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source: palm/trunk/SCRIPTS/palmrun @ 2506

Last change on this file since 2506 was 2506, checked in by raasch, 7 years ago
new options -V and -W plus other small changes in PALM scripts
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 85.9 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 2506 2017-09-29 08:30:37Z raasch $
[2506]	29	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	30	# host configuration added to SOURCES_FOR_RUN_... folder name
	31	# host_identifier renamed host_configuration
	32	# option -W added to allow for job dependencies
	33	#
	34	# 2501 2017-09-26 11:41:55Z raasch
[2501]	35	# default value for number of cores (option -X) set to 1
	36	# bugfix for mechanism which overwrites configuration file settings with values
	37	# provided by palmrun options
	38	#
	39	# 2499 2017-09-22 16:47:58Z kanani
[2499]	40	# option -h named configuration identifier
	41	#
	42	# 2480 2017-09-19 06:24:14Z maronga
[2480]	43	# bugfix for last revision
	44	#
	45	# 2479 2017-09-19 06:12:16Z raasch
[2479]	46	# option -A (project account number) added
	47	#
	48	# 2422 2017-09-08 08:25:41Z raasch
[2410]	49	# initial revision
[2380]	50	#
	51	#--------------------------------------------------------------------------------#
	52	# palmrun - script for running PALM jobs on local and remote hosts
	53	#--------------------------------------------------------------------------------#
	54
	55
	56
	57	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	58
	59	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	60	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	61	# (TOO MANY ARGUMENTS - PROBLEM)
	62	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	63
	64	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	65	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	66	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	67	# SCRIPT-OPTION ARGUMENTS
	68	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	69	typeset -i icycle inode ival maxcycle mpi_tasks
	70	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	71
	72	activation_string_list=""
	73	AddFilenames=""
	74	combine_plot_fields=true
	75	compiler_name=""
	76	compiler_name_ser=""
	77	compiler_options=""
[2501]	78	cores=1
[2380]	79	cores_atmos=0
	80	cores_ocean=0
	81	coupled_dist=""
	82	cpp_options=""
	83	cpumax=0
[2506]	84	create_batch_job=false
[2380]	85	create_jobfile_only=false
	86	create_remote_batch_job=false
	87	dashes=" ----------------------------------------------------------------------------"
	88	defaultqueue=""
[2506]	89	delete_temporary_catalog=true
[2380]	90	do_compile=true
	91	do_trace=false
	92	executable=""
	93	execute_command=""
	94	execution_error=false
	95	fileconnection_file=.palm.iofiles
	96	fname=test
	97	global_revision=""
[2506]	98	host_configuration="default"
[2380]	99	hostfile=""
	100	hp=""
	101	keep_data_from_previous_run=false
	102	link_local_input=false
	103	link_local_output=false
[2388]	104	linker_options=""
[2385]	105	local_jobcatalog=""
[2380]	106	locat=normal
	107	makefile=""
	108	max_par_io_str=""
	109	prc=$0
	110	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	111	do
	112	prc=`echo $prc \| cut -f2- -d"/"`
	113	done
	114	module_calls=""
[2506]	115	palmrun_memory=""
[2380]	116	palmrun_script_name=$prc
	117	openmp=false
[2506]	118	previous_job=""
[2479]	119	project_account=""
[2380]	120	queue=none
	121	restart_run=false
	122	return_address=""
[2385]	123	remote_jobcatalog=""
[2380]	124	remote_username=""
	125	running_in_batch_mode=false
	126	run_coupled_model=false
	127	run_id=""
	128	silent=false
	129	source_list=""
	130	source_path=""
[2501]	131	tasks_per_node=0
[2380]	132	threads_per_task=1
	133	tmpcreate=false
	134	transfer_problems=false
[2384]	135	user_source_path=""
[2506]	136	use_existing_sources_folder=""
[2380]	137	use_openmp=false
[2422]	138	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	139	working_directory=`pwd`
	140	write_binary=""
	141	TOPT=""
	142
	143
	144	# ERROR HANDLING IN CASE OF EXIT
[2404]	145	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	146	then
	147
	148	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	149	(( i = 0 ))
	150	while (( i < iec ))
	151	do
	152	(( i = i + 1 ))
	153	printf "\n *** Execution of ERROR-command:\n"
	154	printf " >>> ${err_command[$i]}\n"
	155	eval ${err_command[$i]}
	156	done
[2405]	157	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	158	printf "\n\n+++ palmrun killed \n\n"
	159	elif [[ $locat != control_c ]]
	160	then
	161	printf "\n\n --> palmrun finished\n\n"
	162	if [[ $running_on_remote = true ]]
	163	then
	164	printf " Bye, bye $remote_username !!\n\n"
	165	else
	166	printf " Bye, bye $local_username !!\n\n"
	167	fi
	168	fi' exit
	169
	170
	171	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	172	trap 'cd; rm -rf $TEMPDIR
[2380]	173	printf "\n+++ palmrun killed by \"^C\" \n\n"
	174	locat=control_c
	175	exit
	176	' 2
	177
	178
	179	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	180	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	181	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]	182	do
	183	case $option in
	184	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	185	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	186	(b) create_batch_job=true; prc="$prc -b";;
	187	(B) delete_temporary_catalog=false; prc="$prc -B";;
	188	(C) restart_run=true; prc="$prc -C";;
	189	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	190	(F) create_jobfile_only=true;;
	191	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	192	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	193	(j) running_in_batch_mode=true;;
	194	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	195	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	196	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	197	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	198	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	199	(r) run_id=$OPTARG;;
	200	(R) return_address=$OPTARG;;
	201	(s) source_list=$OPTARG;;
[2501]	202	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	203	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	204	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	205	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	206	(v) silent=true; prc="$prc -v";;
[2506]	207	(V) use_existing_sources_folder="-V";;
[2380]	208	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	209	(W) previous_job=$OPTARG;;
[2380]	210	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	211	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	212	(y) ocean_file_appendix=true; prc="$prc -y";;
	213	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	214	(Z) combine_plot_fields=false; prc="$prc -Z";;
	215	(\?) printf "\n +++ unknown option $OPTARG \n"
	216	printf "\n --> type \"$0 ?\" for available options \n"
	217	locat=parameter;exit;;
	218	esac
	219	done
	220
	221
	222	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	223	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	224	(( to_shift = $OPTIND - 1 ))
	225	shift $to_shift
	226
	227	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	228	if [[ "$1" = "?" ]]
	229	then
	230	(printf "\n *** Description of available palmrun options:\n"
	231	printf "\n Option Description Default-Value"
	232	printf "\n -a activation string list \"\" "
[2479]	233	printf "\n -A project account number ---"
[2380]	234	printf "\n -b batch-job on local machine ---"
	235	printf "\n -B do not delete temporary directory at end ---"
	236	printf "\n -d base name of files attached to program test"
	237	printf "\n -F create batch job file only ---"
[2506]	238	printf "\n -h host configuration \"default\" "
[2380]	239	printf "\n -k keep data from previous run"
	240	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	241	printf "\n -M Makefile name Makefile"
	242	printf "\n -O threads per openMP task ---"
	243	printf "\n -q queue \"$queue\" "
	244	printf "\n -s filenames of routines to be compiled \"\" "
	245	printf "\n must end with .f, .f90, .F, or .c !"
	246	printf "\n use \"..\" for more than one file and wildcards"
	247	printf "\n -s LM compiles all locally modified files"
	248	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	249	printf "\n -T tasks per node ---"
[2380]	250	printf "\n -u username on remote machine \"\" "
	251	printf "\n -v no prompt for confirmation ---"
[2506]	252	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	253	printf "\n -w maximum parallel io streams as given by -X"
[2506]	254	printf "\n -W name of job to wait for ---"
[2380]	255	printf "\n -x tracing of palmrun for debug purposes ---"
	256	printf "\n -X # of processors (on parallel machines) 1"
	257	printf "\n -y add appendix \"_O\" to all local output"
	258	printf "\n files (ocean precursor runs followed by"
	259	printf "\n coupled atmosphere-ocean runs) ---"
	260	printf "\n -Y run coupled model, \"#1 #2\" with"
	261	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	262	printf "\n -Z skip combine_plot_fields at the end of "
	263	printf "\n the simulation ---"
	264	printf "\n "
	265	printf "\n Possible values of positional parameter <modus>:"
	266	printf "\n \"?\" - this outline \n\n") \| more
	267	exit
	268	elif [[ "$1" != "" ]]
	269	then
	270	printf "\n +++ positional parameter $1 unknown \n"
	271	locat=parameter; exit
	272	fi
	273
	274
	275
	276	# SHORT STARTING MESSAGE
	277	printf "\n*** $version "
	278	printf "\n will be executed. Please wait ..."
