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source: palm/trunk/SCRIPTS/palmrun @ 4319

Last change on this file since 4319 was 4303, checked in by raasch, 5 years ago
Abort if temporary working catalog / SOURCES_FOR_RUN catalog cannot be created
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 105.4 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 4303 2019-11-25 08:55:18Z suehring $
[4303]	29	# Abort if temporary working catalog cannot be created
	30	#
	31	# 3982 2019-05-16 11:07:31Z raasch
[3982]	32	# bugfix: -b is not added in automatically generated batch jobs for remote hosts
	33	#
	34	# 3917 2019-04-18 11:46:37Z raasch
[3917]	35	# in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has
	36	# been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied
	37	# into the temporary working catalog
	38	#
	39	# 3860 2019-04-04 06:23:27Z raasch
[3860]	40	# check added, that it is not allowed to set option -b if the configuration file has been setup
	41	# for running batch jobs on remote hosts,
	42	# local time added to terminal output before and after saving output files
	43	#
	44	# 3725 2019-02-07 10:11:02Z raasch
[3725]	45	# error messages for failed restarts extended
	46	#
	47	# 3682 2019-01-18 17:01:54Z knoop
[3665]	48	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	49	# of login messages on specific systems
	50	#
	51	# 3574 2018-11-28 13:14:39Z raasch
[3574]	52	# syntax-error in last commit fixed
	53	#
	54	# 3573 2018-11-28 13:03:44Z raasch
[3573]	55	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	56	# removed,
	57	# r3570 reverted
	58	#
	59	# 3570 2018-11-27 17:44:21Z kanani
[3570]	60	# Rename job-id by run_id
	61	#
	62	# 3555 2018-11-22 13:50:37Z raasch
[3555]	63	# sed-command to remove repeated space-characters replaced by tr-command, to
	64	# guarantee mac compatible
	65	#
	66	# 3549 2018-11-21 15:44:44Z raasch
[3549]	67	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	68	# of login messages on specific systems
	69	#
	70	# 3534 2018-11-19 15:35:16Z raasch
[3534]	71	# batch_scp for sending back the job protocol file is called via login-node if
	72	# a login-node has been set in the config-file
	73	# ssh-calls rearranged to avoid output of system/user-profile messages
	74	#
	75	# 3505 2018-11-08 09:14:30Z raasch
[3505]	76	# job folders are created in case that they do not exist
	77	#
	78	# 3455 2018-10-30 14:12:31Z raasch
[3455]	79	# options -h and -d renamed -c and -r, respectively
	80	#
	81	# 3402 2018-10-23 11:49:24Z knoop
[3346]	82	# job_id is set for compatibility reasons with older versions of config files
	83	#
	84	# 3313 2018-10-06 15:22:48Z knoop
[3294]	85	# more detailed error message for outdated fileconnection file
	86	#
	87	# 3236 2018-09-10 09:07:06Z raasch
[3236]	88	# warning issued in case of file connection file version mismatch,
	89	# host_configuration renamed configuration_identifier,
	90	# "host identifier" in header output renamed "config. identifier",
	91	# jobname renamed run_identifier,
	92	# run_id renamed run_id_number
	93	# job_id renamed run_id
	94	# option -r renamed -i
	95	#
	96	# 3151 2018-07-19 08:45:38Z raasch
[3151]	97	# removed additional listing of files to be compiled, print PALM code revision
	98	# in header
	99	#
	100	# 3132 2018-07-16 11:44:58Z raasch
[3132]	101	# create consistent error messages in case of failed restarts,
	102	# check existence of remote job catalog
	103	#
	104	# 3043 2018-05-25 10:47:54Z raasch
[3043]	105	# check for setting of fast_io_catalog
	106	#
	107	# 3033 2018-05-23 15:26:19Z raasch
[3025]	108	# -T option not required for interactive runs (tasks per node =
	109	# total number of cores is assumed as default, if option is not given),
	110	# reformatting of a few messages,
	111	# bugfix: destination output directory is created if attribute "pe" is set in
	112	# .palm.iofiles
	113	#
	114	# 2718 2018-01-02 08:49:38Z maronga
[2993]	115	# bugfix of r2990
	116	#
	117	# 2718 2018-01-02 08:49:38Z maronga
[2990]	118	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	119	# not in the working directory from where palmrun is called
	120	#
	121	# 2718 2018-01-02 08:49:38Z maronga
[2957]	122	# svfout in the activation string will be replaced now by svfin in case of
	123	# automatic restarts
	124	#
	125	# 2718 2018-01-02 08:49:38Z maronga
[2906]	126	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	127	# the possible output or input of sky view factors
	128	#
	129	# 2718 2018-01-02 08:49:38Z maronga
[2834]	130	# "fname" renamed to "jobname"
	131	#
	132	# 2718 2018-01-02 08:49:38Z maronga
[2799]	133	# parameters are allowed in output commands (OC:)
	134	#
	135	# 2718 2018-01-02 08:49:38Z maronga
[2789]	136	# bugfix: exit if no queue has been given neither with option -q nor in the
	137	# configuration file
	138	#
	139	# 2718 2018-01-02 08:49:38Z maronga
[2762]	140	# file connection file from trunk/SCRIPTS is taken by default
	141	#
	142	# 2718 2018-01-02 08:49:38Z maronga
[2716]	143	# Corrected "Former revisions" section
	144	#
	145	# 2696 2017-12-14 17:12:51Z kanani
	146	# Change in file header (GPL part)
	147	#
	148	# 2693 2017-12-13 12:33:49Z raasch
[2693]	149	# replacement of variables given by {{<variable>}} in configuration file is now
	150	# done in a more general way, variable names are written in small letters
	151	#
	152	# 2670 2017-12-06 16:32:19Z raasch
[2670]	153	# test printouts removed
	154	#
	155	# 2669 2017-12-06 16:03:27Z raasch
[2669]	156	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	157	# removed,
	158	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	159	# files,
	160	# informative messages in case of missing optional input files shortened
	161	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	162	#
	163	# 2638 2017-11-23 12:44:23Z raasch
[2610]	164	# use of wildcards in file connection statements enabled
	165	#
	166	# 2605 2017-11-09 15:31:46Z raasch
[2605]	167	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	168	# will not be sent with the job file any more, but copied into the
[2610]	169	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	170	#
	171	# 2600 2017-11-01 14:11:20Z raasch
[2600]	172	# cycle numbers are made three digits wide
	173	#
	174	# 2566 2017-10-20 08:50:47Z raasch
[2566]	175	# execute command for combine_plot_fields added
	176	# "TEMPDIR" renamed "tempdir"
	177	# temporary working directory for local batch jobs is created immediately within
	178	# the user's palmrun call, due to a requirement of the "grid engine" batch
	179	# system, where the working directory is given with batch directive -wd and must
	180	# already exist when the job is submitted,
	181	# informative messages in non-trace mode reduced and partly reformatted
	182	#
	183	# 2551 2017-10-18 07:25:11Z raasch
[2551]	184	# TEMPDIR added as replacement string to be used in batch directives
	185	#
	186	# 2512 2017-10-04 08:26:59Z raasch
[2507]	187	# bugfix for determining cycle numbers of NetCDF input files
	188	#
	189	# 2506 2017-09-29 08:30:37Z raasch
[2506]	190	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	191	# host configuration added to SOURCES_FOR_RUN_... folder name
	192	# host_identifier renamed host_configuration
	193	# option -W added to allow for job dependencies
	194	#
	195	# 2501 2017-09-26 11:41:55Z raasch
[2501]	196	# default value for number of cores (option -X) set to 1
	197	# bugfix for mechanism which overwrites configuration file settings with values
	198	# provided by palmrun options
	199	#
	200	# 2499 2017-09-22 16:47:58Z kanani
[2499]	201	# option -h named configuration identifier
	202	#
	203	# 2480 2017-09-19 06:24:14Z maronga
[2480]	204	# bugfix for last revision
	205	#
	206	# 2479 2017-09-19 06:12:16Z raasch
[2479]	207	# option -A (project account number) added
	208	#
	209	# 2422 2017-09-08 08:25:41Z raasch
[2410]	210	# initial revision
[2380]	211	#
	212	#--------------------------------------------------------------------------------#
	213	# palmrun - script for running PALM jobs on local and remote hosts
	214	#--------------------------------------------------------------------------------#
	215
	216
	217
	218	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	219
	220	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	221	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	222	# (TOO MANY ARGUMENTS - PROBLEM)
	223	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	224
[2610]	225	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	226	typeset -i nr_of_output_files=0
[2380]	227	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	228	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	229	# SCRIPT-OPTION ARGUMENTS
	230	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	231	typeset -i icycle inode ival maxcycle mpi_tasks
	232	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	233
	234	activation_string_list=""
	235	AddFilenames=""
	236	combine_plot_fields=true
	237	compiler_name=""
	238	compiler_name_ser=""
	239	compiler_options=""
[3236]	240	configuration_identifier="default"
[2501]	241	cores=1
[2380]	242	cores_atmos=0
	243	cores_ocean=0
	244	coupled_dist=""
	245	cpp_options=""
	246	cpumax=0
[2506]	247	create_batch_job=false
[2380]	248	create_jobfile_only=false
	249	create_remote_batch_job=false
	250	dashes=" ----------------------------------------------------------------------------"
	251	defaultqueue=""
[2506]	252	delete_temporary_catalog=true
[2380]	253	do_compile=true
	254	do_trace=false
	255	executable=""
	256	execute_command=""
	257	execution_error=false
[2762]	258	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	259	global_revision=""
	260	hostfile=""
	261	hp=""
	262	keep_data_from_previous_run=false
	263	link_local_input=false
	264	link_local_output=false
[2388]	265	linker_options=""
[2385]	266	local_jobcatalog=""
[2380]	267	locat=normal
	268	makefile=""
	269	max_par_io_str=""
	270	prc=$0
	271	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	272	do
	273	prc=`echo $prc \| cut -f2- -d"/"`
	274	done
	275	module_calls=""
[2506]	276	palmrun_memory=""
[2380]	277	palmrun_script_name=$prc
	278	openmp=false
[2506]	279	previous_job=""
[2479]	280	project_account=""
[2380]	281	queue=none
[2906]	282	read_svf=""
[2380]	283	restart_run=false
	284	return_address=""
[2385]	285	remote_jobcatalog=""
[2380]	286	remote_username=""
	287	running_in_batch_mode=false
[3313]	288	running_in_test_mode=false
[2380]	289	run_coupled_model=false
	290	run_id=""
[3236]	291	run_id_number=""
	292	run_identifier=test
[2380]	293	silent=false
	294	source_list=""
	295	source_path=""
[2501]	296	tasks_per_node=0
[2380]	297	threads_per_task=1
	298	transfer_problems=false
[2384]	299	user_source_path=""
[2506]	300	use_existing_sources_folder=""
[2380]	301	use_openmp=false
[3033]	302	version="palmrun 1.0 Rev$Rev: 4303 $"
[2380]	303	working_directory=`pwd`
	304	write_binary=""
[2906]	305	write_svf=""
[2380]	306
	307
	308	# ERROR HANDLING IN CASE OF EXIT
[2404]	309	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	310	then
	311
	312	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	313	(( i = 0 ))
	314	while (( i < iec ))
	315	do
	316	(( i = i + 1 ))
	317	printf "\n *** Execution of ERROR-command:\n"
	318	printf " >>> ${err_command[$i]}\n"
	319	eval ${err_command[$i]}
	320	done
[2566]	321	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	322	printf "\n\n+++ palmrun crashed \n\n"
	323	exit 1
	324	elif [[ $locat != normal ]]
[2380]	325	then
[3312]	326	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	327	printf "\n+++ palmrun killed by \"^C\" \n\n"
