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source: palm/trunk/SCRIPTS/palmrun @ 2566

Last change on this file since 2566 was 2566, checked in by raasch, 7 years ago
palmrun adjusted for grid engine batch systems, informative messages reduced and reformatted
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 86.8 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 2566 2017-10-20 08:50:47Z raasch $
[2566]	29	# execute command for combine_plot_fields added
	30	# "TEMPDIR" renamed "tempdir"
	31	# temporary working directory for local batch jobs is created immediately within
	32	# the user's palmrun call, due to a requirement of the "grid engine" batch
	33	# system, where the working directory is given with batch directive -wd and must
	34	# already exist when the job is submitted,
	35	# informative messages in non-trace mode reduced and partly reformatted
	36	#
	37	# 2551 2017-10-18 07:25:11Z raasch
[2551]	38	# TEMPDIR added as replacement string to be used in batch directives
	39	#
	40	# 2512 2017-10-04 08:26:59Z raasch
[2507]	41	# bugfix for determining cycle numbers of NetCDF input files
	42	#
	43	# 2506 2017-09-29 08:30:37Z raasch
[2506]	44	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	45	# host configuration added to SOURCES_FOR_RUN_... folder name
	46	# host_identifier renamed host_configuration
	47	# option -W added to allow for job dependencies
	48	#
	49	# 2501 2017-09-26 11:41:55Z raasch
[2501]	50	# default value for number of cores (option -X) set to 1
	51	# bugfix for mechanism which overwrites configuration file settings with values
	52	# provided by palmrun options
	53	#
	54	# 2499 2017-09-22 16:47:58Z kanani
[2499]	55	# option -h named configuration identifier
	56	#
	57	# 2480 2017-09-19 06:24:14Z maronga
[2480]	58	# bugfix for last revision
	59	#
	60	# 2479 2017-09-19 06:12:16Z raasch
[2479]	61	# option -A (project account number) added
	62	#
	63	# 2422 2017-09-08 08:25:41Z raasch
[2410]	64	# initial revision
[2380]	65	#
	66	#--------------------------------------------------------------------------------#
	67	# palmrun - script for running PALM jobs on local and remote hosts
	68	#--------------------------------------------------------------------------------#
	69
	70
	71
	72	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	73
	74	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	75	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	76	# (TOO MANY ARGUMENTS - PROBLEM)
	77	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	78
	79	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	80	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	81	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	82	# SCRIPT-OPTION ARGUMENTS
	83	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	84	typeset -i icycle inode ival maxcycle mpi_tasks
	85	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	86
	87	activation_string_list=""
	88	AddFilenames=""
	89	combine_plot_fields=true
	90	compiler_name=""
	91	compiler_name_ser=""
	92	compiler_options=""
[2501]	93	cores=1
[2380]	94	cores_atmos=0
	95	cores_ocean=0
	96	coupled_dist=""
	97	cpp_options=""
	98	cpumax=0
[2506]	99	create_batch_job=false
[2380]	100	create_jobfile_only=false
	101	create_remote_batch_job=false
	102	dashes=" ----------------------------------------------------------------------------"
	103	defaultqueue=""
[2506]	104	delete_temporary_catalog=true
[2380]	105	do_compile=true
	106	do_trace=false
	107	executable=""
	108	execute_command=""
	109	execution_error=false
	110	fileconnection_file=.palm.iofiles
	111	fname=test
	112	global_revision=""
[2506]	113	host_configuration="default"
[2380]	114	hostfile=""
	115	hp=""
	116	keep_data_from_previous_run=false
	117	link_local_input=false
	118	link_local_output=false
[2388]	119	linker_options=""
[2385]	120	local_jobcatalog=""
[2380]	121	locat=normal
	122	makefile=""
	123	max_par_io_str=""
	124	prc=$0
	125	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	126	do
	127	prc=`echo $prc \| cut -f2- -d"/"`
	128	done
	129	module_calls=""
[2506]	130	palmrun_memory=""
[2380]	131	palmrun_script_name=$prc
	132	openmp=false
[2506]	133	previous_job=""
[2479]	134	project_account=""
[2380]	135	queue=none
	136	restart_run=false
	137	return_address=""
[2385]	138	remote_jobcatalog=""
[2380]	139	remote_username=""
	140	running_in_batch_mode=false
	141	run_coupled_model=false
	142	run_id=""
	143	silent=false
	144	source_list=""
	145	source_path=""
[2501]	146	tasks_per_node=0
[2380]	147	threads_per_task=1
	148	transfer_problems=false
[2384]	149	user_source_path=""
[2506]	150	use_existing_sources_folder=""
[2380]	151	use_openmp=false
[2422]	152	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	153	working_directory=`pwd`
	154	write_binary=""
	155	TOPT=""
	156
	157
	158	# ERROR HANDLING IN CASE OF EXIT
[2404]	159	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	160	then
	161
	162	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	163	(( i = 0 ))
	164	while (( i < iec ))
	165	do
	166	(( i = i + 1 ))
	167	printf "\n *** Execution of ERROR-command:\n"
	168	printf " >>> ${err_command[$i]}\n"
	169	eval ${err_command[$i]}
	170	done
[2566]	171	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	172	printf "\n\n+++ palmrun killed \n\n"
	173	elif [[ $locat != control_c ]]
	174	then
[2566]	175	printf "\n --> palmrun finished\n\n"
[2380]	176	fi' exit
	177
	178
	179	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	180	trap 'cd; rm -rf $tempdir
[2380]	181	printf "\n+++ palmrun killed by \"^C\" \n\n"
	182	locat=control_c
	183	exit
	184	' 2
	185
	186
	187	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	188	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	189	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	190	do
	191	case $option in
	192	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	193	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	194	(b) create_batch_job=true; prc="$prc -b";;
	195	(B) delete_temporary_catalog=false; prc="$prc -B";;
	196	(C) restart_run=true; prc="$prc -C";;
	197	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	198	(F) create_jobfile_only=true;;
	199	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	200	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	201	(j) running_in_batch_mode=true;;
	202	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	203	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	204	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	205	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	206	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	207	(r) run_id=$OPTARG;;
	208	(R) return_address=$OPTARG;;
	209	(s) source_list=$OPTARG;;
[2501]	210	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	211	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	212	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	213	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	214	(v) silent=true; prc="$prc -v";;
[2506]	215	(V) use_existing_sources_folder="-V";;
[2380]	216	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	217	(W) previous_job=$OPTARG;;
[2380]	218	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	219	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	220	(y) ocean_file_appendix=true; prc="$prc -y";;
	221	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	222	(Z) combine_plot_fields=false; prc="$prc -Z";;
	223	(\?) printf "\n +++ unknown option $OPTARG \n"
	224	printf "\n --> type \"$0 ?\" for available options \n"
	225	locat=parameter;exit;;
	226	esac
	227	done
	228
	229
	230	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	231	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	232	(( to_shift = $OPTIND - 1 ))
	233	shift $to_shift
	234
	235	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	236	if [[ "$1" = "?" ]]
	237	then
	238	(printf "\n *** Description of available palmrun options:\n"
	239	printf "\n Option Description Default-Value"
	240	printf "\n -a activation string list \"\" "
[2479]	241	printf "\n -A project account number ---"
[2380]	242	printf "\n -b batch-job on local machine ---"
	243	printf "\n -B do not delete temporary directory at end ---"
	244	printf "\n -d base name of files attached to program test"
	245	printf "\n -F create batch job file only ---"
[2506]	246	printf "\n -h host configuration \"default\" "
[2380]	247	printf "\n -k keep data from previous run"
	248	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	249	printf "\n -M Makefile name Makefile"
	250	printf "\n -O threads per openMP task ---"
	251	printf "\n -q queue \"$queue\" "
	252	printf "\n -s filenames of routines to be compiled \"\" "
	253	printf "\n must end with .f, .f90, .F, or .c !"
	254	printf "\n use \"..\" for more than one file and wildcards"
	255	printf "\n -s LM compiles all locally modified files"
	256	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	257	printf "\n -T tasks per node ---"
[2380]	258	printf "\n -u username on remote machine \"\" "
	259	printf "\n -v no prompt for confirmation ---"
[2506]	260	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	261	printf "\n -w maximum parallel io streams as given by -X"
[2506]	262	printf "\n -W name of job to wait for ---"
[2380]	263	printf "\n -x tracing of palmrun for debug purposes ---"
	264	printf "\n -X # of processors (on parallel machines) 1"
	265	printf "\n -y add appendix \"_O\" to all local output"
	266	printf "\n files (ocean precursor runs followed by"
	267	printf "\n coupled atmosphere-ocean runs) ---"
	268	printf "\n -Y run coupled model, \"#1 #2\" with"
	269	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	270	printf "\n -Z skip combine_plot_fields at the end of "
	271	printf "\n the simulation ---"
	272	printf "\n "
	273	printf "\n Possible values of positional parameter <modus>:"
	274	printf "\n \"?\" - this outline \n\n") \| more
	275	exit
	276	elif [[ "$1" != "" ]]
	277	then
	278	printf "\n +++ positional parameter $1 unknown \n"
	279	locat=parameter; exit
	280	fi
	281
	282
	283
	284	# SHORT STARTING MESSAGE
	285	printf "\n*** $version "
	286	printf "\n will be executed. Please wait ..."
