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source: palm/trunk/SCRIPTS/palmrun @ 2516

Last change on this file since 2516 was 2512, checked in by raasch, 7 years ago
upper bounds of cross section and 3d output changed from nx+1,ny+1 to nx,ny; no output if redundant ghost layer data to NetCDF files
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 86.0 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 2512 2017-10-04 08:26:59Z suehring $
[2507]	29	# bugfix for determining cycle numbers of NetCDF input files
	30	#
	31	# 2506 2017-09-29 08:30:37Z raasch
[2506]	32	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	33	# host configuration added to SOURCES_FOR_RUN_... folder name
	34	# host_identifier renamed host_configuration
	35	# option -W added to allow for job dependencies
	36	#
	37	# 2501 2017-09-26 11:41:55Z raasch
[2501]	38	# default value for number of cores (option -X) set to 1
	39	# bugfix for mechanism which overwrites configuration file settings with values
	40	# provided by palmrun options
	41	#
	42	# 2499 2017-09-22 16:47:58Z kanani
[2499]	43	# option -h named configuration identifier
	44	#
	45	# 2480 2017-09-19 06:24:14Z maronga
[2480]	46	# bugfix for last revision
	47	#
	48	# 2479 2017-09-19 06:12:16Z raasch
[2479]	49	# option -A (project account number) added
	50	#
	51	# 2422 2017-09-08 08:25:41Z raasch
[2410]	52	# initial revision
[2380]	53	#
	54	#--------------------------------------------------------------------------------#
	55	# palmrun - script for running PALM jobs on local and remote hosts
	56	#--------------------------------------------------------------------------------#
	57
	58
	59
	60	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	61
	62	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	63	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	64	# (TOO MANY ARGUMENTS - PROBLEM)
	65	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	66
	67	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	68	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	69	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	70	# SCRIPT-OPTION ARGUMENTS
	71	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	72	typeset -i icycle inode ival maxcycle mpi_tasks
	73	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	74
	75	activation_string_list=""
	76	AddFilenames=""
	77	combine_plot_fields=true
	78	compiler_name=""
	79	compiler_name_ser=""
	80	compiler_options=""
[2501]	81	cores=1
[2380]	82	cores_atmos=0
	83	cores_ocean=0
	84	coupled_dist=""
	85	cpp_options=""
	86	cpumax=0
[2506]	87	create_batch_job=false
[2380]	88	create_jobfile_only=false
	89	create_remote_batch_job=false
	90	dashes=" ----------------------------------------------------------------------------"
	91	defaultqueue=""
[2506]	92	delete_temporary_catalog=true
[2380]	93	do_compile=true
	94	do_trace=false
	95	executable=""
	96	execute_command=""
	97	execution_error=false
	98	fileconnection_file=.palm.iofiles
	99	fname=test
	100	global_revision=""
[2506]	101	host_configuration="default"
[2380]	102	hostfile=""
	103	hp=""
	104	keep_data_from_previous_run=false
	105	link_local_input=false
	106	link_local_output=false
[2388]	107	linker_options=""
[2385]	108	local_jobcatalog=""
[2380]	109	locat=normal
	110	makefile=""
	111	max_par_io_str=""
	112	prc=$0
	113	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	114	do
	115	prc=`echo $prc \| cut -f2- -d"/"`
	116	done
	117	module_calls=""
[2506]	118	palmrun_memory=""
[2380]	119	palmrun_script_name=$prc
	120	openmp=false
[2506]	121	previous_job=""
[2479]	122	project_account=""
[2380]	123	queue=none
	124	restart_run=false
	125	return_address=""
[2385]	126	remote_jobcatalog=""
[2380]	127	remote_username=""
	128	running_in_batch_mode=false
	129	run_coupled_model=false
	130	run_id=""
	131	silent=false
	132	source_list=""
	133	source_path=""
[2501]	134	tasks_per_node=0
[2380]	135	threads_per_task=1
	136	tmpcreate=false
	137	transfer_problems=false
[2384]	138	user_source_path=""
[2506]	139	use_existing_sources_folder=""
[2380]	140	use_openmp=false
[2422]	141	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	142	working_directory=`pwd`
	143	write_binary=""
	144	TOPT=""
	145
	146
	147	# ERROR HANDLING IN CASE OF EXIT
[2404]	148	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	149	then
	150
	151	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	152	(( i = 0 ))
	153	while (( i < iec ))
	154	do
	155	(( i = i + 1 ))
	156	printf "\n *** Execution of ERROR-command:\n"
	157	printf " >>> ${err_command[$i]}\n"
	158	eval ${err_command[$i]}
	159	done
[2405]	160	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	161	printf "\n\n+++ palmrun killed \n\n"
	162	elif [[ $locat != control_c ]]
	163	then
	164	printf "\n\n --> palmrun finished\n\n"
	165	if [[ $running_on_remote = true ]]
	166	then
	167	printf " Bye, bye $remote_username !!\n\n"
	168	else
	169	printf " Bye, bye $local_username !!\n\n"
	170	fi
	171	fi' exit
	172
	173
	174	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	175	trap 'cd; rm -rf $TEMPDIR
[2380]	176	printf "\n+++ palmrun killed by \"^C\" \n\n"
	177	locat=control_c
	178	exit
	179	' 2
	180
	181
	182	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	183	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	184	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]	185	do
	186	case $option in
	187	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	188	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	189	(b) create_batch_job=true; prc="$prc -b";;
	190	(B) delete_temporary_catalog=false; prc="$prc -B";;
	191	(C) restart_run=true; prc="$prc -C";;
	192	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	193	(F) create_jobfile_only=true;;
	194	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	195	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	196	(j) running_in_batch_mode=true;;
	197	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	198	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	199	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	200	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	201	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	202	(r) run_id=$OPTARG;;
	203	(R) return_address=$OPTARG;;
	204	(s) source_list=$OPTARG;;
[2501]	205	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	206	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	207	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	208	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	209	(v) silent=true; prc="$prc -v";;
[2506]	210	(V) use_existing_sources_folder="-V";;
[2380]	211	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	212	(W) previous_job=$OPTARG;;
[2380]	213	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	214	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	215	(y) ocean_file_appendix=true; prc="$prc -y";;
	216	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	217	(Z) combine_plot_fields=false; prc="$prc -Z";;
	218	(\?) printf "\n +++ unknown option $OPTARG \n"
	219	printf "\n --> type \"$0 ?\" for available options \n"
	220	locat=parameter;exit;;
	221	esac
	222	done
	223
	224
	225	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	226	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	227	(( to_shift = $OPTIND - 1 ))
	228	shift $to_shift
	229
	230	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	231	if [[ "$1" = "?" ]]
	232	then
	233	(printf "\n *** Description of available palmrun options:\n"
	234	printf "\n Option Description Default-Value"
	235	printf "\n -a activation string list \"\" "
[2479]	236	printf "\n -A project account number ---"
[2380]	237	printf "\n -b batch-job on local machine ---"
	238	printf "\n -B do not delete temporary directory at end ---"
	239	printf "\n -d base name of files attached to program test"
	240	printf "\n -F create batch job file only ---"
[2506]	241	printf "\n -h host configuration \"default\" "
[2380]	242	printf "\n -k keep data from previous run"
	243	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	244	printf "\n -M Makefile name Makefile"
	245	printf "\n -O threads per openMP task ---"
	246	printf "\n -q queue \"$queue\" "
	247	printf "\n -s filenames of routines to be compiled \"\" "
	248	printf "\n must end with .f, .f90, .F, or .c !"
	249	printf "\n use \"..\" for more than one file and wildcards"
	250	printf "\n -s LM compiles all locally modified files"
	251	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	252	printf "\n -T tasks per node ---"
[2380]	253	printf "\n -u username on remote machine \"\" "
	254	printf "\n -v no prompt for confirmation ---"
[2506]	255	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	256	printf "\n -w maximum parallel io streams as given by -X"
[2506]	257	printf "\n -W name of job to wait for ---"
[2380]	258	printf "\n -x tracing of palmrun for debug purposes ---"
	259	printf "\n -X # of processors (on parallel machines) 1"
	260	printf "\n -y add appendix \"_O\" to all local output"
	261	printf "\n files (ocean precursor runs followed by"
	262	printf "\n coupled atmosphere-ocean runs) ---"
	263	printf "\n -Y run coupled model, \"#1 #2\" with"
	264	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	265	printf "\n -Z skip combine_plot_fields at the end of "
	266	printf "\n the simulation ---"
	267	printf "\n "
	268	printf "\n Possible values of positional parameter <modus>:"
	269	printf "\n \"?\" - this outline \n\n") \| more
	270	exit
	271	elif [[ "$1" != "" ]]
	272	then
	273	printf "\n +++ positional parameter $1 unknown \n"
	274	locat=parameter; exit
	275	fi
	276
	277
	278
	279	# SHORT STARTING MESSAGE
	280	printf "\n*** $version "
	281	printf "\n will be executed. Please wait ..."
