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source: palm/trunk/SCRIPTS/palmrun @ 2397

Last change on this file since 2397 was 2396, checked in by knoop, 7 years ago
Bugfix: in palmrun and palmbuild
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 81.9 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 2396 2017-09-04 16:15:48Z suehring $
	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	tmp_data_catalog=""
	113	transfer_problems=false
[2384]	114	user_source_path=""
[2380]	115	use_openmp=false
	116	version="palmrun 0.9 Rev$Rev: 2303 $"
	117	working_directory=`pwd`
	118	write_binary=""
	119	TOPT=""
	120
	121
	122	# ERROR HANDLING IN CASE OF EXIT
	123	trap 'rm -rf $working_directory/tmp_mrun
	124	if [[ $locat != normal && $locat != control_c ]]
	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
	136	if [[ $tmpcreate = true ]]
	137	then
	138	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	139	fi
	140	printf "\n\n+++ palmrun killed \n\n"
	141	elif [[ $locat != control_c ]]
	142	then
	143	printf "\n\n --> palmrun finished\n\n"
	144	if [[ $running_on_remote = true ]]
	145	then
	146	printf " Bye, bye $remote_username !!\n\n"
	147	else
	148	printf " Bye, bye $local_username !!\n\n"
	149	fi
	150	fi' exit
	151
	152
	153	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
	154	trap 'rm -rf $working_directory/tmp_mrun
	155	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
	156	printf "\n+++ palmrun killed by \"^C\" \n\n"
	157	locat=control_c
	158	exit
	159	' 2
	160
	161
	162	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	163	# BEEN SET
	164	if [[ "$PALM_BIN" = "" ]]
	165	then
	166	printf "\n +++ environment variable PALM_BIN has not been set"
	167	printf "\n please set it to the directory where the PALM scripts are located"
	168	locat=palm_bin; exit
	169	fi
	170	export PATH=$PALM_BIN:$PATH
	171
	172
	173
	174	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	175	# WHICH WILL BE USED TO START RESTART-JOBS
	176	while getopts :a:bBc:Cd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
	177	do
	178	case $option in
	179	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
	180	(b) create_batch_job=true; prc="$prc -b";;
	181	(B) delete_temporary_catalog=false; prc="$prc -B";;
	182	(c) config_file=$OPTARG; prc="$prc -c$OPTARG";;
	183	(C) restart_run=true; prc="$prc -C";;
	184	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	185	(F) create_jobfile_only=true;;
	186	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
	187	(h) host=$OPTARG; prc="$prc -h$OPTARG";;
	188	(j) running_in_batch_mode=true;;
	189	(k) keep_data_from_previous_run=true; prc="$prc -k";;
	190	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
	191	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	192	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	193	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	194	(r) run_id=$OPTARG;;
	195	(R) return_address=$OPTARG;;
	196	(s) source_list=$OPTARG;;
	197	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
	198	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	199	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	200	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	201	(v) silent=true; prc="$prc -v";;
	202	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
	203	(x) do_trace=true;set -x; prc="$prc -x";;
	204	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
	205	(y) ocean_file_appendix=true; prc="$prc -y";;
	206	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	207	(Z) combine_plot_fields=false; prc="$prc -Z";;
	208	(\?) printf "\n +++ unknown option $OPTARG \n"
	209	printf "\n --> type \"$0 ?\" for available options \n"
	210	locat=parameter;exit;;
	211	esac
	212	done
	213
	214
	215	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	216	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	217	(( to_shift = $OPTIND - 1 ))
	218	shift $to_shift
	219
	220	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	221	if [[ "$1" = "?" ]]
	222	then
	223	(printf "\n *** Description of available palmrun options:\n"
	224	printf "\n Option Description Default-Value"
	225	printf "\n -a activation string list \"\" "
	226	printf "\n -b batch-job on local machine ---"
	227	printf "\n -B do not delete temporary directory at end ---"
[2384]	228	printf "\n -c configuration file .palm.config.default"
[2380]	229	printf "\n -d base name of files attached to program test"
	230	printf "\n -F create batch job file only ---"
	231	printf "\n -h execution host \"default\" "
	232	printf "\n -k keep data from previous run"
	233	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	234	printf "\n -M Makefile name Makefile"
	235	printf "\n -O threads per openMP task ---"
	236	printf "\n -q queue \"$queue\" "
	237	printf "\n -s filenames of routines to be compiled \"\" "
	238	printf "\n must end with .f, .f90, .F, or .c !"
	239	printf "\n use \"..\" for more than one file and wildcards"
	240	printf "\n -s LM compiles all locally modified files"
	241	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	242	printf "\n -T tasks per node ---"
[2380]	243	printf "\n -u username on remote machine \"\" "
	244	printf "\n -v no prompt for confirmation ---"
	245	printf "\n -w maximum parallel io streams as given by -X"
	246	printf "\n -x tracing of palmrun for debug purposes ---"
	247	printf "\n -X # of processors (on parallel machines) 1"
	248	printf "\n -y add appendix \"_O\" to all local output"
	249	printf "\n files (ocean precursor runs followed by"
	250	printf "\n coupled atmosphere-ocean runs) ---"
	251	printf "\n -Y run coupled model, \"#1 #2\" with"
	252	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	253	printf "\n -Z skip combine_plot_fields at the end of "
	254	printf "\n the simulation ---"
	255	printf "\n "
	256	printf "\n Possible values of positional parameter <modus>:"
	257	printf "\n \"?\" - this outline \n\n") \| more
	258	exit
	259	elif [[ "$1" != "" ]]
	260	then
	261	printf "\n +++ positional parameter $1 unknown \n"
	262	locat=parameter; exit
	263	fi
	264
	265
	266
	267	# SHORT STARTING MESSAGE
	268	printf "\n*** $version "
	269	printf "\n will be executed. Please wait ..."
	270
	271
	272	# BUILD THE CONFIGURATION-FILE NAME
	273	if [[ "$config_file" = "" ]]
	274	then
	275	config_file=.palm.config.$host
	276	fi
	277
	278
	279	# CHECK, IF CONFIGURATION FILE EXISTS
	280	if [[ ! -f $config_file ]]
	281	then
	282	printf "\n\n +++ configuration file: "
	283	printf "\n $config_file"
	284	printf "\n does not exist"
	285	locat=connect; exit
	286	fi
	287
	288
	289	# CHECK, IF FILE CONNECTION FILE EXISTS
	290	if [[ ! -f $fileconnection_file ]]
	291	then
	292	printf "\n\n +++ file connection file: "
	293	printf "\n $fileconnection_file"
	294	printf "\n does not exist"
	295	locat=connect; exit
	296	fi
	297
	298
	299	# READ AND EVALUATE THE CONFIGURATION-FILE
	300	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	301
	302	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	303	while read line
	304	do
	305
	306	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	307	eval line=\"$line\"
	308
	309
	310	# INTERPRET THE LINE
	311	if [[ "$(echo $line)" = "" ]]
	312	then
	313
	314	# EMPTY LINE, NO ACTION
	315	continue
	316
	317	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	318	then
	319
	320	# LINE IS A COMMENT LINE
	321	continue
	322
	323	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	324	then
	325
	326	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	327	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	328	value=`echo $line \| cut -d" " -s -f2-`
	329
	330
	331	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	332	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	333	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	334	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	335	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	336	# CONFIGURATION-FILE.
