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source: palm/trunk/SCRIPTS/palmrun @ 3303

Last change on this file since 3303 was 3294, checked in by raasch, 6 years ago
modularization of the ocean code
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 99.9 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	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	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[3032]	28	# $Id: palmrun 3294 2018-10-01 02:37:10Z raasch $
[3294]	29	# more detailed error message for outdated fileconnection file
	30	#
	31	# 3236 2018-09-10 09:07:06Z raasch
[3236]	32	# warning issued in case of file connection file version mismatch,
	33	# host_configuration renamed configuration_identifier,
	34	# "host identifier" in header output renamed "config. identifier",
	35	# jobname renamed run_identifier,
	36	# run_id renamed run_id_number
	37	# job_id renamed run_id
	38	# option -r renamed -i
	39	#
	40	# 3151 2018-07-19 08:45:38Z raasch
[3151]	41	# removed additional listing of files to be compiled, print PALM code revision
	42	# in header
	43	#
	44	# 3132 2018-07-16 11:44:58Z raasch
[3132]	45	# create consistent error messages in case of failed restarts,
	46	# check existence of remote job catalog
	47	#
	48	# 3043 2018-05-25 10:47:54Z raasch
[3043]	49	# check for setting of fast_io_catalog
	50	#
	51	# 3033 2018-05-23 15:26:19Z raasch
[3025]	52	# -T option not required for interactive runs (tasks per node =
	53	# total number of cores is assumed as default, if option is not given),
	54	# reformatting of a few messages,
	55	# bugfix: destination output directory is created if attribute "pe" is set in
	56	# .palm.iofiles
	57	#
	58	# 2718 2018-01-02 08:49:38Z maronga
[2993]	59	# bugfix of r2990
	60	#
	61	# 2718 2018-01-02 08:49:38Z maronga
[2990]	62	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	63	# not in the working directory from where palmrun is called
	64	#
	65	# 2718 2018-01-02 08:49:38Z maronga
[2957]	66	# svfout in the activation string will be replaced now by svfin in case of
	67	# automatic restarts
	68	#
	69	# 2718 2018-01-02 08:49:38Z maronga
[2906]	70	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	71	# the possible output or input of sky view factors
	72	#
	73	# 2718 2018-01-02 08:49:38Z maronga
[2834]	74	# "fname" renamed to "jobname"
	75	#
	76	# 2718 2018-01-02 08:49:38Z maronga
[2799]	77	# parameters are allowed in output commands (OC:)
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2789]	80	# bugfix: exit if no queue has been given neither with option -q nor in the
	81	# configuration file
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2762]	84	# file connection file from trunk/SCRIPTS is taken by default
	85	#
	86	# 2718 2018-01-02 08:49:38Z maronga
[2716]	87	# Corrected "Former revisions" section
	88	#
	89	# 2696 2017-12-14 17:12:51Z kanani
	90	# Change in file header (GPL part)
	91	#
	92	# 2693 2017-12-13 12:33:49Z raasch
[2693]	93	# replacement of variables given by {{<variable>}} in configuration file is now
	94	# done in a more general way, variable names are written in small letters
	95	#
	96	# 2670 2017-12-06 16:32:19Z raasch
[2670]	97	# test printouts removed
	98	#
	99	# 2669 2017-12-06 16:03:27Z raasch
[2669]	100	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	101	# removed,
	102	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	103	# files,
	104	# informative messages in case of missing optional input files shortened
	105	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	106	#
	107	# 2638 2017-11-23 12:44:23Z raasch
[2610]	108	# use of wildcards in file connection statements enabled
	109	#
	110	# 2605 2017-11-09 15:31:46Z raasch
[2605]	111	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	112	# will not be sent with the job file any more, but copied into the
[2610]	113	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	114	#
	115	# 2600 2017-11-01 14:11:20Z raasch
[2600]	116	# cycle numbers are made three digits wide
	117	#
	118	# 2566 2017-10-20 08:50:47Z raasch
[2566]	119	# execute command for combine_plot_fields added
	120	# "TEMPDIR" renamed "tempdir"
	121	# temporary working directory for local batch jobs is created immediately within
	122	# the user's palmrun call, due to a requirement of the "grid engine" batch
	123	# system, where the working directory is given with batch directive -wd and must
	124	# already exist when the job is submitted,
	125	# informative messages in non-trace mode reduced and partly reformatted
	126	#
	127	# 2551 2017-10-18 07:25:11Z raasch
[2551]	128	# TEMPDIR added as replacement string to be used in batch directives
	129	#
	130	# 2512 2017-10-04 08:26:59Z raasch
[2507]	131	# bugfix for determining cycle numbers of NetCDF input files
	132	#
	133	# 2506 2017-09-29 08:30:37Z raasch
[2506]	134	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	135	# host configuration added to SOURCES_FOR_RUN_... folder name
	136	# host_identifier renamed host_configuration
	137	# option -W added to allow for job dependencies
	138	#
	139	# 2501 2017-09-26 11:41:55Z raasch
[2501]	140	# default value for number of cores (option -X) set to 1
	141	# bugfix for mechanism which overwrites configuration file settings with values
	142	# provided by palmrun options
	143	#
	144	# 2499 2017-09-22 16:47:58Z kanani
[2499]	145	# option -h named configuration identifier
	146	#
	147	# 2480 2017-09-19 06:24:14Z maronga
[2480]	148	# bugfix for last revision
	149	#
	150	# 2479 2017-09-19 06:12:16Z raasch
[2479]	151	# option -A (project account number) added
	152	#
	153	# 2422 2017-09-08 08:25:41Z raasch
[2410]	154	# initial revision
[2380]	155	#
	156	#--------------------------------------------------------------------------------#
	157	# palmrun - script for running PALM jobs on local and remote hosts
	158	#--------------------------------------------------------------------------------#
	159
	160
	161
	162	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	163
	164	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	165	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	166	# (TOO MANY ARGUMENTS - PROBLEM)
	167	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	168
[2610]	169	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	170	typeset -i nr_of_output_files=0
[2380]	171	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	172	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	173	# SCRIPT-OPTION ARGUMENTS
	174	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	175	typeset -i icycle inode ival maxcycle mpi_tasks
	176	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	177
	178	activation_string_list=""
	179	AddFilenames=""
	180	combine_plot_fields=true
	181	compiler_name=""
	182	compiler_name_ser=""
	183	compiler_options=""
[3236]	184	configuration_identifier="default"
[2501]	185	cores=1
[2380]	186	cores_atmos=0
	187	cores_ocean=0
	188	coupled_dist=""
	189	cpp_options=""
	190	cpumax=0
[2506]	191	create_batch_job=false
[2380]	192	create_jobfile_only=false
	193	create_remote_batch_job=false
	194	dashes=" ----------------------------------------------------------------------------"
	195	defaultqueue=""
[2506]	196	delete_temporary_catalog=true
[2380]	197	do_compile=true
	198	do_trace=false
	199	executable=""
	200	execute_command=""
	201	execution_error=false
[2762]	202	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	203	global_revision=""
	204	hostfile=""
	205	hp=""
	206	keep_data_from_previous_run=false
	207	link_local_input=false
	208	link_local_output=false
[2388]	209	linker_options=""
[2385]	210	local_jobcatalog=""
[2380]	211	locat=normal
	212	makefile=""
	213	max_par_io_str=""
	214	prc=$0
	215	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	216	do
	217	prc=`echo $prc \| cut -f2- -d"/"`
	218	done
	219	module_calls=""
[2506]	220	palmrun_memory=""
[2380]	221	palmrun_script_name=$prc
	222	openmp=false
[2506]	223	previous_job=""
[2479]	224	project_account=""
[2380]	225	queue=none
[2906]	226	read_svf=""
[2380]	227	restart_run=false
	228	return_address=""
[2385]	229	remote_jobcatalog=""
[2380]	230	remote_username=""
	231	running_in_batch_mode=false
	232	run_coupled_model=false
	233	run_id=""
[3236]	234	run_id_number=""
	235	run_identifier=test
[2380]	236	silent=false
	237	source_list=""
	238	source_path=""
[2501]	239	tasks_per_node=0
[2380]	240	threads_per_task=1
	241	transfer_problems=false
[2384]	242	user_source_path=""
[2506]	243	use_existing_sources_folder=""
[2380]	244	use_openmp=false
[3033]	245	version="palmrun 1.0 Rev$Rev: 3294 $"
[2380]	246	working_directory=`pwd`
	247	write_binary=""
[2906]	248	write_svf=""
[2380]	249
	250
	251	# ERROR HANDLING IN CASE OF EXIT
[2404]	252	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	253	then
	254
	255	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	256	(( i = 0 ))
	257	while (( i < iec ))
	258	do
	259	(( i = i + 1 ))
	260	printf "\n *** Execution of ERROR-command:\n"
	261	printf " >>> ${err_command[$i]}\n"
	262	eval ${err_command[$i]}
	263	done
[2566]	264	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	265	printf "\n\n+++ palmrun killed \n\n"
	266	elif [[ $locat != control_c ]]
	267	then
[2566]	268	printf "\n --> palmrun finished\n\n"
[2380]	269	fi' exit
	270
	271
	272	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	273	trap 'cd; rm -rf $tempdir
[2380]	274	printf "\n+++ palmrun killed by \"^C\" \n\n"
	275	locat=control_c
	276	exit
	277	' 2
	278
	279
	280	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	281	# WHICH WILL BE USED TO START RESTART-JOBS
[3236]	282	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	283	do
	284	case $option in
	285	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	286	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	287	(b) create_batch_job=true; prc="$prc -b";;
	288	(B) delete_temporary_catalog=false; prc="$prc -B";;
	289	(C) restart_run=true; prc="$prc -C";;
[3236]	290	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	291	(F) create_jobfile_only=true;;
	292	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	293	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
	294	(i) run_id_number=$OPTARG;;
[2380]	295	(j) running_in_batch_mode=true;;
	296	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	297	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	298	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	299	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	300	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	301	(R) return_address=$OPTARG;;
	302	(s) source_list=$OPTARG;;
[2501]	303	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	304	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	305	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	306	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	307	(v) silent=true; prc="$prc -v";;
[2506]	308	(V) use_existing_sources_folder="-V";;
[2380]	309	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	310	(W) previous_job=$OPTARG;;
[2380]	311	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	312	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	313	(y) ocean_file_appendix=true; prc="$prc -y";;
	314	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	315	(Z) combine_plot_fields=false; prc="$prc -Z";;
	316	(\?) printf "\n +++ unknown option $OPTARG \n"
	317	printf "\n --> type \"$0 ?\" for available options \n"
	318	locat=parameter;exit;;
	319	esac
	320	done
	321
	322
	323	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	324	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	325	(( to_shift = $OPTIND - 1 ))
	326	shift $to_shift
	327
	328	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	329	if [[ "$1" = "?" ]]
	330	then
	331	(printf "\n *** Description of available palmrun options:\n"
	332	printf "\n Option Description Default-Value"
	333	printf "\n -a activation string list \"\" "
[2479]	334	printf "\n -A project account number ---"
[2380]	335	printf "\n -b batch-job on local machine ---"
	336	printf "\n -B do not delete temporary directory at end ---"
[3025]	337	printf "\n -d run identifier test"
[2380]	338	printf "\n -F create batch job file only ---"
[2506]	339	printf "\n -h host configuration \"default\" "
[2380]	340	printf "\n -k keep data from previous run"
	341	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	342	printf "\n -M Makefile name Makefile"
	343	printf "\n -O threads per openMP task ---"
	344	printf "\n -q queue \"$queue\" "
	345	printf "\n -s filenames of routines to be compiled \"\" "
	346	printf "\n must end with .f, .f90, .F, or .c !"