	279
	280
[2506]	281	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	282	config_file=.palm.config.$host_configuration
	283	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	284
	285
	286	# CHECK, IF CONFIGURATION FILE EXISTS
	287	if [[ ! -f $config_file ]]
	288	then
	289	printf "\n\n +++ configuration file: "
	290	printf "\n $config_file"
	291	printf "\n does not exist"
	292	locat=connect; exit
	293	fi
	294
	295
	296	# CHECK, IF FILE CONNECTION FILE EXISTS
	297	if [[ ! -f $fileconnection_file ]]
	298	then
	299	printf "\n\n +++ file connection file: "
	300	printf "\n $fileconnection_file"
	301	printf "\n does not exist"
	302	locat=connect; exit
	303	fi
	304
	305
[2404]	306	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	307	if [[ "$activation_string_list" = "" ]]
	308	then
	309	printf "\n\n +++ no activation string list given: "
	310	printf "\n please set palmrun option \"-a\" "
	311	locat=palmrun_option; exit
	312	fi
	313
	314
	315	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	316	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	317	then
	318	write_binary=true
	319	else
	320	write_binary=false
	321	fi
	322
	323
[2380]	324	# READ AND EVALUATE THE CONFIGURATION-FILE
	325	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	326
	327	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	328	while read line
	329	do
	330
	331	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	332	eval line=\"$line\"
	333
	334
	335	# INTERPRET THE LINE
	336	if [[ "$(echo $line)" = "" ]]
	337	then
	338
	339	# EMPTY LINE, NO ACTION
	340	continue
	341
	342	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	343	then
	344
	345	# LINE IS A COMMENT LINE
	346	continue
	347
	348	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	349	then
	350
	351	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	352	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	353	value=`echo $line \| cut -d" " -s -f2-`
	354
	355
	356	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	357	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	358	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	359	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	360	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	361	# CONFIGURATION-FILE.
	362	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	363	then
	364	eval export $var="\$value"
	365
	366	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	367	if [[ $do_trace = true ]]
	368	then
	369	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	370	fi
	371	fi
	372
	373	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	374	then
	375
	376	# LINE DEFINES BATCH-DIRECTIVE
	377	(( ibd = ibd + 1 ))
	378	line=$(echo $line \| cut -c4-)
	379	batch_directive[$ibd]="$line"
	380
	381	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	382	then
	383
	384	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	385	# REMOTE TO A LOCAL HOST
	386	(( ibdt = ibdt + 1 ))
	387	line=$(echo $line \| cut -c5-)
	388	batch_directive_transfer[$ibdt]="$line"
	389
	390	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	391	then
	392
	393	# LINE DEFINES ERROR-COMMAND
	394	(( iec = iec + 1 ))
	395	line=$(echo $line \| cut -c4-)
	396	err_command[$iec]="$line"
	397
	398	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	399	then
	400
	401	# LINE DEFINES INPUT-COMMAND
	402	(( iic = iic + 1 ))
	403	line=$(echo $line \| cut -c4-)
	404	in_command[$iic]="$line"
	405
	406	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	407	then
	408
	409	# LINE DEFINES OUTPUT-COMMAND
	410	(( ioc = ioc + 1 ))
	411	line=$(echo $line \| cut -c4-)
	412	out_command[$ioc]="$line"
	413
	414	else
	415
	416	# SKIP ALL OTHER LINES
	417	continue
	418
	419	fi
	420
	421	done < $config_file
	422
	423
	424	# CHECK SETTING OF REQUIRED PARAMETERS
	425	if [[ "$compiler_name" = "" ]]
	426	then
	427	printf "\n +++ no compiler name found in $config_file"
	428	printf "\n Please add line \"compiler_name ...\" to that file."
	429	locat=config_file; exit
	430	fi
	431	if [[ "$compiler_name_ser" = "" ]]
	432	then
	433	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	434	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	435	locat=config_file; exit
	436	fi
	437	if [[ "$compiler_options" = "" ]]
	438	then
	439	printf "\n +++ no compiler options found in $config_file"
	440	printf "\n Please add line \"compiler_options ...\" to that file."
	441	locat=config_file; exit
	442	fi
[2388]	443	if [[ "$linker_options" = "" ]]
[2380]	444	then
[2388]	445	printf "\n +++ no linker options found in $config_file"
	446	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	447	locat=config_file; exit
	448	fi
	449	if [[ "$execute_command" = "" ]]
	450	then
	451	printf "\n +++ no execute command found in $config_file"
	452	printf "\n Please add line \"execute_command ...\" to that file."
	453	locat=config_file; exit
	454	fi
	455
	456	if [[ "$hostfile" != "" ]]
	457	then
	458	if [[ $hostfile != auto && ! -f $hostfile ]]
	459	then
	460	printf "\n +++ no hostfile \"$hostfile\" found"
	461	printf "\n Please check line \"hostfile ...\" in $config_file"
	462	locat=config_file; exit
	463	fi
	464	fi
	465
	466
	467	# DETERMINE THE CALL STATUS
	468	if [[ "$return_address" != "" ]]
	469	then
	470
	471	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	472	# BATCH MODE AND ...
	473	running_on_remote=true
	474
	475	else
	476
	477	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	478	if [[ "$remote_ip" != "" ]]
	479	then
	480
	481	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	482	create_remote_batch_job=true
	483
	484	fi
	485	running_on_remote=false
	486	fi
	487
	488
	489
	490	# READ AND EVALUATE THE I/O-FILE LIST
	491	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	492
	493	# READ THE FILE CONNECTION FILE LINE BY LINE
	494	while read line
	495	do
	496
	497	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	498	eval line=\"$line\"
	499
	500
	501	# INTERPRET THE LINE
	502	if [[ "$(echo $line)" = "" ]]
	503	then
	504	# EMPTY LINE, NO ACTION
	505	continue
	506
	507	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	508	then
	509
	510	# LINE IS A COMMENT LINE
	511	true
	512
	513	else
	514
	515	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	516	# s2a: in/out - field
	517	# s2b: loc - field (optional)
	518	# s2c: tr/ar - field (optional)
	519	s1=`echo $line \| cut -d" " -f1`
	520	s2=`echo $line \| cut -d" " -s -f2`
	521	s2a=$(echo $s2 \| cut -d":" -f1)
	522	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	523	then
	524	s2b=""
	525	s2c=""
	526	else
	527	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	528	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	529	fi
	530	s3=`echo $line \| cut -d" " -f3`
	531	s4=`echo $line \| cut -d" " -s -f4`
	532	s5=`echo $line \| cut -d" " -s -f5`
	533	s6=`echo $line \| cut -d" " -s -f6`
	534
	535
	536	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	537	# INPUT- OR OUTPUT-LIST.
	538	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	539	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	540	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	541	# IS NOT CHECKED AND STORED.
	542	IFSALT="$IFS"; IFS="$IFS:"
	543	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	544	then
	545	found=false
	546	for actual in $activation_string_list
	547	do
	548	for formal in $s3
	549	do
	550	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	551	done
	552	done
	553	if [[ $found = true ]]
	554	then
	555	(( iin = iin + 1 ))
	556	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	557	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	558	extin[$iin]=$s6
	559	fi
	560	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	561	then
	562	found=false
	563	for actual in $activation_string_list
	564	do
	565	for formal in $s3
	566	do
	567	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	568	done
	569	done
	570	if [[ $found = true ]]
	571	then
	572	(( iout = iout + 1 ))
	573	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	574	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	575	fi
	576	elif [[ "$s2a" != in && "$s2a" != out ]]
	577	then
	578	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	579	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	580	locat=connect; exit
	581	fi
	582	IFS="$IFSALT"
	583	fi
	584
	585	done < $fileconnection_file
	586
	587
	588
[2501]	589	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	590	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	591	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	592	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	593	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	594	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	595
	596
	597
[2380]	598	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	599	if [[ $run_coupled_model = true ]]
	600	then
	601
	602	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	603	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	604
	605	if (( $cores_ocean + $cores_atmos != $cores ))
	606	then
	607
	608	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	609	printf "\n PEs (total) : $cores"
	610	printf "\n PEs (atmosphere): $cores_atmos"
	611	printf "\n PEs (ocean) : $cores_ocean"
	612	locat=coupling; exit
	613
	614	fi
	615
	616	fi
	617
	618
	619	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	620	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	621	# FOLDER
	622	if [[ $running_in_batch_mode = true ]]
	623	then
	624
[2506]	625	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	626	then
[2506]	627	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	628	printf "\n Please check the output of the palmrun-call"
	629	printf "\n that you did on your local host."