	282
	283
[2506]	284	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	285	config_file=.palm.config.$host_configuration
	286	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	287
	288
	289	# CHECK, IF CONFIGURATION FILE EXISTS
	290	if [[ ! -f $config_file ]]
	291	then
	292	printf "\n\n +++ configuration file: "
	293	printf "\n $config_file"
	294	printf "\n does not exist"
	295	locat=connect; exit
	296	fi
	297
	298
	299	# CHECK, IF FILE CONNECTION FILE EXISTS
	300	if [[ ! -f $fileconnection_file ]]
	301	then
	302	printf "\n\n +++ file connection file: "
	303	printf "\n $fileconnection_file"
	304	printf "\n does not exist"
	305	locat=connect; exit
	306	fi
	307
	308
[2404]	309	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	310	if [[ "$activation_string_list" = "" ]]
	311	then
	312	printf "\n\n +++ no activation string list given: "
	313	printf "\n please set palmrun option \"-a\" "
	314	locat=palmrun_option; exit
	315	fi
	316
	317
	318	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	319	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	320	then
	321	write_binary=true
	322	else
	323	write_binary=false
	324	fi
	325
	326
[2380]	327	# READ AND EVALUATE THE CONFIGURATION-FILE
	328	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	329
	330	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	331	while read line
	332	do
	333
	334	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	335	eval line=\"$line\"
	336
	337
	338	# INTERPRET THE LINE
	339	if [[ "$(echo $line)" = "" ]]
	340	then
	341
	342	# EMPTY LINE, NO ACTION
	343	continue
	344
	345	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	346	then
	347
	348	# LINE IS A COMMENT LINE
	349	continue
	350
	351	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	352	then
	353
	354	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	355	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	356	value=`echo $line \| cut -d" " -s -f2-`
	357
	358
	359	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	360	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	361	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	362	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	363	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	364	# CONFIGURATION-FILE.
	365	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	366	then
	367	eval export $var="\$value"
	368
	369	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	370	if [[ $do_trace = true ]]
	371	then
	372	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	373	fi
	374	fi
	375
	376	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	377	then
	378
	379	# LINE DEFINES BATCH-DIRECTIVE
	380	(( ibd = ibd + 1 ))
	381	line=$(echo $line \| cut -c4-)
	382	batch_directive[$ibd]="$line"
	383
	384	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	385	then
	386
	387	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	388	# REMOTE TO A LOCAL HOST
	389	(( ibdt = ibdt + 1 ))
	390	line=$(echo $line \| cut -c5-)
	391	batch_directive_transfer[$ibdt]="$line"
	392
	393	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	394	then
	395
	396	# LINE DEFINES ERROR-COMMAND
	397	(( iec = iec + 1 ))
	398	line=$(echo $line \| cut -c4-)
	399	err_command[$iec]="$line"
	400
	401	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	402	then
	403
	404	# LINE DEFINES INPUT-COMMAND
	405	(( iic = iic + 1 ))
	406	line=$(echo $line \| cut -c4-)
	407	in_command[$iic]="$line"
	408
	409	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	410	then
	411
	412	# LINE DEFINES OUTPUT-COMMAND
	413	(( ioc = ioc + 1 ))
	414	line=$(echo $line \| cut -c4-)
	415	out_command[$ioc]="$line"
	416
	417	else
	418
	419	# SKIP ALL OTHER LINES
	420	continue
	421
	422	fi
	423
	424	done < $config_file
	425
	426
	427	# CHECK SETTING OF REQUIRED PARAMETERS
	428	if [[ "$compiler_name" = "" ]]
	429	then
	430	printf "\n +++ no compiler name found in $config_file"
	431	printf "\n Please add line \"compiler_name ...\" to that file."
	432	locat=config_file; exit
	433	fi
	434	if [[ "$compiler_name_ser" = "" ]]
	435	then
	436	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	437	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	438	locat=config_file; exit
	439	fi
	440	if [[ "$compiler_options" = "" ]]
	441	then
	442	printf "\n +++ no compiler options found in $config_file"
	443	printf "\n Please add line \"compiler_options ...\" to that file."
	444	locat=config_file; exit
	445	fi
[2388]	446	if [[ "$linker_options" = "" ]]
[2380]	447	then
[2388]	448	printf "\n +++ no linker options found in $config_file"
	449	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	450	locat=config_file; exit
	451	fi
	452	if [[ "$execute_command" = "" ]]
	453	then
	454	printf "\n +++ no execute command found in $config_file"
	455	printf "\n Please add line \"execute_command ...\" to that file."
	456	locat=config_file; exit
	457	fi
	458
	459	if [[ "$hostfile" != "" ]]
	460	then
	461	if [[ $hostfile != auto && ! -f $hostfile ]]
	462	then
	463	printf "\n +++ no hostfile \"$hostfile\" found"
	464	printf "\n Please check line \"hostfile ...\" in $config_file"
	465	locat=config_file; exit
	466	fi
	467	fi
	468
	469
	470	# DETERMINE THE CALL STATUS
	471	if [[ "$return_address" != "" ]]
	472	then
	473
	474	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	475	# BATCH MODE AND ...
	476	running_on_remote=true
	477
	478	else
	479
	480	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	481	if [[ "$remote_ip" != "" ]]
	482	then
	483
	484	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	485	create_remote_batch_job=true
	486
	487	fi
	488	running_on_remote=false
	489	fi
	490
	491
	492
	493	# READ AND EVALUATE THE I/O-FILE LIST
	494	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	495
	496	# READ THE FILE CONNECTION FILE LINE BY LINE
	497	while read line
	498	do
	499
	500	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	501	eval line=\"$line\"
	502
	503
	504	# INTERPRET THE LINE
	505	if [[ "$(echo $line)" = "" ]]
	506	then
	507	# EMPTY LINE, NO ACTION
	508	continue
	509
	510	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	511	then
	512
	513	# LINE IS A COMMENT LINE
	514	true
	515
	516	else
	517
	518	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	519	# s2a: in/out - field
	520	# s2b: loc - field (optional)
	521	# s2c: tr/ar - field (optional)
	522	s1=`echo $line \| cut -d" " -f1`
	523	s2=`echo $line \| cut -d" " -s -f2`
	524	s2a=$(echo $s2 \| cut -d":" -f1)
	525	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	526	then
	527	s2b=""
	528	s2c=""
	529	else
	530	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	531	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	532	fi
	533	s3=`echo $line \| cut -d" " -f3`
	534	s4=`echo $line \| cut -d" " -s -f4`
	535	s5=`echo $line \| cut -d" " -s -f5`
	536	s6=`echo $line \| cut -d" " -s -f6`
	537
	538
	539	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	540	# INPUT- OR OUTPUT-LIST.
	541	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	542	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	543	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	544	# IS NOT CHECKED AND STORED.
	545	IFSALT="$IFS"; IFS="$IFS:"
	546	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	547	then
	548	found=false
	549	for actual in $activation_string_list
	550	do
	551	for formal in $s3
	552	do
	553	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	554	done
	555	done
	556	if [[ $found = true ]]
	557	then
	558	(( iin = iin + 1 ))
	559	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	560	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	561	extin[$iin]=$s6
	562	fi
	563	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	564	then
	565	found=false
	566	for actual in $activation_string_list
	567	do
	568	for formal in $s3
	569	do
	570	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	571	done
	572	done
	573	if [[ $found = true ]]
	574	then
	575	(( iout = iout + 1 ))
	576	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	577	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	578	fi
	579	elif [[ "$s2a" != in && "$s2a" != out ]]
	580	then
	581	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	582	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	583	locat=connect; exit
	584	fi
	585	IFS="$IFSALT"
	586	fi
	587
	588	done < $fileconnection_file
	589
	590
	591
[2501]	592	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	593	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	594	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	595	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	596	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	597	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	598
	599
	600
[2380]	601	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	602	if [[ $run_coupled_model = true ]]
	603	then
	604
	605	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	606	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	607
	608	if (( $cores_ocean + $cores_atmos != $cores ))
	609	then
	610
	611	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	612	printf "\n PEs (total) : $cores"
	613	printf "\n PEs (atmosphere): $cores_atmos"
	614	printf "\n PEs (ocean) : $cores_ocean"
	615	locat=coupling; exit
	616
	617	fi
	618
	619	fi
	620
	621
	622	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	623	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	624	# FOLDER
	625	if [[ $running_in_batch_mode = true ]]
	626	then
	627
[2506]	628	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	629	then
[2506]	630	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	631	printf "\n Please check the output of the palmrun-call"
	632	printf "\n that you did on your local host."