	347	printf "\n use \"..\" for more than one file and wildcards"
	348	printf "\n -s LM compiles all locally modified files"
	349	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	350	printf "\n -T tasks per node ---"
[2380]	351	printf "\n -u username on remote machine \"\" "
	352	printf "\n -v no prompt for confirmation ---"
[2506]	353	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	354	printf "\n -w maximum parallel io streams as given by -X"
[2506]	355	printf "\n -W name of job to wait for ---"
[2380]	356	printf "\n -x tracing of palmrun for debug purposes ---"
	357	printf "\n -X # of processors (on parallel machines) 1"
	358	printf "\n -y add appendix \"_O\" to all local output"
	359	printf "\n files (ocean precursor runs followed by"
	360	printf "\n coupled atmosphere-ocean runs) ---"
	361	printf "\n -Y run coupled model, \"#1 #2\" with"
	362	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	363	printf "\n -Z skip combine_plot_fields at the end of "
	364	printf "\n the simulation ---"
	365	printf "\n "
	366	printf "\n Possible values of positional parameter <modus>:"
	367	printf "\n \"?\" - this outline \n\n") \| more
	368	exit
	369	elif [[ "$1" != "" ]]
	370	then
	371	printf "\n +++ positional parameter $1 unknown \n"
	372	locat=parameter; exit
	373	fi
	374
	375
	376
	377	# SHORT STARTING MESSAGE
	378	printf "\n*** $version "
	379	printf "\n will be executed. Please wait ..."
	380
	381
[3236]	382	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
	383	export fname=$run_identifier
	384	export jobname=$run_identifier
[2834]	385
	386
[2506]	387	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	388	config_file=.palm.config.$configuration_identifier
	389	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	390
	391
	392	# CHECK, IF CONFIGURATION FILE EXISTS
	393	if [[ ! -f $config_file ]]
	394	then
	395	printf "\n\n +++ configuration file: "
	396	printf "\n $config_file"
	397	printf "\n does not exist"
	398	locat=connect; exit
	399	fi
	400
	401
[2762]	402	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	403	if [[ -f .palm.iofiles ]]
	404	then
[3236]	405
	406	# CHECK VERSION MISMATCH
	407	if [[ $running_in_batch_mode != true ]]
	408	then
	409	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	410	then
	411	printf "\n\n +++ WARNING: A file connection file has been found in your"
	412	printf "\n working directory, but its revision does not match"
	413	printf "\n the revision of the default (trunk) version."
[3294]	414	printf "\n You may need to update your connection file"
	415	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	416	fi
	417	fi
	418
[2762]	419	fileconnection_file=.palm.iofiles
[3236]	420
[2762]	421	fi
	422
	423
[2380]	424	# CHECK, IF FILE CONNECTION FILE EXISTS
	425	if [[ ! -f $fileconnection_file ]]
	426	then
	427	printf "\n\n +++ file connection file: "
	428	printf "\n $fileconnection_file"
	429	printf "\n does not exist"
	430	locat=connect; exit
	431	fi
	432
	433
[2404]	434	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	435	if [[ "$activation_string_list" = "" ]]
	436	then
	437	printf "\n\n +++ no activation string list given: "
	438	printf "\n please set palmrun option \"-a\" "
	439	locat=palmrun_option; exit
	440	fi
	441
	442
	443	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	444	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	445	then
	446	write_binary=true
	447	else
	448	write_binary=false
	449	fi
	450
[2906]	451	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	452	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	453	then
	454	write_svf=true
	455	else
	456	write_svf=false
	457	fi
[2404]	458
[2906]	459	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	460	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	461	then
	462	read_svf=true
	463	else
	464	read_svf=false
	465	fi
	466
	467
[2380]	468	# READ AND EVALUATE THE CONFIGURATION-FILE
	469	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	470
	471	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	472	while read line
	473	do
	474
	475	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	476	eval line=\"$line\"
	477
	478
	479	# INTERPRET THE LINE
	480	if [[ "$(echo $line)" = "" ]]
	481	then
	482
	483	# EMPTY LINE, NO ACTION
	484	continue
	485
	486	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	487	then
	488
	489	# LINE IS A COMMENT LINE
	490	continue
	491
	492	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	493	then
	494
	495	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	496	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	497	value=`echo $line \| cut -d" " -s -f2-`
	498
	499
	500	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	501	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	502	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	503	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	504	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	505	# CONFIGURATION-FILE.
	506	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	507	then
	508	eval export $var="\$value"
	509
	510	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	511	if [[ $do_trace = true ]]
	512	then
	513	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	514	fi
	515	fi
	516
	517	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	518	then
	519
	520	# LINE DEFINES BATCH-DIRECTIVE
	521	(( ibd = ibd + 1 ))
	522	line=$(echo $line \| cut -c4-)
	523	batch_directive[$ibd]="$line"
	524
	525	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	526	then
	527
	528	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	529	# REMOTE TO A LOCAL HOST
	530	(( ibdt = ibdt + 1 ))
	531	line=$(echo $line \| cut -c5-)
	532	batch_directive_transfer[$ibdt]="$line"
	533
	534	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	535	then
	536
	537	# LINE DEFINES ERROR-COMMAND
	538	(( iec = iec + 1 ))
	539	line=$(echo $line \| cut -c4-)
	540	err_command[$iec]="$line"
	541
	542	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	543	then
	544
	545	# LINE DEFINES INPUT-COMMAND
	546	(( iic = iic + 1 ))
	547	line=$(echo $line \| cut -c4-)
	548	in_command[$iic]="$line"
	549
	550	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	551	then
	552
	553	# LINE DEFINES OUTPUT-COMMAND
	554	(( ioc = ioc + 1 ))
	555	line=$(echo $line \| cut -c4-)
	556	out_command[$ioc]="$line"
	557
	558	else
	559
	560	# SKIP ALL OTHER LINES
	561	continue
	562
	563	fi
	564
	565	done < $config_file
	566
	567
	568	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	569	if [[ "$fast_io_catalog" = "" ]]
	570	then
	571	printf "\n +++ no fast_io_catalog found in $config_file"
	572	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	573	locat=config_file; exit
	574	fi
[2380]	575	if [[ "$compiler_name" = "" ]]
	576	then
	577	printf "\n +++ no compiler name found in $config_file"
	578	printf "\n Please add line \"compiler_name ...\" to that file."
	579	locat=config_file; exit
	580	fi
	581	if [[ "$compiler_name_ser" = "" ]]
	582	then
	583	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	584	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	585	locat=config_file; exit
	586	fi
	587	if [[ "$compiler_options" = "" ]]
	588	then
	589	printf "\n +++ no compiler options found in $config_file"
	590	printf "\n Please add line \"compiler_options ...\" to that file."
	591	locat=config_file; exit
	592	fi
[2388]	593	if [[ "$linker_options" = "" ]]
[2380]	594	then
[2388]	595	printf "\n +++ no linker options found in $config_file"
	596	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	597	locat=config_file; exit
	598	fi
	599	if [[ "$execute_command" = "" ]]
	600	then
	601	printf "\n +++ no execute command found in $config_file"
	602	printf "\n Please add line \"execute_command ...\" to that file."
	603	locat=config_file; exit
	604	fi
	605
	606	if [[ "$hostfile" != "" ]]
	607	then
	608	if [[ $hostfile != auto && ! -f $hostfile ]]
	609	then
	610	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	611	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	612	locat=config_file; exit
	613	fi
	614	fi
	615
	616
	617	# DETERMINE THE CALL STATUS
	618	if [[ "$return_address" != "" ]]
	619	then
	620
	621	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	622	# BATCH MODE AND ...
	623	running_on_remote=true
	624
	625	else
	626
	627	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	628	if [[ "$remote_ip" != "" ]]
	629	then
	630
	631	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	632	create_remote_batch_job=true
	633
[3132]	634	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	635	if [[ "$remote_jobcatalog" = "" ]]
	636	then
	637	printf "\n +++ no remote jobcatalog found in $config_file"
	638	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	639	locat=config_file; exit
	640	fi
	641
	642
[2380]	643	fi
	644	running_on_remote=false
	645	fi
	646
	647
	648
	649	# READ AND EVALUATE THE I/O-FILE LIST
	650	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	651
	652	# READ THE FILE CONNECTION FILE LINE BY LINE
	653	while read line
	654	do
	655
[2669]	656	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	657	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	658
	659	# INTERPRET THE LINE
	660	if [[ "$(echo $line)" = "" ]]
	661	then
	662	# EMPTY LINE, NO ACTION
	663	continue
	664
	665	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	666	then
	667
	668	# LINE IS A COMMENT LINE
	669	true
	670
	671	else
	672
	673	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	674	# s2a: in/out - field
[2669]	675	# s2b: action - field (optional)
	676	s1=`echo "$line" \| cut -d" " -f1`
	677	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	678	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	679	then
[2669]	680	s2a=$s2
[2380]	681	s2b=""
	682	else
[2669]	683	s2a=`echo $s2 \| cut -d":" -f1`
	684	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	685	fi
[2669]	686	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	687	s4=`echo "$line" \| cut -d" " -s -f4`
	688	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	689	s5=`echo "$line" \| cut -d" " -s -f5`
	690	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	691
	692
	693	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	694	# INPUT- OR OUTPUT-LIST.
