Home

Context Navigation

source: palm/trunk/SCRIPTS/palmrun @ 3658

Last change on this file since 3658 was 3574, checked in by raasch, 6 years ago
syntax-error in last commit fixed
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.8 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[3032]	28	# $Id: palmrun 3574 2018-11-28 13:14:39Z knoop $
[3574]	29	# syntax-error in last commit fixed
	30	#
	31	# 3573 2018-11-28 13:03:44Z raasch
[3573]	32	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	33	# removed,
	34	# r3570 reverted
	35	#
	36	# 3570 2018-11-27 17:44:21Z kanani
[3570]	37	# Rename job-id by run_id
	38	#
	39	# 3555 2018-11-22 13:50:37Z raasch
[3555]	40	# sed-command to remove repeated space-characters replaced by tr-command, to
	41	# guarantee mac compatible
	42	#
	43	# 3549 2018-11-21 15:44:44Z raasch
[3549]	44	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	45	# of login messages on specific systems
	46	#
	47	# 3534 2018-11-19 15:35:16Z raasch
[3534]	48	# batch_scp for sending back the job protocol file is called via login-node if
	49	# a login-node has been set in the config-file
	50	# ssh-calls rearranged to avoid output of system/user-profile messages
	51	#
	52	# 3505 2018-11-08 09:14:30Z raasch
[3505]	53	# job folders are created in case that they do not exist
	54	#
	55	# 3455 2018-10-30 14:12:31Z raasch
[3455]	56	# options -h and -d renamed -c and -r, respectively
	57	#
	58	# 3402 2018-10-23 11:49:24Z knoop
[3346]	59	# job_id is set for compatibility reasons with older versions of config files
	60	#
	61	# 3313 2018-10-06 15:22:48Z knoop
[3294]	62	# more detailed error message for outdated fileconnection file
	63	#
	64	# 3236 2018-09-10 09:07:06Z raasch
[3236]	65	# warning issued in case of file connection file version mismatch,
	66	# host_configuration renamed configuration_identifier,
	67	# "host identifier" in header output renamed "config. identifier",
	68	# jobname renamed run_identifier,
	69	# run_id renamed run_id_number
	70	# job_id renamed run_id
	71	# option -r renamed -i
	72	#
	73	# 3151 2018-07-19 08:45:38Z raasch
[3151]	74	# removed additional listing of files to be compiled, print PALM code revision
	75	# in header
	76	#
	77	# 3132 2018-07-16 11:44:58Z raasch
[3132]	78	# create consistent error messages in case of failed restarts,
	79	# check existence of remote job catalog
	80	#
	81	# 3043 2018-05-25 10:47:54Z raasch
[3043]	82	# check for setting of fast_io_catalog
	83	#
	84	# 3033 2018-05-23 15:26:19Z raasch
[3025]	85	# -T option not required for interactive runs (tasks per node =
	86	# total number of cores is assumed as default, if option is not given),
	87	# reformatting of a few messages,
	88	# bugfix: destination output directory is created if attribute "pe" is set in
	89	# .palm.iofiles
	90	#
	91	# 2718 2018-01-02 08:49:38Z maronga
[2993]	92	# bugfix of r2990
	93	#
	94	# 2718 2018-01-02 08:49:38Z maronga
[2990]	95	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	96	# not in the working directory from where palmrun is called
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2957]	99	# svfout in the activation string will be replaced now by svfin in case of
	100	# automatic restarts
	101	#
	102	# 2718 2018-01-02 08:49:38Z maronga
[2906]	103	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	104	# the possible output or input of sky view factors
	105	#
	106	# 2718 2018-01-02 08:49:38Z maronga
[2834]	107	# "fname" renamed to "jobname"
	108	#
	109	# 2718 2018-01-02 08:49:38Z maronga
[2799]	110	# parameters are allowed in output commands (OC:)
	111	#
	112	# 2718 2018-01-02 08:49:38Z maronga
[2789]	113	# bugfix: exit if no queue has been given neither with option -q nor in the
	114	# configuration file
	115	#
	116	# 2718 2018-01-02 08:49:38Z maronga
[2762]	117	# file connection file from trunk/SCRIPTS is taken by default
	118	#
	119	# 2718 2018-01-02 08:49:38Z maronga
[2716]	120	# Corrected "Former revisions" section
	121	#
	122	# 2696 2017-12-14 17:12:51Z kanani
	123	# Change in file header (GPL part)
	124	#
	125	# 2693 2017-12-13 12:33:49Z raasch
[2693]	126	# replacement of variables given by {{<variable>}} in configuration file is now
	127	# done in a more general way, variable names are written in small letters
	128	#
	129	# 2670 2017-12-06 16:32:19Z raasch
[2670]	130	# test printouts removed
	131	#
	132	# 2669 2017-12-06 16:03:27Z raasch
[2669]	133	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	134	# removed,
	135	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	136	# files,
	137	# informative messages in case of missing optional input files shortened
	138	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	139	#
	140	# 2638 2017-11-23 12:44:23Z raasch
[2610]	141	# use of wildcards in file connection statements enabled
	142	#
	143	# 2605 2017-11-09 15:31:46Z raasch
[2605]	144	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	145	# will not be sent with the job file any more, but copied into the
[2610]	146	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	147	#
	148	# 2600 2017-11-01 14:11:20Z raasch
[2600]	149	# cycle numbers are made three digits wide
	150	#
	151	# 2566 2017-10-20 08:50:47Z raasch
[2566]	152	# execute command for combine_plot_fields added
	153	# "TEMPDIR" renamed "tempdir"
	154	# temporary working directory for local batch jobs is created immediately within
	155	# the user's palmrun call, due to a requirement of the "grid engine" batch
	156	# system, where the working directory is given with batch directive -wd and must
	157	# already exist when the job is submitted,
	158	# informative messages in non-trace mode reduced and partly reformatted
	159	#
	160	# 2551 2017-10-18 07:25:11Z raasch
[2551]	161	# TEMPDIR added as replacement string to be used in batch directives
	162	#
	163	# 2512 2017-10-04 08:26:59Z raasch
[2507]	164	# bugfix for determining cycle numbers of NetCDF input files
	165	#
	166	# 2506 2017-09-29 08:30:37Z raasch
[2506]	167	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	168	# host configuration added to SOURCES_FOR_RUN_... folder name
	169	# host_identifier renamed host_configuration
	170	# option -W added to allow for job dependencies
	171	#
	172	# 2501 2017-09-26 11:41:55Z raasch
[2501]	173	# default value for number of cores (option -X) set to 1
	174	# bugfix for mechanism which overwrites configuration file settings with values
	175	# provided by palmrun options
	176	#
	177	# 2499 2017-09-22 16:47:58Z kanani
[2499]	178	# option -h named configuration identifier
	179	#
	180	# 2480 2017-09-19 06:24:14Z maronga
[2480]	181	# bugfix for last revision
	182	#
	183	# 2479 2017-09-19 06:12:16Z raasch
[2479]	184	# option -A (project account number) added
	185	#
	186	# 2422 2017-09-08 08:25:41Z raasch
[2410]	187	# initial revision
[2380]	188	#
	189	#--------------------------------------------------------------------------------#
	190	# palmrun - script for running PALM jobs on local and remote hosts
	191	#--------------------------------------------------------------------------------#
	192
	193
	194
	195	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	196
	197	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	198	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	199	# (TOO MANY ARGUMENTS - PROBLEM)
	200	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	201
[2610]	202	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	203	typeset -i nr_of_output_files=0
[2380]	204	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	205	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	206	# SCRIPT-OPTION ARGUMENTS
	207	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	208	typeset -i icycle inode ival maxcycle mpi_tasks
	209	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	210
	211	activation_string_list=""
	212	AddFilenames=""
	213	combine_plot_fields=true
	214	compiler_name=""
	215	compiler_name_ser=""
	216	compiler_options=""
[3236]	217	configuration_identifier="default"
[2501]	218	cores=1
[2380]	219	cores_atmos=0
	220	cores_ocean=0
	221	coupled_dist=""
	222	cpp_options=""
	223	cpumax=0
[2506]	224	create_batch_job=false
[2380]	225	create_jobfile_only=false
	226	create_remote_batch_job=false
	227	dashes=" ----------------------------------------------------------------------------"
	228	defaultqueue=""
[2506]	229	delete_temporary_catalog=true
[2380]	230	do_compile=true
	231	do_trace=false
	232	executable=""
	233	execute_command=""
	234	execution_error=false
[2762]	235	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	236	global_revision=""
	237	hostfile=""
	238	hp=""
	239	keep_data_from_previous_run=false
	240	link_local_input=false
	241	link_local_output=false
[2388]	242	linker_options=""
[2385]	243	local_jobcatalog=""
[2380]	244	locat=normal
	245	makefile=""
	246	max_par_io_str=""
	247	prc=$0
	248	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	249	do
	250	prc=`echo $prc \| cut -f2- -d"/"`
	251	done
	252	module_calls=""
[2506]	253	palmrun_memory=""
[2380]	254	palmrun_script_name=$prc
	255	openmp=false
[2506]	256	previous_job=""
[2479]	257	project_account=""
[2380]	258	queue=none
[2906]	259	read_svf=""
[2380]	260	restart_run=false
	261	return_address=""
[2385]	262	remote_jobcatalog=""
[2380]	263	remote_username=""
	264	running_in_batch_mode=false
[3313]	265	running_in_test_mode=false
[2380]	266	run_coupled_model=false
	267	run_id=""
[3236]	268	run_id_number=""
	269	run_identifier=test
[2380]	270	silent=false
	271	source_list=""
	272	source_path=""
[2501]	273	tasks_per_node=0
[2380]	274	threads_per_task=1
	275	transfer_problems=false
[2384]	276	user_source_path=""
[2506]	277	use_existing_sources_folder=""
[2380]	278	use_openmp=false
[3033]	279	version="palmrun 1.0 Rev$Rev: 3574 $"
[2380]	280	working_directory=`pwd`
	281	write_binary=""
[2906]	282	write_svf=""
[2380]	283
	284
	285	# ERROR HANDLING IN CASE OF EXIT
[2404]	286	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	287	then
	288
	289	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	290	(( i = 0 ))
	291	while (( i < iec ))
	292	do
	293	(( i = i + 1 ))
	294	printf "\n *** Execution of ERROR-command:\n"
	295	printf " >>> ${err_command[$i]}\n"
	296	eval ${err_command[$i]}
	297	done
[2566]	298	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	299	printf "\n\n+++ palmrun crashed \n\n"
	300	exit 1
	301	elif [[ $locat != normal ]]
[2380]	302	then
[3312]	303	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	304	printf "\n+++ palmrun killed by \"^C\" \n\n"
	305	exit 2
	306	else
[2566]	307	printf "\n --> palmrun finished\n\n"
[3312]	308	exit 0
[2380]	309	fi' exit
	310
	311
	312	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	313	trap 'locat=control_c
	314	exit 1
[2380]	315	' 2
	316
	317
	318	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	319	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	320	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]	321	do
	322	case $option in
	323	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	324	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	325	(b) create_batch_job=true; prc="$prc -b";;
	326	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	327	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	328	(C) restart_run=true; prc="$prc -C";;
	329	(F) create_jobfile_only=true;;
	330	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	331	(i) run_id_number=$OPTARG;;
[2380]	332	(j) running_in_batch_mode=true;;
	333	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	334	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	335	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	336	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	337	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	338	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	339	(R) return_address=$OPTARG;;
	340	(s) source_list=$OPTARG;;
[2501]	341	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	342	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	343	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	344	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	345	(v) silent=true; prc="$prc -v";;
[2506]	346	(V) use_existing_sources_folder="-V";;
[2380]	347	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	348	(W) previous_job=$OPTARG;;
[2380]	349	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	350	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	351	(y) ocean_file_appendix=true; prc="$prc -y";;
	352	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	353	(z) running_in_test_mode=true;;
[2380]	354	(Z) combine_plot_fields=false; prc="$prc -Z";;
	355	(\?) printf "\n +++ unknown option $OPTARG \n"
	356	printf "\n --> type \"$0 ?\" for available options \n"
	357	locat=parameter;exit;;
	358	esac
	359	done
	360
	361
	362	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	363	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	364	(( to_shift = $OPTIND - 1 ))
	365	shift $to_shift
	366
	367	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	368	if [[ "$1" = "?" ]]
	369	then
	370	(printf "\n *** Description of available palmrun options:\n"
	371	printf "\n Option Description Default-Value"
	372	printf "\n -a activation string list \"\" "
[2479]	373	printf "\n -A project account number ---"
[2380]	374	printf "\n -b batch-job on local machine ---"
	375	printf "\n -B do not delete temporary directory at end ---"
[3455]	376	printf "\n -c configuration identifier \"default\" "
[2380]	377	printf "\n -F create batch job file only ---"
	378	printf "\n -k keep data from previous run"
	379	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	380	printf "\n -M Makefile name Makefile"
	381	printf "\n -O threads per openMP task ---"
	382	printf "\n -q queue \"$queue\" "
[3455]	383	printf "\n -r run identifier test"
[2380]	384	printf "\n -s filenames of routines to be compiled \"\" "
	385	printf "\n must end with .f, .f90, .F, or .c !"