	633	locat=SOURCES_FOR_RUN; exit
	634	fi
	635
	636	else
	637
	638	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	639	# AUTOMATIC RESTART RUN
	640	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	641	if [[ $restart_run = false ]]
	642	then
	643
	644	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	645	# THE LOCAL HOST
	646	if [[ ! -d $source_path ]]
	647	then
	648	printf "\n\n +++ source path \"$source_path\" on local host"
	649	printf "\n \"$(hostname)\" does not exist"
	650	locat=source_path; exit
	651	fi
	652
[2506]	653	rm -rf $sources_for_run_catalog
	654	mkdir -p $sources_for_run_catalog
[2380]	655
	656	if [[ "$source_list" = LM ]]
	657	then
	658
	659	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	660	source_list=""
	661	cd $source_path
	662
	663
[2512]	664	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	665	if [[ ! -d ../.svn ]]
[2380]	666	then
	667	printf "\n\n +++ source directory"
	668	printf "\n \"$source_path\" "
	669	printf "\n is not under control of \"subversion\"."
[2512]	670	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	671	fi
	672
	673
	674	# LIST ALL MODIFIED SOURCE CODE FILES
	675	Filenames=""
[2404]	676	svn status > tmp_svnstatus
[2380]	677	while read line
	678	do
	679	firstc=`echo $line \| cut -c1`
	680	if [[ $firstc = M \|\| $firstc = "?" ]]
	681	then
	682	Name=`echo "$line" \| cut -c8-`
	683	extension=`echo $Name \| cut -d. -f2`
	684	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	685	then
	686	Filenames="$Filenames "$Name
	687	fi
	688	fi
[2404]	689	done < tmp_svnstatus
	690	rm -rf tmp_svnstatus
[2380]	691
	692
	693	# COPY FILES TO SOURCES_FOR_RUN_...
	694	for filename in $Filenames
	695	do
[2506]	696	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	697	source_list=$source_list"$filename "
	698	done
	699
	700	cd - > /dev/null
	701
	702
	703	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	704	elif [[ "$source_list" != "" ]]
	705	then
	706
	707	cd $source_path
	708
	709	for filename in $source_list
	710	do
	711
	712	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	713	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	714	then
	715	printf "\n +++ source code file: $filename"
	716	printf "\n must not contain (\"/\") "
	717	locat=source; exit
	718	fi
	719
	720	if [[ ! -f $filename ]]
	721	then
	722	printf "\n +++ source code file: $filename"
	723	printf "\n does not exist"
	724	locat=source; exit
	725	else
[2506]	726	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	727	fi
	728
	729	done
	730
	731	cd - > /dev/null
	732
	733	fi
	734
	735	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	736	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	737	if [[ ! -f $makefile ]]
	738	then
	739	printf "\n +++ file \"$makefile\" does not exist"
	740	locat=make; exit
	741	else
[2506]	742	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	743	fi
	744
	745
	746	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	747	if [[ "$user_source_path" != "" ]]
[2380]	748	then
	749
	750	# DOES THE DIRECTORY EXIST?
[2384]	751	if [[ ! -d $user_source_path ]]
[2380]	752	then
	753
	754	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	755	printf "\n \"$user_source_path\" "
[2380]	756	printf "\n does not exist or is not a directory."
	757	printf "\n No source code will be used from this directory!\n"
[2384]	758	user_source_path=""
[2380]	759	if [[ $silent == false ]]
	760	then
	761	sleep 2
	762	fi
	763
	764	else
	765
[2384]	766	cd $user_source_path
[2380]	767	found=false
	768
	769	Names=$(ls -1 *.f90 2>&1)
	770	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	771	Names=$(ls -1 *.F90 2>&1)
	772	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	773	Names=$(ls -1 *.F 2>&1)
	774	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	775	Names=$(ls -1 *.f 2>&1)
	776	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	777	Names=$(ls -1 *.c 2>&1)
	778	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	779
	780	cd - > /dev/null
[2506]	781	cd $sources_for_run_catalog
[2380]	782
	783	# COPY MAKEFILE IF EXISTING
[2384]	784	if [[ -f $user_source_path/Makefile ]]
[2380]	785	then
	786	printf "\n\n *** user Makefile from directory"
[2384]	787	printf "\n \"$user_source_path\" is used \n"
[2380]	788	if [[ $silent == false ]]
	789	then
	790	sleep 1
	791	fi
[2384]	792	cp $user_source_path/Makefile .
[2380]	793	fi
	794
	795	for filename in $AddFilenames
	796	do
	797	if [[ -f $filename ]]
	798	then
	799	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	800	printf "\n source code directory \"$user_source_path\" "
[2380]	801	printf "\n but was also given with option \"-s\" which means that it should be taken"
	802	printf "\n from directory \"$source_path\"."
	803	locat=source; exit
	804	fi
	805
[2384]	806	cp $user_source_path/$filename .
[2380]	807	source_list="$source_list $filename"
	808
	809	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	810	if [[ $(grep -c $filename Makefile) = 0 ]]
	811	then
	812	printf "\n\n +++ user file \"$filename\" "
	813	printf "\n is not listed in Makefile \n"
	814	locat=source; exit
	815	else
	816
	817	if [[ $found = false ]]
	818	then
	819	found=true
	820	printf "\n\n *** following user file(s) added to the"
	821	printf " files to be translated:\n "
	822	fi
	823	printf "$filename "
	824	if [[ $silent == false ]]
	825	then
	826	sleep 0.5
	827	fi
	828
	829	fi
	830	done
	831	[[ $found = true ]] && printf "\n"
	832	cd - > /dev/null
	833	fi
	834	fi
	835
	836	# COPY CONFIGURATION FILES
[2506]	837	cp $config_file $sources_for_run_catalog
	838	cp $fileconnection_file $sources_for_run_catalog
[2380]	839
	840	# COPY SHELLSCRIPTS
[2506]	841	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	842	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	843
	844	fi
	845
	846	fi
	847
	848	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	849	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	850	if [[ "$global_revision" = "" ]]
	851	then
	852	global_revision=`svnversion $source_path 2>/dev/null`
	853	global_revision="Rev: $global_revision"
	854	fi
	855
	856
	857	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	858	if [[ -n $cores ]]
	859	then
	860
	861	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	862	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	863	if [[ $tasks_per_node = 0 ]]
[2380]	864	then
	865	printf "\n"
	866	printf "\n +++ option \"-T\" (tasks per node) is missing"
	867	printf "\n set -T option or define tasks_per_node in the config file"
	868	locat=tasks_per_node; (( iec = 0 )); exit
	869	fi
	870
	871	if (( cores < tasks_per_node ))
	872	then
	873	printf "\n"
	874	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	875	printf "\n given values: -T $tasks_per_node -X $cores"
	876	locat=tasks_per_node; (( iec = 0 )); exit
	877	fi
	878
	879	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	880	(( mpi_tasks = cores / threads_per_task ))
	881	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	882	(( ii = cores / tasks_per_node ))
	883	(( remaining_cores = cores - ii * tasks_per_node ))
	884	if (( remaining_cores > 0 ))
	885	then
	886	printf "\n"
	887	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	888	printf "\n divisor of the total number of cores (option \"-X\")"
	889	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	890	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	891	(( nodes = nodes + 1 ))
	892	fi
	893
	894	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	895	if [[ "$tasks_per_node" != "" ]]
	896	then
	897	TOPT="-T $tasks_per_node"
	898	fi
	899
	900	fi
	901
	902
	903	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	904	if [[ "$maximum_parallel_io_streams" = "" ]]
	905	then
	906	maximum_parallel_io_streams=$cores
	907	fi
	908
	909
	910	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	911	if [[ "$scp_port" != "" ]]
	912	then
	913	PORTOPT="-P $scp_port"
	914	SSH_PORTOPT="-p $scp_port"
	915	fi
	916
	917
	918	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	919	# CONFIG-FILE
	920	if [[ "$ssh_key" != "" ]]
	921	then
	922	ssh_key="-i $HOME/.ssh/$ssh_key"
	923	fi
	924
	925
	926	# SET QUEUE, IF NOT GIVEN
	927	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	928	then
	929
	930	if [[ $queue = none && "$defaultqueue" = "" ]]
	931	then
	932	printf "\n"
	933	printf "\n +++ no default queue given in configuration file and no queue"
	934	printf "\n given with option -q"
	935	fi
	936	if [[ $queue = none ]]
	937	then
	938	queue=$defaultqueue
	939	fi
	940
	941	fi
	942
	943
	944	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	945	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	946	(( i = 0 ))
	947	while (( i < iin ))
	948	do
	949	(( i = i + 1 ))
	950	(( maxcycle = 0 ))
	951
