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source: palm/trunk/SCRIPTS/mrun @ 1345

Last change on this file since 1345 was 1328, checked in by maronga, 11 years ago
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File size: 174.6 KB

Rev	Line
[1103]	1	#!/bin/ksh
[1046]	2
[1059]	3	# mrun - script for running PALM jobs
	4
[1046]	5	#--------------------------------------------------------------------------------#
	6	# This file is part of PALM.
	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	#
[1310]	19	# Copyright 1997-2014 Leibniz Universitaet Hannover
[1046]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
[1090]	23	# ------------------
[1305]	24	#
[1328]	25	#
[1200]	26	# Former revisions:
	27	# -----------------
	28	# $Id: mrun 1328 2014-03-21 11:00:33Z kanani $
	29	#
[1328]	30	# 1320 2014-03-20 08:40:49Z raasch
	31	# check namelist file set false by default
	32	#
[1305]	33	# 1304 2014-03-12 10:29:42Z raasch
	34	# ulimit option changed from -Ss to -s
	35	#
	36	# bugfix: missing "fi" in r1289
	37	#
[1290]	38	# 1289 2014-03-04 07:12:34Z raasch
	39	# comments translated to English
	40	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	41	# export of variables for palm and interpret_config removed
	42	#
[1282]	43	# 1281 2014-02-01 07:55:49Z raasch
	44	# rsync-copy restricted to Cray machines, since command is unavailable on some
	45	# other systems
	46	#
[1280]	47	# 1279 2014-01-28 12:10:14Z raasch
	48	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	49	# in order to remove annoying restrictions concerning the number of processors which
	50	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	51	# restriction, one of the nodes will be filled with less than the given number of
	52	# tasks per node. A respective warning is given.
	53	#
[1275]	54	# 1274 2014-01-09 13:14:54Z heinze
	55	# adjustments for lccrayh
	56	#
[1273]	57	# 1272 2014-01-08 10:19:32Z witha
	58	# small adjustment for lcflow
	59	#
[1271]	60	# 1270 2013-12-16 11:05:01Z fricke
	61	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	62	#
[1256]	63	# 1255 2013-11-07 14:43:35Z raasch
	64	# further adjustments for lccrayb remote access
	65	#
[1242]	66	# 1241 2013-10-30 11:36:58Z heinze
	67	# Enable use of nudging input and input of large scale forcing from
	68	# external files
	69	#
[1230]	70	# 1229 2013-09-20 06:55:19Z raasch
	71	# further adjustments for lccrayb
	72	#
[1225]	73	# 1224 2013-09-16 07:27:23Z raasch
	74	# first adjustments for lccrayb
	75	#
[1211]	76	# 1210 2013-08-14 10:58:20Z raasch
	77	# fftw support added
	78	#
[1203]	79	# 1201 2013-07-10 16:17:59Z witha
	80	# adjustments for Forwind cluster (lcflow)
	81	#
[1200]	82	# 1199 2013-07-05 14:52:22Z raasch
[1199]	83	# adjustments for CSC Helsinki (lccrayf),
	84	# executables for batch jobs can be created in advance, in order to avoid calling
	85	# the compiler within the batch job (only works if batch jobs are submitted on
	86	# local host)
[1104]	87	#
[1191]	88	# 1190 2013-06-25 09:39:21Z heinze
	89	# enable use of automatic restarts for ibmh
[1185]	90	# use of cluster/express queue enabled (ibmh)
[1104]	91	#
[1125]	92	# 1124 2013-04-09 15:46:52Z raasch
	93	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	94	# side effect may lead to data loss while getopts is reading the script-option arguments
	95	#
[1123]	96	# 1122 2013-04-09 08:37:16Z heinze
	97	# Bugfix: change type of variable last_char
	98	#
[1121]	99	# 1119 2013-04-05 15:11:19Z raasch
	100	# Bugfix for setting -T option for subjob
	101	#
[1109]	102	# 1108 2013-03-05 07:03:32Z raasch
	103	# bugfix for coupled runs on lckyut/lckyuh
	104	#
[1107]	105	# 1106 2013-03-04 05:31:38Z raasch
	106	# --stdin argument for mpiexec on lckyuh
	107	# -y and -Y settings output to header
	108	#
[1104]	109	# 1103 2013-02-20 02:15:53Z raasch
[1103]	110	# default script runs again under ksh, because of unsolved problems with read
	111	# from stdin: when bash script is called from a ksh, message "read error: 0:
	112	# Resource temporarily unavailable" appears and script does not stop,
	113	# further bash compatibility adjustments,
	114	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	115	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	116	#
[1102]	117	# 1101 2013-02-17 10:20:21Z raasch
	118	# script now running under bash instead of ksh, which required small adjustments
	119	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	120	# read from stdin),
	121	# cross compilername on lckyuh compute nodes replaced by real compiler name
	122	#
[1100]	123	# 1099 2013-02-10 01:47:43Z raasch
	124	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	125	# and for Forwind cluster (lcflow)
	126	# small further adjustments for lckyut
	127	#
[1096]	128	# 1094 2013-02-03 01:52:12Z raasch
	129	# explicit ssh/scp port can be set in config file with environment variable
	130	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	131	# decalpha parts (yonsei) removed
	132	#
[1091]	133	# 2013-02-02 07:06:13Z raasch
[1099]	134	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	135	#
[1084]	136	# 1083 2013-01-04 10:22:09Z maronga
	137	# bugfix in parameter file check (read %cpp_options was missing)
	138	#
[1070]	139	# 1069 2012-11-28 16:18:43Z maronga
	140	# bugfix: coupling mode was always set to mpi2, typos removed
	141	#
[1059]	142	# 1058 2012-11-21 07:00:35Z raasch
	143	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	144	# nodes
	145	#
[1047]	146	# 1046 2012-11-09 14:38:45Z maronga
	147	# code put under GPL (PALM 3.9)
	148	#
[1090]	149	# 21/03/94 - Siggi - first version finished
	150	# 03/03/94 - Siggi - script development started
	151	#
[1059]	152	#--------------------------------------------------------------------------------#
[1090]	153	# mrun - script for running PALM jobs
	154	#--------------------------------------------------------------------------------#
[1]	155
[1047]	156
[1]	157
[1289]	158	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	159
[1289]	160	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	161	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	162	# (TOO MANY ARGUMENTS - PROBLEM)
	163	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	164
	165	AddFilenames=""
	166	additional_conditions=""
	167	add_source_path=""
	168	afname=""
	169	archive_save=true
	170	archive_system=none
[1320]	171	check_namelist_files=false
[920]	172	combine_plot_fields=true
[1]	173	compiler_name=""
	174	cond1=""
	175	cond2=""
	176	config_file=.mrun.config
[206]	177	coupled_dist=""
	178	coupled_mode="mpi1"
[1]	179	cpp_opts=""
[82]	180	cpp_options=""
[1]	181	cpumax=0
	182	cpurest=0
[1199]	183	create_executable_for_batch=false
[1]	184	delete_temporary_catalog=true
	185	do_batch=false
	186	do_compile=true
	187	do_remote=false
	188	do_stagein=true
	189	do_stageout=true
	190	do_trace=false
[352]	191	email_notification="none"
[1]	192	exclude=""
	193	executable=""
	194	execution_error=false
[1210]	195	fftw_inc=""
	196	fftw_lib=""
	197	fftw_support=false
[1289]	198	fname=test
[1]	199	fromhost=""
[78]	200	global_revision=""
[122]	201	group_number=none
[1]	202	host=""
	203	host_file=""
	204	hp=""
	205	ignore_archive_error=false
	206	input_list=""
	207	interpreted_config_file=""
[164]	208	job_catalog="~/job_queue"
[1]	209	job_on_file=""
	210	keep_data_from_previous_run=false
[183]	211	link_local_input=false
[149]	212	link_local_output=false
[1]	213	localhost_realname=$(hostname)
[260]	214	local_dvrserver_running=.FALSE.
[1]	215	locat=normal
	216	mainprog=""
	217	makefile=""
[759]	218	max_par_io_str=""
[1]	219	mc=$0
	220	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	221	do
	222	mc=`echo $mc \| cut -f2- -d"/"`
	223	done
[493]	224	module_calls=""
[1]	225	mrun_script_name=$mc
[82]	226	netcdf_inc=""
	227	netcdf_lib=""
[1]	228	netcdf_support=false
	229	node_usage=default
	230	numprocs=""
[206]	231	numprocs_atmos=0
	232	numprocs_ocean=0
[1]	233	OOPT=""
	234	openmp=false
	235	output_list=""
	236	package_list=""
	237	queue=none
	238	read_from_config=""
[5]	239	restart_run=false
[622]	240	if [[ `hostname` = rte10 ]]
[1]	241	then
[1103]	242	return_addres=133.5.185.60
	243	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
[693]	244	elif [[ `hostname` = climate0 ]]
	245	then
[1103]	246	return_addres=165.132.26.68
	247	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
[1021]	248	elif [[ `hostname` = urban00 ]]
	249	then
[1103]	250	return_addres=147.46.30.151
	251	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
[622]	252	else
	253	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	254	fi
	255	return_password=""
	256	return_username=$LOGNAME
	257	remotecall=false
	258	remote_username=""
[102]	259	run_coupled_model=false
[1]	260	run_mode=""
[397]	261	store_on_archive_system=false
[1289]	262	dashes=" ----------------------------------------------------------------------------"
[1]	263	silent=false
	264	source_list=""
	265	source_path=SOURCE
	266	tasks_per_node=""
	267	threads_per_task=1
	268	tmpcreate=false
	269	tmp_data_catalog=""
	270	transfer_problems=false
	271	usern=$LOGNAME
[377]	272	use_openmp=false
[1289]	273	version="MRUN 2.1 Rev$Rev: 1328 $"
[1]	274	working_directory=`pwd`
	275	TOPT=""
	276	XOPT=""
	277	zeit=$( date \| cut -c 12-19 )
	278
[1124]	279	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	280	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	281	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	282	# SCRIPT-OPTION ARGUMENTS
[1279]	283	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
[1]	284
	285
	286
[1289]	287	# ERROR HANDLING IN CASE OF EXIT
[83]	288	trap 'rm -rf $working_directory/tmp_mrun
[1289]	289	if [[ $locat != normal && $locat != control_c ]]
[1]	290	then
	291
[1289]	292	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	293	(( i = 0 ))
	294	while (( i < iec ))
	295	do
	296	(( i = i + 1 ))
	297	printf "\n *** Execution of ERROR-command:\n"
	298	printf " >>> ${err_command[$i]}\n"
	299	eval ${err_command[$i]}
	300	done
[1101]	301	if [[ -n $interpreted_config_file ]]
	302	then
[1]	303	rm -rf $interpreted_config_file
	304	fi
[1101]	305	if [[ -n .mrun_environment ]]
	306	then
[71]	307	rm -rf .mrun_environment
	308	fi
[1]	309	if [[ $tmpcreate = true ]]
	310	then
	311	printf "\n *** Contents of \"$TEMPDIR\":\n"
	312	ls -al; cd
	313	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	314	fi
[260]	315	if [[ "$dvrserver_id" != "" ]]
	316	then
	317	echo "+++ killing dvrserver_id=$dvrserver_id"
	318	kill $dvrserver_id
	319	fi
[1]	320	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	321	then
	322	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	323	fi
	324	printf "\n\n+++ MRUN killed \n\n"
	325	elif [[ $locat != control_c ]]
	326	then
	327	printf "\n\n --> all actions finished\n\n"
	328	printf " Bye, bye $usern !!\n\n"
	329	fi' exit
	330
	331
[1289]	332	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	333	trap 'rm -rf $working_directory/tmp_mrun
[807]	334	rm -rf $working_directory/tmp_check_namelist_files
[69]	335	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	336	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	337	then
	338	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	339	fi
[260]	340	if [[ "$dvrserver_id" != "" ]]
	341	then
	342	echo "+++ killing dvrserver_id=$dvrserver_id"
	343	kill $dvrserver_id
	344	fi
[1]	345	printf "\n+++ MRUN killed by \"^C\" \n\n"
	346	locat=control_c
	347	exit
	348	' 2
	349
	350
[22]	351	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	352	# BEEN SET
	353	if [[ "$PALM_BIN" = "" ]]
	354	then
	355	printf "\n +++ environment variable PALM_BIN has not been set"
	356	printf "\n please set it to the directory where the PALM scripts are located"
	357	locat=palm_bin; exit
	358	fi
[180]	359	export PATH=$PALM_BIN:$PATH
[22]	360
	361
[1]	362
[1289]	363	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	364	# WHICH WILL BE USED TO START RESTART-JOBS
[920]	365	while getopts :a:AbBc:Cd:D:Fg:G:h:H:i:IkK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
[1]	366	do
	367	case $option in
	368	(a) afname=$OPTARG;;
[397]	369	(A) store_on_archive_system=true; mc="$mc -A";;
[1]	370	(b) do_batch=true; mc="$mc -b";;
	371	(B) delete_temporary_catalog=false; mc="$mc -B";;
	372	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	373	(C) restart_run=true; mc="$mc -C";;
[1]	374	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[210]	375	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
[79]	376	(F) job_on_file="-D"; mc="$mc -F";;
[122]	377	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	378	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	379	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	380	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	381	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	382	(I) ignore_archive_error=true; mc="$mc -I";;
	383	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	384	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	385	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	386	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	387	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
	388	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	389	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	390	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	391	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	392	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	393	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
	394	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
	395	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	396	(S) read_from_config=false; mc="$mc -S";;
	397	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	398	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	399	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	400	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	401	(v) silent=true; mc="$mc -v";;
[759]	402	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	403	(x) do_trace=true;set -x; mc="$mc -x";;
	404	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	405	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	406	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	407	(z) check_namelist_files=false; mc="$mc -z";;
[920]	408	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	409	(\?) printf "\n +++ unknown option $OPTARG \n"
	410	printf "\n --> type \"$0 ?\" for available options \n"
	411	locat=parameter;exit;;
	412	esac
	413	done
	414
	415
[1289]	416	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	417	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	418	(( to_shift = $OPTIND - 1 ))
	419	shift $to_shift
[1]	420
[1289]	421	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	422	if [[ "$1" = "?" ]]
	423	then
	424	(printf "\n *** mrun can be called as follows:\n"
[920]	425	printf "\n $mrun_script_name -b -c.. -d.. -D.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -z -Z <modus> \n"
[1]	426	printf "\n Description of available options:\n"
	427	printf "\n Option Description Default-Value"
	428	printf "\n -a base name of input files equiv. -d"
[400]	429	printf "\n -A archiving when using file-attribute fl"
[1]	430	printf "\n -b batch-job on local machine ---"
	431	printf "\n -B do not delete temporary directory at end ---"
	432	printf "\n -c configuration file .mrun.config"
	433	printf "\n -d base name of files attached to program test"
	434	printf "\n -D preprocessor(cpp)-directives \"\" "
	435	printf "\n -F create remote job file only ---"
	436	printf "\n -h execution host $localhost_realname"
	437	printf "\n -i INPUT control list \"\" "
	438	printf "\n -I archiving errors of previous batch-jobs"
	439	printf "\n will be ignored"
	440	printf "\n -k keep data from previous run"
	441	printf "\n -K additional conditions for controling"
	442	printf "\n usage of conditional code and"
	443	printf "\n env-variables in configuration file \"\" "
	444	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	445	printf "\n -M Makefile name Makefile"
	446	printf "\n -n node usage (shared/not_shared) depending on -h"
	447	printf "\n -o OUTPUT control list \"\" "
[1304]	448	printf "\n -O threads per openMP task ---"
[1]	449	printf "\n -p software package list \"\" "
	450	printf "\n -q queue \"$queue\" "
	451	printf "\n -r run control list (combines -i -o) \"\" "
	452	printf "\n -s filenames of routines to be compiled \"\" "
	453	printf "\n must end with .f, .f90, .F, or .c !"
	454	printf "\n use \"..\" for more than one file and wildcards"
[837]	455	printf "\n -s LM compiles all locally modified files"
[1]	456	printf "\n -S config file interpreted by shellscript ---"
	457	printf "\n -t allowed cpu-time in seconds (batch) 0"
	458	printf "\n -T tasks per node depending on -h"
	459	printf "\n -u username on remote machine \"\" "
	460	printf "\n -v no prompt for confirmation ---"
[759]	461	printf "\n -w maximum parallel io streams as given by -X"
[1]	462	printf "\n -x tracing of mrun for debug purposes ---"
	463	printf "\n -X # of processors (on parallel machines) 1"
[291]	464	printf "\n -y add appendix \"_O\" to all local output"
	465	printf "\n files (ocean precursor runs followed by"
	466	printf "\n coupled atmosphere-ocean runs) ---"
[206]	467	printf "\n -Y run coupled model, \"#1 #2\" with"
	468	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	469	printf "\n -z disable a priori parameter file check ---"
	470	printf "\n -Z skip combine_plot_fields at the end of "
	471	printf "\n the simulation ---"
[1]	472	printf "\n "
	473	printf "\n Possible values of positional parameter <modus>:"
	474	printf "\n \"?\" - this outline \n\n") \| more
	475	exit
	476	elif [[ "$1" != "" ]]
	477	then
	478	printf "\n +++ positional parameter $1 unknown \n"
	479	locat=parameter; exit
	480	fi
	481
	482
	483
[1289]	484	# SHORT STARTING MESSAGE
[1]	485	printf "\n*** $version "
	486	printf "\n will be executed. Please wait ..."