	386	printf "\n use \"..\" for more than one file and wildcards"
	387	printf "\n -s LM compiles all locally modified files"
	388	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	389	printf "\n -T tasks per node ---"
[2380]	390	printf "\n -u username on remote machine \"\" "
	391	printf "\n -v no prompt for confirmation ---"
[2506]	392	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	393	printf "\n -w maximum parallel io streams as given by -X"
[2506]	394	printf "\n -W name of job to wait for ---"
[2380]	395	printf "\n -x tracing of palmrun for debug purposes ---"
	396	printf "\n -X # of processors (on parallel machines) 1"
	397	printf "\n -y add appendix \"_O\" to all local output"
	398	printf "\n files (ocean precursor runs followed by"
	399	printf "\n coupled atmosphere-ocean runs) ---"
	400	printf "\n -Y run coupled model, \"#1 #2\" with"
	401	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	402	printf "\n -Z skip combine_plot_fields at the end of "
	403	printf "\n the simulation ---"
	404	printf "\n "
	405	printf "\n Possible values of positional parameter <modus>:"
	406	printf "\n \"?\" - this outline \n\n") \| more
	407	exit
	408	elif [[ "$1" != "" ]]
	409	then
	410	printf "\n +++ positional parameter $1 unknown \n"
	411	locat=parameter; exit
	412	fi
	413
	414
	415
	416	# SHORT STARTING MESSAGE
	417	printf "\n*** $version "
	418	printf "\n will be executed. Please wait ..."
	419
	420
[2506]	421	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	422	config_file=.palm.config.$configuration_identifier
	423	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	424
	425
	426	# CHECK, IF CONFIGURATION FILE EXISTS
	427	if [[ ! -f $config_file ]]
	428	then
	429	printf "\n\n +++ configuration file: "
	430	printf "\n $config_file"
	431	printf "\n does not exist"
	432	locat=connect; exit
	433	fi
	434
	435
[2762]	436	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	437	if [[ -f .palm.iofiles ]]
	438	then
[3236]	439
	440	# CHECK VERSION MISMATCH
[3573]	441	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	442	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	443	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	444	then
	445	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	446	then
	447	printf "\n\n +++ WARNING: A file connection file has been found in your"
	448	printf "\n working directory, but its revision does not match"
	449	printf "\n the revision of the default (trunk) version."
[3294]	450	printf "\n You may need to update your connection file"
	451	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	452	fi
	453	fi
	454
[2762]	455	fileconnection_file=.palm.iofiles
[3236]	456
[2762]	457	fi
	458
	459
[2380]	460	# CHECK, IF FILE CONNECTION FILE EXISTS
	461	if [[ ! -f $fileconnection_file ]]
	462	then
	463	printf "\n\n +++ file connection file: "
	464	printf "\n $fileconnection_file"
	465	printf "\n does not exist"
	466	locat=connect; exit
	467	fi
	468
	469
[2404]	470	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	471	if [[ "$activation_string_list" = "" ]]
	472	then
	473	printf "\n\n +++ no activation string list given: "
	474	printf "\n please set palmrun option \"-a\" "
	475	locat=palmrun_option; exit
	476	fi
	477
	478
	479	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	480	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	481	then
	482	write_binary=true
	483	else
	484	write_binary=false
	485	fi
	486
[2906]	487	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	488	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	489	then
	490	write_svf=true
	491	else
	492	write_svf=false
	493	fi
[2404]	494
[2906]	495	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	496	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	497	then
	498	read_svf=true
	499	else
	500	read_svf=false
	501	fi
	502
	503
[2380]	504	# READ AND EVALUATE THE CONFIGURATION-FILE
	505	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	506
	507	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	508	while read line
	509	do
	510
	511	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	512	eval line=\"$line\"
	513
	514
	515	# INTERPRET THE LINE
	516	if [[ "$(echo $line)" = "" ]]
	517	then
	518
	519	# EMPTY LINE, NO ACTION
	520	continue
	521
	522	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	523	then
	524
	525	# LINE IS A COMMENT LINE
	526	continue
	527
	528	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	529	then
	530
	531	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	532	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	533	value=`echo $line \| cut -d" " -s -f2-`
	534
	535
	536	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	537	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	538	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	539	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	540	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	541	# CONFIGURATION-FILE.
	542	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	543	then
	544	eval export $var="\$value"
	545
	546	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	547	if [[ $do_trace = true ]]
	548	then
	549	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	550	fi
	551	fi
	552
	553	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	554	then
	555
	556	# LINE DEFINES BATCH-DIRECTIVE
	557	(( ibd = ibd + 1 ))
	558	line=$(echo $line \| cut -c4-)
	559	batch_directive[$ibd]="$line"
	560
	561	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	562	then
	563
	564	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	565	# REMOTE TO A LOCAL HOST
	566	(( ibdt = ibdt + 1 ))
	567	line=$(echo $line \| cut -c5-)
	568	batch_directive_transfer[$ibdt]="$line"
	569
	570	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	571	then
	572
	573	# LINE DEFINES ERROR-COMMAND
	574	(( iec = iec + 1 ))
	575	line=$(echo $line \| cut -c4-)
	576	err_command[$iec]="$line"
	577
	578	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	579	then
	580
	581	# LINE DEFINES INPUT-COMMAND
	582	(( iic = iic + 1 ))
	583	line=$(echo $line \| cut -c4-)
	584	in_command[$iic]="$line"
	585
	586	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	587	then
	588
	589	# LINE DEFINES OUTPUT-COMMAND
	590	(( ioc = ioc + 1 ))
	591	line=$(echo $line \| cut -c4-)
	592	out_command[$ioc]="$line"
	593
	594	else
	595
	596	# SKIP ALL OTHER LINES
	597	continue
	598
	599	fi
	600
	601	done < $config_file
	602
	603
	604	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	605	if [[ "$fast_io_catalog" = "" ]]
	606	then
	607	printf "\n +++ no fast_io_catalog found in $config_file"
	608	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	609	locat=config_file; exit
	610	fi
[2380]	611	if [[ "$compiler_name" = "" ]]
	612	then
	613	printf "\n +++ no compiler name found in $config_file"
	614	printf "\n Please add line \"compiler_name ...\" to that file."
	615	locat=config_file; exit
	616	fi
	617	if [[ "$compiler_name_ser" = "" ]]
	618	then
	619	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	620	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	621	locat=config_file; exit
	622	fi
	623	if [[ "$compiler_options" = "" ]]
	624	then
	625	printf "\n +++ no compiler options found in $config_file"
	626	printf "\n Please add line \"compiler_options ...\" to that file."
	627	locat=config_file; exit
	628	fi
[2388]	629	if [[ "$linker_options" = "" ]]
[2380]	630	then
[2388]	631	printf "\n +++ no linker options found in $config_file"
	632	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	633	locat=config_file; exit
	634	fi
	635	if [[ "$execute_command" = "" ]]
	636	then
	637	printf "\n +++ no execute command found in $config_file"
	638	printf "\n Please add line \"execute_command ...\" to that file."
	639	locat=config_file; exit
	640	fi
	641
	642	if [[ "$hostfile" != "" ]]
	643	then
	644	if [[ $hostfile != auto && ! -f $hostfile ]]
	645	then
	646	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	647	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	648	locat=config_file; exit
	649	fi
	650	fi
	651
	652
	653	# DETERMINE THE CALL STATUS
	654	if [[ "$return_address" != "" ]]
	655	then
	656
	657	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	658	# BATCH MODE AND ...
