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source: palm/trunk/SCRIPTS/palmrun @ 4173

Last change on this file since 4173 was 3982, checked in by raasch, 6 years ago
bugfix: -b is not added in automatically generated batch jobs for remote hosts
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 104.4 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 3982 2019-05-16 11:07:31Z gronemeier $
[3982]	29	# bugfix: -b is not added in automatically generated batch jobs for remote hosts
	30	#
	31	# 3917 2019-04-18 11:46:37Z raasch
[3917]	32	# in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has
	33	# been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied
	34	# into the temporary working catalog
	35	#
	36	# 3860 2019-04-04 06:23:27Z raasch
[3860]	37	# check added, that it is not allowed to set option -b if the configuration file has been setup
	38	# for running batch jobs on remote hosts,
	39	# local time added to terminal output before and after saving output files
	40	#
	41	# 3725 2019-02-07 10:11:02Z raasch
[3725]	42	# error messages for failed restarts extended
	43	#
	44	# 3682 2019-01-18 17:01:54Z knoop
[3665]	45	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	46	# of login messages on specific systems
	47	#
	48	# 3574 2018-11-28 13:14:39Z raasch
[3574]	49	# syntax-error in last commit fixed
	50	#
	51	# 3573 2018-11-28 13:03:44Z raasch
[3573]	52	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	53	# removed,
	54	# r3570 reverted
	55	#
	56	# 3570 2018-11-27 17:44:21Z kanani
[3570]	57	# Rename job-id by run_id
	58	#
	59	# 3555 2018-11-22 13:50:37Z raasch
[3555]	60	# sed-command to remove repeated space-characters replaced by tr-command, to
	61	# guarantee mac compatible
	62	#
	63	# 3549 2018-11-21 15:44:44Z raasch
[3549]	64	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	65	# of login messages on specific systems
	66	#
	67	# 3534 2018-11-19 15:35:16Z raasch
[3534]	68	# batch_scp for sending back the job protocol file is called via login-node if
	69	# a login-node has been set in the config-file
	70	# ssh-calls rearranged to avoid output of system/user-profile messages
	71	#
	72	# 3505 2018-11-08 09:14:30Z raasch
[3505]	73	# job folders are created in case that they do not exist
	74	#
	75	# 3455 2018-10-30 14:12:31Z raasch
[3455]	76	# options -h and -d renamed -c and -r, respectively
	77	#
	78	# 3402 2018-10-23 11:49:24Z knoop
[3346]	79	# job_id is set for compatibility reasons with older versions of config files
	80	#
	81	# 3313 2018-10-06 15:22:48Z knoop
[3294]	82	# more detailed error message for outdated fileconnection file
	83	#
	84	# 3236 2018-09-10 09:07:06Z raasch
[3236]	85	# warning issued in case of file connection file version mismatch,
	86	# host_configuration renamed configuration_identifier,
	87	# "host identifier" in header output renamed "config. identifier",
	88	# jobname renamed run_identifier,
	89	# run_id renamed run_id_number
	90	# job_id renamed run_id
	91	# option -r renamed -i
	92	#
	93	# 3151 2018-07-19 08:45:38Z raasch
[3151]	94	# removed additional listing of files to be compiled, print PALM code revision
	95	# in header
	96	#
	97	# 3132 2018-07-16 11:44:58Z raasch
[3132]	98	# create consistent error messages in case of failed restarts,
	99	# check existence of remote job catalog
	100	#
	101	# 3043 2018-05-25 10:47:54Z raasch
[3043]	102	# check for setting of fast_io_catalog
	103	#
	104	# 3033 2018-05-23 15:26:19Z raasch
[3025]	105	# -T option not required for interactive runs (tasks per node =
	106	# total number of cores is assumed as default, if option is not given),
	107	# reformatting of a few messages,
	108	# bugfix: destination output directory is created if attribute "pe" is set in
	109	# .palm.iofiles
	110	#
	111	# 2718 2018-01-02 08:49:38Z maronga
[2993]	112	# bugfix of r2990
	113	#
	114	# 2718 2018-01-02 08:49:38Z maronga
[2990]	115	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	116	# not in the working directory from where palmrun is called
	117	#
	118	# 2718 2018-01-02 08:49:38Z maronga
[2957]	119	# svfout in the activation string will be replaced now by svfin in case of
	120	# automatic restarts
	121	#
	122	# 2718 2018-01-02 08:49:38Z maronga
[2906]	123	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	124	# the possible output or input of sky view factors
	125	#
	126	# 2718 2018-01-02 08:49:38Z maronga
[2834]	127	# "fname" renamed to "jobname"
	128	#
	129	# 2718 2018-01-02 08:49:38Z maronga
[2799]	130	# parameters are allowed in output commands (OC:)
	131	#
	132	# 2718 2018-01-02 08:49:38Z maronga
[2789]	133	# bugfix: exit if no queue has been given neither with option -q nor in the
	134	# configuration file
	135	#
	136	# 2718 2018-01-02 08:49:38Z maronga
[2762]	137	# file connection file from trunk/SCRIPTS is taken by default
	138	#
	139	# 2718 2018-01-02 08:49:38Z maronga
[2716]	140	# Corrected "Former revisions" section
	141	#
	142	# 2696 2017-12-14 17:12:51Z kanani
	143	# Change in file header (GPL part)
	144	#
	145	# 2693 2017-12-13 12:33:49Z raasch
[2693]	146	# replacement of variables given by {{<variable>}} in configuration file is now
	147	# done in a more general way, variable names are written in small letters
	148	#
	149	# 2670 2017-12-06 16:32:19Z raasch
[2670]	150	# test printouts removed
	151	#
	152	# 2669 2017-12-06 16:03:27Z raasch
[2669]	153	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	154	# removed,
	155	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	156	# files,
	157	# informative messages in case of missing optional input files shortened
	158	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	159	#
	160	# 2638 2017-11-23 12:44:23Z raasch
[2610]	161	# use of wildcards in file connection statements enabled
	162	#
	163	# 2605 2017-11-09 15:31:46Z raasch
[2605]	164	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	165	# will not be sent with the job file any more, but copied into the
[2610]	166	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	167	#
	168	# 2600 2017-11-01 14:11:20Z raasch
[2600]	169	# cycle numbers are made three digits wide
	170	#
	171	# 2566 2017-10-20 08:50:47Z raasch
[2566]	172	# execute command for combine_plot_fields added
	173	# "TEMPDIR" renamed "tempdir"
	174	# temporary working directory for local batch jobs is created immediately within
	175	# the user's palmrun call, due to a requirement of the "grid engine" batch
	176	# system, where the working directory is given with batch directive -wd and must
	177	# already exist when the job is submitted,
	178	# informative messages in non-trace mode reduced and partly reformatted
	179	#
	180	# 2551 2017-10-18 07:25:11Z raasch
[2551]	181	# TEMPDIR added as replacement string to be used in batch directives
	182	#
	183	# 2512 2017-10-04 08:26:59Z raasch
[2507]	184	# bugfix for determining cycle numbers of NetCDF input files
	185	#
	186	# 2506 2017-09-29 08:30:37Z raasch
[2506]	187	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	188	# host configuration added to SOURCES_FOR_RUN_... folder name
	189	# host_identifier renamed host_configuration
	190	# option -W added to allow for job dependencies
	191	#
	192	# 2501 2017-09-26 11:41:55Z raasch
[2501]	193	# default value for number of cores (option -X) set to 1
	194	# bugfix for mechanism which overwrites configuration file settings with values
	195	# provided by palmrun options
	196	#
	197	# 2499 2017-09-22 16:47:58Z kanani
[2499]	198	# option -h named configuration identifier
	199	#
	200	# 2480 2017-09-19 06:24:14Z maronga
[2480]	201	# bugfix for last revision
	202	#
	203	# 2479 2017-09-19 06:12:16Z raasch
[2479]	204	# option -A (project account number) added
	205	#
	206	# 2422 2017-09-08 08:25:41Z raasch
[2410]	207	# initial revision
[2380]	208	#
	209	#--------------------------------------------------------------------------------#
	210	# palmrun - script for running PALM jobs on local and remote hosts
	211	#--------------------------------------------------------------------------------#
	212
	213
	214
	215	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	216
	217	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	218	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	219	# (TOO MANY ARGUMENTS - PROBLEM)
	220	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	221
[2610]	222	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	223	typeset -i nr_of_output_files=0
[2380]	224	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	225	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	226	# SCRIPT-OPTION ARGUMENTS
	227	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	228	typeset -i icycle inode ival maxcycle mpi_tasks
	229	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	230
	231	activation_string_list=""
	232	AddFilenames=""
	233	combine_plot_fields=true
	234	compiler_name=""
	235	compiler_name_ser=""
	236	compiler_options=""
[3236]	237	configuration_identifier="default"
[2501]	238	cores=1
[2380]	239	cores_atmos=0
	240	cores_ocean=0
	241	coupled_dist=""
	242	cpp_options=""
	243	cpumax=0
[2506]	244	create_batch_job=false
[2380]	245	create_jobfile_only=false
	246	create_remote_batch_job=false
	247	dashes=" ----------------------------------------------------------------------------"
	248	defaultqueue=""
[2506]	249	delete_temporary_catalog=true
[2380]	250	do_compile=true
	251	do_trace=false
	252	executable=""
	253	execute_command=""
	254	execution_error=false
[2762]	255	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	256	global_revision=""
	257	hostfile=""
	258	hp=""
	259	keep_data_from_previous_run=false
	260	link_local_input=false
	261	link_local_output=false
[2388]	262	linker_options=""
[2385]	263	local_jobcatalog=""
[2380]	264	locat=normal
	265	makefile=""
	266	max_par_io_str=""
	267	prc=$0
	268	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	269	do
	270	prc=`echo $prc \| cut -f2- -d"/"`
	271	done
	272	module_calls=""
[2506]	273	palmrun_memory=""
[2380]	274	palmrun_script_name=$prc
	275	openmp=false
[2506]	276	previous_job=""
[2479]	277	project_account=""
[2380]	278	queue=none
[2906]	279	read_svf=""
[2380]	280	restart_run=false
	281	return_address=""
[2385]	282	remote_jobcatalog=""
[2380]	283	remote_username=""
	284	running_in_batch_mode=false
[3313]	285	running_in_test_mode=false
[2380]	286	run_coupled_model=false
	287	run_id=""
[3236]	288	run_id_number=""
	289	run_identifier=test
[2380]	290	silent=false
	291	source_list=""
	292	source_path=""
[2501]	293	tasks_per_node=0
[2380]	294	threads_per_task=1
	295	transfer_problems=false
[2384]	296	user_source_path=""
[2506]	297	use_existing_sources_folder=""
[2380]	298	use_openmp=false
[3033]	299	version="palmrun 1.0 Rev$Rev: 3982 $"
[2380]	300	working_directory=`pwd`
	301	write_binary=""
[2906]	302	write_svf=""
[2380]	303
	304
	305	# ERROR HANDLING IN CASE OF EXIT
[2404]	306	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	307	then
	308
	309	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	310	(( i = 0 ))
	311	while (( i < iec ))
	312	do
	313	(( i = i + 1 ))
	314	printf "\n *** Execution of ERROR-command:\n"
	315	printf " >>> ${err_command[$i]}\n"
	316	eval ${err_command[$i]}
	317	done
[2566]	318	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	319	printf "\n\n+++ palmrun crashed \n\n"
	320	exit 1
	321	elif [[ $locat != normal ]]
[2380]	322	then
[3312]	323	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	324	printf "\n+++ palmrun killed by \"^C\" \n\n"
	325	exit 2
	326	else
