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source: palm/trunk/SCRIPTS/palmrun @ 2504

Last change on this file since 2504 was 2501, checked in by raasch, 7 years ago
default value for number of cores (option -X) set to 1, bugfix for mechanism which overwrites configuration file settings with values provided by palmrun options
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 85.2 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 2501 2017-09-26 11:41:55Z maronga $
[2501]	29	# default value for number of cores (option -X) set to 1
	30	# bugfix for mechanism which overwrites configuration file settings with values
	31	# provided by palmrun options
	32	#
	33	# 2499 2017-09-22 16:47:58Z kanani
[2499]	34	# option -h named configuration identifier
	35	#
	36	# 2480 2017-09-19 06:24:14Z maronga
[2480]	37	# bugfix for last revision
	38	#
	39	# 2479 2017-09-19 06:12:16Z raasch
[2479]	40	# option -A (project account number) added
	41	#
	42	# 2422 2017-09-08 08:25:41Z raasch
[2410]	43	# initial revision
[2380]	44	#
	45	#--------------------------------------------------------------------------------#
	46	# palmrun - script for running PALM jobs on local and remote hosts
	47	#--------------------------------------------------------------------------------#
	48
	49
	50
	51	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	52
	53	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	54	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	55	# (TOO MANY ARGUMENTS - PROBLEM)
	56	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	57
	58	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	59	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	60	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	61	# SCRIPT-OPTION ARGUMENTS
	62	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	63	typeset -i icycle inode ival maxcycle mpi_tasks
	64	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	65
	66	activation_string_list=""
	67	AddFilenames=""
	68	combine_plot_fields=true
	69	compiler_name=""
	70	compiler_name_ser=""
	71	compiler_options=""
[2501]	72	cores=1
[2380]	73	cores_atmos=0
	74	cores_ocean=0
	75	coupled_dist=""
	76	cpp_options=""
	77	cpumax=0
	78	create_jobfile_only=false
	79	delete_temporary_catalog=true
	80	create_batch_job=false
	81	create_remote_batch_job=false
	82	dashes=" ----------------------------------------------------------------------------"
	83	defaultqueue=""
	84	do_compile=true
	85	do_trace=false
	86	executable=""
	87	execute_command=""
	88	execution_error=false
	89	fileconnection_file=.palm.iofiles
	90	fname=test
	91	global_revision=""
[2420]	92	host_identifier="default"
[2380]	93	hostfile=""
	94	hp=""
	95	keep_data_from_previous_run=false
	96	link_local_input=false
	97	link_local_output=false
[2388]	98	linker_options=""
[2385]	99	local_jobcatalog=""
[2380]	100	locat=normal
	101	makefile=""
	102	max_par_io_str=""
	103	prc=$0
	104	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	105	do
	106	prc=`echo $prc \| cut -f2- -d"/"`
	107	done
	108	module_calls=""
	109	palmrun_script_name=$prc
	110	openmp=false
[2479]	111	project_account=""
[2380]	112	queue=none
	113	restart_run=false
	114	return_address=""
[2385]	115	remote_jobcatalog=""
[2380]	116	remote_username=""
	117	running_in_batch_mode=false
	118	run_coupled_model=false
	119	run_id=""
	120	silent=false
	121	source_list=""
	122	source_path=""
[2501]	123	tasks_per_node=0
[2380]	124	threads_per_task=1
	125	tmpcreate=false
	126	transfer_problems=false
[2384]	127	user_source_path=""
[2380]	128	use_openmp=false
[2422]	129	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	130	working_directory=`pwd`
	131	write_binary=""
	132	TOPT=""
	133
	134
	135	# ERROR HANDLING IN CASE OF EXIT
[2404]	136	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	137	then
	138
	139	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	140	(( i = 0 ))
	141	while (( i < iec ))
	142	do
	143	(( i = i + 1 ))
	144	printf "\n *** Execution of ERROR-command:\n"
	145	printf " >>> ${err_command[$i]}\n"
	146	eval ${err_command[$i]}
	147	done
[2405]	148	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	149	printf "\n\n+++ palmrun killed \n\n"
	150	elif [[ $locat != control_c ]]
	151	then
	152	printf "\n\n --> palmrun finished\n\n"
	153	if [[ $running_on_remote = true ]]
	154	then
	155	printf " Bye, bye $remote_username !!\n\n"
	156	else
	157	printf " Bye, bye $local_username !!\n\n"
	158	fi
	159	fi' exit
	160
	161
	162	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	163	trap 'cd; rm -rf $TEMPDIR
[2380]	164	printf "\n+++ palmrun killed by \"^C\" \n\n"
	165	locat=control_c
	166	exit
	167	' 2
	168
	169
	170	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	171	# WHICH WILL BE USED TO START RESTART-JOBS
[2479]	172	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
[2380]	173	do
	174	case $option in
	175	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	176	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	177	(b) create_batch_job=true; prc="$prc -b";;
	178	(B) delete_temporary_catalog=false; prc="$prc -B";;
	179	(C) restart_run=true; prc="$prc -C";;
	180	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	181	(F) create_jobfile_only=true;;
	182	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2420]	183	(h) host_identifier=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	184	(j) running_in_batch_mode=true;;
	185	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	186	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	187	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	188	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	189	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	190	(r) run_id=$OPTARG;;
	191	(R) return_address=$OPTARG;;
	192	(s) source_list=$OPTARG;;
[2501]	193	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	194	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	195	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	196	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	197	(v) silent=true; prc="$prc -v";;
	198	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
	199	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	200	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	201	(y) ocean_file_appendix=true; prc="$prc -y";;
	202	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	203	(Z) combine_plot_fields=false; prc="$prc -Z";;
	204	(\?) printf "\n +++ unknown option $OPTARG \n"
	205	printf "\n --> type \"$0 ?\" for available options \n"
	206	locat=parameter;exit;;
	207	esac
	208	done
	209
	210
	211	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	212	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	213	(( to_shift = $OPTIND - 1 ))
	214	shift $to_shift
	215
	216	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	217	if [[ "$1" = "?" ]]
	218	then
	219	(printf "\n *** Description of available palmrun options:\n"
	220	printf "\n Option Description Default-Value"
	221	printf "\n -a activation string list \"\" "
[2479]	222	printf "\n -A project account number ---"
[2380]	223	printf "\n -b batch-job on local machine ---"
	224	printf "\n -B do not delete temporary directory at end ---"
	225	printf "\n -d base name of files attached to program test"
	226	printf "\n -F create batch job file only ---"
[2499]	227	printf "\n -h configuration identifier \"default\" "
[2380]	228	printf "\n -k keep data from previous run"
	229	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	230	printf "\n -M Makefile name Makefile"
	231	printf "\n -O threads per openMP task ---"
	232	printf "\n -q queue \"$queue\" "
	233	printf "\n -s filenames of routines to be compiled \"\" "
	234	printf "\n must end with .f, .f90, .F, or .c !"
	235	printf "\n use \"..\" for more than one file and wildcards"
	236	printf "\n -s LM compiles all locally modified files"
	237	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	238	printf "\n -T tasks per node ---"
[2380]	239	printf "\n -u username on remote machine \"\" "
	240	printf "\n -v no prompt for confirmation ---"
	241	printf "\n -w maximum parallel io streams as given by -X"
	242	printf "\n -x tracing of palmrun for debug purposes ---"
	243	printf "\n -X # of processors (on parallel machines) 1"
	244	printf "\n -y add appendix \"_O\" to all local output"
	245	printf "\n files (ocean precursor runs followed by"
	246	printf "\n coupled atmosphere-ocean runs) ---"
	247	printf "\n -Y run coupled model, \"#1 #2\" with"
	248	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	249	printf "\n -Z skip combine_plot_fields at the end of "
	250	printf "\n the simulation ---"
	251	printf "\n "
	252	printf "\n Possible values of positional parameter <modus>:"
	253	printf "\n \"?\" - this outline \n\n") \| more
	254	exit
	255	elif [[ "$1" != "" ]]
	256	then
	257	printf "\n +++ positional parameter $1 unknown \n"
	258	locat=parameter; exit
	259	fi
	260
	261
	262
	263	# SHORT STARTING MESSAGE
	264	printf "\n*** $version "
	265	printf "\n will be executed. Please wait ..."
