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source: palm/trunk/SCRIPTS/palmrun @ 3704

Last change on this file since 3704 was 3682, checked in by knoop, 6 years ago
Extended palmtest to use custom MPI execution commands
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.8 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 3682 2019-01-18 17:01:54Z suehring $
[3665]	29	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	30	# of login messages on specific systems
	31	#
	32	# 3574 2018-11-28 13:14:39Z raasch
[3574]	33	# syntax-error in last commit fixed
	34	#
	35	# 3573 2018-11-28 13:03:44Z raasch
[3573]	36	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	37	# removed,
	38	# r3570 reverted
	39	#
	40	# 3570 2018-11-27 17:44:21Z kanani
[3570]	41	# Rename job-id by run_id
	42	#
	43	# 3555 2018-11-22 13:50:37Z raasch
[3555]	44	# sed-command to remove repeated space-characters replaced by tr-command, to
	45	# guarantee mac compatible
	46	#
	47	# 3549 2018-11-21 15:44:44Z raasch
[3549]	48	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	49	# of login messages on specific systems
	50	#
	51	# 3534 2018-11-19 15:35:16Z raasch
[3534]	52	# batch_scp for sending back the job protocol file is called via login-node if
	53	# a login-node has been set in the config-file
	54	# ssh-calls rearranged to avoid output of system/user-profile messages
	55	#
	56	# 3505 2018-11-08 09:14:30Z raasch
[3505]	57	# job folders are created in case that they do not exist
	58	#
	59	# 3455 2018-10-30 14:12:31Z raasch
[3455]	60	# options -h and -d renamed -c and -r, respectively
	61	#
	62	# 3402 2018-10-23 11:49:24Z knoop
[3346]	63	# job_id is set for compatibility reasons with older versions of config files
	64	#
	65	# 3313 2018-10-06 15:22:48Z knoop
[3294]	66	# more detailed error message for outdated fileconnection file
	67	#
	68	# 3236 2018-09-10 09:07:06Z raasch
[3236]	69	# warning issued in case of file connection file version mismatch,
	70	# host_configuration renamed configuration_identifier,
	71	# "host identifier" in header output renamed "config. identifier",
	72	# jobname renamed run_identifier,
	73	# run_id renamed run_id_number
	74	# job_id renamed run_id
	75	# option -r renamed -i
	76	#
	77	# 3151 2018-07-19 08:45:38Z raasch
[3151]	78	# removed additional listing of files to be compiled, print PALM code revision
	79	# in header
	80	#
	81	# 3132 2018-07-16 11:44:58Z raasch
[3132]	82	# create consistent error messages in case of failed restarts,
	83	# check existence of remote job catalog
	84	#
	85	# 3043 2018-05-25 10:47:54Z raasch
[3043]	86	# check for setting of fast_io_catalog
	87	#
	88	# 3033 2018-05-23 15:26:19Z raasch
[3025]	89	# -T option not required for interactive runs (tasks per node =
	90	# total number of cores is assumed as default, if option is not given),
	91	# reformatting of a few messages,
	92	# bugfix: destination output directory is created if attribute "pe" is set in
	93	# .palm.iofiles
	94	#
	95	# 2718 2018-01-02 08:49:38Z maronga
[2993]	96	# bugfix of r2990
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2990]	99	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	100	# not in the working directory from where palmrun is called
	101	#
	102	# 2718 2018-01-02 08:49:38Z maronga
[2957]	103	# svfout in the activation string will be replaced now by svfin in case of
	104	# automatic restarts
	105	#
	106	# 2718 2018-01-02 08:49:38Z maronga
[2906]	107	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	108	# the possible output or input of sky view factors
	109	#
	110	# 2718 2018-01-02 08:49:38Z maronga
[2834]	111	# "fname" renamed to "jobname"
	112	#
	113	# 2718 2018-01-02 08:49:38Z maronga
[2799]	114	# parameters are allowed in output commands (OC:)
	115	#
	116	# 2718 2018-01-02 08:49:38Z maronga
[2789]	117	# bugfix: exit if no queue has been given neither with option -q nor in the
	118	# configuration file
	119	#
	120	# 2718 2018-01-02 08:49:38Z maronga
[2762]	121	# file connection file from trunk/SCRIPTS is taken by default
	122	#
	123	# 2718 2018-01-02 08:49:38Z maronga
[2716]	124	# Corrected "Former revisions" section
	125	#
	126	# 2696 2017-12-14 17:12:51Z kanani
	127	# Change in file header (GPL part)
	128	#
	129	# 2693 2017-12-13 12:33:49Z raasch
[2693]	130	# replacement of variables given by {{<variable>}} in configuration file is now
	131	# done in a more general way, variable names are written in small letters
	132	#
	133	# 2670 2017-12-06 16:32:19Z raasch
[2670]	134	# test printouts removed
	135	#
	136	# 2669 2017-12-06 16:03:27Z raasch
[2669]	137	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	138	# removed,
	139	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	140	# files,
	141	# informative messages in case of missing optional input files shortened
	142	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	143	#
	144	# 2638 2017-11-23 12:44:23Z raasch
[2610]	145	# use of wildcards in file connection statements enabled
	146	#
	147	# 2605 2017-11-09 15:31:46Z raasch
[2605]	148	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	149	# will not be sent with the job file any more, but copied into the
[2610]	150	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	151	#
	152	# 2600 2017-11-01 14:11:20Z raasch
[2600]	153	# cycle numbers are made three digits wide
	154	#
	155	# 2566 2017-10-20 08:50:47Z raasch
[2566]	156	# execute command for combine_plot_fields added
	157	# "TEMPDIR" renamed "tempdir"
	158	# temporary working directory for local batch jobs is created immediately within
	159	# the user's palmrun call, due to a requirement of the "grid engine" batch
	160	# system, where the working directory is given with batch directive -wd and must
	161	# already exist when the job is submitted,
	162	# informative messages in non-trace mode reduced and partly reformatted
	163	#
	164	# 2551 2017-10-18 07:25:11Z raasch
[2551]	165	# TEMPDIR added as replacement string to be used in batch directives
	166	#
	167	# 2512 2017-10-04 08:26:59Z raasch
[2507]	168	# bugfix for determining cycle numbers of NetCDF input files
	169	#
	170	# 2506 2017-09-29 08:30:37Z raasch
[2506]	171	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	172	# host configuration added to SOURCES_FOR_RUN_... folder name
	173	# host_identifier renamed host_configuration
	174	# option -W added to allow for job dependencies
	175	#
	176	# 2501 2017-09-26 11:41:55Z raasch
[2501]	177	# default value for number of cores (option -X) set to 1
	178	# bugfix for mechanism which overwrites configuration file settings with values
	179	# provided by palmrun options
	180	#
	181	# 2499 2017-09-22 16:47:58Z kanani
[2499]	182	# option -h named configuration identifier
	183	#
	184	# 2480 2017-09-19 06:24:14Z maronga
[2480]	185	# bugfix for last revision
	186	#
	187	# 2479 2017-09-19 06:12:16Z raasch
[2479]	188	# option -A (project account number) added
	189	#
	190	# 2422 2017-09-08 08:25:41Z raasch
[2410]	191	# initial revision
[2380]	192	#
	193	#--------------------------------------------------------------------------------#
	194	# palmrun - script for running PALM jobs on local and remote hosts
	195	#--------------------------------------------------------------------------------#
	196
	197
	198
	199	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	200
	201	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	202	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	203	# (TOO MANY ARGUMENTS - PROBLEM)
	204	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	205
[2610]	206	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	207	typeset -i nr_of_output_files=0
[2380]	208	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	209	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	210	# SCRIPT-OPTION ARGUMENTS
	211	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	212	typeset -i icycle inode ival maxcycle mpi_tasks
	213	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	214
	215	activation_string_list=""
	216	AddFilenames=""
	217	combine_plot_fields=true
	218	compiler_name=""
	219	compiler_name_ser=""
	220	compiler_options=""
[3236]	221	configuration_identifier="default"
[2501]	222	cores=1
[2380]	223	cores_atmos=0
	224	cores_ocean=0
	225	coupled_dist=""
	226	cpp_options=""
	227	cpumax=0
[2506]	228	create_batch_job=false
[2380]	229	create_jobfile_only=false
	230	create_remote_batch_job=false
	231	dashes=" ----------------------------------------------------------------------------"
	232	defaultqueue=""
[2506]	233	delete_temporary_catalog=true
[2380]	234	do_compile=true
	235	do_trace=false
	236	executable=""
	237	execute_command=""
	238	execution_error=false
[2762]	239	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	240	global_revision=""
	241	hostfile=""
	242	hp=""
	243	keep_data_from_previous_run=false
	244	link_local_input=false
	245	link_local_output=false
[2388]	246	linker_options=""
[2385]	247	local_jobcatalog=""
[2380]	248	locat=normal
	249	makefile=""
	250	max_par_io_str=""
	251	prc=$0
	252	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	253	do
	254	prc=`echo $prc \| cut -f2- -d"/"`
	255	done
	256	module_calls=""
[2506]	257	palmrun_memory=""
[2380]	258	palmrun_script_name=$prc
	259	openmp=false
[2506]	260	previous_job=""
[2479]	261	project_account=""
[2380]	262	queue=none
[2906]	263	read_svf=""
[2380]	264	restart_run=false
	265	return_address=""
[2385]	266	remote_jobcatalog=""
[2380]	267	remote_username=""
	268	running_in_batch_mode=false
[3313]	269	running_in_test_mode=false
[2380]	270	run_coupled_model=false
	271	run_id=""
[3236]	272	run_id_number=""
	273	run_identifier=test
[2380]	274	silent=false
	275	source_list=""
	276	source_path=""
[2501]	277	tasks_per_node=0
[2380]	278	threads_per_task=1
	279	transfer_problems=false
[2384]	280	user_source_path=""
[2506]	281	use_existing_sources_folder=""
[2380]	282	use_openmp=false
[3033]	283	version="palmrun 1.0 Rev$Rev: 3682 $"
[2380]	284	working_directory=`pwd`
	285	write_binary=""
[2906]	286	write_svf=""
[2380]	287
	288
	289	# ERROR HANDLING IN CASE OF EXIT
[2404]	290	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	291	then
	292
	293	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	294	(( i = 0 ))
	295	while (( i < iec ))
	296	do
	297	(( i = i + 1 ))
	298	printf "\n *** Execution of ERROR-command:\n"
	299	printf " >>> ${err_command[$i]}\n"
	300	eval ${err_command[$i]}
	301	done
[2566]	302	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	303	printf "\n\n+++ palmrun crashed \n\n"
	304	exit 1
	305	elif [[ $locat != normal ]]
[2380]	306	then
[3312]	307	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	308	printf "\n+++ palmrun killed by \"^C\" \n\n"
	309	exit 2
	310	else
[2566]	311	printf "\n --> palmrun finished\n\n"
[3312]	312	exit 0
[2380]	313	fi' exit
	314
	315
	316	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	317	trap 'locat=control_c
	318	exit 1
[2380]	319	' 2
	320
	321
	322	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	323	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	324	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	325	do
	326	case $option in
	327	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	328	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	329	(b) create_batch_job=true; prc="$prc -b";;
	330	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	331	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	332	(C) restart_run=true; prc="$prc -C";;
	333	(F) create_jobfile_only=true;;
	334	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	335	(i) run_id_number=$OPTARG;;
[2380]	336	(j) running_in_batch_mode=true;;
	337	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	338	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	339	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	340	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	341	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	342	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	343	(R) return_address=$OPTARG;;
	344	(s) source_list=$OPTARG;;
[2501]	345	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	346	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	347	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	348	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	349	(v) silent=true; prc="$prc -v";;
[2506]	350	(V) use_existing_sources_folder="-V";;
[2380]	351	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	352	(W) previous_job=$OPTARG;;
[2380]	353	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	354	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	355	(y) ocean_file_appendix=true; prc="$prc -y";;
	356	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	357	(z) running_in_test_mode=true;;
[2380]	358	(Z) combine_plot_fields=false; prc="$prc -Z";;
	359	(\?) printf "\n +++ unknown option $OPTARG \n"
	360	printf "\n --> type \"$0 ?\" for available options \n"
	361	locat=parameter;exit;;
	362	esac
	363	done
	364
	365
	366	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	367	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	368	(( to_shift = $OPTIND - 1 ))
	369	shift $to_shift
	370
	371	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	372	if [[ "$1" = "?" ]]
	373	then
	374	(printf "\n *** Description of available palmrun options:\n"
	375	printf "\n Option Description Default-Value"
	376	printf "\n -a activation string list \"\" "
[2479]	377	printf "\n -A project account number ---"
[2380]	378	printf "\n -b batch-job on local machine ---"
	379	printf "\n -B do not delete temporary directory at end ---"
[3455]	380	printf "\n -c configuration identifier \"default\" "
[2380]	381	printf "\n -F create batch job file only ---"
	382	printf "\n -k keep data from previous run"
	383	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	384	printf "\n -M Makefile name Makefile"
	385	printf "\n -O threads per openMP task ---"
	386	printf "\n -q queue \"$queue\" "
[3455]	387	printf "\n -r run identifier test"
[2380]	388	printf "\n -s filenames of routines to be compiled \"\" "
	389	printf "\n must end with .f, .f90, .F, or .c !"