	659	running_on_remote=true
	660
	661	else
	662
	663	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	664	if [[ "$remote_ip" != "" ]]
	665	then
	666
	667	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	668	create_remote_batch_job=true
	669
[3132]	670	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	671	if [[ "$remote_jobcatalog" = "" ]]
	672	then
	673	printf "\n +++ no remote jobcatalog found in $config_file"
	674	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	675	locat=config_file; exit
	676	fi
	677
	678
[2380]	679	fi
	680	running_on_remote=false
	681	fi
	682
	683
	684
	685	# READ AND EVALUATE THE I/O-FILE LIST
	686	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	687
	688	# READ THE FILE CONNECTION FILE LINE BY LINE
	689	while read line
	690	do
	691
[2669]	692	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	693	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	694	line=`echo "$line" \| tr -s " "`
[2380]	695
	696	# INTERPRET THE LINE
	697	if [[ "$(echo $line)" = "" ]]
	698	then
	699	# EMPTY LINE, NO ACTION
	700	continue
	701
	702	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	703	then
	704
	705	# LINE IS A COMMENT LINE
	706	true
	707
	708	else
	709
	710	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	711	# s2a: in/out - field
[2669]	712	# s2b: action - field (optional)
	713	s1=`echo "$line" \| cut -d" " -f1`
	714	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	715	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	716	then
[2669]	717	s2a=$s2
[2380]	718	s2b=""
	719	else
[2669]	720	s2a=`echo $s2 \| cut -d":" -f1`
	721	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	722	fi
[2669]	723	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	724	s4=`echo "$line" \| cut -d" " -s -f4`
	725	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	726	s5=`echo "$line" \| cut -d" " -s -f5`
	727	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	728
	729
	730	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	731	# INPUT- OR OUTPUT-LIST.
	732	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	733	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	734	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	735	# IS NOT CHECKED AND STORED.
[2610]	736	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	737	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	738	then
	739	found=false
	740	for actual in $activation_string_list
	741	do
	742	for formal in $s3
	743	do
	744	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	745	done
	746	done
	747	if [[ $found = true ]]
	748	then
	749	(( iin = iin + 1 ))
[2669]	750	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	751	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	752	if [[ "$s2a" = inopt ]]
	753	then
	754	optin_pre[$iin]=yes
	755	else
	756	optin_pre[$iin]=no
	757	fi
[2605]	758
	759	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	760	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	761	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	762	then
[2610]	763	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	764	fi
	765
[2610]	766	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	767	# THE WILDCARD FROM THE ENDING
	768	if [[ "${s5: -1}" = "*" ]]
	769	then
[2669]	770	if [[ "$s2b" = "di" ]]
[2610]	771	then
	772	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	773	printf "\n see file \"$fileconnection_file\", line"
	774	printf "\n$line"
	775	locat=iofiles_file; exit
	776	fi
	777	multin[$iin]=true
	778	string=${endin_pre[$iin]}
	779	endin_pre[$iin]="${string%?}"
	780	else
	781	multin[$iin]=false
	782	fi
[2380]	783	fi
[2669]	784	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	785	then
	786	found=false
	787	for actual in $activation_string_list
	788	do
	789	for formal in $s3
	790	do
[2670]	791	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	792	done
	793	done
	794	if [[ $found = true ]]
	795	then
	796	(( iout = iout + 1 ))
[2669]	797	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	798	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	799
[2669]	800	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	801	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	802	if [[ $formal = wildcard ]]
	803	then
	804	warnout_pre[$iout]=false
	805	else
	806	warnout_pre[$iout]=true
	807	fi
	808
[2610]	809	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	810	# THE WILDCARD FROM THE LOCAL FILENAME
	811	if [[ "${s1: -1}" = "*" ]]
	812	then
[2669]	813	if [[ "$s2b" = "di" ]]
[2610]	814	then
	815	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	816	printf "\n see file \"$fileconnection_file\", line"
	817	printf "\n$line"
	818	locat=iofiles_file; exit
	819	fi
	820	multout[$iout]=true
	821	string=${localout_pre[$iout]}
	822	localout_pre[$iout]="${string%?}"
	823	else
	824	multout[$iout]=false
	825	fi
[2380]	826	fi
[2669]	827	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	828	then
[2669]	829	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	830	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	831	locat=connect; exit
	832	fi
	833	IFS="$IFSALT"
	834	fi
	835
	836	done < $fileconnection_file
	837
	838
	839
[2501]	840	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	841	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	842	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	843	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	844	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	845	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	846
	847
	848
[2380]	849	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	850	if [[ $run_coupled_model = true ]]
	851	then
	852
	853	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	854	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	855
	856	if (( $cores_ocean + $cores_atmos != $cores ))
	857	then
	858
	859	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	860	printf "\n PEs (total) : $cores"
	861	printf "\n PEs (atmosphere): $cores_atmos"
	862	printf "\n PEs (ocean) : $cores_ocean"
	863	locat=coupling; exit
	864
	865	fi
	866
	867	fi
	868
	869
	870	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	871	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	872	# FOLDER
	873	if [[ $running_in_batch_mode = true ]]
	874	then
	875
[2506]	876	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	877	then
[2506]	878	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	879	printf "\n Please check the output of the palmrun-call"
	880	printf "\n that you did on your local host."
	881	locat=SOURCES_FOR_RUN; exit
	882	fi
	883
	884	else
	885
	886	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	887	# AUTOMATIC RESTART RUN
	888	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	889	if [[ $restart_run = false ]]
	890	then
	891
	892	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	893	# THE LOCAL HOST
	894	if [[ ! -d $source_path ]]
	895	then
	896	printf "\n\n +++ source path \"$source_path\" on local host"
	897	printf "\n \"$(hostname)\" does not exist"
	898	locat=source_path; exit
	899	fi
	900
[2990]	901	rm -rf ${base_directory}/${sources_for_run_catalog}
	902	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	903
	904	if [[ "$source_list" = LM ]]
	905	then
	906
	907	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	908	source_list=""
	909	cd $source_path
	910
	911
[2512]	912	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	913	if [[ ! -d ../.svn ]]
[2380]	914	then
	915	printf "\n\n +++ source directory"
	916	printf "\n \"$source_path\" "
	917	printf "\n is not under control of \"subversion\"."
[2512]	918	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	919	fi
	920
	921
	922	# LIST ALL MODIFIED SOURCE CODE FILES
	923	Filenames=""
[2404]	924	svn status > tmp_svnstatus
[2380]	925	while read line
	926	do
	927	firstc=`echo $line \| cut -c1`
	928	if [[ $firstc = M \|\| $firstc = "?" ]]
	929	then
	930	Name=`echo "$line" \| cut -c8-`
	931	extension=`echo $Name \| cut -d. -f2`
	932	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	933	then
	934	Filenames="$Filenames "$Name
	935	fi
	936	fi
[2404]	937	done < tmp_svnstatus
	938	rm -rf tmp_svnstatus
[2380]	939
	940
	941	# COPY FILES TO SOURCES_FOR_RUN_...
	942	for filename in $Filenames
	943	do
[2990]	944	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	945	source_list=$source_list"$filename "
	946	done
	947
	948	cd - > /dev/null
	949
	950
	951	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	952	elif [[ "$source_list" != "" ]]
	953	then
	954
	955	cd $source_path
	956
	957	for filename in $source_list
	958	do
	959
	960	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	961	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	962	then
	963	printf "\n +++ source code file: $filename"
	964	printf "\n must not contain (\"/\") "
	965	locat=source; exit
	966	fi
	967
	968	if [[ ! -f $filename ]]
	969	then
	970	printf "\n +++ source code file: $filename"
	971	printf "\n does not exist"
	972	locat=source; exit
	973	else
[2990]	974	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	975	fi
	976
	977	done
	978
	979	cd - > /dev/null
	980
	981	fi
	982
	983	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	984	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	985	if [[ ! -f $makefile ]]
	986	then
	987	printf "\n +++ file \"$makefile\" does not exist"
	988	locat=make; exit
	989	else
[2990]	990	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	991	fi
	992
	993
	994	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	995	if [[ "$user_source_path" != "" ]]
[2380]	996	then
	997
	998	# DOES THE DIRECTORY EXIST?
[2384]	999	if [[ ! -d $user_source_path ]]
[2380]	1000	then
	1001
	1002	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1003	printf "\n \"$user_source_path\" "
[2380]	1004	printf "\n does not exist or is not a directory."
	1005	printf "\n No source code will be used from this directory!\n"
[2384]	1006	user_source_path=""
[2380]	1007	if [[ $silent == false ]]
	1008	then
	1009	sleep 2
	1010	fi
	1011
	1012	else
	1013
[2384]	1014	cd $user_source_path
[2380]	1015
	1016	Names=$(ls -1 *.f90 2>&1)
	1017	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1018	Names=$(ls -1 *.F90 2>&1)
	1019	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1020	Names=$(ls -1 *.F 2>&1)
	1021	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1022	Names=$(ls -1 *.f 2>&1)
	1023	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1024	Names=$(ls -1 *.c 2>&1)
	1025	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1026
	1027	cd - > /dev/null
[2990]	1028	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1029
	1030	# COPY MAKEFILE IF EXISTING
[2384]	1031	if [[ -f $user_source_path/Makefile ]]
[2380]	1032	then
	1033	printf "\n\n *** user Makefile from directory"
[2384]	1034	printf "\n \"$user_source_path\" is used \n"
[2380]	1035	if [[ $silent == false ]]
	1036	then
	1037	sleep 1
	1038	fi
[2384]	1039	cp $user_source_path/Makefile .
[2380]	1040	fi
	1041
	1042	for filename in $AddFilenames
	1043	do
	1044	if [[ -f $filename ]]
	1045	then
	1046	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1047	printf "\n source code directory \"$user_source_path\" "
[2380]	1048	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1049	printf "\n from directory \"$source_path\"."
	1050	locat=source; exit
	1051	fi
	1052
[2384]	1053	cp $user_source_path/$filename .
