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source: palm/trunk/SCRIPTS/palmrun @ 2429

Last change on this file since 2429 was 2422, checked in by raasch, 7 years ago
new palm-scripts set to version number 1.0, further check for consistent restart settings
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 84.3 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 2422 2017-09-08 08:25:41Z gronemeier $
[2410]	29	# initial revision
[2380]	30	#
	31	#--------------------------------------------------------------------------------#
	32	# palmrun - script for running PALM jobs on local and remote hosts
	33	#--------------------------------------------------------------------------------#
	34
	35
	36
	37	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	38
	39	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	40	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	41	# (TOO MANY ARGUMENTS - PROBLEM)
	42	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	43
	44	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	45	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	46	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	47	# SCRIPT-OPTION ARGUMENTS
	48	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	49	typeset -i icycle inode ival maxcycle mpi_tasks
	50	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	51
	52	activation_string_list=""
	53	AddFilenames=""
	54	combine_plot_fields=true
	55	compiler_name=""
	56	compiler_name_ser=""
	57	compiler_options=""
	58	cores=""
	59	cores_atmos=0
	60	cores_ocean=0
	61	coupled_dist=""
	62	cpp_options=""
	63	cpumax=0
	64	create_jobfile_only=false
	65	delete_temporary_catalog=true
	66	create_batch_job=false
	67	create_remote_batch_job=false
	68	dashes=" ----------------------------------------------------------------------------"
	69	defaultqueue=""
	70	do_compile=true
	71	do_trace=false
	72	executable=""
	73	execute_command=""
	74	execution_error=false
	75	fileconnection_file=.palm.iofiles
	76	fname=test
	77	global_revision=""
[2420]	78	host_identifier="default"
[2380]	79	hostfile=""
	80	hp=""
	81	keep_data_from_previous_run=false
	82	link_local_input=false
	83	link_local_output=false
[2388]	84	linker_options=""
[2385]	85	local_jobcatalog=""
[2380]	86	locat=normal
	87	makefile=""
	88	max_par_io_str=""
	89	prc=$0
	90	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	91	do
	92	prc=`echo $prc \| cut -f2- -d"/"`
	93	done
	94	module_calls=""
	95	palmrun_script_name=$prc
	96	openmp=false
	97	queue=none
	98	restart_run=false
	99	return_address=""
[2385]	100	remote_jobcatalog=""
[2380]	101	remote_username=""
	102	running_in_batch_mode=false
	103	run_coupled_model=false
	104	run_id=""
	105	silent=false
	106	source_list=""
	107	source_path=""
	108	tasks_per_node=""
	109	threads_per_task=1
	110	tmpcreate=false
	111	transfer_problems=false
[2384]	112	user_source_path=""
[2380]	113	use_openmp=false
[2422]	114	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	115	working_directory=`pwd`
	116	write_binary=""
	117	TOPT=""
	118
	119
	120	# ERROR HANDLING IN CASE OF EXIT
[2404]	121	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	122	then
	123
	124	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	125	(( i = 0 ))
	126	while (( i < iec ))
	127	do
	128	(( i = i + 1 ))
	129	printf "\n *** Execution of ERROR-command:\n"
	130	printf " >>> ${err_command[$i]}\n"
	131	eval ${err_command[$i]}
	132	done
[2405]	133	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	134	printf "\n\n+++ palmrun killed \n\n"
	135	elif [[ $locat != control_c ]]
	136	then
	137	printf "\n\n --> palmrun finished\n\n"
	138	if [[ $running_on_remote = true ]]
	139	then
	140	printf " Bye, bye $remote_username !!\n\n"
	141	else
	142	printf " Bye, bye $local_username !!\n\n"
	143	fi
	144	fi' exit
	145
	146
	147	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	148	trap 'cd; rm -rf $TEMPDIR
[2380]	149	printf "\n+++ palmrun killed by \"^C\" \n\n"
	150	locat=control_c
	151	exit
	152	' 2
	153
	154
	155	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	156	# WHICH WILL BE USED TO START RESTART-JOBS
[2420]	157	while getopts :a:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
[2380]	158	do
	159	case $option in
	160	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
	161	(b) create_batch_job=true; prc="$prc -b";;
	162	(B) delete_temporary_catalog=false; prc="$prc -B";;
	163	(C) restart_run=true; prc="$prc -C";;
	164	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	165	(F) create_jobfile_only=true;;
	166	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2420]	167	(h) host_identifier=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	168	(j) running_in_batch_mode=true;;
	169	(k) keep_data_from_previous_run=true; prc="$prc -k";;
	170	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
	171	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	172	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	173	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	174	(r) run_id=$OPTARG;;
	175	(R) return_address=$OPTARG;;
	176	(s) source_list=$OPTARG;;
	177	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
	178	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	179	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	180	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	181	(v) silent=true; prc="$prc -v";;
	182	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
	183	(x) do_trace=true;set -x; prc="$prc -x";;
	184	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
	185	(y) ocean_file_appendix=true; prc="$prc -y";;
	186	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	187	(Z) combine_plot_fields=false; prc="$prc -Z";;
	188	(\?) printf "\n +++ unknown option $OPTARG \n"
	189	printf "\n --> type \"$0 ?\" for available options \n"
	190	locat=parameter;exit;;
	191	esac
	192	done
	193
	194
	195	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	196	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	197	(( to_shift = $OPTIND - 1 ))
	198	shift $to_shift
	199
	200	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	201	if [[ "$1" = "?" ]]
	202	then
	203	(printf "\n *** Description of available palmrun options:\n"
	204	printf "\n Option Description Default-Value"
	205	printf "\n -a activation string list \"\" "
	206	printf "\n -b batch-job on local machine ---"
	207	printf "\n -B do not delete temporary directory at end ---"
	208	printf "\n -d base name of files attached to program test"
	209	printf "\n -F create batch job file only ---"
[2420]	210	printf "\n -h host identifier \"default\" "
[2380]	211	printf "\n -k keep data from previous run"
	212	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	213	printf "\n -M Makefile name Makefile"
	214	printf "\n -O threads per openMP task ---"
	215	printf "\n -q queue \"$queue\" "
	216	printf "\n -s filenames of routines to be compiled \"\" "
	217	printf "\n must end with .f, .f90, .F, or .c !"
	218	printf "\n use \"..\" for more than one file and wildcards"
	219	printf "\n -s LM compiles all locally modified files"
	220	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	221	printf "\n -T tasks per node ---"
[2380]	222	printf "\n -u username on remote machine \"\" "
	223	printf "\n -v no prompt for confirmation ---"
	224	printf "\n -w maximum parallel io streams as given by -X"
	225	printf "\n -x tracing of palmrun for debug purposes ---"
	226	printf "\n -X # of processors (on parallel machines) 1"
	227	printf "\n -y add appendix \"_O\" to all local output"
	228	printf "\n files (ocean precursor runs followed by"
	229	printf "\n coupled atmosphere-ocean runs) ---"
	230	printf "\n -Y run coupled model, \"#1 #2\" with"
	231	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	232	printf "\n -Z skip combine_plot_fields at the end of "
	233	printf "\n the simulation ---"
	234	printf "\n "
	235	printf "\n Possible values of positional parameter <modus>:"
	236	printf "\n \"?\" - this outline \n\n") \| more
	237	exit
	238	elif [[ "$1" != "" ]]
	239	then
	240	printf "\n +++ positional parameter $1 unknown \n"
	241	locat=parameter; exit
	242	fi
	243
	244
	245
	246	# SHORT STARTING MESSAGE
	247	printf "\n*** $version "
	248	printf "\n will be executed. Please wait ..."
	249
	250
	251	# BUILD THE CONFIGURATION-FILE NAME
[2420]	252	config_file=.palm.config.$host_identifier
[2380]	253
	254
	255	# CHECK, IF CONFIGURATION FILE EXISTS
	256	if [[ ! -f $config_file ]]
	257	then
	258	printf "\n\n +++ configuration file: "
	259	printf "\n $config_file"
	260	printf "\n does not exist"
	261	locat=connect; exit
	262	fi
	263
	264
	265	# CHECK, IF FILE CONNECTION FILE EXISTS
	266	if [[ ! -f $fileconnection_file ]]
	267	then
	268	printf "\n\n +++ file connection file: "
	269	printf "\n $fileconnection_file"
	270	printf "\n does not exist"
	271	locat=connect; exit
	272	fi
	273
	274
[2404]	275	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	276	if [[ "$activation_string_list" = "" ]]
	277	then
	278	printf "\n\n +++ no activation string list given: "
	279	printf "\n please set palmrun option \"-a\" "
	280	locat=palmrun_option; exit
	281	fi
	282
	283
	284	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	285	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	286	then
	287	write_binary=true
	288	else
	289	write_binary=false
	290	fi
	291
	292
[2380]	293	# READ AND EVALUATE THE CONFIGURATION-FILE
	294	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	295
	296	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	297	while read line
	298	do
	299
	300	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	301	eval line=\"$line\"
	302
	303
	304	# INTERPRET THE LINE
	305	if [[ "$(echo $line)" = "" ]]
	306	then
	307
	308	# EMPTY LINE, NO ACTION
	309	continue
	310
	311	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	312	then
	313
	314	# LINE IS A COMMENT LINE
	315	continue
	316
	317	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	318	then
	319
	320	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	321	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	322	value=`echo $line \| cut -d" " -s -f2-`
	323
	324
	325	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	326	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	327	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	328	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	329	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	330	# CONFIGURATION-FILE.