	390	printf "\n use \"..\" for more than one file and wildcards"
	391	printf "\n -s LM compiles all locally modified files"
	392	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	393	printf "\n -T tasks per node ---"
[2380]	394	printf "\n -u username on remote machine \"\" "
	395	printf "\n -v no prompt for confirmation ---"
[2506]	396	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	397	printf "\n -w maximum parallel io streams as given by -X"
[2506]	398	printf "\n -W name of job to wait for ---"
[2380]	399	printf "\n -x tracing of palmrun for debug purposes ---"
	400	printf "\n -X # of processors (on parallel machines) 1"
	401	printf "\n -y add appendix \"_O\" to all local output"
	402	printf "\n files (ocean precursor runs followed by"
	403	printf "\n coupled atmosphere-ocean runs) ---"
	404	printf "\n -Y run coupled model, \"#1 #2\" with"
	405	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	406	printf "\n -Z skip combine_plot_fields at the end of "
	407	printf "\n the simulation ---"
	408	printf "\n "
	409	printf "\n Possible values of positional parameter <modus>:"
	410	printf "\n \"?\" - this outline \n\n") \| more
	411	exit
	412	elif [[ "$1" != "" ]]
	413	then
	414	printf "\n +++ positional parameter $1 unknown \n"
	415	locat=parameter; exit
	416	fi
	417
	418
	419
	420	# SHORT STARTING MESSAGE
	421	printf "\n*** $version "
	422	printf "\n will be executed. Please wait ..."
	423
	424
[2506]	425	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	426	config_file=.palm.config.$configuration_identifier
	427	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	428
	429
	430	# CHECK, IF CONFIGURATION FILE EXISTS
	431	if [[ ! -f $config_file ]]
	432	then
	433	printf "\n\n +++ configuration file: "
	434	printf "\n $config_file"
	435	printf "\n does not exist"
	436	locat=connect; exit
	437	fi
	438
	439
[2762]	440	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	441	if [[ -f .palm.iofiles ]]
	442	then
[3236]	443
	444	# CHECK VERSION MISMATCH
[3573]	445	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	446	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	447	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	448	then
	449	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	450	then
	451	printf "\n\n +++ WARNING: A file connection file has been found in your"
	452	printf "\n working directory, but its revision does not match"
	453	printf "\n the revision of the default (trunk) version."
[3294]	454	printf "\n You may need to update your connection file"
	455	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	456	fi
	457	fi
	458
[2762]	459	fileconnection_file=.palm.iofiles
[3236]	460
[2762]	461	fi
	462
	463
[2380]	464	# CHECK, IF FILE CONNECTION FILE EXISTS
	465	if [[ ! -f $fileconnection_file ]]
	466	then
	467	printf "\n\n +++ file connection file: "
	468	printf "\n $fileconnection_file"
	469	printf "\n does not exist"
	470	locat=connect; exit
	471	fi
	472
	473
[2404]	474	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	475	if [[ "$activation_string_list" = "" ]]
	476	then
	477	printf "\n\n +++ no activation string list given: "
	478	printf "\n please set palmrun option \"-a\" "
	479	locat=palmrun_option; exit
	480	fi
	481
	482
	483	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	484	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	485	then
	486	write_binary=true
	487	else
	488	write_binary=false
	489	fi
	490
[2906]	491	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	492	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	493	then
	494	write_svf=true
	495	else
	496	write_svf=false
	497	fi
[2404]	498
[2906]	499	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	500	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	501	then
	502	read_svf=true
	503	else
	504	read_svf=false
	505	fi
	506
	507
[2380]	508	# READ AND EVALUATE THE CONFIGURATION-FILE
	509	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	510
	511	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	512	while read line
	513	do
	514
	515	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	516	eval line=\"$line\"
	517
	518
	519	# INTERPRET THE LINE
	520	if [[ "$(echo $line)" = "" ]]
	521	then
	522
	523	# EMPTY LINE, NO ACTION
	524	continue
	525
	526	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	527	then
	528
	529	# LINE IS A COMMENT LINE
	530	continue
	531
	532	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	533	then
	534
	535	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	536	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	537	value=`echo $line \| cut -d" " -s -f2-`
	538
	539
	540	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	541	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	542	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	543	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	544	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	545	# CONFIGURATION-FILE.
	546	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	547	then
	548	eval export $var="\$value"
	549
	550	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	551	if [[ $do_trace = true ]]
	552	then
	553	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	554	fi
	555	fi
	556
	557	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	558	then
	559
	560	# LINE DEFINES BATCH-DIRECTIVE
	561	(( ibd = ibd + 1 ))
	562	line=$(echo $line \| cut -c4-)
	563	batch_directive[$ibd]="$line"
	564
	565	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	566	then
	567
	568	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	569	# REMOTE TO A LOCAL HOST
	570	(( ibdt = ibdt + 1 ))
	571	line=$(echo $line \| cut -c5-)
	572	batch_directive_transfer[$ibdt]="$line"
	573
	574	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	575	then
	576
	577	# LINE DEFINES ERROR-COMMAND
	578	(( iec = iec + 1 ))
	579	line=$(echo $line \| cut -c4-)
	580	err_command[$iec]="$line"
	581
	582	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	583	then
	584
	585	# LINE DEFINES INPUT-COMMAND
	586	(( iic = iic + 1 ))
	587	line=$(echo $line \| cut -c4-)
	588	in_command[$iic]="$line"
	589
	590	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	591	then
	592
	593	# LINE DEFINES OUTPUT-COMMAND
	594	(( ioc = ioc + 1 ))
	595	line=$(echo $line \| cut -c4-)
	596	out_command[$ioc]="$line"
	597
	598	else
	599
	600	# SKIP ALL OTHER LINES
	601	continue
	602
	603	fi
	604
	605	done < $config_file
	606
	607
	608	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	609	if [[ "$fast_io_catalog" = "" ]]
	610	then
	611	printf "\n +++ no fast_io_catalog found in $config_file"
	612	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	613	locat=config_file; exit
	614	fi
[2380]	615	if [[ "$compiler_name" = "" ]]
	616	then
	617	printf "\n +++ no compiler name found in $config_file"
	618	printf "\n Please add line \"compiler_name ...\" to that file."
	619	locat=config_file; exit
	620	fi
	621	if [[ "$compiler_name_ser" = "" ]]
	622	then
	623	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	624	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	625	locat=config_file; exit
	626	fi
	627	if [[ "$compiler_options" = "" ]]
	628	then
	629	printf "\n +++ no compiler options found in $config_file"
	630	printf "\n Please add line \"compiler_options ...\" to that file."
	631	locat=config_file; exit
	632	fi
	633	if [[ "$execute_command" = "" ]]
	634	then
	635	printf "\n +++ no execute command found in $config_file"
	636	printf "\n Please add line \"execute_command ...\" to that file."
	637	locat=config_file; exit
	638	fi
	639
	640	if [[ "$hostfile" != "" ]]
	641	then
	642	if [[ $hostfile != auto && ! -f $hostfile ]]
	643	then
	644	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	645	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	646	locat=config_file; exit
	647	fi
	648	fi
	649
	650
	651	# DETERMINE THE CALL STATUS
	652	if [[ "$return_address" != "" ]]
	653	then
	654
	655	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	656	# BATCH MODE AND ...