	952	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	953	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	954	if [[ "${actionin[$i]}" = di ]]
	955	then
	956	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	957	# HOST ONLY
	958	eval filename=${pathin[$i]}/${endin[$i]}
	959	else
	960	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	961	# HOST ONLY
	962	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	963	fi
	964	eval pathname=${pathin[$i]}
	965
	966	# CHECK IF FILE EXISTS
	967	if ! ls $filename* 1>/dev/null 2>&1
	968	then
	969
	970	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	971	if [[ "${transin[$i]}" != "locopt" ]]
	972	then
	973	printf "\n\n +++ INPUT-file: "
	974	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	975	then
	976	printf "\n $filename"
	977	else
	978	printf "\n $filename.${extin[$i]}"
	979	fi
	980	printf "\n does not exist\n"
	981	locat=input; exit
	982	else
	983	transin[$i]="unavailable"
	984	fi
	985	else
	986
	987	# DETERMINE THE FILE'S CYCLE NUMBER
	988	ls -1 -d $filename > filelist 2>/dev/null
	989	ls -1 -d $filename.* >> filelist 2>/dev/null
	990	while read line
	991	do
	992	# filename without path (i.e. after the last "/")
	993	basefilename=$(basename ${line})
	994
	995	# check if there is an extension
	996	extension=${basefilename##*.}
[2507]	997	if [[ "$extension" = "${extin[$i]}" ]]
[2380]	998	then
[2507]	999	basefilename=${basefilename%.*}
[2380]	1000	fi
	1001
	1002	# check for an existing cycle number
	1003	cycle=${basefilename##*.}
	1004	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1005	then
	1006	(( icycle = $cycle ))
	1007	else
	1008	(( icycle = 0 ))
	1009	fi
	1010
	1011	if (( icycle > maxcycle ))
	1012	then
	1013	(( maxcycle = icycle ))
	1014	fi
	1015
	1016	done <filelist
	1017	rm filelist
	1018
	1019	# APPEND CYCLE NUMBER TO FILENAME
	1020	if (( maxcycle > 0 ))
	1021	then
	1022	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1023	then
	1024	filename=${filename}.$maxcycle.${extin[$i]}
	1025	else
	1026	filename=${filename}.$maxcycle
	1027	fi
	1028	else
	1029	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1030	then
	1031	filename=${filename}.${extin[$i]}
	1032	fi
	1033	fi
	1034
	1035	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1036	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1037	absnamein[$i]=$filename
	1038	if (( maxcycle > 0 ))
	1039	then
	1040	if [[ "${actionin[$i]}" = di ]]
	1041	then
	1042	frelin[$i]=${endin[$i]}.$maxcycle
	1043	else
	1044	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1045	fi
	1046	else
	1047	if [[ "${actionin[$i]}" = di ]]
	1048	then
	1049	frelin[$i]=${endin[$i]}
	1050	else
	1051	frelin[$i]=${fname}${endin[$i]}
	1052	fi
	1053	fi
	1054
	1055	fi
	1056	done
	1057
	1058
	1059	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1060	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1061	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1062	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1063	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1064	# REMOTE HOST)
	1065	(( i = 0 ))
	1066	while (( i < iout ))
	1067	do
	1068	(( i = i + 1 ))
	1069	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1070	then
	1071	if [[ "${actionout[$i]}" = tr ]]
	1072	then
	1073	actionout[$i]=""
	1074	elif [[ "${actionout[$i]}" = trpe ]]
	1075	then
	1076	actionout[$i]=pe
	1077	elif [[ "${actionout[$i]}" = tra ]]
	1078	then
	1079	actionout[$i]=a
	1080	fi
	1081	(( maxcycle = 0 ))
	1082	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1083	eval catalogname=${pathout[$i]}
	1084	if ! ls $filename* 1>/dev/null 2>&1
	1085	then
	1086
	1087	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1088	if cat /dev/null > $filename
	1089	then
	1090	rm $filename
	1091	else
	1092
	1093	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1094	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1095	if [[ ! -d $catalogname ]]
	1096	then
	1097	if mkdir -p $catalogname
	1098	then
	1099	printf "\n\n *** directory:"
	1100	printf "\n $catalogname"
	1101	printf "\n was created\n"
	1102	else
	1103	printf "\n\n +++ OUTPUT-file:"
	1104	printf "\n $filename"
	1105	printf "\n cannot be created, because directory does not exist"
	1106	printf "\n and cannot be created either"
	1107	printf "\n"
	1108	locat=output ; exit
	1109	fi 2>/dev/null
	1110	else
	1111	printf "\n\n +++ OUTPUT-file:"
	1112	printf "\n $filename"
	1113	printf "\n cannot be created, although directory exists"
	1114	printf "\n"
	1115	locat=output ; exit
	1116	fi
	1117	fi 2>/dev/null
	1118	else
	1119
	1120	# DETERMINE THE CYCLE NUMBER
	1121	ls -1 -d $filename > filelist 2>/dev/null
	1122	ls -1 -d $filename.* >> filelist 2>/dev/null
	1123	while read line
	1124	do
	1125
	1126	# filename without path (i.e. after the last "/")
	1127	basefilename=$(basename ${line})
	1128
	1129	# check if there is an extension
	1130	extension=${basefilename##*.}
	1131	if [[ "$extension" = "${extout[$i]}" ]]
	1132	then
	1133	basefilename=${basefilename%.*}
	1134	fi
	1135
	1136	# check for an existing cycle number
	1137	cycle=${basefilename##*.}
	1138	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1139	then
	1140	(( icycle = $cycle + 1 ))
	1141	else
	1142	(( icycle = 1 ))
	1143	fi
	1144
	1145	if (( icycle > maxcycle ))
	1146	then
	1147	(( maxcycle = icycle ))
	1148	fi
	1149
	1150	done <filelist
	1151	rm filelist
	1152	fi
	1153
	1154	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1155	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1156	if [[ "${actionout[$i]}" != a ]]
	1157	then
	1158	if (( maxcycle > 0 ))
	1159	then
	1160	filename_tmp=${filename}.$maxcycle
	1161	if cat /dev/null > $filename_tmp
	1162	then
	1163	rm $filename_tmp
	1164	else
	1165	printf "\n +++ OUTPUT-file:"
	1166	printf "\n $filename_tmp"
	1167	printf "\n cannot be created"
	1168	locat=output ; exit
	1169	fi
	1170	fi
	1171	else
	1172	(( maxcycle = maxcycle - 1 ))
	1173	fi
	1174
	1175	(( cycnum[$i] = maxcycle ))
	1176	pathout[$i]=$filename
	1177
	1178	fi
	1179	done
	1180
	1181
	1182	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1183	if [[ $running_in_batch_mode = false ]]
	1184	then
	1185	run_id=$RANDOM
	1186	job_id=${fname}.$run_id
	1187
[2404]	1188	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1189	fi
	1190
	1191
	1192	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1193	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1194	then
	1195
	1196	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1197	if [[ $ibd = 0 ]]
	1198	then
	1199	printf "\n"
	1200	printf "\n +++ no batch directives found in configuration file"
	1201	locat=config_file_batch_directives; (( iec = 0 )); exit
	1202	fi
	1203
	1204	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1205	done=false
[2384]	1206	cputime=$cpumax
[2380]	1207	while [[ $done = false ]]
	1208	do
[2384]	1209	if (( cputime == 0 ))
[2380]	1210	then
	1211	printf "\n +++ cpu-time is undefined"
	1212	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1213	printf "\n >>> "
[2384]	1214	read cputime 1>/dev/null 2>&1
[2380]	1215	else
	1216	done=true
	1217	fi
	1218	done
[2420]	1219	cpumax=$cputime
[2380]	1220
	1221	# CHECK THE MEMORY DEMAND
	1222	done=false
	1223	while [[ $done = false ]]
	1224	do
	1225	if (( memory == 0 ))
	1226	then
	1227	printf "\n +++ memory demand is undefined"
	1228	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1229	printf "\n >>> "
	1230	read memory 1>/dev/null 2>&1
	1231	else
	1232	done=true
	1233	fi
	1234	done
	1235
	1236	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1237	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1238	then
	1239	while [[ -z $remote_username ]]
	1240	do
[2420]	1241	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1242	printf "\n >>> Please type username:"
	1243	printf "\n >>> "
	1244	read remote_username
	1245	done
	1246	fi
	1247
	1248	else
	1249
[2420]	1250	if [[ $running_in_batch_mode = false ]]
	1251	then
	1252	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1253	cpumax=$cputime
	1254	else
	1255	cputime=$cpumax
	1256	fi
[2380]	1257
	1258	fi
	1259
	1260
	1261	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1262	(( cpu_hours = cputime / 3600 ))
	1263	(( resttime = cputime - cpu_hours * 3600 ))
	1264	(( cpu_minutes = resttime / 60 ))
	1265	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1266	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1267
	1268
	1269	# OUTPUT OF THE PALMRUN-HEADER
	1270	calltime=$(date)
	1271	printf "\n"
	1272	printf "#------------------------------------------------------------------------# \n"
	1273	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1274	printf "\| \| \n"
	1275	column1="called on:"; column2=$(hostname)
	1276	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1277	if [[ $create_remote_batch_job = true ]]
	1278	then
