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source: palm/trunk/SCRIPTS/mrun @ 1949

Last change on this file since 1949 was 1945, checked in by raasch, 9 years ago
last commit documented
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Rev	Line
[1841]	1	#!/bin/bash
[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	#
[1753]	19	# Copyright 1997-2015 Leibniz Universitaet Hannover
[1046]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
[1090]	23	# ------------------
[1945]	24	#
[1805]	25	#
	26	# Former revisions:
	27	# -----------------
	28	# $Id: mrun 1945 2016-06-15 07:17:24Z maronga $
[1867]	29	#
[1945]	30	# 1944 2016-06-15 06:29:00Z raasch
	31	# adjustments for using HLRN ssh-keys
	32	#
[1941]	33	# 1940 2016-06-14 05:15:20Z raasch $
	34	# adjustments for lckiaps
	35	#
[1867]	36	# 1866 2016-04-15 06:50:59Z raasch
	37	# adjusted for lcocean
[1805]	38	#
[1842]	39	# 1841 2016-04-07 19:14:06Z raasch
	40	# script now running under bash
	41	#
[1805]	42	# 1804 2016-04-05 16:30:18Z maronga
[1779]	43	# test: implementing an execute mechanism where the execute command is given in the
	44	# configuration file
	45	# ROPTS removed from execution commands
	46	# Warnings about missing optional files or user code changed to informative messages
[1804]	47	# Removed parameter file check
[1305]	48	#
[1756]	49	# 1755 2016-02-22 13:53:39Z maronga
	50	# Minor bugfix to last commit
	51	#
[1754]	52	# 1753 2016-02-22 13:49:49Z maronga
	53	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
	54	#
[1623]	55	# 1622 2015-07-20 06:21:36Z heinze
	56	# bugfix for Mistral (lcbullhh)
	57	#
	58	# 1621 2015-07-17 11:39:33Z heinze
[1621]	59	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
[1200]	60	#
[1610]	61	# 1609 2015-07-03 15:37:58Z maronga
	62	# Modified the random number of the temporary working directory to match the
	63	# queuing system number on HLRN-III (lccray*).
	64	#
[1605]	65	# 1604 2015-06-23 15:48:03Z suehring
	66	# Enable coupled runs for lcmuk
	67	#
[1599]	68	# 1598 2015-05-29 06:45:40Z raasch
	69	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
	70	#
[1550]	71	# 1549 2015-01-30 14:26:16Z suehring
	72	# Enable interactive debug sessions with allinea debugger
	73	#
[1548]	74	# 1547 2015-01-29 15:09:12Z witha
	75	# adjustments for ForWind computing cluster (lcflow)
	76	#
[1492]	77	# 1491 2014-11-12 08:12:57Z heinze
	78	# correct setting of batch_job allowed for ibm-machines
	79	#
[1469]	80	# 1468 2014-09-24 14:06:57Z maronga
	81	# Typo removed (addres->address)
	82	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
	83	# Added support for restart runs (remote) for lcxe6
	84	#
[1443]	85	# 1442 2014-07-28 07:09:10Z raasch
	86	# default queues for HLRN-III (lccrayb/lccrayh) defined
	87	#
[1423]	88	# 1422 2014-07-02 10:01:25Z kanani
	89	# automatic restarts enabled for lccrayb,
	90	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
	91	#
[1421]	92	# 1420 2014-06-10 06:24:14Z raasch
	93	# -j1 option added to aprung command for lccrayf (CSC)
	94	#
[1403]	95	# 1402 2014-05-09 14:25:13Z raasch
	96	# batch_job added to envpar-NAMELIST
	97	#
[1358]	98	# 1357 2014-04-11 15:02:03Z witha
	99	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
	100	# possible)
	101	#
[1328]	102	# 1320 2014-03-20 08:40:49Z raasch
	103	# check namelist file set false by default
	104	#
[1305]	105	# 1304 2014-03-12 10:29:42Z raasch
	106	# ulimit option changed from -Ss to -s
	107	#
	108	# bugfix: missing "fi" in r1289
	109	#
[1290]	110	# 1289 2014-03-04 07:12:34Z raasch
	111	# comments translated to English
	112	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	113	# export of variables for palm and interpret_config removed
	114	#
[1282]	115	# 1281 2014-02-01 07:55:49Z raasch
	116	# rsync-copy restricted to Cray machines, since command is unavailable on some
	117	# other systems
	118	#
[1280]	119	# 1279 2014-01-28 12:10:14Z raasch
	120	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	121	# in order to remove annoying restrictions concerning the number of processors which
	122	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	123	# restriction, one of the nodes will be filled with less than the given number of
	124	# tasks per node. A respective warning is given.