	630	locat=SOURCES_FOR_RUN; exit
	631	fi
	632
	633	else
	634
	635	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	636	# AUTOMATIC RESTART RUN
	637	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	638	if [[ $restart_run = false ]]
	639	then
	640
	641	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	642	# THE LOCAL HOST
	643	if [[ ! -d $source_path ]]
	644	then
	645	printf "\n\n +++ source path \"$source_path\" on local host"
	646	printf "\n \"$(hostname)\" does not exist"
	647	locat=source_path; exit
	648	fi
	649
[2506]	650	rm -rf $sources_for_run_catalog
	651	mkdir -p $sources_for_run_catalog
[2380]	652
	653	if [[ "$source_list" = LM ]]
	654	then
	655
	656	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	657	source_list=""
	658	cd $source_path
	659
	660
	661	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	662	if [[ ! -d .svn ]]
	663	then
	664	printf "\n\n +++ source directory"
	665	printf "\n \"$source_path\" "
	666	printf "\n is not under control of \"subversion\"."
	667	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	668	fi
	669
	670
	671	# LIST ALL MODIFIED SOURCE CODE FILES
	672	Filenames=""
[2404]	673	svn status > tmp_svnstatus
[2380]	674	while read line
	675	do
	676	firstc=`echo $line \| cut -c1`
	677	if [[ $firstc = M \|\| $firstc = "?" ]]
	678	then
	679	Name=`echo "$line" \| cut -c8-`
	680	extension=`echo $Name \| cut -d. -f2`
	681	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	682	then
	683	Filenames="$Filenames "$Name
	684	fi
	685	fi
[2404]	686	done < tmp_svnstatus
	687	rm -rf tmp_svnstatus
[2380]	688
	689
	690	# COPY FILES TO SOURCES_FOR_RUN_...
	691	for filename in $Filenames
	692	do
[2506]	693	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	694	source_list=$source_list"$filename "
	695	done
	696
	697	cd - > /dev/null
	698
	699
	700	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	701	elif [[ "$source_list" != "" ]]
	702	then
	703
	704	cd $source_path
	705
	706	for filename in $source_list
	707	do
	708
	709	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	710	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	711	then
	712	printf "\n +++ source code file: $filename"
	713	printf "\n must not contain (\"/\") "
	714	locat=source; exit
	715	fi
	716
	717	if [[ ! -f $filename ]]
	718	then
	719	printf "\n +++ source code file: $filename"
	720	printf "\n does not exist"
	721	locat=source; exit
	722	else
[2506]	723	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	724	fi
	725
	726	done
	727
	728	cd - > /dev/null
	729
	730	fi
	731
	732	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	733	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	734	if [[ ! -f $makefile ]]
	735	then
	736	printf "\n +++ file \"$makefile\" does not exist"
	737	locat=make; exit
	738	else
[2506]	739	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	740	fi
	741
	742
	743	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	744	if [[ "$user_source_path" != "" ]]
[2380]	745	then
	746
	747	# DOES THE DIRECTORY EXIST?
[2384]	748	if [[ ! -d $user_source_path ]]
[2380]	749	then
	750
	751	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	752	printf "\n \"$user_source_path\" "
[2380]	753	printf "\n does not exist or is not a directory."
	754	printf "\n No source code will be used from this directory!\n"
[2384]	755	user_source_path=""
[2380]	756	if [[ $silent == false ]]
	757	then
	758	sleep 2
	759	fi
	760
	761	else
	762
[2384]	763	cd $user_source_path
[2380]	764	found=false
	765
	766	Names=$(ls -1 *.f90 2>&1)
	767	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	768	Names=$(ls -1 *.F90 2>&1)
	769	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	770	Names=$(ls -1 *.F 2>&1)
	771	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	772	Names=$(ls -1 *.f 2>&1)
	773	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	774	Names=$(ls -1 *.c 2>&1)
	775	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	776
	777	cd - > /dev/null
[2506]	778	cd $sources_for_run_catalog
[2380]	779
	780	# COPY MAKEFILE IF EXISTING
[2384]	781	if [[ -f $user_source_path/Makefile ]]
[2380]	782	then
	783	printf "\n\n *** user Makefile from directory"
[2384]	784	printf "\n \"$user_source_path\" is used \n"
[2380]	785	if [[ $silent == false ]]
	786	then
	787	sleep 1
	788	fi
[2384]	789	cp $user_source_path/Makefile .
[2380]	790	fi
	791
	792	for filename in $AddFilenames
	793	do
	794	if [[ -f $filename ]]
	795	then
	796	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	797	printf "\n source code directory \"$user_source_path\" "
[2380]	798	printf "\n but was also given with option \"-s\" which means that it should be taken"
	799	printf "\n from directory \"$source_path\"."
	800	locat=source; exit
	801	fi
	802
[2384]	803	cp $user_source_path/$filename .
[2380]	804	source_list="$source_list $filename"
	805
	806	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	807	if [[ $(grep -c $filename Makefile) = 0 ]]
	808	then
	809	printf "\n\n +++ user file \"$filename\" "
	810	printf "\n is not listed in Makefile \n"
	811	locat=source; exit
	812	else
	813
	814	if [[ $found = false ]]
	815	then
	816	found=true
	817	printf "\n\n *** following user file(s) added to the"
	818	printf " files to be translated:\n "
	819	fi
	820	printf "$filename "
	821	if [[ $silent == false ]]
	822	then
	823	sleep 0.5
	824	fi
	825
	826	fi
	827	done
	828	[[ $found = true ]] && printf "\n"
	829	cd - > /dev/null
	830	fi
	831	fi
	832
	833	# COPY CONFIGURATION FILES
[2506]	834	cp $config_file $sources_for_run_catalog
	835	cp $fileconnection_file $sources_for_run_catalog
[2380]	836
	837	# COPY SHELLSCRIPTS
[2506]	838	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	839	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	840
	841	fi
	842
	843	fi
	844
	845	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	846	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	847	if [[ "$global_revision" = "" ]]
	848	then
	849	global_revision=`svnversion $source_path 2>/dev/null`
	850	global_revision="Rev: $global_revision"
	851	fi
	852
	853
	854	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	855	if [[ -n $cores ]]
	856	then
	857
	858	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	859	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	860	if [[ $tasks_per_node = 0 ]]
[2380]	861	then
	862	printf "\n"
	863	printf "\n +++ option \"-T\" (tasks per node) is missing"
	864	printf "\n set -T option or define tasks_per_node in the config file"
	865	locat=tasks_per_node; (( iec = 0 )); exit
	866	fi
	867
	868	if (( cores < tasks_per_node ))
	869	then
	870	printf "\n"
	871	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	872	printf "\n given values: -T $tasks_per_node -X $cores"
	873	locat=tasks_per_node; (( iec = 0 )); exit
	874	fi
	875
	876	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	877	(( mpi_tasks = cores / threads_per_task ))
	878	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	879	(( ii = cores / tasks_per_node ))
	880	(( remaining_cores = cores - ii * tasks_per_node ))
	881	if (( remaining_cores > 0 ))
	882	then
	883	printf "\n"
	884	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	885	printf "\n divisor of the total number of cores (option \"-X\")"
	886	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	887	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	888	(( nodes = nodes + 1 ))
	889	fi
	890
	891	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	892	if [[ "$tasks_per_node" != "" ]]
	893	then
	894	TOPT="-T $tasks_per_node"
	895	fi
	896
	897	fi
	898
	899
	900	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	901	if [[ "$maximum_parallel_io_streams" = "" ]]
	902	then
	903	maximum_parallel_io_streams=$cores
	904	fi
	905
	906
	907	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	908	if [[ "$scp_port" != "" ]]
	909	then
	910	PORTOPT="-P $scp_port"
	911	SSH_PORTOPT="-p $scp_port"
	912	fi
	913
	914
	915	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	916	# CONFIG-FILE
	917	if [[ "$ssh_key" != "" ]]
	918	then
	919	ssh_key="-i $HOME/.ssh/$ssh_key"
	920	fi
	921
	922
	923	# SET QUEUE, IF NOT GIVEN
	924	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	925	then
	926
	927	if [[ $queue = none && "$defaultqueue" = "" ]]
	928	then
	929	printf "\n"
	930	printf "\n +++ no default queue given in configuration file and no queue"
	931	printf "\n given with option -q"
	932	fi
	933	if [[ $queue = none ]]
	934	then
	935	queue=$defaultqueue
	936	fi
	937
	938	fi
	939
	940
	941	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	942	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	943	(( i = 0 ))
	944	while (( i < iin ))
	945	do
	946	(( i = i + 1 ))
	947	(( maxcycle = 0 ))
	948