	331	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	332	then
	333	eval export $var="\$value"
	334
	335	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	336	if [[ $do_trace = true ]]
	337	then
	338	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	339	fi
	340	fi
	341
	342	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	343	then
	344
	345	# LINE DEFINES BATCH-DIRECTIVE
	346	(( ibd = ibd + 1 ))
	347	line=$(echo $line \| cut -c4-)
	348	batch_directive[$ibd]="$line"
	349
	350	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	351	then
	352
	353	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	354	# REMOTE TO A LOCAL HOST
	355	(( ibdt = ibdt + 1 ))
	356	line=$(echo $line \| cut -c5-)
	357	batch_directive_transfer[$ibdt]="$line"
	358
	359	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	360	then
	361
	362	# LINE DEFINES ERROR-COMMAND
	363	(( iec = iec + 1 ))
	364	line=$(echo $line \| cut -c4-)
	365	err_command[$iec]="$line"
	366
	367	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	368	then
	369
	370	# LINE DEFINES INPUT-COMMAND
	371	(( iic = iic + 1 ))
	372	line=$(echo $line \| cut -c4-)
	373	in_command[$iic]="$line"
	374
	375	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	376	then
	377
	378	# LINE DEFINES OUTPUT-COMMAND
	379	(( ioc = ioc + 1 ))
	380	line=$(echo $line \| cut -c4-)
	381	out_command[$ioc]="$line"
	382
	383	else
	384
	385	# SKIP ALL OTHER LINES
	386	continue
	387
	388	fi
	389
	390	done < $config_file
	391
	392
	393	# CHECK SETTING OF REQUIRED PARAMETERS
	394	if [[ "$compiler_name" = "" ]]
	395	then
	396	printf "\n +++ no compiler name found in $config_file"
	397	printf "\n Please add line \"compiler_name ...\" to that file."
	398	locat=config_file; exit
	399	fi
	400	if [[ "$compiler_name_ser" = "" ]]
	401	then
	402	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	403	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	404	locat=config_file; exit
	405	fi
	406	if [[ "$compiler_options" = "" ]]
	407	then
	408	printf "\n +++ no compiler options found in $config_file"
	409	printf "\n Please add line \"compiler_options ...\" to that file."
	410	locat=config_file; exit
	411	fi
[2388]	412	if [[ "$linker_options" = "" ]]
[2380]	413	then
[2388]	414	printf "\n +++ no linker options found in $config_file"
	415	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	416	locat=config_file; exit
	417	fi
	418	if [[ "$execute_command" = "" ]]
	419	then
	420	printf "\n +++ no execute command found in $config_file"
	421	printf "\n Please add line \"execute_command ...\" to that file."
	422	locat=config_file; exit
	423	fi
	424
	425	if [[ "$hostfile" != "" ]]
	426	then
	427	if [[ $hostfile != auto && ! -f $hostfile ]]
	428	then
	429	printf "\n +++ no hostfile \"$hostfile\" found"
	430	printf "\n Please check line \"hostfile ...\" in $config_file"
	431	locat=config_file; exit
	432	fi
	433	fi
	434
	435
	436	# DETERMINE THE CALL STATUS
	437	if [[ "$return_address" != "" ]]
	438	then
	439
	440	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	441	# BATCH MODE AND ...
	442	running_on_remote=true
	443
	444	else
	445
	446	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	447	if [[ "$remote_ip" != "" ]]
	448	then
	449
	450	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	451	create_remote_batch_job=true
	452
	453	fi
	454	running_on_remote=false
	455	fi
	456
	457
	458
	459	# READ AND EVALUATE THE I/O-FILE LIST
	460	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	461
	462	# READ THE FILE CONNECTION FILE LINE BY LINE
	463	while read line
	464	do
	465
	466	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	467	eval line=\"$line\"
	468
	469
	470	# INTERPRET THE LINE
	471	if [[ "$(echo $line)" = "" ]]
	472	then
	473	# EMPTY LINE, NO ACTION
	474	continue
	475
	476	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	477	then
	478
	479	# LINE IS A COMMENT LINE
	480	true
	481
	482	else
	483
	484	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	485	# s2a: in/out - field
	486	# s2b: loc - field (optional)
	487	# s2c: tr/ar - field (optional)
	488	s1=`echo $line \| cut -d" " -f1`
	489	s2=`echo $line \| cut -d" " -s -f2`
	490	s2a=$(echo $s2 \| cut -d":" -f1)
	491	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	492	then
	493	s2b=""
	494	s2c=""
	495	else
	496	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	497	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	498	fi
	499	s3=`echo $line \| cut -d" " -f3`
	500	s4=`echo $line \| cut -d" " -s -f4`
	501	s5=`echo $line \| cut -d" " -s -f5`
	502	s6=`echo $line \| cut -d" " -s -f6`
	503
	504
	505	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	506	# INPUT- OR OUTPUT-LIST.
	507	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	508	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	509	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	510	# IS NOT CHECKED AND STORED.
	511	IFSALT="$IFS"; IFS="$IFS:"
	512	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	513	then
	514	found=false
	515	for actual in $activation_string_list
	516	do
	517	for formal in $s3
	518	do
	519	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	520	done
	521	done
	522	if [[ $found = true ]]
	523	then
	524	(( iin = iin + 1 ))
	525	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	526	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	527	extin[$iin]=$s6
	528	fi
	529	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	530	then
	531	found=false
	532	for actual in $activation_string_list
	533	do
	534	for formal in $s3
	535	do
	536	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	537	done
	538	done
	539	if [[ $found = true ]]
	540	then
	541	(( iout = iout + 1 ))
	542	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	543	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	544	fi
	545	elif [[ "$s2a" != in && "$s2a" != out ]]
	546	then
	547	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	548	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	549	locat=connect; exit
	550	fi
	551	IFS="$IFSALT"
	552	fi
	553
	554	done < $fileconnection_file
	555
	556
	557
	558	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	559	if [[ $run_coupled_model = true ]]
	560	then
	561
	562	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	563	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	564
	565	if (( $cores_ocean + $cores_atmos != $cores ))
	566	then
	567
	568	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	569	printf "\n PEs (total) : $cores"
	570	printf "\n PEs (atmosphere): $cores_atmos"
	571	printf "\n PEs (ocean) : $cores_ocean"
	572	locat=coupling; exit
	573
	574	fi
	575
	576	fi
	577
	578
	579	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
	580	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
	581	palmrun_memory=$memory
	582	palmrun_cpumax=$cpumax
	583	palmrun_cores=$cores
	584
	585
	586	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
	587	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
	588	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
	589	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	590	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	591	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	592
	593
	594
	595	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	596	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	597	# FOLDER
	598	if [[ $running_in_batch_mode = true ]]
	599	then
	600
[2404]	601	if [[ ! -d ${fast_io_catalog}/SOURCES_FOR_RUN_$fname ]]
[2380]	602	then
[2404]	603	printf "\n +++ directory ${fast_io_catalog}/SOURCES_FOR_RUN_$fname is missing"
[2380]	604	printf "\n Please check the output of the palmrun-call"
	605	printf "\n that you did on your local host."
	606	locat=SOURCES_FOR_RUN; exit
	607	fi
	608
	609	else
	610
	611	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	612	# AUTOMATIC RESTART RUN
	613	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	614	if [[ $restart_run = false ]]
	615	then
	616
	617	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	618	# THE LOCAL HOST
	619	if [[ ! -d $source_path ]]
	620	then
	621	printf "\n\n +++ source path \"$source_path\" on local host"
	622	printf "\n \"$(hostname)\" does not exist"
	623	locat=source_path; exit
	624	fi
	625
[2396]	626	rm -rf SOURCES_FOR_RUN_$fname
	627	mkdir -p SOURCES_FOR_RUN_$fname
[2380]	628
	629	if [[ "$source_list" = LM ]]
	630	then
	631
	632	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	633	source_list=""
	634	cd $source_path
	635
	636
	637	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	638	if [[ ! -d .svn ]]
	639	then
	640	printf "\n\n +++ source directory"
	641	printf "\n \"$source_path\" "
	642	printf "\n is not under control of \"subversion\"."