	695	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	696	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	697	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	698	# IS NOT CHECKED AND STORED.
[2610]	699	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	700	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	701	then
	702	found=false
	703	for actual in $activation_string_list
	704	do
	705	for formal in $s3
	706	do
	707	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	708	done
	709	done
	710	if [[ $found = true ]]
	711	then
	712	(( iin = iin + 1 ))
[2669]	713	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	714	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	715	if [[ "$s2a" = inopt ]]
	716	then
	717	optin_pre[$iin]=yes
	718	else
	719	optin_pre[$iin]=no
	720	fi
[2605]	721
	722	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	723	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	724	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	725	then
[2610]	726	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	727	fi
	728
[2610]	729	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	730	# THE WILDCARD FROM THE ENDING
	731	if [[ "${s5: -1}" = "*" ]]
	732	then
[2669]	733	if [[ "$s2b" = "di" ]]
[2610]	734	then
	735	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	736	printf "\n see file \"$fileconnection_file\", line"
	737	printf "\n$line"
	738	locat=iofiles_file; exit
	739	fi
	740	multin[$iin]=true
	741	string=${endin_pre[$iin]}
	742	endin_pre[$iin]="${string%?}"
	743	else
	744	multin[$iin]=false
	745	fi
[2380]	746	fi
[2669]	747	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	748	then
	749	found=false
	750	for actual in $activation_string_list
	751	do
	752	for formal in $s3
	753	do
[2670]	754	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	755	done
	756	done
	757	if [[ $found = true ]]
	758	then
	759	(( iout = iout + 1 ))
[2669]	760	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	761	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	762
[2669]	763	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	764	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	765	if [[ $formal = wildcard ]]
	766	then
	767	warnout_pre[$iout]=false
	768	else
	769	warnout_pre[$iout]=true
	770	fi
	771
[2610]	772	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	773	# THE WILDCARD FROM THE LOCAL FILENAME
	774	if [[ "${s1: -1}" = "*" ]]
	775	then
[2669]	776	if [[ "$s2b" = "di" ]]
[2610]	777	then
	778	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	779	printf "\n see file \"$fileconnection_file\", line"
	780	printf "\n$line"
	781	locat=iofiles_file; exit
	782	fi
	783	multout[$iout]=true
	784	string=${localout_pre[$iout]}
	785	localout_pre[$iout]="${string%?}"
	786	else
	787	multout[$iout]=false
	788	fi
[2380]	789	fi
[2669]	790	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	791	then
[2669]	792	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	793	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	794	locat=connect; exit
	795	fi
	796	IFS="$IFSALT"
	797	fi
	798
	799	done < $fileconnection_file
	800
	801
	802
[2501]	803	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	804	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	805	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	806	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	807	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	808	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	809
	810
	811
[2380]	812	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	813	if [[ $run_coupled_model = true ]]
	814	then
	815
	816	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	817	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	818
	819	if (( $cores_ocean + $cores_atmos != $cores ))
	820	then
	821
	822	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	823	printf "\n PEs (total) : $cores"
	824	printf "\n PEs (atmosphere): $cores_atmos"
	825	printf "\n PEs (ocean) : $cores_ocean"
	826	locat=coupling; exit
	827
	828	fi
	829
	830	fi
	831
	832
	833	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	834	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	835	# FOLDER
	836	if [[ $running_in_batch_mode = true ]]
	837	then
	838
[2506]	839	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	840	then
[2506]	841	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	842	printf "\n Please check the output of the palmrun-call"
	843	printf "\n that you did on your local host."
	844	locat=SOURCES_FOR_RUN; exit
	845	fi
	846
	847	else
	848
	849	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	850	# AUTOMATIC RESTART RUN
	851	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	852	if [[ $restart_run = false ]]
	853	then
	854
	855	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	856	# THE LOCAL HOST
	857	if [[ ! -d $source_path ]]
	858	then
	859	printf "\n\n +++ source path \"$source_path\" on local host"
	860	printf "\n \"$(hostname)\" does not exist"
	861	locat=source_path; exit
	862	fi
	863
[2990]	864	rm -rf ${base_directory}/${sources_for_run_catalog}
	865	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	866
	867	if [[ "$source_list" = LM ]]
	868	then
	869
	870	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	871	source_list=""
	872	cd $source_path
	873
	874
[2512]	875	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	876	if [[ ! -d ../.svn ]]
[2380]	877	then
	878	printf "\n\n +++ source directory"
	879	printf "\n \"$source_path\" "
	880	printf "\n is not under control of \"subversion\"."
[2512]	881	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	882	fi
	883
	884
	885	# LIST ALL MODIFIED SOURCE CODE FILES
	886	Filenames=""
[2404]	887	svn status > tmp_svnstatus
[2380]	888	while read line
	889	do
	890	firstc=`echo $line \| cut -c1`
	891	if [[ $firstc = M \|\| $firstc = "?" ]]
	892	then
	893	Name=`echo "$line" \| cut -c8-`
	894	extension=`echo $Name \| cut -d. -f2`
	895	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	896	then
	897	Filenames="$Filenames "$Name
	898	fi
	899	fi
[2404]	900	done < tmp_svnstatus
	901	rm -rf tmp_svnstatus
[2380]	902
	903
	904	# COPY FILES TO SOURCES_FOR_RUN_...
	905	for filename in $Filenames
	906	do
[2990]	907	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	908	source_list=$source_list"$filename "
	909	done
	910
	911	cd - > /dev/null
	912
	913
	914	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	915	elif [[ "$source_list" != "" ]]
	916	then
	917
	918	cd $source_path
	919
	920	for filename in $source_list
	921	do
	922
	923	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	924	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	925	then
	926	printf "\n +++ source code file: $filename"
	927	printf "\n must not contain (\"/\") "
	928	locat=source; exit
	929	fi
	930
	931	if [[ ! -f $filename ]]
	932	then
	933	printf "\n +++ source code file: $filename"
	934	printf "\n does not exist"
	935	locat=source; exit
	936	else
[2990]	937	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	938	fi
	939
	940	done
	941
	942	cd - > /dev/null
	943
	944	fi
	945
	946	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	947	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	948	if [[ ! -f $makefile ]]
	949	then
	950	printf "\n +++ file \"$makefile\" does not exist"
	951	locat=make; exit
	952	else
[2990]	953	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	954	fi
	955
	956
	957	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	958	if [[ "$user_source_path" != "" ]]
[2380]	959	then
	960
	961	# DOES THE DIRECTORY EXIST?
[2384]	962	if [[ ! -d $user_source_path ]]
[2380]	963	then
	964
	965	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	966	printf "\n \"$user_source_path\" "
[2380]	967	printf "\n does not exist or is not a directory."
	968	printf "\n No source code will be used from this directory!\n"
[2384]	969	user_source_path=""
[2380]	970	if [[ $silent == false ]]
	971	then
	972	sleep 2
	973	fi
	974
	975	else
	976
[2384]	977	cd $user_source_path
[2380]	978
	979	Names=$(ls -1 *.f90 2>&1)
	980	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	981	Names=$(ls -1 *.F90 2>&1)
	982	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	983	Names=$(ls -1 *.F 2>&1)
	984	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	985	Names=$(ls -1 *.f 2>&1)
	986	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	987	Names=$(ls -1 *.c 2>&1)
	988	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	989
	990	cd - > /dev/null
[2990]	991	cd ${base_directory}/${sources_for_run_catalog}
[2380]	992
	993	# COPY MAKEFILE IF EXISTING
[2384]	994	if [[ -f $user_source_path/Makefile ]]
[2380]	995	then
	996	printf "\n\n *** user Makefile from directory"
[2384]	997	printf "\n \"$user_source_path\" is used \n"
[2380]	998	if [[ $silent == false ]]
	999	then
	1000	sleep 1
	1001	fi
[2384]	1002	cp $user_source_path/Makefile .
[2380]	1003	fi
	1004
	1005	for filename in $AddFilenames
	1006	do
	1007	if [[ -f $filename ]]
	1008	then
	1009	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1010	printf "\n source code directory \"$user_source_path\" "
[2380]	1011	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1012	printf "\n from directory \"$source_path\"."
	1013	locat=source; exit
	1014	fi
	1015
[2384]	1016	cp $user_source_path/$filename .