	287
	288
[2506]	289	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	290	config_file=.palm.config.$host_configuration
	291	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	292
	293
	294	# CHECK, IF CONFIGURATION FILE EXISTS
	295	if [[ ! -f $config_file ]]
	296	then
	297	printf "\n\n +++ configuration file: "
	298	printf "\n $config_file"
	299	printf "\n does not exist"
	300	locat=connect; exit
	301	fi
	302
	303
	304	# CHECK, IF FILE CONNECTION FILE EXISTS
	305	if [[ ! -f $fileconnection_file ]]
	306	then
	307	printf "\n\n +++ file connection file: "
	308	printf "\n $fileconnection_file"
	309	printf "\n does not exist"
	310	locat=connect; exit
	311	fi
	312
	313
[2404]	314	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	315	if [[ "$activation_string_list" = "" ]]
	316	then
	317	printf "\n\n +++ no activation string list given: "
	318	printf "\n please set palmrun option \"-a\" "
	319	locat=palmrun_option; exit
	320	fi
	321
	322
	323	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	324	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	325	then
	326	write_binary=true
	327	else
	328	write_binary=false
	329	fi
	330
	331
[2380]	332	# READ AND EVALUATE THE CONFIGURATION-FILE
	333	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	334
	335	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	336	while read line
	337	do
	338
	339	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	340	eval line=\"$line\"
	341
	342
	343	# INTERPRET THE LINE
	344	if [[ "$(echo $line)" = "" ]]
	345	then
	346
	347	# EMPTY LINE, NO ACTION
	348	continue
	349
	350	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	351	then
	352
	353	# LINE IS A COMMENT LINE
	354	continue
	355
	356	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	357	then
	358
	359	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	360	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	361	value=`echo $line \| cut -d" " -s -f2-`
	362
	363
	364	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	365	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	366	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	367	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	368	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	369	# CONFIGURATION-FILE.
	370	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	371	then
	372	eval export $var="\$value"
	373
	374	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	375	if [[ $do_trace = true ]]
	376	then
	377	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	378	fi
	379	fi
	380
	381	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	382	then
	383
	384	# LINE DEFINES BATCH-DIRECTIVE
	385	(( ibd = ibd + 1 ))
	386	line=$(echo $line \| cut -c4-)
	387	batch_directive[$ibd]="$line"
	388
	389	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	390	then
	391
	392	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	393	# REMOTE TO A LOCAL HOST
	394	(( ibdt = ibdt + 1 ))
	395	line=$(echo $line \| cut -c5-)
	396	batch_directive_transfer[$ibdt]="$line"
	397
	398	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	399	then
	400
	401	# LINE DEFINES ERROR-COMMAND
	402	(( iec = iec + 1 ))
	403	line=$(echo $line \| cut -c4-)
	404	err_command[$iec]="$line"
	405
	406	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	407	then
	408
	409	# LINE DEFINES INPUT-COMMAND
	410	(( iic = iic + 1 ))
	411	line=$(echo $line \| cut -c4-)
	412	in_command[$iic]="$line"
	413
	414	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	415	then
	416
	417	# LINE DEFINES OUTPUT-COMMAND
	418	(( ioc = ioc + 1 ))
	419	line=$(echo $line \| cut -c4-)
	420	out_command[$ioc]="$line"
	421
	422	else
	423
	424	# SKIP ALL OTHER LINES
	425	continue
	426
	427	fi
	428
	429	done < $config_file
	430
	431
	432	# CHECK SETTING OF REQUIRED PARAMETERS
	433	if [[ "$compiler_name" = "" ]]
	434	then
	435	printf "\n +++ no compiler name found in $config_file"
	436	printf "\n Please add line \"compiler_name ...\" to that file."
	437	locat=config_file; exit
	438	fi
	439	if [[ "$compiler_name_ser" = "" ]]
	440	then
	441	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	442	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	443	locat=config_file; exit
	444	fi
	445	if [[ "$compiler_options" = "" ]]
	446	then
	447	printf "\n +++ no compiler options found in $config_file"
	448	printf "\n Please add line \"compiler_options ...\" to that file."
	449	locat=config_file; exit
	450	fi
[2388]	451	if [[ "$linker_options" = "" ]]
[2380]	452	then
[2388]	453	printf "\n +++ no linker options found in $config_file"
	454	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	455	locat=config_file; exit
	456	fi
	457	if [[ "$execute_command" = "" ]]
	458	then
	459	printf "\n +++ no execute command found in $config_file"
	460	printf "\n Please add line \"execute_command ...\" to that file."
	461	locat=config_file; exit
	462	fi
	463
	464	if [[ "$hostfile" != "" ]]
	465	then
	466	if [[ $hostfile != auto && ! -f $hostfile ]]
	467	then
	468	printf "\n +++ no hostfile \"$hostfile\" found"
	469	printf "\n Please check line \"hostfile ...\" in $config_file"
	470	locat=config_file; exit
	471	fi
	472	fi
	473
	474
	475	# DETERMINE THE CALL STATUS
	476	if [[ "$return_address" != "" ]]
	477	then
	478
	479	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	480	# BATCH MODE AND ...
	481	running_on_remote=true
	482
	483	else
	484
	485	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	486	if [[ "$remote_ip" != "" ]]
	487	then
	488
	489	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	490	create_remote_batch_job=true
	491
	492	fi
	493	running_on_remote=false
	494	fi
	495
	496
	497
	498	# READ AND EVALUATE THE I/O-FILE LIST
	499	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	500
	501	# READ THE FILE CONNECTION FILE LINE BY LINE
	502	while read line
	503	do
	504
	505	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	506	eval line=\"$line\"
	507
	508
	509	# INTERPRET THE LINE
	510	if [[ "$(echo $line)" = "" ]]
	511	then
	512	# EMPTY LINE, NO ACTION
	513	continue
	514
	515	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	516	then
	517
	518	# LINE IS A COMMENT LINE
	519	true
	520
	521	else
	522
	523	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	524	# s2a: in/out - field
	525	# s2b: loc - field (optional)
	526	# s2c: tr/ar - field (optional)
	527	s1=`echo $line \| cut -d" " -f1`
	528	s2=`echo $line \| cut -d" " -s -f2`
	529	s2a=$(echo $s2 \| cut -d":" -f1)
	530	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	531	then
	532	s2b=""
	533	s2c=""
	534	else
	535	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	536	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	537	fi
	538	s3=`echo $line \| cut -d" " -f3`
	539	s4=`echo $line \| cut -d" " -s -f4`
	540	s5=`echo $line \| cut -d" " -s -f5`
	541	s6=`echo $line \| cut -d" " -s -f6`
	542
	543
	544	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	545	# INPUT- OR OUTPUT-LIST.
	546	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	547	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	548	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	549	# IS NOT CHECKED AND STORED.
	550	IFSALT="$IFS"; IFS="$IFS:"
	551	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	552	then
	553	found=false
	554	for actual in $activation_string_list
	555	do
	556	for formal in $s3
	557	do
	558	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	559	done
	560	done
	561	if [[ $found = true ]]
	562	then
	563	(( iin = iin + 1 ))
	564	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	565	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	566	extin[$iin]=$s6
	567	fi
	568	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	569	then
	570	found=false
	571	for actual in $activation_string_list
	572	do
	573	for formal in $s3
	574	do
	575	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	576	done
	577	done
	578	if [[ $found = true ]]
	579	then
	580	(( iout = iout + 1 ))
	581	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	582	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	583	fi
	584	elif [[ "$s2a" != in && "$s2a" != out ]]
	585	then
	586	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	587	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	588	locat=connect; exit
	589	fi
	590	IFS="$IFSALT"
	591	fi
	592
	593	done < $fileconnection_file
	594
	595
	596
[2501]	597	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	598	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	599	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	600	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	601	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	602	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	603
	604
	605
[2380]	606	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	607	if [[ $run_coupled_model = true ]]
	608	then
	609
	610	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	611	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	612
	613	if (( $cores_ocean + $cores_atmos != $cores ))
	614	then
	615
	616	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	617	printf "\n PEs (total) : $cores"
	618	printf "\n PEs (atmosphere): $cores_atmos"
	619	printf "\n PEs (ocean) : $cores_ocean"
	620	locat=coupling; exit
	621
	622	fi
	623
	624	fi
	625
	626
	627	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	628	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	629	# FOLDER
	630	if [[ $running_in_batch_mode = true ]]
	631	then
	632
[2506]	633	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	634	then
[2506]	635	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	636	printf "\n Please check the output of the palmrun-call"
	637	printf "\n that you did on your local host."
