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source: palm/trunk/SCRIPTS/palmrun @ 2420

Last change on this file since 2420 was 2420, checked in by raasch, 7 years ago
PALM_BIN setting removed from new scripts
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 82.3 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
	6	# This file is part of PALM.
	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
	19	# Copyright 2017 Leibniz Universitaet Hannover
	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
	28	# $Id: palmrun 2420 2017-09-07 06:20:11Z raasch $
[2410]	29	# initial revision
[2380]	30	#
[2410]	31	# 2405 2017-09-05 11:17:46Z raasch
	32	#
[2380]	33	#
	34	#--------------------------------------------------------------------------------#
	35	# palmrun - script for running PALM jobs on local and remote hosts
	36	#--------------------------------------------------------------------------------#
	37
	38
	39
	40	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	41
	42	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	43	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	44	# (TOO MANY ARGUMENTS - PROBLEM)
	45	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	46
	47	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
	48	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	49	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	50	# SCRIPT-OPTION ARGUMENTS
	51	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	52	typeset -i icycle inode ival maxcycle mpi_tasks
	53	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	54
	55	activation_string_list=""
	56	AddFilenames=""
	57	combine_plot_fields=true
	58	compiler_name=""
	59	compiler_name_ser=""
	60	compiler_options=""
	61	cores=""
	62	cores_atmos=0
	63	cores_ocean=0
	64	coupled_dist=""
	65	cpp_options=""
	66	cpumax=0
	67	create_jobfile_only=false
	68	delete_temporary_catalog=true
	69	create_batch_job=false
	70	create_remote_batch_job=false
	71	dashes=" ----------------------------------------------------------------------------"
	72	defaultqueue=""
	73	do_compile=true
	74	do_trace=false
	75	executable=""
	76	execute_command=""
	77	execution_error=false
	78	fileconnection_file=.palm.iofiles
	79	fname=test
	80	global_revision=""
[2420]	81	host_identifier="default"
[2380]	82	hostfile=""
	83	hp=""
	84	keep_data_from_previous_run=false
	85	link_local_input=false
	86	link_local_output=false
[2388]	87	linker_options=""
[2385]	88	local_jobcatalog=""
[2380]	89	locat=normal
	90	makefile=""
	91	max_par_io_str=""
	92	prc=$0
	93	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	94	do
	95	prc=`echo $prc \| cut -f2- -d"/"`
	96	done
	97	module_calls=""
	98	palmrun_script_name=$prc
	99	openmp=false
	100	queue=none
	101	restart_run=false
	102	return_address=""
[2385]	103	remote_jobcatalog=""
[2380]	104	remote_username=""
	105	running_in_batch_mode=false
	106	run_coupled_model=false
	107	run_id=""
	108	silent=false
	109	source_list=""
	110	source_path=""
	111	tasks_per_node=""
	112	threads_per_task=1
	113	tmpcreate=false
	114	transfer_problems=false
[2384]	115	user_source_path=""
[2380]	116	use_openmp=false
	117	version="palmrun 0.9 Rev$Rev: 2303 $"
	118	working_directory=`pwd`
	119	write_binary=""
	120	TOPT=""
	121
	122
	123	# ERROR HANDLING IN CASE OF EXIT
[2404]	124	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	125	then
	126
	127	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	128	(( i = 0 ))
	129	while (( i < iec ))
	130	do
	131	(( i = i + 1 ))
	132	printf "\n *** Execution of ERROR-command:\n"
	133	printf " >>> ${err_command[$i]}\n"
	134	eval ${err_command[$i]}
	135	done
[2405]	136	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $TEMPDIR)
[2380]	137	printf "\n\n+++ palmrun killed \n\n"
	138	elif [[ $locat != control_c ]]
	139	then
	140	printf "\n\n --> palmrun finished\n\n"
	141	if [[ $running_on_remote = true ]]
	142	then
	143	printf " Bye, bye $remote_username !!\n\n"
	144	else
	145	printf " Bye, bye $local_username !!\n\n"
	146	fi
	147	fi' exit
	148
	149
	150	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2405]	151	trap 'cd; rm -rf $TEMPDIR
[2380]	152	printf "\n+++ palmrun killed by \"^C\" \n\n"
	153	locat=control_c
	154	exit
	155	' 2
	156
	157
	158	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	159	# WHICH WILL BE USED TO START RESTART-JOBS
[2420]	160	while getopts :a:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
[2380]	161	do
	162	case $option in
	163	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
	164	(b) create_batch_job=true; prc="$prc -b";;
	165	(B) delete_temporary_catalog=false; prc="$prc -B";;
	166	(C) restart_run=true; prc="$prc -C";;
	167	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	168	(F) create_jobfile_only=true;;
	169	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2420]	170	(h) host_identifier=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	171	(j) running_in_batch_mode=true;;
	172	(k) keep_data_from_previous_run=true; prc="$prc -k";;
	173	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
	174	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	175	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	176	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	177	(r) run_id=$OPTARG;;
	178	(R) return_address=$OPTARG;;
	179	(s) source_list=$OPTARG;;
	180	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
	181	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	182	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	183	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	184	(v) silent=true; prc="$prc -v";;
	185	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
	186	(x) do_trace=true;set -x; prc="$prc -x";;
	187	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
	188	(y) ocean_file_appendix=true; prc="$prc -y";;
	189	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	190	(Z) combine_plot_fields=false; prc="$prc -Z";;
	191	(\?) printf "\n +++ unknown option $OPTARG \n"
	192	printf "\n --> type \"$0 ?\" for available options \n"
	193	locat=parameter;exit;;
	194	esac
	195	done
	196
	197
	198	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	199	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	200	(( to_shift = $OPTIND - 1 ))
	201	shift $to_shift
	202
	203	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	204	if [[ "$1" = "?" ]]
	205	then
	206	(printf "\n *** Description of available palmrun options:\n"
	207	printf "\n Option Description Default-Value"
	208	printf "\n -a activation string list \"\" "
	209	printf "\n -b batch-job on local machine ---"
	210	printf "\n -B do not delete temporary directory at end ---"
	211	printf "\n -d base name of files attached to program test"
	212	printf "\n -F create batch job file only ---"
[2420]	213	printf "\n -h host identifier \"default\" "
[2380]	214	printf "\n -k keep data from previous run"
	215	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	216	printf "\n -M Makefile name Makefile"
	217	printf "\n -O threads per openMP task ---"
	218	printf "\n -q queue \"$queue\" "
	219	printf "\n -s filenames of routines to be compiled \"\" "
	220	printf "\n must end with .f, .f90, .F, or .c !"
	221	printf "\n use \"..\" for more than one file and wildcards"
	222	printf "\n -s LM compiles all locally modified files"
	223	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	224	printf "\n -T tasks per node ---"
[2380]	225	printf "\n -u username on remote machine \"\" "
	226	printf "\n -v no prompt for confirmation ---"
	227	printf "\n -w maximum parallel io streams as given by -X"
	228	printf "\n -x tracing of palmrun for debug purposes ---"
	229	printf "\n -X # of processors (on parallel machines) 1"
	230	printf "\n -y add appendix \"_O\" to all local output"
	231	printf "\n files (ocean precursor runs followed by"
	232	printf "\n coupled atmosphere-ocean runs) ---"
	233	printf "\n -Y run coupled model, \"#1 #2\" with"
	234	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	235	printf "\n -Z skip combine_plot_fields at the end of "
	236	printf "\n the simulation ---"
	237	printf "\n "
	238	printf "\n Possible values of positional parameter <modus>:"
	239	printf "\n \"?\" - this outline \n\n") \| more
	240	exit
	241	elif [[ "$1" != "" ]]
	242	then
	243	printf "\n +++ positional parameter $1 unknown \n"
	244	locat=parameter; exit
	245	fi
	246
	247
	248
	249	# SHORT STARTING MESSAGE
	250	printf "\n*** $version "
	251	printf "\n will be executed. Please wait ..."