	643	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	644	fi
	645
	646
	647	# LIST ALL MODIFIED SOURCE CODE FILES
	648	Filenames=""
[2404]	649	svn status > tmp_svnstatus
[2380]	650	while read line
	651	do
	652	firstc=`echo $line \| cut -c1`
	653	if [[ $firstc = M \|\| $firstc = "?" ]]
	654	then
	655	Name=`echo "$line" \| cut -c8-`
	656	extension=`echo $Name \| cut -d. -f2`
	657	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	658	then
	659	Filenames="$Filenames "$Name
	660	fi
	661	fi
[2404]	662	done < tmp_svnstatus
	663	rm -rf tmp_svnstatus
[2380]	664
	665
	666	# COPY FILES TO SOURCES_FOR_RUN_...
	667	for filename in $Filenames
	668	do
	669	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	670	source_list=$source_list"$filename "
	671	done
	672
	673	cd - > /dev/null
	674
	675
	676	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	677	elif [[ "$source_list" != "" ]]
	678	then
	679
	680	cd $source_path
	681
	682	for filename in $source_list
	683	do
	684
	685	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	686	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	687	then
	688	printf "\n +++ source code file: $filename"
	689	printf "\n must not contain (\"/\") "
	690	locat=source; exit
	691	fi
	692
	693	if [[ ! -f $filename ]]
	694	then
	695	printf "\n +++ source code file: $filename"
	696	printf "\n does not exist"
	697	locat=source; exit
	698	else
	699	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	700	fi
	701
	702	done
	703
	704	cd - > /dev/null
	705
	706	fi
	707
	708	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	709	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	710	if [[ ! -f $makefile ]]
	711	then
	712	printf "\n +++ file \"$makefile\" does not exist"
	713	locat=make; exit
	714	else
	715	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	716	fi
	717
	718
	719	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	720	if [[ "$user_source_path" != "" ]]
[2380]	721	then
	722
	723	# DOES THE DIRECTORY EXIST?
[2384]	724	if [[ ! -d $user_source_path ]]
[2380]	725	then
	726
	727	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	728	printf "\n \"$user_source_path\" "
[2380]	729	printf "\n does not exist or is not a directory."
	730	printf "\n No source code will be used from this directory!\n"
[2384]	731	user_source_path=""
[2380]	732	if [[ $silent == false ]]
	733	then
	734	sleep 2
	735	fi
	736
	737	else
	738
[2384]	739	cd $user_source_path
[2380]	740	found=false
	741
	742	Names=$(ls -1 *.f90 2>&1)
	743	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	744	Names=$(ls -1 *.F90 2>&1)
	745	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	746	Names=$(ls -1 *.F 2>&1)
	747	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	748	Names=$(ls -1 *.f 2>&1)
	749	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	750	Names=$(ls -1 *.c 2>&1)
	751	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	752
	753	cd - > /dev/null
	754	cd SOURCES_FOR_RUN_$fname
	755
	756	# COPY MAKEFILE IF EXISTING
[2384]	757	if [[ -f $user_source_path/Makefile ]]
[2380]	758	then
	759	printf "\n\n *** user Makefile from directory"
[2384]	760	printf "\n \"$user_source_path\" is used \n"
[2380]	761	if [[ $silent == false ]]
	762	then
	763	sleep 1
	764	fi
[2384]	765	cp $user_source_path/Makefile .
[2380]	766	fi
	767
	768	for filename in $AddFilenames
	769	do
	770	if [[ -f $filename ]]
	771	then
	772	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	773	printf "\n source code directory \"$user_source_path\" "
[2380]	774	printf "\n but was also given with option \"-s\" which means that it should be taken"
	775	printf "\n from directory \"$source_path\"."
	776	locat=source; exit
	777	fi
	778
[2384]	779	cp $user_source_path/$filename .
[2380]	780	source_list="$source_list $filename"
	781
	782	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	783	if [[ $(grep -c $filename Makefile) = 0 ]]
	784	then
	785	printf "\n\n +++ user file \"$filename\" "
	786	printf "\n is not listed in Makefile \n"
	787	locat=source; exit
	788	else
	789
	790	if [[ $found = false ]]
	791	then
	792	found=true
	793	printf "\n\n *** following user file(s) added to the"
	794	printf " files to be translated:\n "
	795	fi
	796	printf "$filename "
	797	if [[ $silent == false ]]
	798	then
	799	sleep 0.5
	800	fi
	801
	802	fi
	803	done
	804	[[ $found = true ]] && printf "\n"
	805	cd - > /dev/null
	806	fi
	807	fi
	808
	809	# COPY CONFIGURATION FILES
	810	cp $config_file SOURCES_FOR_RUN_$fname
	811	cp $fileconnection_file SOURCES_FOR_RUN_$fname
	812
	813	# COPY SHELLSCRIPTS
	814	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
	815	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
	816
	817	fi
	818
	819	fi
	820
	821	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	822	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	823	if [[ "$global_revision" = "" ]]
	824	then
	825	global_revision=`svnversion $source_path 2>/dev/null`
	826	global_revision="Rev: $global_revision"
	827	fi
	828
	829
	830	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	831	if [[ -n $cores ]]
	832	then
	833
	834	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	835	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2384]	836	if [[ "$tasks_per_node" = "" ]]
[2380]	837	then
	838	printf "\n"
	839	printf "\n +++ option \"-T\" (tasks per node) is missing"
	840	printf "\n set -T option or define tasks_per_node in the config file"
	841	locat=tasks_per_node; (( iec = 0 )); exit
	842	fi
	843
	844	if (( cores < tasks_per_node ))
	845	then
	846	printf "\n"
	847	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	848	printf "\n given values: -T $tasks_per_node -X $cores"
	849	locat=tasks_per_node; (( iec = 0 )); exit
	850	fi
	851
	852	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	853	(( mpi_tasks = cores / threads_per_task ))
	854	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	855	(( ii = cores / tasks_per_node ))
	856	(( remaining_cores = cores - ii * tasks_per_node ))
	857	if (( remaining_cores > 0 ))
	858	then
	859	printf "\n"
	860	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	861	printf "\n divisor of the total number of cores (option \"-X\")"
	862	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	863	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	864	(( nodes = nodes + 1 ))
	865	fi
	866
	867	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	868	if [[ "$tasks_per_node" != "" ]]
	869	then
	870	TOPT="-T $tasks_per_node"
	871	fi
	872
	873	fi
	874
	875
	876	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	877	if [[ "$maximum_parallel_io_streams" = "" ]]
	878	then
	879	maximum_parallel_io_streams=$cores
	880	fi
	881
	882
	883	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	884	if [[ "$scp_port" != "" ]]
	885	then
	886	PORTOPT="-P $scp_port"
	887	SSH_PORTOPT="-p $scp_port"
	888	fi
	889
	890
	891	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	892	# CONFIG-FILE
	893	if [[ "$ssh_key" != "" ]]
	894	then
	895	ssh_key="-i $HOME/.ssh/$ssh_key"
	896	fi
	897
	898
	899	# SET QUEUE, IF NOT GIVEN
	900	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	901	then
	902
	903	if [[ $queue = none && "$defaultqueue" = "" ]]
	904	then
	905	printf "\n"
	906	printf "\n +++ no default queue given in configuration file and no queue"
	907	printf "\n given with option -q"
	908	fi
	909	if [[ $queue = none ]]
	910	then
	911	queue=$defaultqueue
	912	fi
	913
	914	fi
	915
	916
	917	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	918	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	919	(( i = 0 ))
	920	while (( i < iin ))
	921	do
	922	(( i = i + 1 ))
	923	(( maxcycle = 0 ))
	924
	925	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	926	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	927	if [[ "${actionin[$i]}" = di ]]
	928	then
	929	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	930	# HOST ONLY
	931	eval filename=${pathin[$i]}/${endin[$i]}
	932	else
	933	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	934	# HOST ONLY
	935	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	936	fi
	937	eval pathname=${pathin[$i]}
	938
	939	# CHECK IF FILE EXISTS
	940	if ! ls $filename* 1>/dev/null 2>&1
	941	then
	942
	943	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	944	if [[ "${transin[$i]}" != "locopt" ]]
	945	then
	946	printf "\n\n +++ INPUT-file: "
	947	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	948	then
	949	printf "\n $filename"