	337	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	338	then
	339	eval export $var="\$value"
	340
	341	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	342	if [[ $do_trace = true ]]
	343	then
	344	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	345	fi
	346	fi
	347
	348	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	349	then
	350
	351	# LINE DEFINES BATCH-DIRECTIVE
	352	(( ibd = ibd + 1 ))
	353	line=$(echo $line \| cut -c4-)
	354	batch_directive[$ibd]="$line"
	355
	356	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	357	then
	358
	359	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	360	# REMOTE TO A LOCAL HOST
	361	(( ibdt = ibdt + 1 ))
	362	line=$(echo $line \| cut -c5-)
	363	batch_directive_transfer[$ibdt]="$line"
	364
	365	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	366	then
	367
	368	# LINE DEFINES ERROR-COMMAND
	369	(( iec = iec + 1 ))
	370	line=$(echo $line \| cut -c4-)
	371	err_command[$iec]="$line"
	372
	373	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	374	then
	375
	376	# LINE DEFINES INPUT-COMMAND
	377	(( iic = iic + 1 ))
	378	line=$(echo $line \| cut -c4-)
	379	in_command[$iic]="$line"
	380
	381	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	382	then
	383
	384	# LINE DEFINES OUTPUT-COMMAND
	385	(( ioc = ioc + 1 ))
	386	line=$(echo $line \| cut -c4-)
	387	out_command[$ioc]="$line"
	388
	389	else
	390
	391	# SKIP ALL OTHER LINES
	392	continue
	393
	394	fi
	395
	396	done < $config_file
	397
	398
	399	# CHECK SETTING OF REQUIRED PARAMETERS
	400	if [[ "$compiler_name" = "" ]]
	401	then
	402	printf "\n +++ no compiler name found in $config_file"
	403	printf "\n Please add line \"compiler_name ...\" to that file."
	404	locat=config_file; exit
	405	fi
	406	if [[ "$compiler_name_ser" = "" ]]
	407	then
	408	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	409	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	410	locat=config_file; exit
	411	fi
	412	if [[ "$compiler_options" = "" ]]
	413	then
	414	printf "\n +++ no compiler options found in $config_file"
	415	printf "\n Please add line \"compiler_options ...\" to that file."
	416	locat=config_file; exit
	417	fi
[2388]	418	if [[ "$linker_options" = "" ]]
[2380]	419	then
[2388]	420	printf "\n +++ no linker options found in $config_file"
	421	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	422	locat=config_file; exit
	423	fi
	424	if [[ "$execute_command" = "" ]]
	425	then
	426	printf "\n +++ no execute command found in $config_file"
	427	printf "\n Please add line \"execute_command ...\" to that file."
	428	locat=config_file; exit
	429	fi
	430
	431	if [[ "$hostfile" != "" ]]
	432	then
	433	if [[ $hostfile != auto && ! -f $hostfile ]]
	434	then
	435	printf "\n +++ no hostfile \"$hostfile\" found"
	436	printf "\n Please check line \"hostfile ...\" in $config_file"
	437	locat=config_file; exit
	438	fi
	439	fi
	440
	441	if [[ "$write_binary" = "" ]]
	442	then
	443	write_binary=false
	444	fi
	445
	446	# DETERMINE THE CALL STATUS
	447	if [[ "$return_address" != "" ]]
	448	then
	449
	450	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	451	# BATCH MODE AND ...
	452	running_on_remote=true
	453	host_name=$remote_hostname
	454
	455	else
	456
	457	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	458	if [[ "$remote_ip" != "" ]]
	459	then
	460
	461	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	462	create_remote_batch_job=true
	463
	464	fi
	465	host_name=$local_hostname
	466	running_on_remote=false
	467	fi
	468
	469
	470
	471	# READ AND EVALUATE THE I/O-FILE LIST
	472	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	473
	474	# READ THE FILE CONNECTION FILE LINE BY LINE
	475	while read line
	476	do
	477
	478	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	479	eval line=\"$line\"
	480
	481
	482	# INTERPRET THE LINE
	483	if [[ "$(echo $line)" = "" ]]
	484	then
	485	# EMPTY LINE, NO ACTION
	486	continue
	487
	488	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	489	then
	490
	491	# LINE IS A COMMENT LINE
	492	true
	493
	494	else
	495
	496	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	497	# s2a: in/out - field
	498	# s2b: loc - field (optional)
	499	# s2c: tr/ar - field (optional)
	500	s1=`echo $line \| cut -d" " -f1`
	501	s2=`echo $line \| cut -d" " -s -f2`
	502	s2a=$(echo $s2 \| cut -d":" -f1)
	503	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	504	then
	505	s2b=""
	506	s2c=""
	507	else
	508	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	509	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	510	fi
	511	s3=`echo $line \| cut -d" " -f3`
	512	s4=`echo $line \| cut -d" " -s -f4`
	513	s5=`echo $line \| cut -d" " -s -f5`
	514	s6=`echo $line \| cut -d" " -s -f6`
	515
	516
	517	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	518	# INPUT- OR OUTPUT-LIST.
	519	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	520	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	521	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	522	# IS NOT CHECKED AND STORED.
	523	IFSALT="$IFS"; IFS="$IFS:"
	524	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	525	then
	526	found=false
	527	for actual in $activation_string_list
	528	do
	529	for formal in $s3
	530	do
	531	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	532	done
	533	done
	534	if [[ $found = true ]]
	535	then
	536	(( iin = iin + 1 ))
	537	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	538	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	539	extin[$iin]=$s6
	540	fi
	541	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	542	then
	543	found=false
	544	for actual in $activation_string_list
	545	do
	546	for formal in $s3
	547	do
	548	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	549	done
	550	done
	551	if [[ $found = true ]]
	552	then
	553	(( iout = iout + 1 ))
	554	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	555	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	556	fi
	557	elif [[ "$s2a" != in && "$s2a" != out ]]
	558	then
	559	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	560	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	561	locat=connect; exit
	562	fi
	563	IFS="$IFSALT"
	564	fi
	565
	566	done < $fileconnection_file
	567
	568
	569
	570	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	571	if [[ $run_coupled_model = true ]]
	572	then
	573
	574	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	575	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	576
	577	if (( $cores_ocean + $cores_atmos != $cores ))
	578	then
	579
	580	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	581	printf "\n PEs (total) : $cores"
	582	printf "\n PEs (atmosphere): $cores_atmos"
	583	printf "\n PEs (ocean) : $cores_ocean"
	584	locat=coupling; exit
	585
	586	fi
	587
	588	fi
	589
	590
	591	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
	592	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
	593	palmrun_memory=$memory
	594	palmrun_cpumax=$cpumax
	595	palmrun_cores=$cores
	596
	597
	598	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
	599	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
	600	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
	601	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	602	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	603	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	604
	605
	606
	607	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	608	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	609	# FOLDER
	610	if [[ $running_in_batch_mode = true ]]
	611	then
	612
	613	if [[ ! -d ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname ]]
	614	then
	615	printf "\n +++ directory ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname is missing"
	616	printf "\n Please check the output of the palmrun-call"
	617	printf "\n that you did on your local host."
