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source: palm/trunk/SCRIPTS/palmrun @ 2600

Last change on this file since 2600 was 2600, checked in by raasch, 7 years ago
small changes concerning r2599, cycle number are now three digits wide
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 87.5 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 2600 2017-11-01 14:11:20Z raasch $
[2600]	29	# cycle numbers are made three digits wide
	30	#
	31	# 2566 2017-10-20 08:50:47Z raasch
[2566]	32	# execute command for combine_plot_fields added
	33	# "TEMPDIR" renamed "tempdir"
	34	# temporary working directory for local batch jobs is created immediately within
	35	# the user's palmrun call, due to a requirement of the "grid engine" batch
	36	# system, where the working directory is given with batch directive -wd and must
	37	# already exist when the job is submitted,
	38	# informative messages in non-trace mode reduced and partly reformatted
	39	#
	40	# 2551 2017-10-18 07:25:11Z raasch
[2551]	41	# TEMPDIR added as replacement string to be used in batch directives
	42	#
	43	# 2512 2017-10-04 08:26:59Z raasch
[2507]	44	# bugfix for determining cycle numbers of NetCDF input files
	45	#
	46	# 2506 2017-09-29 08:30:37Z raasch
[2506]	47	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	48	# host configuration added to SOURCES_FOR_RUN_... folder name
	49	# host_identifier renamed host_configuration
	50	# option -W added to allow for job dependencies
	51	#
	52	# 2501 2017-09-26 11:41:55Z raasch
[2501]	53	# default value for number of cores (option -X) set to 1
	54	# bugfix for mechanism which overwrites configuration file settings with values
	55	# provided by palmrun options
	56	#
	57	# 2499 2017-09-22 16:47:58Z kanani
[2499]	58	# option -h named configuration identifier
	59	#
	60	# 2480 2017-09-19 06:24:14Z maronga
[2480]	61	# bugfix for last revision
	62	#
	63	# 2479 2017-09-19 06:12:16Z raasch
[2479]	64	# option -A (project account number) added
	65	#
	66	# 2422 2017-09-08 08:25:41Z raasch
[2410]	67	# initial revision
[2380]	68	#
	69	#--------------------------------------------------------------------------------#
	70	# palmrun - script for running PALM jobs on local and remote hosts
	71	#--------------------------------------------------------------------------------#
	72
	73
	74
	75	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	76
	77	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	78	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	79	# (TOO MANY ARGUMENTS - PROBLEM)
	80	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	81
	82	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	83	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	84	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	85	# SCRIPT-OPTION ARGUMENTS
	86	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	87	typeset -i icycle inode ival maxcycle mpi_tasks
	88	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	89
	90	activation_string_list=""
	91	AddFilenames=""
	92	combine_plot_fields=true
	93	compiler_name=""
	94	compiler_name_ser=""
	95	compiler_options=""
[2501]	96	cores=1
[2380]	97	cores_atmos=0
	98	cores_ocean=0
	99	coupled_dist=""
	100	cpp_options=""
	101	cpumax=0
[2506]	102	create_batch_job=false
[2380]	103	create_jobfile_only=false
	104	create_remote_batch_job=false
	105	dashes=" ----------------------------------------------------------------------------"
	106	defaultqueue=""
[2506]	107	delete_temporary_catalog=true
[2380]	108	do_compile=true
	109	do_trace=false
	110	executable=""
	111	execute_command=""
	112	execution_error=false
	113	fileconnection_file=.palm.iofiles
	114	fname=test
	115	global_revision=""
[2506]	116	host_configuration="default"
[2380]	117	hostfile=""
	118	hp=""
	119	keep_data_from_previous_run=false
	120	link_local_input=false
	121	link_local_output=false
[2388]	122	linker_options=""
[2385]	123	local_jobcatalog=""
[2380]	124	locat=normal
	125	makefile=""
	126	max_par_io_str=""
	127	prc=$0
	128	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	129	do
	130	prc=`echo $prc \| cut -f2- -d"/"`
	131	done
	132	module_calls=""
[2506]	133	palmrun_memory=""
[2380]	134	palmrun_script_name=$prc
	135	openmp=false
[2506]	136	previous_job=""
[2479]	137	project_account=""
[2380]	138	queue=none
	139	restart_run=false
	140	return_address=""
[2385]	141	remote_jobcatalog=""
[2380]	142	remote_username=""
	143	running_in_batch_mode=false
	144	run_coupled_model=false
	145	run_id=""
	146	silent=false
	147	source_list=""
	148	source_path=""
[2501]	149	tasks_per_node=0
[2380]	150	threads_per_task=1
	151	transfer_problems=false
[2384]	152	user_source_path=""
[2506]	153	use_existing_sources_folder=""
[2380]	154	use_openmp=false
[2422]	155	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	156	working_directory=`pwd`
	157	write_binary=""
	158	TOPT=""
	159
	160
	161	# ERROR HANDLING IN CASE OF EXIT
[2404]	162	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	163	then
	164
	165	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	166	(( i = 0 ))
	167	while (( i < iec ))
	168	do
	169	(( i = i + 1 ))
	170	printf "\n *** Execution of ERROR-command:\n"
	171	printf " >>> ${err_command[$i]}\n"
	172	eval ${err_command[$i]}
	173	done
[2566]	174	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	175	printf "\n\n+++ palmrun killed \n\n"
	176	elif [[ $locat != control_c ]]
	177	then
[2566]	178	printf "\n --> palmrun finished\n\n"
[2380]	179	fi' exit
	180
	181
	182	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	183	trap 'cd; rm -rf $tempdir
[2380]	184	printf "\n+++ palmrun killed by \"^C\" \n\n"
	185	locat=control_c
	186	exit
	187	' 2
	188
	189
	190	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	191	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	192	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]	193	do
	194	case $option in
	195	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	196	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	197	(b) create_batch_job=true; prc="$prc -b";;
	198	(B) delete_temporary_catalog=false; prc="$prc -B";;
	199	(C) restart_run=true; prc="$prc -C";;
	200	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	201	(F) create_jobfile_only=true;;
	202	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	203	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	204	(j) running_in_batch_mode=true;;
	205	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	206	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	207	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	208	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	209	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	210	(r) run_id=$OPTARG;;
	211	(R) return_address=$OPTARG;;
	212	(s) source_list=$OPTARG;;
[2501]	213	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	214	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	215	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	216	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	217	(v) silent=true; prc="$prc -v";;
[2506]	218	(V) use_existing_sources_folder="-V";;
[2380]	219	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	220	(W) previous_job=$OPTARG;;
[2380]	221	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	222	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	223	(y) ocean_file_appendix=true; prc="$prc -y";;
	224	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	225	(Z) combine_plot_fields=false; prc="$prc -Z";;
	226	(\?) printf "\n +++ unknown option $OPTARG \n"
	227	printf "\n --> type \"$0 ?\" for available options \n"
	228	locat=parameter;exit;;
	229	esac
	230	done
	231
	232
	233	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	234	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	235	(( to_shift = $OPTIND - 1 ))
	236	shift $to_shift
	237
	238	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	239	if [[ "$1" = "?" ]]
	240	then
	241	(printf "\n *** Description of available palmrun options:\n"
	242	printf "\n Option Description Default-Value"
	243	printf "\n -a activation string list \"\" "
[2479]	244	printf "\n -A project account number ---"
[2380]	245	printf "\n -b batch-job on local machine ---"
	246	printf "\n -B do not delete temporary directory at end ---"
	247	printf "\n -d base name of files attached to program test"
	248	printf "\n -F create batch job file only ---"
[2506]	249	printf "\n -h host configuration \"default\" "
[2380]	250	printf "\n -k keep data from previous run"
	251	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	252	printf "\n -M Makefile name Makefile"
	253	printf "\n -O threads per openMP task ---"
	254	printf "\n -q queue \"$queue\" "
	255	printf "\n -s filenames of routines to be compiled \"\" "
	256	printf "\n must end with .f, .f90, .F, or .c !"
	257	printf "\n use \"..\" for more than one file and wildcards"
	258	printf "\n -s LM compiles all locally modified files"
	259	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	260	printf "\n -T tasks per node ---"
[2380]	261	printf "\n -u username on remote machine \"\" "
	262	printf "\n -v no prompt for confirmation ---"
[2506]	263	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	264	printf "\n -w maximum parallel io streams as given by -X"
[2506]	265	printf "\n -W name of job to wait for ---"
[2380]	266	printf "\n -x tracing of palmrun for debug purposes ---"
	267	printf "\n -X # of processors (on parallel machines) 1"
	268	printf "\n -y add appendix \"_O\" to all local output"
	269	printf "\n files (ocean precursor runs followed by"
	270	printf "\n coupled atmosphere-ocean runs) ---"
	271	printf "\n -Y run coupled model, \"#1 #2\" with"
	272	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	273	printf "\n -Z skip combine_plot_fields at the end of "
	274	printf "\n the simulation ---"
	275	printf "\n "
	276	printf "\n Possible values of positional parameter <modus>:"
	277	printf "\n \"?\" - this outline \n\n") \| more
	278	exit
	279	elif [[ "$1" != "" ]]
	280	then
	281	printf "\n +++ positional parameter $1 unknown \n"
	282	locat=parameter; exit
	283	fi
	284
	285
	286
	287	# SHORT STARTING MESSAGE
	288	printf "\n*** $version "
	289	printf "\n will be executed. Please wait ..."