	950	else
	951	printf "\n $filename.${extin[$i]}"
	952	fi
	953	printf "\n does not exist\n"
	954	locat=input; exit
	955	else
	956	transin[$i]="unavailable"
	957	fi
	958	else
	959
	960	# DETERMINE THE FILE'S CYCLE NUMBER
	961	ls -1 -d $filename > filelist 2>/dev/null
	962	ls -1 -d $filename.* >> filelist 2>/dev/null
	963	while read line
	964	do
	965	# filename without path (i.e. after the last "/")
	966	basefilename=$(basename ${line})
	967
	968	# check if there is an extension
	969	extension=${basefilename##*.}
	970	if [[ "$extension" = "$extin[$i]" ]]
	971	then
	972	basefilename=${basefilename&.*}
	973	fi
	974
	975	# check for an existing cycle number
	976	cycle=${basefilename##*.}
	977	if [[ $cycle =~ ^-?[0-9]+$ ]]
	978	then
	979	(( icycle = $cycle ))
	980	else
	981	(( icycle = 0 ))
	982	fi
	983
	984	if (( icycle > maxcycle ))
	985	then
	986	(( maxcycle = icycle ))
	987	fi
	988
	989	done <filelist
	990	rm filelist
	991
	992	# APPEND CYCLE NUMBER TO FILENAME
	993	if (( maxcycle > 0 ))
	994	then
	995	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	996	then
	997	filename=${filename}.$maxcycle.${extin[$i]}
	998	else
	999	filename=${filename}.$maxcycle
	1000	fi
	1001	else
	1002	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1003	then
	1004	filename=${filename}.${extin[$i]}
	1005	fi
	1006	fi
	1007
	1008	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1009	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1010	absnamein[$i]=$filename
	1011	if (( maxcycle > 0 ))
	1012	then
	1013	if [[ "${actionin[$i]}" = di ]]
	1014	then
	1015	frelin[$i]=${endin[$i]}.$maxcycle
	1016	else
	1017	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1018	fi
	1019	else
	1020	if [[ "${actionin[$i]}" = di ]]
	1021	then
	1022	frelin[$i]=${endin[$i]}
	1023	else
	1024	frelin[$i]=${fname}${endin[$i]}
	1025	fi
	1026	fi
	1027
	1028	fi
	1029	done
	1030
	1031
	1032	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1033	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1034	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1035	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1036	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1037	# REMOTE HOST)
	1038	(( i = 0 ))
	1039	while (( i < iout ))
	1040	do
	1041	(( i = i + 1 ))
	1042	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1043	then
	1044	if [[ "${actionout[$i]}" = tr ]]
	1045	then
	1046	actionout[$i]=""
	1047	elif [[ "${actionout[$i]}" = trpe ]]
	1048	then
	1049	actionout[$i]=pe
	1050	elif [[ "${actionout[$i]}" = tra ]]
	1051	then
	1052	actionout[$i]=a
	1053	fi
	1054	(( maxcycle = 0 ))
	1055	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1056	eval catalogname=${pathout[$i]}
	1057	if ! ls $filename* 1>/dev/null 2>&1
	1058	then
	1059
	1060	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1061	if cat /dev/null > $filename
	1062	then
	1063	rm $filename
	1064	else
	1065
	1066	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1067	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1068	if [[ ! -d $catalogname ]]
	1069	then
	1070	if mkdir -p $catalogname
	1071	then
	1072	printf "\n\n *** directory:"
	1073	printf "\n $catalogname"
	1074	printf "\n was created\n"
	1075	else
	1076	printf "\n\n +++ OUTPUT-file:"
	1077	printf "\n $filename"
	1078	printf "\n cannot be created, because directory does not exist"
	1079	printf "\n and cannot be created either"
	1080	printf "\n"
	1081	locat=output ; exit
	1082	fi 2>/dev/null
	1083	else
	1084	printf "\n\n +++ OUTPUT-file:"
	1085	printf "\n $filename"
	1086	printf "\n cannot be created, although directory exists"
	1087	printf "\n"
	1088	locat=output ; exit
	1089	fi
	1090	fi 2>/dev/null
	1091	else
	1092
	1093	# DETERMINE THE CYCLE NUMBER
	1094	ls -1 -d $filename > filelist 2>/dev/null
	1095	ls -1 -d $filename.* >> filelist 2>/dev/null
	1096	while read line
	1097	do
	1098
	1099	# filename without path (i.e. after the last "/")
	1100	basefilename=$(basename ${line})
	1101
	1102	# check if there is an extension
	1103	extension=${basefilename##*.}
	1104	if [[ "$extension" = "${extout[$i]}" ]]
	1105	then
	1106	basefilename=${basefilename%.*}
	1107	fi
	1108
	1109	# check for an existing cycle number
	1110	cycle=${basefilename##*.}
	1111	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1112	then
	1113	(( icycle = $cycle + 1 ))
	1114	else
	1115	(( icycle = 1 ))
	1116	fi
	1117
	1118	if (( icycle > maxcycle ))
	1119	then
	1120	(( maxcycle = icycle ))
	1121	fi
	1122
	1123	done <filelist
	1124	rm filelist
	1125	fi
	1126
	1127	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1128	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1129	if [[ "${actionout[$i]}" != a ]]
	1130	then
	1131	if (( maxcycle > 0 ))
	1132	then
	1133	filename_tmp=${filename}.$maxcycle
	1134	if cat /dev/null > $filename_tmp
	1135	then
	1136	rm $filename_tmp
	1137	else
	1138	printf "\n +++ OUTPUT-file:"
	1139	printf "\n $filename_tmp"
	1140	printf "\n cannot be created"
	1141	locat=output ; exit
	1142	fi
	1143	fi
	1144	else
	1145	(( maxcycle = maxcycle - 1 ))
	1146	fi
	1147
	1148	(( cycnum[$i] = maxcycle ))
	1149	pathout[$i]=$filename
	1150
	1151	fi
	1152	done
	1153
	1154
	1155	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1156	if [[ $running_in_batch_mode = false ]]
	1157	then
	1158	run_id=$RANDOM
	1159	job_id=${fname}.$run_id
	1160
[2404]	1161	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1162	fi
	1163
	1164
	1165	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1166	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1167	then
	1168
	1169	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1170	if [[ $ibd = 0 ]]
	1171	then
	1172	printf "\n"
	1173	printf "\n +++ no batch directives found in configuration file"
	1174	locat=config_file_batch_directives; (( iec = 0 )); exit
	1175	fi
	1176
	1177	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1178	done=false
[2384]	1179	cputime=$cpumax
[2380]	1180	while [[ $done = false ]]
	1181	do
[2384]	1182	if (( cputime == 0 ))
[2380]	1183	then
	1184	printf "\n +++ cpu-time is undefined"
	1185	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1186	printf "\n >>> "
[2384]	1187	read cputime 1>/dev/null 2>&1
[2380]	1188	else
	1189	done=true
	1190	fi
	1191	done
[2420]	1192	cpumax=$cputime
[2380]	1193
	1194	# CHECK THE MEMORY DEMAND
	1195	done=false
	1196	while [[ $done = false ]]
	1197	do
	1198	if (( memory == 0 ))
	1199	then
	1200	printf "\n +++ memory demand is undefined"
	1201	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1202	printf "\n >>> "
	1203	read memory 1>/dev/null 2>&1
	1204	else
	1205	done=true
	1206	fi
	1207	done
	1208
	1209	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1210	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1211	then
	1212	while [[ -z $remote_username ]]
	1213	do
[2420]	1214	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1215	printf "\n >>> Please type username:"
	1216	printf "\n >>> "
	1217	read remote_username
	1218	done
	1219	fi
	1220
	1221	else
	1222
[2420]	1223	if [[ $running_in_batch_mode = false ]]
	1224	then
	1225	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1226	cpumax=$cputime
	1227	else
	1228	cputime=$cpumax
	1229	fi
[2380]	1230
	1231	fi
	1232
	1233
	1234	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1235	(( cpu_hours = cputime / 3600 ))
	1236	(( resttime = cputime - cpu_hours * 3600 ))
	1237	(( cpu_minutes = resttime / 60 ))
	1238	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1239	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1240
	1241
	1242	# OUTPUT OF THE PALMRUN-HEADER
	1243	calltime=$(date)
	1244	printf "\n"
	1245	printf "#------------------------------------------------------------------------# \n"
	1246	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1247	printf "\| \| \n"
	1248	column1="called on:"; column2=$(hostname)
	1249	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1250	if [[ $create_remote_batch_job = true ]]
	1251	then
[2420]	1252	column1="execution on:"; column2="$host_identifier (username: $remote_username)"
[2380]	1253	else
	1254	if [[ $running_on_remote = true ]]
	1255	then
[2420]	1256	column1="execution on:"; column2="$host_identifier (IP:$remote_ip)"
[2380]	1257	else
[2420]	1258	column1="execution on:"; column2="$host_identifier (IP:$local_ip)"
[2380]	1259	fi
	1260	fi
	1261	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1262
	1263	column1="running in:"
	1264	if [[ $running_in_batch_mode = true ]]