[2380]	1017	source_list="$source_list $filename"
	1018
	1019	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1020	if [[ $(grep -c $filename Makefile) = 0 ]]
	1021	then
	1022	printf "\n\n +++ user file \"$filename\" "
	1023	printf "\n is not listed in Makefile \n"
	1024	locat=source; exit
	1025	fi
	1026	done
	1027	cd - > /dev/null
	1028	fi
	1029	fi
	1030
	1031	# COPY CONFIGURATION FILES
[2990]	1032	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1033	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1034
	1035	# COPY SHELLSCRIPTS
[2990]	1036	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1037	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1038
	1039	fi
	1040
	1041	fi
	1042
[2605]	1043
[2380]	1044	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1045	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1046	if [[ "$global_revision" = "" ]]
	1047	then
	1048	global_revision=`svnversion $source_path 2>/dev/null`
	1049	global_revision="Rev: $global_revision"
	1050	fi
	1051
	1052
	1053	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1054	if [[ -n $cores ]]
	1055	then
	1056
	1057	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1058	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1059	if [[ $tasks_per_node = 0 ]]
[2380]	1060	then
[3025]	1061	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1062	then
	1063	printf "\n"
	1064	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1065	printf "\n set -T option or define tasks_per_node in the config file"
	1066	locat=tasks_per_node; (( iec = 0 )); exit
	1067	else
	1068	# DEFAULT FOR INTERACTIVE RUN
	1069	tasks_per_node=$cores
	1070	fi
[2380]	1071	fi
	1072
	1073	if (( cores < tasks_per_node ))
	1074	then
	1075	printf "\n"
	1076	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1077	printf "\n given values: -T $tasks_per_node -X $cores"
	1078	locat=tasks_per_node; (( iec = 0 )); exit
	1079	fi
	1080
	1081	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1082	(( mpi_tasks = cores / threads_per_task ))
	1083	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1084	(( ii = cores / tasks_per_node ))
	1085	(( remaining_cores = cores - ii * tasks_per_node ))
	1086	if (( remaining_cores > 0 ))
	1087	then
	1088	printf "\n"
	1089	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1090	printf "\n divisor of the total number of cores (option \"-X\")"
	1091	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1092	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1093	(( nodes = nodes + 1 ))
	1094	fi
	1095
	1096	fi
	1097
	1098
	1099	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1100	if [[ "$maximum_parallel_io_streams" = "" ]]
	1101	then
	1102	maximum_parallel_io_streams=$cores
	1103	fi
	1104
	1105
	1106	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1107	if [[ "$scp_port" != "" ]]
	1108	then
	1109	PORTOPT="-P $scp_port"
	1110	SSH_PORTOPT="-p $scp_port"
	1111	fi
	1112
	1113
	1114	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1115	# CONFIG-FILE
	1116	if [[ "$ssh_key" != "" ]]
	1117	then
	1118	ssh_key="-i $HOME/.ssh/$ssh_key"
	1119	fi
	1120
	1121
	1122	# SET QUEUE, IF NOT GIVEN
	1123	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1124	then
	1125
	1126	if [[ $queue = none && "$defaultqueue" = "" ]]
	1127	then
	1128	printf "\n"
	1129	printf "\n +++ no default queue given in configuration file and no queue"
	1130	printf "\n given with option -q"
[2789]	1131	locat=queue; exit
[2380]	1132	fi
	1133	if [[ $queue = none ]]
	1134	then
	1135	queue=$defaultqueue
	1136	fi
	1137
	1138	fi
	1139
	1140
	1141	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1142	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1143	(( i = 0 ))
[2610]	1144	(( nr_of_input_files = 0 ))
[2380]	1145	while (( i < iin ))
	1146	do
	1147	(( i = i + 1 ))
	1148
	1149	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1150	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1151	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1152	then
[2610]	1153	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1154	else
[3236]	1155	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1156	fi
	1157
[2610]	1158
[2380]	1159	# CHECK IF FILE EXISTS
	1160	if ! ls $filename* 1>/dev/null 2>&1
	1161	then
	1162
[2669]	1163	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1164	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1165	then
	1166	printf "\n\n +++ INPUT-file: "
[2610]	1167	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1168	then
	1169	printf "\n $filename"
	1170	else
[2610]	1171	printf "\n $filename.${extin_pre[$i]}"
[2380]	1172	fi
	1173	printf "\n does not exist\n"
	1174	locat=input; exit
	1175	else
[2610]	1176	(( nr_of_input_files = nr_of_input_files + 1 ))
	1177	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1178	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1179	actionin[$nr_of_input_files]="unavailable"
[2610]	1180	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1181	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1182	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1183	fi
[2605]	1184
[2380]	1185	else
	1186
[3236]	1187	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1188	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1189	# ENDINGS
[2610]	1190	if [[ "${multin[$i]}" = true ]]
	1191	then
	1192	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1193	ls -1 -d ${filename} > filelist 2>/dev/null
	1194	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1195	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1196
[2610]	1197	endings=""
	1198	while read line
	1199	do
	1200	# filename without path (i.e. after the last "/")
	1201	basefilename=$(basename ${line})
[2380]	1202
[2610]	1203	# check if there is an extension and remove it
	1204	ext=${basefilename##*.}
	1205	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1206	then
	1207	basefilename=${basefilename%.*}
	1208	fi
[2380]	1209
[2610]	1210	# check for an existing cycle number and remove it
	1211	cycle=${basefilename##*.}
	1212	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1213	then
	1214	basefilename=${basefilename%.*}
	1215	fi
[2600]	1216
[3236]	1217	# remove the run_identifier from the beginning
	1218	length_run_identifier=${#run_identifier}
	1219	ending=${basefilename:${length_run_identifier}}
[2610]	1220
	1221	# remove the ending given in the .iofiles from the beginning
	1222	endingstring="${endin_pre[$i]}"
	1223	length_ending=${#endingstring}
	1224	ending=${ending:${length_ending}}
	1225
	1226	if [[ "$ending" = "" ]]
[2600]	1227	then
[2610]	1228	# standard ending as given in the .iofiles
	1229	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1230	then
	1231	endings="$endings DEFAULT"
	1232	fi
[2600]	1233	else
[2610]	1234	# ending must start with "_", otherwise its a different file
	1235	if [[ "${ending:0:1}" = "_" ]]
	1236	then
	1237	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1238	then
	1239	endings="$endings $ending"
	1240	fi
	1241	fi
[2600]	1242	fi
[2610]	1243
	1244	done <filelist
[2380]	1245
[2610]	1246	rm filelist
[2380]	1247
[2600]	1248	else
[2610]	1249
	1250	# SINGLE NAME
	1251	endings=DEFAULT
	1252
[2600]	1253	fi
	1254
[2610]	1255	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1256	for ending in $endings
	1257	do
	1258
	1259	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1260	if [[ $ending = DEFAULT ]]
[2380]	1261	then
[2610]	1262	ending=""
	1263	fi
	1264
	1265	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1266	(( nr_of_input_files = nr_of_input_files + 1 ))
	1267	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1268	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1269	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1270	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1271	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1272	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1273
	1274
	1275	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1276	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1277	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1278	then
	1279	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1280	else
[3236]	1281	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1282	fi
[2610]	1283
	1284	# DETERMINE THE FILE'S CYCLE NUMBER
	1285	(( maxcycle = 0 ))
	1286	ls -1 -d $filename > filelist 2>/dev/null
	1287	ls -1 -d $filename.* >> filelist 2>/dev/null
	1288	while read line
	1289	do
	1290	# filename without path (i.e. after the last "/")
	1291	basefilename=$(basename ${line})
	1292
	1293	# check if there is an extension
	1294	extension=${basefilename##*.}
	1295	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1296	then
	1297	basefilename=${basefilename%.*}
	1298	fi
	1299
	1300	# check for an existing cycle number
	1301	cycle=${basefilename##*.}
	1302	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1303	then
[2669]	1304	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1305	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1306	(( icycle = $((10#$cycle)) ))
[2610]	1307	else
	1308	(( icycle = 0 ))
	1309	fi
	1310
	1311	if (( icycle > maxcycle ))
	1312	then
	1313	(( maxcycle = icycle ))
	1314
	1315	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1316	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1317	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1318	then
	1319	leading_zero=true
	1320	else
	1321	leading_zero=false
	1322	fi
	1323	fi
	1324
	1325	done <filelist
	1326	rm filelist
	1327
	1328	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1329	if [[ $leading_zero = true ]]
[2380]	1330	then
[2610]	1331	cyclestring=`printf "%03d" $maxcycle`
	1332	else
	1333	cyclestring=$maxcycle
[2380]	1334	fi
[2610]	1335
	1336	# APPEND CYCLE NUMBER TO FILENAME
	1337	if (( maxcycle > 0 ))
[2380]	1338	then
[2610]	1339	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1340	then
	1341	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1342	else
	1343	filename=${filename}.$cyclestring
	1344	fi
[2380]	1345	else
[2610]	1346	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1347	then
	1348	filename=${filename}.${extin[$nr_of_input_files]}
	1349	fi
[2380]	1350	fi
[2610]	1351
	1352	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1353	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1354	absnamein[$nr_of_input_files]=$filename
	1355	if (( maxcycle > 0 ))
[2380]	1356	then
[2610]	1357	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1358	then
	1359	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1360	else
[3236]	1361	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1362	fi
[2380]	1363	else
[2610]	1364	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1365	then
	1366	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1367	else
[3236]	1368	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1369	fi
[2380]	1370	fi
	1371
[2610]	1372	done
	1373
[2380]	1374	fi
[2610]	1375
[2380]	1376	done
	1377
[2610]	1378
[2380]	1379	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1380	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1381	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1382	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1383	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1384	# REMOTE HOST)
	1385	(( i = 0 ))
	1386	while (( i < iout ))
	1387	do
	1388	(( i = i + 1 ))
[2610]	1389	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1390	then
[2610]	1391	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1392	then
[2610]	1393	actionout_pre[$i]=""
	1394	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1395	then
[2610]	1396	actionout_pre[$i]=pe
	1397	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1398	then
[2610]	1399	actionout_pre[$i]=a
[2380]	1400	fi
	1401	(( maxcycle = 0 ))
[3236]	1402	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1403	eval catalogname=${pathout_pre[$i]}
[2380]	1404	if ! ls $filename* 1>/dev/null 2>&1