	657	running_on_remote=true
	658
	659	else
	660
	661	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	662	if [[ "$remote_ip" != "" ]]
	663	then
	664
	665	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	666	create_remote_batch_job=true
	667
[3132]	668	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	669	if [[ "$remote_jobcatalog" = "" ]]
	670	then
	671	printf "\n +++ no remote jobcatalog found in $config_file"
	672	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	673	locat=config_file; exit
	674	fi
	675
	676
[2380]	677	fi
	678	running_on_remote=false
	679	fi
	680
	681
	682
	683	# READ AND EVALUATE THE I/O-FILE LIST
	684	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	685
	686	# READ THE FILE CONNECTION FILE LINE BY LINE
	687	while read line
	688	do
	689
[2669]	690	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	691	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	692	line=`echo "$line" \| tr -s " "`
[2380]	693
	694	# INTERPRET THE LINE
	695	if [[ "$(echo $line)" = "" ]]
	696	then
	697	# EMPTY LINE, NO ACTION
	698	continue
	699
	700	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	701	then
	702
	703	# LINE IS A COMMENT LINE
	704	true
	705
	706	else
	707
	708	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	709	# s2a: in/out - field
[2669]	710	# s2b: action - field (optional)
	711	s1=`echo "$line" \| cut -d" " -f1`
	712	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	713	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	714	then
[2669]	715	s2a=$s2
[2380]	716	s2b=""
	717	else
[2669]	718	s2a=`echo $s2 \| cut -d":" -f1`
	719	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	720	fi
[2669]	721	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	722	s4=`echo "$line" \| cut -d" " -s -f4`
	723	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	724	s5=`echo "$line" \| cut -d" " -s -f5`
	725	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	726
	727
	728	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	729	# INPUT- OR OUTPUT-LIST.
	730	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	731	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	732	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	733	# IS NOT CHECKED AND STORED.
[2610]	734	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	735	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	736	then
	737	found=false
	738	for actual in $activation_string_list
	739	do
	740	for formal in $s3
	741	do
	742	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	743	done
	744	done
	745	if [[ $found = true ]]
	746	then
	747	(( iin = iin + 1 ))
[2669]	748	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	749	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	750	if [[ "$s2a" = inopt ]]
	751	then
	752	optin_pre[$iin]=yes
	753	else
	754	optin_pre[$iin]=no
	755	fi
[2605]	756
	757	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	758	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	759	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	760	then
[2610]	761	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	762	fi
	763
[2610]	764	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	765	# THE WILDCARD FROM THE ENDING
	766	if [[ "${s5: -1}" = "*" ]]
	767	then
[2669]	768	if [[ "$s2b" = "di" ]]
[2610]	769	then
	770	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	771	printf "\n see file \"$fileconnection_file\", line"
	772	printf "\n$line"
	773	locat=iofiles_file; exit
	774	fi
	775	multin[$iin]=true
	776	string=${endin_pre[$iin]}
	777	endin_pre[$iin]="${string%?}"
	778	else
	779	multin[$iin]=false
	780	fi
[2380]	781	fi
[2669]	782	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	783	then
	784	found=false
	785	for actual in $activation_string_list
	786	do
	787	for formal in $s3
	788	do
[2670]	789	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	790	done
	791	done
	792	if [[ $found = true ]]
	793	then
	794	(( iout = iout + 1 ))
[2669]	795	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	796	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	797
[2669]	798	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	799	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	800	if [[ $formal = wildcard ]]
	801	then
	802	warnout_pre[$iout]=false
	803	else
	804	warnout_pre[$iout]=true
	805	fi
	806
[2610]	807	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	808	# THE WILDCARD FROM THE LOCAL FILENAME
	809	if [[ "${s1: -1}" = "*" ]]
	810	then
[2669]	811	if [[ "$s2b" = "di" ]]
[2610]	812	then
	813	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	814	printf "\n see file \"$fileconnection_file\", line"
	815	printf "\n$line"
	816	locat=iofiles_file; exit
	817	fi
	818	multout[$iout]=true
	819	string=${localout_pre[$iout]}
	820	localout_pre[$iout]="${string%?}"
	821	else
	822	multout[$iout]=false
	823	fi
[2380]	824	fi
[2669]	825	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	826	then
[2669]	827	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	828	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	829	locat=connect; exit
	830	fi
	831	IFS="$IFSALT"
	832	fi
	833
	834	done < $fileconnection_file
	835
	836
	837
[2501]	838	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	839	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	840	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	841	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	842	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	843	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	844
	845
	846
[2380]	847	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	848	if [[ $run_coupled_model = true ]]
	849	then
	850
	851	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	852	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	853
	854	if (( $cores_ocean + $cores_atmos != $cores ))
	855	then
	856
	857	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	858	printf "\n PEs (total) : $cores"
	859	printf "\n PEs (atmosphere): $cores_atmos"
	860	printf "\n PEs (ocean) : $cores_ocean"
	861	locat=coupling; exit
	862
	863	fi
	864
	865	fi
	866
	867
	868	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	869	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	870	# FOLDER
	871	if [[ $running_in_batch_mode = true ]]
	872	then
	873
[2506]	874	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	875	then
[2506]	876	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	877	printf "\n Please check the output of the palmrun-call"
	878	printf "\n that you did on your local host."
	879	locat=SOURCES_FOR_RUN; exit
	880	fi
	881
	882	else
	883
	884	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	885	# AUTOMATIC RESTART RUN
	886	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	887	if [[ $restart_run = false ]]
	888	then
	889
	890	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	891	# THE LOCAL HOST
	892	if [[ ! -d $source_path ]]
	893	then
	894	printf "\n\n +++ source path \"$source_path\" on local host"
	895	printf "\n \"$(hostname)\" does not exist"
	896	locat=source_path; exit
	897	fi
	898
[2990]	899	rm -rf ${base_directory}/${sources_for_run_catalog}
	900	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	901
	902	if [[ "$source_list" = LM ]]
	903	then
	904
	905	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	906	source_list=""
	907	cd $source_path
	908
	909
[2512]	910	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	911	if [[ ! -d ../.svn ]]
[2380]	912	then
	913	printf "\n\n +++ source directory"
	914	printf "\n \"$source_path\" "
	915	printf "\n is not under control of \"subversion\"."
[2512]	916	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	917	fi
	918
	919
	920	# LIST ALL MODIFIED SOURCE CODE FILES
	921	Filenames=""
[2404]	922	svn status > tmp_svnstatus
[2380]	923	while read line
	924	do
	925	firstc=`echo $line \| cut -c1`
	926	if [[ $firstc = M \|\| $firstc = "?" ]]
	927	then
	928	Name=`echo "$line" \| cut -c8-`
	929	extension=`echo $Name \| cut -d. -f2`
	930	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	931	then
	932	Filenames="$Filenames "$Name
	933	fi
	934	fi
[2404]	935	done < tmp_svnstatus
	936	rm -rf tmp_svnstatus
[2380]	937
	938
	939	# COPY FILES TO SOURCES_FOR_RUN_...
	940	for filename in $Filenames
	941	do
[2990]	942	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	943	source_list=$source_list"$filename "
	944	done
	945
	946	cd - > /dev/null
	947
	948
	949	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	950	elif [[ "$source_list" != "" ]]
	951	then
	952
	953	cd $source_path
	954
	955	for filename in $source_list
	956	do
	957
	958	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	959	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	960	then
	961	printf "\n +++ source code file: $filename"
	962	printf "\n must not contain (\"/\") "
	963	locat=source; exit
	964	fi
	965
	966	if [[ ! -f $filename ]]
	967	then
	968	printf "\n +++ source code file: $filename"
	969	printf "\n does not exist"
	970	locat=source; exit
	971	else
[2990]	972	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	973	fi
	974
	975	done
	976
	977	cd - > /dev/null
	978
	979	fi
	980
	981	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	982	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	983	if [[ ! -f $makefile ]]
	984	then
	985	printf "\n +++ file \"$makefile\" does not exist"
	986	locat=make; exit
	987	else
[2990]	988	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	989	fi
	990
	991
	992	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	993	if [[ "$user_source_path" != "" ]]
[2380]	994	then
	995
	996	# DOES THE DIRECTORY EXIST?
[2384]	997	if [[ ! -d $user_source_path ]]
[2380]	998	then
	999
	1000	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1001	printf "\n \"$user_source_path\" "
[2380]	1002	printf "\n does not exist or is not a directory."
	1003	printf "\n No source code will be used from this directory!\n"
[2384]	1004	user_source_path=""
[2380]	1005	if [[ $silent == false ]]
	1006	then
	1007	sleep 2
	1008	fi
	1009
	1010	else
	1011
[2384]	1012	cd $user_source_path
[2380]	1013
	1014	Names=$(ls -1 *.f90 2>&1)
	1015	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1016	Names=$(ls -1 *.F90 2>&1)
	1017	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1018	Names=$(ls -1 *.F 2>&1)
	1019	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1020	Names=$(ls -1 *.f 2>&1)
	1021	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1022	Names=$(ls -1 *.c 2>&1)
	1023	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1024
	1025	cd - > /dev/null
[2990]	1026	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1027
	1028	# COPY MAKEFILE IF EXISTING
[2384]	1029	if [[ -f $user_source_path/Makefile ]]
[2380]	1030	then
	1031	printf "\n\n *** user Makefile from directory"
[2384]	1032	printf "\n \"$user_source_path\" is used \n"
[2380]	1033	if [[ $silent == false ]]
	1034	then
	1035	sleep 1
	1036	fi
[2384]	1037	cp $user_source_path/Makefile .
[2380]	1038	fi
	1039
	1040	for filename in $AddFilenames
	1041	do
	1042	if [[ -f $filename ]]
	1043	then
	1044	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1045	printf "\n source code directory \"$user_source_path\" "
[2380]	1046	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1047	printf "\n from directory \"$source_path\"."
	1048	locat=source; exit
	1049	fi
	1050
[2384]	1051	cp $user_source_path/$filename .
