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source: palm/trunk/SCRIPTS/palmrun @ 3936

Last change on this file since 3936 was 3917, checked in by raasch, 6 years ago
in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied into the temporary working catalog
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 104.2 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 3917 2019-04-18 11:46:37Z kanani $
[3917]	29	# in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has
	30	# been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied
	31	# into the temporary working catalog
	32	#
	33	# 3860 2019-04-04 06:23:27Z raasch
[3860]	34	# check added, that it is not allowed to set option -b if the configuration file has been setup
	35	# for running batch jobs on remote hosts,
	36	# local time added to terminal output before and after saving output files
	37	#
	38	# 3725 2019-02-07 10:11:02Z raasch
[3725]	39	# error messages for failed restarts extended
	40	#
	41	# 3682 2019-01-18 17:01:54Z knoop
[3665]	42	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	43	# of login messages on specific systems
	44	#
	45	# 3574 2018-11-28 13:14:39Z raasch
[3574]	46	# syntax-error in last commit fixed
	47	#
	48	# 3573 2018-11-28 13:03:44Z raasch
[3573]	49	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	50	# removed,
	51	# r3570 reverted
	52	#
	53	# 3570 2018-11-27 17:44:21Z kanani
[3570]	54	# Rename job-id by run_id
	55	#
	56	# 3555 2018-11-22 13:50:37Z raasch
[3555]	57	# sed-command to remove repeated space-characters replaced by tr-command, to
	58	# guarantee mac compatible
	59	#
	60	# 3549 2018-11-21 15:44:44Z raasch
[3549]	61	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	62	# of login messages on specific systems
	63	#
	64	# 3534 2018-11-19 15:35:16Z raasch
[3534]	65	# batch_scp for sending back the job protocol file is called via login-node if
	66	# a login-node has been set in the config-file
	67	# ssh-calls rearranged to avoid output of system/user-profile messages
	68	#
	69	# 3505 2018-11-08 09:14:30Z raasch
[3505]	70	# job folders are created in case that they do not exist
	71	#
	72	# 3455 2018-10-30 14:12:31Z raasch
[3455]	73	# options -h and -d renamed -c and -r, respectively
	74	#
	75	# 3402 2018-10-23 11:49:24Z knoop
[3346]	76	# job_id is set for compatibility reasons with older versions of config files
	77	#
	78	# 3313 2018-10-06 15:22:48Z knoop
[3294]	79	# more detailed error message for outdated fileconnection file
	80	#
	81	# 3236 2018-09-10 09:07:06Z raasch
[3236]	82	# warning issued in case of file connection file version mismatch,
	83	# host_configuration renamed configuration_identifier,
	84	# "host identifier" in header output renamed "config. identifier",
	85	# jobname renamed run_identifier,
	86	# run_id renamed run_id_number
	87	# job_id renamed run_id
	88	# option -r renamed -i
	89	#
	90	# 3151 2018-07-19 08:45:38Z raasch
[3151]	91	# removed additional listing of files to be compiled, print PALM code revision
	92	# in header
	93	#
	94	# 3132 2018-07-16 11:44:58Z raasch
[3132]	95	# create consistent error messages in case of failed restarts,
	96	# check existence of remote job catalog
	97	#
	98	# 3043 2018-05-25 10:47:54Z raasch
[3043]	99	# check for setting of fast_io_catalog
	100	#
	101	# 3033 2018-05-23 15:26:19Z raasch
[3025]	102	# -T option not required for interactive runs (tasks per node =
	103	# total number of cores is assumed as default, if option is not given),
	104	# reformatting of a few messages,
	105	# bugfix: destination output directory is created if attribute "pe" is set in
	106	# .palm.iofiles
	107	#
	108	# 2718 2018-01-02 08:49:38Z maronga
[2993]	109	# bugfix of r2990
	110	#
	111	# 2718 2018-01-02 08:49:38Z maronga
[2990]	112	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	113	# not in the working directory from where palmrun is called
	114	#
	115	# 2718 2018-01-02 08:49:38Z maronga
[2957]	116	# svfout in the activation string will be replaced now by svfin in case of
	117	# automatic restarts
	118	#
	119	# 2718 2018-01-02 08:49:38Z maronga
[2906]	120	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	121	# the possible output or input of sky view factors
	122	#
	123	# 2718 2018-01-02 08:49:38Z maronga
[2834]	124	# "fname" renamed to "jobname"
	125	#
	126	# 2718 2018-01-02 08:49:38Z maronga
[2799]	127	# parameters are allowed in output commands (OC:)
	128	#
	129	# 2718 2018-01-02 08:49:38Z maronga
[2789]	130	# bugfix: exit if no queue has been given neither with option -q nor in the
	131	# configuration file
	132	#
	133	# 2718 2018-01-02 08:49:38Z maronga
[2762]	134	# file connection file from trunk/SCRIPTS is taken by default
	135	#
	136	# 2718 2018-01-02 08:49:38Z maronga
[2716]	137	# Corrected "Former revisions" section
	138	#
	139	# 2696 2017-12-14 17:12:51Z kanani
	140	# Change in file header (GPL part)
	141	#
	142	# 2693 2017-12-13 12:33:49Z raasch
[2693]	143	# replacement of variables given by {{<variable>}} in configuration file is now
	144	# done in a more general way, variable names are written in small letters
	145	#
	146	# 2670 2017-12-06 16:32:19Z raasch
[2670]	147	# test printouts removed
	148	#
	149	# 2669 2017-12-06 16:03:27Z raasch
[2669]	150	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	151	# removed,
	152	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	153	# files,
	154	# informative messages in case of missing optional input files shortened
	155	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	156	#
	157	# 2638 2017-11-23 12:44:23Z raasch
[2610]	158	# use of wildcards in file connection statements enabled
	159	#
	160	# 2605 2017-11-09 15:31:46Z raasch
[2605]	161	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	162	# will not be sent with the job file any more, but copied into the
[2610]	163	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	164	#
	165	# 2600 2017-11-01 14:11:20Z raasch
[2600]	166	# cycle numbers are made three digits wide
	167	#
	168	# 2566 2017-10-20 08:50:47Z raasch
[2566]	169	# execute command for combine_plot_fields added
	170	# "TEMPDIR" renamed "tempdir"
	171	# temporary working directory for local batch jobs is created immediately within
	172	# the user's palmrun call, due to a requirement of the "grid engine" batch
	173	# system, where the working directory is given with batch directive -wd and must
	174	# already exist when the job is submitted,
	175	# informative messages in non-trace mode reduced and partly reformatted
	176	#
	177	# 2551 2017-10-18 07:25:11Z raasch
[2551]	178	# TEMPDIR added as replacement string to be used in batch directives
	179	#
	180	# 2512 2017-10-04 08:26:59Z raasch
[2507]	181	# bugfix for determining cycle numbers of NetCDF input files
	182	#
	183	# 2506 2017-09-29 08:30:37Z raasch
[2506]	184	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	185	# host configuration added to SOURCES_FOR_RUN_... folder name
	186	# host_identifier renamed host_configuration
	187	# option -W added to allow for job dependencies
	188	#
	189	# 2501 2017-09-26 11:41:55Z raasch
[2501]	190	# default value for number of cores (option -X) set to 1
	191	# bugfix for mechanism which overwrites configuration file settings with values
	192	# provided by palmrun options
	193	#
	194	# 2499 2017-09-22 16:47:58Z kanani
[2499]	195	# option -h named configuration identifier
	196	#
	197	# 2480 2017-09-19 06:24:14Z maronga
[2480]	198	# bugfix for last revision
	199	#
	200	# 2479 2017-09-19 06:12:16Z raasch
[2479]	201	# option -A (project account number) added
	202	#
	203	# 2422 2017-09-08 08:25:41Z raasch
[2410]	204	# initial revision
[2380]	205	#
	206	#--------------------------------------------------------------------------------#
	207	# palmrun - script for running PALM jobs on local and remote hosts
	208	#--------------------------------------------------------------------------------#
	209
	210
	211
	212	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	213
	214	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	215	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	216	# (TOO MANY ARGUMENTS - PROBLEM)
	217	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	218
[2610]	219	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	220	typeset -i nr_of_output_files=0
[2380]	221	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	222	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	223	# SCRIPT-OPTION ARGUMENTS
	224	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	225	typeset -i icycle inode ival maxcycle mpi_tasks
	226	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	227
	228	activation_string_list=""
	229	AddFilenames=""
	230	combine_plot_fields=true
	231	compiler_name=""
	232	compiler_name_ser=""
	233	compiler_options=""
[3236]	234	configuration_identifier="default"
[2501]	235	cores=1
[2380]	236	cores_atmos=0
	237	cores_ocean=0
	238	coupled_dist=""
	239	cpp_options=""
	240	cpumax=0
[2506]	241	create_batch_job=false
[2380]	242	create_jobfile_only=false
	243	create_remote_batch_job=false
	244	dashes=" ----------------------------------------------------------------------------"
	245	defaultqueue=""
[2506]	246	delete_temporary_catalog=true
[2380]	247	do_compile=true
	248	do_trace=false
	249	executable=""
	250	execute_command=""
	251	execution_error=false
[2762]	252	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	253	global_revision=""
	254	hostfile=""
	255	hp=""
	256	keep_data_from_previous_run=false
	257	link_local_input=false
	258	link_local_output=false
[2388]	259	linker_options=""
[2385]	260	local_jobcatalog=""
[2380]	261	locat=normal
	262	makefile=""
	263	max_par_io_str=""
	264	prc=$0
	265	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	266	do
	267	prc=`echo $prc \| cut -f2- -d"/"`
	268	done
	269	module_calls=""
[2506]	270	palmrun_memory=""
[2380]	271	palmrun_script_name=$prc
	272	openmp=false
[2506]	273	previous_job=""
[2479]	274	project_account=""
[2380]	275	queue=none
[2906]	276	read_svf=""
[2380]	277	restart_run=false
	278	return_address=""
[2385]	279	remote_jobcatalog=""
[2380]	280	remote_username=""
	281	running_in_batch_mode=false
[3313]	282	running_in_test_mode=false
[2380]	283	run_coupled_model=false
	284	run_id=""
[3236]	285	run_id_number=""
	286	run_identifier=test
[2380]	287	silent=false
	288	source_list=""
	289	source_path=""
[2501]	290	tasks_per_node=0
[2380]	291	threads_per_task=1
	292	transfer_problems=false
[2384]	293	user_source_path=""
[2506]	294	use_existing_sources_folder=""
[2380]	295	use_openmp=false
[3033]	296	version="palmrun 1.0 Rev$Rev: 3917 $"
[2380]	297	working_directory=`pwd`
	298	write_binary=""
[2906]	299	write_svf=""
[2380]	300
	301
	302	# ERROR HANDLING IN CASE OF EXIT
[2404]	303	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	304	then
	305
	306	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	307	(( i = 0 ))
	308	while (( i < iec ))
	309	do
	310	(( i = i + 1 ))
	311	printf "\n *** Execution of ERROR-command:\n"
	312	printf " >>> ${err_command[$i]}\n"
	313	eval ${err_command[$i]}
	314	done
[2566]	315	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	316	printf "\n\n+++ palmrun crashed \n\n"
	317	exit 1
	318	elif [[ $locat != normal ]]
[2380]	319	then
[3312]	320	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	321	printf "\n+++ palmrun killed by \"^C\" \n\n"
	322	exit 2
	323	else
[2566]	324	printf "\n --> palmrun finished\n\n"
[3312]	325	exit 0