	487
	488
[82]	489
[1289]	490	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	491	if [[ ! -f $config_file ]]
	492	then
	493	printf "\n\n +++ configuration file: "
	494	printf "\n $config_file"
	495	printf "\n does not exist"
	496	locat=connect; exit
	497	fi
	498
	499
[1289]	500	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	501	line=""
	502	grep "%host_identifier" $config_file > tmp_mrun
	503	while read line
	504	do
[206]	505	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	506	then
	507	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	508	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	509	if [[ $localhost_realname = $HOSTNAME ]]
[82]	510	then
	511	localhost=$host_identifier
	512	break
	513	fi
	514	fi
	515	done < tmp_mrun
	516
	517	if [[ "$localhost" = "" ]]
	518	then
	519	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	520	printf "\n for local host \"$localhost_realname\"."
	521	printf "\n Please add line"
	522	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	523	printf "\n to the configuration file."
	524	locat=localhost; exit
	525	fi
	526
	527
[1289]	528	# SET HOST-SPECIFIC VARIABLES
[82]	529	case $localhost_realname in
[397]	530	(r1\|r2\|h01\|b01) archive_system=tivoli;;
[82]	531	(cs*) archive_system=ut;;
	532	esac
	533
	534
[1289]	535	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	536	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	537	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	538	[[ "$afname" = "" ]] && afname=$fname
	539
	540
[1289]	541	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	542	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	543	# STATEMENTS IN THE CONFIGURATION FILE
[1]	544	if [[ "$run_mode" != "" ]]
	545	then
	546	input_list="$input_list $run_mode"
	547	output_list="$output_list $run_mode"
	548	fi
	549
	550
[1289]	551	# ??? is this (and the respective option -H) really required ???
	552	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	553	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	554	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	555	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	556	if [[ "$fromhost" = "" ]]
	557	then
	558	fromhost=$localhost
	559	fi
	560
	561
[1289]	562	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	563	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	564	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
	565	# TO BE SUBMITTED (I.E. do_bacth=true)
[1]	566	if [[ -n $host && "$host" != $localhost ]]
	567	then
	568	do_batch=true
	569	do_remote=true
	570	case $host in
[1289]	571	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	572	(*) printf "\n"
[83]	573	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	574	printf "\n is not available"
[1]	575	locat=nqs; (( iec = 0 )); exit;;
	576	esac
	577	else
	578	host=$localhost
	579	fi
	580
	581
[1289]	582	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	583	if [[ -n $additional_conditions ]]
	584	then
[69]	585	cond1=`echo $additional_conditions \| cut -d" " -f1`
	586	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	587	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	588	if [[ -n $dummy ]]
	589	then
	590	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	591	locat=options; exit
	592	fi
[503]	593	block=_$cond1
	594	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	595	fi
	596
	597
[1289]	598	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
[206]	599	if [[ $run_coupled_model = true ]]
	600	then
	601
[1289]	602	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	603	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	604
	605	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	606	then
	607
[1289]	608	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	609	printf "\n PEs (total) : $numprocs"
	610	printf "\n PEs (atmosphere): $numprocs_atmos"
	611	printf "\n PEs (ocean) : $numprocs_ocean"
	612	locat=coupling; exit
[206]	613
[1289]	614	fi
[206]	615
	616
	617	# GET coupled_mode FROM THE CONFIG FILE
	618	line=""
	619	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
	620	while read line
	621	do
[1069]	622	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
[206]	623	then
	624	coupled_mode="mpi2"
	625	fi
	626	done < tmp_mrun
	627
	628	fi
	629
	630
[1289]	631	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
[1]	632	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
	633	then
	634	if [[ $ignore_archive_error = false ]]
	635	then
	636	printf "\n +++ data archiving of previous run failed"
	637	printf "\n see directory \~/job_queue on remote machine"
	638	locat=archive; exit
	639	else
	640	printf "\n +++ warning: data archiving in a previous run failed"
	641	printf "\n MRUN continues, trying to get backup copy"
	642	fi
	643	fi
	644
	645
[1289]	646	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	647	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	648	mrun_memory=$memory
	649	mrun_group_number=$group_number
	650	mrun_cpumax=$cpumax
	651	mrun_numprocs=$numprocs
[1]	652
[1099]	653
[1289]	654	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
	655	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
[1]	656	if [[ "$read_from_config" = false ]]
	657	then
	658
	659	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	660
	661	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	662	while read zeile
	663	do
	664	[[ $silent = false ]] && printf "."
	665
	666
[1289]	667	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	668	eval zeile=\"$zeile\"
	669
	670
[1289]	671	# INTERPRET THE LINE
[21]	672	if [[ "$(echo $zeile)" = "" ]]
[1]	673	then
[1289]	674	# EMPTY LINE, NO ACTION
[21]	675	continue
[1]	676
[21]	677	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	678	then
	679
[1289]	680	# LINE IS A COMMENT LINE
[1]	681	true
	682
	683	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	684	then
	685
[1289]	686	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	687	zeile=$(echo $zeile \| cut -c2-)
[69]	688	var=`echo $zeile \| cut -d" " -f1`
	689	value=`echo $zeile \| cut -d" " -s -f2`
	690	for_host=`echo $zeile \| cut -d" " -s -f3`
	691	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	692	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	693
	694	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	695	then
	696
[1289]	697	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	698	# "::" IS REPLACED BY ":".
[1]	699	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	700
	701
[1289]	702	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	703	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	704	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	705	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	706	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	707	# CONFIGURATION-FILE.
[1]	708	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	709	then
	710	eval $var=\$value
	711
[1289]	712	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	713	if [[ $do_trace = true ]]
	714	then
	715	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	716	fi
	717	fi
	718
[1289]	719	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	720	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	721	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	722	# MUST HAVE TO BE STARTED
[1]	723	if [[ $var = host ]]
	724	then
	725	if [[ -n $host && "$host" != $localhost ]]
	726	then
	727	do_batch=true
	728	do_remote=true
	729	case $host in
[1289]	730	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[83]	731	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	732	printf "\n is not available"
[1]	733	locat=nqs; exit;;
	734	esac
	735	else
	736	host=$localhost
	737	fi
	738	fi
	739
[1289]	740	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	741	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	742	# BY MRUN (E.G. subjob)
[1]	743	export $var
	744	fi
	745
	746
	747
	748
	749	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	750	then
	751
[1289]	752	# LINE DEFINES ERROR-COMMAND
[1]	753	(( iec = iec + 1 ))
	754	zeile=$(echo $zeile \| cut -c4-)
	755	err_command[$iec]="$zeile"
	756
	757	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	758	then
	759
[1289]	760	# LINE DEFINES INPUT-COMMAND
[1]	761	(( iic = iic + 1 ))
	762	zeile=$(echo $zeile \| cut -c4-)
	763	in_command[$iic]="$zeile"
	764
	765	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	766	then
	767
[1289]	768	# LINE DEFINES OUTPUT-COMMAND
[1]	769	(( ioc = ioc + 1 ))
	770	zeile=$(echo $zeile \| cut -c4-)
	771	out_command[$ioc]="$zeile"
	772
	773	else
	774
[1289]	775	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	776	# s2a: in/out - field
	777	# s2b: loc - field (optional)
	778	# s2c: tr/ar - field (optional)
[69]	779	s1=`echo $zeile \| cut -d" " -f1`
	780	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	781	s2a=$(echo $s2 \| cut -d":" -f1)
	782	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	783	then
	784	s2b=""
	785	s2c=""
	786	else
[69]	787	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	788	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	789	fi
[69]	790	s3=`echo $zeile \| cut -d" " -f3`
	791	s4=`echo $zeile \| cut -d" " -s -f4`
	792	s5=`echo $zeile \| cut -d" " -s -f5`
	793	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	794
	795
[1289]	796	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	797	# INPUT- OR OUTPUT-LIST.
	798	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	799	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	800	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	801	# IS NOT CHECKED AND STORED.
[1]	802	IFSALT="$IFS"; IFS="$IFS:"
	803	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	804	then
	805	found=false
	806	for actual in $input_list
	807	do
	808	for formal in $s3
	809	do
	810	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	811	done
	812	done
	813	if [[ $found = true ]]
	814	then
	815	(( iin = iin + 1 ))
	816	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	817	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	818	extin[$iin]=$s6
	819	fi
	820	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	821	then
	822	found=false
	823	for actual in $output_list
	824	do
	825	for formal in $s3
	826	do
	827	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	828	done
	829	done
	830	if [[ $found = true ]]
	831	then
	832	(( iout = iout + 1 ))
	833	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	834	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	835	fi
	836	elif [[ "$s2a" != in && "$s2a" != out ]]
	837	then
	838	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	839	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	840	locat=connect; exit
	841	fi
	842	IFS="$IFSALT"
	843	fi
	844	done < $config_file
	845
	846	else
	847
	848
[1289]	849	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	850	[[ $silent = false ]] && printf "..."
[1289]	851	interpreted_config_file=.icf.$RANDOM
[1]	852
	853
[69]	854
[1289]	855	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[69]	856	cat > .mrun_environment << %%END%%
	857	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	858	config_file = '$config_file', do_remote = '$do_remote',
	859	do_trace = '$do_trace', host = '$host',
	860	input_list = '$input_list', icf = '$interpreted_config_file',
	861	localhost = '$localhost', output_list = '$output_list' /
	862
	863	%%END%%
	864
[1289]	865	if [[ "$host" != $localhost ]]
[66]	866	then
[503]	867
[1289]	868	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	869	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	870	if [[ $? != 0 ]]
[503]	871	then
[1289]	872	printf "\n\n +++ no interpret_config found"
	873	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	874	locat=interpret_config; exit
	875	fi
	876	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	877	$interpret_config_executable
[503]	878
[1289]	879	else
[503]	880
[1289]	881	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	882	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	883	then
	884	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	885	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	886	locat=interpret_config; exit
[503]	887	else
[1289]	888	interpret_config${block}.x
	889	fi
[503]	890
[66]	891	fi
[71]	892	rm .mrun_environment
[1]	893
[71]	894
[1289]	895	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	896	chmod u+x $interpreted_config_file
	897	export PATH=$PATH:.
	898	. $interpreted_config_file
[71]	899	rm $interpreted_config_file
[1]	900
[1099]	901	fi
[71]	902
[69]	903
[1289]	904	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	905	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	906	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	907	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	908	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	909	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	910	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	911
	912
[1289]	913	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	914	# FOR SOURCE-FILES TO BE COMPILED.
	915	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	916	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	917	if [[ "$SOURCES_COMPLETE" = "" ]]
	918	then
	919
[1289]	920	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	921	# HAS BEEN DEFINED
[1]	922	source_path=""
	923	line=""
	924	grep "%source_path" $config_file > tmp_mrun
	925	while read line
	926	do
	927	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	928	then
	929	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	930	then
	931	global_source_path=`echo $line \| cut -d" " -f2`
	932	fi
	933	fi
	934	done < tmp_mrun
	935
	936	line=""
	937	found=false
	938	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	939	while read line
	940	do
	941	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	942	then
	943	if [[ $found = true ]]
	944	then
	945	printf "\n\n +++ more than one source path found in configuration file"
	946	printf "\n for local host \"$localhost\" "
	947	locat=source_path; exit
	948	fi
	949	source_path=`echo $line \| cut -d" " -f2`
	950	found=true
	951	fi
	952	done < tmp_mrun
	953	rm tmp_mrun
	954
	955	if [[ "$source_path" = "" ]]
	956	then
	957	if [[ "$global_source_path" != "" ]]
	958	then
	959	source_path=$global_source_path
	960	else
	961	printf "\n\n +++ no source path found in configuration file"
	962	printf "\n for local host \"$localhost\" "
	963	locat=source_path; exit
	964	fi
	965	fi
	966	eval source_path=$source_path
	967
	968	if [[ ! -d $source_path ]]
	969	then
	970	printf "\n\n +++ source path \"$source_path\" on local host"
	971	printf "\n \"$localhost\" does not exist"
	972	locat=source_path; exit
	973	fi
	974
	975	fi
	976
	977
[1289]	978	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	979	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	980	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	981	then
	982	global_revision=`svnversion $source_path 2>/dev/null`
	983	global_revision="Rev: $global_revision"
	984	fi
[1]	985
[78]	986
[1289]	987	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	988	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	989	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	990	if [[ -n $host && "$host" != $localhost ]]
	991	then
	992	do_batch=true
	993	do_remote=true
	994	case $host in
[1289]	995	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	996	(*) printf "\n"
[83]	997	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	998	printf "\n is not available"
[1]	999	locat=nqs; (( iec = 0 )); exit;;
	1000	esac
	1001	else
	1002	host=$localhost
	1003	fi
	1004
	1005
[1289]	1006	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1007	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1008	then
	1009
[1289]	1010	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1011	if [[ ! -n $numprocs ]]
	1012	then
	1013	printf "\n"
	1014	printf "\n +++ option \"-K parallel\" requires additional specification"
	1015	printf "\n of the number of processors to be used by"
	1016	printf "\n mrun-option \"-X\" or by environment-variable"
	1017	printf "\n \"numprocs\" in the configuration file"
	1018	locat=numprocs; (( iec = 0 )); exit
	1019	fi
	1020
[1289]	1021	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1022	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[1039]	1023	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
[1]	1024	then
[759]	1025	printf "\n"
	1026	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1027	printf "\n set -T option or define tasks_per_node in the config file"
	1028	locat=tasks_per_node; (( iec = 0 )); exit
	1029	fi
[1279]	1030
	1031	if (( numprocs < tasks_per_node ))
	1032	then
	1033	printf "\n"
	1034	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1035	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1036	locat=tasks_per_node; (( iec = 0 )); exit
	1037	fi
	1038
[1039]	1039	if [[ $host != lcflow && $host != lcxt5m ]]
[759]	1040	then
[1279]	1041	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1042	(( ival = $tasks_per_node ))
	1043	(( pes = numprocs ))
	1044	(( ii = pes / ival ))
[1279]	1045	(( remaining_pes = pes - ii * ival ))
	1046	if (( remaining_pes > 0 ))
[848]	1047	then
	1048	printf "\n"
[1279]	1049	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1050	printf "\n divisor of the total number of processors (option \"-X\")"
	1051	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1052	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1053	(( nodes = nodes + 1 ))
[848]	1054	fi
[1]	1055	fi
	1056
[759]	1057
[377]	1058	# SETTINGS FOR SUBJOB-COMMAND
[1]	1059	OOPT="-O $threads_per_task"
	1060
[1289]	1061	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1062	if [[ "$tasks_per_node" != "" ]]
	1063	then
[1119]	1064	TOPT="-T $tasks_per_node"
[1]	1065	fi
	1066
[1289]	1067	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1068	if [[ $node_usage = default ]]
	1069	then
	1070	if [[ $host = ibms ]]
	1071	then
	1072	node_usage=shared
	1073	else
	1074	node_usage=not_shared
	1075	fi
	1076	fi
[181]	1077
[635]	1078	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1079	then
	1080	printf "\n"
	1081	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1082	printf "\n \"shared\" or \"not_shared\""
	1083	locat=tasks_per_node; (( iec = 0 )); exit
	1084	fi
	1085
	1086	fi
	1087
[1289]	1088	# CHECK IF HOSTFILE EXISTS
[1]	1089	if [[ -n $hostfile ]]
	1090	then
	1091	if [[ ! -f $hostfile ]]
	1092	then
	1093	printf "\n"
	1094	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1095	locat=hostfile; exit
	1096	fi
	1097	fi
	1098
	1099
[1289]	1100	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1101	if [[ "$maximum_parallel_io_streams" = "" ]]
	1102	then
	1103	maximum_parallel_io_streams=$numprocs
	1104	fi
[1]	1105
[759]	1106
[1289]	1107	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1108	if [[ "$scp_port" != "" ]]
	1109	then
	1110	PORTOPT="-P $scp_port"
	1111	SSH_PORTOPT="-p $scp_port"
	1112	fi
	1113
	1114
[1289]	1115	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1116	if [[ $queue = none ]]
	1117	then
	1118	case $host in
[1184]	1119	(ibmh) queue=cluster;;
[693]	1120	(ibmkisti) queue=class.32plus;;
[1040]	1121	(lckiaps) queue=normal;;
[440]	1122	(lckyoto) queue=ph;;
[1099]	1123	(lckyuh) queue=fx-single;;
	1124	(lckyut) queue=cx-single;;
[635]	1125	(lctit) queue=S;;
[1]	1126	(nech) queue=none;;
	1127	(unics) queue=unics;;
	1128	esac
	1129	fi
	1130
	1131
[1289]	1132	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1133	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1134	(( i = 0 ))
	1135	while (( i < iin ))
	1136	do
	1137	(( i = i + 1 ))
	1138	(( maxcycle = 0 ))
	1139
[1289]	1140	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1141	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1142	if [[ "${actionin[$i]}" = di ]]
	1143	then
[1289]	1144	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1145	# HOST ONLY
[1]	1146	eval filename=${pathin[$i]}/${endin[$i]}
	1147	else
[1289]	1148	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1149	# HOST ONLY
[1]	1150	eval filename=${pathin[$i]}/${afname}${endin[$i]}
	1151	fi
[892]	1152	eval pathname=${pathin[$i]}
[1]	1153
[1289]	1154	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
[920]	1155	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
	1156	then
	1157	filename_input=$filename
	1158	fi
[892]	1159
[1289]	1160	# CHECK IF FILE EXISTS
[1]	1161	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
[746]	1162	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
[1]	1163	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
	1164	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
	1165	then
[1289]	1166
	1167	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[1]	1168	if [[ "${transin[$i]}" != "locopt" ]]
	1169	then
	1170	printf "\n\n +++ INPUT-file: "
	1171	if [[ "${extin[$i]}" = "" ]]
	1172	then
	1173	printf "\n $filename"
	1174	else
	1175	printf "\n $filename.${extin[$i]}"
	1176	fi
	1177	printf "\n does not exist\n"
	1178	locat=input; exit
	1179	else
	1180	transin[$i]="unavailable"
	1181	fi
	1182	else
	1183
[1289]	1184	# DETERMINE THE FILE'S CYCLE NUMBER
[1]	1185	ls -1 -d $filename > filelist 2>/dev/null
	1186	ls -1 -d $filename.* >> filelist 2>/dev/null
	1187	while read zeile
	1188	do
[1101]	1189	cycle=$(echo $zeile \| cut -f2 -d".")