	125	#
[1275]	126	# 1274 2014-01-09 13:14:54Z heinze
	127	# adjustments for lccrayh
	128	#
[1273]	129	# 1272 2014-01-08 10:19:32Z witha
	130	# small adjustment for lcflow
	131	#
[1271]	132	# 1270 2013-12-16 11:05:01Z fricke
	133	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	134	#
[1256]	135	# 1255 2013-11-07 14:43:35Z raasch
	136	# further adjustments for lccrayb remote access
	137	#
[1242]	138	# 1241 2013-10-30 11:36:58Z heinze
	139	# Enable use of nudging input and input of large scale forcing from
	140	# external files
	141	#
[1230]	142	# 1229 2013-09-20 06:55:19Z raasch
	143	# further adjustments for lccrayb
	144	#
[1225]	145	# 1224 2013-09-16 07:27:23Z raasch
	146	# first adjustments for lccrayb
	147	#
[1211]	148	# 1210 2013-08-14 10:58:20Z raasch
	149	# fftw support added
	150	#
[1203]	151	# 1201 2013-07-10 16:17:59Z witha
	152	# adjustments for Forwind cluster (lcflow)
	153	#
[1200]	154	# 1199 2013-07-05 14:52:22Z raasch
[1199]	155	# adjustments for CSC Helsinki (lccrayf),
	156	# executables for batch jobs can be created in advance, in order to avoid calling
	157	# the compiler within the batch job (only works if batch jobs are submitted on
	158	# local host)
[1104]	159	#
[1191]	160	# 1190 2013-06-25 09:39:21Z heinze
	161	# enable use of automatic restarts for ibmh
[1185]	162	# use of cluster/express queue enabled (ibmh)
[1104]	163	#
[1125]	164	# 1124 2013-04-09 15:46:52Z raasch
	165	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	166	# side effect may lead to data loss while getopts is reading the script-option arguments
	167	#
[1123]	168	# 1122 2013-04-09 08:37:16Z heinze
	169	# Bugfix: change type of variable last_char
	170	#
[1121]	171	# 1119 2013-04-05 15:11:19Z raasch
	172	# Bugfix for setting -T option for subjob
	173	#
[1109]	174	# 1108 2013-03-05 07:03:32Z raasch
	175	# bugfix for coupled runs on lckyut/lckyuh
	176	#
[1107]	177	# 1106 2013-03-04 05:31:38Z raasch
	178	# --stdin argument for mpiexec on lckyuh
	179	# -y and -Y settings output to header
	180	#
[1104]	181	# 1103 2013-02-20 02:15:53Z raasch
[1103]	182	# default script runs again under ksh, because of unsolved problems with read
	183	# from stdin: when bash script is called from a ksh, message "read error: 0:
	184	# Resource temporarily unavailable" appears and script does not stop,
	185	# further bash compatibility adjustments,
	186	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	187	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	188	#
[1102]	189	# 1101 2013-02-17 10:20:21Z raasch
	190	# script now running under bash instead of ksh, which required small adjustments
	191	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	192	# read from stdin),
	193	# cross compilername on lckyuh compute nodes replaced by real compiler name
	194	#
[1100]	195	# 1099 2013-02-10 01:47:43Z raasch
	196	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	197	# and for Forwind cluster (lcflow)
	198	# small further adjustments for lckyut
	199	#
[1096]	200	# 1094 2013-02-03 01:52:12Z raasch
	201	# explicit ssh/scp port can be set in config file with environment variable
	202	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	203	# decalpha parts (yonsei) removed
	204	#
[1091]	205	# 2013-02-02 07:06:13Z raasch
[1099]	206	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	207	#
[1084]	208	# 1083 2013-01-04 10:22:09Z maronga
	209	# bugfix in parameter file check (read %cpp_options was missing)
	210	#
[1070]	211	# 1069 2012-11-28 16:18:43Z maronga
	212	# bugfix: coupling mode was always set to mpi2, typos removed
	213	#
[1059]	214	# 1058 2012-11-21 07:00:35Z raasch
	215	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	216	# nodes
	217	#
[1047]	218	# 1046 2012-11-09 14:38:45Z maronga
	219	# code put under GPL (PALM 3.9)
	220	#
[1090]	221	# 21/03/94 - Siggi - first version finished
	222	# 03/03/94 - Siggi - script development started
	223	#
[1059]	224	#--------------------------------------------------------------------------------#
[1090]	225	# mrun - script for running PALM jobs
	226	#--------------------------------------------------------------------------------#
[1]	227
[1047]	228
[1]	229
[1289]	230	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	231
[1289]	232	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	233	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	234	# (TOO MANY ARGUMENTS - PROBLEM)
	235	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	236
	237	AddFilenames=""
	238	additional_conditions=""
	239	add_source_path=""
	240	afname=""
	241	archive_save=true
	242	archive_system=none
[1320]	243	check_namelist_files=false
[920]	244	combine_plot_fields=true
[1]	245	compiler_name=""
	246	cond1=""
	247	cond2=""
	248	config_file=.mrun.config
[206]	249	coupled_dist=""
	250	coupled_mode="mpi1"
[1]	251	cpp_opts=""
[82]	252	cpp_options=""
[1]	253	cpumax=0
	254	cpurest=0
[1199]	255	create_executable_for_batch=false
[1]	256	delete_temporary_catalog=true
	257	do_batch=false
	258	do_compile=true
	259	do_remote=false
	260	do_stagein=true
	261	do_stageout=true
	262	do_trace=false
[352]	263	email_notification="none"
[1]	264	exclude=""
	265	executable=""
[1779]	266	execute_command="none"
[1]	267	execution_error=false
[1210]	268	fftw_inc=""
	269	fftw_lib=""
	270	fftw_support=false
[1289]	271	fname=test
[1]	272	fromhost=""
[78]	273	global_revision=""
[122]	274	group_number=none
[1]	275	host=""
	276	host_file=""
	277	hp=""
	278	ignore_archive_error=false
	279	input_list=""
	280	interpreted_config_file=""
[164]	281	job_catalog="~/job_queue"
[1]	282	job_on_file=""
	283	keep_data_from_previous_run=false
[183]	284	link_local_input=false
[149]	285	link_local_output=false
[1]	286	localhost_realname=$(hostname)
[260]	287	local_dvrserver_running=.FALSE.