	1265	then
	1266	column2="batch job mode"
	1267	else
	1268	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1269	then
	1270	column2="job creation mode"
	1271	else
	1272	column2="interactive run mode"
	1273	fi
	1274	fi
	1275	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1276
	1277	if [[ -n $cores ]]
	1278	then
	1279	if [[ $run_coupled_model = false ]]
	1280	then
	1281	column1="number of cores:"; column2=$cores
	1282	else
	1283	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1284	fi
	1285	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1286	fi
	1287	if [[ -n $tasks_per_node ]]
	1288	then
	1289	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1290	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1291	if (( remaining_cores > 0 ))
	1292	then
	1293	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1294	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1295	fi
	1296	fi
	1297	if [[ $maximum_parallel_io_streams != $cores ]]
	1298	then
	1299	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1300	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1301	fi
	1302	if [[ $use_openmp = true ]]
	1303	then
	1304	column1="threads per task:"; column2="$threads_per_task"
	1305	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1306	fi
[2384]	1307	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1308	then
	1309	column1="job cpu time (h:m:s):"; column2="$timestring"
	1310	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1311	fi
[2380]	1312	printf "\| \| \n"
	1313	if [[ "$source_list" != "" ]]
	1314	then
	1315	if [[ "$make_options" != "" ]]
	1316	then
	1317	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1318	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1319	line=$(echo "$make_options" \| cut -c46-)
	1320	while [[ "$line" != "" ]]
	1321	do
	1322	column1=""
	1323	column2=$(echo "$line" \| cut -c-45)
	1324	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1325	line=$(echo "$line" \| cut -c46-)
	1326	done
	1327	fi
	1328	fi
	1329
	1330	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1331	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1332	line=$(echo "$cpp_options" \| cut -c46-)
	1333	while [[ "$line" != "" ]]
	1334	do
	1335	column1=""
	1336	column2=$(echo "$line" \| cut -c-45)
	1337	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1338	line=$(echo "$line" \| cut -c46-)
	1339	done
	1340
	1341	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1342	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1343	line=$(echo "$compiler_options" \| cut -c46-)
	1344	while [[ "$line" != "" ]]
	1345	do
	1346	column1=""
	1347	column2=$(echo "$line" \| cut -c-45)
	1348	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1349	line=$(echo "$line" \| cut -c46-)
	1350	done
	1351
[2388]	1352	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1353	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1354	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1355	while [[ "$line" != "" ]]
	1356	do
	1357	column1=""
	1358	column2=$(echo "$line" \| cut -c-45)
	1359	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1360	line=$(echo "$line" \| cut -c46-)
	1361	done
	1362
	1363	if [[ "$login_init_cmd" != "" ]]
	1364	then
	1365	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1366	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1367	line=$(echo "$login_init_cmd" \| cut -c46-)
	1368	while [[ "$line" != "" ]]
	1369	do
	1370	column1=""
	1371	column2=$(echo "$line" \| cut -c-45)
	1372	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1373	line=$(echo "$line" \| cut -c46-)
	1374	done
	1375	fi
	1376
	1377	if [[ "$module_commands" != "" ]]
	1378	then
	1379	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1380	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1381	line=$(echo "$module_commands" \| cut -c46-)
	1382	while [[ "$line" != "" ]]
	1383	do
	1384	column1=""
	1385	column2=$(echo "$line" \| cut -c-45)
	1386	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1387	line=$(echo "$line" \| cut -c46-)
	1388	done
	1389	fi
	1390	printf "\| \| \n"
	1391	column1="base name of files:"; column2=$fname
	1392	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1393	column1="activation string list:"; column2=$(echo $activation_string_list)
	1394	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1395
	1396	if [[ "$ocean_file_appendix" = true ]]
	1397	then
	1398	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1399	fi
	1400
	1401	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
	1402	then
	1403	column1="memory demand / PE":; column2="$memory MB"
	1404	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1405	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
	1406	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1407	fi
	1408
	1409	if [[ "$source_list" != "" ]]
	1410	then
	1411	printf "\| \| \n"
	1412	printf "\| Files to be compiled: \| \n"
	1413	line=$source_list
	1414	while [[ "$line" != "" ]]
	1415	do
	1416	linestart=$(echo $line \| cut -c-70)
	1417	printf "\| %-70s \| \n" "$linestart"
	1418	line=$(echo "$line" \| cut -c71-)
	1419	done
	1420	fi
	1421	printf "#------------------------------------------------------------------------#"
	1422
	1423
	1424
	1425	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1426	if [[ $do_trace = true ]]
	1427	then
	1428	(( i = 0 ))
	1429	while (( i < iin ))
	1430	do
	1431	(( i = i + 1 ))
	1432	if (( i == 1 ))
	1433	then
	1434	printf "\n\n >>> INPUT-file assignments:\n"
	1435	fi
	1436	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1437	done
	1438	(( i = 0 ))
	1439	while (( i < iout ))
	1440	do
	1441	(( i = i + 1 ))
	1442	if (( i == 1 ))
	1443	then
	1444	printf "\n\n >>> OUTPUT-file assignments:\n"
	1445	fi
	1446	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1447	done
	1448	(( i = 0 ))
	1449	while (( i < iic ))
	1450	do
	1451	(( i = i + 1 ))
	1452	if (( i == 1 ))
	1453	then
	1454	printf "\n\n >>> INPUT-commands:\n"
	1455	fi
	1456	printf "\n ${in_command[$i]}"
	1457	done
	1458	(( i = 0 ))
	1459	while (( i < ioc ))
	1460	do
	1461	(( i = i + 1 ))
	1462	if (( i == 1 ))
	1463	then
	1464	printf "\n\n >>> OUTPUT-commands:\n"
	1465	fi
	1466	printf "\n ${out_command[$i]}"
	1467	done
	1468	fi
	1469
	1470	# QUERY FOR CONTINUE
	1471	if [[ $silent = false && $running_in_batch_mode = false ]]
	1472	then
	1473	antwort=dummy
	1474	printf "\n\n"
	1475	printf " >>> everything o.k. (y/n) ? "
	1476	while read antwort
	1477	do
	1478	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1479	then
	1480	printf " >>> everything o.k. (y/n) ? "
	1481	else
	1482	break
	1483	fi
	1484	done
	1485	if [[ $antwort = n \|\| $antwort = N ]]
	1486	then
	1487	locat=user_abort; (( iec = 0 )); exit
	1488	fi
	1489	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1490	then
	1491	printf " *** batch-job will be created and submitted"
	1492	else
	1493	printf " *** PALMRUN will now continue to execute on this machine"
	1494	fi
	1495	fi
	1496
	1497
	1498
	1499	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1500	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1501	then
	1502
	1503	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1504	then
	1505	printf "\n\n *** creating executable and other sources for the remote host"
	1506	else
	1507	printf "\n\n *** creating executable and other sources for the local host"
	1508	fi
	1509
[2422]	1510	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1511	# IT SHALL BE CREATED
	1512	ask_for_make_depository=false
	1513	if [[ $create_remote_batch_job = true ]]
	1514	then
	1515
	1516	line=`grep %base_directory $config_file`
	1517	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_identifier}
	1518	echo "make_depository=$make_depository"
	1519	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_identifier}_last_make_protokoll
	1520
	1521	if [[ $(grep -c "depository not found" ${host_identifier}_last_make_protokoll) != 0 ]]
	1522	then
	1523	printf "\n\n +++ make depository \"${make_depository}\""
	1524	printf "\n on remote host not found!"
	1525	ask_for_make_depository=true
	1526	fi
	1527	rm ${host_identifier}_last_make_protokoll
	1528
	1529	else
	1530
	1531	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
	1532	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_identifier}
	1533	if [[ ! -d ${make_depository} ]]
	1534	then
	1535	printf "\n\n +++ make depository \"${make_depository}\""
	1536	printf "\n on local host not found!"