	328	exit 2
	329	else
[2566]	330	printf "\n --> palmrun finished\n\n"
[3312]	331	exit 0
[2380]	332	fi' exit
	333
	334
	335	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	336	trap 'locat=control_c
	337	exit 1
[2380]	338	' 2
	339
	340
	341	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	342	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	343	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]	344	do
	345	case $option in
	346	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	347	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	348	(b) create_batch_job=true; prc="$prc -b";;
	349	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	350	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	351	(C) restart_run=true; prc="$prc -C";;
	352	(F) create_jobfile_only=true;;
	353	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	354	(i) run_id_number=$OPTARG;;
[2380]	355	(j) running_in_batch_mode=true;;
	356	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	357	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	358	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	359	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	360	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	361	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	362	(R) return_address=$OPTARG;;
	363	(s) source_list=$OPTARG;;
[2501]	364	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	365	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	366	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	367	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	368	(v) silent=true; prc="$prc -v";;
[2506]	369	(V) use_existing_sources_folder="-V";;
[2380]	370	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	371	(W) previous_job=$OPTARG;;
[2380]	372	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	373	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	374	(y) ocean_file_appendix=true; prc="$prc -y";;
	375	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	376	(z) running_in_test_mode=true;;
[2380]	377	(Z) combine_plot_fields=false; prc="$prc -Z";;
	378	(\?) printf "\n +++ unknown option $OPTARG \n"
	379	printf "\n --> type \"$0 ?\" for available options \n"
	380	locat=parameter;exit;;
	381	esac
	382	done
	383
	384
	385	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	386	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	387	(( to_shift = $OPTIND - 1 ))
	388	shift $to_shift
	389
	390	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	391	if [[ "$1" = "?" ]]
	392	then
	393	(printf "\n *** Description of available palmrun options:\n"
	394	printf "\n Option Description Default-Value"
	395	printf "\n -a activation string list \"\" "
[2479]	396	printf "\n -A project account number ---"
[2380]	397	printf "\n -b batch-job on local machine ---"
	398	printf "\n -B do not delete temporary directory at end ---"
[3455]	399	printf "\n -c configuration identifier \"default\" "
[2380]	400	printf "\n -F create batch job file only ---"
	401	printf "\n -k keep data from previous run"
	402	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	403	printf "\n -M Makefile name Makefile"
	404	printf "\n -O threads per openMP task ---"
	405	printf "\n -q queue \"$queue\" "
[3455]	406	printf "\n -r run identifier test"
[2380]	407	printf "\n -s filenames of routines to be compiled \"\" "
	408	printf "\n must end with .f, .f90, .F, or .c !"
	409	printf "\n use \"..\" for more than one file and wildcards"
	410	printf "\n -s LM compiles all locally modified files"
	411	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	412	printf "\n -T tasks per node ---"
[2380]	413	printf "\n -u username on remote machine \"\" "
	414	printf "\n -v no prompt for confirmation ---"
[2506]	415	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	416	printf "\n -w maximum parallel io streams as given by -X"
[2506]	417	printf "\n -W name of job to wait for ---"
[2380]	418	printf "\n -x tracing of palmrun for debug purposes ---"
	419	printf "\n -X # of processors (on parallel machines) 1"
	420	printf "\n -y add appendix \"_O\" to all local output"
	421	printf "\n files (ocean precursor runs followed by"
	422	printf "\n coupled atmosphere-ocean runs) ---"
	423	printf "\n -Y run coupled model, \"#1 #2\" with"
	424	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	425	printf "\n -Z skip combine_plot_fields at the end of "
	426	printf "\n the simulation ---"
	427	printf "\n "
	428	printf "\n Possible values of positional parameter <modus>:"
	429	printf "\n \"?\" - this outline \n\n") \| more
	430	exit
	431	elif [[ "$1" != "" ]]
	432	then
	433	printf "\n +++ positional parameter $1 unknown \n"
	434	locat=parameter; exit
	435	fi
	436
	437
	438
	439	# SHORT STARTING MESSAGE
	440	printf "\n*** $version "
	441	printf "\n will be executed. Please wait ..."
	442
	443
[2506]	444	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	445	config_file=.palm.config.$configuration_identifier
	446	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	447
	448
	449	# CHECK, IF CONFIGURATION FILE EXISTS
	450	if [[ ! -f $config_file ]]
	451	then
	452	printf "\n\n +++ configuration file: "
	453	printf "\n $config_file"
	454	printf "\n does not exist"
	455	locat=connect; exit
	456	fi
	457
	458
[2762]	459	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	460	if [[ -f .palm.iofiles ]]
	461	then
[3236]	462
	463	# CHECK VERSION MISMATCH
[3573]	464	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	465	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	466	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	467	then
	468	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	469	then
	470	printf "\n\n +++ WARNING: A file connection file has been found in your"
	471	printf "\n working directory, but its revision does not match"
	472	printf "\n the revision of the default (trunk) version."
[3294]	473	printf "\n You may need to update your connection file"
	474	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	475	fi
	476	fi
	477
[2762]	478	fileconnection_file=.palm.iofiles
[3236]	479
[2762]	480	fi
	481
	482
[2380]	483	# CHECK, IF FILE CONNECTION FILE EXISTS
	484	if [[ ! -f $fileconnection_file ]]
	485	then
	486	printf "\n\n +++ file connection file: "
	487	printf "\n $fileconnection_file"
	488	printf "\n does not exist"
	489	locat=connect; exit
	490	fi
	491
	492
[2404]	493	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	494	if [[ "$activation_string_list" = "" ]]
	495	then
	496	printf "\n\n +++ no activation string list given: "
	497	printf "\n please set palmrun option \"-a\" "
	498	locat=palmrun_option; exit
	499	fi
	500
	501
	502	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	503	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	504	then
	505	write_binary=true
	506	else
	507	write_binary=false
	508	fi
	509
[2906]	510	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	511	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	512	then
	513	write_svf=true
	514	else
	515	write_svf=false
	516	fi
[2404]	517
[2906]	518	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	519	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	520	then
	521	read_svf=true
	522	else
	523	read_svf=false
	524	fi
	525
	526
[2380]	527	# READ AND EVALUATE THE CONFIGURATION-FILE
	528	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	529
	530	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	531	while read line
	532	do
	533
	534	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	535	eval line=\"$line\"
	536
	537
	538	# INTERPRET THE LINE
	539	if [[ "$(echo $line)" = "" ]]
	540	then
	541
	542	# EMPTY LINE, NO ACTION
	543	continue
	544
	545	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	546	then
	547
	548	# LINE IS A COMMENT LINE
	549	continue
	550
	551	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	552	then
	553
	554	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	555	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	556	value=`echo $line \| cut -d" " -s -f2-`
	557
	558
	559	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	560	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	561	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	562	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	563	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	564	# CONFIGURATION-FILE.
	565	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	566	then
	567	eval export $var="\$value"
	568
	569	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	570	if [[ $do_trace = true ]]
	571	then
	572	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	573	fi
	574	fi
	575
	576	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	577	then
	578
	579	# LINE DEFINES BATCH-DIRECTIVE
	580	(( ibd = ibd + 1 ))
	581	line=$(echo $line \| cut -c4-)
	582	batch_directive[$ibd]="$line"
	583
	584	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	585	then
	586
	587	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	588	# REMOTE TO A LOCAL HOST
	589	(( ibdt = ibdt + 1 ))
	590	line=$(echo $line \| cut -c5-)
	591	batch_directive_transfer[$ibdt]="$line"
	592
	593	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	594	then
	595
	596	# LINE DEFINES ERROR-COMMAND
	597	(( iec = iec + 1 ))
	598	line=$(echo $line \| cut -c4-)
	599	err_command[$iec]="$line"
	600
	601	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	602	then
	603
	604	# LINE DEFINES INPUT-COMMAND
	605	(( iic = iic + 1 ))
	606	line=$(echo $line \| cut -c4-)
	607	in_command[$iic]="$line"
	608
	609	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	610	then
	611
	612	# LINE DEFINES OUTPUT-COMMAND
	613	(( ioc = ioc + 1 ))
	614	line=$(echo $line \| cut -c4-)
	615	out_command[$ioc]="$line"
	616
	617	else
	618
	619	# SKIP ALL OTHER LINES
	620	continue
	621
	622	fi
	623
	624	done < $config_file
	625
	626
	627	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	628	if [[ "$fast_io_catalog" = "" ]]
	629	then
[3860]	630	printf "\n\n +++ no fast_io_catalog found in $config_file"
[3043]	631	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	632	locat=config_file; exit
	633	fi
[2380]	634	if [[ "$compiler_name" = "" ]]
	635	then
[3860]	636	printf "\n\n +++ no compiler name found in $config_file"
[2380]	637	printf "\n Please add line \"compiler_name ...\" to that file."
	638	locat=config_file; exit
	639	fi
	640	if [[ "$compiler_name_ser" = "" ]]
	641	then
[3860]	642	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
[2380]	643	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	644	locat=config_file; exit
	645	fi
	646	if [[ "$compiler_options" = "" ]]
	647	then
[3860]	648	printf "\n\n +++ no compiler options found in $config_file"
[2380]	649	printf "\n Please add line \"compiler_options ...\" to that file."
	650	locat=config_file; exit
	651	fi
	652	if [[ "$execute_command" = "" ]]
	653	then
[3860]	654	printf "\n\n +++ no execute command found in $config_file"
[2380]	655	printf "\n Please add line \"execute_command ...\" to that file."
	656	locat=config_file; exit
	657	fi
	658
	659	if [[ "$hostfile" != "" ]]
	660	then
	661	if [[ $hostfile != auto && ! -f $hostfile ]]
	662	then
[3860]	663	printf "\n\n +++ no hostfile \"$hostfile\" found"
[3151]	664	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	665	locat=config_file; exit
	666	fi
	667	fi
	668
	669
	670	# DETERMINE THE CALL STATUS
	671	if [[ "$return_address" != "" ]]
	672	then
	673
	674	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	675	# BATCH MODE AND ...