[1]	288	locat=normal
	289	mainprog=""
	290	makefile=""
[759]	291	max_par_io_str=""
[1]	292	mc=$0
	293	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	294	do
	295	mc=`echo $mc \| cut -f2- -d"/"`
	296	done
[493]	297	module_calls=""
[1]	298	mrun_script_name=$mc
[82]	299	netcdf_inc=""
	300	netcdf_lib=""
[1]	301	netcdf_support=false
	302	node_usage=default
	303	numprocs=""
[206]	304	numprocs_atmos=0
	305	numprocs_ocean=0
[1]	306	OOPT=""
	307	openmp=false
	308	output_list=""
	309	package_list=""
	310	queue=none
	311	read_from_config=""
[5]	312	restart_run=false
[622]	313	if [[ `hostname` = rte10 ]]
[1]	314	then
[1468]	315	return_address=133.5.185.60
	316	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[693]	317	elif [[ `hostname` = climate0 ]]
	318	then
[1468]	319	return_address=165.132.26.68
	320	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1866]	321	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
	322	then
	323	return_address="schultzl-Latitude-E6540"
	324	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1021]	325	elif [[ `hostname` = urban00 ]]
	326	then
[1468]	327	return_address=147.46.30.151
	328	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[622]	329	else
[1468]	330	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	331	fi
	332	return_password=""
	333	return_username=$LOGNAME
	334	remotecall=false
	335	remote_username=""
[102]	336	run_coupled_model=false
[1]	337	run_mode=""
[397]	338	store_on_archive_system=false
[1289]	339	dashes=" ----------------------------------------------------------------------------"
[1]	340	silent=false
	341	source_list=""
	342	source_path=SOURCE
	343	tasks_per_node=""
	344	threads_per_task=1
	345	tmpcreate=false
	346	tmp_data_catalog=""
	347	transfer_problems=false
	348	usern=$LOGNAME
[377]	349	use_openmp=false
[1289]	350	version="MRUN 2.1 Rev$Rev: 1945 $"
[1]	351	working_directory=`pwd`
	352	TOPT=""
	353	XOPT=""
	354	zeit=$( date \| cut -c 12-19 )
	355
[1124]	356	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	357	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	358	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	359	# SCRIPT-OPTION ARGUMENTS
[1279]	360	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]	361
[1289]	362	# ERROR HANDLING IN CASE OF EXIT
[83]	363	trap 'rm -rf $working_directory/tmp_mrun
[1289]	364	if [[ $locat != normal && $locat != control_c ]]
[1]	365	then
	366
[1289]	367	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	368	(( i = 0 ))
	369	while (( i < iec ))
	370	do
	371	(( i = i + 1 ))
	372	printf "\n *** Execution of ERROR-command:\n"
	373	printf " >>> ${err_command[$i]}\n"
	374	eval ${err_command[$i]}
	375	done
[1101]	376	if [[ -n $interpreted_config_file ]]
	377	then
[1]	378	rm -rf $interpreted_config_file
	379	fi
[1101]	380	if [[ -n .mrun_environment ]]
	381	then
[71]	382	rm -rf .mrun_environment
	383	fi
[1]	384	if [[ $tmpcreate = true ]]
	385	then
	386	printf "\n *** Contents of \"$TEMPDIR\":\n"
	387	ls -al; cd
	388	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	389	fi
[260]	390	if [[ "$dvrserver_id" != "" ]]
	391	then
	392	echo "+++ killing dvrserver_id=$dvrserver_id"
	393	kill $dvrserver_id
	394	fi
[1]	395	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	396	then
	397	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	398	fi
	399	printf "\n\n+++ MRUN killed \n\n"
	400	elif [[ $locat != control_c ]]
	401	then
	402	printf "\n\n --> all actions finished\n\n"
	403	printf " Bye, bye $usern !!\n\n"
	404	fi' exit
	405
	406
[1289]	407	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	408	trap 'rm -rf $working_directory/tmp_mrun
[807]	409	rm -rf $working_directory/tmp_check_namelist_files
[69]	410	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	411	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	412	then
	413	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	414	fi
[260]	415	if [[ "$dvrserver_id" != "" ]]
	416	then
	417	echo "+++ killing dvrserver_id=$dvrserver_id"
	418	kill $dvrserver_id
	419	fi
[1]	420	printf "\n+++ MRUN killed by \"^C\" \n\n"
	421	locat=control_c
	422	exit
	423	' 2
	424
	425
[22]	426	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	427	# BEEN SET
	428	if [[ "$PALM_BIN" = "" ]]
	429	then
	430	printf "\n +++ environment variable PALM_BIN has not been set"
	431	printf "\n please set it to the directory where the PALM scripts are located"
	432	locat=palm_bin; exit
	433	fi
[180]	434	export PATH=$PALM_BIN:$PATH
[22]	435
	436
[1]	437
[1289]	438	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	439	# WHICH WILL BE USED TO START RESTART-JOBS
[920]	440	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]	441	do
	442	case $option in
	443	(a) afname=$OPTARG;;
[397]	444	(A) store_on_archive_system=true; mc="$mc -A";;
[1]	445	(b) do_batch=true; mc="$mc -b";;
	446	(B) delete_temporary_catalog=false; mc="$mc -B";;
	447	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	448	(C) restart_run=true; mc="$mc -C";;
[1]	449	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[210]	450	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
[79]	451	(F) job_on_file="-D"; mc="$mc -F";;
[122]	452	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	453	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	454	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	455	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	456	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	457	(I) ignore_archive_error=true; mc="$mc -I";;
	458	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	459	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	460	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	461	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	462	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
	463	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	464	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	465	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	466	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	467	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	468	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
[1468]	469	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
[1]	470	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	471	(S) read_from_config=false; mc="$mc -S";;
	472	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	473	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	474	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	475	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	476	(v) silent=true; mc="$mc -v";;
[759]	477	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	478	(x) do_trace=true;set -x; mc="$mc -x";;
	479	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	480	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	481	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	482	(z) check_namelist_files=false; mc="$mc -z";;
[920]	483	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	484	(\?) printf "\n +++ unknown option $OPTARG \n"
	485	printf "\n --> type \"$0 ?\" for available options \n"
	486	locat=parameter;exit;;
	487	esac
	488	done
	489
	490
[1289]	491	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	492	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	493	(( to_shift = $OPTIND - 1 ))
	494	shift $to_shift
[1]	495
[1289]	496	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	497	if [[ "$1" = "?" ]]
	498	then
	499	(printf "\n *** mrun can be called as follows:\n"
[1804]	500	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 <modus> \n"
[1]	501	printf "\n Description of available options:\n"
	502	printf "\n Option Description Default-Value"
	503	printf "\n -a base name of input files equiv. -d"
[400]	504	printf "\n -A archiving when using file-attribute fl"
[1]	505	printf "\n -b batch-job on local machine ---"
	506	printf "\n -B do not delete temporary directory at end ---"
	507	printf "\n -c configuration file .mrun.config"
	508	printf "\n -d base name of files attached to program test"
	509	printf "\n -D preprocessor(cpp)-directives \"\" "
	510	printf "\n -F create remote job file only ---"
	511	printf "\n -h execution host $localhost_realname"
	512	printf "\n -i INPUT control list \"\" "
	513	printf "\n -I archiving errors of previous batch-jobs"
	514	printf "\n will be ignored"
	515	printf "\n -k keep data from previous run"
	516	printf "\n -K additional conditions for controling"
	517	printf "\n usage of conditional code and"
	518	printf "\n env-variables in configuration file \"\" "
	519	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	520	printf "\n -M Makefile name Makefile"
	521	printf "\n -n node usage (shared/not_shared) depending on -h"
	522	printf "\n -o OUTPUT control list \"\" "
[1304]	523	printf "\n -O threads per openMP task ---"
[1]	524	printf "\n -p software package list \"\" "
	525	printf "\n -q queue \"$queue\" "
	526	printf "\n -r run control list (combines -i -o) \"\" "
	527	printf "\n -s filenames of routines to be compiled \"\" "
	528	printf "\n must end with .f, .f90, .F, or .c !"