[2380]	1054	source_list="$source_list $filename"
	1055
	1056	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1057	if [[ $(grep -c $filename Makefile) = 0 ]]
	1058	then
	1059	printf "\n\n +++ user file \"$filename\" "
	1060	printf "\n is not listed in Makefile \n"
	1061	locat=source; exit
	1062	fi
	1063	done
	1064	cd - > /dev/null
	1065	fi
	1066	fi
	1067
	1068	# COPY CONFIGURATION FILES
[2990]	1069	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1070	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1071
	1072	# COPY SHELLSCRIPTS
[2990]	1073	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1074	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1075
	1076	fi
	1077
	1078	fi
	1079
[2605]	1080
[2380]	1081	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1082	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1083	if [[ "$global_revision" = "" ]]
	1084	then
	1085	global_revision=`svnversion $source_path 2>/dev/null`
	1086	global_revision="Rev: $global_revision"
	1087	fi
	1088
	1089
	1090	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1091	if [[ -n $cores ]]
	1092	then
	1093
	1094	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1095	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1096	if [[ $tasks_per_node = 0 ]]
[2380]	1097	then
[3025]	1098	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1099	then
	1100	printf "\n"
	1101	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1102	printf "\n set -T option or define tasks_per_node in the config file"
	1103	locat=tasks_per_node; (( iec = 0 )); exit
	1104	else
	1105	# DEFAULT FOR INTERACTIVE RUN
	1106	tasks_per_node=$cores
	1107	fi
[2380]	1108	fi
	1109
	1110	if (( cores < tasks_per_node ))
	1111	then
	1112	printf "\n"
	1113	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1114	printf "\n given values: -T $tasks_per_node -X $cores"
	1115	locat=tasks_per_node; (( iec = 0 )); exit
	1116	fi
	1117
	1118	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1119	(( mpi_tasks = cores / threads_per_task ))
	1120	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1121	(( ii = cores / tasks_per_node ))
	1122	(( remaining_cores = cores - ii * tasks_per_node ))
	1123	if (( remaining_cores > 0 ))
	1124	then
	1125	printf "\n"
	1126	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1127	printf "\n divisor of the total number of cores (option \"-X\")"
	1128	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1129	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1130	(( nodes = nodes + 1 ))
	1131	fi
	1132
	1133	fi
	1134
	1135
	1136	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1137	if [[ "$maximum_parallel_io_streams" = "" ]]
	1138	then
	1139	maximum_parallel_io_streams=$cores
	1140	fi
	1141
	1142
	1143	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1144	if [[ "$scp_port" != "" ]]
	1145	then
	1146	PORTOPT="-P $scp_port"
	1147	SSH_PORTOPT="-p $scp_port"
	1148	fi
	1149
	1150
	1151	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1152	# CONFIG-FILE
	1153	if [[ "$ssh_key" != "" ]]
	1154	then
	1155	ssh_key="-i $HOME/.ssh/$ssh_key"
	1156	fi
	1157
	1158
	1159	# SET QUEUE, IF NOT GIVEN
	1160	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1161	then
	1162
	1163	if [[ $queue = none && "$defaultqueue" = "" ]]
	1164	then
	1165	printf "\n"
	1166	printf "\n +++ no default queue given in configuration file and no queue"
	1167	printf "\n given with option -q"
[2789]	1168	locat=queue; exit
[2380]	1169	fi
	1170	if [[ $queue = none ]]
	1171	then
	1172	queue=$defaultqueue
	1173	fi
	1174
	1175	fi
	1176
	1177
	1178	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1179	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1180	(( i = 0 ))
[2610]	1181	(( nr_of_input_files = 0 ))
[2380]	1182	while (( i < iin ))
	1183	do
	1184	(( i = i + 1 ))
	1185
	1186	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1187	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1188	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1189	then
[2610]	1190	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1191	else
[3236]	1192	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1193	fi
	1194
[2610]	1195
[2380]	1196	# CHECK IF FILE EXISTS
	1197	if ! ls $filename* 1>/dev/null 2>&1
	1198	then
	1199
[2669]	1200	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1201	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1202	then
	1203	printf "\n\n +++ INPUT-file: "
[2610]	1204	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1205	then
	1206	printf "\n $filename"
	1207	else
[2610]	1208	printf "\n $filename.${extin_pre[$i]}"
[2380]	1209	fi
	1210	printf "\n does not exist\n"
	1211	locat=input; exit
	1212	else
[2610]	1213	(( nr_of_input_files = nr_of_input_files + 1 ))
	1214	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1215	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1216	actionin[$nr_of_input_files]="unavailable"
[2610]	1217	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1218	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1219	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1220	fi
[2605]	1221
[2380]	1222	else
	1223
[3236]	1224	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1225	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1226	# ENDINGS
[2610]	1227	if [[ "${multin[$i]}" = true ]]
	1228	then
	1229	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1230	ls -1 -d ${filename} > filelist 2>/dev/null
	1231	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1232	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1233
[2610]	1234	endings=""
	1235	while read line
	1236	do
	1237	# filename without path (i.e. after the last "/")
	1238	basefilename=$(basename ${line})
[2380]	1239
[2610]	1240	# check if there is an extension and remove it
	1241	ext=${basefilename##*.}
	1242	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1243	then
	1244	basefilename=${basefilename%.*}
	1245	fi
[2380]	1246
[2610]	1247	# check for an existing cycle number and remove it
	1248	cycle=${basefilename##*.}
	1249	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1250	then
	1251	basefilename=${basefilename%.*}
	1252	fi
[2600]	1253
[3236]	1254	# remove the run_identifier from the beginning
	1255	length_run_identifier=${#run_identifier}
	1256	ending=${basefilename:${length_run_identifier}}
[2610]	1257
	1258	# remove the ending given in the .iofiles from the beginning
	1259	endingstring="${endin_pre[$i]}"
	1260	length_ending=${#endingstring}
	1261	ending=${ending:${length_ending}}
	1262
	1263	if [[ "$ending" = "" ]]
[2600]	1264	then
[2610]	1265	# standard ending as given in the .iofiles
	1266	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1267	then
	1268	endings="$endings DEFAULT"
	1269	fi
[2600]	1270	else
[2610]	1271	# ending must start with "_", otherwise its a different file
	1272	if [[ "${ending:0:1}" = "_" ]]
	1273	then
	1274	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1275	then
	1276	endings="$endings $ending"
	1277	fi
	1278	fi
[2600]	1279	fi
[2610]	1280
	1281	done <filelist
[2380]	1282
[2610]	1283	rm filelist
[2380]	1284
[2600]	1285	else
[2610]	1286
	1287	# SINGLE NAME
	1288	endings=DEFAULT
	1289
[2600]	1290	fi
	1291
[2610]	1292	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1293	for ending in $endings
	1294	do
	1295
	1296	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1297	if [[ $ending = DEFAULT ]]
[2380]	1298	then
[2610]	1299	ending=""
	1300	fi
	1301
	1302	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1303	(( nr_of_input_files = nr_of_input_files + 1 ))
	1304	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1305	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1306	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1307	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1308	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1309	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1310
	1311
	1312	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1313	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1314	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1315	then
	1316	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1317	else
[3236]	1318	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1319	fi
[2610]	1320
	1321	# DETERMINE THE FILE'S CYCLE NUMBER
	1322	(( maxcycle = 0 ))
	1323	ls -1 -d $filename > filelist 2>/dev/null
	1324	ls -1 -d $filename.* >> filelist 2>/dev/null
	1325	while read line
	1326	do
	1327	# filename without path (i.e. after the last "/")
	1328	basefilename=$(basename ${line})
	1329
	1330	# check if there is an extension
	1331	extension=${basefilename##*.}
	1332	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1333	then
	1334	basefilename=${basefilename%.*}
	1335	fi
	1336
	1337	# check for an existing cycle number
	1338	cycle=${basefilename##*.}
	1339	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1340	then
[2669]	1341	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1342	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1343	(( icycle = $((10#$cycle)) ))
[2610]	1344	else
	1345	(( icycle = 0 ))
	1346	fi
	1347
	1348	if (( icycle > maxcycle ))
	1349	then
	1350	(( maxcycle = icycle ))
	1351
	1352	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1353	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1354	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1355	then
	1356	leading_zero=true
	1357	else
	1358	leading_zero=false
	1359	fi
	1360	fi
	1361
	1362	done <filelist
	1363	rm filelist
	1364
	1365	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1366	if [[ $leading_zero = true ]]
[2380]	1367	then
[2610]	1368	cyclestring=`printf "%03d" $maxcycle`
	1369	else
	1370	cyclestring=$maxcycle
[2380]	1371	fi
[2610]	1372
	1373	# APPEND CYCLE NUMBER TO FILENAME
	1374	if (( maxcycle > 0 ))
[2380]	1375	then
[2610]	1376	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1377	then
	1378	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1379	else
	1380	filename=${filename}.$cyclestring
	1381	fi
[2380]	1382	else
[2610]	1383	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1384	then
	1385	filename=${filename}.${extin[$nr_of_input_files]}
	1386	fi
[2380]	1387	fi
[2610]	1388
	1389	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1390	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1391	absnamein[$nr_of_input_files]=$filename
	1392	if (( maxcycle > 0 ))
[2380]	1393	then
[2610]	1394	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1395	then
	1396	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1397	else
[3236]	1398	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1399	fi
[2380]	1400	else
[2610]	1401	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1402	then
	1403	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1404	else
[3236]	1405	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1406	fi
[2380]	1407	fi
	1408
[2610]	1409	done
	1410
[2380]	1411	fi
[2610]	1412
[2380]	1413	done
	1414
[2610]	1415
[2380]	1416	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1417	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1418	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1419	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1420	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1421	# REMOTE HOST)
	1422	(( i = 0 ))
	1423	while (( i < iout ))
	1424	do
	1425	(( i = i + 1 ))
[2610]	1426	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1427	then
[2610]	1428	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1429	then
[2610]	1430	actionout_pre[$i]=""
	1431	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1432	then
[2610]	1433	actionout_pre[$i]=pe
	1434	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1435	then
[2610]	1436	actionout_pre[$i]=a
[2380]	1437	fi
	1438	(( maxcycle = 0 ))
[3236]	1439	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1440	eval catalogname=${pathout_pre[$i]}
[2380]	1441	if ! ls $filename* 1>/dev/null 2>&1
	1442	then
	1443