	676	running_on_remote=true
	677
	678	else
	679
	680	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	681	if [[ "$remote_ip" != "" ]]
	682	then
	683
	684	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	685	create_remote_batch_job=true
	686
[3132]	687	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	688	if [[ "$remote_jobcatalog" = "" ]]
	689	then
[3860]	690	printf "\n\n +++ no remote jobcatalog found in $config_file"
[3132]	691	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	692	locat=config_file; exit
	693	fi
	694
[3860]	695	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
	696	if [[ $create_batch_job = true ]]
	697	then
	698	printf "\n\n +++ option -b must not be set because configuration file has been setup"
	699	printf "\n for running jobs on a remote host"
	700	locat=config_file; exit
	701	fi
	702
[2380]	703	fi
	704	running_on_remote=false
	705	fi
	706
	707
	708
	709	# READ AND EVALUATE THE I/O-FILE LIST
	710	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	711
	712	# READ THE FILE CONNECTION FILE LINE BY LINE
	713	while read line
	714	do
	715
[2669]	716	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	717	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	718	line=`echo "$line" \| tr -s " "`
[2380]	719
	720	# INTERPRET THE LINE
	721	if [[ "$(echo $line)" = "" ]]
	722	then
	723	# EMPTY LINE, NO ACTION
	724	continue
	725
	726	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	727	then
	728
	729	# LINE IS A COMMENT LINE
	730	true
	731
	732	else
	733
	734	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	735	# s2a: in/out - field
[2669]	736	# s2b: action - field (optional)
	737	s1=`echo "$line" \| cut -d" " -f1`
	738	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	739	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	740	then
[2669]	741	s2a=$s2
[2380]	742	s2b=""
	743	else
[2669]	744	s2a=`echo $s2 \| cut -d":" -f1`
	745	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	746	fi
[2669]	747	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	748	s4=`echo "$line" \| cut -d" " -s -f4`
	749	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	750	s5=`echo "$line" \| cut -d" " -s -f5`
	751	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	752
	753
	754	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	755	# INPUT- OR OUTPUT-LIST.
	756	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	757	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	758	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	759	# IS NOT CHECKED AND STORED.
[2610]	760	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	761	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	762	then
	763	found=false
	764	for actual in $activation_string_list
	765	do
	766	for formal in $s3
	767	do
	768	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	769	done
	770	done
	771	if [[ $found = true ]]
	772	then
	773	(( iin = iin + 1 ))
[2669]	774	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	775	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	776	if [[ "$s2a" = inopt ]]
	777	then
	778	optin_pre[$iin]=yes
	779	else
	780	optin_pre[$iin]=no
	781	fi
[2605]	782
	783	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	784	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	785	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	786	then
[2610]	787	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	788	fi
	789
[2610]	790	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	791	# THE WILDCARD FROM THE ENDING
	792	if [[ "${s5: -1}" = "*" ]]
	793	then
[2669]	794	if [[ "$s2b" = "di" ]]
[2610]	795	then
	796	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	797	printf "\n see file \"$fileconnection_file\", line"
	798	printf "\n$line"
	799	locat=iofiles_file; exit
	800	fi
	801	multin[$iin]=true
	802	string=${endin_pre[$iin]}
	803	endin_pre[$iin]="${string%?}"
	804	else
	805	multin[$iin]=false
	806	fi
[2380]	807	fi
[2669]	808	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	809	then
	810	found=false
	811	for actual in $activation_string_list
	812	do
	813	for formal in $s3
	814	do
[2670]	815	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	816	done
	817	done
	818	if [[ $found = true ]]
	819	then
	820	(( iout = iout + 1 ))
[2669]	821	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	822	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	823
[2669]	824	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	825	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	826	if [[ $formal = wildcard ]]
	827	then
	828	warnout_pre[$iout]=false
	829	else
	830	warnout_pre[$iout]=true
	831	fi
	832
[2610]	833	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	834	# THE WILDCARD FROM THE LOCAL FILENAME
	835	if [[ "${s1: -1}" = "*" ]]
	836	then
[2669]	837	if [[ "$s2b" = "di" ]]
[2610]	838	then
	839	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	840	printf "\n see file \"$fileconnection_file\", line"
	841	printf "\n$line"
	842	locat=iofiles_file; exit
	843	fi
	844	multout[$iout]=true
	845	string=${localout_pre[$iout]}
	846	localout_pre[$iout]="${string%?}"
	847	else
	848	multout[$iout]=false
	849	fi
[2380]	850	fi
[2669]	851	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	852	then
[2669]	853	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	854	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	855	locat=connect; exit
	856	fi
	857	IFS="$IFSALT"
	858	fi
	859
	860	done < $fileconnection_file
	861
	862
	863
[2501]	864	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	865	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	866	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	867	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	868	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	869	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	870
	871
	872
[2380]	873	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	874	if [[ $run_coupled_model = true ]]
	875	then
	876
	877	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	878	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	879
	880	if (( $cores_ocean + $cores_atmos != $cores ))
	881	then
	882
	883	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	884	printf "\n PEs (total) : $cores"
	885	printf "\n PEs (atmosphere): $cores_atmos"
	886	printf "\n PEs (ocean) : $cores_ocean"
	887	locat=coupling; exit
	888
	889	fi
	890
	891	fi
	892
	893
	894	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	895	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	896	# FOLDER
	897	if [[ $running_in_batch_mode = true ]]
	898	then
	899
[2506]	900	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	901	then
[2506]	902	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	903	printf "\n Please check the output of the palmrun-call"
	904	printf "\n that you did on your local host."
	905	locat=SOURCES_FOR_RUN; exit
	906	fi
	907
	908	else
	909
	910	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	911	# AUTOMATIC RESTART RUN
	912	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	913	if [[ $restart_run = false ]]
	914	then
	915
	916	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	917	# THE LOCAL HOST
	918	if [[ ! -d $source_path ]]
	919	then
	920	printf "\n\n +++ source path \"$source_path\" on local host"
	921	printf "\n \"$(hostname)\" does not exist"
	922	locat=source_path; exit
	923	fi
	924
[2990]	925	rm -rf ${base_directory}/${sources_for_run_catalog}
	926	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	927
	928	if [[ "$source_list" = LM ]]
	929	then
	930
	931	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	932	source_list=""
	933	cd $source_path
	934
	935
[2512]	936	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	937	if [[ ! -d ../.svn ]]
[2380]	938	then
	939	printf "\n\n +++ source directory"
	940	printf "\n \"$source_path\" "
	941	printf "\n is not under control of \"subversion\"."
[2512]	942	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	943	fi
	944
	945
	946	# LIST ALL MODIFIED SOURCE CODE FILES
	947	Filenames=""
[2404]	948	svn status > tmp_svnstatus
[2380]	949	while read line
	950	do
	951	firstc=`echo $line \| cut -c1`
	952	if [[ $firstc = M \|\| $firstc = "?" ]]
	953	then
	954	Name=`echo "$line" \| cut -c8-`
	955	extension=`echo $Name \| cut -d. -f2`
	956	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	957	then
	958	Filenames="$Filenames "$Name
	959	fi
	960	fi
[2404]	961	done < tmp_svnstatus
	962	rm -rf tmp_svnstatus
[2380]	963
	964
	965	# COPY FILES TO SOURCES_FOR_RUN_...
	966	for filename in $Filenames
	967	do
[2990]	968	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	969	source_list=$source_list"$filename "
	970	done
	971
	972	cd - > /dev/null
	973
	974
	975	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	976	elif [[ "$source_list" != "" ]]
	977	then
	978
	979	cd $source_path
	980
	981	for filename in $source_list
	982	do
	983
	984	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	985	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	986	then
	987	printf "\n +++ source code file: $filename"
	988	printf "\n must not contain (\"/\") "
	989	locat=source; exit
	990	fi
	991
	992	if [[ ! -f $filename ]]
	993	then
	994	printf "\n +++ source code file: $filename"
	995	printf "\n does not exist"
	996	locat=source; exit
	997	else
[2990]	998	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	999	fi
	1000
	1001	done
	1002
	1003	cd - > /dev/null
	1004
	1005	fi
	1006
	1007	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1008	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1009	if [[ ! -f $makefile ]]
	1010	then
	1011	printf "\n +++ file \"$makefile\" does not exist"
	1012	locat=make; exit
	1013	else
[2990]	1014	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	1015	fi
	1016
	1017
	1018	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	1019	if [[ "$user_source_path" != "" ]]
[2380]	1020	then
	1021
	1022	# DOES THE DIRECTORY EXIST?
[2384]	1023	if [[ ! -d $user_source_path ]]
[2380]	1024	then
	1025
	1026	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1027	printf "\n \"$user_source_path\" "
[2380]	1028	printf "\n does not exist or is not a directory."
	1029	printf "\n No source code will be used from this directory!\n"
[2384]	1030	user_source_path=""
[2380]	1031	if [[ $silent == false ]]
	1032	then
	1033	sleep 2
	1034	fi
	1035
	1036	else
	1037
[2384]	1038	cd $user_source_path
[2380]	1039
	1040	Names=$(ls -1 *.f90 2>&1)
	1041	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1042	Names=$(ls -1 *.F90 2>&1)
	1043	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1044	Names=$(ls -1 *.F 2>&1)
	1045	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1046	Names=$(ls -1 *.f 2>&1)
	1047	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1048	Names=$(ls -1 *.c 2>&1)
	1049	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1050
	1051	cd - > /dev/null
[2990]	1052	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1053
	1054	# COPY MAKEFILE IF EXISTING
[2384]	1055	if [[ -f $user_source_path/Makefile ]]
[2380]	1056	then
	1057	printf "\n\n *** user Makefile from directory"
[2384]	1058	printf "\n \"$user_source_path\" is used \n"
[2380]	1059	if [[ $silent == false ]]
	1060	then
	1061	sleep 1
	1062	fi
[2384]	1063	cp $user_source_path/Makefile .
[2380]	1064	fi
	1065
	1066	for filename in $AddFilenames
	1067	do
	1068	if [[ -f $filename ]]
	1069	then
	1070	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1071	printf "\n source code directory \"$user_source_path\" "
[2380]	1072	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1073	printf "\n from directory \"$source_path\"."
	1074	locat=source; exit
	1075	fi
	1076
[2384]	1077	cp $user_source_path/$filename .
[2380]	1078	source_list="$source_list $filename"
	1079
	1080	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1081	if [[ $(grep -c $filename Makefile) = 0 ]]
	1082	then
	1083	printf "\n\n +++ user file \"$filename\" "
	1084	printf "\n is not listed in Makefile \n"
	1085	locat=source; exit
	1086	fi
	1087	done
	1088	cd - > /dev/null
	1089	fi
	1090	fi
	1091
	1092	# COPY CONFIGURATION FILES
[2990]	1093	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1094	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1095
	1096	# COPY SHELLSCRIPTS
[2990]	1097	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1098	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1099
	1100	fi
	1101
	1102	fi
	1103
[2605]	1104
[2380]	1105	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1106	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1107	if [[ "$global_revision" = "" ]]
	1108	then
	1109	global_revision=`svnversion $source_path 2>/dev/null`
	1110	global_revision="Rev: $global_revision"
	1111	fi
	1112
	1113
	1114	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1115	if [[ -n $cores ]]
	1116	then
	1117
	1118	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1119	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1120	if [[ $tasks_per_node = 0 ]]
[2380]	1121	then
[3025]	1122	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1123	then
	1124	printf "\n"
	1125	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1126	printf "\n set -T option or define tasks_per_node in the config file"
	1127	locat=tasks_per_node; (( iec = 0 )); exit
	1128	else
	1129	# DEFAULT FOR INTERACTIVE RUN
	1130	tasks_per_node=$cores
	1131	fi
[2380]	1132	fi
	1133
	1134	if (( cores < tasks_per_node ))
	1135	then
	1136	printf "\n"
	1137	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1138	printf "\n given values: -T $tasks_per_node -X $cores"
	1139	locat=tasks_per_node; (( iec = 0 )); exit
	1140	fi
	1141
	1142	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1143	(( mpi_tasks = cores / threads_per_task ))
	1144	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1145	(( ii = cores / tasks_per_node ))
	1146	(( remaining_cores = cores - ii * tasks_per_node ))
	1147	if (( remaining_cores > 0 ))
	1148	then
	1149	printf "\n"
	1150	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1151	printf "\n divisor of the total number of cores (option \"-X\")"
	1152	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1153	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1154	(( nodes = nodes + 1 ))
	1155	fi
	1156
	1157	fi
	1158
	1159
	1160	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1161	if [[ "$maximum_parallel_io_streams" = "" ]]
	1162	then
	1163	maximum_parallel_io_streams=$cores
	1164	fi
	1165
	1166
	1167	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1168	if [[ "$scp_port" != "" ]]
	1169	then
	1170	PORTOPT="-P $scp_port"
	1171	SSH_PORTOPT="-p $scp_port"
	1172	fi
	1173
	1174
	1175	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1176	# CONFIG-FILE
	1177	if [[ "$ssh_key" != "" ]]
	1178	then
	1179	ssh_key="-i $HOME/.ssh/$ssh_key"
	1180	fi
	1181
	1182
	1183	# SET QUEUE, IF NOT GIVEN
	1184	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1185	then
	1186
	1187	if [[ $queue = none && "$defaultqueue" = "" ]]
	1188	then
	1189	printf "\n"
	1190	printf "\n +++ no default queue given in configuration file and no queue"
	1191	printf "\n given with option -q"
[2789]	1192	locat=queue; exit
[2380]	1193	fi
	1194	if [[ $queue = none ]]
	1195	then
	1196	queue=$defaultqueue
	1197	fi
	1198
	1199	fi
	1200
	1201
	1202	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1203	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1204	(( i = 0 ))
[2610]	1205	(( nr_of_input_files = 0 ))
[2380]	1206	while (( i < iin ))
	1207	do
	1208	(( i = i + 1 ))
	1209
	1210	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1211	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1212	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1213	then
[2610]	1214	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1215	else
[3236]	1216	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1217	fi
	1218
[2610]	1219
[2380]	1220	# CHECK IF FILE EXISTS
	1221	if ! ls $filename* 1>/dev/null 2>&1
	1222	then
	1223
[2669]	1224	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1225	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1226	then
	1227	printf "\n\n +++ INPUT-file: "
[2610]	1228	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1229	then
	1230	printf "\n $filename"
	1231	else
[2610]	1232	printf "\n $filename.${extin_pre[$i]}"
[2380]	1233	fi
	1234	printf "\n does not exist\n"
	1235	locat=input; exit
	1236	else
[2610]	1237	(( nr_of_input_files = nr_of_input_files + 1 ))
	1238	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1239	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1240	actionin[$nr_of_input_files]="unavailable"
[2610]	1241	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1242	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1243	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1244	fi
[2605]	1245
[2380]	1246	else
	1247
[3236]	1248	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1249	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1250	# ENDINGS
[2610]	1251	if [[ "${multin[$i]}" = true ]]
	1252	then
	1253	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1254	ls -1 -d ${filename} > filelist 2>/dev/null
	1255	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1256	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1257
[2610]	1258	endings=""
	1259	while read line
	1260	do
	1261	# filename without path (i.e. after the last "/")
	1262	basefilename=$(basename ${line})
[2380]	1263
[2610]	1264	# check if there is an extension and remove it
	1265	ext=${basefilename##*.}
	1266	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1267	then
	1268	basefilename=${basefilename%.*}
	1269	fi
[2380]	1270
[2610]	1271	# check for an existing cycle number and remove it
	1272	cycle=${basefilename##*.}
	1273	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1274	then
	1275	basefilename=${basefilename%.*}
	1276	fi
[2600]	1277
[3236]	1278	# remove the run_identifier from the beginning
	1279	length_run_identifier=${#run_identifier}
	1280	ending=${basefilename:${length_run_identifier}}
[2610]	1281
	1282	# remove the ending given in the .iofiles from the beginning
	1283	endingstring="${endin_pre[$i]}"
	1284	length_ending=${#endingstring}
	1285	ending=${ending:${length_ending}}
	1286
	1287	if [[ "$ending" = "" ]]
[2600]	1288	then
[2610]	1289	# standard ending as given in the .iofiles
	1290	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1291	then
	1292	endings="$endings DEFAULT"
	1293	fi
[2600]	1294	else
[2610]	1295	# ending must start with "_", otherwise its a different file
	1296	if [[ "${ending:0:1}" = "_" ]]
	1297	then
	1298	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1299	then
	1300	endings="$endings $ending"
	1301	fi
	1302	fi
[2600]	1303	fi
[2610]	1304
	1305	done <filelist
[2380]	1306
[2610]	1307	rm filelist
[2380]	1308
[2600]	1309	else
[2610]	1310
	1311	# SINGLE NAME
	1312	endings=DEFAULT
	1313
[2600]	1314	fi
	1315
[2610]	1316	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1317	for ending in $endings
	1318	do
	1319
	1320	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1321	if [[ $ending = DEFAULT ]]
[2380]	1322	then
[2610]	1323	ending=""
	1324	fi
	1325
	1326	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1327	(( nr_of_input_files = nr_of_input_files + 1 ))
	1328	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1329	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1330	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1331	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1332	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1333	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1334
	1335
	1336	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1337	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1338	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1339	then
	1340	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1341	else
[3236]	1342	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1343	fi
[2610]	1344
	1345	# DETERMINE THE FILE'S CYCLE NUMBER
	1346	(( maxcycle = 0 ))
	1347	ls -1 -d $filename > filelist 2>/dev/null
	1348	ls -1 -d $filename.* >> filelist 2>/dev/null
	1349	while read line
	1350	do
	1351	# filename without path (i.e. after the last "/")
	1352	basefilename=$(basename ${line})
	1353
	1354	# check if there is an extension
	1355	extension=${basefilename##*.}
	1356	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1357	then
	1358	basefilename=${basefilename%.*}
	1359	fi
	1360
	1361	# check for an existing cycle number
	1362	cycle=${basefilename##*.}
	1363	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1364	then
[2669]	1365	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1366	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1367	(( icycle = $((10#$cycle)) ))
[2610]	1368	else
	1369	(( icycle = 0 ))
	1370	fi
	1371
	1372	if (( icycle > maxcycle ))
	1373	then
	1374	(( maxcycle = icycle ))
	1375
	1376	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1377	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1378	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1379	then
	1380	leading_zero=true
	1381	else
	1382	leading_zero=false
	1383	fi
	1384	fi
	1385
	1386	done <filelist
	1387	rm filelist
	1388
	1389	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1390	if [[ $leading_zero = true ]]
[2380]	1391	then
[2610]	1392	cyclestring=`printf "%03d" $maxcycle`
	1393	else
	1394	cyclestring=$maxcycle
[2380]	1395	fi
[2610]	1396
	1397	# APPEND CYCLE NUMBER TO FILENAME
	1398	if (( maxcycle > 0 ))
[2380]	1399	then
[2610]	1400	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1401	then
	1402	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1403	else
	1404	filename=${filename}.$cyclestring
	1405	fi
[2380]	1406	else
[2610]	1407	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1408	then
	1409	filename=${filename}.${extin[$nr_of_input_files]}
	1410	fi
[2380]	1411	fi
[2610]	1412
	1413	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1414	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1415	absnamein[$nr_of_input_files]=$filename
	1416	if (( maxcycle > 0 ))
[2380]	1417	then
[2610]	1418	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1419	then
	1420	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1421	else
[3236]	1422	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1423	fi
[2380]	1424	else
[2610]	1425	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1426	then
	1427	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1428	else
[3236]	1429	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1430	fi
[2380]	1431	fi
	1432
[2610]	1433	done
	1434
[2380]	1435	fi
[2610]	1436
[2380]	1437	done
	1438
[2610]	1439
[2380]	1440	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1441	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1442	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1443	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1444	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1445	# REMOTE HOST)
	1446	(( i = 0 ))
	1447	while (( i < iout ))
	1448	do
	1449	(( i = i + 1 ))
[2610]	1450	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1451	then
[2610]	1452	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1453	then
[2610]	1454	actionout_pre[$i]=""
	1455	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1456	then
[2610]	1457	actionout_pre[$i]=pe
	1458	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1459	then
[2610]	1460	actionout_pre[$i]=a
[2380]	1461	fi
	1462	(( maxcycle = 0 ))
[3236]	1463	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1464	eval catalogname=${pathout_pre[$i]}
[2380]	1465	if ! ls $filename* 1>/dev/null 2>&1
	1466	then
	1467
	1468	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1469	if cat /dev/null > $filename
	1470	then
	1471	rm $filename
	1472	else
	1473
	1474	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1475	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1476	if [[ ! -d $catalogname ]]