[1]	1190	if [[ "$cycle" = "$zeile" ]]
	1191	then
	1192	(( icycle = 0 ))
	1193	elif [[ "$cycle" = "${extin[$i]}" ]]
	1194	then
	1195	(( icycle = 0 ))
	1196	else
	1197	(( icycle = $cycle ))
	1198	fi
	1199	if (( icycle > maxcycle ))
	1200	then
	1201	(( maxcycle = icycle ))
	1202	file_to_be_used=$zeile
	1203	fi
	1204	done <filelist
	1205	rm filelist
	1206
[1289]	1207	# APPEND CYCLE NUMBER TO FILENAME
[1]	1208	if (( maxcycle > 0 ))
	1209	then
	1210	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1211	then
	1212	filename=${filename}.$maxcycle.${extin[$i]}
	1213	else
	1214	filename=${filename}.$maxcycle
	1215	fi
	1216	else
	1217	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1218	then
	1219	filename=${filename}.${extin[$i]}
	1220	fi
	1221	fi
	1222
[1289]	1223	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1224	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
[1]	1225	absnamein[$i]=$filename
	1226	if (( maxcycle > 0 ))
	1227	then
	1228	if [[ "${actionin[$i]}" = di ]]
	1229	then
	1230	frelin[$i]=${endin[$i]}.$maxcycle
	1231	else
	1232	frelin[$i]=${afname}${endin[$i]}.$maxcycle
	1233	fi
	1234	else
	1235	if [[ "${actionin[$i]}" = di ]]
	1236	then
	1237	frelin[$i]=${endin[$i]}
	1238	else
	1239	frelin[$i]=${afname}${endin[$i]}
	1240	fi
	1241	fi
	1242
	1243	fi
	1244	done
[920]	1245
[1289]	1246	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1247	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1248	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1249	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1250	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1251	# REMOTE HOST)
[1]	1252	(( i = 0 ))
	1253	while (( i < iout ))
	1254	do
	1255	(( i = i + 1 ))
	1256	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1257	then
[260]	1258	if [[ "${actionout[$i]}" = tr ]]
[1]	1259	then
	1260	actionout[$i]=""
[260]	1261	elif [[ "${actionout[$i]}" = trpe ]]
	1262	then
	1263	actionout[$i]=pe
[1]	1264	elif [[ "${actionout[$i]}" = tra ]]
	1265	then
	1266	actionout[$i]=a
	1267	fi
	1268	(( maxcycle = 0 ))
	1269	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1270	eval catalogname=${pathout[$i]}
	1271	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
[746]	1272	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
[1]	1273	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
	1274	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
	1275	then
	1276
[1289]	1277	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
[1]	1278	if cat /dev/null > $filename
	1279	then
	1280	rm $filename
	1281	else
	1282
[1289]	1283	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1284	# IF IT DOES NOT EXIST, TRY TO CREATE IT
[1]	1285	if [[ ! -d $catalogname ]]
	1286	then
	1287	if mkdir -p $catalogname
	1288	then
	1289	printf "\n\n *** directory:"
	1290	printf "\n $catalogname"
	1291	printf "\n was created\n"
	1292	else
	1293	printf "\n\n +++ OUTPUT-file:"
	1294	printf "\n $filename"
	1295	printf "\n cannot be created, because directory does not exist"
	1296	printf "\n and cannot be created either"
	1297	printf "\n"
	1298	locat=output ; exit
	1299	fi 2>/dev/null
	1300	else
	1301	printf "\n\n +++ OUTPUT-file:"
	1302	printf "\n $filename"
	1303	printf "\n cannot be created, although directory exists"
	1304	printf "\n"
	1305	locat=output ; exit
	1306	fi
	1307	fi 2>/dev/null
	1308	else
	1309
[1289]	1310	# DETERMINE THE CYCLE NUMBER
[1]	1311	ls -1 -d $filename > filelist 2>/dev/null
	1312	ls -1 -d $filename.* >> filelist 2>/dev/null
	1313	while read zeile
	1314	do
[1101]	1315	cycle=$(echo $zeile \| cut -f2 -d".")
[1]	1316	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
	1317	then
	1318	(( icycle = 1 ))
	1319	else
	1320	(( icycle = $cycle + 1 ))
	1321	fi
	1322	if (( icycle > maxcycle ))
	1323	then
	1324	(( maxcycle = icycle ))
	1325	fi
	1326	done <filelist
	1327	rm filelist
	1328	fi
	1329
[1289]	1330	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1331	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1332	if [[ "${actionout[$i]}" != a ]]
	1333	then
	1334	if (( maxcycle > 0 ))
	1335	then
	1336	filename=${filename}.$maxcycle
	1337	if cat /dev/null > $filename
	1338	then
	1339	rm $filename
	1340	else
	1341	printf "\n +++ OUTPUT-file:"
	1342	printf "\n $filename"
	1343	printf "\n cannot be created"
	1344	locat=output ; exit
	1345	fi
	1346	fi
	1347	else
	1348	(( maxcycle = maxcycle - 1 ))
	1349	if (( maxcycle > 0 ))
	1350	then
	1351	filename=${filename}.$maxcycle
	1352	fi
	1353	fi
	1354
[1289]	1355	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1356	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
	1357	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
[1]	1358	pathout[$i]=$filename
	1359	if (( maxcycle > 0 ))
	1360	then
	1361	frelout[$i]=${fname}${endout[$i]}.$maxcycle
	1362	else
	1363	frelout[$i]=${fname}${endout[$i]}
	1364	fi
	1365
	1366	fi
	1367	done
	1368
	1369
[1289]	1370	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1371	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1372	then
[260]	1373	if [[ "$dvr_inc" = "" ]]
[83]	1374	then
[260]	1375	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1376	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1377	locat=dvr; exit
[83]	1378	fi
[260]	1379	if [[ "$dvr_lib" = "" ]]
[83]	1380	then
[260]	1381	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1382	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1383	locat=dvr; exit
[83]	1384	fi
	1385	fi
	1386
	1387
[1289]	1388	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1389	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1390	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1391	then
	1392	printf "\n +++ neither main program nor executable defined"
	1393	locat=source; exit
	1394	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1395	then
	1396	printf "\n +++ main program as well as executable defined"
	1397	locat=source; exit
	1398	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1399	then
	1400	do_compile=false
	1401	fi
	1402
	1403
[1289]	1404	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1405	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1406	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1407	then
	1408	rm -rf SOURCES_FOR_RUN_$fname
	1409	mkdir SOURCES_FOR_RUN_$fname
	1410	fi
	1411
	1412
[1289]	1413	# COLLECT ALL ROUTINES TO BE COMPILED
	1414	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1415	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1416	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1417	then
	1418
[5]	1419	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1420
[838]	1421	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1422	then
	1423
[1289]	1424	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1425	source_list=""
	1426	cd $source_path
	1427
	1428
[1289]	1429	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1430	if [[ ! -d .svn ]]
	1431	then
	1432	printf "\n\n +++ source directory"
	1433	printf "\n \"$source_path\" "
	1434	printf "\n is not under control of \"subversion\"."
[306]	1435	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1436	fi
	1437
	1438
[1289]	1439	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1440	Filenames=""
[69]	1441	svn status > tmp_mrun
	1442	while read line
[5]	1443	do
	1444	firstc=`echo $line \| cut -c1`
	1445	if [[ $firstc = M \|\| $firstc = "?" ]]
	1446	then
	1447	Name=`echo "$line" \| cut -c8-`
	1448	extension=`echo $Name \| cut -d. -f2`
	1449	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1450	then
	1451	Filenames="$Filenames "$Name
	1452	fi
	1453	fi
[69]	1454	done < tmp_mrun
[5]	1455
	1456
[1289]	1457	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1458	for dateiname in $Filenames
	1459	do
	1460	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1461	source_list=$source_list"$dateiname "
	1462	done
	1463
	1464	cd - > /dev/null
	1465
	1466
[1289]	1467	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1468	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1469	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1470	then
	1471
	1472	cd $source_path
	1473
	1474	for filename in $source_list
	1475	do
	1476
[1289]	1477	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1478	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1479	then
	1480	printf "\n +++ source code file: $filename"
	1481	printf "\n must not contain (\"/\") "
	1482	locat=source; exit
	1483	fi
	1484
	1485	if [[ ! -f $filename ]]
	1486	then
	1487	printf "\n +++ source code file: $filename"
	1488	printf "\n does not exist"
	1489	locat=source; exit
	1490	else
	1491	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1492	fi
	1493
	1494	done
	1495
	1496	cd - > /dev/null
	1497
	1498	fi
	1499
	1500
[1289]	1501	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1502	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1503	if [[ $restart_run != true ]]
[1]	1504	then
	1505
	1506	if [[ ! -f "$source_path/$mainprog" ]]
	1507	then
	1508	printf "\n\n +++ main program: $mainprog"
	1509	printf "\n does not exist in source directory"
	1510	printf "\n \"$source_path\"\n"
	1511	locat=source; exit
	1512	else
	1513	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1514	then
	1515	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1516	source_list=${mainprog}" $source_list"
	1517	fi
	1518	fi
	1519	fi
	1520
	1521
[1289]	1522	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1523	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1524	if [[ "$restart_run" != true ]]
	1525	then
	1526	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1527	if [[ ! -f $makefile ]]
	1528	then
	1529	printf "\n +++ file \"$makefile\" does not exist"
	1530	locat=make; exit
	1531	else
	1532	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1533	fi
	1534	fi
	1535
	1536
[1289]	1537	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1538	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1539	then
	1540
[1289]	1541	# DOES THE DIRECTORY EXIST?
[1]	1542	if [[ ! -d $add_source_path ]]
	1543	then
	1544	printf "\n\n +++ WARNING: additional source code directory"
	1545	printf "\n \"$add_source_path\" "
	1546	printf "\n does not exist or is not a directory."
	1547	printf "\n No source code will be used from this directory!\n"
	1548	add_source_path=""
[931]	1549	if [[ $silent == false ]]
	1550	then
	1551	sleep 3
	1552	fi
[1]	1553	else
	1554
	1555	cd $add_source_path
[211]	1556	found=false
[1]	1557
	1558	Names=$(ls -1 *.f90 2>&1)
	1559	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1560	Names=$(ls -1 *.F90 2>&1)
	1561	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1562	Names=$(ls -1 *.F 2>&1)
	1563	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1564	Names=$(ls -1 *.f 2>&1)
	1565	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1566	Names=$(ls -1 *.c 2>&1)
	1567	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1568
	1569	cd - > /dev/null
	1570	cd SOURCES_FOR_RUN_$fname
	1571
[211]	1572	# COPY MAKEFILE IF EXISTING
	1573	if [[ -f $add_source_path/Makefile ]]
	1574	then
	1575	printf "\n\n *** user Makefile from directory"
	1576	printf "\n \"$add_source_path\" is used \n"
[931]	1577	if [[ $silent == false ]]
	1578	then
	1579	sleep 1
	1580	fi
[211]	1581	cp $add_source_path/Makefile .
	1582	fi
	1583
[1]	1584	for dateiname in $AddFilenames
	1585	do
	1586	if [[ -f $dateiname ]]
	1587	then
	1588	printf "\n +++ source code file \"$dateiname\" found in additional"
	1589	printf "\n source code directory \"$add_source_path\" "
[211]	1590	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1591	printf "\n from directory \"$source_path\"."
[1]	1592	locat=source; exit
	1593	fi
	1594
	1595	cp $add_source_path/$dateiname .
