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source: palm/trunk/SCRIPTS/palmrun @ 2481

Last change on this file since 2481 was 2480, checked in by maronga, 7 years ago
added support for specifying project account in PBS
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 85.1 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 2480 2017-09-19 06:24:14Z raasch $
[2480]	29	# bugfix for last revision
	30	#
	31	# 2479 2017-09-19 06:12:16Z raasch
[2479]	32	# option -A (project account number) added
	33	#
	34	# 2422 2017-09-08 08:25:41Z raasch
[2410]	35	# initial revision
[2380]	36	#
	37	#--------------------------------------------------------------------------------#
	38	# palmrun - script for running PALM jobs on local and remote hosts
	39	#--------------------------------------------------------------------------------#
	40
	41
	42
	43	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	44
	45	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	46	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	47	# (TOO MANY ARGUMENTS - PROBLEM)
	48	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	49
	50	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	51	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	52	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	53	# SCRIPT-OPTION ARGUMENTS
	54	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	55	typeset -i icycle inode ival maxcycle mpi_tasks
	56	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	57
	58	activation_string_list=""
	59	AddFilenames=""
	60	combine_plot_fields=true
	61	compiler_name=""
	62	compiler_name_ser=""
	63	compiler_options=""
	64	cores=""
	65	cores_atmos=0
	66	cores_ocean=0
	67	coupled_dist=""
	68	cpp_options=""
	69	cpumax=0
	70	create_jobfile_only=false
	71	delete_temporary_catalog=true
	72	create_batch_job=false
	73	create_remote_batch_job=false
	74	dashes=" ----------------------------------------------------------------------------"
	75	defaultqueue=""
	76	do_compile=true
	77	do_trace=false
	78	executable=""
	79	execute_command=""
	80	execution_error=false
	81	fileconnection_file=.palm.iofiles
	82	fname=test
	83	global_revision=""
[2420]	84	host_identifier="default"
[2380]	85	hostfile=""
	86	hp=""
	87	keep_data_from_previous_run=false
	88	link_local_input=false
	89	link_local_output=false
[2388]	90	linker_options=""
[2385]	91	local_jobcatalog=""
[2380]	92	locat=normal
	93	makefile=""
	94	max_par_io_str=""
	95	prc=$0
	96	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	97	do
	98	prc=`echo $prc \| cut -f2- -d"/"`
	99	done
	100	module_calls=""
	101	palmrun_script_name=$prc
	102	openmp=false
[2479]	103	project_account=""
[2380]	104	queue=none
	105	restart_run=false
	106	return_address=""
[2385]	107	remote_jobcatalog=""
[2380]	108	remote_username=""
	109	running_in_batch_mode=false
	110	run_coupled_model=false
	111	run_id=""
	112	silent=false
	113	source_list=""
	114	source_path=""
	115	tasks_per_node=""
	116	threads_per_task=1
	117	tmpcreate=false
	118	transfer_problems=false
[2384]	119	user_source_path=""
[2380]	120	use_openmp=false
[2422]	121	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	122	working_directory=`pwd`
	123	write_binary=""
	124	TOPT=""
	125
	126
	127	# ERROR HANDLING IN CASE OF EXIT
[2404]	128	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	129	then
	130
	131	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	132	(( i = 0 ))
	133	while (( i < iec ))
	134	do
	135	(( i = i + 1 ))
	136	printf "\n *** Execution of ERROR-command:\n"
	137	printf " >>> ${err_command[$i]}\n"
	138	eval ${err_command[$i]}
	139	done
[2405]	140	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	141	printf "\n\n+++ palmrun killed \n\n"
	142	elif [[ $locat != control_c ]]
	143	then
	144	printf "\n\n --> palmrun finished\n\n"
	145	if [[ $running_on_remote = true ]]
	146	then
	147	printf " Bye, bye $remote_username !!\n\n"
	148	else
	149	printf " Bye, bye $local_username !!\n\n"
	150	fi
	151	fi' exit
	152
	153
	154	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	155	trap 'cd; rm -rf $TEMPDIR
[2380]	156	printf "\n+++ palmrun killed by \"^C\" \n\n"
	157	locat=control_c
	158	exit
	159	' 2
	160
	161
	162	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	163	# WHICH WILL BE USED TO START RESTART-JOBS
[2479]	164	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
[2380]	165	do
	166	case $option in
	167	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	168	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	169	(b) create_batch_job=true; prc="$prc -b";;
	170	(B) delete_temporary_catalog=false; prc="$prc -B";;
	171	(C) restart_run=true; prc="$prc -C";;
	172	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	173	(F) create_jobfile_only=true;;
	174	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2420]	175	(h) host_identifier=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	176	(j) running_in_batch_mode=true;;
	177	(k) keep_data_from_previous_run=true; prc="$prc -k";;
	178	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
	179	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	180	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	181	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	182	(r) run_id=$OPTARG;;
	183	(R) return_address=$OPTARG;;
	184	(s) source_list=$OPTARG;;
	185	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
	186	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	187	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	188	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	189	(v) silent=true; prc="$prc -v";;
	190	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
	191	(x) do_trace=true;set -x; prc="$prc -x";;
	192	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
	193	(y) ocean_file_appendix=true; prc="$prc -y";;
	194	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	195	(Z) combine_plot_fields=false; prc="$prc -Z";;
	196	(\?) printf "\n +++ unknown option $OPTARG \n"
	197	printf "\n --> type \"$0 ?\" for available options \n"
	198	locat=parameter;exit;;
	199	esac
	200	done
	201
	202
	203	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	204	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	205	(( to_shift = $OPTIND - 1 ))
	206	shift $to_shift
	207
	208	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	209	if [[ "$1" = "?" ]]
	210	then
	211	(printf "\n *** Description of available palmrun options:\n"
	212	printf "\n Option Description Default-Value"
	213	printf "\n -a activation string list \"\" "
[2479]	214	printf "\n -A project account number ---"
[2380]	215	printf "\n -b batch-job on local machine ---"
	216	printf "\n -B do not delete temporary directory at end ---"
	217	printf "\n -d base name of files attached to program test"
	218	printf "\n -F create batch job file only ---"
[2420]	219	printf "\n -h host identifier \"default\" "
[2380]	220	printf "\n -k keep data from previous run"
	221	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	222	printf "\n -M Makefile name Makefile"
	223	printf "\n -O threads per openMP task ---"
	224	printf "\n -q queue \"$queue\" "
	225	printf "\n -s filenames of routines to be compiled \"\" "
	226	printf "\n must end with .f, .f90, .F, or .c !"
	227	printf "\n use \"..\" for more than one file and wildcards"
	228	printf "\n -s LM compiles all locally modified files"
	229	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	230	printf "\n -T tasks per node ---"
[2380]	231	printf "\n -u username on remote machine \"\" "
	232	printf "\n -v no prompt for confirmation ---"
	233	printf "\n -w maximum parallel io streams as given by -X"
	234	printf "\n -x tracing of palmrun for debug purposes ---"
	235	printf "\n -X # of processors (on parallel machines) 1"
	236	printf "\n -y add appendix \"_O\" to all local output"
	237	printf "\n files (ocean precursor runs followed by"
	238	printf "\n coupled atmosphere-ocean runs) ---"
	239	printf "\n -Y run coupled model, \"#1 #2\" with"
	240	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	241	printf "\n -Z skip combine_plot_fields at the end of "
	242	printf "\n the simulation ---"
	243	printf "\n "
	244	printf "\n Possible values of positional parameter <modus>:"
	245	printf "\n \"?\" - this outline \n\n") \| more
	246	exit
	247	elif [[ "$1" != "" ]]
	248	then
	249	printf "\n +++ positional parameter $1 unknown \n"
	250	locat=parameter; exit
	251	fi
	252
	253
	254
	255	# SHORT STARTING MESSAGE
	256	printf "\n*** $version "
	257	printf "\n will be executed. Please wait ..."