	1477	then
	1478	if mkdir -p $catalogname
	1479	then
	1480	printf "\n\n *** directory:"
	1481	printf "\n $catalogname"
	1482	printf "\n was created\n"
	1483	else
	1484	printf "\n\n +++ OUTPUT-file:"
	1485	printf "\n $filename"
	1486	printf "\n cannot be created, because directory does not exist"
	1487	printf "\n and cannot be created either"
	1488	printf "\n"
	1489	locat=output ; exit
	1490	fi 2>/dev/null
	1491	else
	1492	printf "\n\n +++ OUTPUT-file:"
	1493	printf "\n $filename"
	1494	printf "\n cannot be created, although directory exists"
	1495	printf "\n"
	1496	locat=output ; exit
	1497	fi
	1498	fi 2>/dev/null
	1499
	1500	fi
	1501
	1502	fi
	1503	done
	1504
	1505
	1506	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1507	if [[ $running_in_batch_mode = false ]]
	1508	then
[3236]	1509	run_id_number=$RANDOM
	1510	run_id=${run_identifier}.$run_id_number
[2380]	1511
[3236]	1512	tempdir=$fast_io_catalog/$run_id
[3346]	1513
	1514	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1515	export job_id=$run_id
	1516
[2380]	1517	fi
	1518
	1519
	1520	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1521	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1522	then
	1523
	1524	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1525	if [[ $ibd = 0 ]]
	1526	then
	1527	printf "\n"
	1528	printf "\n +++ no batch directives found in configuration file"
	1529	locat=config_file_batch_directives; (( iec = 0 )); exit
	1530	fi
	1531
	1532	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1533	done=false
[2384]	1534	cputime=$cpumax
[2380]	1535	while [[ $done = false ]]
	1536	do
[2384]	1537	if (( cputime == 0 ))
[2380]	1538	then
	1539	printf "\n +++ cpu-time is undefined"
	1540	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1541	printf "\n >>> "
[2384]	1542	read cputime 1>/dev/null 2>&1
[2380]	1543	else
	1544	done=true
	1545	fi
	1546	done
[2420]	1547	cpumax=$cputime
[2380]	1548
	1549	# CHECK THE MEMORY DEMAND
	1550	done=false
	1551	while [[ $done = false ]]
	1552	do
	1553	if (( memory == 0 ))
	1554	then
	1555	printf "\n +++ memory demand is undefined"
	1556	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1557	printf "\n >>> "
	1558	read memory 1>/dev/null 2>&1
	1559	else
	1560	done=true
	1561	fi
	1562	done
	1563
	1564	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1565	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1566	then
	1567	while [[ -z $remote_username ]]
	1568	do
[2420]	1569	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1570	printf "\n >>> Please type username:"
	1571	printf "\n >>> "
	1572	read remote_username
	1573	done
	1574	fi
	1575
	1576	else
	1577
[2420]	1578	if [[ $running_in_batch_mode = false ]]
	1579	then
	1580	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1581	cpumax=$cputime
	1582	else
	1583	cputime=$cpumax
	1584	fi
[2380]	1585
	1586	fi
	1587
	1588
	1589	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1590	(( cpu_hours = cputime / 3600 ))
	1591	(( resttime = cputime - cpu_hours * 3600 ))
	1592	(( cpu_minutes = resttime / 60 ))
	1593	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1594	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1595
	1596
	1597	# OUTPUT OF THE PALMRUN-HEADER
	1598	calltime=$(date)
	1599	printf "\n"
	1600	printf "#------------------------------------------------------------------------# \n"
	1601	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1602	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1603	printf "\| \| \n"
	1604	column1="called on:"; column2=$(hostname)
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	if [[ $create_remote_batch_job = true ]]
	1607	then
[3236]	1608	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1609	else
	1610	if [[ $running_on_remote = true ]]
	1611	then
[3236]	1612	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1613	else
[3236]	1614	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1615	fi
	1616	fi
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1618
	1619	column1="running in:"
	1620	if [[ $running_in_batch_mode = true ]]
	1621	then
	1622	column2="batch job mode"
	1623	else
	1624	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1625	then
	1626	column2="job creation mode"
	1627	else
	1628	column2="interactive run mode"
	1629	fi
	1630	fi
	1631	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1632
[2479]	1633	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1634	then
[2480]	1635	if [[ "$project_account" != "" ]]
[2479]	1636	then
	1637	column1="project account number:"
	1638	column2="$project_account"
	1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1640	fi
	1641	fi
	1642
[2380]	1643	if [[ -n $cores ]]
	1644	then
	1645	if [[ $run_coupled_model = false ]]
	1646	then
	1647	column1="number of cores:"; column2=$cores
	1648	else
	1649	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1650	fi
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	fi
	1653	if [[ -n $tasks_per_node ]]
	1654	then
	1655	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1657	if (( remaining_cores > 0 ))
	1658	then
	1659	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1661	fi
	1662	fi
	1663	if [[ $maximum_parallel_io_streams != $cores ]]
	1664	then
	1665	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1666	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1667	fi
	1668	if [[ $use_openmp = true ]]
	1669	then
	1670	column1="threads per task:"; column2="$threads_per_task"
	1671	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1672	fi
[2384]	1673	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1674	then
[2506]	1675	column1="memory demand / PE":; column2="$memory MB"
	1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1677	column1="job cpu time (h:m:s):"; column2="$timestring"
	1678	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1679	fi
[2380]	1680	printf "\| \| \n"
	1681	if [[ "$source_list" != "" ]]
	1682	then
	1683	if [[ "$make_options" != "" ]]
	1684	then
	1685	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1687	line=$(echo "$make_options" \| cut -c46-)
	1688	while [[ "$line" != "" ]]
	1689	do
	1690	column1=""
	1691	column2=$(echo "$line" \| cut -c-45)
	1692	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1693	line=$(echo "$line" \| cut -c46-)
	1694	done
	1695	fi
	1696	fi
	1697
	1698	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1699	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1700	line=$(echo "$cpp_options" \| cut -c46-)
	1701	while [[ "$line" != "" ]]
	1702	do
	1703	column1=""
	1704	column2=$(echo "$line" \| cut -c-45)
	1705	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1706	line=$(echo "$line" \| cut -c46-)
	1707	done
	1708
	1709	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1711	line=$(echo "$compiler_options" \| cut -c46-)
	1712	while [[ "$line" != "" ]]
	1713	do
	1714	column1=""
	1715	column2=$(echo "$line" \| cut -c-45)
	1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1717	line=$(echo "$line" \| cut -c46-)
	1718	done
	1719
[2388]	1720	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1721	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1722	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1723	while [[ "$line" != "" ]]
	1724	do
	1725	column1=""
	1726	column2=$(echo "$line" \| cut -c-45)
	1727	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1728	line=$(echo "$line" \| cut -c46-)
	1729	done
	1730
	1731	if [[ "$login_init_cmd" != "" ]]
	1732	then
	1733	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1734	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1735	line=$(echo "$login_init_cmd" \| cut -c46-)
	1736	while [[ "$line" != "" ]]
	1737	do
	1738	column1=""
	1739	column2=$(echo "$line" \| cut -c-45)
	1740	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1741	line=$(echo "$line" \| cut -c46-)
	1742	done
	1743	fi
	1744
	1745	if [[ "$module_commands" != "" ]]
	1746	then
	1747	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1748	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1749	line=$(echo "$module_commands" \| cut -c46-)
	1750	while [[ "$line" != "" ]]
	1751	do
	1752	column1=""
	1753	column2=$(echo "$line" \| cut -c-45)
	1754	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1755	line=$(echo "$line" \| cut -c46-)
	1756	done
	1757	fi
	1758	printf "\| \| \n"
[3236]	1759	column1="run identifier:"; column2=$run_identifier
[2380]	1760	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1761	column1="activation string list:"; column2=$(echo $activation_string_list)
	1762	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1763
	1764	if [[ "$ocean_file_appendix" = true ]]
	1765	then
	1766	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1767	fi
	1768
	1769	if [[ "$source_list" != "" ]]
	1770	then
	1771	printf "\| \| \n"
	1772	printf "\| Files to be compiled: \| \n"
	1773	line=$source_list
	1774	while [[ "$line" != "" ]]
	1775	do
	1776	linestart=$(echo $line \| cut -c-70)
	1777	printf "\| %-70s \| \n" "$linestart"
	1778	line=$(echo "$line" \| cut -c71-)
	1779	done
	1780	fi
	1781	printf "#------------------------------------------------------------------------#"
	1782
	1783
	1784
	1785	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1786	if [[ $do_trace = true ]]
	1787	then
	1788	(( i = 0 ))
[2610]	1789	while (( i < nr_of_input_files ))
[2380]	1790	do
	1791	(( i = i + 1 ))
	1792	if (( i == 1 ))
	1793	then
	1794	printf "\n\n >>> INPUT-file assignments:\n"
	1795	fi
	1796	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1797	done
	1798	(( i = 0 ))
	1799	while (( i < iout ))
	1800	do
	1801	(( i = i + 1 ))
	1802	if (( i == 1 ))
	1803	then
	1804	printf "\n\n >>> OUTPUT-file assignments:\n"
	1805	fi
	1806	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1807	done
	1808	(( i = 0 ))
	1809	while (( i < iic ))
	1810	do
	1811	(( i = i + 1 ))
	1812	if (( i == 1 ))
	1813	then
	1814	printf "\n\n >>> INPUT-commands:\n"
	1815	fi
	1816	printf "\n ${in_command[$i]}"
	1817	done
	1818	(( i = 0 ))
	1819	while (( i < ioc ))
	1820	do
	1821	(( i = i + 1 ))
	1822	if (( i == 1 ))
	1823	then
	1824	printf "\n\n >>> OUTPUT-commands:\n"
	1825	fi
	1826	printf "\n ${out_command[$i]}"
	1827	done
	1828	fi
	1829
	1830	# QUERY FOR CONTINUE
	1831	if [[ $silent = false && $running_in_batch_mode = false ]]
	1832	then
	1833	antwort=dummy
	1834	printf "\n\n"
	1835	printf " >>> everything o.k. (y/n) ? "
	1836	while read antwort
	1837	do
	1838	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1839	then
	1840	printf " >>> everything o.k. (y/n) ? "
	1841	else
	1842	break
	1843	fi
	1844	done
	1845	if [[ $antwort = n \|\| $antwort = N ]]
	1846	then
	1847	locat=user_abort; (( iec = 0 )); exit
	1848	fi
	1849	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1850	then
[2566]	1851	printf "\n *** batch-job will be created and submitted"
[2380]	1852	else
[2566]	1853	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1854	fi
	1855	fi
	1856
	1857
	1858
	1859	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1860	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1861	then
	1862
	1863	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1864	then
[2566]	1865	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1866	else
[2566]	1867	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1868	fi
	1869
[2422]	1870	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1871	# IT SHALL BE CREATED
	1872	ask_for_make_depository=false
	1873	if [[ $create_remote_batch_job = true ]]
	1874	then
	1875
	1876	line=`grep %base_directory $config_file`
[3236]	1877	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1878	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1879
[3236]	1880	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1881	then
	1882	printf "\n\n +++ make depository \"${make_depository}\""
	1883	printf "\n on remote host not found!"
	1884	ask_for_make_depository=true
	1885	fi
[3236]	1886	rm ${configuration_identifier}_last_make_protokoll
[2422]	1887
	1888	else
	1889
	1890	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1891	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1892	if [[ ! -d ${make_depository} ]]
	1893	then
	1894	printf "\n\n +++ make depository \"${make_depository}\""
	1895	printf "\n on local host not found!"
	1896	ask_for_make_depository=true
	1897	fi
	1898
	1899	fi
	1900
	1901	if [[ $ask_for_make_depository = true ]]
	1902	then
	1903
	1904	antwort=dummy
	1905	printf "\n\n"
	1906	printf " >>> Create a new one (y/n) ? "
	1907	while read antwort
	1908	do
	1909	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1910	then
	1911	printf " >>> Create a new one (y/n) ? "
	1912	else
	1913	break
	1914	fi
	1915	done
	1916	if [[ $antwort = n \|\| $antwort = N ]]
	1917	then
	1918	locat=user_abort; (( iec = 0 )); exit
	1919	fi
	1920
[2566]	1921	if [[ $do_trace = true ]]
	1922	then
[3455]	1923	palmbuild -c $configuration_identifier
[2566]	1924	else
[3455]	1925	palmbuild -v -c $configuration_identifier
[2566]	1926	fi
[2422]	1927
[3312]	1928	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1929	then
	1930
	1931	# ABORT IN CASE OF COMPILATION PROBLEMS
	1932	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1933	locat=make_depository
	1934	exit
	1935	else
	1936	echo " *** now continue with creating executable and other sources"
	1937	fi
	1938
	1939	fi
	1940
[2566]	1941	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1942	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1943
[3312]	1944	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1945	then
	1946
	1947	# ABORT IN CASE OF COMPILATION PROBLEMS
	1948	printf "\n +++ error while creating executable and/or other sources"
	1949	locat=execution
[2990]	1950	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1951	exit
	1952
	1953	else
	1954
[2566]	1955	printf " *** executable and other sources created\n"
[2990]	1956	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1957
	1958	fi
	1959
	1960	fi
	1961
	1962
[2669]	1963	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1964	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1965	if [[ $create_remote_batch_job = true ]]
	1966	then
	1967	(( i = 0 ))
[2610]	1968	while (( i < nr_of_input_files ))
[2605]	1969	do
	1970	(( i = i + 1 ))
[2669]	1971	if [[ "${actionin[$i]}" = tr ]]
[2605]	1972	then
	1973	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1974	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1975	fi
	1976	done
	1977	if (( i > 0 ))
	1978	then
[3025]	1979	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1980	fi
	1981	fi
	1982
	1983
[2380]	1984	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1985	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1986	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1987	then
	1988
	1989	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1990	if [[ $running_in_batch_mode = false ]]
	1991	then
[3917]	1992	# CREATE THE DIRECTORY
[2566]	1993	mkdir -p $tempdir
[4303]	1994	if [[ $? != 0 ]]
	1995	then
	1996	printf "\n +++ temporary working directory cannot be created."
	1997	printf "\n Check setting of variable fast_io_catalog in your config file."
	1998	locat=execution
	1999	exit
	2000	fi
[2566]	2001	chmod go+rx $tempdir
	2002	cd $tempdir
	2003	printf "\n *** changed to temporary directory: $tempdir"
[2380]	2004
	2005	else
	2006
	2007	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	2008	printf "\n *** running in temporary directory: $tempdir"
[2380]	2009
	2010	fi
	2011
	2012
	2013	# PROVIDE THE INPUT FILES
	2014	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	2015	optional_files_missing=false
[2380]	2016	(( i = 0 ))
[2610]	2017	while (( i < nr_of_input_files ))
[2380]	2018	do
	2019	(( i = i + 1 ))
	2020	if (( i == 1 ))
	2021	then
	2022	printf "\n\n *** providing INPUT-files:\n$dashes"
	2023	fi
	2024
	2025
	2026	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	2027	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2028	then
[2669]	2029	optional_files_missing=true
[2380]	2030	continue
	2031	fi
	2032
	2033	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2034	files_for_cores=false; filetype=file
	2035	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2036	then
	2037	files_for_cores=true; filetype=files
	2038	actionin[$i]=""
	2039	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2040	then
	2041	actionin[$i]=""
	2042	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2043	then
	2044	files_for_cores=true; filetype=files
	2045	actionin[$i]="ln"
	2046	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2047	then
	2048	actionin[$i]="ln"
	2049	fi
	2050
	2051	if [[ $files_for_cores = true ]]
	2052	then
	2053	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2054	else
	2055	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2056	fi
	2057
	2058	# INPUT-FILES TO BE LINKED
	2059	if [[ "${actionin[$i]}" = ln ]]
	2060	then
	2061
	2062	printf "\n $filetype will be linked"
	2063	if [[ $files_for_cores = false ]]
	2064	then
	2065	if [[ -f "${absnamein[$i]}" ]]
	2066	then
	2067	ln ${absnamein[$i]} ${localin[$i]}
	2068	got_tmp[$i]=true
	2069	fi
	2070	else
	2071	if [[ -d "${absnamein[$i]}" ]]
	2072	then
[2396]	2073	mkdir -p ${localin[$i]}
[2380]	2074	cd ${absnamein[$i]}
	2075	for file in $(ls *)
	2076	do
[2566]	2077	ln $file $tempdir/${localin[$i]}
[2380]	2078	done >\|/dev/null 2>&1
[2566]	2079	cd $tempdir
[2380]	2080	fi
	2081
	2082	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2083	if [[ ! -f "${localin[$i]}/_000000" ]]
	2084	then
	2085	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2086	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2087	fi
	2088
	2089	got_tmp[$i]=true
	2090	fi
	2091	fi
	2092
	2093	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2094	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2095	then
	2096
	2097	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2098	then
	2099
	2100	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2101	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2102	printf "\n file will be provided for $cores processors"
[2396]	2103	mkdir -p ${localin[$i]}
[2380]	2104	ival=$cores
	2105	(( ii = 0 ))
	2106	while (( ii <= ival-1 ))
	2107	do
	2108	if (( ii < 10 ))
	2109	then
	2110	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2111	elif (( ii < 100 ))
	2112	then
	2113	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2114	elif (( ii < 1000 ))
	2115	then
	2116	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2117	else
	2118	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2119	fi
	2120	(( ii = ii + 1 ))
	2121	done
	2122
	2123	else
	2124
	2125	if [[ $files_for_cores = true ]]
	2126	then
	2127
	2128	# PROVIDE FILES FOR EACH CORE
	2129	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2130	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2131	printf "\n providing $cores files for the respective cores"
[2396]	2132	mkdir -p ${localin[$i]}
[2380]	2133	if [[ $link_local_input = true ]]
	2134	then
	2135	printf " files will be linked\n"
	2136	cd ${absnamein[$i]}
	2137	for file in $(ls *)
	2138	do
	2139	ln -f $file ${localin[$i]}
	2140	done
[2566]	2141	cd $tempdir
[2380]	2142	fi
	2143
	2144	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2145	if [[ ! -f "${localin[$i]}/_000000" ]]
	2146	then
	2147	if [[ $link_local_input = true ]]
	2148	then
	2149	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2150	fi
	2151	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2152	fi
	2153
	2154	else
	2155
	2156	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2157	if [[ $link_local_input = true ]]
	2158	then
	2159	printf " file will be linked\n"
	2160	ln -f ${absnamein[$i]} ${localin[$i]}
	2161	fi
[2605]	2162	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2163	if [[ ! -f "${localin[$i]}" ]]
	2164	then
	2165	if [[ $link_local_input = true ]]
	2166	then
	2167	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2168	fi
[2669]	2169	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2170	then
	2171	mv ${absnamein[$i]} ${localin[$i]}
	2172	else
	2173	cp ${absnamein[$i]} ${localin[$i]}
	2174	fi
[2380]	2175	fi
	2176	fi
	2177	fi
	2178	fi
	2179
	2180	done
	2181	if (( i != 0 ))
	2182	then
[2669]	2183	if [[ $optional_files_missing = true ]]
	2184	then
	2185	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2186	fi
[2380]	2187	printf "\n$dashes\n *** all INPUT-files provided \n"
	2188	fi
	2189
[3917]	2190	# NOW COPY FILES (.f90, .o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY
	2191	# WORKING DIRECTORY
	2192	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
[2380]	2193
[3917]	2194
[2380]	2195	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2196	(( i = 0 ))
	2197	while (( i < iic ))
	2198	do
	2199	(( i = i + 1 ))
	2200	if (( i == 1 ))
	2201	then
	2202	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2203	fi
	2204	printf "\n >>> ${in_command[$i]}"
	2205	eval ${in_command[$i]}
	2206	if (( i == iic ))
	2207	then
	2208	printf "\n$dashes\n"
	2209	fi
	2210	done
	2211
	2212
[3313]	2213	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2214	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2215	then
	2216	progress_bar_disabled=true
	2217	else
	2218	progress_bar_disabled=false
	2219	fi
	2220
	2221
[2380]	2222	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2223	# (FILE ENVPAR WILL BE READ BY PALM)
	2224	cat > ENVPAR << EOF
[3236]	2225	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2226	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2227	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2228	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2229	maximum_cpu_time_allowed = ${cpumax}.,
	2230	revision = '$global_revision',
[3313]	2231	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2232
	2233	EOF
	2234
	2235
	2236	# STARTING THE EXECUTABLE
	2237	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2238	PATH=$PATH:$tempdir
[2380]	2239
	2240
	2241	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2242	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2243	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2244	eval line=\"$line\"
	2245	execute_command="$line"
	2246
	2247
	2248	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2249	if [[ "$execute_command_for_combine" = "" ]]
	2250	then
	2251	eval line2=\"$line2\"
	2252	execute_command_for_combine="$line2"
	2253	fi
	2254
[2380]	2255
	2256
	2257	# PROVIDE A HOSTFILE, IF REQUIRED
	2258	if [[ "$hostfile" != "" ]]
	2259	then
	2260
	2261	if [[ $hostfile = auto ]]
	2262	then
	2263	# CREATE A NEW HOSTFILE
	2264	(( ii = 1 ))
	2265	while (( ii <= cores / threads_per_task ))
	2266	do
	2267	echo $(hostname) >> hostfile
	2268	(( ii = ii + 1 ))
	2269	done
	2270	if (( cores / threads_per_task == 0 ))
	2271	then
	2272	echo $(hostname) >> hostfile
	2273	fi
	2274
	2275	else
	2276	cp $hostfile hostfile
	2277	fi
	2278	eval line=\"`head -n $ii hostfile`\"
	2279	printf "\n *** running on: $line"
	2280	fi
	2281
	2282
	2283
	2284	# SET THE NUMBER OF OPENMP-THREADS
	2285	if [[ $use_openmp = true ]]
	2286	then
	2287	export OMP_NUM_THREADS=$threads_per_task
	2288	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2289	else
	2290	export OMP_NUM_THREADS=1
	2291	fi
	2292
	2293
[2610]	2294	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2295	if [[ $run_coupled_model = false ]]
	2296	then
	2297	if [[ "$ocean_file_appendix" = true ]]
	2298	then
	2299	echo "precursor_ocean" > coupling_steering
	2300	else
	2301	echo "precursor_atmos" > coupling_steering
	2302	fi
	2303	else
	2304	(( iia = $cores_atmos / $threads_per_task ))
	2305	(( iio = $cores_ocean / $threads_per_task ))
	2306	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2307	printf "\n\n"
	2308	echo "coupled_run $iia $iio" > coupling_steering
	2309	fi
	2310
	2311	printf "\n *** execute command:"
	2312	printf "\n \"$execute_command\" \n\n"
	2313
	2314
[3393]	2315	if [[ $progress_bar_disabled = true ]]
[2380]	2316	then
[3402]	2317	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2318	exit_code=${PIPESTATUS[0]}
	2319	else
	2320	$execute_command < coupling_steering &> >(tee STDOUT)
	2321	exit_code=${PIPESTATUS[0]}
	2322	fi
[2380]	2323
[3393]	2324	if [[ ${exit_code} != 0 ]]
	2325	then
	2326
[2380]	2327	# ABORT IN CASE OF RUNTIME ERRORS
	2328	printf "\n +++ runtime error occured"
	2329	locat=execution
	2330	exit
	2331
	2332	else
	2333
	2334	printf "\n$dashes\n *** execution finished \n"
	2335
	2336	fi
	2337
	2338
	2339	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2340	# BY EACH CORE INTO ONE FILE
	2341	if [[ ! -f combine_plot_fields.x ]]
	2342	then
	2343
	2344	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2345	printf "\n 2d- and/or 3d-data may be incomplete!"
	2346	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2347
	2348	elif [[ "$combine_plot_fields" == true ]]
	2349	then
	2350
	2351	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2352	$execute_command_for_combine
	2353
	2354	else
	2355
	2356	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2357	# DATA OUTPUT
[2380]	2358	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2359	fi
	2360
	2361
	2362
	2363	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2364	(( i = 0 ))
	2365	while (( i < ioc ))
	2366	do
	2367	(( i = i + 1 ))
	2368	if (( i == 1 ))
	2369	then
	2370	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2371	fi
[2799]	2372
	2373	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2374	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2375
[2380]	2376	printf "\n >>> ${out_command[$i]}"
	2377	eval ${out_command[$i]}
	2378	if (( i == ioc ))
	2379	then
	2380	printf "\n$dashes\n"
	2381	fi
	2382	done
	2383
	2384
[2610]	2385	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2386	# WILDCARDS
[2380]	2387	(( i = 0 ))
[2610]	2388	(( nr_of_output_files = 0 ))
	2389
[2380]	2390	while (( i < iout ))
	2391	do
[2610]	2392
[2380]	2393	(( i = i + 1 ))
[2610]	2394
	2395	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2396	# CREATE A LIST FOR THE DETECTED ENDINGS
	2397	if [[ "${multout[$i]}" = true ]]
	2398	then
	2399	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2400	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2401	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2402
	2403	endings="DEFAULT"
	2404	while read line
	2405	do
	2406	# remove the local name from the beginning
	2407	localnamestring="${localout_pre[$i]}"
	2408	length_localname=${#localnamestring}
	2409	ending=${line:${length_localname}}
	2410
	2411	if [[ "$ending" != "" ]]
	2412	then
	2413	endings="$endings $ending"
	2414	fi
	2415
	2416	done <filelist
	2417
	2418	rm filelist
	2419
	2420	else
	2421
	2422	# SINGLE NAME
	2423	endings=DEFAULT
	2424
	2425	fi
	2426
	2427	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2428	for ending in $endings
	2429	do
	2430
	2431	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2432	if [[ $ending = DEFAULT ]]
	2433	then
	2434	ending=""
	2435	fi
	2436
	2437	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2438	(( nr_of_output_files = nr_of_output_files + 1 ))
	2439	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2440	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2441	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2442	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2443	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2444	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2445	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2446
	2447	done
	2448
	2449	done
	2450
	2451
	2452
	2453
	2454	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2455	(( i = 0 ))
	2456	while (( i < nr_of_output_files ))
	2457	do
	2458	(( i = i + 1 ))
[2380]	2459	if (( i == 1 ))
	2460	then
[3860]	2461	timestring=`date +%H:%M:%S`
	2462	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
[2380]	2463
	2464	# GET RUN NUMBER ASSIGNED BY PALM
	2465	if [[ -f RUN_NUMBER ]]
	2466	then
	2467	read run_number < RUN_NUMBER
	2468	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2469	usecycle_option="-U $run_number"
	2470	else
	2471	run_number=0
	2472	usecycle_option=""
	2473	fi
	2474	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2475	then
[2404]	2476	printf "\n *** in case of SCP transfers to local host"
	2477	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2478	fi
	2479	printf "\n$dashes"
	2480	fi
	2481
	2482	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2483	then
	2484
[3236]	2485	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2486
	2487	# DETERMINE THE CYCLE NUMBER
	2488	ls -1 -d $filename > filelist 2>/dev/null
	2489	ls -1 -d $filename.* >> filelist 2>/dev/null
	2490	while read line
	2491	do
	2492
	2493	# filename without path (i.e. after the last "/")
	2494	basefilename=$(basename ${line})
	2495
	2496	# check if there is an extension
	2497	extension=${basefilename##*.}
	2498	if [[ "$extension" = "${extout[$i]}" ]]
	2499	then
	2500	basefilename=${basefilename%.*}
	2501	fi
	2502
	2503	# check for an existing cycle number
	2504	cycle=${basefilename##*.}
	2505	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2506	then
[2669]	2507	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2508	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2509	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2510	else
	2511	(( icycle = 1 ))
	2512	fi
	2513
	2514	if (( icycle > maxcycle ))
	2515	then
	2516	(( maxcycle = icycle ))
	2517	fi
	2518
	2519	done <filelist
	2520	rm filelist
	2521
	2522
	2523	# SET THE CYCLE NUMBER
	2524	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2525	if [[ "${actionout[$i]}" = a ]]
	2526	then
	2527	(( maxcycle = maxcycle - 1 ))
	2528	fi
	2529
	2530	(( cycnum[$i] = maxcycle ))
	2531	pathout[$i]=$filename
	2532
	2533
	2534	# ADD CYCLE NUMBER TO FILENAME
	2535	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2536	if [[ "${actionout[$i]}" != "a" ]]
	2537	then
	2538	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2539	# WITH AN EXISTING CYCLE NUMBER
	2540	if (( run_number >= cycnum[$i] ))
	2541	then
	2542	(( cycnum[$i] = run_number ))
	2543	else
	2544	if (( run_number > 0 ))
	2545	then
	2546	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2547	fi
	2548	fi
	2549	fi
	2550	if (( cycnum[$i] > 0 ))
	2551	then
[2600]	2552	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2553	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2554	fi
	2555	fi
	2556
	2557	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2558	files_for_cores=false; filetype=file
	2559	link_local_output=false
	2560	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2561	then
	2562	files_for_cores=true; filetype=directory
	2563	actionout[$i]=""
	2564	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2565	then
	2566	actionout[$i]=""
	2567	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2568	then
	2569	files_for_cores=true; filetype=directory
	2570	link_local_output=true
	2571	actionout[$i]=""
	2572	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2573	then
	2574	link_local_output
	2575	actionout[$i]=""
	2576	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2577	then
	2578	files_for_cores=true; filetype=directory
	2579	actionout[$i]="tr"
	2580	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2581	then
	2582	actionout[$i]="tr"
	2583	fi
	2584
	2585	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2586	then
[2669]	2587	if [[ ${warnout[$i]} = true ]]
	2588	then
	2589	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2590	fi
[2380]	2591	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2592	then
[2669]	2593	if [[ ${warnout[$i]} = true ]]
	2594	then
	2595	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2596	fi
[2380]	2597	else
	2598
	2599
	2600	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2601	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2602	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2603	then
	2604	if [[ $running_on_remote = true ]]
	2605	then
	2606
	2607	# SET OPTIONS FOR TRANSFER
	2608	if [[ "${actionout[$i]}" = tr ]]
	2609	then
	2610	if [[ $files_for_cores = false ]]
	2611	then
	2612	catalog_option=""
	2613	catalog_string=""
	2614	else
	2615	catalog_option="-c"
	2616	catalog_string="/"
	2617	fi
	2618	append_option=""
	2619	append_string=""
	2620	else
	2621	append_option="-A"
	2622	append_string="append"
	2623	fi
	2624
	2625	transfer_failed=false
	2626	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2627	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2628
	2629	# TRANSFER VIA SCP
	2630	if [[ "$remote_loginnode" != "" ]]
	2631	then
[3534]	2632	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]	2633	else
[3236]	2634	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]	2635	fi
[3312]	2636	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2637
	2638
	2639	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2640	if [[ $transfer_failed = true ]]
	2641	then
	2642	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2643	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2644
	2645	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2646	eval local_catalog=${pathout[$i]}
	2647	if [[ ! -d $local_catalog ]]
	2648	then
	2649	printf " *** local directory does not exist. Trying to create:\n"
	2650	printf " $local_catalog \n"
	2651	mkdir -p $local_catalog
	2652	fi
[3236]	2653	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2654	transfer_problems=true
	2655	fi
	2656
	2657	else
	2658
	2659	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2660	# BE COPIED OR APPENDED ON THIS MACHINE
	2661	if [[ "${actionout[$i]}" = tr ]]
	2662	then
	2663	actionout[$i]=""
	2664	else
	2665	actionout[$i]="a"
	2666	fi
	2667	fi
	2668	fi
	2669
	2670
	2671	# APPEND ON THIS MACHINE
	2672	if [[ "${actionout[$i]}" = "a" ]]
	2673	then
	2674	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2675	then
	2676	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2677	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2678	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2679	else
	2680	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2681	printf "\n ${pathout[$i]}\n"
	2682	cat ${localout[$i]} >> ${pathout[$i]}
	2683	fi
	2684	fi
	2685
	2686	# COPY ON THIS MACHINE
	2687	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2688	# ON DIFFERENT FILE-SYSTEMS
	2689	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2690	then
	2691
	2692	# COPY IN CASE OF RUNS ON SINGLE CORES
	2693	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2694	then
	2695	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2696	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2697	if [[ $link_local_output = true ]]
	2698	then
	2699	printf " file will be linked\n"
	2700	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2701	fi
	2702	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2703	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2704	then
	2705	if [[ $link_local_output = true ]]
	2706	then
	2707	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2708	fi
	2709	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2710	else
	2711	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2712	fi
	2713	else
	2714	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2715	printf "\n ${pathout[$i]}\n"
	2716	if [[ $link_local_output = true ]]
	2717	then
	2718	printf " file will be linked\n"
	2719	ln -f ${localout[$i]} ${pathout[$i]}
	2720	fi
	2721	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2722	if [[ ! -f "${pathout[$i]}" ]]
	2723	then
	2724	if [[ $link_local_output = true ]]
	2725	then
	2726	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2727	fi
	2728	cp ${localout[$i]} ${pathout[$i]}
	2729	else
	2730	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2731	fi
	2732	fi
	2733
	2734	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2735	then
	2736
	2737	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2738	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2739	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2740	printf "\n ${pathout[$i]}\n"
	2741	if [[ $link_local_output = true ]]
	2742	then
	2743	printf " files will be linked\n"
[2396]	2744	mkdir -p ${pathout[$i]}
[2380]	2745	cd ${localout[$i]}
	2746	for file in $(ls *)
	2747	do
	2748	ln -f $file ${pathout[$i]}
	2749	done >\|/dev/null 2>&1
[2566]	2750	cd $tempdir
[2380]	2751	fi
	2752
	2753	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2754	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2755	then
	2756	if [[ $link_local_output = true ]]
	2757	then
	2758	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2759	fi
[3025]	2760	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2761	cp -r ${localout[$i]}/* ${pathout[$i]}
	2762	fi
	2763
	2764	fi
	2765	fi
	2766	done
	2767
	2768	if (( i != 0 ))
	2769	then
[3860]	2770	timestring=`date +%H:%M:%S`
[2380]	2771	if [[ $transfer_problems = true ]]
	2772	then
[3860]	2773	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
[2380]	2774	printf "\n +++ WARNING: some data transfers failed! \n"
	2775	else
[3860]	2776	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
[2380]	2777	fi
	2778	fi
	2779
	2780
	2781	# IF REQUIRED, START A RESTART-JOB
	2782	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2783	if [[ -f CONTINUE_RUN ]]
	2784	then
	2785
	2786	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2787	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2788	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2789	# -b START A BATCH JOB
	2790	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2791	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
[3982]	2792	[[ $(echo $prc \| grep -c "\-b") = 0 && $running_on_remote = false ]] && prc="$prc -b"
[2380]	2793
[2957]	2794	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2795	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2796	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2797	then
	2798	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2799	fi
[2380]	2800
	2801	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2802	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2803	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2804	then
[2381]	2805	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2806	fi
	2807
	2808
	2809	# START THE RESTART-JOB
	2810	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2811	echo " $prc"
	2812	printf "\n$dashes\n"
	2813	if [[ $running_on_remote = true ]]
	2814	then
	2815
	2816	echo "*** ssh will be used to initiate restart-runs!"
	2817	echo " return_address=\"$return_address\" "
	2818	echo " return_username=\"$local_username\" "
	2819
	2820	if [[ "$remote_loginnode" != "" ]]
	2821	then
[3534]	2822	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]	2823	else
[3534]	2824	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2825	fi
	2826
	2827	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2828	sleep 30
	2829
	2830	else
	2831
	2832	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2833	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2834
	2835	fi
	2836
[3132]	2837	# CHECK, IF RESTART JOB HAS BEEN STARTED
[3725]	2838	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
[3132]	2839	then
	2840	printf "\n$dashes\n +++ creating restart run failed \n"
	2841	locat=create_restart
[3455]	2842	rm palmrun_restart.log
[3132]	2843	exit
[3725]	2844	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
	2845	then
	2846	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
	2847	locat=create_restart
	2848	rm palmrun_restart.log
	2849	exit
[3132]	2850	else
	2851	printf "\n$dashes\n *** restart run initiated \n"
	2852	rm palmrun_restart.log
	2853	fi
[2380]	2854
[3132]	2855
[2380]	2856	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2857	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2858	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2859	# MAY BE VERY HUGE)
	2860	(( i = 0 ))
[2610]	2861	while (( i < nr_of_input_files ))
[2380]	2862	do
	2863	(( i = i + 1 ))
	2864	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2865	then
	2866	rm -r ${absnamein[$i]}
	2867	fi
	2868	done
	2869
	2870	fi
	2871
	2872
	2873	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2874	cd $HOME
[2566]	2875	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2876
	2877
	2878	else
	2879
	2880
	2881	# PREPARING ACTIONS,
	2882	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2883
	2884	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2885	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2886	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2887	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2888	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2889	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2890	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2891	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2892	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2893	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2894	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2895	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2896	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2897	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2898	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2899	if [[ $create_remote_batch_job = true ]]
	2900	then
	2901	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2902	if [[ $do_trace = true ]]
	2903	then
	2904	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2905	fi
[2380]	2906	elif [[ $create_batch_job = true ]]
	2907	then
	2908	palmrun_com=${palmrun_com}" -j"
[2420]	2909	if [[ $do_trace = true ]]
	2910	then
	2911	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2912	fi
[2380]	2913	fi
	2914
	2915
	2916	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2917	# REMOTE HOST
[3236]	2918	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2919	job_protocol_file=$job_protocol_file_local
	2920	if [[ $create_remote_batch_job = true ]]
	2921	then
[3236]	2922	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2923	job_protocol_file=$job_protocol_file_remote
	2924	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2925	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2926	fi
	2927
	2928
	2929	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2930	jobfile=jobfile.$run_id_number
[2380]	2931
	2932
	2933	# FIRST CREATE THE BATCH DIRECTIVES
	2934	(( i = 0 ))
	2935	while (( i < ibd ))
	2936	do
	2937	(( i = i + 1 ))
[2693]	2938	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2939	eval line=\"$line\"
	2940	echo "$line" >> $jobfile
	2941	done
	2942	echo " " >> $jobfile
	2943
	2944
	2945	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2946	# PROTOCOL
	2947	if [[ $create_remote_batch_job = true ]]
	2948	then
[3236]	2949	echo "set +vx" >> $jobfile
	2950	echo "trap '" >> $jobfile
	2951	echo "set +vx" >> $jobfile
	2952	echo "cd ${remote_jobcatalog}" >> $jobfile
	2953	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2954
	2955	# ADD THE BATCH DIRECTIVES
	2956	(( i = 0 ))
	2957	while (( i < ibdt ))
	2958	do
	2959	(( i = i + 1 ))
[2693]	2960	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2961	eval line=\"$line\"
	2962	echo "$line" >> $jobfile
	2963	done
	2964	echo " " >> $jobfile
	2965
	2966	echo "set -x" >> $jobfile
[3534]	2967	if [[ "$remote_loginnode" != "" ]]
	2968	then
	2969	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}\" " >> $jobfile
	2970	else
	2971	echo "${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
	2972	fi
[2380]	2973	echo "%%END%%" >> $jobfile
	2974	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2975	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2976	echo "rm $scpjob_file" >> $jobfile
[2404]	2977	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2978	echo "set -x" >> $jobfile
	2979	echo " ' exit" >> $jobfile
	2980	fi
	2981
	2982
	2983	# ACTIVATE ERROR-TRACEBACK
	2984	if [[ $do_trace = true ]]
	2985	then
	2986	echo "set -x" >> $jobfile
	2987	else
	2988	echo "set +vx" >> $jobfile
	2989	fi
	2990
	2991
	2992	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2993	if [[ "$login_init_cmd" != "" ]]
	2994	then
	2995	echo "$login_init_cmd" >> $jobfile
	2996	fi
	2997	if [[ "$module_commands" != "" ]]
	2998	then
	2999	echo "$module_commands" >> $jobfile
	3000	fi
	3001
	3002
	3003	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	3004	if [[ $create_remote_batch_job = true ]]
	3005	then
	3006	echo "mkdir $tempdir" >> $jobfile
[4303]	3007	echo "if [[ \$? != 0 ]]" >> $jobfile
	3008	echo "then" >> $jobfile
	3009	echo " echo \"+++ temporary working directory cannot be created.\" " >> $jobfile
	3010	echo " echo \" Check setting of variable fast_io_catalog in your config file.\" " >> $jobfile
	3011	echo " exit" >> $jobfile
	3012	echo "fi" >> $jobfile
[2566]	3013	echo "chmod go+rx $tempdir" >> $jobfile
	3014	else
	3015	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	3016	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	3017	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	3018	mkdir $tempdir
[4303]	3019	if [[ $? != 0 ]]
	3020	then
	3021	printf "\n +++ temporary working directory cannot be created."
	3022	printf "\n Check setting of variable fast_io_catalog in your config file."
	3023	locat=execution
	3024	exit
	3025	fi
[2566]	3026	chmod go+rx $tempdir
	3027	fi
	3028	echo "cd $tempdir" >> $jobfile
	3029	echo "export tempdir=$tempdir" >> $jobfile
[3917]	3030	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile
	3031	echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile
[2380]	3032	echo "export execute_palmrun=true" >> $jobfile
	3033
	3034
	3035	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3036	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	3037	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	3038	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3039	echo "export LOCAL_PWD" >> $jobfile
	3040
	3041
	3042	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	3043	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	3044	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	3045
	3046
	3047	# CALL PALMRUN WITHIN THE JOB
	3048	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	3049	echo "set -x" >> $jobfile
	3050	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3051
	3052
	3053	# TRANSFER JOBFILE TO THE TARGET HOST
	3054	if [[ $create_jobfile_only = false ]]
	3055	then
	3056
[3505]	3057	# CREATE LOCAL JOB FOLDER
	3058	eval local_jobcatalog=$local_jobcatalog
	3059	if [[ ! -d $local_jobcatalog ]]
	3060	then
	3061	echo " "
	3062	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3063	mkdir $local_jobcatalog
	3064	fi
	3065
[2380]	3066	if [[ $create_remote_batch_job = true ]]
	3067	then
	3068
[2420]	3069	echo " "
[2566]	3070	echo " *** transfer of job to remote host via scp"
[3505]	3071
	3072	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3073	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3074
	3075	# COPY THE JOB FILE
[2420]	3076	if [[ $do_trace = true ]]
	3077	then
[3236]	3078	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3079	fi
[3236]	3080	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3081
[3505]	3082	# SUBMIT THE JOB
[3574]	3083	printf " *** submit the job (output of submit command, \n"
[3573]	3084	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3085	if [[ $do_trace = true ]]
	3086	then
[3665]	3087	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]	3088	fi
[3665]	3089	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]	3090
	3091	elif [[ $create_batch_job = true ]]
	3092	then
	3093
[2385]	3094	eval local_jobcatalog=$local_jobcatalog
[3236]	3095	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3096	cd $local_jobcatalog
[2380]	3097	echo " "
[2420]	3098	echo " *** submit the job"
	3099	if [[ $do_trace = true ]]
	3100	then
[3236]	3101	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3102	fi
[3236]	3103	$submit_command ${configuration_identifier}_${run_id}
	3104	rm ${configuration_identifier}_${run_id}
[2380]	3105	cd - > /dev/null
	3106
	3107	fi
	3108
	3109	rm -rf $jobfile
	3110
	3111	else
	3112
	3113	printf "\n *** jobfile created under name \"$jobfile\" "
	3114	printf "\n no batch-job has been sent!"
	3115
	3116	fi
	3117
	3118	fi # END OF REMOTE-PART

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