	618	locat=SOURCES_FOR_RUN; exit
	619	fi
	620
	621	else
	622
	623	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	624	# AUTOMATIC RESTART RUN
	625	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	626	if [[ $restart_run = false ]]
	627	then
	628
	629	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	630	# THE LOCAL HOST
	631	if [[ ! -d $source_path ]]
	632	then
	633	printf "\n\n +++ source path \"$source_path\" on local host"
	634	printf "\n \"$(hostname)\" does not exist"
	635	locat=source_path; exit
	636	fi
	637
[2396]	638	rm -rf SOURCES_FOR_RUN_$fname
	639	mkdir -p SOURCES_FOR_RUN_$fname
[2380]	640
	641	if [[ "$source_list" = LM ]]
	642	then
	643
	644	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	645	source_list=""
	646	cd $source_path
	647
	648
	649	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
	650	if [[ ! -d .svn ]]
	651	then
	652	printf "\n\n +++ source directory"
	653	printf "\n \"$source_path\" "
	654	printf "\n is not under control of \"subversion\"."
	655	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
	656	fi
	657
	658
	659	# LIST ALL MODIFIED SOURCE CODE FILES
	660	Filenames=""
	661	svn status > tmp_mrun
	662	while read line
	663	do
	664	firstc=`echo $line \| cut -c1`
	665	if [[ $firstc = M \|\| $firstc = "?" ]]
	666	then
	667	Name=`echo "$line" \| cut -c8-`
	668	extension=`echo $Name \| cut -d. -f2`
	669	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	670	then
	671	Filenames="$Filenames "$Name
	672	fi
	673	fi
	674	done < tmp_mrun
	675
	676
	677	# COPY FILES TO SOURCES_FOR_RUN_...
	678	for filename in $Filenames
	679	do
	680	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	681	source_list=$source_list"$filename "
	682	done
	683
	684	cd - > /dev/null
	685
	686
	687	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	688	elif [[ "$source_list" != "" ]]
	689	then
	690
	691	cd $source_path
	692
	693	for filename in $source_list
	694	do
	695
	696	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	697	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	698	then
	699	printf "\n +++ source code file: $filename"
	700	printf "\n must not contain (\"/\") "
	701	locat=source; exit
	702	fi
	703
	704	if [[ ! -f $filename ]]
	705	then
	706	printf "\n +++ source code file: $filename"
	707	printf "\n does not exist"
	708	locat=source; exit
	709	else
	710	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	711	fi
	712
	713	done
	714
	715	cd - > /dev/null
	716
	717	fi
	718
	719	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	720	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	721	if [[ ! -f $makefile ]]
	722	then
	723	printf "\n +++ file \"$makefile\" does not exist"
	724	locat=make; exit
	725	else
	726	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	727	fi
	728
	729
	730	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	731	if [[ "$user_source_path" != "" ]]
[2380]	732	then
	733
	734	# DOES THE DIRECTORY EXIST?
[2384]	735	if [[ ! -d $user_source_path ]]
[2380]	736	then
	737
	738	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	739	printf "\n \"$user_source_path\" "
[2380]	740	printf "\n does not exist or is not a directory."
	741	printf "\n No source code will be used from this directory!\n"
[2384]	742	user_source_path=""
[2380]	743	if [[ $silent == false ]]
	744	then
	745	sleep 2
	746	fi
	747
	748	else
	749
[2384]	750	cd $user_source_path
[2380]	751	found=false
	752
	753	Names=$(ls -1 *.f90 2>&1)
	754	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	755	Names=$(ls -1 *.F90 2>&1)
	756	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	757	Names=$(ls -1 *.F 2>&1)
	758	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	759	Names=$(ls -1 *.f 2>&1)
	760	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	761	Names=$(ls -1 *.c 2>&1)
	762	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	763
	764	cd - > /dev/null
	765	cd SOURCES_FOR_RUN_$fname
	766
	767	# COPY MAKEFILE IF EXISTING
[2384]	768	if [[ -f $user_source_path/Makefile ]]
[2380]	769	then
	770	printf "\n\n *** user Makefile from directory"
[2384]	771	printf "\n \"$user_source_path\" is used \n"
[2380]	772	if [[ $silent == false ]]
	773	then
	774	sleep 1
	775	fi
[2384]	776	cp $user_source_path/Makefile .
[2380]	777	fi
	778
	779	for filename in $AddFilenames
	780	do
	781	if [[ -f $filename ]]
	782	then
	783	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	784	printf "\n source code directory \"$user_source_path\" "
[2380]	785	printf "\n but was also given with option \"-s\" which means that it should be taken"
	786	printf "\n from directory \"$source_path\"."
	787	locat=source; exit
	788	fi
	789
[2384]	790	cp $user_source_path/$filename .
[2380]	791	source_list="$source_list $filename"
	792
	793	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	794	if [[ $(grep -c $filename Makefile) = 0 ]]
	795	then
	796	printf "\n\n +++ user file \"$filename\" "
	797	printf "\n is not listed in Makefile \n"
	798	locat=source; exit
	799	else
	800
	801	if [[ $found = false ]]
	802	then
	803	found=true
	804	printf "\n\n *** following user file(s) added to the"
	805	printf " files to be translated:\n "
	806	fi
	807	printf "$filename "
	808	if [[ $silent == false ]]
	809	then
	810	sleep 0.5
	811	fi
	812
	813	fi
	814	done
	815	[[ $found = true ]] && printf "\n"
	816	cd - > /dev/null
	817	fi
	818	fi
	819
	820	# COPY CONFIGURATION FILES
	821	cp $config_file SOURCES_FOR_RUN_$fname
	822	cp $fileconnection_file SOURCES_FOR_RUN_$fname
	823
	824	# COPY SHELLSCRIPTS
	825	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
	826	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
	827
	828	fi
	829
	830	fi
	831
	832	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	833	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	834	if [[ "$global_revision" = "" ]]
	835	then
	836	global_revision=`svnversion $source_path 2>/dev/null`
	837	global_revision="Rev: $global_revision"
	838	fi
	839
	840
	841	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	842	if [[ -n $cores ]]
	843	then
	844
	845	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	846	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2384]	847	if [[ "$tasks_per_node" = "" ]]
[2380]	848	then
	849	printf "\n"
	850	printf "\n +++ option \"-T\" (tasks per node) is missing"
	851	printf "\n set -T option or define tasks_per_node in the config file"
	852	locat=tasks_per_node; (( iec = 0 )); exit
	853	fi
	854
	855	if (( cores < tasks_per_node ))
	856	then
	857	printf "\n"
	858	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	859	printf "\n given values: -T $tasks_per_node -X $cores"
	860	locat=tasks_per_node; (( iec = 0 )); exit
	861	fi
	862
	863	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	864	(( mpi_tasks = cores / threads_per_task ))
	865	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	866	(( ii = cores / tasks_per_node ))
	867	(( remaining_cores = cores - ii * tasks_per_node ))