	1444	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1445	if cat /dev/null > $filename
	1446	then
	1447	rm $filename
	1448	else
	1449
	1450	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1451	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1452	if [[ ! -d $catalogname ]]
	1453	then
	1454	if mkdir -p $catalogname
	1455	then
	1456	printf "\n\n *** directory:"
	1457	printf "\n $catalogname"
	1458	printf "\n was created\n"
	1459	else
	1460	printf "\n\n +++ OUTPUT-file:"
	1461	printf "\n $filename"
	1462	printf "\n cannot be created, because directory does not exist"
	1463	printf "\n and cannot be created either"
	1464	printf "\n"
	1465	locat=output ; exit
	1466	fi 2>/dev/null
	1467	else
	1468	printf "\n\n +++ OUTPUT-file:"
	1469	printf "\n $filename"
	1470	printf "\n cannot be created, although directory exists"
	1471	printf "\n"
	1472	locat=output ; exit
	1473	fi
	1474	fi 2>/dev/null
	1475
	1476	fi
	1477
	1478	fi
	1479	done
	1480
	1481
	1482	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1483	if [[ $running_in_batch_mode = false ]]
	1484	then
[3236]	1485	run_id_number=$RANDOM
	1486	run_id=${run_identifier}.$run_id_number
[2380]	1487
[3236]	1488	tempdir=$fast_io_catalog/$run_id
[3346]	1489
	1490	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1491	export job_id=$run_id
	1492
[2380]	1493	fi
	1494
	1495
	1496	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1497	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1498	then
	1499
	1500	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1501	if [[ $ibd = 0 ]]
	1502	then
	1503	printf "\n"
	1504	printf "\n +++ no batch directives found in configuration file"
	1505	locat=config_file_batch_directives; (( iec = 0 )); exit
	1506	fi
	1507
	1508	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1509	done=false
[2384]	1510	cputime=$cpumax
[2380]	1511	while [[ $done = false ]]
	1512	do
[2384]	1513	if (( cputime == 0 ))
[2380]	1514	then
	1515	printf "\n +++ cpu-time is undefined"
	1516	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1517	printf "\n >>> "
[2384]	1518	read cputime 1>/dev/null 2>&1
[2380]	1519	else
	1520	done=true
	1521	fi
	1522	done
[2420]	1523	cpumax=$cputime
[2380]	1524
	1525	# CHECK THE MEMORY DEMAND
	1526	done=false
	1527	while [[ $done = false ]]
	1528	do
	1529	if (( memory == 0 ))
	1530	then
	1531	printf "\n +++ memory demand is undefined"
	1532	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1533	printf "\n >>> "
	1534	read memory 1>/dev/null 2>&1
	1535	else
	1536	done=true
	1537	fi
	1538	done
	1539
	1540	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1541	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1542	then
	1543	while [[ -z $remote_username ]]
	1544	do
[2420]	1545	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1546	printf "\n >>> Please type username:"
	1547	printf "\n >>> "
	1548	read remote_username
	1549	done
	1550	fi
	1551
	1552	else
	1553
[2420]	1554	if [[ $running_in_batch_mode = false ]]
	1555	then
	1556	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1557	cpumax=$cputime
	1558	else
	1559	cputime=$cpumax
	1560	fi
[2380]	1561
	1562	fi
	1563
	1564
	1565	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1566	(( cpu_hours = cputime / 3600 ))
	1567	(( resttime = cputime - cpu_hours * 3600 ))
	1568	(( cpu_minutes = resttime / 60 ))
	1569	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1570	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1571
	1572
	1573	# OUTPUT OF THE PALMRUN-HEADER
	1574	calltime=$(date)
	1575	printf "\n"
	1576	printf "#------------------------------------------------------------------------# \n"
	1577	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1578	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1579	printf "\| \| \n"
	1580	column1="called on:"; column2=$(hostname)
	1581	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1582	if [[ $create_remote_batch_job = true ]]
	1583	then
[3236]	1584	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1585	else
	1586	if [[ $running_on_remote = true ]]
	1587	then
[3236]	1588	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1589	else
[3236]	1590	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1591	fi
	1592	fi
	1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1594
	1595	column1="running in:"
	1596	if [[ $running_in_batch_mode = true ]]
	1597	then
	1598	column2="batch job mode"
	1599	else
	1600	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1601	then
	1602	column2="job creation mode"
	1603	else
	1604	column2="interactive run mode"
	1605	fi
	1606	fi
	1607	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1608
[2479]	1609	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1610	then
[2480]	1611	if [[ "$project_account" != "" ]]
[2479]	1612	then
	1613	column1="project account number:"
	1614	column2="$project_account"
	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1616	fi
	1617	fi
	1618
[2380]	1619	if [[ -n $cores ]]
	1620	then
	1621	if [[ $run_coupled_model = false ]]
	1622	then
	1623	column1="number of cores:"; column2=$cores
	1624	else
	1625	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1626	fi
	1627	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1628	fi
	1629	if [[ -n $tasks_per_node ]]
	1630	then
	1631	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1633	if (( remaining_cores > 0 ))
	1634	then
	1635	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1637	fi
	1638	fi
	1639	if [[ $maximum_parallel_io_streams != $cores ]]
	1640	then
	1641	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1642	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1643	fi
	1644	if [[ $use_openmp = true ]]
	1645	then
	1646	column1="threads per task:"; column2="$threads_per_task"
	1647	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1648	fi
[2384]	1649	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1650	then
[2506]	1651	column1="memory demand / PE":; column2="$memory MB"
	1652	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1653	column1="job cpu time (h:m:s):"; column2="$timestring"
	1654	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1655	fi
[2380]	1656	printf "\| \| \n"
	1657	if [[ "$source_list" != "" ]]
	1658	then
	1659	if [[ "$make_options" != "" ]]
	1660	then
	1661	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1663	line=$(echo "$make_options" \| cut -c46-)
	1664	while [[ "$line" != "" ]]
	1665	do
	1666	column1=""
	1667	column2=$(echo "$line" \| cut -c-45)
	1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1669	line=$(echo "$line" \| cut -c46-)
	1670	done
	1671	fi
	1672	fi
	1673
	1674	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	line=$(echo "$cpp_options" \| cut -c46-)
	1677	while [[ "$line" != "" ]]
	1678	do
	1679	column1=""
	1680	column2=$(echo "$line" \| cut -c-45)
	1681	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1682	line=$(echo "$line" \| cut -c46-)
	1683	done
	1684
	1685	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1687	line=$(echo "$compiler_options" \| cut -c46-)
	1688	while [[ "$line" != "" ]]
	1689	do
	1690	column1=""
	1691	column2=$(echo "$line" \| cut -c-45)
	1692	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1693	line=$(echo "$line" \| cut -c46-)
	1694	done
	1695
[2388]	1696	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1698	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1699	while [[ "$line" != "" ]]
	1700	do
	1701	column1=""
	1702	column2=$(echo "$line" \| cut -c-45)
	1703	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1704	line=$(echo "$line" \| cut -c46-)
	1705	done
	1706
	1707	if [[ "$login_init_cmd" != "" ]]
	1708	then
	1709	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1711	line=$(echo "$login_init_cmd" \| cut -c46-)
	1712	while [[ "$line" != "" ]]
	1713	do
	1714	column1=""
	1715	column2=$(echo "$line" \| cut -c-45)
	1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1717	line=$(echo "$line" \| cut -c46-)
	1718	done
	1719	fi
	1720
	1721	if [[ "$module_commands" != "" ]]
	1722	then
	1723	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1724	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1725	line=$(echo "$module_commands" \| cut -c46-)
	1726	while [[ "$line" != "" ]]
	1727	do
	1728	column1=""
	1729	column2=$(echo "$line" \| cut -c-45)
	1730	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1731	line=$(echo "$line" \| cut -c46-)
	1732	done
	1733	fi
	1734	printf "\| \| \n"
[3236]	1735	column1="run identifier:"; column2=$run_identifier
[2380]	1736	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1737	column1="activation string list:"; column2=$(echo $activation_string_list)
	1738	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1739
	1740	if [[ "$ocean_file_appendix" = true ]]
	1741	then
	1742	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1743	fi
	1744
	1745	if [[ "$source_list" != "" ]]
	1746	then
	1747	printf "\| \| \n"
	1748	printf "\| Files to be compiled: \| \n"
	1749	line=$source_list
	1750	while [[ "$line" != "" ]]
	1751	do
	1752	linestart=$(echo $line \| cut -c-70)
	1753	printf "\| %-70s \| \n" "$linestart"
	1754	line=$(echo "$line" \| cut -c71-)
	1755	done
	1756	fi
	1757	printf "#------------------------------------------------------------------------#"
	1758
	1759
	1760
	1761	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1762	if [[ $do_trace = true ]]
	1763	then
	1764	(( i = 0 ))
[2610]	1765	while (( i < nr_of_input_files ))
[2380]	1766	do
	1767	(( i = i + 1 ))
	1768	if (( i == 1 ))
	1769	then
	1770	printf "\n\n >>> INPUT-file assignments:\n"
	1771	fi
	1772	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1773	done
	1774	(( i = 0 ))
	1775	while (( i < iout ))
	1776	do
	1777	(( i = i + 1 ))
	1778	if (( i == 1 ))
	1779	then
	1780	printf "\n\n >>> OUTPUT-file assignments:\n"
	1781	fi
	1782	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1783	done
	1784	(( i = 0 ))
	1785	while (( i < iic ))
	1786	do
	1787	(( i = i + 1 ))
	1788	if (( i == 1 ))
	1789	then
	1790	printf "\n\n >>> INPUT-commands:\n"
	1791	fi
	1792	printf "\n ${in_command[$i]}"
	1793	done
	1794	(( i = 0 ))
	1795	while (( i < ioc ))
	1796	do
	1797	(( i = i + 1 ))
	1798	if (( i == 1 ))
	1799	then
	1800	printf "\n\n >>> OUTPUT-commands:\n"
	1801	fi
	1802	printf "\n ${out_command[$i]}"
	1803	done
	1804	fi
	1805
	1806	# QUERY FOR CONTINUE
	1807	if [[ $silent = false && $running_in_batch_mode = false ]]
	1808	then
	1809	antwort=dummy
	1810	printf "\n\n"
	1811	printf " >>> everything o.k. (y/n) ? "
	1812	while read antwort
	1813	do
	1814	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1815	then
	1816	printf " >>> everything o.k. (y/n) ? "
	1817	else
	1818	break
	1819	fi
	1820	done
	1821	if [[ $antwort = n \|\| $antwort = N ]]
	1822	then
	1823	locat=user_abort; (( iec = 0 )); exit
	1824	fi
	1825	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1826	then
[2566]	1827	printf "\n *** batch-job will be created and submitted"
[2380]	1828	else
[2566]	1829	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1830	fi
	1831	fi
	1832
	1833
	1834
	1835	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1836	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1837	then
	1838
	1839	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1840	then
[2566]	1841	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1842	else
[2566]	1843	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1844	fi
	1845
[2422]	1846	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1847	# IT SHALL BE CREATED
	1848	ask_for_make_depository=false
	1849	if [[ $create_remote_batch_job = true ]]
	1850	then
	1851
	1852	line=`grep %base_directory $config_file`
[3236]	1853	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1854	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1855
[3236]	1856	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1857	then
	1858	printf "\n\n +++ make depository \"${make_depository}\""
	1859	printf "\n on remote host not found!"