	949	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	950	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	951	if [[ "${actionin[$i]}" = di ]]
	952	then
	953	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	954	# HOST ONLY
	955	eval filename=${pathin[$i]}/${endin[$i]}
	956	else
	957	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	958	# HOST ONLY
	959	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	960	fi
	961	eval pathname=${pathin[$i]}
	962
	963	# CHECK IF FILE EXISTS
	964	if ! ls $filename* 1>/dev/null 2>&1
	965	then
	966
	967	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	968	if [[ "${transin[$i]}" != "locopt" ]]
	969	then
	970	printf "\n\n +++ INPUT-file: "
	971	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	972	then
	973	printf "\n $filename"
	974	else
	975	printf "\n $filename.${extin[$i]}"
	976	fi
	977	printf "\n does not exist\n"
	978	locat=input; exit
	979	else
	980	transin[$i]="unavailable"
	981	fi
	982	else
	983
	984	# DETERMINE THE FILE'S CYCLE NUMBER
	985	ls -1 -d $filename > filelist 2>/dev/null
	986	ls -1 -d $filename.* >> filelist 2>/dev/null
	987	while read line
	988	do
	989	# filename without path (i.e. after the last "/")
	990	basefilename=$(basename ${line})
	991
	992	# check if there is an extension
	993	extension=${basefilename##*.}
	994	if [[ "$extension" = "$extin[$i]" ]]
	995	then
	996	basefilename=${basefilename&.*}
	997	fi
	998
	999	# check for an existing cycle number
	1000	cycle=${basefilename##*.}
	1001	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1002	then
	1003	(( icycle = $cycle ))
	1004	else
	1005	(( icycle = 0 ))
	1006	fi
	1007
	1008	if (( icycle > maxcycle ))
	1009	then
	1010	(( maxcycle = icycle ))
	1011	fi
	1012
	1013	done <filelist
	1014	rm filelist
	1015
	1016	# APPEND CYCLE NUMBER TO FILENAME
	1017	if (( maxcycle > 0 ))
	1018	then
	1019	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1020	then
	1021	filename=${filename}.$maxcycle.${extin[$i]}
	1022	else
	1023	filename=${filename}.$maxcycle
	1024	fi
	1025	else
	1026	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1027	then
	1028	filename=${filename}.${extin[$i]}
	1029	fi
	1030	fi
	1031
	1032	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1033	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1034	absnamein[$i]=$filename
	1035	if (( maxcycle > 0 ))
	1036	then
	1037	if [[ "${actionin[$i]}" = di ]]
	1038	then
	1039	frelin[$i]=${endin[$i]}.$maxcycle
	1040	else
	1041	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1042	fi
	1043	else
	1044	if [[ "${actionin[$i]}" = di ]]
	1045	then
	1046	frelin[$i]=${endin[$i]}
	1047	else
	1048	frelin[$i]=${fname}${endin[$i]}
	1049	fi
	1050	fi
	1051
	1052	fi
	1053	done
	1054
	1055
	1056	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1057	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1058	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1059	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1060	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1061	# REMOTE HOST)
	1062	(( i = 0 ))
	1063	while (( i < iout ))
	1064	do
	1065	(( i = i + 1 ))
	1066	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1067	then
	1068	if [[ "${actionout[$i]}" = tr ]]
	1069	then
	1070	actionout[$i]=""
	1071	elif [[ "${actionout[$i]}" = trpe ]]
	1072	then
	1073	actionout[$i]=pe
	1074	elif [[ "${actionout[$i]}" = tra ]]
	1075	then
	1076	actionout[$i]=a
	1077	fi
	1078	(( maxcycle = 0 ))
	1079	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1080	eval catalogname=${pathout[$i]}
	1081	if ! ls $filename* 1>/dev/null 2>&1
	1082	then
	1083
	1084	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1085	if cat /dev/null > $filename
	1086	then
	1087	rm $filename
	1088	else
	1089
	1090	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1091	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1092	if [[ ! -d $catalogname ]]
	1093	then
	1094	if mkdir -p $catalogname
	1095	then
	1096	printf "\n\n *** directory:"
	1097	printf "\n $catalogname"
	1098	printf "\n was created\n"
	1099	else
	1100	printf "\n\n +++ OUTPUT-file:"
	1101	printf "\n $filename"
	1102	printf "\n cannot be created, because directory does not exist"
	1103	printf "\n and cannot be created either"
	1104	printf "\n"
	1105	locat=output ; exit
	1106	fi 2>/dev/null
	1107	else
	1108	printf "\n\n +++ OUTPUT-file:"
	1109	printf "\n $filename"
	1110	printf "\n cannot be created, although directory exists"
	1111	printf "\n"
	1112	locat=output ; exit
	1113	fi
	1114	fi 2>/dev/null
	1115	else
	1116
	1117	# DETERMINE THE CYCLE NUMBER
	1118	ls -1 -d $filename > filelist 2>/dev/null
	1119	ls -1 -d $filename.* >> filelist 2>/dev/null
	1120	while read line
	1121	do
	1122
	1123	# filename without path (i.e. after the last "/")
	1124	basefilename=$(basename ${line})
	1125
	1126	# check if there is an extension
	1127	extension=${basefilename##*.}
	1128	if [[ "$extension" = "${extout[$i]}" ]]
	1129	then
	1130	basefilename=${basefilename%.*}
	1131	fi
	1132
	1133	# check for an existing cycle number
	1134	cycle=${basefilename##*.}
	1135	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1136	then
	1137	(( icycle = $cycle + 1 ))
	1138	else
	1139	(( icycle = 1 ))
	1140	fi
	1141
	1142	if (( icycle > maxcycle ))
	1143	then
	1144	(( maxcycle = icycle ))
	1145	fi
	1146
	1147	done <filelist
	1148	rm filelist
	1149	fi
	1150
	1151	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1152	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1153	if [[ "${actionout[$i]}" != a ]]
	1154	then
	1155	if (( maxcycle > 0 ))
	1156	then
	1157	filename_tmp=${filename}.$maxcycle
	1158	if cat /dev/null > $filename_tmp
	1159	then
	1160	rm $filename_tmp
	1161	else
	1162	printf "\n +++ OUTPUT-file:"
	1163	printf "\n $filename_tmp"
	1164	printf "\n cannot be created"
	1165	locat=output ; exit
	1166	fi
	1167	fi
	1168	else
	1169	(( maxcycle = maxcycle - 1 ))
	1170	fi
	1171
	1172	(( cycnum[$i] = maxcycle ))
	1173	pathout[$i]=$filename
	1174
	1175	fi
	1176	done
	1177
	1178
	1179	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1180	if [[ $running_in_batch_mode = false ]]
	1181	then
	1182	run_id=$RANDOM
	1183	job_id=${fname}.$run_id
	1184
[2404]	1185	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1186	fi
	1187
	1188
	1189	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1190	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1191	then
	1192
	1193	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1194	if [[ $ibd = 0 ]]
	1195	then
	1196	printf "\n"
	1197	printf "\n +++ no batch directives found in configuration file"
	1198	locat=config_file_batch_directives; (( iec = 0 )); exit
	1199	fi
	1200
	1201	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1202	done=false
[2384]	1203	cputime=$cpumax
[2380]	1204	while [[ $done = false ]]
	1205	do
[2384]	1206	if (( cputime == 0 ))
[2380]	1207	then
	1208	printf "\n +++ cpu-time is undefined"
	1209	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1210	printf "\n >>> "
[2384]	1211	read cputime 1>/dev/null 2>&1
[2380]	1212	else
	1213	done=true
	1214	fi
	1215	done
[2420]	1216	cpumax=$cputime
[2380]	1217
	1218	# CHECK THE MEMORY DEMAND
	1219	done=false
	1220	while [[ $done = false ]]
	1221	do
	1222	if (( memory == 0 ))
	1223	then
	1224	printf "\n +++ memory demand is undefined"
	1225	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1226	printf "\n >>> "
	1227	read memory 1>/dev/null 2>&1
	1228	else
	1229	done=true
	1230	fi
	1231	done
	1232
	1233	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1234	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1235	then
	1236	while [[ -z $remote_username ]]
	1237	do
[2420]	1238	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1239	printf "\n >>> Please type username:"
	1240	printf "\n >>> "
	1241	read remote_username
	1242	done
	1243	fi
	1244
	1245	else
	1246
[2420]	1247	if [[ $running_in_batch_mode = false ]]
	1248	then
	1249	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1250	cpumax=$cputime
	1251	else
	1252	cputime=$cpumax
	1253	fi
[2380]	1254
	1255	fi
	1256
	1257
	1258	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1259	(( cpu_hours = cputime / 3600 ))
	1260	(( resttime = cputime - cpu_hours * 3600 ))
	1261	(( cpu_minutes = resttime / 60 ))
	1262	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1263	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1264
	1265
	1266	# OUTPUT OF THE PALMRUN-HEADER
	1267	calltime=$(date)
	1268	printf "\n"
	1269	printf "#------------------------------------------------------------------------# \n"
	1270	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1271	printf "\| \| \n"
	1272	column1="called on:"; column2=$(hostname)
	1273	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1274	if [[ $create_remote_batch_job = true ]]
	1275	then
[2506]	1276	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1277	else