	1405	then
	1406
	1407	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1408	if cat /dev/null > $filename
	1409	then
	1410	rm $filename
	1411	else
	1412
	1413	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1414	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1415	if [[ ! -d $catalogname ]]
	1416	then
	1417	if mkdir -p $catalogname
	1418	then
	1419	printf "\n\n *** directory:"
	1420	printf "\n $catalogname"
	1421	printf "\n was created\n"
	1422	else
	1423	printf "\n\n +++ OUTPUT-file:"
	1424	printf "\n $filename"
	1425	printf "\n cannot be created, because directory does not exist"
	1426	printf "\n and cannot be created either"
	1427	printf "\n"
	1428	locat=output ; exit
	1429	fi 2>/dev/null
	1430	else
	1431	printf "\n\n +++ OUTPUT-file:"
	1432	printf "\n $filename"
	1433	printf "\n cannot be created, although directory exists"
	1434	printf "\n"
	1435	locat=output ; exit
	1436	fi
	1437	fi 2>/dev/null
	1438
	1439	fi
	1440
	1441	fi
	1442	done
	1443
	1444
	1445	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1446	if [[ $running_in_batch_mode = false ]]
	1447	then
[3236]	1448	run_id_number=$RANDOM
	1449	run_id=${run_identifier}.$run_id_number
[2380]	1450
[3236]	1451	tempdir=$fast_io_catalog/$run_id
[2380]	1452	fi
	1453
	1454
	1455	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1456	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1457	then
	1458
	1459	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1460	if [[ $ibd = 0 ]]
	1461	then
	1462	printf "\n"
	1463	printf "\n +++ no batch directives found in configuration file"
	1464	locat=config_file_batch_directives; (( iec = 0 )); exit
	1465	fi
	1466
	1467	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1468	done=false
[2384]	1469	cputime=$cpumax
[2380]	1470	while [[ $done = false ]]
	1471	do
[2384]	1472	if (( cputime == 0 ))
[2380]	1473	then
	1474	printf "\n +++ cpu-time is undefined"
	1475	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1476	printf "\n >>> "
[2384]	1477	read cputime 1>/dev/null 2>&1
[2380]	1478	else
	1479	done=true
	1480	fi
	1481	done
[2420]	1482	cpumax=$cputime
[2380]	1483
	1484	# CHECK THE MEMORY DEMAND
	1485	done=false
	1486	while [[ $done = false ]]
	1487	do
	1488	if (( memory == 0 ))
	1489	then
	1490	printf "\n +++ memory demand is undefined"
	1491	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1492	printf "\n >>> "
	1493	read memory 1>/dev/null 2>&1
	1494	else
	1495	done=true
	1496	fi
	1497	done
	1498
	1499	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1500	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1501	then
	1502	while [[ -z $remote_username ]]
	1503	do
[2420]	1504	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1505	printf "\n >>> Please type username:"
	1506	printf "\n >>> "
	1507	read remote_username
	1508	done
	1509	fi
	1510
	1511	else
	1512
[2420]	1513	if [[ $running_in_batch_mode = false ]]
	1514	then
	1515	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1516	cpumax=$cputime
	1517	else
	1518	cputime=$cpumax
	1519	fi
[2380]	1520
	1521	fi
	1522
	1523
	1524	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1525	(( cpu_hours = cputime / 3600 ))
	1526	(( resttime = cputime - cpu_hours * 3600 ))
	1527	(( cpu_minutes = resttime / 60 ))
	1528	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1529	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1530
	1531
	1532	# OUTPUT OF THE PALMRUN-HEADER
	1533	calltime=$(date)
	1534	printf "\n"
	1535	printf "#------------------------------------------------------------------------# \n"
	1536	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1537	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1538	printf "\| \| \n"
	1539	column1="called on:"; column2=$(hostname)
	1540	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1541	if [[ $create_remote_batch_job = true ]]
	1542	then
[3236]	1543	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1544	else
	1545	if [[ $running_on_remote = true ]]
	1546	then
[3236]	1547	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1548	else
[3236]	1549	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1550	fi
	1551	fi
	1552	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1553
	1554	column1="running in:"
	1555	if [[ $running_in_batch_mode = true ]]
	1556	then
	1557	column2="batch job mode"
	1558	else
	1559	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1560	then
	1561	column2="job creation mode"
	1562	else
	1563	column2="interactive run mode"
	1564	fi
	1565	fi
	1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1567
[2479]	1568	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1569	then
[2480]	1570	if [[ "$project_account" != "" ]]
[2479]	1571	then
	1572	column1="project account number:"
	1573	column2="$project_account"
	1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1575	fi
	1576	fi
	1577
[2380]	1578	if [[ -n $cores ]]
	1579	then
	1580	if [[ $run_coupled_model = false ]]
	1581	then
	1582	column1="number of cores:"; column2=$cores
	1583	else
	1584	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1585	fi
	1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1587	fi
	1588	if [[ -n $tasks_per_node ]]
	1589	then
	1590	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1592	if (( remaining_cores > 0 ))
	1593	then
	1594	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1596	fi
	1597	fi
	1598	if [[ $maximum_parallel_io_streams != $cores ]]
	1599	then
	1600	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1601	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1602	fi
	1603	if [[ $use_openmp = true ]]
	1604	then
	1605	column1="threads per task:"; column2="$threads_per_task"
	1606	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1607	fi
[2384]	1608	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1609	then
[2506]	1610	column1="memory demand / PE":; column2="$memory MB"
	1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1612	column1="job cpu time (h:m:s):"; column2="$timestring"
	1613	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1614	fi
[2380]	1615	printf "\| \| \n"
	1616	if [[ "$source_list" != "" ]]
	1617	then
	1618	if [[ "$make_options" != "" ]]
	1619	then
	1620	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1622	line=$(echo "$make_options" \| cut -c46-)
	1623	while [[ "$line" != "" ]]
	1624	do
	1625	column1=""
	1626	column2=$(echo "$line" \| cut -c-45)
	1627	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1628	line=$(echo "$line" \| cut -c46-)
	1629	done
	1630	fi
	1631	fi
	1632
	1633	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1635	line=$(echo "$cpp_options" \| cut -c46-)
	1636	while [[ "$line" != "" ]]
	1637	do
	1638	column1=""
	1639	column2=$(echo "$line" \| cut -c-45)
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	line=$(echo "$line" \| cut -c46-)
	1642	done
	1643
	1644	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1646	line=$(echo "$compiler_options" \| cut -c46-)
	1647	while [[ "$line" != "" ]]
	1648	do
	1649	column1=""
	1650	column2=$(echo "$line" \| cut -c-45)
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	line=$(echo "$line" \| cut -c46-)
	1653	done
	1654
[2388]	1655	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1657	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1658	while [[ "$line" != "" ]]
	1659	do
	1660	column1=""
	1661	column2=$(echo "$line" \| cut -c-45)
	1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1663	line=$(echo "$line" \| cut -c46-)
	1664	done
	1665
	1666	if [[ "$login_init_cmd" != "" ]]
	1667	then
	1668	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1669	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1670	line=$(echo "$login_init_cmd" \| cut -c46-)
	1671	while [[ "$line" != "" ]]
	1672	do
	1673	column1=""
	1674	column2=$(echo "$line" \| cut -c-45)
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	line=$(echo "$line" \| cut -c46-)
	1677	done
	1678	fi
	1679
	1680	if [[ "$module_commands" != "" ]]
	1681	then
	1682	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1683	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1684	line=$(echo "$module_commands" \| cut -c46-)
	1685	while [[ "$line" != "" ]]
	1686	do
	1687	column1=""
	1688	column2=$(echo "$line" \| cut -c-45)
	1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1690	line=$(echo "$line" \| cut -c46-)
	1691	done
	1692	fi
	1693	printf "\| \| \n"
[3236]	1694	column1="run identifier:"; column2=$run_identifier
[2380]	1695	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1696	column1="activation string list:"; column2=$(echo $activation_string_list)
	1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1698
	1699	if [[ "$ocean_file_appendix" = true ]]
	1700	then
	1701	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1702	fi
	1703
	1704	if [[ "$source_list" != "" ]]
	1705	then
	1706	printf "\| \| \n"
	1707	printf "\| Files to be compiled: \| \n"
	1708	line=$source_list
	1709	while [[ "$line" != "" ]]
	1710	do
	1711	linestart=$(echo $line \| cut -c-70)
	1712	printf "\| %-70s \| \n" "$linestart"
	1713	line=$(echo "$line" \| cut -c71-)
	1714	done
	1715	fi
	1716	printf "#------------------------------------------------------------------------#"
	1717
	1718
	1719
	1720	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1721	if [[ $do_trace = true ]]
	1722	then
	1723	(( i = 0 ))
[2610]	1724	while (( i < nr_of_input_files ))
[2380]	1725	do
	1726	(( i = i + 1 ))
	1727	if (( i == 1 ))
	1728	then
	1729	printf "\n\n >>> INPUT-file assignments:\n"
	1730	fi
	1731	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1732	done
	1733	(( i = 0 ))
	1734	while (( i < iout ))
	1735	do
	1736	(( i = i + 1 ))
	1737	if (( i == 1 ))
	1738	then
	1739	printf "\n\n >>> OUTPUT-file assignments:\n"
	1740	fi
	1741	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1742	done
	1743	(( i = 0 ))
	1744	while (( i < iic ))
	1745	do
	1746	(( i = i + 1 ))
	1747	if (( i == 1 ))
	1748	then
	1749	printf "\n\n >>> INPUT-commands:\n"
	1750	fi
	1751	printf "\n ${in_command[$i]}"
	1752	done
	1753	(( i = 0 ))
	1754	while (( i < ioc ))
	1755	do
	1756	(( i = i + 1 ))
	1757	if (( i == 1 ))
	1758	then
	1759	printf "\n\n >>> OUTPUT-commands:\n"
	1760	fi
	1761	printf "\n ${out_command[$i]}"
	1762	done
	1763	fi
	1764
	1765	# QUERY FOR CONTINUE
	1766	if [[ $silent = false && $running_in_batch_mode = false ]]
	1767	then
	1768	antwort=dummy
	1769	printf "\n\n"
	1770	printf " >>> everything o.k. (y/n) ? "
	1771	while read antwort
	1772	do
	1773	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1774	then
	1775	printf " >>> everything o.k. (y/n) ? "
	1776	else
	1777	break
	1778	fi
	1779	done
	1780	if [[ $antwort = n \|\| $antwort = N ]]
	1781	then
	1782	locat=user_abort; (( iec = 0 )); exit
	1783	fi
	1784	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1785	then
[2566]	1786	printf "\n *** batch-job will be created and submitted"
[2380]	1787	else
[2566]	1788	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1789	fi
	1790	fi
	1791
	1792
	1793
	1794	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1795	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1796	then
	1797
	1798	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1799	then
[2566]	1800	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1801	else
[2566]	1802	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1803	fi
	1804
[2422]	1805	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1806	# IT SHALL BE CREATED
	1807	ask_for_make_depository=false
	1808	if [[ $create_remote_batch_job = true ]]
	1809	then
	1810
	1811	line=`grep %base_directory $config_file`
[3236]	1812	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1813	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1814
[3236]	1815	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1816	then
	1817	printf "\n\n +++ make depository \"${make_depository}\""
	1818	printf "\n on remote host not found!"