	529	printf "\n use \"..\" for more than one file and wildcards"
[837]	530	printf "\n -s LM compiles all locally modified files"
[1]	531	printf "\n -S config file interpreted by shellscript ---"
	532	printf "\n -t allowed cpu-time in seconds (batch) 0"
	533	printf "\n -T tasks per node depending on -h"
	534	printf "\n -u username on remote machine \"\" "
	535	printf "\n -v no prompt for confirmation ---"
[759]	536	printf "\n -w maximum parallel io streams as given by -X"
[1]	537	printf "\n -x tracing of mrun for debug purposes ---"
	538	printf "\n -X # of processors (on parallel machines) 1"
[291]	539	printf "\n -y add appendix \"_O\" to all local output"
	540	printf "\n files (ocean precursor runs followed by"
	541	printf "\n coupled atmosphere-ocean runs) ---"
[206]	542	printf "\n -Y run coupled model, \"#1 #2\" with"
	543	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	544	printf "\n -Z skip combine_plot_fields at the end of "
	545	printf "\n the simulation ---"
[1]	546	printf "\n "
	547	printf "\n Possible values of positional parameter <modus>:"
	548	printf "\n \"?\" - this outline \n\n") \| more
	549	exit
	550	elif [[ "$1" != "" ]]
	551	then
	552	printf "\n +++ positional parameter $1 unknown \n"
	553	locat=parameter; exit
	554	fi
	555
	556
	557
[1289]	558	# SHORT STARTING MESSAGE
[1]	559	printf "\n*** $version "
	560	printf "\n will be executed. Please wait ..."
	561
	562
[82]	563
[1289]	564	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	565	if [[ ! -f $config_file ]]
	566	then
	567	printf "\n\n +++ configuration file: "
	568	printf "\n $config_file"
	569	printf "\n does not exist"
	570	locat=connect; exit
	571	fi
	572
	573
[1289]	574	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	575	line=""
	576	grep "%host_identifier" $config_file > tmp_mrun
	577	while read line
	578	do
[206]	579	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	580	then
	581	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	582	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	583	if [[ $localhost_realname = $HOSTNAME ]]
[82]	584	then
	585	localhost=$host_identifier
	586	break
	587	fi
	588	fi
	589	done < tmp_mrun
	590
	591	if [[ "$localhost" = "" ]]
	592	then
	593	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	594	printf "\n for local host \"$localhost_realname\"."
	595	printf "\n Please add line"
	596	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	597	printf "\n to the configuration file."
	598	locat=localhost; exit
	599	fi
	600
	601
[1289]	602	# SET HOST-SPECIFIC VARIABLES
[82]	603	case $localhost_realname in
[397]	604	(r1\|r2\|h01\|b01) archive_system=tivoli;;
[82]	605	(cs*) archive_system=ut;;
	606	esac
	607
	608
[1289]	609	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	610	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	611	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	612	[[ "$afname" = "" ]] && afname=$fname
	613
	614
[1289]	615	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	616	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	617	# STATEMENTS IN THE CONFIGURATION FILE
[1]	618	if [[ "$run_mode" != "" ]]
	619	then
	620	input_list="$input_list $run_mode"
	621	output_list="$output_list $run_mode"
	622	fi
	623
	624
[1289]	625	# ??? is this (and the respective option -H) really required ???
	626	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	627	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	628	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	629	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	630	if [[ "$fromhost" = "" ]]
	631	then
	632	fromhost=$localhost
	633	fi
	634
	635
[1289]	636	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	637	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	638	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
[1609]	639	# TO BE SUBMITTED (I.E. do_batch=true)
[1]	640	if [[ -n $host && "$host" != $localhost ]]
	641	then
	642	do_batch=true
	643	do_remote=true
	644	case $host in
[1866]	645	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	646	(*) printf "\n"
[83]	647	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	648	printf "\n is not available"
[1]	649	locat=nqs; (( iec = 0 )); exit;;
	650	esac
	651	else
	652	host=$localhost
	653	fi
	654
	655
[1289]	656	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	657	if [[ -n $additional_conditions ]]
	658	then
[69]	659	cond1=`echo $additional_conditions \| cut -d" " -f1`
	660	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	661	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	662	if [[ -n $dummy ]]
	663	then
	664	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	665	locat=options; exit
	666	fi
[503]	667	block=_$cond1
	668	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	669	fi
	670
	671
[1289]	672	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
[206]	673	if [[ $run_coupled_model = true ]]
	674	then
	675
[1289]	676	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	677	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	678
	679	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	680	then
	681
[1289]	682	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	683	printf "\n PEs (total) : $numprocs"
	684	printf "\n PEs (atmosphere): $numprocs_atmos"
	685	printf "\n PEs (ocean) : $numprocs_ocean"
	686	locat=coupling; exit
[206]	687
[1289]	688	fi
[206]	689
	690
	691	# GET coupled_mode FROM THE CONFIG FILE
	692	line=""
	693	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
	694	while read line
	695	do
[1779]	696	echo line=\"$line\"
	697	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
[206]	698	then
	699	coupled_mode="mpi2"
	700	fi
	701	done < tmp_mrun
	702
	703	fi
	704
[1289]	705	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
[1]	706	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
	707	then
	708	if [[ $ignore_archive_error = false ]]
	709	then
	710	printf "\n +++ data archiving of previous run failed"
	711	printf "\n see directory \~/job_queue on remote machine"
	712	locat=archive; exit
	713	else
	714	printf "\n +++ warning: data archiving in a previous run failed"
	715	printf "\n MRUN continues, trying to get backup copy"
	716	fi
	717	fi
	718
	719
[1289]	720	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	721	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	722	mrun_memory=$memory
	723	mrun_group_number=$group_number
	724	mrun_cpumax=$cpumax
	725	mrun_numprocs=$numprocs
[1]	726
[1099]	727
[1289]	728	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
[1468]	729	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
[1]	730	if [[ "$read_from_config" = false ]]
	731	then
	732	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	733
	734	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	735	while read zeile
	736	do
	737	[[ $silent = false ]] && printf "."