[2380]	1052	source_list="$source_list $filename"
	1053
	1054	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1055	if [[ $(grep -c $filename Makefile) = 0 ]]
	1056	then
	1057	printf "\n\n +++ user file \"$filename\" "
	1058	printf "\n is not listed in Makefile \n"
	1059	locat=source; exit
	1060	fi
	1061	done
	1062	cd - > /dev/null
	1063	fi
	1064	fi
	1065
	1066	# COPY CONFIGURATION FILES
[2990]	1067	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1068	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1069
	1070	# COPY SHELLSCRIPTS
[2990]	1071	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1072	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1073
	1074	fi
	1075
	1076	fi
	1077
[2605]	1078
[2380]	1079	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1080	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1081	if [[ "$global_revision" = "" ]]
	1082	then
	1083	global_revision=`svnversion $source_path 2>/dev/null`
	1084	global_revision="Rev: $global_revision"
	1085	fi
	1086
	1087
	1088	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1089	if [[ -n $cores ]]
	1090	then
	1091
	1092	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1093	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1094	if [[ $tasks_per_node = 0 ]]
[2380]	1095	then
[3025]	1096	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1097	then
	1098	printf "\n"
	1099	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1100	printf "\n set -T option or define tasks_per_node in the config file"
	1101	locat=tasks_per_node; (( iec = 0 )); exit
	1102	else
	1103	# DEFAULT FOR INTERACTIVE RUN
	1104	tasks_per_node=$cores
	1105	fi
[2380]	1106	fi
	1107
	1108	if (( cores < tasks_per_node ))
	1109	then
	1110	printf "\n"
	1111	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1112	printf "\n given values: -T $tasks_per_node -X $cores"
	1113	locat=tasks_per_node; (( iec = 0 )); exit
	1114	fi
	1115
	1116	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1117	(( mpi_tasks = cores / threads_per_task ))
	1118	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1119	(( ii = cores / tasks_per_node ))
	1120	(( remaining_cores = cores - ii * tasks_per_node ))
	1121	if (( remaining_cores > 0 ))
	1122	then
	1123	printf "\n"
	1124	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1125	printf "\n divisor of the total number of cores (option \"-X\")"
	1126	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1127	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1128	(( nodes = nodes + 1 ))
	1129	fi
	1130
	1131	fi
	1132
	1133
	1134	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1135	if [[ "$maximum_parallel_io_streams" = "" ]]
	1136	then
	1137	maximum_parallel_io_streams=$cores
	1138	fi
	1139
	1140
	1141	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1142	if [[ "$scp_port" != "" ]]
	1143	then
	1144	PORTOPT="-P $scp_port"
	1145	SSH_PORTOPT="-p $scp_port"
	1146	fi
	1147
	1148
	1149	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1150	# CONFIG-FILE
	1151	if [[ "$ssh_key" != "" ]]
	1152	then
	1153	ssh_key="-i $HOME/.ssh/$ssh_key"
	1154	fi
	1155
	1156
	1157	# SET QUEUE, IF NOT GIVEN
	1158	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1159	then
	1160
	1161	if [[ $queue = none && "$defaultqueue" = "" ]]
	1162	then
	1163	printf "\n"
	1164	printf "\n +++ no default queue given in configuration file and no queue"
	1165	printf "\n given with option -q"
[2789]	1166	locat=queue; exit
[2380]	1167	fi
	1168	if [[ $queue = none ]]
	1169	then
	1170	queue=$defaultqueue
	1171	fi
	1172
	1173	fi
	1174
	1175
	1176	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1177	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1178	(( i = 0 ))
[2610]	1179	(( nr_of_input_files = 0 ))
[2380]	1180	while (( i < iin ))
	1181	do
	1182	(( i = i + 1 ))
	1183
	1184	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1185	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1186	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1187	then
[2610]	1188	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1189	else
[3236]	1190	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1191	fi
	1192
[2610]	1193
[2380]	1194	# CHECK IF FILE EXISTS
	1195	if ! ls $filename* 1>/dev/null 2>&1
	1196	then
	1197
[2669]	1198	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1199	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1200	then
	1201	printf "\n\n +++ INPUT-file: "
[2610]	1202	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1203	then
	1204	printf "\n $filename"
	1205	else
[2610]	1206	printf "\n $filename.${extin_pre[$i]}"
[2380]	1207	fi
	1208	printf "\n does not exist\n"
	1209	locat=input; exit
	1210	else
[2610]	1211	(( nr_of_input_files = nr_of_input_files + 1 ))
	1212	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1213	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1214	actionin[$nr_of_input_files]="unavailable"
[2610]	1215	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1216	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1217	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1218	fi
[2605]	1219
[2380]	1220	else
	1221
[3236]	1222	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1223	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1224	# ENDINGS
[2610]	1225	if [[ "${multin[$i]}" = true ]]
	1226	then
	1227	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1228	ls -1 -d ${filename} > filelist 2>/dev/null
	1229	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1230	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1231
[2610]	1232	endings=""
	1233	while read line
	1234	do
	1235	# filename without path (i.e. after the last "/")
	1236	basefilename=$(basename ${line})
[2380]	1237
[2610]	1238	# check if there is an extension and remove it
	1239	ext=${basefilename##*.}
	1240	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1241	then
	1242	basefilename=${basefilename%.*}
	1243	fi
[2380]	1244
[2610]	1245	# check for an existing cycle number and remove it
	1246	cycle=${basefilename##*.}
	1247	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1248	then
	1249	basefilename=${basefilename%.*}
	1250	fi
[2600]	1251
[3236]	1252	# remove the run_identifier from the beginning
	1253	length_run_identifier=${#run_identifier}
	1254	ending=${basefilename:${length_run_identifier}}
[2610]	1255
	1256	# remove the ending given in the .iofiles from the beginning
	1257	endingstring="${endin_pre[$i]}"
	1258	length_ending=${#endingstring}
	1259	ending=${ending:${length_ending}}
	1260
	1261	if [[ "$ending" = "" ]]
[2600]	1262	then
[2610]	1263	# standard ending as given in the .iofiles
	1264	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1265	then
	1266	endings="$endings DEFAULT"
	1267	fi
[2600]	1268	else
[2610]	1269	# ending must start with "_", otherwise its a different file
	1270	if [[ "${ending:0:1}" = "_" ]]
	1271	then
	1272	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1273	then
	1274	endings="$endings $ending"
	1275	fi
	1276	fi
[2600]	1277	fi
[2610]	1278
	1279	done <filelist
[2380]	1280
[2610]	1281	rm filelist
[2380]	1282
[2600]	1283	else
[2610]	1284
	1285	# SINGLE NAME
	1286	endings=DEFAULT
	1287
[2600]	1288	fi
	1289
[2610]	1290	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1291	for ending in $endings
	1292	do
	1293
	1294	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1295	if [[ $ending = DEFAULT ]]
[2380]	1296	then
[2610]	1297	ending=""
	1298	fi
	1299
	1300	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1301	(( nr_of_input_files = nr_of_input_files + 1 ))
	1302	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1303	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1304	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1305	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1306	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1307	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1308
	1309
	1310	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1311	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1312	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1313	then
	1314	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1315	else
[3236]	1316	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1317	fi
[2610]	1318
	1319	# DETERMINE THE FILE'S CYCLE NUMBER
	1320	(( maxcycle = 0 ))
	1321	ls -1 -d $filename > filelist 2>/dev/null
	1322	ls -1 -d $filename.* >> filelist 2>/dev/null
	1323	while read line
	1324	do
	1325	# filename without path (i.e. after the last "/")
	1326	basefilename=$(basename ${line})
	1327
	1328	# check if there is an extension
	1329	extension=${basefilename##*.}
	1330	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1331	then
	1332	basefilename=${basefilename%.*}
	1333	fi
	1334
	1335	# check for an existing cycle number
	1336	cycle=${basefilename##*.}
	1337	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1338	then
[2669]	1339	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1340	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1341	(( icycle = $((10#$cycle)) ))
[2610]	1342	else
	1343	(( icycle = 0 ))
	1344	fi
	1345
	1346	if (( icycle > maxcycle ))
	1347	then
	1348	(( maxcycle = icycle ))
	1349
	1350	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1351	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1352	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1353	then
	1354	leading_zero=true
	1355	else
	1356	leading_zero=false
	1357	fi
	1358	fi
	1359
	1360	done <filelist
	1361	rm filelist
	1362
	1363	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1364	if [[ $leading_zero = true ]]
[2380]	1365	then
[2610]	1366	cyclestring=`printf "%03d" $maxcycle`
	1367	else
	1368	cyclestring=$maxcycle
[2380]	1369	fi
[2610]	1370
	1371	# APPEND CYCLE NUMBER TO FILENAME
	1372	if (( maxcycle > 0 ))
[2380]	1373	then
[2610]	1374	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1375	then
	1376	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1377	else
	1378	filename=${filename}.$cyclestring
	1379	fi
[2380]	1380	else
[2610]	1381	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1382	then
	1383	filename=${filename}.${extin[$nr_of_input_files]}
	1384	fi
[2380]	1385	fi
[2610]	1386
	1387	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1388	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1389	absnamein[$nr_of_input_files]=$filename
	1390	if (( maxcycle > 0 ))
[2380]	1391	then
[2610]	1392	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1393	then
	1394	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1395	else
[3236]	1396	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1397	fi
[2380]	1398	else
[2610]	1399	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1400	then
	1401	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1402	else
[3236]	1403	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1404	fi
[2380]	1405	fi
	1406
[2610]	1407	done
	1408
[2380]	1409	fi
[2610]	1410
[2380]	1411	done
	1412
[2610]	1413
[2380]	1414	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1415	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1416	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1417	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1418	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1419	# REMOTE HOST)
	1420	(( i = 0 ))
	1421	while (( i < iout ))
	1422	do
	1423	(( i = i + 1 ))
[2610]	1424	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1425	then
[2610]	1426	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1427	then
[2610]	1428	actionout_pre[$i]=""
	1429	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1430	then
[2610]	1431	actionout_pre[$i]=pe
	1432	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1433	then
[2610]	1434	actionout_pre[$i]=a
[2380]	1435	fi
	1436	(( maxcycle = 0 ))
[3236]	1437	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1438	eval catalogname=${pathout_pre[$i]}
[2380]	1439	if ! ls $filename* 1>/dev/null 2>&1
	1440	then
	1441
