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source: palm/trunk/SCRIPTS/palmrun @ 2404

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

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