[2506]	1279	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1280	else
	1281	if [[ $running_on_remote = true ]]
	1282	then
[2506]	1283	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1284	else
[2506]	1285	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1286	fi
	1287	fi
	1288	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1289
	1290	column1="running in:"
	1291	if [[ $running_in_batch_mode = true ]]
	1292	then
	1293	column2="batch job mode"
	1294	else
	1295	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1296	then
	1297	column2="job creation mode"
	1298	else
	1299	column2="interactive run mode"
	1300	fi
	1301	fi
	1302	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1303
[2479]	1304	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1305	then
[2480]	1306	if [[ "$project_account" != "" ]]
[2479]	1307	then
	1308	column1="project account number:"
	1309	column2="$project_account"
	1310	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1311	fi
	1312	fi
	1313
[2380]	1314	if [[ -n $cores ]]
	1315	then
	1316	if [[ $run_coupled_model = false ]]
	1317	then
	1318	column1="number of cores:"; column2=$cores
	1319	else
	1320	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1321	fi
	1322	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1323	fi
	1324	if [[ -n $tasks_per_node ]]
	1325	then
	1326	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1327	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1328	if (( remaining_cores > 0 ))
	1329	then
	1330	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1331	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1332	fi
	1333	fi
	1334	if [[ $maximum_parallel_io_streams != $cores ]]
	1335	then
	1336	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1337	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1338	fi
	1339	if [[ $use_openmp = true ]]
	1340	then
	1341	column1="threads per task:"; column2="$threads_per_task"
	1342	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1343	fi
[2384]	1344	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1345	then
[2506]	1346	column1="memory demand / PE":; column2="$memory MB"
	1347	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1348	column1="job cpu time (h:m:s):"; column2="$timestring"
	1349	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1350	fi
[2380]	1351	printf "\| \| \n"
	1352	if [[ "$source_list" != "" ]]
	1353	then
	1354	if [[ "$make_options" != "" ]]
	1355	then
	1356	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1357	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1358	line=$(echo "$make_options" \| cut -c46-)
	1359	while [[ "$line" != "" ]]
	1360	do
	1361	column1=""
	1362	column2=$(echo "$line" \| cut -c-45)
	1363	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1364	line=$(echo "$line" \| cut -c46-)
	1365	done
	1366	fi
	1367	fi
	1368
	1369	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1370	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1371	line=$(echo "$cpp_options" \| cut -c46-)
	1372	while [[ "$line" != "" ]]
	1373	do
	1374	column1=""
	1375	column2=$(echo "$line" \| cut -c-45)
	1376	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1377	line=$(echo "$line" \| cut -c46-)
	1378	done
	1379
	1380	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1381	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1382	line=$(echo "$compiler_options" \| cut -c46-)
	1383	while [[ "$line" != "" ]]
	1384	do
	1385	column1=""
	1386	column2=$(echo "$line" \| cut -c-45)
	1387	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1388	line=$(echo "$line" \| cut -c46-)
	1389	done
	1390
[2388]	1391	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1392	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1393	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1394	while [[ "$line" != "" ]]
	1395	do
	1396	column1=""
	1397	column2=$(echo "$line" \| cut -c-45)
	1398	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1399	line=$(echo "$line" \| cut -c46-)
	1400	done
	1401
	1402	if [[ "$login_init_cmd" != "" ]]
	1403	then
	1404	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1405	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1406	line=$(echo "$login_init_cmd" \| cut -c46-)
	1407	while [[ "$line" != "" ]]
	1408	do
	1409	column1=""
	1410	column2=$(echo "$line" \| cut -c-45)
	1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1412	line=$(echo "$line" \| cut -c46-)
	1413	done
	1414	fi
	1415
	1416	if [[ "$module_commands" != "" ]]
	1417	then
	1418	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1419	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1420	line=$(echo "$module_commands" \| cut -c46-)
	1421	while [[ "$line" != "" ]]
	1422	do
	1423	column1=""
	1424	column2=$(echo "$line" \| cut -c-45)
	1425	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1426	line=$(echo "$line" \| cut -c46-)
	1427	done
	1428	fi
	1429	printf "\| \| \n"
	1430	column1="base name of files:"; column2=$fname
	1431	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1432	column1="activation string list:"; column2=$(echo $activation_string_list)
	1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1434
	1435	if [[ "$ocean_file_appendix" = true ]]
	1436	then
	1437	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1438	fi
	1439
	1440	if [[ "$source_list" != "" ]]
	1441	then
	1442	printf "\| \| \n"
	1443	printf "\| Files to be compiled: \| \n"
	1444	line=$source_list
	1445	while [[ "$line" != "" ]]
	1446	do
	1447	linestart=$(echo $line \| cut -c-70)
	1448	printf "\| %-70s \| \n" "$linestart"
	1449	line=$(echo "$line" \| cut -c71-)
	1450	done
	1451	fi
	1452	printf "#------------------------------------------------------------------------#"
	1453
	1454
	1455
	1456	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1457	if [[ $do_trace = true ]]
	1458	then
	1459	(( i = 0 ))
	1460	while (( i < iin ))
	1461	do
	1462	(( i = i + 1 ))
	1463	if (( i == 1 ))
	1464	then
	1465	printf "\n\n >>> INPUT-file assignments:\n"
	1466	fi
	1467	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1468	done
	1469	(( i = 0 ))
	1470	while (( i < iout ))
	1471	do
	1472	(( i = i + 1 ))
	1473	if (( i == 1 ))
	1474	then
	1475	printf "\n\n >>> OUTPUT-file assignments:\n"
	1476	fi
	1477	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1478	done
	1479	(( i = 0 ))
	1480	while (( i < iic ))
	1481	do
	1482	(( i = i + 1 ))
	1483	if (( i == 1 ))
	1484	then
	1485	printf "\n\n >>> INPUT-commands:\n"
	1486	fi
	1487	printf "\n ${in_command[$i]}"
	1488	done
	1489	(( i = 0 ))
	1490	while (( i < ioc ))
	1491	do
	1492	(( i = i + 1 ))
	1493	if (( i == 1 ))
	1494	then
	1495	printf "\n\n >>> OUTPUT-commands:\n"
	1496	fi
	1497	printf "\n ${out_command[$i]}"
	1498	done
	1499	fi
	1500
	1501	# QUERY FOR CONTINUE
	1502	if [[ $silent = false && $running_in_batch_mode = false ]]
	1503	then
	1504	antwort=dummy
	1505	printf "\n\n"
	1506	printf " >>> everything o.k. (y/n) ? "
	1507	while read antwort
	1508	do
	1509	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1510	then
	1511	printf " >>> everything o.k. (y/n) ? "
	1512	else
	1513	break
	1514	fi
	1515	done
	1516	if [[ $antwort = n \|\| $antwort = N ]]
	1517	then
	1518	locat=user_abort; (( iec = 0 )); exit
	1519	fi
	1520	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1521	then
	1522	printf " *** batch-job will be created and submitted"
	1523	else
	1524	printf " *** PALMRUN will now continue to execute on this machine"
	1525	fi
	1526	fi
	1527
	1528
	1529
	1530	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1531	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1532	then
	1533
	1534	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1535	then
	1536	printf "\n\n *** creating executable and other sources for the remote host"
	1537	else
	1538	printf "\n\n *** creating executable and other sources for the local host"
	1539	fi
	1540
[2422]	1541	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1542	# IT SHALL BE CREATED
	1543	ask_for_make_depository=false
	1544	if [[ $create_remote_batch_job = true ]]
	1545	then
	1546
	1547	line=`grep %base_directory $config_file`
[2506]	1548	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1549	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]	1550
[2506]	1551	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1552	then
	1553	printf "\n\n +++ make depository \"${make_depository}\""
	1554	printf "\n on remote host not found!"
	1555	ask_for_make_depository=true
	1556	fi
[2506]	1557	rm ${host_configuration}_last_make_protokoll
[2422]	1558
	1559	else
	1560
	1561	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1562	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1563	if [[ ! -d ${make_depository} ]]
	1564	then
	1565	printf "\n\n +++ make depository \"${make_depository}\""
	1566	printf "\n on local host not found!"