	1278	if [[ $running_on_remote = true ]]
	1279	then
[2506]	1280	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1281	else
[2506]	1282	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1283	fi
	1284	fi
	1285	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1286
	1287	column1="running in:"
	1288	if [[ $running_in_batch_mode = true ]]
	1289	then
	1290	column2="batch job mode"
	1291	else
	1292	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1293	then
	1294	column2="job creation mode"
	1295	else
	1296	column2="interactive run mode"
	1297	fi
	1298	fi
	1299	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1300
[2479]	1301	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1302	then
[2480]	1303	if [[ "$project_account" != "" ]]
[2479]	1304	then
	1305	column1="project account number:"
	1306	column2="$project_account"
	1307	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1308	fi
	1309	fi
	1310
[2380]	1311	if [[ -n $cores ]]
	1312	then
	1313	if [[ $run_coupled_model = false ]]
	1314	then
	1315	column1="number of cores:"; column2=$cores
	1316	else
	1317	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1318	fi
	1319	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1320	fi
	1321	if [[ -n $tasks_per_node ]]
	1322	then
	1323	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1324	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1325	if (( remaining_cores > 0 ))
	1326	then
	1327	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1328	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1329	fi
	1330	fi
	1331	if [[ $maximum_parallel_io_streams != $cores ]]
	1332	then
	1333	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1334	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1335	fi
	1336	if [[ $use_openmp = true ]]
	1337	then
	1338	column1="threads per task:"; column2="$threads_per_task"
	1339	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1340	fi
[2384]	1341	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1342	then
[2506]	1343	column1="memory demand / PE":; column2="$memory MB"
	1344	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1345	column1="job cpu time (h:m:s):"; column2="$timestring"
	1346	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1347	fi
[2380]	1348	printf "\| \| \n"
	1349	if [[ "$source_list" != "" ]]
	1350	then
	1351	if [[ "$make_options" != "" ]]
	1352	then
	1353	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1354	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1355	line=$(echo "$make_options" \| cut -c46-)
	1356	while [[ "$line" != "" ]]
	1357	do
	1358	column1=""
	1359	column2=$(echo "$line" \| cut -c-45)
	1360	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1361	line=$(echo "$line" \| cut -c46-)
	1362	done
	1363	fi
	1364	fi
	1365
	1366	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1367	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1368	line=$(echo "$cpp_options" \| cut -c46-)
	1369	while [[ "$line" != "" ]]
	1370	do
	1371	column1=""
	1372	column2=$(echo "$line" \| cut -c-45)
	1373	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1374	line=$(echo "$line" \| cut -c46-)
	1375	done
	1376
	1377	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1378	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1379	line=$(echo "$compiler_options" \| cut -c46-)
	1380	while [[ "$line" != "" ]]
	1381	do
	1382	column1=""
	1383	column2=$(echo "$line" \| cut -c-45)
	1384	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1385	line=$(echo "$line" \| cut -c46-)
	1386	done
	1387
[2388]	1388	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1389	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1390	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1391	while [[ "$line" != "" ]]
	1392	do
	1393	column1=""
	1394	column2=$(echo "$line" \| cut -c-45)
	1395	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1396	line=$(echo "$line" \| cut -c46-)
	1397	done
	1398
	1399	if [[ "$login_init_cmd" != "" ]]
	1400	then
	1401	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1402	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1403	line=$(echo "$login_init_cmd" \| cut -c46-)
	1404	while [[ "$line" != "" ]]
	1405	do
	1406	column1=""
	1407	column2=$(echo "$line" \| cut -c-45)
	1408	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1409	line=$(echo "$line" \| cut -c46-)
	1410	done
	1411	fi
	1412
	1413	if [[ "$module_commands" != "" ]]
	1414	then
	1415	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1416	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1417	line=$(echo "$module_commands" \| cut -c46-)
	1418	while [[ "$line" != "" ]]
	1419	do
	1420	column1=""
	1421	column2=$(echo "$line" \| cut -c-45)
	1422	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1423	line=$(echo "$line" \| cut -c46-)
	1424	done
	1425	fi
	1426	printf "\| \| \n"
	1427	column1="base name of files:"; column2=$fname
	1428	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1429	column1="activation string list:"; column2=$(echo $activation_string_list)
	1430	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1431
	1432	if [[ "$ocean_file_appendix" = true ]]
	1433	then
	1434	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1435	fi
	1436
	1437	if [[ "$source_list" != "" ]]
	1438	then
	1439	printf "\| \| \n"
	1440	printf "\| Files to be compiled: \| \n"
	1441	line=$source_list
	1442	while [[ "$line" != "" ]]
	1443	do
	1444	linestart=$(echo $line \| cut -c-70)
	1445	printf "\| %-70s \| \n" "$linestart"
	1446	line=$(echo "$line" \| cut -c71-)
	1447	done
	1448	fi
	1449	printf "#------------------------------------------------------------------------#"
	1450
	1451
	1452
	1453	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1454	if [[ $do_trace = true ]]
	1455	then
	1456	(( i = 0 ))
	1457	while (( i < iin ))
	1458	do
	1459	(( i = i + 1 ))
	1460	if (( i == 1 ))
	1461	then
	1462	printf "\n\n >>> INPUT-file assignments:\n"
	1463	fi
	1464	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1465	done
	1466	(( i = 0 ))
	1467	while (( i < iout ))
	1468	do
	1469	(( i = i + 1 ))
	1470	if (( i == 1 ))
	1471	then
	1472	printf "\n\n >>> OUTPUT-file assignments:\n"
	1473	fi
	1474	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1475	done
	1476	(( i = 0 ))
	1477	while (( i < iic ))
	1478	do
	1479	(( i = i + 1 ))
	1480	if (( i == 1 ))
	1481	then
	1482	printf "\n\n >>> INPUT-commands:\n"
	1483	fi
	1484	printf "\n ${in_command[$i]}"
	1485	done
	1486	(( i = 0 ))
	1487	while (( i < ioc ))
	1488	do
	1489	(( i = i + 1 ))
	1490	if (( i == 1 ))
	1491	then
	1492	printf "\n\n >>> OUTPUT-commands:\n"
	1493	fi
	1494	printf "\n ${out_command[$i]}"
	1495	done
	1496	fi
	1497
	1498	# QUERY FOR CONTINUE
	1499	if [[ $silent = false && $running_in_batch_mode = false ]]
	1500	then
	1501	antwort=dummy
	1502	printf "\n\n"
	1503	printf " >>> everything o.k. (y/n) ? "
	1504	while read antwort
	1505	do
	1506	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1507	then
	1508	printf " >>> everything o.k. (y/n) ? "
	1509	else
	1510	break
	1511	fi
	1512	done
	1513	if [[ $antwort = n \|\| $antwort = N ]]
	1514	then
	1515	locat=user_abort; (( iec = 0 )); exit
	1516	fi
	1517	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1518	then
	1519	printf " *** batch-job will be created and submitted"
	1520	else
	1521	printf " *** PALMRUN will now continue to execute on this machine"
	1522	fi
	1523	fi
	1524
	1525
	1526
	1527	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1528	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1529	then
	1530
	1531	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1532	then
	1533	printf "\n\n *** creating executable and other sources for the remote host"
	1534	else
	1535	printf "\n\n *** creating executable and other sources for the local host"
	1536	fi
	1537
[2422]	1538	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1539	# IT SHALL BE CREATED
	1540	ask_for_make_depository=false
	1541	if [[ $create_remote_batch_job = true ]]
	1542	then
	1543
	1544	line=`grep %base_directory $config_file`
[2506]	1545	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1546	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]	1547
[2506]	1548	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1549	then
	1550	printf "\n\n +++ make depository \"${make_depository}\""
	1551	printf "\n on remote host not found!"
	1552	ask_for_make_depository=true
	1553	fi
[2506]	1554	rm ${host_configuration}_last_make_protokoll
[2422]	1555
	1556	else
	1557
	1558	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1559	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1560	if [[ ! -d ${make_depository} ]]
	1561	then
	1562	printf "\n\n +++ make depository \"${make_depository}\""
	1563	printf "\n on local host not found!"