	290
	291
[2506]	292	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	293	config_file=.palm.config.$host_configuration
	294	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	295
	296
	297	# CHECK, IF CONFIGURATION FILE EXISTS
	298	if [[ ! -f $config_file ]]
	299	then
	300	printf "\n\n +++ configuration file: "
	301	printf "\n $config_file"
	302	printf "\n does not exist"
	303	locat=connect; exit
	304	fi
	305
	306
	307	# CHECK, IF FILE CONNECTION FILE EXISTS
	308	if [[ ! -f $fileconnection_file ]]
	309	then
	310	printf "\n\n +++ file connection file: "
	311	printf "\n $fileconnection_file"
	312	printf "\n does not exist"
	313	locat=connect; exit
	314	fi
	315
	316
[2404]	317	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	318	if [[ "$activation_string_list" = "" ]]
	319	then
	320	printf "\n\n +++ no activation string list given: "
	321	printf "\n please set palmrun option \"-a\" "
	322	locat=palmrun_option; exit
	323	fi
	324
	325
	326	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	327	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	328	then
	329	write_binary=true
	330	else
	331	write_binary=false
	332	fi
	333
	334
[2380]	335	# READ AND EVALUATE THE CONFIGURATION-FILE
	336	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	337
	338	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	339	while read line
	340	do
	341
	342	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	343	eval line=\"$line\"
	344
	345
	346	# INTERPRET THE LINE
	347	if [[ "$(echo $line)" = "" ]]
	348	then
	349
	350	# EMPTY LINE, NO ACTION
	351	continue
	352
	353	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	354	then
	355
	356	# LINE IS A COMMENT LINE
	357	continue
	358
	359	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	360	then
	361
	362	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	363	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	364	value=`echo $line \| cut -d" " -s -f2-`
	365
	366
	367	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	368	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	369	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	370	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	371	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	372	# CONFIGURATION-FILE.
	373	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	374	then
	375	eval export $var="\$value"
	376
	377	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	378	if [[ $do_trace = true ]]
	379	then
	380	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	381	fi
	382	fi
	383
	384	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	385	then
	386
	387	# LINE DEFINES BATCH-DIRECTIVE
	388	(( ibd = ibd + 1 ))
	389	line=$(echo $line \| cut -c4-)
	390	batch_directive[$ibd]="$line"
	391
	392	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	393	then
	394
	395	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	396	# REMOTE TO A LOCAL HOST
	397	(( ibdt = ibdt + 1 ))
	398	line=$(echo $line \| cut -c5-)
	399	batch_directive_transfer[$ibdt]="$line"
	400
	401	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	402	then
	403
	404	# LINE DEFINES ERROR-COMMAND
	405	(( iec = iec + 1 ))
	406	line=$(echo $line \| cut -c4-)
	407	err_command[$iec]="$line"
	408
	409	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	410	then
	411
	412	# LINE DEFINES INPUT-COMMAND
	413	(( iic = iic + 1 ))
	414	line=$(echo $line \| cut -c4-)
	415	in_command[$iic]="$line"
	416
	417	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	418	then
	419
	420	# LINE DEFINES OUTPUT-COMMAND
	421	(( ioc = ioc + 1 ))
	422	line=$(echo $line \| cut -c4-)
	423	out_command[$ioc]="$line"
	424
	425	else
	426
	427	# SKIP ALL OTHER LINES
	428	continue
	429
	430	fi
	431
	432	done < $config_file
	433
	434
	435	# CHECK SETTING OF REQUIRED PARAMETERS
	436	if [[ "$compiler_name" = "" ]]
	437	then
	438	printf "\n +++ no compiler name found in $config_file"
	439	printf "\n Please add line \"compiler_name ...\" to that file."
	440	locat=config_file; exit
	441	fi
	442	if [[ "$compiler_name_ser" = "" ]]
	443	then
	444	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	445	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	446	locat=config_file; exit
	447	fi
	448	if [[ "$compiler_options" = "" ]]
	449	then
	450	printf "\n +++ no compiler options found in $config_file"
	451	printf "\n Please add line \"compiler_options ...\" to that file."
	452	locat=config_file; exit
	453	fi
[2388]	454	if [[ "$linker_options" = "" ]]
[2380]	455	then
[2388]	456	printf "\n +++ no linker options found in $config_file"
	457	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	458	locat=config_file; exit
	459	fi
	460	if [[ "$execute_command" = "" ]]
	461	then
	462	printf "\n +++ no execute command found in $config_file"
	463	printf "\n Please add line \"execute_command ...\" to that file."
	464	locat=config_file; exit
	465	fi
	466
	467	if [[ "$hostfile" != "" ]]
	468	then
	469	if [[ $hostfile != auto && ! -f $hostfile ]]
	470	then
	471	printf "\n +++ no hostfile \"$hostfile\" found"
	472	printf "\n Please check line \"hostfile ...\" in $config_file"
	473	locat=config_file; exit
	474	fi
	475	fi
	476
	477
	478	# DETERMINE THE CALL STATUS
	479	if [[ "$return_address" != "" ]]
	480	then
	481
	482	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	483	# BATCH MODE AND ...
	484	running_on_remote=true
	485
	486	else
	487
	488	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	489	if [[ "$remote_ip" != "" ]]
	490	then
	491
	492	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	493	create_remote_batch_job=true
	494
	495	fi
	496	running_on_remote=false
	497	fi
	498
	499
	500
	501	# READ AND EVALUATE THE I/O-FILE LIST
	502	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	503
	504	# READ THE FILE CONNECTION FILE LINE BY LINE
	505	while read line
	506	do
	507
	508	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	509	eval line=\"$line\"
	510
	511
	512	# INTERPRET THE LINE
	513	if [[ "$(echo $line)" = "" ]]
	514	then
	515	# EMPTY LINE, NO ACTION
	516	continue
	517
	518	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	519	then
	520
	521	# LINE IS A COMMENT LINE
	522	true
	523
	524	else
	525
	526	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	527	# s2a: in/out - field
	528	# s2b: loc - field (optional)
	529	# s2c: tr/ar - field (optional)
	530	s1=`echo $line \| cut -d" " -f1`
	531	s2=`echo $line \| cut -d" " -s -f2`
	532	s2a=$(echo $s2 \| cut -d":" -f1)
	533	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	534	then
	535	s2b=""
	536	s2c=""
	537	else
	538	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	539	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	540	fi
	541	s3=`echo $line \| cut -d" " -f3`
	542	s4=`echo $line \| cut -d" " -s -f4`
	543	s5=`echo $line \| cut -d" " -s -f5`
	544	s6=`echo $line \| cut -d" " -s -f6`
	545
	546
	547	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	548	# INPUT- OR OUTPUT-LIST.
	549	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	550	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	551	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	552	# IS NOT CHECKED AND STORED.
	553	IFSALT="$IFS"; IFS="$IFS:"
	554	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	555	then
	556	found=false
	557	for actual in $activation_string_list
	558	do
	559	for formal in $s3
	560	do
	561	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	562	done
	563	done
	564	if [[ $found = true ]]
	565	then
	566	(( iin = iin + 1 ))
	567	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	568	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	569	extin[$iin]=$s6
	570	fi
	571	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	572	then
	573	found=false
	574	for actual in $activation_string_list
	575	do
	576	for formal in $s3
	577	do
	578	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	579	done
	580	done
	581	if [[ $found = true ]]
	582	then
	583	(( iout = iout + 1 ))
	584	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	585	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	586	fi
	587	elif [[ "$s2a" != in && "$s2a" != out ]]
	588	then
	589	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	590	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	591	locat=connect; exit
	592	fi
	593	IFS="$IFSALT"
	594	fi
	595
	596	done < $fileconnection_file
	597
	598
	599
[2501]	600	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	601	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	602	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	603	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	604	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	605	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	606
	607
	608
[2380]	609	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	610	if [[ $run_coupled_model = true ]]
	611	then
	612
	613	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	614	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	615
	616	if (( $cores_ocean + $cores_atmos != $cores ))
	617	then
	618
	619	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	620	printf "\n PEs (total) : $cores"
	621	printf "\n PEs (atmosphere): $cores_atmos"
	622	printf "\n PEs (ocean) : $cores_ocean"
	623	locat=coupling; exit
	624
	625	fi
	626
	627	fi
	628
	629
	630	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	631	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	632	# FOLDER
	633	if [[ $running_in_batch_mode = true ]]
	634	then
	635
[2506]	636	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	637	then
[2506]	638	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	639	printf "\n Please check the output of the palmrun-call"
	640	printf "\n that you did on your local host."