	638	locat=SOURCES_FOR_RUN; exit
	639	fi
	640
	641	else
	642
	643	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	644	# AUTOMATIC RESTART RUN
	645	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	646	if [[ $restart_run = false ]]
	647	then
	648
	649	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	650	# THE LOCAL HOST
	651	if [[ ! -d $source_path ]]
	652	then
	653	printf "\n\n +++ source path \"$source_path\" on local host"
	654	printf "\n \"$(hostname)\" does not exist"
	655	locat=source_path; exit
	656	fi
	657
[2506]	658	rm -rf $sources_for_run_catalog
	659	mkdir -p $sources_for_run_catalog
[2380]	660
	661	if [[ "$source_list" = LM ]]
	662	then
	663
	664	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	665	source_list=""
	666	cd $source_path
	667
	668
[2512]	669	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	670	if [[ ! -d ../.svn ]]
[2380]	671	then
	672	printf "\n\n +++ source directory"
	673	printf "\n \"$source_path\" "
	674	printf "\n is not under control of \"subversion\"."
[2512]	675	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	676	fi
	677
	678
	679	# LIST ALL MODIFIED SOURCE CODE FILES
	680	Filenames=""
[2404]	681	svn status > tmp_svnstatus
[2380]	682	while read line
	683	do
	684	firstc=`echo $line \| cut -c1`
	685	if [[ $firstc = M \|\| $firstc = "?" ]]
	686	then
	687	Name=`echo "$line" \| cut -c8-`
	688	extension=`echo $Name \| cut -d. -f2`
	689	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	690	then
	691	Filenames="$Filenames "$Name
	692	fi
	693	fi
[2404]	694	done < tmp_svnstatus
	695	rm -rf tmp_svnstatus
[2380]	696
	697
	698	# COPY FILES TO SOURCES_FOR_RUN_...
	699	for filename in $Filenames
	700	do
[2506]	701	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	702	source_list=$source_list"$filename "
	703	done
	704
	705	cd - > /dev/null
	706
	707
	708	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	709	elif [[ "$source_list" != "" ]]
	710	then
	711
	712	cd $source_path
	713
	714	for filename in $source_list
	715	do
	716
	717	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	718	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	719	then
	720	printf "\n +++ source code file: $filename"
	721	printf "\n must not contain (\"/\") "
	722	locat=source; exit
	723	fi
	724
	725	if [[ ! -f $filename ]]
	726	then
	727	printf "\n +++ source code file: $filename"
	728	printf "\n does not exist"
	729	locat=source; exit
	730	else
[2506]	731	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	732	fi
	733
	734	done
	735
	736	cd - > /dev/null
	737
	738	fi
	739
	740	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	741	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	742	if [[ ! -f $makefile ]]
	743	then
	744	printf "\n +++ file \"$makefile\" does not exist"
	745	locat=make; exit
	746	else
[2506]	747	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	748	fi
	749
	750
	751	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	752	if [[ "$user_source_path" != "" ]]
[2380]	753	then
	754
	755	# DOES THE DIRECTORY EXIST?
[2384]	756	if [[ ! -d $user_source_path ]]
[2380]	757	then
	758
	759	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	760	printf "\n \"$user_source_path\" "
[2380]	761	printf "\n does not exist or is not a directory."
	762	printf "\n No source code will be used from this directory!\n"
[2384]	763	user_source_path=""
[2380]	764	if [[ $silent == false ]]
	765	then
	766	sleep 2
	767	fi
	768
	769	else
	770
[2384]	771	cd $user_source_path
[2380]	772	found=false
	773
	774	Names=$(ls -1 *.f90 2>&1)
	775	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	776	Names=$(ls -1 *.F90 2>&1)
	777	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	778	Names=$(ls -1 *.F 2>&1)
	779	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	780	Names=$(ls -1 *.f 2>&1)
	781	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	782	Names=$(ls -1 *.c 2>&1)
	783	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	784
	785	cd - > /dev/null
[2506]	786	cd $sources_for_run_catalog
[2380]	787
	788	# COPY MAKEFILE IF EXISTING
[2384]	789	if [[ -f $user_source_path/Makefile ]]
[2380]	790	then
	791	printf "\n\n *** user Makefile from directory"
[2384]	792	printf "\n \"$user_source_path\" is used \n"
[2380]	793	if [[ $silent == false ]]
	794	then
	795	sleep 1
	796	fi
[2384]	797	cp $user_source_path/Makefile .
[2380]	798	fi
	799
	800	for filename in $AddFilenames
	801	do
	802	if [[ -f $filename ]]
	803	then
	804	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	805	printf "\n source code directory \"$user_source_path\" "
[2380]	806	printf "\n but was also given with option \"-s\" which means that it should be taken"
	807	printf "\n from directory \"$source_path\"."
	808	locat=source; exit
	809	fi
	810
[2384]	811	cp $user_source_path/$filename .
[2380]	812	source_list="$source_list $filename"
	813
	814	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	815	if [[ $(grep -c $filename Makefile) = 0 ]]
	816	then
	817	printf "\n\n +++ user file \"$filename\" "
	818	printf "\n is not listed in Makefile \n"
	819	locat=source; exit
	820	else
	821
	822	if [[ $found = false ]]
	823	then
	824	found=true
	825	printf "\n\n *** following user file(s) added to the"
	826	printf " files to be translated:\n "
	827	fi
	828	printf "$filename "
	829	if [[ $silent == false ]]
	830	then
	831	sleep 0.5
	832	fi
	833
	834	fi
	835	done
	836	[[ $found = true ]] && printf "\n"
	837	cd - > /dev/null
	838	fi
	839	fi
	840
	841	# COPY CONFIGURATION FILES
[2506]	842	cp $config_file $sources_for_run_catalog
	843	cp $fileconnection_file $sources_for_run_catalog
[2380]	844
	845	# COPY SHELLSCRIPTS
[2506]	846	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	847	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	848
	849	fi
	850
	851	fi
	852
	853	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	854	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	855	if [[ "$global_revision" = "" ]]
	856	then
	857	global_revision=`svnversion $source_path 2>/dev/null`
	858	global_revision="Rev: $global_revision"
	859	fi
	860
	861
	862	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	863	if [[ -n $cores ]]
	864	then
	865
	866	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	867	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	868	if [[ $tasks_per_node = 0 ]]
[2380]	869	then
	870	printf "\n"
	871	printf "\n +++ option \"-T\" (tasks per node) is missing"
	872	printf "\n set -T option or define tasks_per_node in the config file"
	873	locat=tasks_per_node; (( iec = 0 )); exit
	874	fi
	875
	876	if (( cores < tasks_per_node ))
	877	then
	878	printf "\n"
	879	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	880	printf "\n given values: -T $tasks_per_node -X $cores"
	881	locat=tasks_per_node; (( iec = 0 )); exit
	882	fi
	883
	884	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	885	(( mpi_tasks = cores / threads_per_task ))
	886	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	887	(( ii = cores / tasks_per_node ))
	888	(( remaining_cores = cores - ii * tasks_per_node ))
	889	if (( remaining_cores > 0 ))
	890	then
	891	printf "\n"
	892	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	893	printf "\n divisor of the total number of cores (option \"-X\")"
	894	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	895	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	896	(( nodes = nodes + 1 ))
	897	fi
	898
	899	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	900	if [[ "$tasks_per_node" != "" ]]
	901	then
	902	TOPT="-T $tasks_per_node"
	903	fi
	904
	905	fi
	906
	907
	908	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	909	if [[ "$maximum_parallel_io_streams" = "" ]]
	910	then
	911	maximum_parallel_io_streams=$cores
	912	fi
	913
	914
	915	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	916	if [[ "$scp_port" != "" ]]
	917	then
	918	PORTOPT="-P $scp_port"
	919	SSH_PORTOPT="-p $scp_port"
	920	fi
	921
	922
	923	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	924	# CONFIG-FILE
	925	if [[ "$ssh_key" != "" ]]
	926	then
	927	ssh_key="-i $HOME/.ssh/$ssh_key"
	928	fi
	929
	930
	931	# SET QUEUE, IF NOT GIVEN
	932	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	933	then
	934
	935	if [[ $queue = none && "$defaultqueue" = "" ]]
	936	then
	937	printf "\n"
	938	printf "\n +++ no default queue given in configuration file and no queue"
	939	printf "\n given with option -q"
	940	fi
	941	if [[ $queue = none ]]
	942	then
	943	queue=$defaultqueue
	944	fi
	945
	946	fi
	947
	948
	949	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	950	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	951	(( i = 0 ))
	952	while (( i < iin ))
	953	do
	954	(( i = i + 1 ))
	955	(( maxcycle = 0 ))
	956