	1442	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1443	if cat /dev/null > $filename
	1444	then
	1445	rm $filename
	1446	else
	1447
	1448	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1449	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1450	if [[ ! -d $catalogname ]]
	1451	then
	1452	if mkdir -p $catalogname
	1453	then
	1454	printf "\n\n *** directory:"
	1455	printf "\n $catalogname"
	1456	printf "\n was created\n"
	1457	else
	1458	printf "\n\n +++ OUTPUT-file:"
	1459	printf "\n $filename"
	1460	printf "\n cannot be created, because directory does not exist"
	1461	printf "\n and cannot be created either"
	1462	printf "\n"
	1463	locat=output ; exit
	1464	fi 2>/dev/null
	1465	else
	1466	printf "\n\n +++ OUTPUT-file:"
	1467	printf "\n $filename"
	1468	printf "\n cannot be created, although directory exists"
	1469	printf "\n"
	1470	locat=output ; exit
	1471	fi
	1472	fi 2>/dev/null
	1473
	1474	fi
	1475
	1476	fi
	1477	done
	1478
	1479
	1480	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1481	if [[ $running_in_batch_mode = false ]]
	1482	then
[3236]	1483	run_id_number=$RANDOM
	1484	run_id=${run_identifier}.$run_id_number
[2380]	1485
[3236]	1486	tempdir=$fast_io_catalog/$run_id
[3346]	1487
	1488	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1489	export job_id=$run_id
	1490
[2380]	1491	fi
	1492
	1493
	1494	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1495	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1496	then
	1497
	1498	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1499	if [[ $ibd = 0 ]]
	1500	then
	1501	printf "\n"
	1502	printf "\n +++ no batch directives found in configuration file"
	1503	locat=config_file_batch_directives; (( iec = 0 )); exit
	1504	fi
	1505
	1506	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1507	done=false
[2384]	1508	cputime=$cpumax
[2380]	1509	while [[ $done = false ]]
	1510	do
[2384]	1511	if (( cputime == 0 ))
[2380]	1512	then
	1513	printf "\n +++ cpu-time is undefined"
	1514	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1515	printf "\n >>> "
[2384]	1516	read cputime 1>/dev/null 2>&1
[2380]	1517	else
	1518	done=true
	1519	fi
	1520	done
[2420]	1521	cpumax=$cputime
[2380]	1522
	1523	# CHECK THE MEMORY DEMAND
	1524	done=false
	1525	while [[ $done = false ]]
	1526	do
	1527	if (( memory == 0 ))
	1528	then
	1529	printf "\n +++ memory demand is undefined"
	1530	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1531	printf "\n >>> "
	1532	read memory 1>/dev/null 2>&1
	1533	else
	1534	done=true
	1535	fi
	1536	done
	1537
	1538	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1539	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1540	then
	1541	while [[ -z $remote_username ]]
	1542	do
[2420]	1543	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1544	printf "\n >>> Please type username:"
	1545	printf "\n >>> "
	1546	read remote_username
	1547	done
	1548	fi
	1549
	1550	else
	1551
[2420]	1552	if [[ $running_in_batch_mode = false ]]
	1553	then
	1554	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1555	cpumax=$cputime
	1556	else
	1557	cputime=$cpumax
	1558	fi
[2380]	1559
	1560	fi
	1561
	1562
	1563	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1564	(( cpu_hours = cputime / 3600 ))
	1565	(( resttime = cputime - cpu_hours * 3600 ))
	1566	(( cpu_minutes = resttime / 60 ))
	1567	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1568	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1569
	1570
	1571	# OUTPUT OF THE PALMRUN-HEADER
	1572	calltime=$(date)
	1573	printf "\n"
	1574	printf "#------------------------------------------------------------------------# \n"
	1575	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1576	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1577	printf "\| \| \n"
	1578	column1="called on:"; column2=$(hostname)
	1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1580	if [[ $create_remote_batch_job = true ]]
	1581	then
[3236]	1582	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1583	else
	1584	if [[ $running_on_remote = true ]]
	1585	then
[3236]	1586	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1587	else
[3236]	1588	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1589	fi
	1590	fi
	1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1592
	1593	column1="running in:"
	1594	if [[ $running_in_batch_mode = true ]]
	1595	then
	1596	column2="batch job mode"
	1597	else
	1598	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1599	then
	1600	column2="job creation mode"
	1601	else
	1602	column2="interactive run mode"
	1603	fi
	1604	fi
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606
[2479]	1607	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1608	then
[2480]	1609	if [[ "$project_account" != "" ]]
[2479]	1610	then
	1611	column1="project account number:"
	1612	column2="$project_account"
	1613	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1614	fi
	1615	fi
	1616
[2380]	1617	if [[ -n $cores ]]
	1618	then
	1619	if [[ $run_coupled_model = false ]]
	1620	then
	1621	column1="number of cores:"; column2=$cores
	1622	else
	1623	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1624	fi
	1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1626	fi
	1627	if [[ -n $tasks_per_node ]]
	1628	then
	1629	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1631	if (( remaining_cores > 0 ))
	1632	then
	1633	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1635	fi
	1636	fi
	1637	if [[ $maximum_parallel_io_streams != $cores ]]
	1638	then
	1639	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	fi
	1642	if [[ $use_openmp = true ]]
	1643	then
	1644	column1="threads per task:"; column2="$threads_per_task"
	1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1646	fi
[2384]	1647	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1648	then
[2506]	1649	column1="memory demand / PE":; column2="$memory MB"
	1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1651	column1="job cpu time (h:m:s):"; column2="$timestring"
	1652	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1653	fi
[2380]	1654	printf "\| \| \n"
	1655	if [[ "$source_list" != "" ]]
	1656	then
	1657	if [[ "$make_options" != "" ]]
	1658	then
	1659	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1661	line=$(echo "$make_options" \| cut -c46-)
	1662	while [[ "$line" != "" ]]
	1663	do
	1664	column1=""
	1665	column2=$(echo "$line" \| cut -c-45)
	1666	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1667	line=$(echo "$line" \| cut -c46-)
	1668	done
	1669	fi
	1670	fi
	1671
	1672	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1674	line=$(echo "$cpp_options" \| cut -c46-)
	1675	while [[ "$line" != "" ]]
	1676	do
	1677	column1=""
	1678	column2=$(echo "$line" \| cut -c-45)
	1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1680	line=$(echo "$line" \| cut -c46-)
	1681	done
	1682
	1683	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1684	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1685	line=$(echo "$compiler_options" \| cut -c46-)
	1686	while [[ "$line" != "" ]]
	1687	do
	1688	column1=""
	1689	column2=$(echo "$line" \| cut -c-45)
	1690	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1691	line=$(echo "$line" \| cut -c46-)
	1692	done
	1693
[2388]	1694	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1695	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1696	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1697	while [[ "$line" != "" ]]
	1698	do
	1699	column1=""
	1700	column2=$(echo "$line" \| cut -c-45)
	1701	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1702	line=$(echo "$line" \| cut -c46-)
	1703	done
	1704
	1705	if [[ "$login_init_cmd" != "" ]]
	1706	then
	1707	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1709	line=$(echo "$login_init_cmd" \| cut -c46-)
	1710	while [[ "$line" != "" ]]
	1711	do
	1712	column1=""
	1713	column2=$(echo "$line" \| cut -c-45)
	1714	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1715	line=$(echo "$line" \| cut -c46-)
	1716	done
	1717	fi
	1718
	1719	if [[ "$module_commands" != "" ]]
	1720	then
	1721	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1722	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1723	line=$(echo "$module_commands" \| cut -c46-)
	1724	while [[ "$line" != "" ]]
	1725	do
	1726	column1=""
	1727	column2=$(echo "$line" \| cut -c-45)
	1728	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1729	line=$(echo "$line" \| cut -c46-)
	1730	done
	1731	fi
	1732	printf "\| \| \n"
[3236]	1733	column1="run identifier:"; column2=$run_identifier
[2380]	1734	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1735	column1="activation string list:"; column2=$(echo $activation_string_list)
	1736	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1737
	1738	if [[ "$ocean_file_appendix" = true ]]
	1739	then
	1740	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1741	fi
	1742
	1743	if [[ "$source_list" != "" ]]
	1744	then
	1745	printf "\| \| \n"
	1746	printf "\| Files to be compiled: \| \n"
	1747	line=$source_list
	1748	while [[ "$line" != "" ]]
	1749	do
	1750	linestart=$(echo $line \| cut -c-70)
	1751	printf "\| %-70s \| \n" "$linestart"
	1752	line=$(echo "$line" \| cut -c71-)
	1753	done
	1754	fi
	1755	printf "#------------------------------------------------------------------------#"
	1756
	1757
	1758
	1759	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1760	if [[ $do_trace = true ]]
	1761	then
	1762	(( i = 0 ))
[2610]	1763	while (( i < nr_of_input_files ))
[2380]	1764	do
	1765	(( i = i + 1 ))
	1766	if (( i == 1 ))
	1767	then
	1768	printf "\n\n >>> INPUT-file assignments:\n"
	1769	fi
	1770	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1771	done
	1772	(( i = 0 ))
	1773	while (( i < iout ))
	1774	do
	1775	(( i = i + 1 ))
	1776	if (( i == 1 ))
	1777	then
	1778	printf "\n\n >>> OUTPUT-file assignments:\n"
	1779	fi
	1780	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1781	done
	1782	(( i = 0 ))
	1783	while (( i < iic ))
	1784	do
	1785	(( i = i + 1 ))
	1786	if (( i == 1 ))
	1787	then
	1788	printf "\n\n >>> INPUT-commands:\n"
	1789	fi
	1790	printf "\n ${in_command[$i]}"
	1791	done
	1792	(( i = 0 ))
	1793	while (( i < ioc ))
	1794	do
	1795	(( i = i + 1 ))
	1796	if (( i == 1 ))
	1797	then
	1798	printf "\n\n >>> OUTPUT-commands:\n"
	1799	fi
	1800	printf "\n ${out_command[$i]}"
	1801	done
	1802	fi
	1803
	1804	# QUERY FOR CONTINUE
	1805	if [[ $silent = false && $running_in_batch_mode = false ]]
	1806	then
	1807	antwort=dummy
	1808	printf "\n\n"
	1809	printf " >>> everything o.k. (y/n) ? "
	1810	while read antwort
	1811	do
	1812	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1813	then
	1814	printf " >>> everything o.k. (y/n) ? "
	1815	else
	1816	break
	1817	fi
	1818	done
	1819	if [[ $antwort = n \|\| $antwort = N ]]
	1820	then
	1821	locat=user_abort; (( iec = 0 )); exit
	1822	fi
	1823	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1824	then
[2566]	1825	printf "\n *** batch-job will be created and submitted"
[2380]	1826	else
[2566]	1827	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1828	fi
	1829	fi
	1830
	1831
	1832
	1833	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1834	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1835	then
	1836
	1837	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1838	then
[2566]	1839	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1840	else
[2566]	1841	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1842	fi
	1843
[2422]	1844	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1845	# IT SHALL BE CREATED
	1846	ask_for_make_depository=false
	1847	if [[ $create_remote_batch_job = true ]]
	1848	then
	1849
	1850	line=`grep %base_directory $config_file`
[3236]	1851	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1852	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1853
[3236]	1854	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1855	then
	1856	printf "\n\n +++ make depository \"${make_depository}\""
	1857	printf "\n on remote host not found!"