	258
	259
	260	# BUILD THE CONFIGURATION-FILE NAME
[2420]	261	config_file=.palm.config.$host_identifier
[2380]	262
	263
	264	# CHECK, IF CONFIGURATION FILE EXISTS
	265	if [[ ! -f $config_file ]]
	266	then
	267	printf "\n\n +++ configuration file: "
	268	printf "\n $config_file"
	269	printf "\n does not exist"
	270	locat=connect; exit
	271	fi
	272
	273
	274	# CHECK, IF FILE CONNECTION FILE EXISTS
	275	if [[ ! -f $fileconnection_file ]]
	276	then
	277	printf "\n\n +++ file connection file: "
	278	printf "\n $fileconnection_file"
	279	printf "\n does not exist"
	280	locat=connect; exit
	281	fi
	282
	283
[2404]	284	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	285	if [[ "$activation_string_list" = "" ]]
	286	then
	287	printf "\n\n +++ no activation string list given: "
	288	printf "\n please set palmrun option \"-a\" "
	289	locat=palmrun_option; exit
	290	fi
	291
	292
	293	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	294	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	295	then
	296	write_binary=true
	297	else
	298	write_binary=false
	299	fi
	300
	301
[2380]	302	# READ AND EVALUATE THE CONFIGURATION-FILE
	303	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	304
	305	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	306	while read line
	307	do
	308
	309	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	310	eval line=\"$line\"
	311
	312
	313	# INTERPRET THE LINE
	314	if [[ "$(echo $line)" = "" ]]
	315	then
	316
	317	# EMPTY LINE, NO ACTION
	318	continue
	319
	320	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	321	then
	322
	323	# LINE IS A COMMENT LINE
	324	continue
	325
	326	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	327	then
	328
	329	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	330	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	331	value=`echo $line \| cut -d" " -s -f2-`
	332
	333
	334	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	335	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	336	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	337	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	338	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	339	# CONFIGURATION-FILE.
	340	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	341	then
	342	eval export $var="\$value"
	343
	344	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	345	if [[ $do_trace = true ]]
	346	then
	347	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	348	fi
	349	fi
	350
	351	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	352	then
	353
	354	# LINE DEFINES BATCH-DIRECTIVE
	355	(( ibd = ibd + 1 ))
	356	line=$(echo $line \| cut -c4-)
	357	batch_directive[$ibd]="$line"
	358
	359	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	360	then
	361
	362	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	363	# REMOTE TO A LOCAL HOST
	364	(( ibdt = ibdt + 1 ))
	365	line=$(echo $line \| cut -c5-)
	366	batch_directive_transfer[$ibdt]="$line"
	367
	368	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	369	then
	370
	371	# LINE DEFINES ERROR-COMMAND
	372	(( iec = iec + 1 ))
	373	line=$(echo $line \| cut -c4-)
	374	err_command[$iec]="$line"
	375
	376	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	377	then
	378
	379	# LINE DEFINES INPUT-COMMAND
	380	(( iic = iic + 1 ))
	381	line=$(echo $line \| cut -c4-)
	382	in_command[$iic]="$line"
	383
	384	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	385	then
	386
	387	# LINE DEFINES OUTPUT-COMMAND
	388	(( ioc = ioc + 1 ))
	389	line=$(echo $line \| cut -c4-)
	390	out_command[$ioc]="$line"
	391
	392	else
	393
	394	# SKIP ALL OTHER LINES
	395	continue
	396
	397	fi
	398
	399	done < $config_file
	400
	401
	402	# CHECK SETTING OF REQUIRED PARAMETERS
	403	if [[ "$compiler_name" = "" ]]
	404	then
	405	printf "\n +++ no compiler name found in $config_file"
	406	printf "\n Please add line \"compiler_name ...\" to that file."
	407	locat=config_file; exit
	408	fi
	409	if [[ "$compiler_name_ser" = "" ]]
	410	then
	411	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	412	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	413	locat=config_file; exit
	414	fi
	415	if [[ "$compiler_options" = "" ]]
	416	then
	417	printf "\n +++ no compiler options found in $config_file"
	418	printf "\n Please add line \"compiler_options ...\" to that file."
	419	locat=config_file; exit
	420	fi
[2388]	421	if [[ "$linker_options" = "" ]]
[2380]	422	then
[2388]	423	printf "\n +++ no linker options found in $config_file"
	424	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	425	locat=config_file; exit
	426	fi
	427	if [[ "$execute_command" = "" ]]
	428	then
	429	printf "\n +++ no execute command found in $config_file"
	430	printf "\n Please add line \"execute_command ...\" to that file."
	431	locat=config_file; exit
	432	fi
	433
	434	if [[ "$hostfile" != "" ]]
	435	then
	436	if [[ $hostfile != auto && ! -f $hostfile ]]
	437	then
	438	printf "\n +++ no hostfile \"$hostfile\" found"
	439	printf "\n Please check line \"hostfile ...\" in $config_file"
	440	locat=config_file; exit
	441	fi
	442	fi
	443
	444
	445	# DETERMINE THE CALL STATUS
	446	if [[ "$return_address" != "" ]]
	447	then
	448
	449	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	450	# BATCH MODE AND ...
	451	running_on_remote=true
	452
	453	else
	454
	455	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	456	if [[ "$remote_ip" != "" ]]
	457	then
	458
	459	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	460	create_remote_batch_job=true
	461
	462	fi
	463	running_on_remote=false
	464	fi
	465
	466
	467
	468	# READ AND EVALUATE THE I/O-FILE LIST
	469	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	470
	471	# READ THE FILE CONNECTION FILE LINE BY LINE
	472	while read line
	473	do
	474
	475	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	476	eval line=\"$line\"
	477
	478
	479	# INTERPRET THE LINE
	480	if [[ "$(echo $line)" = "" ]]
	481	then
	482	# EMPTY LINE, NO ACTION
	483	continue
	484
	485	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	486	then
	487
	488	# LINE IS A COMMENT LINE
	489	true
	490
	491	else
	492
	493	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	494	# s2a: in/out - field
	495	# s2b: loc - field (optional)
	496	# s2c: tr/ar - field (optional)
	497	s1=`echo $line \| cut -d" " -f1`
	498	s2=`echo $line \| cut -d" " -s -f2`
	499	s2a=$(echo $s2 \| cut -d":" -f1)
	500	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	501	then
	502	s2b=""
	503	s2c=""
	504	else
	505	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	506	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	507	fi
	508	s3=`echo $line \| cut -d" " -f3`
	509	s4=`echo $line \| cut -d" " -s -f4`
	510	s5=`echo $line \| cut -d" " -s -f5`
	511	s6=`echo $line \| cut -d" " -s -f6`
	512
	513
	514	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	515	# INPUT- OR OUTPUT-LIST.
	516	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	517	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	518	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	519	# IS NOT CHECKED AND STORED.
	520	IFSALT="$IFS"; IFS="$IFS:"
	521	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	522	then
	523	found=false
	524	for actual in $activation_string_list
	525	do
	526	for formal in $s3
	527	do
	528	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	529	done
	530	done
	531	if [[ $found = true ]]
	532	then
	533	(( iin = iin + 1 ))
	534	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	535	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	536	extin[$iin]=$s6
	537	fi
	538	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	539	then
	540	found=false
	541	for actual in $activation_string_list
	542	do
	543	for formal in $s3
	544	do
	545	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	546	done
	547	done
	548	if [[ $found = true ]]
	549	then
	550	(( iout = iout + 1 ))
	551	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	552	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	553	fi
	554	elif [[ "$s2a" != in && "$s2a" != out ]]
	555	then
	556	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	557	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	558	locat=connect; exit
	559	fi
	560	IFS="$IFSALT"
	561	fi
	562
	563	done < $fileconnection_file
	564
	565
	566
	567	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	568	if [[ $run_coupled_model = true ]]
	569	then
	570
	571	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	572	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	573
	574	if (( $cores_ocean + $cores_atmos != $cores ))
	575	then
	576
	577	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	578	printf "\n PEs (total) : $cores"
	579	printf "\n PEs (atmosphere): $cores_atmos"
	580	printf "\n PEs (ocean) : $cores_ocean"
	581	locat=coupling; exit
	582
	583	fi
	584
	585	fi
	586
	587
	588	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
	589	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
	590	palmrun_memory=$memory
	591	palmrun_cpumax=$cpumax
	592	palmrun_cores=$cores
	593
	594
	595	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
	596	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
	597	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
	598	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	599	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	600	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	601
	602
	603
	604	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	605	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	606	# FOLDER
	607	if [[ $running_in_batch_mode = true ]]
	608	then
	609
[2404]	610	if [[ ! -d ${fast_io_catalog}/SOURCES_FOR_RUN_$fname ]]
[2380]	611	then
[2404]	612	printf "\n +++ directory ${fast_io_catalog}/SOURCES_FOR_RUN_$fname is missing"
[2380]	613	printf "\n Please check the output of the palmrun-call"
	614	printf "\n that you did on your local host."
	615	locat=SOURCES_FOR_RUN; exit
	616	fi
	617
	618	else
	619
	620	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	621	# AUTOMATIC RESTART RUN
	622	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	623	if [[ $restart_run = false ]]
	624	then
	625
	626	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	627	# THE LOCAL HOST
	628	if [[ ! -d $source_path ]]
	629	then
	630	printf "\n\n +++ source path \"$source_path\" on local host"
	631	printf "\n \"$(hostname)\" does not exist"
	632	locat=source_path; exit
	633	fi
	634
[2396]	635	rm -rf SOURCES_FOR_RUN_$fname
	636	mkdir -p SOURCES_FOR_RUN_$fname
[2380]	637
	638	if [[ "$source_list" = LM ]]
	639	then
	640
	641	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	642	source_list=""
	643	cd $source_path
	644
	645
	646	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	647	if [[ ! -d .svn ]]
	648	then
	649	printf "\n\n +++ source directory"
	650	printf "\n \"$source_path\" "
	651	printf "\n is not under control of \"subversion\"."