	957	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	958	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	959	if [[ "${actionin[$i]}" = di ]]
	960	then
	961	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	962	# HOST ONLY
	963	eval filename=${pathin[$i]}/${endin[$i]}
	964	else
	965	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	966	# HOST ONLY
	967	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	968	fi
	969	eval pathname=${pathin[$i]}
	970
	971	# CHECK IF FILE EXISTS
	972	if ! ls $filename* 1>/dev/null 2>&1
	973	then
	974
	975	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	976	if [[ "${transin[$i]}" != "locopt" ]]
	977	then
	978	printf "\n\n +++ INPUT-file: "
	979	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	980	then
	981	printf "\n $filename"
	982	else
	983	printf "\n $filename.${extin[$i]}"
	984	fi
	985	printf "\n does not exist\n"
	986	locat=input; exit
	987	else
	988	transin[$i]="unavailable"
	989	fi
	990	else
	991
	992	# DETERMINE THE FILE'S CYCLE NUMBER
	993	ls -1 -d $filename > filelist 2>/dev/null
	994	ls -1 -d $filename.* >> filelist 2>/dev/null
	995	while read line
	996	do
	997	# filename without path (i.e. after the last "/")
	998	basefilename=$(basename ${line})
	999
	1000	# check if there is an extension
	1001	extension=${basefilename##*.}
[2507]	1002	if [[ "$extension" = "${extin[$i]}" ]]
[2380]	1003	then
[2507]	1004	basefilename=${basefilename%.*}
[2380]	1005	fi
	1006
	1007	# check for an existing cycle number
	1008	cycle=${basefilename##*.}
	1009	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1010	then
	1011	(( icycle = $cycle ))
	1012	else
	1013	(( icycle = 0 ))
	1014	fi
	1015
	1016	if (( icycle > maxcycle ))
	1017	then
	1018	(( maxcycle = icycle ))
	1019	fi
	1020
	1021	done <filelist
	1022	rm filelist
	1023
	1024	# APPEND CYCLE NUMBER TO FILENAME
	1025	if (( maxcycle > 0 ))
	1026	then
	1027	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1028	then
	1029	filename=${filename}.$maxcycle.${extin[$i]}
	1030	else
	1031	filename=${filename}.$maxcycle
	1032	fi
	1033	else
	1034	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1035	then
	1036	filename=${filename}.${extin[$i]}
	1037	fi
	1038	fi
	1039
	1040	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1041	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1042	absnamein[$i]=$filename
	1043	if (( maxcycle > 0 ))
	1044	then
	1045	if [[ "${actionin[$i]}" = di ]]
	1046	then
	1047	frelin[$i]=${endin[$i]}.$maxcycle
	1048	else
	1049	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1050	fi
	1051	else
	1052	if [[ "${actionin[$i]}" = di ]]
	1053	then
	1054	frelin[$i]=${endin[$i]}
	1055	else
	1056	frelin[$i]=${fname}${endin[$i]}
	1057	fi
	1058	fi
	1059
	1060	fi
	1061	done
	1062
	1063
	1064	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1065	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1066	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1067	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1068	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1069	# REMOTE HOST)
	1070	(( i = 0 ))
	1071	while (( i < iout ))
	1072	do
	1073	(( i = i + 1 ))
	1074	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1075	then
	1076	if [[ "${actionout[$i]}" = tr ]]
	1077	then
	1078	actionout[$i]=""
	1079	elif [[ "${actionout[$i]}" = trpe ]]
	1080	then
	1081	actionout[$i]=pe
	1082	elif [[ "${actionout[$i]}" = tra ]]
	1083	then
	1084	actionout[$i]=a
	1085	fi
	1086	(( maxcycle = 0 ))
	1087	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1088	eval catalogname=${pathout[$i]}
	1089	if ! ls $filename* 1>/dev/null 2>&1
	1090	then
	1091
	1092	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1093	if cat /dev/null > $filename
	1094	then
	1095	rm $filename
	1096	else
	1097
	1098	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1099	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1100	if [[ ! -d $catalogname ]]
	1101	then
	1102	if mkdir -p $catalogname
	1103	then
	1104	printf "\n\n *** directory:"
	1105	printf "\n $catalogname"
	1106	printf "\n was created\n"
	1107	else
	1108	printf "\n\n +++ OUTPUT-file:"
	1109	printf "\n $filename"
	1110	printf "\n cannot be created, because directory does not exist"
	1111	printf "\n and cannot be created either"
	1112	printf "\n"
	1113	locat=output ; exit
	1114	fi 2>/dev/null
	1115	else
	1116	printf "\n\n +++ OUTPUT-file:"
	1117	printf "\n $filename"
	1118	printf "\n cannot be created, although directory exists"
	1119	printf "\n"
	1120	locat=output ; exit
	1121	fi
	1122	fi 2>/dev/null
	1123	else
	1124
	1125	# DETERMINE THE CYCLE NUMBER
	1126	ls -1 -d $filename > filelist 2>/dev/null
	1127	ls -1 -d $filename.* >> filelist 2>/dev/null
	1128	while read line
	1129	do
	1130
	1131	# filename without path (i.e. after the last "/")
	1132	basefilename=$(basename ${line})
	1133
	1134	# check if there is an extension
	1135	extension=${basefilename##*.}
	1136	if [[ "$extension" = "${extout[$i]}" ]]
	1137	then
	1138	basefilename=${basefilename%.*}
	1139	fi
	1140
	1141	# check for an existing cycle number
	1142	cycle=${basefilename##*.}
	1143	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1144	then
	1145	(( icycle = $cycle + 1 ))
	1146	else
	1147	(( icycle = 1 ))
	1148	fi
	1149
	1150	if (( icycle > maxcycle ))
	1151	then
	1152	(( maxcycle = icycle ))
	1153	fi
	1154
	1155	done <filelist
	1156	rm filelist
	1157	fi
	1158
	1159	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1160	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1161	if [[ "${actionout[$i]}" != a ]]
	1162	then
	1163	if (( maxcycle > 0 ))
	1164	then
	1165	filename_tmp=${filename}.$maxcycle
	1166	if cat /dev/null > $filename_tmp
	1167	then
	1168	rm $filename_tmp
	1169	else
	1170	printf "\n +++ OUTPUT-file:"
	1171	printf "\n $filename_tmp"
	1172	printf "\n cannot be created"
	1173	locat=output ; exit
	1174	fi
	1175	fi
	1176	else
	1177	(( maxcycle = maxcycle - 1 ))
	1178	fi
	1179
	1180	(( cycnum[$i] = maxcycle ))
	1181	pathout[$i]=$filename
	1182
	1183	fi
	1184	done
	1185
	1186
	1187	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1188	if [[ $running_in_batch_mode = false ]]
	1189	then
	1190	run_id=$RANDOM
	1191	job_id=${fname}.$run_id
	1192
[2566]	1193	tempdir=$fast_io_catalog/$job_id
[2380]	1194	fi
	1195
	1196
	1197	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1198	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1199	then
	1200
	1201	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1202	if [[ $ibd = 0 ]]
	1203	then
	1204	printf "\n"
	1205	printf "\n +++ no batch directives found in configuration file"
	1206	locat=config_file_batch_directives; (( iec = 0 )); exit
	1207	fi
	1208
	1209	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1210	done=false
[2384]	1211	cputime=$cpumax
[2380]	1212	while [[ $done = false ]]
	1213	do
[2384]	1214	if (( cputime == 0 ))
[2380]	1215	then
	1216	printf "\n +++ cpu-time is undefined"
	1217	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1218	printf "\n >>> "
[2384]	1219	read cputime 1>/dev/null 2>&1
[2380]	1220	else
	1221	done=true
	1222	fi
	1223	done
[2420]	1224	cpumax=$cputime
[2380]	1225
	1226	# CHECK THE MEMORY DEMAND
	1227	done=false
	1228	while [[ $done = false ]]
	1229	do
	1230	if (( memory == 0 ))
	1231	then
	1232	printf "\n +++ memory demand is undefined"
	1233	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1234	printf "\n >>> "
	1235	read memory 1>/dev/null 2>&1
	1236	else
	1237	done=true
	1238	fi
	1239	done
	1240
	1241	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1242	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1243	then
	1244	while [[ -z $remote_username ]]
	1245	do
[2420]	1246	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1247	printf "\n >>> Please type username:"
	1248	printf "\n >>> "
	1249	read remote_username
	1250	done
	1251	fi
	1252
	1253	else
	1254
[2420]	1255	if [[ $running_in_batch_mode = false ]]
	1256	then
	1257	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1258	cpumax=$cputime
	1259	else
	1260	cputime=$cpumax
	1261	fi
[2380]	1262
	1263	fi
	1264
	1265
	1266	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1267	(( cpu_hours = cputime / 3600 ))
	1268	(( resttime = cputime - cpu_hours * 3600 ))
	1269	(( cpu_minutes = resttime / 60 ))
	1270	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1271	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1272
	1273
	1274	# OUTPUT OF THE PALMRUN-HEADER
	1275	calltime=$(date)
	1276	printf "\n"
	1277	printf "#------------------------------------------------------------------------# \n"
	1278	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1279	printf "\| \| \n"
	1280	column1="called on:"; column2=$(hostname)
	1281	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1282	if [[ $create_remote_batch_job = true ]]