	1860	ask_for_make_depository=true
	1861	fi
[3236]	1862	rm ${configuration_identifier}_last_make_protokoll
[2422]	1863
	1864	else
	1865
	1866	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1867	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1868	if [[ ! -d ${make_depository} ]]
	1869	then
	1870	printf "\n\n +++ make depository \"${make_depository}\""
	1871	printf "\n on local host not found!"
	1872	ask_for_make_depository=true
	1873	fi
	1874
	1875	fi
	1876
	1877	if [[ $ask_for_make_depository = true ]]
	1878	then
	1879
	1880	antwort=dummy
	1881	printf "\n\n"
	1882	printf " >>> Create a new one (y/n) ? "
	1883	while read antwort
	1884	do
	1885	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1886	then
	1887	printf " >>> Create a new one (y/n) ? "
	1888	else
	1889	break
	1890	fi
	1891	done
	1892	if [[ $antwort = n \|\| $antwort = N ]]
	1893	then
	1894	locat=user_abort; (( iec = 0 )); exit
	1895	fi
	1896
[2566]	1897	if [[ $do_trace = true ]]
	1898	then
[3455]	1899	palmbuild -c $configuration_identifier
[2566]	1900	else
[3455]	1901	palmbuild -v -c $configuration_identifier
[2566]	1902	fi
[2422]	1903
[3312]	1904	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1905	then
	1906
	1907	# ABORT IN CASE OF COMPILATION PROBLEMS
	1908	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1909	locat=make_depository
	1910	exit
	1911	else
	1912	echo " *** now continue with creating executable and other sources"
	1913	fi
	1914
	1915	fi
	1916
[2566]	1917	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1918	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1919
[3312]	1920	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1921	then
	1922
	1923	# ABORT IN CASE OF COMPILATION PROBLEMS
	1924	printf "\n +++ error while creating executable and/or other sources"
	1925	locat=execution
[2990]	1926	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1927	exit
	1928
	1929	else
	1930
[2566]	1931	printf " *** executable and other sources created\n"
[2990]	1932	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1933
	1934	fi
	1935
	1936	fi
	1937
	1938
[2669]	1939	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1940	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1941	if [[ $create_remote_batch_job = true ]]
	1942	then
	1943	(( i = 0 ))
[2610]	1944	while (( i < nr_of_input_files ))
[2605]	1945	do
	1946	(( i = i + 1 ))
[2669]	1947	if [[ "${actionin[$i]}" = tr ]]
[2605]	1948	then
	1949	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1950	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1951	fi
	1952	done
	1953	if (( i > 0 ))
	1954	then
[3025]	1955	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1956	fi
	1957	fi
	1958
	1959
[2380]	1960	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1961	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1962	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1963	then
	1964
	1965	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1966	if [[ $running_in_batch_mode = false ]]
	1967	then
	1968	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1969	# FOLDER
[2566]	1970	mkdir -p $tempdir
	1971	chmod go+rx $tempdir
	1972	cd $tempdir
	1973	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1974	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1975
	1976	else
	1977
	1978	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1979	printf "\n *** running in temporary directory: $tempdir"
[2380]	1980
	1981	fi
	1982
	1983
	1984	# PROVIDE THE INPUT FILES
	1985	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1986	optional_files_missing=false
[2380]	1987	(( i = 0 ))
[2610]	1988	while (( i < nr_of_input_files ))
[2380]	1989	do
	1990	(( i = i + 1 ))
	1991	if (( i == 1 ))
	1992	then
	1993	printf "\n\n *** providing INPUT-files:\n$dashes"
	1994	fi
	1995
	1996
	1997	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1998	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1999	then
[2669]	2000	optional_files_missing=true
[2380]	2001	continue
	2002	fi
	2003
	2004	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2005	files_for_cores=false; filetype=file
	2006	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2007	then
	2008	files_for_cores=true; filetype=files
	2009	actionin[$i]=""
	2010	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2011	then
	2012	actionin[$i]=""
	2013	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2014	then
	2015	files_for_cores=true; filetype=files
	2016	actionin[$i]="ln"
	2017	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2018	then
	2019	actionin[$i]="ln"
	2020	fi
	2021
	2022	if [[ $files_for_cores = true ]]
	2023	then
	2024	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2025	else
	2026	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2027	fi
	2028
	2029	# INPUT-FILES TO BE LINKED
	2030	if [[ "${actionin[$i]}" = ln ]]
	2031	then
	2032
	2033	printf "\n $filetype will be linked"
	2034	if [[ $files_for_cores = false ]]
	2035	then
	2036	if [[ -f "${absnamein[$i]}" ]]
	2037	then
	2038	ln ${absnamein[$i]} ${localin[$i]}
	2039	got_tmp[$i]=true
	2040	fi
	2041	else
	2042	if [[ -d "${absnamein[$i]}" ]]
	2043	then
[2396]	2044	mkdir -p ${localin[$i]}
[2380]	2045	cd ${absnamein[$i]}
	2046	for file in $(ls *)
	2047	do
[2566]	2048	ln $file $tempdir/${localin[$i]}
[2380]	2049	done >\|/dev/null 2>&1
[2566]	2050	cd $tempdir
[2380]	2051	fi
	2052
	2053	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2054	if [[ ! -f "${localin[$i]}/_000000" ]]
	2055	then
	2056	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2057	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2058	fi
	2059
	2060	got_tmp[$i]=true
	2061	fi
	2062	fi
	2063
	2064	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2065	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2066	then
	2067
	2068	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2069	then
	2070
	2071	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2072	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2073	printf "\n file will be provided for $cores processors"
[2396]	2074	mkdir -p ${localin[$i]}
[2380]	2075	ival=$cores
	2076	(( ii = 0 ))
	2077	while (( ii <= ival-1 ))
	2078	do
	2079	if (( ii < 10 ))
	2080	then
	2081	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2082	elif (( ii < 100 ))
	2083	then
	2084	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2085	elif (( ii < 1000 ))
	2086	then
	2087	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2088	else
	2089	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2090	fi
	2091	(( ii = ii + 1 ))
	2092	done
	2093
	2094	else
	2095
	2096	if [[ $files_for_cores = true ]]
	2097	then
	2098
	2099	# PROVIDE FILES FOR EACH CORE
	2100	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2101	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2102	printf "\n providing $cores files for the respective cores"
[2396]	2103	mkdir -p ${localin[$i]}
[2380]	2104	if [[ $link_local_input = true ]]
	2105	then
	2106	printf " files will be linked\n"
	2107	cd ${absnamein[$i]}
	2108	for file in $(ls *)
	2109	do
	2110	ln -f $file ${localin[$i]}
	2111	done
[2566]	2112	cd $tempdir
[2380]	2113	fi
	2114
	2115	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2116	if [[ ! -f "${localin[$i]}/_000000" ]]
	2117	then
	2118	if [[ $link_local_input = true ]]
	2119	then
	2120	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2121	fi
	2122	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2123	fi
	2124
	2125	else
	2126
	2127	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2128	if [[ $link_local_input = true ]]
	2129	then
	2130	printf " file will be linked\n"
	2131	ln -f ${absnamein[$i]} ${localin[$i]}
	2132	fi
[2605]	2133	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2134	if [[ ! -f "${localin[$i]}" ]]
	2135	then
	2136	if [[ $link_local_input = true ]]
	2137	then
	2138	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2139	fi
[2669]	2140	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2141	then
	2142	mv ${absnamein[$i]} ${localin[$i]}
	2143	else
	2144	cp ${absnamein[$i]} ${localin[$i]}
	2145	fi
[2380]	2146	fi
	2147	fi
	2148	fi
	2149	fi
	2150
	2151	done
	2152	if (( i != 0 ))
	2153	then
[2669]	2154	if [[ $optional_files_missing = true ]]
	2155	then
	2156	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2157	fi
[2380]	2158	printf "\n$dashes\n *** all INPUT-files provided \n"
	2159	fi
	2160
	2161
	2162	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2163	(( i = 0 ))
	2164	while (( i < iic ))
	2165	do
	2166	(( i = i + 1 ))
	2167	if (( i == 1 ))
	2168	then
	2169	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2170	fi
	2171	printf "\n >>> ${in_command[$i]}"
	2172	eval ${in_command[$i]}
	2173	if (( i == iic ))
	2174	then
	2175	printf "\n$dashes\n"
	2176	fi
	2177	done
	2178
	2179
[3313]	2180	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2181	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2182	then
	2183	progress_bar_disabled=true
	2184	else
	2185	progress_bar_disabled=false
	2186	fi
	2187
	2188
[2380]	2189	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2190	# (FILE ENVPAR WILL BE READ BY PALM)
	2191	cat > ENVPAR << EOF
[3236]	2192	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2193	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2194	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2195	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2196	maximum_cpu_time_allowed = ${cpumax}.,
	2197	revision = '$global_revision',
[3313]	2198	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2199
	2200	EOF
	2201
	2202
	2203	# STARTING THE EXECUTABLE
	2204	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2205	PATH=$PATH:$tempdir
[2380]	2206
	2207
	2208	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2209	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2210	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2211	eval line=\"$line\"
	2212	execute_command="$line"
	2213
	2214
	2215	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2216	if [[ "$execute_command_for_combine" = "" ]]
	2217	then
	2218	eval line2=\"$line2\"
	2219	execute_command_for_combine="$line2"
	2220	fi
	2221
[2380]	2222
	2223
	2224	# PROVIDE A HOSTFILE, IF REQUIRED
	2225	if [[ "$hostfile" != "" ]]
	2226	then
	2227
	2228	if [[ $hostfile = auto ]]
	2229	then
	2230	# CREATE A NEW HOSTFILE
	2231	(( ii = 1 ))
	2232	while (( ii <= cores / threads_per_task ))
	2233	do
	2234	echo $(hostname) >> hostfile
	2235	(( ii = ii + 1 ))
	2236	done
	2237	if (( cores / threads_per_task == 0 ))
	2238	then
	2239	echo $(hostname) >> hostfile
	2240	fi
	2241
	2242	else
	2243	cp $hostfile hostfile
	2244	fi
	2245	eval line=\"`head -n $ii hostfile`\"
	2246	printf "\n *** running on: $line"
	2247	fi
	2248
	2249
	2250
	2251	# SET THE NUMBER OF OPENMP-THREADS
	2252	if [[ $use_openmp = true ]]
	2253	then
	2254	export OMP_NUM_THREADS=$threads_per_task
	2255	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2256	else
	2257	export OMP_NUM_THREADS=1
	2258	fi
	2259
	2260
[2610]	2261	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2262	if [[ $run_coupled_model = false ]]
	2263	then
	2264	if [[ "$ocean_file_appendix" = true ]]
	2265	then
	2266	echo "precursor_ocean" > coupling_steering
	2267	else
	2268	echo "precursor_atmos" > coupling_steering
	2269	fi
	2270	else
	2271	(( iia = $cores_atmos / $threads_per_task ))
	2272	(( iio = $cores_ocean / $threads_per_task ))
	2273	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2274	printf "\n\n"
	2275	echo "coupled_run $iia $iio" > coupling_steering
	2276	fi
	2277
	2278	printf "\n *** execute command:"
	2279	printf "\n \"$execute_command\" \n\n"
	2280
	2281
[3393]	2282	if [[ $progress_bar_disabled = true ]]
[2380]	2283	then
[3402]	2284	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2285	exit_code=${PIPESTATUS[0]}
	2286	else
	2287	$execute_command < coupling_steering &> >(tee STDOUT)
	2288	exit_code=${PIPESTATUS[0]}
	2289	fi
[2380]	2290
[3393]	2291	if [[ ${exit_code} != 0 ]]
	2292	then
	2293
[2380]	2294	# ABORT IN CASE OF RUNTIME ERRORS
	2295	printf "\n +++ runtime error occured"
	2296	locat=execution
	2297	exit
	2298
	2299	else
	2300
	2301	printf "\n$dashes\n *** execution finished \n"
	2302
	2303	fi
	2304
	2305
	2306	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2307	# BY EACH CORE INTO ONE FILE
	2308	if [[ ! -f combine_plot_fields.x ]]
	2309	then
	2310
	2311	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2312	printf "\n 2d- and/or 3d-data may be incomplete!"