[2566]	327	printf "\n --> palmrun finished\n\n"
[3312]	328	exit 0
[2380]	329	fi' exit
	330
	331
	332	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	333	trap 'locat=control_c
	334	exit 1
[2380]	335	' 2
	336
	337
	338	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	339	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	340	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]	341	do
	342	case $option in
	343	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	344	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	345	(b) create_batch_job=true; prc="$prc -b";;
	346	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	347	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	348	(C) restart_run=true; prc="$prc -C";;
	349	(F) create_jobfile_only=true;;
	350	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	351	(i) run_id_number=$OPTARG;;
[2380]	352	(j) running_in_batch_mode=true;;
	353	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	354	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	355	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	356	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	357	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	358	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	359	(R) return_address=$OPTARG;;
	360	(s) source_list=$OPTARG;;
[2501]	361	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	362	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	363	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	364	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	365	(v) silent=true; prc="$prc -v";;
[2506]	366	(V) use_existing_sources_folder="-V";;
[2380]	367	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	368	(W) previous_job=$OPTARG;;
[2380]	369	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	370	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	371	(y) ocean_file_appendix=true; prc="$prc -y";;
	372	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	373	(z) running_in_test_mode=true;;
[2380]	374	(Z) combine_plot_fields=false; prc="$prc -Z";;
	375	(\?) printf "\n +++ unknown option $OPTARG \n"
	376	printf "\n --> type \"$0 ?\" for available options \n"
	377	locat=parameter;exit;;
	378	esac
	379	done
	380
	381
	382	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	383	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	384	(( to_shift = $OPTIND - 1 ))
	385	shift $to_shift
	386
	387	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	388	if [[ "$1" = "?" ]]
	389	then
	390	(printf "\n *** Description of available palmrun options:\n"
	391	printf "\n Option Description Default-Value"
	392	printf "\n -a activation string list \"\" "
[2479]	393	printf "\n -A project account number ---"
[2380]	394	printf "\n -b batch-job on local machine ---"
	395	printf "\n -B do not delete temporary directory at end ---"
[3455]	396	printf "\n -c configuration identifier \"default\" "
[2380]	397	printf "\n -F create batch job file only ---"
	398	printf "\n -k keep data from previous run"
	399	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	400	printf "\n -M Makefile name Makefile"
	401	printf "\n -O threads per openMP task ---"
	402	printf "\n -q queue \"$queue\" "
[3455]	403	printf "\n -r run identifier test"
[2380]	404	printf "\n -s filenames of routines to be compiled \"\" "
	405	printf "\n must end with .f, .f90, .F, or .c !"
	406	printf "\n use \"..\" for more than one file and wildcards"
	407	printf "\n -s LM compiles all locally modified files"
	408	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	409	printf "\n -T tasks per node ---"
[2380]	410	printf "\n -u username on remote machine \"\" "
	411	printf "\n -v no prompt for confirmation ---"
[2506]	412	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	413	printf "\n -w maximum parallel io streams as given by -X"
[2506]	414	printf "\n -W name of job to wait for ---"
[2380]	415	printf "\n -x tracing of palmrun for debug purposes ---"
	416	printf "\n -X # of processors (on parallel machines) 1"
	417	printf "\n -y add appendix \"_O\" to all local output"
	418	printf "\n files (ocean precursor runs followed by"
	419	printf "\n coupled atmosphere-ocean runs) ---"
	420	printf "\n -Y run coupled model, \"#1 #2\" with"
	421	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	422	printf "\n -Z skip combine_plot_fields at the end of "
	423	printf "\n the simulation ---"
	424	printf "\n "
	425	printf "\n Possible values of positional parameter <modus>:"
	426	printf "\n \"?\" - this outline \n\n") \| more
	427	exit
	428	elif [[ "$1" != "" ]]
	429	then
	430	printf "\n +++ positional parameter $1 unknown \n"
	431	locat=parameter; exit
	432	fi
	433
	434
	435
	436	# SHORT STARTING MESSAGE
	437	printf "\n*** $version "
	438	printf "\n will be executed. Please wait ..."
	439
	440
[2506]	441	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	442	config_file=.palm.config.$configuration_identifier
	443	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	444
	445
	446	# CHECK, IF CONFIGURATION FILE EXISTS
	447	if [[ ! -f $config_file ]]
	448	then
	449	printf "\n\n +++ configuration file: "
	450	printf "\n $config_file"
	451	printf "\n does not exist"
	452	locat=connect; exit
	453	fi
	454
	455
[2762]	456	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	457	if [[ -f .palm.iofiles ]]
	458	then
[3236]	459
	460	# CHECK VERSION MISMATCH
[3573]	461	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	462	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	463	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	464	then
	465	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	466	then
	467	printf "\n\n +++ WARNING: A file connection file has been found in your"
	468	printf "\n working directory, but its revision does not match"
	469	printf "\n the revision of the default (trunk) version."
[3294]	470	printf "\n You may need to update your connection file"
	471	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	472	fi
	473	fi
	474
[2762]	475	fileconnection_file=.palm.iofiles
[3236]	476
[2762]	477	fi
	478
	479
[2380]	480	# CHECK, IF FILE CONNECTION FILE EXISTS
	481	if [[ ! -f $fileconnection_file ]]
	482	then
	483	printf "\n\n +++ file connection file: "
	484	printf "\n $fileconnection_file"
	485	printf "\n does not exist"
	486	locat=connect; exit
	487	fi
	488
	489
[2404]	490	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	491	if [[ "$activation_string_list" = "" ]]
	492	then
	493	printf "\n\n +++ no activation string list given: "
	494	printf "\n please set palmrun option \"-a\" "
	495	locat=palmrun_option; exit
	496	fi
	497
	498
	499	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	500	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	501	then
	502	write_binary=true
	503	else
	504	write_binary=false
	505	fi
	506
[2906]	507	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	508	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	509	then
	510	write_svf=true
	511	else
	512	write_svf=false
	513	fi
[2404]	514
[2906]	515	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	516	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	517	then
	518	read_svf=true
	519	else
	520	read_svf=false
	521	fi
	522
	523
[2380]	524	# READ AND EVALUATE THE CONFIGURATION-FILE
	525	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	526
	527	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	528	while read line
	529	do
	530
	531	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	532	eval line=\"$line\"
	533
	534
	535	# INTERPRET THE LINE
	536	if [[ "$(echo $line)" = "" ]]
	537	then
	538
	539	# EMPTY LINE, NO ACTION
	540	continue
	541
	542	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	543	then
	544
	545	# LINE IS A COMMENT LINE
	546	continue
	547
	548	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	549	then
	550
	551	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	552	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	553	value=`echo $line \| cut -d" " -s -f2-`
	554
	555
	556	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	557	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	558	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	559	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	560	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	561	# CONFIGURATION-FILE.
	562	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	563	then
	564	eval export $var="\$value"
	565
	566	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	567	if [[ $do_trace = true ]]
	568	then
	569	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	570	fi
	571	fi
	572
	573	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	574	then
	575
	576	# LINE DEFINES BATCH-DIRECTIVE
	577	(( ibd = ibd + 1 ))
	578	line=$(echo $line \| cut -c4-)
	579	batch_directive[$ibd]="$line"
	580
	581	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	582	then
	583
	584	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	585	# REMOTE TO A LOCAL HOST
	586	(( ibdt = ibdt + 1 ))
	587	line=$(echo $line \| cut -c5-)
	588	batch_directive_transfer[$ibdt]="$line"
	589
	590	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	591	then
	592
	593	# LINE DEFINES ERROR-COMMAND
	594	(( iec = iec + 1 ))
	595	line=$(echo $line \| cut -c4-)
	596	err_command[$iec]="$line"
	597
	598	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	599	then
	600
	601	# LINE DEFINES INPUT-COMMAND
	602	(( iic = iic + 1 ))
	603	line=$(echo $line \| cut -c4-)
	604	in_command[$iic]="$line"
	605
	606	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	607	then
	608
	609	# LINE DEFINES OUTPUT-COMMAND
	610	(( ioc = ioc + 1 ))
	611	line=$(echo $line \| cut -c4-)
	612	out_command[$ioc]="$line"
	613
	614	else
	615
	616	# SKIP ALL OTHER LINES
	617	continue
	618
	619	fi
	620
	621	done < $config_file
	622
	623
	624	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	625	if [[ "$fast_io_catalog" = "" ]]
	626	then
[3860]	627	printf "\n\n +++ no fast_io_catalog found in $config_file"
[3043]	628	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	629	locat=config_file; exit
	630	fi
[2380]	631	if [[ "$compiler_name" = "" ]]
	632	then
[3860]	633	printf "\n\n +++ no compiler name found in $config_file"
[2380]	634	printf "\n Please add line \"compiler_name ...\" to that file."
	635	locat=config_file; exit
	636	fi
	637	if [[ "$compiler_name_ser" = "" ]]
	638	then
[3860]	639	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
[2380]	640	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	641	locat=config_file; exit
	642	fi
	643	if [[ "$compiler_options" = "" ]]
	644	then
[3860]	645	printf "\n\n +++ no compiler options found in $config_file"
[2380]	646	printf "\n Please add line \"compiler_options ...\" to that file."
	647	locat=config_file; exit
	648	fi
	649	if [[ "$execute_command" = "" ]]
	650	then
[3860]	651	printf "\n\n +++ no execute command found in $config_file"
[2380]	652	printf "\n Please add line \"execute_command ...\" to that file."
	653	locat=config_file; exit
	654	fi
	655
	656	if [[ "$hostfile" != "" ]]
	657	then
	658	if [[ $hostfile != auto && ! -f $hostfile ]]
	659	then
[3860]	660	printf "\n\n +++ no hostfile \"$hostfile\" found"
[3151]	661	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	662	locat=config_file; exit
	663	fi
	664	fi
	665
	666
	667	# DETERMINE THE CALL STATUS
	668	if [[ "$return_address" != "" ]]
	669	then
	670
	671	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	672	# BATCH MODE AND ...