	868	if (( remaining_cores > 0 ))
	869	then
	870	printf "\n"
	871	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	872	printf "\n divisor of the total number of cores (option \"-X\")"
	873	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	874	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	875	(( nodes = nodes + 1 ))
	876	fi
	877
	878	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	879	if [[ "$tasks_per_node" != "" ]]
	880	then
	881	TOPT="-T $tasks_per_node"
	882	fi
	883
	884	fi
	885
	886
	887	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	888	if [[ "$maximum_parallel_io_streams" = "" ]]
	889	then
	890	maximum_parallel_io_streams=$cores
	891	fi
	892
	893
	894	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	895	if [[ "$scp_port" != "" ]]
	896	then
	897	PORTOPT="-P $scp_port"
	898	SSH_PORTOPT="-p $scp_port"
	899	fi
	900
	901
	902	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	903	# CONFIG-FILE
	904	if [[ "$ssh_key" != "" ]]
	905	then
	906	ssh_key="-i $HOME/.ssh/$ssh_key"
	907	fi
	908
	909
	910	# SET QUEUE, IF NOT GIVEN
	911	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	912	then
	913
	914	if [[ $queue = none && "$defaultqueue" = "" ]]
	915	then
	916	printf "\n"
	917	printf "\n +++ no default queue given in configuration file and no queue"
	918	printf "\n given with option -q"
	919	fi
	920	if [[ $queue = none ]]
	921	then
	922	queue=$defaultqueue
	923	fi
	924
	925	fi
	926
	927
	928	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	929	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	930	(( i = 0 ))
	931	while (( i < iin ))
	932	do
	933	(( i = i + 1 ))
	934	(( maxcycle = 0 ))
	935
	936	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	937	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	938	if [[ "${actionin[$i]}" = di ]]
	939	then
	940	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	941	# HOST ONLY
	942	eval filename=${pathin[$i]}/${endin[$i]}
	943	else
	944	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	945	# HOST ONLY
	946	eval filename=${pathin[$i]}/${fname}${endin[$i]}
	947	fi
	948	eval pathname=${pathin[$i]}
	949
	950	# CHECK IF FILE EXISTS
	951	if ! ls $filename* 1>/dev/null 2>&1
	952	then
	953
	954	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	955	if [[ "${transin[$i]}" != "locopt" ]]
	956	then
	957	printf "\n\n +++ INPUT-file: "
	958	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	959	then
	960	printf "\n $filename"
	961	else
	962	printf "\n $filename.${extin[$i]}"
	963	fi
	964	printf "\n does not exist\n"
	965	locat=input; exit
	966	else
	967	transin[$i]="unavailable"
	968	fi
	969	else
	970
	971	# DETERMINE THE FILE'S CYCLE NUMBER
	972	ls -1 -d $filename > filelist 2>/dev/null
	973	ls -1 -d $filename.* >> filelist 2>/dev/null
	974	while read line
	975	do
	976	# filename without path (i.e. after the last "/")
	977	basefilename=$(basename ${line})
	978
	979	# check if there is an extension
	980	extension=${basefilename##*.}
	981	if [[ "$extension" = "$extin[$i]" ]]
	982	then
	983	basefilename=${basefilename&.*}
	984	fi
	985
	986	# check for an existing cycle number
	987	cycle=${basefilename##*.}
	988	if [[ $cycle =~ ^-?[0-9]+$ ]]
	989	then
	990	(( icycle = $cycle ))
	991	else
	992	(( icycle = 0 ))
	993	fi
	994
	995	if (( icycle > maxcycle ))
	996	then
	997	(( maxcycle = icycle ))
	998	fi
	999
	1000	done <filelist
	1001	rm filelist
	1002
	1003	# APPEND CYCLE NUMBER TO FILENAME
	1004	if (( maxcycle > 0 ))
	1005	then
	1006	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1007	then
	1008	filename=${filename}.$maxcycle.${extin[$i]}
	1009	else
	1010	filename=${filename}.$maxcycle
	1011	fi
	1012	else
	1013	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1014	then
	1015	filename=${filename}.${extin[$i]}
	1016	fi
	1017	fi
	1018
	1019	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1020	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1021	absnamein[$i]=$filename
	1022	if (( maxcycle > 0 ))
	1023	then
	1024	if [[ "${actionin[$i]}" = di ]]
	1025	then
	1026	frelin[$i]=${endin[$i]}.$maxcycle
	1027	else
	1028	frelin[$i]=${fname}${endin[$i]}.$maxcycle
	1029	fi
	1030	else
	1031	if [[ "${actionin[$i]}" = di ]]
	1032	then
	1033	frelin[$i]=${endin[$i]}
	1034	else
	1035	frelin[$i]=${fname}${endin[$i]}
	1036	fi
	1037	fi
	1038
	1039	fi
	1040	done
	1041
	1042
	1043	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1044	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1045	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1046	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1047	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1048	# REMOTE HOST)
	1049	(( i = 0 ))
	1050	while (( i < iout ))
	1051	do
	1052	(( i = i + 1 ))
	1053	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1054	then
	1055	if [[ "${actionout[$i]}" = tr ]]
	1056	then
	1057	actionout[$i]=""
	1058	elif [[ "${actionout[$i]}" = trpe ]]
	1059	then
	1060	actionout[$i]=pe
	1061	elif [[ "${actionout[$i]}" = tra ]]
	1062	then
	1063	actionout[$i]=a
	1064	fi
	1065	(( maxcycle = 0 ))
	1066	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1067	eval catalogname=${pathout[$i]}
	1068	if ! ls $filename* 1>/dev/null 2>&1
	1069	then
	1070
	1071	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1072	if cat /dev/null > $filename
	1073	then
	1074	rm $filename
	1075	else
	1076
	1077	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1078	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1079	if [[ ! -d $catalogname ]]
	1080	then
	1081	if mkdir -p $catalogname
	1082	then
	1083	printf "\n\n *** directory:"
	1084	printf "\n $catalogname"
	1085	printf "\n was created\n"
	1086	else
	1087	printf "\n\n +++ OUTPUT-file:"
	1088	printf "\n $filename"
	1089	printf "\n cannot be created, because directory does not exist"
	1090	printf "\n and cannot be created either"
	1091	printf "\n"
	1092	locat=output ; exit
	1093	fi 2>/dev/null
	1094	else
	1095	printf "\n\n +++ OUTPUT-file:"
	1096	printf "\n $filename"
	1097	printf "\n cannot be created, although directory exists"
	1098	printf "\n"
	1099	locat=output ; exit
	1100	fi
	1101	fi 2>/dev/null
	1102	else
	1103
	1104	# DETERMINE THE CYCLE NUMBER
	1105	ls -1 -d $filename > filelist 2>/dev/null
	1106	ls -1 -d $filename.* >> filelist 2>/dev/null
	1107	while read line
	1108	do
	1109
	1110	# filename without path (i.e. after the last "/")
	1111	basefilename=$(basename ${line})
	1112
	1113	# check if there is an extension
	1114	extension=${basefilename##*.}
	1115	if [[ "$extension" = "${extout[$i]}" ]]
	1116	then
	1117	basefilename=${basefilename%.*}
	1118	fi
	1119
	1120	# check for an existing cycle number
	1121	cycle=${basefilename##*.}
	1122	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1123	then
	1124	(( icycle = $cycle + 1 ))
	1125	else
	1126	(( icycle = 1 ))
	1127	fi
	1128
	1129	if (( icycle > maxcycle ))
	1130	then
	1131	(( maxcycle = icycle ))
	1132	fi
	1133
	1134	done <filelist