	652	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	653	fi
	654
	655
	656	# LIST ALL MODIFIED SOURCE CODE FILES
	657	Filenames=""
[2404]	658	svn status > tmp_svnstatus
[2380]	659	while read line
	660	do
	661	firstc=`echo $line \| cut -c1`
	662	if [[ $firstc = M \|\| $firstc = "?" ]]
	663	then
	664	Name=`echo "$line" \| cut -c8-`
	665	extension=`echo $Name \| cut -d. -f2`
	666	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	667	then
	668	Filenames="$Filenames "$Name
	669	fi
	670	fi
[2404]	671	done < tmp_svnstatus
	672	rm -rf tmp_svnstatus
[2380]	673
	674
	675	# COPY FILES TO SOURCES_FOR_RUN_...
	676	for filename in $Filenames
	677	do
	678	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	679	source_list=$source_list"$filename "
	680	done
	681
	682	cd - > /dev/null
	683
	684
	685	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	686	elif [[ "$source_list" != "" ]]
	687	then
	688
	689	cd $source_path
	690
	691	for filename in $source_list
	692	do
	693
	694	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	695	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	696	then
	697	printf "\n +++ source code file: $filename"
	698	printf "\n must not contain (\"/\") "
	699	locat=source; exit
	700	fi
	701
	702	if [[ ! -f $filename ]]
	703	then
	704	printf "\n +++ source code file: $filename"
	705	printf "\n does not exist"
	706	locat=source; exit
	707	else
	708	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	709	fi
	710
	711	done
	712
	713	cd - > /dev/null
	714
	715	fi
	716
	717	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	718	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	719	if [[ ! -f $makefile ]]
	720	then
	721	printf "\n +++ file \"$makefile\" does not exist"
	722	locat=make; exit
	723	else
	724	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	725	fi
	726
	727
	728	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	729	if [[ "$user_source_path" != "" ]]
[2380]	730	then
	731
	732	# DOES THE DIRECTORY EXIST?
[2384]	733	if [[ ! -d $user_source_path ]]
[2380]	734	then
	735
	736	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	737	printf "\n \"$user_source_path\" "
[2380]	738	printf "\n does not exist or is not a directory."
	739	printf "\n No source code will be used from this directory!\n"
[2384]	740	user_source_path=""
[2380]	741	if [[ $silent == false ]]
	742	then
	743	sleep 2
	744	fi
	745
	746	else
	747
[2384]	748	cd $user_source_path
[2380]	749	found=false
	750
	751	Names=$(ls -1 *.f90 2>&1)
	752	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	753	Names=$(ls -1 *.F90 2>&1)
	754	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	755	Names=$(ls -1 *.F 2>&1)
	756	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	757	Names=$(ls -1 *.f 2>&1)
	758	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	759	Names=$(ls -1 *.c 2>&1)
	760	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	761
	762	cd - > /dev/null
	763	cd SOURCES_FOR_RUN_$fname
	764
	765	# COPY MAKEFILE IF EXISTING
[2384]	766	if [[ -f $user_source_path/Makefile ]]
[2380]	767	then
	768	printf "\n\n *** user Makefile from directory"
[2384]	769	printf "\n \"$user_source_path\" is used \n"
[2380]	770	if [[ $silent == false ]]
	771	then
	772	sleep 1
	773	fi
[2384]	774	cp $user_source_path/Makefile .
[2380]	775	fi
	776
	777	for filename in $AddFilenames
	778	do
	779	if [[ -f $filename ]]
	780	then
	781	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	782	printf "\n source code directory \"$user_source_path\" "
[2380]	783	printf "\n but was also given with option \"-s\" which means that it should be taken"
	784	printf "\n from directory \"$source_path\"."
	785	locat=source; exit
	786	fi
	787
[2384]	788	cp $user_source_path/$filename .
[2380]	789	source_list="$source_list $filename"
	790
	791	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	792	if [[ $(grep -c $filename Makefile) = 0 ]]
	793	then
	794	printf "\n\n +++ user file \"$filename\" "
	795	printf "\n is not listed in Makefile \n"
	796	locat=source; exit
	797	else
	798
	799	if [[ $found = false ]]
	800	then
	801	found=true
	802	printf "\n\n *** following user file(s) added to the"
	803	printf " files to be translated:\n "
	804	fi
	805	printf "$filename "
	806	if [[ $silent == false ]]
	807	then
	808	sleep 0.5
	809	fi
	810
	811	fi
	812	done
	813	[[ $found = true ]] && printf "\n"
	814	cd - > /dev/null
	815	fi
	816	fi
	817
	818	# COPY CONFIGURATION FILES
	819	cp $config_file SOURCES_FOR_RUN_$fname
	820	cp $fileconnection_file SOURCES_FOR_RUN_$fname
	821
	822	# COPY SHELLSCRIPTS
	823	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
	824	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
	825
	826	fi
	827
	828	fi
	829
	830	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	831	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	832	if [[ "$global_revision" = "" ]]
	833	then
	834	global_revision=`svnversion $source_path 2>/dev/null`
	835	global_revision="Rev: $global_revision"
	836	fi
	837
	838
	839	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	840	if [[ -n $cores ]]
	841	then
	842
	843	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	844	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2384]	845	if [[ "$tasks_per_node" = "" ]]
[2380]	846	then
	847	printf "\n"
	848	printf "\n +++ option \"-T\" (tasks per node) is missing"
	849	printf "\n set -T option or define tasks_per_node in the config file"
	850	locat=tasks_per_node; (( iec = 0 )); exit
	851	fi
	852
	853	if (( cores < tasks_per_node ))
	854	then
	855	printf "\n"
	856	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	857	printf "\n given values: -T $tasks_per_node -X $cores"
	858	locat=tasks_per_node; (( iec = 0 )); exit
	859	fi
	860
	861	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	862	(( mpi_tasks = cores / threads_per_task ))
	863	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	864	(( ii = cores / tasks_per_node ))
	865	(( remaining_cores = cores - ii * tasks_per_node ))
	866	if (( remaining_cores > 0 ))
	867	then
	868	printf "\n"
	869	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	870	printf "\n divisor of the total number of cores (option \"-X\")"
	871	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	872	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	873	(( nodes = nodes + 1 ))
	874	fi
	875
	876	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	877	if [[ "$tasks_per_node" != "" ]]
	878	then
	879	TOPT="-T $tasks_per_node"
	880	fi
	881
	882	fi
	883
	884
	885	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	886	if [[ "$maximum_parallel_io_streams" = "" ]]
	887	then
	888	maximum_parallel_io_streams=$cores
	889	fi
	890
	891
	892	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	893	if [[ "$scp_port" != "" ]]
	894	then
	895	PORTOPT="-P $scp_port"
	896	SSH_PORTOPT="-p $scp_port"
	897	fi
	898
	899
	900	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	901	# CONFIG-FILE
	902	if [[ "$ssh_key" != "" ]]
	903	then
	904	ssh_key="-i $HOME/.ssh/$ssh_key"
	905	fi
	906
	907
	908	# SET QUEUE, IF NOT GIVEN
	909	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	910	then
	911
	912	if [[ $queue = none && "$defaultqueue" = "" ]]
	913	then
	914	printf "\n"
	915	printf "\n +++ no default queue given in configuration file and no queue"
	916	printf "\n given with option -q"
	917	fi
	918	if [[ $queue = none ]]
	919	then
	920	queue=$defaultqueue
	921	fi
	922
	923	fi
	924
	925
	926	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	927	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	928	(( i = 0 ))
	929	while (( i < iin ))
	930	do
	931	(( i = i + 1 ))
	932	(( maxcycle = 0 ))
	933
	934	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	935	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	936	if [[ "${actionin[$i]}" = di ]]
	937	then
	938	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	939	# HOST ONLY
	940	eval filename=${pathin[$i]}/${endin[$i]}
	941	else
	942	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	943	# HOST ONLY
	944	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	945	fi
	946	eval pathname=${pathin[$i]}
	947
	948	# CHECK IF FILE EXISTS
	949	if ! ls $filename* 1>/dev/null 2>&1
	950	then
	951
	952	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	953	if [[ "${transin[$i]}" != "locopt" ]]
	954	then
	955	printf "\n\n +++ INPUT-file: "
	956	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	957	then
	958	printf "\n $filename"
	959	else
	960	printf "\n $filename.${extin[$i]}"
	961	fi
	962	printf "\n does not exist\n"