	673	running_on_remote=true
	674
	675	else
	676
	677	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	678	if [[ "$remote_ip" != "" ]]
	679	then
	680
	681	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	682	create_remote_batch_job=true
	683
[3132]	684	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	685	if [[ "$remote_jobcatalog" = "" ]]
	686	then
[3860]	687	printf "\n\n +++ no remote jobcatalog found in $config_file"
[3132]	688	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	689	locat=config_file; exit
	690	fi
	691
[3860]	692	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
	693	if [[ $create_batch_job = true ]]
	694	then
	695	printf "\n\n +++ option -b must not be set because configuration file has been setup"
	696	printf "\n for running jobs on a remote host"
	697	locat=config_file; exit
	698	fi
	699
[2380]	700	fi
	701	running_on_remote=false
	702	fi
	703
	704
	705
	706	# READ AND EVALUATE THE I/O-FILE LIST
	707	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	708
	709	# READ THE FILE CONNECTION FILE LINE BY LINE
	710	while read line
	711	do
	712
[2669]	713	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	714	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	715	line=`echo "$line" \| tr -s " "`
[2380]	716
	717	# INTERPRET THE LINE
	718	if [[ "$(echo $line)" = "" ]]
	719	then
	720	# EMPTY LINE, NO ACTION
	721	continue
	722
	723	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	724	then
	725
	726	# LINE IS A COMMENT LINE
	727	true
	728
	729	else
	730
	731	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	732	# s2a: in/out - field
[2669]	733	# s2b: action - field (optional)
	734	s1=`echo "$line" \| cut -d" " -f1`
	735	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	736	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	737	then
[2669]	738	s2a=$s2
[2380]	739	s2b=""
	740	else
[2669]	741	s2a=`echo $s2 \| cut -d":" -f1`
	742	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	743	fi
[2669]	744	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	745	s4=`echo "$line" \| cut -d" " -s -f4`
	746	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	747	s5=`echo "$line" \| cut -d" " -s -f5`
	748	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	749
	750
	751	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	752	# INPUT- OR OUTPUT-LIST.
	753	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	754	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	755	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	756	# IS NOT CHECKED AND STORED.
[2610]	757	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	758	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	759	then
	760	found=false
	761	for actual in $activation_string_list
	762	do
	763	for formal in $s3
	764	do
	765	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	766	done
	767	done
	768	if [[ $found = true ]]
	769	then
	770	(( iin = iin + 1 ))
[2669]	771	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	772	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	773	if [[ "$s2a" = inopt ]]
	774	then
	775	optin_pre[$iin]=yes
	776	else
	777	optin_pre[$iin]=no
	778	fi
[2605]	779
	780	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	781	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	782	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	783	then
[2610]	784	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	785	fi
	786
[2610]	787	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	788	# THE WILDCARD FROM THE ENDING
	789	if [[ "${s5: -1}" = "*" ]]
	790	then
[2669]	791	if [[ "$s2b" = "di" ]]
[2610]	792	then
	793	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	794	printf "\n see file \"$fileconnection_file\", line"
	795	printf "\n$line"
	796	locat=iofiles_file; exit
	797	fi
	798	multin[$iin]=true
	799	string=${endin_pre[$iin]}
	800	endin_pre[$iin]="${string%?}"
	801	else
	802	multin[$iin]=false
	803	fi
[2380]	804	fi
[2669]	805	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	806	then
	807	found=false
	808	for actual in $activation_string_list
	809	do
	810	for formal in $s3
	811	do
[2670]	812	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	813	done
	814	done
	815	if [[ $found = true ]]
	816	then
	817	(( iout = iout + 1 ))
[2669]	818	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	819	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	820
[2669]	821	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	822	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	823	if [[ $formal = wildcard ]]
	824	then
	825	warnout_pre[$iout]=false
	826	else
	827	warnout_pre[$iout]=true
	828	fi
	829
[2610]	830	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	831	# THE WILDCARD FROM THE LOCAL FILENAME
	832	if [[ "${s1: -1}" = "*" ]]
	833	then
[2669]	834	if [[ "$s2b" = "di" ]]
[2610]	835	then
	836	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	837	printf "\n see file \"$fileconnection_file\", line"
	838	printf "\n$line"
	839	locat=iofiles_file; exit
	840	fi
	841	multout[$iout]=true
	842	string=${localout_pre[$iout]}
	843	localout_pre[$iout]="${string%?}"
	844	else
	845	multout[$iout]=false
	846	fi
[2380]	847	fi
[2669]	848	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	849	then
[2669]	850	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	851	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	852	locat=connect; exit
	853	fi
	854	IFS="$IFSALT"
	855	fi
	856
	857	done < $fileconnection_file
	858
	859
	860
[2501]	861	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	862	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	863	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	864	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	865	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	866	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	867
	868
	869
[2380]	870	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	871	if [[ $run_coupled_model = true ]]
	872	then
	873
	874	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	875	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	876
	877	if (( $cores_ocean + $cores_atmos != $cores ))
	878	then
	879
	880	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	881	printf "\n PEs (total) : $cores"
	882	printf "\n PEs (atmosphere): $cores_atmos"
	883	printf "\n PEs (ocean) : $cores_ocean"
	884	locat=coupling; exit
	885
	886	fi
	887
	888	fi
	889
	890
	891	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	892	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	893	# FOLDER
	894	if [[ $running_in_batch_mode = true ]]
	895	then
	896
[2506]	897	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	898	then
[2506]	899	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	900	printf "\n Please check the output of the palmrun-call"
	901	printf "\n that you did on your local host."
	902	locat=SOURCES_FOR_RUN; exit
	903	fi
	904
	905	else
	906
	907	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	908	# AUTOMATIC RESTART RUN
	909	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	910	if [[ $restart_run = false ]]
	911	then
	912
	913	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	914	# THE LOCAL HOST
	915	if [[ ! -d $source_path ]]
	916	then
	917	printf "\n\n +++ source path \"$source_path\" on local host"
	918	printf "\n \"$(hostname)\" does not exist"
	919	locat=source_path; exit
	920	fi
	921
[2990]	922	rm -rf ${base_directory}/${sources_for_run_catalog}
	923	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	924
	925	if [[ "$source_list" = LM ]]
	926	then
	927
	928	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	929	source_list=""
	930	cd $source_path
	931
	932
[2512]	933	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	934	if [[ ! -d ../.svn ]]
[2380]	935	then
	936	printf "\n\n +++ source directory"
	937	printf "\n \"$source_path\" "
	938	printf "\n is not under control of \"subversion\"."
[2512]	939	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	940	fi
	941
	942
	943	# LIST ALL MODIFIED SOURCE CODE FILES
	944	Filenames=""
[2404]	945	svn status > tmp_svnstatus
[2380]	946	while read line
	947	do
	948	firstc=`echo $line \| cut -c1`
	949	if [[ $firstc = M \|\| $firstc = "?" ]]
	950	then
	951	Name=`echo "$line" \| cut -c8-`
	952	extension=`echo $Name \| cut -d. -f2`
	953	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	954	then
	955	Filenames="$Filenames "$Name
	956	fi
	957	fi
[2404]	958	done < tmp_svnstatus
	959	rm -rf tmp_svnstatus
[2380]	960
	961
	962	# COPY FILES TO SOURCES_FOR_RUN_...
	963	for filename in $Filenames
	964	do
[2990]	965	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	966	source_list=$source_list"$filename "
	967	done
	968
	969	cd - > /dev/null
	970
	971
	972	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	973	elif [[ "$source_list" != "" ]]
	974	then
	975
	976	cd $source_path
	977
	978	for filename in $source_list
	979	do
	980
	981	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	982	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	983	then
	984	printf "\n +++ source code file: $filename"
	985	printf "\n must not contain (\"/\") "
	986	locat=source; exit
	987	fi
	988
	989	if [[ ! -f $filename ]]
	990	then
	991	printf "\n +++ source code file: $filename"
	992	printf "\n does not exist"
	993	locat=source; exit
	994	else
[2990]	995	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	996	fi
	997
	998	done
	999
	1000	cd - > /dev/null
	1001
	1002	fi
	1003
	1004	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1005	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1006	if [[ ! -f $makefile ]]
	1007	then
	1008	printf "\n +++ file \"$makefile\" does not exist"
	1009	locat=make; exit
	1010	else
[2990]	1011	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	1012	fi
	1013
	1014
	1015	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	1016	if [[ "$user_source_path" != "" ]]
[2380]	1017	then
	1018
	1019	# DOES THE DIRECTORY EXIST?
[2384]	1020	if [[ ! -d $user_source_path ]]
[2380]	1021	then
	1022
	1023	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1024	printf "\n \"$user_source_path\" "
[2380]	1025	printf "\n does not exist or is not a directory."
	1026	printf "\n No source code will be used from this directory!\n"
[2384]	1027	user_source_path=""
[2380]	1028	if [[ $silent == false ]]
	1029	then
	1030	sleep 2
	1031	fi
	1032
	1033	else
	1034
[2384]	1035	cd $user_source_path
[2380]	1036
	1037	Names=$(ls -1 *.f90 2>&1)
	1038	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1039	Names=$(ls -1 *.F90 2>&1)
	1040	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1041	Names=$(ls -1 *.F 2>&1)
	1042	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1043	Names=$(ls -1 *.f 2>&1)
	1044	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1045	Names=$(ls -1 *.c 2>&1)
	1046	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1047
	1048	cd - > /dev/null
[2990]	1049	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1050
	1051	# COPY MAKEFILE IF EXISTING
[2384]	1052	if [[ -f $user_source_path/Makefile ]]
[2380]	1053	then
	1054	printf "\n\n *** user Makefile from directory"
[2384]	1055	printf "\n \"$user_source_path\" is used \n"
[2380]	1056	if [[ $silent == false ]]
	1057	then
	1058	sleep 1
	1059	fi
[2384]	1060	cp $user_source_path/Makefile .
[2380]	1061	fi
	1062
	1063	for filename in $AddFilenames
	1064	do
	1065	if [[ -f $filename ]]
	1066	then
	1067	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1068	printf "\n source code directory \"$user_source_path\" "
[2380]	1069	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1070	printf "\n from directory \"$source_path\"."
	1071	locat=source; exit
	1072	fi
	1073
[2384]	1074	cp $user_source_path/$filename .