	1283	then
[2506]	1284	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1285	else
	1286	if [[ $running_on_remote = true ]]
	1287	then
[2506]	1288	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1289	else
[2506]	1290	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1291	fi
	1292	fi
	1293	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1294
	1295	column1="running in:"
	1296	if [[ $running_in_batch_mode = true ]]
	1297	then
	1298	column2="batch job mode"
	1299	else
	1300	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1301	then
	1302	column2="job creation mode"
	1303	else
	1304	column2="interactive run mode"
	1305	fi
	1306	fi
	1307	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1308
[2479]	1309	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1310	then
[2480]	1311	if [[ "$project_account" != "" ]]
[2479]	1312	then
	1313	column1="project account number:"
	1314	column2="$project_account"
	1315	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1316	fi
	1317	fi
	1318
[2380]	1319	if [[ -n $cores ]]
	1320	then
	1321	if [[ $run_coupled_model = false ]]
	1322	then
	1323	column1="number of cores:"; column2=$cores
	1324	else
	1325	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1326	fi
	1327	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1328	fi
	1329	if [[ -n $tasks_per_node ]]
	1330	then
	1331	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1332	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1333	if (( remaining_cores > 0 ))
	1334	then
	1335	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1336	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1337	fi
	1338	fi
	1339	if [[ $maximum_parallel_io_streams != $cores ]]
	1340	then
	1341	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1342	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1343	fi
	1344	if [[ $use_openmp = true ]]
	1345	then
	1346	column1="threads per task:"; column2="$threads_per_task"
	1347	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1348	fi
[2384]	1349	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1350	then
[2506]	1351	column1="memory demand / PE":; column2="$memory MB"
	1352	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1353	column1="job cpu time (h:m:s):"; column2="$timestring"
	1354	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1355	fi
[2380]	1356	printf "\| \| \n"
	1357	if [[ "$source_list" != "" ]]
	1358	then
	1359	if [[ "$make_options" != "" ]]
	1360	then
	1361	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1362	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1363	line=$(echo "$make_options" \| cut -c46-)
	1364	while [[ "$line" != "" ]]
	1365	do
	1366	column1=""
	1367	column2=$(echo "$line" \| cut -c-45)
	1368	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1369	line=$(echo "$line" \| cut -c46-)
	1370	done
	1371	fi
	1372	fi
	1373
	1374	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1375	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1376	line=$(echo "$cpp_options" \| cut -c46-)
	1377	while [[ "$line" != "" ]]
	1378	do
	1379	column1=""
	1380	column2=$(echo "$line" \| cut -c-45)
	1381	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1382	line=$(echo "$line" \| cut -c46-)
	1383	done
	1384
	1385	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1386	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1387	line=$(echo "$compiler_options" \| cut -c46-)
	1388	while [[ "$line" != "" ]]
	1389	do
	1390	column1=""
	1391	column2=$(echo "$line" \| cut -c-45)
	1392	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1393	line=$(echo "$line" \| cut -c46-)
	1394	done
	1395
[2388]	1396	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1398	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1399	while [[ "$line" != "" ]]
	1400	do
	1401	column1=""
	1402	column2=$(echo "$line" \| cut -c-45)
	1403	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1404	line=$(echo "$line" \| cut -c46-)
	1405	done
	1406
	1407	if [[ "$login_init_cmd" != "" ]]
	1408	then
	1409	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1410	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1411	line=$(echo "$login_init_cmd" \| cut -c46-)
	1412	while [[ "$line" != "" ]]
	1413	do
	1414	column1=""
	1415	column2=$(echo "$line" \| cut -c-45)
	1416	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1417	line=$(echo "$line" \| cut -c46-)
	1418	done
	1419	fi
	1420
	1421	if [[ "$module_commands" != "" ]]
	1422	then
	1423	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1424	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1425	line=$(echo "$module_commands" \| cut -c46-)
	1426	while [[ "$line" != "" ]]
	1427	do
	1428	column1=""
	1429	column2=$(echo "$line" \| cut -c-45)
	1430	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1431	line=$(echo "$line" \| cut -c46-)
	1432	done
	1433	fi
	1434	printf "\| \| \n"
	1435	column1="base name of files:"; column2=$fname
	1436	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1437	column1="activation string list:"; column2=$(echo $activation_string_list)
	1438	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1439
	1440	if [[ "$ocean_file_appendix" = true ]]
	1441	then
	1442	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1443	fi
	1444
	1445	if [[ "$source_list" != "" ]]
	1446	then
	1447	printf "\| \| \n"
	1448	printf "\| Files to be compiled: \| \n"
	1449	line=$source_list
	1450	while [[ "$line" != "" ]]
	1451	do
	1452	linestart=$(echo $line \| cut -c-70)
	1453	printf "\| %-70s \| \n" "$linestart"
	1454	line=$(echo "$line" \| cut -c71-)
	1455	done
	1456	fi
	1457	printf "#------------------------------------------------------------------------#"
	1458
	1459
	1460
	1461	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1462	if [[ $do_trace = true ]]
	1463	then
	1464	(( i = 0 ))
	1465	while (( i < iin ))
	1466	do
	1467	(( i = i + 1 ))
	1468	if (( i == 1 ))
	1469	then
	1470	printf "\n\n >>> INPUT-file assignments:\n"
	1471	fi
	1472	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1473	done
	1474	(( i = 0 ))
	1475	while (( i < iout ))
	1476	do
	1477	(( i = i + 1 ))
	1478	if (( i == 1 ))
	1479	then
	1480	printf "\n\n >>> OUTPUT-file assignments:\n"
	1481	fi
	1482	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1483	done
	1484	(( i = 0 ))
	1485	while (( i < iic ))
	1486	do
	1487	(( i = i + 1 ))
	1488	if (( i == 1 ))
	1489	then
	1490	printf "\n\n >>> INPUT-commands:\n"
	1491	fi
	1492	printf "\n ${in_command[$i]}"
	1493	done
	1494	(( i = 0 ))
	1495	while (( i < ioc ))
	1496	do
	1497	(( i = i + 1 ))
	1498	if (( i == 1 ))
	1499	then
	1500	printf "\n\n >>> OUTPUT-commands:\n"
	1501	fi
	1502	printf "\n ${out_command[$i]}"
	1503	done
	1504	fi
	1505
	1506	# QUERY FOR CONTINUE
	1507	if [[ $silent = false && $running_in_batch_mode = false ]]
	1508	then
	1509	antwort=dummy
	1510	printf "\n\n"
	1511	printf " >>> everything o.k. (y/n) ? "
	1512	while read antwort
	1513	do
	1514	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1515	then
	1516	printf " >>> everything o.k. (y/n) ? "
	1517	else
	1518	break
	1519	fi
	1520	done
	1521	if [[ $antwort = n \|\| $antwort = N ]]
	1522	then
	1523	locat=user_abort; (( iec = 0 )); exit
	1524	fi
	1525	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1526	then
[2566]	1527	printf "\n *** batch-job will be created and submitted"
[2380]	1528	else
[2566]	1529	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1530	fi
	1531	fi
	1532
	1533
	1534
	1535	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1536	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1537	then
	1538
	1539	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1540	then
[2566]	1541	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1542	else
[2566]	1543	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1544	fi
	1545
[2422]	1546	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1547	# IT SHALL BE CREATED
	1548	ask_for_make_depository=false
	1549	if [[ $create_remote_batch_job = true ]]
	1550	then
	1551
	1552	line=`grep %base_directory $config_file`
[2506]	1553	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1554	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
[2422]	1555
[2506]	1556	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1557	then
	1558	printf "\n\n +++ make depository \"${make_depository}\""
	1559	printf "\n on remote host not found!"
	1560	ask_for_make_depository=true
	1561	fi
[2506]	1562	rm ${host_configuration}_last_make_protokoll
[2422]	1563
	1564	else
	1565
	1566	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1567	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1568	if [[ ! -d ${make_depository} ]]
	1569	then
	1570	printf "\n\n +++ make depository \"${make_depository}\""
	1571	printf "\n on local host not found!"