	641	locat=SOURCES_FOR_RUN; exit
	642	fi
	643
	644	else
	645
	646	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	647	# AUTOMATIC RESTART RUN
	648	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	649	if [[ $restart_run = false ]]
	650	then
	651
	652	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	653	# THE LOCAL HOST
	654	if [[ ! -d $source_path ]]
	655	then
	656	printf "\n\n +++ source path \"$source_path\" on local host"
	657	printf "\n \"$(hostname)\" does not exist"
	658	locat=source_path; exit
	659	fi
	660
[2506]	661	rm -rf $sources_for_run_catalog
	662	mkdir -p $sources_for_run_catalog
[2380]	663
	664	if [[ "$source_list" = LM ]]
	665	then
	666
	667	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	668	source_list=""
	669	cd $source_path
	670
	671
[2512]	672	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	673	if [[ ! -d ../.svn ]]
[2380]	674	then
	675	printf "\n\n +++ source directory"
	676	printf "\n \"$source_path\" "
	677	printf "\n is not under control of \"subversion\"."
[2512]	678	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	679	fi
	680
	681
	682	# LIST ALL MODIFIED SOURCE CODE FILES
	683	Filenames=""
[2404]	684	svn status > tmp_svnstatus
[2380]	685	while read line
	686	do
	687	firstc=`echo $line \| cut -c1`
	688	if [[ $firstc = M \|\| $firstc = "?" ]]
	689	then
	690	Name=`echo "$line" \| cut -c8-`
	691	extension=`echo $Name \| cut -d. -f2`
	692	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	693	then
	694	Filenames="$Filenames "$Name
	695	fi
	696	fi
[2404]	697	done < tmp_svnstatus
	698	rm -rf tmp_svnstatus
[2380]	699
	700
	701	# COPY FILES TO SOURCES_FOR_RUN_...
	702	for filename in $Filenames
	703	do
[2506]	704	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	705	source_list=$source_list"$filename "
	706	done
	707
	708	cd - > /dev/null
	709
	710
	711	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	712	elif [[ "$source_list" != "" ]]
	713	then
	714
	715	cd $source_path
	716
	717	for filename in $source_list
	718	do
	719
	720	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	721	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	722	then
	723	printf "\n +++ source code file: $filename"
	724	printf "\n must not contain (\"/\") "
	725	locat=source; exit
	726	fi
	727
	728	if [[ ! -f $filename ]]
	729	then
	730	printf "\n +++ source code file: $filename"
	731	printf "\n does not exist"
	732	locat=source; exit
	733	else
[2506]	734	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	735	fi
	736
	737	done
	738
	739	cd - > /dev/null
	740
	741	fi
	742
	743	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	744	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	745	if [[ ! -f $makefile ]]
	746	then
	747	printf "\n +++ file \"$makefile\" does not exist"
	748	locat=make; exit
	749	else
[2506]	750	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	751	fi
	752
	753
	754	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	755	if [[ "$user_source_path" != "" ]]
[2380]	756	then
	757
	758	# DOES THE DIRECTORY EXIST?
[2384]	759	if [[ ! -d $user_source_path ]]
[2380]	760	then
	761
	762	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	763	printf "\n \"$user_source_path\" "
[2380]	764	printf "\n does not exist or is not a directory."
	765	printf "\n No source code will be used from this directory!\n"
[2384]	766	user_source_path=""
[2380]	767	if [[ $silent == false ]]
	768	then
	769	sleep 2
	770	fi
	771
	772	else
	773
[2384]	774	cd $user_source_path
[2380]	775	found=false
	776
	777	Names=$(ls -1 *.f90 2>&1)
	778	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	779	Names=$(ls -1 *.F90 2>&1)
	780	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	781	Names=$(ls -1 *.F 2>&1)
	782	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	783	Names=$(ls -1 *.f 2>&1)
	784	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	785	Names=$(ls -1 *.c 2>&1)
	786	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	787
	788	cd - > /dev/null
[2506]	789	cd $sources_for_run_catalog
[2380]	790
	791	# COPY MAKEFILE IF EXISTING
[2384]	792	if [[ -f $user_source_path/Makefile ]]
[2380]	793	then
	794	printf "\n\n *** user Makefile from directory"
[2384]	795	printf "\n \"$user_source_path\" is used \n"
[2380]	796	if [[ $silent == false ]]
	797	then
	798	sleep 1
	799	fi
[2384]	800	cp $user_source_path/Makefile .
[2380]	801	fi
	802
	803	for filename in $AddFilenames
	804	do
	805	if [[ -f $filename ]]
	806	then
	807	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	808	printf "\n source code directory \"$user_source_path\" "
[2380]	809	printf "\n but was also given with option \"-s\" which means that it should be taken"
	810	printf "\n from directory \"$source_path\"."
	811	locat=source; exit
	812	fi
	813
[2384]	814	cp $user_source_path/$filename .
[2380]	815	source_list="$source_list $filename"
	816
	817	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	818	if [[ $(grep -c $filename Makefile) = 0 ]]
	819	then
	820	printf "\n\n +++ user file \"$filename\" "
	821	printf "\n is not listed in Makefile \n"
	822	locat=source; exit
	823	else
	824
	825	if [[ $found = false ]]
	826	then
	827	found=true
	828	printf "\n\n *** following user file(s) added to the"
	829	printf " files to be translated:\n "
	830	fi
	831	printf "$filename "
	832	if [[ $silent == false ]]
	833	then
	834	sleep 0.5
	835	fi
	836
	837	fi
	838	done
	839	[[ $found = true ]] && printf "\n"
	840	cd - > /dev/null
	841	fi
	842	fi
	843
	844	# COPY CONFIGURATION FILES
[2506]	845	cp $config_file $sources_for_run_catalog
	846	cp $fileconnection_file $sources_for_run_catalog
[2380]	847
	848	# COPY SHELLSCRIPTS
[2506]	849	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	850	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	851
	852	fi
	853
	854	fi
	855
	856	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	857	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	858	if [[ "$global_revision" = "" ]]
	859	then
	860	global_revision=`svnversion $source_path 2>/dev/null`
	861	global_revision="Rev: $global_revision"
	862	fi
	863
	864
	865	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	866	if [[ -n $cores ]]
	867	then
	868
	869	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	870	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	871	if [[ $tasks_per_node = 0 ]]
[2380]	872	then
	873	printf "\n"
	874	printf "\n +++ option \"-T\" (tasks per node) is missing"
	875	printf "\n set -T option or define tasks_per_node in the config file"
	876	locat=tasks_per_node; (( iec = 0 )); exit
	877	fi
	878
	879	if (( cores < tasks_per_node ))
	880	then
	881	printf "\n"
	882	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	883	printf "\n given values: -T $tasks_per_node -X $cores"
	884	locat=tasks_per_node; (( iec = 0 )); exit
	885	fi
	886
	887	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	888	(( mpi_tasks = cores / threads_per_task ))
	889	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	890	(( ii = cores / tasks_per_node ))
	891	(( remaining_cores = cores - ii * tasks_per_node ))
	892	if (( remaining_cores > 0 ))
	893	then
	894	printf "\n"
	895	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	896	printf "\n divisor of the total number of cores (option \"-X\")"
	897	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	898	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	899	(( nodes = nodes + 1 ))
	900	fi
	901
	902	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	903	if [[ "$tasks_per_node" != "" ]]
	904	then
	905	TOPT="-T $tasks_per_node"
	906	fi
	907
	908	fi
	909
	910
	911	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	912	if [[ "$maximum_parallel_io_streams" = "" ]]
	913	then
	914	maximum_parallel_io_streams=$cores
	915	fi
	916
	917
	918	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	919	if [[ "$scp_port" != "" ]]
	920	then
	921	PORTOPT="-P $scp_port"
	922	SSH_PORTOPT="-p $scp_port"
	923	fi
	924
	925
	926	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	927	# CONFIG-FILE
	928	if [[ "$ssh_key" != "" ]]
	929	then
	930	ssh_key="-i $HOME/.ssh/$ssh_key"
	931	fi
	932
	933
	934	# SET QUEUE, IF NOT GIVEN
	935	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	936	then
	937
	938	if [[ $queue = none && "$defaultqueue" = "" ]]
	939	then
	940	printf "\n"
	941	printf "\n +++ no default queue given in configuration file and no queue"
	942	printf "\n given with option -q"
	943	fi
	944	if [[ $queue = none ]]
	945	then
	946	queue=$defaultqueue
	947	fi
	948
	949	fi
	950
	951
	952	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	953	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	954	(( i = 0 ))
	955	while (( i < iin ))
	956	do
	957	(( i = i + 1 ))
	958	(( maxcycle = 0 ))
	959
	960	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	961	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	962	if [[ "${actionin[$i]}" = di ]]
	963	then
	964	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	965	# HOST ONLY