	252
	253
	254	# BUILD THE CONFIGURATION-FILE NAME
[2420]	255	config_file=.palm.config.$host_identifier
[2380]	256
	257
	258	# CHECK, IF CONFIGURATION FILE EXISTS
	259	if [[ ! -f $config_file ]]
	260	then
	261	printf "\n\n +++ configuration file: "
	262	printf "\n $config_file"
	263	printf "\n does not exist"
	264	locat=connect; exit
	265	fi
	266
	267
	268	# CHECK, IF FILE CONNECTION FILE EXISTS
	269	if [[ ! -f $fileconnection_file ]]
	270	then
	271	printf "\n\n +++ file connection file: "
	272	printf "\n $fileconnection_file"
	273	printf "\n does not exist"
	274	locat=connect; exit
	275	fi
	276
	277
[2404]	278	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	279	if [[ "$activation_string_list" = "" ]]
	280	then
	281	printf "\n\n +++ no activation string list given: "
	282	printf "\n please set palmrun option \"-a\" "
	283	locat=palmrun_option; exit
	284	fi
	285
	286
	287	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	288	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	289	then
	290	write_binary=true
	291	else
	292	write_binary=false
	293	fi
	294
	295
[2380]	296	# READ AND EVALUATE THE CONFIGURATION-FILE
	297	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	298
	299	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	300	while read line
	301	do
	302
	303	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	304	eval line=\"$line\"
	305
	306
	307	# INTERPRET THE LINE
	308	if [[ "$(echo $line)" = "" ]]
	309	then
	310
	311	# EMPTY LINE, NO ACTION
	312	continue
	313
	314	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	315	then
	316
	317	# LINE IS A COMMENT LINE
	318	continue
	319
	320	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	321	then
	322
	323	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	324	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	325	value=`echo $line \| cut -d" " -s -f2-`
	326
	327
	328	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	329	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	330	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	331	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	332	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	333	# CONFIGURATION-FILE.
	334	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	335	then
	336	eval export $var="\$value"
	337
	338	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	339	if [[ $do_trace = true ]]
	340	then
	341	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	342	fi
	343	fi
	344
	345	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	346	then
	347
	348	# LINE DEFINES BATCH-DIRECTIVE
	349	(( ibd = ibd + 1 ))
	350	line=$(echo $line \| cut -c4-)
	351	batch_directive[$ibd]="$line"
	352
	353	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	354	then
	355
	356	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	357	# REMOTE TO A LOCAL HOST
	358	(( ibdt = ibdt + 1 ))
	359	line=$(echo $line \| cut -c5-)
	360	batch_directive_transfer[$ibdt]="$line"
	361
	362	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	363	then
	364
	365	# LINE DEFINES ERROR-COMMAND
	366	(( iec = iec + 1 ))
	367	line=$(echo $line \| cut -c4-)
	368	err_command[$iec]="$line"
	369
	370	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	371	then
	372
	373	# LINE DEFINES INPUT-COMMAND
	374	(( iic = iic + 1 ))
	375	line=$(echo $line \| cut -c4-)
	376	in_command[$iic]="$line"
	377
	378	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	379	then
	380
	381	# LINE DEFINES OUTPUT-COMMAND
	382	(( ioc = ioc + 1 ))
	383	line=$(echo $line \| cut -c4-)
	384	out_command[$ioc]="$line"
	385
	386	else
	387
	388	# SKIP ALL OTHER LINES
	389	continue
	390
	391	fi
	392
	393	done < $config_file
	394
	395
	396	# CHECK SETTING OF REQUIRED PARAMETERS
	397	if [[ "$compiler_name" = "" ]]
	398	then
	399	printf "\n +++ no compiler name found in $config_file"
	400	printf "\n Please add line \"compiler_name ...\" to that file."
	401	locat=config_file; exit
	402	fi
	403	if [[ "$compiler_name_ser" = "" ]]
	404	then
	405	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	406	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	407	locat=config_file; exit
	408	fi
	409	if [[ "$compiler_options" = "" ]]
	410	then
	411	printf "\n +++ no compiler options found in $config_file"
	412	printf "\n Please add line \"compiler_options ...\" to that file."
	413	locat=config_file; exit
	414	fi
[2388]	415	if [[ "$linker_options" = "" ]]
[2380]	416	then
[2388]	417	printf "\n +++ no linker options found in $config_file"
	418	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	419	locat=config_file; exit
	420	fi
	421	if [[ "$execute_command" = "" ]]
	422	then
	423	printf "\n +++ no execute command found in $config_file"
	424	printf "\n Please add line \"execute_command ...\" to that file."
	425	locat=config_file; exit
	426	fi
	427
	428	if [[ "$hostfile" != "" ]]
	429	then
	430	if [[ $hostfile != auto && ! -f $hostfile ]]
	431	then
	432	printf "\n +++ no hostfile \"$hostfile\" found"
	433	printf "\n Please check line \"hostfile ...\" in $config_file"
	434	locat=config_file; exit
	435	fi
	436	fi
	437
	438
	439	# DETERMINE THE CALL STATUS
	440	if [[ "$return_address" != "" ]]
	441	then
	442
	443	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	444	# BATCH MODE AND ...
	445	running_on_remote=true
	446
	447	else
	448
	449	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	450	if [[ "$remote_ip" != "" ]]
	451	then
	452
	453	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	454	create_remote_batch_job=true
	455
	456	fi
	457	running_on_remote=false
	458	fi
	459
	460
	461
	462	# READ AND EVALUATE THE I/O-FILE LIST
	463	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	464
	465	# READ THE FILE CONNECTION FILE LINE BY LINE
	466	while read line
	467	do
	468
	469	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	470	eval line=\"$line\"
	471
	472
	473	# INTERPRET THE LINE
	474	if [[ "$(echo $line)" = "" ]]
	475	then
	476	# EMPTY LINE, NO ACTION
	477	continue
	478
	479	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	480	then
	481
	482	# LINE IS A COMMENT LINE
	483	true
	484
	485	else
	486
	487	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	488	# s2a: in/out - field
	489	# s2b: loc - field (optional)
	490	# s2c: tr/ar - field (optional)
	491	s1=`echo $line \| cut -d" " -f1`
	492	s2=`echo $line \| cut -d" " -s -f2`
	493	s2a=$(echo $s2 \| cut -d":" -f1)
	494	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	495	then
	496	s2b=""
	497	s2c=""
	498	else
	499	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	500	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	501	fi
	502	s3=`echo $line \| cut -d" " -f3`
	503	s4=`echo $line \| cut -d" " -s -f4`
	504	s5=`echo $line \| cut -d" " -s -f5`
	505	s6=`echo $line \| cut -d" " -s -f6`
	506
	507
	508	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	509	# INPUT- OR OUTPUT-LIST.
	510	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	511	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	512	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	513	# IS NOT CHECKED AND STORED.
	514	IFSALT="$IFS"; IFS="$IFS:"
	515	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	516	then
	517	found=false
	518	for actual in $activation_string_list
	519	do
	520	for formal in $s3
	521	do
	522	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	523	done
	524	done
	525	if [[ $found = true ]]
	526	then
	527	(( iin = iin + 1 ))
	528	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	529	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	530	extin[$iin]=$s6
	531	fi
	532	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	533	then
	534	found=false
	535	for actual in $activation_string_list
	536	do
	537	for formal in $s3
	538	do
	539	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	540	done
	541	done
	542	if [[ $found = true ]]
	543	then
	544	(( iout = iout + 1 ))
	545	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	546	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	547	fi
	548	elif [[ "$s2a" != in && "$s2a" != out ]]
	549	then
	550	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	551	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	552	locat=connect; exit
	553	fi
	554	IFS="$IFSALT"
	555	fi
	556
	557	done < $fileconnection_file
	558
	559
	560
	561	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	562	if [[ $run_coupled_model = true ]]
	563	then
	564
	565	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	566	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	567
	568	if (( $cores_ocean + $cores_atmos != $cores ))
	569	then
	570
	571	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	572	printf "\n PEs (total) : $cores"
	573	printf "\n PEs (atmosphere): $cores_atmos"
	574	printf "\n PEs (ocean) : $cores_ocean"
	575	locat=coupling; exit
	576
	577	fi
	578
	579	fi
	580
	581
	582	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
	583	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
	584	palmrun_memory=$memory
	585	palmrun_cpumax=$cpumax
	586	palmrun_cores=$cores
	587
	588
	589	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
	590	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
	591	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
	592	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	593	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	594	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	595
	596
	597
	598	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	599	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	600	# FOLDER
	601	if [[ $running_in_batch_mode = true ]]
	602	then
	603
[2404]	604	if [[ ! -d ${fast_io_catalog}/SOURCES_FOR_RUN_$fname ]]
[2380]	605	then
[2404]	606	printf "\n +++ directory ${fast_io_catalog}/SOURCES_FOR_RUN_$fname is missing"
[2380]	607	printf "\n Please check the output of the palmrun-call"
	608	printf "\n that you did on your local host."