	963	locat=input; exit
	964	else
	965	transin[$i]="unavailable"
	966	fi
	967	else
	968
	969	# DETERMINE THE FILE'S CYCLE NUMBER
	970	ls -1 -d $filename > filelist 2>/dev/null
	971	ls -1 -d $filename.* >> filelist 2>/dev/null
	972	while read line
	973	do
	974	# filename without path (i.e. after the last "/")
	975	basefilename=$(basename ${line})
	976
	977	# check if there is an extension
	978	extension=${basefilename##*.}
	979	if [[ "$extension" = "$extin[$i]" ]]
	980	then
	981	basefilename=${basefilename&.*}
	982	fi
	983
	984	# check for an existing cycle number
	985	cycle=${basefilename##*.}
	986	if [[ $cycle =~ ^-?[0-9]+$ ]]
	987	then
	988	(( icycle = $cycle ))
	989	else
	990	(( icycle = 0 ))
	991	fi
	992
	993	if (( icycle > maxcycle ))
	994	then
	995	(( maxcycle = icycle ))
	996	fi
	997
	998	done <filelist
	999	rm filelist
	1000
	1001	# APPEND CYCLE NUMBER TO FILENAME
	1002	if (( maxcycle > 0 ))
	1003	then
	1004	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1005	then
	1006	filename=${filename}.$maxcycle.${extin[$i]}
	1007	else
	1008	filename=${filename}.$maxcycle
	1009	fi
	1010	else
	1011	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1012	then
	1013	filename=${filename}.${extin[$i]}
	1014	fi
	1015	fi
	1016
	1017	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1018	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1019	absnamein[$i]=$filename
	1020	if (( maxcycle > 0 ))
	1021	then
	1022	if [[ "${actionin[$i]}" = di ]]
	1023	then
	1024	frelin[$i]=${endin[$i]}.$maxcycle
	1025	else
	1026	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1027	fi
	1028	else
	1029	if [[ "${actionin[$i]}" = di ]]
	1030	then
	1031	frelin[$i]=${endin[$i]}
	1032	else
	1033	frelin[$i]=${fname}${endin[$i]}
	1034	fi
	1035	fi
	1036
	1037	fi
	1038	done
	1039
	1040
	1041	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1042	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1043	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1044	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1045	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1046	# REMOTE HOST)
	1047	(( i = 0 ))
	1048	while (( i < iout ))
	1049	do
	1050	(( i = i + 1 ))
	1051	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1052	then
	1053	if [[ "${actionout[$i]}" = tr ]]
	1054	then
	1055	actionout[$i]=""
	1056	elif [[ "${actionout[$i]}" = trpe ]]
	1057	then
	1058	actionout[$i]=pe
	1059	elif [[ "${actionout[$i]}" = tra ]]
	1060	then
	1061	actionout[$i]=a
	1062	fi
	1063	(( maxcycle = 0 ))
	1064	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1065	eval catalogname=${pathout[$i]}
	1066	if ! ls $filename* 1>/dev/null 2>&1
	1067	then
	1068
	1069	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1070	if cat /dev/null > $filename
	1071	then
	1072	rm $filename
	1073	else
	1074
	1075	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1076	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1077	if [[ ! -d $catalogname ]]
	1078	then
	1079	if mkdir -p $catalogname
	1080	then
	1081	printf "\n\n *** directory:"
	1082	printf "\n $catalogname"
	1083	printf "\n was created\n"
	1084	else
	1085	printf "\n\n +++ OUTPUT-file:"
	1086	printf "\n $filename"
	1087	printf "\n cannot be created, because directory does not exist"
	1088	printf "\n and cannot be created either"
	1089	printf "\n"
	1090	locat=output ; exit
	1091	fi 2>/dev/null
	1092	else
	1093	printf "\n\n +++ OUTPUT-file:"
	1094	printf "\n $filename"
	1095	printf "\n cannot be created, although directory exists"
	1096	printf "\n"
	1097	locat=output ; exit
	1098	fi
	1099	fi 2>/dev/null
	1100	else
	1101
	1102	# DETERMINE THE CYCLE NUMBER
	1103	ls -1 -d $filename > filelist 2>/dev/null
	1104	ls -1 -d $filename.* >> filelist 2>/dev/null
	1105	while read line
	1106	do
	1107
	1108	# filename without path (i.e. after the last "/")
	1109	basefilename=$(basename ${line})
	1110
	1111	# check if there is an extension
	1112	extension=${basefilename##*.}
	1113	if [[ "$extension" = "${extout[$i]}" ]]
	1114	then
	1115	basefilename=${basefilename%.*}
	1116	fi
	1117
	1118	# check for an existing cycle number
	1119	cycle=${basefilename##*.}
	1120	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1121	then
	1122	(( icycle = $cycle + 1 ))
	1123	else
	1124	(( icycle = 1 ))
	1125	fi
	1126
	1127	if (( icycle > maxcycle ))
	1128	then
	1129	(( maxcycle = icycle ))
	1130	fi
	1131
	1132	done <filelist
	1133	rm filelist
	1134	fi
	1135
	1136	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1137	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1138	if [[ "${actionout[$i]}" != a ]]
	1139	then
	1140	if (( maxcycle > 0 ))
	1141	then
	1142	filename_tmp=${filename}.$maxcycle
	1143	if cat /dev/null > $filename_tmp
	1144	then
	1145	rm $filename_tmp
	1146	else
	1147	printf "\n +++ OUTPUT-file:"
	1148	printf "\n $filename_tmp"
	1149	printf "\n cannot be created"
	1150	locat=output ; exit
	1151	fi
	1152	fi
	1153	else
	1154	(( maxcycle = maxcycle - 1 ))
	1155	fi
	1156
	1157	(( cycnum[$i] = maxcycle ))
	1158	pathout[$i]=$filename
	1159
	1160	fi
	1161	done
	1162
	1163
	1164	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1165	if [[ $running_in_batch_mode = false ]]
	1166	then
	1167	run_id=$RANDOM
	1168	job_id=${fname}.$run_id
	1169
[2404]	1170	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1171	fi
	1172
	1173
	1174	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1175	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1176	then
	1177
	1178	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1179	if [[ $ibd = 0 ]]
	1180	then
	1181	printf "\n"
	1182	printf "\n +++ no batch directives found in configuration file"
	1183	locat=config_file_batch_directives; (( iec = 0 )); exit
	1184	fi
	1185
	1186	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1187	done=false
[2384]	1188	cputime=$cpumax
[2380]	1189	while [[ $done = false ]]
	1190	do
[2384]	1191	if (( cputime == 0 ))
[2380]	1192	then
	1193	printf "\n +++ cpu-time is undefined"
	1194	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1195	printf "\n >>> "
[2384]	1196	read cputime 1>/dev/null 2>&1
[2380]	1197	else
	1198	done=true
	1199	fi
	1200	done
[2420]	1201	cpumax=$cputime
[2380]	1202
	1203	# CHECK THE MEMORY DEMAND
	1204	done=false
	1205	while [[ $done = false ]]
	1206	do
	1207	if (( memory == 0 ))
	1208	then
	1209	printf "\n +++ memory demand is undefined"
	1210	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1211	printf "\n >>> "
	1212	read memory 1>/dev/null 2>&1
	1213	else
	1214	done=true
	1215	fi
	1216	done
	1217
	1218	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1219	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1220	then
	1221	while [[ -z $remote_username ]]
	1222	do
[2420]	1223	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1224	printf "\n >>> Please type username:"
	1225	printf "\n >>> "
	1226	read remote_username
	1227	done
	1228	fi
	1229
	1230	else
	1231
[2420]	1232	if [[ $running_in_batch_mode = false ]]
	1233	then
	1234	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1235	cpumax=$cputime
	1236	else
	1237	cputime=$cpumax
	1238	fi
[2380]	1239
	1240	fi
	1241
	1242
	1243	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1244	(( cpu_hours = cputime / 3600 ))
	1245	(( resttime = cputime - cpu_hours * 3600 ))
	1246	(( cpu_minutes = resttime / 60 ))
	1247	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1248	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1249
	1250
	1251	# OUTPUT OF THE PALMRUN-HEADER
	1252	calltime=$(date)
	1253	printf "\n"
	1254	printf "#------------------------------------------------------------------------# \n"
	1255	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1256	printf "\| \| \n"
	1257	column1="called on:"; column2=$(hostname)
	1258	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1259	if [[ $create_remote_batch_job = true ]]
	1260	then
[2420]	1261	column1="execution on:"; column2="$host_identifier (username: $remote_username)"
[2380]	1262	else
	1263	if [[ $running_on_remote = true ]]
	1264	then
[2420]	1265	column1="execution on:"; column2="$host_identifier (IP:$remote_ip)"
[2380]	1266	else
[2420]	1267	column1="execution on:"; column2="$host_identifier (IP:$local_ip)"
[2380]	1268	fi
	1269	fi
	1270	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1271
	1272	column1="running in:"
	1273	if [[ $running_in_batch_mode = true ]]
	1274	then
	1275	column2="batch job mode"
	1276	else
	1277	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1278	then
	1279	column2="job creation mode"
	1280	else