	738
	739
[1289]	740	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	741	eval zeile=\"$zeile\"
	742
	743
[1289]	744	# INTERPRET THE LINE
[21]	745	if [[ "$(echo $zeile)" = "" ]]
[1]	746	then
[1289]	747	# EMPTY LINE, NO ACTION
[21]	748	continue
[1]	749
[21]	750	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	751	then
	752
[1289]	753	# LINE IS A COMMENT LINE
[1]	754	true
	755
	756	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	757	then
	758
[1289]	759	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	760	zeile=$(echo $zeile \| cut -c2-)
[69]	761	var=`echo $zeile \| cut -d" " -f1`
	762	value=`echo $zeile \| cut -d" " -s -f2`
	763	for_host=`echo $zeile \| cut -d" " -s -f3`
	764	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	765	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	766
	767	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	768	then
	769
[1289]	770	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	771	# "::" IS REPLACED BY ":".
[1]	772	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	773
	774
[1289]	775	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	776	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	777	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	778	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	779	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	780	# CONFIGURATION-FILE.
[1]	781	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	782	then
	783	eval $var=\$value
	784
[1289]	785	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	786	if [[ $do_trace = true ]]
	787	then
	788	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	789	fi
	790	fi
	791
[1289]	792	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	793	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	794	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	795	# MUST HAVE TO BE STARTED
[1]	796	if [[ $var = host ]]
	797	then
	798	if [[ -n $host && "$host" != $localhost ]]
	799	then
	800	do_batch=true
	801	do_remote=true
	802	case $host in
[1866]	803	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[83]	804	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	805	printf "\n is not available"
[1]	806	locat=nqs; exit;;
	807	esac
	808	else
	809	host=$localhost
	810	fi
	811	fi
	812
[1289]	813	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	814	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	815	# BY MRUN (E.G. subjob)
[1]	816	export $var
	817	fi
	818
	819
	820
	821
	822	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	823	then
	824
[1289]	825	# LINE DEFINES ERROR-COMMAND
[1]	826	(( iec = iec + 1 ))
	827	zeile=$(echo $zeile \| cut -c4-)
	828	err_command[$iec]="$zeile"
	829
	830	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	831	then
	832
[1289]	833	# LINE DEFINES INPUT-COMMAND
[1]	834	(( iic = iic + 1 ))
	835	zeile=$(echo $zeile \| cut -c4-)
	836	in_command[$iic]="$zeile"
	837
	838	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	839	then
	840
[1289]	841	# LINE DEFINES OUTPUT-COMMAND
[1]	842	(( ioc = ioc + 1 ))
	843	zeile=$(echo $zeile \| cut -c4-)
	844	out_command[$ioc]="$zeile"
	845
	846	else
	847
[1289]	848	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	849	# s2a: in/out - field
	850	# s2b: loc - field (optional)
	851	# s2c: tr/ar - field (optional)
[69]	852	s1=`echo $zeile \| cut -d" " -f1`
	853	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	854	s2a=$(echo $s2 \| cut -d":" -f1)
	855	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	856	then
	857	s2b=""
	858	s2c=""
	859	else
[69]	860	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	861	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	862	fi
[69]	863	s3=`echo $zeile \| cut -d" " -f3`
	864	s4=`echo $zeile \| cut -d" " -s -f4`
	865	s5=`echo $zeile \| cut -d" " -s -f5`
	866	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	867
	868
[1289]	869	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	870	# INPUT- OR OUTPUT-LIST.
	871	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	872	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	873	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	874	# IS NOT CHECKED AND STORED.
[1]	875	IFSALT="$IFS"; IFS="$IFS:"
	876	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	877	then
	878	found=false
	879	for actual in $input_list
	880	do
	881	for formal in $s3
	882	do
	883	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	884	done
	885	done
	886	if [[ $found = true ]]
	887	then
	888	(( iin = iin + 1 ))
	889	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	890	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	891	extin[$iin]=$s6
	892	fi
	893	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	894	then
	895	found=false
	896	for actual in $output_list
	897	do
	898	for formal in $s3
	899	do
	900	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	901	done
	902	done
	903	if [[ $found = true ]]
	904	then
	905	(( iout = iout + 1 ))
	906	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	907	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	908	fi
	909	elif [[ "$s2a" != in && "$s2a" != out ]]
	910	then
	911	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	912	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	913	locat=connect; exit
	914	fi
	915	IFS="$IFSALT"
	916	fi
	917	done < $config_file
	918
	919	else
	920
[1289]	921	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	922	[[ $silent = false ]] && printf "..."
