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source: palm/trunk/SCRIPTS/palmrun @ 3799

Last change on this file since 3799 was 3725, checked in by raasch, 6 years ago
modifications to avoid compiler warnings about unused variables, temperton-fft: GOTO statements replaced, file re-formatted corresponding to coding standards, ssh-calls for compilations on remote systems modified to avoid output of login messages on specific systems changed again (palmbuild, reverted as before r3549), error messages for failed restarts extended (palmrun)
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.1 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 3725 2019-02-07 10:11:02Z forkel $
[3725]	29	# error messages for failed restarts extended
	30	#
	31	# 3682 2019-01-18 17:01:54Z knoop
[3665]	32	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	33	# of login messages on specific systems
	34	#
	35	# 3574 2018-11-28 13:14:39Z raasch
[3574]	36	# syntax-error in last commit fixed
	37	#
	38	# 3573 2018-11-28 13:03:44Z raasch
[3573]	39	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	40	# removed,
	41	# r3570 reverted
	42	#
	43	# 3570 2018-11-27 17:44:21Z kanani
[3570]	44	# Rename job-id by run_id
	45	#
	46	# 3555 2018-11-22 13:50:37Z raasch
[3555]	47	# sed-command to remove repeated space-characters replaced by tr-command, to
	48	# guarantee mac compatible
	49	#
	50	# 3549 2018-11-21 15:44:44Z raasch
[3549]	51	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	52	# of login messages on specific systems
	53	#
	54	# 3534 2018-11-19 15:35:16Z raasch
[3534]	55	# batch_scp for sending back the job protocol file is called via login-node if
	56	# a login-node has been set in the config-file
	57	# ssh-calls rearranged to avoid output of system/user-profile messages
	58	#
	59	# 3505 2018-11-08 09:14:30Z raasch
[3505]	60	# job folders are created in case that they do not exist
	61	#
	62	# 3455 2018-10-30 14:12:31Z raasch
[3455]	63	# options -h and -d renamed -c and -r, respectively
	64	#
	65	# 3402 2018-10-23 11:49:24Z knoop
[3346]	66	# job_id is set for compatibility reasons with older versions of config files
	67	#
	68	# 3313 2018-10-06 15:22:48Z knoop
[3294]	69	# more detailed error message for outdated fileconnection file
	70	#
	71	# 3236 2018-09-10 09:07:06Z raasch
[3236]	72	# warning issued in case of file connection file version mismatch,
	73	# host_configuration renamed configuration_identifier,
	74	# "host identifier" in header output renamed "config. identifier",
	75	# jobname renamed run_identifier,
	76	# run_id renamed run_id_number
	77	# job_id renamed run_id
	78	# option -r renamed -i
	79	#
	80	# 3151 2018-07-19 08:45:38Z raasch
[3151]	81	# removed additional listing of files to be compiled, print PALM code revision
	82	# in header
	83	#
	84	# 3132 2018-07-16 11:44:58Z raasch
[3132]	85	# create consistent error messages in case of failed restarts,
	86	# check existence of remote job catalog
	87	#
	88	# 3043 2018-05-25 10:47:54Z raasch
[3043]	89	# check for setting of fast_io_catalog
	90	#
	91	# 3033 2018-05-23 15:26:19Z raasch
[3025]	92	# -T option not required for interactive runs (tasks per node =
	93	# total number of cores is assumed as default, if option is not given),
	94	# reformatting of a few messages,
	95	# bugfix: destination output directory is created if attribute "pe" is set in
	96	# .palm.iofiles
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2993]	99	# bugfix of r2990
	100	#
	101	# 2718 2018-01-02 08:49:38Z maronga
[2990]	102	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	103	# not in the working directory from where palmrun is called
	104	#
	105	# 2718 2018-01-02 08:49:38Z maronga
[2957]	106	# svfout in the activation string will be replaced now by svfin in case of
	107	# automatic restarts
	108	#
	109	# 2718 2018-01-02 08:49:38Z maronga
[2906]	110	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	111	# the possible output or input of sky view factors
	112	#
	113	# 2718 2018-01-02 08:49:38Z maronga
[2834]	114	# "fname" renamed to "jobname"
	115	#
	116	# 2718 2018-01-02 08:49:38Z maronga
[2799]	117	# parameters are allowed in output commands (OC:)
	118	#
	119	# 2718 2018-01-02 08:49:38Z maronga
[2789]	120	# bugfix: exit if no queue has been given neither with option -q nor in the
	121	# configuration file
	122	#
	123	# 2718 2018-01-02 08:49:38Z maronga
[2762]	124	# file connection file from trunk/SCRIPTS is taken by default
	125	#
	126	# 2718 2018-01-02 08:49:38Z maronga
[2716]	127	# Corrected "Former revisions" section
	128	#
	129	# 2696 2017-12-14 17:12:51Z kanani
	130	# Change in file header (GPL part)
	131	#
	132	# 2693 2017-12-13 12:33:49Z raasch
[2693]	133	# replacement of variables given by {{<variable>}} in configuration file is now
	134	# done in a more general way, variable names are written in small letters
	135	#
	136	# 2670 2017-12-06 16:32:19Z raasch
[2670]	137	# test printouts removed
	138	#
	139	# 2669 2017-12-06 16:03:27Z raasch
[2669]	140	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	141	# removed,
	142	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	143	# files,
	144	# informative messages in case of missing optional input files shortened
	145	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	146	#
	147	# 2638 2017-11-23 12:44:23Z raasch
[2610]	148	# use of wildcards in file connection statements enabled
	149	#
	150	# 2605 2017-11-09 15:31:46Z raasch
[2605]	151	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	152	# will not be sent with the job file any more, but copied into the
[2610]	153	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	154	#
	155	# 2600 2017-11-01 14:11:20Z raasch
[2600]	156	# cycle numbers are made three digits wide
	157	#
	158	# 2566 2017-10-20 08:50:47Z raasch
[2566]	159	# execute command for combine_plot_fields added
	160	# "TEMPDIR" renamed "tempdir"
	161	# temporary working directory for local batch jobs is created immediately within
	162	# the user's palmrun call, due to a requirement of the "grid engine" batch
	163	# system, where the working directory is given with batch directive -wd and must
	164	# already exist when the job is submitted,
	165	# informative messages in non-trace mode reduced and partly reformatted
	166	#
	167	# 2551 2017-10-18 07:25:11Z raasch
[2551]	168	# TEMPDIR added as replacement string to be used in batch directives
	169	#
	170	# 2512 2017-10-04 08:26:59Z raasch
[2507]	171	# bugfix for determining cycle numbers of NetCDF input files
	172	#
	173	# 2506 2017-09-29 08:30:37Z raasch
[2506]	174	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	175	# host configuration added to SOURCES_FOR_RUN_... folder name
	176	# host_identifier renamed host_configuration
	177	# option -W added to allow for job dependencies
	178	#
	179	# 2501 2017-09-26 11:41:55Z raasch
[2501]	180	# default value for number of cores (option -X) set to 1
	181	# bugfix for mechanism which overwrites configuration file settings with values
	182	# provided by palmrun options
	183	#
	184	# 2499 2017-09-22 16:47:58Z kanani
[2499]	185	# option -h named configuration identifier
	186	#
	187	# 2480 2017-09-19 06:24:14Z maronga
[2480]	188	# bugfix for last revision
	189	#
	190	# 2479 2017-09-19 06:12:16Z raasch
[2479]	191	# option -A (project account number) added
	192	#
	193	# 2422 2017-09-08 08:25:41Z raasch
[2410]	194	# initial revision
[2380]	195	#
	196	#--------------------------------------------------------------------------------#
	197	# palmrun - script for running PALM jobs on local and remote hosts
	198	#--------------------------------------------------------------------------------#
	199
	200
	201
	202	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	203
	204	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	205	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	206	# (TOO MANY ARGUMENTS - PROBLEM)
	207	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	208
[2610]	209	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	210	typeset -i nr_of_output_files=0
[2380]	211	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	212	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	213	# SCRIPT-OPTION ARGUMENTS
	214	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	215	typeset -i icycle inode ival maxcycle mpi_tasks
	216	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	217
	218	activation_string_list=""
	219	AddFilenames=""
	220	combine_plot_fields=true
	221	compiler_name=""
	222	compiler_name_ser=""
	223	compiler_options=""
[3236]	224	configuration_identifier="default"
[2501]	225	cores=1
[2380]	226	cores_atmos=0
	227	cores_ocean=0
	228	coupled_dist=""
	229	cpp_options=""
	230	cpumax=0
[2506]	231	create_batch_job=false
[2380]	232	create_jobfile_only=false
	233	create_remote_batch_job=false
	234	dashes=" ----------------------------------------------------------------------------"
	235	defaultqueue=""
[2506]	236	delete_temporary_catalog=true
[2380]	237	do_compile=true
	238	do_trace=false
	239	executable=""
	240	execute_command=""
	241	execution_error=false
[2762]	242	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	243	global_revision=""
	244	hostfile=""
	245	hp=""
	246	keep_data_from_previous_run=false
	247	link_local_input=false
	248	link_local_output=false
[2388]	249	linker_options=""
[2385]	250	local_jobcatalog=""
[2380]	251	locat=normal
	252	makefile=""
	253	max_par_io_str=""
	254	prc=$0
	255	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	256	do
	257	prc=`echo $prc \| cut -f2- -d"/"`
	258	done
	259	module_calls=""
[2506]	260	palmrun_memory=""
[2380]	261	palmrun_script_name=$prc
	262	openmp=false
[2506]	263	previous_job=""
[2479]	264	project_account=""
[2380]	265	queue=none
[2906]	266	read_svf=""
[2380]	267	restart_run=false
	268	return_address=""
[2385]	269	remote_jobcatalog=""
[2380]	270	remote_username=""
	271	running_in_batch_mode=false
[3313]	272	running_in_test_mode=false
[2380]	273	run_coupled_model=false
	274	run_id=""
[3236]	275	run_id_number=""
	276	run_identifier=test
[2380]	277	silent=false
	278	source_list=""
	279	source_path=""
[2501]	280	tasks_per_node=0
[2380]	281	threads_per_task=1
	282	transfer_problems=false
[2384]	283	user_source_path=""
[2506]	284	use_existing_sources_folder=""
[2380]	285	use_openmp=false
[3033]	286	version="palmrun 1.0 Rev$Rev: 3725 $"
[2380]	287	working_directory=`pwd`
	288	write_binary=""
[2906]	289	write_svf=""
[2380]	290
	291
	292	# ERROR HANDLING IN CASE OF EXIT
[2404]	293	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	294	then
	295
	296	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	297	(( i = 0 ))
	298	while (( i < iec ))
	299	do
	300	(( i = i + 1 ))
	301	printf "\n *** Execution of ERROR-command:\n"
	302	printf " >>> ${err_command[$i]}\n"
	303	eval ${err_command[$i]}
	304	done
[2566]	305	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	306	printf "\n\n+++ palmrun crashed \n\n"
	307	exit 1
	308	elif [[ $locat != normal ]]
[2380]	309	then
[3312]	310	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	311	printf "\n+++ palmrun killed by \"^C\" \n\n"
	312	exit 2
	313	else
[2566]	314	printf "\n --> palmrun finished\n\n"
[3312]	315	exit 0
[2380]	316	fi' exit
	317
	318
	319	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	320	trap 'locat=control_c
