{TEMPDIR}}/$tempdir/g'`
[2380]	2473	eval line=\"$line\"
	2474	echo "$line" >> $jobfile
	2475	done
	2476	echo " " >> $jobfile
	2477
	2478
	2479	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2480	# PROTOCOL
	2481	if [[ $create_remote_batch_job = true ]]
	2482	then
	2483	echo "set +vx" >> $jobfile
	2484	echo "trap '" >> $jobfile
	2485	echo "set +vx" >> $jobfile
	2486	echo "cd ${remote_jobcatalog}" >> $jobfile
	2487	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2488
	2489	# ADD THE BATCH DIRECTIVES
	2490	(( i = 0 ))
	2491	while (( i < ibdt ))
	2492	do
	2493	(( i = i + 1 ))
[2506]	2494	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2495	eval line=\"$line\"
	2496	echo "$line" >> $jobfile
	2497	done
	2498	echo " " >> $jobfile
	2499
	2500	echo "set -x" >> $jobfile
[2506]	2501	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
[2380]	2502	echo "%%END%%" >> $jobfile
	2503	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2504	echo "$submit_command $scpjob_file" >> $jobfile
	2505	echo "rm $scpjob_file" >> $jobfile
[2404]	2506	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2507	echo "set -x" >> $jobfile
	2508	echo " ' exit" >> $jobfile
	2509	fi
	2510
	2511
	2512	# ACTIVATE ERROR-TRACEBACK
	2513	if [[ $do_trace = true ]]
	2514	then
	2515	echo "set -x" >> $jobfile
	2516	else
	2517	echo "set +vx" >> $jobfile
	2518	fi
	2519
	2520
	2521	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2522	if [[ "$login_init_cmd" != "" ]]
	2523	then
	2524	echo "$login_init_cmd" >> $jobfile
	2525	fi
	2526	if [[ "$module_commands" != "" ]]
	2527	then
	2528	echo "$module_commands" >> $jobfile
	2529	fi
	2530
	2531
	2532	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2533	if [[ $create_remote_batch_job = true ]]
	2534	then
	2535	echo "mkdir $tempdir" >> $jobfile
	2536	echo "chmod go+rx $tempdir" >> $jobfile
	2537	else
	2538	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2539	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2540	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2541	mkdir $tempdir
	2542	chmod go+rx $tempdir
	2543	fi
	2544	echo "cd $tempdir" >> $jobfile
	2545	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2546	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2547	echo "export PATH=.:\$PATH" >> $jobfile
	2548	echo "export execute_palmrun=true" >> $jobfile
	2549
	2550
	2551	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2552	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2553	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2554	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2555	echo "export LOCAL_PWD" >> $jobfile
	2556
	2557
	2558	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2559	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2560	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2561
	2562
	2563	# CALL PALMRUN WITHIN THE JOB
	2564	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2565	echo "set -x" >> $jobfile
	2566	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2567
	2568
	2569	# TRANSFER JOBFILE TO THE TARGET HOST
	2570	if [[ $create_jobfile_only = false ]]
	2571	then
	2572
	2573	if [[ $create_remote_batch_job = true ]]
	2574	then
	2575
[2420]	2576	echo " "
[2566]	2577	echo " *** transfer of job to remote host via scp"
[2420]	2578	if [[ $do_trace = true ]]
	2579	then
[2506]	2580	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2581	fi
[2566]	2582	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2583
[2566]	2584	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2585	if [[ $do_trace = true ]]
	2586	then
[2506]	2587	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2588	fi
[2506]	2589	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2590
	2591	elif [[ $create_batch_job = true ]]
	2592	then
	2593
[2385]	2594	eval local_jobcatalog=$local_jobcatalog
[2506]	2595	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2596	cd $local_jobcatalog
[2380]	2597	echo " "
[2420]	2598	echo " *** submit the job"
	2599	if [[ $do_trace = true ]]
	2600	then
[2506]	2601	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2602	fi
[2506]	2603	$submit_command ${host_configuration}_${job_id}
	2604	rm ${host_configuration}_${job_id}
[2380]	2605	cd - > /dev/null
	2606
	2607	fi
	2608
	2609	rm -rf $jobfile
	2610
	2611	else
	2612
	2613	printf "\n *** jobfile created under name \"$jobfile\" "
	2614	printf "\n no batch-job has been sent!"
	2615
	2616	fi
	2617
	2618	fi # END OF REMOTE-PART

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