	1819	ask_for_make_depository=true
	1820	fi
[3236]	1821	rm ${configuration_identifier}_last_make_protokoll
[2422]	1822
	1823	else
	1824
	1825	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1826	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1827	if [[ ! -d ${make_depository} ]]
	1828	then
	1829	printf "\n\n +++ make depository \"${make_depository}\""
	1830	printf "\n on local host not found!"
	1831	ask_for_make_depository=true
	1832	fi
	1833
	1834	fi
	1835
	1836	if [[ $ask_for_make_depository = true ]]
	1837	then
	1838
	1839	antwort=dummy
	1840	printf "\n\n"
	1841	printf " >>> Create a new one (y/n) ? "
	1842	while read antwort
	1843	do
	1844	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1845	then
	1846	printf " >>> Create a new one (y/n) ? "
	1847	else
	1848	break
	1849	fi
	1850	done
	1851	if [[ $antwort = n \|\| $antwort = N ]]
	1852	then
	1853	locat=user_abort; (( iec = 0 )); exit
	1854	fi
	1855
[2566]	1856	if [[ $do_trace = true ]]
	1857	then
[3236]	1858	palmbuild -h $configuration_identifier
[2566]	1859	else
[3236]	1860	palmbuild -v -h $configuration_identifier
[2566]	1861	fi
[2422]	1862
	1863	if [[ $? != 0 ]]
	1864	then
	1865
	1866	# ABORT IN CASE OF COMPILATION PROBLEMS
	1867	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1868	locat=make_depository
	1869	exit
	1870	else
	1871	echo " *** now continue with creating executable and other sources"
	1872	fi
	1873
	1874	fi
	1875
[2566]	1876	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3236]	1877	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
[2380]	1878
	1879	if [[ $? != 0 ]]
	1880	then
	1881
	1882	# ABORT IN CASE OF COMPILATION PROBLEMS
	1883	printf "\n +++ error while creating executable and/or other sources"
	1884	locat=execution
[2990]	1885	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1886	exit
	1887
	1888	else
	1889
[2566]	1890	printf " *** executable and other sources created\n"
[2990]	1891	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1892
	1893	fi
	1894
	1895	fi
	1896
	1897
[2669]	1898	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1899	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1900	if [[ $create_remote_batch_job = true ]]
	1901	then
	1902	(( i = 0 ))
[2610]	1903	while (( i < nr_of_input_files ))
[2605]	1904	do
	1905	(( i = i + 1 ))
[2669]	1906	if [[ "${actionin[$i]}" = tr ]]
[2605]	1907	then
	1908	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1909	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1910	fi
	1911	done
	1912	if (( i > 0 ))
	1913	then
[3025]	1914	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1915	fi
	1916	fi
	1917
	1918
[2380]	1919	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1920	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1921	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1922	then
	1923
	1924	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1925	if [[ $running_in_batch_mode = false ]]
	1926	then
	1927	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1928	# FOLDER
[2566]	1929	mkdir -p $tempdir
	1930	chmod go+rx $tempdir
	1931	cd $tempdir
	1932	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1933	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1934
	1935	else
	1936
	1937	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1938	printf "\n *** running in temporary directory: $tempdir"
[2380]	1939
	1940	fi
	1941
	1942
	1943	# PROVIDE THE INPUT FILES
	1944	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1945	optional_files_missing=false
[2380]	1946	(( i = 0 ))
[2610]	1947	while (( i < nr_of_input_files ))
[2380]	1948	do
	1949	(( i = i + 1 ))
	1950	if (( i == 1 ))
	1951	then
	1952	printf "\n\n *** providing INPUT-files:\n$dashes"
	1953	fi
	1954
	1955
	1956	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1957	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1958	then
[2669]	1959	optional_files_missing=true
[2380]	1960	continue
	1961	fi
	1962
	1963	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1964	files_for_cores=false; filetype=file
	1965	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1966	then
	1967	files_for_cores=true; filetype=files
	1968	actionin[$i]=""
	1969	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1970	then
	1971	actionin[$i]=""
	1972	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1973	then
	1974	files_for_cores=true; filetype=files
	1975	actionin[$i]="ln"
	1976	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1977	then
	1978	actionin[$i]="ln"
	1979	fi
	1980
	1981	if [[ $files_for_cores = true ]]
	1982	then
	1983	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1984	else
	1985	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1986	fi
	1987
	1988	# INPUT-FILES TO BE LINKED
	1989	if [[ "${actionin[$i]}" = ln ]]
	1990	then
	1991
	1992	printf "\n $filetype will be linked"
	1993	if [[ $files_for_cores = false ]]
	1994	then
	1995	if [[ -f "${absnamein[$i]}" ]]
	1996	then
	1997	ln ${absnamein[$i]} ${localin[$i]}
	1998	got_tmp[$i]=true
	1999	fi
	2000	else
	2001	if [[ -d "${absnamein[$i]}" ]]
	2002	then
[2396]	2003	mkdir -p ${localin[$i]}
[2380]	2004	cd ${absnamein[$i]}
	2005	for file in $(ls *)
	2006	do
[2566]	2007	ln $file $tempdir/${localin[$i]}
[2380]	2008	done >\|/dev/null 2>&1
[2566]	2009	cd $tempdir
[2380]	2010	fi
	2011
	2012	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2013	if [[ ! -f "${localin[$i]}/_000000" ]]
	2014	then
	2015	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2016	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2017	fi
	2018
	2019	got_tmp[$i]=true
	2020	fi
	2021	fi
	2022
	2023	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2024	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2025	then
	2026
	2027	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2028	then
	2029
	2030	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2031	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2032	printf "\n file will be provided for $cores processors"
[2396]	2033	mkdir -p ${localin[$i]}
[2380]	2034	ival=$cores
	2035	(( ii = 0 ))
	2036	while (( ii <= ival-1 ))
	2037	do
	2038	if (( ii < 10 ))
	2039	then
	2040	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2041	elif (( ii < 100 ))
	2042	then
	2043	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2044	elif (( ii < 1000 ))
	2045	then
	2046	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2047	else
	2048	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2049	fi
	2050	(( ii = ii + 1 ))
	2051	done
	2052
	2053	else
	2054
	2055	if [[ $files_for_cores = true ]]
	2056	then
	2057
	2058	# PROVIDE FILES FOR EACH CORE
	2059	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2060	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2061	printf "\n providing $cores files for the respective cores"
[2396]	2062	mkdir -p ${localin[$i]}
[2380]	2063	if [[ $link_local_input = true ]]
	2064	then
	2065	printf " files will be linked\n"
	2066	cd ${absnamein[$i]}
	2067	for file in $(ls *)
	2068	do
	2069	ln -f $file ${localin[$i]}
	2070	done
[2566]	2071	cd $tempdir
[2380]	2072	fi
	2073
	2074	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2075	if [[ ! -f "${localin[$i]}/_000000" ]]
	2076	then
	2077	if [[ $link_local_input = true ]]
	2078	then
	2079	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2080	fi
	2081	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2082	fi
	2083
	2084	else
	2085
	2086	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2087	if [[ $link_local_input = true ]]
	2088	then
	2089	printf " file will be linked\n"
	2090	ln -f ${absnamein[$i]} ${localin[$i]}
	2091	fi
[2605]	2092	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2093	if [[ ! -f "${localin[$i]}" ]]
	2094	then
	2095	if [[ $link_local_input = true ]]
	2096	then
	2097	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2098	fi
[2669]	2099	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2100	then
	2101	mv ${absnamein[$i]} ${localin[$i]}
	2102	else
	2103	cp ${absnamein[$i]} ${localin[$i]}
	2104	fi
[2380]	2105	fi
	2106	fi
	2107	fi
	2108	fi
	2109
	2110	done
	2111	if (( i != 0 ))
	2112	then
[2669]	2113	if [[ $optional_files_missing = true ]]
	2114	then
	2115	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2116	fi
[2380]	2117	printf "\n$dashes\n *** all INPUT-files provided \n"
	2118	fi
	2119
	2120
	2121	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2122	(( i = 0 ))
	2123	while (( i < iic ))
	2124	do
	2125	(( i = i + 1 ))
	2126	if (( i == 1 ))
	2127	then
	2128	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2129	fi
	2130	printf "\n >>> ${in_command[$i]}"
	2131	eval ${in_command[$i]}
	2132	if (( i == iic ))
	2133	then
	2134	printf "\n$dashes\n"
	2135	fi
	2136	done
	2137
	2138
	2139	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2140	# (FILE ENVPAR WILL BE READ BY PALM)
	2141	cat > ENVPAR << EOF
[3236]	2142	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2143	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2144	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2145	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2146	maximum_cpu_time_allowed = ${cpumax}.,
	2147	revision = '$global_revision',
	2148	batch_job = .${running_in_batch_mode}. /
	2149
	2150	EOF
	2151
	2152
	2153	# STARTING THE EXECUTABLE
	2154	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2155	PATH=$PATH:$tempdir
[2380]	2156
	2157
	2158	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2159	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2160	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2161	eval line=\"$line\"
	2162	execute_command="$line"
	2163
	2164
	2165	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2166	if [[ "$execute_command_for_combine" = "" ]]
	2167	then
	2168	eval line2=\"$line2\"
	2169	execute_command_for_combine="$line2"
	2170	fi
	2171
[2380]	2172
	2173
	2174	# PROVIDE A HOSTFILE, IF REQUIRED
	2175	if [[ "$hostfile" != "" ]]
	2176	then
	2177
	2178	if [[ $hostfile = auto ]]
	2179	then
	2180	# CREATE A NEW HOSTFILE
	2181	(( ii = 1 ))
	2182	while (( ii <= cores / threads_per_task ))
	2183	do
	2184	echo $(hostname) >> hostfile
	2185	(( ii = ii + 1 ))
	2186	done
	2187	if (( cores / threads_per_task == 0 ))
	2188	then
	2189	echo $(hostname) >> hostfile
	2190	fi
	2191
	2192	else
	2193	cp $hostfile hostfile
	2194	fi
	2195	eval line=\"`head -n $ii hostfile`\"
	2196	printf "\n *** running on: $line"
	2197	fi
	2198
	2199
	2200
	2201	# SET THE NUMBER OF OPENMP-THREADS
	2202	if [[ $use_openmp = true ]]
	2203	then
	2204	export OMP_NUM_THREADS=$threads_per_task
	2205	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2206	else
	2207	export OMP_NUM_THREADS=1
	2208	fi
	2209
	2210
[2610]	2211	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2212	if [[ $run_coupled_model = false ]]
	2213	then
	2214	if [[ "$ocean_file_appendix" = true ]]
	2215	then
	2216	echo "precursor_ocean" > coupling_steering
	2217	else
	2218	echo "precursor_atmos" > coupling_steering
	2219	fi
	2220	else
	2221	(( iia = $cores_atmos / $threads_per_task ))
	2222	(( iio = $cores_ocean / $threads_per_task ))
	2223	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2224	printf "\n\n"
	2225	echo "coupled_run $iia $iio" > coupling_steering
	2226	fi
	2227
	2228	printf "\n *** execute command:"
	2229	printf "\n \"$execute_command\" \n\n"
	2230
	2231	$execute_command < coupling_steering
	2232
	2233	if [[ $? != 0 ]]
	2234	then
	2235
	2236	# ABORT IN CASE OF RUNTIME ERRORS
	2237	printf "\n +++ runtime error occured"
	2238	locat=execution
	2239	exit
	2240
	2241	else
	2242
	2243	printf "\n$dashes\n *** execution finished \n"
	2244
	2245	fi
	2246
	2247
	2248	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2249	# BY EACH CORE INTO ONE FILE
	2250	if [[ ! -f combine_plot_fields.x ]]
	2251	then
	2252
	2253	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2254	printf "\n 2d- and/or 3d-data may be incomplete!"