	609	locat=SOURCES_FOR_RUN; exit
	610	fi
	611
	612	else
	613
	614	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	615	# AUTOMATIC RESTART RUN
	616	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	617	if [[ $restart_run = false ]]
	618	then
	619
	620	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	621	# THE LOCAL HOST
	622	if [[ ! -d $source_path ]]
	623	then
	624	printf "\n\n +++ source path \"$source_path\" on local host"
	625	printf "\n \"$(hostname)\" does not exist"
	626	locat=source_path; exit
	627	fi
	628
[2396]	629	rm -rf SOURCES_FOR_RUN_$fname
	630	mkdir -p SOURCES_FOR_RUN_$fname
[2380]	631
	632	if [[ "$source_list" = LM ]]
	633	then
	634
	635	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	636	source_list=""
	637	cd $source_path
	638
	639
	640	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	641	if [[ ! -d .svn ]]
	642	then
	643	printf "\n\n +++ source directory"
	644	printf "\n \"$source_path\" "
	645	printf "\n is not under control of \"subversion\"."
	646	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	647	fi
	648
	649
	650	# LIST ALL MODIFIED SOURCE CODE FILES
	651	Filenames=""
[2404]	652	svn status > tmp_svnstatus
[2380]	653	while read line
	654	do
	655	firstc=`echo $line \| cut -c1`
	656	if [[ $firstc = M \|\| $firstc = "?" ]]
	657	then
	658	Name=`echo "$line" \| cut -c8-`
	659	extension=`echo $Name \| cut -d. -f2`
	660	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	661	then
	662	Filenames="$Filenames "$Name
	663	fi
	664	fi
[2404]	665	done < tmp_svnstatus
	666	rm -rf tmp_svnstatus
[2380]	667
	668
	669	# COPY FILES TO SOURCES_FOR_RUN_...
	670	for filename in $Filenames
	671	do
	672	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	673	source_list=$source_list"$filename "
	674	done
	675
	676	cd - > /dev/null
	677
	678
	679	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	680	elif [[ "$source_list" != "" ]]
	681	then
	682
	683	cd $source_path
	684
	685	for filename in $source_list
	686	do
	687
	688	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	689	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	690	then
	691	printf "\n +++ source code file: $filename"
	692	printf "\n must not contain (\"/\") "
	693	locat=source; exit
	694	fi
	695
	696	if [[ ! -f $filename ]]
	697	then
	698	printf "\n +++ source code file: $filename"
	699	printf "\n does not exist"
	700	locat=source; exit
	701	else
	702	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	703	fi
	704
	705	done
	706
	707	cd - > /dev/null
	708
	709	fi
	710
	711	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	712	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	713	if [[ ! -f $makefile ]]
	714	then
	715	printf "\n +++ file \"$makefile\" does not exist"
	716	locat=make; exit
	717	else
	718	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	719	fi
	720
	721
	722	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	723	if [[ "$user_source_path" != "" ]]
[2380]	724	then
	725
	726	# DOES THE DIRECTORY EXIST?
[2384]	727	if [[ ! -d $user_source_path ]]
[2380]	728	then
	729
	730	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	731	printf "\n \"$user_source_path\" "
[2380]	732	printf "\n does not exist or is not a directory."
	733	printf "\n No source code will be used from this directory!\n"
[2384]	734	user_source_path=""
[2380]	735	if [[ $silent == false ]]
	736	then
	737	sleep 2
	738	fi
	739
	740	else
	741
[2384]	742	cd $user_source_path
[2380]	743	found=false
	744
	745	Names=$(ls -1 *.f90 2>&1)
	746	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	747	Names=$(ls -1 *.F90 2>&1)
	748	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	749	Names=$(ls -1 *.F 2>&1)
	750	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	751	Names=$(ls -1 *.f 2>&1)
	752	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	753	Names=$(ls -1 *.c 2>&1)
	754	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	755
	756	cd - > /dev/null
	757	cd SOURCES_FOR_RUN_$fname
	758
	759	# COPY MAKEFILE IF EXISTING
[2384]	760	if [[ -f $user_source_path/Makefile ]]
[2380]	761	then
	762	printf "\n\n *** user Makefile from directory"
[2384]	763	printf "\n \"$user_source_path\" is used \n"
[2380]	764	if [[ $silent == false ]]
	765	then
	766	sleep 1
	767	fi
[2384]	768	cp $user_source_path/Makefile .
[2380]	769	fi
	770
	771	for filename in $AddFilenames
	772	do
	773	if [[ -f $filename ]]
	774	then
	775	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	776	printf "\n source code directory \"$user_source_path\" "
[2380]	777	printf "\n but was also given with option \"-s\" which means that it should be taken"
	778	printf "\n from directory \"$source_path\"."
	779	locat=source; exit
	780	fi
	781
[2384]	782	cp $user_source_path/$filename .
[2380]	783	source_list="$source_list $filename"
	784
	785	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	786	if [[ $(grep -c $filename Makefile) = 0 ]]
	787	then
	788	printf "\n\n +++ user file \"$filename\" "
	789	printf "\n is not listed in Makefile \n"
	790	locat=source; exit
	791	else
	792
	793	if [[ $found = false ]]
	794	then
	795	found=true
	796	printf "\n\n *** following user file(s) added to the"
	797	printf " files to be translated:\n "
	798	fi
	799	printf "$filename "
	800	if [[ $silent == false ]]
	801	then
	802	sleep 0.5
	803	fi
	804
	805	fi
	806	done
	807	[[ $found = true ]] && printf "\n"
	808	cd - > /dev/null
	809	fi
	810	fi
	811
	812	# COPY CONFIGURATION FILES
	813	cp $config_file SOURCES_FOR_RUN_$fname
	814	cp $fileconnection_file SOURCES_FOR_RUN_$fname
	815
	816	# COPY SHELLSCRIPTS
	817	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
	818	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
	819
	820	fi
	821
	822	fi
	823
	824	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	825	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	826	if [[ "$global_revision" = "" ]]
	827	then
	828	global_revision=`svnversion $source_path 2>/dev/null`
	829	global_revision="Rev: $global_revision"
	830	fi
	831
	832
	833	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	834	if [[ -n $cores ]]
	835	then
	836
	837	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	838	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2384]	839	if [[ "$tasks_per_node" = "" ]]
[2380]	840	then
	841	printf "\n"
	842	printf "\n +++ option \"-T\" (tasks per node) is missing"
	843	printf "\n set -T option or define tasks_per_node in the config file"
	844	locat=tasks_per_node; (( iec = 0 )); exit
	845	fi
	846
	847	if (( cores < tasks_per_node ))
	848	then
	849	printf "\n"
	850	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	851	printf "\n given values: -T $tasks_per_node -X $cores"
	852	locat=tasks_per_node; (( iec = 0 )); exit
	853	fi
	854
	855	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	856	(( mpi_tasks = cores / threads_per_task ))
	857	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	858	(( ii = cores / tasks_per_node ))
	859	(( remaining_cores = cores - ii * tasks_per_node ))
	860	if (( remaining_cores > 0 ))
	861	then
	862	printf "\n"
	863	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	864	printf "\n divisor of the total number of cores (option \"-X\")"
	865	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	866	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	867	(( nodes = nodes + 1 ))
	868	fi
	869
	870	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	871	if [[ "$tasks_per_node" != "" ]]
	872	then
	873	TOPT="-T $tasks_per_node"
	874	fi
	875
	876	fi
	877
	878
	879	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	880	if [[ "$maximum_parallel_io_streams" = "" ]]
	881	then
	882	maximum_parallel_io_streams=$cores
	883	fi
	884
	885
	886	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	887	if [[ "$scp_port" != "" ]]
	888	then
	889	PORTOPT="-P $scp_port"
	890	SSH_PORTOPT="-p $scp_port"
	891	fi
	892
	893
	894	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	895	# CONFIG-FILE
	896	if [[ "$ssh_key" != "" ]]
	897	then
	898	ssh_key="-i $HOME/.ssh/$ssh_key"
	899	fi
	900
	901
	902	# SET QUEUE, IF NOT GIVEN
	903	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	904	then
	905
	906	if [[ $queue = none && "$defaultqueue" = "" ]]
	907	then
	908	printf "\n"
	909	printf "\n +++ no default queue given in configuration file and no queue"
	910	printf "\n given with option -q"
	911	fi
	912	if [[ $queue = none ]]
	913	then
	914	queue=$defaultqueue
	915	fi
	916
	917	fi
	918
	919
	920	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	921	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	922	(( i = 0 ))
	923	while (( i < iin ))
	924	do
	925	(( i = i + 1 ))
	926	(( maxcycle = 0 ))
	927
	928	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	929	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	930	if [[ "${actionin[$i]}" = di ]]
	931	then
	932	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	933	# HOST ONLY
	934	eval filename=${pathin[$i]}/${endin[$i]}
	935	else
	936	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	937	# HOST ONLY