	321	exit 1
[2380]	322	' 2
	323
	324
	325	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	326	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	327	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]	328	do
	329	case $option in
	330	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	331	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	332	(b) create_batch_job=true; prc="$prc -b";;
	333	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	334	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	335	(C) restart_run=true; prc="$prc -C";;
	336	(F) create_jobfile_only=true;;
	337	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	338	(i) run_id_number=$OPTARG;;
[2380]	339	(j) running_in_batch_mode=true;;
	340	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	341	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	342	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	343	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	344	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	345	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	346	(R) return_address=$OPTARG;;
	347	(s) source_list=$OPTARG;;
[2501]	348	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	349	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	350	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	351	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	352	(v) silent=true; prc="$prc -v";;
[2506]	353	(V) use_existing_sources_folder="-V";;
[2380]	354	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	355	(W) previous_job=$OPTARG;;
[2380]	356	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	357	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	358	(y) ocean_file_appendix=true; prc="$prc -y";;
	359	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	360	(z) running_in_test_mode=true;;
[2380]	361	(Z) combine_plot_fields=false; prc="$prc -Z";;
	362	(\?) printf "\n +++ unknown option $OPTARG \n"
	363	printf "\n --> type \"$0 ?\" for available options \n"
	364	locat=parameter;exit;;
	365	esac
	366	done
	367
	368
	369	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	370	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	371	(( to_shift = $OPTIND - 1 ))
	372	shift $to_shift
	373
	374	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	375	if [[ "$1" = "?" ]]
	376	then
	377	(printf "\n *** Description of available palmrun options:\n"
	378	printf "\n Option Description Default-Value"
	379	printf "\n -a activation string list \"\" "
[2479]	380	printf "\n -A project account number ---"
[2380]	381	printf "\n -b batch-job on local machine ---"
	382	printf "\n -B do not delete temporary directory at end ---"
[3455]	383	printf "\n -c configuration identifier \"default\" "
[2380]	384	printf "\n -F create batch job file only ---"
	385	printf "\n -k keep data from previous run"
	386	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	387	printf "\n -M Makefile name Makefile"
	388	printf "\n -O threads per openMP task ---"
	389	printf "\n -q queue \"$queue\" "
[3455]	390	printf "\n -r run identifier test"
[2380]	391	printf "\n -s filenames of routines to be compiled \"\" "
	392	printf "\n must end with .f, .f90, .F, or .c !"
	393	printf "\n use \"..\" for more than one file and wildcards"
	394	printf "\n -s LM compiles all locally modified files"
	395	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	396	printf "\n -T tasks per node ---"
[2380]	397	printf "\n -u username on remote machine \"\" "
	398	printf "\n -v no prompt for confirmation ---"
[2506]	399	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	400	printf "\n -w maximum parallel io streams as given by -X"
[2506]	401	printf "\n -W name of job to wait for ---"
[2380]	402	printf "\n -x tracing of palmrun for debug purposes ---"
	403	printf "\n -X # of processors (on parallel machines) 1"
	404	printf "\n -y add appendix \"_O\" to all local output"
	405	printf "\n files (ocean precursor runs followed by"
	406	printf "\n coupled atmosphere-ocean runs) ---"
	407	printf "\n -Y run coupled model, \"#1 #2\" with"
	408	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	409	printf "\n -Z skip combine_plot_fields at the end of "
	410	printf "\n the simulation ---"
	411	printf "\n "
	412	printf "\n Possible values of positional parameter <modus>:"
	413	printf "\n \"?\" - this outline \n\n") \| more
	414	exit
	415	elif [[ "$1" != "" ]]
	416	then
	417	printf "\n +++ positional parameter $1 unknown \n"
	418	locat=parameter; exit
	419	fi
	420
	421
	422
	423	# SHORT STARTING MESSAGE
	424	printf "\n*** $version "
	425	printf "\n will be executed. Please wait ..."
	426
	427
[2506]	428	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	429	config_file=.palm.config.$configuration_identifier
	430	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	431
	432
	433	# CHECK, IF CONFIGURATION FILE EXISTS
	434	if [[ ! -f $config_file ]]
	435	then
	436	printf "\n\n +++ configuration file: "
	437	printf "\n $config_file"
	438	printf "\n does not exist"
	439	locat=connect; exit
	440	fi
	441
	442
[2762]	443	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	444	if [[ -f .palm.iofiles ]]
	445	then
[3236]	446
	447	# CHECK VERSION MISMATCH
[3573]	448	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	449	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	450	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	451	then
	452	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	453	then
	454	printf "\n\n +++ WARNING: A file connection file has been found in your"
	455	printf "\n working directory, but its revision does not match"
	456	printf "\n the revision of the default (trunk) version."
[3294]	457	printf "\n You may need to update your connection file"
	458	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	459	fi
	460	fi
	461
[2762]	462	fileconnection_file=.palm.iofiles
[3236]	463
[2762]	464	fi
	465
	466
[2380]	467	# CHECK, IF FILE CONNECTION FILE EXISTS
	468	if [[ ! -f $fileconnection_file ]]
	469	then
	470	printf "\n\n +++ file connection file: "
	471	printf "\n $fileconnection_file"
	472	printf "\n does not exist"
	473	locat=connect; exit
	474	fi
	475
	476
[2404]	477	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	478	if [[ "$activation_string_list" = "" ]]
	479	then
	480	printf "\n\n +++ no activation string list given: "
	481	printf "\n please set palmrun option \"-a\" "
	482	locat=palmrun_option; exit
	483	fi
	484
	485
	486	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	487	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	488	then
	489	write_binary=true
	490	else
	491	write_binary=false
	492	fi
	493
[2906]	494	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	495	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	496	then
	497	write_svf=true
	498	else
	499	write_svf=false
	500	fi
[2404]	501
[2906]	502	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	503	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	504	then
	505	read_svf=true
	506	else
	507	read_svf=false
	508	fi
	509
	510
[2380]	511	# READ AND EVALUATE THE CONFIGURATION-FILE
	512	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	513
	514	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	515	while read line
	516	do
	517
	518	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	519	eval line=\"$line\"
	520
	521
	522	# INTERPRET THE LINE
	523	if [[ "$(echo $line)" = "" ]]
	524	then
	525
	526	# EMPTY LINE, NO ACTION
	527	continue
	528
	529	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	530	then
	531
	532	# LINE IS A COMMENT LINE
	533	continue
	534
	535	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	536	then
	537
	538	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	539	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	540	value=`echo $line \| cut -d" " -s -f2-`
	541
	542
	543	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	544	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	545	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	546	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	547	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	548	# CONFIGURATION-FILE.
	549	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	550	then
	551	eval export $var="\$value"
	552
	553	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	554	if [[ $do_trace = true ]]
	555	then
	556	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	557	fi
	558	fi
	559
	560	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	561	then
	562
	563	# LINE DEFINES BATCH-DIRECTIVE
	564	(( ibd = ibd + 1 ))
	565	line=$(echo $line \| cut -c4-)
	566	batch_directive[$ibd]="$line"
	567
	568	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	569	then
	570
	571	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	572	# REMOTE TO A LOCAL HOST
	573	(( ibdt = ibdt + 1 ))
	574	line=$(echo $line \| cut -c5-)
	575	batch_directive_transfer[$ibdt]="$line"
	576
	577	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	578	then
	579
	580	# LINE DEFINES ERROR-COMMAND
	581	(( iec = iec + 1 ))
	582	line=$(echo $line \| cut -c4-)
	583	err_command[$iec]="$line"
	584
	585	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	586	then
	587
	588	# LINE DEFINES INPUT-COMMAND
	589	(( iic = iic + 1 ))
	590	line=$(echo $line \| cut -c4-)
	591	in_command[$iic]="$line"
	592
	593	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	594	then
	595
	596	# LINE DEFINES OUTPUT-COMMAND
	597	(( ioc = ioc + 1 ))
	598	line=$(echo $line \| cut -c4-)
	599	out_command[$ioc]="$line"
	600
	601	else
	602
	603	# SKIP ALL OTHER LINES
	604	continue
	605
	606	fi
	607
	608	done < $config_file
	609
	610
	611	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	612	if [[ "$fast_io_catalog" = "" ]]
	613	then
	614	printf "\n +++ no fast_io_catalog found in $config_file"
	615	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	616	locat=config_file; exit
	617	fi
[2380]	618	if [[ "$compiler_name" = "" ]]
	619	then
	620	printf "\n +++ no compiler name found in $config_file"
	621	printf "\n Please add line \"compiler_name ...\" to that file."
	622	locat=config_file; exit
	623	fi
	624	if [[ "$compiler_name_ser" = "" ]]
	625	then
	626	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	627	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	628	locat=config_file; exit
	629	fi
	630	if [[ "$compiler_options" = "" ]]
	631	then
	632	printf "\n +++ no compiler options found in $config_file"
	633	printf "\n Please add line \"compiler_options ...\" to that file."
	634	locat=config_file; exit
	635	fi
	636	if [[ "$execute_command" = "" ]]
	637	then
	638	printf "\n +++ no execute command found in $config_file"
	639	printf "\n Please add line \"execute_command ...\" to that file."
	640	locat=config_file; exit
	641	fi
	642
	643	if [[ "$hostfile" != "" ]]
	644	then
	645	if [[ $hostfile != auto && ! -f $hostfile ]]
	646	then
	647	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	648	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	649	locat=config_file; exit
	650	fi
	651	fi
	652
	653
	654	# DETERMINE THE CALL STATUS
	655	if [[ "$return_address" != "" ]]
	656	then
	657
	658	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	659	# BATCH MODE AND ...