	1596	source_list="$source_list $dateiname"
	1597
[211]	1598	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1599	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1600	then
	1601	printf "\n\n +++ user file \"$dateiname\" "
	1602	printf "\n is not listed in Makefile \n"
	1603	locat=source; exit
	1604	else
	1605
	1606	if [[ $found = false ]]
[1]	1607	then
[211]	1608	found=true
	1609	printf "\n\n *** following user file(s) added to the"
	1610	printf " files to be translated:\n "
[1]	1611	fi
[211]	1612	printf "$dateiname "
[931]	1613	if [[ $silent == false ]]
	1614	then
	1615	sleep 0.5
	1616	fi
	1617
[1]	1618	fi
	1619	done
[211]	1620	[[ $found = true ]] && printf "\n"
[1]	1621	cd - > /dev/null
	1622	fi
	1623	fi
	1624
	1625
[1289]	1626	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1627	# TO THE LIST OF FILES TO BE COMPILED
[5]	1628	if [[ $restart_run != true && -n $package_list ]]
[1]	1629	then
	1630
	1631	cd $source_path
	1632
	1633	for package in $package_list
	1634	do
	1635
	1636	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1637
[1289]	1638	# DETERMINE FILES BELONGING TO THE PACKAGE
	1639	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1640	# THE NAME OF THE DIRECTORY
[1]	1641	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1642
	1643
[1289]	1644	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1645	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1646	for source_list_name in $package_source_list
	1647	do
	1648	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1649	then
	1650
[1289]	1651	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1652	ending=`echo $source_list_name \| cut -f2 -d.`
	1653	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1654	then
	1655	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1656	source_list="$source_list $source_list_name"
	1657	fi
	1658	fi
	1659	done
	1660	done
	1661
	1662	cd - > /dev/null
	1663	fi
	1664
	1665	fi # do_compile=true
	1666
	1667
[1289]	1668	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1669	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1670	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1671	then
	1672
[1289]	1673	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[1]	1674	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1675	then
[82]	1676	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1677	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1678	then
[82]	1679	cpp_options="$cpp_options -D__nec"
	1680	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1681	then
	1682	cpp_options="$cpp_options -D__lc"
[1]	1683	else
[82]	1684	cpp_options="$cpp_options -D__$localhost"
[1]	1685	fi
[83]	1686
[1289]	1687	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[1]	1688	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1689	then
[82]	1690	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1691	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1692	else
[82]	1693	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1694	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1695	fi
[83]	1696
[1289]	1697	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1698	if [[ -n $package_list ]]
	1699	then
	1700	for package in $package_list
	1701	do
	1702	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1703	then
	1704	if [[ $package != "dvrp_graphics+1PE" ]]
	1705	then
[82]	1706	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1707	else
[82]	1708	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1709	export use_seperate_pe_for_dvrp_output=true
	1710	fi
	1711	else
	1712	if [[ $package != "dvrp_graphics+1PE" ]]
	1713	then
[82]	1714	cpp_options="$cpp_options -D__$package"
[1]	1715	else
[82]	1716	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1717	export use_seperate_pe_for_dvrp_output=true
	1718	fi
	1719	fi
	1720	done
	1721	fi
[83]	1722
[1289]	1723	# SET DIRECTIVES GIVEN BY OPTION -D
[1]	1724	if [[ -n $cpp_opts ]]
	1725	then
	1726	for popts in $cpp_opts
	1727	do
[82]	1728	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1729	then
	1730	cpp_options="${cpp_options},-D__$popts=__$popts"
	1731	else
	1732	cpp_options="$cpp_options -D__$popts"
	1733	fi
[1]	1734	done
	1735	fi
	1736
	1737	else
	1738
	1739
[1289]	1740	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1741	if [[ $do_remote = false ]]
	1742	then
	1743	if [[ ! -f $executable ]]
	1744	then
	1745	printf "\n +++ executable file: $executable"
	1746	printf "\n does not exist"
	1747	locat=executable; exit
	1748	fi
	1749	fi
	1750	fi
	1751
	1752
[1289]	1753	# DETERMINE THE JOB MODE
[635]	1754	if [[ "$ENVIRONMENT" = BATCH ]]
[1]	1755	then
	1756	jobmo=BATCH
	1757	else
	1758	jobmo=INTERACTIVE
	1759	fi
	1760
	1761
[1289]	1762	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1763	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1764	then
	1765	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1766	printf "\n please submit batch job using mrun option \"-b\" \n"
	1767	locat=normal; exit
	1768	fi
	1769
	1770
[1289]	1771	# CHECK, IF USER DEFINED A COMPILER
[1]	1772	if [[ "$compiler_name" = "" ]]
	1773	then
[82]	1774
[220]	1775	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1776	locat=compiler_name; exit
	1777
[1]	1778	fi
	1779
	1780
[1289]	1781	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1]	1782	kennung=$RANDOM
	1783	if [[ "$tmp_user_catalog" = "" ]]
	1784	then
[312]	1785	if [[ $localhost = ibmh ]]
[1]	1786	then
[312]	1787	tmp_user_catalog=$SCRATCH
[1]	1788	elif [[ $localhost = nech ]]
	1789	then
	1790	tmp_user_catalog=$WRKSHR
	1791	else
	1792	tmp_user_catalog=/tmp
	1793	fi
	1794	fi
	1795	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1796
	1797
[1289]	1798	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1799	if [[ "$tmp_data_catalog" = "" ]]
	1800	then
[622]	1801	if [[ $localhost = nech ]]
[1]	1802	then
	1803	tmp_data_catalog=$WRKSHR/mrun_restart_data
	1804	else
	1805	tmp_data_catalog=/tmp/mrun_restart_data
	1806	fi
	1807	fi
	1808
	1809
[1289]	1810	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1811	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1812	then
	1813	eval fopts=\"$fopts\"
	1814	eval lopts=\"$lopts\"
	1815	fi
	1816
	1817
	1818
[1289]	1819	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1820	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1821	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1]	1822	ROPTS="$ropts"
[1289]	1823	# if [[ ( $(echo $host \| cut -c1-3) = nec \|\| $(echo $host \| cut -c1-3) = ibm \|\| $host = lckyoto \|\| $host = lctit \|\| $host = lcflow \|\| $host = lcxe6 \|\| $host = lcxt5m \|\| $host = lck \|\| $host = lckiaps \|\| $host = lckordi \|\| $host = lcsb \|\| $host ) && -n $numprocs ]]
[1090]	1824	# then
[1]	1825	XOPT="-X $numprocs"
[1090]	1826	# fi
[1]	1827
	1828
	1829
[1289]	1830	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1831	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1832	done=false
	1833	while [[ $done = false ]]
	1834	do
	1835	cputime=$cpumax
	1836	if (( $cputime == 0 ))
	1837	then
[246]	1838	if [[ $do_batch = true ]]
	1839	then
	1840	printf "\n +++ cpu-time is undefined"
	1841	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1842	printf "\n >>> "
	1843	read cputime 1>/dev/null 2>&1
	1844	else
	1845	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1846	fi
[1]	1847	else
	1848	done=true
	1849	fi
	1850	cpumax=$cputime
	1851	done
	1852
	1853	(( minuten = cputime / 60 ))
	1854	(( sekunden = cputime - minuten * 60 ))
	1855
	1856
[1289]	1857	# CHECK THE MEMORY DEMAND
[1]	1858	if [[ $do_batch = true ]]
	1859	then
	1860	done=false
	1861	while [[ $done = false ]]
	1862	do
	1863	if (( memory == 0 ))
	1864	then
	1865	printf "\n +++ memory demand is undefined"
	1866	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1867	printf "\n >>> "
	1868	read memory 1>/dev/null 2>&1
	1869	else
	1870	done=true
	1871	fi
	1872	done
	1873	fi
	1874
	1875
[1289]	1876	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	1877	if [[ $do_remote = true && -z $remote_username ]]
	1878	then
	1879	while [[ -z $remote_username ]]
	1880	do
	1881	printf "\n +++ username on remote host \"$host\" is undefined"
	1882	printf "\n >>> Please type username:"
	1883	printf "\n >>> "
	1884	read remote_username
	1885	done
	1886	mc="$mc -u$remote_username"
	1887	fi
	1888
[892]	1889	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	1890	if [[ "$login_init_cmd" != "" ]]
	1891	then
	1892	export init_cmds="${login_init_cmd};"
	1893	fi
[221]	1894
[892]	1895
[1289]	1896	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	1897	if [[ "$modules" != "" ]]
	1898	then
[678]	1899	if [[ $host = lctit ]]
	1900	then
	1901	export module_calls=". $modules"
	1902	else
	1903	export module_calls="module load ${modules};"
	1904	fi
[493]	1905	fi
	1906
	1907
[555]	1908
[1289]	1909	# OUTPUT OF THE MRUN-HEADER
[1]	1910	calltime=$(date)
	1911	printf "\n"
[1101]	1912	printf "#------------------------------------------------------------------------# \n"
	1913	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1914	printf "\| \| \n"
[1]	1915	spalte1="called on:"; spalte2=$localhost_realname
[1101]	1916	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	1917	if [[ $do_remote = true ]]
[1]	1918	then
[1289]	1919	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	1920	else
[1289]	1921	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	1922	fi
[1101]	1923	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	1924	if [[ -n $numprocs ]]
	1925	then
[1106]	1926	if [[ $run_coupled_model = false ]]
	1927	then
	1928	spalte1="number of PEs:"; spalte2=$numprocs
	1929	else
	1930	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	1931	fi
[1101]	1932	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	1933	fi
	1934	if [[ -n $tasks_per_node ]]
	1935	then
	1936	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	1937	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	1938	if (( remaining_pes > 0 ))
	1939	then
	1940	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	1941	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1942	fi
[1]	1943	fi
[759]	1944	if [[ $maximum_parallel_io_streams != $numprocs ]]
	1945	then
	1946	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	1947	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	1948	fi
[622]	1949	if [[ $use_openmp = true ]]
[1]	1950	then
	1951	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	1952	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	1953	fi
[1101]	1954	printf "\| \| \n"
[1]	1955	if [[ $do_compile = true ]]
	1956	then
[475]	1957	if [[ "$mopts" != "" ]]
	1958	then
[1101]	1959	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	1960	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1961	zeile=$(echo "$mopts" \| cut -c46-)
[475]	1962	while [[ "$zeile" != "" ]]
	1963	do
	1964	spalte1=""
[1101]	1965	spalte2=$(echo "$zeile" \| cut -c-45)
	1966	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1967	zeile=$(echo "$zeile" \| cut -c46-)
[475]	1968	done
	1969	fi
	1970
[1101]	1971	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	1972	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1973	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	1974	while [[ "$zeile" != "" ]]
	1975	do
	1976	spalte1=""
[1101]	1977	spalte2=$(echo "$zeile" \| cut -c-45)
	1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1979	zeile=$(echo "$zeile" \| cut -c46-)
[1]	1980	done
	1981
[1101]	1982	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	1983	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1984	zeile=$(echo "$fopts" \| cut -c46-)
[1]	1985	while [[ "$zeile" != "" ]]
	1986	do
	1987	spalte1=""
[1101]	1988	spalte2=$(echo "$zeile" \| cut -c-45)
	1989	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1990	zeile=$(echo "$zeile" \| cut -c46-)
[1]	1991	done
	1992
[1101]	1993	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	1995	zeile=$(echo "$lopts" \| cut -c46-)
[1]	1996	while [[ "$zeile" != "" ]]
	1997	do
	1998	spalte1=""
[1101]	1999	spalte2=$(echo "$zeile" \| cut -c-45)
	2000	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2001	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2002	done
	2003
[1101]	2004	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2005	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2006	zeile=$(echo "$modules" \| cut -c46-)
[493]	2007	while [[ "$zeile" != "" ]]
	2008	do
	2009	spalte1=""
[1101]	2010	spalte2=$(echo "$zeile" \| cut -c-45)
	2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2012	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2013	done
	2014
[1101]	2015	spalte1="main program:"; spalte2=$mainprog
	2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2017	else
	2018	spalte1=executable:; spalte2=$executable
[1101]	2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2020	fi
[1101]	2021	printf "\| \| \n"
	2022	spalte1="base name of files:"; spalte2=$fname
	2023	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2024	if [[ $fname != $afname ]]
	2025	then
[1101]	2026	spalte1="base name of input files:"; spalte2=$afname
	2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2028	fi
[1101]	2029	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2031	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2033
[1106]	2034	if [[ "$ocean_file_appendix" = true ]]
	2035	then
	2036	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2037	fi
	2038
[1]	2039	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2040	then
	2041	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2042	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2043	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2045	fi
	2046
	2047	if [[ $do_compile = true ]]
	2048	then
[1101]	2049	printf "\| \| \n"
	2050	printf "\| Files to be compiled: \| \n"
[1]	2051	zeile=$source_list
	2052	while [[ "$zeile" != "" ]]
	2053	do
[1101]	2054	linestart=$(echo $zeile \| cut -c-70)
	2055	printf "\| %-70s \| \n" "$linestart"
	2056	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2057	done
	2058	fi
[1101]	2059	printf "#------------------------------------------------------------------------#"
[1]	2060
	2061
	2062
[1289]	2063	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2064	if [[ $do_trace = true ]]
	2065	then
	2066	(( i = 0 ))
	2067	while (( i < iin ))
	2068	do
	2069	(( i = i + 1 ))
	2070	if (( i == 1 ))
	2071	then
	2072	printf "\n\n >>> INPUT-file assignments:\n"
	2073	fi
	2074	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2075	done
	2076	(( i = 0 ))
	2077	while (( i < iout ))
	2078	do
	2079	(( i = i + 1 ))
	2080	if (( i == 1 ))
	2081	then
	2082	printf "\n\n >>> OUTPUT-file assignments:\n"
	2083	fi
	2084	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2085	done
	2086	(( i = 0 ))
	2087	while (( i < iic ))
	2088	do
	2089	(( i = i + 1 ))
	2090	if (( i == 1 ))
	2091	then
	2092	printf "\n\n >>> INPUT-commands:\n"
	2093	fi
	2094	printf "\n ${in_command[$i]}"
	2095	done
	2096	(( i = 0 ))
	2097	while (( i < ioc ))
	2098	do
	2099	(( i = i + 1 ))
	2100	if (( i == 1 ))
	2101	then
	2102	printf "\n\n >>> OUTPUT-commands:\n"
	2103	fi
	2104	printf "\n ${out_command[$i]}"
	2105	done
	2106	fi
	2107
	2108
[1289]	2109	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2110	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2111	then
	2112	antwort=dummy
	2113	printf "\n\n"
[1101]	2114	printf " >>> everything o.k. (y/n) ? "
	2115	while read antwort
[1]	2116	do
[1101]	2117	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2118	then
	2119	printf " >>> everything o.k. (y/n) ? "
	2120	else
	2121	break
	2122	fi
[1]	2123	done
	2124	if [[ $antwort = n \|\| $antwort = N ]]
	2125	then
	2126	locat=user_abort; (( iec = 0 )); exit
	2127	fi
	2128	if [[ $do_batch = true ]]
	2129	then
	2130	printf " >>> batch-job will be created and submitted"
	2131	else
[1289]	2132	printf " >>> MRUN will now continue to execute on this machine"
[1]	2133	fi
	2134	fi
	2135
[841]	2136
[1101]	2137	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
	2138	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
[841]	2139	check_depository="${working_directory}/trunk/UTIL"
	2140	check_sources="${working_directory}/tmp_check_namelist_files"
[818]	2141	skip_check=false
[841]	2142
[1101]	2143	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
[920]	2144	if [[ ! -f $check_depository/check_namelist_files.tar ]]
[841]	2145	then
[1101]	2146	skip_check=true
	2147	reason="run on remote host or parameter file check has not been compiled."
[920]	2148	fi
	2149	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
	2150	then
[1101]	2151	skip_check=true
	2152	reason="parameter file check has not been compiled."
[892]	2153	fi
[841]	2154
[1101]	2155	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
[892]	2156	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
	2157	then
[1101]	2158	skip_check=true
	2159	reason="serial run."
[841]	2160	fi
	2161
[1101]	2162	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
	2163	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
	2164	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
	2165	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
[892]	2166	if [[ $check_namelist_files == false ]]
[807]	2167	then
[1101]	2168	skip_check=true
	2169	reason="-z option set."
[815]	2170	fi
[892]	2171
	2172	if [[ $fromhost != $localhost ]]
[815]	2173	then
[1101]	2174	skip_check=true
	2175	reason="submitting host is local host."
[892]	2176	fi
[1]	2177
[892]	2178	if [[ $run_coupled_model == true ]]
	2179	then
	2180	skip_check=true
	2181	reason="coupled run."
	2182	fi
[1]	2183
[892]	2184	if [[ $restart_run == true ]]
	2185	then
	2186	skip_check=true
	2187	reason="restart run."
	2188	fi
[807]	2189
[1101]	2190	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
[1122]	2191	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
	2192	last_char=`echo $filename_input \| cut -c $last_char_int`
[892]	2193	if [[ "$last_char" == "f" ]]
	2194	then
	2195	skip_check=true
[1069]	2196	reason="restart run."
[892]	2197	fi
[807]	2198
[892]	2199	if [[ $skip_check == false ]]
	2200	then
	2201	tmp_check=${working_directory}/tmp_check
[841]	2202
[1241]	2203	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
[1101]	2204	# NOT NECESSARILY REQUIRED
[818]	2205	line=""
	2206	found=false
[892]	2207	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
[818]	2208	while read line1
	2209	do
	2210	line="$line1"
	2211	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2212	then
	2213	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
	2214	found=true
	2215	fi
	2216	done < $tmp_check
[807]	2217
[818]	2218	if [[ $found = false ]]
	2219	then
	2220	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
	2221	fi
	2222
[1241]	2223	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
	2224	# NOT NECESSARILY REQUIRED
	2225	line=""
	2226	found=false
	2227	grep "NUDGING_DATA" $config_file > $tmp_check
	2228	while read line1
	2229	do
	2230	line="$line1"
	2231	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2232	then
	2233	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
	2234	found=true
	2235	fi
	2236	done < $tmp_check
	2237
	2238	if [[ $found = false ]]
	2239	then
	2240	printf "\n +++ no NUDGING list entry found in the configuration file."
	2241	fi
	2242
	2243	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
	2244	# NOT NECESSARILY REQUIRED
	2245	line=""
	2246	found=false
	2247	grep "LSF_DATA" $config_file > $tmp_check
	2248	while read line1
	2249	do
	2250	line="$line1"
	2251	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2252	then
	2253	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
	2254	found=true
	2255	fi
	2256	done < $tmp_check
	2257
	2258	if [[ $found = false ]]
	2259	then
	2260	printf "\n +++ no LSF list entry found in the configuration file."
	2261	fi
	2262
[807]	2263	rm -rf ${working_directory}/tmp_check
	2264
[1241]	2265	# CHECK IF THE P3DF FILE MUST BE CHECKED
[807]	2266	for item in $input_list
	2267	do
[892]	2268	if [[ "$item" == "restart" ]]
[807]	2269	then
	2270	check_restart=1
	2271	else
	2272	check_restart=0
	2273	fi
	2274	done
	2275
[1101]	2276	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
	2277	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
[807]	2278	then
[920]	2279	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
[807]	2280	locat=check_namelist; exit
	2281	fi
	2282
[1101]	2283	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
[807]	2284	if [[ $check_restart == 1 ]]
	2285	then
[892]	2286
[920]	2287	filenamef="${filename_input}f"
[892]	2288	if [[ ! -f $filenamef ]]
[807]	2289	then
[892]	2290	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
[807]	2291	check_restart=0
	2292	answer=dummy
	2293	printf "\n\n"
	2294
[818]	2295	if [[ $silent == false ]]
[807]	2296	then
[818]	2297	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
	2298	do
	2299	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
	2300	read answer
	2301	done
	2302	if [[ $answer = a \|\| $answer = A ]]
	2303	then
	2304	printf "\n +++ Aborting...."
	2305	locat=normal; exit
	2306	fi
[807]	2307	fi
	2308	else
	2309	check_restart=1
	2310	fi
	2311	fi
	2312
[1101]	2313	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
[807]	2314	mkdir $check_sources
	2315	cd $check_sources
	2316
[892]	2317
[1101]	2318	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
[892]	2319	if [[ -d $add_source_path ]]
[807]	2320	then
	2321	printf "\n\n *** copying files from $check_depository"
	2322	cp $check_depository/check_namelist_files.tar ./
	2323
	2324	printf "\n\n *** untar of makefile and source files in $check_sources"
	2325	tar -xf check_namelist_files.tar > /dev/null 2>&1
	2326
	2327	printf "\n\n *** adding user code."
[892]	2328	cp $add_source_path/* ./
[807]	2329	touch check_namelist_files.f90
	2330
[1101]	2331	# GET COMPILER OPTIONS AND PERFORM MAKE
[807]	2332	printf "\n\n *** compiling code if necessary...\n"
[1045]	2333
[1101]	2334	# workaround for batch jobs on local machine (lcxe6)
[1045]	2335	if [[ $do_batch == true && $do_remote == false ]]
	2336	then
	2337	eval $init_cmds
	2338	fi
	2339
[1101]	2340	# GET CHECK OPTIONS
[1083]	2341	line=""
	2342	found=false
	2343
	2344	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
	2345
	2346	while read line1
	2347	do
	2348
	2349	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
	2350	then
	2351	line="$line1"
	2352	fi
	2353
	2354	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2355	then
[1289]	2356	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
[1101]	2357	line="$line "
[1083]	2358	copts_check=`echo $line \| cut -d" " -s -f2 \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g' \| sed 's/-D[^ ]* //g' \| sed 's/ -D.*//g'`
	2359	found=true
	2360	fi
	2361
	2362	done < $tmp_check
	2363	copts_check="$copts_check -D__check -D__parallel"
	2364
[807]	2365	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
	2366
[1101]	2367	# GET MAKE OUTPUT
[807]	2368	if [[ $? != 0 ]]
	2369	then
[815]	2370	printf "\n +++ error during make."
	2371	answer=dummy
	2372	printf "\n\n"
[818]	2373	if [[ $silent == false ]]
[815]	2374	then
[818]	2375	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
	2376	do
	2377	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
	2378	read answer
	2379	done
	2380	if [[ $answer = a \|\| $answer = A ]]
	2381	then
	2382	printf "\n +++ Aborting..."
	2383	rm -rf $check_sources
	2384	locat=normal; exit
	2385	else
	2386	skip_check=true
	2387	fi
[815]	2388	else
	2389	skip_check=true
	2390	fi
[807]	2391	fi
	2392	else
	2393	cp $PALM_BIN/check_namelist_files.x ./
	2394	fi
	2395
[920]	2396	cp $filename_input ./PARIN
[807]	2397	if [[ $check_restart == 1 ]]
	2398	then
[892]	2399	cp $filenamef ./PARINF
[807]	2400	fi
	2401
[892]	2402	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
[818]	2403	then
	2404	printf "\n *** adding topography data"
[892]	2405	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
[818]	2406
[1101]	2407	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
	2408	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
	2409	# WHICH REQUIRE SUFFICIENT MEMORY
[818]	2410	ulimit -s unlimited
	2411	fi
	2412
[1241]	2413	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
	2414	then
	2415	printf "\n *** adding nudging data"
	2416	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
	2417	fi
	2418
	2419	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
	2420	then
	2421	printf "\n *** adding large scale forcing data"
	2422	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
	2423	fi
	2424
[1101]	2425	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
[807]	2426	cat > ENVPAR << %%END%%
[823]	2427	&envpar run_identifier = '$fname', host = '$host',
[807]	2428	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
	2429	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2430	maximum_cpu_time_allowed = ${cpumax}.,
	2431	revision = '$global_revision',
	2432	local_dvrserver_running = $local_dvrserver_running /
	2433
	2434	%%END%%
	2435
[1101]	2436	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
	2437	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
	2438	then
[807]	2439	printf "\n +++ WARNING: check_namelist_files.x not found."
	2440	answer=dummy
	2441	printf "\n\n"
[818]	2442
	2443	if [[ $silent == false ]]
[807]	2444	then
[818]	2445	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
	2446	do
	2447	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
	2448	read answer
	2449	done
	2450	if [[ $answer = a \|\| $answer = A ]]
	2451	then
	2452	printf "\n +++ Aborting..."
	2453	rm -rf $check_sources
	2454	locat=normal; exit
	2455	else
[1101]	2456	printf "\n *** skipping parameter file check."
[818]	2457	fi
	2458	fi
	2459
[815]	2460	elif [[ $skip_check == false ]]
	2461	then
[1101]	2462	# STARTING THE PARAMETER FILE CHECK
[807]	2463	printf "\n\n *** starting parameter file check..."
	2464
[1101]	2465	# CHECKING THE P3D FILE
[920]	2466	printf "\n\n (1) checking $filename_input"
[931]	2467	echo "$numprocs 0 0" > VARIN
[807]	2468	errors=`./check_namelist_files.x < VARIN 2>&1`
	2469
	2470	check_error=false
	2471	if [[ "$errors" == "" ]]
	2472	then
	2473	printf " --> o.k."
	2474	else
	2475	printf " --> failed."
	2476	check_error=true
	2477	printf "\n\n $errors"
	2478	fi
	2479
[1101]	2480	# CHECKING THE PD3F FILE IF NECESSARY
[807]	2481	if [[ $check_restart == 1 && $check_error == false ]]
	2482	then
[892]	2483	printf "\n\n (2) checking $filenamef"
[807]	2484
[1101]	2485	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
	2486	# IN &INIPAR LIST
[807]	2487	found=false
[1101]	2488	cat PARINF \| while read line
[807]	2489	do
	2490	line=$(echo $line\|sed 's/ //g')
	2491	if [[ $line == "&inipar" ]]
	2492	then
	2493	start_search=true
	2494	fi
	2495
	2496	if [[ $start_search == true ]]
	2497	then
	2498	if [[ $line == "initializing_actions='read_restart_data'" ]]
	2499	then
	2500	found=true
	2501	break
	2502	fi
	2503	fi
	2504
	2505	if [[ $line == "/" ]]
	2506	then
	2507	start_search=false
	2508	fi
	2509
	2510	done
	2511
	2512	if [[ $found = false ]]
	2513	then
	2514	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
	2515	printf "\n in &inipar list in $fname$p3df_suffix."
	2516	rm -rf $check_sources
	2517	locat=check_namelist; exit
	2518	fi
	2519
[1101]	2520	# READ max_user_pr FROM FILES
[931]	2521	if [[ -f parin_for_check ]]
	2522	then
	2523	read max_pr_user < parin_for_check
	2524	else
	2525	max_user_pr=0
	2526	fi
	2527
	2528	echo "$numprocs 1 $max_pr_user" > VARIN
[807]	2529	errors=`./check_namelist_files.x < VARIN 2>&1`
	2530
	2531	if [[ "$errors" == "" ]]
	2532	then
	2533	printf " --> o.k."
	2534	else
	2535	printf " --> failed."
	2536	check_error=true
	2537	printf "\n\n $errors"
	2538	fi
	2539	fi
	2540
[1101]	2541	# REPORT ERRORS AND CONTINUE/EXIT
[807]	2542	if [[ $check_error == true ]]
	2543	then
	2544	printf "\n +++ errors found in the parameter file!\n"
	2545	answer=dummy
	2546	printf "\n\n"
	2547
	2548	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
	2549	do
[1101]	2550	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
	2551	read answer
[807]	2552	done
	2553
	2554	if [[ $answer = a \|\| $answer = A ]]
	2555	then
	2556	printf "\n +++ Aborting..."
	2557	rm -rf $check_sources
	2558	locat=normal; exit
	2559	fi
	2560	else
	2561	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
	2562	fi
	2563	rm -rf $check_sources
	2564	fi
	2565	else
[1103]	2566	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
[807]	2567	fi
	2568
[818]	2569	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
	2570	rm -rf $check_sources
[807]	2571	cd $working_directory
	2572
[892]	2573
[1199]	2574	# DETERMINE PATH FOR MAKE DEPOSITORY
	2575	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2576	then
	2577
	2578	line=""
	2579	grep "%depository_path" $config_file > tmp_mrun
	2580	while read line
	2581	do
	2582	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2583	then
	2584	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2585	then
	2586	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2587	fi
	2588	fi
	2589	done < tmp_mrun
	2590
	2591	line=""
	2592	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2593	while read line
	2594	do
	2595	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2596	then
	2597	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2598	then
	2599	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2600	fi
	2601	fi
	2602	done < tmp_mrun
	2603
	2604	if [[ "$local_depository_path" = "" ]]
	2605	then
	2606	if [[ "$global_depository_path" != "" ]]
	2607	then
	2608	local_depository_path=$global_depository_path
	2609	else
	2610	printf "\n\n +++ no depository path found in configuration file"
	2611	printf "\n for local host \"$localhost\" "
	2612	printf "\n please set \"\%depository_path\" in configuration file\n"
	2613	locat=config_file; exit
	2614	fi
	2615	fi
	2616	eval local_depository_path=$local_depository_path
	2617	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2618	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2619
	2620
	2621	basename=`echo $mainprog \| cut -f1 -d"."`
	2622	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2623	if [[ ! -f $make_depository ]]
	2624	then
	2625	printf "\n"
	2626	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2627	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2628	fi
	2629
	2630	fi
	2631
	2632
[1289]	2633	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2634	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2635	if [[ $do_batch = false ]]
	2636	then
	2637
	2638
[1289]	2639	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2640	mkdir -p $TEMPDIR
	2641	chmod go+rx $TEMPDIR
	2642	tmpcreate=true
	2643
	2644
[1289]	2645	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2646	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2647	if [[ $do_compile = true ]]
	2648	then
	2649
	2650	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
	2651	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
	2652	if [[ $localhost = nech ]]
	2653	then
	2654	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
	2655	if mkdir -p $TEMPDIR_COMPILE
	2656	then
	2657	printf "\n *** \"$TEMPDIR_COMPILE\" "
	2658	printf "\n is generated as temporary directory for cross compiling\n"
	2659	else
	2660	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
	2661	printf "\n needed for cross compilation failed"
	2662	locat=compile
	2663	exit
	2664	fi
	2665	else
	2666	TEMPDIR_COMPILE=$TEMPDIR
	2667	fi
	2668
[1199]	2669	cp $make_depository $TEMPDIR_COMPILE
	2670	cd $TEMPDIR_COMPILE
	2671	tar -xf $make_depository > /dev/null 2>&1
	2672	cd - > /dev/null
[1]	2673
[1255]	2674	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2675	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2676	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2677	then
	2678	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2679	else
	2680	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2681	fi
[82]	2682
[1]	2683	else
[475]	2684
[1]	2685	cp $executable ${TEMPDIR}/a.out
[475]	2686
[1]	2687	fi
	2688
	2689
[1289]	2690	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2691	cd $TEMPDIR
[1]	2692	printf "\n *** changed to temporary directory: $TEMPDIR"
	2693
	2694
[1289]	2695	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
	2696	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
	2697	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
	2698	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
[1]	2699	(( i = 0 ))
	2700	while (( i < iout ))
	2701	do
	2702	(( i = i + 1 ))
	2703	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
	2704	then
	2705	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
	2706	else
	2707	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
	2708	fi
	2709	done
	2710
	2711
[1289]	2712	# IF REQUIRED, START WITH COMPILING
[1]	2713	if [[ $do_compile = true ]]
	2714	then
	2715
	2716
[1199]	2717	if [[ -f a.out ]]
[475]	2718	then
[82]	2719
[1199]	2720	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2721	printf "\n\n\n *** executable a.out found"
	2722	printf "\n no compilation required \n"
	2723
[1]	2724	else
[807]	2725
[1199]	2726	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2727	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2728	printf " *** compilation with make using following options:\n"
	2729	printf " make depository: $make_depository"
	2730	if [[ "$mopts" != "" ]]
	2731	then
	2732	printf " make options: $mopts\n"
	2733	fi
	2734	printf " compilername: $compiler_name\n"
	2735	printf " compiler options: $fopts\n"
	2736	printf " preprocessor directives: $cpp_options \n"
	2737	printf " linker options: $lopts \n"
	2738	if [[ "$modules" != "" ]]
	2739	then
	2740	printf " modules to be load: $modules \n"
	2741	fi
	2742	printf " source code files: $source_list \n"
[1]	2743
[1199]	2744	if [[ $localhost = nech ]]
	2745	then
	2746	ssh $SSH_PORTOPT 136.172.44.192 -l $usern "$init_cmds $module_calls cd \$HOME/work/${usern}.$kennung; sxmake $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
	2747	cp $TEMPDIR_COMPILE/a.out .
	2748	[[ $? != 0 ]] && compile_error=true
	2749	rm -rf $TEMPDIR_COMPILE
	2750	elif [[ $localhost = ibmh ]]
	2751	then
	2752	printf " compiler is called via ssh on \"plogin1\" \n"
	2753	ssh $SSH_PORTOPT plogin1 -l $usern "$init_cmds export PATH=/sw/ibm/xlf/13.1.0.8/usr/bin:$PATH; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
	2754	[[ ! -f a.out ]] && compile_error=true
[1289]	2755	continue # STATUS=1, IF a.out EXISTS
[1199]	2756	elif [[ $localhost = lcflow ]]
	2757	then
	2758	printf " compiler is called via ssh on \"flow\" \n"
[1201]	2759	/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
[1272]	2760	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
	2761	[[ "$check_for_file" = "" ]] && compile_error=true
[1289]	2762	continue # STATUS=1, IF a.out EXISTS
[1274]	2763	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2764	then
	2765	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2766	else
	2767	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2768	[[ "$module_calls" != "" ]] && eval $module_calls
	2769	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2770	fi
[181]	2771
[1199]	2772	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2773	then
	2774	printf "\n +++ error occured while compiling or linking"
	2775	locat=compile
	2776
[181]	2777	exit
[1199]	2778	else
[1289]	2779	printf "$dashes\n *** compilation finished \n"
[1199]	2780	fi
	2781
[1]	2782	fi
[1199]	2783
[1]	2784	fi
	2785
	2786
[1289]	2787	# PROVIDE THE INPUT FILES
	2788	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2789	(( i = 0 ))
	2790	while (( i < iin ))
	2791	do
	2792	(( i = i + 1 ))
	2793	if (( i == 1 ))
	2794	then
[1289]	2795	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2796	fi
	2797
	2798
[1289]	2799	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2800	if [[ "${transin[$i]}" = unavailable ]]
	2801	then
	2802	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2803	then
	2804	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2805	printf "\n is not available!"
	2806	else
	2807	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2808	printf "\n is not available!"
	2809	fi
	2810	continue
	2811	fi
	2812
[1289]	2813	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2814	files_for_pes=false; datentyp=file
	2815	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2816	then
	2817	files_for_pes=true; datentyp=directory
	2818	actionin[$i]=""
	2819	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2820	then
	2821	actionin[$i]=""
	2822	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
	2823	then
	2824	files_for_pes=true; datentyp=directory
	2825	actionin[$i]="ar"
	2826	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
	2827	then
	2828	actionin[$i]="ar"
	2829	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
	2830	then
	2831	files_for_pes=true; datentyp=directory
	2832	actionin[$i]="fl"
	2833	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
	2834	then
	2835	actionin[$i]="fl"
	2836	fi
	2837
	2838	if [[ $files_for_pes = true ]]
	2839	then
	2840	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2841	else
	2842	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2843	fi
	2844
[1289]	2845	# INPUT-FILE FOR A RESTART RUN.
	2846	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
	2847	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
[1]	2848	if [[ "${actionin[$i]}" = fl ]]
	2849	then
	2850	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
	2851	if [[ $files_for_pes = false ]]
	2852	then
	2853	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
	2854	then
	2855	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
	2856	got_tmp[$i]=true
	2857	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
	2858	then
	2859	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
	2860	printf "\n *** trying to use backup copy in \"$WORK\" "
	2861	cp $WORK/${frelin[$i]} ${localin[$i]}
	2862	else
	2863	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
	2864	printf "\n or \"$tmp_data_catalog\" does not exist!"
	2865	printf "\n *** trying to get copy from archive"
	2866	actionin[$i]=ar
	2867	fi
	2868	else
	2869	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
	2870	then
	2871	mkdir ${localin[$i]}
[149]	2872	cd $tmp_data_catalog/${frelin[$i]}
	2873	for file in $(ls *)
	2874	do
	2875	ln $file $TEMPDIR/${localin[$i]}
	2876	done
	2877	cd $TEMPDIR
[1]	2878	got_tmp[$i]=true
	2879	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
	2880	then
	2881	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
	2882	printf "\n *** trying to use backup copy in \"$WORK\" "
	2883	cp -r $WORK/${frelin[$i]} ${localin[$i]}
	2884	else
	2885	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
	2886	printf "\n or \"$tmp_data_catalog\" does not exist!"
	2887	printf "\n *** trying to get copy from archive"
	2888	actionin[$i]=ar
	2889	fi
	2890	fi
	2891	fi
	2892
	2893
[1289]	2894	# FILE IS STORED ON THE ARCHIVE SYSTEM
[1]	2895	if [[ "${actionin[$i]}" = ar ]]
	2896	then
	2897
	2898	if [[ $files_for_pes = false ]]
	2899	then
	2900	printf "\n file will be restored from archive-system ($archive_system)!"
	2901	else
	2902	printf "\n directory will be restored from archive-system ($archive_system)!"
	2903	fi
	2904
	2905	file_restored=false
	2906
	2907	if [[ $archive_system = asterix ]]
	2908	then
	2909	do_stagein=true
	2910	(( stagein_anz = 0 ))
	2911	while [[ $do_stagein = true ]]
	2912	do
	2913	if [[ $files_for_pes = false ]]
	2914	then
	2915	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
	2916	else
	2917	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
	2918	fi
	2919	cat STAGEIN_OUTPUT
	2920	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
	2921	then
	2922	file_restored=true
	2923	do_stagein=false
	2924	else
	2925	(( stagein_anz = stagein_anz + 1 ))
	2926	if (( stagein_anz == 10 ))
	2927	then
	2928	printf "\n +++ stagein stoped after 10 tries"
	2929	locat=stage
	2930	exit
	2931	fi
	2932	printf "\n +++ restoring from archive failed, trying again:"
	2933	sleep 900
	2934	fi
	2935	done
	2936	elif [[ $archive_system = DMF ]]
	2937	then
	2938	if [[ $files_for_pes = false ]]
	2939	then
	2940	printf "\n +++ restoring of single files impossible with $archive_system !\n"
	2941	locat=DMF
	2942	exit
	2943	else
	2944	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
	2945	cp -r $ARCHIVE/${frelin[$i]} $PWD
	2946	file_restored=true
	2947	fi
	2948	elif [[ $archive_system = tivoli ]]
	2949	then
	2950	if [[ $files_for_pes = false ]]
	2951	then
[1289]	2952	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
[1]	2953	else
	2954	(( inode = 0 ))
	2955	while (( inode < nodes ))
	2956	do
[1289]	2957	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
[1]	2958	(( inode = inode + 1 ))
	2959	done
	2960	fi
	2961	file_restored=true
	2962	elif [[ $archive_system = ut ]]
	2963	then
	2964	if [[ $files_for_pes = false ]]
	2965	then
	2966	cp $UT/${frelin[$i]} .
	2967	else
	2968	(( inode = 0 ))
	2969	while (( inode < nodes ))
	2970	do
	2971	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
	2972	(( inode = inode + 1 ))
	2973	done
	2974	fi
	2975	file_restored=true
	2976	else
	2977	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
	2978	locat=rearchive
	2979	exit
	2980	fi
	2981
	2982	if [[ $file_restored = true ]]
	2983	then
	2984
[1289]	2985	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
	2986	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
[1]	2987	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
	2988	if [[ $files_for_pes = false ]]
	2989	then
	2990	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
	2991	else
	2992	mkdir $tmp_data_catalog/${frelin[$i]}
	2993	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
	2994	fi
	2995	got_tmp[$i]=true
	2996
[1289]	2997	# PROVIDE THE FILE UNDER ITS LOCAL NAME
[1]	2998	mv ${frelin[$i]} ${localin[$i]}
	2999
	3000	fi
	3001	fi
	3002
	3003
[1289]	3004	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	3005	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	3006	then
	3007
	3008	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	3009	then
	3010
[1289]	3011	# FILE COPIES ARE PROVIDED FOR ALL CORES
	3012	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	3013	printf "\n file will be provided for $numprocs processors"
	3014	mkdir ${localin[$i]}
	3015	ival=$numprocs
	3016	(( ii = 0 ))
	3017	while (( ii <= ival-1 ))
	3018	do
	3019	if (( ii < 10 ))
	3020	then
	3021	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	3022	elif (( ii < 100 ))
	3023	then
	3024	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	3025	elif (( ii < 1000 ))
	3026	then
	3027	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	3028	else
	3029	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	3030	fi
	3031	(( ii = ii + 1 ))
	3032	done
	3033
	3034	else
	3035
	3036	if [[ $files_for_pes = true ]]
	3037	then
	3038
[1289]	3039	# PROVIDE FILES FOR EACH CORE
	3040	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	3041	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	3042	printf "\n providing $numprocs files for the respective processors"
	3043	mkdir ${localin[$i]}
[183]	3044	if [[ $link_local_input = true ]]
	3045	then
	3046	printf " using ln -f\n"
	3047	cd ${absnamein[$i]}
	3048	for file in $(ls *)
	3049	do
	3050	ln -f $file ${localin[$i]}
	3051	done
	3052	cd $TEMPDIR
	3053	fi
[1289]	3054
	3055	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[183]	3056	if [[ ! -f "${localin[$i]}/_0000" ]]
	3057	then
	3058	if [[ $link_local_input = true ]]
	3059	then
	3060	printf " ln failed for .../_0000, using cp...\n"
	3061	fi
	3062	cp -r ${absnamein[$i]}/* ${localin[$i]}
	3063	fi
[1]	3064
	3065	else
[1289]	3066
	3067	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[183]	3068	if [[ $link_local_input = true ]]
	3069	then
	3070	printf " using ln -f\n"
	3071	ln -f ${absnamein[$i]} ${localin[$i]}
	3072	fi
	3073	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	3074	if [[ ! -f "${localin[$i]}" ]]
	3075	then
	3076	if [[ $link_local_input = true ]]
	3077	then
	3078	printf " ln failed, using cp...\n"
	3079	fi
	3080	cp ${absnamein[$i]} ${localin[$i]}
	3081	fi
[1]	3082	fi
	3083	fi
	3084	fi
	3085
	3086	done
	3087	if (( i != 0 ))
	3088	then
[1289]	3089	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	3090	fi
	3091
	3092
[1289]	3093	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3094	(( i = 0 ))
	3095	while (( i < iic ))
	3096	do
	3097	(( i = i + 1 ))
	3098	if (( i == 1 ))
	3099	then
[1289]	3100	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	3101	fi
	3102	printf "\n >>> ${in_command[$i]}"
	3103	eval ${in_command[$i]}
	3104	if (( i == iic ))
	3105	then
[1289]	3106	printf "\n$dashes\n"
[1]	3107	fi
	3108	done
	3109
	3110
[1289]	3111	# SET THE REMAINING CPU-TIME
[1]	3112	cpurest=${cpumax}.
	3113
	3114
[260]	3115	# START DVR STREAMING SERVER
	3116	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3117	then
	3118	if [[ "$dvr_server" != "" ]]
	3119	then
	3120
	3121	printf "\n\n *** preparing the dvr streaming server configuration file"
	3122
[1289]	3123	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	3124	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	3125	if [[ "$running_dvrserver_id" != "" ]]
	3126	then
	3127
[261]	3128	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	3129	printf "\n This server is used instead starting a new one!"
[261]	3130	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	3131
	3132	else
	3133
	3134	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	3135	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	3136	then
	3137	cp ${PALM_BIN}/.dvrserver.config .
	3138
[1289]	3139	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	3140	user_id=`id -u`
	3141	group_id=`id -g`
[1289]	3142
	3143	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	3144	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	3145	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	3146	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	3147	mv .dvrserver.3 .dvrserver.config
	3148	rm .dvrserver.1 .dvrserver.2
	3149
[1289]	3150	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	3151	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	3152	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	3153	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	3154	local_dvrserver_running=.TRUE.
	3155	else
	3156	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	3157	printf "\n \"$PALM_BIN\" "
	3158	locat=dvr
	3159	exit
	3160	fi
	3161
	3162	fi
	3163
	3164	else
	3165	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	3166	fi
	3167	fi
	3168
	3169
[1289]	3170	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	3171	# (FILE ENVPAR WILL BE READ BY PALM)
[260]	3172	cat > ENVPAR << %%END%%
	3173	&envpar run_identifier = '$fname', host = '$localhost',
	3174	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
[759]	3175	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	3176	maximum_cpu_time_allowed = ${cpumax}.,
	3177	revision = '$global_revision',
	3178	local_dvrserver_running = $local_dvrserver_running /
	3179
	3180	%%END%%
	3181
	3182
[1289]	3183	# STARTING THE EXECUTABLE
	3184	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	3185	PATH=$PATH:$TEMPDIR
	3186
[1289]	3187	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
[359]	3188	if [[ "$mpi_debug" = true ]]
	3189	then
	3190	export MPI_CHECK_ARGS=1
	3191	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
	3192	fi
	3193
[693]	3194	if [[ "$totalview" = true ]]
	3195	then
	3196	printf "\n *** totalview debugger will be used"
	3197	tv_opt="-tv"
	3198	else
	3199	tv_opt=""
	3200	fi
	3201
[1]	3202	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
	3203	then
	3204	if [[ "$ENVIRONMENT" = BATCH ]]
	3205	then
[1289]	3206	continue
[1]	3207	fi
[1096]	3208	if [[ $localhost = ibmh ]]
[1]	3209	then
	3210
	3211	# SETUP THE IBM MPI ENVIRONMENT
	3212	export MP_SHARED_MEMORY=yes
	3213	export AIXTHREADS_SCOPE=S
	3214	export OMP_NUM_THREADS=$threads_per_task
	3215	export AUTHSTATE=files
	3216	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	3217
	3218	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	3219	export MP_ADAPTER_USE=shared
	3220	export MP_CPU_USE=multiple
	3221	export MP_TIMEOUT=1200
	3222
	3223	unset MP_TASK_AFFINITY
	3224
	3225	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
	3226	#(( ii = 1 ))
	3227	#while (( ii <= $numprocs ))
	3228	#do
	3229	# echo $localhost_realname >> hostfile
	3230	# (( ii = ii + 1 ))
	3231	#done
	3232	#export MP_HOSTFILE=hostfile
	3233
	3234	if [[ "$LOADLBATCH" = yes ]]
	3235	then
	3236	totalview poe a.out $ROPTS
	3237	else
	3238	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
	3239	export TVDSVRLAUNCHCMD=ssh
	3240	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
	3241	fi
[622]	3242
[1295]	3243	fi # END DEBUG MODE
	3244
[1]	3245	else
[622]	3246
[1289]	3247	# NORMAL EXECUTION
[1]	3248	if [[ -n $numprocs ]]
	3249	then
[1289]	3250
[1]	3251	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	3252	if [[ $(echo $host \| cut -c1-3) = ibm ]]
	3253	then
[1289]	3254
[1]	3255	# SETUP THE IBM MPI ENVIRONMENT
[693]	3256	if [[ $host != ibmh && $host != ibmkisti ]]
[312]	3257	then
	3258	export MP_SHARED_MEMORY=yes
	3259	export AIXTHREAD_SCOPE=S
	3260	export OMP_NUM_THREADS=$threads_per_task
	3261	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	3262	export AUTHSTATE=files
	3263	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	3264	# export MP_PRINTENV=yes
[1]	3265
[1289]	3266	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	3267	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
[312]	3268	export MP_WAIT_MODE=poll
	3269	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
	3270	fi
[693]	3271
	3272	if [[ $host = ibmkisti ]]
	3273	then
	3274	export LANG=en_US
	3275	export MP_SHARED_MEMORY=yes
[696]	3276	if [[ $threads_per_task = 1 ]]
	3277	then
	3278	export MP_SINGLE_THREAD=yes
	3279	export MEMORY_AFFINITY=MCM
	3280	else
	3281	export OMP_NUM_THREADS=$threads_per_task
	3282	fi
[693]	3283	fi
	3284
[1]	3285	if [[ "$LOADLBATCH" = yes ]]
	3286	then
	3287	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	3288	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
	3289	then
[102]	3290	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
[1]	3291	else
[343]	3292	if [[ $run_coupled_model = false ]]
	3293	then
	3294	if [[ "$ocean_file_appendix" = true ]]
	3295	then
	3296	echo "precursor_ocean" > runfile_atmos
	3297	else
	3298	echo "precursor_atmos" > runfile_atmos
	3299	fi
	3300	else
	3301	(( iia = $numprocs_atmos / $threads_per_task ))
	3302	(( iio = $numprocs_ocean / $threads_per_task ))
	3303	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3304	printf "\n using $coupled_mode coupling"
	3305	printf "\n\n"
	3306	echo "coupled_run $iia $iio" > runfile_atmos
	3307	fi
	3308	poe ./a.out $ROPTS < runfile_atmos
[1]	3309	fi
	3310	else
[622]	3311	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[1]	3312	then
[102]	3313	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
[1289]	3314	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
[1]	3315	then
	3316	if [[ -f $hostfile ]]
	3317	then
	3318	cp $hostfile hostfile
	3319	else
	3320	(( ii = 1 ))
	3321	while (( ii <= $numprocs ))
	3322	do
	3323	echo $localhost_realname >> hostfile
	3324	(( ii = ii + 1 ))
	3325	done
	3326	fi
	3327	export MP_HOSTFILE=hostfile
[331]	3328	if [[ $run_coupled_model = false ]]
	3329	then
	3330	if [[ "$ocean_file_appendix" = true ]]
	3331	then
	3332	echo "precursor_ocean" > runfile_atmos
	3333	else
	3334	echo "precursor_atmos" > runfile_atmos
	3335	fi
	3336	else
	3337	(( iia = $numprocs_atmos / $threads_per_task ))
	3338	(( iio = $numprocs_ocean / $threads_per_task ))
	3339	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3340	printf "\n using $coupled_mode coupling"
	3341	printf "\n\n"
	3342	echo "coupled_run $iia $iio" > runfile_atmos
	3343	fi
	3344
[1289]	3345	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
	3346
[1]	3347	else
	3348	if [[ "$host_file" = "" ]]
	3349	then
	3350	printf "\n +++ no hostfile given in configuration file"
	3351	locat=config_file
	3352	exit
	3353	else
	3354	eval host_file=$host_file
	3355	fi
	3356	export MP_HOSTFILE=$host_file
[102]	3357	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
[1]	3358	fi
	3359	fi
[1289]	3360	elif [[ $host = nech ]]
[1]	3361	then
	3362	(( ii = nodes ))
	3363	if [[ $ii = 1 ]]
	3364	then
	3365	export F_ERRCNT=0 # acceptable number of errors before program is stopped
	3366	export MPIPROGINF=YES
[61]	3367	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
[1]	3368	echo "*** execution on single node with mpirun"
[102]	3369	mpirun -np $numprocs ./a.out $ROPTS
[1]	3370	else
	3371	(( i = 0 ))
	3372	while (( i < ii ))
	3373	do
	3374	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
	3375	(( i = i + 1 ))
	3376	done
	3377
	3378	echo "#!/bin/sh" > mpi_exec_shell
	3379	echo " " >> mpi_exec_shell
	3380	echo "set -u" >> mpi_exec_shell
	3381	echo "F_ERRCNT=0" >> mpi_exec_shell
	3382	echo "MPIPROGINV=YES" >> mpi_exec_shell
	3383	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
	3384	echo "cpurest=$cpurest" >> mpi_exec_shell
	3385	echo "fname=$fname" >> mpi_exec_shell
	3386	echo "localhost=$localhost" >> mpi_exec_shell
	3387	echo "return_addres=$return_addres" >> mpi_exec_shell
	3388	echo "return_username=$return_username" >> mpi_exec_shell
	3389	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
	3390	echo "write_binary=$write_binary" >> mpi_exec_shell
	3391	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
	3392	echo " " >> mpi_exec_shell
	3393	echo "export F_ERRCNT" >> mpi_exec_shell
	3394	echo "export MPIPROGINV" >> mpi_exec_shell
	3395	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
	3396	echo "export cpurest" >> mpi_exec_shell
	3397	echo "export fname" >> mpi_exec_shell
	3398	echo "export localhost" >> mpi_exec_shell
	3399	echo "export return_addres" >> mpi_exec_shell
	3400	echo "export return_username" >> mpi_exec_shell
	3401	echo "export tasks_per_node" >> mpi_exec_shell
	3402	echo "export write_binary" >> mpi_exec_shell
	3403	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
	3404	echo " " >> mpi_exec_shell
[102]	3405	echo "exec ./a.out" >> mpi_exec_shell
[1]	3406
	3407	chmod u+x mpi_exec_shell
	3408	export MPIPROGINF=YES
	3409	mpirun -f multinode_config &
	3410	wait
	3411
	3412	fi
[440]	3413	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	3414	then
	3415
	3416	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	3417	# DOES NOT EXIST
[1289]	3418	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
[1]	3419	then
[179]	3420	if [[ -f $hostfile ]]
	3421	then
	3422	cp $hostfile hostfile
[746]	3423	(( ii = $numprocs / $threads_per_task ))
[179]	3424	else
	3425	(( ii = 1 ))
	3426	while (( ii <= $numprocs / $threads_per_task ))
	3427	do
	3428	echo $localhost_realname >> hostfile
	3429	(( ii = ii + 1 ))
	3430	done
	3431	fi
	3432	eval zeile=\"`head -n $ii hostfile`\"
	3433	printf "\n *** running on: $zeile"
[1]	3434	fi
[179]	3435
[1]	3436	(( ii = $numprocs / $threads_per_task ))
	3437	export OMP_NUM_THREADS=$threads_per_task
[1289]	3438
[1]	3439	if [[ $threads_per_task != 1 ]]
	3440	then
[1289]	3441	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	3442	# MAY ABORT
[1304]	3443	ulimit -s unlimited
[405]	3444	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[1]	3445	fi
[102]	3446	if [[ $run_coupled_model = false ]]
[1]	3447	then
[291]	3448	if [[ "$ocean_file_appendix" = true ]]
	3449	then
	3450	echo "precursor_ocean" > runfile_atmos
	3451	else
	3452	echo "precursor_atmos" > runfile_atmos
	3453	fi
[102]	3454	printf "\n\n"
[388]	3455
[1289]	3456	if [[ $host = lccrayb \|\| $host = lccrayh ]]
[1224]	3457	then
	3458	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
	3459	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
	3460	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
[1197]	3461	elif [[ $host = lccrayf ]]
	3462	then
	3463	aprun -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
[892]	3464	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
[179]	3465	then
[544]	3466	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
[755]	3467	elif [[ $host = lcflow ]]
	3468	then
[1201]	3469	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
[1021]	3470	elif [[ $host = lcsb ]]
	3471	then
	3472	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
[1040]	3473	elif [[ $host = lckiaps ]]
	3474	then
	3475	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
[1090]	3476	elif [[ $host = lckyu* ]]
	3477	then
[1106]	3478	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
[164]	3479	else
[1106]	3480	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
[164]	3481	fi
[1]	3482	else
[164]	3483
[1289]	3484	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
[206]	3485	(( iia = $numprocs_atmos / $threads_per_task ))
	3486	(( iio = $numprocs_ocean / $threads_per_task ))
	3487	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3488	printf "\n using $coupled_mode coupling"
[102]	3489	printf "\n\n"
[164]	3490
[206]	3491	if [[ $coupled_mode = "mpi2" ]]
[164]	3492	then
[206]	3493	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
	3494	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
[197]	3495
[1289]	3496	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
[206]	3497	then
[197]	3498
[206]	3499	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
	3500	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
	3501
	3502	else
	3503	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
	3504	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
	3505	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
	3506	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
	3507	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
	3508	fi
	3509	wait
	3510
[164]	3511	else
	3512
[206]	3513	echo "coupled_run $iia $iio" > runfile_atmos
	3514
[1289]	3515	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
[206]	3516	then
	3517
	3518	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
	3519
[718]	3520	elif [[ $host = lck \|\| $host = lckordi ]]
[367]	3521	then
[1108]	3522
	3523	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
	3524
	3525	elif [[ $host = lckyu* ]]
	3526	then
	3527
	3528	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
	3529
[206]	3530	fi
	3531	wait
[164]	3532	fi
[102]	3533
[206]	3534	fi
[1289]	3535
[440]	3536	elif [[ $host = lckyoto ]]
	3537	then
	3538	set -xv
	3539	export P4_RSHCOMMAND=plesh
	3540	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3541	if [[ "$ENVIRONMENT" = BATCH ]]
	3542	then
[505]	3543	if [[ "$cond2" = fujitsu ]]
	3544	then
	3545	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
	3546	elif [[ "cond2" = pgi ]]
	3547	then
	3548	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
	3549	else
	3550	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
	3551	fi
[440]	3552	else
[505]	3553	if [[ "$cond2" = "" ]]
	3554	then
	3555	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
	3556	else
	3557	mpirun -np $numprocs ./a.out $ROPTS
	3558	fi
[440]	3559	fi
	3560	set +xv
[1289]	3561
[1]	3562	elif [[ $host = lctit ]]
	3563	then
[678]	3564	export OMP_NUM_THREADS=$threads_per_task
	3565	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3566	if [[ "$threads_per_task" != 1 ]]
	3567	then
	3568	export MV2_ENABLE_AFFINITY=0
	3569	fi
	3570	echo "----- PBS_NODEFILE content:"
	3571	cat $PBS_NODEFILE
	3572	echo "-----"
	3573	(( ii = $numprocs / $threads_per_task ))
	3574	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
	3575	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
[1]	3576	else
[102]	3577	mpprun -n $numprocs a.out $ROPTS
[1]	3578	fi
	3579	else
[102]	3580	a.out $ROPTS
[1]	3581	fi
	3582	fi
[1289]	3583
	3584	if [[ $? != 0 ]]
[1]	3585	then
	3586
[1289]	3587	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3588	printf "\n +++ runtime error occured"
	3589	locat=execution
	3590	exit
[1289]	3591
[1]	3592	else
[260]	3593
[1289]	3594	printf "\n$dashes\n *** execution finished \n"
	3595
	3596	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3597	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3598	if [[ "$dvrserver_id" != "" ]]
	3599	then
	3600	kill $dvrserver_id
	3601	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3602
[1289]	3603	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3604	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3605	if [[ -d DATA_DVR ]]
	3606	then
[261]	3607
[1289]	3608	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3609	# DIRECTORY
[262]	3610	cp .dvrserver.config DATA_DVR
	3611
[1289]	3612	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3613	# SEQUENCE MODE DATA TOO)
[262]	3614	process_dvr_output -d DATA_DVR -f $fname -s
	3615
	3616	else
	3617
[1289]	3618	# PROCESS THE LOCAL OUTPUT
[262]	3619	process_dvr_output -l -d DATA_DVR -f $fname
	3620
	3621	fi
	3622
	3623	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3624	then
	3625
[1289]	3626	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3627	process_dvr_output -l -d DATA_DVR -f $fname
	3628
[260]	3629	fi
[1]	3630	fi
	3631
	3632
	3633
[1289]	3634	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3635	# BY EACH CORE INTO ONE FILE
[920]	3636	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3637	then
	3638	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3639	printf "\n 2d- and/or 3d-data may be incomplete!"
	3640	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3641	elif [[ "$combine_plot_fields" == true ]]
	3642	then
[1270]	3643	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3644	then
	3645	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
	3646	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
	3647	else
	3648	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3649	combine_plot_fields${block}.x
	3650	fi
[920]	3651	else
[1289]	3652
	3653	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3654	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3655	# ??? koennen wir das streichen ???
[920]	3656	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3657	fi
[503]	3658
	3659
	3660
[1289]	3661	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3662	(( i = 0 ))
	3663	while (( i < ioc ))
	3664	do
	3665	(( i = i + 1 ))
	3666	if (( i == 1 ))
	3667	then
[1289]	3668	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3669	fi
	3670	printf "\n >>> ${out_command[$i]}"
	3671	eval ${out_command[$i]}
	3672	if (( i == ioc ))
	3673	then
[1289]	3674	printf "\n$dashes\n"
[1]	3675	fi
	3676	done
	3677
	3678
[1289]	3679	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3680	if [[ $do_trace = true ]]
	3681	then
	3682	printf "\n\n"
	3683	ls -al
	3684	fi
	3685
	3686
	3687
[1289]	3688	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3689	(( i = 0 ))
	3690	while (( i < iout ))
	3691	do
	3692	(( i = i + 1 ))
	3693	if (( i == 1 ))
	3694	then
[1289]	3695	printf "\n\n *** saving OUTPUT-files:\n$dashes"
[1]	3696	fi
	3697
[1289]	3698	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3699	files_for_pes=false; filetyp=file
	3700	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3701	then
	3702	files_for_pes=true; filetyp=directory
	3703	actionout[$i]=""
	3704	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3705	then
	3706	actionout[$i]=""
	3707	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
	3708	then
	3709	files_for_pes=true; filetyp=directory
	3710	actionout[$i]="ar"
	3711	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
	3712	then
	3713	actionout[$i]="ar"
	3714	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
	3715	then
	3716	files_for_pes=true; filetyp=directory
	3717	actionout[$i]="fl"
	3718	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
	3719	then
	3720	actionout[$i]="fl"
	3721	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3722	then
	3723	files_for_pes=true; filetyp=directory
	3724	actionout[$i]="tr"
	3725	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3726	then
	3727	actionout[$i]="tr"
	3728	fi
	3729
	3730	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3731	then
	3732	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3733	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3734	then
	3735	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3736	else
	3737
	3738
[1289]	3739	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3740	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3741	if [[ "${actionout[$i]}" = tr ]]
	3742	then
	3743	if [[ $localhost != $fromhost ]]
	3744	then
	3745	if [[ $files_for_pes = false ]]
	3746	then
	3747	cps=""
	3748	cst=""
	3749	else
	3750	cps=-c
	3751	cst="/"
	3752	fi
[622]	3753	if [[ $localhost = nech ]]
[1]	3754	then
	3755
[1289]	3756	# TRANSFER IN SEPERATE JOB
	3757	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3758	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3759	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3760	if [[ $files_for_pes = false ]]
	3761	then
	3762	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3763	else
	3764	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
	3765	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
	3766	fi
	3767
	3768	echo "set -x" > transfer_${localout[$i]}
	3769	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3770
	3771	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
	3772	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
	3773	printf "\n or higher cycle\n"
[1094]	3774	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
[82]	3775
[1]	3776	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3777
	3778	if [[ $localhost = nech ]]
	3779	then
[1094]	3780	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
[1]	3781	else
	3782	if [[ "$LOGNAME" = b323013 ]]
	3783	then
[1094]	3784	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3785	else
[1094]	3786	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3787	fi
	3788	fi
	3789
	3790	else
	3791
[1289]	3792	# TRANSFER WITHIN THIS JOB
[1]	3793	transfer_failed=false
[82]	3794	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3795	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
[1255]	3796	if [[ $localhost = lccrayb ]]
	3797	then
	3798	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1274]	3799	elif [[ $localhost = lccrayh ]]
	3800	then
	3801	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1255]	3802	else
	3803	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3804	fi
[82]	3805	[[ $? != 0 ]] && transfer_failed=true
[1]	3806
[1289]	3807	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3808	if [[ $transfer_failed = true ]]
	3809	then
[1289]	3810	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3811	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3812
[1289]	3813	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3814	eval local_catalog=${pathout[$i]}
	3815	if [[ ! -d $local_catalog ]]
	3816	then
	3817	printf " *** local directory does not exist. Trying to create:\n"
	3818	printf " $local_catalog \n"
	3819	mkdir -p $local_catalog
	3820	fi
	3821	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3822	transfer_problems=true
	3823	fi
	3824	fi
	3825	else
	3826
[1289]	3827	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3828	actionout[$i]=""
	3829	fi
	3830	fi
	3831
	3832
[1289]	3833	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3834	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3835	if [[ "${actionout[$i]}" = tra ]]
	3836	then
	3837	if [[ $localhost != $fromhost ]]
	3838	then
[622]	3839	if [[ $localhost = ibmh \|\| $localhost = nech ]]
[1]	3840	then
	3841
[1289]	3842	# TRANSFER IN SEPERATE JOB
	3843	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3844	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3845	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3846	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3847
	3848	echo "set -x" > transfer_${localout[$i]}
	3849	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3850
	3851	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3852	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3853	printf "\n or higher cycle\n"
[1094]	3854	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
[82]	3855
[1]	3856	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3857
	3858	if [[ $localhost = nech ]]
	3859	then
[1094]	3860	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
[1]	3861	else
	3862	if [[ $LOGNAME = b323013 ]]
	3863	then
[1094]	3864	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3865	else
[1094]	3866	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3867	fi
	3868	fi
	3869
	3870	else
	3871
[1289]	3872	# TRANSFER WITHIN THIS JOB
[1]	3873	transfer_failed=false
[82]	3874	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3875	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3876	if [[ $localhost = lccrayb ]]
	3877	then
	3878	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1274]	3879	elif [[ $localhost = lccrayh ]]
	3880	then
	3881	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1255]	3882	else
	3883	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3884	fi
[82]	3885	[[ $? != 0 ]] && transfer_failed=true
[1]	3886
[1289]	3887	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3888	if [[ $transfer_failed = true ]]
	3889	then
[1289]	3890	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3891	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3892
[1289]	3893	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3894	eval local_catalog=${pathout[$i]}
	3895	if [[ ! -d $local_catalog ]]
	3896	then
	3897	printf " *** local directory does not exist. Trying to create:\n"
	3898	printf " $local_catalog \n"
	3899	mkdir -p $local_catalog
	3900	fi
	3901
	3902	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3903	transfer_problems=true
	3904	fi
	3905	fi
	3906	else
	3907
[1289]	3908	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3909	actionout[$i]=a
	3910	fi
	3911	fi
	3912
	3913
[1289]	3914	# OUTPUT-FILE FOR A RESTART-RUN.
	3915	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
	3916	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
	3917	# AS LAST ACTION, ARCHIVING IS INITIATED.
[1]	3918	if [[ "${actionout[$i]}" = fl ]]
	3919	then
	3920	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	3921	chmod g+rx $tmp_data_catalog
	3922	if [[ $files_for_pes = false ]]
	3923	then
	3924	printf "\n >>> OUTPUT: ${localout[$i]} to"
	3925	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
	3926	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
	3927	else
	3928	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
	3929	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
	3930	mkdir $tmp_data_catalog/${frelout[$i]}
[149]	3931	cd ${localout[$i]}
	3932	for file in $(ls *)
	3933	do
	3934	ln -f $file $tmp_data_catalog/${frelout[$i]}
	3935	done
	3936	cd $TEMPDIR
[1]	3937	fi
	3938
	3939
[1289]	3940	# CREATE AND SUBMIT ARCHIVING-JOB
[1]	3941	if [[ $store_on_archive_system = true ]]
	3942	then
	3943
	3944	if [[ $archive_system = asterix ]]
	3945	then
	3946	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3947	if [[ $files_for_pes = false ]]
	3948	then
	3949	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3950	else
	3951	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3952	fi
	3953	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3954	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
	3955	echo "then" >> archive_${frelout[$i]}
	3956	echo " do_stageout=false" >> archive_${frelout[$i]}
	3957	echo "else" >> archive_${frelout[$i]}
	3958	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
	3959	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
	3960	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
	3961	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
	3962	if [[ $files_for_pes = false ]]
	3963	then
	3964	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
	3965	else
	3966	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
	3967	fi
	3968	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
	3969	echo "fi" >> archive_${frelout[$i]}
	3970	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3971	elif [[ $archive_system = DMF ]]
	3972	then
	3973	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3974	if [[ $files_for_pes = false ]]
	3975	then
	3976	printf "\n +++ archiving of single files impossible with $archive_system !\n"
	3977	locat=DMF
	3978	exit
	3979	else
[1289]	3980	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
[1]	3981	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
	3982	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
	3983	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
	3984	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
	3985	fi
	3986	elif [[ $archive_system = tivoli ]]
	3987	then
	3988	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3989	if [[ $files_for_pes = false ]]
	3990	then
[1289]	3991	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
[1]	3992	echo "set -x" >> archive_${frelout[$i]}
	3993	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3994	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3995	else
	3996
	3997	echo "set -x" >> archive_${frelout[$i]}
	3998	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
	3999	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	4000	cd $tmp_data_catalog
	4001	all_files=`ls -1 ${frelout[$i]}/*`
	4002	cd - > /dev/null
	4003	(( inode = 0 ))
	4004	(( tp1 = tasks_per_node + 1 ))
	4005	while (( inode < nodes ))
	4006	do
	4007	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
	4008	all_files=`echo $all_files \| cut -d" " -f$tp1-`
[1289]	4009	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
[1]	4010	(( inode = inode + 1 ))
	4011	done
	4012	fi
	4013	elif [[ $archive_system = ut ]]
	4014	then
	4015	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	4016	if [[ $files_for_pes = false ]]
	4017	then
[1289]	4018	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
[1]	4019	echo "set -x" >> archive_${frelout[$i]}
	4020	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	4021	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	4022	else
	4023
	4024	echo "set -x" >> archive_${frelout[$i]}
	4025	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
	4026	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
	4027	cd $tmp_data_catalog
	4028	all_files=`ls -1 ${frelout[$i]}/*`
	4029	cd - > /dev/null
	4030	(( inode = 0 ))
	4031	(( tp1 = tasks_per_node + 1 ))
	4032	while (( inode < nodes ))
	4033	do
	4034	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
	4035	all_files=`echo $all_files \| cut -d" " -f$tp1-`
	4036	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
	4037	(( inode = inode + 1 ))
	4038	done
	4039	fi
	4040	elif [[ $archive_system = none ]]
	4041	then
	4042	printf " +++ archiving on $localhost not available!\n"
	4043	fi
	4044
	4045	if [[ $archive_system != none ]]
	4046	then
[1289]	4047	if [[ $localhost = nech ]]
[1]	4048	then
[1094]	4049	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
[1]	4050	fi
	4051	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	4052	fi
	4053	else
[399]	4054	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
[1]	4055	fi
	4056
	4057
[1289]	4058	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
	4059	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
	4060	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
	4061	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
	4062	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
[1]	4063	if [[ $files_for_pes = false ]]
	4064	then
	4065	cat /dev/null > ${pathout[$i]}
	4066	else
	4067	mkdir -p ${pathout[$i]}
	4068	fi
	4069
	4070	fi
	4071
	4072
[1289]	4073	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
	4074	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
	4075	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
[1]	4076	if [[ "${actionout[$i]}" = ar ]]
	4077	then
	4078	if [[ $files_for_pes = false ]]
	4079	then
	4080	printf "\n >>> OUTPUT: ${localout[$i]} to"
	4081	printf "\n ${pathout[$i]}"
	4082	printf "\n File will be copied to archive-system ($archive_system) !\n"
	4083	else
	4084	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	4085	printf "\n ${pathout[$i]}"
	4086	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
	4087	fi
	4088	mv ${localout[$i]} ${frelout[$i]}
	4089
	4090	file_saved=false
	4091
	4092	if [[ $archive_system = asterix ]]
	4093	then
	4094	do_stageout=true
	4095	(( stageout_anz = 0 ))
	4096	while [[ $do_stageout = true ]]
	4097	do
	4098	if [[ $files_for_pes = false ]]
	4099	then
	4100	stageout ${frelout[$i]} > STAGE_OUTPUT
	4101	else
	4102	stageout -t ${frelout[$i]} > STAGE_OUTPUT
	4103	fi
	4104	cat STAGE_OUTPUT
	4105	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
	4106	then
	4107	file_saved=true
	4108	do_stageout=false
	4109	else
	4110	if [[ $files_for_pes = false ]]
	4111	then
	4112	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
	4113	else
	4114	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
	4115	fi
	4116	(( stageout_anz = stageout_anz + 1 ))
	4117	if (( stageout_anz == 10 ))
	4118	then
	4119	printf "\n +++ stoped after 10 unsuccessful tries!"
	4120	archive_save=false
	4121	do_stageout=false
	4122	else
	4123	printf "\n *** new try to store on archive after 15 min:"
	4124	sleep 900
	4125	fi
	4126	fi
	4127	done
	4128	elif [[ $archive_system = DMF ]]
	4129	then
	4130	if [[ $files_for_pes = false ]]
	4131	then
	4132	printf "\n +++ archiving of single files impossible on $archive_system!\n"
	4133	locat=DMF
	4134	exit
	4135	else
	4136	rm -rf $ARCHIVE/${frelout[$i]}
	4137	cp -r ${frelout[$i]} $ARCHIVE
	4138	fi
	4139	file_saved=true
	4140	elif [[ $archive_system = tivoli ]]
	4141	then
[1289]	4142	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
	4143	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
	4144	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
	4145	# WHEN THE ARCHIVE-JOB IS EXECUTED
[1]	4146	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	4147	chmod g+rx $tmp_data_catalog
	4148	if [[ $files_for_pes = false ]]
	4149	then
	4150	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
	4151	else
	4152	mkdir $tmp_data_catalog/${frelout[$i]}
	4153	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
	4154	fi
	4155
[1289]	4156	# GENERATE AND SUBMIT BATCH-JOB
	4157	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
	4158	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
[1]	4159	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
	4160	if [[ $files_for_pes = false ]]
	4161	then
	4162	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	4163	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	4164	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	4165	else
	4166	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
	4167	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
	4168	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	4169	fi
	4170
[1094]	4171	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
[1]	4172	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	4173	file_saved=true
	4174
	4175	elif [[ $archive_system = ut ]]
	4176	then
[1289]	4177	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
	4178	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
	4179	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
	4180	# WHEN THE ARCHIVE-JOB IS EXECUTED
[1]	4181	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	4182	chmod g+rx $tmp_data_catalog
	4183	if [[ $files_for_pes = false ]]
	4184	then
	4185	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
	4186	else
	4187	mkdir $tmp_data_catalog/${frelout[$i]}
	4188	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
	4189	fi
	4190
[1289]	4191	# GENERATE AND SUBMIT BATCH-JOB
	4192	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
	4193	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
[1]	4194	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
	4195	if [[ $files_for_pes = false ]]
	4196	then
	4197	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	4198	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	4199	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	4200	else
	4201	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
	4202	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
	4203	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	4204	fi
	4205
[1094]	4206	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
[1]	4207	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	4208	file_saved=true
	4209
	4210	else
	4211	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
	4212	archive_save=false
	4213	fi
[1289]	4214
	4215	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
	4216	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
	4217	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
	4218	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
	4219	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
[1]	4220	if [[ $file_saved = true ]]
	4221	then
	4222	if [[ $files_for_pes = false ]]
	4223	then
	4224	cat /dev/null > ${pathout[$i]}
	4225	else
	4226	mkdir -p ${pathout[$i]}
	4227	fi
	4228	fi
[1289]	4229
[1]	4230	fi
	4231
[1289]	4232	# APPEND ON THIS MACHINE
[1]	4233	if [[ "${actionout[$i]}" = "a" ]]
	4234	then
[741]	4235	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	4236	then
	4237	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	4238	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	4239	else
	4240	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	4241	cat ${localout[$i]} >> ${pathout[$i]}
	4242	fi
[1]	4243	fi
	4244
[1289]	4245	# COPY ON THIS MACHINE
	4246	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	4247	# ON DIFFERENT FILE-SYSTEMS
[1]	4248	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	4249	then
	4250
[1289]	4251	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	4252	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	4253	then
	4254	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[149]	4255	if [[ $link_local_output = true ]]
	4256	then
	4257	printf " using ln -f\n"
	4258	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	4259	fi
	4260	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	4261	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	4262	then
	4263	if [[ $link_local_output = true ]]
	4264	then
	4265	printf " ln failed, using cp...\n"
	4266	fi
	4267	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	4268	fi
[1]	4269	else
	4270	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[149]	4271	if [[ $link_local_output = true ]]
	4272	then
	4273	printf " using ln -f\n"
	4274	ln -f ${localout[$i]} ${pathout[$i]}
	4275	fi
	4276	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	4277	if [[ ! -f "${pathout[$i]}" ]]
	4278	then
	4279	if [[ $link_local_output = true ]]
	4280	then
	4281	printf " ln failed, using cp...\n"
	4282	fi
	4283	cp ${localout[$i]} ${pathout[$i]}
	4284	fi
[1]	4285	fi
	4286
	4287	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	4288	then
	4289
[1289]	4290	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	4291	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	4292	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[149]	4293	if [[ $link_local_output = true ]]
	4294	then
	4295	printf " using ln -f\n"
	4296	mkdir ${pathout[$i]}
	4297	cd ${localout[$i]}
	4298	for file in $(ls *)
	4299	do
	4300	ln -f $file ${pathout[$i]}
	4301	done
	4302	cd $TEMPDIR
	4303	fi
[1289]	4304
	4305	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[149]	4306	if [[ ! -f "${pathout[$i]}/_0000" ]]
	4307	then
	4308	if [[ $link_local_output = true ]]
	4309	then
	4310	printf " ln failed for .../_0000, using cp...\n"
	4311	fi
	4312	cp -r ${localout[$i]} ${pathout[$i]}
	4313	fi
[1]	4314
	4315	fi
	4316	fi
	4317	done
	4318	if (( i != 0 ))
	4319	then
	4320	if [[ $transfer_problems = true ]]
	4321	then
[1289]	4322	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	4323	printf "\n +++ WARNING: some data transfers failed! \n"
	4324	else
[1289]	4325	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	4326	fi
	4327	fi
	4328
	4329
[1289]	4330	# IF REQUIRED, START A RESTART-JOB
	4331	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	4332	if [[ -f CONTINUE_RUN ]]
	4333	then
	4334
	4335	if [[ $archive_save = true ]]
	4336	then
	4337
[1289]	4338	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	4339	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	4340	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	4341	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
[1]	4342	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	4343	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	4344	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	4345	if [[ $(echo $mc \| grep -c "#") != 0 ]]
	4346	then
	4347	mc=`echo $mc \| sed 's/#/f/g'`
	4348	fi
	4349
	4350
[1289]	4351	# START THE RESTART-JOB
[1]	4352	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
	4353	echo " $mc"
[1289]	4354	printf "\n$dashes\n"
[1]	4355	if [[ $localhost != $fromhost ]]
	4356	then
	4357
[1289]	4358	if [[ $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
[1]	4359	then
	4360	echo "*** ssh will be used to initiate restart-runs!"
	4361	echo " return_addres=\"$return_addres\" "
	4362	echo " return_username=\"$return_username\" "
[635]	4363	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
[1]	4364	then
[1190]	4365	if [[ $localhost = ibmh ]]
	4366	then
	4367	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1255]	4368	elif [[ $localhost = lccrayb ]]
	4369	then
	4370	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1274]	4371	elif [[ $localhost = lccrayh ]]
	4372	then
	4373	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
	4374
[1190]	4375	else
	4376	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	4377	fi
[1]	4378	else
[693]	4379	if [[ $localhost = ibmkisti ]]
	4380	then
[1094]	4381	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1255]	4382	elif [[ $localhost = lcflow ]]
	4383	then
	4384	/usr/bin/ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	4385	elif [[ $localhost = lccrayb ]]
	4386	then
	4387	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1274]	4388	elif [[ $localhost = lccrayh ]]
	4389	then
	4390	ssh $usern@130.75.4.1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[693]	4391	else
[1255]	4392	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
[693]	4393	fi
[1]	4394	fi
	4395	else
	4396	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	4397	locat=restart; exit
	4398	fi
	4399
[1289]	4400	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
[399]	4401	if [[ $queue = special1q ]]
	4402	then
	4403	sleep 120
	4404	else
	4405	sleep 30
	4406	fi
[1]	4407
	4408	else
	4409
[1289]	4410	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	4411	# USING SSH)
[1]	4412	cd $LOCAL_PWD
[1289]	4413	if [[ $localhost = lckyuh ]]
[108]	4414	then
[1103]	4415	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	4416	printf "\n please restart job manually using command:\n"
	4417	printf "\n \"$mc\" "
[108]	4418	else
[1289]	4419	eval $mc # THE ' MUST BE EVALUATED
[108]	4420	fi
[1]	4421	cd - > /dev/null
	4422	fi
[1103]	4423	if [[ $localhost = lckyuh ]]
	4424	then
[1289]	4425	printf "\n$dashes\n *** restart-run to be initiated manually\n"
[1103]	4426	else
[1289]	4427	printf "\n$dashes\n *** restart-run initiated \n"
[1103]	4428	fi
[1]	4429
	4430
[1289]	4431	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	4432	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	4433	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	4434	# MAY BE VERY HUGE)
[1]	4435	(( i = 0 ))
	4436	while (( i < iin ))
	4437	do
	4438	(( i = i + 1 ))
	4439	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	4440	then
	4441	rm -r $tmp_data_catalog/${frelin[$i]}
	4442	fi
	4443	done
	4444
	4445	else
	4446
	4447	printf "\n +++ no restart-run possible, since errors occured"
	4448	printf "\n during the archive process"
	4449	fi
	4450
	4451	fi
	4452
	4453
	4454
[1289]	4455	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	4456	if [[ "$email_notification" != "none" ]]
[1]	4457	then
	4458
	4459	if [[ $localhost != $fromhost ]]
	4460	then
	4461	if [[ -f CONTINUE_RUN ]]
	4462	then
	4463	echo "PALM restart run necessary" > email_text
	4464	echo "description header of actual run:" >> email_text
	4465	cat CONTINUE_RUN >> email_text
	4466	echo "mrun-command to restart:" >> email_text
	4467	echo "$mc" >> email_text
	4468	else
	4469	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	4470	fi
	4471	mail $email_notification < email_text
	4472	printf "\n *** email notification sent to \"$email_notification\" "
	4473	fi
	4474	fi
	4475
	4476
	4477
[1289]	4478	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	4479	cd $HOME
	4480	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	4481
	4482	else
	4483
	4484
[1289]	4485	# PREPARING ACTIONS,
	4486	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	4487
[1289]	4488	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[821]	4489	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_addres -U $return_username -u $remote_username"
[1]	4490	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
[79]	4491	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	4492	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	4493	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	4494	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	4495	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
	4496	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	4497	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	4498	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	4499	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	4500	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	4501	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	4502	if [[ $use_openmp = true ]]
	4503	then
[622]	4504	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	4505	fi
[759]	4506	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[397]	4507	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
[1]	4508	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	4509	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	4510	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	4511	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	4512	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	4513	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[920]	4514	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	4515	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	4516	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	4517	if [[ $do_remote = true ]]
	4518	then
	4519	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	4520	fi
	4521
	4522
[1289]	4523	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	4524	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	4525	then
	4526
	4527	printf "\n *** creating the executable for batch job\n"
	4528
[1289]	4529	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	4530	if [[ $host != $localhost ]]
	4531	then
	4532	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	4533	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	4534	locat=create_executable; exit
	4535	fi
	4536
	4537	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4538	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4539
	4540	cp $make_depository .
	4541	tar -xf $make_depository > /dev/null 2>&1
	4542	cp ../* . > /dev/null 2>&1
	4543
	4544	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	4545
	4546	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	4547	then
	4548	printf "\n +++ error occured while compiling or linking"
	4549	locat=compile
	4550	exit
	4551	fi
	4552
	4553	mv a.out ..
	4554	cd - > /dev/null 2>&1
	4555	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4556
	4557	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	4558
	4559	fi
	4560
	4561
[1289]	4562	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	4563	jobfile=jobfile.$RANDOM
	4564
	4565
[1289]	4566	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	4567	echo "mkdir $TEMPDIR" >> $jobfile
	4568	echo "cd $TEMPDIR" >> $jobfile
	4569
	4570
[1289]	4571	# ACTIVATE ERROR-TRACEBACK
[1]	4572	if [[ $do_trace = true ]]
	4573	then
	4574	echo "set -x" >> $jobfile
	4575	else
	4576	echo "set +vx" >> $jobfile
	4577	fi
	4578
	4579
[1289]	4580	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	4581	if [[ "$init_cmds" != "" ]]
	4582	then
	4583	echo "$init_cmds" >> $jobfile
	4584	fi
	4585	if [[ "$module_calls" != "" ]]
	4586	then
	4587	echo "$module_calls" >> $jobfile
	4588	fi
	4589
	4590
[1289]	4591	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	4592	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	4593	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	4594	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	4595	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	4596	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	4597	# QUEUEING-SYSTEMS
	4598	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
[1]	4599	then
	4600
[1289]	4601	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	4602	if [[ $restart_run != true ]]
	4603	then
	4604	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	4605	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	4606	fi
[1]	4607
[1289]	4608	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	4609	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	4610	echo "set -x" >> $jobfile
[693]	4611	if [[ $host = $localhost ]]
	4612	then
[1199]	4613
	4614	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	4615	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	4616	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	4617	then
	4618	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	4619	else
	4620	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	4621	fi
[1199]	4622
[693]	4623	else
[1255]	4624	if [[ $host = ibmkisti ]]
[693]	4625	then
[1289]	4626	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	4627	echo "localdir=\`pwd\`" >> $jobfile
[1094]	4628	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1255]	4629	elif [[ $host = lccrayb ]]
	4630	then
	4631	echo "localdir=\`pwd\`" >> $jobfile
	4632	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	4633	elif [[ $host = lccrayh ]]
	4634	then
	4635	echo "localdir=\`pwd\`" >> $jobfile
	4636	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	4637
[1255]	4638	else
	4639	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	4640	fi
	4641	fi
[193]	4642	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	4643
[1289]	4644	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	4645	# WORKING DIRECTORY OF THE JOB
[193]	4646	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	4647	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	4648	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	4649	echo "execute_mrun=true" >> $jobfile
	4650	echo " " >> $jobfile
	4651
[191]	4652	else
	4653
[1289]	4654	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	4655	if [[ $do_compile = true ]]
	4656	then
	4657
	4658	source_catalog=SOURCES_FOR_RUN_$fname
	4659
[1289]	4660	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	4661	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	4662	echo "export SOURCES_COMPLETE=true" >> $jobfile
	4663	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	4664
	4665	for filename in $source_list
	4666	do
[1289]	4667	# BACKSLASH IS USED FOR MASKING
[191]	4668	echo "cat > $filename << \"%END%\"" >> $jobfile
	4669	cat $source_catalog/$filename >> $jobfile
	4670	echo " " >> $jobfile
	4671	echo "%END%" >> $jobfile
	4672	echo " " >> $jobfile
	4673	done
	4674
[1289]	4675	# BACKSLASH IS USED FOR MASKING
[191]	4676	echo "cat > Makefile << \"%END%\"" >> $jobfile
	4677	cat $source_catalog/Makefile >> $jobfile
[1]	4678	echo " " >> $jobfile
	4679	echo "%END%" >> $jobfile
	4680	echo " " >> $jobfile
	4681
[191]	4682	echo "cd - > /dev/null" >> $jobfile
[1]	4683
[191]	4684	fi
[1]	4685
	4686
[1289]	4687	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	4688	# BACKSLASH IS USED FOR MASKING
	4689	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	4690	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	4691	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	4692	if [[ $host = lckyuh ]]
	4693	then
[1289]	4694	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	4695	sed 's/frtpx/frt/g' $config_file >> $jobfile
	4696	else
	4697	sed 's/#$.*//g' $config_file >> $jobfile
	4698	fi
[191]	4699	echo "%END%" >> $jobfile
	4700	echo " " >> $jobfile
[1]	4701
	4702
[1289]	4703	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	4704	# BACKSLASH IS USED FOR MASKING
[1101]	4705	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	4706	if [[ $host = lckyuh ]]
	4707	then
	4708	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	4709	else
	4710	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	4711	fi
[1101]	4712	echo "%END%" >> $jobfile
[191]	4713	echo "chmod u+x $mrun_script_name" >> $jobfile
	4714	echo "execute_mrun=true" >> $jobfile
	4715	echo " " >> $jobfile
[1]	4716
	4717	fi
	4718
[191]	4719
[1289]	4720	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	4721	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	4722	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	4723	if [[ $do_remote = true ]]
	4724	then
	4725	(( i = 0 ))
	4726	while (( i < iin ))
	4727	do
	4728	(( i = i + 1 ))
	4729	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	4730	if [[ "${transin[$i]}" = job ]]
	4731	then
	4732	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	4733	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	4734	echo " " >> $jobfile
	4735	echo "%END%" >> $jobfile
	4736	else
[1094]	4737	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	4738	fi
	4739
[1289]	4740	# CHECK, IF FILE COULD BE CREATED
[1]	4741	echo "if [[ \$? = 1 ]]" >> $jobfile
	4742	echo "then" >> $jobfile
	4743	echo " echo \" \" " >> $jobfile
	4744	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	4745	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	4746	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	4747	echo " execute_mrun=false" >> $jobfile
	4748	echo "fi" >> $jobfile
	4749	done
	4750	fi
	4751
[1289]	4752	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	4753	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	4754	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	4755	echo "LOCAL_PWD=$working_directory" >> $jobfile
	4756	echo "export LOCAL_PWD" >> $jobfile
	4757
[1289]	4758	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	4759	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	4760	echo "export LOCAL_MRUN_PATH" >> $jobfile
	4761
[1289]	4762	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
	4763	if [[ $host = lcflow \|\| $localhost = lcflow ]]
[66]	4764	then
[1099]	4765	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	4766	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[66]	4767	fi
[1]	4768
[1289]	4769	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	4770	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	4771	echo "set -x" >> $jobfile
	4772	echo "queue=$queue" >> $jobfile
[1]	4773	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	4774	echo 'ls -al; echo `pwd`' >> $jobfile
	4775	echo "cd \$HOME" >> $jobfile
	4776	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	4777
	4778
	4779
	4780
[1289]	4781	# START THE JOB USING SUBJOB-COMMAND
[1]	4782	if [[ $silent = false ]]
	4783	then
	4784	printf "\n "
	4785	else
	4786	printf "\n\n"
	4787	fi
	4788
[1094]	4789	subjob $job_on_file -h $host -u $remote_username -g $group_number -q $queue -m $memory -N $node_usage -t $cpumax $XOPT $TOPT $OOPT -n $fname -v -c $job_catalog -e $email_notification $PORTOPT $jobfile
[1]	4790	rm -rf $jobfile
	4791
	4792
[1289]	4793	fi # END OF REMOTE-PART

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