	938	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	939	fi
	940	eval pathname=${pathin[$i]}
	941
	942	# CHECK IF FILE EXISTS
	943	if ! ls $filename* 1>/dev/null 2>&1
	944	then
	945
	946	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	947	if [[ "${transin[$i]}" != "locopt" ]]
	948	then
	949	printf "\n\n +++ INPUT-file: "
	950	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	951	then
	952	printf "\n $filename"
	953	else
	954	printf "\n $filename.${extin[$i]}"
	955	fi
	956	printf "\n does not exist\n"
	957	locat=input; exit
	958	else
	959	transin[$i]="unavailable"
	960	fi
	961	else
	962
	963	# DETERMINE THE FILE'S CYCLE NUMBER
	964	ls -1 -d $filename > filelist 2>/dev/null
	965	ls -1 -d $filename.* >> filelist 2>/dev/null
	966	while read line
	967	do
	968	# filename without path (i.e. after the last "/")
	969	basefilename=$(basename ${line})
	970
	971	# check if there is an extension
	972	extension=${basefilename##*.}
	973	if [[ "$extension" = "$extin[$i]" ]]
	974	then
	975	basefilename=${basefilename&.*}
	976	fi
	977
	978	# check for an existing cycle number
	979	cycle=${basefilename##*.}
	980	if [[ $cycle =~ ^-?[0-9]+$ ]]
	981	then
	982	(( icycle = $cycle ))
	983	else
	984	(( icycle = 0 ))
	985	fi
	986
	987	if (( icycle > maxcycle ))
	988	then
	989	(( maxcycle = icycle ))
	990	fi
	991
	992	done <filelist
	993	rm filelist
	994
	995	# APPEND CYCLE NUMBER TO FILENAME
	996	if (( maxcycle > 0 ))
	997	then
	998	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	999	then
	1000	filename=${filename}.$maxcycle.${extin[$i]}
	1001	else
	1002	filename=${filename}.$maxcycle
	1003	fi
	1004	else
	1005	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1006	then
	1007	filename=${filename}.${extin[$i]}
	1008	fi
	1009	fi
	1010
	1011	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1012	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1013	absnamein[$i]=$filename
	1014	if (( maxcycle > 0 ))
	1015	then
	1016	if [[ "${actionin[$i]}" = di ]]
	1017	then
	1018	frelin[$i]=${endin[$i]}.$maxcycle
	1019	else
	1020	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1021	fi
	1022	else
	1023	if [[ "${actionin[$i]}" = di ]]
	1024	then
	1025	frelin[$i]=${endin[$i]}
	1026	else
	1027	frelin[$i]=${fname}${endin[$i]}
	1028	fi
	1029	fi
	1030
	1031	fi
	1032	done
	1033
	1034
	1035	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1036	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1037	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1038	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1039	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1040	# REMOTE HOST)
	1041	(( i = 0 ))
	1042	while (( i < iout ))
	1043	do
	1044	(( i = i + 1 ))
	1045	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1046	then
	1047	if [[ "${actionout[$i]}" = tr ]]
	1048	then
	1049	actionout[$i]=""
	1050	elif [[ "${actionout[$i]}" = trpe ]]
	1051	then
	1052	actionout[$i]=pe
	1053	elif [[ "${actionout[$i]}" = tra ]]
	1054	then
	1055	actionout[$i]=a
	1056	fi
	1057	(( maxcycle = 0 ))
	1058	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1059	eval catalogname=${pathout[$i]}
	1060	if ! ls $filename* 1>/dev/null 2>&1
	1061	then
	1062
	1063	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1064	if cat /dev/null > $filename
	1065	then
	1066	rm $filename
	1067	else
	1068
	1069	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1070	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1071	if [[ ! -d $catalogname ]]
	1072	then
	1073	if mkdir -p $catalogname
	1074	then
	1075	printf "\n\n *** directory:"
	1076	printf "\n $catalogname"
	1077	printf "\n was created\n"
	1078	else
	1079	printf "\n\n +++ OUTPUT-file:"
	1080	printf "\n $filename"
	1081	printf "\n cannot be created, because directory does not exist"
	1082	printf "\n and cannot be created either"
	1083	printf "\n"
	1084	locat=output ; exit
	1085	fi 2>/dev/null
	1086	else
	1087	printf "\n\n +++ OUTPUT-file:"
	1088	printf "\n $filename"
	1089	printf "\n cannot be created, although directory exists"
	1090	printf "\n"
	1091	locat=output ; exit
	1092	fi
	1093	fi 2>/dev/null
	1094	else
	1095
	1096	# DETERMINE THE CYCLE NUMBER
	1097	ls -1 -d $filename > filelist 2>/dev/null
	1098	ls -1 -d $filename.* >> filelist 2>/dev/null
	1099	while read line
	1100	do
	1101
	1102	# filename without path (i.e. after the last "/")
	1103	basefilename=$(basename ${line})
	1104
	1105	# check if there is an extension
	1106	extension=${basefilename##*.}
	1107	if [[ "$extension" = "${extout[$i]}" ]]
	1108	then
	1109	basefilename=${basefilename%.*}
	1110	fi
	1111
	1112	# check for an existing cycle number
	1113	cycle=${basefilename##*.}
	1114	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1115	then
	1116	(( icycle = $cycle + 1 ))
	1117	else
	1118	(( icycle = 1 ))
	1119	fi
	1120
	1121	if (( icycle > maxcycle ))
	1122	then
	1123	(( maxcycle = icycle ))
	1124	fi
	1125
	1126	done <filelist
	1127	rm filelist
	1128	fi
	1129
	1130	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1131	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1132	if [[ "${actionout[$i]}" != a ]]
	1133	then
	1134	if (( maxcycle > 0 ))
	1135	then
	1136	filename_tmp=${filename}.$maxcycle
	1137	if cat /dev/null > $filename_tmp
	1138	then
	1139	rm $filename_tmp
	1140	else
	1141	printf "\n +++ OUTPUT-file:"
	1142	printf "\n $filename_tmp"
	1143	printf "\n cannot be created"
	1144	locat=output ; exit
	1145	fi
	1146	fi
	1147	else
	1148	(( maxcycle = maxcycle - 1 ))
	1149	fi
	1150
	1151	(( cycnum[$i] = maxcycle ))
	1152	pathout[$i]=$filename
	1153
	1154	fi
	1155	done
	1156
	1157
	1158	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1159	if [[ $running_in_batch_mode = false ]]
	1160	then
	1161	run_id=$RANDOM
	1162	job_id=${fname}.$run_id
	1163
[2404]	1164	TEMPDIR=$fast_io_catalog/$job_id
[2380]	1165	fi
	1166
	1167
	1168	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1169	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1170	then
	1171
	1172	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1173	if [[ $ibd = 0 ]]
	1174	then
	1175	printf "\n"
	1176	printf "\n +++ no batch directives found in configuration file"
	1177	locat=config_file_batch_directives; (( iec = 0 )); exit
	1178	fi
	1179
	1180	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1181	done=false
[2384]	1182	cputime=$cpumax
[2380]	1183	while [[ $done = false ]]
	1184	do
[2384]	1185	if (( cputime == 0 ))
[2380]	1186	then
	1187	printf "\n +++ cpu-time is undefined"
	1188	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1189	printf "\n >>> "
[2384]	1190	read cputime 1>/dev/null 2>&1
[2380]	1191	else
	1192	done=true
	1193	fi
	1194	done
[2420]	1195	cpumax=$cputime
[2380]	1196
	1197	# CHECK THE MEMORY DEMAND
	1198	done=false
	1199	while [[ $done = false ]]
	1200	do
	1201	if (( memory == 0 ))
	1202	then
	1203	printf "\n +++ memory demand is undefined"
	1204	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1205	printf "\n >>> "
	1206	read memory 1>/dev/null 2>&1
	1207	else
	1208	done=true
	1209	fi
	1210	done
	1211
	1212	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1213	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1214	then
	1215	while [[ -z $remote_username ]]
	1216	do
[2420]	1217	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1218	printf "\n >>> Please type username:"
	1219	printf "\n >>> "
	1220	read remote_username
	1221	done
	1222	fi
	1223
	1224	else
	1225
[2420]	1226	if [[ $running_in_batch_mode = false ]]
	1227	then
	1228	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1229	cpumax=$cputime
	1230	else
	1231	cputime=$cpumax
	1232	fi
[2380]	1233
	1234	fi
	1235
	1236
	1237	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1238	(( cpu_hours = cputime / 3600 ))
	1239	(( resttime = cputime - cpu_hours * 3600 ))
	1240	(( cpu_minutes = resttime / 60 ))
	1241	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1242	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1243
	1244
	1245	# OUTPUT OF THE PALMRUN-HEADER
	1246	calltime=$(date)
	1247	printf "\n"
	1248	printf "#------------------------------------------------------------------------# \n"
	1249	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1250	printf "\| \| \n"
	1251	column1="called on:"; column2=$(hostname)
	1252	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1253	if [[ $create_remote_batch_job = true ]]
	1254	then
[2420]	1255	column1="execution on:"; column2="$host_identifier (username: $remote_username)"
[2380]	1256	else
	1257	if [[ $running_on_remote = true ]]
	1258	then
[2420]	1259	column1="execution on:"; column2="$host_identifier (IP:$remote_ip)"
[2380]	1260	else
[2420]	1261	column1="execution on:"; column2="$host_identifier (IP:$local_ip)"
[2380]	1262	fi
	1263	fi
	1264	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1265
	1266	column1="running in:"
	1267	if [[ $running_in_batch_mode = true ]]
	1268	then
	1269	column2="batch job mode"
	1270	else
	1271	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1272	then