	1572	ask_for_make_depository=true
	1573	fi
	1574
	1575	fi
	1576
	1577	if [[ $ask_for_make_depository = true ]]
	1578	then
	1579
	1580	antwort=dummy
	1581	printf "\n\n"
	1582	printf " >>> Create a new one (y/n) ? "
	1583	while read antwort
	1584	do
	1585	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1586	then
	1587	printf " >>> Create a new one (y/n) ? "
	1588	else
	1589	break
	1590	fi
	1591	done
	1592	if [[ $antwort = n \|\| $antwort = N ]]
	1593	then
	1594	locat=user_abort; (( iec = 0 )); exit
	1595	fi
	1596
[2566]	1597	if [[ $do_trace = true ]]
	1598	then
	1599	palmbuild -h $host_configuration
	1600	else
	1601	palmbuild -v -h $host_configuration
	1602	fi
[2422]	1603
	1604	if [[ $? != 0 ]]
	1605	then
	1606
	1607	# ABORT IN CASE OF COMPILATION PROBLEMS
	1608	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1609	locat=make_depository
	1610	exit
	1611	else
	1612	echo " *** now continue with creating executable and other sources"
	1613	fi
	1614
	1615	fi
	1616
[2566]	1617	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1618	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1619
	1620	if [[ $? != 0 ]]
	1621	then
	1622
	1623	# ABORT IN CASE OF COMPILATION PROBLEMS
	1624	printf "\n +++ error while creating executable and/or other sources"
	1625	locat=execution
[2506]	1626	rm -rf $sources_for_run_catalog
[2380]	1627	exit
	1628
	1629	else
	1630
[2566]	1631	printf " *** executable and other sources created\n"
[2506]	1632	rm -rf $sources_for_run_catalog
[2380]	1633
	1634	fi
	1635
	1636	fi
	1637
	1638
	1639	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1640	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1641	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1642	then
	1643
	1644	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1645	if [[ $running_in_batch_mode = false ]]
	1646	then
	1647	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1648	# FOLDER
[2566]	1649	mkdir -p $tempdir
	1650	chmod go+rx $tempdir
	1651	cd $tempdir
	1652	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1653	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1654
	1655	else
	1656
	1657	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1658	printf "\n *** running in temporary directory: $tempdir"
[2380]	1659
	1660	fi
	1661
	1662
	1663	# PROVIDE THE INPUT FILES
	1664	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1665	(( i = 0 ))
	1666	while (( i < iin ))
	1667	do
	1668	(( i = i + 1 ))
	1669	if (( i == 1 ))
	1670	then
	1671	printf "\n\n *** providing INPUT-files:\n$dashes"
	1672	fi
	1673
	1674
	1675	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1676	if [[ "${transin[$i]}" = unavailable ]]
	1677	then
	1678	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1679	then
	1680	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1681	printf "\n is not available!"
	1682	else
	1683	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1684	printf "\n is not available!"
	1685	fi
	1686	continue
	1687	fi
	1688
	1689	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1690	files_for_cores=false; filetype=file
	1691	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1692	then
	1693	files_for_cores=true; filetype=files
	1694	actionin[$i]=""
	1695	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1696	then
	1697	actionin[$i]=""
	1698	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1699	then
	1700	files_for_cores=true; filetype=files
	1701	actionin[$i]="ln"
	1702	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1703	then
	1704	actionin[$i]="ln"
	1705	fi
	1706
	1707	if [[ $files_for_cores = true ]]
	1708	then
	1709	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1710	else
	1711	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1712	fi
	1713
	1714	# INPUT-FILES TO BE LINKED
	1715	if [[ "${actionin[$i]}" = ln ]]
	1716	then
	1717
	1718	printf "\n $filetype will be linked"
	1719	if [[ $files_for_cores = false ]]
	1720	then
	1721	if [[ -f "${absnamein[$i]}" ]]
	1722	then
	1723	ln ${absnamein[$i]} ${localin[$i]}
	1724	got_tmp[$i]=true
	1725	fi
	1726	else
	1727	if [[ -d "${absnamein[$i]}" ]]
	1728	then
[2396]	1729	mkdir -p ${localin[$i]}
[2380]	1730	cd ${absnamein[$i]}
	1731	for file in $(ls *)
	1732	do
[2566]	1733	ln $file $tempdir/${localin[$i]}
[2380]	1734	done >\|/dev/null 2>&1
[2566]	1735	cd $tempdir
[2380]	1736	fi
	1737
	1738	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1739	if [[ ! -f "${localin[$i]}/_000000" ]]
	1740	then
	1741	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1742	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1743	fi
	1744
	1745	got_tmp[$i]=true
	1746	fi
	1747	fi
	1748
	1749	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1750	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1751	then
	1752
	1753	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1754	then
	1755
	1756	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1757	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1758	printf "\n file will be provided for $cores processors"
[2396]	1759	mkdir -p ${localin[$i]}
[2380]	1760	ival=$cores
	1761	(( ii = 0 ))
	1762	while (( ii <= ival-1 ))
	1763	do
	1764	if (( ii < 10 ))
	1765	then
	1766	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1767	elif (( ii < 100 ))
	1768	then
	1769	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1770	elif (( ii < 1000 ))
	1771	then
	1772	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1773	else
	1774	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1775	fi
	1776	(( ii = ii + 1 ))
	1777	done
	1778
	1779	else
	1780
	1781	if [[ $files_for_cores = true ]]
	1782	then
	1783
	1784	# PROVIDE FILES FOR EACH CORE
	1785	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1786	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1787	printf "\n providing $cores files for the respective cores"
[2396]	1788	mkdir -p ${localin[$i]}
[2380]	1789	if [[ $link_local_input = true ]]
	1790	then
	1791	printf " files will be linked\n"
	1792	cd ${absnamein[$i]}
	1793	for file in $(ls *)
	1794	do
	1795	ln -f $file ${localin[$i]}
	1796	done
[2566]	1797	cd $tempdir
[2380]	1798	fi
	1799
	1800	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1801	if [[ ! -f "${localin[$i]}/_000000" ]]
	1802	then
	1803	if [[ $link_local_input = true ]]
	1804	then
	1805	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1806	fi
	1807	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1808	fi
	1809
	1810	else
	1811
	1812	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1813	if [[ $link_local_input = true ]]
	1814	then
	1815	printf " file will be linked\n"
	1816	ln -f ${absnamein[$i]} ${localin[$i]}
	1817	fi
	1818	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1819	if [[ ! -f "${localin[$i]}" ]]
	1820	then
	1821	if [[ $link_local_input = true ]]
	1822	then
	1823	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1824	fi
	1825	cp ${absnamein[$i]} ${localin[$i]}
	1826	fi
	1827	fi
	1828	fi
	1829	fi
	1830
	1831	done
	1832	if (( i != 0 ))
	1833	then
	1834	printf "\n$dashes\n *** all INPUT-files provided \n"
	1835	fi
	1836
	1837
	1838	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1839	(( i = 0 ))
	1840	while (( i < iic ))
	1841	do
	1842	(( i = i + 1 ))
	1843	if (( i == 1 ))
	1844	then
	1845	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1846	fi
	1847	printf "\n >>> ${in_command[$i]}"
	1848	eval ${in_command[$i]}
	1849	if (( i == iic ))
	1850	then
	1851	printf "\n$dashes\n"
	1852	fi
	1853	done
	1854
	1855
	1856	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1857	# (FILE ENVPAR WILL BE READ BY PALM)
	1858	cat > ENVPAR << EOF
[2506]	1859	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	1860	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1861	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1862	maximum_cpu_time_allowed = ${cpumax}.,
	1863	revision = '$global_revision',
	1864	batch_job = .${running_in_batch_mode}. /
	1865
	1866	EOF
	1867
	1868
	1869	# STARTING THE EXECUTABLE
	1870	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	1871	PATH=$PATH:$tempdir
[2380]	1872
	1873
	1874	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1875	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1876	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1877	eval line=\"$line\"
	1878	execute_command="$line"
	1879
	1880
	1881	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	1882	if [[ "$execute_command_for_combine" = "" ]]
	1883	then
	1884	eval line2=\"$line2\"
	1885	execute_command_for_combine="$line2"
	1886	fi
	1887
[2380]	1888
	1889
	1890	# PROVIDE A HOSTFILE, IF REQUIRED
	1891	if [[ "$hostfile" != "" ]]
	1892	then
	1893
	1894	if [[ $hostfile = auto ]]
	1895	then
	1896	# CREATE A NEW HOSTFILE
	1897	(( ii = 1 ))
	1898	while (( ii <= cores / threads_per_task ))
	1899	do
	1900	echo $(hostname) >> hostfile
	1901	(( ii = ii + 1 ))
	1902	done
	1903	if (( cores / threads_per_task == 0 ))
	1904	then
	1905	echo $(hostname) >> hostfile
	1906	fi
	1907
	1908	else
	1909	cp $hostfile hostfile
	1910	fi
	1911	eval line=\"`head -n $ii hostfile`\"
	1912	printf "\n *** running on: $line"
	1913	fi
	1914
	1915
	1916
	1917	# SET THE NUMBER OF OPENMP-THREADS
	1918	if [[ $use_openmp = true ]]
	1919	then
	1920	export OMP_NUM_THREADS=$threads_per_task
	1921	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1922	else
	1923	export OMP_NUM_THREADS=1
	1924	fi
	1925
	1926
	1927	# PROVIDE DATA FOR
	1928	if [[ $run_coupled_model = false ]]
	1929	then
	1930	if [[ "$ocean_file_appendix" = true ]]
	1931	then
	1932	echo "precursor_ocean" > coupling_steering
	1933	else
	1934	echo "precursor_atmos" > coupling_steering
	1935	fi
	1936	else
	1937	(( iia = $cores_atmos / $threads_per_task ))
	1938	(( iio = $cores_ocean / $threads_per_task ))
	1939	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1940	printf "\n\n"
	1941	echo "coupled_run $iia $iio" > coupling_steering
	1942	fi
	1943
	1944	printf "\n *** execute command:"
	1945	printf "\n \"$execute_command\" \n\n"
	1946
	1947	$execute_command < coupling_steering
	1948
	1949	if [[ $? != 0 ]]
	1950	then
	1951
	1952	# ABORT IN CASE OF RUNTIME ERRORS
	1953	printf "\n +++ runtime error occured"
	1954	locat=execution
	1955	exit
	1956
	1957	else
	1958
	1959	printf "\n$dashes\n *** execution finished \n"
	1960
	1961	fi
	1962
	1963
	1964	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1965	# BY EACH CORE INTO ONE FILE
	1966	if [[ ! -f combine_plot_fields.x ]]
	1967	then
	1968
	1969	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1970	printf "\n 2d- and/or 3d-data may be incomplete!"