	1135	rm filelist
	1136	fi
	1137
	1138	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1139	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
	1140	if [[ "${actionout[$i]}" != a ]]
	1141	then
	1142	if (( maxcycle > 0 ))
	1143	then
	1144	filename_tmp=${filename}.$maxcycle
	1145	if cat /dev/null > $filename_tmp
	1146	then
	1147	rm $filename_tmp
	1148	else
	1149	printf "\n +++ OUTPUT-file:"
	1150	printf "\n $filename_tmp"
	1151	printf "\n cannot be created"
	1152	locat=output ; exit
	1153	fi
	1154	fi
	1155	else
	1156	(( maxcycle = maxcycle - 1 ))
	1157	fi
	1158
	1159	(( cycnum[$i] = maxcycle ))
	1160	pathout[$i]=$filename
	1161
	1162	fi
	1163	done
	1164
	1165
	1166	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1167	if [[ $running_in_batch_mode = false ]]
	1168	then
	1169	run_id=$RANDOM
	1170	job_id=${fname}.$run_id
	1171
	1172	TEMPDIR=$tmp_user_catalog/$job_id
	1173	fi
	1174
	1175
	1176	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1177	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1178	then
	1179
	1180	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1181	if [[ $ibd = 0 ]]
	1182	then
	1183	printf "\n"
	1184	printf "\n +++ no batch directives found in configuration file"
	1185	locat=config_file_batch_directives; (( iec = 0 )); exit
	1186	fi
	1187
	1188	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1189	done=false
[2384]	1190	cputime=$cpumax
[2380]	1191	while [[ $done = false ]]
	1192	do
[2384]	1193	if (( cputime == 0 ))
[2380]	1194	then
	1195	printf "\n +++ cpu-time is undefined"
	1196	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1197	printf "\n >>> "
[2384]	1198	read cputime 1>/dev/null 2>&1
[2380]	1199	else
	1200	done=true
	1201	fi
	1202	done
	1203
	1204	# CHECK THE MEMORY DEMAND
	1205	done=false
	1206	while [[ $done = false ]]
	1207	do
	1208	if (( memory == 0 ))
	1209	then
	1210	printf "\n +++ memory demand is undefined"
	1211	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1212	printf "\n >>> "
	1213	read memory 1>/dev/null 2>&1
	1214	else
	1215	done=true
	1216	fi
	1217	done
	1218
	1219	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1220	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1221	then
	1222	while [[ -z $remote_username ]]
	1223	do
	1224	printf "\n +++ username on remote host \"$remote_ip\" is undefined"
	1225	printf "\n >>> Please type username:"
	1226	printf "\n >>> "
	1227	read remote_username
	1228	done
	1229	fi
	1230
	1231	else
	1232
	1233	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1234
	1235	fi
	1236	cpumax=$cputime
	1237
	1238
	1239	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1240	(( cpu_hours = cputime / 3600 ))
	1241	(( resttime = cputime - cpu_hours * 3600 ))
	1242	(( cpu_minutes = resttime / 60 ))
	1243	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1244	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1245
	1246
	1247	# OUTPUT OF THE PALMRUN-HEADER
	1248	calltime=$(date)
	1249	printf "\n"
	1250	printf "#------------------------------------------------------------------------# \n"
	1251	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1252	printf "\| \| \n"
	1253	column1="called on:"; column2=$(hostname)
	1254	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1255	if [[ $create_remote_batch_job = true ]]
	1256	then
	1257	column1="execution on:"; column2="$remote_hostname (username: $remote_username)"
	1258	else
	1259	if [[ $running_on_remote = true ]]
	1260	then
	1261	column1="execution on:"; column2="$remote_hostname"
	1262	else
	1263	column1="execution on:"; column2="$local_hostname"
	1264	fi
	1265	fi
	1266	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1267
	1268	column1="running in:"
	1269	if [[ $running_in_batch_mode = true ]]
	1270	then
	1271	column2="batch job mode"
	1272	else
	1273	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1274	then
	1275	column2="job creation mode"
	1276	else
	1277	column2="interactive run mode"
	1278	fi
	1279	fi
	1280	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1281
	1282	if [[ -n $cores ]]
	1283	then
	1284	if [[ $run_coupled_model = false ]]
	1285	then
	1286	column1="number of cores:"; column2=$cores
	1287	else
	1288	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1289	fi
	1290	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1291	fi
	1292	if [[ -n $tasks_per_node ]]
	1293	then
	1294	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1295	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1296	if (( remaining_cores > 0 ))
	1297	then
	1298	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1299	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1300	fi
	1301	fi
	1302	if [[ $maximum_parallel_io_streams != $cores ]]
	1303	then
	1304	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1305	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1306	fi
	1307	if [[ $use_openmp = true ]]
	1308	then
	1309	column1="threads per task:"; column2="$threads_per_task"
	1310	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1311	fi
[2384]	1312	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1313	then
	1314	column1="job cpu time (h:m:s):"; column2="$timestring"
	1315	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1316	fi
[2380]	1317	printf "\| \| \n"
	1318	if [[ "$source_list" != "" ]]
	1319	then
	1320	if [[ "$make_options" != "" ]]
	1321	then
	1322	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1323	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1324	line=$(echo "$make_options" \| cut -c46-)
	1325	while [[ "$line" != "" ]]
	1326	do
	1327	column1=""
	1328	column2=$(echo "$line" \| cut -c-45)
	1329	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1330	line=$(echo "$line" \| cut -c46-)
	1331	done
	1332	fi
	1333	fi
	1334
	1335	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1336	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1337	line=$(echo "$cpp_options" \| cut -c46-)
	1338	while [[ "$line" != "" ]]
	1339	do
	1340	column1=""
	1341	column2=$(echo "$line" \| cut -c-45)
	1342	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1343	line=$(echo "$line" \| cut -c46-)
	1344	done
	1345
	1346	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1347	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1348	line=$(echo "$compiler_options" \| cut -c46-)
	1349	while [[ "$line" != "" ]]
	1350	do
	1351	column1=""
	1352	column2=$(echo "$line" \| cut -c-45)
	1353	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1354	line=$(echo "$line" \| cut -c46-)
	1355	done
	1356
[2388]	1357	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1358	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1359	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1360	while [[ "$line" != "" ]]
	1361	do
	1362	column1=""
	1363	column2=$(echo "$line" \| cut -c-45)
	1364	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1365	line=$(echo "$line" \| cut -c46-)
	1366	done
	1367
	1368	if [[ "$login_init_cmd" != "" ]]