[2380]	326	fi' exit
	327
	328
	329	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	330	trap 'locat=control_c
	331	exit 1
[2380]	332	' 2
	333
	334
	335	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	336	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	337	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]	338	do
	339	case $option in
	340	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	341	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	342	(b) create_batch_job=true; prc="$prc -b";;
	343	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	344	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	345	(C) restart_run=true; prc="$prc -C";;
	346	(F) create_jobfile_only=true;;
	347	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	348	(i) run_id_number=$OPTARG;;
[2380]	349	(j) running_in_batch_mode=true;;
	350	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	351	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	352	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	353	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	354	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	355	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	356	(R) return_address=$OPTARG;;
	357	(s) source_list=$OPTARG;;
[2501]	358	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	359	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	360	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	361	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	362	(v) silent=true; prc="$prc -v";;
[2506]	363	(V) use_existing_sources_folder="-V";;
[2380]	364	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	365	(W) previous_job=$OPTARG;;
[2380]	366	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	367	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	368	(y) ocean_file_appendix=true; prc="$prc -y";;
	369	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	370	(z) running_in_test_mode=true;;
[2380]	371	(Z) combine_plot_fields=false; prc="$prc -Z";;
	372	(\?) printf "\n +++ unknown option $OPTARG \n"
	373	printf "\n --> type \"$0 ?\" for available options \n"
	374	locat=parameter;exit;;
	375	esac
	376	done
	377
	378
	379	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	380	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	381	(( to_shift = $OPTIND - 1 ))
	382	shift $to_shift
	383
	384	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	385	if [[ "$1" = "?" ]]
	386	then
	387	(printf "\n *** Description of available palmrun options:\n"
	388	printf "\n Option Description Default-Value"
	389	printf "\n -a activation string list \"\" "
[2479]	390	printf "\n -A project account number ---"
[2380]	391	printf "\n -b batch-job on local machine ---"
	392	printf "\n -B do not delete temporary directory at end ---"
[3455]	393	printf "\n -c configuration identifier \"default\" "
[2380]	394	printf "\n -F create batch job file only ---"
	395	printf "\n -k keep data from previous run"
	396	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	397	printf "\n -M Makefile name Makefile"
	398	printf "\n -O threads per openMP task ---"
	399	printf "\n -q queue \"$queue\" "
[3455]	400	printf "\n -r run identifier test"
[2380]	401	printf "\n -s filenames of routines to be compiled \"\" "
	402	printf "\n must end with .f, .f90, .F, or .c !"
	403	printf "\n use \"..\" for more than one file and wildcards"
	404	printf "\n -s LM compiles all locally modified files"
	405	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	406	printf "\n -T tasks per node ---"
[2380]	407	printf "\n -u username on remote machine \"\" "
	408	printf "\n -v no prompt for confirmation ---"
[2506]	409	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	410	printf "\n -w maximum parallel io streams as given by -X"
[2506]	411	printf "\n -W name of job to wait for ---"
[2380]	412	printf "\n -x tracing of palmrun for debug purposes ---"
	413	printf "\n -X # of processors (on parallel machines) 1"
	414	printf "\n -y add appendix \"_O\" to all local output"
	415	printf "\n files (ocean precursor runs followed by"
	416	printf "\n coupled atmosphere-ocean runs) ---"
	417	printf "\n -Y run coupled model, \"#1 #2\" with"
	418	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	419	printf "\n -Z skip combine_plot_fields at the end of "
	420	printf "\n the simulation ---"
	421	printf "\n "
	422	printf "\n Possible values of positional parameter <modus>:"
	423	printf "\n \"?\" - this outline \n\n") \| more
	424	exit
	425	elif [[ "$1" != "" ]]
	426	then
	427	printf "\n +++ positional parameter $1 unknown \n"
	428	locat=parameter; exit
	429	fi
	430
	431
	432
	433	# SHORT STARTING MESSAGE
	434	printf "\n*** $version "
	435	printf "\n will be executed. Please wait ..."
	436
	437
[2506]	438	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	439	config_file=.palm.config.$configuration_identifier
	440	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	441
	442
	443	# CHECK, IF CONFIGURATION FILE EXISTS
	444	if [[ ! -f $config_file ]]
	445	then
	446	printf "\n\n +++ configuration file: "
	447	printf "\n $config_file"
	448	printf "\n does not exist"
	449	locat=connect; exit
	450	fi
	451
	452
[2762]	453	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	454	if [[ -f .palm.iofiles ]]
	455	then
[3236]	456
	457	# CHECK VERSION MISMATCH
[3573]	458	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	459	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	460	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	461	then
	462	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	463	then
	464	printf "\n\n +++ WARNING: A file connection file has been found in your"
	465	printf "\n working directory, but its revision does not match"
	466	printf "\n the revision of the default (trunk) version."
[3294]	467	printf "\n You may need to update your connection file"
	468	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	469	fi
	470	fi
	471
[2762]	472	fileconnection_file=.palm.iofiles
[3236]	473
[2762]	474	fi
	475
	476
[2380]	477	# CHECK, IF FILE CONNECTION FILE EXISTS
	478	if [[ ! -f $fileconnection_file ]]
	479	then
	480	printf "\n\n +++ file connection file: "
	481	printf "\n $fileconnection_file"
	482	printf "\n does not exist"
	483	locat=connect; exit
	484	fi
	485
	486
[2404]	487	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	488	if [[ "$activation_string_list" = "" ]]
	489	then
	490	printf "\n\n +++ no activation string list given: "
	491	printf "\n please set palmrun option \"-a\" "
	492	locat=palmrun_option; exit
	493	fi
	494
	495
	496	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	497	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	498	then
	499	write_binary=true
	500	else
	501	write_binary=false
	502	fi
	503
[2906]	504	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	505	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	506	then
	507	write_svf=true
	508	else
	509	write_svf=false
	510	fi
[2404]	511
[2906]	512	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	513	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	514	then
	515	read_svf=true
	516	else
	517	read_svf=false
	518	fi
	519
	520
[2380]	521	# READ AND EVALUATE THE CONFIGURATION-FILE
	522	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	523
	524	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	525	while read line
	526	do
	527
	528	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	529	eval line=\"$line\"
	530
	531
	532	# INTERPRET THE LINE
	533	if [[ "$(echo $line)" = "" ]]
	534	then
	535
	536	# EMPTY LINE, NO ACTION
	537	continue
	538
	539	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	540	then
	541
	542	# LINE IS A COMMENT LINE
	543	continue
	544
	545	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	546	then
	547
	548	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	549	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	550	value=`echo $line \| cut -d" " -s -f2-`
	551
	552
	553	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	554	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	555	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	556	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	557	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	558	# CONFIGURATION-FILE.
	559	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	560	then
	561	eval export $var="\$value"
	562
	563	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	564	if [[ $do_trace = true ]]
	565	then
	566	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	567	fi
	568	fi
	569
	570	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	571	then
	572
	573	# LINE DEFINES BATCH-DIRECTIVE
	574	(( ibd = ibd + 1 ))
	575	line=$(echo $line \| cut -c4-)
	576	batch_directive[$ibd]="$line"
	577
	578	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	579	then
	580
	581	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	582	# REMOTE TO A LOCAL HOST
	583	(( ibdt = ibdt + 1 ))
	584	line=$(echo $line \| cut -c5-)
	585	batch_directive_transfer[$ibdt]="$line"
	586
	587	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	588	then
	589
	590	# LINE DEFINES ERROR-COMMAND
	591	(( iec = iec + 1 ))
	592	line=$(echo $line \| cut -c4-)
	593	err_command[$iec]="$line"
	594
	595	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	596	then
	597
	598	# LINE DEFINES INPUT-COMMAND
	599	(( iic = iic + 1 ))
	600	line=$(echo $line \| cut -c4-)
	601	in_command[$iic]="$line"
	602
	603	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	604	then
	605
	606	# LINE DEFINES OUTPUT-COMMAND
	607	(( ioc = ioc + 1 ))
	608	line=$(echo $line \| cut -c4-)
	609	out_command[$ioc]="$line"
	610
	611	else
	612
	613	# SKIP ALL OTHER LINES
	614	continue
	615
	616	fi
	617
	618	done < $config_file
	619
	620
	621	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	622	if [[ "$fast_io_catalog" = "" ]]
	623	then
[3860]	624	printf "\n\n +++ no fast_io_catalog found in $config_file"
[3043]	625	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	626	locat=config_file; exit
	627	fi
[2380]	628	if [[ "$compiler_name" = "" ]]
	629	then
[3860]	630	printf "\n\n +++ no compiler name found in $config_file"
[2380]	631	printf "\n Please add line \"compiler_name ...\" to that file."
	632	locat=config_file; exit
	633	fi
	634	if [[ "$compiler_name_ser" = "" ]]
	635	then
[3860]	636	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
[2380]	637	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	638	locat=config_file; exit
	639	fi
	640	if [[ "$compiler_options" = "" ]]
	641	then
[3860]	642	printf "\n\n +++ no compiler options found in $config_file"
[2380]	643	printf "\n Please add line \"compiler_options ...\" to that file."
	644	locat=config_file; exit
	645	fi
	646	if [[ "$execute_command" = "" ]]
	647	then
[3860]	648	printf "\n\n +++ no execute command found in $config_file"
[2380]	649	printf "\n Please add line \"execute_command ...\" to that file."
	650	locat=config_file; exit
	651	fi
	652
	653	if [[ "$hostfile" != "" ]]
	654	then
	655	if [[ $hostfile != auto && ! -f $hostfile ]]
	656	then
[3860]	657	printf "\n\n +++ no hostfile \"$hostfile\" found"
[3151]	658	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	659	locat=config_file; exit
	660	fi
	661	fi
	662
	663
	664	# DETERMINE THE CALL STATUS
	665	if [[ "$return_address" != "" ]]
	666	then
	667
	668	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	669	# BATCH MODE AND ...
	670	running_on_remote=true
	671
	672	else
	673
	674	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	675	if [[ "$remote_ip" != "" ]]
	676	then
	677
	678	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	679	create_remote_batch_job=true
	680
[3132]	681	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	682	if [[ "$remote_jobcatalog" = "" ]]
	683	then
[3860]	684	printf "\n\n +++ no remote jobcatalog found in $config_file"
[3132]	685	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	686	locat=config_file; exit
	687	fi
	688
[3860]	689	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
	690	if [[ $create_batch_job = true ]]
	691	then
	692	printf "\n\n +++ option -b must not be set because configuration file has been setup"
	693	printf "\n for running jobs on a remote host"
	694	locat=config_file; exit
	695	fi
	696
[2380]	697	fi
	698	running_on_remote=false
	699	fi
	700
	701
	702
	703	# READ AND EVALUATE THE I/O-FILE LIST
	704	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	705
	706	# READ THE FILE CONNECTION FILE LINE BY LINE
	707	while read line
	708	do
	709
[2669]	710	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	711	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	712	line=`echo "$line" \| tr -s " "`
[2380]	713
	714	# INTERPRET THE LINE
	715	if [[ "$(echo $line)" = "" ]]
	716	then
	717	# EMPTY LINE, NO ACTION
	718	continue
	719
	720	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	721	then
	722
	723	# LINE IS A COMMENT LINE
	724	true
	725
	726	else
	727
	728	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	729	# s2a: in/out - field
[2669]	730	# s2b: action - field (optional)
	731	s1=`echo "$line" \| cut -d" " -f1`
	732	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	733	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	734	then
[2669]	735	s2a=$s2
[2380]	736	s2b=""
	737	else
[2669]	738	s2a=`echo $s2 \| cut -d":" -f1`
	739	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	740	fi
[2669]	741	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	742	s4=`echo "$line" \| cut -d" " -s -f4`
	743	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	744	s5=`echo "$line" \| cut -d" " -s -f5`
	745	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	746
	747
	748	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	749	# INPUT- OR OUTPUT-LIST.
	750	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	751	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	752	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	753	# IS NOT CHECKED AND STORED.
[2610]	754	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	755	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	756	then
	757	found=false
	758	for actual in $activation_string_list
	759	do
	760	for formal in $s3
	761	do
	762	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	763	done
	764	done
	765	if [[ $found = true ]]
	766	then
	767	(( iin = iin + 1 ))
[2669]	768	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	769	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	770	if [[ "$s2a" = inopt ]]
	771	then
	772	optin_pre[$iin]=yes
	773	else
	774	optin_pre[$iin]=no
	775	fi
[2605]	776
	777	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	778	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	779	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	780	then
[2610]	781	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	782	fi
	783
[2610]	784	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	785	# THE WILDCARD FROM THE ENDING
	786	if [[ "${s5: -1}" = "*" ]]
	787	then
[2669]	788	if [[ "$s2b" = "di" ]]
[2610]	789	then
	790	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	791	printf "\n see file \"$fileconnection_file\", line"
	792	printf "\n$line"
	793	locat=iofiles_file; exit
	794	fi
	795	multin[$iin]=true
	796	string=${endin_pre[$iin]}
	797	endin_pre[$iin]="${string%?}"
	798	else
	799	multin[$iin]=false
	800	fi
[2380]	801	fi
[2669]	802	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	803	then
	804	found=false
	805	for actual in $activation_string_list
	806	do
	807	for formal in $s3
	808	do
[2670]	809	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	810	done
	811	done
	812	if [[ $found = true ]]
	813	then
	814	(( iout = iout + 1 ))
[2669]	815	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	816	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	817
[2669]	818	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	819	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	820	if [[ $formal = wildcard ]]
	821	then
	822	warnout_pre[$iout]=false
	823	else
	824	warnout_pre[$iout]=true
	825	fi
	826
[2610]	827	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	828	# THE WILDCARD FROM THE LOCAL FILENAME
	829	if [[ "${s1: -1}" = "*" ]]
	830	then
[2669]	831	if [[ "$s2b" = "di" ]]
[2610]	832	then
	833	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	834	printf "\n see file \"$fileconnection_file\", line"
	835	printf "\n$line"
	836	locat=iofiles_file; exit
	837	fi
	838	multout[$iout]=true
	839	string=${localout_pre[$iout]}
	840	localout_pre[$iout]="${string%?}"
	841	else
	842	multout[$iout]=false
	843	fi
[2380]	844	fi
[2669]	845	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	846	then
[2669]	847	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	848	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	849	locat=connect; exit
	850	fi
	851	IFS="$IFSALT"
	852	fi
	853
	854	done < $fileconnection_file
	855
	856
	857
[2501]	858	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	859	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	860	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	861	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	862	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	863	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	864
	865
	866
[2380]	867	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	868	if [[ $run_coupled_model = true ]]
	869	then
	870
	871	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	872	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	873
	874	if (( $cores_ocean + $cores_atmos != $cores ))
	875	then
	876
	877	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	878	printf "\n PEs (total) : $cores"
	879	printf "\n PEs (atmosphere): $cores_atmos"
	880	printf "\n PEs (ocean) : $cores_ocean"
	881	locat=coupling; exit
	882
	883	fi
	884
	885	fi
	886
	887
	888	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	889	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	890	# FOLDER
	891	if [[ $running_in_batch_mode = true ]]
	892	then
	893
[2506]	894	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	895	then
[2506]	896	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	897	printf "\n Please check the output of the palmrun-call"
	898	printf "\n that you did on your local host."
	899	locat=SOURCES_FOR_RUN; exit
	900	fi
	901
	902	else
	903
	904	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	905	# AUTOMATIC RESTART RUN
	906	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	907	if [[ $restart_run = false ]]
	908	then
	909
	910	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	911	# THE LOCAL HOST
	912	if [[ ! -d $source_path ]]
	913	then
	914	printf "\n\n +++ source path \"$source_path\" on local host"
	915	printf "\n \"$(hostname)\" does not exist"
	916	locat=source_path; exit
	917	fi
	918
[2990]	919	rm -rf ${base_directory}/${sources_for_run_catalog}
	920	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	921
	922	if [[ "$source_list" = LM ]]
	923	then
	924
	925	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	926	source_list=""
	927	cd $source_path
	928
	929
[2512]	930	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	931	if [[ ! -d ../.svn ]]
[2380]	932	then
	933	printf "\n\n +++ source directory"
	934	printf "\n \"$source_path\" "
	935	printf "\n is not under control of \"subversion\"."
[2512]	936	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	937	fi
	938
	939
	940	# LIST ALL MODIFIED SOURCE CODE FILES
	941	Filenames=""
[2404]	942	svn status > tmp_svnstatus
[2380]	943	while read line
	944	do
	945	firstc=`echo $line \| cut -c1`
	946	if [[ $firstc = M \|\| $firstc = "?" ]]
	947	then
	948	Name=`echo "$line" \| cut -c8-`
	949	extension=`echo $Name \| cut -d. -f2`
	950	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	951	then
	952	Filenames="$Filenames "$Name
	953	fi
	954	fi
[2404]	955	done < tmp_svnstatus
	956	rm -rf tmp_svnstatus
[2380]	957
	958
	959	# COPY FILES TO SOURCES_FOR_RUN_...
	960	for filename in $Filenames
	961	do
[2990]	962	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	963	source_list=$source_list"$filename "
	964	done
	965
	966	cd - > /dev/null
	967
	968
	969	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	970	elif [[ "$source_list" != "" ]]
	971	then
	972
	973	cd $source_path
	974
	975	for filename in $source_list
	976	do
	977
	978	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	979	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	980	then
	981	printf "\n +++ source code file: $filename"
	982	printf "\n must not contain (\"/\") "
	983	locat=source; exit
	984	fi
	985
	986	if [[ ! -f $filename ]]
	987	then
	988	printf "\n +++ source code file: $filename"
	989	printf "\n does not exist"
	990	locat=source; exit
	991	else
[2990]	992	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	993	fi
	994
	995	done
	996
	997	cd - > /dev/null
	998
	999	fi
	1000
	1001	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1002	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1003	if [[ ! -f $makefile ]]
	1004	then
	1005	printf "\n +++ file \"$makefile\" does not exist"
	1006	locat=make; exit
	1007	else
[2990]	1008	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	1009	fi
	1010
	1011
	1012	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	1013	if [[ "$user_source_path" != "" ]]
[2380]	1014	then
	1015
	1016	# DOES THE DIRECTORY EXIST?
[2384]	1017	if [[ ! -d $user_source_path ]]
[2380]	1018	then
	1019
	1020	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1021	printf "\n \"$user_source_path\" "
[2380]	1022	printf "\n does not exist or is not a directory."
	1023	printf "\n No source code will be used from this directory!\n"
[2384]	1024	user_source_path=""
[2380]	1025	if [[ $silent == false ]]
	1026	then
	1027	sleep 2
	1028	fi
	1029
	1030	else
	1031
[2384]	1032	cd $user_source_path
[2380]	1033
	1034	Names=$(ls -1 *.f90 2>&1)
	1035	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1036	Names=$(ls -1 *.F90 2>&1)
	1037	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1038	Names=$(ls -1 *.F 2>&1)
	1039	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1040	Names=$(ls -1 *.f 2>&1)
	1041	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1042	Names=$(ls -1 *.c 2>&1)
	1043	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1044
	1045	cd - > /dev/null
[2990]	1046	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1047
	1048	# COPY MAKEFILE IF EXISTING
[2384]	1049	if [[ -f $user_source_path/Makefile ]]
[2380]	1050	then
	1051	printf "\n\n *** user Makefile from directory"
[2384]	1052	printf "\n \"$user_source_path\" is used \n"
[2380]	1053	if [[ $silent == false ]]
	1054	then
	1055	sleep 1
	1056	fi
[2384]	1057	cp $user_source_path/Makefile .
[2380]	1058	fi
	1059
	1060	for filename in $AddFilenames
	1061	do
	1062	if [[ -f $filename ]]
	1063	then
	1064	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1065	printf "\n source code directory \"$user_source_path\" "
[2380]	1066	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1067	printf "\n from directory \"$source_path\"."
	1068	locat=source; exit
	1069	fi
	1070
[2384]	1071	cp $user_source_path/$filename .
[2380]	1072	source_list="$source_list $filename"
	1073
	1074	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1075	if [[ $(grep -c $filename Makefile) = 0 ]]
	1076	then
	1077	printf "\n\n +++ user file \"$filename\" "
	1078	printf "\n is not listed in Makefile \n"
	1079	locat=source; exit
	1080	fi
	1081	done
	1082	cd - > /dev/null
	1083	fi
	1084	fi
	1085
	1086	# COPY CONFIGURATION FILES
[2990]	1087	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1088	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1089
	1090	# COPY SHELLSCRIPTS
[2990]	1091	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1092	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1093
	1094	fi
	1095
	1096	fi
	1097
[2605]	1098
[2380]	1099	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1100	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1101	if [[ "$global_revision" = "" ]]
	1102	then
	1103	global_revision=`svnversion $source_path 2>/dev/null`
	1104	global_revision="Rev: $global_revision"
	1105	fi
	1106
	1107
	1108	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1109	if [[ -n $cores ]]
	1110	then
	1111
	1112	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1113	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1114	if [[ $tasks_per_node = 0 ]]
[2380]	1115	then
[3025]	1116	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1117	then
	1118	printf "\n"
	1119	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1120	printf "\n set -T option or define tasks_per_node in the config file"
	1121	locat=tasks_per_node; (( iec = 0 )); exit
	1122	else
	1123	# DEFAULT FOR INTERACTIVE RUN
	1124	tasks_per_node=$cores
	1125	fi
[2380]	1126	fi
	1127
	1128	if (( cores < tasks_per_node ))
	1129	then
	1130	printf "\n"
	1131	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1132	printf "\n given values: -T $tasks_per_node -X $cores"
	1133	locat=tasks_per_node; (( iec = 0 )); exit
	1134	fi
	1135
	1136	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1137	(( mpi_tasks = cores / threads_per_task ))
	1138	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1139	(( ii = cores / tasks_per_node ))
	1140	(( remaining_cores = cores - ii * tasks_per_node ))
	1141	if (( remaining_cores > 0 ))
	1142	then
	1143	printf "\n"
	1144	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1145	printf "\n divisor of the total number of cores (option \"-X\")"
	1146	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1147	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1148	(( nodes = nodes + 1 ))
	1149	fi
	1150
	1151	fi
	1152
	1153
	1154	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1155	if [[ "$maximum_parallel_io_streams" = "" ]]
	1156	then
	1157	maximum_parallel_io_streams=$cores
	1158	fi
	1159
	1160
	1161	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1162	if [[ "$scp_port" != "" ]]
	1163	then
	1164	PORTOPT="-P $scp_port"
	1165	SSH_PORTOPT="-p $scp_port"
	1166	fi
	1167
	1168
	1169	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1170	# CONFIG-FILE
	1171	if [[ "$ssh_key" != "" ]]
	1172	then
	1173	ssh_key="-i $HOME/.ssh/$ssh_key"
	1174	fi
	1175
	1176
	1177	# SET QUEUE, IF NOT GIVEN
	1178	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1179	then
	1180
	1181	if [[ $queue = none && "$defaultqueue" = "" ]]
	1182	then
	1183	printf "\n"
	1184	printf "\n +++ no default queue given in configuration file and no queue"
	1185	printf "\n given with option -q"
[2789]	1186	locat=queue; exit
[2380]	1187	fi
	1188	if [[ $queue = none ]]
	1189	then
	1190	queue=$defaultqueue
	1191	fi
	1192
	1193	fi
	1194
	1195
	1196	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1197	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1198	(( i = 0 ))
[2610]	1199	(( nr_of_input_files = 0 ))
[2380]	1200	while (( i < iin ))
	1201	do
	1202	(( i = i + 1 ))
	1203
	1204	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1205	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1206	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1207	then
[2610]	1208	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1209	else
[3236]	1210	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1211	fi
	1212
[2610]	1213
[2380]	1214	# CHECK IF FILE EXISTS
	1215	if ! ls $filename* 1>/dev/null 2>&1
	1216	then
	1217
[2669]	1218	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1219	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1220	then
	1221	printf "\n\n +++ INPUT-file: "
[2610]	1222	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1223	then
	1224	printf "\n $filename"
	1225	else
[2610]	1226	printf "\n $filename.${extin_pre[$i]}"
[2380]	1227	fi
	1228	printf "\n does not exist\n"
	1229	locat=input; exit
	1230	else
[2610]	1231	(( nr_of_input_files = nr_of_input_files + 1 ))
	1232	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1233	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1234	actionin[$nr_of_input_files]="unavailable"
[2610]	1235	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1236	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1237	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1238	fi
[2605]	1239
[2380]	1240	else
	1241
[3236]	1242	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1243	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1244	# ENDINGS
[2610]	1245	if [[ "${multin[$i]}" = true ]]
	1246	then
	1247	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1248	ls -1 -d ${filename} > filelist 2>/dev/null
	1249	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1250	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1251
[2610]	1252	endings=""
	1253	while read line
	1254	do
	1255	# filename without path (i.e. after the last "/")
	1256	basefilename=$(basename ${line})
[2380]	1257
[2610]	1258	# check if there is an extension and remove it
	1259	ext=${basefilename##*.}
	1260	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1261	then
	1262	basefilename=${basefilename%.*}
	1263	fi
[2380]	1264
[2610]	1265	# check for an existing cycle number and remove it
	1266	cycle=${basefilename##*.}
	1267	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1268	then
	1269	basefilename=${basefilename%.*}
	1270	fi
[2600]	1271
[3236]	1272	# remove the run_identifier from the beginning
	1273	length_run_identifier=${#run_identifier}
	1274	ending=${basefilename:${length_run_identifier}}
[2610]	1275
	1276	# remove the ending given in the .iofiles from the beginning
	1277	endingstring="${endin_pre[$i]}"
	1278	length_ending=${#endingstring}
	1279	ending=${ending:${length_ending}}
	1280
	1281	if [[ "$ending" = "" ]]
[2600]	1282	then
[2610]	1283	# standard ending as given in the .iofiles
	1284	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1285	then
	1286	endings="$endings DEFAULT"
	1287	fi
[2600]	1288	else
[2610]	1289	# ending must start with "_", otherwise its a different file
	1290	if [[ "${ending:0:1}" = "_" ]]
	1291	then
	1292	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1293	then
	1294	endings="$endings $ending"
	1295	fi
	1296	fi
[2600]	1297	fi
[2610]	1298
	1299	done <filelist
[2380]	1300
[2610]	1301	rm filelist
[2380]	1302
[2600]	1303	else
[2610]	1304
	1305	# SINGLE NAME
	1306	endings=DEFAULT
	1307
[2600]	1308	fi
	1309
[2610]	1310	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1311	for ending in $endings
	1312	do
	1313
	1314	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1315	if [[ $ending = DEFAULT ]]
[2380]	1316	then
[2610]	1317	ending=""
	1318	fi
	1319
	1320	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1321	(( nr_of_input_files = nr_of_input_files + 1 ))
	1322	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1323	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1324	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1325	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1326	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1327	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1328
	1329
	1330	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1331	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1332	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1333	then
	1334	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1335	else
[3236]	1336	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1337	fi
[2610]	1338
	1339	# DETERMINE THE FILE'S CYCLE NUMBER
	1340	(( maxcycle = 0 ))
	1341	ls -1 -d $filename > filelist 2>/dev/null
	1342	ls -1 -d $filename.* >> filelist 2>/dev/null
	1343	while read line
	1344	do
	1345	# filename without path (i.e. after the last "/")
	1346	basefilename=$(basename ${line})
	1347
	1348	# check if there is an extension
	1349	extension=${basefilename##*.}
	1350	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1351	then
	1352	basefilename=${basefilename%.*}
	1353	fi
	1354
	1355	# check for an existing cycle number
	1356	cycle=${basefilename##*.}
	1357	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1358	then
[2669]	1359	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1360	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1361	(( icycle = $((10#$cycle)) ))
[2610]	1362	else
	1363	(( icycle = 0 ))
	1364	fi
	1365
	1366	if (( icycle > maxcycle ))
	1367	then
	1368	(( maxcycle = icycle ))
	1369
	1370	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1371	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1372	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1373	then
	1374	leading_zero=true
	1375	else
	1376	leading_zero=false
	1377	fi
	1378	fi
	1379
	1380	done <filelist
	1381	rm filelist
	1382
	1383	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1384	if [[ $leading_zero = true ]]
[2380]	1385	then
[2610]	1386	cyclestring=`printf "%03d" $maxcycle`
	1387	else
	1388	cyclestring=$maxcycle
[2380]	1389	fi
[2610]	1390
	1391	# APPEND CYCLE NUMBER TO FILENAME
	1392	if (( maxcycle > 0 ))
[2380]	1393	then
[2610]	1394	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1395	then
	1396	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1397	else
	1398	filename=${filename}.$cyclestring
	1399	fi
[2380]	1400	else
[2610]	1401	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1402	then
	1403	filename=${filename}.${extin[$nr_of_input_files]}
	1404	fi
[2380]	1405	fi
[2610]	1406
	1407	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1408	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1409	absnamein[$nr_of_input_files]=$filename
	1410	if (( maxcycle > 0 ))
[2380]	1411	then
[2610]	1412	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1413	then
	1414	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1415	else
[3236]	1416	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1417	fi
[2380]	1418	else
[2610]	1419	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1420	then
	1421	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1422	else
[3236]	1423	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1424	fi
[2380]	1425	fi
	1426
[2610]	1427	done
	1428
[2380]	1429	fi
[2610]	1430
[2380]	1431	done
	1432
[2610]	1433
[2380]	1434	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1435	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1436	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1437	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1438	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1439	# REMOTE HOST)
	1440	(( i = 0 ))
	1441	while (( i < iout ))
	1442	do
	1443	(( i = i + 1 ))
[2610]	1444	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1445	then
[2610]	1446	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1447	then
[2610]	1448	actionout_pre[$i]=""
	1449	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1450	then
[2610]	1451	actionout_pre[$i]=pe
	1452	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1453	then
[2610]	1454	actionout_pre[$i]=a
[2380]	1455	fi
	1456	(( maxcycle = 0 ))
[3236]	1457	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1458	eval catalogname=${pathout_pre[$i]}
[2380]	1459	if ! ls $filename* 1>/dev/null 2>&1
	1460	then
	1461
	1462	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1463	if cat /dev/null > $filename
	1464	then
	1465	rm $filename
	1466	else
	1467
	1468	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1469	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1470	if [[ ! -d $catalogname ]]
	1471	then
	1472	if mkdir -p $catalogname
	1473	then
	1474	printf "\n\n *** directory:"
	1475	printf "\n $catalogname"
	1476	printf "\n was created\n"
	1477	else
	1478	printf "\n\n +++ OUTPUT-file:"
	1479	printf "\n $filename"
	1480	printf "\n cannot be created, because directory does not exist"
	1481	printf "\n and cannot be created either"
	1482	printf "\n"
	1483	locat=output ; exit
	1484	fi 2>/dev/null
	1485	else
	1486	printf "\n\n +++ OUTPUT-file:"
	1487	printf "\n $filename"
	1488	printf "\n cannot be created, although directory exists"
	1489	printf "\n"
	1490	locat=output ; exit
	1491	fi
	1492	fi 2>/dev/null
	1493
	1494	fi
	1495
	1496	fi
	1497	done
	1498
	1499
	1500	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1501	if [[ $running_in_batch_mode = false ]]
	1502	then
[3236]	1503	run_id_number=$RANDOM
	1504	run_id=${run_identifier}.$run_id_number
[2380]	1505
[3236]	1506	tempdir=$fast_io_catalog/$run_id
[3346]	1507
	1508	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1509	export job_id=$run_id
	1510
[2380]	1511	fi
	1512
	1513
	1514	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1515	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1516	then
	1517
	1518	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1519	if [[ $ibd = 0 ]]
	1520	then
	1521	printf "\n"
	1522	printf "\n +++ no batch directives found in configuration file"
	1523	locat=config_file_batch_directives; (( iec = 0 )); exit
	1524	fi
	1525
	1526	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1527	done=false
[2384]	1528	cputime=$cpumax
[2380]	1529	while [[ $done = false ]]
	1530	do
[2384]	1531	if (( cputime == 0 ))
[2380]	1532	then
	1533	printf "\n +++ cpu-time is undefined"
	1534	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1535	printf "\n >>> "
[2384]	1536	read cputime 1>/dev/null 2>&1
[2380]	1537	else
	1538	done=true
	1539	fi
	1540	done
[2420]	1541	cpumax=$cputime
[2380]	1542
	1543	# CHECK THE MEMORY DEMAND
	1544	done=false
	1545	while [[ $done = false ]]
	1546	do
	1547	if (( memory == 0 ))
	1548	then
	1549	printf "\n +++ memory demand is undefined"
	1550	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1551	printf "\n >>> "
	1552	read memory 1>/dev/null 2>&1
	1553	else
	1554	done=true
	1555	fi
	1556	done
	1557
	1558	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1559	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1560	then
	1561	while [[ -z $remote_username ]]
	1562	do
[2420]	1563	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1564	printf "\n >>> Please type username:"
	1565	printf "\n >>> "
	1566	read remote_username
	1567	done
	1568	fi
	1569
	1570	else
	1571
[2420]	1572	if [[ $running_in_batch_mode = false ]]
	1573	then
	1574	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1575	cpumax=$cputime
	1576	else
	1577	cputime=$cpumax
	1578	fi
[2380]	1579
	1580	fi
	1581
	1582
	1583	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1584	(( cpu_hours = cputime / 3600 ))
	1585	(( resttime = cputime - cpu_hours * 3600 ))
	1586	(( cpu_minutes = resttime / 60 ))
	1587	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1588	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1589
	1590
	1591	# OUTPUT OF THE PALMRUN-HEADER
	1592	calltime=$(date)
	1593	printf "\n"
	1594	printf "#------------------------------------------------------------------------# \n"
	1595	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1596	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1597	printf "\| \| \n"
	1598	column1="called on:"; column2=$(hostname)
	1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1600	if [[ $create_remote_batch_job = true ]]
	1601	then
[3236]	1602	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1603	else
	1604	if [[ $running_on_remote = true ]]
	1605	then
[3236]	1606	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1607	else
[3236]	1608	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1609	fi
	1610	fi
	1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1612
	1613	column1="running in:"
	1614	if [[ $running_in_batch_mode = true ]]
	1615	then
	1616	column2="batch job mode"
	1617	else
	1618	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1619	then
	1620	column2="job creation mode"
	1621	else
	1622	column2="interactive run mode"
	1623	fi
	1624	fi
	1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1626
[2479]	1627	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1628	then
[2480]	1629	if [[ "$project_account" != "" ]]
[2479]	1630	then
	1631	column1="project account number:"
	1632	column2="$project_account"
	1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1634	fi
	1635	fi
	1636
[2380]	1637	if [[ -n $cores ]]
	1638	then
	1639	if [[ $run_coupled_model = false ]]
	1640	then
	1641	column1="number of cores:"; column2=$cores
	1642	else
	1643	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1644	fi
	1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1646	fi
	1647	if [[ -n $tasks_per_node ]]
	1648	then
	1649	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1651	if (( remaining_cores > 0 ))
	1652	then
	1653	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1654	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1655	fi
	1656	fi
	1657	if [[ $maximum_parallel_io_streams != $cores ]]
	1658	then
	1659	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1661	fi
	1662	if [[ $use_openmp = true ]]
	1663	then
	1664	column1="threads per task:"; column2="$threads_per_task"
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1666	fi
[2384]	1667	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1668	then
[2506]	1669	column1="memory demand / PE":; column2="$memory MB"
	1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1671	column1="job cpu time (h:m:s):"; column2="$timestring"
	1672	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1673	fi
[2380]	1674	printf "\| \| \n"
	1675	if [[ "$source_list" != "" ]]
	1676	then
	1677	if [[ "$make_options" != "" ]]
	1678	then
	1679	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1680	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1681	line=$(echo "$make_options" \| cut -c46-)
	1682	while [[ "$line" != "" ]]
	1683	do
	1684	column1=""
	1685	column2=$(echo "$line" \| cut -c-45)
	1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1687	line=$(echo "$line" \| cut -c46-)
	1688	done
	1689	fi
	1690	fi
	1691
	1692	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1694	line=$(echo "$cpp_options" \| cut -c46-)
	1695	while [[ "$line" != "" ]]
	1696	do
	1697	column1=""
	1698	column2=$(echo "$line" \| cut -c-45)
	1699	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1700	line=$(echo "$line" \| cut -c46-)
	1701	done
	1702
	1703	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1704	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1705	line=$(echo "$compiler_options" \| cut -c46-)
	1706	while [[ "$line" != "" ]]
	1707	do
	1708	column1=""
	1709	column2=$(echo "$line" \| cut -c-45)
	1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1711	line=$(echo "$line" \| cut -c46-)
	1712	done
	1713
[2388]	1714	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1715	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1716	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1717	while [[ "$line" != "" ]]
	1718	do
	1719	column1=""
	1720	column2=$(echo "$line" \| cut -c-45)
	1721	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1722	line=$(echo "$line" \| cut -c46-)
	1723	done
	1724
	1725	if [[ "$login_init_cmd" != "" ]]
	1726	then
	1727	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1728	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1729	line=$(echo "$login_init_cmd" \| cut -c46-)
	1730	while [[ "$line" != "" ]]
	1731	do
	1732	column1=""
	1733	column2=$(echo "$line" \| cut -c-45)
	1734	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1735	line=$(echo "$line" \| cut -c46-)
	1736	done
	1737	fi
	1738
	1739	if [[ "$module_commands" != "" ]]
	1740	then
	1741	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1742	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1743	line=$(echo "$module_commands" \| cut -c46-)
	1744	while [[ "$line" != "" ]]
	1745	do
	1746	column1=""
	1747	column2=$(echo "$line" \| cut -c-45)
	1748	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1749	line=$(echo "$line" \| cut -c46-)
	1750	done
	1751	fi
	1752	printf "\| \| \n"
[3236]	1753	column1="run identifier:"; column2=$run_identifier
[2380]	1754	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1755	column1="activation string list:"; column2=$(echo $activation_string_list)
	1756	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1757
	1758	if [[ "$ocean_file_appendix" = true ]]
	1759	then
	1760	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1761	fi
	1762
	1763	if [[ "$source_list" != "" ]]
	1764	then
	1765	printf "\| \| \n"
	1766	printf "\| Files to be compiled: \| \n"
	1767	line=$source_list
	1768	while [[ "$line" != "" ]]
	1769	do
	1770	linestart=$(echo $line \| cut -c-70)
	1771	printf "\| %-70s \| \n" "$linestart"
	1772	line=$(echo "$line" \| cut -c71-)
	1773	done
	1774	fi
	1775	printf "#------------------------------------------------------------------------#"
	1776
	1777
	1778
	1779	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1780	if [[ $do_trace = true ]]
	1781	then
	1782	(( i = 0 ))
[2610]	1783	while (( i < nr_of_input_files ))
[2380]	1784	do
	1785	(( i = i + 1 ))
	1786	if (( i == 1 ))
	1787	then
	1788	printf "\n\n >>> INPUT-file assignments:\n"
	1789	fi
	1790	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1791	done
	1792	(( i = 0 ))
	1793	while (( i < iout ))
	1794	do
	1795	(( i = i + 1 ))
	1796	if (( i == 1 ))
	1797	then
	1798	printf "\n\n >>> OUTPUT-file assignments:\n"
	1799	fi
	1800	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1801	done
	1802	(( i = 0 ))
	1803	while (( i < iic ))
	1804	do
	1805	(( i = i + 1 ))
	1806	if (( i == 1 ))
	1807	then
	1808	printf "\n\n >>> INPUT-commands:\n"
	1809	fi
	1810	printf "\n ${in_command[$i]}"
	1811	done
	1812	(( i = 0 ))
	1813	while (( i < ioc ))
	1814	do
	1815	(( i = i + 1 ))
	1816	if (( i == 1 ))
	1817	then
	1818	printf "\n\n >>> OUTPUT-commands:\n"
	1819	fi
	1820	printf "\n ${out_command[$i]}"
	1821	done
	1822	fi
	1823
	1824	# QUERY FOR CONTINUE
	1825	if [[ $silent = false && $running_in_batch_mode = false ]]
	1826	then
	1827	antwort=dummy
	1828	printf "\n\n"
	1829	printf " >>> everything o.k. (y/n) ? "
	1830	while read antwort
	1831	do
	1832	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1833	then
	1834	printf " >>> everything o.k. (y/n) ? "
	1835	else
	1836	break
	1837	fi
	1838	done
	1839	if [[ $antwort = n \|\| $antwort = N ]]
	1840	then
	1841	locat=user_abort; (( iec = 0 )); exit
	1842	fi
	1843	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1844	then
[2566]	1845	printf "\n *** batch-job will be created and submitted"
[2380]	1846	else
[2566]	1847	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1848	fi
	1849	fi
	1850
	1851
	1852
	1853	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1854	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1855	then
	1856
	1857	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1858	then
[2566]	1859	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1860	else
[2566]	1861	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1862	fi
	1863
[2422]	1864	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1865	# IT SHALL BE CREATED
	1866	ask_for_make_depository=false
	1867	if [[ $create_remote_batch_job = true ]]
	1868	then
	1869
	1870	line=`grep %base_directory $config_file`
[3236]	1871	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1872	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1873
[3236]	1874	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1875	then
	1876	printf "\n\n +++ make depository \"${make_depository}\""
	1877	printf "\n on remote host not found!"
	1878	ask_for_make_depository=true
	1879	fi
[3236]	1880	rm ${configuration_identifier}_last_make_protokoll
[2422]	1881
	1882	else
	1883
	1884	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1885	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1886	if [[ ! -d ${make_depository} ]]
	1887	then
	1888	printf "\n\n +++ make depository \"${make_depository}\""
	1889	printf "\n on local host not found!"
	1890	ask_for_make_depository=true
	1891	fi
	1892
	1893	fi
	1894
	1895	if [[ $ask_for_make_depository = true ]]
	1896	then
	1897
	1898	antwort=dummy
	1899	printf "\n\n"
	1900	printf " >>> Create a new one (y/n) ? "
	1901	while read antwort
	1902	do
	1903	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1904	then
	1905	printf " >>> Create a new one (y/n) ? "
	1906	else
	1907	break
	1908	fi
	1909	done
	1910	if [[ $antwort = n \|\| $antwort = N ]]
	1911	then
	1912	locat=user_abort; (( iec = 0 )); exit
	1913	fi
	1914
[2566]	1915	if [[ $do_trace = true ]]
	1916	then
[3455]	1917	palmbuild -c $configuration_identifier
[2566]	1918	else
[3455]	1919	palmbuild -v -c $configuration_identifier
[2566]	1920	fi
[2422]	1921
[3312]	1922	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1923	then
	1924
	1925	# ABORT IN CASE OF COMPILATION PROBLEMS
	1926	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1927	locat=make_depository
	1928	exit
	1929	else
	1930	echo " *** now continue with creating executable and other sources"
	1931	fi
	1932
	1933	fi
	1934
[2566]	1935	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1936	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1937
[3312]	1938	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1939	then
	1940
	1941	# ABORT IN CASE OF COMPILATION PROBLEMS
	1942	printf "\n +++ error while creating executable and/or other sources"
	1943	locat=execution
[2990]	1944	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1945	exit
	1946
	1947	else
	1948
[2566]	1949	printf " *** executable and other sources created\n"
[2990]	1950	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1951
	1952	fi
	1953
	1954	fi
	1955
	1956
[2669]	1957	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1958	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1959	if [[ $create_remote_batch_job = true ]]
	1960	then
	1961	(( i = 0 ))
[2610]	1962	while (( i < nr_of_input_files ))
[2605]	1963	do
	1964	(( i = i + 1 ))
[2669]	1965	if [[ "${actionin[$i]}" = tr ]]
[2605]	1966	then
	1967	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1968	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1969	fi
	1970	done
	1971	if (( i > 0 ))
	1972	then
[3025]	1973	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1974	fi
	1975	fi
	1976
	1977
[2380]	1978	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1979	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1980	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1981	then
	1982
	1983	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1984	if [[ $running_in_batch_mode = false ]]
	1985	then
[3917]	1986	# CREATE THE DIRECTORY
[2566]	1987	mkdir -p $tempdir
	1988	chmod go+rx $tempdir
	1989	cd $tempdir
	1990	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1991
	1992	else
	1993
	1994	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1995	printf "\n *** running in temporary directory: $tempdir"
[2380]	1996
	1997	fi
	1998
	1999
	2000	# PROVIDE THE INPUT FILES
	2001	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	2002	optional_files_missing=false
[2380]	2003	(( i = 0 ))
[2610]	2004	while (( i < nr_of_input_files ))
[2380]	2005	do
	2006	(( i = i + 1 ))
	2007	if (( i == 1 ))
	2008	then
	2009	printf "\n\n *** providing INPUT-files:\n$dashes"
	2010	fi
	2011
	2012
	2013	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	2014	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2015	then
[2669]	2016	optional_files_missing=true
[2380]	2017	continue
	2018	fi
	2019
	2020	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2021	files_for_cores=false; filetype=file
	2022	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2023	then
	2024	files_for_cores=true; filetype=files
	2025	actionin[$i]=""
	2026	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2027	then
	2028	actionin[$i]=""
	2029	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2030	then
	2031	files_for_cores=true; filetype=files
	2032	actionin[$i]="ln"
	2033	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2034	then
	2035	actionin[$i]="ln"
	2036	fi
	2037
	2038	if [[ $files_for_cores = true ]]
	2039	then
	2040	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2041	else
	2042	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2043	fi
	2044
	2045	# INPUT-FILES TO BE LINKED
	2046	if [[ "${actionin[$i]}" = ln ]]
	2047	then
	2048
	2049	printf "\n $filetype will be linked"
	2050	if [[ $files_for_cores = false ]]
	2051	then
	2052	if [[ -f "${absnamein[$i]}" ]]
	2053	then
	2054	ln ${absnamein[$i]} ${localin[$i]}
	2055	got_tmp[$i]=true
	2056	fi
	2057	else
	2058	if [[ -d "${absnamein[$i]}" ]]
	2059	then
[2396]	2060	mkdir -p ${localin[$i]}
[2380]	2061	cd ${absnamein[$i]}
	2062	for file in $(ls *)
	2063	do
[2566]	2064	ln $file $tempdir/${localin[$i]}
[2380]	2065	done >\|/dev/null 2>&1
[2566]	2066	cd $tempdir
[2380]	2067	fi
	2068
	2069	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2070	if [[ ! -f "${localin[$i]}/_000000" ]]
	2071	then
	2072	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2073	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2074	fi
	2075
	2076	got_tmp[$i]=true
	2077	fi
	2078	fi
	2079
	2080	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2081	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2082	then
	2083
	2084	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2085	then
	2086
	2087	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2088	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2089	printf "\n file will be provided for $cores processors"
[2396]	2090	mkdir -p ${localin[$i]}
[2380]	2091	ival=$cores
	2092	(( ii = 0 ))
	2093	while (( ii <= ival-1 ))
	2094	do
	2095	if (( ii < 10 ))
	2096	then
	2097	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2098	elif (( ii < 100 ))
	2099	then
	2100	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2101	elif (( ii < 1000 ))
	2102	then
	2103	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2104	else
	2105	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2106	fi
	2107	(( ii = ii + 1 ))
	2108	done
	2109
	2110	else
	2111
	2112	if [[ $files_for_cores = true ]]
	2113	then
	2114
	2115	# PROVIDE FILES FOR EACH CORE
	2116	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2117	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2118	printf "\n providing $cores files for the respective cores"
[2396]	2119	mkdir -p ${localin[$i]}
[2380]	2120	if [[ $link_local_input = true ]]
	2121	then
	2122	printf " files will be linked\n"
	2123	cd ${absnamein[$i]}
	2124	for file in $(ls *)
	2125	do
	2126	ln -f $file ${localin[$i]}
	2127	done
[2566]	2128	cd $tempdir
[2380]	2129	fi
	2130
	2131	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2132	if [[ ! -f "${localin[$i]}/_000000" ]]
	2133	then
	2134	if [[ $link_local_input = true ]]
	2135	then
	2136	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2137	fi
	2138	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2139	fi
	2140
	2141	else
	2142
	2143	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2144	if [[ $link_local_input = true ]]
	2145	then
	2146	printf " file will be linked\n"
	2147	ln -f ${absnamein[$i]} ${localin[$i]}
	2148	fi
[2605]	2149	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2150	if [[ ! -f "${localin[$i]}" ]]
	2151	then
	2152	if [[ $link_local_input = true ]]
	2153	then
	2154	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2155	fi
[2669]	2156	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2157	then
	2158	mv ${absnamein[$i]} ${localin[$i]}
	2159	else
	2160	cp ${absnamein[$i]} ${localin[$i]}
	2161	fi
[2380]	2162	fi
	2163	fi
	2164	fi
	2165	fi
	2166
	2167	done
	2168	if (( i != 0 ))
	2169	then
[2669]	2170	if [[ $optional_files_missing = true ]]
	2171	then
	2172	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2173	fi
[2380]	2174	printf "\n$dashes\n *** all INPUT-files provided \n"
	2175	fi
	2176
[3917]	2177	# NOW COPY FILES (.f90, .o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY
	2178	# WORKING DIRECTORY
	2179	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
[2380]	2180
[3917]	2181
[2380]	2182	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2183	(( i = 0 ))
	2184	while (( i < iic ))
	2185	do
	2186	(( i = i + 1 ))
	2187	if (( i == 1 ))
	2188	then
	2189	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2190	fi
	2191	printf "\n >>> ${in_command[$i]}"
	2192	eval ${in_command[$i]}
	2193	if (( i == iic ))
	2194	then
	2195	printf "\n$dashes\n"
	2196	fi
	2197	done
	2198
	2199
[3313]	2200	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2201	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2202	then
	2203	progress_bar_disabled=true
	2204	else
	2205	progress_bar_disabled=false
	2206	fi
	2207
	2208
[2380]	2209	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2210	# (FILE ENVPAR WILL BE READ BY PALM)
	2211	cat > ENVPAR << EOF
[3236]	2212	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2213	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2214	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2215	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2216	maximum_cpu_time_allowed = ${cpumax}.,
	2217	revision = '$global_revision',
[3313]	2218	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2219
	2220	EOF
	2221
	2222
	2223	# STARTING THE EXECUTABLE
	2224	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2225	PATH=$PATH:$tempdir
[2380]	2226
	2227
	2228	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2229	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2230	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2231	eval line=\"$line\"
	2232	execute_command="$line"
	2233
	2234
	2235	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2236	if [[ "$execute_command_for_combine" = "" ]]
	2237	then
	2238	eval line2=\"$line2\"
	2239	execute_command_for_combine="$line2"
	2240	fi
	2241
[2380]	2242
	2243
	2244	# PROVIDE A HOSTFILE, IF REQUIRED
	2245	if [[ "$hostfile" != "" ]]
	2246	then
	2247
	2248	if [[ $hostfile = auto ]]
	2249	then
	2250	# CREATE A NEW HOSTFILE
	2251	(( ii = 1 ))
	2252	while (( ii <= cores / threads_per_task ))
	2253	do
	2254	echo $(hostname) >> hostfile
	2255	(( ii = ii + 1 ))
	2256	done
	2257	if (( cores / threads_per_task == 0 ))
	2258	then
	2259	echo $(hostname) >> hostfile
	2260	fi
	2261
	2262	else
	2263	cp $hostfile hostfile
	2264	fi
	2265	eval line=\"`head -n $ii hostfile`\"
	2266	printf "\n *** running on: $line"
	2267	fi
	2268
	2269
	2270
	2271	# SET THE NUMBER OF OPENMP-THREADS
	2272	if [[ $use_openmp = true ]]
	2273	then
	2274	export OMP_NUM_THREADS=$threads_per_task
	2275	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2276	else
	2277	export OMP_NUM_THREADS=1
	2278	fi
	2279
	2280
[2610]	2281	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2282	if [[ $run_coupled_model = false ]]
	2283	then
	2284	if [[ "$ocean_file_appendix" = true ]]
	2285	then
	2286	echo "precursor_ocean" > coupling_steering
	2287	else
	2288	echo "precursor_atmos" > coupling_steering
	2289	fi
	2290	else
	2291	(( iia = $cores_atmos / $threads_per_task ))
	2292	(( iio = $cores_ocean / $threads_per_task ))
	2293	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2294	printf "\n\n"
	2295	echo "coupled_run $iia $iio" > coupling_steering
	2296	fi
	2297
	2298	printf "\n *** execute command:"
	2299	printf "\n \"$execute_command\" \n\n"
	2300
	2301
[3393]	2302	if [[ $progress_bar_disabled = true ]]
[2380]	2303	then
[3402]	2304	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2305	exit_code=${PIPESTATUS[0]}
	2306	else
	2307	$execute_command < coupling_steering &> >(tee STDOUT)
	2308	exit_code=${PIPESTATUS[0]}
	2309	fi
[2380]	2310
[3393]	2311	if [[ ${exit_code} != 0 ]]
	2312	then
	2313
[2380]	2314	# ABORT IN CASE OF RUNTIME ERRORS
	2315	printf "\n +++ runtime error occured"
	2316	locat=execution
	2317	exit
	2318
	2319	else
	2320
	2321	printf "\n$dashes\n *** execution finished \n"
	2322
	2323	fi
	2324
	2325
	2326	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2327	# BY EACH CORE INTO ONE FILE
	2328	if [[ ! -f combine_plot_fields.x ]]
	2329	then
	2330
	2331	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2332	printf "\n 2d- and/or 3d-data may be incomplete!"
	2333	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2334
	2335	elif [[ "$combine_plot_fields" == true ]]
	2336	then
	2337
	2338	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2339	$execute_command_for_combine
	2340
	2341	else
	2342
	2343	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2344	# DATA OUTPUT
[2380]	2345	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2346	fi
	2347
	2348
	2349
	2350	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2351	(( i = 0 ))
	2352	while (( i < ioc ))
	2353	do
	2354	(( i = i + 1 ))
	2355	if (( i == 1 ))
	2356	then
	2357	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2358	fi
[2799]	2359
	2360	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2361	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2362
[2380]	2363	printf "\n >>> ${out_command[$i]}"
	2364	eval ${out_command[$i]}
	2365	if (( i == ioc ))
	2366	then
	2367	printf "\n$dashes\n"
	2368	fi
	2369	done
	2370
	2371
[2610]	2372	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2373	# WILDCARDS
[2380]	2374	(( i = 0 ))
[2610]	2375	(( nr_of_output_files = 0 ))
	2376
[2380]	2377	while (( i < iout ))
	2378	do
[2610]	2379
[2380]	2380	(( i = i + 1 ))
[2610]	2381
	2382	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2383	# CREATE A LIST FOR THE DETECTED ENDINGS
	2384	if [[ "${multout[$i]}" = true ]]
	2385	then
	2386	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2387	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2388	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2389
	2390	endings="DEFAULT"
	2391	while read line
	2392	do
	2393	# remove the local name from the beginning
	2394	localnamestring="${localout_pre[$i]}"
	2395	length_localname=${#localnamestring}
	2396	ending=${line:${length_localname}}
	2397
	2398	if [[ "$ending" != "" ]]
	2399	then
	2400	endings="$endings $ending"
	2401	fi
	2402
	2403	done <filelist
	2404
	2405	rm filelist
	2406
	2407	else
	2408
	2409	# SINGLE NAME
	2410	endings=DEFAULT
	2411
	2412	fi
	2413
	2414	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2415	for ending in $endings
	2416	do
	2417
	2418	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2419	if [[ $ending = DEFAULT ]]
	2420	then
	2421	ending=""
	2422	fi
	2423
	2424	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2425	(( nr_of_output_files = nr_of_output_files + 1 ))
	2426	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2427	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2428	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2429	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2430	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2431	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2432	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2433
	2434	done
	2435
	2436	done
	2437
	2438
	2439
	2440
	2441	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2442	(( i = 0 ))
	2443	while (( i < nr_of_output_files ))
	2444	do
	2445	(( i = i + 1 ))
[2380]	2446	if (( i == 1 ))
	2447	then
[3860]	2448	timestring=`date +%H:%M:%S`
	2449	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
[2380]	2450
	2451	# GET RUN NUMBER ASSIGNED BY PALM
	2452	if [[ -f RUN_NUMBER ]]
	2453	then
	2454	read run_number < RUN_NUMBER
	2455	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2456	usecycle_option="-U $run_number"
	2457	else
	2458	run_number=0
	2459	usecycle_option=""
	2460	fi
	2461	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2462	then
[2404]	2463	printf "\n *** in case of SCP transfers to local host"
	2464	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2465	fi
	2466	printf "\n$dashes"
	2467	fi
	2468
	2469	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2470	then
	2471
[3236]	2472	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2473
	2474	# DETERMINE THE CYCLE NUMBER
	2475	ls -1 -d $filename > filelist 2>/dev/null
	2476	ls -1 -d $filename.* >> filelist 2>/dev/null
	2477	while read line
	2478	do
	2479
	2480	# filename without path (i.e. after the last "/")
	2481	basefilename=$(basename ${line})
	2482
	2483	# check if there is an extension
	2484	extension=${basefilename##*.}
	2485	if [[ "$extension" = "${extout[$i]}" ]]
	2486	then
	2487	basefilename=${basefilename%.*}
	2488	fi
	2489
	2490	# check for an existing cycle number
	2491	cycle=${basefilename##*.}
	2492	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2493	then
[2669]	2494	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2495	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2496	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2497	else
	2498	(( icycle = 1 ))
	2499	fi
	2500
	2501	if (( icycle > maxcycle ))
	2502	then
	2503	(( maxcycle = icycle ))
	2504	fi
	2505
	2506	done <filelist
	2507	rm filelist
	2508
	2509
	2510	# SET THE CYCLE NUMBER
	2511	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2512	if [[ "${actionout[$i]}" = a ]]
	2513	then
	2514	(( maxcycle = maxcycle - 1 ))
	2515	fi
	2516
	2517	(( cycnum[$i] = maxcycle ))
	2518	pathout[$i]=$filename
	2519
	2520
	2521	# ADD CYCLE NUMBER TO FILENAME
	2522	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2523	if [[ "${actionout[$i]}" != "a" ]]
	2524	then
	2525	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2526	# WITH AN EXISTING CYCLE NUMBER
	2527	if (( run_number >= cycnum[$i] ))
	2528	then
	2529	(( cycnum[$i] = run_number ))
	2530	else
	2531	if (( run_number > 0 ))
	2532	then
	2533	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2534	fi
	2535	fi
	2536	fi
	2537	if (( cycnum[$i] > 0 ))
	2538	then
[2600]	2539	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2540	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2541	fi
	2542	fi
	2543
	2544	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2545	files_for_cores=false; filetype=file
	2546	link_local_output=false
	2547	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2548	then
	2549	files_for_cores=true; filetype=directory
	2550	actionout[$i]=""
	2551	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2552	then
	2553	actionout[$i]=""
	2554	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2555	then
	2556	files_for_cores=true; filetype=directory
	2557	link_local_output=true
	2558	actionout[$i]=""
	2559	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2560	then
	2561	link_local_output
	2562	actionout[$i]=""
	2563	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2564	then
	2565	files_for_cores=true; filetype=directory
	2566	actionout[$i]="tr"
	2567	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2568	then
	2569	actionout[$i]="tr"
	2570	fi
	2571
	2572	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2573	then
[2669]	2574	if [[ ${warnout[$i]} = true ]]
	2575	then
	2576	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2577	fi
[2380]	2578	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2579	then
[2669]	2580	if [[ ${warnout[$i]} = true ]]
	2581	then
	2582	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2583	fi
[2380]	2584	else
	2585
	2586
	2587	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2588	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2589	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2590	then
	2591	if [[ $running_on_remote = true ]]
	2592	then
	2593
	2594	# SET OPTIONS FOR TRANSFER
	2595	if [[ "${actionout[$i]}" = tr ]]
	2596	then
	2597	if [[ $files_for_cores = false ]]
	2598	then
	2599	catalog_option=""
	2600	catalog_string=""
	2601	else
	2602	catalog_option="-c"
	2603	catalog_string="/"
	2604	fi
	2605	append_option=""
	2606	append_string=""
	2607	else
	2608	append_option="-A"
	2609	append_string="append"
	2610	fi
	2611
	2612	transfer_failed=false
	2613	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2614	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2615
	2616	# TRANSFER VIA SCP
	2617	if [[ "$remote_loginnode" != "" ]]
	2618	then
[3534]	2619	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]	2620	else
[3236]	2621	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]	2622	fi
[3312]	2623	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2624
	2625
	2626	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2627	if [[ $transfer_failed = true ]]
	2628	then
	2629	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2630	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2631
	2632	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2633	eval local_catalog=${pathout[$i]}
	2634	if [[ ! -d $local_catalog ]]
	2635	then
	2636	printf " *** local directory does not exist. Trying to create:\n"
	2637	printf " $local_catalog \n"
	2638	mkdir -p $local_catalog
	2639	fi
[3236]	2640	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2641	transfer_problems=true
	2642	fi
	2643
	2644	else
	2645
	2646	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2647	# BE COPIED OR APPENDED ON THIS MACHINE
	2648	if [[ "${actionout[$i]}" = tr ]]
	2649	then
	2650	actionout[$i]=""
	2651	else
	2652	actionout[$i]="a"
	2653	fi
	2654	fi
	2655	fi
	2656
	2657
	2658	# APPEND ON THIS MACHINE
	2659	if [[ "${actionout[$i]}" = "a" ]]
	2660	then
	2661	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2662	then
	2663	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2664	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2665	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2666	else
	2667	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2668	printf "\n ${pathout[$i]}\n"
	2669	cat ${localout[$i]} >> ${pathout[$i]}
	2670	fi
	2671	fi
	2672
	2673	# COPY ON THIS MACHINE
	2674	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2675	# ON DIFFERENT FILE-SYSTEMS
	2676	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2677	then
	2678
	2679	# COPY IN CASE OF RUNS ON SINGLE CORES
	2680	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2681	then
	2682	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2683	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2684	if [[ $link_local_output = true ]]
	2685	then
	2686	printf " file will be linked\n"
	2687	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2688	fi
	2689	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2690	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2691	then
	2692	if [[ $link_local_output = true ]]
	2693	then
	2694	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2695	fi
	2696	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2697	else
	2698	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2699	fi
	2700	else
	2701	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2702	printf "\n ${pathout[$i]}\n"
	2703	if [[ $link_local_output = true ]]
	2704	then
	2705	printf " file will be linked\n"
	2706	ln -f ${localout[$i]} ${pathout[$i]}
	2707	fi
	2708	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2709	if [[ ! -f "${pathout[$i]}" ]]
	2710	then
	2711	if [[ $link_local_output = true ]]
	2712	then
	2713	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2714	fi
	2715	cp ${localout[$i]} ${pathout[$i]}
	2716	else
	2717	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2718	fi
	2719	fi
	2720
	2721	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2722	then
	2723
	2724	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2725	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2726	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2727	printf "\n ${pathout[$i]}\n"
	2728	if [[ $link_local_output = true ]]
	2729	then
	2730	printf " files will be linked\n"
[2396]	2731	mkdir -p ${pathout[$i]}
[2380]	2732	cd ${localout[$i]}
	2733	for file in $(ls *)
	2734	do
	2735	ln -f $file ${pathout[$i]}
	2736	done >\|/dev/null 2>&1
[2566]	2737	cd $tempdir
[2380]	2738	fi
	2739
	2740	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2741	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2742	then
	2743	if [[ $link_local_output = true ]]
	2744	then
	2745	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2746	fi
[3025]	2747	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2748	cp -r ${localout[$i]}/* ${pathout[$i]}
	2749	fi
	2750
	2751	fi
	2752	fi
	2753	done
	2754
	2755	if (( i != 0 ))
	2756	then
[3860]	2757	timestring=`date +%H:%M:%S`
[2380]	2758	if [[ $transfer_problems = true ]]
	2759	then
[3860]	2760	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
[2380]	2761	printf "\n +++ WARNING: some data transfers failed! \n"
	2762	else
[3860]	2763	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
[2380]	2764	fi
	2765	fi
	2766
	2767
	2768	# IF REQUIRED, START A RESTART-JOB
	2769	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2770	if [[ -f CONTINUE_RUN ]]
	2771	then
	2772
	2773	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2774	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2775	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2776	# -b START A BATCH JOB
	2777	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2778	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2779	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2780
[2957]	2781	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2782	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2783	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2784	then
	2785	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2786	fi
[2380]	2787
	2788	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2789	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2790	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2791	then
[2381]	2792	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2793	fi
	2794
	2795
	2796	# START THE RESTART-JOB
	2797	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2798	echo " $prc"
	2799	printf "\n$dashes\n"
	2800	if [[ $running_on_remote = true ]]
	2801	then
	2802
	2803	echo "*** ssh will be used to initiate restart-runs!"
	2804	echo " return_address=\"$return_address\" "
	2805	echo " return_username=\"$local_username\" "
	2806
	2807	if [[ "$remote_loginnode" != "" ]]
	2808	then
[3534]	2809	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]	2810	else
[3534]	2811	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2812	fi
	2813
	2814	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2815	sleep 30
	2816
	2817	else
	2818
	2819	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2820	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2821
	2822	fi
	2823
[3132]	2824	# CHECK, IF RESTART JOB HAS BEEN STARTED
[3725]	2825	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
[3132]	2826	then
	2827	printf "\n$dashes\n +++ creating restart run failed \n"
	2828	locat=create_restart
[3455]	2829	rm palmrun_restart.log
[3132]	2830	exit
[3725]	2831	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
	2832	then
	2833	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
	2834	locat=create_restart
	2835	rm palmrun_restart.log
	2836	exit
[3132]	2837	else
	2838	printf "\n$dashes\n *** restart run initiated \n"
	2839	rm palmrun_restart.log
	2840	fi
[2380]	2841
[3132]	2842
[2380]	2843	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2844	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2845	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2846	# MAY BE VERY HUGE)
	2847	(( i = 0 ))
[2610]	2848	while (( i < nr_of_input_files ))
[2380]	2849	do
	2850	(( i = i + 1 ))
	2851	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2852	then
	2853	rm -r ${absnamein[$i]}
	2854	fi
	2855	done
	2856
	2857	fi
	2858
	2859
	2860	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2861	cd $HOME
[2566]	2862	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2863
	2864
	2865	else
	2866
	2867
	2868	# PREPARING ACTIONS,
	2869	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2870
	2871	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2872	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2873	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2874	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2875	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2876	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2877	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2878	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2879	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2880	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2881	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2882	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2883	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2884	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2885	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2886	if [[ $create_remote_batch_job = true ]]
	2887	then
	2888	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2889	if [[ $do_trace = true ]]
	2890	then
	2891	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2892	fi
[2380]	2893	elif [[ $create_batch_job = true ]]
	2894	then
	2895	palmrun_com=${palmrun_com}" -j"
[2420]	2896	if [[ $do_trace = true ]]
	2897	then
	2898	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2899	fi
[2380]	2900	fi
	2901
	2902
	2903	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2904	# REMOTE HOST
[3236]	2905	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2906	job_protocol_file=$job_protocol_file_local
	2907	if [[ $create_remote_batch_job = true ]]
	2908	then
[3236]	2909	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2910	job_protocol_file=$job_protocol_file_remote
	2911	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2912	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2913	fi
	2914
	2915
	2916	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2917	jobfile=jobfile.$run_id_number
[2380]	2918
	2919
	2920	# FIRST CREATE THE BATCH DIRECTIVES
	2921	(( i = 0 ))
	2922	while (( i < ibd ))
	2923	do
	2924	(( i = i + 1 ))
[2693]	2925	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2926	eval line=\"$line\"
	2927	echo "$line" >> $jobfile
	2928	done
	2929	echo " " >> $jobfile
	2930
	2931
	2932	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2933	# PROTOCOL
	2934	if [[ $create_remote_batch_job = true ]]
	2935	then
[3236]	2936	echo "set +vx" >> $jobfile
	2937	echo "trap '" >> $jobfile
	2938	echo "set +vx" >> $jobfile
	2939	echo "cd ${remote_jobcatalog}" >> $jobfile
	2940	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2941
	2942	# ADD THE BATCH DIRECTIVES
	2943	(( i = 0 ))
	2944	while (( i < ibdt ))
	2945	do
	2946	(( i = i + 1 ))
[2693]	2947	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2948	eval line=\"$line\"
	2949	echo "$line" >> $jobfile
	2950	done
	2951	echo " " >> $jobfile
	2952
	2953	echo "set -x" >> $jobfile
[3534]	2954	if [[ "$remote_loginnode" != "" ]]
	2955	then
	2956	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}\" " >> $jobfile
	2957	else
	2958	echo "${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
	2959	fi
[2380]	2960	echo "%%END%%" >> $jobfile
	2961	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2962	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2963	echo "rm $scpjob_file" >> $jobfile
[2404]	2964	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2965	echo "set -x" >> $jobfile
	2966	echo " ' exit" >> $jobfile
	2967	fi
	2968
	2969
	2970	# ACTIVATE ERROR-TRACEBACK
	2971	if [[ $do_trace = true ]]
	2972	then
	2973	echo "set -x" >> $jobfile
	2974	else
	2975	echo "set +vx" >> $jobfile
	2976	fi
	2977
	2978
	2979	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2980	if [[ "$login_init_cmd" != "" ]]
	2981	then
	2982	echo "$login_init_cmd" >> $jobfile
	2983	fi
	2984	if [[ "$module_commands" != "" ]]
	2985	then
	2986	echo "$module_commands" >> $jobfile
	2987	fi
	2988
	2989
	2990	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2991	if [[ $create_remote_batch_job = true ]]
	2992	then
	2993	echo "mkdir $tempdir" >> $jobfile
	2994	echo "chmod go+rx $tempdir" >> $jobfile
	2995	else
	2996	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2997	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2998	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2999	mkdir $tempdir
	3000	chmod go+rx $tempdir
	3001	fi
	3002	echo "cd $tempdir" >> $jobfile
	3003	echo "export tempdir=$tempdir" >> $jobfile
[3917]	3004	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile
	3005	echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile
[2380]	3006	echo "export execute_palmrun=true" >> $jobfile
	3007
	3008
	3009	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3010	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	3011	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	3012	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3013	echo "export LOCAL_PWD" >> $jobfile
	3014
	3015
	3016	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	3017	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	3018	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	3019
	3020
	3021	# CALL PALMRUN WITHIN THE JOB
	3022	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	3023	echo "set -x" >> $jobfile
	3024	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3025
	3026
	3027	# TRANSFER JOBFILE TO THE TARGET HOST
	3028	if [[ $create_jobfile_only = false ]]
	3029	then
	3030
[3505]	3031	# CREATE LOCAL JOB FOLDER
	3032	eval local_jobcatalog=$local_jobcatalog
	3033	if [[ ! -d $local_jobcatalog ]]
	3034	then
	3035	echo " "
	3036	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3037	mkdir $local_jobcatalog
	3038	fi
	3039
[2380]	3040	if [[ $create_remote_batch_job = true ]]
	3041	then
	3042
[2420]	3043	echo " "
[2566]	3044	echo " *** transfer of job to remote host via scp"
[3505]	3045
	3046	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3047	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3048
	3049	# COPY THE JOB FILE
[2420]	3050	if [[ $do_trace = true ]]
	3051	then
[3236]	3052	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3053	fi
[3236]	3054	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3055
[3505]	3056	# SUBMIT THE JOB
[3574]	3057	printf " *** submit the job (output of submit command, \n"
[3573]	3058	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3059	if [[ $do_trace = true ]]
	3060	then
[3665]	3061	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]	3062	fi
[3665]	3063	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]	3064
	3065	elif [[ $create_batch_job = true ]]
	3066	then
	3067
[2385]	3068	eval local_jobcatalog=$local_jobcatalog
[3236]	3069	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3070	cd $local_jobcatalog
[2380]	3071	echo " "
[2420]	3072	echo " *** submit the job"
	3073	if [[ $do_trace = true ]]
	3074	then
[3236]	3075	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3076	fi
[3236]	3077	$submit_command ${configuration_identifier}_${run_id}
	3078	rm ${configuration_identifier}_${run_id}
[2380]	3079	cd - > /dev/null
	3080
	3081	fi
	3082
	3083	rm -rf $jobfile
	3084
	3085	else
	3086
	3087	printf "\n *** jobfile created under name \"$jobfile\" "
	3088	printf "\n no batch-job has been sent!"
	3089
	3090	fi
	3091
	3092	fi # END OF REMOTE-PART

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