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source: palm/trunk/SCRIPTS/mrun @ 1321

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

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