	1369	then
	1370	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1371	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1372	line=$(echo "$login_init_cmd" \| cut -c46-)
	1373	while [[ "$line" != "" ]]
	1374	do
	1375	column1=""
	1376	column2=$(echo "$line" \| cut -c-45)
	1377	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1378	line=$(echo "$line" \| cut -c46-)
	1379	done
	1380	fi
	1381
	1382	if [[ "$module_commands" != "" ]]
	1383	then
	1384	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1385	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1386	line=$(echo "$module_commands" \| cut -c46-)
	1387	while [[ "$line" != "" ]]
	1388	do
	1389	column1=""
	1390	column2=$(echo "$line" \| cut -c-45)
	1391	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1392	line=$(echo "$line" \| cut -c46-)
	1393	done
	1394	fi
	1395	printf "\| \| \n"
	1396	column1="base name of files:"; column2=$fname
	1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1398	column1="activation string list:"; column2=$(echo $activation_string_list)
	1399	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1400
	1401	if [[ "$ocean_file_appendix" = true ]]
	1402	then
	1403	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1404	fi
	1405
	1406	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
	1407	then
	1408	column1="memory demand / PE":; column2="$memory MB"
	1409	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1410	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
	1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1412	fi
	1413
	1414	if [[ "$source_list" != "" ]]
	1415	then
	1416	printf "\| \| \n"
	1417	printf "\| Files to be compiled: \| \n"
	1418	line=$source_list
	1419	while [[ "$line" != "" ]]
	1420	do
	1421	linestart=$(echo $line \| cut -c-70)
	1422	printf "\| %-70s \| \n" "$linestart"
	1423	line=$(echo "$line" \| cut -c71-)
	1424	done
	1425	fi
	1426	printf "#------------------------------------------------------------------------#"
	1427
	1428
	1429
	1430	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1431	if [[ $do_trace = true ]]
	1432	then
	1433	(( i = 0 ))
	1434	while (( i < iin ))
	1435	do
	1436	(( i = i + 1 ))
	1437	if (( i == 1 ))
	1438	then
	1439	printf "\n\n >>> INPUT-file assignments:\n"
	1440	fi
	1441	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1442	done
	1443	(( i = 0 ))
	1444	while (( i < iout ))
	1445	do
	1446	(( i = i + 1 ))
	1447	if (( i == 1 ))
	1448	then
	1449	printf "\n\n >>> OUTPUT-file assignments:\n"
	1450	fi
	1451	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1452	done
	1453	(( i = 0 ))
	1454	while (( i < iic ))
	1455	do
	1456	(( i = i + 1 ))
	1457	if (( i == 1 ))
	1458	then
	1459	printf "\n\n >>> INPUT-commands:\n"
	1460	fi
	1461	printf "\n ${in_command[$i]}"
	1462	done
	1463	(( i = 0 ))
	1464	while (( i < ioc ))
	1465	do
	1466	(( i = i + 1 ))
	1467	if (( i == 1 ))
	1468	then
	1469	printf "\n\n >>> OUTPUT-commands:\n"
	1470	fi
	1471	printf "\n ${out_command[$i]}"
	1472	done
	1473	fi
	1474
	1475	# QUERY FOR CONTINUE
	1476	if [[ $silent = false && $running_in_batch_mode = false ]]
	1477	then
	1478	antwort=dummy
	1479	printf "\n\n"
	1480	printf " >>> everything o.k. (y/n) ? "
	1481	while read antwort
	1482	do
	1483	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1484	then
	1485	printf " >>> everything o.k. (y/n) ? "
	1486	else
	1487	break
	1488	fi
	1489	done
	1490	if [[ $antwort = n \|\| $antwort = N ]]
	1491	then
	1492	locat=user_abort; (( iec = 0 )); exit
	1493	fi
	1494	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1495	then
	1496	printf " *** batch-job will be created and submitted"
	1497	else
	1498	printf " *** PALMRUN will now continue to execute on this machine"
	1499	fi
	1500	fi
	1501
	1502
	1503
	1504	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1505	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1506	then
	1507
	1508	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1509	then
	1510	printf "\n\n *** creating executable and other sources for the remote host"
	1511	else
	1512	printf "\n\n *** creating executable and other sources for the local host"
	1513	fi
	1514
	1515	palmbuild -v -h $host -d $fname
	1516	rm -rf SOURCES_FOR_RUN_$fname
	1517
	1518	if [[ $? != 0 ]]
	1519	then
	1520
	1521	# ABORT IN CASE OF COMPILATION PROBLEMS
	1522	printf "\n +++ error while creating executable and/or other sources"
	1523	locat=execution
	1524	exit
	1525
	1526	else
	1527
	1528	printf "\n$dashes\n *** executable and other sources created\n"
	1529
	1530	fi
	1531
	1532	fi
	1533
	1534
	1535	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1536	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1537	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1538	then
	1539
	1540	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1541	if [[ $running_in_batch_mode = false ]]
	1542	then
	1543	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1544	# FOLDER
	1545	mkdir -p $TEMPDIR
	1546	chmod go+rx $TEMPDIR
	1547	tmpcreate=true
	1548	cd $TEMPDIR
	1549	cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
	1550	printf "\n *** changed to temporary directory: $TEMPDIR"
	1551
	1552	else
	1553
	1554	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
	1555	printf "\n *** running in temporary directory: $TEMPDIR"
	1556
	1557	fi
	1558
	1559
	1560	# PROVIDE THE INPUT FILES
	1561	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1562	(( i = 0 ))
	1563	while (( i < iin ))
	1564	do
	1565	(( i = i + 1 ))
	1566	if (( i == 1 ))
	1567	then
	1568	printf "\n\n *** providing INPUT-files:\n$dashes"
	1569	fi
	1570
	1571
	1572	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1573	if [[ "${transin[$i]}" = unavailable ]]
	1574	then
	1575	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1576	then
	1577	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1578	printf "\n is not available!"
	1579	else
	1580	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1581	printf "\n is not available!"
	1582	fi
	1583	continue
	1584	fi
	1585
	1586	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1587	files_for_cores=false; filetype=file
	1588	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1589	then
	1590	files_for_cores=true; filetype=files
	1591	actionin[$i]=""
	1592	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1593	then
	1594	actionin[$i]=""
	1595	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1596	then
	1597	files_for_cores=true; filetype=files
	1598	actionin[$i]="ln"
	1599	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1600	then
	1601	actionin[$i]="ln"
	1602	fi
	1603
	1604	if [[ $files_for_cores = true ]]
	1605	then
	1606	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1607	else
	1608	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1609	fi
	1610
	1611	# INPUT-FILES TO BE LINKED
	1612	if [[ "${actionin[$i]}" = ln ]]
	1613	then
	1614
	1615	printf "\n $filetype will be linked"
	1616	if [[ $files_for_cores = false ]]