	1858	ask_for_make_depository=true
	1859	fi
[3236]	1860	rm ${configuration_identifier}_last_make_protokoll
[2422]	1861
	1862	else
	1863
	1864	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1865	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1866	if [[ ! -d ${make_depository} ]]
	1867	then
	1868	printf "\n\n +++ make depository \"${make_depository}\""
	1869	printf "\n on local host not found!"
	1870	ask_for_make_depository=true
	1871	fi
	1872
	1873	fi
	1874
	1875	if [[ $ask_for_make_depository = true ]]
	1876	then
	1877
	1878	antwort=dummy
	1879	printf "\n\n"
	1880	printf " >>> Create a new one (y/n) ? "
	1881	while read antwort
	1882	do
	1883	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1884	then
	1885	printf " >>> Create a new one (y/n) ? "
	1886	else
	1887	break
	1888	fi
	1889	done
	1890	if [[ $antwort = n \|\| $antwort = N ]]
	1891	then
	1892	locat=user_abort; (( iec = 0 )); exit
	1893	fi
	1894
[2566]	1895	if [[ $do_trace = true ]]
	1896	then
[3455]	1897	palmbuild -c $configuration_identifier
[2566]	1898	else
[3455]	1899	palmbuild -v -c $configuration_identifier
[2566]	1900	fi
[2422]	1901
[3312]	1902	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1903	then
	1904
	1905	# ABORT IN CASE OF COMPILATION PROBLEMS
	1906	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1907	locat=make_depository
	1908	exit
	1909	else
	1910	echo " *** now continue with creating executable and other sources"
	1911	fi
	1912
	1913	fi
	1914
[2566]	1915	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1916	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1917
[3312]	1918	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1919	then
	1920
	1921	# ABORT IN CASE OF COMPILATION PROBLEMS
	1922	printf "\n +++ error while creating executable and/or other sources"
	1923	locat=execution
[2990]	1924	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1925	exit
	1926
	1927	else
	1928
[2566]	1929	printf " *** executable and other sources created\n"
[2990]	1930	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1931
	1932	fi
	1933
	1934	fi
	1935
	1936
[2669]	1937	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1938	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1939	if [[ $create_remote_batch_job = true ]]
	1940	then
	1941	(( i = 0 ))
[2610]	1942	while (( i < nr_of_input_files ))
[2605]	1943	do
	1944	(( i = i + 1 ))
[2669]	1945	if [[ "${actionin[$i]}" = tr ]]
[2605]	1946	then
	1947	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1948	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1949	fi
	1950	done
	1951	if (( i > 0 ))
	1952	then
[3025]	1953	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1954	fi
	1955	fi
	1956
	1957
[2380]	1958	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1959	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1960	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1961	then
	1962
	1963	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1964	if [[ $running_in_batch_mode = false ]]
	1965	then
	1966	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1967	# FOLDER
[2566]	1968	mkdir -p $tempdir
	1969	chmod go+rx $tempdir
	1970	cd $tempdir
	1971	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1972	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1973
	1974	else
	1975
	1976	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1977	printf "\n *** running in temporary directory: $tempdir"
[2380]	1978
	1979	fi
	1980
	1981
	1982	# PROVIDE THE INPUT FILES
	1983	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1984	optional_files_missing=false
[2380]	1985	(( i = 0 ))
[2610]	1986	while (( i < nr_of_input_files ))
[2380]	1987	do
	1988	(( i = i + 1 ))
	1989	if (( i == 1 ))
	1990	then
	1991	printf "\n\n *** providing INPUT-files:\n$dashes"
	1992	fi
	1993
	1994
	1995	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1996	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1997	then
[2669]	1998	optional_files_missing=true
[2380]	1999	continue
	2000	fi
	2001
	2002	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2003	files_for_cores=false; filetype=file
	2004	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2005	then
	2006	files_for_cores=true; filetype=files
	2007	actionin[$i]=""
	2008	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2009	then
	2010	actionin[$i]=""
	2011	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2012	then
	2013	files_for_cores=true; filetype=files
	2014	actionin[$i]="ln"
	2015	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2016	then
	2017	actionin[$i]="ln"
	2018	fi
	2019
	2020	if [[ $files_for_cores = true ]]
	2021	then
	2022	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2023	else
	2024	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2025	fi
	2026
	2027	# INPUT-FILES TO BE LINKED
	2028	if [[ "${actionin[$i]}" = ln ]]
	2029	then
	2030
	2031	printf "\n $filetype will be linked"
	2032	if [[ $files_for_cores = false ]]
	2033	then
	2034	if [[ -f "${absnamein[$i]}" ]]
	2035	then
	2036	ln ${absnamein[$i]} ${localin[$i]}
	2037	got_tmp[$i]=true
	2038	fi
	2039	else
	2040	if [[ -d "${absnamein[$i]}" ]]
	2041	then
[2396]	2042	mkdir -p ${localin[$i]}
[2380]	2043	cd ${absnamein[$i]}
	2044	for file in $(ls *)
	2045	do
[2566]	2046	ln $file $tempdir/${localin[$i]}
[2380]	2047	done >\|/dev/null 2>&1
[2566]	2048	cd $tempdir
[2380]	2049	fi
	2050
	2051	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2052	if [[ ! -f "${localin[$i]}/_000000" ]]
	2053	then
	2054	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2055	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2056	fi
	2057
	2058	got_tmp[$i]=true
	2059	fi
	2060	fi
	2061
	2062	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2063	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2064	then
	2065
	2066	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2067	then
	2068
	2069	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2070	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2071	printf "\n file will be provided for $cores processors"
[2396]	2072	mkdir -p ${localin[$i]}
[2380]	2073	ival=$cores
	2074	(( ii = 0 ))
	2075	while (( ii <= ival-1 ))
	2076	do
	2077	if (( ii < 10 ))
	2078	then
	2079	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2080	elif (( ii < 100 ))
	2081	then
	2082	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2083	elif (( ii < 1000 ))
	2084	then
	2085	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2086	else
	2087	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2088	fi
	2089	(( ii = ii + 1 ))
	2090	done
	2091
	2092	else
	2093
	2094	if [[ $files_for_cores = true ]]
	2095	then
	2096
	2097	# PROVIDE FILES FOR EACH CORE
	2098	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2099	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2100	printf "\n providing $cores files for the respective cores"
[2396]	2101	mkdir -p ${localin[$i]}
[2380]	2102	if [[ $link_local_input = true ]]
	2103	then
	2104	printf " files will be linked\n"
	2105	cd ${absnamein[$i]}
	2106	for file in $(ls *)
	2107	do
	2108	ln -f $file ${localin[$i]}
	2109	done
[2566]	2110	cd $tempdir
[2380]	2111	fi
	2112
	2113	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2114	if [[ ! -f "${localin[$i]}/_000000" ]]
	2115	then
	2116	if [[ $link_local_input = true ]]
	2117	then
	2118	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2119	fi
	2120	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2121	fi
	2122
	2123	else
	2124
	2125	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2126	if [[ $link_local_input = true ]]
	2127	then
	2128	printf " file will be linked\n"
	2129	ln -f ${absnamein[$i]} ${localin[$i]}
	2130	fi
[2605]	2131	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2132	if [[ ! -f "${localin[$i]}" ]]
	2133	then
	2134	if [[ $link_local_input = true ]]
	2135	then
	2136	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2137	fi
[2669]	2138	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2139	then
	2140	mv ${absnamein[$i]} ${localin[$i]}
	2141	else
	2142	cp ${absnamein[$i]} ${localin[$i]}
	2143	fi
[2380]	2144	fi
	2145	fi
	2146	fi
	2147	fi
	2148
	2149	done
	2150	if (( i != 0 ))
	2151	then
[2669]	2152	if [[ $optional_files_missing = true ]]
	2153	then
	2154	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2155	fi
[2380]	2156	printf "\n$dashes\n *** all INPUT-files provided \n"
	2157	fi
	2158
	2159
	2160	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2161	(( i = 0 ))
	2162	while (( i < iic ))
	2163	do
	2164	(( i = i + 1 ))
	2165	if (( i == 1 ))
	2166	then
	2167	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2168	fi
	2169	printf "\n >>> ${in_command[$i]}"
	2170	eval ${in_command[$i]}
	2171	if (( i == iic ))
	2172	then
	2173	printf "\n$dashes\n"
	2174	fi
	2175	done
	2176
	2177
[3313]	2178	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2179	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2180	then
	2181	progress_bar_disabled=true
	2182	else
	2183	progress_bar_disabled=false
	2184	fi
	2185
	2186
[2380]	2187	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2188	# (FILE ENVPAR WILL BE READ BY PALM)
	2189	cat > ENVPAR << EOF
[3236]	2190	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2191	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2192	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2193	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2194	maximum_cpu_time_allowed = ${cpumax}.,
	2195	revision = '$global_revision',
[3313]	2196	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2197
	2198	EOF
	2199
	2200
	2201	# STARTING THE EXECUTABLE
	2202	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2203	PATH=$PATH:$tempdir
[2380]	2204
	2205
	2206	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2207	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2208	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2209	eval line=\"$line\"
	2210	execute_command="$line"
	2211
	2212
	2213	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2214	if [[ "$execute_command_for_combine" = "" ]]
	2215	then
	2216	eval line2=\"$line2\"
	2217	execute_command_for_combine="$line2"
	2218	fi
	2219
[2380]	2220
	2221
	2222	# PROVIDE A HOSTFILE, IF REQUIRED
	2223	if [[ "$hostfile" != "" ]]
	2224	then
	2225
	2226	if [[ $hostfile = auto ]]
	2227	then
	2228	# CREATE A NEW HOSTFILE
	2229	(( ii = 1 ))
	2230	while (( ii <= cores / threads_per_task ))
	2231	do
	2232	echo $(hostname) >> hostfile
	2233	(( ii = ii + 1 ))
	2234	done
	2235	if (( cores / threads_per_task == 0 ))
	2236	then
	2237	echo $(hostname) >> hostfile
	2238	fi
	2239
	2240	else
	2241	cp $hostfile hostfile
	2242	fi
	2243	eval line=\"`head -n $ii hostfile`\"
	2244	printf "\n *** running on: $line"
	2245	fi
	2246
	2247
	2248
	2249	# SET THE NUMBER OF OPENMP-THREADS
	2250	if [[ $use_openmp = true ]]
	2251	then
	2252	export OMP_NUM_THREADS=$threads_per_task
	2253	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2254	else
	2255	export OMP_NUM_THREADS=1
	2256	fi
	2257
	2258
[2610]	2259	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2260	if [[ $run_coupled_model = false ]]
	2261	then
	2262	if [[ "$ocean_file_appendix" = true ]]
	2263	then
	2264	echo "precursor_ocean" > coupling_steering
	2265	else
	2266	echo "precursor_atmos" > coupling_steering
	2267	fi
	2268	else
	2269	(( iia = $cores_atmos / $threads_per_task ))
	2270	(( iio = $cores_ocean / $threads_per_task ))
	2271	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2272	printf "\n\n"
	2273	echo "coupled_run $iia $iio" > coupling_steering
	2274	fi
	2275
	2276	printf "\n *** execute command:"
	2277	printf "\n \"$execute_command\" \n\n"
	2278
	2279
[3393]	2280	if [[ $progress_bar_disabled = true ]]
[2380]	2281	then
[3402]	2282	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2283	exit_code=${PIPESTATUS[0]}
	2284	else
	2285	$execute_command < coupling_steering &> >(tee STDOUT)
	2286	exit_code=${PIPESTATUS[0]}
	2287	fi
[2380]	2288
[3393]	2289	if [[ ${exit_code} != 0 ]]
	2290	then
	2291
[2380]	2292	# ABORT IN CASE OF RUNTIME ERRORS
	2293	printf "\n +++ runtime error occured"
	2294	locat=execution
	2295	exit
	2296
	2297	else
	2298
	2299	printf "\n$dashes\n *** execution finished \n"
	2300
	2301	fi
	2302
	2303
	2304	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2305	# BY EACH CORE INTO ONE FILE
	2306	if [[ ! -f combine_plot_fields.x ]]
	2307	then
	2308
	2309	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2310	printf "\n 2d- and/or 3d-data may be incomplete!"