	1564	ask_for_make_depository=true
	1565	fi
	1566
	1567	fi
	1568
	1569	if [[ $ask_for_make_depository = true ]]
	1570	then
	1571
	1572	antwort=dummy
	1573	printf "\n\n"
	1574	printf " >>> Create a new one (y/n) ? "
	1575	while read antwort
	1576	do
	1577	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1578	then
	1579	printf " >>> Create a new one (y/n) ? "
	1580	else
	1581	break
	1582	fi
	1583	done
	1584	if [[ $antwort = n \|\| $antwort = N ]]
	1585	then
	1586	locat=user_abort; (( iec = 0 )); exit
	1587	fi
	1588
[2506]	1589	palmbuild -v -h $host_configuration
[2422]	1590
	1591	if [[ $? != 0 ]]
	1592	then
	1593
	1594	# ABORT IN CASE OF COMPILATION PROBLEMS
	1595	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1596	locat=make_depository
	1597	exit
	1598	else
	1599	echo " *** now continue with creating executable and other sources"
	1600	fi
	1601
	1602	fi
	1603
[2506]	1604	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1605
	1606	if [[ $? != 0 ]]
	1607	then
	1608
	1609	# ABORT IN CASE OF COMPILATION PROBLEMS
	1610	printf "\n +++ error while creating executable and/or other sources"
	1611	locat=execution
[2506]	1612	rm -rf $sources_for_run_catalog
[2380]	1613	exit
	1614
	1615	else
	1616
	1617	printf "\n$dashes\n *** executable and other sources created\n"
[2506]	1618	rm -rf $sources_for_run_catalog
[2380]	1619
	1620	fi
	1621
	1622	fi
	1623
	1624
	1625	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1626	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1627	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1628	then
	1629
	1630	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1631	if [[ $running_in_batch_mode = false ]]
	1632	then
	1633	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1634	# FOLDER
	1635	mkdir -p $TEMPDIR
	1636	chmod go+rx $TEMPDIR
	1637	tmpcreate=true
	1638	cd $TEMPDIR
[2506]	1639	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $TEMPDIR
[2380]	1640	printf "\n *** changed to temporary directory: $TEMPDIR"
	1641
	1642	else
	1643
	1644	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1645	printf "\n *** running in temporary directory: $TEMPDIR"
	1646
	1647	fi
	1648
	1649
	1650	# PROVIDE THE INPUT FILES
	1651	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1652	(( i = 0 ))
	1653	while (( i < iin ))
	1654	do
	1655	(( i = i + 1 ))
	1656	if (( i == 1 ))
	1657	then
	1658	printf "\n\n *** providing INPUT-files:\n$dashes"
	1659	fi
	1660
	1661
	1662	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1663	if [[ "${transin[$i]}" = unavailable ]]
	1664	then
	1665	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1666	then
	1667	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1668	printf "\n is not available!"
	1669	else
	1670	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1671	printf "\n is not available!"
	1672	fi
	1673	continue
	1674	fi
	1675
	1676	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1677	files_for_cores=false; filetype=file
	1678	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1679	then
	1680	files_for_cores=true; filetype=files
	1681	actionin[$i]=""
	1682	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1683	then
	1684	actionin[$i]=""
	1685	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1686	then
	1687	files_for_cores=true; filetype=files
	1688	actionin[$i]="ln"
	1689	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1690	then
	1691	actionin[$i]="ln"
	1692	fi
	1693
	1694	if [[ $files_for_cores = true ]]
	1695	then
	1696	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1697	else
	1698	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1699	fi
	1700
	1701	# INPUT-FILES TO BE LINKED
	1702	if [[ "${actionin[$i]}" = ln ]]
	1703	then
	1704
	1705	printf "\n $filetype will be linked"
	1706	if [[ $files_for_cores = false ]]
	1707	then
	1708	if [[ -f "${absnamein[$i]}" ]]
	1709	then
	1710	ln ${absnamein[$i]} ${localin[$i]}
	1711	got_tmp[$i]=true
	1712	fi
	1713	else
	1714	if [[ -d "${absnamein[$i]}" ]]
	1715	then
[2396]	1716	mkdir -p ${localin[$i]}
[2380]	1717	cd ${absnamein[$i]}
	1718	for file in $(ls *)
	1719	do
	1720	ln $file $TEMPDIR/${localin[$i]}
	1721	done >\|/dev/null 2>&1
	1722	cd $TEMPDIR
	1723	fi
	1724
	1725	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1726	if [[ ! -f "${localin[$i]}/_000000" ]]
	1727	then
	1728	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1729	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1730	fi
	1731
	1732	got_tmp[$i]=true
	1733	fi
	1734	fi
	1735
	1736	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1737	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1738	then
	1739
	1740	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1741	then
	1742
	1743	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1744	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1745	printf "\n file will be provided for $cores processors"
[2396]	1746	mkdir -p ${localin[$i]}
[2380]	1747	ival=$cores
	1748	(( ii = 0 ))
	1749	while (( ii <= ival-1 ))
	1750	do
	1751	if (( ii < 10 ))
	1752	then
	1753	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1754	elif (( ii < 100 ))
	1755	then
	1756	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1757	elif (( ii < 1000 ))
	1758	then
	1759	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1760	else
	1761	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1762	fi
	1763	(( ii = ii + 1 ))
	1764	done
	1765
	1766	else
	1767
	1768	if [[ $files_for_cores = true ]]
	1769	then
	1770
	1771	# PROVIDE FILES FOR EACH CORE
	1772	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1773	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1774	printf "\n providing $cores files for the respective cores"
[2396]	1775	mkdir -p ${localin[$i]}
[2380]	1776	if [[ $link_local_input = true ]]
	1777	then
	1778	printf " files will be linked\n"
	1779	cd ${absnamein[$i]}
	1780	for file in $(ls *)
	1781	do
	1782	ln -f $file ${localin[$i]}
	1783	done
	1784	cd $TEMPDIR
	1785	fi
	1786
	1787	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1788	if [[ ! -f "${localin[$i]}/_000000" ]]
	1789	then
	1790	if [[ $link_local_input = true ]]
	1791	then
	1792	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1793	fi
	1794	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1795	fi
	1796
	1797	else
	1798
	1799	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1800	if [[ $link_local_input = true ]]
	1801	then
	1802	printf " file will be linked\n"
	1803	ln -f ${absnamein[$i]} ${localin[$i]}
	1804	fi
	1805	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1806	if [[ ! -f "${localin[$i]}" ]]
	1807	then
	1808	if [[ $link_local_input = true ]]
	1809	then
	1810	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1811	fi
	1812	cp ${absnamein[$i]} ${localin[$i]}
	1813	fi
	1814	fi
	1815	fi
	1816	fi
	1817
	1818	done
	1819	if (( i != 0 ))
	1820	then
	1821	printf "\n$dashes\n *** all INPUT-files provided \n"
	1822	fi
	1823
	1824
	1825	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1826	(( i = 0 ))
	1827	while (( i < iic ))
	1828	do
	1829	(( i = i + 1 ))
	1830	if (( i == 1 ))
	1831	then
	1832	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1833	fi
	1834	printf "\n >>> ${in_command[$i]}"
	1835	eval ${in_command[$i]}
	1836	if (( i == iic ))
	1837	then
	1838	printf "\n$dashes\n"
	1839	fi
	1840	done
	1841
	1842
	1843	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1844	# (FILE ENVPAR WILL BE READ BY PALM)
	1845	cat > ENVPAR << EOF
[2506]	1846	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	1847	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1848	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1849	maximum_cpu_time_allowed = ${cpumax}.,
	1850	revision = '$global_revision',
	1851	batch_job = .${running_in_batch_mode}. /
	1852
	1853	EOF
	1854
	1855
	1856	# STARTING THE EXECUTABLE
	1857	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1858	PATH=$PATH:$TEMPDIR
	1859
	1860
	1861	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1862	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1863	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1864	eval line=\"$line\"
	1865	execute_command="$line"
	1866
	1867
	1868	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1869	eval line2=\"$line2\"
	1870	execute_command_for_combine="$line2"
	1871
	1872
	1873	# PROVIDE A HOSTFILE, IF REQUIRED
	1874	if [[ "$hostfile" != "" ]]
	1875	then
	1876
	1877	if [[ $hostfile = auto ]]
	1878	then
	1879	# CREATE A NEW HOSTFILE
	1880	(( ii = 1 ))
	1881	while (( ii <= cores / threads_per_task ))
	1882	do
	1883	echo $(hostname) >> hostfile
	1884	(( ii = ii + 1 ))
	1885	done
	1886	if (( cores / threads_per_task == 0 ))
	1887	then
	1888	echo $(hostname) >> hostfile
	1889	fi
	1890
	1891	else
	1892	cp $hostfile hostfile
	1893	fi
	1894	eval line=\"`head -n $ii hostfile`\"
	1895	printf "\n *** running on: $line"
	1896	fi
	1897
	1898
	1899
	1900	# SET THE NUMBER OF OPENMP-THREADS
	1901	if [[ $use_openmp = true ]]
	1902	then
	1903	export OMP_NUM_THREADS=$threads_per_task
	1904	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1905	else
	1906	export OMP_NUM_THREADS=1
	1907	fi
	1908
	1909
	1910	# PROVIDE DATA FOR
	1911	if [[ $run_coupled_model = false ]]
	1912	then
	1913	if [[ "$ocean_file_appendix" = true ]]
	1914	then
	1915	echo "precursor_ocean" > coupling_steering
	1916	else
	1917	echo "precursor_atmos" > coupling_steering
	1918	fi
	1919	else
	1920	(( iia = $cores_atmos / $threads_per_task ))
	1921	(( iio = $cores_ocean / $threads_per_task ))
	1922	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1923	printf "\n\n"
	1924	echo "coupled_run $iia $iio" > coupling_steering
	1925	fi
	1926
	1927	printf "\n *** execute command:"
	1928	printf "\n \"$execute_command\" \n\n"
	1929
	1930	$execute_command < coupling_steering
	1931
	1932	if [[ $? != 0 ]]
	1933	then
	1934
	1935	# ABORT IN CASE OF RUNTIME ERRORS
	1936	printf "\n +++ runtime error occured"
	1937	locat=execution
	1938	exit
	1939
	1940	else
	1941
	1942	printf "\n$dashes\n *** execution finished \n"
	1943
	1944	fi
	1945
	1946
	1947	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1948	# BY EACH CORE INTO ONE FILE
	1949	if [[ ! -f combine_plot_fields.x ]]
	1950	then
	1951
	1952	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1953	printf "\n 2d- and/or 3d-data may be incomplete!"