	2313	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2314
	2315	elif [[ "$combine_plot_fields" == true ]]
	2316	then
	2317
	2318	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2319	$execute_command_for_combine
	2320
	2321	else
	2322
	2323	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2324	# DATA OUTPUT
[2380]	2325	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2326	fi
	2327
	2328
	2329
	2330	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2331	(( i = 0 ))
	2332	while (( i < ioc ))
	2333	do
	2334	(( i = i + 1 ))
	2335	if (( i == 1 ))
	2336	then
	2337	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2338	fi
[2799]	2339
	2340	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2341	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2342
[2380]	2343	printf "\n >>> ${out_command[$i]}"
	2344	eval ${out_command[$i]}
	2345	if (( i == ioc ))
	2346	then
	2347	printf "\n$dashes\n"
	2348	fi
	2349	done
	2350
	2351
[2610]	2352	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2353	# WILDCARDS
[2380]	2354	(( i = 0 ))
[2610]	2355	(( nr_of_output_files = 0 ))
	2356
[2380]	2357	while (( i < iout ))
	2358	do
[2610]	2359
[2380]	2360	(( i = i + 1 ))
[2610]	2361
	2362	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2363	# CREATE A LIST FOR THE DETECTED ENDINGS
	2364	if [[ "${multout[$i]}" = true ]]
	2365	then
	2366	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2367	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2368	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2369
	2370	endings="DEFAULT"
	2371	while read line
	2372	do
	2373	# remove the local name from the beginning
	2374	localnamestring="${localout_pre[$i]}"
	2375	length_localname=${#localnamestring}
	2376	ending=${line:${length_localname}}
	2377
	2378	if [[ "$ending" != "" ]]
	2379	then
	2380	endings="$endings $ending"
	2381	fi
	2382
	2383	done <filelist
	2384
	2385	rm filelist
	2386
	2387	else
	2388
	2389	# SINGLE NAME
	2390	endings=DEFAULT
	2391
	2392	fi
	2393
	2394	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2395	for ending in $endings
	2396	do
	2397
	2398	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2399	if [[ $ending = DEFAULT ]]
	2400	then
	2401	ending=""
	2402	fi
	2403
	2404	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2405	(( nr_of_output_files = nr_of_output_files + 1 ))
	2406	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2407	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2408	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2409	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2410	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2411	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2412	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2413
	2414	done
	2415
	2416	done
	2417
	2418
	2419
	2420
	2421	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2422	(( i = 0 ))
	2423	while (( i < nr_of_output_files ))
	2424	do
	2425	(( i = i + 1 ))
[2380]	2426	if (( i == 1 ))
	2427	then
	2428	printf "\n\n *** saving OUTPUT-files:"
	2429
	2430	# GET RUN NUMBER ASSIGNED BY PALM
	2431	if [[ -f RUN_NUMBER ]]
	2432	then
	2433	read run_number < RUN_NUMBER
	2434	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2435	usecycle_option="-U $run_number"
	2436	else
	2437	run_number=0
	2438	usecycle_option=""
	2439	fi
	2440	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2441	then
[2404]	2442	printf "\n *** in case of SCP transfers to local host"
	2443	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2444	fi
	2445	printf "\n$dashes"
	2446	fi
	2447
	2448	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2449	then
	2450
[3236]	2451	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2452
	2453	# DETERMINE THE CYCLE NUMBER
	2454	ls -1 -d $filename > filelist 2>/dev/null
	2455	ls -1 -d $filename.* >> filelist 2>/dev/null
	2456	while read line
	2457	do
	2458
	2459	# filename without path (i.e. after the last "/")
	2460	basefilename=$(basename ${line})
	2461
	2462	# check if there is an extension
	2463	extension=${basefilename##*.}
	2464	if [[ "$extension" = "${extout[$i]}" ]]
	2465	then
	2466	basefilename=${basefilename%.*}
	2467	fi
	2468
	2469	# check for an existing cycle number
	2470	cycle=${basefilename##*.}
	2471	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2472	then
[2669]	2473	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2474	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2475	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2476	else
	2477	(( icycle = 1 ))
	2478	fi
	2479
	2480	if (( icycle > maxcycle ))
	2481	then
	2482	(( maxcycle = icycle ))
	2483	fi
	2484
	2485	done <filelist
	2486	rm filelist
	2487
	2488
	2489	# SET THE CYCLE NUMBER
	2490	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2491	if [[ "${actionout[$i]}" = a ]]
	2492	then
	2493	(( maxcycle = maxcycle - 1 ))
	2494	fi
	2495
	2496	(( cycnum[$i] = maxcycle ))
	2497	pathout[$i]=$filename
	2498
	2499
	2500	# ADD CYCLE NUMBER TO FILENAME
	2501	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2502	if [[ "${actionout[$i]}" != "a" ]]
	2503	then
	2504	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2505	# WITH AN EXISTING CYCLE NUMBER
	2506	if (( run_number >= cycnum[$i] ))
	2507	then
	2508	(( cycnum[$i] = run_number ))
	2509	else
	2510	if (( run_number > 0 ))
	2511	then
	2512	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2513	fi
	2514	fi
	2515	fi
	2516	if (( cycnum[$i] > 0 ))
	2517	then
[2600]	2518	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2519	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2520	fi
	2521	fi
	2522
	2523	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2524	files_for_cores=false; filetype=file
	2525	link_local_output=false
	2526	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2527	then
	2528	files_for_cores=true; filetype=directory
	2529	actionout[$i]=""
	2530	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2531	then
	2532	actionout[$i]=""
	2533	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2534	then
	2535	files_for_cores=true; filetype=directory
	2536	link_local_output=true
	2537	actionout[$i]=""
	2538	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2539	then
	2540	link_local_output
	2541	actionout[$i]=""
	2542	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2543	then
	2544	files_for_cores=true; filetype=directory
	2545	actionout[$i]="tr"
	2546	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2547	then
	2548	actionout[$i]="tr"
	2549	fi
	2550
	2551	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2552	then
[2669]	2553	if [[ ${warnout[$i]} = true ]]
	2554	then
	2555	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2556	fi
[2380]	2557	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2558	then
[2669]	2559	if [[ ${warnout[$i]} = true ]]
	2560	then
	2561	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2562	fi
[2380]	2563	else
	2564
	2565
	2566	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2567	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2568	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2569	then
	2570	if [[ $running_on_remote = true ]]
	2571	then
	2572
	2573	# SET OPTIONS FOR TRANSFER
	2574	if [[ "${actionout[$i]}" = tr ]]
	2575	then
	2576	if [[ $files_for_cores = false ]]
	2577	then
	2578	catalog_option=""
	2579	catalog_string=""
	2580	else
	2581	catalog_option="-c"
	2582	catalog_string="/"
	2583	fi
	2584	append_option=""
	2585	append_string=""
	2586	else
	2587	append_option="-A"
	2588	append_string="append"
	2589	fi
	2590
	2591	transfer_failed=false
	2592	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2593	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2594
	2595	# TRANSFER VIA SCP
	2596	if [[ "$remote_loginnode" != "" ]]
	2597	then
[3534]	2598	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]	2599	else
[3236]	2600	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]	2601	fi
[3312]	2602	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2603
	2604
	2605	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2606	if [[ $transfer_failed = true ]]
	2607	then
	2608	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2609	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2610
	2611	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2612	eval local_catalog=${pathout[$i]}
	2613	if [[ ! -d $local_catalog ]]
	2614	then
	2615	printf " *** local directory does not exist. Trying to create:\n"
	2616	printf " $local_catalog \n"
	2617	mkdir -p $local_catalog
	2618	fi
[3236]	2619	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2620	transfer_problems=true
	2621	fi
	2622
	2623	else
	2624
	2625	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2626	# BE COPIED OR APPENDED ON THIS MACHINE
	2627	if [[ "${actionout[$i]}" = tr ]]
	2628	then
	2629	actionout[$i]=""
	2630	else
	2631	actionout[$i]="a"
	2632	fi
	2633	fi
	2634	fi
	2635
	2636
	2637	# APPEND ON THIS MACHINE
	2638	if [[ "${actionout[$i]}" = "a" ]]
	2639	then
	2640	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2641	then
	2642	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2643	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2644	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2645	else
	2646	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2647	printf "\n ${pathout[$i]}\n"
	2648	cat ${localout[$i]} >> ${pathout[$i]}
	2649	fi
	2650	fi
	2651
	2652	# COPY ON THIS MACHINE
	2653	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2654	# ON DIFFERENT FILE-SYSTEMS
	2655	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2656	then
	2657
	2658	# COPY IN CASE OF RUNS ON SINGLE CORES
	2659	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2660	then
	2661	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2662	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2663	if [[ $link_local_output = true ]]
	2664	then
	2665	printf " file will be linked\n"
	2666	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2667	fi
	2668	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2669	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2670	then
	2671	if [[ $link_local_output = true ]]
	2672	then
	2673	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2674	fi
	2675	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2676	else
	2677	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2678	fi
	2679	else
	2680	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2681	printf "\n ${pathout[$i]}\n"
	2682	if [[ $link_local_output = true ]]
	2683	then
	2684	printf " file will be linked\n"
	2685	ln -f ${localout[$i]} ${pathout[$i]}
	2686	fi
	2687	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2688	if [[ ! -f "${pathout[$i]}" ]]
	2689	then
	2690	if [[ $link_local_output = true ]]
	2691	then
	2692	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2693	fi
	2694	cp ${localout[$i]} ${pathout[$i]}
	2695	else
	2696	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2697	fi
	2698	fi
	2699
	2700	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2701	then
	2702
	2703	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2704	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2705	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2706	printf "\n ${pathout[$i]}\n"
	2707	if [[ $link_local_output = true ]]
	2708	then
	2709	printf " files will be linked\n"
[2396]	2710	mkdir -p ${pathout[$i]}
[2380]	2711	cd ${localout[$i]}
	2712	for file in $(ls *)
	2713	do
	2714	ln -f $file ${pathout[$i]}
	2715	done >\|/dev/null 2>&1
[2566]	2716	cd $tempdir
[2380]	2717	fi
	2718
	2719	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2720	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2721	then
	2722	if [[ $link_local_output = true ]]
	2723	then
	2724	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2725	fi
[3025]	2726	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2727	cp -r ${localout[$i]}/* ${pathout[$i]}
	2728	fi
	2729
	2730	fi
	2731	fi
	2732	done
	2733
	2734	if (( i != 0 ))
	2735	then
	2736	if [[ $transfer_problems = true ]]
	2737	then
	2738	printf "\n$dashes\n *** OUTPUT-files saved"
	2739	printf "\n +++ WARNING: some data transfers failed! \n"
	2740	else
	2741	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2742	fi
	2743	fi
	2744
	2745
	2746	# IF REQUIRED, START A RESTART-JOB
	2747	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2748	if [[ -f CONTINUE_RUN ]]
	2749	then
	2750
	2751	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2752	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2753	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2754	# -b START A BATCH JOB
	2755	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2756	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2757	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2758
[2957]	2759	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2760	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2761	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2762	then
	2763	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2764	fi
[2380]	2765
	2766	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2767	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2768	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2769	then
[2381]	2770	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2771	fi
	2772
	2773
	2774	# START THE RESTART-JOB
	2775	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2776	echo " $prc"
	2777	printf "\n$dashes\n"
	2778	if [[ $running_on_remote = true ]]
	2779	then
	2780
	2781	echo "*** ssh will be used to initiate restart-runs!"