	1971	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1972
	1973	elif [[ "$combine_plot_fields" == true ]]
	1974	then
	1975
	1976	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1977	$execute_command_for_combine
	1978
	1979	else
	1980
	1981	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1982	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1983	# ??? koennen wir das streichen ???
	1984	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1985	fi
	1986
	1987
	1988
	1989	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1990	(( i = 0 ))
	1991	while (( i < ioc ))
	1992	do
	1993	(( i = i + 1 ))
	1994	if (( i == 1 ))
	1995	then
	1996	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1997	fi
	1998	printf "\n >>> ${out_command[$i]}"
	1999	eval ${out_command[$i]}
	2000	if (( i == ioc ))
	2001	then
	2002	printf "\n$dashes\n"
	2003	fi
	2004	done
	2005
	2006
	2007	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2008	(( i = 0 ))
	2009	while (( i < iout ))
	2010	do
	2011	(( i = i + 1 ))
	2012	if (( i == 1 ))
	2013	then
	2014	printf "\n\n *** saving OUTPUT-files:"
	2015
	2016	# GET RUN NUMBER ASSIGNED BY PALM
	2017	if [[ -f RUN_NUMBER ]]
	2018	then
	2019	read run_number < RUN_NUMBER
	2020	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2021	usecycle_option="-U $run_number"
	2022	else
	2023	run_number=0
	2024	usecycle_option=""
	2025	fi
	2026	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2027	then
[2404]	2028	printf "\n *** in case of SCP transfers to local host"
	2029	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2030	fi
	2031	printf "\n$dashes"
	2032	fi
	2033
	2034	# ADD CYCLE NUMBER TO FILENAME
	2035	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2036	then
	2037
	2038	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2039	if [[ "${actionout[$i]}" != "a" ]]
	2040	then
	2041	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2042	# WITH AN EXISTING CYCLE NUMBER
	2043	if (( run_number >= cycnum[$i] ))
	2044	then
	2045	(( cycnum[$i] = run_number ))
	2046	else
	2047	if (( run_number > 0 ))
	2048	then
	2049	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2050	fi
	2051	fi
	2052	fi
	2053	if (( cycnum[$i] > 0 ))
	2054	then
	2055	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2056	fi
	2057	fi
	2058
	2059	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2060	files_for_cores=false; filetype=file
	2061	link_local_output=false
	2062	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2063	then
	2064	files_for_cores=true; filetype=directory
	2065	actionout[$i]=""
	2066	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2067	then
	2068	actionout[$i]=""
	2069	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2070	then
	2071	files_for_cores=true; filetype=directory
	2072	link_local_output=true
	2073	actionout[$i]=""
	2074	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2075	then
	2076	link_local_output
	2077	actionout[$i]=""
	2078	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2079	then
	2080	files_for_cores=true; filetype=directory
	2081	actionout[$i]="tr"
	2082	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2083	then
	2084	actionout[$i]="tr"
	2085	fi
	2086
	2087	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2088	then
	2089	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2090	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2091	then
	2092	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2093	else
	2094
	2095
	2096	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2097	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2098	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2099	then
	2100	if [[ $running_on_remote = true ]]
	2101	then
	2102
	2103	# SET OPTIONS FOR TRANSFER
	2104	if [[ "${actionout[$i]}" = tr ]]
	2105	then
	2106	if [[ $files_for_cores = false ]]
	2107	then
	2108	catalog_option=""
	2109	catalog_string=""
	2110	else
	2111	catalog_option="-c"
	2112	catalog_string="/"
	2113	fi
	2114	append_option=""
	2115	append_string=""
	2116	else
	2117	append_option="-A"
	2118	append_string="append"
	2119	fi
	2120
	2121	transfer_failed=false
	2122	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2123	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2124
	2125	# TRANSFER VIA SCP
	2126	if [[ "$remote_loginnode" != "" ]]
	2127	then
[2566]	2128	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2129	else
[2506]	2130	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2131	fi
	2132	[[ $? != 0 ]] && transfer_failed=true
	2133
	2134
	2135	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2136	if [[ $transfer_failed = true ]]
	2137	then
	2138	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2139	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2140
	2141	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2142	eval local_catalog=${pathout[$i]}
	2143	if [[ ! -d $local_catalog ]]
	2144	then
	2145	printf " *** local directory does not exist. Trying to create:\n"
	2146	printf " $local_catalog \n"
	2147	mkdir -p $local_catalog
	2148	fi
[2506]	2149	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2150	transfer_problems=true
	2151	fi
	2152
	2153	else
	2154
	2155	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2156	# BE COPIED OR APPENDED ON THIS MACHINE
	2157	if [[ "${actionout[$i]}" = tr ]]
	2158	then
	2159	actionout[$i]=""
	2160	else
	2161	actionout[$i]="a"
	2162	fi
	2163	fi
	2164	fi
	2165
	2166
	2167	# APPEND ON THIS MACHINE
	2168	if [[ "${actionout[$i]}" = "a" ]]
	2169	then
	2170	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2171	then
	2172	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2173	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2174	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2175	else
	2176	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2177	printf "\n ${pathout[$i]}\n"
	2178	cat ${localout[$i]} >> ${pathout[$i]}
	2179	fi
	2180	fi
	2181
	2182	# COPY ON THIS MACHINE
	2183	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2184	# ON DIFFERENT FILE-SYSTEMS
	2185	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2186	then
	2187
	2188	# COPY IN CASE OF RUNS ON SINGLE CORES
	2189	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2190	then
	2191	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2192	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2193	if [[ $link_local_output = true ]]
	2194	then
	2195	printf " file will be linked\n"
	2196	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2197	fi
	2198	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2199	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2200	then
	2201	if [[ $link_local_output = true ]]
	2202	then
	2203	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2204	fi
	2205	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2206	else
	2207	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2208	fi
	2209	else
	2210	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2211	printf "\n ${pathout[$i]}\n"
	2212	if [[ $link_local_output = true ]]
	2213	then
	2214	printf " file will be linked\n"
	2215	ln -f ${localout[$i]} ${pathout[$i]}
	2216	fi
	2217	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2218	if [[ ! -f "${pathout[$i]}" ]]
	2219	then
	2220	if [[ $link_local_output = true ]]
	2221	then
	2222	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2223	fi
	2224	cp ${localout[$i]} ${pathout[$i]}
	2225	else
	2226	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2227	fi
	2228	fi
	2229
	2230	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2231	then
	2232
	2233	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2234	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2235	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2236	printf "\n ${pathout[$i]}\n"
	2237	if [[ $link_local_output = true ]]
	2238	then
	2239	printf " files will be linked\n"
[2396]	2240	mkdir -p ${pathout[$i]}
[2380]	2241	cd ${localout[$i]}
	2242	for file in $(ls *)
	2243	do
	2244	ln -f $file ${pathout[$i]}
	2245	done >\|/dev/null 2>&1
[2566]	2246	cd $tempdir
[2380]	2247	fi
	2248
	2249	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2250	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2251	then
	2252	if [[ $link_local_output = true ]]
	2253	then
	2254	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2255	fi
	2256	cp -r ${localout[$i]}/* ${pathout[$i]}
	2257	fi
	2258
	2259	fi
	2260	fi
	2261	done
	2262
	2263	if (( i != 0 ))
	2264	then
	2265	if [[ $transfer_problems = true ]]
	2266	then
	2267	printf "\n$dashes\n *** OUTPUT-files saved"
	2268	printf "\n +++ WARNING: some data transfers failed! \n"
	2269	else
	2270	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2271	fi
	2272	fi
	2273
	2274
	2275	# IF REQUIRED, START A RESTART-JOB
	2276	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2277	if [[ -f CONTINUE_RUN ]]
	2278	then
	2279
	2280	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2281	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2282	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2283	# -b START A BATCH JOB
	2284	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2285	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2286	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2287
	2288
	2289	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2290	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2291	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2292	then
[2381]	2293	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2294	fi
	2295
	2296
	2297	# START THE RESTART-JOB
	2298	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2299	echo " $prc"
	2300	printf "\n$dashes\n"
	2301	if [[ $running_on_remote = true ]]
	2302	then
	2303
	2304	echo "*** ssh will be used to initiate restart-runs!"