	1567	ask_for_make_depository=true
	1568	fi
	1569
	1570	fi
	1571
	1572	if [[ $ask_for_make_depository = true ]]
	1573	then
	1574
	1575	antwort=dummy
	1576	printf "\n\n"
	1577	printf " >>> Create a new one (y/n) ? "
	1578	while read antwort
	1579	do
	1580	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1581	then
	1582	printf " >>> Create a new one (y/n) ? "
	1583	else
	1584	break
	1585	fi
	1586	done
	1587	if [[ $antwort = n \|\| $antwort = N ]]
	1588	then
	1589	locat=user_abort; (( iec = 0 )); exit
	1590	fi
	1591
[2506]	1592	palmbuild -v -h $host_configuration
[2422]	1593
	1594	if [[ $? != 0 ]]
	1595	then
	1596
	1597	# ABORT IN CASE OF COMPILATION PROBLEMS
	1598	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1599	locat=make_depository
	1600	exit
	1601	else
	1602	echo " *** now continue with creating executable and other sources"
	1603	fi
	1604
	1605	fi
	1606
[2506]	1607	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1608
	1609	if [[ $? != 0 ]]
	1610	then
	1611
	1612	# ABORT IN CASE OF COMPILATION PROBLEMS
	1613	printf "\n +++ error while creating executable and/or other sources"
	1614	locat=execution
[2506]	1615	rm -rf $sources_for_run_catalog
[2380]	1616	exit
	1617
	1618	else
	1619
	1620	printf "\n$dashes\n *** executable and other sources created\n"
[2506]	1621	rm -rf $sources_for_run_catalog
[2380]	1622
	1623	fi
	1624
	1625	fi
	1626
	1627
	1628	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1629	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1630	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1631	then
	1632
	1633	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1634	if [[ $running_in_batch_mode = false ]]
	1635	then
	1636	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1637	# FOLDER
	1638	mkdir -p $TEMPDIR
	1639	chmod go+rx $TEMPDIR
	1640	tmpcreate=true
	1641	cd $TEMPDIR
[2506]	1642	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $TEMPDIR
[2380]	1643	printf "\n *** changed to temporary directory: $TEMPDIR"
	1644
	1645	else
	1646
	1647	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1648	printf "\n *** running in temporary directory: $TEMPDIR"
	1649
	1650	fi
	1651
	1652
	1653	# PROVIDE THE INPUT FILES
	1654	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1655	(( i = 0 ))
	1656	while (( i < iin ))
	1657	do
	1658	(( i = i + 1 ))
	1659	if (( i == 1 ))
	1660	then
	1661	printf "\n\n *** providing INPUT-files:\n$dashes"
	1662	fi
	1663
	1664
	1665	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1666	if [[ "${transin[$i]}" = unavailable ]]
	1667	then
	1668	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1669	then
	1670	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1671	printf "\n is not available!"
	1672	else
	1673	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1674	printf "\n is not available!"
	1675	fi
	1676	continue
	1677	fi
	1678
	1679	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1680	files_for_cores=false; filetype=file
	1681	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1682	then
	1683	files_for_cores=true; filetype=files
	1684	actionin[$i]=""
	1685	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1686	then
	1687	actionin[$i]=""
	1688	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1689	then
	1690	files_for_cores=true; filetype=files
	1691	actionin[$i]="ln"
	1692	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1693	then
	1694	actionin[$i]="ln"
	1695	fi
	1696
	1697	if [[ $files_for_cores = true ]]
	1698	then
	1699	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1700	else
	1701	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1702	fi
	1703
	1704	# INPUT-FILES TO BE LINKED
	1705	if [[ "${actionin[$i]}" = ln ]]
	1706	then
	1707
	1708	printf "\n $filetype will be linked"
	1709	if [[ $files_for_cores = false ]]
	1710	then
	1711	if [[ -f "${absnamein[$i]}" ]]
	1712	then
	1713	ln ${absnamein[$i]} ${localin[$i]}
	1714	got_tmp[$i]=true
	1715	fi
	1716	else
	1717	if [[ -d "${absnamein[$i]}" ]]
	1718	then
[2396]	1719	mkdir -p ${localin[$i]}
[2380]	1720	cd ${absnamein[$i]}
	1721	for file in $(ls *)
	1722	do
	1723	ln $file $TEMPDIR/${localin[$i]}
	1724	done >\|/dev/null 2>&1
	1725	cd $TEMPDIR
	1726	fi
	1727
	1728	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1729	if [[ ! -f "${localin[$i]}/_000000" ]]
	1730	then
	1731	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1732	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1733	fi
	1734
	1735	got_tmp[$i]=true
	1736	fi
	1737	fi
	1738
	1739	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1740	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1741	then
	1742
	1743	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1744	then
	1745
	1746	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1747	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1748	printf "\n file will be provided for $cores processors"
[2396]	1749	mkdir -p ${localin[$i]}
[2380]	1750	ival=$cores
	1751	(( ii = 0 ))
	1752	while (( ii <= ival-1 ))
	1753	do
	1754	if (( ii < 10 ))
	1755	then
	1756	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1757	elif (( ii < 100 ))
	1758	then
	1759	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1760	elif (( ii < 1000 ))
	1761	then
	1762	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1763	else
	1764	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1765	fi
	1766	(( ii = ii + 1 ))
	1767	done
	1768
	1769	else
	1770
	1771	if [[ $files_for_cores = true ]]
	1772	then
	1773
	1774	# PROVIDE FILES FOR EACH CORE
	1775	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1776	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1777	printf "\n providing $cores files for the respective cores"
[2396]	1778	mkdir -p ${localin[$i]}
[2380]	1779	if [[ $link_local_input = true ]]
	1780	then
	1781	printf " files will be linked\n"
	1782	cd ${absnamein[$i]}
	1783	for file in $(ls *)
	1784	do
	1785	ln -f $file ${localin[$i]}
	1786	done
	1787	cd $TEMPDIR
	1788	fi
	1789
	1790	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1791	if [[ ! -f "${localin[$i]}/_000000" ]]
	1792	then
	1793	if [[ $link_local_input = true ]]
	1794	then
	1795	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1796	fi
	1797	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1798	fi
	1799
	1800	else
	1801
	1802	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1803	if [[ $link_local_input = true ]]
	1804	then
	1805	printf " file will be linked\n"
	1806	ln -f ${absnamein[$i]} ${localin[$i]}
	1807	fi
	1808	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1809	if [[ ! -f "${localin[$i]}" ]]
	1810	then
	1811	if [[ $link_local_input = true ]]
	1812	then
	1813	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1814	fi
	1815	cp ${absnamein[$i]} ${localin[$i]}
	1816	fi
	1817	fi
	1818	fi
	1819	fi
	1820
	1821	done
	1822	if (( i != 0 ))
	1823	then
	1824	printf "\n$dashes\n *** all INPUT-files provided \n"
	1825	fi
	1826
	1827
	1828	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1829	(( i = 0 ))
	1830	while (( i < iic ))
	1831	do
	1832	(( i = i + 1 ))
	1833	if (( i == 1 ))
	1834	then
	1835	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1836	fi
	1837	printf "\n >>> ${in_command[$i]}"
	1838	eval ${in_command[$i]}
	1839	if (( i == iic ))
	1840	then
	1841	printf "\n$dashes\n"
	1842	fi
	1843	done
	1844
	1845
	1846	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1847	# (FILE ENVPAR WILL BE READ BY PALM)
	1848	cat > ENVPAR << EOF
[2506]	1849	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	1850	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1851	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1852	maximum_cpu_time_allowed = ${cpumax}.,
	1853	revision = '$global_revision',
	1854	batch_job = .${running_in_batch_mode}. /
	1855
	1856	EOF
	1857
	1858
	1859	# STARTING THE EXECUTABLE
	1860	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1861	PATH=$PATH:$TEMPDIR
	1862
	1863
	1864	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1865	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1866	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1867	eval line=\"$line\"
	1868	execute_command="$line"
	1869
	1870
	1871	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1872	eval line2=\"$line2\"
	1873	execute_command_for_combine="$line2"
	1874
	1875
	1876	# PROVIDE A HOSTFILE, IF REQUIRED
	1877	if [[ "$hostfile" != "" ]]
	1878	then
	1879
	1880	if [[ $hostfile = auto ]]
	1881	then
	1882	# CREATE A NEW HOSTFILE
	1883	(( ii = 1 ))
	1884	while (( ii <= cores / threads_per_task ))
	1885	do
	1886	echo $(hostname) >> hostfile
	1887	(( ii = ii + 1 ))
	1888	done
	1889	if (( cores / threads_per_task == 0 ))
	1890	then
	1891	echo $(hostname) >> hostfile
	1892	fi
	1893
	1894	else
	1895	cp $hostfile hostfile
	1896	fi
	1897	eval line=\"`head -n $ii hostfile`\"
	1898	printf "\n *** running on: $line"
	1899	fi
	1900
	1901
	1902
	1903	# SET THE NUMBER OF OPENMP-THREADS
	1904	if [[ $use_openmp = true ]]
	1905	then
	1906	export OMP_NUM_THREADS=$threads_per_task
	1907	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1908	else
	1909	export OMP_NUM_THREADS=1
	1910	fi
	1911
	1912
	1913	# PROVIDE DATA FOR
	1914	if [[ $run_coupled_model = false ]]
	1915	then
	1916	if [[ "$ocean_file_appendix" = true ]]
	1917	then
	1918	echo "precursor_ocean" > coupling_steering
	1919	else
	1920	echo "precursor_atmos" > coupling_steering
	1921	fi
	1922	else
	1923	(( iia = $cores_atmos / $threads_per_task ))
	1924	(( iio = $cores_ocean / $threads_per_task ))
	1925	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1926	printf "\n\n"
	1927	echo "coupled_run $iia $iio" > coupling_steering
	1928	fi
	1929
	1930	printf "\n *** execute command:"
	1931	printf "\n \"$execute_command\" \n\n"
	1932
	1933	$execute_command < coupling_steering
	1934
	1935	if [[ $? != 0 ]]
	1936	then
	1937
	1938	# ABORT IN CASE OF RUNTIME ERRORS
	1939	printf "\n +++ runtime error occured"
	1940	locat=execution
	1941	exit
	1942
	1943	else
	1944
	1945	printf "\n$dashes\n *** execution finished \n"
	1946
	1947	fi
	1948
	1949
	1950	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1951	# BY EACH CORE INTO ONE FILE
	1952	if [[ ! -f combine_plot_fields.x ]]
	1953	then
	1954
	1955	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1956	printf "\n 2d- and/or 3d-data may be incomplete!"