	1281	column2="interactive run mode"
	1282	fi
	1283	fi
	1284	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1285
[2479]	1286	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1287	then
[2480]	1288	if [[ "$project_account" != "" ]]
[2479]	1289	then
	1290	column1="project account number:"
	1291	column2="$project_account"
	1292	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1293	fi
	1294	fi
	1295
[2380]	1296	if [[ -n $cores ]]
	1297	then
	1298	if [[ $run_coupled_model = false ]]
	1299	then
	1300	column1="number of cores:"; column2=$cores
	1301	else
	1302	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1303	fi
	1304	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1305	fi
	1306	if [[ -n $tasks_per_node ]]
	1307	then
	1308	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1309	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1310	if (( remaining_cores > 0 ))
	1311	then
	1312	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1313	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1314	fi
	1315	fi
	1316	if [[ $maximum_parallel_io_streams != $cores ]]
	1317	then
	1318	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1319	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1320	fi
	1321	if [[ $use_openmp = true ]]
	1322	then
	1323	column1="threads per task:"; column2="$threads_per_task"
	1324	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1325	fi
[2384]	1326	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1327	then
	1328	column1="job cpu time (h:m:s):"; column2="$timestring"
	1329	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1330	fi
[2380]	1331	printf "\| \| \n"
	1332	if [[ "$source_list" != "" ]]
	1333	then
	1334	if [[ "$make_options" != "" ]]
	1335	then
	1336	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1337	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1338	line=$(echo "$make_options" \| cut -c46-)
	1339	while [[ "$line" != "" ]]
	1340	do
	1341	column1=""
	1342	column2=$(echo "$line" \| cut -c-45)
	1343	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1344	line=$(echo "$line" \| cut -c46-)
	1345	done
	1346	fi
	1347	fi
	1348
	1349	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1350	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1351	line=$(echo "$cpp_options" \| cut -c46-)
	1352	while [[ "$line" != "" ]]
	1353	do
	1354	column1=""
	1355	column2=$(echo "$line" \| cut -c-45)
	1356	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1357	line=$(echo "$line" \| cut -c46-)
	1358	done
	1359
	1360	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1361	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1362	line=$(echo "$compiler_options" \| cut -c46-)
	1363	while [[ "$line" != "" ]]
	1364	do
	1365	column1=""
	1366	column2=$(echo "$line" \| cut -c-45)
	1367	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1368	line=$(echo "$line" \| cut -c46-)
	1369	done
	1370
[2388]	1371	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1372	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1373	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1374	while [[ "$line" != "" ]]
	1375	do
	1376	column1=""
	1377	column2=$(echo "$line" \| cut -c-45)
	1378	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1379	line=$(echo "$line" \| cut -c46-)
	1380	done
	1381
	1382	if [[ "$login_init_cmd" != "" ]]
	1383	then
	1384	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1385	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1386	line=$(echo "$login_init_cmd" \| cut -c46-)
	1387	while [[ "$line" != "" ]]
	1388	do
	1389	column1=""
	1390	column2=$(echo "$line" \| cut -c-45)
	1391	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1392	line=$(echo "$line" \| cut -c46-)
	1393	done
	1394	fi
	1395
	1396	if [[ "$module_commands" != "" ]]
	1397	then
	1398	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1399	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1400	line=$(echo "$module_commands" \| cut -c46-)
	1401	while [[ "$line" != "" ]]
	1402	do
	1403	column1=""
	1404	column2=$(echo "$line" \| cut -c-45)
	1405	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1406	line=$(echo "$line" \| cut -c46-)
	1407	done
	1408	fi
	1409	printf "\| \| \n"
	1410	column1="base name of files:"; column2=$fname
	1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1412	column1="activation string list:"; column2=$(echo $activation_string_list)
	1413	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1414
	1415	if [[ "$ocean_file_appendix" = true ]]
	1416	then
	1417	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1418	fi
	1419
	1420	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
	1421	then
	1422	column1="memory demand / PE":; column2="$memory MB"
	1423	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1424	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
	1425	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1426	fi
	1427
	1428	if [[ "$source_list" != "" ]]
	1429	then
	1430	printf "\| \| \n"
	1431	printf "\| Files to be compiled: \| \n"
	1432	line=$source_list
	1433	while [[ "$line" != "" ]]
	1434	do
	1435	linestart=$(echo $line \| cut -c-70)
	1436	printf "\| %-70s \| \n" "$linestart"
	1437	line=$(echo "$line" \| cut -c71-)
	1438	done
	1439	fi
	1440	printf "#------------------------------------------------------------------------#"
	1441
	1442
	1443
	1444	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1445	if [[ $do_trace = true ]]
	1446	then
	1447	(( i = 0 ))
	1448	while (( i < iin ))
	1449	do
	1450	(( i = i + 1 ))
	1451	if (( i == 1 ))
	1452	then
	1453	printf "\n\n >>> INPUT-file assignments:\n"
	1454	fi
	1455	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1456	done
	1457	(( i = 0 ))
	1458	while (( i < iout ))
	1459	do
	1460	(( i = i + 1 ))
	1461	if (( i == 1 ))
	1462	then
	1463	printf "\n\n >>> OUTPUT-file assignments:\n"
	1464	fi
	1465	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1466	done
	1467	(( i = 0 ))
	1468	while (( i < iic ))
	1469	do
	1470	(( i = i + 1 ))
	1471	if (( i == 1 ))
	1472	then
	1473	printf "\n\n >>> INPUT-commands:\n"
	1474	fi
	1475	printf "\n ${in_command[$i]}"
	1476	done
	1477	(( i = 0 ))
	1478	while (( i < ioc ))
	1479	do
	1480	(( i = i + 1 ))
	1481	if (( i == 1 ))
	1482	then
	1483	printf "\n\n >>> OUTPUT-commands:\n"
	1484	fi
	1485	printf "\n ${out_command[$i]}"
	1486	done
	1487	fi
	1488
	1489	# QUERY FOR CONTINUE
	1490	if [[ $silent = false && $running_in_batch_mode = false ]]
	1491	then
	1492	antwort=dummy
	1493	printf "\n\n"
	1494	printf " >>> everything o.k. (y/n) ? "
	1495	while read antwort
	1496	do
	1497	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1498	then
	1499	printf " >>> everything o.k. (y/n) ? "
	1500	else
	1501	break
	1502	fi
	1503	done
	1504	if [[ $antwort = n \|\| $antwort = N ]]
	1505	then
	1506	locat=user_abort; (( iec = 0 )); exit
	1507	fi
	1508	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1509	then
	1510	printf " *** batch-job will be created and submitted"
	1511	else
	1512	printf " *** PALMRUN will now continue to execute on this machine"
	1513	fi
	1514	fi
	1515
	1516
	1517
	1518	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1519	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1520	then
	1521
	1522	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1523	then
	1524	printf "\n\n *** creating executable and other sources for the remote host"
	1525	else
	1526	printf "\n\n *** creating executable and other sources for the local host"
	1527	fi
	1528
[2422]	1529	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1530	# IT SHALL BE CREATED
	1531	ask_for_make_depository=false
	1532	if [[ $create_remote_batch_job = true ]]
	1533	then
	1534
	1535	line=`grep %base_directory $config_file`
	1536	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_identifier}
	1537	echo "make_depository=$make_depository"
	1538	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_identifier}_last_make_protokoll
	1539
	1540	if [[ $(grep -c "depository not found" ${host_identifier}_last_make_protokoll) != 0 ]]
	1541	then
	1542	printf "\n\n +++ make depository \"${make_depository}\""
	1543	printf "\n on remote host not found!"
	1544	ask_for_make_depository=true
	1545	fi
	1546	rm ${host_identifier}_last_make_protokoll
	1547
	1548	else
	1549
	1550	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
	1551	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_identifier}
	1552	if [[ ! -d ${make_depository} ]]
	1553	then
	1554	printf "\n\n +++ make depository \"${make_depository}\""
	1555	printf "\n on local host not found!"
	1556	ask_for_make_depository=true
	1557	fi
	1558
	1559	fi
	1560
	1561	if [[ $ask_for_make_depository = true ]]
	1562	then
	1563
	1564	antwort=dummy
	1565	printf "\n\n"
	1566	printf " >>> Create a new one (y/n) ? "
	1567	while read antwort
	1568	do
	1569	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1570	then
	1571	printf " >>> Create a new one (y/n) ? "
	1572	else
	1573	break
	1574	fi
	1575	done
	1576	if [[ $antwort = n \|\| $antwort = N ]]
	1577	then
	1578	locat=user_abort; (( iec = 0 )); exit
	1579	fi
	1580
	1581	palmbuild -v -h $host_identifier
	1582
	1583	if [[ $? != 0 ]]
	1584	then
	1585
	1586	# ABORT IN CASE OF COMPILATION PROBLEMS
	1587	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1588	locat=make_depository
	1589	exit
	1590	else
	1591	echo " *** now continue with creating executable and other sources"
	1592	fi
	1593
	1594	fi
	1595
[2420]	1596	palmbuild -v -h $host_identifier -d $fname
[2380]	1597
	1598	if [[ $? != 0 ]]
	1599	then
	1600
	1601	# ABORT IN CASE OF COMPILATION PROBLEMS
	1602	printf "\n +++ error while creating executable and/or other sources"
	1603	locat=execution
[2420]	1604	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1605	exit
	1606
	1607	else
	1608
	1609	printf "\n$dashes\n *** executable and other sources created\n"
[2420]	1610	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1611
	1612	fi
	1613
	1614	fi
	1615
	1616
	1617	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1618	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1619	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1620	then
	1621
	1622	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1623	if [[ $running_in_batch_mode = false ]]
	1624	then
	1625	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1626	# FOLDER
	1627	mkdir -p $TEMPDIR
	1628	chmod go+rx $TEMPDIR
	1629	tmpcreate=true
	1630	cd $TEMPDIR
[2404]	1631	cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
[2380]	1632	printf "\n *** changed to temporary directory: $TEMPDIR"
	1633
	1634	else
	1635
	1636	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1637	printf "\n *** running in temporary directory: $TEMPDIR"
	1638
	1639	fi
	1640
	1641
	1642	# PROVIDE THE INPUT FILES
	1643	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1644	(( i = 0 ))
	1645	while (( i < iin ))
	1646	do
	1647	(( i = i + 1 ))
	1648	if (( i == 1 ))
	1649	then
	1650	printf "\n\n *** providing INPUT-files:\n$dashes"
	1651	fi
	1652
	1653
	1654	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1655	if [[ "${transin[$i]}" = unavailable ]]
	1656	then
	1657	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1658	then
	1659	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1660	printf "\n is not available!"
	1661	else
	1662	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1663	printf "\n is not available!"
	1664	fi
	1665	continue
	1666	fi
	1667
	1668	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1669	files_for_cores=false; filetype=file
	1670	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1671	then
	1672	files_for_cores=true; filetype=files
	1673	actionin[$i]=""
	1674	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1675	then
	1676	actionin[$i]=""
	1677	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1678	then
	1679	files_for_cores=true; filetype=files
	1680	actionin[$i]="ln"
	1681	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1682	then
	1683	actionin[$i]="ln"
	1684	fi
	1685
	1686	if [[ $files_for_cores = true ]]
	1687	then
	1688	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1689	else
	1690	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1691	fi
	1692
	1693	# INPUT-FILES TO BE LINKED
	1694	if [[ "${actionin[$i]}" = ln ]]
	1695	then
	1696
	1697	printf "\n $filetype will be linked"
	1698	if [[ $files_for_cores = false ]]
	1699	then
	1700	if [[ -f "${absnamein[$i]}" ]]
	1701	then
	1702	ln ${absnamein[$i]} ${localin[$i]}
	1703	got_tmp[$i]=true
	1704	fi
	1705	else
	1706	if [[ -d "${absnamein[$i]}" ]]
	1707	then
[2396]	1708	mkdir -p ${localin[$i]}
[2380]	1709	cd ${absnamein[$i]}
	1710	for file in $(ls *)
	1711	do
	1712	ln $file $TEMPDIR/${localin[$i]}
	1713	done >\|/dev/null 2>&1
	1714	cd $TEMPDIR
	1715	fi
	1716
	1717	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1718	if [[ ! -f "${localin[$i]}/_000000" ]]
	1719	then
	1720	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1721	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1722	fi
	1723
	1724	got_tmp[$i]=true
	1725	fi
	1726	fi
	1727
	1728	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1729	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1730	then
	1731
	1732	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1733	then
	1734
	1735	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1736	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1737	printf "\n file will be provided for $cores processors"
[2396]	1738	mkdir -p ${localin[$i]}
[2380]	1739	ival=$cores
	1740	(( ii = 0 ))
	1741	while (( ii <= ival-1 ))
	1742	do
	1743	if (( ii < 10 ))
	1744	then
	1745	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1746	elif (( ii < 100 ))
	1747	then
	1748	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1749	elif (( ii < 1000 ))
	1750	then
	1751	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1752	else
	1753	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1754	fi
	1755	(( ii = ii + 1 ))
	1756	done
	1757
	1758	else
	1759
	1760	if [[ $files_for_cores = true ]]
	1761	then
	1762
	1763	# PROVIDE FILES FOR EACH CORE
	1764	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1765	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1766	printf "\n providing $cores files for the respective cores"
[2396]	1767	mkdir -p ${localin[$i]}
[2380]	1768	if [[ $link_local_input = true ]]
	1769	then
	1770	printf " files will be linked\n"
	1771	cd ${absnamein[$i]}
	1772	for file in $(ls *)
	1773	do
	1774	ln -f $file ${localin[$i]}
	1775	done
	1776	cd $TEMPDIR
	1777	fi
	1778
	1779	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1780	if [[ ! -f "${localin[$i]}/_000000" ]]
	1781	then
	1782	if [[ $link_local_input = true ]]
	1783	then
	1784	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1785	fi
	1786	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1787	fi
	1788
	1789	else
	1790
	1791	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1792	if [[ $link_local_input = true ]]
	1793	then
	1794	printf " file will be linked\n"
	1795	ln -f ${absnamein[$i]} ${localin[$i]}
	1796	fi
	1797	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1798	if [[ ! -f "${localin[$i]}" ]]
	1799	then
	1800	if [[ $link_local_input = true ]]
	1801	then
	1802	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1803	fi
	1804	cp ${absnamein[$i]} ${localin[$i]}
	1805	fi
	1806	fi
	1807	fi
	1808	fi
	1809
	1810	done
	1811	if (( i != 0 ))
	1812	then
	1813	printf "\n$dashes\n *** all INPUT-files provided \n"
	1814	fi
	1815
	1816
	1817	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1818	(( i = 0 ))
	1819	while (( i < iic ))
	1820	do
	1821	(( i = i + 1 ))
	1822	if (( i == 1 ))
	1823	then
	1824	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1825	fi
	1826	printf "\n >>> ${in_command[$i]}"
	1827	eval ${in_command[$i]}
	1828	if (( i == iic ))
	1829	then
	1830	printf "\n$dashes\n"
	1831	fi
	1832	done
	1833
	1834
	1835	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1836	# (FILE ENVPAR WILL BE READ BY PALM)
	1837	cat > ENVPAR << EOF
[2420]	1838	&envpar run_identifier = '$fname', host = '$host_identifier',
[2380]	1839	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1840	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1841	maximum_cpu_time_allowed = ${cpumax}.,
	1842	revision = '$global_revision',
	1843	batch_job = .${running_in_batch_mode}. /
	1844
	1845	EOF
	1846
	1847
	1848	# STARTING THE EXECUTABLE
	1849	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1850	PATH=$PATH:$TEMPDIR
	1851
	1852
	1853	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1854	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1855	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1856	eval line=\"$line\"
	1857	execute_command="$line"
	1858
	1859
	1860	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1861	eval line2=\"$line2\"
	1862	execute_command_for_combine="$line2"
	1863
	1864
	1865	# PROVIDE A HOSTFILE, IF REQUIRED
	1866	if [[ "$hostfile" != "" ]]
	1867	then
	1868
	1869	if [[ $hostfile = auto ]]
	1870	then
	1871	# CREATE A NEW HOSTFILE
	1872	(( ii = 1 ))
	1873	while (( ii <= cores / threads_per_task ))
	1874	do
	1875	echo $(hostname) >> hostfile
	1876	(( ii = ii + 1 ))
	1877	done
	1878	if (( cores / threads_per_task == 0 ))
	1879	then
	1880	echo $(hostname) >> hostfile
	1881	fi
	1882
	1883	else
	1884	cp $hostfile hostfile
	1885	fi
	1886	eval line=\"`head -n $ii hostfile`\"
	1887	printf "\n *** running on: $line"
	1888	fi
	1889
	1890
	1891
	1892	# SET THE NUMBER OF OPENMP-THREADS
	1893	if [[ $use_openmp = true ]]
	1894	then
	1895	export OMP_NUM_THREADS=$threads_per_task
	1896	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1897	else
	1898	export OMP_NUM_THREADS=1
	1899	fi
	1900
	1901
	1902	# PROVIDE DATA FOR
	1903	if [[ $run_coupled_model = false ]]
	1904	then
	1905	if [[ "$ocean_file_appendix" = true ]]
	1906	then
	1907	echo "precursor_ocean" > coupling_steering
	1908	else
	1909	echo "precursor_atmos" > coupling_steering
	1910	fi
	1911	else
	1912	(( iia = $cores_atmos / $threads_per_task ))
	1913	(( iio = $cores_ocean / $threads_per_task ))
	1914	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1915	printf "\n\n"
	1916	echo "coupled_run $iia $iio" > coupling_steering
	1917	fi
	1918
	1919	printf "\n *** execute command:"
	1920	printf "\n \"$execute_command\" \n\n"
	1921
	1922	$execute_command < coupling_steering
	1923
	1924	if [[ $? != 0 ]]
	1925	then
	1926
	1927	# ABORT IN CASE OF RUNTIME ERRORS
	1928	printf "\n +++ runtime error occured"
	1929	locat=execution
	1930	exit
	1931
	1932	else
	1933
	1934	printf "\n$dashes\n *** execution finished \n"
	1935
	1936	fi
	1937
	1938
	1939	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1940	# BY EACH CORE INTO ONE FILE
	1941	if [[ ! -f combine_plot_fields.x ]]
	1942	then
	1943
	1944	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1945	printf "\n 2d- and/or 3d-data may be incomplete!"
	1946	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1947
	1948	elif [[ "$combine_plot_fields" == true ]]
	1949	then
	1950
	1951	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1952	$execute_command_for_combine
	1953
	1954	else
	1955
	1956	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1957	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1958	# ??? koennen wir das streichen ???
	1959	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1960	fi
	1961
	1962
	1963
	1964	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1965	(( i = 0 ))
	1966	while (( i < ioc ))
	1967	do
	1968	(( i = i + 1 ))
	1969	if (( i == 1 ))
	1970	then
	1971	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1972	fi
	1973	printf "\n >>> ${out_command[$i]}"
	1974	eval ${out_command[$i]}
	1975	if (( i == ioc ))
	1976	then
	1977	printf "\n$dashes\n"
	1978	fi
	1979	done
	1980
	1981
	1982	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1983	if [[ $do_trace = true ]]
	1984	then
	1985	printf "\n\n"
	1986	ls -al
	1987	fi
	1988
	1989
	1990	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1991	(( i = 0 ))
	1992	while (( i < iout ))
	1993	do
	1994	(( i = i + 1 ))
	1995	if (( i == 1 ))
	1996	then
	1997	printf "\n\n *** saving OUTPUT-files:"
	1998
	1999	# GET RUN NUMBER ASSIGNED BY PALM
	2000	if [[ -f RUN_NUMBER ]]
	2001	then
	2002	read run_number < RUN_NUMBER
	2003	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2004	usecycle_option="-U $run_number"
	2005	else
	2006	run_number=0
	2007	usecycle_option=""
	2008	fi
	2009	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2010	then
[2404]	2011	printf "\n *** in case of SCP transfers to local host"
	2012	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2013	fi
	2014	printf "\n$dashes"
	2015	fi
	2016
	2017	# ADD CYCLE NUMBER TO FILENAME
	2018	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2019	then
	2020
	2021	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2022	if [[ "${actionout[$i]}" != "a" ]]
	2023	then
	2024	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2025	# WITH AN EXISTING CYCLE NUMBER
	2026	if (( run_number >= cycnum[$i] ))
	2027	then
	2028	(( cycnum[$i] = run_number ))
	2029	else
	2030	if (( run_number > 0 ))
	2031	then
	2032	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2033	fi
	2034	fi
	2035	fi
	2036	if (( cycnum[$i] > 0 ))
	2037	then
	2038	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2039	fi
	2040	fi
	2041
	2042	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2043	files_for_cores=false; filetype=file
	2044	link_local_output=false
	2045	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2046	then
	2047	files_for_cores=true; filetype=directory
	2048	actionout[$i]=""
	2049	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2050	then
	2051	actionout[$i]=""
	2052	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2053	then
	2054	files_for_cores=true; filetype=directory
	2055	link_local_output=true
	2056	actionout[$i]=""
	2057	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2058	then
	2059	link_local_output
	2060	actionout[$i]=""
	2061	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2062	then
	2063	files_for_cores=true; filetype=directory
	2064	actionout[$i]="tr"
	2065	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2066	then
	2067	actionout[$i]="tr"
	2068	fi
	2069
	2070	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2071	then
	2072	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2073	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2074	then
	2075	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2076	else
	2077
	2078
	2079	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2080	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2081	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2082	then
	2083	if [[ $running_on_remote = true ]]
	2084	then
	2085
	2086	# SET OPTIONS FOR TRANSFER
	2087	if [[ "${actionout[$i]}" = tr ]]
	2088	then
	2089	if [[ $files_for_cores = false ]]
	2090	then
	2091	catalog_option=""
	2092	catalog_string=""
	2093	else
	2094	catalog_option="-c"
	2095	catalog_string="/"
	2096	fi
	2097	append_option=""
	2098	append_string=""
	2099	else
	2100	append_option="-A"
	2101	append_string="append"
	2102	fi
	2103
	2104	transfer_failed=false
	2105	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2420]	2106	printf "\n ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2107
	2108	# TRANSFER VIA SCP
	2109	if [[ "$remote_loginnode" != "" ]]
	2110	then
[2420]	2111	echo "cd $TEMPDIR; ${fast_io_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_identifier}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2112	else
[2420]	2113	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_identifier}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2114	fi
	2115	[[ $? != 0 ]] && transfer_failed=true
	2116
	2117
	2118	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2119	if [[ $transfer_failed = true ]]
	2120	then
	2121	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2420]	2122	printf " ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id\n"
[2380]	2123
	2124	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2125	eval local_catalog=${pathout[$i]}
	2126	if [[ ! -d $local_catalog ]]
	2127	then
	2128	printf " *** local directory does not exist. Trying to create:\n"
	2129	printf " $local_catalog \n"
	2130	mkdir -p $local_catalog
	2131	fi
[2420]	2132	eval cp ${localout[$i]} ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id
[2380]	2133	transfer_problems=true
	2134	fi
	2135
	2136	else
	2137
	2138	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2139	# BE COPIED OR APPENDED ON THIS MACHINE
	2140	if [[ "${actionout[$i]}" = tr ]]
	2141	then
	2142	actionout[$i]=""
	2143	else
	2144	actionout[$i]="a"
	2145	fi
	2146	fi
	2147	fi
	2148
	2149
	2150	# APPEND ON THIS MACHINE
	2151	if [[ "${actionout[$i]}" = "a" ]]
	2152	then
	2153	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2154	then
	2155	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2156	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2157	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2158	else
	2159	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2160	printf "\n ${pathout[$i]}\n"
	2161	cat ${localout[$i]} >> ${pathout[$i]}
	2162	fi
	2163	fi
	2164
	2165	# COPY ON THIS MACHINE
	2166	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2167	# ON DIFFERENT FILE-SYSTEMS
	2168	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2169	then
	2170
	2171	# COPY IN CASE OF RUNS ON SINGLE CORES
	2172	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2173	then
	2174	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2175	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2176	if [[ $link_local_output = true ]]
	2177	then
	2178	printf " file will be linked\n"
	2179	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2180	fi
	2181	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2182	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2183	then
	2184	if [[ $link_local_output = true ]]
	2185	then
	2186	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2187	fi
	2188	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2189	else
	2190	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2191	fi
	2192	else
	2193	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2194	printf "\n ${pathout[$i]}\n"
	2195	if [[ $link_local_output = true ]]
	2196	then
	2197	printf " file will be linked\n"
	2198	ln -f ${localout[$i]} ${pathout[$i]}
	2199	fi
	2200	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2201	if [[ ! -f "${pathout[$i]}" ]]
	2202	then
	2203	if [[ $link_local_output = true ]]
	2204	then
	2205	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2206	fi
	2207	cp ${localout[$i]} ${pathout[$i]}
	2208	else
	2209	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2210	fi
	2211	fi
	2212
	2213	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2214	then
	2215
	2216	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2217	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2218	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2219	printf "\n ${pathout[$i]}\n"
	2220	if [[ $link_local_output = true ]]
	2221	then
	2222	printf " files will be linked\n"
[2396]	2223	mkdir -p ${pathout[$i]}
[2380]	2224	cd ${localout[$i]}
	2225	for file in $(ls *)
	2226	do
	2227	ln -f $file ${pathout[$i]}
	2228	done >\|/dev/null 2>&1
	2229	cd $TEMPDIR
	2230	fi
	2231
	2232	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2233	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2234	then
	2235	if [[ $link_local_output = true ]]
	2236	then
	2237	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2238	fi
	2239	cp -r ${localout[$i]}/* ${pathout[$i]}
	2240	fi
	2241
	2242	fi
	2243	fi
	2244	done
	2245
	2246	if (( i != 0 ))
	2247	then
	2248	if [[ $transfer_problems = true ]]
	2249	then
	2250	printf "\n$dashes\n *** OUTPUT-files saved"
	2251	printf "\n +++ WARNING: some data transfers failed! \n"
	2252	else
	2253	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2254	fi
	2255	fi
	2256
	2257
	2258	# IF REQUIRED, START A RESTART-JOB
	2259	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2260	if [[ -f CONTINUE_RUN ]]
	2261	then
	2262
	2263	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2264	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2265	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2266	# -b START A BATCH JOB
	2267	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2268	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2269	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2270
	2271
	2272	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2273	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2274	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2275	then
[2381]	2276	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2277	fi
	2278
	2279
	2280	# START THE RESTART-JOB
	2281	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2282	echo " $prc"
	2283	printf "\n$dashes\n"
	2284	if [[ $running_on_remote = true ]]
	2285	then
	2286
	2287	echo "*** ssh will be used to initiate restart-runs!"
	2288	echo " return_address=\"$return_address\" "
	2289	echo " return_username=\"$local_username\" "
	2290
	2291	if [[ "$remote_loginnode" != "" ]]
	2292	then
[2420]	2293	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]	2294	else
[2420]	2295	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2296	fi
	2297
	2298	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2299	sleep 30
	2300
	2301	else
	2302
	2303	# START THE RESTART JOB ON THE LOCAL HOST
	2304	eval $prc # THE ' MUST BE EVALUATED
	2305	cd - > /dev/null
	2306
	2307	fi
	2308	printf "\n$dashes\n *** restart-run initiated \n"
	2309
	2310
	2311	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2312	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2313	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2314	# MAY BE VERY HUGE)
	2315	(( i = 0 ))
	2316	while (( i < iin ))
	2317	do
	2318	(( i = i + 1 ))
	2319	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2320	then
	2321	rm -r ${absnamein[$i]}
	2322	fi
	2323	done
	2324
	2325	fi
	2326
	2327
	2328	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2329	cd $HOME
	2330	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2331
	2332
	2333	else
	2334
	2335
	2336	# PREPARING ACTIONS,
	2337	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2338
	2339	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2420]	2340	palmrun_com="$palmrun_script_name -d $fname -h $host_identifier -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2341	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2342	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2343	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2344	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2345	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2346	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
	2347	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
	2348	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2349	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2350	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2351	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2352	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2353	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2354	if [[ $create_remote_batch_job = true ]]
	2355	then
	2356	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2357	if [[ $do_trace = true ]]
	2358	then
	2359	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2360	fi
[2380]	2361	elif [[ $create_batch_job = true ]]
	2362	then
	2363	palmrun_com=${palmrun_com}" -j"
[2420]	2364	if [[ $do_trace = true ]]
	2365	then
	2366	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2367	fi
[2380]	2368	fi
	2369
	2370
	2371	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2372	# REMOTE HOST
[2420]	2373	job_protocol_file_local=${local_jobcatalog}/${host_identifier}_${job_id}
[2380]	2374	job_protocol_file=$job_protocol_file_local
	2375	if [[ $create_remote_batch_job = true ]]
	2376	then
[2420]	2377	job_protocol_file_remote=${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2378	job_protocol_file=$job_protocol_file_remote
	2379	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2380	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2381	fi
	2382
	2383
	2384	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2385	jobfile=jobfile.$run_id
	2386
	2387
	2388	# FIRST CREATE THE BATCH DIRECTIVES
	2389	(( i = 0 ))
	2390	while (( i < ibd ))
	2391	do
	2392	(( i = i + 1 ))
[2479]	2393	line=`echo "${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}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2394	eval line=\"$line\"
	2395	echo "$line" >> $jobfile
	2396	done
	2397	echo " " >> $jobfile
	2398
	2399
	2400	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2401	# PROTOCOL
	2402	if [[ $create_remote_batch_job = true ]]
	2403	then
	2404	echo "set +vx" >> $jobfile
	2405	echo "trap '" >> $jobfile
	2406	echo "set +vx" >> $jobfile
	2407	echo "cd ${remote_jobcatalog}" >> $jobfile
	2408	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2409
	2410	# ADD THE BATCH DIRECTIVES
	2411	(( i = 0 ))
	2412	while (( i < ibdt ))
	2413	do
	2414	(( i = i + 1 ))
[2479]	2415	line=`echo "${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}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2416	eval line=\"$line\"
	2417	echo "$line" >> $jobfile
	2418	done
	2419	echo " " >> $jobfile
	2420
	2421	echo "set -x" >> $jobfile
[2420]	2422	echo "${fast_io_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_identifier}_${fname}" >> $jobfile
[2380]	2423	echo "%%END%%" >> $jobfile
	2424	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2425	echo "$submit_command $scpjob_file" >> $jobfile
	2426	echo "rm $scpjob_file" >> $jobfile
[2404]	2427	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2428	echo "set -x" >> $jobfile
	2429	echo " ' exit" >> $jobfile
	2430	fi
	2431
	2432
	2433	# ACTIVATE ERROR-TRACEBACK
	2434	if [[ $do_trace = true ]]
	2435	then
	2436	echo "set -x" >> $jobfile
	2437	else
	2438	echo "set +vx" >> $jobfile
	2439	fi
	2440
	2441
	2442	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2443	if [[ "$login_init_cmd" != "" ]]
	2444	then
	2445	echo "$login_init_cmd" >> $jobfile
	2446	fi
	2447	if [[ "$module_commands" != "" ]]
	2448	then
	2449	echo "$module_commands" >> $jobfile
	2450	fi
	2451
	2452
	2453	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2454	echo "mkdir $TEMPDIR" >> $jobfile
	2455	echo "cd $TEMPDIR" >> $jobfile
	2456	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2404]	2457	echo "cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
[2380]	2458	echo "export PATH=.:\$PATH" >> $jobfile
	2459	echo "export execute_palmrun=true" >> $jobfile
	2460
	2461
	2462	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2463	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2464	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2465	if [[ $create_remote_batch_job = true ]]
	2466	then
	2467	(( i = 0 ))
	2468	while (( i < iin ))
	2469	do
	2470	(( i = i + 1 ))
	2471	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2472	if [[ "${transin[$i]}" = job ]]
	2473	then
	2474	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2475	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2476	echo " " >> $jobfile
	2477	echo "%END%" >> $jobfile
	2478	else
	2479	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2480	fi
	2481
	2482	# CHECK, IF FILE COULD BE CREATED
	2483	echo "if [[ \$? = 1 ]]" >> $jobfile
	2484	echo "then" >> $jobfile
	2485	echo " echo \" \" " >> $jobfile
	2486	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2420]	2487	echo " echo \" please check, if directory exists on $host_identifier!\" " >> $jobfile
[2380]	2488	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2489	echo " execute_palmrun=false" >> $jobfile
	2490	echo "fi" >> $jobfile
	2491	done
	2492	fi
	2493
	2494
	2495	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2496	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2497	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2498	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2499	echo "export LOCAL_PWD" >> $jobfile
	2500
	2501
	2502	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2503	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2504	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2505
	2506
	2507	# CALL PALMRUN WITHIN THE JOB
	2508	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2509	echo "set -x" >> $jobfile
	2510	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2511
	2512
	2513	# TRANSFER JOBFILE TO THE TARGET HOST
	2514	if [[ $create_jobfile_only = false ]]
	2515	then
	2516
	2517	if [[ $create_remote_batch_job = true ]]
	2518	then
	2519
[2420]	2520	echo " "
	2521	echo " *** transfer of job to remote host via scp"
	2522	if [[ $do_trace = true ]]
	2523	then
	2524	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}"
	2525	fi
	2526	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2527
	2528	echo " "
[2420]	2529	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2530	if [[ $do_trace = true ]]
	2531	then
	2532	echo " cd $remote_jobcatalog; $submit_command ${host_identifier}_${job_id}; rm ${host_identifier}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
	2533	fi
	2534	echo "cd $remote_jobcatalog; $submit_command ${host_identifier}_${job_id}; rm ${host_identifier}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2535
	2536	elif [[ $create_batch_job = true ]]
	2537	then
	2538
[2385]	2539	eval local_jobcatalog=$local_jobcatalog
[2420]	2540	cp $jobfile ${local_jobcatalog}/${host_identifier}_${job_id}
[2385]	2541	cd $local_jobcatalog
[2380]	2542	echo " "
[2420]	2543	echo " *** submit the job"
	2544	if [[ $do_trace = true ]]
	2545	then
	2546	echo "$submit_command ${host_identifier}_${job_id}"
	2547	fi
	2548	$submit_command ${host_identifier}_${job_id}
	2549	rm ${host_identifier}_${job_id}
[2380]	2550	cd - > /dev/null
	2551
	2552	fi
	2553
	2554	rm -rf $jobfile
	2555
	2556	else
	2557
	2558	printf "\n *** jobfile created under name \"$jobfile\" "
	2559	printf "\n no batch-job has been sent!"
	2560
	2561	fi
	2562
	2563	fi # END OF REMOTE-PART

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