	966	eval filename=${pathin[$i]}/${endin[$i]}
	967	else
	968	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	969	# HOST ONLY
	970	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	971	fi
	972	eval pathname=${pathin[$i]}
	973
	974	# CHECK IF FILE EXISTS
	975	if ! ls $filename* 1>/dev/null 2>&1
	976	then
	977
	978	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	979	if [[ "${transin[$i]}" != "locopt" ]]
	980	then
	981	printf "\n\n +++ INPUT-file: "
	982	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	983	then
	984	printf "\n $filename"
	985	else
	986	printf "\n $filename.${extin[$i]}"
	987	fi
	988	printf "\n does not exist\n"
	989	locat=input; exit
	990	else
	991	transin[$i]="unavailable"
	992	fi
	993	else
	994
	995	# DETERMINE THE FILE'S CYCLE NUMBER
	996	ls -1 -d $filename > filelist 2>/dev/null
	997	ls -1 -d $filename.* >> filelist 2>/dev/null
	998	while read line
	999	do
	1000	# filename without path (i.e. after the last "/")
	1001	basefilename=$(basename ${line})
	1002
	1003	# check if there is an extension
	1004	extension=${basefilename##*.}
[2507]	1005	if [[ "$extension" = "${extin[$i]}" ]]
[2380]	1006	then
[2507]	1007	basefilename=${basefilename%.*}
[2380]	1008	fi
	1009
	1010	# check for an existing cycle number
	1011	cycle=${basefilename##*.}
	1012	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1013	then
	1014	(( icycle = $cycle ))
	1015	else
	1016	(( icycle = 0 ))
	1017	fi
	1018
	1019	if (( icycle > maxcycle ))
	1020	then
	1021	(( maxcycle = icycle ))
[2600]	1022
	1023	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1024	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1025	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1026	then
	1027	leading_zero=true
	1028	else
	1029	leading_zero=false
	1030	fi
[2380]	1031	fi
	1032
	1033	done <filelist
	1034	rm filelist
	1035
[2600]	1036	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1037	if [[ $leading_zero = true ]]
	1038	then
	1039	cyclestring=`printf "%03d" $maxcycle`
	1040	else
	1041	cyclestring=$maxcycle
	1042	fi
	1043
[2380]	1044	# APPEND CYCLE NUMBER TO FILENAME
	1045	if (( maxcycle > 0 ))
	1046	then
	1047	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1048	then
[2600]	1049	filename=${filename}.$cyclestring.${extin[$i]}
[2380]	1050	else
[2600]	1051	filename=${filename}.$cyclestring
[2380]	1052	fi
	1053	else
	1054	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1055	then
	1056	filename=${filename}.${extin[$i]}
	1057	fi
	1058	fi
	1059
	1060	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1061	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1062	absnamein[$i]=$filename
	1063	if (( maxcycle > 0 ))
	1064	then
	1065	if [[ "${actionin[$i]}" = di ]]
	1066	then
[2600]	1067	frelin[$i]=${endin[$i]}.$cyclestring
[2380]	1068	else
[2600]	1069	frelin[$i]=${fname}${endin[$i]}.$cyclestring
[2380]	1070	fi
	1071	else
	1072	if [[ "${actionin[$i]}" = di ]]
	1073	then
	1074	frelin[$i]=${endin[$i]}
	1075	else
	1076	frelin[$i]=${fname}${endin[$i]}
	1077	fi
	1078	fi
	1079
	1080	fi
	1081	done
	1082
	1083
	1084	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1085	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1086	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1087	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1088	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1089	# REMOTE HOST)
	1090	(( i = 0 ))
	1091	while (( i < iout ))
	1092	do
	1093	(( i = i + 1 ))
	1094	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1095	then
	1096	if [[ "${actionout[$i]}" = tr ]]
	1097	then
	1098	actionout[$i]=""
	1099	elif [[ "${actionout[$i]}" = trpe ]]
	1100	then
	1101	actionout[$i]=pe
	1102	elif [[ "${actionout[$i]}" = tra ]]
	1103	then
	1104	actionout[$i]=a
	1105	fi
	1106	(( maxcycle = 0 ))
	1107	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1108	eval catalogname=${pathout[$i]}
	1109	if ! ls $filename* 1>/dev/null 2>&1
	1110	then
	1111
	1112	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1113	if cat /dev/null > $filename
	1114	then
	1115	rm $filename
	1116	else
	1117
	1118	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1119	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1120	if [[ ! -d $catalogname ]]
	1121	then
	1122	if mkdir -p $catalogname
	1123	then
	1124	printf "\n\n *** directory:"
	1125	printf "\n $catalogname"
	1126	printf "\n was created\n"
	1127	else
	1128	printf "\n\n +++ OUTPUT-file:"
	1129	printf "\n $filename"
	1130	printf "\n cannot be created, because directory does not exist"
	1131	printf "\n and cannot be created either"
	1132	printf "\n"
	1133	locat=output ; exit
	1134	fi 2>/dev/null
	1135	else
	1136	printf "\n\n +++ OUTPUT-file:"
	1137	printf "\n $filename"
	1138	printf "\n cannot be created, although directory exists"
	1139	printf "\n"
	1140	locat=output ; exit
	1141	fi
	1142	fi 2>/dev/null
	1143	else
	1144
	1145	# DETERMINE THE CYCLE NUMBER
	1146	ls -1 -d $filename > filelist 2>/dev/null
	1147	ls -1 -d $filename.* >> filelist 2>/dev/null
	1148	while read line
	1149	do
	1150
	1151	# filename without path (i.e. after the last "/")
	1152	basefilename=$(basename ${line})
	1153
	1154	# check if there is an extension
	1155	extension=${basefilename##*.}
	1156	if [[ "$extension" = "${extout[$i]}" ]]
	1157	then
	1158	basefilename=${basefilename%.*}
	1159	fi
	1160
	1161	# check for an existing cycle number
	1162	cycle=${basefilename##*.}
	1163	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1164	then
	1165	(( icycle = $cycle + 1 ))
	1166	else
	1167	(( icycle = 1 ))
	1168	fi
	1169
	1170	if (( icycle > maxcycle ))
	1171	then
	1172	(( maxcycle = icycle ))
	1173	fi
	1174
	1175	done <filelist
	1176	rm filelist
	1177	fi
	1178
	1179	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1180	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1181	if [[ "${actionout[$i]}" != a ]]
	1182	then
[2600]	1183	cyclestring=`printf "%03d" $maxcycle`
[2380]	1184	if (( maxcycle > 0 ))
	1185	then
[2600]	1186	filename_tmp=${filename}.$cyclestring
[2380]	1187	if cat /dev/null > $filename_tmp
	1188	then
	1189	rm $filename_tmp
	1190	else
	1191	printf "\n +++ OUTPUT-file:"
	1192	printf "\n $filename_tmp"
	1193	printf "\n cannot be created"
	1194	locat=output ; exit
	1195	fi
	1196	fi
	1197	else
	1198	(( maxcycle = maxcycle - 1 ))
	1199	fi
	1200
	1201	(( cycnum[$i] = maxcycle ))
	1202	pathout[$i]=$filename
	1203
	1204	fi
	1205	done
	1206
	1207
	1208	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1209	if [[ $running_in_batch_mode = false ]]
	1210	then
	1211	run_id=$RANDOM
	1212	job_id=${fname}.$run_id
	1213
[2566]	1214	tempdir=$fast_io_catalog/$job_id
[2380]	1215	fi
	1216
	1217
	1218	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1219	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1220	then
	1221
	1222	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1223	if [[ $ibd = 0 ]]
	1224	then
	1225	printf "\n"
	1226	printf "\n +++ no batch directives found in configuration file"
	1227	locat=config_file_batch_directives; (( iec = 0 )); exit
	1228	fi
	1229
	1230	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1231	done=false
[2384]	1232	cputime=$cpumax
[2380]	1233	while [[ $done = false ]]
	1234	do
[2384]	1235	if (( cputime == 0 ))
[2380]	1236	then
	1237	printf "\n +++ cpu-time is undefined"
	1238	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1239	printf "\n >>> "
[2384]	1240	read cputime 1>/dev/null 2>&1
[2380]	1241	else
	1242	done=true
	1243	fi
	1244	done
[2420]	1245	cpumax=$cputime
[2380]	1246
	1247	# CHECK THE MEMORY DEMAND
	1248	done=false
	1249	while [[ $done = false ]]
	1250	do
	1251	if (( memory == 0 ))
	1252	then
	1253	printf "\n +++ memory demand is undefined"
	1254	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1255	printf "\n >>> "
	1256	read memory 1>/dev/null 2>&1
	1257	else
	1258	done=true
	1259	fi
	1260	done
	1261
	1262	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1263	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1264	then
	1265	while [[ -z $remote_username ]]
	1266	do
[2420]	1267	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1268	printf "\n >>> Please type username:"
	1269	printf "\n >>> "
	1270	read remote_username
	1271	done
	1272	fi
	1273
	1274	else
	1275
[2420]	1276	if [[ $running_in_batch_mode = false ]]
	1277	then
	1278	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1279	cpumax=$cputime
	1280	else
	1281	cputime=$cpumax
	1282	fi
[2380]	1283
	1284	fi
	1285
	1286
	1287	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1288	(( cpu_hours = cputime / 3600 ))
	1289	(( resttime = cputime - cpu_hours * 3600 ))
	1290	(( cpu_minutes = resttime / 60 ))
	1291	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1292	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1293
	1294
	1295	# OUTPUT OF THE PALMRUN-HEADER
	1296	calltime=$(date)
	1297	printf "\n"
	1298	printf "#------------------------------------------------------------------------# \n"