	1957	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1958
	1959	elif [[ "$combine_plot_fields" == true ]]
	1960	then
	1961
	1962	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1963	$execute_command_for_combine
	1964
	1965	else
	1966
	1967	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1968	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1969	# ??? koennen wir das streichen ???
	1970	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1971	fi
	1972
	1973
	1974
	1975	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1976	(( i = 0 ))
	1977	while (( i < ioc ))
	1978	do
	1979	(( i = i + 1 ))
	1980	if (( i == 1 ))
	1981	then
	1982	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1983	fi
	1984	printf "\n >>> ${out_command[$i]}"
	1985	eval ${out_command[$i]}
	1986	if (( i == ioc ))
	1987	then
	1988	printf "\n$dashes\n"
	1989	fi
	1990	done
	1991
	1992
	1993	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1994	if [[ $do_trace = true ]]
	1995	then
	1996	printf "\n\n"
	1997	ls -al
	1998	fi
	1999
	2000
	2001	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2002	(( i = 0 ))
	2003	while (( i < iout ))
	2004	do
	2005	(( i = i + 1 ))
	2006	if (( i == 1 ))
	2007	then
	2008	printf "\n\n *** saving OUTPUT-files:"
	2009
	2010	# GET RUN NUMBER ASSIGNED BY PALM
	2011	if [[ -f RUN_NUMBER ]]
	2012	then
	2013	read run_number < RUN_NUMBER
	2014	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2015	usecycle_option="-U $run_number"
	2016	else
	2017	run_number=0
	2018	usecycle_option=""
	2019	fi
	2020	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2021	then
[2404]	2022	printf "\n *** in case of SCP transfers to local host"
	2023	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2024	fi
	2025	printf "\n$dashes"
	2026	fi
	2027
	2028	# ADD CYCLE NUMBER TO FILENAME
	2029	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2030	then
	2031
	2032	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2033	if [[ "${actionout[$i]}" != "a" ]]
	2034	then
	2035	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2036	# WITH AN EXISTING CYCLE NUMBER
	2037	if (( run_number >= cycnum[$i] ))
	2038	then
	2039	(( cycnum[$i] = run_number ))
	2040	else
	2041	if (( run_number > 0 ))
	2042	then
	2043	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2044	fi
	2045	fi
	2046	fi
	2047	if (( cycnum[$i] > 0 ))
	2048	then
	2049	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2050	fi
	2051	fi
	2052
	2053	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2054	files_for_cores=false; filetype=file
	2055	link_local_output=false
	2056	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2057	then
	2058	files_for_cores=true; filetype=directory
	2059	actionout[$i]=""
	2060	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2061	then
	2062	actionout[$i]=""
	2063	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2064	then
	2065	files_for_cores=true; filetype=directory
	2066	link_local_output=true
	2067	actionout[$i]=""
	2068	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2069	then
	2070	link_local_output
	2071	actionout[$i]=""
	2072	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2073	then
	2074	files_for_cores=true; filetype=directory
	2075	actionout[$i]="tr"
	2076	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2077	then
	2078	actionout[$i]="tr"
	2079	fi
	2080
	2081	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2082	then
	2083	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2084	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2085	then
	2086	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2087	else
	2088
	2089
	2090	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2091	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2092	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2093	then
	2094	if [[ $running_on_remote = true ]]
	2095	then
	2096
	2097	# SET OPTIONS FOR TRANSFER
	2098	if [[ "${actionout[$i]}" = tr ]]
	2099	then
	2100	if [[ $files_for_cores = false ]]
	2101	then
	2102	catalog_option=""
	2103	catalog_string=""
	2104	else
	2105	catalog_option="-c"
	2106	catalog_string="/"
	2107	fi
	2108	append_option=""
	2109	append_string=""
	2110	else
	2111	append_option="-A"
	2112	append_string="append"
	2113	fi
	2114
	2115	transfer_failed=false
	2116	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2117	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2118
	2119	# TRANSFER VIA SCP
	2120	if [[ "$remote_loginnode" != "" ]]
	2121	then
[2506]	2122	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]	2123	else
[2506]	2124	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]	2125	fi
	2126	[[ $? != 0 ]] && transfer_failed=true
	2127
	2128
	2129	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2130	if [[ $transfer_failed = true ]]
	2131	then
	2132	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2133	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2134
	2135	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2136	eval local_catalog=${pathout[$i]}
	2137	if [[ ! -d $local_catalog ]]
	2138	then
	2139	printf " *** local directory does not exist. Trying to create:\n"
	2140	printf " $local_catalog \n"
	2141	mkdir -p $local_catalog
	2142	fi
[2506]	2143	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2144	transfer_problems=true
	2145	fi
	2146
	2147	else
	2148
	2149	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2150	# BE COPIED OR APPENDED ON THIS MACHINE
	2151	if [[ "${actionout[$i]}" = tr ]]
	2152	then
	2153	actionout[$i]=""
	2154	else
	2155	actionout[$i]="a"
	2156	fi
	2157	fi
	2158	fi
	2159
	2160
	2161	# APPEND ON THIS MACHINE
	2162	if [[ "${actionout[$i]}" = "a" ]]
	2163	then
	2164	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2165	then
	2166	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2167	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2168	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2169	else
	2170	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2171	printf "\n ${pathout[$i]}\n"
	2172	cat ${localout[$i]} >> ${pathout[$i]}
	2173	fi
	2174	fi
	2175
	2176	# COPY ON THIS MACHINE
	2177	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2178	# ON DIFFERENT FILE-SYSTEMS
	2179	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2180	then
	2181
	2182	# COPY IN CASE OF RUNS ON SINGLE CORES
	2183	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2184	then
	2185	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2186	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2187	if [[ $link_local_output = true ]]
	2188	then
	2189	printf " file will be linked\n"
	2190	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2191	fi
	2192	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2193	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2194	then
	2195	if [[ $link_local_output = true ]]
	2196	then
	2197	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2198	fi
	2199	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2200	else
	2201	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2202	fi
	2203	else
	2204	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2205	printf "\n ${pathout[$i]}\n"
	2206	if [[ $link_local_output = true ]]
	2207	then
	2208	printf " file will be linked\n"
	2209	ln -f ${localout[$i]} ${pathout[$i]}
	2210	fi
	2211	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2212	if [[ ! -f "${pathout[$i]}" ]]
	2213	then
	2214	if [[ $link_local_output = true ]]
	2215	then
	2216	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2217	fi
	2218	cp ${localout[$i]} ${pathout[$i]}
	2219	else
	2220	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2221	fi
	2222	fi
	2223
	2224	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2225	then
	2226
	2227	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2228	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2229	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2230	printf "\n ${pathout[$i]}\n"
	2231	if [[ $link_local_output = true ]]
	2232	then
	2233	printf " files will be linked\n"
[2396]	2234	mkdir -p ${pathout[$i]}
[2380]	2235	cd ${localout[$i]}
	2236	for file in $(ls *)
	2237	do
	2238	ln -f $file ${pathout[$i]}
	2239	done >\|/dev/null 2>&1
	2240	cd $TEMPDIR
	2241	fi
	2242
	2243	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2244	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2245	then
	2246	if [[ $link_local_output = true ]]
	2247	then
	2248	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2249	fi
	2250	cp -r ${localout[$i]}/* ${pathout[$i]}
	2251	fi
	2252
	2253	fi
	2254	fi
	2255	done
	2256
	2257	if (( i != 0 ))
	2258	then
	2259	if [[ $transfer_problems = true ]]
	2260	then
	2261	printf "\n$dashes\n *** OUTPUT-files saved"
	2262	printf "\n +++ WARNING: some data transfers failed! \n"
	2263	else
	2264	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2265	fi
	2266	fi
	2267
	2268
	2269	# IF REQUIRED, START A RESTART-JOB
	2270	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2271	if [[ -f CONTINUE_RUN ]]
	2272	then
	2273
	2274	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2275	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2276	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2277	# -b START A BATCH JOB
	2278	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2279	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2280	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2281
	2282
	2283	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2284	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2285	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2286	then
[2381]	2287	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2288	fi
	2289
	2290
	2291	# START THE RESTART-JOB
	2292	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2293	echo " $prc"
	2294	printf "\n$dashes\n"
	2295	if [[ $running_on_remote = true ]]
	2296	then
	2297
	2298	echo "*** ssh will be used to initiate restart-runs!"