	1273	column2="job creation mode"
	1274	else
	1275	column2="interactive run mode"
	1276	fi
	1277	fi
	1278	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1279
	1280	if [[ -n $cores ]]
	1281	then
	1282	if [[ $run_coupled_model = false ]]
	1283	then
	1284	column1="number of cores:"; column2=$cores
	1285	else
	1286	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1287	fi
	1288	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1289	fi
	1290	if [[ -n $tasks_per_node ]]
	1291	then
	1292	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1293	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1294	if (( remaining_cores > 0 ))
	1295	then
	1296	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1297	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1298	fi
	1299	fi
	1300	if [[ $maximum_parallel_io_streams != $cores ]]
	1301	then
	1302	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1303	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1304	fi
	1305	if [[ $use_openmp = true ]]
	1306	then
	1307	column1="threads per task:"; column2="$threads_per_task"
	1308	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1309	fi
[2384]	1310	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1311	then
	1312	column1="job cpu time (h:m:s):"; column2="$timestring"
	1313	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1314	fi
[2380]	1315	printf "\| \| \n"
	1316	if [[ "$source_list" != "" ]]
	1317	then
	1318	if [[ "$make_options" != "" ]]
	1319	then
	1320	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1321	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1322	line=$(echo "$make_options" \| cut -c46-)
	1323	while [[ "$line" != "" ]]
	1324	do
	1325	column1=""
	1326	column2=$(echo "$line" \| cut -c-45)
	1327	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1328	line=$(echo "$line" \| cut -c46-)
	1329	done
	1330	fi
	1331	fi
	1332
	1333	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1334	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1335	line=$(echo "$cpp_options" \| cut -c46-)
	1336	while [[ "$line" != "" ]]
	1337	do
	1338	column1=""
	1339	column2=$(echo "$line" \| cut -c-45)
	1340	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1341	line=$(echo "$line" \| cut -c46-)
	1342	done
	1343
	1344	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1345	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1346	line=$(echo "$compiler_options" \| cut -c46-)
	1347	while [[ "$line" != "" ]]
	1348	do
	1349	column1=""
	1350	column2=$(echo "$line" \| cut -c-45)
	1351	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1352	line=$(echo "$line" \| cut -c46-)
	1353	done
	1354
[2388]	1355	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1356	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1357	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1358	while [[ "$line" != "" ]]
	1359	do
	1360	column1=""
	1361	column2=$(echo "$line" \| cut -c-45)
	1362	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1363	line=$(echo "$line" \| cut -c46-)
	1364	done
	1365
	1366	if [[ "$login_init_cmd" != "" ]]
	1367	then
	1368	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1369	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1370	line=$(echo "$login_init_cmd" \| cut -c46-)
	1371	while [[ "$line" != "" ]]
	1372	do
	1373	column1=""
	1374	column2=$(echo "$line" \| cut -c-45)
	1375	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1376	line=$(echo "$line" \| cut -c46-)
	1377	done
	1378	fi
	1379
	1380	if [[ "$module_commands" != "" ]]
	1381	then
	1382	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1384	line=$(echo "$module_commands" \| cut -c46-)
	1385	while [[ "$line" != "" ]]
	1386	do
	1387	column1=""
	1388	column2=$(echo "$line" \| cut -c-45)
	1389	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1390	line=$(echo "$line" \| cut -c46-)
	1391	done
	1392	fi
	1393	printf "\| \| \n"
	1394	column1="base name of files:"; column2=$fname
	1395	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1396	column1="activation string list:"; column2=$(echo $activation_string_list)
	1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1398
	1399	if [[ "$ocean_file_appendix" = true ]]
	1400	then
	1401	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1402	fi
	1403
	1404	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
	1405	then
	1406	column1="memory demand / PE":; column2="$memory MB"
	1407	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1408	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
	1409	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1410	fi
	1411
	1412	if [[ "$source_list" != "" ]]
	1413	then
	1414	printf "\| \| \n"
	1415	printf "\| Files to be compiled: \| \n"
	1416	line=$source_list
	1417	while [[ "$line" != "" ]]
	1418	do
	1419	linestart=$(echo $line \| cut -c-70)
	1420	printf "\| %-70s \| \n" "$linestart"
	1421	line=$(echo "$line" \| cut -c71-)
	1422	done
	1423	fi
	1424	printf "#------------------------------------------------------------------------#"
	1425
	1426
	1427
	1428	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1429	if [[ $do_trace = true ]]
	1430	then
	1431	(( i = 0 ))
	1432	while (( i < iin ))
	1433	do
	1434	(( i = i + 1 ))
	1435	if (( i == 1 ))
	1436	then
	1437	printf "\n\n >>> INPUT-file assignments:\n"
	1438	fi
	1439	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1440	done
	1441	(( i = 0 ))
	1442	while (( i < iout ))
	1443	do
	1444	(( i = i + 1 ))
	1445	if (( i == 1 ))
	1446	then
	1447	printf "\n\n >>> OUTPUT-file assignments:\n"
	1448	fi
	1449	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1450	done
	1451	(( i = 0 ))
	1452	while (( i < iic ))
	1453	do
	1454	(( i = i + 1 ))
	1455	if (( i == 1 ))
	1456	then
	1457	printf "\n\n >>> INPUT-commands:\n"
	1458	fi
	1459	printf "\n ${in_command[$i]}"
	1460	done
	1461	(( i = 0 ))
	1462	while (( i < ioc ))
	1463	do
	1464	(( i = i + 1 ))
	1465	if (( i == 1 ))
	1466	then
	1467	printf "\n\n >>> OUTPUT-commands:\n"
	1468	fi
	1469	printf "\n ${out_command[$i]}"
	1470	done
	1471	fi
	1472
	1473	# QUERY FOR CONTINUE
	1474	if [[ $silent = false && $running_in_batch_mode = false ]]
	1475	then
	1476	antwort=dummy
	1477	printf "\n\n"
	1478	printf " >>> everything o.k. (y/n) ? "
	1479	while read antwort
	1480	do
	1481	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1482	then
	1483	printf " >>> everything o.k. (y/n) ? "
	1484	else
	1485	break
	1486	fi
	1487	done
	1488	if [[ $antwort = n \|\| $antwort = N ]]
	1489	then
	1490	locat=user_abort; (( iec = 0 )); exit
	1491	fi
	1492	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1493	then
	1494	printf " *** batch-job will be created and submitted"
	1495	else
	1496	printf " *** PALMRUN will now continue to execute on this machine"
	1497	fi
	1498	fi
	1499
	1500
	1501
	1502	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1503	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1504	then
	1505
	1506	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1507	then
	1508	printf "\n\n *** creating executable and other sources for the remote host"
	1509	else
	1510	printf "\n\n *** creating executable and other sources for the local host"
	1511	fi
	1512
[2420]	1513	palmbuild -v -h $host_identifier -d $fname
[2380]	1514
	1515	if [[ $? != 0 ]]
	1516	then
	1517
	1518	# ABORT IN CASE OF COMPILATION PROBLEMS
	1519	printf "\n +++ error while creating executable and/or other sources"
	1520	locat=execution
[2420]	1521	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1522	exit
	1523
	1524	else
	1525
	1526	printf "\n$dashes\n *** executable and other sources created\n"
[2420]	1527	rm -rf SOURCES_FOR_RUN_$fname
[2380]	1528
	1529	fi
	1530
	1531	fi
	1532
	1533
	1534	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1535	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1536	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1537	then
	1538
	1539	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1540	if [[ $running_in_batch_mode = false ]]
	1541	then
	1542	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1543	# FOLDER
	1544	mkdir -p $TEMPDIR
	1545	chmod go+rx $TEMPDIR
	1546	tmpcreate=true
	1547	cd $TEMPDIR
[2404]	1548	cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
[2380]	1549	printf "\n *** changed to temporary directory: $TEMPDIR"
	1550
	1551	else
	1552
	1553	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1554	printf "\n *** running in temporary directory: $TEMPDIR"
	1555
	1556	fi
	1557
	1558
	1559	# PROVIDE THE INPUT FILES
	1560	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1561	(( i = 0 ))
	1562	while (( i < iin ))
	1563	do
	1564	(( i = i + 1 ))
	1565	if (( i == 1 ))
	1566	then
	1567	printf "\n\n *** providing INPUT-files:\n$dashes"
	1568	fi
	1569
	1570
	1571	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1572	if [[ "${transin[$i]}" = unavailable ]]
	1573	then
	1574	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1575	then
	1576	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1577	printf "\n is not available!"