	1299	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1300	printf "\| \| \n"
	1301	column1="called on:"; column2=$(hostname)
	1302	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1303	if [[ $create_remote_batch_job = true ]]
	1304	then
[2506]	1305	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1306	else
	1307	if [[ $running_on_remote = true ]]
	1308	then
[2506]	1309	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1310	else
[2506]	1311	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1312	fi
	1313	fi
	1314	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1315
	1316	column1="running in:"
	1317	if [[ $running_in_batch_mode = true ]]
	1318	then
	1319	column2="batch job mode"
	1320	else
	1321	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1322	then
	1323	column2="job creation mode"
	1324	else
	1325	column2="interactive run mode"
	1326	fi
	1327	fi
	1328	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1329
[2479]	1330	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1331	then
[2480]	1332	if [[ "$project_account" != "" ]]
[2479]	1333	then
	1334	column1="project account number:"
	1335	column2="$project_account"
	1336	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1337	fi
	1338	fi
	1339
[2380]	1340	if [[ -n $cores ]]
	1341	then
	1342	if [[ $run_coupled_model = false ]]
	1343	then
	1344	column1="number of cores:"; column2=$cores
	1345	else
	1346	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1347	fi
	1348	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1349	fi
	1350	if [[ -n $tasks_per_node ]]
	1351	then
	1352	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1353	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1354	if (( remaining_cores > 0 ))
	1355	then
	1356	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1357	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1358	fi
	1359	fi
	1360	if [[ $maximum_parallel_io_streams != $cores ]]
	1361	then
	1362	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1363	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1364	fi
	1365	if [[ $use_openmp = true ]]
	1366	then
	1367	column1="threads per task:"; column2="$threads_per_task"
	1368	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1369	fi
[2384]	1370	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1371	then
[2506]	1372	column1="memory demand / PE":; column2="$memory MB"
	1373	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1374	column1="job cpu time (h:m:s):"; column2="$timestring"
	1375	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1376	fi
[2380]	1377	printf "\| \| \n"
	1378	if [[ "$source_list" != "" ]]
	1379	then
	1380	if [[ "$make_options" != "" ]]
	1381	then
	1382	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1384	line=$(echo "$make_options" \| cut -c46-)
	1385	while [[ "$line" != "" ]]
	1386	do
	1387	column1=""
	1388	column2=$(echo "$line" \| cut -c-45)
	1389	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1390	line=$(echo "$line" \| cut -c46-)
	1391	done
	1392	fi
	1393	fi
	1394
	1395	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1396	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1397	line=$(echo "$cpp_options" \| cut -c46-)
	1398	while [[ "$line" != "" ]]
	1399	do
	1400	column1=""
	1401	column2=$(echo "$line" \| cut -c-45)
	1402	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1403	line=$(echo "$line" \| cut -c46-)
	1404	done
	1405
	1406	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1407	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1408	line=$(echo "$compiler_options" \| cut -c46-)
	1409	while [[ "$line" != "" ]]
	1410	do
	1411	column1=""
	1412	column2=$(echo "$line" \| cut -c-45)
	1413	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1414	line=$(echo "$line" \| cut -c46-)
	1415	done
	1416
[2388]	1417	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1418	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1419	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1420	while [[ "$line" != "" ]]
	1421	do
	1422	column1=""
	1423	column2=$(echo "$line" \| cut -c-45)
	1424	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1425	line=$(echo "$line" \| cut -c46-)
	1426	done
	1427
	1428	if [[ "$login_init_cmd" != "" ]]
	1429	then
	1430	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1431	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1432	line=$(echo "$login_init_cmd" \| cut -c46-)
	1433	while [[ "$line" != "" ]]
	1434	do
	1435	column1=""
	1436	column2=$(echo "$line" \| cut -c-45)
	1437	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1438	line=$(echo "$line" \| cut -c46-)
	1439	done
	1440	fi
	1441
	1442	if [[ "$module_commands" != "" ]]
	1443	then
	1444	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1446	line=$(echo "$module_commands" \| cut -c46-)
	1447	while [[ "$line" != "" ]]
	1448	do
	1449	column1=""
	1450	column2=$(echo "$line" \| cut -c-45)
	1451	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1452	line=$(echo "$line" \| cut -c46-)
	1453	done
	1454	fi
	1455	printf "\| \| \n"
	1456	column1="base name of files:"; column2=$fname
	1457	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1458	column1="activation string list:"; column2=$(echo $activation_string_list)
	1459	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1460
	1461	if [[ "$ocean_file_appendix" = true ]]
	1462	then
	1463	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1464	fi
	1465
	1466	if [[ "$source_list" != "" ]]
	1467	then
	1468	printf "\| \| \n"
	1469	printf "\| Files to be compiled: \| \n"
	1470	line=$source_list
	1471	while [[ "$line" != "" ]]
	1472	do
	1473	linestart=$(echo $line \| cut -c-70)
	1474	printf "\| %-70s \| \n" "$linestart"
	1475	line=$(echo "$line" \| cut -c71-)
	1476	done
	1477	fi
	1478	printf "#------------------------------------------------------------------------#"
	1479
	1480
	1481
	1482	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1483	if [[ $do_trace = true ]]
	1484	then
	1485	(( i = 0 ))
	1486	while (( i < iin ))
	1487	do
	1488	(( i = i + 1 ))
	1489	if (( i == 1 ))
	1490	then
	1491	printf "\n\n >>> INPUT-file assignments:\n"
	1492	fi
	1493	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1494	done
	1495	(( i = 0 ))
	1496	while (( i < iout ))
	1497	do
	1498	(( i = i + 1 ))
	1499	if (( i == 1 ))
	1500	then
	1501	printf "\n\n >>> OUTPUT-file assignments:\n"
	1502	fi
	1503	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1504	done
	1505	(( i = 0 ))
	1506	while (( i < iic ))
	1507	do
	1508	(( i = i + 1 ))
	1509	if (( i == 1 ))
	1510	then
	1511	printf "\n\n >>> INPUT-commands:\n"
	1512	fi
	1513	printf "\n ${in_command[$i]}"
	1514	done
	1515	(( i = 0 ))
	1516	while (( i < ioc ))
	1517	do
	1518	(( i = i + 1 ))
	1519	if (( i == 1 ))
	1520	then
	1521	printf "\n\n >>> OUTPUT-commands:\n"
	1522	fi
	1523	printf "\n ${out_command[$i]}"
	1524	done
	1525	fi
	1526
	1527	# QUERY FOR CONTINUE
	1528	if [[ $silent = false && $running_in_batch_mode = false ]]
	1529	then
	1530	antwort=dummy
	1531	printf "\n\n"
	1532	printf " >>> everything o.k. (y/n) ? "
	1533	while read antwort
	1534	do
	1535	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1536	then
	1537	printf " >>> everything o.k. (y/n) ? "
	1538	else
	1539	break
	1540	fi
	1541	done
	1542	if [[ $antwort = n \|\| $antwort = N ]]
	1543	then
	1544	locat=user_abort; (( iec = 0 )); exit
	1545	fi
	1546	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1547	then
[2566]	1548	printf "\n *** batch-job will be created and submitted"
[2380]	1549	else
[2566]	1550	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1551	fi
	1552	fi
	1553
	1554
	1555
	1556	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1557	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1558	then
	1559
	1560	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1561	then
[2566]	1562	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1563	else
[2566]	1564	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1565	fi
	1566
[2422]	1567	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1568	# IT SHALL BE CREATED
	1569	ask_for_make_depository=false
	1570	if [[ $create_remote_batch_job = true ]]
	1571	then
	1572
	1573	line=`grep %base_directory $config_file`
[2506]	1574	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1575	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]	1576
[2506]	1577	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1578	then
	1579	printf "\n\n +++ make depository \"${make_depository}\""
	1580	printf "\n on remote host not found!"
	1581	ask_for_make_depository=true
	1582	fi
[2506]	1583	rm ${host_configuration}_last_make_protokoll
[2422]	1584
	1585	else
	1586
	1587	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1588	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1589	if [[ ! -d ${make_depository} ]]
	1590	then
	1591	printf "\n\n +++ make depository \"${make_depository}\""
	1592	printf "\n on local host not found!"