	2305	echo " return_address=\"$return_address\" "
	2306	echo " return_username=\"$local_username\" "
	2307
	2308	if [[ "$remote_loginnode" != "" ]]
	2309	then
[2420]	2310	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]	2311	else
[2420]	2312	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2313	fi
	2314
	2315	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2316	sleep 30
	2317
	2318	else
	2319
	2320	# START THE RESTART JOB ON THE LOCAL HOST
	2321	eval $prc # THE ' MUST BE EVALUATED
	2322	cd - > /dev/null
	2323
	2324	fi
	2325	printf "\n$dashes\n *** restart-run initiated \n"
	2326
	2327
	2328	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2329	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2330	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2331	# MAY BE VERY HUGE)
	2332	(( i = 0 ))
	2333	while (( i < iin ))
	2334	do
	2335	(( i = i + 1 ))
	2336	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2337	then
	2338	rm -r ${absnamein[$i]}
	2339	fi
	2340	done
	2341
	2342	fi
	2343
	2344
	2345	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2346	cd $HOME
[2566]	2347	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2348
	2349
	2350	else
	2351
	2352
	2353	# PREPARING ACTIONS,
	2354	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2355
	2356	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2357	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2358	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2359	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2360	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2361	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2362	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2363	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2364	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2365	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2366	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2367	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2368	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2369	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2370	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2371	if [[ $create_remote_batch_job = true ]]
	2372	then
	2373	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2374	if [[ $do_trace = true ]]
	2375	then
	2376	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2377	fi
[2380]	2378	elif [[ $create_batch_job = true ]]
	2379	then
	2380	palmrun_com=${palmrun_com}" -j"
[2420]	2381	if [[ $do_trace = true ]]
	2382	then
	2383	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2384	fi
[2380]	2385	fi
	2386
	2387
	2388	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2389	# REMOTE HOST
[2506]	2390	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2391	job_protocol_file=$job_protocol_file_local
	2392	if [[ $create_remote_batch_job = true ]]
	2393	then
[2506]	2394	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2395	job_protocol_file=$job_protocol_file_remote
	2396	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2397	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2398	fi
	2399
	2400
	2401	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2402	jobfile=jobfile.$run_id
	2403
	2404
	2405	# FIRST CREATE THE BATCH DIRECTIVES
	2406	(( i = 0 ))
	2407	while (( i < ibd ))
	2408	do
	2409	(( i = i + 1 ))
[2566]	2410	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' \| sed 's/{{PREVIOUS_JOB}}/$previous_job/g' \| sed 's/{{TEMPDIR}}/$tempdir/g'`
[2380]	2411	eval line=\"$line\"
	2412	echo "$line" >> $jobfile
	2413	done
	2414	echo " " >> $jobfile
	2415
	2416
	2417	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2418	# PROTOCOL
	2419	if [[ $create_remote_batch_job = true ]]
	2420	then
	2421	echo "set +vx" >> $jobfile
	2422	echo "trap '" >> $jobfile
	2423	echo "set +vx" >> $jobfile
	2424	echo "cd ${remote_jobcatalog}" >> $jobfile
	2425	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2426
	2427	# ADD THE BATCH DIRECTIVES
	2428	(( i = 0 ))
	2429	while (( i < ibdt ))
	2430	do
	2431	(( i = i + 1 ))
[2506]	2432	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2433	eval line=\"$line\"
	2434	echo "$line" >> $jobfile
	2435	done
	2436	echo " " >> $jobfile
	2437
	2438	echo "set -x" >> $jobfile
[2506]	2439	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
[2380]	2440	echo "%%END%%" >> $jobfile
	2441	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2442	echo "$submit_command $scpjob_file" >> $jobfile
	2443	echo "rm $scpjob_file" >> $jobfile
[2404]	2444	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2445	echo "set -x" >> $jobfile
	2446	echo " ' exit" >> $jobfile
	2447	fi
	2448
	2449
	2450	# ACTIVATE ERROR-TRACEBACK
	2451	if [[ $do_trace = true ]]
	2452	then
	2453	echo "set -x" >> $jobfile
	2454	else
	2455	echo "set +vx" >> $jobfile
	2456	fi
	2457
	2458
	2459	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2460	if [[ "$login_init_cmd" != "" ]]
	2461	then
	2462	echo "$login_init_cmd" >> $jobfile
	2463	fi
	2464	if [[ "$module_commands" != "" ]]
	2465	then
	2466	echo "$module_commands" >> $jobfile
	2467	fi
	2468
	2469
	2470	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2471	if [[ $create_remote_batch_job = true ]]
	2472	then
	2473	echo "mkdir $tempdir" >> $jobfile
	2474	echo "chmod go+rx $tempdir" >> $jobfile
	2475	else
	2476	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2477	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2478	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2479	mkdir $tempdir
	2480	chmod go+rx $tempdir
	2481	fi
	2482	echo "cd $tempdir" >> $jobfile
	2483	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2484	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2485	echo "export PATH=.:\$PATH" >> $jobfile
	2486	echo "export execute_palmrun=true" >> $jobfile
	2487
	2488
	2489	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2490	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2491	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2492	if [[ $create_remote_batch_job = true ]]
	2493	then
	2494	(( i = 0 ))
	2495	while (( i < iin ))
	2496	do
	2497	(( i = i + 1 ))
	2498	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2499	if [[ "${transin[$i]}" = job ]]
	2500	then
	2501	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2502	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2503	echo " " >> $jobfile
	2504	echo "%END%" >> $jobfile
	2505	else
	2506	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2507	fi
	2508
	2509	# CHECK, IF FILE COULD BE CREATED
	2510	echo "if [[ \$? = 1 ]]" >> $jobfile
	2511	echo "then" >> $jobfile
	2512	echo " echo \" \" " >> $jobfile
	2513	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2506]	2514	echo " echo \" please check, if directory exists on $host_configuration!\" " >> $jobfile
[2380]	2515	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2516	echo " execute_palmrun=false" >> $jobfile
	2517	echo "fi" >> $jobfile
	2518	done
	2519	fi
	2520
	2521
	2522	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2523	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2524	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2525	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2526	echo "export LOCAL_PWD" >> $jobfile
	2527
	2528
	2529	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2530	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2531	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2532
	2533
	2534	# CALL PALMRUN WITHIN THE JOB
	2535	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2536	echo "set -x" >> $jobfile
	2537	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2538
	2539
	2540	# TRANSFER JOBFILE TO THE TARGET HOST
	2541	if [[ $create_jobfile_only = false ]]
	2542	then
	2543
	2544	if [[ $create_remote_batch_job = true ]]
	2545	then
	2546
[2420]	2547	echo " "
[2566]	2548	echo " *** transfer of job to remote host via scp"
[2420]	2549	if [[ $do_trace = true ]]
	2550	then
[2506]	2551	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2552	fi
[2566]	2553	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2554
[2566]	2555	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2556	if [[ $do_trace = true ]]
	2557	then
[2506]	2558	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2559	fi
[2506]	2560	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2561
	2562	elif [[ $create_batch_job = true ]]
	2563	then
	2564
[2385]	2565	eval local_jobcatalog=$local_jobcatalog
[2506]	2566	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2567	cd $local_jobcatalog
[2380]	2568	echo " "
[2420]	2569	echo " *** submit the job"
	2570	if [[ $do_trace = true ]]
	2571	then
[2506]	2572	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2573	fi
[2506]	2574	$submit_command ${host_configuration}_${job_id}
	2575	rm ${host_configuration}_${job_id}
[2380]	2576	cd - > /dev/null
	2577
	2578	fi
	2579
	2580	rm -rf $jobfile
	2581
	2582	else
	2583
	2584	printf "\n *** jobfile created under name \"$jobfile\" "
	2585	printf "\n no batch-job has been sent!"
	2586
	2587	fi
	2588
	2589	fi # END OF REMOTE-PART

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