	660	running_on_remote=true
	661
	662	else
	663
	664	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	665	if [[ "$remote_ip" != "" ]]
	666	then
	667
	668	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	669	create_remote_batch_job=true
	670
[3132]	671	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	672	if [[ "$remote_jobcatalog" = "" ]]
	673	then
	674	printf "\n +++ no remote jobcatalog found in $config_file"
	675	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	676	locat=config_file; exit
	677	fi
	678
	679
[2380]	680	fi
	681	running_on_remote=false
	682	fi
	683
	684
	685
	686	# READ AND EVALUATE THE I/O-FILE LIST
	687	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	688
	689	# READ THE FILE CONNECTION FILE LINE BY LINE
	690	while read line
	691	do
	692
[2669]	693	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	694	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	695	line=`echo "$line" \| tr -s " "`
[2380]	696
	697	# INTERPRET THE LINE
	698	if [[ "$(echo $line)" = "" ]]
	699	then
	700	# EMPTY LINE, NO ACTION
	701	continue
	702
	703	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	704	then
	705
	706	# LINE IS A COMMENT LINE
	707	true
	708
	709	else
	710
	711	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	712	# s2a: in/out - field
[2669]	713	# s2b: action - field (optional)
	714	s1=`echo "$line" \| cut -d" " -f1`
	715	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	716	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	717	then
[2669]	718	s2a=$s2
[2380]	719	s2b=""
	720	else
[2669]	721	s2a=`echo $s2 \| cut -d":" -f1`
	722	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	723	fi
[2669]	724	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	725	s4=`echo "$line" \| cut -d" " -s -f4`
	726	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	727	s5=`echo "$line" \| cut -d" " -s -f5`
	728	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	729
	730
	731	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	732	# INPUT- OR OUTPUT-LIST.
	733	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	734	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	735	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	736	# IS NOT CHECKED AND STORED.
[2610]	737	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	738	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	739	then
	740	found=false
	741	for actual in $activation_string_list
	742	do
	743	for formal in $s3
	744	do
	745	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	746	done
	747	done
	748	if [[ $found = true ]]
	749	then
	750	(( iin = iin + 1 ))
[2669]	751	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	752	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	753	if [[ "$s2a" = inopt ]]
	754	then
	755	optin_pre[$iin]=yes
	756	else
	757	optin_pre[$iin]=no
	758	fi
[2605]	759
	760	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	761	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	762	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	763	then
[2610]	764	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	765	fi
	766
[2610]	767	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	768	# THE WILDCARD FROM THE ENDING
	769	if [[ "${s5: -1}" = "*" ]]
	770	then
[2669]	771	if [[ "$s2b" = "di" ]]
[2610]	772	then
	773	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	774	printf "\n see file \"$fileconnection_file\", line"
	775	printf "\n$line"
	776	locat=iofiles_file; exit
	777	fi
	778	multin[$iin]=true
	779	string=${endin_pre[$iin]}
	780	endin_pre[$iin]="${string%?}"
	781	else
	782	multin[$iin]=false
	783	fi
[2380]	784	fi
[2669]	785	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	786	then
	787	found=false
	788	for actual in $activation_string_list
	789	do
	790	for formal in $s3
	791	do
[2670]	792	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	793	done
	794	done
	795	if [[ $found = true ]]
	796	then
	797	(( iout = iout + 1 ))
[2669]	798	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	799	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	800
[2669]	801	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	802	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	803	if [[ $formal = wildcard ]]
	804	then
	805	warnout_pre[$iout]=false
	806	else
	807	warnout_pre[$iout]=true
	808	fi
	809
[2610]	810	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	811	# THE WILDCARD FROM THE LOCAL FILENAME
	812	if [[ "${s1: -1}" = "*" ]]
	813	then
[2669]	814	if [[ "$s2b" = "di" ]]
[2610]	815	then
	816	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	817	printf "\n see file \"$fileconnection_file\", line"
	818	printf "\n$line"
	819	locat=iofiles_file; exit
	820	fi
	821	multout[$iout]=true
	822	string=${localout_pre[$iout]}
	823	localout_pre[$iout]="${string%?}"
	824	else
	825	multout[$iout]=false
	826	fi
[2380]	827	fi
[2669]	828	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	829	then
[2669]	830	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	831	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	832	locat=connect; exit
	833	fi
	834	IFS="$IFSALT"
	835	fi
	836
	837	done < $fileconnection_file
	838
	839
	840
[2501]	841	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	842	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	843	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	844	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	845	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	846	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	847
	848
	849
[2380]	850	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	851	if [[ $run_coupled_model = true ]]
	852	then
	853
	854	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	855	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	856
	857	if (( $cores_ocean + $cores_atmos != $cores ))
	858	then
	859
	860	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	861	printf "\n PEs (total) : $cores"
	862	printf "\n PEs (atmosphere): $cores_atmos"
	863	printf "\n PEs (ocean) : $cores_ocean"
	864	locat=coupling; exit
	865
	866	fi
	867
	868	fi
	869
	870
	871	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	872	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	873	# FOLDER
	874	if [[ $running_in_batch_mode = true ]]
	875	then
	876
[2506]	877	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	878	then
[2506]	879	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	880	printf "\n Please check the output of the palmrun-call"
	881	printf "\n that you did on your local host."
	882	locat=SOURCES_FOR_RUN; exit
	883	fi
	884
	885	else
	886
	887	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	888	# AUTOMATIC RESTART RUN
	889	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	890	if [[ $restart_run = false ]]
	891	then
	892
	893	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	894	# THE LOCAL HOST
	895	if [[ ! -d $source_path ]]
	896	then
	897	printf "\n\n +++ source path \"$source_path\" on local host"
	898	printf "\n \"$(hostname)\" does not exist"
	899	locat=source_path; exit
	900	fi
	901
[2990]	902	rm -rf ${base_directory}/${sources_for_run_catalog}
	903	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	904
	905	if [[ "$source_list" = LM ]]
	906	then
	907
	908	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	909	source_list=""
	910	cd $source_path
	911
	912
[2512]	913	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	914	if [[ ! -d ../.svn ]]
[2380]	915	then
	916	printf "\n\n +++ source directory"
	917	printf "\n \"$source_path\" "
	918	printf "\n is not under control of \"subversion\"."
[2512]	919	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	920	fi
	921
	922
	923	# LIST ALL MODIFIED SOURCE CODE FILES
	924	Filenames=""
[2404]	925	svn status > tmp_svnstatus
[2380]	926	while read line
	927	do
	928	firstc=`echo $line \| cut -c1`
	929	if [[ $firstc = M \|\| $firstc = "?" ]]
	930	then
	931	Name=`echo "$line" \| cut -c8-`
	932	extension=`echo $Name \| cut -d. -f2`
	933	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	934	then
	935	Filenames="$Filenames "$Name
	936	fi
	937	fi
[2404]	938	done < tmp_svnstatus
	939	rm -rf tmp_svnstatus
[2380]	940
	941
	942	# COPY FILES TO SOURCES_FOR_RUN_...
	943	for filename in $Filenames
	944	do
[2990]	945	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	946	source_list=$source_list"$filename "
	947	done
	948
	949	cd - > /dev/null
	950
	951
	952	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	953	elif [[ "$source_list" != "" ]]
	954	then
	955
	956	cd $source_path
	957
	958	for filename in $source_list
	959	do
	960
	961	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	962	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	963	then
	964	printf "\n +++ source code file: $filename"
	965	printf "\n must not contain (\"/\") "
	966	locat=source; exit
	967	fi
	968
	969	if [[ ! -f $filename ]]
	970	then
	971	printf "\n +++ source code file: $filename"
	972	printf "\n does not exist"
	973	locat=source; exit
	974	else
[2990]	975	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	976	fi
	977
	978	done
	979
	980	cd - > /dev/null
	981
	982	fi
	983
	984	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	985	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	986	if [[ ! -f $makefile ]]
	987	then
	988	printf "\n +++ file \"$makefile\" does not exist"
	989	locat=make; exit
	990	else
[2990]	991	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	992	fi
	993
	994
	995	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	996	if [[ "$user_source_path" != "" ]]
[2380]	997	then
	998
	999	# DOES THE DIRECTORY EXIST?
[2384]	1000	if [[ ! -d $user_source_path ]]
[2380]	1001	then
	1002
	1003	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1004	printf "\n \"$user_source_path\" "
[2380]	1005	printf "\n does not exist or is not a directory."
	1006	printf "\n No source code will be used from this directory!\n"
[2384]	1007	user_source_path=""
[2380]	1008	if [[ $silent == false ]]
	1009	then
	1010	sleep 2
	1011	fi
	1012
	1013	else
	1014
[2384]	1015	cd $user_source_path
[2380]	1016
	1017	Names=$(ls -1 *.f90 2>&1)
	1018	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1019	Names=$(ls -1 *.F90 2>&1)
	1020	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1021	Names=$(ls -1 *.F 2>&1)
	1022	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1023	Names=$(ls -1 *.f 2>&1)
	1024	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1025	Names=$(ls -1 *.c 2>&1)
	1026	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1027
	1028	cd - > /dev/null
[2990]	1029	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1030
	1031	# COPY MAKEFILE IF EXISTING
[2384]	1032	if [[ -f $user_source_path/Makefile ]]
[2380]	1033	then
	1034	printf "\n\n *** user Makefile from directory"
[2384]	1035	printf "\n \"$user_source_path\" is used \n"
[2380]	1036	if [[ $silent == false ]]
	1037	then
	1038	sleep 1
	1039	fi
[2384]	1040	cp $user_source_path/Makefile .
[2380]	1041	fi
	1042
	1043	for filename in $AddFilenames
	1044	do
	1045	if [[ -f $filename ]]
	1046	then
	1047	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1048	printf "\n source code directory \"$user_source_path\" "
[2380]	1049	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1050	printf "\n from directory \"$source_path\"."
	1051	locat=source; exit
	1052	fi
	1053
[2384]	1054	cp $user_source_path/$filename .
[2380]	1055	source_list="$source_list $filename"
	1056
	1057	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1058	if [[ $(grep -c $filename Makefile) = 0 ]]
	1059	then
	1060	printf "\n\n +++ user file \"$filename\" "
	1061	printf "\n is not listed in Makefile \n"
	1062	locat=source; exit
	1063	fi
	1064	done
	1065	cd - > /dev/null
	1066	fi
	1067	fi
	1068
	1069	# COPY CONFIGURATION FILES
[2990]	1070	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1071	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1072
	1073	# COPY SHELLSCRIPTS
[2990]	1074	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1075	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1076
	1077	fi
	1078
	1079	fi
	1080
[2605]	1081
[2380]	1082	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1083	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1084	if [[ "$global_revision" = "" ]]
	1085	then
	1086	global_revision=`svnversion $source_path 2>/dev/null`
	1087	global_revision="Rev: $global_revision"
	1088	fi
	1089
	1090
	1091	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1092	if [[ -n $cores ]]
	1093	then
	1094
	1095	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1096	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1097	if [[ $tasks_per_node = 0 ]]
[2380]	1098	then
[3025]	1099	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1100	then
	1101	printf "\n"
	1102	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1103	printf "\n set -T option or define tasks_per_node in the config file"
	1104	locat=tasks_per_node; (( iec = 0 )); exit
	1105	else
	1106	# DEFAULT FOR INTERACTIVE RUN
	1107	tasks_per_node=$cores
	1108	fi
[2380]	1109	fi
	1110
	1111	if (( cores < tasks_per_node ))
	1112	then
	1113	printf "\n"
	1114	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1115	printf "\n given values: -T $tasks_per_node -X $cores"
	1116	locat=tasks_per_node; (( iec = 0 )); exit
	1117	fi
	1118
	1119	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1120	(( mpi_tasks = cores / threads_per_task ))
	1121	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1122	(( ii = cores / tasks_per_node ))
	1123	(( remaining_cores = cores - ii * tasks_per_node ))
	1124	if (( remaining_cores > 0 ))
	1125	then
	1126	printf "\n"
	1127	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1128	printf "\n divisor of the total number of cores (option \"-X\")"
	1129	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1130	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1131	(( nodes = nodes + 1 ))
	1132	fi
	1133
	1134	fi
	1135
	1136
	1137	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1138	if [[ "$maximum_parallel_io_streams" = "" ]]
	1139	then
	1140	maximum_parallel_io_streams=$cores
	1141	fi
	1142
	1143
	1144	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1145	if [[ "$scp_port" != "" ]]
	1146	then
	1147	PORTOPT="-P $scp_port"
	1148	SSH_PORTOPT="-p $scp_port"
	1149	fi
	1150
	1151
	1152	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1153	# CONFIG-FILE
	1154	if [[ "$ssh_key" != "" ]]
	1155	then
	1156	ssh_key="-i $HOME/.ssh/$ssh_key"
	1157	fi
	1158
	1159
	1160	# SET QUEUE, IF NOT GIVEN
	1161	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1162	then
	1163
	1164	if [[ $queue = none && "$defaultqueue" = "" ]]
	1165	then
	1166	printf "\n"
	1167	printf "\n +++ no default queue given in configuration file and no queue"
	1168	printf "\n given with option -q"
[2789]	1169	locat=queue; exit
[2380]	1170	fi
	1171	if [[ $queue = none ]]
	1172	then
	1173	queue=$defaultqueue
	1174	fi
	1175
	1176	fi
	1177
	1178
	1179	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1180	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1181	(( i = 0 ))
[2610]	1182	(( nr_of_input_files = 0 ))
[2380]	1183	while (( i < iin ))
	1184	do
	1185	(( i = i + 1 ))
	1186
	1187	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1188	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1189	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1190	then
[2610]	1191	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1192	else
[3236]	1193	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1194	fi
	1195
[2610]	1196
[2380]	1197	# CHECK IF FILE EXISTS
	1198	if ! ls $filename* 1>/dev/null 2>&1
	1199	then
	1200
[2669]	1201	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1202	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1203	then
	1204	printf "\n\n +++ INPUT-file: "
[2610]	1205	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1206	then
	1207	printf "\n $filename"
	1208	else
[2610]	1209	printf "\n $filename.${extin_pre[$i]}"
[2380]	1210	fi
	1211	printf "\n does not exist\n"
	1212	locat=input; exit
	1213	else
[2610]	1214	(( nr_of_input_files = nr_of_input_files + 1 ))
	1215	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1216	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1217	actionin[$nr_of_input_files]="unavailable"
[2610]	1218	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1219	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1220	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1221	fi
[2605]	1222
[2380]	1223	else
	1224
[3236]	1225	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1226	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1227	# ENDINGS
[2610]	1228	if [[ "${multin[$i]}" = true ]]
	1229	then
	1230	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1231	ls -1 -d ${filename} > filelist 2>/dev/null
	1232	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1233	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1234
[2610]	1235	endings=""
	1236	while read line
	1237	do
	1238	# filename without path (i.e. after the last "/")
	1239	basefilename=$(basename ${line})
[2380]	1240
[2610]	1241	# check if there is an extension and remove it
	1242	ext=${basefilename##*.}
	1243	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1244	then
	1245	basefilename=${basefilename%.*}
	1246	fi
[2380]	1247
[2610]	1248	# check for an existing cycle number and remove it
	1249	cycle=${basefilename##*.}
	1250	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1251	then
	1252	basefilename=${basefilename%.*}
	1253	fi
[2600]	1254
[3236]	1255	# remove the run_identifier from the beginning
	1256	length_run_identifier=${#run_identifier}
	1257	ending=${basefilename:${length_run_identifier}}
[2610]	1258
	1259	# remove the ending given in the .iofiles from the beginning
	1260	endingstring="${endin_pre[$i]}"
	1261	length_ending=${#endingstring}
	1262	ending=${ending:${length_ending}}
	1263
	1264	if [[ "$ending" = "" ]]
[2600]	1265	then
[2610]	1266	# standard ending as given in the .iofiles
	1267	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1268	then
	1269	endings="$endings DEFAULT"
	1270	fi
[2600]	1271	else
[2610]	1272	# ending must start with "_", otherwise its a different file
	1273	if [[ "${ending:0:1}" = "_" ]]
	1274	then
	1275	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1276	then
	1277	endings="$endings $ending"
	1278	fi
	1279	fi
[2600]	1280	fi
[2610]	1281
	1282	done <filelist
[2380]	1283
[2610]	1284	rm filelist
[2380]	1285
[2600]	1286	else
[2610]	1287
	1288	# SINGLE NAME
	1289	endings=DEFAULT
	1290
[2600]	1291	fi
	1292
[2610]	1293	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1294	for ending in $endings
	1295	do
	1296
	1297	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1298	if [[ $ending = DEFAULT ]]
[2380]	1299	then
[2610]	1300	ending=""
	1301	fi
	1302
	1303	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1304	(( nr_of_input_files = nr_of_input_files + 1 ))
	1305	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1306	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1307	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1308	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1309	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1310	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1311
	1312
	1313	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1314	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1315	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1316	then
	1317	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1318	else
[3236]	1319	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1320	fi
[2610]	1321
	1322	# DETERMINE THE FILE'S CYCLE NUMBER
	1323	(( maxcycle = 0 ))
	1324	ls -1 -d $filename > filelist 2>/dev/null
	1325	ls -1 -d $filename.* >> filelist 2>/dev/null
	1326	while read line
	1327	do
	1328	# filename without path (i.e. after the last "/")
	1329	basefilename=$(basename ${line})
	1330
	1331	# check if there is an extension
	1332	extension=${basefilename##*.}
	1333	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1334	then
	1335	basefilename=${basefilename%.*}
	1336	fi
	1337
	1338	# check for an existing cycle number
	1339	cycle=${basefilename##*.}
	1340	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1341	then
[2669]	1342	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1343	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1344	(( icycle = $((10#$cycle)) ))
[2610]	1345	else
	1346	(( icycle = 0 ))
	1347	fi
	1348
	1349	if (( icycle > maxcycle ))
	1350	then
	1351	(( maxcycle = icycle ))
	1352
	1353	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1354	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1355	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1356	then
	1357	leading_zero=true
	1358	else
	1359	leading_zero=false
	1360	fi
	1361	fi
	1362
	1363	done <filelist
	1364	rm filelist
	1365
	1366	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1367	if [[ $leading_zero = true ]]
[2380]	1368	then
[2610]	1369	cyclestring=`printf "%03d" $maxcycle`
	1370	else
	1371	cyclestring=$maxcycle
[2380]	1372	fi
[2610]	1373
	1374	# APPEND CYCLE NUMBER TO FILENAME
	1375	if (( maxcycle > 0 ))
[2380]	1376	then
[2610]	1377	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1378	then
	1379	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1380	else
	1381	filename=${filename}.$cyclestring
	1382	fi
[2380]	1383	else
[2610]	1384	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1385	then
	1386	filename=${filename}.${extin[$nr_of_input_files]}
	1387	fi
[2380]	1388	fi
[2610]	1389
	1390	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1391	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1392	absnamein[$nr_of_input_files]=$filename
	1393	if (( maxcycle > 0 ))
[2380]	1394	then
[2610]	1395	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1396	then
	1397	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1398	else
[3236]	1399	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1400	fi
[2380]	1401	else
[2610]	1402	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1403	then
	1404	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1405	else
[3236]	1406	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1407	fi
[2380]	1408	fi
	1409
[2610]	1410	done
	1411
[2380]	1412	fi
[2610]	1413
[2380]	1414	done
	1415
[2610]	1416
[2380]	1417	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1418	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1419	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1420	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1421	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1422	# REMOTE HOST)
	1423	(( i = 0 ))
	1424	while (( i < iout ))
	1425	do
	1426	(( i = i + 1 ))
[2610]	1427	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1428	then
[2610]	1429	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1430	then
[2610]	1431	actionout_pre[$i]=""
	1432	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1433	then
[2610]	1434	actionout_pre[$i]=pe
	1435	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1436	then
[2610]	1437	actionout_pre[$i]=a
[2380]	1438	fi
	1439	(( maxcycle = 0 ))
[3236]	1440	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1441	eval catalogname=${pathout_pre[$i]}
[2380]	1442	if ! ls $filename* 1>/dev/null 2>&1
	1443	then
	1444
	1445	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1446	if cat /dev/null > $filename
	1447	then
	1448	rm $filename
	1449	else
	1450
	1451	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1452	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1453	if [[ ! -d $catalogname ]]
	1454	then
	1455	if mkdir -p $catalogname
	1456	then
	1457	printf "\n\n *** directory:"
	1458	printf "\n $catalogname"
	1459	printf "\n was created\n"
	1460	else
	1461	printf "\n\n +++ OUTPUT-file:"
	1462	printf "\n $filename"
	1463	printf "\n cannot be created, because directory does not exist"
	1464	printf "\n and cannot be created either"
	1465	printf "\n"
	1466	locat=output ; exit
	1467	fi 2>/dev/null
	1468	else
	1469	printf "\n\n +++ OUTPUT-file:"
	1470	printf "\n $filename"
	1471	printf "\n cannot be created, although directory exists"
	1472	printf "\n"
	1473	locat=output ; exit
	1474	fi
	1475	fi 2>/dev/null
	1476
	1477	fi
	1478
	1479	fi
	1480	done
	1481
	1482
	1483	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1484	if [[ $running_in_batch_mode = false ]]
	1485	then
[3236]	1486	run_id_number=$RANDOM
	1487	run_id=${run_identifier}.$run_id_number
[2380]	1488
[3236]	1489	tempdir=$fast_io_catalog/$run_id
[3346]	1490
	1491	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1492	export job_id=$run_id
	1493
[2380]	1494	fi
	1495
	1496
	1497	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1498	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1499	then
	1500
	1501	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1502	if [[ $ibd = 0 ]]
	1503	then
	1504	printf "\n"
	1505	printf "\n +++ no batch directives found in configuration file"
	1506	locat=config_file_batch_directives; (( iec = 0 )); exit
	1507	fi
	1508
	1509	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1510	done=false
[2384]	1511	cputime=$cpumax
[2380]	1512	while [[ $done = false ]]
	1513	do
[2384]	1514	if (( cputime == 0 ))
[2380]	1515	then
	1516	printf "\n +++ cpu-time is undefined"
	1517	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1518	printf "\n >>> "
[2384]	1519	read cputime 1>/dev/null 2>&1
[2380]	1520	else
	1521	done=true
	1522	fi
	1523	done
[2420]	1524	cpumax=$cputime
[2380]	1525
	1526	# CHECK THE MEMORY DEMAND
	1527	done=false
	1528	while [[ $done = false ]]
	1529	do
	1530	if (( memory == 0 ))
	1531	then
	1532	printf "\n +++ memory demand is undefined"
	1533	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1534	printf "\n >>> "
	1535	read memory 1>/dev/null 2>&1
	1536	else
	1537	done=true
	1538	fi
	1539	done
	1540
	1541	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1542	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1543	then
	1544	while [[ -z $remote_username ]]
	1545	do
[2420]	1546	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1547	printf "\n >>> Please type username:"
	1548	printf "\n >>> "
	1549	read remote_username
	1550	done
	1551	fi
	1552
	1553	else
	1554
[2420]	1555	if [[ $running_in_batch_mode = false ]]
	1556	then
	1557	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1558	cpumax=$cputime
	1559	else
	1560	cputime=$cpumax
	1561	fi
[2380]	1562
	1563	fi
	1564
	1565
	1566	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1567	(( cpu_hours = cputime / 3600 ))
	1568	(( resttime = cputime - cpu_hours * 3600 ))
	1569	(( cpu_minutes = resttime / 60 ))
	1570	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1571	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1572
	1573
	1574	# OUTPUT OF THE PALMRUN-HEADER
	1575	calltime=$(date)
	1576	printf "\n"
	1577	printf "#------------------------------------------------------------------------# \n"
	1578	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1579	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1580	printf "\| \| \n"
	1581	column1="called on:"; column2=$(hostname)
	1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1583	if [[ $create_remote_batch_job = true ]]
	1584	then
[3236]	1585	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1586	else
	1587	if [[ $running_on_remote = true ]]
	1588	then
[3236]	1589	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1590	else
[3236]	1591	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1592	fi
	1593	fi
	1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1595
	1596	column1="running in:"
	1597	if [[ $running_in_batch_mode = true ]]
	1598	then
	1599	column2="batch job mode"
	1600	else
	1601	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1602	then
	1603	column2="job creation mode"
	1604	else
	1605	column2="interactive run mode"
	1606	fi
	1607	fi
	1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1609
[2479]	1610	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1611	then
[2480]	1612	if [[ "$project_account" != "" ]]
[2479]	1613	then
	1614	column1="project account number:"
	1615	column2="$project_account"
	1616	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1617	fi
	1618	fi
	1619
[2380]	1620	if [[ -n $cores ]]
	1621	then
	1622	if [[ $run_coupled_model = false ]]
	1623	then
	1624	column1="number of cores:"; column2=$cores
	1625	else
	1626	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1627	fi
	1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1629	fi
	1630	if [[ -n $tasks_per_node ]]
	1631	then
	1632	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1634	if (( remaining_cores > 0 ))
	1635	then
	1636	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1638	fi
	1639	fi
	1640	if [[ $maximum_parallel_io_streams != $cores ]]
	1641	then
	1642	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1644	fi
	1645	if [[ $use_openmp = true ]]
	1646	then
	1647	column1="threads per task:"; column2="$threads_per_task"
	1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1649	fi
[2384]	1650	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1651	then
[2506]	1652	column1="memory demand / PE":; column2="$memory MB"
	1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1654	column1="job cpu time (h:m:s):"; column2="$timestring"
	1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1656	fi
[2380]	1657	printf "\| \| \n"
	1658	if [[ "$source_list" != "" ]]
	1659	then
	1660	if [[ "$make_options" != "" ]]
	1661	then
	1662	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1664	line=$(echo "$make_options" \| cut -c46-)
	1665	while [[ "$line" != "" ]]
	1666	do
	1667	column1=""
	1668	column2=$(echo "$line" \| cut -c-45)
	1669	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1670	line=$(echo "$line" \| cut -c46-)
	1671	done
	1672	fi
	1673	fi
	1674
	1675	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1677	line=$(echo "$cpp_options" \| cut -c46-)
	1678	while [[ "$line" != "" ]]
	1679	do
	1680	column1=""
	1681	column2=$(echo "$line" \| cut -c-45)
	1682	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1683	line=$(echo "$line" \| cut -c46-)
	1684	done
	1685
	1686	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1687	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1688	line=$(echo "$compiler_options" \| cut -c46-)
	1689	while [[ "$line" != "" ]]
	1690	do
	1691	column1=""
	1692	column2=$(echo "$line" \| cut -c-45)
	1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1694	line=$(echo "$line" \| cut -c46-)
	1695	done
	1696
[2388]	1697	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1698	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1699	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1700	while [[ "$line" != "" ]]
	1701	do
	1702	column1=""
	1703	column2=$(echo "$line" \| cut -c-45)
	1704	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1705	line=$(echo "$line" \| cut -c46-)
	1706	done
	1707
	1708	if [[ "$login_init_cmd" != "" ]]
	1709	then
	1710	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1712	line=$(echo "$login_init_cmd" \| cut -c46-)
	1713	while [[ "$line" != "" ]]
	1714	do
	1715	column1=""
	1716	column2=$(echo "$line" \| cut -c-45)
	1717	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1718	line=$(echo "$line" \| cut -c46-)
	1719	done
	1720	fi
	1721
	1722	if [[ "$module_commands" != "" ]]
	1723	then
	1724	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1725	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1726	line=$(echo "$module_commands" \| cut -c46-)
	1727	while [[ "$line" != "" ]]
	1728	do
	1729	column1=""
	1730	column2=$(echo "$line" \| cut -c-45)
	1731	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1732	line=$(echo "$line" \| cut -c46-)
	1733	done
	1734	fi
	1735	printf "\| \| \n"
[3236]	1736	column1="run identifier:"; column2=$run_identifier
[2380]	1737	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1738	column1="activation string list:"; column2=$(echo $activation_string_list)
	1739	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1740
	1741	if [[ "$ocean_file_appendix" = true ]]
	1742	then
	1743	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1744	fi
	1745
	1746	if [[ "$source_list" != "" ]]
	1747	then
	1748	printf "\| \| \n"
	1749	printf "\| Files to be compiled: \| \n"
	1750	line=$source_list
	1751	while [[ "$line" != "" ]]
	1752	do
	1753	linestart=$(echo $line \| cut -c-70)
	1754	printf "\| %-70s \| \n" "$linestart"
	1755	line=$(echo "$line" \| cut -c71-)
	1756	done
	1757	fi
	1758	printf "#------------------------------------------------------------------------#"
	1759
	1760
	1761
	1762	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1763	if [[ $do_trace = true ]]
	1764	then
	1765	(( i = 0 ))
[2610]	1766	while (( i < nr_of_input_files ))
[2380]	1767	do
	1768	(( i = i + 1 ))
	1769	if (( i == 1 ))
	1770	then
	1771	printf "\n\n >>> INPUT-file assignments:\n"
	1772	fi
	1773	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1774	done
	1775	(( i = 0 ))
	1776	while (( i < iout ))
	1777	do
	1778	(( i = i + 1 ))
	1779	if (( i == 1 ))
	1780	then
	1781	printf "\n\n >>> OUTPUT-file assignments:\n"
	1782	fi
	1783	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1784	done
	1785	(( i = 0 ))
	1786	while (( i < iic ))
	1787	do
	1788	(( i = i + 1 ))
	1789	if (( i == 1 ))
	1790	then
	1791	printf "\n\n >>> INPUT-commands:\n"
	1792	fi
	1793	printf "\n ${in_command[$i]}"
	1794	done
	1795	(( i = 0 ))
	1796	while (( i < ioc ))
	1797	do
	1798	(( i = i + 1 ))
	1799	if (( i == 1 ))
	1800	then
	1801	printf "\n\n >>> OUTPUT-commands:\n"
	1802	fi
	1803	printf "\n ${out_command[$i]}"
	1804	done
	1805	fi
	1806
	1807	# QUERY FOR CONTINUE
	1808	if [[ $silent = false && $running_in_batch_mode = false ]]
	1809	then
	1810	antwort=dummy
	1811	printf "\n\n"
	1812	printf " >>> everything o.k. (y/n) ? "
	1813	while read antwort
	1814	do
	1815	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1816	then
	1817	printf " >>> everything o.k. (y/n) ? "
	1818	else
	1819	break
	1820	fi
	1821	done
	1822	if [[ $antwort = n \|\| $antwort = N ]]
	1823	then
	1824	locat=user_abort; (( iec = 0 )); exit
	1825	fi
	1826	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1827	then
[2566]	1828	printf "\n *** batch-job will be created and submitted"
[2380]	1829	else
[2566]	1830	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1831	fi
	1832	fi
	1833
	1834
	1835
	1836	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1837	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1838	then
	1839
	1840	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1841	then
[2566]	1842	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1843	else
[2566]	1844	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1845	fi
	1846
[2422]	1847	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1848	# IT SHALL BE CREATED
	1849	ask_for_make_depository=false
	1850	if [[ $create_remote_batch_job = true ]]
	1851	then
	1852
	1853	line=`grep %base_directory $config_file`
[3236]	1854	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1855	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1856
[3236]	1857	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1858	then
	1859	printf "\n\n +++ make depository \"${make_depository}\""
	1860	printf "\n on remote host not found!"
	1861	ask_for_make_depository=true
	1862	fi
[3236]	1863	rm ${configuration_identifier}_last_make_protokoll
[2422]	1864
	1865	else
	1866
	1867	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1868	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1869	if [[ ! -d ${make_depository} ]]
	1870	then
	1871	printf "\n\n +++ make depository \"${make_depository}\""
	1872	printf "\n on local host not found!"
	1873	ask_for_make_depository=true
	1874	fi
	1875
	1876	fi
	1877
	1878	if [[ $ask_for_make_depository = true ]]
	1879	then
	1880
	1881	antwort=dummy
	1882	printf "\n\n"
	1883	printf " >>> Create a new one (y/n) ? "
	1884	while read antwort
	1885	do
	1886	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1887	then
	1888	printf " >>> Create a new one (y/n) ? "
	1889	else
	1890	break
	1891	fi
	1892	done
	1893	if [[ $antwort = n \|\| $antwort = N ]]
	1894	then
	1895	locat=user_abort; (( iec = 0 )); exit
	1896	fi
	1897
[2566]	1898	if [[ $do_trace = true ]]
	1899	then
[3455]	1900	palmbuild -c $configuration_identifier
[2566]	1901	else
[3455]	1902	palmbuild -v -c $configuration_identifier
[2566]	1903	fi
[2422]	1904
[3312]	1905	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1906	then
	1907
	1908	# ABORT IN CASE OF COMPILATION PROBLEMS
	1909	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1910	locat=make_depository
	1911	exit
	1912	else
	1913	echo " *** now continue with creating executable and other sources"
	1914	fi
	1915
	1916	fi
	1917
[2566]	1918	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1919	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1920
[3312]	1921	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1922	then
	1923
	1924	# ABORT IN CASE OF COMPILATION PROBLEMS
	1925	printf "\n +++ error while creating executable and/or other sources"
	1926	locat=execution
[2990]	1927	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1928	exit
	1929
	1930	else
	1931
[2566]	1932	printf " *** executable and other sources created\n"
[2990]	1933	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1934
	1935	fi
	1936
	1937	fi
	1938
	1939
[2669]	1940	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1941	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1942	if [[ $create_remote_batch_job = true ]]
	1943	then
	1944	(( i = 0 ))
[2610]	1945	while (( i < nr_of_input_files ))
[2605]	1946	do
	1947	(( i = i + 1 ))
[2669]	1948	if [[ "${actionin[$i]}" = tr ]]
[2605]	1949	then
	1950	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1951	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1952	fi
	1953	done
	1954	if (( i > 0 ))
	1955	then
[3025]	1956	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1957	fi
	1958	fi
	1959
	1960
[2380]	1961	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1962	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1963	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1964	then
	1965
	1966	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1967	if [[ $running_in_batch_mode = false ]]
	1968	then
	1969	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1970	# FOLDER
[2566]	1971	mkdir -p $tempdir
	1972	chmod go+rx $tempdir
	1973	cd $tempdir
	1974	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1975	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1976
	1977	else
	1978
	1979	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1980	printf "\n *** running in temporary directory: $tempdir"
[2380]	1981
	1982	fi
	1983
	1984
	1985	# PROVIDE THE INPUT FILES
	1986	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1987	optional_files_missing=false
[2380]	1988	(( i = 0 ))
[2610]	1989	while (( i < nr_of_input_files ))
[2380]	1990	do
	1991	(( i = i + 1 ))
	1992	if (( i == 1 ))
	1993	then
	1994	printf "\n\n *** providing INPUT-files:\n$dashes"
	1995	fi
	1996
	1997
	1998	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1999	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2000	then
[2669]	2001	optional_files_missing=true
[2380]	2002	continue
	2003	fi
	2004
	2005	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2006	files_for_cores=false; filetype=file
	2007	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2008	then
	2009	files_for_cores=true; filetype=files
	2010	actionin[$i]=""
	2011	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2012	then
	2013	actionin[$i]=""
	2014	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2015	then
	2016	files_for_cores=true; filetype=files
	2017	actionin[$i]="ln"
	2018	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2019	then
	2020	actionin[$i]="ln"
	2021	fi
	2022
	2023	if [[ $files_for_cores = true ]]
	2024	then
	2025	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2026	else
	2027	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2028	fi
	2029
	2030	# INPUT-FILES TO BE LINKED
	2031	if [[ "${actionin[$i]}" = ln ]]
	2032	then
	2033
	2034	printf "\n $filetype will be linked"
	2035	if [[ $files_for_cores = false ]]
	2036	then
	2037	if [[ -f "${absnamein[$i]}" ]]
	2038	then
	2039	ln ${absnamein[$i]} ${localin[$i]}
	2040	got_tmp[$i]=true
	2041	fi
	2042	else
	2043	if [[ -d "${absnamein[$i]}" ]]
	2044	then
[2396]	2045	mkdir -p ${localin[$i]}
[2380]	2046	cd ${absnamein[$i]}
	2047	for file in $(ls *)
	2048	do
[2566]	2049	ln $file $tempdir/${localin[$i]}
[2380]	2050	done >\|/dev/null 2>&1
[2566]	2051	cd $tempdir
[2380]	2052	fi
	2053
	2054	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2055	if [[ ! -f "${localin[$i]}/_000000" ]]
	2056	then
	2057	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2058	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2059	fi
	2060
	2061	got_tmp[$i]=true
	2062	fi
	2063	fi
	2064
	2065	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2066	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2067	then
	2068
	2069	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2070	then
	2071
	2072	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2073	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2074	printf "\n file will be provided for $cores processors"
[2396]	2075	mkdir -p ${localin[$i]}
[2380]	2076	ival=$cores
	2077	(( ii = 0 ))
	2078	while (( ii <= ival-1 ))
	2079	do
	2080	if (( ii < 10 ))
	2081	then
	2082	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2083	elif (( ii < 100 ))
	2084	then
	2085	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2086	elif (( ii < 1000 ))
	2087	then
	2088	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2089	else
	2090	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2091	fi
	2092	(( ii = ii + 1 ))
	2093	done
	2094
	2095	else
	2096
	2097	if [[ $files_for_cores = true ]]
	2098	then
	2099
	2100	# PROVIDE FILES FOR EACH CORE
	2101	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2102	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2103	printf "\n providing $cores files for the respective cores"
[2396]	2104	mkdir -p ${localin[$i]}
[2380]	2105	if [[ $link_local_input = true ]]
	2106	then
	2107	printf " files will be linked\n"
	2108	cd ${absnamein[$i]}
	2109	for file in $(ls *)
	2110	do
	2111	ln -f $file ${localin[$i]}
	2112	done
[2566]	2113	cd $tempdir
[2380]	2114	fi
	2115
	2116	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2117	if [[ ! -f "${localin[$i]}/_000000" ]]
	2118	then
	2119	if [[ $link_local_input = true ]]
	2120	then
	2121	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2122	fi
	2123	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2124	fi
	2125
	2126	else
	2127
	2128	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2129	if [[ $link_local_input = true ]]
	2130	then
	2131	printf " file will be linked\n"
	2132	ln -f ${absnamein[$i]} ${localin[$i]}
	2133	fi
[2605]	2134	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2135	if [[ ! -f "${localin[$i]}" ]]
	2136	then
	2137	if [[ $link_local_input = true ]]
	2138	then
	2139	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2140	fi
[2669]	2141	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2142	then
	2143	mv ${absnamein[$i]} ${localin[$i]}
	2144	else
	2145	cp ${absnamein[$i]} ${localin[$i]}
	2146	fi
[2380]	2147	fi
	2148	fi
	2149	fi
	2150	fi
	2151
	2152	done
	2153	if (( i != 0 ))
	2154	then
[2669]	2155	if [[ $optional_files_missing = true ]]
	2156	then
	2157	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2158	fi
[2380]	2159	printf "\n$dashes\n *** all INPUT-files provided \n"
	2160	fi
	2161
	2162
	2163	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2164	(( i = 0 ))
	2165	while (( i < iic ))
	2166	do
	2167	(( i = i + 1 ))
	2168	if (( i == 1 ))
	2169	then
	2170	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2171	fi
	2172	printf "\n >>> ${in_command[$i]}"
	2173	eval ${in_command[$i]}
	2174	if (( i == iic ))
	2175	then
	2176	printf "\n$dashes\n"
	2177	fi
	2178	done
	2179
	2180
[3313]	2181	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2182	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2183	then
	2184	progress_bar_disabled=true
	2185	else
	2186	progress_bar_disabled=false
	2187	fi
	2188
	2189
[2380]	2190	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2191	# (FILE ENVPAR WILL BE READ BY PALM)
	2192	cat > ENVPAR << EOF
[3236]	2193	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2194	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2195	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2196	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2197	maximum_cpu_time_allowed = ${cpumax}.,
	2198	revision = '$global_revision',
[3313]	2199	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2200
	2201	EOF
	2202
	2203
	2204	# STARTING THE EXECUTABLE
	2205	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2206	PATH=$PATH:$tempdir
[2380]	2207
	2208
	2209	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2210	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2211	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2212	eval line=\"$line\"
	2213	execute_command="$line"
	2214
	2215
	2216	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2217	if [[ "$execute_command_for_combine" = "" ]]
	2218	then
	2219	eval line2=\"$line2\"
	2220	execute_command_for_combine="$line2"
	2221	fi
	2222
[2380]	2223
	2224
	2225	# PROVIDE A HOSTFILE, IF REQUIRED
	2226	if [[ "$hostfile" != "" ]]
	2227	then
	2228
	2229	if [[ $hostfile = auto ]]
	2230	then
	2231	# CREATE A NEW HOSTFILE
	2232	(( ii = 1 ))
	2233	while (( ii <= cores / threads_per_task ))
	2234	do
	2235	echo $(hostname) >> hostfile
	2236	(( ii = ii + 1 ))
	2237	done
	2238	if (( cores / threads_per_task == 0 ))
	2239	then
	2240	echo $(hostname) >> hostfile
	2241	fi
	2242
	2243	else
	2244	cp $hostfile hostfile
	2245	fi
	2246	eval line=\"`head -n $ii hostfile`\"
	2247	printf "\n *** running on: $line"
	2248	fi
	2249
	2250
	2251
	2252	# SET THE NUMBER OF OPENMP-THREADS
	2253	if [[ $use_openmp = true ]]
	2254	then
	2255	export OMP_NUM_THREADS=$threads_per_task
	2256	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2257	else
	2258	export OMP_NUM_THREADS=1
	2259	fi
	2260
	2261
[2610]	2262	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2263	if [[ $run_coupled_model = false ]]
	2264	then
	2265	if [[ "$ocean_file_appendix" = true ]]
	2266	then
	2267	echo "precursor_ocean" > coupling_steering
	2268	else
	2269	echo "precursor_atmos" > coupling_steering
	2270	fi
	2271	else
	2272	(( iia = $cores_atmos / $threads_per_task ))
	2273	(( iio = $cores_ocean / $threads_per_task ))
	2274	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2275	printf "\n\n"
	2276	echo "coupled_run $iia $iio" > coupling_steering
	2277	fi
	2278
	2279	printf "\n *** execute command:"
	2280	printf "\n \"$execute_command\" \n\n"
	2281
	2282
[3393]	2283	if [[ $progress_bar_disabled = true ]]
[2380]	2284	then
[3402]	2285	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2286	exit_code=${PIPESTATUS[0]}
	2287	else
	2288	$execute_command < coupling_steering &> >(tee STDOUT)
	2289	exit_code=${PIPESTATUS[0]}
	2290	fi
[2380]	2291
[3393]	2292	if [[ ${exit_code} != 0 ]]
	2293	then
	2294
[2380]	2295	# ABORT IN CASE OF RUNTIME ERRORS
	2296	printf "\n +++ runtime error occured"
	2297	locat=execution
	2298	exit
	2299
	2300	else
	2301
	2302	printf "\n$dashes\n *** execution finished \n"
	2303
	2304	fi
	2305
	2306
	2307	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2308	# BY EACH CORE INTO ONE FILE
	2309	if [[ ! -f combine_plot_fields.x ]]
	2310	then
	2311
	2312	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2313	printf "\n 2d- and/or 3d-data may be incomplete!"
	2314	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2315
	2316	elif [[ "$combine_plot_fields" == true ]]
	2317	then
	2318
	2319	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2320	$execute_command_for_combine
	2321
	2322	else
	2323
	2324	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2325	# DATA OUTPUT
[2380]	2326	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2327	fi
	2328
	2329
	2330
	2331	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2332	(( i = 0 ))
	2333	while (( i < ioc ))
	2334	do
	2335	(( i = i + 1 ))
	2336	if (( i == 1 ))
	2337	then
	2338	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2339	fi
[2799]	2340
	2341	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2342	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2343
[2380]	2344	printf "\n >>> ${out_command[$i]}"
	2345	eval ${out_command[$i]}
	2346	if (( i == ioc ))
	2347	then
	2348	printf "\n$dashes\n"
	2349	fi
	2350	done
	2351
	2352
[2610]	2353	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2354	# WILDCARDS
[2380]	2355	(( i = 0 ))
[2610]	2356	(( nr_of_output_files = 0 ))
	2357
[2380]	2358	while (( i < iout ))
	2359	do
[2610]	2360
[2380]	2361	(( i = i + 1 ))
[2610]	2362
	2363	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2364	# CREATE A LIST FOR THE DETECTED ENDINGS
	2365	if [[ "${multout[$i]}" = true ]]
	2366	then
	2367	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2368	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2369	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2370
	2371	endings="DEFAULT"
	2372	while read line
	2373	do
	2374	# remove the local name from the beginning
	2375	localnamestring="${localout_pre[$i]}"
	2376	length_localname=${#localnamestring}
	2377	ending=${line:${length_localname}}
	2378
	2379	if [[ "$ending" != "" ]]
	2380	then
	2381	endings="$endings $ending"
	2382	fi
	2383
	2384	done <filelist
	2385
	2386	rm filelist
	2387
	2388	else
	2389
	2390	# SINGLE NAME
	2391	endings=DEFAULT
	2392
	2393	fi
	2394
	2395	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2396	for ending in $endings
	2397	do
	2398
	2399	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2400	if [[ $ending = DEFAULT ]]
	2401	then
	2402	ending=""
	2403	fi
	2404
	2405	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2406	(( nr_of_output_files = nr_of_output_files + 1 ))
	2407	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2408	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2409	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2410	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2411	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2412	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2413	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2414
	2415	done
	2416
	2417	done
	2418
	2419
	2420
	2421
	2422	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2423	(( i = 0 ))
	2424	while (( i < nr_of_output_files ))
	2425	do
	2426	(( i = i + 1 ))
[2380]	2427	if (( i == 1 ))
	2428	then
	2429	printf "\n\n *** saving OUTPUT-files:"
	2430
	2431	# GET RUN NUMBER ASSIGNED BY PALM
	2432	if [[ -f RUN_NUMBER ]]
	2433	then
	2434	read run_number < RUN_NUMBER
	2435	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2436	usecycle_option="-U $run_number"
	2437	else
	2438	run_number=0
	2439	usecycle_option=""
	2440	fi
	2441	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2442	then
[2404]	2443	printf "\n *** in case of SCP transfers to local host"
	2444	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2445	fi
	2446	printf "\n$dashes"
	2447	fi
	2448
	2449	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2450	then
	2451
[3236]	2452	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2453
	2454	# DETERMINE THE CYCLE NUMBER
	2455	ls -1 -d $filename > filelist 2>/dev/null
	2456	ls -1 -d $filename.* >> filelist 2>/dev/null
	2457	while read line
	2458	do
	2459
	2460	# filename without path (i.e. after the last "/")
	2461	basefilename=$(basename ${line})
	2462
	2463	# check if there is an extension
	2464	extension=${basefilename##*.}
	2465	if [[ "$extension" = "${extout[$i]}" ]]
	2466	then
	2467	basefilename=${basefilename%.*}
	2468	fi
	2469
	2470	# check for an existing cycle number
	2471	cycle=${basefilename##*.}
	2472	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2473	then
[2669]	2474	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2475	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2476	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2477	else
	2478	(( icycle = 1 ))
	2479	fi
	2480
	2481	if (( icycle > maxcycle ))
	2482	then
	2483	(( maxcycle = icycle ))
	2484	fi
	2485
	2486	done <filelist
	2487	rm filelist
	2488
	2489
	2490	# SET THE CYCLE NUMBER
	2491	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2492	if [[ "${actionout[$i]}" = a ]]
	2493	then
	2494	(( maxcycle = maxcycle - 1 ))
	2495	fi
	2496
	2497	(( cycnum[$i] = maxcycle ))
	2498	pathout[$i]=$filename
	2499
	2500
	2501	# ADD CYCLE NUMBER TO FILENAME
	2502	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2503	if [[ "${actionout[$i]}" != "a" ]]
	2504	then
	2505	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2506	# WITH AN EXISTING CYCLE NUMBER
	2507	if (( run_number >= cycnum[$i] ))
	2508	then
	2509	(( cycnum[$i] = run_number ))
	2510	else
	2511	if (( run_number > 0 ))
	2512	then
	2513	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2514	fi
	2515	fi
	2516	fi
	2517	if (( cycnum[$i] > 0 ))
	2518	then
[2600]	2519	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2520	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2521	fi
	2522	fi
	2523
	2524	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2525	files_for_cores=false; filetype=file
	2526	link_local_output=false
	2527	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2528	then
	2529	files_for_cores=true; filetype=directory
	2530	actionout[$i]=""
	2531	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2532	then
	2533	actionout[$i]=""
	2534	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2535	then
	2536	files_for_cores=true; filetype=directory
	2537	link_local_output=true
	2538	actionout[$i]=""
	2539	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2540	then
	2541	link_local_output
	2542	actionout[$i]=""
	2543	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2544	then
	2545	files_for_cores=true; filetype=directory
	2546	actionout[$i]="tr"
	2547	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2548	then
	2549	actionout[$i]="tr"
	2550	fi
	2551
	2552	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2553	then
[2669]	2554	if [[ ${warnout[$i]} = true ]]
	2555	then
	2556	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2557	fi
[2380]	2558	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2559	then
[2669]	2560	if [[ ${warnout[$i]} = true ]]
	2561	then
	2562	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2563	fi
[2380]	2564	else
	2565
	2566
	2567	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2568	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2569	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2570	then
	2571	if [[ $running_on_remote = true ]]
	2572	then
	2573
	2574	# SET OPTIONS FOR TRANSFER
	2575	if [[ "${actionout[$i]}" = tr ]]
	2576	then
	2577	if [[ $files_for_cores = false ]]
	2578	then
	2579	catalog_option=""
	2580	catalog_string=""
	2581	else
	2582	catalog_option="-c"
	2583	catalog_string="/"
	2584	fi
	2585	append_option=""
	2586	append_string=""
	2587	else
	2588	append_option="-A"
	2589	append_string="append"
	2590	fi
	2591
	2592	transfer_failed=false
	2593	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2594	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2595
	2596	# TRANSFER VIA SCP
	2597	if [[ "$remote_loginnode" != "" ]]
	2598	then
[3534]	2599	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]	2600	else
[3236]	2601	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]	2602	fi
[3312]	2603	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2604
	2605
	2606	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2607	if [[ $transfer_failed = true ]]
	2608	then
	2609	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2610	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2611
	2612	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2613	eval local_catalog=${pathout[$i]}
	2614	if [[ ! -d $local_catalog ]]
	2615	then
	2616	printf " *** local directory does not exist. Trying to create:\n"
	2617	printf " $local_catalog \n"
	2618	mkdir -p $local_catalog
	2619	fi
[3236]	2620	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2621	transfer_problems=true
	2622	fi
	2623
	2624	else
	2625
	2626	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2627	# BE COPIED OR APPENDED ON THIS MACHINE
	2628	if [[ "${actionout[$i]}" = tr ]]
	2629	then
	2630	actionout[$i]=""
	2631	else
	2632	actionout[$i]="a"
	2633	fi
	2634	fi
	2635	fi
	2636
	2637
	2638	# APPEND ON THIS MACHINE
	2639	if [[ "${actionout[$i]}" = "a" ]]
	2640	then
	2641	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2642	then
	2643	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2644	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2645	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2646	else
	2647	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2648	printf "\n ${pathout[$i]}\n"
	2649	cat ${localout[$i]} >> ${pathout[$i]}
	2650	fi
	2651	fi
	2652
	2653	# COPY ON THIS MACHINE
	2654	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2655	# ON DIFFERENT FILE-SYSTEMS
	2656	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2657	then
	2658
	2659	# COPY IN CASE OF RUNS ON SINGLE CORES
	2660	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2661	then
	2662	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2663	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2664	if [[ $link_local_output = true ]]
	2665	then
	2666	printf " file will be linked\n"
	2667	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2668	fi
	2669	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2670	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2671	then
	2672	if [[ $link_local_output = true ]]
	2673	then
	2674	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2675	fi
	2676	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2677	else
	2678	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2679	fi
	2680	else
	2681	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2682	printf "\n ${pathout[$i]}\n"
	2683	if [[ $link_local_output = true ]]
	2684	then
	2685	printf " file will be linked\n"
	2686	ln -f ${localout[$i]} ${pathout[$i]}
	2687	fi
	2688	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2689	if [[ ! -f "${pathout[$i]}" ]]
	2690	then
	2691	if [[ $link_local_output = true ]]
	2692	then
	2693	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2694	fi
	2695	cp ${localout[$i]} ${pathout[$i]}
	2696	else
	2697	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2698	fi
	2699	fi
	2700
	2701	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2702	then
	2703
	2704	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2705	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2706	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2707	printf "\n ${pathout[$i]}\n"
	2708	if [[ $link_local_output = true ]]
	2709	then
	2710	printf " files will be linked\n"
[2396]	2711	mkdir -p ${pathout[$i]}
[2380]	2712	cd ${localout[$i]}
	2713	for file in $(ls *)
	2714	do
	2715	ln -f $file ${pathout[$i]}
	2716	done >\|/dev/null 2>&1
[2566]	2717	cd $tempdir
[2380]	2718	fi
	2719
	2720	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2721	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2722	then
	2723	if [[ $link_local_output = true ]]
	2724	then
	2725	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2726	fi
[3025]	2727	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2728	cp -r ${localout[$i]}/* ${pathout[$i]}
	2729	fi
	2730
	2731	fi
	2732	fi
	2733	done
	2734
	2735	if (( i != 0 ))
	2736	then
	2737	if [[ $transfer_problems = true ]]
	2738	then
	2739	printf "\n$dashes\n *** OUTPUT-files saved"
	2740	printf "\n +++ WARNING: some data transfers failed! \n"
	2741	else
	2742	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2743	fi
	2744	fi
	2745
	2746
	2747	# IF REQUIRED, START A RESTART-JOB
	2748	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2749	if [[ -f CONTINUE_RUN ]]
	2750	then
	2751
	2752	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2753	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2754	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2755	# -b START A BATCH JOB
	2756	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2757	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2758	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2759
[2957]	2760	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2761	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2762	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2763	then
	2764	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2765	fi
[2380]	2766
	2767	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2768	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2769	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2770	then
[2381]	2771	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2772	fi
	2773
	2774
	2775	# START THE RESTART-JOB
	2776	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2777	echo " $prc"
	2778	printf "\n$dashes\n"
	2779	if [[ $running_on_remote = true ]]
	2780	then
	2781
	2782	echo "*** ssh will be used to initiate restart-runs!"
	2783	echo " return_address=\"$return_address\" "
	2784	echo " return_username=\"$local_username\" "
	2785
	2786	if [[ "$remote_loginnode" != "" ]]
	2787	then
[3534]	2788	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]	2789	else
[3534]	2790	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2791	fi
	2792
	2793	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2794	sleep 30
	2795
	2796	else
	2797
	2798	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2799	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2800
	2801	fi
	2802
[3132]	2803	# CHECK, IF RESTART JOB HAS BEEN STARTED
[3725]	2804	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
[3132]	2805	then
	2806	printf "\n$dashes\n +++ creating restart run failed \n"
	2807	locat=create_restart
[3455]	2808	rm palmrun_restart.log
[3132]	2809	exit
[3725]	2810	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
	2811	then
	2812	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
	2813	locat=create_restart
	2814	rm palmrun_restart.log
	2815	exit
[3132]	2816	else
	2817	printf "\n$dashes\n *** restart run initiated \n"
	2818	rm palmrun_restart.log
	2819	fi
[2380]	2820
[3132]	2821
[2380]	2822	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2823	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2824	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2825	# MAY BE VERY HUGE)
	2826	(( i = 0 ))
[2610]	2827	while (( i < nr_of_input_files ))
[2380]	2828	do
	2829	(( i = i + 1 ))
	2830	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2831	then
	2832	rm -r ${absnamein[$i]}
	2833	fi
	2834	done
	2835
	2836	fi
	2837
	2838
	2839	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2840	cd $HOME
[2566]	2841	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2842
	2843
	2844	else
	2845
	2846
	2847	# PREPARING ACTIONS,
	2848	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2849
	2850	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2851	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2852	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2853	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2854	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2855	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2856	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2857	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2858	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2859	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2860	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2861	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2862	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2863	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2864	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2865	if [[ $create_remote_batch_job = true ]]
	2866	then
	2867	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2868	if [[ $do_trace = true ]]
	2869	then
	2870	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2871	fi
[2380]	2872	elif [[ $create_batch_job = true ]]
	2873	then
	2874	palmrun_com=${palmrun_com}" -j"
[2420]	2875	if [[ $do_trace = true ]]
	2876	then
	2877	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2878	fi
[2380]	2879	fi
	2880
	2881
	2882	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2883	# REMOTE HOST
[3236]	2884	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2885	job_protocol_file=$job_protocol_file_local
	2886	if [[ $create_remote_batch_job = true ]]
	2887	then
[3236]	2888	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2889	job_protocol_file=$job_protocol_file_remote
	2890	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2891	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2892	fi
	2893
	2894
	2895	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2896	jobfile=jobfile.$run_id_number
[2380]	2897
	2898
	2899	# FIRST CREATE THE BATCH DIRECTIVES
	2900	(( i = 0 ))
	2901	while (( i < ibd ))
	2902	do
	2903	(( i = i + 1 ))
[2693]	2904	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2905	eval line=\"$line\"
	2906	echo "$line" >> $jobfile
	2907	done
	2908	echo " " >> $jobfile
	2909
	2910
	2911	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2912	# PROTOCOL
	2913	if [[ $create_remote_batch_job = true ]]
	2914	then
[3236]	2915	echo "set +vx" >> $jobfile
	2916	echo "trap '" >> $jobfile
	2917	echo "set +vx" >> $jobfile
	2918	echo "cd ${remote_jobcatalog}" >> $jobfile
	2919	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2920
	2921	# ADD THE BATCH DIRECTIVES
	2922	(( i = 0 ))
	2923	while (( i < ibdt ))
	2924	do
	2925	(( i = i + 1 ))
[2693]	2926	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2927	eval line=\"$line\"
	2928	echo "$line" >> $jobfile
	2929	done
	2930	echo " " >> $jobfile
	2931
	2932	echo "set -x" >> $jobfile
[3534]	2933	if [[ "$remote_loginnode" != "" ]]
	2934	then
	2935	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}\" " >> $jobfile
	2936	else
	2937	echo "${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
	2938	fi
[2380]	2939	echo "%%END%%" >> $jobfile
	2940	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2941	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2942	echo "rm $scpjob_file" >> $jobfile
[2404]	2943	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2944	echo "set -x" >> $jobfile
	2945	echo " ' exit" >> $jobfile
	2946	fi
	2947
	2948
	2949	# ACTIVATE ERROR-TRACEBACK
	2950	if [[ $do_trace = true ]]
	2951	then
	2952	echo "set -x" >> $jobfile
	2953	else
	2954	echo "set +vx" >> $jobfile
	2955	fi
	2956
	2957
	2958	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2959	if [[ "$login_init_cmd" != "" ]]
	2960	then
	2961	echo "$login_init_cmd" >> $jobfile
	2962	fi
	2963	if [[ "$module_commands" != "" ]]
	2964	then
	2965	echo "$module_commands" >> $jobfile
	2966	fi
	2967
	2968
	2969	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2970	if [[ $create_remote_batch_job = true ]]
	2971	then
	2972	echo "mkdir $tempdir" >> $jobfile
	2973	echo "chmod go+rx $tempdir" >> $jobfile
	2974	else
	2975	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2976	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2977	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2978	mkdir $tempdir
	2979	chmod go+rx $tempdir
	2980	fi
	2981	echo "cd $tempdir" >> $jobfile
	2982	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2983	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2984	echo "export PATH=.:\$PATH" >> $jobfile
	2985	echo "export execute_palmrun=true" >> $jobfile
	2986
	2987
	2988	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2989	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2990	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2991	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2992	echo "export LOCAL_PWD" >> $jobfile
	2993
	2994
	2995	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2996	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2997	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2998
	2999
	3000	# CALL PALMRUN WITHIN THE JOB
	3001	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	3002	echo "set -x" >> $jobfile
	3003	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3004
	3005
	3006	# TRANSFER JOBFILE TO THE TARGET HOST
	3007	if [[ $create_jobfile_only = false ]]
	3008	then
	3009
[3505]	3010	# CREATE LOCAL JOB FOLDER
	3011	eval local_jobcatalog=$local_jobcatalog
	3012	if [[ ! -d $local_jobcatalog ]]
	3013	then
	3014	echo " "
	3015	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3016	mkdir $local_jobcatalog
	3017	fi
	3018
[2380]	3019	if [[ $create_remote_batch_job = true ]]
	3020	then
	3021
[2420]	3022	echo " "
[2566]	3023	echo " *** transfer of job to remote host via scp"
[3505]	3024
	3025	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3026	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3027
	3028	# COPY THE JOB FILE
[2420]	3029	if [[ $do_trace = true ]]
	3030	then
[3236]	3031	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3032	fi
[3236]	3033	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3034
[3505]	3035	# SUBMIT THE JOB
[3574]	3036	printf " *** submit the job (output of submit command, \n"
[3573]	3037	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3038	if [[ $do_trace = true ]]
	3039	then
[3665]	3040	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]	3041	fi
[3665]	3042	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]	3043
	3044	elif [[ $create_batch_job = true ]]
	3045	then
	3046
[2385]	3047	eval local_jobcatalog=$local_jobcatalog
[3236]	3048	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3049	cd $local_jobcatalog
[2380]	3050	echo " "
[2420]	3051	echo " *** submit the job"
	3052	if [[ $do_trace = true ]]
	3053	then
[3236]	3054	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3055	fi
[3236]	3056	$submit_command ${configuration_identifier}_${run_id}
	3057	rm ${configuration_identifier}_${run_id}
[2380]	3058	cd - > /dev/null
	3059
	3060	fi
	3061
	3062	rm -rf $jobfile
	3063
	3064	else
	3065
	3066	printf "\n *** jobfile created under name \"$jobfile\" "
	3067	printf "\n no batch-job has been sent!"
	3068
	3069	fi
	3070
	3071	fi # END OF REMOTE-PART

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