	2255	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2256
	2257	elif [[ "$combine_plot_fields" == true ]]
	2258	then
	2259
	2260	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2261	$execute_command_for_combine
	2262
	2263	else
	2264
	2265	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2266	# DATA OUTPUT
[2380]	2267	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2268	fi
	2269
	2270
	2271
	2272	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2273	(( i = 0 ))
	2274	while (( i < ioc ))
	2275	do
	2276	(( i = i + 1 ))
	2277	if (( i == 1 ))
	2278	then
	2279	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2280	fi
[2799]	2281
	2282	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2283	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2284
[2380]	2285	printf "\n >>> ${out_command[$i]}"
	2286	eval ${out_command[$i]}
	2287	if (( i == ioc ))
	2288	then
	2289	printf "\n$dashes\n"
	2290	fi
	2291	done
	2292
	2293
[2610]	2294	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2295	# WILDCARDS
[2380]	2296	(( i = 0 ))
[2610]	2297	(( nr_of_output_files = 0 ))
	2298
[2380]	2299	while (( i < iout ))
	2300	do
[2610]	2301
[2380]	2302	(( i = i + 1 ))
[2610]	2303
	2304	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2305	# CREATE A LIST FOR THE DETECTED ENDINGS
	2306	if [[ "${multout[$i]}" = true ]]
	2307	then
	2308	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2309	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2310	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2311
	2312	endings="DEFAULT"
	2313	while read line
	2314	do
	2315	# remove the local name from the beginning
	2316	localnamestring="${localout_pre[$i]}"
	2317	length_localname=${#localnamestring}
	2318	ending=${line:${length_localname}}
	2319
	2320	if [[ "$ending" != "" ]]
	2321	then
	2322	endings="$endings $ending"
	2323	fi
	2324
	2325	done <filelist
	2326
	2327	rm filelist
	2328
	2329	else
	2330
	2331	# SINGLE NAME
	2332	endings=DEFAULT
	2333
	2334	fi
	2335
	2336	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2337	for ending in $endings
	2338	do
	2339
	2340	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2341	if [[ $ending = DEFAULT ]]
	2342	then
	2343	ending=""
	2344	fi
	2345
	2346	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2347	(( nr_of_output_files = nr_of_output_files + 1 ))
	2348	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2349	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2350	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2351	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2352	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2353	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2354	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2355
	2356	done
	2357
	2358	done
	2359
	2360
	2361
	2362
	2363	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2364	(( i = 0 ))
	2365	while (( i < nr_of_output_files ))
	2366	do
	2367	(( i = i + 1 ))
[2380]	2368	if (( i == 1 ))
	2369	then
	2370	printf "\n\n *** saving OUTPUT-files:"
	2371
	2372	# GET RUN NUMBER ASSIGNED BY PALM
	2373	if [[ -f RUN_NUMBER ]]
	2374	then
	2375	read run_number < RUN_NUMBER
	2376	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2377	usecycle_option="-U $run_number"
	2378	else
	2379	run_number=0
	2380	usecycle_option=""
	2381	fi
	2382	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2383	then
[2404]	2384	printf "\n *** in case of SCP transfers to local host"
	2385	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2386	fi
	2387	printf "\n$dashes"
	2388	fi
	2389
	2390	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2391	then
	2392
[3236]	2393	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2394
	2395	# DETERMINE THE CYCLE NUMBER
	2396	ls -1 -d $filename > filelist 2>/dev/null
	2397	ls -1 -d $filename.* >> filelist 2>/dev/null
	2398	while read line
	2399	do
	2400
	2401	# filename without path (i.e. after the last "/")
	2402	basefilename=$(basename ${line})
	2403
	2404	# check if there is an extension
	2405	extension=${basefilename##*.}
	2406	if [[ "$extension" = "${extout[$i]}" ]]
	2407	then
	2408	basefilename=${basefilename%.*}
	2409	fi
	2410
	2411	# check for an existing cycle number
	2412	cycle=${basefilename##*.}
	2413	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2414	then
[2669]	2415	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2416	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2417	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2418	else
	2419	(( icycle = 1 ))
	2420	fi
	2421
	2422	if (( icycle > maxcycle ))
	2423	then
	2424	(( maxcycle = icycle ))
	2425	fi
	2426
	2427	done <filelist
	2428	rm filelist
	2429
	2430
	2431	# SET THE CYCLE NUMBER
	2432	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2433	if [[ "${actionout[$i]}" = a ]]
	2434	then
	2435	(( maxcycle = maxcycle - 1 ))
	2436	fi
	2437
	2438	(( cycnum[$i] = maxcycle ))
	2439	pathout[$i]=$filename
	2440
	2441
	2442	# ADD CYCLE NUMBER TO FILENAME
	2443	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2444	if [[ "${actionout[$i]}" != "a" ]]
	2445	then
	2446	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2447	# WITH AN EXISTING CYCLE NUMBER
	2448	if (( run_number >= cycnum[$i] ))
	2449	then
	2450	(( cycnum[$i] = run_number ))
	2451	else
	2452	if (( run_number > 0 ))
	2453	then
	2454	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2455	fi
	2456	fi
	2457	fi
	2458	if (( cycnum[$i] > 0 ))
	2459	then
[2600]	2460	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2461	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2462	fi
	2463	fi
	2464
	2465	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2466	files_for_cores=false; filetype=file
	2467	link_local_output=false
	2468	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2469	then
	2470	files_for_cores=true; filetype=directory
	2471	actionout[$i]=""
	2472	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2473	then
	2474	actionout[$i]=""
	2475	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2476	then
	2477	files_for_cores=true; filetype=directory
	2478	link_local_output=true
	2479	actionout[$i]=""
	2480	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2481	then
	2482	link_local_output
	2483	actionout[$i]=""
	2484	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2485	then
	2486	files_for_cores=true; filetype=directory
	2487	actionout[$i]="tr"
	2488	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2489	then
	2490	actionout[$i]="tr"
	2491	fi
	2492
	2493	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2494	then
[2669]	2495	if [[ ${warnout[$i]} = true ]]
	2496	then
	2497	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2498	fi
[2380]	2499	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2500	then
[2669]	2501	if [[ ${warnout[$i]} = true ]]
	2502	then
	2503	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2504	fi
[2380]	2505	else
	2506
	2507
	2508	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2509	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2510	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2511	then
	2512	if [[ $running_on_remote = true ]]
	2513	then
	2514
	2515	# SET OPTIONS FOR TRANSFER
	2516	if [[ "${actionout[$i]}" = tr ]]
	2517	then
	2518	if [[ $files_for_cores = false ]]
	2519	then
	2520	catalog_option=""
	2521	catalog_string=""
	2522	else
	2523	catalog_option="-c"
	2524	catalog_string="/"
	2525	fi
	2526	append_option=""
	2527	append_string=""
	2528	else
	2529	append_option="-A"
	2530	append_string="append"
	2531	fi
	2532
	2533	transfer_failed=false
	2534	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2535	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2536
	2537	# TRANSFER VIA SCP
	2538	if [[ "$remote_loginnode" != "" ]]
	2539	then
[3236]	2540	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2541	else
[3236]	2542	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
[2380]	2543	fi
	2544	[[ $? != 0 ]] && transfer_failed=true
	2545
	2546
	2547	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2548	if [[ $transfer_failed = true ]]
	2549	then
	2550	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2551	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2552
	2553	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2554	eval local_catalog=${pathout[$i]}
	2555	if [[ ! -d $local_catalog ]]
	2556	then
	2557	printf " *** local directory does not exist. Trying to create:\n"
	2558	printf " $local_catalog \n"
	2559	mkdir -p $local_catalog
	2560	fi
[3236]	2561	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2562	transfer_problems=true
	2563	fi
	2564
	2565	else
	2566
	2567	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2568	# BE COPIED OR APPENDED ON THIS MACHINE
	2569	if [[ "${actionout[$i]}" = tr ]]
	2570	then
	2571	actionout[$i]=""
	2572	else
	2573	actionout[$i]="a"
	2574	fi
	2575	fi
	2576	fi
	2577
	2578
	2579	# APPEND ON THIS MACHINE
	2580	if [[ "${actionout[$i]}" = "a" ]]
	2581	then
	2582	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2583	then
	2584	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2585	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2586	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2587	else
	2588	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2589	printf "\n ${pathout[$i]}\n"
	2590	cat ${localout[$i]} >> ${pathout[$i]}
	2591	fi
	2592	fi
	2593
	2594	# COPY ON THIS MACHINE
	2595	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2596	# ON DIFFERENT FILE-SYSTEMS
	2597	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2598	then
	2599
	2600	# COPY IN CASE OF RUNS ON SINGLE CORES
	2601	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2602	then
	2603	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2604	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2605	if [[ $link_local_output = true ]]
	2606	then
	2607	printf " file will be linked\n"
	2608	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2609	fi
	2610	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2611	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2612	then
	2613	if [[ $link_local_output = true ]]
	2614	then
	2615	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2616	fi
	2617	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2618	else
	2619	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2620	fi
	2621	else
	2622	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2623	printf "\n ${pathout[$i]}\n"
	2624	if [[ $link_local_output = true ]]
	2625	then
	2626	printf " file will be linked\n"
	2627	ln -f ${localout[$i]} ${pathout[$i]}
	2628	fi
	2629	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2630	if [[ ! -f "${pathout[$i]}" ]]
	2631	then
	2632	if [[ $link_local_output = true ]]
	2633	then
	2634	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2635	fi
	2636	cp ${localout[$i]} ${pathout[$i]}
	2637	else
	2638	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2639	fi
	2640	fi
	2641