	1593	ask_for_make_depository=true
	1594	fi
	1595
	1596	fi
	1597
	1598	if [[ $ask_for_make_depository = true ]]
	1599	then
	1600
	1601	antwort=dummy
	1602	printf "\n\n"
	1603	printf " >>> Create a new one (y/n) ? "
	1604	while read antwort
	1605	do
	1606	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1607	then
	1608	printf " >>> Create a new one (y/n) ? "
	1609	else
	1610	break
	1611	fi
	1612	done
	1613	if [[ $antwort = n \|\| $antwort = N ]]
	1614	then
	1615	locat=user_abort; (( iec = 0 )); exit
	1616	fi
	1617
[2566]	1618	if [[ $do_trace = true ]]
	1619	then
	1620	palmbuild -h $host_configuration
	1621	else
	1622	palmbuild -v -h $host_configuration
	1623	fi
[2422]	1624
	1625	if [[ $? != 0 ]]
	1626	then
	1627
	1628	# ABORT IN CASE OF COMPILATION PROBLEMS
	1629	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1630	locat=make_depository
	1631	exit
	1632	else
	1633	echo " *** now continue with creating executable and other sources"
	1634	fi
	1635
	1636	fi
	1637
[2566]	1638	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1639	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1640
	1641	if [[ $? != 0 ]]
	1642	then
	1643
	1644	# ABORT IN CASE OF COMPILATION PROBLEMS
	1645	printf "\n +++ error while creating executable and/or other sources"
	1646	locat=execution
[2506]	1647	rm -rf $sources_for_run_catalog
[2380]	1648	exit
	1649
	1650	else
	1651
[2566]	1652	printf " *** executable and other sources created\n"
[2506]	1653	rm -rf $sources_for_run_catalog
[2380]	1654
	1655	fi
	1656
	1657	fi
	1658
	1659
	1660	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1661	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1662	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1663	then
	1664
	1665	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1666	if [[ $running_in_batch_mode = false ]]
	1667	then
	1668	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1669	# FOLDER
[2566]	1670	mkdir -p $tempdir
	1671	chmod go+rx $tempdir
	1672	cd $tempdir
	1673	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1674	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1675
	1676	else
	1677
	1678	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1679	printf "\n *** running in temporary directory: $tempdir"
[2380]	1680
	1681	fi
	1682
	1683
	1684	# PROVIDE THE INPUT FILES
	1685	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1686	(( i = 0 ))
	1687	while (( i < iin ))
	1688	do
	1689	(( i = i + 1 ))
	1690	if (( i == 1 ))
	1691	then
	1692	printf "\n\n *** providing INPUT-files:\n$dashes"
	1693	fi
	1694
	1695
	1696	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1697	if [[ "${transin[$i]}" = unavailable ]]
	1698	then
	1699	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1700	then
	1701	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1702	printf "\n is not available!"
	1703	else
	1704	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1705	printf "\n is not available!"
	1706	fi
	1707	continue
	1708	fi
	1709
	1710	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1711	files_for_cores=false; filetype=file
	1712	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1713	then
	1714	files_for_cores=true; filetype=files
	1715	actionin[$i]=""
	1716	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1717	then
	1718	actionin[$i]=""
	1719	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1720	then
	1721	files_for_cores=true; filetype=files
	1722	actionin[$i]="ln"
	1723	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1724	then
	1725	actionin[$i]="ln"
	1726	fi
	1727
	1728	if [[ $files_for_cores = true ]]
	1729	then
	1730	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1731	else
	1732	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1733	fi
	1734
	1735	# INPUT-FILES TO BE LINKED
	1736	if [[ "${actionin[$i]}" = ln ]]
	1737	then
	1738
	1739	printf "\n $filetype will be linked"
	1740	if [[ $files_for_cores = false ]]
	1741	then
	1742	if [[ -f "${absnamein[$i]}" ]]
	1743	then
	1744	ln ${absnamein[$i]} ${localin[$i]}
	1745	got_tmp[$i]=true
	1746	fi
	1747	else
	1748	if [[ -d "${absnamein[$i]}" ]]
	1749	then
[2396]	1750	mkdir -p ${localin[$i]}
[2380]	1751	cd ${absnamein[$i]}
	1752	for file in $(ls *)
	1753	do
[2566]	1754	ln $file $tempdir/${localin[$i]}
[2380]	1755	done >\|/dev/null 2>&1
[2566]	1756	cd $tempdir
[2380]	1757	fi
	1758
	1759	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1760	if [[ ! -f "${localin[$i]}/_000000" ]]
	1761	then
	1762	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1763	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1764	fi
	1765
	1766	got_tmp[$i]=true
	1767	fi
	1768	fi
	1769
	1770	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1771	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1772	then
	1773
	1774	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1775	then
	1776
	1777	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1778	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1779	printf "\n file will be provided for $cores processors"
[2396]	1780	mkdir -p ${localin[$i]}
[2380]	1781	ival=$cores
	1782	(( ii = 0 ))
	1783	while (( ii <= ival-1 ))
	1784	do
	1785	if (( ii < 10 ))
	1786	then
	1787	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1788	elif (( ii < 100 ))
	1789	then
	1790	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1791	elif (( ii < 1000 ))
	1792	then
	1793	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1794	else
	1795	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1796	fi
	1797	(( ii = ii + 1 ))
	1798	done
	1799
	1800	else
	1801
	1802	if [[ $files_for_cores = true ]]
	1803	then
	1804
	1805	# PROVIDE FILES FOR EACH CORE
	1806	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1807	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1808	printf "\n providing $cores files for the respective cores"
[2396]	1809	mkdir -p ${localin[$i]}
[2380]	1810	if [[ $link_local_input = true ]]
	1811	then
	1812	printf " files will be linked\n"
	1813	cd ${absnamein[$i]}
	1814	for file in $(ls *)
	1815	do
	1816	ln -f $file ${localin[$i]}
	1817	done
[2566]	1818	cd $tempdir
[2380]	1819	fi
	1820
	1821	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1822	if [[ ! -f "${localin[$i]}/_000000" ]]
	1823	then
	1824	if [[ $link_local_input = true ]]
	1825	then
	1826	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1827	fi
	1828	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1829	fi
	1830
	1831	else
	1832
	1833	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1834	if [[ $link_local_input = true ]]
	1835	then
	1836	printf " file will be linked\n"
	1837	ln -f ${absnamein[$i]} ${localin[$i]}
	1838	fi
	1839	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1840	if [[ ! -f "${localin[$i]}" ]]
	1841	then
	1842	if [[ $link_local_input = true ]]
	1843	then
	1844	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1845	fi
	1846	cp ${absnamein[$i]} ${localin[$i]}
	1847	fi
	1848	fi
	1849	fi
	1850	fi
	1851
	1852	done
	1853	if (( i != 0 ))
	1854	then
	1855	printf "\n$dashes\n *** all INPUT-files provided \n"
	1856	fi
	1857
	1858
	1859	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1860	(( i = 0 ))
	1861	while (( i < iic ))
	1862	do
	1863	(( i = i + 1 ))
	1864	if (( i == 1 ))
	1865	then
	1866	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1867	fi
	1868	printf "\n >>> ${in_command[$i]}"
	1869	eval ${in_command[$i]}
	1870	if (( i == iic ))
	1871	then
	1872	printf "\n$dashes\n"
	1873	fi
	1874	done
	1875
	1876
	1877	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1878	# (FILE ENVPAR WILL BE READ BY PALM)
	1879	cat > ENVPAR << EOF
[2506]	1880	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	1881	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1882	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1883	maximum_cpu_time_allowed = ${cpumax}.,
	1884	revision = '$global_revision',
	1885	batch_job = .${running_in_batch_mode}. /
	1886
	1887	EOF
	1888
	1889
	1890	# STARTING THE EXECUTABLE
	1891	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	1892	PATH=$PATH:$tempdir
[2380]	1893
	1894
	1895	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1896	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1897	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1898	eval line=\"$line\"
	1899	execute_command="$line"
	1900
	1901
	1902	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	1903	if [[ "$execute_command_for_combine" = "" ]]
	1904	then
	1905	eval line2=\"$line2\"
	1906	execute_command_for_combine="$line2"
	1907	fi
	1908
[2380]	1909
	1910
	1911	# PROVIDE A HOSTFILE, IF REQUIRED
	1912	if [[ "$hostfile" != "" ]]
	1913	then
	1914
	1915	if [[ $hostfile = auto ]]
	1916	then
	1917	# CREATE A NEW HOSTFILE
	1918	(( ii = 1 ))
	1919	while (( ii <= cores / threads_per_task ))
	1920	do
	1921	echo $(hostname) >> hostfile
	1922	(( ii = ii + 1 ))
	1923	done
	1924	if (( cores / threads_per_task == 0 ))
	1925	then
	1926	echo $(hostname) >> hostfile
	1927	fi
	1928
	1929	else
	1930	cp $hostfile hostfile
	1931	fi
	1932	eval line=\"`head -n $ii hostfile`\"
	1933	printf "\n *** running on: $line"
	1934	fi
	1935
	1936
	1937
	1938	# SET THE NUMBER OF OPENMP-THREADS
	1939	if [[ $use_openmp = true ]]
	1940	then
	1941	export OMP_NUM_THREADS=$threads_per_task
	1942	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1943	else
	1944	export OMP_NUM_THREADS=1
	1945	fi
	1946
	1947
	1948	# PROVIDE DATA FOR
	1949	if [[ $run_coupled_model = false ]]
	1950	then
	1951	if [[ "$ocean_file_appendix" = true ]]
	1952	then
	1953	echo "precursor_ocean" > coupling_steering
	1954	else
	1955	echo "precursor_atmos" > coupling_steering
	1956	fi
	1957	else
	1958	(( iia = $cores_atmos / $threads_per_task ))
	1959	(( iio = $cores_ocean / $threads_per_task ))
	1960	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1961	printf "\n\n"
	1962	echo "coupled_run $iia $iio" > coupling_steering
	1963	fi
	1964
	1965	printf "\n *** execute command:"
	1966	printf "\n \"$execute_command\" \n\n"
	1967
	1968	$execute_command < coupling_steering
	1969
	1970	if [[ $? != 0 ]]
	1971	then
	1972
	1973	# ABORT IN CASE OF RUNTIME ERRORS
	1974	printf "\n +++ runtime error occured"
	1975	locat=execution
	1976	exit
	1977
	1978	else
	1979
	1980	printf "\n$dashes\n *** execution finished \n"
	1981
	1982	fi
	1983
	1984
	1985	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1986	# BY EACH CORE INTO ONE FILE
	1987	if [[ ! -f combine_plot_fields.x ]]
	1988	then
	1989
	1990	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1991	printf "\n 2d- and/or 3d-data may be incomplete!"