	266
	267
	268	# BUILD THE CONFIGURATION-FILE NAME
[2420]	269	config_file=.palm.config.$host_identifier
[2380]	270
	271
	272	# CHECK, IF CONFIGURATION FILE EXISTS
	273	if [[ ! -f $config_file ]]
	274	then
	275	printf "\n\n +++ configuration file: "
	276	printf "\n $config_file"
	277	printf "\n does not exist"
	278	locat=connect; exit
	279	fi
	280
	281
	282	# CHECK, IF FILE CONNECTION FILE EXISTS
	283	if [[ ! -f $fileconnection_file ]]
	284	then
	285	printf "\n\n +++ file connection file: "
	286	printf "\n $fileconnection_file"
	287	printf "\n does not exist"
	288	locat=connect; exit
	289	fi
	290
	291
[2404]	292	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	293	if [[ "$activation_string_list" = "" ]]
	294	then
	295	printf "\n\n +++ no activation string list given: "
	296	printf "\n please set palmrun option \"-a\" "
	297	locat=palmrun_option; exit
	298	fi
	299
	300
	301	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	302	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	303	then
	304	write_binary=true
	305	else
	306	write_binary=false
	307	fi
	308
	309
[2380]	310	# READ AND EVALUATE THE CONFIGURATION-FILE
	311	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	312
	313	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	314	while read line
	315	do
	316
	317	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	318	eval line=\"$line\"
	319
	320
	321	# INTERPRET THE LINE
	322	if [[ "$(echo $line)" = "" ]]
	323	then
	324
	325	# EMPTY LINE, NO ACTION
	326	continue
	327
	328	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	329	then
	330
	331	# LINE IS A COMMENT LINE
	332	continue
	333
	334	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	335	then
	336
	337	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	338	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	339	value=`echo $line \| cut -d" " -s -f2-`
	340
	341
	342	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	343	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	344	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	345	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	346	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	347	# CONFIGURATION-FILE.
	348	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	349	then
	350	eval export $var="\$value"
	351
	352	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	353	if [[ $do_trace = true ]]
	354	then
	355	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	356	fi
	357	fi
	358
	359	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	360	then
	361
	362	# LINE DEFINES BATCH-DIRECTIVE
	363	(( ibd = ibd + 1 ))
	364	line=$(echo $line \| cut -c4-)
	365	batch_directive[$ibd]="$line"
	366
	367	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	368	then
	369
	370	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	371	# REMOTE TO A LOCAL HOST
	372	(( ibdt = ibdt + 1 ))
	373	line=$(echo $line \| cut -c5-)
	374	batch_directive_transfer[$ibdt]="$line"
	375
	376	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	377	then
	378
	379	# LINE DEFINES ERROR-COMMAND
	380	(( iec = iec + 1 ))
	381	line=$(echo $line \| cut -c4-)
	382	err_command[$iec]="$line"
	383
	384	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	385	then
	386
	387	# LINE DEFINES INPUT-COMMAND
	388	(( iic = iic + 1 ))
	389	line=$(echo $line \| cut -c4-)
	390	in_command[$iic]="$line"
	391
	392	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	393	then
	394
	395	# LINE DEFINES OUTPUT-COMMAND
	396	(( ioc = ioc + 1 ))
	397	line=$(echo $line \| cut -c4-)
	398	out_command[$ioc]="$line"
	399
	400	else
	401
	402	# SKIP ALL OTHER LINES
	403	continue
	404
	405	fi
	406
	407	done < $config_file
	408
	409
	410	# CHECK SETTING OF REQUIRED PARAMETERS
	411	if [[ "$compiler_name" = "" ]]
	412	then
	413	printf "\n +++ no compiler name found in $config_file"
	414	printf "\n Please add line \"compiler_name ...\" to that file."
	415	locat=config_file; exit
	416	fi
	417	if [[ "$compiler_name_ser" = "" ]]
	418	then
	419	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	420	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	421	locat=config_file; exit
	422	fi
	423	if [[ "$compiler_options" = "" ]]
	424	then
	425	printf "\n +++ no compiler options found in $config_file"
	426	printf "\n Please add line \"compiler_options ...\" to that file."
	427	locat=config_file; exit
	428	fi
[2388]	429	if [[ "$linker_options" = "" ]]
[2380]	430	then
[2388]	431	printf "\n +++ no linker options found in $config_file"
	432	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	433	locat=config_file; exit
	434	fi
	435	if [[ "$execute_command" = "" ]]
	436	then
	437	printf "\n +++ no execute command found in $config_file"
	438	printf "\n Please add line \"execute_command ...\" to that file."
	439	locat=config_file; exit
	440	fi
	441
	442	if [[ "$hostfile" != "" ]]
	443	then
	444	if [[ $hostfile != auto && ! -f $hostfile ]]
	445	then
	446	printf "\n +++ no hostfile \"$hostfile\" found"
	447	printf "\n Please check line \"hostfile ...\" in $config_file"
	448	locat=config_file; exit
	449	fi
	450	fi
	451
	452
	453	# DETERMINE THE CALL STATUS
	454	if [[ "$return_address" != "" ]]
	455	then
	456
	457	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	458	# BATCH MODE AND ...
	459	running_on_remote=true
	460
	461	else
	462
	463	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	464	if [[ "$remote_ip" != "" ]]
	465	then
	466
	467	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	468	create_remote_batch_job=true
	469
	470	fi
	471	running_on_remote=false
	472	fi
	473
	474
	475
	476	# READ AND EVALUATE THE I/O-FILE LIST
	477	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	478
	479	# READ THE FILE CONNECTION FILE LINE BY LINE
	480	while read line
	481	do
	482
	483	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	484	eval line=\"$line\"
	485
	486
	487	# INTERPRET THE LINE
	488	if [[ "$(echo $line)" = "" ]]
	489	then
	490	# EMPTY LINE, NO ACTION
	491	continue
	492
	493	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	494	then
	495
	496	# LINE IS A COMMENT LINE
	497	true
	498
	499	else
	500
	501	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	502	# s2a: in/out - field
	503	# s2b: loc - field (optional)
	504	# s2c: tr/ar - field (optional)
	505	s1=`echo $line \| cut -d" " -f1`
	506	s2=`echo $line \| cut -d" " -s -f2`
	507	s2a=$(echo $s2 \| cut -d":" -f1)
	508	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	509	then
	510	s2b=""
	511	s2c=""
	512	else
	513	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	514	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	515	fi
	516	s3=`echo $line \| cut -d" " -f3`
	517	s4=`echo $line \| cut -d" " -s -f4`
	518	s5=`echo $line \| cut -d" " -s -f5`
	519	s6=`echo $line \| cut -d" " -s -f6`
	520
	521
	522	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	523	# INPUT- OR OUTPUT-LIST.
	524	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	525	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	526	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	527	# IS NOT CHECKED AND STORED.
	528	IFSALT="$IFS"; IFS="$IFS:"
	529	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	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 [[ $found = true ]]
	540	then
	541	(( iin = iin + 1 ))
	542	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	543	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	544	extin[$iin]=$s6
	545	fi
	546	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	547	then
	548	found=false
	549	for actual in $activation_string_list
	550	do
	551	for formal in $s3
	552	do
	553	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	554	done
	555	done
	556	if [[ $found = true ]]
	557	then
	558	(( iout = iout + 1 ))
	559	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	560	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	561	fi
	562	elif [[ "$s2a" != in && "$s2a" != out ]]
	563	then
	564	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	565	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	566	locat=connect; exit
	567	fi
	568	IFS="$IFSALT"
	569	fi
	570
	571	done < $fileconnection_file
	572
	573
	574
[2501]	575	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
	576	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
	577	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	578	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	579	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	580	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	581
	582
	583
[2380]	584	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	585	if [[ $run_coupled_model = true ]]
	586	then
	587
	588	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	589	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	590
	591	if (( $cores_ocean + $cores_atmos != $cores ))
	592	then
	593
	594	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	595	printf "\n PEs (total) : $cores"
	596	printf "\n PEs (atmosphere): $cores_atmos"
	597	printf "\n PEs (ocean) : $cores_ocean"
	598	locat=coupling; exit
	599
	600	fi
	601
	602	fi
	603
	604
	605	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	606	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	607	# FOLDER
	608	if [[ $running_in_batch_mode = true ]]
	609	then
	610
[2404]	611	if [[ ! -d ${fast_io_catalog}/SOURCES_FOR_RUN_$fname ]]
[2380]	612	then
[2404]	613	printf "\n +++ directory ${fast_io_catalog}/SOURCES_FOR_RUN_$fname is missing"
[2380]	614	printf "\n Please check the output of the palmrun-call"
	615	printf "\n that you did on your local host."
	616	locat=SOURCES_FOR_RUN; exit
	617	fi
	618
	619	else
	620
	621	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	622	# AUTOMATIC RESTART RUN
	623	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	624	if [[ $restart_run = false ]]
	625	then
	626
	627	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	628	# THE LOCAL HOST
	629	if [[ ! -d $source_path ]]
	630	then
	631	printf "\n\n +++ source path \"$source_path\" on local host"
	632	printf "\n \"$(hostname)\" does not exist"
	633	locat=source_path; exit
	634	fi
	635
[2396]	636	rm -rf SOURCES_FOR_RUN_$fname
	637	mkdir -p SOURCES_FOR_RUN_$fname
[2380]	638
	639	if [[ "$source_list" = LM ]]
	640	then
	641
	642	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	643	source_list=""
	644	cd $source_path
	645
	646
	647	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	648	if [[ ! -d .svn ]]
	649	then
	650	printf "\n\n +++ source directory"
	651	printf "\n \"$source_path\" "
	652	printf "\n is not under control of \"subversion\"."