	1537	ask_for_make_depository=true
	1538	fi
	1539
	1540	fi
	1541
	1542	if [[ $ask_for_make_depository = true ]]
	1543	then
	1544
	1545	antwort=dummy
	1546	printf "\n\n"
	1547	printf " >>> Create a new one (y/n) ? "
	1548	while read antwort
	1549	do
	1550	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1551	then
	1552	printf " >>> Create a new one (y/n) ? "
	1553	else
	1554	break
	1555	fi
	1556	done
	1557	if [[ $antwort = n \|\| $antwort = N ]]
	1558	then
	1559	locat=user_abort; (( iec = 0 )); exit
	1560	fi
	1561
	1562	palmbuild -v -h $host_identifier
	1563
	1564	if [[ $? != 0 ]]
	1565	then
	1566
	1567	# ABORT IN CASE OF COMPILATION PROBLEMS
	1568	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1569	locat=make_depository
	1570	exit
	1571	else
	1572	echo " *** now continue with creating executable and other sources"
	1573	fi
	1574
	1575	fi
	1576
[2420]	1577	palmbuild -v -h $host_identifier -d $fname
[2380]	1578
	1579	if [[ $? != 0 ]]
	1580	then
	1581
	1582	# ABORT IN CASE OF COMPILATION PROBLEMS
	1583	printf "\n +++ error while creating executable and/or other sources"
	1584	locat=execution
[2420]	1585	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1586	exit
	1587
	1588	else
	1589
	1590	printf "\n$dashes\n *** executable and other sources created\n"
[2420]	1591	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1592
	1593	fi
	1594
	1595	fi
	1596
	1597
	1598	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1599	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1600	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1601	then
	1602
	1603	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1604	if [[ $running_in_batch_mode = false ]]
	1605	then
	1606	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1607	# FOLDER
	1608	mkdir -p $TEMPDIR
	1609	chmod go+rx $TEMPDIR
	1610	tmpcreate=true
	1611	cd $TEMPDIR
[2404]	1612	cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
[2380]	1613	printf "\n *** changed to temporary directory: $TEMPDIR"
	1614
	1615	else
	1616
	1617	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1618	printf "\n *** running in temporary directory: $TEMPDIR"
	1619
	1620	fi
	1621
	1622
	1623	# PROVIDE THE INPUT FILES
	1624	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1625	(( i = 0 ))
	1626	while (( i < iin ))
	1627	do
	1628	(( i = i + 1 ))
	1629	if (( i == 1 ))
	1630	then
	1631	printf "\n\n *** providing INPUT-files:\n$dashes"
	1632	fi
	1633
	1634
	1635	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1636	if [[ "${transin[$i]}" = unavailable ]]
	1637	then
	1638	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1639	then
	1640	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1641	printf "\n is not available!"
	1642	else
	1643	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1644	printf "\n is not available!"
	1645	fi
	1646	continue
	1647	fi
	1648
	1649	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1650	files_for_cores=false; filetype=file
	1651	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1652	then
	1653	files_for_cores=true; filetype=files
	1654	actionin[$i]=""
	1655	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1656	then
	1657	actionin[$i]=""
	1658	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1659	then
	1660	files_for_cores=true; filetype=files
	1661	actionin[$i]="ln"
	1662	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1663	then
	1664	actionin[$i]="ln"
	1665	fi
	1666
	1667	if [[ $files_for_cores = true ]]
	1668	then
	1669	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1670	else
	1671	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1672	fi
	1673
	1674	# INPUT-FILES TO BE LINKED
	1675	if [[ "${actionin[$i]}" = ln ]]
	1676	then
	1677
	1678	printf "\n $filetype will be linked"
	1679	if [[ $files_for_cores = false ]]
	1680	then
	1681	if [[ -f "${absnamein[$i]}" ]]
	1682	then
	1683	ln ${absnamein[$i]} ${localin[$i]}
	1684	got_tmp[$i]=true
	1685	fi
	1686	else
	1687	if [[ -d "${absnamein[$i]}" ]]
	1688	then
[2396]	1689	mkdir -p ${localin[$i]}
[2380]	1690	cd ${absnamein[$i]}
	1691	for file in $(ls *)
	1692	do
	1693	ln $file $TEMPDIR/${localin[$i]}
	1694	done >\|/dev/null 2>&1
	1695	cd $TEMPDIR
	1696	fi
	1697
	1698	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1699	if [[ ! -f "${localin[$i]}/_000000" ]]
	1700	then
	1701	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1702	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1703	fi
	1704
	1705	got_tmp[$i]=true
	1706	fi
	1707	fi
	1708
	1709	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1710	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1711	then
	1712
	1713	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1714	then
	1715
	1716	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1717	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1718	printf "\n file will be provided for $cores processors"
[2396]	1719	mkdir -p ${localin[$i]}
[2380]	1720	ival=$cores
	1721	(( ii = 0 ))
	1722	while (( ii <= ival-1 ))
	1723	do
	1724	if (( ii < 10 ))
	1725	then
	1726	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1727	elif (( ii < 100 ))
	1728	then
	1729	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1730	elif (( ii < 1000 ))
	1731	then
	1732	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1733	else
	1734	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1735	fi
	1736	(( ii = ii + 1 ))
	1737	done
	1738
	1739	else
	1740
	1741	if [[ $files_for_cores = true ]]
	1742	then
	1743
	1744	# PROVIDE FILES FOR EACH CORE
	1745	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1746	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1747	printf "\n providing $cores files for the respective cores"
[2396]	1748	mkdir -p ${localin[$i]}
[2380]	1749	if [[ $link_local_input = true ]]
	1750	then
	1751	printf " files will be linked\n"
	1752	cd ${absnamein[$i]}
	1753	for file in $(ls *)
	1754	do
	1755	ln -f $file ${localin[$i]}
	1756	done
	1757	cd $TEMPDIR
	1758	fi
	1759
	1760	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1761	if [[ ! -f "${localin[$i]}/_000000" ]]
	1762	then
	1763	if [[ $link_local_input = true ]]
	1764	then
	1765	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1766	fi
	1767	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1768	fi
	1769
	1770	else
	1771
	1772	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1773	if [[ $link_local_input = true ]]
	1774	then
	1775	printf " file will be linked\n"
	1776	ln -f ${absnamein[$i]} ${localin[$i]}
	1777	fi
	1778	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1779	if [[ ! -f "${localin[$i]}" ]]
	1780	then
	1781	if [[ $link_local_input = true ]]
	1782	then
	1783	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1784	fi
	1785	cp ${absnamein[$i]} ${localin[$i]}
	1786	fi
	1787	fi
	1788	fi
	1789	fi
	1790
	1791	done
	1792	if (( i != 0 ))
	1793	then
	1794	printf "\n$dashes\n *** all INPUT-files provided \n"
	1795	fi
	1796
	1797
	1798	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1799	(( i = 0 ))
	1800	while (( i < iic ))
	1801	do
	1802	(( i = i + 1 ))
	1803	if (( i == 1 ))
	1804	then
	1805	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1806	fi
	1807	printf "\n >>> ${in_command[$i]}"
	1808	eval ${in_command[$i]}
	1809	if (( i == iic ))
	1810	then
	1811	printf "\n$dashes\n"
	1812	fi
	1813	done
	1814
	1815
	1816	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1817	# (FILE ENVPAR WILL BE READ BY PALM)
	1818	cat > ENVPAR << EOF
[2420]	1819	&envpar run_identifier = '$fname', host = '$host_identifier',
[2380]	1820	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1821	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1822	maximum_cpu_time_allowed = ${cpumax}.,
	1823	revision = '$global_revision',
	1824	batch_job = .${running_in_batch_mode}. /
	1825
	1826	EOF
	1827
	1828
	1829	# STARTING THE EXECUTABLE
	1830	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1831	PATH=$PATH:$TEMPDIR
	1832
	1833
	1834	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1835	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1836	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1837	eval line=\"$line\"
	1838	execute_command="$line"
	1839
	1840
	1841	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1842	eval line2=\"$line2\"
	1843	execute_command_for_combine="$line2"
	1844
	1845
	1846	# PROVIDE A HOSTFILE, IF REQUIRED
	1847	if [[ "$hostfile" != "" ]]
	1848	then
	1849
	1850	if [[ $hostfile = auto ]]
	1851	then
	1852	# CREATE A NEW HOSTFILE
	1853	(( ii = 1 ))
	1854	while (( ii <= cores / threads_per_task ))
	1855	do
	1856	echo $(hostname) >> hostfile
	1857	(( ii = ii + 1 ))
	1858	done
	1859	if (( cores / threads_per_task == 0 ))
	1860	then
	1861	echo $(hostname) >> hostfile
	1862	fi
	1863
	1864	else
	1865	cp $hostfile hostfile
	1866	fi
	1867	eval line=\"`head -n $ii hostfile`\"
	1868	printf "\n *** running on: $line"
	1869	fi
	1870
	1871
	1872
	1873	# SET THE NUMBER OF OPENMP-THREADS
	1874	if [[ $use_openmp = true ]]
	1875	then
	1876	export OMP_NUM_THREADS=$threads_per_task
	1877	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1878	else
	1879	export OMP_NUM_THREADS=1
	1880	fi
	1881
	1882
	1883	# PROVIDE DATA FOR
	1884	if [[ $run_coupled_model = false ]]
	1885	then
	1886	if [[ "$ocean_file_appendix" = true ]]
	1887	then
	1888	echo "precursor_ocean" > coupling_steering
	1889	else
	1890	echo "precursor_atmos" > coupling_steering
	1891	fi
	1892	else
	1893	(( iia = $cores_atmos / $threads_per_task ))
	1894	(( iio = $cores_ocean / $threads_per_task ))
	1895	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1896	printf "\n\n"
	1897	echo "coupled_run $iia $iio" > coupling_steering
	1898	fi
	1899
	1900	printf "\n *** execute command:"
	1901	printf "\n \"$execute_command\" \n\n"
	1902
	1903	$execute_command < coupling_steering
	1904
	1905	if [[ $? != 0 ]]
	1906	then
	1907
	1908	# ABORT IN CASE OF RUNTIME ERRORS
	1909	printf "\n +++ runtime error occured"
	1910	locat=execution
	1911	exit
	1912
	1913	else
	1914
	1915	printf "\n$dashes\n *** execution finished \n"
	1916
	1917	fi
	1918
	1919
	1920	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1921	# BY EACH CORE INTO ONE FILE
	1922	if [[ ! -f combine_plot_fields.x ]]
	1923	then
	1924
	1925	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1926	printf "\n 2d- and/or 3d-data may be incomplete!"