	1954	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1955
	1956	elif [[ "$combine_plot_fields" == true ]]
	1957	then
	1958
	1959	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1960	$execute_command_for_combine
	1961
	1962	else
	1963
	1964	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1965	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1966	# ??? koennen wir das streichen ???
	1967	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1968	fi
	1969
	1970
	1971
	1972	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1973	(( i = 0 ))
	1974	while (( i < ioc ))
	1975	do
	1976	(( i = i + 1 ))
	1977	if (( i == 1 ))
	1978	then
	1979	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1980	fi
	1981	printf "\n >>> ${out_command[$i]}"
	1982	eval ${out_command[$i]}
	1983	if (( i == ioc ))
	1984	then
	1985	printf "\n$dashes\n"
	1986	fi
	1987	done
	1988
	1989
	1990	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1991	if [[ $do_trace = true ]]
	1992	then
	1993	printf "\n\n"
	1994	ls -al
	1995	fi
	1996
	1997
	1998	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1999	(( i = 0 ))
	2000	while (( i < iout ))
	2001	do
	2002	(( i = i + 1 ))
	2003	if (( i == 1 ))
	2004	then
	2005	printf "\n\n *** saving OUTPUT-files:"
	2006
	2007	# GET RUN NUMBER ASSIGNED BY PALM
	2008	if [[ -f RUN_NUMBER ]]
	2009	then
	2010	read run_number < RUN_NUMBER
	2011	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2012	usecycle_option="-U $run_number"
	2013	else
	2014	run_number=0
	2015	usecycle_option=""
	2016	fi
	2017	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2018	then
[2404]	2019	printf "\n *** in case of SCP transfers to local host"
	2020	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2021	fi
	2022	printf "\n$dashes"
	2023	fi
	2024
	2025	# ADD CYCLE NUMBER TO FILENAME
	2026	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2027	then
	2028
	2029	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2030	if [[ "${actionout[$i]}" != "a" ]]
	2031	then
	2032	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2033	# WITH AN EXISTING CYCLE NUMBER
	2034	if (( run_number >= cycnum[$i] ))
	2035	then
	2036	(( cycnum[$i] = run_number ))
	2037	else
	2038	if (( run_number > 0 ))
	2039	then
	2040	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2041	fi
	2042	fi
	2043	fi
	2044	if (( cycnum[$i] > 0 ))
	2045	then
	2046	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2047	fi
	2048	fi
	2049
	2050	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2051	files_for_cores=false; filetype=file
	2052	link_local_output=false
	2053	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2054	then
	2055	files_for_cores=true; filetype=directory
	2056	actionout[$i]=""
	2057	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2058	then
	2059	actionout[$i]=""
	2060	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2061	then
	2062	files_for_cores=true; filetype=directory
	2063	link_local_output=true
	2064	actionout[$i]=""
	2065	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2066	then
	2067	link_local_output
	2068	actionout[$i]=""
	2069	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2070	then
	2071	files_for_cores=true; filetype=directory
	2072	actionout[$i]="tr"
	2073	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2074	then
	2075	actionout[$i]="tr"
	2076	fi
	2077
	2078	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2079	then
	2080	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2081	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2082	then
	2083	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2084	else
	2085
	2086
	2087	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2088	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2089	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2090	then
	2091	if [[ $running_on_remote = true ]]
	2092	then
	2093
	2094	# SET OPTIONS FOR TRANSFER
	2095	if [[ "${actionout[$i]}" = tr ]]
	2096	then
	2097	if [[ $files_for_cores = false ]]
	2098	then
	2099	catalog_option=""
	2100	catalog_string=""
	2101	else
	2102	catalog_option="-c"
	2103	catalog_string="/"
	2104	fi
	2105	append_option=""
	2106	append_string=""
	2107	else
	2108	append_option="-A"
	2109	append_string="append"
	2110	fi
	2111
	2112	transfer_failed=false
	2113	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2114	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2115
	2116	# TRANSFER VIA SCP
	2117	if [[ "$remote_loginnode" != "" ]]
	2118	then
[2506]	2119	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]	2120	else
[2506]	2121	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]	2122	fi
	2123	[[ $? != 0 ]] && transfer_failed=true
	2124
	2125
	2126	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2127	if [[ $transfer_failed = true ]]
	2128	then
	2129	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2130	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2131
	2132	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2133	eval local_catalog=${pathout[$i]}
	2134	if [[ ! -d $local_catalog ]]
	2135	then
	2136	printf " *** local directory does not exist. Trying to create:\n"
	2137	printf " $local_catalog \n"
	2138	mkdir -p $local_catalog
	2139	fi
[2506]	2140	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2141	transfer_problems=true
	2142	fi
	2143
	2144	else
	2145
	2146	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2147	# BE COPIED OR APPENDED ON THIS MACHINE
	2148	if [[ "${actionout[$i]}" = tr ]]
	2149	then
	2150	actionout[$i]=""
	2151	else
	2152	actionout[$i]="a"
	2153	fi
	2154	fi
	2155	fi
	2156
	2157
	2158	# APPEND ON THIS MACHINE
	2159	if [[ "${actionout[$i]}" = "a" ]]
	2160	then
	2161	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2162	then
	2163	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2164	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2165	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2166	else
	2167	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2168	printf "\n ${pathout[$i]}\n"
	2169	cat ${localout[$i]} >> ${pathout[$i]}
	2170	fi
	2171	fi
	2172
	2173	# COPY ON THIS MACHINE
	2174	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2175	# ON DIFFERENT FILE-SYSTEMS
	2176	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2177	then
	2178
	2179	# COPY IN CASE OF RUNS ON SINGLE CORES
	2180	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2181	then
	2182	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2183	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2184	if [[ $link_local_output = true ]]
	2185	then
	2186	printf " file will be linked\n"
	2187	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2188	fi
	2189	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2190	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2191	then
	2192	if [[ $link_local_output = true ]]
	2193	then
	2194	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2195	fi
	2196	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2197	else
	2198	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2199	fi
	2200	else
	2201	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2202	printf "\n ${pathout[$i]}\n"
	2203	if [[ $link_local_output = true ]]
	2204	then
	2205	printf " file will be linked\n"
	2206	ln -f ${localout[$i]} ${pathout[$i]}
	2207	fi
	2208	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2209	if [[ ! -f "${pathout[$i]}" ]]
	2210	then
	2211	if [[ $link_local_output = true ]]
	2212	then
	2213	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2214	fi
	2215	cp ${localout[$i]} ${pathout[$i]}
	2216	else
	2217	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2218	fi
	2219	fi
	2220
	2221	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2222	then
	2223
	2224	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2225	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2226	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2227	printf "\n ${pathout[$i]}\n"
	2228	if [[ $link_local_output = true ]]
	2229	then
	2230	printf " files will be linked\n"
[2396]	2231	mkdir -p ${pathout[$i]}
[2380]	2232	cd ${localout[$i]}
	2233	for file in $(ls *)
	2234	do
	2235	ln -f $file ${pathout[$i]}
	2236	done >\|/dev/null 2>&1
	2237	cd $TEMPDIR
	2238	fi
	2239
	2240	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2241	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2242	then
	2243	if [[ $link_local_output = true ]]
	2244	then
	2245	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2246	fi
	2247	cp -r ${localout[$i]}/* ${pathout[$i]}
	2248	fi
	2249
	2250	fi
	2251	fi
	2252	done
	2253
	2254	if (( i != 0 ))
	2255	then
	2256	if [[ $transfer_problems = true ]]
	2257	then
	2258	printf "\n$dashes\n *** OUTPUT-files saved"
	2259	printf "\n +++ WARNING: some data transfers failed! \n"
	2260	else
	2261	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2262	fi
	2263	fi
	2264
	2265
	2266	# IF REQUIRED, START A RESTART-JOB
	2267	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2268	if [[ -f CONTINUE_RUN ]]
	2269	then
	2270
	2271	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2272	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2273	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2274	# -b START A BATCH JOB
	2275	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2276	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2277	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2278
	2279
	2280	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2281	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2282	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2283	then
[2381]	2284	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2285	fi
	2286
	2287
	2288	# START THE RESTART-JOB
	2289	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2290	echo " $prc"
	2291	printf "\n$dashes\n"
	2292	if [[ $running_on_remote = true ]]
	2293	then
	2294
	2295	echo "*** ssh will be used to initiate restart-runs!"
	2296	echo " return_address=\"$return_address\" "
	2297	echo " return_username=\"$local_username\" "
	2298
	2299	if [[ "$remote_loginnode" != "" ]]
	2300	then
[2420]	2301	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]	2302	else
[2420]	2303	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2304	fi
	2305
	2306	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2307	sleep 30
	2308
	2309	else
	2310
	2311	# START THE RESTART JOB ON THE LOCAL HOST
	2312	eval $prc # THE ' MUST BE EVALUATED
	2313	cd - > /dev/null
	2314
	2315	fi
	2316	printf "\n$dashes\n *** restart-run initiated \n"
	2317
	2318
	2319	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2320	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2321	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2322	# MAY BE VERY HUGE)
	2323	(( i = 0 ))
	2324	while (( i < iin ))
	2325	do
	2326	(( i = i + 1 ))
	2327	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2328	then
	2329	rm -r ${absnamein[$i]}
	2330	fi
	2331	done
	2332
	2333	fi
	2334
	2335
	2336	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2337	cd $HOME
	2338	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2339
	2340
	2341	else
	2342
	2343
	2344	# PREPARING ACTIONS,
	2345	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2346
	2347	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2348	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2349	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2350	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2351	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2352	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2353	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2354	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2355	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2356	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2357	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2358	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2359	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2360	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2361	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2362	if [[ $create_remote_batch_job = true ]]
	2363	then
	2364	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2365	if [[ $do_trace = true ]]
	2366	then
	2367	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2368	fi
[2380]	2369	elif [[ $create_batch_job = true ]]
	2370	then
	2371	palmrun_com=${palmrun_com}" -j"
[2420]	2372	if [[ $do_trace = true ]]
	2373	then
	2374	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2375	fi
[2380]	2376	fi
	2377
	2378
	2379	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2380	# REMOTE HOST
[2506]	2381	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2382	job_protocol_file=$job_protocol_file_local
	2383	if [[ $create_remote_batch_job = true ]]
	2384	then
[2506]	2385	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2386	job_protocol_file=$job_protocol_file_remote
	2387	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2388	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2389	fi
	2390
	2391
	2392	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2393	jobfile=jobfile.$run_id
	2394
	2395
	2396	# FIRST CREATE THE BATCH DIRECTIVES
	2397	(( i = 0 ))
	2398	while (( i < ibd ))
	2399	do
	2400	(( i = i + 1 ))
[2506]	2401	line=`echo "${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}}/$previous_job/g'`
[2380]	2402	eval line=\"$line\"
	2403	echo "$line" >> $jobfile
	2404	done
	2405	echo " " >> $jobfile
	2406
	2407
	2408	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2409	# PROTOCOL
	2410	if [[ $create_remote_batch_job = true ]]
	2411	then
	2412	echo "set +vx" >> $jobfile
	2413	echo "trap '" >> $jobfile
	2414	echo "set +vx" >> $jobfile
	2415	echo "cd ${remote_jobcatalog}" >> $jobfile
	2416	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2417
	2418	# ADD THE BATCH DIRECTIVES
	2419	(( i = 0 ))
	2420	while (( i < ibdt ))
	2421	do
	2422	(( i = i + 1 ))
[2506]	2423	line=`echo "${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]	2424	eval line=\"$line\"
	2425	echo "$line" >> $jobfile
	2426	done
	2427	echo " " >> $jobfile
	2428
	2429	echo "set -x" >> $jobfile
[2506]	2430	echo "${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]	2431	echo "%%END%%" >> $jobfile
	2432	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2433	echo "$submit_command $scpjob_file" >> $jobfile
	2434	echo "rm $scpjob_file" >> $jobfile
[2404]	2435	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2436	echo "set -x" >> $jobfile
	2437	echo " ' exit" >> $jobfile
	2438	fi
	2439
	2440
	2441	# ACTIVATE ERROR-TRACEBACK
	2442	if [[ $do_trace = true ]]
	2443	then
	2444	echo "set -x" >> $jobfile
	2445	else
	2446	echo "set +vx" >> $jobfile
	2447	fi
	2448
	2449
	2450	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2451	if [[ "$login_init_cmd" != "" ]]
	2452	then
	2453	echo "$login_init_cmd" >> $jobfile
	2454	fi
	2455	if [[ "$module_commands" != "" ]]
	2456	then
	2457	echo "$module_commands" >> $jobfile
	2458	fi
	2459
	2460
	2461	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2462	echo "mkdir $TEMPDIR" >> $jobfile
	2463	echo "cd $TEMPDIR" >> $jobfile
	2464	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2506]	2465	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2466	echo "export PATH=.:\$PATH" >> $jobfile
	2467	echo "export execute_palmrun=true" >> $jobfile
	2468
	2469
	2470	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2471	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2472	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2473	if [[ $create_remote_batch_job = true ]]
	2474	then
	2475	(( i = 0 ))
	2476	while (( i < iin ))
	2477	do
	2478	(( i = i + 1 ))
	2479	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2480	if [[ "${transin[$i]}" = job ]]
	2481	then
	2482	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2483	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2484	echo " " >> $jobfile
	2485	echo "%END%" >> $jobfile
	2486	else
	2487	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2488	fi
	2489
	2490	# CHECK, IF FILE COULD BE CREATED
	2491	echo "if [[ \$? = 1 ]]" >> $jobfile
	2492	echo "then" >> $jobfile
	2493	echo " echo \" \" " >> $jobfile
	2494	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2506]	2495	echo " echo \" please check, if directory exists on $host_configuration!\" " >> $jobfile
[2380]	2496	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2497	echo " execute_palmrun=false" >> $jobfile
	2498	echo "fi" >> $jobfile
	2499	done
	2500	fi
	2501
	2502
	2503	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2504	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2505	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2506	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2507	echo "export LOCAL_PWD" >> $jobfile
	2508
	2509
	2510	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2511	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2512	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2513
	2514
	2515	# CALL PALMRUN WITHIN THE JOB
	2516	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2517	echo "set -x" >> $jobfile
	2518	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2519
	2520
	2521	# TRANSFER JOBFILE TO THE TARGET HOST
	2522	if [[ $create_jobfile_only = false ]]
	2523	then
	2524
	2525	if [[ $create_remote_batch_job = true ]]
	2526	then
	2527
[2420]	2528	echo " "
	2529	echo " *** transfer of job to remote host via scp"
	2530	if [[ $do_trace = true ]]
	2531	then
[2506]	2532	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2533	fi
[2506]	2534	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2535
	2536	echo " "
[2420]	2537	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2538	if [[ $do_trace = true ]]
	2539	then
[2506]	2540	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]	2541	fi
[2506]	2542	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]	2543
	2544	elif [[ $create_batch_job = true ]]
	2545	then
	2546
[2385]	2547	eval local_jobcatalog=$local_jobcatalog
[2506]	2548	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2549	cd $local_jobcatalog
[2380]	2550	echo " "
[2420]	2551	echo " *** submit the job"
	2552	if [[ $do_trace = true ]]
	2553	then
[2506]	2554	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2555	fi
[2506]	2556	$submit_command ${host_configuration}_${job_id}
	2557	rm ${host_configuration}_${job_id}
[2380]	2558	cd - > /dev/null
	2559
	2560	fi
	2561
	2562	rm -rf $jobfile
	2563
	2564	else
	2565
	2566	printf "\n *** jobfile created under name \"$jobfile\" "
	2567	printf "\n no batch-job has been sent!"
	2568
	2569	fi
	2570
	2571	fi # END OF REMOTE-PART

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