	653	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	654	fi
	655
	656
	657	# LIST ALL MODIFIED SOURCE CODE FILES
	658	Filenames=""
[2404]	659	svn status > tmp_svnstatus
[2380]	660	while read line
	661	do
	662	firstc=`echo $line \| cut -c1`
	663	if [[ $firstc = M \|\| $firstc = "?" ]]
	664	then
	665	Name=`echo "$line" \| cut -c8-`
	666	extension=`echo $Name \| cut -d. -f2`
	667	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	668	then
	669	Filenames="$Filenames "$Name
	670	fi
	671	fi
[2404]	672	done < tmp_svnstatus
	673	rm -rf tmp_svnstatus
[2380]	674
	675
	676	# COPY FILES TO SOURCES_FOR_RUN_...
	677	for filename in $Filenames
	678	do
	679	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	680	source_list=$source_list"$filename "
	681	done
	682
	683	cd - > /dev/null
	684
	685
	686	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	687	elif [[ "$source_list" != "" ]]
	688	then
	689
	690	cd $source_path
	691
	692	for filename in $source_list
	693	do
	694
	695	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	696	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	697	then
	698	printf "\n +++ source code file: $filename"
	699	printf "\n must not contain (\"/\") "
	700	locat=source; exit
	701	fi
	702
	703	if [[ ! -f $filename ]]
	704	then
	705	printf "\n +++ source code file: $filename"
	706	printf "\n does not exist"
	707	locat=source; exit
	708	else
	709	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	710	fi
	711
	712	done
	713
	714	cd - > /dev/null
	715
	716	fi
	717
	718	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	719	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	720	if [[ ! -f $makefile ]]
	721	then
	722	printf "\n +++ file \"$makefile\" does not exist"
	723	locat=make; exit
	724	else
	725	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	726	fi
	727
	728
	729	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	730	if [[ "$user_source_path" != "" ]]
[2380]	731	then
	732
	733	# DOES THE DIRECTORY EXIST?
[2384]	734	if [[ ! -d $user_source_path ]]
[2380]	735	then
	736
	737	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	738	printf "\n \"$user_source_path\" "
[2380]	739	printf "\n does not exist or is not a directory."
	740	printf "\n No source code will be used from this directory!\n"
[2384]	741	user_source_path=""
[2380]	742	if [[ $silent == false ]]
	743	then
	744	sleep 2
	745	fi
	746
	747	else
	748
[2384]	749	cd $user_source_path
[2380]	750	found=false
	751
	752	Names=$(ls -1 *.f90 2>&1)
	753	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	754	Names=$(ls -1 *.F90 2>&1)
	755	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	756	Names=$(ls -1 *.F 2>&1)
	757	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	758	Names=$(ls -1 *.f 2>&1)
	759	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	760	Names=$(ls -1 *.c 2>&1)
	761	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	762
	763	cd - > /dev/null
	764	cd SOURCES_FOR_RUN_$fname
	765
	766	# COPY MAKEFILE IF EXISTING
[2384]	767	if [[ -f $user_source_path/Makefile ]]
[2380]	768	then
	769	printf "\n\n *** user Makefile from directory"
[2384]	770	printf "\n \"$user_source_path\" is used \n"
[2380]	771	if [[ $silent == false ]]
	772	then
	773	sleep 1
	774	fi
[2384]	775	cp $user_source_path/Makefile .
[2380]	776	fi
	777
	778	for filename in $AddFilenames
	779	do
	780	if [[ -f $filename ]]
	781	then
	782	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	783	printf "\n source code directory \"$user_source_path\" "
[2380]	784	printf "\n but was also given with option \"-s\" which means that it should be taken"
	785	printf "\n from directory \"$source_path\"."
	786	locat=source; exit
	787	fi
	788
[2384]	789	cp $user_source_path/$filename .
[2380]	790	source_list="$source_list $filename"
	791
	792	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	793	if [[ $(grep -c $filename Makefile) = 0 ]]
	794	then
	795	printf "\n\n +++ user file \"$filename\" "
	796	printf "\n is not listed in Makefile \n"
	797	locat=source; exit
	798	else
	799
	800	if [[ $found = false ]]
	801	then
	802	found=true
	803	printf "\n\n *** following user file(s) added to the"
	804	printf " files to be translated:\n "
	805	fi
	806	printf "$filename "
	807	if [[ $silent == false ]]
	808	then
	809	sleep 0.5
	810	fi
	811
	812	fi
	813	done
	814	[[ $found = true ]] && printf "\n"
	815	cd - > /dev/null
	816	fi
	817	fi
	818
	819	# COPY CONFIGURATION FILES
	820	cp $config_file SOURCES_FOR_RUN_$fname
	821	cp $fileconnection_file SOURCES_FOR_RUN_$fname
	822
	823	# COPY SHELLSCRIPTS
	824	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
	825	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
	826
	827	fi
	828
	829	fi
	830
	831	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	832	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	833	if [[ "$global_revision" = "" ]]
	834	then
	835	global_revision=`svnversion $source_path 2>/dev/null`
	836	global_revision="Rev: $global_revision"
	837	fi
	838
	839
	840	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	841	if [[ -n $cores ]]
	842	then
	843
	844	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	845	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	846	if [[ $tasks_per_node = 0 ]]
[2380]	847	then
	848	printf "\n"
	849	printf "\n +++ option \"-T\" (tasks per node) is missing"
	850	printf "\n set -T option or define tasks_per_node in the config file"
	851	locat=tasks_per_node; (( iec = 0 )); exit
	852	fi
	853
	854	if (( cores < tasks_per_node ))
	855	then
	856	printf "\n"
	857	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	858	printf "\n given values: -T $tasks_per_node -X $cores"
	859	locat=tasks_per_node; (( iec = 0 )); exit
	860	fi
	861
	862	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	863	(( mpi_tasks = cores / threads_per_task ))
	864	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	865	(( ii = cores / tasks_per_node ))
	866	(( remaining_cores = cores - ii * tasks_per_node ))
	867	if (( remaining_cores > 0 ))
	868	then
	869	printf "\n"
	870	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	871	printf "\n divisor of the total number of cores (option \"-X\")"
	872	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	873	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	874	(( nodes = nodes + 1 ))
	875	fi
	876
	877	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	878	if [[ "$tasks_per_node" != "" ]]
	879	then
	880	TOPT="-T $tasks_per_node"
	881	fi
	882
	883	fi
	884
	885
	886	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	887	if [[ "$maximum_parallel_io_streams" = "" ]]
	888	then
	889	maximum_parallel_io_streams=$cores
	890	fi
	891
	892
	893	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	894	if [[ "$scp_port" != "" ]]
	895	then
	896	PORTOPT="-P $scp_port"
	897	SSH_PORTOPT="-p $scp_port"
	898	fi
	899
	900
	901	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	902	# CONFIG-FILE
	903	if [[ "$ssh_key" != "" ]]
	904	then
	905	ssh_key="-i $HOME/.ssh/$ssh_key"
	906	fi
	907
	908
	909	# SET QUEUE, IF NOT GIVEN
	910	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	911	then
	912
	913	if [[ $queue = none && "$defaultqueue" = "" ]]
	914	then
	915	printf "\n"
	916	printf "\n +++ no default queue given in configuration file and no queue"
	917	printf "\n given with option -q"
	918	fi
	919	if [[ $queue = none ]]
	920	then
	921	queue=$defaultqueue
	922	fi
	923
	924	fi
	925
	926
	927	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	928	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	929	(( i = 0 ))
	930	while (( i < iin ))
	931	do
	932	(( i = i + 1 ))
	933	(( maxcycle = 0 ))
	934
	935	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	936	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	937	if [[ "${actionin[$i]}" = di ]]
	938	then
	939	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	940	# HOST ONLY
	941	eval filename=${pathin[$i]}/${endin[$i]}
	942	else
	943	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	944	# HOST ONLY
	945	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	946	fi
	947	eval pathname=${pathin[$i]}
	948
	949	# CHECK IF FILE EXISTS
	950	if ! ls $filename* 1>/dev/null 2>&1
	951	then
	952
	953	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	954	if [[ "${transin[$i]}" != "locopt" ]]
	955	then
	956	printf "\n\n +++ INPUT-file: "
	957	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	958	then
	959	printf "\n $filename"