	1927	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1928
	1929	elif [[ "$combine_plot_fields" == true ]]
	1930	then
	1931
	1932	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1933	$execute_command_for_combine
	1934
	1935	else
	1936
	1937	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1938	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1939	# ??? koennen wir das streichen ???
	1940	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1941	fi
	1942
	1943
	1944
	1945	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1946	(( i = 0 ))
	1947	while (( i < ioc ))
	1948	do
	1949	(( i = i + 1 ))
	1950	if (( i == 1 ))
	1951	then
	1952	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1953	fi
	1954	printf "\n >>> ${out_command[$i]}"
	1955	eval ${out_command[$i]}
	1956	if (( i == ioc ))
	1957	then
	1958	printf "\n$dashes\n"
	1959	fi
	1960	done
	1961
	1962
	1963	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1964	if [[ $do_trace = true ]]
	1965	then
	1966	printf "\n\n"
	1967	ls -al
	1968	fi
	1969
	1970
	1971	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1972	(( i = 0 ))
	1973	while (( i < iout ))
	1974	do
	1975	(( i = i + 1 ))
	1976	if (( i == 1 ))
	1977	then
	1978	printf "\n\n *** saving OUTPUT-files:"
	1979
	1980	# GET RUN NUMBER ASSIGNED BY PALM
	1981	if [[ -f RUN_NUMBER ]]
	1982	then
	1983	read run_number < RUN_NUMBER
	1984	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	1985	usecycle_option="-U $run_number"
	1986	else
	1987	run_number=0
	1988	usecycle_option=""
	1989	fi
	1990	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	1991	then
[2404]	1992	printf "\n *** in case of SCP transfers to local host"
	1993	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	1994	fi
	1995	printf "\n$dashes"
	1996	fi
	1997
	1998	# ADD CYCLE NUMBER TO FILENAME
	1999	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2000	then
	2001
	2002	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2003	if [[ "${actionout[$i]}" != "a" ]]
	2004	then
	2005	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2006	# WITH AN EXISTING CYCLE NUMBER
	2007	if (( run_number >= cycnum[$i] ))
	2008	then
	2009	(( cycnum[$i] = run_number ))
	2010	else
	2011	if (( run_number > 0 ))
	2012	then
	2013	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2014	fi
	2015	fi
	2016	fi
	2017	if (( cycnum[$i] > 0 ))
	2018	then
	2019	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2020	fi
	2021	fi
	2022
	2023	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2024	files_for_cores=false; filetype=file
	2025	link_local_output=false
	2026	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2027	then
	2028	files_for_cores=true; filetype=directory
	2029	actionout[$i]=""
	2030	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2031	then
	2032	actionout[$i]=""
	2033	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2034	then
	2035	files_for_cores=true; filetype=directory
	2036	link_local_output=true
	2037	actionout[$i]=""
	2038	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2039	then
	2040	link_local_output
	2041	actionout[$i]=""
	2042	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2043	then
	2044	files_for_cores=true; filetype=directory
	2045	actionout[$i]="tr"
	2046	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2047	then
	2048	actionout[$i]="tr"
	2049	fi
	2050
	2051	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2052	then
	2053	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2054	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2055	then
	2056	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2057	else
	2058
	2059
	2060	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2061	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2062	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2063	then
	2064	if [[ $running_on_remote = true ]]
	2065	then
	2066
	2067	# SET OPTIONS FOR TRANSFER
	2068	if [[ "${actionout[$i]}" = tr ]]
	2069	then
	2070	if [[ $files_for_cores = false ]]
	2071	then
	2072	catalog_option=""
	2073	catalog_string=""
	2074	else
	2075	catalog_option="-c"
	2076	catalog_string="/"
	2077	fi
	2078	append_option=""
	2079	append_string=""
	2080	else
	2081	append_option="-A"
	2082	append_string="append"
	2083	fi
	2084
	2085	transfer_failed=false
	2086	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2420]	2087	printf "\n ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2088
	2089	# TRANSFER VIA SCP
	2090	if [[ "$remote_loginnode" != "" ]]
	2091	then
[2420]	2092	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]	2093	else
[2420]	2094	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]	2095	fi
	2096	[[ $? != 0 ]] && transfer_failed=true
	2097
	2098
	2099	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2100	if [[ $transfer_failed = true ]]
	2101	then
	2102	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2420]	2103	printf " ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id\n"
[2380]	2104
	2105	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2106	eval local_catalog=${pathout[$i]}
	2107	if [[ ! -d $local_catalog ]]
	2108	then
	2109	printf " *** local directory does not exist. Trying to create:\n"
	2110	printf " $local_catalog \n"
	2111	mkdir -p $local_catalog
	2112	fi
[2420]	2113	eval cp ${localout[$i]} ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id
[2380]	2114	transfer_problems=true
	2115	fi
	2116
	2117	else
	2118
	2119	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2120	# BE COPIED OR APPENDED ON THIS MACHINE
	2121	if [[ "${actionout[$i]}" = tr ]]
	2122	then
	2123	actionout[$i]=""
	2124	else
	2125	actionout[$i]="a"
	2126	fi
	2127	fi
	2128	fi
	2129
	2130
	2131	# APPEND ON THIS MACHINE
	2132	if [[ "${actionout[$i]}" = "a" ]]
	2133	then
	2134	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2135	then
	2136	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2137	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2138	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2139	else
	2140	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2141	printf "\n ${pathout[$i]}\n"
	2142	cat ${localout[$i]} >> ${pathout[$i]}
	2143	fi
	2144	fi
	2145
	2146	# COPY ON THIS MACHINE
	2147	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2148	# ON DIFFERENT FILE-SYSTEMS
	2149	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2150	then
	2151
	2152	# COPY IN CASE OF RUNS ON SINGLE CORES
	2153	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2154	then
	2155	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2156	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2157	if [[ $link_local_output = true ]]
	2158	then
	2159	printf " file will be linked\n"
	2160	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2161	fi
	2162	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2163	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2164	then
	2165	if [[ $link_local_output = true ]]
	2166	then
	2167	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2168	fi
	2169	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2170	else
	2171	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2172	fi
	2173	else
	2174	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2175	printf "\n ${pathout[$i]}\n"
	2176	if [[ $link_local_output = true ]]
	2177	then
	2178	printf " file will be linked\n"
	2179	ln -f ${localout[$i]} ${pathout[$i]}
	2180	fi
	2181	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2182	if [[ ! -f "${pathout[$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]}
	2189	else
	2190	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2191	fi
	2192	fi
	2193
	2194	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2195	then
	2196
	2197	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2198	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2199	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2200	printf "\n ${pathout[$i]}\n"
	2201	if [[ $link_local_output = true ]]
	2202	then
	2203	printf " files will be linked\n"
[2396]	2204	mkdir -p ${pathout[$i]}
[2380]	2205	cd ${localout[$i]}
	2206	for file in $(ls *)
	2207	do
	2208	ln -f $file ${pathout[$i]}
	2209	done >\|/dev/null 2>&1
	2210	cd $TEMPDIR
	2211	fi
	2212
	2213	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2214	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2215	then
	2216	if [[ $link_local_output = true ]]
	2217	then
	2218	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2219	fi
	2220	cp -r ${localout[$i]}/* ${pathout[$i]}
	2221	fi
	2222
	2223	fi
	2224	fi
	2225	done
	2226
	2227	if (( i != 0 ))
	2228	then
	2229	if [[ $transfer_problems = true ]]
	2230	then
	2231	printf "\n$dashes\n *** OUTPUT-files saved"
	2232	printf "\n +++ WARNING: some data transfers failed! \n"
	2233	else
	2234	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2235	fi
	2236	fi
	2237
	2238
	2239	# IF REQUIRED, START A RESTART-JOB
	2240	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2241	if [[ -f CONTINUE_RUN ]]
	2242	then
	2243
	2244	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2245	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2246	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2247	# -b START A BATCH JOB
	2248	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2249	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2250	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2251
	2252
	2253	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2254	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2255	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2256	then
[2381]	2257	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2258	fi
	2259
	2260
	2261	# START THE RESTART-JOB
	2262	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2263	echo " $prc"
	2264	printf "\n$dashes\n"
	2265	if [[ $running_on_remote = true ]]
	2266	then
	2267
	2268	echo "*** ssh will be used to initiate restart-runs!"