[1289]	923	interpreted_config_file=.icf.$RANDOM
[1]	924
	925
[1917]	926
[1289]	927	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[69]	928	cat > .mrun_environment << %%END%%
	929	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	930	config_file = '$config_file', do_remote = '$do_remote',
	931	do_trace = '$do_trace', host = '$host',
	932	input_list = '$input_list', icf = '$interpreted_config_file',
	933	localhost = '$localhost', output_list = '$output_list' /
	934
	935	%%END%%
	936
[1289]	937	if [[ "$host" != $localhost ]]
[66]	938	then
[503]	939
[1289]	940	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	941	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	942	if [[ $? != 0 ]]
[503]	943	then
[1289]	944	printf "\n\n +++ no interpret_config found"
	945	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	946	locat=interpret_config; exit
	947	fi
	948	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	949	$interpret_config_executable
[503]	950
[1289]	951	else
[503]	952
[1289]	953	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	954	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	955	then
	956	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	957	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	958	locat=interpret_config; exit
[503]	959	else
[1289]	960	interpret_config${block}.x
	961	fi
[503]	962
[66]	963	fi
[71]	964	rm .mrun_environment
[1]	965
[1917]	966
[1289]	967	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	968	chmod u+x $interpreted_config_file
	969	export PATH=$PATH:.
	970	. $interpreted_config_file
[71]	971	rm $interpreted_config_file
[1]	972
[1099]	973	fi
[71]	974
[1917]	975
[1289]	976	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	977	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	978	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	979	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	980	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	981	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	982	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	983
	984
[1289]	985	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	986	# FOR SOURCE-FILES TO BE COMPILED.
	987	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	988	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	989	if [[ "$SOURCES_COMPLETE" = "" ]]
	990	then
	991
[1289]	992	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	993	# HAS BEEN DEFINED
[1]	994	source_path=""
	995	line=""
	996	grep "%source_path" $config_file > tmp_mrun
	997	while read line
	998	do
	999	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1000	then
	1001	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	1002	then
	1003	global_source_path=`echo $line \| cut -d" " -f2`
	1004	fi
	1005	fi
	1006	done < tmp_mrun
	1007
	1008	line=""
	1009	found=false
	1010	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	1011	while read line
	1012	do
	1013	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1014	then
	1015	if [[ $found = true ]]
	1016	then
	1017	printf "\n\n +++ more than one source path found in configuration file"
	1018	printf "\n for local host \"$localhost\" "
	1019	locat=source_path; exit
	1020	fi
	1021	source_path=`echo $line \| cut -d" " -f2`
	1022	found=true
	1023	fi
	1024	done < tmp_mrun
	1025	rm tmp_mrun
	1026
	1027	if [[ "$source_path" = "" ]]
	1028	then
	1029	if [[ "$global_source_path" != "" ]]
	1030	then
	1031	source_path=$global_source_path
	1032	else
	1033	printf "\n\n +++ no source path found in configuration file"
	1034	printf "\n for local host \"$localhost\" "
	1035	locat=source_path; exit
	1036	fi
	1037	fi
	1038	eval source_path=$source_path
	1039
	1040	if [[ ! -d $source_path ]]
	1041	then
	1042	printf "\n\n +++ source path \"$source_path\" on local host"
	1043	printf "\n \"$localhost\" does not exist"
	1044	locat=source_path; exit
	1045	fi
	1046
	1047	fi
	1048
	1049
[1289]	1050	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1051	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1052	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	1053	then
	1054	global_revision=`svnversion $source_path 2>/dev/null`
	1055	global_revision="Rev: $global_revision"
	1056	fi
[1]	1057
[78]	1058
[1289]	1059	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	1060	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	1061	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	1062	if [[ -n $host && "$host" != $localhost ]]
	1063	then
	1064	do_batch=true
	1065	do_remote=true
	1066	case $host in
[1866]	1067	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	1068	(*) printf "\n"
[83]	1069	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	1070	printf "\n is not available"
[1]	1071	locat=nqs; (( iec = 0 )); exit;;
	1072	esac
	1073	else
	1074	host=$localhost
	1075	fi
	1076
	1077
[1620]	1078
[1289]	1079	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1080	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1081	then
	1082
[1289]	1083	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1084	if [[ ! -n $numprocs ]]
	1085	then
	1086	printf "\n"
	1087	printf "\n +++ option \"-K parallel\" requires additional specification"
	1088	printf "\n of the number of processors to be used by"
	1089	printf "\n mrun-option \"-X\" or by environment-variable"
	1090	printf "\n \"numprocs\" in the configuration file"
	1091	locat=numprocs; (( iec = 0 )); exit
	1092	fi
	1093
[1289]	1094	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1095	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[1039]	1096	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
[1]	1097	then
[759]	1098	printf "\n"
	1099	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1100	printf "\n set -T option or define tasks_per_node in the config file"
	1101	locat=tasks_per_node; (( iec = 0 )); exit
	1102	fi
[1279]	1103
	1104	if (( numprocs < tasks_per_node ))
	1105	then
	1106	printf "\n"
	1107	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1108	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1109	locat=tasks_per_node; (( iec = 0 )); exit
	1110	fi
	1111
[1039]	1112	if [[ $host != lcflow && $host != lcxt5m ]]
[759]	1113	then
[1279]	1114	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1115	(( ival = $tasks_per_node ))