	1617	then
	1618	if [[ -f "${absnamein[$i]}" ]]
	1619	then
	1620	ln ${absnamein[$i]} ${localin[$i]}
	1621	got_tmp[$i]=true
	1622	fi
	1623	else
	1624	if [[ -d "${absnamein[$i]}" ]]
	1625	then
[2396]	1626	mkdir -p ${localin[$i]}
[2380]	1627	cd ${absnamein[$i]}
	1628	for file in $(ls *)
	1629	do
	1630	ln $file $TEMPDIR/${localin[$i]}
	1631	done >\|/dev/null 2>&1
	1632	cd $TEMPDIR
	1633	fi
	1634
	1635	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1636	if [[ ! -f "${localin[$i]}/_000000" ]]
	1637	then
	1638	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1639	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1640	fi
	1641
	1642	got_tmp[$i]=true
	1643	fi
	1644	fi
	1645
	1646	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1647	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1648	then
	1649
	1650	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1651	then
	1652
	1653	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1654	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1655	printf "\n file will be provided for $cores processors"
[2396]	1656	mkdir -p ${localin[$i]}
[2380]	1657	ival=$cores
	1658	(( ii = 0 ))
	1659	while (( ii <= ival-1 ))
	1660	do
	1661	if (( ii < 10 ))
	1662	then
	1663	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1664	elif (( ii < 100 ))
	1665	then
	1666	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1667	elif (( ii < 1000 ))
	1668	then
	1669	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1670	else
	1671	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1672	fi
	1673	(( ii = ii + 1 ))
	1674	done
	1675
	1676	else
	1677
	1678	if [[ $files_for_cores = true ]]
	1679	then
	1680
	1681	# PROVIDE FILES FOR EACH CORE
	1682	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1683	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1684	printf "\n providing $cores files for the respective cores"
[2396]	1685	mkdir -p ${localin[$i]}
[2380]	1686	if [[ $link_local_input = true ]]
	1687	then
	1688	printf " files will be linked\n"
	1689	cd ${absnamein[$i]}
	1690	for file in $(ls *)
	1691	do
	1692	ln -f $file ${localin[$i]}
	1693	done
	1694	cd $TEMPDIR
	1695	fi
	1696
	1697	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1698	if [[ ! -f "${localin[$i]}/_000000" ]]
	1699	then
	1700	if [[ $link_local_input = true ]]
	1701	then
	1702	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1703	fi
	1704	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1705	fi
	1706
	1707	else
	1708
	1709	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1710	if [[ $link_local_input = true ]]
	1711	then
	1712	printf " file will be linked\n"
	1713	ln -f ${absnamein[$i]} ${localin[$i]}
	1714	fi
	1715	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	1716	if [[ ! -f "${localin[$i]}" ]]
	1717	then
	1718	if [[ $link_local_input = true ]]
	1719	then
	1720	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1721	fi
	1722	cp ${absnamein[$i]} ${localin[$i]}
	1723	fi
	1724	fi
	1725	fi
	1726	fi
	1727
	1728	done
	1729	if (( i != 0 ))
	1730	then
	1731	printf "\n$dashes\n *** all INPUT-files provided \n"
	1732	fi
	1733
	1734
	1735	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1736	(( i = 0 ))
	1737	while (( i < iic ))
	1738	do
	1739	(( i = i + 1 ))
	1740	if (( i == 1 ))
	1741	then
	1742	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1743	fi
	1744	printf "\n >>> ${in_command[$i]}"
	1745	eval ${in_command[$i]}
	1746	if (( i == iic ))
	1747	then
	1748	printf "\n$dashes\n"
	1749	fi
	1750	done
	1751
	1752
	1753	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	1754	# (FILE ENVPAR WILL BE READ BY PALM)
	1755	cat > ENVPAR << EOF
	1756	&envpar run_identifier = '$fname', host = '$host',
	1757	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	1758	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	1759	maximum_cpu_time_allowed = ${cpumax}.,
	1760	revision = '$global_revision',
	1761	batch_job = .${running_in_batch_mode}. /
	1762
	1763	EOF
	1764
	1765
	1766	# STARTING THE EXECUTABLE
	1767	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
	1768	PATH=$PATH:$TEMPDIR
	1769
	1770
	1771	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	1772	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	1773	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	1774	eval line=\"$line\"
	1775	execute_command="$line"
	1776
	1777
	1778	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
	1779	eval line2=\"$line2\"
	1780	execute_command_for_combine="$line2"
	1781
	1782
	1783	# PROVIDE A HOSTFILE, IF REQUIRED
	1784	if [[ "$hostfile" != "" ]]
	1785	then
	1786
	1787	if [[ $hostfile = auto ]]
	1788	then
	1789	# CREATE A NEW HOSTFILE
	1790	(( ii = 1 ))
	1791	while (( ii <= cores / threads_per_task ))
	1792	do
	1793	echo $(hostname) >> hostfile
	1794	(( ii = ii + 1 ))
	1795	done
	1796	if (( cores / threads_per_task == 0 ))
	1797	then
	1798	echo $(hostname) >> hostfile
	1799	fi
	1800
	1801	else
	1802	cp $hostfile hostfile
	1803	fi
	1804	eval line=\"`head -n $ii hostfile`\"
	1805	printf "\n *** running on: $line"
	1806	fi
	1807
	1808
	1809
	1810	# SET THE NUMBER OF OPENMP-THREADS
	1811	if [[ $use_openmp = true ]]
	1812	then
	1813	export OMP_NUM_THREADS=$threads_per_task
	1814	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	1815	else
	1816	export OMP_NUM_THREADS=1
	1817	fi
	1818
	1819
	1820	# PROVIDE DATA FOR
	1821	if [[ $run_coupled_model = false ]]
	1822	then
	1823	if [[ "$ocean_file_appendix" = true ]]
	1824	then
	1825	echo "precursor_ocean" > coupling_steering
	1826	else
	1827	echo "precursor_atmos" > coupling_steering
	1828	fi
	1829	else
	1830	(( iia = $cores_atmos / $threads_per_task ))
	1831	(( iio = $cores_ocean / $threads_per_task ))
	1832	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	1833	printf "\n\n"
	1834	echo "coupled_run $iia $iio" > coupling_steering
	1835	fi
	1836
	1837	printf "\n *** execute command:"
	1838	printf "\n \"$execute_command\" \n\n"
	1839
	1840	$execute_command < coupling_steering
	1841
	1842	if [[ $? != 0 ]]
	1843	then
	1844
	1845	# ABORT IN CASE OF RUNTIME ERRORS
	1846	printf "\n +++ runtime error occured"
	1847	locat=execution
	1848	exit
	1849
	1850	else
	1851
	1852	printf "\n$dashes\n *** execution finished \n"
	1853
	1854	fi
	1855
	1856
	1857	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	1858	# BY EACH CORE INTO ONE FILE
	1859	if [[ ! -f combine_plot_fields.x ]]
	1860	then
	1861
	1862	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	1863	printf "\n 2d- and/or 3d-data may be incomplete!"
	1864	printf "\n Your previous palmbuild may have failed. Please check.\n"
	1865
	1866	elif [[ "$combine_plot_fields" == true ]]
	1867	then
	1868
	1869	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	1870	$execute_command_for_combine
	1871
	1872	else
	1873
	1874	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	1875	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	1876	# ??? koennen wir das streichen ???