	1578	else
	1579	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1580	printf "\n is not available!"
	1581	fi
	1582	continue
	1583	fi
	1584
	1585	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1586	files_for_cores=false; filetype=file
	1587	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1588	then
	1589	files_for_cores=true; filetype=files
	1590	actionin[$i]=""
	1591	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1592	then
	1593	actionin[$i]=""
	1594	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1595	then
	1596	files_for_cores=true; filetype=files
	1597	actionin[$i]="ln"
	1598	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1599	then
	1600	actionin[$i]="ln"
	1601	fi
	1602
	1603	if [[ $files_for_cores = true ]]
	1604	then
	1605	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1606	else
	1607	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1608	fi
	1609
	1610	# INPUT-FILES TO BE LINKED
	1611	if [[ "${actionin[$i]}" = ln ]]
	1612	then
	1613
	1614	printf "\n $filetype will be linked"
	1615	if [[ $files_for_cores = false ]]
	1616	then
	1617	if [[ -f "${absnamein[$i]}" ]]
	1618	then
	1619	ln ${absnamein[$i]} ${localin[$i]}
	1620	got_tmp[$i]=true
	1621	fi
	1622	else
	1623	if [[ -d "${absnamein[$i]}" ]]
	1624	then
[2396]	1625	mkdir -p ${localin[$i]}
[2380]	1626	cd ${absnamein[$i]}
	1627	for file in $(ls *)
	1628	do
	1629	ln $file $TEMPDIR/${localin[$i]}
	1630	done >\|/dev/null 2>&1
	1631	cd $TEMPDIR
	1632	fi
	1633
	1634	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1635	if [[ ! -f "${localin[$i]}/_000000" ]]
	1636	then
	1637	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1638	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1639	fi
	1640
	1641	got_tmp[$i]=true
	1642	fi
	1643	fi
	1644
	1645	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1646	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1647	then
	1648
	1649	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1650	then
	1651
	1652	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1653	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1654	printf "\n file will be provided for $cores processors"
[2396]	1655	mkdir -p ${localin[$i]}
[2380]	1656	ival=$cores
	1657	(( ii = 0 ))
	1658	while (( ii <= ival-1 ))
	1659	do
	1660	if (( ii < 10 ))
	1661	then
	1662	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1663	elif (( ii < 100 ))
	1664	then
	1665	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1666	elif (( ii < 1000 ))
	1667	then
	1668	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1669	else
	1670	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1671	fi
	1672	(( ii = ii + 1 ))
	1673	done
	1674
	1675	else
	1676
	1677	if [[ $files_for_cores = true ]]
	1678	then
	1679
	1680	# PROVIDE FILES FOR EACH CORE
	1681	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1682	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1683	printf "\n providing $cores files for the respective cores"
[2396]	1684	mkdir -p ${localin[$i]}
[2380]	1685	if [[ $link_local_input = true ]]
	1686	then
	1687	printf " files will be linked\n"
	1688	cd ${absnamein[$i]}
	1689	for file in $(ls *)
	1690	do
	1691	ln -f $file ${localin[$i]}
	1692	done
	1693	cd $TEMPDIR
	1694	fi
	1695
	1696	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1697	if [[ ! -f "${localin[$i]}/_000000" ]]
	1698	then
	1699	if [[ $link_local_input = true ]]
	1700	then
	1701	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1702	fi
	1703	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1704	fi
	1705
	1706	else
	1707
	1708	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1709	if [[ $link_local_input = true ]]
	1710	then
	1711	printf " file will be linked\n"
	1712	ln -f ${absnamein[$i]} ${localin[$i]}
	1713	fi
	1714	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1715	if [[ ! -f "${localin[$i]}" ]]
	1716	then
	1717	if [[ $link_local_input = true ]]
	1718	then
	1719	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1720	fi
	1721	cp ${absnamein[$i]} ${localin[$i]}
	1722	fi
	1723	fi
	1724	fi
	1725	fi
	1726
	1727	done
	1728	if (( i != 0 ))
	1729	then
	1730	printf "\n$dashes\n *** all INPUT-files provided \n"
	1731	fi
	1732
	1733
	1734	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1735	(( i = 0 ))
	1736	while (( i < iic ))
	1737	do
	1738	(( i = i + 1 ))
	1739	if (( i == 1 ))
	1740	then
	1741	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1742	fi
	1743	printf "\n >>> ${in_command[$i]}"
	1744	eval ${in_command[$i]}
	1745	if (( i == iic ))
	1746	then
	1747	printf "\n$dashes\n"
	1748	fi
	1749	done
	1750
	1751
	1752	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1753	# (FILE ENVPAR WILL BE READ BY PALM)
	1754	cat > ENVPAR << EOF
[2420]	1755	&envpar run_identifier = '$fname', host = '$host_identifier',
[2380]	1756	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1757	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1758	maximum_cpu_time_allowed = ${cpumax}.,
	1759	revision = '$global_revision',
	1760	batch_job = .${running_in_batch_mode}. /
	1761
	1762	EOF
	1763
	1764
	1765	# STARTING THE EXECUTABLE
	1766	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1767	PATH=$PATH:$TEMPDIR
	1768
	1769
	1770	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1771	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1772	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1773	eval line=\"$line\"
	1774	execute_command="$line"
	1775
	1776
	1777	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1778	eval line2=\"$line2\"
	1779	execute_command_for_combine="$line2"
	1780
	1781
	1782	# PROVIDE A HOSTFILE, IF REQUIRED
	1783	if [[ "$hostfile" != "" ]]
	1784	then
	1785
	1786	if [[ $hostfile = auto ]]
	1787	then
	1788	# CREATE A NEW HOSTFILE
	1789	(( ii = 1 ))
	1790	while (( ii <= cores / threads_per_task ))
	1791	do
	1792	echo $(hostname) >> hostfile
	1793	(( ii = ii + 1 ))
	1794	done
	1795	if (( cores / threads_per_task == 0 ))
	1796	then
	1797	echo $(hostname) >> hostfile
	1798	fi
	1799
	1800	else
	1801	cp $hostfile hostfile
	1802	fi
	1803	eval line=\"`head -n $ii hostfile`\"
	1804	printf "\n *** running on: $line"
	1805	fi
	1806
	1807
	1808
	1809	# SET THE NUMBER OF OPENMP-THREADS
	1810	if [[ $use_openmp = true ]]
	1811	then
	1812	export OMP_NUM_THREADS=$threads_per_task
	1813	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1814	else
	1815	export OMP_NUM_THREADS=1
	1816	fi
	1817
	1818
	1819	# PROVIDE DATA FOR
	1820	if [[ $run_coupled_model = false ]]
	1821	then
	1822	if [[ "$ocean_file_appendix" = true ]]
	1823	then
	1824	echo "precursor_ocean" > coupling_steering
	1825	else
	1826	echo "precursor_atmos" > coupling_steering
	1827	fi
	1828	else
	1829	(( iia = $cores_atmos / $threads_per_task ))
	1830	(( iio = $cores_ocean / $threads_per_task ))
	1831	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1832	printf "\n\n"
	1833	echo "coupled_run $iia $iio" > coupling_steering
	1834	fi
	1835
	1836	printf "\n *** execute command:"
	1837	printf "\n \"$execute_command\" \n\n"
	1838
	1839	$execute_command < coupling_steering
	1840
	1841	if [[ $? != 0 ]]
	1842	then
	1843
	1844	# ABORT IN CASE OF RUNTIME ERRORS
	1845	printf "\n +++ runtime error occured"
	1846	locat=execution
	1847	exit
	1848
	1849	else
	1850
	1851	printf "\n$dashes\n *** execution finished \n"
	1852
	1853	fi
	1854
	1855
	1856	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1857	# BY EACH CORE INTO ONE FILE
	1858	if [[ ! -f combine_plot_fields.x ]]
	1859	then
	1860
	1861	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1862	printf "\n 2d- and/or 3d-data may be incomplete!"