	2269	echo " return_address=\"$return_address\" "
	2270	echo " return_username=\"$local_username\" "
	2271
	2272	if [[ "$remote_loginnode" != "" ]]
	2273	then
[2420]	2274	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]	2275	else
[2420]	2276	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2277	fi
	2278
	2279	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2280	sleep 30
	2281
	2282	else
	2283
	2284	# START THE RESTART JOB ON THE LOCAL HOST
	2285	eval $prc # THE ' MUST BE EVALUATED
	2286	cd - > /dev/null
	2287
	2288	fi
	2289	printf "\n$dashes\n *** restart-run initiated \n"
	2290
	2291
	2292	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2293	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2294	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2295	# MAY BE VERY HUGE)
	2296	(( i = 0 ))
	2297	while (( i < iin ))
	2298	do
	2299	(( i = i + 1 ))
	2300	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2301	then
	2302	rm -r ${absnamein[$i]}
	2303	fi
	2304	done
	2305
	2306	fi
	2307
	2308
	2309	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2310	cd $HOME
	2311	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2312
	2313
	2314	else
	2315
	2316
	2317	# PREPARING ACTIONS,
	2318	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2319
	2320	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2420]	2321	palmrun_com="$palmrun_script_name -d $fname -h $host_identifier -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2322	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2323	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2324	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2325	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2326	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2327	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
	2328	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
	2329	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2330	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2331	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2332	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2333	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
	2334	if [[ $create_remote_batch_job = true ]]
	2335	then
	2336	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2337	if [[ $do_trace = true ]]
	2338	then
	2339	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2340	fi
[2380]	2341	elif [[ $create_batch_job = true ]]
	2342	then
	2343	palmrun_com=${palmrun_com}" -j"
[2420]	2344	if [[ $do_trace = true ]]
	2345	then
	2346	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2347	fi
[2380]	2348	fi
	2349
	2350
	2351	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2352	# REMOTE HOST
[2420]	2353	job_protocol_file_local=${local_jobcatalog}/${host_identifier}_${job_id}
[2380]	2354	job_protocol_file=$job_protocol_file_local
	2355	if [[ $create_remote_batch_job = true ]]
	2356	then
[2420]	2357	job_protocol_file_remote=${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2358	job_protocol_file=$job_protocol_file_remote
	2359	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2360	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2361	fi
	2362
	2363
	2364	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2365	jobfile=jobfile.$run_id
	2366
	2367
	2368	# FIRST CREATE THE BATCH DIRECTIVES
	2369	(( i = 0 ))
	2370	while (( i < ibd ))
	2371	do
	2372	(( i = i + 1 ))
[2420]	2373	line=`echo "${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}}/$memory/g'`
[2380]	2374	eval line=\"$line\"
	2375	echo "$line" >> $jobfile
	2376	done
	2377	echo " " >> $jobfile
	2378
	2379
	2380	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2381	# PROTOCOL
	2382	if [[ $create_remote_batch_job = true ]]
	2383	then
	2384	echo "set +vx" >> $jobfile
	2385	echo "trap '" >> $jobfile
	2386	echo "set +vx" >> $jobfile
	2387	echo "cd ${remote_jobcatalog}" >> $jobfile
	2388	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2389
	2390	# ADD THE BATCH DIRECTIVES
	2391	(( i = 0 ))
	2392	while (( i < ibdt ))
	2393	do
	2394	(( i = i + 1 ))
[2420]	2395	line=`echo "${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}}/$fname/g'`
[2380]	2396	eval line=\"$line\"
	2397	echo "$line" >> $jobfile
	2398	done
	2399	echo " " >> $jobfile
	2400
	2401	echo "set -x" >> $jobfile
[2420]	2402	echo "${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]	2403	echo "%%END%%" >> $jobfile
	2404	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2405	echo "$submit_command $scpjob_file" >> $jobfile
	2406	echo "rm $scpjob_file" >> $jobfile
[2404]	2407	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2408	echo "set -x" >> $jobfile
	2409	echo " ' exit" >> $jobfile
	2410	fi
	2411
	2412
	2413	# ACTIVATE ERROR-TRACEBACK
	2414	if [[ $do_trace = true ]]
	2415	then
	2416	echo "set -x" >> $jobfile
	2417	else
	2418	echo "set +vx" >> $jobfile
	2419	fi
	2420
	2421
	2422	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2423	if [[ "$login_init_cmd" != "" ]]
	2424	then
	2425	echo "$login_init_cmd" >> $jobfile
	2426	fi
	2427	if [[ "$module_commands" != "" ]]
	2428	then
	2429	echo "$module_commands" >> $jobfile
	2430	fi
	2431
	2432
	2433	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2434	echo "mkdir $TEMPDIR" >> $jobfile
	2435	echo "cd $TEMPDIR" >> $jobfile
	2436	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2404]	2437	echo "cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
[2380]	2438	echo "export PATH=.:\$PATH" >> $jobfile
	2439	echo "export execute_palmrun=true" >> $jobfile
	2440
	2441
	2442	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2443	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2444	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2445	if [[ $create_remote_batch_job = true ]]
	2446	then
	2447	(( i = 0 ))
	2448	while (( i < iin ))
	2449	do
	2450	(( i = i + 1 ))
	2451	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2452	if [[ "${transin[$i]}" = job ]]
	2453	then
	2454	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2455	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2456	echo " " >> $jobfile
	2457	echo "%END%" >> $jobfile
	2458	else
	2459	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2460	fi
	2461
	2462	# CHECK, IF FILE COULD BE CREATED
	2463	echo "if [[ \$? = 1 ]]" >> $jobfile
	2464	echo "then" >> $jobfile
	2465	echo " echo \" \" " >> $jobfile
	2466	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2420]	2467	echo " echo \" please check, if directory exists on $host_identifier!\" " >> $jobfile
[2380]	2468	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2469	echo " execute_palmrun=false" >> $jobfile
	2470	echo "fi" >> $jobfile
	2471	done
	2472	fi
	2473
	2474
	2475	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2476	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2477	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2478	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2479	echo "export LOCAL_PWD" >> $jobfile
	2480
	2481
	2482	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2483	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2484	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2485
	2486
	2487	# CALL PALMRUN WITHIN THE JOB
	2488	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2489	echo "set -x" >> $jobfile
	2490	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2491
	2492
	2493	# TRANSFER JOBFILE TO THE TARGET HOST
	2494	if [[ $create_jobfile_only = false ]]
	2495	then
	2496
	2497	if [[ $create_remote_batch_job = true ]]
	2498	then
	2499
[2420]	2500	echo " "
	2501	echo " *** transfer of job to remote host via scp"
	2502	if [[ $do_trace = true ]]
	2503	then
	2504	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}"
	2505	fi
	2506	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2507
	2508	echo " "
[2420]	2509	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2510	if [[ $do_trace = true ]]
	2511	then
	2512	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"
	2513	fi
	2514	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]	2515
	2516	elif [[ $create_batch_job = true ]]
	2517	then
	2518
[2385]	2519	eval local_jobcatalog=$local_jobcatalog
[2420]	2520	cp $jobfile ${local_jobcatalog}/${host_identifier}_${job_id}
[2385]	2521	cd $local_jobcatalog
[2380]	2522	echo " "
[2420]	2523	echo " *** submit the job"
	2524	if [[ $do_trace = true ]]
	2525	then
	2526	echo "$submit_command ${host_identifier}_${job_id}"
	2527	fi
	2528	$submit_command ${host_identifier}_${job_id}
	2529	rm ${host_identifier}_${job_id}
[2380]	2530	cd - > /dev/null
	2531
	2532	fi
	2533
	2534	rm -rf $jobfile
	2535
	2536	else
	2537
	2538	printf "\n *** jobfile created under name \"$jobfile\" "
	2539	printf "\n no batch-job has been sent!"
	2540
	2541	fi
	2542
	2543	fi # END OF REMOTE-PART

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