	960	else
	961	printf "\n $filename.${extin[$i]}"
	962	fi
	963	printf "\n does not exist\n"
	964	locat=input; exit
	965	else
	966	transin[$i]="unavailable"
	967	fi
	968	else
	969
	970	# DETERMINE THE FILE'S CYCLE NUMBER
	971	ls -1 -d $filename > filelist 2>/dev/null
	972	ls -1 -d $filename.* >> filelist 2>/dev/null
	973	while read line
	974	do
	975	# filename without path (i.e. after the last "/")
	976	basefilename=$(basename ${line})
	977
	978	# check if there is an extension
	979	extension=${basefilename##*.}
	980	if [[ "$extension" = "$extin[$i]" ]]
	981	then
	982	basefilename=${basefilename&.*}
	983	fi
	984
	985	# check for an existing cycle number
	986	cycle=${basefilename##*.}
	987	if [[ $cycle =~ ^-?[0-9]+$ ]]
	988	then
	989	(( icycle = $cycle ))
	990	else
	991	(( icycle = 0 ))
	992	fi
	993
	994	if (( icycle > maxcycle ))
	995	then
	996	(( maxcycle = icycle ))
	997	fi
	998
	999	done <filelist
	1000	rm filelist
	1001
	1002	# APPEND CYCLE NUMBER TO FILENAME
	1003	if (( maxcycle > 0 ))
	1004	then
	1005	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1006	then
	1007	filename=${filename}.$maxcycle.${extin[$i]}
	1008	else
	1009	filename=${filename}.$maxcycle
	1010	fi
	1011	else
	1012	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1013	then
	1014	filename=${filename}.${extin[$i]}
	1015	fi
	1016	fi
	1017
	1018	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1019	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1020	absnamein[$i]=$filename
	1021	if (( maxcycle > 0 ))
	1022	then
	1023	if [[ "${actionin[$i]}" = di ]]
	1024	then
	1025	frelin[$i]=${endin[$i]}.$maxcycle
	1026	else
	1027	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1028	fi
	1029	else
	1030	if [[ "${actionin[$i]}" = di ]]
	1031	then
	1032	frelin[$i]=${endin[$i]}
	1033	else
	1034	frelin[$i]=${fname}${endin[$i]}
	1035	fi
	1036	fi
	1037
	1038	fi
	1039	done
	1040
	1041
	1042	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1043	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1044	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1045	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1046	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1047	# REMOTE HOST)
	1048	(( i = 0 ))
	1049	while (( i < iout ))
	1050	do
	1051	(( i = i + 1 ))
	1052	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1053	then
	1054	if [[ "${actionout[$i]}" = tr ]]
	1055	then
	1056	actionout[$i]=""
	1057	elif [[ "${actionout[$i]}" = trpe ]]
	1058	then
	1059	actionout[$i]=pe
	1060	elif [[ "${actionout[$i]}" = tra ]]
	1061	then
	1062	actionout[$i]=a
	1063	fi
	1064	(( maxcycle = 0 ))
	1065	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1066	eval catalogname=${pathout[$i]}
	1067	if ! ls $filename* 1>/dev/null 2>&1
	1068	then
	1069
	1070	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1071	if cat /dev/null > $filename
	1072	then
	1073	rm $filename
	1074	else
	1075
	1076	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1077	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1078	if [[ ! -d $catalogname ]]
	1079	then
	1080	if mkdir -p $catalogname
	1081	then
	1082	printf "\n\n *** directory:"
	1083	printf "\n $catalogname"
	1084	printf "\n was created\n"
	1085	else
	1086	printf "\n\n +++ OUTPUT-file:"
	1087	printf "\n $filename"
	1088	printf "\n cannot be created, because directory does not exist"
	1089	printf "\n and cannot be created either"
	1090	printf "\n"
	1091	locat=output ; exit
	1092	fi 2>/dev/null
	1093	else
	1094	printf "\n\n +++ OUTPUT-file:"
	1095	printf "\n $filename"
	1096	printf "\n cannot be created, although directory exists"
	1097	printf "\n"
	1098	locat=output ; exit
	1099	fi
	1100	fi 2>/dev/null
	1101	else
	1102
	1103	# DETERMINE THE CYCLE NUMBER
	1104	ls -1 -d $filename > filelist 2>/dev/null
	1105	ls -1 -d $filename.* >> filelist 2>/dev/null
	1106	while read line
	1107	do
	1108
	1109	# filename without path (i.e. after the last "/")
	1110	basefilename=$(basename ${line})
	1111
	1112	# check if there is an extension
	1113	extension=${basefilename##*.}
	1114	if [[ "$extension" = "${extout[$i]}" ]]
	1115	then
	1116	basefilename=${basefilename%.*}
	1117	fi
	1118
	1119	# check for an existing cycle number
	1120	cycle=${basefilename##*.}
	1121	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1122	then
	1123	(( icycle = $cycle + 1 ))
	1124	else
	1125	(( icycle = 1 ))
	1126	fi
	1127
	1128	if (( icycle > maxcycle ))
	1129	then
	1130	(( maxcycle = icycle ))
	1131	fi
	1132
	1133	done <filelist
	1134	rm filelist
	1135	fi
	1136
	1137	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1138	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1139	if [[ "${actionout[$i]}" != a ]]
	1140	then
	1141	if (( maxcycle > 0 ))
	1142	then
	1143	filename_tmp=${filename}.$maxcycle
	1144	if cat /dev/null > $filename_tmp
	1145	then
	1146	rm $filename_tmp
	1147	else
	1148	printf "\n +++ OUTPUT-file:"
	1149	printf "\n $filename_tmp"
	1150	printf "\n cannot be created"
	1151	locat=output ; exit
	1152	fi
	1153	fi
	1154	else
	1155	(( maxcycle = maxcycle - 1 ))
	1156	fi
	1157
	1158	(( cycnum[$i] = maxcycle ))
	1159	pathout[$i]=$filename
	1160
	1161	fi
	1162	done
	1163
	1164
	1165	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1166	if [[ $running_in_batch_mode = false ]]
	1167	then
	1168	run_id=$RANDOM
	1169	job_id=${fname}.$run_id
	1170
[2404]	1171	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1172	fi
	1173
	1174
	1175	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1176	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1177	then
	1178
	1179	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1180	if [[ $ibd = 0 ]]
	1181	then
	1182	printf "\n"
	1183	printf "\n +++ no batch directives found in configuration file"
	1184	locat=config_file_batch_directives; (( iec = 0 )); exit
	1185	fi
	1186
	1187	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1188	done=false
[2384]	1189	cputime=$cpumax
[2380]	1190	while [[ $done = false ]]
	1191	do
[2384]	1192	if (( cputime == 0 ))
[2380]	1193	then
	1194	printf "\n +++ cpu-time is undefined"
	1195	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1196	printf "\n >>> "
[2384]	1197	read cputime 1>/dev/null 2>&1
[2380]	1198	else
	1199	done=true
	1200	fi
	1201	done
[2420]	1202	cpumax=$cputime
[2380]	1203
	1204	# CHECK THE MEMORY DEMAND
	1205	done=false
	1206	while [[ $done = false ]]
	1207	do
	1208	if (( memory == 0 ))
	1209	then
	1210	printf "\n +++ memory demand is undefined"
	1211	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1212	printf "\n >>> "
	1213	read memory 1>/dev/null 2>&1
	1214	else
	1215	done=true
	1216	fi
	1217	done
	1218
	1219	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1220	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1221	then
	1222	while [[ -z $remote_username ]]
	1223	do
[2420]	1224	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1225	printf "\n >>> Please type username:"
	1226	printf "\n >>> "
	1227	read remote_username
	1228	done
	1229	fi
	1230
	1231	else
	1232
[2420]	1233	if [[ $running_in_batch_mode = false ]]
	1234	then
	1235	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1236	cpumax=$cputime
	1237	else
	1238	cputime=$cpumax
	1239	fi
[2380]	1240
	1241	fi
	1242
	1243
	1244	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1245	(( cpu_hours = cputime / 3600 ))
	1246	(( resttime = cputime - cpu_hours * 3600 ))
	1247	(( cpu_minutes = resttime / 60 ))
	1248	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1249	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1250
	1251
	1252	# OUTPUT OF THE PALMRUN-HEADER
	1253	calltime=$(date)
	1254	printf "\n"
	1255	printf "#------------------------------------------------------------------------# \n"
	1256	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1257	printf "\| \| \n"
	1258	column1="called on:"; column2=$(hostname)
	1259	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1260	if [[ $create_remote_batch_job = true ]]
	1261	then
[2420]	1262	column1="execution on:"; column2="$host_identifier (username: $remote_username)"
[2380]	1263	else
	1264	if [[ $running_on_remote = true ]]
	1265	then
[2420]	1266	column1="execution on:"; column2="$host_identifier (IP:$remote_ip)"
[2380]	1267	else
[2420]	1268	column1="execution on:"; column2="$host_identifier (IP:$local_ip)"
[2380]	1269	fi
	1270	fi
	1271	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1272
	1273	column1="running in:"
	1274	if [[ $running_in_batch_mode = true ]]