	1863	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1864
	1865	elif [[ "$combine_plot_fields" == true ]]
	1866	then
	1867
	1868	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1869	$execute_command_for_combine
	1870
	1871	else
	1872
	1873	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1874	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1875	# ??? koennen wir das streichen ???
	1876	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1877	fi
	1878
	1879
	1880
	1881	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1882	(( i = 0 ))
	1883	while (( i < ioc ))
	1884	do
	1885	(( i = i + 1 ))
	1886	if (( i == 1 ))
	1887	then
	1888	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1889	fi
	1890	printf "\n >>> ${out_command[$i]}"
	1891	eval ${out_command[$i]}
	1892	if (( i == ioc ))
	1893	then
	1894	printf "\n$dashes\n"
	1895	fi
	1896	done
	1897
	1898
	1899	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1900	if [[ $do_trace = true ]]
	1901	then
	1902	printf "\n\n"
	1903	ls -al
	1904	fi
	1905
	1906
	1907	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1908	(( i = 0 ))
	1909	while (( i < iout ))
	1910	do
	1911	(( i = i + 1 ))
	1912	if (( i == 1 ))
	1913	then
	1914	printf "\n\n *** saving OUTPUT-files:"
	1915
	1916	# GET RUN NUMBER ASSIGNED BY PALM
	1917	if [[ -f RUN_NUMBER ]]
	1918	then
	1919	read run_number < RUN_NUMBER
	1920	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	1921	usecycle_option="-U $run_number"
	1922	else
	1923	run_number=0
	1924	usecycle_option=""
	1925	fi
	1926	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	1927	then
[2404]	1928	printf "\n *** in case of SCP transfers to local host"
	1929	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	1930	fi
	1931	printf "\n$dashes"
	1932	fi
	1933
	1934	# ADD CYCLE NUMBER TO FILENAME
	1935	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1936	then
	1937
	1938	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	1939	if [[ "${actionout[$i]}" != "a" ]]
	1940	then
	1941	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	1942	# WITH AN EXISTING CYCLE NUMBER
	1943	if (( run_number >= cycnum[$i] ))
	1944	then
	1945	(( cycnum[$i] = run_number ))
	1946	else
	1947	if (( run_number > 0 ))
	1948	then
	1949	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	1950	fi
	1951	fi
	1952	fi
	1953	if (( cycnum[$i] > 0 ))
	1954	then
	1955	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	1956	fi
	1957	fi
	1958
	1959	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1960	files_for_cores=false; filetype=file
	1961	link_local_output=false
	1962	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	1963	then
	1964	files_for_cores=true; filetype=directory
	1965	actionout[$i]=""
	1966	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	1967	then
	1968	actionout[$i]=""
	1969	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	1970	then
	1971	files_for_cores=true; filetype=directory
	1972	link_local_output=true
	1973	actionout[$i]=""
	1974	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	1975	then
	1976	link_local_output
	1977	actionout[$i]=""
	1978	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	1979	then
	1980	files_for_cores=true; filetype=directory
	1981	actionout[$i]="tr"
	1982	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	1983	then
	1984	actionout[$i]="tr"
	1985	fi
	1986
	1987	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	1988	then
	1989	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	1990	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	1991	then
	1992	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	1993	else
	1994
	1995
	1996	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	1997	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	1998	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	1999	then
	2000	if [[ $running_on_remote = true ]]
	2001	then
	2002
	2003	# SET OPTIONS FOR TRANSFER
	2004	if [[ "${actionout[$i]}" = tr ]]
	2005	then
	2006	if [[ $files_for_cores = false ]]
	2007	then
	2008	catalog_option=""
	2009	catalog_string=""
	2010	else
	2011	catalog_option="-c"
	2012	catalog_string="/"
	2013	fi
	2014	append_option=""
	2015	append_string=""
	2016	else
	2017	append_option="-A"
	2018	append_string="append"
	2019	fi
	2020
	2021	transfer_failed=false
	2022	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2420]	2023	printf "\n ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2024
	2025	# TRANSFER VIA SCP
	2026	if [[ "$remote_loginnode" != "" ]]
	2027	then
[2420]	2028	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]	2029	else
[2420]	2030	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]	2031	fi
	2032	[[ $? != 0 ]] && transfer_failed=true
	2033
	2034
	2035	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2036	if [[ $transfer_failed = true ]]
	2037	then
	2038	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2420]	2039	printf " ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id\n"
[2380]	2040
	2041	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2042	eval local_catalog=${pathout[$i]}
	2043	if [[ ! -d $local_catalog ]]
	2044	then
	2045	printf " *** local directory does not exist. Trying to create:\n"
	2046	printf " $local_catalog \n"
	2047	mkdir -p $local_catalog
	2048	fi
[2420]	2049	eval cp ${localout[$i]} ${pathout[$i]}/${host_identifier}_${fname}${endout[$i]}_$run_id
[2380]	2050	transfer_problems=true
	2051	fi
	2052
	2053	else
	2054
	2055	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2056	# BE COPIED OR APPENDED ON THIS MACHINE
	2057	if [[ "${actionout[$i]}" = tr ]]
	2058	then
	2059	actionout[$i]=""
	2060	else
	2061	actionout[$i]="a"
	2062	fi
	2063	fi
	2064	fi
	2065
	2066
	2067	# APPEND ON THIS MACHINE
	2068	if [[ "${actionout[$i]}" = "a" ]]
	2069	then
	2070	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2071	then
	2072	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2073	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2074	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2075	else
	2076	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2077	printf "\n ${pathout[$i]}\n"
	2078	cat ${localout[$i]} >> ${pathout[$i]}
	2079	fi
	2080	fi
	2081
	2082	# COPY ON THIS MACHINE
	2083	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2084	# ON DIFFERENT FILE-SYSTEMS
	2085	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2086	then
	2087
	2088	# COPY IN CASE OF RUNS ON SINGLE CORES
	2089	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2090	then
	2091	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2092	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2093	if [[ $link_local_output = true ]]
	2094	then
	2095	printf " file will be linked\n"
	2096	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2097	fi
	2098	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2099	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2100	then
	2101	if [[ $link_local_output = true ]]
	2102	then
	2103	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2104	fi
	2105	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2106	else
	2107	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2108	fi
	2109	else
	2110	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2111	printf "\n ${pathout[$i]}\n"
	2112	if [[ $link_local_output = true ]]
	2113	then
	2114	printf " file will be linked\n"
	2115	ln -f ${localout[$i]} ${pathout[$i]}
	2116	fi
	2117	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2118	if [[ ! -f "${pathout[$i]}" ]]
	2119	then
	2120	if [[ $link_local_output = true ]]
	2121	then
	2122	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2123	fi
	2124	cp ${localout[$i]} ${pathout[$i]}
	2125	else
	2126	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2127	fi
	2128	fi
	2129
	2130	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2131	then
	2132
	2133	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2134	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2135	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2136	printf "\n ${pathout[$i]}\n"
	2137	if [[ $link_local_output = true ]]
	2138	then
	2139	printf " files will be linked\n"
[2396]	2140	mkdir -p ${pathout[$i]}
[2380]	2141	cd ${localout[$i]}
	2142	for file in $(ls *)
	2143	do
	2144	ln -f $file ${pathout[$i]}
	2145	done >\|/dev/null 2>&1
	2146	cd $TEMPDIR
	2147	fi
	2148
	2149	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2150	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2151	then
	2152	if [[ $link_local_output = true ]]
	2153	then
	2154	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2155	fi
	2156	cp -r ${localout[$i]}/* ${pathout[$i]}
	2157	fi
	2158
	2159	fi
	2160	fi
	2161	done
	2162
	2163	if (( i != 0 ))
	2164	then
	2165	if [[ $transfer_problems = true ]]
	2166	then
	2167	printf "\n$dashes\n *** OUTPUT-files saved"
	2168	printf "\n +++ WARNING: some data transfers failed! \n"
	2169	else
	2170	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2171	fi
	2172	fi
	2173
	2174
	2175	# IF REQUIRED, START A RESTART-JOB
	2176	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2177	if [[ -f CONTINUE_RUN ]]
	2178	then
	2179
	2180	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2181	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2182	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2183	# -b START A BATCH JOB
	2184	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2185	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2186	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2187
	2188
	2189	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2190	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2191	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2192	then
[2381]	2193	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2194	fi
	2195
	2196
	2197	# START THE RESTART-JOB
	2198	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2199	echo " $prc"
	2200	printf "\n$dashes\n"
	2201	if [[ $running_on_remote = true ]]
	2202	then
	2203
	2204	echo "*** ssh will be used to initiate restart-runs!"