	1116	(( pes = numprocs ))
	1117	(( ii = pes / ival ))
[1279]	1118	(( remaining_pes = pes - ii * ival ))
	1119	if (( remaining_pes > 0 ))
[848]	1120	then
	1121	printf "\n"
[1279]	1122	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1123	printf "\n divisor of the total number of processors (option \"-X\")"
	1124	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1125	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1126	(( nodes = nodes + 1 ))
[848]	1127	fi
[1]	1128	fi
	1129
[759]	1130
[377]	1131	# SETTINGS FOR SUBJOB-COMMAND
[1]	1132	OOPT="-O $threads_per_task"
	1133
[1289]	1134	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1135	if [[ "$tasks_per_node" != "" ]]
	1136	then
[1119]	1137	TOPT="-T $tasks_per_node"
[1]	1138	fi
	1139
[1289]	1140	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1141	if [[ $node_usage = default ]]
	1142	then
	1143	if [[ $host = ibms ]]
	1144	then
	1145	node_usage=shared
	1146	else
	1147	node_usage=not_shared
	1148	fi
	1149	fi
[181]	1150
[635]	1151	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1152	then
	1153	printf "\n"
	1154	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1155	printf "\n \"shared\" or \"not_shared\""
	1156	locat=tasks_per_node; (( iec = 0 )); exit
	1157	fi
	1158
	1159	fi
	1160
[1289]	1161	# CHECK IF HOSTFILE EXISTS
[1]	1162	if [[ -n $hostfile ]]
	1163	then
	1164	if [[ ! -f $hostfile ]]
	1165	then
	1166	printf "\n"
	1167	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1168	locat=hostfile; exit
	1169	fi
	1170	fi
	1171
	1172
[1289]	1173	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1174	if [[ "$maximum_parallel_io_streams" = "" ]]
	1175	then
	1176	maximum_parallel_io_streams=$numprocs
	1177	fi
[1]	1178
[759]	1179
[1289]	1180	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1181	if [[ "$scp_port" != "" ]]
	1182	then
	1183	PORTOPT="-P $scp_port"
	1184	SSH_PORTOPT="-p $scp_port"
	1185	fi
	1186
	1187
[1944]	1188	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1189	# CONFIG-FILE
	1190	if [[ "$ssh_key" != "" ]]
	1191	then
	1192	ssh_key="-i $HOME/.ssh/$ssh_key"
	1193	fi
	1194
	1195
[1289]	1196	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1197	if [[ $queue = none ]]
	1198	then
	1199	case $host in
[1184]	1200	(ibmh) queue=cluster;;
[693]	1201	(ibmkisti) queue=class.32plus;;
[1620]	1202	(lcbullhh) queue=compute;;
[1442]	1203	(lccrayb) queue=mpp1q;;
	1204	(lccrayh) queue=mpp1q;;
[1040]	1205	(lckiaps) queue=normal;;
[440]	1206	(lckyoto) queue=ph;;
[1099]	1207	(lckyuh) queue=fx-single;;
	1208	(lckyut) queue=cx-single;;
[635]	1209	(lctit) queue=S;;
[1]	1210	(nech) queue=none;;
	1211	(unics) queue=unics;;
	1212	esac
	1213	fi
	1214
	1215
[1289]	1216	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1217	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1218	(( i = 0 ))
	1219	while (( i < iin ))
	1220	do
	1221	(( i = i + 1 ))
	1222	(( maxcycle = 0 ))
	1223
[1289]	1224	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1225	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1226	if [[ "${actionin[$i]}" = di ]]
	1227	then
[1289]	1228	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1229	# HOST ONLY
[1]	1230	eval filename=${pathin[$i]}/${endin[$i]}
	1231	else
[1289]	1232	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1233	# HOST ONLY
[1]	1234	eval filename=${pathin[$i]}/${afname}${endin[$i]}
	1235	fi
[892]	1236	eval pathname=${pathin[$i]}
[1]	1237
[1289]	1238	# CHECK IF FILE EXISTS
[1]	1239	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
[746]	1240	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
[1]	1241	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
	1242	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
	1243	then
[1289]	1244
	1245	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[1]	1246	if [[ "${transin[$i]}" != "locopt" ]]
	1247	then
	1248	printf "\n\n +++ INPUT-file: "
	1249	if [[ "${extin[$i]}" = "" ]]
	1250	then
	1251	printf "\n $filename"
	1252	else
	1253	printf "\n $filename.${extin[$i]}"
	1254	fi
	1255	printf "\n does not exist\n"
	1256	locat=input; exit
	1257	else
	1258	transin[$i]="unavailable"
	1259	fi
	1260	else
	1261
[1289]	1262	# DETERMINE THE FILE'S CYCLE NUMBER
[1]	1263	ls -1 -d $filename > filelist 2>/dev/null
	1264	ls -1 -d $filename.* >> filelist 2>/dev/null
	1265	while read zeile
	1266	do
[1101]	1267	cycle=$(echo $zeile \| cut -f2 -d".")
[1]	1268	if [[ "$cycle" = "$zeile" ]]
	1269	then
	1270	(( icycle = 0 ))
	1271	elif [[ "$cycle" = "${extin[$i]}" ]]
	1272	then
	1273	(( icycle = 0 ))
	1274	else
	1275	(( icycle = $cycle ))
	1276	fi
	1277	if (( icycle > maxcycle ))
	1278	then
	1279	(( maxcycle = icycle ))
	1280	file_to_be_used=$zeile
	1281	fi
	1282	done <filelist
	1283	rm filelist
	1284
[1289]	1285	# APPEND CYCLE NUMBER TO FILENAME
[1]	1286	if (( maxcycle > 0 ))
	1287	then
	1288	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1289	then
	1290	filename=${filename}.$maxcycle.${extin[$i]}
	1291	else
	1292	filename=${filename}.$maxcycle
	1293	fi
	1294	else
	1295	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1296	then
	1297	filename=${filename}.${extin[$i]}
	1298	fi
	1299	fi
	1300
[1289]	1301	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1302	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
[1]	1303	absnamein[$i]=$filename
	1304	if (( maxcycle > 0 ))
	1305	then
	1306	if [[ "${actionin[$i]}" = di ]]
	1307	then
	1308	frelin[$i]=${endin[$i]}.$maxcycle
	1309	else
	1310	frelin[$i]=${afname}${endin[$i]}.$maxcycle
	1311	fi
	1312	else
	1313	if [[ "${actionin[$i]}" = di ]]
	1314	then
	1315	frelin[$i]=${endin[$i]}
	1316	else
	1317	frelin[$i]=${afname}${endin[$i]}
	1318	fi
	1319	fi
	1320
	1321	fi
	1322	done
[920]	1323
[1289]	1324	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1325	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1326	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1327	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1328	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1329	# REMOTE HOST)
[1]	1330	(( i = 0 ))
	1331	while (( i < iout ))
	1332	do
	1333	(( i = i + 1 ))
	1334	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1335	then
[260]	1336	if [[ "${actionout[$i]}" = tr ]]
[1]	1337	then