[2380]	1075	source_list="$source_list $filename"
	1076
	1077	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1078	if [[ $(grep -c $filename Makefile) = 0 ]]
	1079	then
	1080	printf "\n\n +++ user file \"$filename\" "
	1081	printf "\n is not listed in Makefile \n"
	1082	locat=source; exit
	1083	fi
	1084	done
	1085	cd - > /dev/null
	1086	fi
	1087	fi
	1088
	1089	# COPY CONFIGURATION FILES
[2990]	1090	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1091	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1092
	1093	# COPY SHELLSCRIPTS
[2990]	1094	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1095	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1096
	1097	fi
	1098
	1099	fi
	1100
[2605]	1101
[2380]	1102	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1103	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1104	if [[ "$global_revision" = "" ]]
	1105	then
	1106	global_revision=`svnversion $source_path 2>/dev/null`
	1107	global_revision="Rev: $global_revision"
	1108	fi
	1109
	1110
	1111	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1112	if [[ -n $cores ]]
	1113	then
	1114
	1115	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1116	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1117	if [[ $tasks_per_node = 0 ]]
[2380]	1118	then
[3025]	1119	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1120	then
	1121	printf "\n"
	1122	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1123	printf "\n set -T option or define tasks_per_node in the config file"
	1124	locat=tasks_per_node; (( iec = 0 )); exit
	1125	else
	1126	# DEFAULT FOR INTERACTIVE RUN
	1127	tasks_per_node=$cores
	1128	fi
[2380]	1129	fi
	1130
	1131	if (( cores < tasks_per_node ))
	1132	then
	1133	printf "\n"
	1134	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1135	printf "\n given values: -T $tasks_per_node -X $cores"
	1136	locat=tasks_per_node; (( iec = 0 )); exit
	1137	fi
	1138
	1139	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1140	(( mpi_tasks = cores / threads_per_task ))
	1141	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1142	(( ii = cores / tasks_per_node ))
	1143	(( remaining_cores = cores - ii * tasks_per_node ))
	1144	if (( remaining_cores > 0 ))
	1145	then
	1146	printf "\n"
	1147	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1148	printf "\n divisor of the total number of cores (option \"-X\")"
	1149	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1150	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1151	(( nodes = nodes + 1 ))
	1152	fi
	1153
	1154	fi
	1155
	1156
	1157	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1158	if [[ "$maximum_parallel_io_streams" = "" ]]
	1159	then
	1160	maximum_parallel_io_streams=$cores
	1161	fi
	1162
	1163
	1164	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1165	if [[ "$scp_port" != "" ]]
	1166	then
	1167	PORTOPT="-P $scp_port"
	1168	SSH_PORTOPT="-p $scp_port"
	1169	fi
	1170
	1171
	1172	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1173	# CONFIG-FILE
	1174	if [[ "$ssh_key" != "" ]]
	1175	then
	1176	ssh_key="-i $HOME/.ssh/$ssh_key"
	1177	fi
	1178
	1179
	1180	# SET QUEUE, IF NOT GIVEN
	1181	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1182	then
	1183
	1184	if [[ $queue = none && "$defaultqueue" = "" ]]
	1185	then
	1186	printf "\n"
	1187	printf "\n +++ no default queue given in configuration file and no queue"
	1188	printf "\n given with option -q"
[2789]	1189	locat=queue; exit
[2380]	1190	fi
	1191	if [[ $queue = none ]]
	1192	then
	1193	queue=$defaultqueue
	1194	fi
	1195
	1196	fi
	1197
	1198
	1199	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1200	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1201	(( i = 0 ))
[2610]	1202	(( nr_of_input_files = 0 ))
[2380]	1203	while (( i < iin ))
	1204	do
	1205	(( i = i + 1 ))
	1206
	1207	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1208	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1209	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1210	then
[2610]	1211	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1212	else
[3236]	1213	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1214	fi
	1215
[2610]	1216
[2380]	1217	# CHECK IF FILE EXISTS
	1218	if ! ls $filename* 1>/dev/null 2>&1
	1219	then
	1220
[2669]	1221	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1222	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1223	then
	1224	printf "\n\n +++ INPUT-file: "
[2610]	1225	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1226	then
	1227	printf "\n $filename"
	1228	else
[2610]	1229	printf "\n $filename.${extin_pre[$i]}"
[2380]	1230	fi
	1231	printf "\n does not exist\n"
	1232	locat=input; exit
	1233	else
[2610]	1234	(( nr_of_input_files = nr_of_input_files + 1 ))
	1235	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1236	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1237	actionin[$nr_of_input_files]="unavailable"
[2610]	1238	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1239	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1240	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1241	fi
[2605]	1242
[2380]	1243	else
	1244
[3236]	1245	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1246	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1247	# ENDINGS
[2610]	1248	if [[ "${multin[$i]}" = true ]]
	1249	then
	1250	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1251	ls -1 -d ${filename} > filelist 2>/dev/null
	1252	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1253	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1254
[2610]	1255	endings=""
	1256	while read line
	1257	do
	1258	# filename without path (i.e. after the last "/")
	1259	basefilename=$(basename ${line})
[2380]	1260
[2610]	1261	# check if there is an extension and remove it
	1262	ext=${basefilename##*.}
	1263	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1264	then
	1265	basefilename=${basefilename%.*}
	1266	fi
[2380]	1267
[2610]	1268	# check for an existing cycle number and remove it
	1269	cycle=${basefilename##*.}
	1270	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1271	then
	1272	basefilename=${basefilename%.*}
	1273	fi
[2600]	1274
[3236]	1275	# remove the run_identifier from the beginning
	1276	length_run_identifier=${#run_identifier}
	1277	ending=${basefilename:${length_run_identifier}}
[2610]	1278
	1279	# remove the ending given in the .iofiles from the beginning
	1280	endingstring="${endin_pre[$i]}"
	1281	length_ending=${#endingstring}
	1282	ending=${ending:${length_ending}}
	1283
	1284	if [[ "$ending" = "" ]]
[2600]	1285	then
[2610]	1286	# standard ending as given in the .iofiles
	1287	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1288	then
	1289	endings="$endings DEFAULT"
	1290	fi
[2600]	1291	else
[2610]	1292	# ending must start with "_", otherwise its a different file
	1293	if [[ "${ending:0:1}" = "_" ]]
	1294	then
	1295	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1296	then
	1297	endings="$endings $ending"
	1298	fi
	1299	fi
[2600]	1300	fi
[2610]	1301
	1302	done <filelist
[2380]	1303
[2610]	1304	rm filelist
[2380]	1305
[2600]	1306	else
[2610]	1307
	1308	# SINGLE NAME
	1309	endings=DEFAULT
	1310
[2600]	1311	fi
	1312
[2610]	1313	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1314	for ending in $endings
	1315	do
	1316
	1317	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1318	if [[ $ending = DEFAULT ]]
[2380]	1319	then
[2610]	1320	ending=""
	1321	fi
	1322
	1323	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1324	(( nr_of_input_files = nr_of_input_files + 1 ))
	1325	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1326	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1327	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1328	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1329	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1330	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1331
	1332
	1333	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1334	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1335	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1336	then
	1337	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1338	else
[3236]	1339	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1340	fi
[2610]	1341
	1342	# DETERMINE THE FILE'S CYCLE NUMBER
	1343	(( maxcycle = 0 ))
	1344	ls -1 -d $filename > filelist 2>/dev/null
	1345	ls -1 -d $filename.* >> filelist 2>/dev/null
	1346	while read line
	1347	do
	1348	# filename without path (i.e. after the last "/")
	1349	basefilename=$(basename ${line})
	1350
	1351	# check if there is an extension
	1352	extension=${basefilename##*.}
	1353	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1354	then
	1355	basefilename=${basefilename%.*}
	1356	fi
	1357
	1358	# check for an existing cycle number
	1359	cycle=${basefilename##*.}
	1360	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1361	then
[2669]	1362	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1363	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1364	(( icycle = $((10#$cycle)) ))
[2610]	1365	else
	1366	(( icycle = 0 ))
	1367	fi
	1368
	1369	if (( icycle > maxcycle ))
	1370	then
	1371	(( maxcycle = icycle ))
	1372
	1373	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1374	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1375	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1376	then
	1377	leading_zero=true
	1378	else
	1379	leading_zero=false
	1380	fi
	1381	fi
	1382
	1383	done <filelist
	1384	rm filelist
	1385
	1386	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1387	if [[ $leading_zero = true ]]
[2380]	1388	then
[2610]	1389	cyclestring=`printf "%03d" $maxcycle`
	1390	else
	1391	cyclestring=$maxcycle
[2380]	1392	fi
[2610]	1393
	1394	# APPEND CYCLE NUMBER TO FILENAME
	1395	if (( maxcycle > 0 ))
[2380]	1396	then
[2610]	1397	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1398	then
	1399	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1400	else
	1401	filename=${filename}.$cyclestring
	1402	fi
[2380]	1403	else
[2610]	1404	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1405	then
	1406	filename=${filename}.${extin[$nr_of_input_files]}
	1407	fi
[2380]	1408	fi
[2610]	1409
	1410	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1411	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1412	absnamein[$nr_of_input_files]=$filename
	1413	if (( maxcycle > 0 ))
[2380]	1414	then
[2610]	1415	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1416	then
	1417	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1418	else
[3236]	1419	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1420	fi
[2380]	1421	else
[2610]	1422	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1423	then
	1424	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1425	else
[3236]	1426	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1427	fi
[2380]	1428	fi
	1429
[2610]	1430	done
	1431
[2380]	1432	fi
[2610]	1433
[2380]	1434	done
	1435
[2610]	1436
[2380]	1437	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1438	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1439	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1440	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1441	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1442	# REMOTE HOST)
	1443	(( i = 0 ))
	1444	while (( i < iout ))
	1445	do
	1446	(( i = i + 1 ))
[2610]	1447	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1448	then
[2610]	1449	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1450	then
[2610]	1451	actionout_pre[$i]=""
	1452	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1453	then
[2610]	1454	actionout_pre[$i]=pe
	1455	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1456	then
[2610]	1457	actionout_pre[$i]=a
[2380]	1458	fi
	1459	(( maxcycle = 0 ))
[3236]	1460	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1461	eval catalogname=${pathout_pre[$i]}
[2380]	1462	if ! ls $filename* 1>/dev/null 2>&1
	1463	then
	1464
	1465	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1466	if cat /dev/null > $filename
	1467	then