	2782	echo " return_address=\"$return_address\" "
	2783	echo " return_username=\"$local_username\" "
	2784
	2785	if [[ "$remote_loginnode" != "" ]]
	2786	then
[3534]	2787	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]	2788	else
[3534]	2789	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2790	fi
	2791
	2792	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2793	sleep 30
	2794
	2795	else
	2796
	2797	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2798	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2799
	2800	fi
	2801
[3132]	2802	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2803	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2804	then
	2805	printf "\n$dashes\n +++ creating restart run failed \n"
	2806	locat=create_restart
[3455]	2807	rm palmrun_restart.log
[3132]	2808	exit
	2809	else
	2810	printf "\n$dashes\n *** restart run initiated \n"
	2811	rm palmrun_restart.log
	2812	fi
[2380]	2813
[3132]	2814
[2380]	2815	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2816	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2817	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2818	# MAY BE VERY HUGE)
	2819	(( i = 0 ))
[2610]	2820	while (( i < nr_of_input_files ))
[2380]	2821	do
	2822	(( i = i + 1 ))
	2823	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2824	then
	2825	rm -r ${absnamein[$i]}
	2826	fi
	2827	done
	2828
	2829	fi
	2830
	2831
	2832	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2833	cd $HOME
[2566]	2834	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2835
	2836
	2837	else
	2838
	2839
	2840	# PREPARING ACTIONS,
	2841	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2842
	2843	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2844	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2845	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2846	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2847	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2848	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2849	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2850	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2851	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2852	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2853	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2854	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2855	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2856	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2857	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2858	if [[ $create_remote_batch_job = true ]]
	2859	then
	2860	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2861	if [[ $do_trace = true ]]
	2862	then
	2863	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2864	fi
[2380]	2865	elif [[ $create_batch_job = true ]]
	2866	then
	2867	palmrun_com=${palmrun_com}" -j"
[2420]	2868	if [[ $do_trace = true ]]
	2869	then
	2870	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2871	fi
[2380]	2872	fi
	2873
	2874
	2875	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2876	# REMOTE HOST
[3236]	2877	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2878	job_protocol_file=$job_protocol_file_local
	2879	if [[ $create_remote_batch_job = true ]]
	2880	then
[3236]	2881	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2882	job_protocol_file=$job_protocol_file_remote
	2883	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2884	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2885	fi
	2886
	2887
	2888	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2889	jobfile=jobfile.$run_id_number
[2380]	2890
	2891
	2892	# FIRST CREATE THE BATCH DIRECTIVES
	2893	(( i = 0 ))
	2894	while (( i < ibd ))
	2895	do
	2896	(( i = i + 1 ))
[2693]	2897	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2898	eval line=\"$line\"
	2899	echo "$line" >> $jobfile
	2900	done
	2901	echo " " >> $jobfile
	2902
	2903
	2904	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2905	# PROTOCOL
	2906	if [[ $create_remote_batch_job = true ]]
	2907	then
[3236]	2908	echo "set +vx" >> $jobfile
	2909	echo "trap '" >> $jobfile
	2910	echo "set +vx" >> $jobfile
	2911	echo "cd ${remote_jobcatalog}" >> $jobfile
	2912	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2913
	2914	# ADD THE BATCH DIRECTIVES
	2915	(( i = 0 ))
	2916	while (( i < ibdt ))
	2917	do
	2918	(( i = i + 1 ))
[2693]	2919	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2920	eval line=\"$line\"
	2921	echo "$line" >> $jobfile
	2922	done
	2923	echo " " >> $jobfile
	2924
	2925	echo "set -x" >> $jobfile
[3534]	2926	if [[ "$remote_loginnode" != "" ]]
	2927	then
	2928	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}\" " >> $jobfile
	2929	else
	2930	echo "${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
	2931	fi
[2380]	2932	echo "%%END%%" >> $jobfile
	2933	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2934	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2935	echo "rm $scpjob_file" >> $jobfile
[2404]	2936	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2937	echo "set -x" >> $jobfile
	2938	echo " ' exit" >> $jobfile
	2939	fi
	2940
	2941
	2942	# ACTIVATE ERROR-TRACEBACK
	2943	if [[ $do_trace = true ]]
	2944	then
	2945	echo "set -x" >> $jobfile
	2946	else
	2947	echo "set +vx" >> $jobfile
	2948	fi
	2949
	2950
	2951	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2952	if [[ "$login_init_cmd" != "" ]]
	2953	then
	2954	echo "$login_init_cmd" >> $jobfile
	2955	fi
	2956	if [[ "$module_commands" != "" ]]
	2957	then
	2958	echo "$module_commands" >> $jobfile
	2959	fi
	2960
	2961
	2962	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2963	if [[ $create_remote_batch_job = true ]]
	2964	then
	2965	echo "mkdir $tempdir" >> $jobfile
	2966	echo "chmod go+rx $tempdir" >> $jobfile
	2967	else
	2968	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2969	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2970	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2971	mkdir $tempdir
	2972	chmod go+rx $tempdir
	2973	fi
	2974	echo "cd $tempdir" >> $jobfile
	2975	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2976	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2977	echo "export PATH=.:\$PATH" >> $jobfile
	2978	echo "export execute_palmrun=true" >> $jobfile
	2979
	2980
	2981	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2982	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2983	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2984	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2985	echo "export LOCAL_PWD" >> $jobfile
	2986
	2987
	2988	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2989	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2990	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2991
	2992
	2993	# CALL PALMRUN WITHIN THE JOB
	2994	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2995	echo "set -x" >> $jobfile
	2996	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2997
	2998
	2999	# TRANSFER JOBFILE TO THE TARGET HOST
	3000	if [[ $create_jobfile_only = false ]]
	3001	then
	3002
[3505]	3003	# CREATE LOCAL JOB FOLDER
	3004	eval local_jobcatalog=$local_jobcatalog
	3005	if [[ ! -d $local_jobcatalog ]]
	3006	then
	3007	echo " "
	3008	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3009	mkdir $local_jobcatalog
	3010	fi
	3011
[2380]	3012	if [[ $create_remote_batch_job = true ]]
	3013	then
	3014
[2420]	3015	echo " "
[2566]	3016	echo " *** transfer of job to remote host via scp"
[3505]	3017
	3018	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3019	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3020
	3021	# COPY THE JOB FILE
[2420]	3022	if [[ $do_trace = true ]]
	3023	then
[3236]	3024	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3025	fi
[3236]	3026	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3027
[3505]	3028	# SUBMIT THE JOB
[3574]	3029	printf " *** submit the job (output of submit command, \n"
[3573]	3030	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3031	if [[ $do_trace = true ]]
	3032	then
[3549]	3033	echo " echo \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null"
[2420]	3034	fi
[3549]	3035	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null
[2380]	3036
	3037	elif [[ $create_batch_job = true ]]
	3038	then
	3039
[2385]	3040	eval local_jobcatalog=$local_jobcatalog
[3236]	3041	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3042	cd $local_jobcatalog
[2380]	3043	echo " "
[2420]	3044	echo " *** submit the job"
	3045	if [[ $do_trace = true ]]
	3046	then
[3236]	3047	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3048	fi
[3236]	3049	$submit_command ${configuration_identifier}_${run_id}
	3050	rm ${configuration_identifier}_${run_id}
[2380]	3051	cd - > /dev/null
	3052
	3053	fi
	3054
	3055	rm -rf $jobfile
	3056
	3057	else
	3058
	3059	printf "\n *** jobfile created under name \"$jobfile\" "
	3060	printf "\n no batch-job has been sent!"
	3061
	3062	fi
	3063
	3064	fi # END OF REMOTE-PART

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |