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source: palm/trunk/SCRIPTS/palmrun @ 3864

Last change on this file since 3864 was 3860, checked in by raasch, 6 years ago
check added, that it is not allowed to set option -b if the configuration file has been setup for running batch jobs on remote hosts, local time added to terminal output before and after saving output files
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.9 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 3860 2019-04-04 06:23:27Z monakurppa $
[3860]	29	# check added, that it is not allowed to set option -b if the configuration file has been setup
	30	# for running batch jobs on remote hosts,
	31	# local time added to terminal output before and after saving output files
	32	#
	33	# 3725 2019-02-07 10:11:02Z raasch
[3725]	34	# error messages for failed restarts extended
	35	#
	36	# 3682 2019-01-18 17:01:54Z knoop
[3665]	37	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
	38	# of login messages on specific systems
	39	#
	40	# 3574 2018-11-28 13:14:39Z raasch
[3574]	41	# syntax-error in last commit fixed
	42	#
	43	# 3573 2018-11-28 13:03:44Z raasch
[3573]	44	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
	45	# removed,
	46	# r3570 reverted
	47	#
	48	# 3570 2018-11-27 17:44:21Z kanani
[3570]	49	# Rename job-id by run_id
	50	#
	51	# 3555 2018-11-22 13:50:37Z raasch
[3555]	52	# sed-command to remove repeated space-characters replaced by tr-command, to
	53	# guarantee mac compatible
	54	#
	55	# 3549 2018-11-21 15:44:44Z raasch
[3549]	56	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	57	# of login messages on specific systems
	58	#
	59	# 3534 2018-11-19 15:35:16Z raasch
[3534]	60	# batch_scp for sending back the job protocol file is called via login-node if
	61	# a login-node has been set in the config-file
	62	# ssh-calls rearranged to avoid output of system/user-profile messages
	63	#
	64	# 3505 2018-11-08 09:14:30Z raasch
[3505]	65	# job folders are created in case that they do not exist
	66	#
	67	# 3455 2018-10-30 14:12:31Z raasch
[3455]	68	# options -h and -d renamed -c and -r, respectively
	69	#
	70	# 3402 2018-10-23 11:49:24Z knoop
[3346]	71	# job_id is set for compatibility reasons with older versions of config files
	72	#
	73	# 3313 2018-10-06 15:22:48Z knoop
[3294]	74	# more detailed error message for outdated fileconnection file
	75	#
	76	# 3236 2018-09-10 09:07:06Z raasch
[3236]	77	# warning issued in case of file connection file version mismatch,
	78	# host_configuration renamed configuration_identifier,
	79	# "host identifier" in header output renamed "config. identifier",
	80	# jobname renamed run_identifier,
	81	# run_id renamed run_id_number
	82	# job_id renamed run_id
	83	# option -r renamed -i
	84	#
	85	# 3151 2018-07-19 08:45:38Z raasch
[3151]	86	# removed additional listing of files to be compiled, print PALM code revision
	87	# in header
	88	#
	89	# 3132 2018-07-16 11:44:58Z raasch
[3132]	90	# create consistent error messages in case of failed restarts,
	91	# check existence of remote job catalog
	92	#
	93	# 3043 2018-05-25 10:47:54Z raasch
[3043]	94	# check for setting of fast_io_catalog
	95	#
	96	# 3033 2018-05-23 15:26:19Z raasch
[3025]	97	# -T option not required for interactive runs (tasks per node =
	98	# total number of cores is assumed as default, if option is not given),
	99	# reformatting of a few messages,
	100	# bugfix: destination output directory is created if attribute "pe" is set in
	101	# .palm.iofiles
	102	#
	103	# 2718 2018-01-02 08:49:38Z maronga
[2993]	104	# bugfix of r2990
	105	#
	106	# 2718 2018-01-02 08:49:38Z maronga
[2990]	107	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	108	# not in the working directory from where palmrun is called
	109	#
	110	# 2718 2018-01-02 08:49:38Z maronga
[2957]	111	# svfout in the activation string will be replaced now by svfin in case of
	112	# automatic restarts
	113	#
	114	# 2718 2018-01-02 08:49:38Z maronga
[2906]	115	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	116	# the possible output or input of sky view factors
	117	#
	118	# 2718 2018-01-02 08:49:38Z maronga
[2834]	119	# "fname" renamed to "jobname"
	120	#
	121	# 2718 2018-01-02 08:49:38Z maronga
[2799]	122	# parameters are allowed in output commands (OC:)
	123	#
	124	# 2718 2018-01-02 08:49:38Z maronga
[2789]	125	# bugfix: exit if no queue has been given neither with option -q nor in the
	126	# configuration file
	127	#
	128	# 2718 2018-01-02 08:49:38Z maronga
[2762]	129	# file connection file from trunk/SCRIPTS is taken by default
	130	#
	131	# 2718 2018-01-02 08:49:38Z maronga
[2716]	132	# Corrected "Former revisions" section
	133	#
	134	# 2696 2017-12-14 17:12:51Z kanani
	135	# Change in file header (GPL part)
	136	#
	137	# 2693 2017-12-13 12:33:49Z raasch
[2693]	138	# replacement of variables given by {{<variable>}} in configuration file is now
	139	# done in a more general way, variable names are written in small letters
	140	#
	141	# 2670 2017-12-06 16:32:19Z raasch
[2670]	142	# test printouts removed
	143	#
	144	# 2669 2017-12-06 16:03:27Z raasch
[2669]	145	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	146	# removed,
	147	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	148	# files,
	149	# informative messages in case of missing optional input files shortened
	150	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	151	#
	152	# 2638 2017-11-23 12:44:23Z raasch
[2610]	153	# use of wildcards in file connection statements enabled
	154	#
	155	# 2605 2017-11-09 15:31:46Z raasch
[2605]	156	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	157	# will not be sent with the job file any more, but copied into the
[2610]	158	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	159	#
	160	# 2600 2017-11-01 14:11:20Z raasch
[2600]	161	# cycle numbers are made three digits wide
	162	#
	163	# 2566 2017-10-20 08:50:47Z raasch
[2566]	164	# execute command for combine_plot_fields added
	165	# "TEMPDIR" renamed "tempdir"
	166	# temporary working directory for local batch jobs is created immediately within
	167	# the user's palmrun call, due to a requirement of the "grid engine" batch
	168	# system, where the working directory is given with batch directive -wd and must
	169	# already exist when the job is submitted,
	170	# informative messages in non-trace mode reduced and partly reformatted
	171	#
	172	# 2551 2017-10-18 07:25:11Z raasch
[2551]	173	# TEMPDIR added as replacement string to be used in batch directives
	174	#
	175	# 2512 2017-10-04 08:26:59Z raasch
[2507]	176	# bugfix for determining cycle numbers of NetCDF input files
	177	#
	178	# 2506 2017-09-29 08:30:37Z raasch
[2506]	179	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	180	# host configuration added to SOURCES_FOR_RUN_... folder name
	181	# host_identifier renamed host_configuration
	182	# option -W added to allow for job dependencies
	183	#
	184	# 2501 2017-09-26 11:41:55Z raasch
[2501]	185	# default value for number of cores (option -X) set to 1
	186	# bugfix for mechanism which overwrites configuration file settings with values
	187	# provided by palmrun options
	188	#
	189	# 2499 2017-09-22 16:47:58Z kanani
[2499]	190	# option -h named configuration identifier
	191	#
	192	# 2480 2017-09-19 06:24:14Z maronga
[2480]	193	# bugfix for last revision
	194	#
	195	# 2479 2017-09-19 06:12:16Z raasch
[2479]	196	# option -A (project account number) added
	197	#
	198	# 2422 2017-09-08 08:25:41Z raasch
[2410]	199	# initial revision
[2380]	200	#
	201	#--------------------------------------------------------------------------------#
	202	# palmrun - script for running PALM jobs on local and remote hosts
	203	#--------------------------------------------------------------------------------#
	204
	205
	206
	207	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	208
	209	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	210	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	211	# (TOO MANY ARGUMENTS - PROBLEM)
	212	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	213
[2610]	214	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	215	typeset -i nr_of_output_files=0
[2380]	216	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	217	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	218	# SCRIPT-OPTION ARGUMENTS
	219	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	220	typeset -i icycle inode ival maxcycle mpi_tasks
	221	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	222
	223	activation_string_list=""
	224	AddFilenames=""
	225	combine_plot_fields=true
	226	compiler_name=""
	227	compiler_name_ser=""
	228	compiler_options=""
[3236]	229	configuration_identifier="default"
[2501]	230	cores=1
[2380]	231	cores_atmos=0
	232	cores_ocean=0
	233	coupled_dist=""
	234	cpp_options=""
	235	cpumax=0
[2506]	236	create_batch_job=false
[2380]	237	create_jobfile_only=false
	238	create_remote_batch_job=false
	239	dashes=" ----------------------------------------------------------------------------"
	240	defaultqueue=""
[2506]	241	delete_temporary_catalog=true
[2380]	242	do_compile=true
	243	do_trace=false
	244	executable=""
	245	execute_command=""
	246	execution_error=false
[2762]	247	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	248	global_revision=""
	249	hostfile=""
	250	hp=""
	251	keep_data_from_previous_run=false
	252	link_local_input=false
	253	link_local_output=false
[2388]	254	linker_options=""
[2385]	255	local_jobcatalog=""
[2380]	256	locat=normal
	257	makefile=""
	258	max_par_io_str=""
	259	prc=$0
	260	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	261	do
	262	prc=`echo $prc \| cut -f2- -d"/"`
	263	done
	264	module_calls=""
[2506]	265	palmrun_memory=""
[2380]	266	palmrun_script_name=$prc
	267	openmp=false
[2506]	268	previous_job=""
[2479]	269	project_account=""
[2380]	270	queue=none
[2906]	271	read_svf=""
[2380]	272	restart_run=false
	273	return_address=""
[2385]	274	remote_jobcatalog=""
[2380]	275	remote_username=""
	276	running_in_batch_mode=false
[3313]	277	running_in_test_mode=false
[2380]	278	run_coupled_model=false
	279	run_id=""
[3236]	280	run_id_number=""
	281	run_identifier=test
[2380]	282	silent=false
	283	source_list=""
	284	source_path=""
[2501]	285	tasks_per_node=0
[2380]	286	threads_per_task=1
	287	transfer_problems=false
[2384]	288	user_source_path=""
[2506]	289	use_existing_sources_folder=""
[2380]	290	use_openmp=false
[3033]	291	version="palmrun 1.0 Rev$Rev: 3860 $"
[2380]	292	working_directory=`pwd`
	293	write_binary=""
[2906]	294	write_svf=""
[2380]	295
	296
	297	# ERROR HANDLING IN CASE OF EXIT
[2404]	298	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	299	then
	300
	301	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	302	(( i = 0 ))
	303	while (( i < iec ))
	304	do
	305	(( i = i + 1 ))
	306	printf "\n *** Execution of ERROR-command:\n"
	307	printf " >>> ${err_command[$i]}\n"
	308	eval ${err_command[$i]}
	309	done
[2566]	310	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	311	printf "\n\n+++ palmrun crashed \n\n"
	312	exit 1
	313	elif [[ $locat != normal ]]
[2380]	314	then
[3312]	315	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	316	printf "\n+++ palmrun killed by \"^C\" \n\n"
	317	exit 2
	318	else
[2566]	319	printf "\n --> palmrun finished\n\n"
[3312]	320	exit 0
[2380]	321	fi' exit
	322
	323
	324	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	325	trap 'locat=control_c
	326	exit 1
[2380]	327	' 2
	328
	329
	330	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	331	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	332	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]	333	do
	334	case $option in
	335	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	336	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	337	(b) create_batch_job=true; prc="$prc -b";;
	338	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	339	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	340	(C) restart_run=true; prc="$prc -C";;
	341	(F) create_jobfile_only=true;;
	342	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	343	(i) run_id_number=$OPTARG;;
[2380]	344	(j) running_in_batch_mode=true;;
	345	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	346	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	347	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	348	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	349	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	350	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	351	(R) return_address=$OPTARG;;
	352	(s) source_list=$OPTARG;;
[2501]	353	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	354	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	355	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	356	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	357	(v) silent=true; prc="$prc -v";;
[2506]	358	(V) use_existing_sources_folder="-V";;
[2380]	359	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	360	(W) previous_job=$OPTARG;;
[2380]	361	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	362	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	363	(y) ocean_file_appendix=true; prc="$prc -y";;
	364	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	365	(z) running_in_test_mode=true;;
[2380]	366	(Z) combine_plot_fields=false; prc="$prc -Z";;
	367	(\?) printf "\n +++ unknown option $OPTARG \n"
	368	printf "\n --> type \"$0 ?\" for available options \n"
	369	locat=parameter;exit;;
	370	esac
	371	done
	372
	373
	374	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	375	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	376	(( to_shift = $OPTIND - 1 ))
	377	shift $to_shift
	378
	379	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	380	if [[ "$1" = "?" ]]
	381	then
	382	(printf "\n *** Description of available palmrun options:\n"
	383	printf "\n Option Description Default-Value"
	384	printf "\n -a activation string list \"\" "
[2479]	385	printf "\n -A project account number ---"
[2380]	386	printf "\n -b batch-job on local machine ---"
	387	printf "\n -B do not delete temporary directory at end ---"
[3455]	388	printf "\n -c configuration identifier \"default\" "
[2380]	389	printf "\n -F create batch job file only ---"
	390	printf "\n -k keep data from previous run"
	391	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	392	printf "\n -M Makefile name Makefile"
	393	printf "\n -O threads per openMP task ---"
	394	printf "\n -q queue \"$queue\" "
[3455]	395	printf "\n -r run identifier test"
[2380]	396	printf "\n -s filenames of routines to be compiled \"\" "
	397	printf "\n must end with .f, .f90, .F, or .c !"
	398	printf "\n use \"..\" for more than one file and wildcards"
	399	printf "\n -s LM compiles all locally modified files"
	400	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	401	printf "\n -T tasks per node ---"
[2380]	402	printf "\n -u username on remote machine \"\" "
	403	printf "\n -v no prompt for confirmation ---"
[2506]	404	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	405	printf "\n -w maximum parallel io streams as given by -X"
[2506]	406	printf "\n -W name of job to wait for ---"
[2380]	407	printf "\n -x tracing of palmrun for debug purposes ---"
	408	printf "\n -X # of processors (on parallel machines) 1"
	409	printf "\n -y add appendix \"_O\" to all local output"
	410	printf "\n files (ocean precursor runs followed by"
	411	printf "\n coupled atmosphere-ocean runs) ---"
	412	printf "\n -Y run coupled model, \"#1 #2\" with"
	413	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	414	printf "\n -Z skip combine_plot_fields at the end of "
	415	printf "\n the simulation ---"
	416	printf "\n "
	417	printf "\n Possible values of positional parameter <modus>:"
	418	printf "\n \"?\" - this outline \n\n") \| more
	419	exit
	420	elif [[ "$1" != "" ]]
	421	then
	422	printf "\n +++ positional parameter $1 unknown \n"
	423	locat=parameter; exit
	424	fi
	425
	426
	427
	428	# SHORT STARTING MESSAGE
	429	printf "\n*** $version "
	430	printf "\n will be executed. Please wait ..."
	431
	432
[2506]	433	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	434	config_file=.palm.config.$configuration_identifier
	435	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	436
	437
	438	# CHECK, IF CONFIGURATION FILE EXISTS
	439	if [[ ! -f $config_file ]]
	440	then
	441	printf "\n\n +++ configuration file: "
	442	printf "\n $config_file"
	443	printf "\n does not exist"
	444	locat=connect; exit
	445	fi
	446
	447
[2762]	448	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	449	if [[ -f .palm.iofiles ]]
	450	then
[3236]	451
	452	# CHECK VERSION MISMATCH
[3573]	453	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
	454	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
	455	if [[ $running_in_batch_mode != true && $restart_run != true ]]
[3236]	456	then
	457	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	458	then
	459	printf "\n\n +++ WARNING: A file connection file has been found in your"
	460	printf "\n working directory, but its revision does not match"
	461	printf "\n the revision of the default (trunk) version."
[3294]	462	printf "\n You may need to update your connection file"
	463	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	464	fi
	465	fi
	466
[2762]	467	fileconnection_file=.palm.iofiles
[3236]	468
[2762]	469	fi
	470
	471
[2380]	472	# CHECK, IF FILE CONNECTION FILE EXISTS
	473	if [[ ! -f $fileconnection_file ]]
	474	then
	475	printf "\n\n +++ file connection file: "
	476	printf "\n $fileconnection_file"
	477	printf "\n does not exist"
	478	locat=connect; exit
	479	fi
	480
	481
[2404]	482	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	483	if [[ "$activation_string_list" = "" ]]
	484	then
	485	printf "\n\n +++ no activation string list given: "
	486	printf "\n please set palmrun option \"-a\" "
	487	locat=palmrun_option; exit
	488	fi
	489
	490
	491	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	492	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	493	then
	494	write_binary=true
	495	else
	496	write_binary=false
	497	fi
	498
[2906]	499	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	500	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	501	then
	502	write_svf=true
	503	else
	504	write_svf=false
	505	fi
[2404]	506
[2906]	507	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	508	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	509	then
	510	read_svf=true
	511	else
	512	read_svf=false
	513	fi
	514
	515
[2380]	516	# READ AND EVALUATE THE CONFIGURATION-FILE
	517	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	518
	519	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	520	while read line
	521	do
	522
	523	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	524	eval line=\"$line\"
	525
	526
	527	# INTERPRET THE LINE
	528	if [[ "$(echo $line)" = "" ]]
	529	then
	530
	531	# EMPTY LINE, NO ACTION
	532	continue
	533
	534	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	535	then
	536
	537	# LINE IS A COMMENT LINE
	538	continue
	539
	540	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	541	then
	542
	543	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	544	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	545	value=`echo $line \| cut -d" " -s -f2-`
	546
	547
	548	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	549	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	550	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	551	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	552	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	553	# CONFIGURATION-FILE.
	554	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	555	then
	556	eval export $var="\$value"
	557
	558	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	559	if [[ $do_trace = true ]]
	560	then
	561	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	562	fi
	563	fi
	564
	565	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	566	then
	567
	568	# LINE DEFINES BATCH-DIRECTIVE
	569	(( ibd = ibd + 1 ))
	570	line=$(echo $line \| cut -c4-)
	571	batch_directive[$ibd]="$line"
	572
	573	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	574	then
	575
	576	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	577	# REMOTE TO A LOCAL HOST
	578	(( ibdt = ibdt + 1 ))
	579	line=$(echo $line \| cut -c5-)
	580	batch_directive_transfer[$ibdt]="$line"
	581
	582	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	583	then
	584
	585	# LINE DEFINES ERROR-COMMAND
	586	(( iec = iec + 1 ))
	587	line=$(echo $line \| cut -c4-)
	588	err_command[$iec]="$line"
	589
	590	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	591	then
	592
	593	# LINE DEFINES INPUT-COMMAND
	594	(( iic = iic + 1 ))
	595	line=$(echo $line \| cut -c4-)
	596	in_command[$iic]="$line"
	597
	598	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	599	then
	600
	601	# LINE DEFINES OUTPUT-COMMAND
	602	(( ioc = ioc + 1 ))
	603	line=$(echo $line \| cut -c4-)
	604	out_command[$ioc]="$line"
	605
	606	else
	607
	608	# SKIP ALL OTHER LINES
	609	continue
	610
	611	fi
	612
	613	done < $config_file
	614
	615
	616	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	617	if [[ "$fast_io_catalog" = "" ]]
	618	then
[3860]	619	printf "\n\n +++ no fast_io_catalog found in $config_file"
[3043]	620	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	621	locat=config_file; exit
	622	fi
[2380]	623	if [[ "$compiler_name" = "" ]]
	624	then
[3860]	625	printf "\n\n +++ no compiler name found in $config_file"
[2380]	626	printf "\n Please add line \"compiler_name ...\" to that file."
	627	locat=config_file; exit
	628	fi
	629	if [[ "$compiler_name_ser" = "" ]]
	630	then
[3860]	631	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
[2380]	632	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	633	locat=config_file; exit
	634	fi
	635	if [[ "$compiler_options" = "" ]]
	636	then
[3860]	637	printf "\n\n +++ no compiler options found in $config_file"
[2380]	638	printf "\n Please add line \"compiler_options ...\" to that file."
	639	locat=config_file; exit
	640	fi
	641	if [[ "$execute_command" = "" ]]
	642	then
[3860]	643	printf "\n\n +++ no execute command found in $config_file"
[2380]	644	printf "\n Please add line \"execute_command ...\" to that file."
	645	locat=config_file; exit
	646	fi
	647
	648	if [[ "$hostfile" != "" ]]
	649	then
	650	if [[ $hostfile != auto && ! -f $hostfile ]]
	651	then
[3860]	652	printf "\n\n +++ no hostfile \"$hostfile\" found"
[3151]	653	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	654	locat=config_file; exit
	655	fi
	656	fi
	657
	658
	659	# DETERMINE THE CALL STATUS
	660	if [[ "$return_address" != "" ]]
	661	then
	662
	663	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	664	# BATCH MODE AND ...
	665	running_on_remote=true
	666
	667	else
	668
	669	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	670	if [[ "$remote_ip" != "" ]]
	671	then
	672
	673	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	674	create_remote_batch_job=true
	675
[3132]	676	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	677	if [[ "$remote_jobcatalog" = "" ]]
	678	then
[3860]	679	printf "\n\n +++ no remote jobcatalog found in $config_file"
[3132]	680	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	681	locat=config_file; exit
	682	fi
	683
[3860]	684	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
	685	if [[ $create_batch_job = true ]]
	686	then
	687	printf "\n\n +++ option -b must not be set because configuration file has been setup"
	688	printf "\n for running jobs on a remote host"
	689	locat=config_file; exit
	690	fi
	691
[2380]	692	fi
	693	running_on_remote=false
	694	fi
	695
	696
	697
	698	# READ AND EVALUATE THE I/O-FILE LIST
	699	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	700
	701	# READ THE FILE CONNECTION FILE LINE BY LINE
	702	while read line
	703	do
	704
[2669]	705	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	706	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	707	line=`echo "$line" \| tr -s " "`
[2380]	708
	709	# INTERPRET THE LINE
	710	if [[ "$(echo $line)" = "" ]]
	711	then
	712	# EMPTY LINE, NO ACTION
	713	continue
	714
	715	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	716	then
	717
	718	# LINE IS A COMMENT LINE
	719	true
	720
	721	else
	722
	723	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	724	# s2a: in/out - field
[2669]	725	# s2b: action - field (optional)
	726	s1=`echo "$line" \| cut -d" " -f1`
	727	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	728	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	729	then
[2669]	730	s2a=$s2
[2380]	731	s2b=""
	732	else
[2669]	733	s2a=`echo $s2 \| cut -d":" -f1`
	734	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	735	fi
[2669]	736	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	737	s4=`echo "$line" \| cut -d" " -s -f4`
	738	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	739	s5=`echo "$line" \| cut -d" " -s -f5`
	740	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	741
	742
	743	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	744	# INPUT- OR OUTPUT-LIST.
	745	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	746	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	747	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	748	# IS NOT CHECKED AND STORED.
[2610]	749	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	750	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	751	then
	752	found=false
	753	for actual in $activation_string_list
	754	do
	755	for formal in $s3
	756	do
	757	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	758	done
	759	done
	760	if [[ $found = true ]]
	761	then
	762	(( iin = iin + 1 ))
[2669]	763	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	764	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	765	if [[ "$s2a" = inopt ]]
	766	then
	767	optin_pre[$iin]=yes
	768	else
	769	optin_pre[$iin]=no
	770	fi
[2605]	771
	772	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	773	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	774	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	775	then
[2610]	776	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	777	fi
	778
[2610]	779	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	780	# THE WILDCARD FROM THE ENDING
	781	if [[ "${s5: -1}" = "*" ]]
	782	then
[2669]	783	if [[ "$s2b" = "di" ]]
[2610]	784	then
	785	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	786	printf "\n see file \"$fileconnection_file\", line"
	787	printf "\n$line"
	788	locat=iofiles_file; exit
	789	fi
	790	multin[$iin]=true
	791	string=${endin_pre[$iin]}
	792	endin_pre[$iin]="${string%?}"
	793	else
	794	multin[$iin]=false
	795	fi
[2380]	796	fi
[2669]	797	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	798	then
	799	found=false
	800	for actual in $activation_string_list
	801	do
	802	for formal in $s3
	803	do
[2670]	804	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	805	done
	806	done
	807	if [[ $found = true ]]
	808	then
	809	(( iout = iout + 1 ))
[2669]	810	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	811	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	812
[2669]	813	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	814	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	815	if [[ $formal = wildcard ]]
	816	then
	817	warnout_pre[$iout]=false
	818	else
	819	warnout_pre[$iout]=true
	820	fi
	821
[2610]	822	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	823	# THE WILDCARD FROM THE LOCAL FILENAME
	824	if [[ "${s1: -1}" = "*" ]]
	825	then
[2669]	826	if [[ "$s2b" = "di" ]]
[2610]	827	then
	828	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	829	printf "\n see file \"$fileconnection_file\", line"
	830	printf "\n$line"
	831	locat=iofiles_file; exit
	832	fi
	833	multout[$iout]=true
	834	string=${localout_pre[$iout]}
	835	localout_pre[$iout]="${string%?}"
	836	else
	837	multout[$iout]=false
	838	fi
[2380]	839	fi
[2669]	840	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	841	then
[2669]	842	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	843	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	844	locat=connect; exit
	845	fi
	846	IFS="$IFSALT"
	847	fi
	848
	849	done < $fileconnection_file
	850
	851
	852
[2501]	853	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	854	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	855	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	856	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	857	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	858	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	859
	860
	861
[2380]	862	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	863	if [[ $run_coupled_model = true ]]
	864	then
	865
	866	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	867	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	868
	869	if (( $cores_ocean + $cores_atmos != $cores ))
	870	then
	871
	872	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	873	printf "\n PEs (total) : $cores"
	874	printf "\n PEs (atmosphere): $cores_atmos"
	875	printf "\n PEs (ocean) : $cores_ocean"
	876	locat=coupling; exit
	877
	878	fi
	879
	880	fi
	881
	882
	883	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	884	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	885	# FOLDER
	886	if [[ $running_in_batch_mode = true ]]
	887	then
	888
[2506]	889	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	890	then
[2506]	891	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	892	printf "\n Please check the output of the palmrun-call"
	893	printf "\n that you did on your local host."
	894	locat=SOURCES_FOR_RUN; exit
	895	fi
	896
	897	else
	898
	899	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	900	# AUTOMATIC RESTART RUN
	901	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	902	if [[ $restart_run = false ]]
	903	then
	904
	905	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	906	# THE LOCAL HOST
	907	if [[ ! -d $source_path ]]
	908	then
	909	printf "\n\n +++ source path \"$source_path\" on local host"
	910	printf "\n \"$(hostname)\" does not exist"
	911	locat=source_path; exit
	912	fi
	913
[2990]	914	rm -rf ${base_directory}/${sources_for_run_catalog}
	915	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	916
	917	if [[ "$source_list" = LM ]]
	918	then
	919
	920	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	921	source_list=""
	922	cd $source_path
	923
	924
[2512]	925	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	926	if [[ ! -d ../.svn ]]
[2380]	927	then
	928	printf "\n\n +++ source directory"
	929	printf "\n \"$source_path\" "
	930	printf "\n is not under control of \"subversion\"."
[2512]	931	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	932	fi
	933
	934
	935	# LIST ALL MODIFIED SOURCE CODE FILES
	936	Filenames=""
[2404]	937	svn status > tmp_svnstatus
[2380]	938	while read line
	939	do
	940	firstc=`echo $line \| cut -c1`
	941	if [[ $firstc = M \|\| $firstc = "?" ]]
	942	then
	943	Name=`echo "$line" \| cut -c8-`
	944	extension=`echo $Name \| cut -d. -f2`
	945	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	946	then
	947	Filenames="$Filenames "$Name
	948	fi
	949	fi
[2404]	950	done < tmp_svnstatus
	951	rm -rf tmp_svnstatus
[2380]	952
	953
	954	# COPY FILES TO SOURCES_FOR_RUN_...
	955	for filename in $Filenames
	956	do
[2990]	957	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	958	source_list=$source_list"$filename "
	959	done
	960
	961	cd - > /dev/null
	962
	963
	964	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	965	elif [[ "$source_list" != "" ]]
	966	then
	967
	968	cd $source_path
	969
	970	for filename in $source_list
	971	do
	972
	973	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	974	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	975	then
	976	printf "\n +++ source code file: $filename"
	977	printf "\n must not contain (\"/\") "
	978	locat=source; exit
	979	fi
	980
	981	if [[ ! -f $filename ]]
	982	then
	983	printf "\n +++ source code file: $filename"
	984	printf "\n does not exist"
	985	locat=source; exit
	986	else
[2990]	987	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	988	fi
	989
	990	done
	991
	992	cd - > /dev/null
	993
	994	fi
	995
	996	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	997	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	998	if [[ ! -f $makefile ]]
	999	then
	1000	printf "\n +++ file \"$makefile\" does not exist"
	1001	locat=make; exit
	1002	else
[2990]	1003	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	1004	fi
	1005
	1006
	1007	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	1008	if [[ "$user_source_path" != "" ]]
[2380]	1009	then
	1010
	1011	# DOES THE DIRECTORY EXIST?
[2384]	1012	if [[ ! -d $user_source_path ]]
[2380]	1013	then
	1014
	1015	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	1016	printf "\n \"$user_source_path\" "
[2380]	1017	printf "\n does not exist or is not a directory."
	1018	printf "\n No source code will be used from this directory!\n"
[2384]	1019	user_source_path=""
[2380]	1020	if [[ $silent == false ]]
	1021	then
	1022	sleep 2
	1023	fi
	1024
	1025	else
	1026
[2384]	1027	cd $user_source_path
[2380]	1028
	1029	Names=$(ls -1 *.f90 2>&1)
	1030	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1031	Names=$(ls -1 *.F90 2>&1)
	1032	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1033	Names=$(ls -1 *.F 2>&1)
	1034	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1035	Names=$(ls -1 *.f 2>&1)
	1036	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1037	Names=$(ls -1 *.c 2>&1)
	1038	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1039
	1040	cd - > /dev/null
[2990]	1041	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1042
	1043	# COPY MAKEFILE IF EXISTING
[2384]	1044	if [[ -f $user_source_path/Makefile ]]
[2380]	1045	then
	1046	printf "\n\n *** user Makefile from directory"
[2384]	1047	printf "\n \"$user_source_path\" is used \n"
[2380]	1048	if [[ $silent == false ]]
	1049	then
	1050	sleep 1
	1051	fi
[2384]	1052	cp $user_source_path/Makefile .
[2380]	1053	fi
	1054
	1055	for filename in $AddFilenames
	1056	do
	1057	if [[ -f $filename ]]
	1058	then
	1059	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1060	printf "\n source code directory \"$user_source_path\" "
[2380]	1061	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1062	printf "\n from directory \"$source_path\"."
	1063	locat=source; exit
	1064	fi
	1065
[2384]	1066	cp $user_source_path/$filename .
[2380]	1067	source_list="$source_list $filename"
	1068
	1069	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1070	if [[ $(grep -c $filename Makefile) = 0 ]]
	1071	then
	1072	printf "\n\n +++ user file \"$filename\" "
	1073	printf "\n is not listed in Makefile \n"
	1074	locat=source; exit
	1075	fi
	1076	done
	1077	cd - > /dev/null
	1078	fi
	1079	fi
	1080
	1081	# COPY CONFIGURATION FILES
[2990]	1082	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1083	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1084
	1085	# COPY SHELLSCRIPTS
[2990]	1086	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1087	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1088
	1089	fi
	1090
	1091	fi
	1092
[2605]	1093
[2380]	1094	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1095	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1096	if [[ "$global_revision" = "" ]]
	1097	then
	1098	global_revision=`svnversion $source_path 2>/dev/null`
	1099	global_revision="Rev: $global_revision"
	1100	fi
	1101
	1102
	1103	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1104	if [[ -n $cores ]]
	1105	then
	1106
	1107	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1108	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1109	if [[ $tasks_per_node = 0 ]]
[2380]	1110	then
[3025]	1111	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1112	then
	1113	printf "\n"
	1114	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1115	printf "\n set -T option or define tasks_per_node in the config file"
	1116	locat=tasks_per_node; (( iec = 0 )); exit
	1117	else
	1118	# DEFAULT FOR INTERACTIVE RUN
	1119	tasks_per_node=$cores
	1120	fi
[2380]	1121	fi
	1122
	1123	if (( cores < tasks_per_node ))
	1124	then
	1125	printf "\n"
	1126	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1127	printf "\n given values: -T $tasks_per_node -X $cores"
	1128	locat=tasks_per_node; (( iec = 0 )); exit
	1129	fi
	1130
	1131	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1132	(( mpi_tasks = cores / threads_per_task ))
	1133	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1134	(( ii = cores / tasks_per_node ))
	1135	(( remaining_cores = cores - ii * tasks_per_node ))
	1136	if (( remaining_cores > 0 ))
	1137	then
	1138	printf "\n"
	1139	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1140	printf "\n divisor of the total number of cores (option \"-X\")"
	1141	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1142	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1143	(( nodes = nodes + 1 ))
	1144	fi
	1145
	1146	fi
	1147
	1148
	1149	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1150	if [[ "$maximum_parallel_io_streams" = "" ]]
	1151	then
	1152	maximum_parallel_io_streams=$cores
	1153	fi
	1154
	1155
	1156	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1157	if [[ "$scp_port" != "" ]]
	1158	then
	1159	PORTOPT="-P $scp_port"
	1160	SSH_PORTOPT="-p $scp_port"
	1161	fi
	1162
	1163
	1164	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1165	# CONFIG-FILE
	1166	if [[ "$ssh_key" != "" ]]
	1167	then
	1168	ssh_key="-i $HOME/.ssh/$ssh_key"
	1169	fi
	1170
	1171
	1172	# SET QUEUE, IF NOT GIVEN
	1173	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1174	then
	1175
	1176	if [[ $queue = none && "$defaultqueue" = "" ]]
	1177	then
	1178	printf "\n"
	1179	printf "\n +++ no default queue given in configuration file and no queue"
	1180	printf "\n given with option -q"
[2789]	1181	locat=queue; exit
[2380]	1182	fi
	1183	if [[ $queue = none ]]
	1184	then
	1185	queue=$defaultqueue
	1186	fi
	1187
	1188	fi
	1189
	1190
	1191	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1192	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1193	(( i = 0 ))
[2610]	1194	(( nr_of_input_files = 0 ))
[2380]	1195	while (( i < iin ))
	1196	do
	1197	(( i = i + 1 ))
	1198
	1199	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1200	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1201	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1202	then
[2610]	1203	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1204	else
[3236]	1205	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1206	fi
	1207
[2610]	1208
[2380]	1209	# CHECK IF FILE EXISTS
	1210	if ! ls $filename* 1>/dev/null 2>&1
	1211	then
	1212
[2669]	1213	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1214	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1215	then
	1216	printf "\n\n +++ INPUT-file: "
[2610]	1217	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1218	then
	1219	printf "\n $filename"
	1220	else
[2610]	1221	printf "\n $filename.${extin_pre[$i]}"
[2380]	1222	fi
	1223	printf "\n does not exist\n"
	1224	locat=input; exit
	1225	else
[2610]	1226	(( nr_of_input_files = nr_of_input_files + 1 ))
	1227	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1228	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1229	actionin[$nr_of_input_files]="unavailable"
[2610]	1230	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1231	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1232	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1233	fi
[2605]	1234
[2380]	1235	else
	1236
[3236]	1237	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1238	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1239	# ENDINGS
[2610]	1240	if [[ "${multin[$i]}" = true ]]
	1241	then
	1242	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1243	ls -1 -d ${filename} > filelist 2>/dev/null
	1244	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1245	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1246
[2610]	1247	endings=""
	1248	while read line
	1249	do
	1250	# filename without path (i.e. after the last "/")
	1251	basefilename=$(basename ${line})
[2380]	1252
[2610]	1253	# check if there is an extension and remove it
	1254	ext=${basefilename##*.}
	1255	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1256	then
	1257	basefilename=${basefilename%.*}
	1258	fi
[2380]	1259
[2610]	1260	# check for an existing cycle number and remove it
	1261	cycle=${basefilename##*.}
	1262	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1263	then
	1264	basefilename=${basefilename%.*}
	1265	fi
[2600]	1266
[3236]	1267	# remove the run_identifier from the beginning
	1268	length_run_identifier=${#run_identifier}
	1269	ending=${basefilename:${length_run_identifier}}
[2610]	1270
	1271	# remove the ending given in the .iofiles from the beginning
	1272	endingstring="${endin_pre[$i]}"
	1273	length_ending=${#endingstring}
	1274	ending=${ending:${length_ending}}
	1275
	1276	if [[ "$ending" = "" ]]
[2600]	1277	then
[2610]	1278	# standard ending as given in the .iofiles
	1279	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1280	then
	1281	endings="$endings DEFAULT"
	1282	fi
[2600]	1283	else
[2610]	1284	# ending must start with "_", otherwise its a different file
	1285	if [[ "${ending:0:1}" = "_" ]]
	1286	then
	1287	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1288	then
	1289	endings="$endings $ending"
	1290	fi
	1291	fi
[2600]	1292	fi
[2610]	1293
	1294	done <filelist
[2380]	1295
[2610]	1296	rm filelist
[2380]	1297
[2600]	1298	else
[2610]	1299
	1300	# SINGLE NAME
	1301	endings=DEFAULT
	1302
[2600]	1303	fi
	1304
[2610]	1305	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1306	for ending in $endings
	1307	do
	1308
	1309	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1310	if [[ $ending = DEFAULT ]]
[2380]	1311	then
[2610]	1312	ending=""
	1313	fi
	1314
	1315	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1316	(( nr_of_input_files = nr_of_input_files + 1 ))
	1317	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1318	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1319	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1320	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1321	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1322	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1323
	1324
	1325	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1326	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1327	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1328	then
	1329	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1330	else
[3236]	1331	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1332	fi
[2610]	1333
	1334	# DETERMINE THE FILE'S CYCLE NUMBER
	1335	(( maxcycle = 0 ))
	1336	ls -1 -d $filename > filelist 2>/dev/null
	1337	ls -1 -d $filename.* >> filelist 2>/dev/null
	1338	while read line
	1339	do
	1340	# filename without path (i.e. after the last "/")
	1341	basefilename=$(basename ${line})
	1342
	1343	# check if there is an extension
	1344	extension=${basefilename##*.}
	1345	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1346	then
	1347	basefilename=${basefilename%.*}
	1348	fi
	1349
	1350	# check for an existing cycle number
	1351	cycle=${basefilename##*.}
	1352	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1353	then
[2669]	1354	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1355	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1356	(( icycle = $((10#$cycle)) ))
[2610]	1357	else
	1358	(( icycle = 0 ))
	1359	fi
	1360
	1361	if (( icycle > maxcycle ))
	1362	then
	1363	(( maxcycle = icycle ))
	1364
	1365	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1366	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1367	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1368	then
	1369	leading_zero=true
	1370	else
	1371	leading_zero=false
	1372	fi
	1373	fi
	1374
	1375	done <filelist
	1376	rm filelist
	1377
	1378	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1379	if [[ $leading_zero = true ]]
[2380]	1380	then
[2610]	1381	cyclestring=`printf "%03d" $maxcycle`
	1382	else
	1383	cyclestring=$maxcycle
[2380]	1384	fi
[2610]	1385
	1386	# APPEND CYCLE NUMBER TO FILENAME
	1387	if (( maxcycle > 0 ))
[2380]	1388	then
[2610]	1389	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1390	then
	1391	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1392	else
	1393	filename=${filename}.$cyclestring
	1394	fi
[2380]	1395	else
[2610]	1396	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1397	then
	1398	filename=${filename}.${extin[$nr_of_input_files]}
	1399	fi
[2380]	1400	fi
[2610]	1401
	1402	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1403	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1404	absnamein[$nr_of_input_files]=$filename
	1405	if (( maxcycle > 0 ))
[2380]	1406	then
[2610]	1407	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1408	then
	1409	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1410	else
[3236]	1411	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1412	fi
[2380]	1413	else
[2610]	1414	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1415	then
	1416	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1417	else
[3236]	1418	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1419	fi
[2380]	1420	fi
	1421
[2610]	1422	done
	1423
[2380]	1424	fi
[2610]	1425
[2380]	1426	done
	1427
[2610]	1428
[2380]	1429	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1430	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1431	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1432	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1433	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1434	# REMOTE HOST)
	1435	(( i = 0 ))
	1436	while (( i < iout ))
	1437	do
	1438	(( i = i + 1 ))
[2610]	1439	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1440	then
[2610]	1441	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1442	then
[2610]	1443	actionout_pre[$i]=""
	1444	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1445	then
[2610]	1446	actionout_pre[$i]=pe
	1447	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1448	then
[2610]	1449	actionout_pre[$i]=a
[2380]	1450	fi
	1451	(( maxcycle = 0 ))
[3236]	1452	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1453	eval catalogname=${pathout_pre[$i]}
[2380]	1454	if ! ls $filename* 1>/dev/null 2>&1
	1455	then
	1456
	1457	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1458	if cat /dev/null > $filename
	1459	then
	1460	rm $filename
	1461	else
	1462
	1463	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1464	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1465	if [[ ! -d $catalogname ]]
	1466	then
	1467	if mkdir -p $catalogname
	1468	then
	1469	printf "\n\n *** directory:"
	1470	printf "\n $catalogname"
	1471	printf "\n was created\n"
	1472	else
	1473	printf "\n\n +++ OUTPUT-file:"
	1474	printf "\n $filename"
	1475	printf "\n cannot be created, because directory does not exist"
	1476	printf "\n and cannot be created either"
	1477	printf "\n"
	1478	locat=output ; exit
	1479	fi 2>/dev/null
	1480	else
	1481	printf "\n\n +++ OUTPUT-file:"
	1482	printf "\n $filename"
	1483	printf "\n cannot be created, although directory exists"
	1484	printf "\n"
	1485	locat=output ; exit
	1486	fi
	1487	fi 2>/dev/null
	1488
	1489	fi
	1490
	1491	fi
	1492	done
	1493
	1494
	1495	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1496	if [[ $running_in_batch_mode = false ]]
	1497	then
[3236]	1498	run_id_number=$RANDOM
	1499	run_id=${run_identifier}.$run_id_number
[2380]	1500
[3236]	1501	tempdir=$fast_io_catalog/$run_id
[3346]	1502
	1503	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1504	export job_id=$run_id
	1505
[2380]	1506	fi
	1507
	1508
	1509	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1510	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1511	then
	1512
	1513	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1514	if [[ $ibd = 0 ]]
	1515	then
	1516	printf "\n"
	1517	printf "\n +++ no batch directives found in configuration file"
	1518	locat=config_file_batch_directives; (( iec = 0 )); exit
	1519	fi
	1520
	1521	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1522	done=false
[2384]	1523	cputime=$cpumax
[2380]	1524	while [[ $done = false ]]
	1525	do
[2384]	1526	if (( cputime == 0 ))
[2380]	1527	then
	1528	printf "\n +++ cpu-time is undefined"
	1529	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1530	printf "\n >>> "
[2384]	1531	read cputime 1>/dev/null 2>&1
[2380]	1532	else
	1533	done=true
	1534	fi
	1535	done
[2420]	1536	cpumax=$cputime
[2380]	1537
	1538	# CHECK THE MEMORY DEMAND
	1539	done=false
	1540	while [[ $done = false ]]
	1541	do
	1542	if (( memory == 0 ))
	1543	then
	1544	printf "\n +++ memory demand is undefined"
	1545	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1546	printf "\n >>> "
	1547	read memory 1>/dev/null 2>&1
	1548	else
	1549	done=true
	1550	fi
	1551	done
	1552
	1553	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1554	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1555	then
	1556	while [[ -z $remote_username ]]
	1557	do
[2420]	1558	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1559	printf "\n >>> Please type username:"
	1560	printf "\n >>> "
	1561	read remote_username
	1562	done
	1563	fi
	1564
	1565	else
	1566
[2420]	1567	if [[ $running_in_batch_mode = false ]]
	1568	then
	1569	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1570	cpumax=$cputime
	1571	else
	1572	cputime=$cpumax
	1573	fi
[2380]	1574
	1575	fi
	1576
	1577
	1578	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1579	(( cpu_hours = cputime / 3600 ))
	1580	(( resttime = cputime - cpu_hours * 3600 ))
	1581	(( cpu_minutes = resttime / 60 ))
	1582	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1583	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1584
	1585
	1586	# OUTPUT OF THE PALMRUN-HEADER
	1587	calltime=$(date)
	1588	printf "\n"
	1589	printf "#------------------------------------------------------------------------# \n"
	1590	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1591	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1592	printf "\| \| \n"
	1593	column1="called on:"; column2=$(hostname)
	1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1595	if [[ $create_remote_batch_job = true ]]
	1596	then
[3236]	1597	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1598	else
	1599	if [[ $running_on_remote = true ]]
	1600	then
[3236]	1601	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1602	else
[3236]	1603	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1604	fi
	1605	fi
	1606	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1607
	1608	column1="running in:"
	1609	if [[ $running_in_batch_mode = true ]]
	1610	then
	1611	column2="batch job mode"
	1612	else
	1613	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1614	then
	1615	column2="job creation mode"
	1616	else
	1617	column2="interactive run mode"
	1618	fi
	1619	fi
	1620	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1621
[2479]	1622	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1623	then
[2480]	1624	if [[ "$project_account" != "" ]]
[2479]	1625	then
	1626	column1="project account number:"
	1627	column2="$project_account"
	1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1629	fi
	1630	fi
	1631
[2380]	1632	if [[ -n $cores ]]
	1633	then
	1634	if [[ $run_coupled_model = false ]]
	1635	then
	1636	column1="number of cores:"; column2=$cores
	1637	else
	1638	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1639	fi
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	fi
	1642	if [[ -n $tasks_per_node ]]
	1643	then
	1644	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1646	if (( remaining_cores > 0 ))
	1647	then
	1648	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1649	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1650	fi
	1651	fi
	1652	if [[ $maximum_parallel_io_streams != $cores ]]
	1653	then
	1654	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1656	fi
	1657	if [[ $use_openmp = true ]]
	1658	then
	1659	column1="threads per task:"; column2="$threads_per_task"
	1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1661	fi
[2384]	1662	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1663	then
[2506]	1664	column1="memory demand / PE":; column2="$memory MB"
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1666	column1="job cpu time (h:m:s):"; column2="$timestring"
	1667	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1668	fi
[2380]	1669	printf "\| \| \n"
	1670	if [[ "$source_list" != "" ]]
	1671	then
	1672	if [[ "$make_options" != "" ]]
	1673	then
	1674	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	line=$(echo "$make_options" \| cut -c46-)
	1677	while [[ "$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	fi
	1685	fi
	1686
	1687	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1688	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1689	line=$(echo "$cpp_options" \| cut -c46-)
	1690	while [[ "$line" != "" ]]
	1691	do
	1692	column1=""
	1693	column2=$(echo "$line" \| cut -c-45)
	1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1695	line=$(echo "$line" \| cut -c46-)
	1696	done
	1697
	1698	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1699	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1700	line=$(echo "$compiler_options" \| cut -c46-)
	1701	while [[ "$line" != "" ]]
	1702	do
	1703	column1=""
	1704	column2=$(echo "$line" \| cut -c-45)
	1705	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1706	line=$(echo "$line" \| cut -c46-)
	1707	done
	1708
[2388]	1709	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1711	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1712	while [[ "$line" != "" ]]
	1713	do
	1714	column1=""
	1715	column2=$(echo "$line" \| cut -c-45)
	1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1717	line=$(echo "$line" \| cut -c46-)
	1718	done
	1719
	1720	if [[ "$login_init_cmd" != "" ]]
	1721	then
	1722	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1723	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1724	line=$(echo "$login_init_cmd" \| cut -c46-)
	1725	while [[ "$line" != "" ]]
	1726	do
	1727	column1=""
	1728	column2=$(echo "$line" \| cut -c-45)
	1729	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1730	line=$(echo "$line" \| cut -c46-)
	1731	done
	1732	fi
	1733
	1734	if [[ "$module_commands" != "" ]]
	1735	then
	1736	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1737	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1738	line=$(echo "$module_commands" \| cut -c46-)
	1739	while [[ "$line" != "" ]]
	1740	do
	1741	column1=""
	1742	column2=$(echo "$line" \| cut -c-45)
	1743	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1744	line=$(echo "$line" \| cut -c46-)
	1745	done
	1746	fi
	1747	printf "\| \| \n"
[3236]	1748	column1="run identifier:"; column2=$run_identifier
[2380]	1749	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1750	column1="activation string list:"; column2=$(echo $activation_string_list)
	1751	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1752
	1753	if [[ "$ocean_file_appendix" = true ]]
	1754	then
	1755	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1756	fi
	1757
	1758	if [[ "$source_list" != "" ]]
	1759	then
	1760	printf "\| \| \n"
	1761	printf "\| Files to be compiled: \| \n"
	1762	line=$source_list
	1763	while [[ "$line" != "" ]]
	1764	do
	1765	linestart=$(echo $line \| cut -c-70)
	1766	printf "\| %-70s \| \n" "$linestart"
	1767	line=$(echo "$line" \| cut -c71-)
	1768	done
	1769	fi
	1770	printf "#------------------------------------------------------------------------#"
	1771
	1772
	1773
	1774	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1775	if [[ $do_trace = true ]]
	1776	then
	1777	(( i = 0 ))
[2610]	1778	while (( i < nr_of_input_files ))
[2380]	1779	do
	1780	(( i = i + 1 ))
	1781	if (( i == 1 ))
	1782	then
	1783	printf "\n\n >>> INPUT-file assignments:\n"
	1784	fi
	1785	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1786	done
	1787	(( i = 0 ))
	1788	while (( i < iout ))
	1789	do
	1790	(( i = i + 1 ))
	1791	if (( i == 1 ))
	1792	then
	1793	printf "\n\n >>> OUTPUT-file assignments:\n"
	1794	fi
	1795	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1796	done
	1797	(( i = 0 ))
	1798	while (( i < iic ))
	1799	do
	1800	(( i = i + 1 ))
	1801	if (( i == 1 ))
	1802	then
	1803	printf "\n\n >>> INPUT-commands:\n"
	1804	fi
	1805	printf "\n ${in_command[$i]}"
	1806	done
	1807	(( i = 0 ))
	1808	while (( i < ioc ))
	1809	do
	1810	(( i = i + 1 ))
	1811	if (( i == 1 ))
	1812	then
	1813	printf "\n\n >>> OUTPUT-commands:\n"
	1814	fi
	1815	printf "\n ${out_command[$i]}"
	1816	done
	1817	fi
	1818
	1819	# QUERY FOR CONTINUE
	1820	if [[ $silent = false && $running_in_batch_mode = false ]]
	1821	then
	1822	antwort=dummy
	1823	printf "\n\n"
	1824	printf " >>> everything o.k. (y/n) ? "
	1825	while read antwort
	1826	do
	1827	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1828	then
	1829	printf " >>> everything o.k. (y/n) ? "
	1830	else
	1831	break
	1832	fi
	1833	done
	1834	if [[ $antwort = n \|\| $antwort = N ]]
	1835	then
	1836	locat=user_abort; (( iec = 0 )); exit
	1837	fi
	1838	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1839	then
[2566]	1840	printf "\n *** batch-job will be created and submitted"
[2380]	1841	else
[2566]	1842	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1843	fi
	1844	fi
	1845
	1846
	1847
	1848	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1849	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1850	then
	1851
	1852	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1853	then
[2566]	1854	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1855	else
[2566]	1856	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1857	fi
	1858
[2422]	1859	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1860	# IT SHALL BE CREATED
	1861	ask_for_make_depository=false
	1862	if [[ $create_remote_batch_job = true ]]
	1863	then
	1864
	1865	line=`grep %base_directory $config_file`
[3236]	1866	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1867	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1868
[3236]	1869	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1870	then
	1871	printf "\n\n +++ make depository \"${make_depository}\""
	1872	printf "\n on remote host not found!"
	1873	ask_for_make_depository=true
	1874	fi
[3236]	1875	rm ${configuration_identifier}_last_make_protokoll
[2422]	1876
	1877	else
	1878
	1879	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1880	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1881	if [[ ! -d ${make_depository} ]]
	1882	then
	1883	printf "\n\n +++ make depository \"${make_depository}\""
	1884	printf "\n on local host not found!"
	1885	ask_for_make_depository=true
	1886	fi
	1887
	1888	fi
	1889
	1890	if [[ $ask_for_make_depository = true ]]
	1891	then
	1892
	1893	antwort=dummy
	1894	printf "\n\n"
	1895	printf " >>> Create a new one (y/n) ? "
	1896	while read antwort
	1897	do
	1898	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1899	then
	1900	printf " >>> Create a new one (y/n) ? "
	1901	else
	1902	break
	1903	fi
	1904	done
	1905	if [[ $antwort = n \|\| $antwort = N ]]
	1906	then
	1907	locat=user_abort; (( iec = 0 )); exit
	1908	fi
	1909
[2566]	1910	if [[ $do_trace = true ]]
	1911	then
[3455]	1912	palmbuild -c $configuration_identifier
[2566]	1913	else
[3455]	1914	palmbuild -v -c $configuration_identifier
[2566]	1915	fi
[2422]	1916
[3312]	1917	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1918	then
	1919
	1920	# ABORT IN CASE OF COMPILATION PROBLEMS
	1921	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1922	locat=make_depository
	1923	exit
	1924	else
	1925	echo " *** now continue with creating executable and other sources"
	1926	fi
	1927
	1928	fi
	1929
[2566]	1930	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1931	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1932
[3312]	1933	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1934	then
	1935
	1936	# ABORT IN CASE OF COMPILATION PROBLEMS
	1937	printf "\n +++ error while creating executable and/or other sources"
	1938	locat=execution
[2990]	1939	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1940	exit
	1941
	1942	else
	1943
[2566]	1944	printf " *** executable and other sources created\n"
[2990]	1945	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1946
	1947	fi
	1948
	1949	fi
	1950
	1951
[2669]	1952	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1953	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1954	if [[ $create_remote_batch_job = true ]]
	1955	then
	1956	(( i = 0 ))
[2610]	1957	while (( i < nr_of_input_files ))
[2605]	1958	do
	1959	(( i = i + 1 ))
[2669]	1960	if [[ "${actionin[$i]}" = tr ]]
[2605]	1961	then
	1962	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1963	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1964	fi
	1965	done
	1966	if (( i > 0 ))
	1967	then
[3025]	1968	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1969	fi
	1970	fi
	1971
	1972
[2380]	1973	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1974	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1975	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1976	then
	1977
	1978	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1979	if [[ $running_in_batch_mode = false ]]
	1980	then
	1981	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1982	# FOLDER
[2566]	1983	mkdir -p $tempdir
	1984	chmod go+rx $tempdir
	1985	cd $tempdir
	1986	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1987	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1988
	1989	else
	1990
	1991	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1992	printf "\n *** running in temporary directory: $tempdir"
[2380]	1993
	1994	fi
	1995
	1996
	1997	# PROVIDE THE INPUT FILES
	1998	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1999	optional_files_missing=false
[2380]	2000	(( i = 0 ))
[2610]	2001	while (( i < nr_of_input_files ))
[2380]	2002	do
	2003	(( i = i + 1 ))
	2004	if (( i == 1 ))
	2005	then
	2006	printf "\n\n *** providing INPUT-files:\n$dashes"
	2007	fi
	2008
	2009
	2010	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	2011	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	2012	then
[2669]	2013	optional_files_missing=true
[2380]	2014	continue
	2015	fi
	2016
	2017	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2018	files_for_cores=false; filetype=file
	2019	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	2020	then
	2021	files_for_cores=true; filetype=files
	2022	actionin[$i]=""
	2023	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2024	then
	2025	actionin[$i]=""
	2026	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2027	then
	2028	files_for_cores=true; filetype=files
	2029	actionin[$i]="ln"
	2030	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2031	then
	2032	actionin[$i]="ln"
	2033	fi
	2034
	2035	if [[ $files_for_cores = true ]]
	2036	then
	2037	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2038	else
	2039	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2040	fi
	2041
	2042	# INPUT-FILES TO BE LINKED
	2043	if [[ "${actionin[$i]}" = ln ]]
	2044	then
	2045
	2046	printf "\n $filetype will be linked"
	2047	if [[ $files_for_cores = false ]]
	2048	then
	2049	if [[ -f "${absnamein[$i]}" ]]
	2050	then
	2051	ln ${absnamein[$i]} ${localin[$i]}
	2052	got_tmp[$i]=true
	2053	fi
	2054	else
	2055	if [[ -d "${absnamein[$i]}" ]]
	2056	then
[2396]	2057	mkdir -p ${localin[$i]}
[2380]	2058	cd ${absnamein[$i]}
	2059	for file in $(ls *)
	2060	do
[2566]	2061	ln $file $tempdir/${localin[$i]}
[2380]	2062	done >\|/dev/null 2>&1
[2566]	2063	cd $tempdir
[2380]	2064	fi
	2065
	2066	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2067	if [[ ! -f "${localin[$i]}/_000000" ]]
	2068	then
	2069	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2070	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2071	fi
	2072
	2073	got_tmp[$i]=true
	2074	fi
	2075	fi
	2076
	2077	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2078	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2079	then
	2080
	2081	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2082	then
	2083
	2084	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2085	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2086	printf "\n file will be provided for $cores processors"
[2396]	2087	mkdir -p ${localin[$i]}
[2380]	2088	ival=$cores
	2089	(( ii = 0 ))
	2090	while (( ii <= ival-1 ))
	2091	do
	2092	if (( ii < 10 ))
	2093	then
	2094	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2095	elif (( ii < 100 ))
	2096	then
	2097	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2098	elif (( ii < 1000 ))
	2099	then
	2100	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2101	else
	2102	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2103	fi
	2104	(( ii = ii + 1 ))
	2105	done
	2106
	2107	else
	2108
	2109	if [[ $files_for_cores = true ]]
	2110	then
	2111
	2112	# PROVIDE FILES FOR EACH CORE
	2113	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2114	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2115	printf "\n providing $cores files for the respective cores"
[2396]	2116	mkdir -p ${localin[$i]}
[2380]	2117	if [[ $link_local_input = true ]]
	2118	then
	2119	printf " files will be linked\n"
	2120	cd ${absnamein[$i]}
	2121	for file in $(ls *)
	2122	do
	2123	ln -f $file ${localin[$i]}
	2124	done
[2566]	2125	cd $tempdir
[2380]	2126	fi
	2127
	2128	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2129	if [[ ! -f "${localin[$i]}/_000000" ]]
	2130	then
	2131	if [[ $link_local_input = true ]]
	2132	then
	2133	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2134	fi
	2135	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2136	fi
	2137
	2138	else
	2139
	2140	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2141	if [[ $link_local_input = true ]]
	2142	then
	2143	printf " file will be linked\n"
	2144	ln -f ${absnamein[$i]} ${localin[$i]}
	2145	fi
[2605]	2146	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2147	if [[ ! -f "${localin[$i]}" ]]
	2148	then
	2149	if [[ $link_local_input = true ]]
	2150	then
	2151	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2152	fi
[2669]	2153	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2154	then
	2155	mv ${absnamein[$i]} ${localin[$i]}
	2156	else
	2157	cp ${absnamein[$i]} ${localin[$i]}
	2158	fi
[2380]	2159	fi
	2160	fi
	2161	fi
	2162	fi
	2163
	2164	done
	2165	if (( i != 0 ))
	2166	then
[2669]	2167	if [[ $optional_files_missing = true ]]
	2168	then
	2169	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2170	fi
[2380]	2171	printf "\n$dashes\n *** all INPUT-files provided \n"
	2172	fi
	2173
	2174
	2175	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2176	(( i = 0 ))
	2177	while (( i < iic ))
	2178	do
	2179	(( i = i + 1 ))
	2180	if (( i == 1 ))
	2181	then
	2182	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2183	fi
	2184	printf "\n >>> ${in_command[$i]}"
	2185	eval ${in_command[$i]}
	2186	if (( i == iic ))
	2187	then
	2188	printf "\n$dashes\n"
	2189	fi
	2190	done
	2191
	2192
[3313]	2193	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2194	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2195	then
	2196	progress_bar_disabled=true
	2197	else
	2198	progress_bar_disabled=false
	2199	fi
	2200
	2201
[2380]	2202	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2203	# (FILE ENVPAR WILL BE READ BY PALM)
	2204	cat > ENVPAR << EOF
[3236]	2205	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2206	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2207	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2208	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2209	maximum_cpu_time_allowed = ${cpumax}.,
	2210	revision = '$global_revision',
[3313]	2211	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2212
	2213	EOF
	2214
	2215
	2216	# STARTING THE EXECUTABLE
	2217	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2218	PATH=$PATH:$tempdir
[2380]	2219
	2220
	2221	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2222	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2223	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2224	eval line=\"$line\"
	2225	execute_command="$line"
	2226
	2227
	2228	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2229	if [[ "$execute_command_for_combine" = "" ]]
	2230	then
	2231	eval line2=\"$line2\"
	2232	execute_command_for_combine="$line2"
	2233	fi
	2234
[2380]	2235
	2236
	2237	# PROVIDE A HOSTFILE, IF REQUIRED
	2238	if [[ "$hostfile" != "" ]]
	2239	then
	2240
	2241	if [[ $hostfile = auto ]]
	2242	then
	2243	# CREATE A NEW HOSTFILE
	2244	(( ii = 1 ))
	2245	while (( ii <= cores / threads_per_task ))
	2246	do
	2247	echo $(hostname) >> hostfile
	2248	(( ii = ii + 1 ))
	2249	done
	2250	if (( cores / threads_per_task == 0 ))
	2251	then
	2252	echo $(hostname) >> hostfile
	2253	fi
	2254
	2255	else
	2256	cp $hostfile hostfile
	2257	fi
	2258	eval line=\"`head -n $ii hostfile`\"
	2259	printf "\n *** running on: $line"
	2260	fi
	2261
	2262
	2263
	2264	# SET THE NUMBER OF OPENMP-THREADS
	2265	if [[ $use_openmp = true ]]
	2266	then
	2267	export OMP_NUM_THREADS=$threads_per_task
	2268	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2269	else
	2270	export OMP_NUM_THREADS=1
	2271	fi
	2272
	2273
[2610]	2274	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2275	if [[ $run_coupled_model = false ]]
	2276	then
	2277	if [[ "$ocean_file_appendix" = true ]]
	2278	then
	2279	echo "precursor_ocean" > coupling_steering
	2280	else
	2281	echo "precursor_atmos" > coupling_steering
	2282	fi
	2283	else
	2284	(( iia = $cores_atmos / $threads_per_task ))
	2285	(( iio = $cores_ocean / $threads_per_task ))
	2286	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2287	printf "\n\n"
	2288	echo "coupled_run $iia $iio" > coupling_steering
	2289	fi
	2290
	2291	printf "\n *** execute command:"
	2292	printf "\n \"$execute_command\" \n\n"
	2293
	2294
[3393]	2295	if [[ $progress_bar_disabled = true ]]
[2380]	2296	then
[3402]	2297	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2298	exit_code=${PIPESTATUS[0]}
	2299	else
	2300	$execute_command < coupling_steering &> >(tee STDOUT)
	2301	exit_code=${PIPESTATUS[0]}
	2302	fi
[2380]	2303
[3393]	2304	if [[ ${exit_code} != 0 ]]
	2305	then
	2306
[2380]	2307	# ABORT IN CASE OF RUNTIME ERRORS
	2308	printf "\n +++ runtime error occured"
	2309	locat=execution
	2310	exit
	2311
	2312	else
	2313
	2314	printf "\n$dashes\n *** execution finished \n"
	2315
	2316	fi
	2317
	2318
	2319	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2320	# BY EACH CORE INTO ONE FILE
	2321	if [[ ! -f combine_plot_fields.x ]]
	2322	then
	2323
	2324	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2325	printf "\n 2d- and/or 3d-data may be incomplete!"
	2326	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2327
	2328	elif [[ "$combine_plot_fields" == true ]]
	2329	then
	2330
	2331	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2332	$execute_command_for_combine
	2333
	2334	else
	2335
	2336	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2337	# DATA OUTPUT
[2380]	2338	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2339	fi
	2340
	2341
	2342
	2343	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2344	(( i = 0 ))
	2345	while (( i < ioc ))
	2346	do
	2347	(( i = i + 1 ))
	2348	if (( i == 1 ))
	2349	then
	2350	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2351	fi
[2799]	2352
	2353	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2354	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2355
[2380]	2356	printf "\n >>> ${out_command[$i]}"
	2357	eval ${out_command[$i]}
	2358	if (( i == ioc ))
	2359	then
	2360	printf "\n$dashes\n"
	2361	fi
	2362	done
	2363
	2364
[2610]	2365	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2366	# WILDCARDS
[2380]	2367	(( i = 0 ))
[2610]	2368	(( nr_of_output_files = 0 ))
	2369
[2380]	2370	while (( i < iout ))
	2371	do
[2610]	2372
[2380]	2373	(( i = i + 1 ))
[2610]	2374
	2375	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2376	# CREATE A LIST FOR THE DETECTED ENDINGS
	2377	if [[ "${multout[$i]}" = true ]]
	2378	then
	2379	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2380	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2381	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2382
	2383	endings="DEFAULT"
	2384	while read line
	2385	do
	2386	# remove the local name from the beginning
	2387	localnamestring="${localout_pre[$i]}"
	2388	length_localname=${#localnamestring}
	2389	ending=${line:${length_localname}}
	2390
	2391	if [[ "$ending" != "" ]]
	2392	then
	2393	endings="$endings $ending"
	2394	fi
	2395
	2396	done <filelist
	2397
	2398	rm filelist
	2399
	2400	else
	2401
	2402	# SINGLE NAME
	2403	endings=DEFAULT
	2404
	2405	fi
	2406
	2407	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2408	for ending in $endings
	2409	do
	2410
	2411	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2412	if [[ $ending = DEFAULT ]]
	2413	then
	2414	ending=""
	2415	fi
	2416
	2417	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2418	(( nr_of_output_files = nr_of_output_files + 1 ))
	2419	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2420	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2421	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2422	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2423	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2424	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2425	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2426
	2427	done
	2428
	2429	done
	2430
	2431
	2432
	2433
	2434	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2435	(( i = 0 ))
	2436	while (( i < nr_of_output_files ))
	2437	do
	2438	(( i = i + 1 ))
[2380]	2439	if (( i == 1 ))
	2440	then
[3860]	2441	timestring=`date +%H:%M:%S`
	2442	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
[2380]	2443
	2444	# GET RUN NUMBER ASSIGNED BY PALM
	2445	if [[ -f RUN_NUMBER ]]
	2446	then
	2447	read run_number < RUN_NUMBER
	2448	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2449	usecycle_option="-U $run_number"
	2450	else
	2451	run_number=0
	2452	usecycle_option=""
	2453	fi
	2454	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2455	then
[2404]	2456	printf "\n *** in case of SCP transfers to local host"
	2457	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2458	fi
	2459	printf "\n$dashes"
	2460	fi
	2461
	2462	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2463	then
	2464
[3236]	2465	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2466
	2467	# DETERMINE THE CYCLE NUMBER
	2468	ls -1 -d $filename > filelist 2>/dev/null
	2469	ls -1 -d $filename.* >> filelist 2>/dev/null
	2470	while read line
	2471	do
	2472
	2473	# filename without path (i.e. after the last "/")
	2474	basefilename=$(basename ${line})
	2475
	2476	# check if there is an extension
	2477	extension=${basefilename##*.}
	2478	if [[ "$extension" = "${extout[$i]}" ]]
	2479	then
	2480	basefilename=${basefilename%.*}
	2481	fi
	2482
	2483	# check for an existing cycle number
	2484	cycle=${basefilename##*.}
	2485	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2486	then
[2669]	2487	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2488	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2489	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2490	else
	2491	(( icycle = 1 ))
	2492	fi
	2493
	2494	if (( icycle > maxcycle ))
	2495	then
	2496	(( maxcycle = icycle ))
	2497	fi
	2498
	2499	done <filelist
	2500	rm filelist
	2501
	2502
	2503	# SET THE CYCLE NUMBER
	2504	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2505	if [[ "${actionout[$i]}" = a ]]
	2506	then
	2507	(( maxcycle = maxcycle - 1 ))
	2508	fi
	2509
	2510	(( cycnum[$i] = maxcycle ))
	2511	pathout[$i]=$filename
	2512
	2513
	2514	# ADD CYCLE NUMBER TO FILENAME
	2515	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2516	if [[ "${actionout[$i]}" != "a" ]]
	2517	then
	2518	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2519	# WITH AN EXISTING CYCLE NUMBER
	2520	if (( run_number >= cycnum[$i] ))
	2521	then
	2522	(( cycnum[$i] = run_number ))
	2523	else
	2524	if (( run_number > 0 ))
	2525	then
	2526	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2527	fi
	2528	fi
	2529	fi
	2530	if (( cycnum[$i] > 0 ))
	2531	then
[2600]	2532	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2533	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2534	fi
	2535	fi
	2536
	2537	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2538	files_for_cores=false; filetype=file
	2539	link_local_output=false
	2540	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2541	then
	2542	files_for_cores=true; filetype=directory
	2543	actionout[$i]=""
	2544	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2545	then
	2546	actionout[$i]=""
	2547	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2548	then
	2549	files_for_cores=true; filetype=directory
	2550	link_local_output=true
	2551	actionout[$i]=""
	2552	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2553	then
	2554	link_local_output
	2555	actionout[$i]=""
	2556	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2557	then
	2558	files_for_cores=true; filetype=directory
	2559	actionout[$i]="tr"
	2560	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2561	then
	2562	actionout[$i]="tr"
	2563	fi
	2564
	2565	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2566	then
[2669]	2567	if [[ ${warnout[$i]} = true ]]
	2568	then
	2569	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2570	fi
[2380]	2571	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2572	then
[2669]	2573	if [[ ${warnout[$i]} = true ]]
	2574	then
	2575	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2576	fi
[2380]	2577	else
	2578
	2579
	2580	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2581	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2582	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2583	then
	2584	if [[ $running_on_remote = true ]]
	2585	then
	2586
	2587	# SET OPTIONS FOR TRANSFER
	2588	if [[ "${actionout[$i]}" = tr ]]
	2589	then
	2590	if [[ $files_for_cores = false ]]
	2591	then
	2592	catalog_option=""
	2593	catalog_string=""
	2594	else
	2595	catalog_option="-c"
	2596	catalog_string="/"
	2597	fi
	2598	append_option=""
	2599	append_string=""
	2600	else
	2601	append_option="-A"
	2602	append_string="append"
	2603	fi
	2604
	2605	transfer_failed=false
	2606	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2607	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2608
	2609	# TRANSFER VIA SCP
	2610	if [[ "$remote_loginnode" != "" ]]
	2611	then
[3534]	2612	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]	2613	else
[3236]	2614	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]	2615	fi
[3312]	2616	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2617
	2618
	2619	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2620	if [[ $transfer_failed = true ]]
	2621	then
	2622	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2623	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2624
	2625	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2626	eval local_catalog=${pathout[$i]}
	2627	if [[ ! -d $local_catalog ]]
	2628	then
	2629	printf " *** local directory does not exist. Trying to create:\n"
	2630	printf " $local_catalog \n"
	2631	mkdir -p $local_catalog
	2632	fi
[3236]	2633	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2634	transfer_problems=true
	2635	fi
	2636
	2637	else
	2638
	2639	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2640	# BE COPIED OR APPENDED ON THIS MACHINE
	2641	if [[ "${actionout[$i]}" = tr ]]
	2642	then
	2643	actionout[$i]=""
	2644	else
	2645	actionout[$i]="a"
	2646	fi
	2647	fi
	2648	fi
	2649
	2650
	2651	# APPEND ON THIS MACHINE
	2652	if [[ "${actionout[$i]}" = "a" ]]
	2653	then
	2654	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2655	then
	2656	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2657	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2658	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2659	else
	2660	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2661	printf "\n ${pathout[$i]}\n"
	2662	cat ${localout[$i]} >> ${pathout[$i]}
	2663	fi
	2664	fi
	2665
	2666	# COPY ON THIS MACHINE
	2667	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2668	# ON DIFFERENT FILE-SYSTEMS
	2669	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2670	then
	2671
	2672	# COPY IN CASE OF RUNS ON SINGLE CORES
	2673	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2674	then
	2675	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2676	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2677	if [[ $link_local_output = true ]]
	2678	then
	2679	printf " file will be linked\n"
	2680	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2681	fi
	2682	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2683	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2684	then
	2685	if [[ $link_local_output = true ]]
	2686	then
	2687	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2688	fi
	2689	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2690	else
	2691	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2692	fi
	2693	else
	2694	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2695	printf "\n ${pathout[$i]}\n"
	2696	if [[ $link_local_output = true ]]
	2697	then
	2698	printf " file will be linked\n"
	2699	ln -f ${localout[$i]} ${pathout[$i]}
	2700	fi
	2701	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2702	if [[ ! -f "${pathout[$i]}" ]]
	2703	then
	2704	if [[ $link_local_output = true ]]
	2705	then
	2706	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2707	fi
	2708	cp ${localout[$i]} ${pathout[$i]}
	2709	else
	2710	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2711	fi
	2712	fi
	2713
	2714	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2715	then
	2716
	2717	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2718	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2719	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2720	printf "\n ${pathout[$i]}\n"
	2721	if [[ $link_local_output = true ]]
	2722	then
	2723	printf " files will be linked\n"
[2396]	2724	mkdir -p ${pathout[$i]}
[2380]	2725	cd ${localout[$i]}
	2726	for file in $(ls *)
	2727	do
	2728	ln -f $file ${pathout[$i]}
	2729	done >\|/dev/null 2>&1
[2566]	2730	cd $tempdir
[2380]	2731	fi
	2732
	2733	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2734	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2735	then
	2736	if [[ $link_local_output = true ]]
	2737	then
	2738	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2739	fi
[3025]	2740	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2741	cp -r ${localout[$i]}/* ${pathout[$i]}
	2742	fi
	2743
	2744	fi
	2745	fi
	2746	done
	2747
	2748	if (( i != 0 ))
	2749	then
[3860]	2750	timestring=`date +%H:%M:%S`
[2380]	2751	if [[ $transfer_problems = true ]]
	2752	then
[3860]	2753	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
[2380]	2754	printf "\n +++ WARNING: some data transfers failed! \n"
	2755	else
[3860]	2756	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
[2380]	2757	fi
	2758	fi
	2759
	2760
	2761	# IF REQUIRED, START A RESTART-JOB
	2762	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2763	if [[ -f CONTINUE_RUN ]]
	2764	then
	2765
	2766	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2767	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2768	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2769	# -b START A BATCH JOB
	2770	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2771	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2772	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2773
[2957]	2774	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2775	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2776	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2777	then
	2778	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2779	fi
[2380]	2780
	2781	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2782	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2783	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2784	then
[2381]	2785	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2786	fi
	2787
	2788
	2789	# START THE RESTART-JOB
	2790	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2791	echo " $prc"
	2792	printf "\n$dashes\n"
	2793	if [[ $running_on_remote = true ]]
	2794	then
	2795
	2796	echo "*** ssh will be used to initiate restart-runs!"
	2797	echo " return_address=\"$return_address\" "
	2798	echo " return_username=\"$local_username\" "
	2799
	2800	if [[ "$remote_loginnode" != "" ]]
	2801	then
[3534]	2802	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]	2803	else
[3534]	2804	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2805	fi
	2806
	2807	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2808	sleep 30
	2809
	2810	else
	2811
	2812	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2813	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2814
	2815	fi
	2816
[3132]	2817	# CHECK, IF RESTART JOB HAS BEEN STARTED
[3725]	2818	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
[3132]	2819	then
	2820	printf "\n$dashes\n +++ creating restart run failed \n"
	2821	locat=create_restart
[3455]	2822	rm palmrun_restart.log
[3132]	2823	exit
[3725]	2824	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
	2825	then
	2826	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
	2827	locat=create_restart
	2828	rm palmrun_restart.log
	2829	exit
[3132]	2830	else
	2831	printf "\n$dashes\n *** restart run initiated \n"
	2832	rm palmrun_restart.log
	2833	fi
[2380]	2834
[3132]	2835
[2380]	2836	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2837	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2838	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2839	# MAY BE VERY HUGE)
	2840	(( i = 0 ))
[2610]	2841	while (( i < nr_of_input_files ))
[2380]	2842	do
	2843	(( i = i + 1 ))
	2844	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2845	then
	2846	rm -r ${absnamein[$i]}
	2847	fi
	2848	done
	2849
	2850	fi
	2851
	2852
	2853	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2854	cd $HOME
[2566]	2855	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2856
	2857
	2858	else
	2859
	2860
	2861	# PREPARING ACTIONS,
	2862	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2863
	2864	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2865	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2866	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2867	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2868	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2869	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2870	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2871	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2872	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2873	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2874	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2875	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2876	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2877	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2878	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2879	if [[ $create_remote_batch_job = true ]]
	2880	then
	2881	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2882	if [[ $do_trace = true ]]
	2883	then
	2884	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2885	fi
[2380]	2886	elif [[ $create_batch_job = true ]]
	2887	then
	2888	palmrun_com=${palmrun_com}" -j"
[2420]	2889	if [[ $do_trace = true ]]
	2890	then
	2891	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2892	fi
[2380]	2893	fi
	2894
	2895
	2896	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2897	# REMOTE HOST
[3236]	2898	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2899	job_protocol_file=$job_protocol_file_local
	2900	if [[ $create_remote_batch_job = true ]]
	2901	then
[3236]	2902	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2903	job_protocol_file=$job_protocol_file_remote
	2904	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2905	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2906	fi
	2907
	2908
	2909	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2910	jobfile=jobfile.$run_id_number
[2380]	2911
	2912
	2913	# FIRST CREATE THE BATCH DIRECTIVES
	2914	(( i = 0 ))
	2915	while (( i < ibd ))
	2916	do
	2917	(( i = i + 1 ))
[2693]	2918	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2919	eval line=\"$line\"
	2920	echo "$line" >> $jobfile
	2921	done
	2922	echo " " >> $jobfile
	2923
	2924
	2925	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2926	# PROTOCOL
	2927	if [[ $create_remote_batch_job = true ]]
	2928	then
[3236]	2929	echo "set +vx" >> $jobfile
	2930	echo "trap '" >> $jobfile
	2931	echo "set +vx" >> $jobfile
	2932	echo "cd ${remote_jobcatalog}" >> $jobfile
	2933	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2934
	2935	# ADD THE BATCH DIRECTIVES
	2936	(( i = 0 ))
	2937	while (( i < ibdt ))
	2938	do
	2939	(( i = i + 1 ))
[2693]	2940	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2941	eval line=\"$line\"
	2942	echo "$line" >> $jobfile
	2943	done
	2944	echo " " >> $jobfile
	2945
	2946	echo "set -x" >> $jobfile
[3534]	2947	if [[ "$remote_loginnode" != "" ]]
	2948	then
	2949	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}\" " >> $jobfile
	2950	else
	2951	echo "${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
	2952	fi
[2380]	2953	echo "%%END%%" >> $jobfile
	2954	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2955	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2956	echo "rm $scpjob_file" >> $jobfile
[2404]	2957	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2958	echo "set -x" >> $jobfile
	2959	echo " ' exit" >> $jobfile
	2960	fi
	2961
	2962
	2963	# ACTIVATE ERROR-TRACEBACK
	2964	if [[ $do_trace = true ]]
	2965	then
	2966	echo "set -x" >> $jobfile
	2967	else
	2968	echo "set +vx" >> $jobfile
	2969	fi
	2970
	2971
	2972	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2973	if [[ "$login_init_cmd" != "" ]]
	2974	then
	2975	echo "$login_init_cmd" >> $jobfile
	2976	fi
	2977	if [[ "$module_commands" != "" ]]
	2978	then
	2979	echo "$module_commands" >> $jobfile
	2980	fi
	2981
	2982
	2983	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2984	if [[ $create_remote_batch_job = true ]]
	2985	then
	2986	echo "mkdir $tempdir" >> $jobfile
	2987	echo "chmod go+rx $tempdir" >> $jobfile
	2988	else
	2989	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2990	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2991	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2992	mkdir $tempdir
	2993	chmod go+rx $tempdir
	2994	fi
	2995	echo "cd $tempdir" >> $jobfile
	2996	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2997	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2998	echo "export PATH=.:\$PATH" >> $jobfile
	2999	echo "export execute_palmrun=true" >> $jobfile
	3000
	3001
	3002	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3003	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	3004	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	3005	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3006	echo "export LOCAL_PWD" >> $jobfile
	3007
	3008
	3009	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	3010	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	3011	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	3012
	3013
	3014	# CALL PALMRUN WITHIN THE JOB
	3015	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	3016	echo "set -x" >> $jobfile
	3017	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	3018
	3019
	3020	# TRANSFER JOBFILE TO THE TARGET HOST
	3021	if [[ $create_jobfile_only = false ]]
	3022	then
	3023
[3505]	3024	# CREATE LOCAL JOB FOLDER
	3025	eval local_jobcatalog=$local_jobcatalog
	3026	if [[ ! -d $local_jobcatalog ]]
	3027	then
	3028	echo " "
	3029	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3030	mkdir $local_jobcatalog
	3031	fi
	3032
[2380]	3033	if [[ $create_remote_batch_job = true ]]
	3034	then
	3035
[2420]	3036	echo " "
[2566]	3037	echo " *** transfer of job to remote host via scp"
[3505]	3038
	3039	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3040	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3041
	3042	# COPY THE JOB FILE
[2420]	3043	if [[ $do_trace = true ]]
	3044	then
[3236]	3045	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3046	fi
[3236]	3047	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3048
[3505]	3049	# SUBMIT THE JOB
[3574]	3050	printf " *** submit the job (output of submit command, \n"
[3573]	3051	printf " e.g. the job-id given by the batch-system, may follow) \n"
[2420]	3052	if [[ $do_trace = true ]]
	3053	then
[3665]	3054	echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" "
[2420]	3055	fi
[3665]	3056	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
[2380]	3057
	3058	elif [[ $create_batch_job = true ]]
	3059	then
	3060
[2385]	3061	eval local_jobcatalog=$local_jobcatalog
[3236]	3062	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3063	cd $local_jobcatalog
[2380]	3064	echo " "
[2420]	3065	echo " *** submit the job"
	3066	if [[ $do_trace = true ]]
	3067	then
[3236]	3068	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3069	fi
[3236]	3070	$submit_command ${configuration_identifier}_${run_id}
	3071	rm ${configuration_identifier}_${run_id}
[2380]	3072	cd - > /dev/null
	3073
	3074	fi
	3075
	3076	rm -rf $jobfile
	3077
	3078	else
	3079
	3080	printf "\n *** jobfile created under name \"$jobfile\" "
	3081	printf "\n no batch-job has been sent!"
	3082
	3083	fi
	3084
	3085	fi # END OF REMOTE-PART

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