	1468	rm $filename
	1469	else
	1470
	1471	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1472	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1473	if [[ ! -d $catalogname ]]
	1474	then
	1475	if mkdir -p $catalogname
	1476	then
	1477	printf "\n\n *** directory:"
	1478	printf "\n $catalogname"
	1479	printf "\n was created\n"
	1480	else
	1481	printf "\n\n +++ OUTPUT-file:"
	1482	printf "\n $filename"
	1483	printf "\n cannot be created, because directory does not exist"
	1484	printf "\n and cannot be created either"
	1485	printf "\n"
	1486	locat=output ; exit
	1487	fi 2>/dev/null
	1488	else
	1489	printf "\n\n +++ OUTPUT-file:"
	1490	printf "\n $filename"
	1491	printf "\n cannot be created, although directory exists"
	1492	printf "\n"
	1493	locat=output ; exit
	1494	fi
	1495	fi 2>/dev/null
	1496
	1497	fi
	1498
	1499	fi
	1500	done
	1501
	1502
	1503	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1504	if [[ $running_in_batch_mode = false ]]
	1505	then
[3236]	1506	run_id_number=$RANDOM
	1507	run_id=${run_identifier}.$run_id_number
[2380]	1508
[3236]	1509	tempdir=$fast_io_catalog/$run_id
[3346]	1510
	1511	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1512	export job_id=$run_id
	1513
[2380]	1514	fi
	1515
	1516
	1517	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1518	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1519	then
	1520
	1521	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1522	if [[ $ibd = 0 ]]
	1523	then
	1524	printf "\n"
	1525	printf "\n +++ no batch directives found in configuration file"
	1526	locat=config_file_batch_directives; (( iec = 0 )); exit
	1527	fi
	1528
	1529	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1530	done=false
[2384]	1531	cputime=$cpumax
[2380]	1532	while [[ $done = false ]]
	1533	do
[2384]	1534	if (( cputime == 0 ))
[2380]	1535	then
	1536	printf "\n +++ cpu-time is undefined"
	1537	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1538	printf "\n >>> "
[2384]	1539	read cputime 1>/dev/null 2>&1
[2380]	1540	else
	1541	done=true
	1542	fi
	1543	done
[2420]	1544	cpumax=$cputime
[2380]	1545
	1546	# CHECK THE MEMORY DEMAND
	1547	done=false
	1548	while [[ $done = false ]]
	1549	do
	1550	if (( memory == 0 ))
	1551	then
	1552	printf "\n +++ memory demand is undefined"
	1553	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1554	printf "\n >>> "
	1555	read memory 1>/dev/null 2>&1
	1556	else
	1557	done=true
	1558	fi
	1559	done
	1560
	1561	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1562	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1563	then
	1564	while [[ -z $remote_username ]]
	1565	do
[2420]	1566	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1567	printf "\n >>> Please type username:"
	1568	printf "\n >>> "
	1569	read remote_username
	1570	done
	1571	fi
	1572
	1573	else
	1574
[2420]	1575	if [[ $running_in_batch_mode = false ]]
	1576	then
	1577	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1578	cpumax=$cputime
	1579	else
	1580	cputime=$cpumax
	1581	fi
[2380]	1582
	1583	fi
	1584
	1585
	1586	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1587	(( cpu_hours = cputime / 3600 ))
	1588	(( resttime = cputime - cpu_hours * 3600 ))
	1589	(( cpu_minutes = resttime / 60 ))
	1590	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1591	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1592
	1593
	1594	# OUTPUT OF THE PALMRUN-HEADER
	1595	calltime=$(date)
	1596	printf "\n"
	1597	printf "#------------------------------------------------------------------------# \n"
	1598	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1599	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1600	printf "\| \| \n"
	1601	column1="called on:"; column2=$(hostname)
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603	if [[ $create_remote_batch_job = true ]]
	1604	then
[3236]	1605	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1606	else
	1607	if [[ $running_on_remote = true ]]
	1608	then
[3236]	1609	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1610	else
[3236]	1611	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1612	fi
	1613	fi
	1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1615
	1616	column1="running in:"
	1617	if [[ $running_in_batch_mode = true ]]
	1618	then
	1619	column2="batch job mode"
	1620	else
	1621	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1622	then
	1623	column2="job creation mode"
	1624	else
	1625	column2="interactive run mode"
	1626	fi
	1627	fi
	1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1629
[2479]	1630	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1631	then
[2480]	1632	if [[ "$project_account" != "" ]]
[2479]	1633	then
	1634	column1="project account number:"
	1635	column2="$project_account"
	1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1637	fi
	1638	fi
	1639
[2380]	1640	if [[ -n $cores ]]
	1641	then
	1642	if [[ $run_coupled_model = false ]]
	1643	then
	1644	column1="number of cores:"; column2=$cores
	1645	else
	1646	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1647	fi
	1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1649	fi
	1650	if [[ -n $tasks_per_node ]]
	1651	then
	1652	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1654	if (( remaining_cores > 0 ))
	1655	then
	1656	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1658	fi
	1659	fi
	1660	if [[ $maximum_parallel_io_streams != $cores ]]
	1661	then
	1662	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1664	fi
	1665	if [[ $use_openmp = true ]]
	1666	then
	1667	column1="threads per task:"; column2="$threads_per_task"
	1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1669	fi
[2384]	1670	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1671	then
[2506]	1672	column1="memory demand / PE":; column2="$memory MB"
	1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1674	column1="job cpu time (h:m:s):"; column2="$timestring"
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	fi
[2380]	1677	printf "\| \| \n"
	1678	if [[ "$source_list" != "" ]]
	1679	then
	1680	if [[ "$make_options" != "" ]]
	1681	then
	1682	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1683	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1684	line=$(echo "$make_options" \| cut -c46-)
	1685	while [[ "$line" != "" ]]
	1686	do
	1687	column1=""
	1688	column2=$(echo "$line" \| cut -c-45)
	1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1690	line=$(echo "$line" \| cut -c46-)
	1691	done
	1692	fi
	1693	fi
	1694
	1695	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1696	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1697	line=$(echo "$cpp_options" \| cut -c46-)
	1698	while [[ "$line" != "" ]]
	1699	do
	1700	column1=""
	1701	column2=$(echo "$line" \| cut -c-45)
	1702	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1703	line=$(echo "$line" \| cut -c46-)
	1704	done
	1705
	1706	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1707	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1708	line=$(echo "$compiler_options" \| cut -c46-)
	1709	while [[ "$line" != "" ]]
	1710	do
	1711	column1=""
	1712	column2=$(echo "$line" \| cut -c-45)
	1713	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1714	line=$(echo "$line" \| cut -c46-)
	1715	done
	1716
[2388]	1717	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1718	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1719	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1720	while [[ "$line" != "" ]]
	1721	do
	1722	column1=""
	1723	column2=$(echo "$line" \| cut -c-45)
	1724	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1725	line=$(echo "$line" \| cut -c46-)
	1726	done
	1727
	1728	if [[ "$login_init_cmd" != "" ]]
	1729	then
	1730	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1731	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1732	line=$(echo "$login_init_cmd" \| cut -c46-)
	1733	while [[ "$line" != "" ]]
	1734	do
	1735	column1=""
	1736	column2=$(echo "$line" \| cut -c-45)
	1737	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1738	line=$(echo "$line" \| cut -c46-)
	1739	done
	1740	fi
	1741
	1742	if [[ "$module_commands" != "" ]]
	1743	then
	1744	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1745	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1746	line=$(echo "$module_commands" \| cut -c46-)
	1747	while [[ "$line" != "" ]]
	1748	do
	1749	column1=""
	1750	column2=$(echo "$line" \| cut -c-45)
	1751	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1752	line=$(echo "$line" \| cut -c46-)
	1753	done
	1754	fi
	1755	printf "\| \| \n"
[3236]	1756	column1="run identifier:"; column2=$run_identifier
[2380]	1757	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1758	column1="activation string list:"; column2=$(echo $activation_string_list)
	1759	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1760
	1761	if [[ "$ocean_file_appendix" = true ]]
	1762	then
	1763	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1764	fi
	1765
	1766	if [[ "$source_list" != "" ]]
	1767	then
	1768	printf "\| \| \n"
	1769	printf "\| Files to be compiled: \| \n"
	1770	line=$source_list
	1771	while [[ "$line" != "" ]]
	1772	do
	1773	linestart=$(echo $line \| cut -c-70)
	1774	printf "\| %-70s \| \n" "$linestart"
	1775	line=$(echo "$line" \| cut -c71-)
	1776	done
	1777	fi
	1778	printf "#------------------------------------------------------------------------#"
	1779
	1780
	1781
	1782	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1783	if [[ $do_trace = true ]]
	1784	then
	1785	(( i = 0 ))
[2610]	1786	while (( i < nr_of_input_files ))
[2380]	1787	do
	1788	(( i = i + 1 ))
	1789	if (( i == 1 ))
	1790	then
	1791	printf "\n\n >>> INPUT-file assignments:\n"
	1792	fi
	1793	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1794	done
	1795	(( i = 0 ))
	1796	while (( i < iout ))
	1797	do
	1798	(( i = i + 1 ))
	1799	if (( i == 1 ))
	1800	then
	1801	printf "\n\n >>> OUTPUT-file assignments:\n"
	1802	fi
	1803	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1804	done
	1805	(( i = 0 ))
	1806	while (( i < iic ))
	1807	do
	1808	(( i = i + 1 ))
	1809	if (( i == 1 ))
	1810	then
	1811	printf "\n\n >>> INPUT-commands:\n"
	1812	fi
	1813	printf "\n ${in_command[$i]}"
	1814	done
	1815	(( i = 0 ))
	1816	while (( i < ioc ))
	1817	do
	1818	(( i = i + 1 ))
	1819	if (( i == 1 ))
	1820	then
	1821	printf "\n\n >>> OUTPUT-commands:\n"
	1822	fi
	1823	printf "\n ${out_command[$i]}"
	1824	done
	1825	fi
	1826
	1827	# QUERY FOR CONTINUE
	1828	if [[ $silent = false && $running_in_batch_mode = false ]]
	1829	then
	1830	antwort=dummy
	1831	printf "\n\n"
	1832	printf " >>> everything o.k. (y/n) ? "
	1833	while read antwort
	1834	do
	1835	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1836	then
	1837	printf " >>> everything o.k. (y/n) ? "
	1838	else
	1839	break
	1840	fi
	1841	done
	1842	if [[ $antwort = n \|\| $antwort = N ]]
	1843	then
	1844	locat=user_abort; (( iec = 0 )); exit
	1845	fi
	1846	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1847	then
[2566]	1848	printf "\n *** batch-job will be created and submitted"
[2380]	1849	else
[2566]	1850	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1851	fi
	1852	fi
	1853
	1854
	1855
	1856	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1857	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1858	then
	1859
	1860	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1861	then
[2566]	1862	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1863	else
[2566]	1864	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1865	fi
	1866
[2422]	1867	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1868	# IT SHALL BE CREATED
	1869	ask_for_make_depository=false
	1870	if [[ $create_remote_batch_job = true ]]
	1871	then
	1872
	1873	line=`grep %base_directory $config_file`
[3236]	1874	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1875	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1876
[3236]	1877	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1878	then
	1879	printf "\n\n +++ make depository \"${make_depository}\""
	1880	printf "\n on remote host not found!"
	1881	ask_for_make_depository=true
	1882	fi
[3236]	1883	rm ${configuration_identifier}_last_make_protokoll
[2422]	1884
	1885	else
	1886
	1887	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1888	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1889	if [[ ! -d ${make_depository} ]]
	1890	then
	1891	printf "\n\n +++ make depository \"${make_depository}\""
	1892	printf "\n on local host not found!"
	1893	ask_for_make_depository=true
	1894	fi
	1895
	1896	fi
	1897
	1898	if [[ $ask_for_make_depository = true ]]
	1899	then
	1900
	1901	antwort=dummy
	1902	printf "\n\n"
	1903	printf " >>> Create a new one (y/n) ? "
	1904	while read antwort
	1905	do
	1906	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1907	then
	1908	printf " >>> Create a new one (y/n) ? "
	1909	else
	1910	break
	1911	fi
	1912	done
	1913	if [[ $antwort = n \|\| $antwort = N ]]
	1914	then
	1915	locat=user_abort; (( iec = 0 )); exit
	1916	fi
	1917
[2566]	1918	if [[ $do_trace = true ]]
	1919	then
[3455]	1920	palmbuild -c $configuration_identifier
[2566]	1921	else
[3455]	1922	palmbuild -v -c $configuration_identifier
[2566]	1923	fi
[2422]	1924
[3312]	1925	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1926	then
	1927
	1928	# ABORT IN CASE OF COMPILATION PROBLEMS
	1929	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1930	locat=make_depository
	1931	exit
	1932	else
	1933	echo " *** now continue with creating executable and other sources"
	1934	fi
	1935
	1936	fi
	1937
[2566]	1938	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1939	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1940
[3312]	1941	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1942	then
	1943
	1944	# ABORT IN CASE OF COMPILATION PROBLEMS
	1945	printf "\n +++ error while creating executable and/or other sources"
	1946	locat=execution
[2990]	1947	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1948	exit
	1949
	1950	else
	1951
[2566]	1952	printf " *** executable and other sources created\n"
[2990]	1953	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1954
	1955	fi
	1956
	1957	fi
	1958
	1959
[2669]	1960	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1961	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1962	if [[ $create_remote_batch_job = true ]]
	1963	then
	1964	(( i = 0 ))
[2610]	1965	while (( i < nr_of_input_files ))
[2605]	1966	do
	1967	(( i = i + 1 ))
[2669]	1968	if [[ "${actionin[$i]}" = tr ]]
[2605]	1969	then
	1970	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1971	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1972	fi
	1973	done
	1974	if (( i > 0 ))
	1975	then
[3025]	1976	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1977	fi
	1978	fi
	1979
	1980
[2380]	1981	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1982	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1983	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1984	then
	1985
	1986	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1987	if [[ $running_in_batch_mode = false ]]
	1988	then
[3917]	1989	# CREATE THE DIRECTORY
[2566]	1990	mkdir -p $tempdir
	1991	chmod go+rx $tempdir
	1992	cd $tempdir
	1993	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1994
	1995	else
	1996
	1997	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1998	printf "\n *** running in temporary directory: $tempdir"
[2380]	1999
	2000	fi
	2001
	2002
	2003	# PROVIDE THE INPUT FILES
	2004	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	2005	optional_files_missing=false
[2380]	2006	(( i = 0 ))
[2610]	2007	while (( i < nr_of_input_files ))
[2380]	2008	do
	2009	(( i = i + 1 ))
	2010	if (( i == 1 ))
	2011	then
	2012	printf "\n\n *** providing INPUT-files:\n$dashes"
	2013	fi
	2014
	2015
	2016	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	2017	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2018	then
[2669]	2019	optional_files_missing=true
[2380]	2020	continue
	2021	fi
	2022
	2023	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2024	files_for_cores=false; filetype=file
	2025	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2026	then
	2027	files_for_cores=true; filetype=files
	2028	actionin[$i]=""
	2029	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2030	then
	2031	actionin[$i]=""
	2032	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2033	then
	2034	files_for_cores=true; filetype=files
	2035	actionin[$i]="ln"
	2036	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2037	then
	2038	actionin[$i]="ln"
	2039	fi
	2040
	2041	if [[ $files_for_cores = true ]]
	2042	then
	2043	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2044	else
	2045	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2046	fi
	2047
	2048	# INPUT-FILES TO BE LINKED
	2049	if [[ "${actionin[$i]}" = ln ]]
	2050	then
	2051
	2052	printf "\n $filetype will be linked"
	2053	if [[ $files_for_cores = false ]]
	2054	then
	2055	if [[ -f "${absnamein[$i]}" ]]
	2056	then
	2057	ln ${absnamein[$i]} ${localin[$i]}
	2058	got_tmp[$i]=true
	2059	fi
	2060	else
	2061	if [[ -d "${absnamein[$i]}" ]]
	2062	then
[2396]	2063	mkdir -p ${localin[$i]}
[2380]	2064	cd ${absnamein[$i]}
	2065	for file in $(ls *)
	2066	do
[2566]	2067	ln $file $tempdir/${localin[$i]}
[2380]	2068	done >\|/dev/null 2>&1
[2566]	2069	cd $tempdir
[2380]	2070	fi
	2071
	2072	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2073	if [[ ! -f "${localin[$i]}/_000000" ]]
	2074	then
	2075	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2076	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2077	fi
	2078
	2079	got_tmp[$i]=true
	2080	fi
	2081	fi
	2082
	2083	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2084	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2085	then
	2086
	2087	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2088	then
	2089
	2090	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2091	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2092	printf "\n file will be provided for $cores processors"
[2396]	2093	mkdir -p ${localin[$i]}
[2380]	2094	ival=$cores
	2095	(( ii = 0 ))
	2096	while (( ii <= ival-1 ))
	2097	do
	2098	if (( ii < 10 ))
	2099	then
	2100	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2101	elif (( ii < 100 ))
	2102	then
	2103	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2104	elif (( ii < 1000 ))
	2105	then
	2106	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2107	else
	2108	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2109	fi
	2110	(( ii = ii + 1 ))
	2111	done
	2112
	2113	else
	2114
	2115	if [[ $files_for_cores = true ]]
	2116	then
	2117
	2118	# PROVIDE FILES FOR EACH CORE
	2119	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2120	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2121	printf "\n providing $cores files for the respective cores"
[2396]	2122	mkdir -p ${localin[$i]}
[2380]	2123	if [[ $link_local_input = true ]]
	2124	then
	2125	printf " files will be linked\n"
	2126	cd ${absnamein[$i]}
	2127	for file in $(ls *)
	2128	do
	2129	ln -f $file ${localin[$i]}
	2130	done
[2566]	2131	cd $tempdir
[2380]	2132	fi
	2133
	2134	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2135	if [[ ! -f "${localin[$i]}/_000000" ]]
	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
	2141	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2142	fi
	2143
	2144	else
	2145
	2146	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2147	if [[ $link_local_input = true ]]
	2148	then
	2149	printf " file will be linked\n"
	2150	ln -f ${absnamein[$i]} ${localin[$i]}
	2151	fi
[2605]	2152	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2153	if [[ ! -f "${localin[$i]}" ]]
	2154	then
	2155	if [[ $link_local_input = true ]]
	2156	then
	2157	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2158	fi
[2669]	2159	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2160	then
	2161	mv ${absnamein[$i]} ${localin[$i]}
	2162	else
	2163	cp ${absnamein[$i]} ${localin[$i]}
	2164	fi
[2380]	2165	fi
	2166	fi
	2167	fi
	2168	fi
	2169
	2170	done
	2171	if (( i != 0 ))
	2172	then
[2669]	2173	if [[ $optional_files_missing = true ]]
	2174	then
	2175	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2176	fi
[2380]	2177	printf "\n$dashes\n *** all INPUT-files provided \n"
	2178	fi
	2179
[3917]	2180	# NOW COPY FILES (.f90, .o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY
	2181	# WORKING DIRECTORY
	2182	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
[2380]	2183
[3917]	2184
[2380]	2185	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2186	(( i = 0 ))
	2187	while (( i < iic ))
	2188	do
	2189	(( i = i + 1 ))
	2190	if (( i == 1 ))
	2191	then
	2192	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2193	fi
	2194	printf "\n >>> ${in_command[$i]}"
	2195	eval ${in_command[$i]}
	2196	if (( i == iic ))
	2197	then
	2198	printf "\n$dashes\n"
	2199	fi
	2200	done
	2201
	2202
[3313]	2203	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2204	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2205	then
	2206	progress_bar_disabled=true
	2207	else
	2208	progress_bar_disabled=false
	2209	fi
	2210
	2211
[2380]	2212	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2213	# (FILE ENVPAR WILL BE READ BY PALM)
	2214	cat > ENVPAR << EOF
[3236]	2215	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2216	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2217	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2218	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2219	maximum_cpu_time_allowed = ${cpumax}.,
	2220	revision = '$global_revision',
[3313]	2221	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2222
	2223	EOF
	2224
	2225
	2226	# STARTING THE EXECUTABLE
	2227	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2228	PATH=$PATH:$tempdir
[2380]	2229
	2230
	2231	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2232	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2233	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2234	eval line=\"$line\"
	2235	execute_command="$line"
	2236
	2237
	2238	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2239	if [[ "$execute_command_for_combine" = "" ]]
	2240	then
	2241	eval line2=\"$line2\"
	2242	execute_command_for_combine="$line2"
	2243	fi
	2244
[2380]	2245
	2246
	2247	# PROVIDE A HOSTFILE, IF REQUIRED
	2248	if [[ "$hostfile" != "" ]]
	2249	then
	2250
	2251	if [[ $hostfile = auto ]]
	2252	then
	2253	# CREATE A NEW HOSTFILE
	2254	(( ii = 1 ))
	2255	while (( ii <= cores / threads_per_task ))
	2256	do
	2257	echo $(hostname) >> hostfile
	2258	(( ii = ii + 1 ))
	2259	done
	2260	if (( cores / threads_per_task == 0 ))
	2261	then
	2262	echo $(hostname) >> hostfile
	2263	fi
	2264
	2265	else
	2266	cp $hostfile hostfile
	2267	fi
	2268	eval line=\"`head -n $ii hostfile`\"
	2269	printf "\n *** running on: $line"
	2270	fi
	2271
	2272
	2273
	2274	# SET THE NUMBER OF OPENMP-THREADS
	2275	if [[ $use_openmp = true ]]
	2276	then
	2277	export OMP_NUM_THREADS=$threads_per_task
	2278	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2279	else
	2280	export OMP_NUM_THREADS=1
	2281	fi
	2282
	2283
[2610]	2284	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2285	if [[ $run_coupled_model = false ]]
	2286	then
	2287	if [[ "$ocean_file_appendix" = true ]]
	2288	then
	2289	echo "precursor_ocean" > coupling_steering
	2290	else
	2291	echo "precursor_atmos" > coupling_steering
	2292	fi
	2293	else
	2294	(( iia = $cores_atmos / $threads_per_task ))
	2295	(( iio = $cores_ocean / $threads_per_task ))
	2296	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2297	printf "\n\n"
	2298	echo "coupled_run $iia $iio" > coupling_steering
	2299	fi
	2300
	2301	printf "\n *** execute command:"
	2302	printf "\n \"$execute_command\" \n\n"
	2303
	2304
[3393]	2305	if [[ $progress_bar_disabled = true ]]
[2380]	2306	then
[3402]	2307	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2308	exit_code=${PIPESTATUS[0]}
	2309	else
	2310	$execute_command < coupling_steering &> >(tee STDOUT)
	2311	exit_code=${PIPESTATUS[0]}
	2312	fi
[2380]	2313
[3393]	2314	if [[ ${exit_code} != 0 ]]
	2315	then
	2316
[2380]	2317	# ABORT IN CASE OF RUNTIME ERRORS
	2318	printf "\n +++ runtime error occured"
	2319	locat=execution
	2320	exit
	2321
	2322	else
	2323
	2324	printf "\n$dashes\n *** execution finished \n"
	2325
	2326	fi
	2327
	2328
	2329	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2330	# BY EACH CORE INTO ONE FILE
	2331	if [[ ! -f combine_plot_fields.x ]]
	2332	then
	2333
	2334	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2335	printf "\n 2d- and/or 3d-data may be incomplete!"
	2336	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2337
	2338	elif [[ "$combine_plot_fields" == true ]]
	2339	then
	2340
	2341	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2342	$execute_command_for_combine
	2343
	2344	else
	2345
	2346	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2347	# DATA OUTPUT
[2380]	2348	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2349	fi
	2350
	2351
	2352
	2353	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2354	(( i = 0 ))
	2355	while (( i < ioc ))
	2356	do
	2357	(( i = i + 1 ))
	2358	if (( i == 1 ))
	2359	then
	2360	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2361	fi
[2799]	2362
	2363	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2364	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2365
[2380]	2366	printf "\n >>> ${out_command[$i]}"
	2367	eval ${out_command[$i]}
	2368	if (( i == ioc ))
	2369	then
	2370	printf "\n$dashes\n"
	2371	fi
	2372	done
	2373
	2374
[2610]	2375	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2376	# WILDCARDS
[2380]	2377	(( i = 0 ))
[2610]	2378	(( nr_of_output_files = 0 ))
	2379
[2380]	2380	while (( i < iout ))
	2381	do
[2610]	2382
[2380]	2383	(( i = i + 1 ))
[2610]	2384
	2385	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2386	# CREATE A LIST FOR THE DETECTED ENDINGS
	2387	if [[ "${multout[$i]}" = true ]]
	2388	then
	2389	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2390	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2391	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2392
	2393	endings="DEFAULT"
	2394	while read line
	2395	do
	2396	# remove the local name from the beginning
	2397	localnamestring="${localout_pre[$i]}"
	2398	length_localname=${#localnamestring}
	2399	ending=${line:${length_localname}}
	2400
	2401	if [[ "$ending" != "" ]]
	2402	then
	2403	endings="$endings $ending"
	2404	fi
	2405
	2406	done <filelist
	2407
	2408	rm filelist
	2409
	2410	else
	2411
	2412	# SINGLE NAME
	2413	endings=DEFAULT
	2414
	2415	fi
	2416
	2417	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2418	for ending in $endings
	2419	do
	2420
	2421	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2422	if [[ $ending = DEFAULT ]]
	2423	then
	2424	ending=""
	2425	fi
	2426
	2427	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2428	(( nr_of_output_files = nr_of_output_files + 1 ))
	2429	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2430	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2431	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2432	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2433	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2434	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2435	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2436
	2437	done
	2438
	2439	done
	2440
	2441
	2442
	2443
	2444	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2445	(( i = 0 ))
	2446	while (( i < nr_of_output_files ))
	2447	do
	2448	(( i = i + 1 ))
[2380]	2449	if (( i == 1 ))
	2450	then
[3860]	2451	timestring=`date +%H:%M:%S`
	2452	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
[2380]	2453
	2454	# GET RUN NUMBER ASSIGNED BY PALM
	2455	if [[ -f RUN_NUMBER ]]
	2456	then
	2457	read run_number < RUN_NUMBER
	2458	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2459	usecycle_option="-U $run_number"
	2460	else
	2461	run_number=0
	2462	usecycle_option=""
	2463	fi
	2464	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2465	then
[2404]	2466	printf "\n *** in case of SCP transfers to local host"
	2467	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2468	fi
	2469	printf "\n$dashes"
	2470	fi
	2471
	2472	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2473	then
	2474
[3236]	2475	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2476
	2477	# DETERMINE THE CYCLE NUMBER
	2478	ls -1 -d $filename > filelist 2>/dev/null
	2479	ls -1 -d $filename.* >> filelist 2>/dev/null
	2480	while read line
	2481	do
	2482
	2483	# filename without path (i.e. after the last "/")
	2484	basefilename=$(basename ${line})
	2485
	2486	# check if there is an extension
	2487	extension=${basefilename##*.}
	2488	if [[ "$extension" = "${extout[$i]}" ]]
	2489	then
	2490	basefilename=${basefilename%.*}
	2491	fi
	2492
	2493	# check for an existing cycle number
	2494	cycle=${basefilename##*.}
	2495	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2496	then
[2669]	2497	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2498	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2499	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2500	else
	2501	(( icycle = 1 ))
	2502	fi
	2503
	2504	if (( icycle > maxcycle ))
	2505	then
	2506	(( maxcycle = icycle ))
	2507	fi
	2508
	2509	done <filelist
	2510	rm filelist
	2511
	2512
	2513	# SET THE CYCLE NUMBER
	2514	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2515	if [[ "${actionout[$i]}" = a ]]
	2516	then
	2517	(( maxcycle = maxcycle - 1 ))
	2518	fi
	2519
	2520	(( cycnum[$i] = maxcycle ))
	2521	pathout[$i]=$filename
	2522
	2523
	2524	# ADD CYCLE NUMBER TO FILENAME
	2525	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2526	if [[ "${actionout[$i]}" != "a" ]]
	2527	then
	2528	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2529	# WITH AN EXISTING CYCLE NUMBER
	2530	if (( run_number >= cycnum[$i] ))
	2531	then
	2532	(( cycnum[$i] = run_number ))
	2533	else
	2534	if (( run_number > 0 ))
	2535	then
	2536	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2537	fi
	2538	fi
	2539	fi
	2540	if (( cycnum[$i] > 0 ))
	2541	then
[2600]	2542	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2543	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2544	fi
	2545	fi
	2546
	2547	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2548	files_for_cores=false; filetype=file
	2549	link_local_output=false
	2550	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2551	then
	2552	files_for_cores=true; filetype=directory
	2553	actionout[$i]=""
	2554	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2555	then
	2556	actionout[$i]=""
	2557	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2558	then
	2559	files_for_cores=true; filetype=directory
	2560	link_local_output=true
	2561	actionout[$i]=""
	2562	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2563	then
	2564	link_local_output
	2565	actionout[$i]=""
	2566	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2567	then
	2568	files_for_cores=true; filetype=directory
	2569	actionout[$i]="tr"
	2570	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2571	then
	2572	actionout[$i]="tr"
	2573	fi
	2574
	2575	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2576	then
[2669]	2577	if [[ ${warnout[$i]} = true ]]
	2578	then
	2579	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2580	fi
[2380]	2581	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2582	then
[2669]	2583	if [[ ${warnout[$i]} = true ]]
	2584	then
	2585	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2586	fi
[2380]	2587	else
	2588
	2589
	2590	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2591	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2592	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2593	then
	2594	if [[ $running_on_remote = true ]]
	2595	then
	2596
	2597	# SET OPTIONS FOR TRANSFER
	2598	if [[ "${actionout[$i]}" = tr ]]
	2599	then
	2600	if [[ $files_for_cores = false ]]
	2601	then
	2602	catalog_option=""
	2603	catalog_string=""
	2604	else
	2605	catalog_option="-c"
	2606	catalog_string="/"
	2607	fi
	2608	append_option=""
	2609	append_string=""
	2610	else
	2611	append_option="-A"
	2612	append_string="append"
	2613	fi
	2614
	2615	transfer_failed=false
	2616	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2617	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2618
	2619	# TRANSFER VIA SCP
	2620	if [[ "$remote_loginnode" != "" ]]
	2621	then
[3534]	2622	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]	2623	else
[3236]	2624	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]	2625	fi
[3312]	2626	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2627
	2628
	2629	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2630	if [[ $transfer_failed = true ]]
	2631	then
	2632	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2633	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2634
	2635	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2636	eval local_catalog=${pathout[$i]}
	2637	if [[ ! -d $local_catalog ]]
	2638	then
	2639	printf " *** local directory does not exist. Trying to create:\n"
	2640	printf " $local_catalog \n"
	2641	mkdir -p $local_catalog
	2642	fi
[3236]	2643	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2644	transfer_problems=true
	2645	fi
	2646
	2647	else
	2648
	2649	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2650	# BE COPIED OR APPENDED ON THIS MACHINE
	2651	if [[ "${actionout[$i]}" = tr ]]
	2652	then
	2653	actionout[$i]=""
	2654	else
	2655	actionout[$i]="a"
	2656	fi
	2657	fi
	2658	fi
	2659
	2660
	2661	# APPEND ON THIS MACHINE
	2662	if [[ "${actionout[$i]}" = "a" ]]
	2663	then
	2664	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2665	then
	2666	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2667	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2668	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2669	else
	2670	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2671	printf "\n ${pathout[$i]}\n"
	2672	cat ${localout[$i]} >> ${pathout[$i]}
	2673	fi
	2674	fi
	2675
	2676	# COPY ON THIS MACHINE
	2677	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2678	# ON DIFFERENT FILE-SYSTEMS
	2679	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2680	then
	2681
	2682	# COPY IN CASE OF RUNS ON SINGLE CORES
	2683	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2684	then
	2685	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2686	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2687	if [[ $link_local_output = true ]]
	2688	then
	2689	printf " file will be linked\n"
	2690	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2691	fi
	2692	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2693	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2694	then
	2695	if [[ $link_local_output = true ]]
	2696	then
	2697	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2698	fi
	2699	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2700	else
	2701	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2702	fi
	2703	else
	2704	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2705	printf "\n ${pathout[$i]}\n"
	2706	if [[ $link_local_output = true ]]
	2707	then
	2708	printf " file will be linked\n"
	2709	ln -f ${localout[$i]} ${pathout[$i]}
	2710	fi
	2711	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2712	if [[ ! -f "${pathout[$i]}" ]]
	2713	then
	2714	if [[ $link_local_output = true ]]
	2715	then
	2716	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2717	fi
	2718	cp ${localout[$i]} ${pathout[$i]}
	2719	else
	2720	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2721	fi
	2722	fi
	2723
	2724	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2725	then
	2726
	2727	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2728	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2729	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2730	printf "\n ${pathout[$i]}\n"
	2731	if [[ $link_local_output = true ]]
	2732	then
	2733	printf " files will be linked\n"
[2396]	2734	mkdir -p ${pathout[$i]}
[2380]	2735	cd ${localout[$i]}
	2736	for file in $(ls *)
	2737	do
	2738	ln -f $file ${pathout[$i]}
	2739	done >\|/dev/null 2>&1
[2566]	2740	cd $tempdir
[2380]	2741	fi
	2742
	2743	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2744	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2745	then
	2746	if [[ $link_local_output = true ]]
	2747	then
	2748	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2749	fi
[3025]	2750	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2751	cp -r ${localout[$i]}/* ${pathout[$i]}
	2752	fi
	2753
	2754	fi
	2755	fi
	2756	done
	2757
	2758	if (( i != 0 ))
	2759	then
[3860]	2760	timestring=`date +%H:%M:%S`
[2380]	2761	if [[ $transfer_problems = true ]]
	2762	then
[3860]	2763	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
[2380]	2764	printf "\n +++ WARNING: some data transfers failed! \n"
	2765	else
[3860]	2766	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
[2380]	2767	fi
	2768	fi
	2769
	2770
	2771	# IF REQUIRED, START A RESTART-JOB
	2772	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2773	if [[ -f CONTINUE_RUN ]]
	2774	then
	2775
	2776	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2777	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2778	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2779	# -b START A BATCH JOB
	2780	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2781	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
[3982]	2782	[[ $(echo $prc \| grep -c "\-b") = 0 && $running_on_remote = false ]] && prc="$prc -b"
[2380]	2783
[2957]	2784	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2785	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2786	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2787	then
	2788	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2789	fi
[2380]	2790
	2791	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2792	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2793	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2794	then
[2381]	2795	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2796	fi
	2797
	2798
	2799	# START THE RESTART-JOB
	2800	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2801	echo " $prc"
	2802	printf "\n$dashes\n"
	2803	if [[ $running_on_remote = true ]]
	2804	then
	2805
	2806	echo "*** ssh will be used to initiate restart-runs!"
	2807	echo " return_address=\"$return_address\" "
	2808	echo " return_username=\"$local_username\" "
	2809
	2810	if [[ "$remote_loginnode" != "" ]]
	2811	then
[3534]	2812	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]	2813	else
[3534]	2814	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2815	fi
	2816
	2817	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2818	sleep 30
	2819
	2820	else
	2821
	2822	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2823	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2824
	2825	fi
	2826
[3132]	2827	# CHECK, IF RESTART JOB HAS BEEN STARTED
[3725]	2828	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
[3132]	2829	then
	2830	printf "\n$dashes\n +++ creating restart run failed \n"
	2831	locat=create_restart
[3455]	2832	rm palmrun_restart.log
[3132]	2833	exit
[3725]	2834	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
	2835	then
	2836	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
	2837	locat=create_restart
	2838	rm palmrun_restart.log
	2839	exit
[3132]	2840	else
	2841	printf "\n$dashes\n *** restart run initiated \n"
	2842	rm palmrun_restart.log
	2843	fi
[2380]	2844
[3132]	2845
[2380]	2846	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2847	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2848	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2849	# MAY BE VERY HUGE)
	2850	(( i = 0 ))
[2610]	2851	while (( i < nr_of_input_files ))
[2380]	2852	do
	2853	(( i = i + 1 ))
	2854	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2855	then
	2856	rm -r ${absnamein[$i]}
	2857	fi
	2858	done
	2859
	2860	fi
	2861
	2862
	2863	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2864	cd $HOME
[2566]	2865	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2866
	2867
	2868	else
	2869
	2870
	2871	# PREPARING ACTIONS,
	2872	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2873
	2874	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2875	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2876	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2877	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2878	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2879	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2880	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2881	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2882	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2883	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2884	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2885	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2886	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2887	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2888	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2889	if [[ $create_remote_batch_job = true ]]
	2890	then
	2891	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2892	if [[ $do_trace = true ]]
	2893	then
	2894	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2895	fi
[2380]	2896	elif [[ $create_batch_job = true ]]
	2897	then
	2898	palmrun_com=${palmrun_com}" -j"
[2420]	2899	if [[ $do_trace = true ]]
	2900	then
	2901	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2902	fi
[2380]	2903	fi
	2904
	2905
	2906	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2907	# REMOTE HOST
[3236]	2908	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2909	job_protocol_file=$job_protocol_file_local
	2910	if [[ $create_remote_batch_job = true ]]
	2911	then
[3236]	2912	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2913	job_protocol_file=$job_protocol_file_remote
	2914	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2915	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2916	fi
	2917
	2918
	2919	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2920	jobfile=jobfile.$run_id_number
[2380]	2921
	2922
	2923	# FIRST CREATE THE BATCH DIRECTIVES
	2924	(( i = 0 ))
	2925	while (( i < ibd ))
	2926	do
	2927	(( i = i + 1 ))
[2693]	2928	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2929	eval line=\"$line\"
	2930	echo "$line" >> $jobfile
	2931	done
	2932	echo " " >> $jobfile
	2933
	2934
	2935	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2936	# PROTOCOL
	2937	if [[ $create_remote_batch_job = true ]]
	2938	then
[3236]	2939	echo "set +vx" >> $jobfile
	2940	echo "trap '" >> $jobfile
	2941	echo "set +vx" >> $jobfile
	2942	echo "cd ${remote_jobcatalog}" >> $jobfile
	2943	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2944
	2945	# ADD THE BATCH DIRECTIVES
	2946	(( i = 0 ))
	2947	while (( i < ibdt ))
	2948	do
	2949	(( i = i + 1 ))
[2693]	2950	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2951	eval line=\"$line\"
	2952	echo "$line" >> $jobfile
	2953	done
	2954	echo " " >> $jobfile
	2955
	2956	echo "set -x" >> $jobfile
[3534]	2957	if [[ "$remote_loginnode" != "" ]]
	2958	then
	2959	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}\" " >> $jobfile
	2960	else
	2961	echo "${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
	2962	fi
[2380]	2963	echo "%%END%%" >> $jobfile
	2964	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2965	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2966	echo "rm $scpjob_file" >> $jobfile
[2404]	2967	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2968	echo "set -x" >> $jobfile
	2969	echo " ' exit" >> $jobfile
	2970	fi
	2971
	2972
	2973	# ACTIVATE ERROR-TRACEBACK
	2974	if [[ $do_trace = true ]]
	2975	then
	2976	echo "set -x" >> $jobfile
	2977	else
	2978	echo "set +vx" >> $jobfile
	2979	fi
	2980
	2981
	2982	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2983	if [[ "$login_init_cmd" != "" ]]
	2984	then
	2985	echo "$login_init_cmd" >> $jobfile
	2986	fi
	2987	if [[ "$module_commands" != "" ]]
	2988	then
	2989	echo "$module_commands" >> $jobfile
	2990	fi
	2991
	2992
	2993	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2994	if [[ $create_remote_batch_job = true ]]
	2995	then
	2996	echo "mkdir $tempdir" >> $jobfile
	2997	echo "chmod go+rx $tempdir" >> $jobfile
	2998	else
	2999	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	3000	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	3001	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	3002	mkdir $tempdir
	3003	chmod go+rx $tempdir
	3004	fi
	3005	echo "cd $tempdir" >> $jobfile
	3006	echo "export tempdir=$tempdir" >> $jobfile
[3917]	3007	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile
	3008	echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile
[2380]	3009	echo "export execute_palmrun=true" >> $jobfile
	3010
	3011
	3012	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3013	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	3014	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	3015	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3016	echo "export LOCAL_PWD" >> $jobfile
	3017
	3018
	3019	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	3020	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	3021	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	3022
	3023
	3024	# CALL PALMRUN WITHIN THE JOB
	3025	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	3026	echo "set -x" >> $jobfile
	3027	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3028
	3029
	3030	# TRANSFER JOBFILE TO THE TARGET HOST
	3031	if [[ $create_jobfile_only = false ]]
	3032	then
	3033
[3505]	3034	# CREATE LOCAL JOB FOLDER
	3035	eval local_jobcatalog=$local_jobcatalog
	3036	if [[ ! -d $local_jobcatalog ]]
	3037	then
	3038	echo " "
	3039	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3040	mkdir $local_jobcatalog
	3041	fi
	3042
[2380]	3043	if [[ $create_remote_batch_job = true ]]
	3044	then
	3045
[2420]	3046	echo " "
[2566]	3047	echo " *** transfer of job to remote host via scp"
[3505]	3048
	3049	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3050	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3051
	3052	# COPY THE JOB FILE
[2420]	3053	if [[ $do_trace = true ]]
	3054	then
[3236]	3055	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3056	fi
[3236]	3057	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3058
[3505]	3059	# SUBMIT THE JOB
[3574]	3060	printf " *** submit the job (output of submit command, \n"
[3573]	3061	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3062	if [[ $do_trace = true ]]
	3063	then
[3665]	3064	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]	3065	fi
[3665]	3066	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]	3067
	3068	elif [[ $create_batch_job = true ]]
	3069	then
	3070
[2385]	3071	eval local_jobcatalog=$local_jobcatalog
[3236]	3072	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3073	cd $local_jobcatalog
[2380]	3074	echo " "
[2420]	3075	echo " *** submit the job"
	3076	if [[ $do_trace = true ]]
	3077	then
[3236]	3078	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3079	fi
[3236]	3080	$submit_command ${configuration_identifier}_${run_id}
	3081	rm ${configuration_identifier}_${run_id}
[2380]	3082	cd - > /dev/null
	3083
	3084	fi
	3085
	3086	rm -rf $jobfile
	3087
	3088	else
	3089
	3090	printf "\n *** jobfile created under name \"$jobfile\" "
	3091	printf "\n no batch-job has been sent!"
	3092
	3093	fi
	3094
	3095	fi # END OF REMOTE-PART

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