	1275	then
	1276	column2="batch job mode"
	1277	else
	1278	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1279	then
	1280	column2="job creation mode"
	1281	else
	1282	column2="interactive run mode"
	1283	fi
	1284	fi
	1285	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1286
[2479]	1287	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1288	then
[2480]	1289	if [[ "$project_account" != "" ]]
[2479]	1290	then
	1291	column1="project account number:"
	1292	column2="$project_account"
	1293	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1294	fi
	1295	fi
	1296
[2380]	1297	if [[ -n $cores ]]
	1298	then
	1299	if [[ $run_coupled_model = false ]]
	1300	then
	1301	column1="number of cores:"; column2=$cores
	1302	else
	1303	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1304	fi
	1305	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1306	fi
	1307	if [[ -n $tasks_per_node ]]
	1308	then
	1309	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1310	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1311	if (( remaining_cores > 0 ))
	1312	then
	1313	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1314	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1315	fi
	1316	fi
	1317	if [[ $maximum_parallel_io_streams != $cores ]]
	1318	then
	1319	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1320	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1321	fi
	1322	if [[ $use_openmp = true ]]
	1323	then
	1324	column1="threads per task:"; column2="$threads_per_task"
	1325	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1326	fi
[2384]	1327	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1328	then
	1329	column1="job cpu time (h:m:s):"; column2="$timestring"
	1330	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1331	fi
[2380]	1332	printf "\| \| \n"
	1333	if [[ "$source_list" != "" ]]
	1334	then
	1335	if [[ "$make_options" != "" ]]
	1336	then
	1337	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1338	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1339	line=$(echo "$make_options" \| cut -c46-)
	1340	while [[ "$line" != "" ]]
	1341	do
	1342	column1=""
	1343	column2=$(echo "$line" \| cut -c-45)
	1344	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1345	line=$(echo "$line" \| cut -c46-)
	1346	done
	1347	fi
	1348	fi
	1349
	1350	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1351	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1352	line=$(echo "$cpp_options" \| cut -c46-)
	1353	while [[ "$line" != "" ]]
	1354	do
	1355	column1=""
	1356	column2=$(echo "$line" \| cut -c-45)
	1357	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1358	line=$(echo "$line" \| cut -c46-)
	1359	done
	1360
	1361	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1362	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1363	line=$(echo "$compiler_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 "$line" \| cut -c46-)
	1370	done
	1371
[2388]	1372	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1373	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1374	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1375	while [[ "$line" != "" ]]
	1376	do
	1377	column1=""
	1378	column2=$(echo "$line" \| cut -c-45)
	1379	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1380	line=$(echo "$line" \| cut -c46-)
	1381	done
	1382
	1383	if [[ "$login_init_cmd" != "" ]]
	1384	then
	1385	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1386	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1387	line=$(echo "$login_init_cmd" \| cut -c46-)
	1388	while [[ "$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	fi
	1396
	1397	if [[ "$module_commands" != "" ]]
	1398	then
	1399	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1400	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1401	line=$(echo "$module_commands" \| cut -c46-)
	1402	while [[ "$line" != "" ]]
	1403	do
	1404	column1=""
	1405	column2=$(echo "$line" \| cut -c-45)
	1406	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1407	line=$(echo "$line" \| cut -c46-)
	1408	done
	1409	fi
	1410	printf "\| \| \n"
	1411	column1="base name of files:"; column2=$fname
	1412	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1413	column1="activation string list:"; column2=$(echo $activation_string_list)
	1414	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1415
	1416	if [[ "$ocean_file_appendix" = true ]]
	1417	then
	1418	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1419	fi
	1420
	1421	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
	1422	then
	1423	column1="memory demand / PE":; column2="$memory MB"
	1424	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1425	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
	1426	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1427	fi
	1428
	1429	if [[ "$source_list" != "" ]]
	1430	then
	1431	printf "\| \| \n"
	1432	printf "\| Files to be compiled: \| \n"
	1433	line=$source_list
	1434	while [[ "$line" != "" ]]
	1435	do
	1436	linestart=$(echo $line \| cut -c-70)
	1437	printf "\| %-70s \| \n" "$linestart"
	1438	line=$(echo "$line" \| cut -c71-)
	1439	done
	1440	fi
	1441	printf "#------------------------------------------------------------------------#"
	1442
	1443
	1444
	1445	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1446	if [[ $do_trace = true ]]
	1447	then
	1448	(( i = 0 ))
	1449	while (( i < iin ))
	1450	do
	1451	(( i = i + 1 ))
	1452	if (( i == 1 ))
	1453	then
	1454	printf "\n\n >>> INPUT-file assignments:\n"
	1455	fi
	1456	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1457	done
	1458	(( i = 0 ))
	1459	while (( i < iout ))
	1460	do
	1461	(( i = i + 1 ))
	1462	if (( i == 1 ))
	1463	then
	1464	printf "\n\n >>> OUTPUT-file assignments:\n"
	1465	fi
	1466	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1467	done
	1468	(( i = 0 ))
	1469	while (( i < iic ))
	1470	do
	1471	(( i = i + 1 ))
	1472	if (( i == 1 ))
	1473	then
	1474	printf "\n\n >>> INPUT-commands:\n"
	1475	fi
	1476	printf "\n ${in_command[$i]}"
	1477	done
	1478	(( i = 0 ))
	1479	while (( i < ioc ))
	1480	do
	1481	(( i = i + 1 ))
	1482	if (( i == 1 ))
	1483	then
	1484	printf "\n\n >>> OUTPUT-commands:\n"
	1485	fi
	1486	printf "\n ${out_command[$i]}"
	1487	done
	1488	fi
	1489
	1490	# QUERY FOR CONTINUE
	1491	if [[ $silent = false && $running_in_batch_mode = false ]]
	1492	then
	1493	antwort=dummy
	1494	printf "\n\n"
	1495	printf " >>> everything o.k. (y/n) ? "
	1496	while read antwort
	1497	do
	1498	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1499	then
	1500	printf " >>> everything o.k. (y/n) ? "
	1501	else
	1502	break
	1503	fi
	1504	done
	1505	if [[ $antwort = n \|\| $antwort = N ]]
	1506	then
	1507	locat=user_abort; (( iec = 0 )); exit
	1508	fi
	1509	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1510	then
	1511	printf " *** batch-job will be created and submitted"
	1512	else
	1513	printf " *** PALMRUN will now continue to execute on this machine"
	1514	fi
	1515	fi
	1516
	1517
	1518
	1519	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1520	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1521	then
	1522
	1523	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1524	then
	1525	printf "\n\n *** creating executable and other sources for the remote host"
	1526	else
	1527	printf "\n\n *** creating executable and other sources for the local host"
	1528	fi
	1529
[2422]	1530	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1531	# IT SHALL BE CREATED
	1532	ask_for_make_depository=false
	1533	if [[ $create_remote_batch_job = true ]]
	1534	then
	1535
	1536	line=`grep %base_directory $config_file`
	1537	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_identifier}
	1538	echo "make_depository=$make_depository"
	1539	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_identifier}_last_make_protokoll
	1540
	1541	if [[ $(grep -c "depository not found" ${host_identifier}_last_make_protokoll) != 0 ]]
	1542	then
	1543	printf "\n\n +++ make depository \"${make_depository}\""
	1544	printf "\n on remote host not found!"
	1545	ask_for_make_depository=true
	1546	fi
	1547	rm ${host_identifier}_last_make_protokoll
	1548
	1549	else
	1550
	1551	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
	1552	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_identifier}
	1553	if [[ ! -d ${make_depository} ]]
	1554	then
	1555	printf "\n\n +++ make depository \"${make_depository}\""
	1556	printf "\n on local host not found!"
	1557	ask_for_make_depository=true
	1558	fi
	1559
	1560	fi
	1561
	1562	if [[ $ask_for_make_depository = true ]]
	1563	then
	1564
	1565	antwort=dummy
	1566	printf "\n\n"
	1567	printf " >>> Create a new one (y/n) ? "
	1568	while read antwort
	1569	do
	1570	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1571	then
	1572	printf " >>> Create a new one (y/n) ? "
	1573	else
	1574	break
	1575	fi
	1576	done
	1577	if [[ $antwort = n \|\| $antwort = N ]]
	1578	then
	1579	locat=user_abort; (( iec = 0 )); exit
	1580	fi
	1581
	1582	palmbuild -v -h $host_identifier
	1583
	1584	if [[ $? != 0 ]]
	1585	then
	1586
	1587	# ABORT IN CASE OF COMPILATION PROBLEMS
	1588	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1589	locat=make_depository
	1590	exit
	1591	else
	1592	echo " *** now continue with creating executable and other sources"
	1593	fi
	1594
	1595	fi
	1596
[2420]	1597	palmbuild -v -h $host_identifier -d $fname
[2380]	1598
	1599	if [[ $? != 0 ]]
	1600	then
	1601
	1602	# ABORT IN CASE OF COMPILATION PROBLEMS
	1603	printf "\n +++ error while creating executable and/or other sources"
	1604	locat=execution
[2420]	1605	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1606	exit
	1607
	1608	else
	1609
	1610	printf "\n$dashes\n *** executable and other sources created\n"
[2420]	1611	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1612
	1613	fi
	1614
	1615	fi
	1616
	1617
	1618	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1619	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1620	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1621	then
	1622
	1623	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1624	if [[ $running_in_batch_mode = false ]]
	1625	then
	1626	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1627	# FOLDER
	1628	mkdir -p $TEMPDIR
	1629	chmod go+rx $TEMPDIR
	1630	tmpcreate=true
	1631	cd $TEMPDIR
[2404]	1632	cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
[2380]	1633	printf "\n *** changed to temporary directory: $TEMPDIR"
	1634
	1635	else
	1636
	1637	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1638	printf "\n *** running in temporary directory: $TEMPDIR"
	1639
	1640	fi
	1641
	1642
	1643	# PROVIDE THE INPUT FILES
	1644	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1645	(( i = 0 ))
	1646	while (( i < iin ))
	1647	do
	1648	(( i = i + 1 ))
	1649	if (( i == 1 ))
	1650	then
	1651	printf "\n\n *** providing INPUT-files:\n$dashes"
	1652	fi
	1653
	1654
	1655	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1656	if [[ "${transin[$i]}" = unavailable ]]
	1657	then
	1658	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1659	then
	1660	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1661	printf "\n is not available!"
	1662	else
	1663	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1664	printf "\n is not available!"
	1665	fi
	1666	continue
	1667	fi
	1668
	1669	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1670	files_for_cores=false; filetype=file
	1671	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1672	then
	1673	files_for_cores=true; filetype=files
	1674	actionin[$i]=""
	1675	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1676	then
	1677	actionin[$i]=""
	1678	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1679	then
	1680	files_for_cores=true; filetype=files
	1681	actionin[$i]="ln"
	1682	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1683	then
	1684	actionin[$i]="ln"
	1685	fi
	1686
	1687	if [[ $files_for_cores = true ]]
	1688	then
	1689	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1690	else
	1691	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1692	fi
	1693
	1694	# INPUT-FILES TO BE LINKED
	1695	if [[ "${actionin[$i]}" = ln ]]
	1696	then
	1697
	1698	printf "\n $filetype will be linked"
	1699	if [[ $files_for_cores = false ]]
	1700	then
	1701	if [[ -f "${absnamein[$i]}" ]]
	1702	then
	1703	ln ${absnamein[$i]} ${localin[$i]}
	1704	got_tmp[$i]=true
	1705	fi
	1706	else
	1707	if [[ -d "${absnamein[$i]}" ]]
	1708	then
[2396]	1709	mkdir -p ${localin[$i]}
[2380]	1710	cd ${absnamein[$i]}
	1711	for file in $(ls *)
	1712	do
	1713	ln $file $TEMPDIR/${localin[$i]}
	1714	done >\|/dev/null 2>&1
	1715	cd $TEMPDIR
	1716	fi
	1717
	1718	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1719	if [[ ! -f "${localin[$i]}/_000000" ]]
	1720	then
	1721	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1722	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1723	fi
	1724
	1725	got_tmp[$i]=true
	1726	fi
	1727	fi
	1728
	1729	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1730	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1731	then
	1732
	1733	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1734	then
	1735
	1736	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1737	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1738	printf "\n file will be provided for $cores processors"
[2396]	1739	mkdir -p ${localin[$i]}
[2380]	1740	ival=$cores
	1741	(( ii = 0 ))
	1742	while (( ii <= ival-1 ))
	1743	do
	1744	if (( ii < 10 ))
	1745	then
	1746	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1747	elif (( ii < 100 ))
	1748	then
	1749	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1750	elif (( ii < 1000 ))
	1751	then
	1752	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1753	else
	1754	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1755	fi
	1756	(( ii = ii + 1 ))
	1757	done
	1758
	1759	else
	1760
	1761	if [[ $files_for_cores = true ]]
	1762	then
	1763
	1764	# PROVIDE FILES FOR EACH CORE
	1765	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1766	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1767	printf "\n providing $cores files for the respective cores"
[2396]	1768	mkdir -p ${localin[$i]}
[2380]	1769	if [[ $link_local_input = true ]]
	1770	then
	1771	printf " files will be linked\n"
	1772	cd ${absnamein[$i]}
	1773	for file in $(ls *)
	1774	do
	1775	ln -f $file ${localin[$i]}
	1776	done
	1777	cd $TEMPDIR
	1778	fi
	1779
	1780	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1781	if [[ ! -f "${localin[$i]}/_000000" ]]
	1782	then
	1783	if [[ $link_local_input = true ]]
	1784	then
	1785	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1786	fi
	1787	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1788	fi
	1789
	1790	else
	1791
	1792	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1793	if [[ $link_local_input = true ]]
	1794	then
	1795	printf " file will be linked\n"
	1796	ln -f ${absnamein[$i]} ${localin[$i]}
	1797	fi
	1798	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1799	if [[ ! -f "${localin[$i]}" ]]
	1800	then
	1801	if [[ $link_local_input = true ]]
	1802	then
	1803	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1804	fi
	1805	cp ${absnamein[$i]} ${localin[$i]}
	1806	fi
	1807	fi
	1808	fi
	1809	fi
	1810
	1811	done
	1812	if (( i != 0 ))
	1813	then
	1814	printf "\n$dashes\n *** all INPUT-files provided \n"
	1815	fi
	1816
	1817
	1818	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1819	(( i = 0 ))
	1820	while (( i < iic ))
	1821	do
	1822	(( i = i + 1 ))
	1823	if (( i == 1 ))
	1824	then
	1825	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1826	fi
	1827	printf "\n >>> ${in_command[$i]}"
	1828	eval ${in_command[$i]}
	1829	if (( i == iic ))
	1830	then
	1831	printf "\n$dashes\n"
	1832	fi
	1833	done
	1834
	1835
	1836	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1837	# (FILE ENVPAR WILL BE READ BY PALM)
	1838	cat > ENVPAR << EOF
[2420]	1839	&envpar run_identifier = '$fname', host = '$host_identifier',
[2380]	1840	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1841	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1842	maximum_cpu_time_allowed = ${cpumax}.,
	1843	revision = '$global_revision',
	1844	batch_job = .${running_in_batch_mode}. /
	1845
	1846	EOF
	1847
	1848
	1849	# STARTING THE EXECUTABLE
	1850	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1851	PATH=$PATH:$TEMPDIR
	1852
	1853
	1854	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1855	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1856	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1857	eval line=\"$line\"
	1858	execute_command="$line"
	1859
	1860
	1861	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1862	eval line2=\"$line2\"
	1863	execute_command_for_combine="$line2"
	1864
	1865
	1866	# PROVIDE A HOSTFILE, IF REQUIRED
	1867	if [[ "$hostfile" != "" ]]
	1868	then
	1869
	1870	if [[ $hostfile = auto ]]
	1871	then
	1872	# CREATE A NEW HOSTFILE
	1873	(( ii = 1 ))
	1874	while (( ii <= cores / threads_per_task ))
	1875	do
	1876	echo $(hostname) >> hostfile
	1877	(( ii = ii + 1 ))
	1878	done
	1879	if (( cores / threads_per_task == 0 ))
	1880	then
	1881	echo $(hostname) >> hostfile
	1882	fi
	1883
	1884	else
	1885	cp $hostfile hostfile
	1886	fi
	1887	eval line=\"`head -n $ii hostfile`\"
	1888	printf "\n *** running on: $line"
	1889	fi
	1890
	1891
	1892
	1893	# SET THE NUMBER OF OPENMP-THREADS
	1894	if [[ $use_openmp = true ]]
	1895	then
	1896	export OMP_NUM_THREADS=$threads_per_task
	1897	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1898	else
	1899	export OMP_NUM_THREADS=1
	1900	fi
	1901
	1902
	1903	# PROVIDE DATA FOR
	1904	if [[ $run_coupled_model = false ]]
	1905	then
	1906	if [[ "$ocean_file_appendix" = true ]]
	1907	then
	1908	echo "precursor_ocean" > coupling_steering
	1909	else
	1910	echo "precursor_atmos" > coupling_steering
	1911	fi
	1912	else
	1913	(( iia = $cores_atmos / $threads_per_task ))
	1914	(( iio = $cores_ocean / $threads_per_task ))
	1915	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1916	printf "\n\n"
	1917	echo "coupled_run $iia $iio" > coupling_steering
	1918	fi
	1919
	1920	printf "\n *** execute command:"
	1921	printf "\n \"$execute_command\" \n\n"
	1922
	1923	$execute_command < coupling_steering
	1924
	1925	if [[ $? != 0 ]]
	1926	then
	1927
	1928	# ABORT IN CASE OF RUNTIME ERRORS
	1929	printf "\n +++ runtime error occured"
	1930	locat=execution
	1931	exit
	1932
	1933	else
	1934
	1935	printf "\n$dashes\n *** execution finished \n"
	1936
	1937	fi
	1938
	1939
	1940	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1941	# BY EACH CORE INTO ONE FILE
	1942	if [[ ! -f combine_plot_fields.x ]]
	1943	then
	1944
	1945	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1946	printf "\n 2d- and/or 3d-data may be incomplete!"
	1947	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1948
	1949	elif [[ "$combine_plot_fields" == true ]]
	1950	then
	1951
	1952	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1953	$execute_command_for_combine
	1954
	1955	else
	1956
	1957	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1958	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1959	# ??? koennen wir das streichen ???
	1960	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1961	fi
	1962
	1963
	1964
	1965	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1966	(( i = 0 ))
	1967	while (( i < ioc ))
	1968	do
	1969	(( i = i + 1 ))
	1970	if (( i == 1 ))
	1971	then
	1972	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1973	fi
	1974	printf "\n >>> ${out_command[$i]}"
	1975	eval ${out_command[$i]}
	1976	if (( i == ioc ))
	1977	then
	1978	printf "\n$dashes\n"
	1979	fi
	1980	done
	1981
	1982
	1983	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1984	if [[ $do_trace = true ]]
	1985	then
	1986	printf "\n\n"
	1987	ls -al
	1988	fi
	1989
	1990
	1991	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1992	(( i = 0 ))
	1993	while (( i < iout ))
	1994	do
	1995	(( i = i + 1 ))
	1996	if (( i == 1 ))
	1997	then
	1998	printf "\n\n *** saving OUTPUT-files:"
	1999
	2000	# GET RUN NUMBER ASSIGNED BY PALM
	2001	if [[ -f RUN_NUMBER ]]
	2002	then
	2003	read run_number < RUN_NUMBER
	2004	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2005	usecycle_option="-U $run_number"
	2006	else
	2007	run_number=0
	2008	usecycle_option=""
	2009	fi
	2010	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2011	then
[2404]	2012	printf "\n *** in case of SCP transfers to local host"
	2013	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2014	fi
	2015	printf "\n$dashes"
	2016	fi
	2017
	2018	# ADD CYCLE NUMBER TO FILENAME
	2019	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2020	then
	2021
	2022	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	2023	if [[ "${actionout[$i]}" != "a" ]]
	2024	then
	2025	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2026	# WITH AN EXISTING CYCLE NUMBER
	2027	if (( run_number >= cycnum[$i] ))
	2028	then
	2029	(( cycnum[$i] = run_number ))
	2030	else
	2031	if (( run_number > 0 ))
	2032	then
	2033	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2034	fi
	2035	fi
	2036	fi
	2037	if (( cycnum[$i] > 0 ))
	2038	then
	2039	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	2040	fi
	2041	fi
	2042
	2043	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2044	files_for_cores=false; filetype=file
	2045	link_local_output=false
	2046	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2047	then
	2048	files_for_cores=true; filetype=directory
	2049	actionout[$i]=""
	2050	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2051	then
	2052	actionout[$i]=""
	2053	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2054	then
	2055	files_for_cores=true; filetype=directory
	2056	link_local_output=true
	2057	actionout[$i]=""
	2058	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2059	then
	2060	link_local_output
	2061	actionout[$i]=""
	2062	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2063	then
	2064	files_for_cores=true; filetype=directory
	2065	actionout[$i]="tr"
	2066	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2067	then
	2068	actionout[$i]="tr"
	2069	fi
	2070
	2071	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2072	then
	2073	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2074	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2075	then
	2076	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2077	else
	2078
	2079
	2080	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2081	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2082	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2083	then
	2084	if [[ $running_on_remote = true ]]
	2085	then
	2086
	2087	# SET OPTIONS FOR TRANSFER
	2088	if [[ "${actionout[$i]}" = tr ]]
	2089	then
	2090	if [[ $files_for_cores = false ]]
	2091	then
	2092	catalog_option=""
	2093	catalog_string=""
	2094	else
	2095	catalog_option="-c"
	2096	catalog_string="/"
	2097	fi
	2098	append_option=""
	2099	append_string=""
	2100	else
	2101	append_option="-A"
	2102	append_string="append"
	2103	fi
	2104
	2105	transfer_failed=false
	2106	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2420]	2107	printf "\n ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2108
	2109	# TRANSFER VIA SCP
	2110	if [[ "$remote_loginnode" != "" ]]
	2111	then
[2420]	2112	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]	2113	else
[2420]	2114	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]	2115	fi
	2116	[[ $? != 0 ]] && transfer_failed=true
	2117
	2118
	2119	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2120	if [[ $transfer_failed = true ]]
	2121	then
	2122	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2420]	2123	printf " ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id\n"
[2380]	2124
	2125	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2126	eval local_catalog=${pathout[$i]}
	2127	if [[ ! -d $local_catalog ]]
	2128	then
	2129	printf " *** local directory does not exist. Trying to create:\n"
	2130	printf " $local_catalog \n"
	2131	mkdir -p $local_catalog
	2132	fi
[2420]	2133	eval cp ${localout[$i]} ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id
[2380]	2134	transfer_problems=true
	2135	fi
	2136
	2137	else
	2138
	2139	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2140	# BE COPIED OR APPENDED ON THIS MACHINE
	2141	if [[ "${actionout[$i]}" = tr ]]
	2142	then
	2143	actionout[$i]=""
	2144	else
	2145	actionout[$i]="a"
	2146	fi
	2147	fi
	2148	fi
	2149
	2150
	2151	# APPEND ON THIS MACHINE
	2152	if [[ "${actionout[$i]}" = "a" ]]
	2153	then
	2154	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2155	then
	2156	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2157	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2158	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2159	else
	2160	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2161	printf "\n ${pathout[$i]}\n"
	2162	cat ${localout[$i]} >> ${pathout[$i]}
	2163	fi
	2164	fi
	2165
	2166	# COPY ON THIS MACHINE
	2167	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2168	# ON DIFFERENT FILE-SYSTEMS
	2169	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2170	then
	2171
	2172	# COPY IN CASE OF RUNS ON SINGLE CORES
	2173	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2174	then
	2175	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2176	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2177	if [[ $link_local_output = true ]]
	2178	then
	2179	printf " file will be linked\n"
	2180	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2181	fi
	2182	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2183	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2184	then
	2185	if [[ $link_local_output = true ]]
	2186	then
	2187	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2188	fi
	2189	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2190	else
	2191	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2192	fi
	2193	else
	2194	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2195	printf "\n ${pathout[$i]}\n"
	2196	if [[ $link_local_output = true ]]
	2197	then
	2198	printf " file will be linked\n"
	2199	ln -f ${localout[$i]} ${pathout[$i]}
	2200	fi
	2201	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2202	if [[ ! -f "${pathout[$i]}" ]]
	2203	then
	2204	if [[ $link_local_output = true ]]
	2205	then
	2206	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2207	fi
	2208	cp ${localout[$i]} ${pathout[$i]}
	2209	else
	2210	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2211	fi
	2212	fi
	2213
	2214	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2215	then
	2216
	2217	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2218	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2219	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2220	printf "\n ${pathout[$i]}\n"
	2221	if [[ $link_local_output = true ]]
	2222	then
	2223	printf " files will be linked\n"
[2396]	2224	mkdir -p ${pathout[$i]}
[2380]	2225	cd ${localout[$i]}
	2226	for file in $(ls *)
	2227	do
	2228	ln -f $file ${pathout[$i]}
	2229	done >\|/dev/null 2>&1
	2230	cd $TEMPDIR
	2231	fi
	2232
	2233	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2234	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2235	then
	2236	if [[ $link_local_output = true ]]
	2237	then
	2238	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2239	fi
	2240	cp -r ${localout[$i]}/* ${pathout[$i]}
	2241	fi
	2242
	2243	fi
	2244	fi
	2245	done
	2246
	2247	if (( i != 0 ))
	2248	then
	2249	if [[ $transfer_problems = true ]]
	2250	then
	2251	printf "\n$dashes\n *** OUTPUT-files saved"
	2252	printf "\n +++ WARNING: some data transfers failed! \n"
	2253	else
	2254	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2255	fi
	2256	fi
	2257
	2258
	2259	# IF REQUIRED, START A RESTART-JOB
	2260	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2261	if [[ -f CONTINUE_RUN ]]
	2262	then
	2263
	2264	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2265	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2266	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2267	# -b START A BATCH JOB
	2268	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2269	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2270	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2271
	2272
	2273	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2274	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2275	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2276	then
[2381]	2277	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2278	fi
	2279
	2280
	2281	# START THE RESTART-JOB
	2282	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2283	echo " $prc"
	2284	printf "\n$dashes\n"
	2285	if [[ $running_on_remote = true ]]
	2286	then
	2287
	2288	echo "*** ssh will be used to initiate restart-runs!"
	2289	echo " return_address=\"$return_address\" "
	2290	echo " return_username=\"$local_username\" "
	2291
	2292	if [[ "$remote_loginnode" != "" ]]
	2293	then
[2420]	2294	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]	2295	else
[2420]	2296	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2297	fi
	2298
	2299	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2300	sleep 30
	2301
	2302	else
	2303
	2304	# START THE RESTART JOB ON THE LOCAL HOST
	2305	eval $prc # THE ' MUST BE EVALUATED
	2306	cd - > /dev/null
	2307
	2308	fi
	2309	printf "\n$dashes\n *** restart-run initiated \n"
	2310
	2311
	2312	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2313	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2314	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2315	# MAY BE VERY HUGE)
	2316	(( i = 0 ))
	2317	while (( i < iin ))
	2318	do
	2319	(( i = i + 1 ))
	2320	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2321	then
	2322	rm -r ${absnamein[$i]}
	2323	fi
	2324	done
	2325
	2326	fi
	2327
	2328
	2329	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2330	cd $HOME
	2331	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2332
	2333
	2334	else
	2335
	2336
	2337	# PREPARING ACTIONS,
	2338	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2339
	2340	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2420]	2341	palmrun_com="$palmrun_script_name -d $fname -h $host_identifier -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2342	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2343	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2344	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2345	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2346	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2347	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2348	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2349	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2350	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2351	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2352	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2353	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2354	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2355	if [[ $create_remote_batch_job = true ]]
	2356	then
	2357	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2358	if [[ $do_trace = true ]]
	2359	then
	2360	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2361	fi
[2380]	2362	elif [[ $create_batch_job = true ]]
	2363	then
	2364	palmrun_com=${palmrun_com}" -j"
[2420]	2365	if [[ $do_trace = true ]]
	2366	then
	2367	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2368	fi
[2380]	2369	fi
	2370
	2371
	2372	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2373	# REMOTE HOST
[2420]	2374	job_protocol_file_local=${local_jobcatalog}/${host_identifier}_${job_id}
[2380]	2375	job_protocol_file=$job_protocol_file_local
	2376	if [[ $create_remote_batch_job = true ]]
	2377	then
[2420]	2378	job_protocol_file_remote=${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2379	job_protocol_file=$job_protocol_file_remote
	2380	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2381	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2382	fi
	2383
	2384
	2385	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2386	jobfile=jobfile.$run_id
	2387
	2388
	2389	# FIRST CREATE THE BATCH DIRECTIVES
	2390	(( i = 0 ))
	2391	while (( i < ibd ))
	2392	do
	2393	(( i = i + 1 ))
[2479]	2394	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2395	eval line=\"$line\"
	2396	echo "$line" >> $jobfile
	2397	done
	2398	echo " " >> $jobfile
	2399
	2400
	2401	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2402	# PROTOCOL
	2403	if [[ $create_remote_batch_job = true ]]
	2404	then
	2405	echo "set +vx" >> $jobfile
	2406	echo "trap '" >> $jobfile
	2407	echo "set +vx" >> $jobfile
	2408	echo "cd ${remote_jobcatalog}" >> $jobfile
	2409	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2410
	2411	# ADD THE BATCH DIRECTIVES
	2412	(( i = 0 ))
	2413	while (( i < ibdt ))
	2414	do
	2415	(( i = i + 1 ))
[2479]	2416	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
[2380]	2417	eval line=\"$line\"
	2418	echo "$line" >> $jobfile
	2419	done
	2420	echo " " >> $jobfile
	2421
	2422	echo "set -x" >> $jobfile
[2420]	2423	echo "${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]	2424	echo "%%END%%" >> $jobfile
	2425	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2426	echo "$submit_command $scpjob_file" >> $jobfile
	2427	echo "rm $scpjob_file" >> $jobfile
[2404]	2428	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2429	echo "set -x" >> $jobfile
	2430	echo " ' exit" >> $jobfile
	2431	fi
	2432
	2433
	2434	# ACTIVATE ERROR-TRACEBACK
	2435	if [[ $do_trace = true ]]
	2436	then
	2437	echo "set -x" >> $jobfile
	2438	else
	2439	echo "set +vx" >> $jobfile
	2440	fi
	2441
	2442
	2443	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2444	if [[ "$login_init_cmd" != "" ]]
	2445	then
	2446	echo "$login_init_cmd" >> $jobfile
	2447	fi
	2448	if [[ "$module_commands" != "" ]]
	2449	then
	2450	echo "$module_commands" >> $jobfile
	2451	fi
	2452
	2453
	2454	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2455	echo "mkdir $TEMPDIR" >> $jobfile
	2456	echo "cd $TEMPDIR" >> $jobfile
	2457	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2404]	2458	echo "cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
[2380]	2459	echo "export PATH=.:\$PATH" >> $jobfile
	2460	echo "export execute_palmrun=true" >> $jobfile
	2461
	2462
	2463	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2464	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2465	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2466	if [[ $create_remote_batch_job = true ]]
	2467	then
	2468	(( i = 0 ))
	2469	while (( i < iin ))
	2470	do
	2471	(( i = i + 1 ))
	2472	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2473	if [[ "${transin[$i]}" = job ]]
	2474	then
	2475	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2476	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2477	echo " " >> $jobfile
	2478	echo "%END%" >> $jobfile
	2479	else
	2480	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2481	fi
	2482
	2483	# CHECK, IF FILE COULD BE CREATED
	2484	echo "if [[ \$? = 1 ]]" >> $jobfile
	2485	echo "then" >> $jobfile
	2486	echo " echo \" \" " >> $jobfile
	2487	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2420]	2488	echo " echo \" please check, if directory exists on $host_identifier!\" " >> $jobfile
[2380]	2489	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2490	echo " execute_palmrun=false" >> $jobfile
	2491	echo "fi" >> $jobfile
	2492	done
	2493	fi
	2494
	2495
	2496	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2497	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2498	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2499	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2500	echo "export LOCAL_PWD" >> $jobfile
	2501
	2502
	2503	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2504	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2505	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2506
	2507
	2508	# CALL PALMRUN WITHIN THE JOB
	2509	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2510	echo "set -x" >> $jobfile
	2511	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2512
	2513
	2514	# TRANSFER JOBFILE TO THE TARGET HOST
	2515	if [[ $create_jobfile_only = false ]]
	2516	then
	2517
	2518	if [[ $create_remote_batch_job = true ]]
	2519	then
	2520
[2420]	2521	echo " "
	2522	echo " *** transfer of job to remote host via scp"
	2523	if [[ $do_trace = true ]]
	2524	then
	2525	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}"
	2526	fi
	2527	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2528
	2529	echo " "
[2420]	2530	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2531	if [[ $do_trace = true ]]
	2532	then
	2533	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"
	2534	fi
	2535	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]	2536
	2537	elif [[ $create_batch_job = true ]]
	2538	then
	2539
[2385]	2540	eval local_jobcatalog=$local_jobcatalog
[2420]	2541	cp $jobfile ${local_jobcatalog}/${host_identifier}_${job_id}
[2385]	2542	cd $local_jobcatalog
[2380]	2543	echo " "
[2420]	2544	echo " *** submit the job"
	2545	if [[ $do_trace = true ]]
	2546	then
	2547	echo "$submit_command ${host_identifier}_${job_id}"
	2548	fi
	2549	$submit_command ${host_identifier}_${job_id}
	2550	rm ${host_identifier}_${job_id}
[2380]	2551	cd - > /dev/null
	2552
	2553	fi
	2554
	2555	rm -rf $jobfile
	2556
	2557	else
	2558
	2559	printf "\n *** jobfile created under name \"$jobfile\" "
	2560	printf "\n no batch-job has been sent!"
	2561
	2562	fi
	2563
	2564	fi # END OF REMOTE-PART

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