	2311	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2312
	2313	elif [[ "$combine_plot_fields" == true ]]
	2314	then
	2315
	2316	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2317	$execute_command_for_combine
	2318
	2319	else
	2320
	2321	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2322	# DATA OUTPUT
[2380]	2323	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2324	fi
	2325
	2326
	2327
	2328	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2329	(( i = 0 ))
	2330	while (( i < ioc ))
	2331	do
	2332	(( i = i + 1 ))
	2333	if (( i == 1 ))
	2334	then
	2335	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2336	fi
[2799]	2337
	2338	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2339	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2340
[2380]	2341	printf "\n >>> ${out_command[$i]}"
	2342	eval ${out_command[$i]}
	2343	if (( i == ioc ))
	2344	then
	2345	printf "\n$dashes\n"
	2346	fi
	2347	done
	2348
	2349
[2610]	2350	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2351	# WILDCARDS
[2380]	2352	(( i = 0 ))
[2610]	2353	(( nr_of_output_files = 0 ))
	2354
[2380]	2355	while (( i < iout ))
	2356	do
[2610]	2357
[2380]	2358	(( i = i + 1 ))
[2610]	2359
	2360	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2361	# CREATE A LIST FOR THE DETECTED ENDINGS
	2362	if [[ "${multout[$i]}" = true ]]
	2363	then
	2364	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2365	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2366	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2367
	2368	endings="DEFAULT"
	2369	while read line
	2370	do
	2371	# remove the local name from the beginning
	2372	localnamestring="${localout_pre[$i]}"
	2373	length_localname=${#localnamestring}
	2374	ending=${line:${length_localname}}
	2375
	2376	if [[ "$ending" != "" ]]
	2377	then
	2378	endings="$endings $ending"
	2379	fi
	2380
	2381	done <filelist
	2382
	2383	rm filelist
	2384
	2385	else
	2386
	2387	# SINGLE NAME
	2388	endings=DEFAULT
	2389
	2390	fi
	2391
	2392	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2393	for ending in $endings
	2394	do
	2395
	2396	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2397	if [[ $ending = DEFAULT ]]
	2398	then
	2399	ending=""
	2400	fi
	2401
	2402	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2403	(( nr_of_output_files = nr_of_output_files + 1 ))
	2404	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2405	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2406	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2407	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2408	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2409	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2410	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2411
	2412	done
	2413
	2414	done
	2415
	2416
	2417
	2418
	2419	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2420	(( i = 0 ))
	2421	while (( i < nr_of_output_files ))
	2422	do
	2423	(( i = i + 1 ))
[2380]	2424	if (( i == 1 ))
	2425	then
	2426	printf "\n\n *** saving OUTPUT-files:"
	2427
	2428	# GET RUN NUMBER ASSIGNED BY PALM
	2429	if [[ -f RUN_NUMBER ]]
	2430	then
	2431	read run_number < RUN_NUMBER
	2432	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2433	usecycle_option="-U $run_number"
	2434	else
	2435	run_number=0
	2436	usecycle_option=""
	2437	fi
	2438	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2439	then
[2404]	2440	printf "\n *** in case of SCP transfers to local host"
	2441	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2442	fi
	2443	printf "\n$dashes"
	2444	fi
	2445
	2446	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2447	then
	2448
[3236]	2449	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2450
	2451	# DETERMINE THE CYCLE NUMBER
	2452	ls -1 -d $filename > filelist 2>/dev/null
	2453	ls -1 -d $filename.* >> filelist 2>/dev/null
	2454	while read line
	2455	do
	2456
	2457	# filename without path (i.e. after the last "/")
	2458	basefilename=$(basename ${line})
	2459
	2460	# check if there is an extension
	2461	extension=${basefilename##*.}
	2462	if [[ "$extension" = "${extout[$i]}" ]]
	2463	then
	2464	basefilename=${basefilename%.*}
	2465	fi
	2466
	2467	# check for an existing cycle number
	2468	cycle=${basefilename##*.}
	2469	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2470	then
[2669]	2471	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2472	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2473	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2474	else
	2475	(( icycle = 1 ))
	2476	fi
	2477
	2478	if (( icycle > maxcycle ))
	2479	then
	2480	(( maxcycle = icycle ))
	2481	fi
	2482
	2483	done <filelist
	2484	rm filelist
	2485
	2486
	2487	# SET THE CYCLE NUMBER
	2488	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2489	if [[ "${actionout[$i]}" = a ]]
	2490	then
	2491	(( maxcycle = maxcycle - 1 ))
	2492	fi
	2493
	2494	(( cycnum[$i] = maxcycle ))
	2495	pathout[$i]=$filename
	2496
	2497
	2498	# ADD CYCLE NUMBER TO FILENAME
	2499	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2500	if [[ "${actionout[$i]}" != "a" ]]
	2501	then
	2502	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2503	# WITH AN EXISTING CYCLE NUMBER
	2504	if (( run_number >= cycnum[$i] ))
	2505	then
	2506	(( cycnum[$i] = run_number ))
	2507	else
	2508	if (( run_number > 0 ))
	2509	then
	2510	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2511	fi
	2512	fi
	2513	fi
	2514	if (( cycnum[$i] > 0 ))
	2515	then
[2600]	2516	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2517	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2518	fi
	2519	fi
	2520
	2521	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2522	files_for_cores=false; filetype=file
	2523	link_local_output=false
	2524	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2525	then
	2526	files_for_cores=true; filetype=directory
	2527	actionout[$i]=""
	2528	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2529	then
	2530	actionout[$i]=""
	2531	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2532	then
	2533	files_for_cores=true; filetype=directory
	2534	link_local_output=true
	2535	actionout[$i]=""
	2536	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2537	then
	2538	link_local_output
	2539	actionout[$i]=""
	2540	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2541	then
	2542	files_for_cores=true; filetype=directory
	2543	actionout[$i]="tr"
	2544	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2545	then
	2546	actionout[$i]="tr"
	2547	fi
	2548
	2549	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2550	then
[2669]	2551	if [[ ${warnout[$i]} = true ]]
	2552	then
	2553	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2554	fi
[2380]	2555	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2556	then
[2669]	2557	if [[ ${warnout[$i]} = true ]]
	2558	then
	2559	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2560	fi
[2380]	2561	else
	2562
	2563
	2564	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2565	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2566	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2567	then
	2568	if [[ $running_on_remote = true ]]
	2569	then
	2570
	2571	# SET OPTIONS FOR TRANSFER
	2572	if [[ "${actionout[$i]}" = tr ]]
	2573	then
	2574	if [[ $files_for_cores = false ]]
	2575	then
	2576	catalog_option=""
	2577	catalog_string=""
	2578	else
	2579	catalog_option="-c"
	2580	catalog_string="/"
	2581	fi
	2582	append_option=""
	2583	append_string=""
	2584	else
	2585	append_option="-A"
	2586	append_string="append"
	2587	fi
	2588
	2589	transfer_failed=false
	2590	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2591	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2592
	2593	# TRANSFER VIA SCP
	2594	if [[ "$remote_loginnode" != "" ]]
	2595	then
[3534]	2596	ssh -q $remote_username@$remote_loginnode "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]}"
[2380]	2597	else
[3236]	2598	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]	2599	fi
[3312]	2600	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2601
	2602
	2603	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2604	if [[ $transfer_failed = true ]]
	2605	then
	2606	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2607	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2608
	2609	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2610	eval local_catalog=${pathout[$i]}
	2611	if [[ ! -d $local_catalog ]]
	2612	then
	2613	printf " *** local directory does not exist. Trying to create:\n"
	2614	printf " $local_catalog \n"
	2615	mkdir -p $local_catalog
	2616	fi
[3236]	2617	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2618	transfer_problems=true
	2619	fi
	2620
	2621	else
	2622
	2623	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2624	# BE COPIED OR APPENDED ON THIS MACHINE
	2625	if [[ "${actionout[$i]}" = tr ]]
	2626	then
	2627	actionout[$i]=""
	2628	else
	2629	actionout[$i]="a"
	2630	fi
	2631	fi
	2632	fi
	2633
	2634
	2635	# APPEND ON THIS MACHINE
	2636	if [[ "${actionout[$i]}" = "a" ]]
	2637	then
	2638	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2639	then
	2640	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2641	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2642	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2643	else
	2644	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2645	printf "\n ${pathout[$i]}\n"
	2646	cat ${localout[$i]} >> ${pathout[$i]}
	2647	fi
	2648	fi
	2649
	2650	# COPY ON THIS MACHINE
	2651	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2652	# ON DIFFERENT FILE-SYSTEMS
	2653	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2654	then
	2655
	2656	# COPY IN CASE OF RUNS ON SINGLE CORES
	2657	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2658	then
	2659	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2660	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2661	if [[ $link_local_output = true ]]
	2662	then
	2663	printf " file will be linked\n"
	2664	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2665	fi
	2666	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2667	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2668	then
	2669	if [[ $link_local_output = true ]]
	2670	then
	2671	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2672	fi
	2673	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2674	else
	2675	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2676	fi
	2677	else
	2678	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2679	printf "\n ${pathout[$i]}\n"
	2680	if [[ $link_local_output = true ]]
	2681	then
	2682	printf " file will be linked\n"
	2683	ln -f ${localout[$i]} ${pathout[$i]}
	2684	fi
	2685	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2686	if [[ ! -f "${pathout[$i]}" ]]
	2687	then
	2688	if [[ $link_local_output = true ]]
	2689	then
	2690	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2691	fi
	2692	cp ${localout[$i]} ${pathout[$i]}
	2693	else
	2694	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2695	fi
	2696	fi
	2697
	2698	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2699	then
	2700
	2701	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2702	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2703	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2704	printf "\n ${pathout[$i]}\n"
	2705	if [[ $link_local_output = true ]]
	2706	then
	2707	printf " files will be linked\n"
[2396]	2708	mkdir -p ${pathout[$i]}
[2380]	2709	cd ${localout[$i]}
	2710	for file in $(ls *)
	2711	do
	2712	ln -f $file ${pathout[$i]}
	2713	done >\|/dev/null 2>&1
[2566]	2714	cd $tempdir
[2380]	2715	fi
	2716
	2717	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2718	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2719	then
	2720	if [[ $link_local_output = true ]]
	2721	then
	2722	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2723	fi
[3025]	2724	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2725	cp -r ${localout[$i]}/* ${pathout[$i]}
	2726	fi
	2727
	2728	fi
	2729	fi
	2730	done
	2731
	2732	if (( i != 0 ))
	2733	then
	2734	if [[ $transfer_problems = true ]]
	2735	then
	2736	printf "\n$dashes\n *** OUTPUT-files saved"
	2737	printf "\n +++ WARNING: some data transfers failed! \n"
	2738	else
	2739	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2740	fi
	2741	fi
	2742
	2743
	2744	# IF REQUIRED, START A RESTART-JOB
	2745	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2746	if [[ -f CONTINUE_RUN ]]
	2747	then
	2748
	2749	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2750	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2751	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2752	# -b START A BATCH JOB
	2753	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2754	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2755	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2756
[2957]	2757	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2758	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2759	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2760	then
	2761	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2762	fi
[2380]	2763
	2764	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2765	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2766	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2767	then
[2381]	2768	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2769	fi
	2770
	2771
	2772	# START THE RESTART-JOB
	2773	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2774	echo " $prc"
	2775	printf "\n$dashes\n"
	2776	if [[ $running_on_remote = true ]]
	2777	then
	2778
	2779	echo "*** ssh will be used to initiate restart-runs!"
	2780	echo " return_address=\"$return_address\" "
	2781	echo " return_username=\"$local_username\" "
	2782
	2783	if [[ "$remote_loginnode" != "" ]]
	2784	then
[3534]	2785	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
[2380]	2786	else
[3534]	2787	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2788	fi
	2789
	2790	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2791	sleep 30
	2792
	2793	else
	2794
	2795	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2796	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2797
	2798	fi
	2799
[3132]	2800	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2801	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2802	then
	2803	printf "\n$dashes\n +++ creating restart run failed \n"
	2804	locat=create_restart
[3455]	2805	rm palmrun_restart.log
[3132]	2806	exit
	2807	else
	2808	printf "\n$dashes\n *** restart run initiated \n"
	2809	rm palmrun_restart.log
	2810	fi
[2380]	2811
[3132]	2812
[2380]	2813	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2814	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2815	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2816	# MAY BE VERY HUGE)
	2817	(( i = 0 ))
[2610]	2818	while (( i < nr_of_input_files ))
[2380]	2819	do
	2820	(( i = i + 1 ))
	2821	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2822	then
	2823	rm -r ${absnamein[$i]}
	2824	fi
	2825	done
	2826
	2827	fi
	2828
	2829
	2830	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2831	cd $HOME
[2566]	2832	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2833
	2834
	2835	else
	2836
	2837
	2838	# PREPARING ACTIONS,
	2839	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2840
	2841	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2842	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2843	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2844	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2845	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2846	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2847	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2848	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2849	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2850	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2851	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2852	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2853	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2854	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2855	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2856	if [[ $create_remote_batch_job = true ]]
	2857	then
	2858	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2859	if [[ $do_trace = true ]]
	2860	then
	2861	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2862	fi
[2380]	2863	elif [[ $create_batch_job = true ]]
	2864	then
	2865	palmrun_com=${palmrun_com}" -j"
[2420]	2866	if [[ $do_trace = true ]]
	2867	then
	2868	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2869	fi
[2380]	2870	fi
	2871
	2872
	2873	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2874	# REMOTE HOST
[3236]	2875	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2876	job_protocol_file=$job_protocol_file_local
	2877	if [[ $create_remote_batch_job = true ]]
	2878	then
[3236]	2879	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2880	job_protocol_file=$job_protocol_file_remote
	2881	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2882	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2883	fi
	2884
	2885
	2886	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2887	jobfile=jobfile.$run_id_number
[2380]	2888
	2889
	2890	# FIRST CREATE THE BATCH DIRECTIVES
	2891	(( i = 0 ))
	2892	while (( i < ibd ))
	2893	do
	2894	(( i = i + 1 ))
[2693]	2895	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2896	eval line=\"$line\"
	2897	echo "$line" >> $jobfile
	2898	done
	2899	echo " " >> $jobfile
	2900
	2901
	2902	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2903	# PROTOCOL
	2904	if [[ $create_remote_batch_job = true ]]
	2905	then
[3236]	2906	echo "set +vx" >> $jobfile
	2907	echo "trap '" >> $jobfile
	2908	echo "set +vx" >> $jobfile
	2909	echo "cd ${remote_jobcatalog}" >> $jobfile
	2910	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2911
	2912	# ADD THE BATCH DIRECTIVES
	2913	(( i = 0 ))
	2914	while (( i < ibdt ))
	2915	do
	2916	(( i = i + 1 ))
[2693]	2917	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2918	eval line=\"$line\"
	2919	echo "$line" >> $jobfile
	2920	done
	2921	echo " " >> $jobfile
	2922
	2923	echo "set -x" >> $jobfile
[3534]	2924	if [[ "$remote_loginnode" != "" ]]
	2925	then
	2926	echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${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}\" " >> $jobfile
	2927	else
	2928	echo "${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
	2929	fi
[2380]	2930	echo "%%END%%" >> $jobfile
	2931	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2932	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2933	echo "rm $scpjob_file" >> $jobfile
[2404]	2934	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2935	echo "set -x" >> $jobfile
	2936	echo " ' exit" >> $jobfile
	2937	fi
	2938
	2939
	2940	# ACTIVATE ERROR-TRACEBACK
	2941	if [[ $do_trace = true ]]
	2942	then
	2943	echo "set -x" >> $jobfile
	2944	else
	2945	echo "set +vx" >> $jobfile
	2946	fi
	2947
	2948
	2949	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2950	if [[ "$login_init_cmd" != "" ]]
	2951	then
	2952	echo "$login_init_cmd" >> $jobfile
	2953	fi
	2954	if [[ "$module_commands" != "" ]]
	2955	then
	2956	echo "$module_commands" >> $jobfile
	2957	fi
	2958
	2959
	2960	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2961	if [[ $create_remote_batch_job = true ]]
	2962	then
	2963	echo "mkdir $tempdir" >> $jobfile
	2964	echo "chmod go+rx $tempdir" >> $jobfile
	2965	else
	2966	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2967	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2968	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2969	mkdir $tempdir
	2970	chmod go+rx $tempdir
	2971	fi
	2972	echo "cd $tempdir" >> $jobfile
	2973	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2974	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2975	echo "export PATH=.:\$PATH" >> $jobfile
	2976	echo "export execute_palmrun=true" >> $jobfile
	2977
	2978
	2979	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2980	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2981	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2982	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2983	echo "export LOCAL_PWD" >> $jobfile
	2984
	2985
	2986	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2987	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2988	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2989
	2990
	2991	# CALL PALMRUN WITHIN THE JOB
	2992	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2993	echo "set -x" >> $jobfile
	2994	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2995
	2996
	2997	# TRANSFER JOBFILE TO THE TARGET HOST
	2998	if [[ $create_jobfile_only = false ]]
	2999	then
	3000
[3505]	3001	# CREATE LOCAL JOB FOLDER
	3002	eval local_jobcatalog=$local_jobcatalog
	3003	if [[ ! -d $local_jobcatalog ]]
	3004	then
	3005	echo " "
	3006	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3007	mkdir $local_jobcatalog
	3008	fi
	3009
[2380]	3010	if [[ $create_remote_batch_job = true ]]
	3011	then
	3012
[2420]	3013	echo " "
[2566]	3014	echo " *** transfer of job to remote host via scp"
[3505]	3015
	3016	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3017	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3018
	3019	# COPY THE JOB FILE
[2420]	3020	if [[ $do_trace = true ]]
	3021	then
[3236]	3022	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3023	fi
[3236]	3024	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3025
[3505]	3026	# SUBMIT THE JOB
[3574]	3027	printf " *** submit the job (output of submit command, \n"
[3573]	3028	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3029	if [[ $do_trace = true ]]
	3030	then
[3665]	3031	echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" "
[2420]	3032	fi
[3665]	3033	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
[2380]	3034
	3035	elif [[ $create_batch_job = true ]]
	3036	then
	3037
[2385]	3038	eval local_jobcatalog=$local_jobcatalog
[3236]	3039	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3040	cd $local_jobcatalog
[2380]	3041	echo " "
[2420]	3042	echo " *** submit the job"
	3043	if [[ $do_trace = true ]]
	3044	then
[3236]	3045	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3046	fi
[3236]	3047	$submit_command ${configuration_identifier}_${run_id}
	3048	rm ${configuration_identifier}_${run_id}
[2380]	3049	cd - > /dev/null
	3050
	3051	fi
	3052
	3053	rm -rf $jobfile
	3054
	3055	else
	3056
	3057	printf "\n *** jobfile created under name \"$jobfile\" "
	3058	printf "\n no batch-job has been sent!"
	3059
	3060	fi
	3061
	3062	fi # END OF REMOTE-PART

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