	1877	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	1878	fi
	1879
	1880
	1881
	1882	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1883	(( i = 0 ))
	1884	while (( i < ioc ))
	1885	do
	1886	(( i = i + 1 ))
	1887	if (( i == 1 ))
	1888	then
	1889	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	1890	fi
	1891	printf "\n >>> ${out_command[$i]}"
	1892	eval ${out_command[$i]}
	1893	if (( i == ioc ))
	1894	then
	1895	printf "\n$dashes\n"
	1896	fi
	1897	done
	1898
	1899
	1900	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
	1901	if [[ $do_trace = true ]]
	1902	then
	1903	printf "\n\n"
	1904	ls -al
	1905	fi
	1906
	1907
	1908	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	1909	(( i = 0 ))
	1910	while (( i < iout ))
	1911	do
	1912	(( i = i + 1 ))
	1913	if (( i == 1 ))
	1914	then
	1915	printf "\n\n *** saving OUTPUT-files:"
	1916
	1917	# GET RUN NUMBER ASSIGNED BY PALM
	1918	if [[ -f RUN_NUMBER ]]
	1919	then
	1920	read run_number < RUN_NUMBER
	1921	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	1922	usecycle_option="-U $run_number"
	1923	else
	1924	run_number=0
	1925	usecycle_option=""
	1926	fi
	1927	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	1928	then
	1929	printf "\n *** SCP transfers to local host via remote login-node \"$remote_loginnode\" "
	1930	fi
	1931	printf "\n$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"
	2023	printf "\n ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}$catalog_string\n"
	2024
	2025	# TRANSFER VIA SCP
	2026	if [[ "$remote_loginnode" != "" ]]
	2027	then
	2028	echo "cd $TEMPDIR; ${tmp_user_catalog}/SOURCES_FOR_RUN_${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
	2029	else
	2030	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]}
	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"
	2039	printf " ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id\n"
	2040
	2041	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2042	eval local_catalog=${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
	2049	eval cp ${localout[$i]} ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id
	2050	transfer_problems=true
	2051	fi
	2052
	2053	else
	2054
	2055	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2056	# BE COPIED OR APPENDED ON THIS MACHINE
	2057	if [[ "${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
	2210	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
	2211	else
	2212	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
	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 $TEMPDIR
	2248
	2249
	2250	else
	2251
	2252
	2253	# PREPARING ACTIONS,
	2254	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2255
	2256	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
	2257	palmrun_com="$palmrun_script_name -c $config_file -d $fname -h $host -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
	2258	[[ "$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"
	2273	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2274	elif [[ $create_batch_job = true ]]
	2275	then
	2276	palmrun_com=${palmrun_com}" -j"
	2277	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2278	fi
	2279
	2280
	2281	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2282	# REMOTE HOST
	2283	job_protocol_file_local=${local_jobcatalog}/${host}_${job_id}
	2284	job_protocol_file=$job_protocol_file_local
	2285	if [[ $create_remote_batch_job = true ]]
	2286	then
	2287	job_protocol_file_remote=${remote_jobcatalog}/${host}_${job_id}
	2288	job_protocol_file=$job_protocol_file_remote
	2289	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2290	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2291	fi
	2292
	2293
	2294	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2295	jobfile=jobfile.$run_id
	2296
	2297
	2298	# FIRST CREATE THE BATCH DIRECTIVES
	2299	(( i = 0 ))
	2300	while (( i < ibd ))
	2301	do
	2302	(( i = i + 1 ))
[2393]	2303	line=`echo "${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}}/$queue/g'`
[2380]	2304	eval line=\"$line\"
	2305	echo "$line" >> $jobfile
	2306	done
	2307	echo " " >> $jobfile
	2308
	2309
	2310	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2311	# PROTOCOL
	2312	if [[ $create_remote_batch_job = true ]]
	2313	then
	2314	echo "set +vx" >> $jobfile
	2315	echo "trap '" >> $jobfile
	2316	echo "set +vx" >> $jobfile
	2317	echo "cd ${remote_jobcatalog}" >> $jobfile
	2318	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2319
	2320	# ADD THE BATCH DIRECTIVES
	2321	(( i = 0 ))
	2322	while (( i < ibdt ))
	2323	do
	2324	(( i = i + 1 ))
[2393]	2325	line=`echo "${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]	2326	eval line=\"$line\"
	2327	echo "$line" >> $jobfile
	2328	done
	2329	echo " " >> $jobfile
	2330
	2331	echo "set -x" >> $jobfile
	2332	echo "${tmp_user_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
	2333	echo "%%END%%" >> $jobfile
	2334	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2335	echo "$submit_command $scpjob_file" >> $jobfile
	2336	echo "rm $scpjob_file" >> $jobfile
	2337	echo "rm $job_transfer_protocol_file" >> $jobfile
	2338	echo "set -x" >> $jobfile
	2339	echo " ' exit" >> $jobfile
	2340	fi
	2341
	2342
	2343	# ACTIVATE ERROR-TRACEBACK
	2344	if [[ $do_trace = true ]]
	2345	then
	2346	echo "set -x" >> $jobfile
	2347	else
	2348	echo "set +vx" >> $jobfile
	2349	fi
	2350
	2351
	2352	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2353	if [[ "$login_init_cmd" != "" ]]
	2354	then
	2355	echo "$login_init_cmd" >> $jobfile
	2356	fi
	2357	if [[ "$module_commands" != "" ]]
	2358	then
	2359	echo "$module_commands" >> $jobfile
	2360	fi
	2361
	2362
	2363	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
	2364	echo "mkdir $TEMPDIR" >> $jobfile
	2365	echo "cd $TEMPDIR" >> $jobfile
	2366	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
	2367	echo "cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
	2368	echo "export PATH=.:\$PATH" >> $jobfile
	2369	echo "export execute_palmrun=true" >> $jobfile
	2370
	2371
	2372	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	2373	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	2374	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
	2375	if [[ $create_remote_batch_job = true ]]
	2376	then
	2377	(( i = 0 ))
	2378	while (( i < iin ))
	2379	do
	2380	(( i = i + 1 ))
	2381	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	2382	if [[ "${transin[$i]}" = job ]]
	2383	then
	2384	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	2385	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	2386	echo " " >> $jobfile
	2387	echo "%END%" >> $jobfile
	2388	else
	2389	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
	2390	fi
	2391
	2392	# CHECK, IF FILE COULD BE CREATED
	2393	echo "if [[ \$? = 1 ]]" >> $jobfile
	2394	echo "then" >> $jobfile
	2395	echo " echo \" \" " >> $jobfile
	2396	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	2397	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	2398	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
	2399	echo " execute_palmrun=false" >> $jobfile
	2400	echo "fi" >> $jobfile
	2401	done
	2402	fi
	2403
	2404
	2405	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2406	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2407	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2408	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2409	echo "export LOCAL_PWD" >> $jobfile
	2410
	2411
	2412	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
	2413	echo "LOCAL_PALMRUN_PATH=$PALM_BIN" >> $jobfile
	2414	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2415
	2416
	2417	# CALL PALMRUN WITHIN THE JOB
	2418	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2419	echo "set -x" >> $jobfile
	2420	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2421
	2422
	2423	# TRANSFER JOBFILE TO THE TARGET HOST
	2424	if [[ $create_jobfile_only = false ]]
	2425	then
	2426
	2427	if [[ $create_remote_batch_job = true ]]
	2428	then
	2429
	2430	echo " *** transfer of job to remote host via scp"
[2385]	2431	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}"
	2432	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}
[2380]	2433
	2434	echo " "
	2435	echo " *** submit the job"
[2385]	2436	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"
	2437	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]	2438
	2439	elif [[ $create_batch_job = true ]]
	2440	then
	2441
[2385]	2442	eval local_jobcatalog=$local_jobcatalog
	2443	cp $jobfile ${local_jobcatalog}/${host}_${job_id}
	2444	cd $local_jobcatalog
[2380]	2445	echo " "
	2446	echo "--- submit the job"
	2447	echo "$submit_command ${host}_${job_id}"
	2448	$submit_command ${host}_${job_id}
	2449	rm ${host}_${job_id}
	2450	cd - > /dev/null
	2451
	2452	fi
	2453
	2454	rm -rf $jobfile
	2455
	2456	else
	2457
	2458	printf "\n *** jobfile created under name \"$jobfile\" "
	2459	printf "\n no batch-job has been sent!"
	2460
	2461	fi
	2462
	2463	fi # END OF REMOTE-PART

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