	2205	echo " return_address=\"$return_address\" "
	2206	echo " return_username=\"$local_username\" "
	2207
	2208	if [[ "$remote_loginnode" != "" ]]
	2209	then
[2420]	2210	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]	2211	else
[2420]	2212	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2213	fi
	2214
	2215	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2216	sleep 30
	2217
	2218	else
	2219
	2220	# START THE RESTART JOB ON THE LOCAL HOST
	2221	eval $prc # THE ' MUST BE EVALUATED
	2222	cd - > /dev/null
	2223
	2224	fi
	2225	printf "\n$dashes\n *** restart-run initiated \n"
	2226
	2227
	2228	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2229	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2230	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2231	# MAY BE VERY HUGE)
	2232	(( i = 0 ))
	2233	while (( i < iin ))
	2234	do
	2235	(( i = i + 1 ))
	2236	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2237	then
	2238	rm -r ${absnamein[$i]}
	2239	fi
	2240	done
	2241
	2242	fi
	2243
	2244
	2245	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2246	cd $HOME
	2247	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	2248
	2249
	2250	else
	2251
	2252
	2253	# PREPARING ACTIONS,
	2254	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2255
	2256	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2420]	2257	palmrun_com="$palmrun_script_name -d $fname -h $host_identifier -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2258	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2259	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2260	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2261	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2262	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2263	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
	2264	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
	2265	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2266	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2267	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2268	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2269	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
	2270	if [[ $create_remote_batch_job = true ]]
	2271	then
	2272	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2273	if [[ $do_trace = true ]]
	2274	then
	2275	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2276	fi
[2380]	2277	elif [[ $create_batch_job = true ]]
	2278	then
	2279	palmrun_com=${palmrun_com}" -j"
[2420]	2280	if [[ $do_trace = true ]]
	2281	then
	2282	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2283	fi
[2380]	2284	fi
	2285
	2286
	2287	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2288	# REMOTE HOST
[2420]	2289	job_protocol_file_local=${local_jobcatalog}/${host_identifier}_${job_id}
[2380]	2290	job_protocol_file=$job_protocol_file_local
	2291	if [[ $create_remote_batch_job = true ]]
	2292	then
[2420]	2293	job_protocol_file_remote=${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2294	job_protocol_file=$job_protocol_file_remote
	2295	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2296	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2297	fi
	2298
	2299
	2300	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2301	jobfile=jobfile.$run_id
	2302
	2303
	2304	# FIRST CREATE THE BATCH DIRECTIVES
	2305	(( i = 0 ))
	2306	while (( i < ibd ))
	2307	do
	2308	(( i = i + 1 ))
[2420]	2309	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g'`
[2380]	2310	eval line=\"$line\"
	2311	echo "$line" >> $jobfile
	2312	done
	2313	echo " " >> $jobfile
	2314
	2315
	2316	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2317	# PROTOCOL
	2318	if [[ $create_remote_batch_job = true ]]
	2319	then
	2320	echo "set +vx" >> $jobfile
	2321	echo "trap '" >> $jobfile
	2322	echo "set +vx" >> $jobfile
	2323	echo "cd ${remote_jobcatalog}" >> $jobfile
	2324	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2325
	2326	# ADD THE BATCH DIRECTIVES
	2327	(( i = 0 ))
	2328	while (( i < ibdt ))
	2329	do
	2330	(( i = i + 1 ))
[2420]	2331	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_IDENTIFIER}}/${host_identifier}/g' \| sed 's/{{FNAME}}/$fname/g'`
[2380]	2332	eval line=\"$line\"
	2333	echo "$line" >> $jobfile
	2334	done
	2335	echo " " >> $jobfile
	2336
	2337	echo "set -x" >> $jobfile
[2420]	2338	echo "${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]	2339	echo "%%END%%" >> $jobfile
	2340	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2341	echo "$submit_command $scpjob_file" >> $jobfile
	2342	echo "rm $scpjob_file" >> $jobfile
[2404]	2343	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2344	echo "set -x" >> $jobfile
	2345	echo " ' exit" >> $jobfile
	2346	fi
	2347
	2348
	2349	# ACTIVATE ERROR-TRACEBACK
	2350	if [[ $do_trace = true ]]
	2351	then
	2352	echo "set -x" >> $jobfile
	2353	else
	2354	echo "set +vx" >> $jobfile
	2355	fi
	2356
	2357
	2358	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2359	if [[ "$login_init_cmd" != "" ]]
	2360	then
	2361	echo "$login_init_cmd" >> $jobfile
	2362	fi
	2363	if [[ "$module_commands" != "" ]]
	2364	then
	2365	echo "$module_commands" >> $jobfile
	2366	fi
	2367
	2368
	2369	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2370	echo "mkdir $TEMPDIR" >> $jobfile
	2371	echo "cd $TEMPDIR" >> $jobfile
	2372	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
[2404]	2373	echo "cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
[2380]	2374	echo "export PATH=.:\$PATH" >> $jobfile
	2375	echo "export execute_palmrun=true" >> $jobfile
	2376
	2377
	2378	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2379	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2380	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2381	if [[ $create_remote_batch_job = true ]]
	2382	then
	2383	(( i = 0 ))
	2384	while (( i < iin ))
	2385	do
	2386	(( i = i + 1 ))
	2387	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2388	if [[ "${transin[$i]}" = job ]]
	2389	then
	2390	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2391	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2392	echo " " >> $jobfile
	2393	echo "%END%" >> $jobfile
	2394	else
	2395	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2396	fi
	2397
	2398	# CHECK, IF FILE COULD BE CREATED
	2399	echo "if [[ \$? = 1 ]]" >> $jobfile
	2400	echo "then" >> $jobfile
	2401	echo " echo \" \" " >> $jobfile
	2402	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
[2420]	2403	echo " echo \" please check, if directory exists on $host_identifier!\" " >> $jobfile
[2380]	2404	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2405	echo " execute_palmrun=false" >> $jobfile
	2406	echo "fi" >> $jobfile
	2407	done
	2408	fi
	2409
	2410
	2411	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2412	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2413	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2414	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2415	echo "export LOCAL_PWD" >> $jobfile
	2416
	2417
	2418	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2419	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2420	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2421
	2422
	2423	# CALL PALMRUN WITHIN THE JOB
	2424	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2425	echo "set -x" >> $jobfile
	2426	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2427
	2428
	2429	# TRANSFER JOBFILE TO THE TARGET HOST
	2430	if [[ $create_jobfile_only = false ]]
	2431	then
	2432
	2433	if [[ $create_remote_batch_job = true ]]
	2434	then
	2435
[2420]	2436	echo " "
	2437	echo " *** transfer of job to remote host via scp"
	2438	if [[ $do_trace = true ]]
	2439	then
	2440	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}"
	2441	fi
	2442	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_identifier}_${job_id}
[2380]	2443
	2444	echo " "
[2420]	2445	echo " *** submit the job (output of submit command, e.g. the job-id, may follow)"
	2446	if [[ $do_trace = true ]]
	2447	then
	2448	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"
	2449	fi
	2450	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]	2451
	2452	elif [[ $create_batch_job = true ]]
	2453	then
	2454
[2385]	2455	eval local_jobcatalog=$local_jobcatalog
[2420]	2456	cp $jobfile ${local_jobcatalog}/${host_identifier}_${job_id}
[2385]	2457	cd $local_jobcatalog
[2380]	2458	echo " "
[2420]	2459	echo " *** submit the job"
	2460	if [[ $do_trace = true ]]
	2461	then
	2462	echo "$submit_command ${host_identifier}_${job_id}"
	2463	fi
	2464	$submit_command ${host_identifier}_${job_id}
	2465	rm ${host_identifier}_${job_id}
[2380]	2466	cd - > /dev/null
	2467
	2468	fi
	2469
	2470	rm -rf $jobfile
	2471
	2472	else
	2473
	2474	printf "\n *** jobfile created under name \"$jobfile\" "
	2475	printf "\n no batch-job has been sent!"
	2476
	2477	fi
	2478
	2479	fi # END OF REMOTE-PART

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