	2299	echo " return_address=\"$return_address\" "
	2300	echo " return_username=\"$local_username\" "
	2301
	2302	if [[ "$remote_loginnode" != "" ]]
	2303	then
[2420]	2304	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]	2305	else
[2420]	2306	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2307	fi
	2308
	2309	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2310	sleep 30
	2311
	2312	else
	2313
	2314	# START THE RESTART JOB ON THE LOCAL HOST
	2315	eval $prc # THE ' MUST BE EVALUATED
	2316	cd - > /dev/null
	2317
	2318	fi
	2319	printf "\n$dashes\n *** restart-run initiated \n"
	2320
	2321
	2322	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2323	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2324	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2325	# MAY BE VERY HUGE)
	2326	(( i = 0 ))
	2327	while (( i < iin ))
	2328	do
	2329	(( i = i + 1 ))
	2330	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2331	then
	2332	rm -r ${absnamein[$i]}
	2333	fi
	2334	done
	2335
	2336	fi
	2337
	2338
	2339	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2340	cd $HOME
	2341	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2342
	2343
	2344	else
	2345
	2346
	2347	# PREPARING ACTIONS,
	2348	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2349
	2350	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2351	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2352	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2353	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2354	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2355	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2356	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2357	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2358	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2359	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2360	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2361	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2362	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2363	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2364	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2365	if [[ $create_remote_batch_job = true ]]
	2366	then
	2367	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2368	if [[ $do_trace = true ]]
	2369	then
	2370	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2371	fi
[2380]	2372	elif [[ $create_batch_job = true ]]
	2373	then
	2374	palmrun_com=${palmrun_com}" -j"
[2420]	2375	if [[ $do_trace = true ]]
	2376	then
	2377	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2378	fi
[2380]	2379	fi
	2380
	2381
	2382	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2383	# REMOTE HOST
[2506]	2384	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2385	job_protocol_file=$job_protocol_file_local
	2386	if [[ $create_remote_batch_job = true ]]
	2387	then
[2506]	2388	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2389	job_protocol_file=$job_protocol_file_remote
	2390	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2391	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2392	fi
	2393
	2394
	2395	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2396	jobfile=jobfile.$run_id
	2397
	2398
	2399	# FIRST CREATE THE BATCH DIRECTIVES
	2400	(( i = 0 ))
	2401	while (( i < ibd ))
	2402	do
	2403	(( i = i + 1 ))
[2506]	2404	line=`echo "${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}}/$previous_job/g'`
[2380]	2405	eval line=\"$line\"
	2406	echo "$line" >> $jobfile
	2407	done
	2408	echo " " >> $jobfile
	2409
	2410
	2411	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2412	# PROTOCOL
	2413	if [[ $create_remote_batch_job = true ]]
	2414	then
	2415	echo "set +vx" >> $jobfile
	2416	echo "trap '" >> $jobfile
	2417	echo "set +vx" >> $jobfile
	2418	echo "cd ${remote_jobcatalog}" >> $jobfile
	2419	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2420
	2421	# ADD THE BATCH DIRECTIVES
	2422	(( i = 0 ))
	2423	while (( i < ibdt ))
	2424	do
	2425	(( i = i + 1 ))
[2506]	2426	line=`echo "${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]	2427	eval line=\"$line\"
	2428	echo "$line" >> $jobfile
	2429	done
	2430	echo " " >> $jobfile
	2431
	2432	echo "set -x" >> $jobfile
[2506]	2433	echo "${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]	2434	echo "%%END%%" >> $jobfile
	2435	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2436	echo "$submit_command $scpjob_file" >> $jobfile
	2437	echo "rm $scpjob_file" >> $jobfile
[2404]	2438	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2439	echo "set -x" >> $jobfile
	2440	echo " ' exit" >> $jobfile
	2441	fi
	2442
	2443
	2444	# ACTIVATE ERROR-TRACEBACK
	2445	if [[ $do_trace = true ]]
	2446	then
	2447	echo "set -x" >> $jobfile
	2448	else
	2449	echo "set +vx" >> $jobfile
	2450	fi
	2451
	2452
	2453	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2454	if [[ "$login_init_cmd" != "" ]]
	2455	then
	2456	echo "$login_init_cmd" >> $jobfile
	2457	fi
	2458	if [[ "$module_commands" != "" ]]
	2459	then
	2460	echo "$module_commands" >> $jobfile
	2461	fi
	2462
	2463
	2464	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2465	echo "mkdir $TEMPDIR" >> $jobfile
	2466	echo "cd $TEMPDIR" >> $jobfile
	2467	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2506]	2468	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2469	echo "export PATH=.:\$PATH" >> $jobfile
	2470	echo "export execute_palmrun=true" >> $jobfile
	2471
	2472
	2473	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2474	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2475	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2476	if [[ $create_remote_batch_job = true ]]
	2477	then
	2478	(( i = 0 ))
	2479	while (( i < iin ))
	2480	do
	2481	(( i = i + 1 ))
	2482	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2483	if [[ "${transin[$i]}" = job ]]
	2484	then
	2485	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2486	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2487	echo " " >> $jobfile
	2488	echo "%END%" >> $jobfile
	2489	else
	2490	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2491	fi
	2492
	2493	# CHECK, IF FILE COULD BE CREATED
	2494	echo "if [[ \$? = 1 ]]" >> $jobfile
	2495	echo "then" >> $jobfile
	2496	echo " echo \" \" " >> $jobfile
	2497	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2506]	2498	echo " echo \" please check, if directory exists on $host_configuration!\" " >> $jobfile
[2380]	2499	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2500	echo " execute_palmrun=false" >> $jobfile
	2501	echo "fi" >> $jobfile
	2502	done
	2503	fi
	2504
	2505
	2506	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2507	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2508	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2509	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2510	echo "export LOCAL_PWD" >> $jobfile
	2511
	2512
	2513	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2514	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2515	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2516
	2517
	2518	# CALL PALMRUN WITHIN THE JOB
	2519	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2520	echo "set -x" >> $jobfile
	2521	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2522
	2523
	2524	# TRANSFER JOBFILE TO THE TARGET HOST
	2525	if [[ $create_jobfile_only = false ]]
	2526	then
	2527
	2528	if [[ $create_remote_batch_job = true ]]
	2529	then
	2530
[2420]	2531	echo " "
	2532	echo " *** transfer of job to remote host via scp"
	2533	if [[ $do_trace = true ]]
	2534	then
[2506]	2535	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2536	fi
[2506]	2537	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2538
	2539	echo " "
[2420]	2540	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2541	if [[ $do_trace = true ]]
	2542	then
[2506]	2543	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]	2544	fi
[2506]	2545	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]	2546
	2547	elif [[ $create_batch_job = true ]]
	2548	then
	2549
[2385]	2550	eval local_jobcatalog=$local_jobcatalog
[2506]	2551	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2552	cd $local_jobcatalog
[2380]	2553	echo " "
[2420]	2554	echo " *** submit the job"
	2555	if [[ $do_trace = true ]]
	2556	then
[2506]	2557	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2558	fi
[2506]	2559	$submit_command ${host_configuration}_${job_id}
	2560	rm ${host_configuration}_${job_id}
[2380]	2561	cd - > /dev/null
	2562
	2563	fi
	2564
	2565	rm -rf $jobfile
	2566
	2567	else
	2568
	2569	printf "\n *** jobfile created under name \"$jobfile\" "
	2570	printf "\n no batch-job has been sent!"
	2571
	2572	fi
	2573
	2574	fi # END OF REMOTE-PART

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