	1992	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1993
	1994	elif [[ "$combine_plot_fields" == true ]]
	1995	then
	1996
	1997	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1998	$execute_command_for_combine
	1999
	2000	else
	2001
	2002	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	2003	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	2004	# ??? koennen wir das streichen ???
	2005	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2006	fi
	2007
	2008
	2009
	2010	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2011	(( i = 0 ))
	2012	while (( i < ioc ))
	2013	do
	2014	(( i = i + 1 ))
	2015	if (( i == 1 ))
	2016	then
	2017	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2018	fi
	2019	printf "\n >>> ${out_command[$i]}"
	2020	eval ${out_command[$i]}
	2021	if (( i == ioc ))
	2022	then
	2023	printf "\n$dashes\n"
	2024	fi
	2025	done
	2026
	2027
	2028	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2029	(( i = 0 ))
	2030	while (( i < iout ))
	2031	do
	2032	(( i = i + 1 ))
	2033	if (( i == 1 ))
	2034	then
	2035	printf "\n\n *** saving OUTPUT-files:"
	2036
	2037	# GET RUN NUMBER ASSIGNED BY PALM
	2038	if [[ -f RUN_NUMBER ]]
	2039	then
	2040	read run_number < RUN_NUMBER
	2041	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2042	usecycle_option="-U $run_number"
	2043	else
	2044	run_number=0
	2045	usecycle_option=""
	2046	fi
	2047	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2048	then
[2404]	2049	printf "\n *** in case of SCP transfers to local host"
	2050	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2051	fi
	2052	printf "\n$dashes"
	2053	fi
	2054
	2055	# ADD CYCLE NUMBER TO FILENAME
	2056	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2057	then
	2058
	2059	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2060	if [[ "${actionout[$i]}" != "a" ]]
	2061	then
	2062	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2063	# WITH AN EXISTING CYCLE NUMBER
	2064	if (( run_number >= cycnum[$i] ))
	2065	then
	2066	(( cycnum[$i] = run_number ))
	2067	else
	2068	if (( run_number > 0 ))
	2069	then
	2070	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2071	fi
	2072	fi
	2073	fi
	2074	if (( cycnum[$i] > 0 ))
	2075	then
[2600]	2076	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2077	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2078	fi
	2079	fi
	2080
	2081	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2082	files_for_cores=false; filetype=file
	2083	link_local_output=false
	2084	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2085	then
	2086	files_for_cores=true; filetype=directory
	2087	actionout[$i]=""
	2088	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2089	then
	2090	actionout[$i]=""
	2091	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2092	then
	2093	files_for_cores=true; filetype=directory
	2094	link_local_output=true
	2095	actionout[$i]=""
	2096	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2097	then
	2098	link_local_output
	2099	actionout[$i]=""
	2100	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2101	then
	2102	files_for_cores=true; filetype=directory
	2103	actionout[$i]="tr"
	2104	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2105	then
	2106	actionout[$i]="tr"
	2107	fi
	2108
	2109	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2110	then
	2111	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2112	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2113	then
	2114	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2115	else
	2116
	2117
	2118	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2119	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2120	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2121	then
	2122	if [[ $running_on_remote = true ]]
	2123	then
	2124
	2125	# SET OPTIONS FOR TRANSFER
	2126	if [[ "${actionout[$i]}" = tr ]]
	2127	then
	2128	if [[ $files_for_cores = false ]]
	2129	then
	2130	catalog_option=""
	2131	catalog_string=""
	2132	else
	2133	catalog_option="-c"
	2134	catalog_string="/"
	2135	fi
	2136	append_option=""
	2137	append_string=""
	2138	else
	2139	append_option="-A"
	2140	append_string="append"
	2141	fi
	2142
	2143	transfer_failed=false
	2144	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2145	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2146
	2147	# TRANSFER VIA SCP
	2148	if [[ "$remote_loginnode" != "" ]]
	2149	then
[2566]	2150	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]	2151	else
[2506]	2152	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]	2153	fi
	2154	[[ $? != 0 ]] && transfer_failed=true
	2155
	2156
	2157	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2158	if [[ $transfer_failed = true ]]
	2159	then
	2160	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2161	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2162
	2163	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2164	eval local_catalog=${pathout[$i]}
	2165	if [[ ! -d $local_catalog ]]
	2166	then
	2167	printf " *** local directory does not exist. Trying to create:\n"
	2168	printf " $local_catalog \n"
	2169	mkdir -p $local_catalog
	2170	fi
[2506]	2171	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2172	transfer_problems=true
	2173	fi
	2174
	2175	else
	2176
	2177	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2178	# BE COPIED OR APPENDED ON THIS MACHINE
	2179	if [[ "${actionout[$i]}" = tr ]]
	2180	then
	2181	actionout[$i]=""
	2182	else
	2183	actionout[$i]="a"
	2184	fi
	2185	fi
	2186	fi
	2187
	2188
	2189	# APPEND ON THIS MACHINE
	2190	if [[ "${actionout[$i]}" = "a" ]]
	2191	then
	2192	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2193	then
	2194	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2195	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2196	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2197	else
	2198	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2199	printf "\n ${pathout[$i]}\n"
	2200	cat ${localout[$i]} >> ${pathout[$i]}
	2201	fi
	2202	fi
	2203
	2204	# COPY ON THIS MACHINE
	2205	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2206	# ON DIFFERENT FILE-SYSTEMS
	2207	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2208	then
	2209
	2210	# COPY IN CASE OF RUNS ON SINGLE CORES
	2211	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2212	then
	2213	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2214	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2215	if [[ $link_local_output = true ]]
	2216	then
	2217	printf " file will be linked\n"
	2218	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2219	fi
	2220	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2221	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2222	then
	2223	if [[ $link_local_output = true ]]
	2224	then
	2225	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2226	fi
	2227	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2228	else
	2229	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2230	fi
	2231	else
	2232	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2233	printf "\n ${pathout[$i]}\n"
	2234	if [[ $link_local_output = true ]]
	2235	then
	2236	printf " file will be linked\n"
	2237	ln -f ${localout[$i]} ${pathout[$i]}
	2238	fi
	2239	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2240	if [[ ! -f "${pathout[$i]}" ]]
	2241	then
	2242	if [[ $link_local_output = true ]]
	2243	then
	2244	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2245	fi
	2246	cp ${localout[$i]} ${pathout[$i]}
	2247	else
	2248	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2249	fi
	2250	fi
	2251
	2252	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2253	then
	2254
	2255	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2256	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2257	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2258	printf "\n ${pathout[$i]}\n"
	2259	if [[ $link_local_output = true ]]
	2260	then
	2261	printf " files will be linked\n"
[2396]	2262	mkdir -p ${pathout[$i]}
[2380]	2263	cd ${localout[$i]}
	2264	for file in $(ls *)
	2265	do
	2266	ln -f $file ${pathout[$i]}
	2267	done >\|/dev/null 2>&1
[2566]	2268	cd $tempdir
[2380]	2269	fi
	2270
	2271	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2272	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2273	then
	2274	if [[ $link_local_output = true ]]
	2275	then
	2276	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2277	fi
	2278	cp -r ${localout[$i]}/* ${pathout[$i]}
	2279	fi
	2280
	2281	fi
	2282	fi
	2283	done
	2284
	2285	if (( i != 0 ))
	2286	then
	2287	if [[ $transfer_problems = true ]]
	2288	then
	2289	printf "\n$dashes\n *** OUTPUT-files saved"
	2290	printf "\n +++ WARNING: some data transfers failed! \n"
	2291	else
	2292	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2293	fi
	2294	fi
	2295
	2296
	2297	# IF REQUIRED, START A RESTART-JOB
	2298	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2299	if [[ -f CONTINUE_RUN ]]
	2300	then
	2301
	2302	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2303	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2304	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2305	# -b START A BATCH JOB
	2306	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2307	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2308	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2309
	2310
	2311	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2312	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2313	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2314	then
[2381]	2315	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2316	fi
	2317
	2318
	2319	# START THE RESTART-JOB
	2320	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2321	echo " $prc"
	2322	printf "\n$dashes\n"
	2323	if [[ $running_on_remote = true ]]
	2324	then
	2325
	2326	echo "*** ssh will be used to initiate restart-runs!"
	2327	echo " return_address=\"$return_address\" "
	2328	echo " return_username=\"$local_username\" "
	2329
	2330	if [[ "$remote_loginnode" != "" ]]
	2331	then
[2420]	2332	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]	2333	else
[2420]	2334	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2335	fi
	2336
	2337	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2338	sleep 30
	2339
	2340	else
	2341
	2342	# START THE RESTART JOB ON THE LOCAL HOST
	2343	eval $prc # THE ' MUST BE EVALUATED
	2344	cd - > /dev/null
	2345
	2346	fi
	2347	printf "\n$dashes\n *** restart-run initiated \n"
	2348
	2349
	2350	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2351	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2352	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2353	# MAY BE VERY HUGE)
	2354	(( i = 0 ))
	2355	while (( i < iin ))
	2356	do
	2357	(( i = i + 1 ))
	2358	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2359	then
	2360	rm -r ${absnamein[$i]}
	2361	fi
	2362	done
	2363
	2364	fi
	2365
	2366
	2367	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2368	cd $HOME
[2566]	2369	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2370
	2371
	2372	else
	2373
	2374
	2375	# PREPARING ACTIONS,
	2376	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2377
	2378	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2379	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2380	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2381	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2382	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2383	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2384	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2385	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2386	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2387	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2388	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2389	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2390	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2391	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2392	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2393	if [[ $create_remote_batch_job = true ]]
	2394	then
	2395	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2396	if [[ $do_trace = true ]]
	2397	then
	2398	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2399	fi
[2380]	2400	elif [[ $create_batch_job = true ]]
	2401	then
	2402	palmrun_com=${palmrun_com}" -j"
[2420]	2403	if [[ $do_trace = true ]]
	2404	then
	2405	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2406	fi
[2380]	2407	fi
	2408
	2409
	2410	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2411	# REMOTE HOST
[2506]	2412	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2413	job_protocol_file=$job_protocol_file_local
	2414	if [[ $create_remote_batch_job = true ]]
	2415	then
[2506]	2416	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2417	job_protocol_file=$job_protocol_file_remote
	2418	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2419	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2420	fi
	2421
	2422
	2423	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2424	jobfile=jobfile.$run_id
	2425
	2426
	2427	# FIRST CREATE THE BATCH DIRECTIVES
	2428	(( i = 0 ))
	2429	while (( i < ibd ))
	2430	do
	2431	(( i = i + 1 ))
[2566]	2432	line=`echo "${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]	2433	eval line=\"$line\"
	2434	echo "$line" >> $jobfile
	2435	done
	2436	echo " " >> $jobfile
	2437
	2438
	2439	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2440	# PROTOCOL
	2441	if [[ $create_remote_batch_job = true ]]
	2442	then
	2443	echo "set +vx" >> $jobfile
	2444	echo "trap '" >> $jobfile
	2445	echo "set +vx" >> $jobfile
	2446	echo "cd ${remote_jobcatalog}" >> $jobfile
	2447	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2448
	2449	# ADD THE BATCH DIRECTIVES
	2450	(( i = 0 ))
	2451	while (( i < ibdt ))
	2452	do
	2453	(( i = i + 1 ))
[2506]	2454	line=`echo "${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]	2455	eval line=\"$line\"
	2456	echo "$line" >> $jobfile
	2457	done
	2458	echo " " >> $jobfile
	2459
	2460	echo "set -x" >> $jobfile
[2506]	2461	echo "${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]	2462	echo "%%END%%" >> $jobfile
	2463	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2464	echo "$submit_command $scpjob_file" >> $jobfile
	2465	echo "rm $scpjob_file" >> $jobfile
[2404]	2466	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2467	echo "set -x" >> $jobfile
	2468	echo " ' exit" >> $jobfile
	2469	fi
	2470
	2471
	2472	# ACTIVATE ERROR-TRACEBACK
	2473	if [[ $do_trace = true ]]
	2474	then
	2475	echo "set -x" >> $jobfile
	2476	else
	2477	echo "set +vx" >> $jobfile
	2478	fi
	2479
	2480
	2481	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2482	if [[ "$login_init_cmd" != "" ]]
	2483	then
	2484	echo "$login_init_cmd" >> $jobfile
	2485	fi
	2486	if [[ "$module_commands" != "" ]]
	2487	then
	2488	echo "$module_commands" >> $jobfile
	2489	fi
	2490
	2491
	2492	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2493	if [[ $create_remote_batch_job = true ]]
	2494	then
	2495	echo "mkdir $tempdir" >> $jobfile
	2496	echo "chmod go+rx $tempdir" >> $jobfile
	2497	else
	2498	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2499	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2500	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2501	mkdir $tempdir
	2502	chmod go+rx $tempdir
	2503	fi
	2504	echo "cd $tempdir" >> $jobfile
	2505	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2506	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2507	echo "export PATH=.:\$PATH" >> $jobfile
	2508	echo "export execute_palmrun=true" >> $jobfile
	2509
	2510
	2511	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2512	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2513	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2514	if [[ $create_remote_batch_job = true ]]
	2515	then
	2516	(( i = 0 ))
	2517	while (( i < iin ))
	2518	do
	2519	(( i = i + 1 ))
	2520	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2521	if [[ "${transin[$i]}" = job ]]
	2522	then
	2523	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2524	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2525	echo " " >> $jobfile
	2526	echo "%END%" >> $jobfile
	2527	else
	2528	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2529	fi
	2530
	2531	# CHECK, IF FILE COULD BE CREATED
	2532	echo "if [[ \$? = 1 ]]" >> $jobfile
	2533	echo "then" >> $jobfile
	2534	echo " echo \" \" " >> $jobfile
	2535	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2506]	2536	echo " echo \" please check, if directory exists on $host_configuration!\" " >> $jobfile
[2380]	2537	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2538	echo " execute_palmrun=false" >> $jobfile
	2539	echo "fi" >> $jobfile
	2540	done
	2541	fi
	2542
	2543
	2544	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2545	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2546	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2547	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2548	echo "export LOCAL_PWD" >> $jobfile
	2549
	2550
	2551	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2552	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2553	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2554
	2555
	2556	# CALL PALMRUN WITHIN THE JOB
	2557	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2558	echo "set -x" >> $jobfile
	2559	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2560
	2561
	2562	# TRANSFER JOBFILE TO THE TARGET HOST
	2563	if [[ $create_jobfile_only = false ]]
	2564	then
	2565
	2566	if [[ $create_remote_batch_job = true ]]
	2567	then
	2568
[2420]	2569	echo " "
[2566]	2570	echo " *** transfer of job to remote host via scp"
[2420]	2571	if [[ $do_trace = true ]]
	2572	then
[2506]	2573	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2574	fi
[2566]	2575	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2576
[2566]	2577	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2578	if [[ $do_trace = true ]]
	2579	then
[2506]	2580	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]	2581	fi
[2506]	2582	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]	2583
	2584	elif [[ $create_batch_job = true ]]
	2585	then
	2586
[2385]	2587	eval local_jobcatalog=$local_jobcatalog
[2506]	2588	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2589	cd $local_jobcatalog
[2380]	2590	echo " "
[2420]	2591	echo " *** submit the job"
	2592	if [[ $do_trace = true ]]
	2593	then
[2506]	2594	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2595	fi
[2506]	2596	$submit_command ${host_configuration}_${job_id}
	2597	rm ${host_configuration}_${job_id}
[2380]	2598	cd - > /dev/null
	2599
	2600	fi
	2601
	2602	rm -rf $jobfile
	2603
	2604	else
	2605
	2606	printf "\n *** jobfile created under name \"$jobfile\" "
	2607	printf "\n no batch-job has been sent!"
	2608
	2609	fi
	2610
	2611	fi # END OF REMOTE-PART

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