	2642	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2643	then
	2644
	2645	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2646	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2647	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2648	printf "\n ${pathout[$i]}\n"
	2649	if [[ $link_local_output = true ]]
	2650	then
	2651	printf " files will be linked\n"
[2396]	2652	mkdir -p ${pathout[$i]}
[2380]	2653	cd ${localout[$i]}
	2654	for file in $(ls *)
	2655	do
	2656	ln -f $file ${pathout[$i]}
	2657	done >\|/dev/null 2>&1
[2566]	2658	cd $tempdir
[2380]	2659	fi
	2660
	2661	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2662	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2663	then
	2664	if [[ $link_local_output = true ]]
	2665	then
	2666	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2667	fi
[3025]	2668	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2669	cp -r ${localout[$i]}/* ${pathout[$i]}
	2670	fi
	2671
	2672	fi
	2673	fi
	2674	done
	2675
	2676	if (( i != 0 ))
	2677	then
	2678	if [[ $transfer_problems = true ]]
	2679	then
	2680	printf "\n$dashes\n *** OUTPUT-files saved"
	2681	printf "\n +++ WARNING: some data transfers failed! \n"
	2682	else
	2683	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2684	fi
	2685	fi
	2686
	2687
	2688	# IF REQUIRED, START A RESTART-JOB
	2689	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2690	if [[ -f CONTINUE_RUN ]]
	2691	then
	2692
	2693	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2694	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2695	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2696	# -b START A BATCH JOB
	2697	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2698	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2699	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2700
[2957]	2701	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2702	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2703	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2704	then
	2705	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2706	fi
[2380]	2707
	2708	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2709	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2710	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2711	then
[2381]	2712	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2713	fi
	2714
	2715
	2716	# START THE RESTART-JOB
	2717	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2718	echo " $prc"
	2719	printf "\n$dashes\n"
	2720	if [[ $running_on_remote = true ]]
	2721	then
	2722
	2723	echo "*** ssh will be used to initiate restart-runs!"
	2724	echo " return_address=\"$return_address\" "
	2725	echo " return_username=\"$local_username\" "
	2726
	2727	if [[ "$remote_loginnode" != "" ]]
	2728	then
[3132]	2729	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode \| tee palmrun_restart.log
[2380]	2730	else
[3132]	2731	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2732	fi
	2733
	2734	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2735	sleep 30
	2736
	2737	else
	2738
	2739	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2740	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2741	cd - > /dev/null
	2742
	2743	fi
	2744
[3132]	2745	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2746	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2747	then
	2748	printf "\n$dashes\n +++ creating restart run failed \n"
	2749	locat=create_restart
	2750	exit
	2751	rm palmrun_restart.log
	2752	else
	2753	printf "\n$dashes\n *** restart run initiated \n"
	2754	rm palmrun_restart.log
	2755	fi
[2380]	2756
[3132]	2757
[2380]	2758	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2759	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2760	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2761	# MAY BE VERY HUGE)
	2762	(( i = 0 ))
[2610]	2763	while (( i < nr_of_input_files ))
[2380]	2764	do
	2765	(( i = i + 1 ))
	2766	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2767	then
	2768	rm -r ${absnamein[$i]}
	2769	fi
	2770	done
	2771
	2772	fi
	2773
	2774
	2775	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2776	cd $HOME
[2566]	2777	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2778
	2779
	2780	else
	2781
	2782
	2783	# PREPARING ACTIONS,
	2784	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2785
	2786	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3236]	2787	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2788	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2789	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2790	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2791	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2792	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2793	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2794	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2795	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2796	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2797	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2798	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2799	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2800	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2801	if [[ $create_remote_batch_job = true ]]
	2802	then
	2803	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2804	if [[ $do_trace = true ]]
	2805	then
	2806	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2807	fi
[2380]	2808	elif [[ $create_batch_job = true ]]
	2809	then
	2810	palmrun_com=${palmrun_com}" -j"
[2420]	2811	if [[ $do_trace = true ]]
	2812	then
	2813	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2814	fi
[2380]	2815	fi
	2816
	2817
	2818	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2819	# REMOTE HOST
[3236]	2820	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2821	job_protocol_file=$job_protocol_file_local
	2822	if [[ $create_remote_batch_job = true ]]
	2823	then
[3236]	2824	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2825	job_protocol_file=$job_protocol_file_remote
	2826	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2827	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2828	fi
	2829
	2830
	2831	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2832	jobfile=jobfile.$run_id_number
[2380]	2833
	2834
	2835	# FIRST CREATE THE BATCH DIRECTIVES
	2836	(( i = 0 ))
	2837	while (( i < ibd ))
	2838	do
	2839	(( i = i + 1 ))
[2693]	2840	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2841	eval line=\"$line\"
	2842	echo "$line" >> $jobfile
	2843	done
	2844	echo " " >> $jobfile
	2845
	2846
	2847	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2848	# PROTOCOL
	2849	if [[ $create_remote_batch_job = true ]]
	2850	then
[3236]	2851	echo "set +vx" >> $jobfile
	2852	echo "trap '" >> $jobfile
	2853	echo "set +vx" >> $jobfile
	2854	echo "cd ${remote_jobcatalog}" >> $jobfile
	2855	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2856
	2857	# ADD THE BATCH DIRECTIVES
	2858	(( i = 0 ))
	2859	while (( i < ibdt ))
	2860	do
	2861	(( i = i + 1 ))
[2693]	2862	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2863	eval line=\"$line\"
	2864	echo "$line" >> $jobfile
	2865	done
	2866	echo " " >> $jobfile
	2867
	2868	echo "set -x" >> $jobfile
[3236]	2869	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
[2380]	2870	echo "%%END%%" >> $jobfile
	2871	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2872	echo "$submit_command $scpjob_file" >> $jobfile
	2873	echo "rm $scpjob_file" >> $jobfile
[2404]	2874	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2875	echo "set -x" >> $jobfile
	2876	echo " ' exit" >> $jobfile
	2877	fi
	2878
	2879
	2880	# ACTIVATE ERROR-TRACEBACK
	2881	if [[ $do_trace = true ]]
	2882	then
	2883	echo "set -x" >> $jobfile
	2884	else
	2885	echo "set +vx" >> $jobfile
	2886	fi
	2887
	2888
	2889	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2890	if [[ "$login_init_cmd" != "" ]]
	2891	then
	2892	echo "$login_init_cmd" >> $jobfile
	2893	fi
	2894	if [[ "$module_commands" != "" ]]
	2895	then
	2896	echo "$module_commands" >> $jobfile
	2897	fi
	2898
	2899
	2900	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2901	if [[ $create_remote_batch_job = true ]]
	2902	then
	2903	echo "mkdir $tempdir" >> $jobfile
	2904	echo "chmod go+rx $tempdir" >> $jobfile
	2905	else
	2906	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2907	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2908	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2909	mkdir $tempdir
	2910	chmod go+rx $tempdir
	2911	fi
	2912	echo "cd $tempdir" >> $jobfile
	2913	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2914	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2915	echo "export PATH=.:\$PATH" >> $jobfile
	2916	echo "export execute_palmrun=true" >> $jobfile
	2917
	2918
	2919	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2920	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2921	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2922	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2923	echo "export LOCAL_PWD" >> $jobfile
	2924
	2925
	2926	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2927	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2928	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2929
	2930
	2931	# CALL PALMRUN WITHIN THE JOB
	2932	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2933	echo "set -x" >> $jobfile
	2934	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2935
	2936
	2937	# TRANSFER JOBFILE TO THE TARGET HOST
	2938	if [[ $create_jobfile_only = false ]]
	2939	then
	2940
	2941	if [[ $create_remote_batch_job = true ]]
	2942	then
	2943
[2420]	2944	echo " "
[2566]	2945	echo " *** transfer of job to remote host via scp"
[2420]	2946	if [[ $do_trace = true ]]
	2947	then
[3236]	2948	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2949	fi
[3236]	2950	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2951
[2566]	2952	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2953	if [[ $do_trace = true ]]
	2954	then
[3236]	2955	echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2956	fi
[3236]	2957	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2958
	2959	elif [[ $create_batch_job = true ]]
	2960	then
	2961
[2385]	2962	eval local_jobcatalog=$local_jobcatalog
[3236]	2963	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	2964	cd $local_jobcatalog
[2380]	2965	echo " "
[2420]	2966	echo " *** submit the job"
	2967	if [[ $do_trace = true ]]
	2968	then
[3236]	2969	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	2970	fi
[3236]	2971	$submit_command ${configuration_identifier}_${run_id}
	2972	rm ${configuration_identifier}_${run_id}
[2380]	2973	cd - > /dev/null
	2974
	2975	fi
	2976
	2977	rm -rf $jobfile
	2978
	2979	else
	2980
	2981	printf "\n *** jobfile created under name \"$jobfile\" "
	2982	printf "\n no batch-job has been sent!"
	2983
	2984	fi
	2985
	2986	fi # END OF REMOTE-PART

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