	1338	actionout[$i]=""
[260]	1339	elif [[ "${actionout[$i]}" = trpe ]]
	1340	then
	1341	actionout[$i]=pe
[1]	1342	elif [[ "${actionout[$i]}" = tra ]]
	1343	then
	1344	actionout[$i]=a
	1345	fi
	1346	(( maxcycle = 0 ))
	1347	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1348	eval catalogname=${pathout[$i]}
	1349	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
[746]	1350	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
[1]	1351	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
	1352	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
	1353	then
	1354
[1289]	1355	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
[1]	1356	if cat /dev/null > $filename
	1357	then
	1358	rm $filename
	1359	else
	1360
[1289]	1361	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1362	# IF IT DOES NOT EXIST, TRY TO CREATE IT
[1]	1363	if [[ ! -d $catalogname ]]
	1364	then
	1365	if mkdir -p $catalogname
	1366	then
	1367	printf "\n\n *** directory:"
	1368	printf "\n $catalogname"
	1369	printf "\n was created\n"
	1370	else
	1371	printf "\n\n +++ OUTPUT-file:"
	1372	printf "\n $filename"
	1373	printf "\n cannot be created, because directory does not exist"
	1374	printf "\n and cannot be created either"
	1375	printf "\n"
	1376	locat=output ; exit
	1377	fi 2>/dev/null
	1378	else
	1379	printf "\n\n +++ OUTPUT-file:"
	1380	printf "\n $filename"
	1381	printf "\n cannot be created, although directory exists"
	1382	printf "\n"
	1383	locat=output ; exit
	1384	fi
	1385	fi 2>/dev/null
	1386	else
	1387
[1289]	1388	# DETERMINE THE CYCLE NUMBER
[1]	1389	ls -1 -d $filename > filelist 2>/dev/null
	1390	ls -1 -d $filename.* >> filelist 2>/dev/null
	1391	while read zeile
	1392	do
[1101]	1393	cycle=$(echo $zeile \| cut -f2 -d".")
[1]	1394	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
	1395	then
	1396	(( icycle = 1 ))
	1397	else
	1398	(( icycle = $cycle + 1 ))
	1399	fi
	1400	if (( icycle > maxcycle ))
	1401	then
	1402	(( maxcycle = icycle ))
	1403	fi
	1404	done <filelist
	1405	rm filelist
	1406	fi
	1407
[1289]	1408	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1409	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1410	if [[ "${actionout[$i]}" != a ]]
	1411	then
	1412	if (( maxcycle > 0 ))
	1413	then
	1414	filename=${filename}.$maxcycle
	1415	if cat /dev/null > $filename
	1416	then
	1417	rm $filename
	1418	else
	1419	printf "\n +++ OUTPUT-file:"
	1420	printf "\n $filename"
	1421	printf "\n cannot be created"
	1422	locat=output ; exit
	1423	fi
	1424	fi
	1425	else
	1426	(( maxcycle = maxcycle - 1 ))
	1427	if (( maxcycle > 0 ))
	1428	then
	1429	filename=${filename}.$maxcycle
	1430	fi
	1431	fi
	1432
[1289]	1433	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1434	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
	1435	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
[1]	1436	pathout[$i]=$filename
	1437	if (( maxcycle > 0 ))
	1438	then
	1439	frelout[$i]=${fname}${endout[$i]}.$maxcycle
	1440	else
	1441	frelout[$i]=${fname}${endout[$i]}
	1442	fi
	1443
	1444	fi
	1445	done
	1446
	1447
[1289]	1448	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1449	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1450	then
[260]	1451	if [[ "$dvr_inc" = "" ]]
[83]	1452	then
[260]	1453	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1454	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1455	locat=dvr; exit
[83]	1456	fi
[260]	1457	if [[ "$dvr_lib" = "" ]]
[83]	1458	then
[260]	1459	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1460	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1461	locat=dvr; exit
[83]	1462	fi
	1463	fi
	1464
	1465
[1289]	1466	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1467	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1468	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1469	then
	1470	printf "\n +++ neither main program nor executable defined"
	1471	locat=source; exit
	1472	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1473	then
	1474	printf "\n +++ main program as well as executable defined"
	1475	locat=source; exit
	1476	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1477	then
	1478	do_compile=false
	1479	fi
	1480
	1481
[1289]	1482	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1483	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1484	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1485	then
	1486	rm -rf SOURCES_FOR_RUN_$fname
	1487	mkdir SOURCES_FOR_RUN_$fname
	1488	fi
	1489
	1490
[1289]	1491	# COLLECT ALL ROUTINES TO BE COMPILED
	1492	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1493	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1494	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1495	then
	1496
[5]	1497	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1498
[838]	1499	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1500	then
	1501
[1289]	1502	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1503	source_list=""
	1504	cd $source_path
	1505
	1506
[1289]	1507	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1508	if [[ ! -d .svn ]]
	1509	then
	1510	printf "\n\n +++ source directory"
	1511	printf "\n \"$source_path\" "
	1512	printf "\n is not under control of \"subversion\"."
[306]	1513	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1514	fi
	1515
	1516
[1289]	1517	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1518	Filenames=""
[69]	1519	svn status > tmp_mrun
	1520	while read line
[5]	1521	do
	1522	firstc=`echo $line \| cut -c1`
	1523	if [[ $firstc = M \|\| $firstc = "?" ]]
	1524	then
	1525	Name=`echo "$line" \| cut -c8-`
	1526	extension=`echo $Name \| cut -d. -f2`
	1527	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1528	then
	1529	Filenames="$Filenames "$Name
	1530	fi
	1531	fi
[69]	1532	done < tmp_mrun
[5]	1533
	1534
[1289]	1535	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1536	for dateiname in $Filenames
	1537	do
	1538	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1539	source_list=$source_list"$dateiname "
	1540	done
	1541
	1542	cd - > /dev/null
	1543
	1544
[1289]	1545	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1546	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1547	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1548	then
	1549
	1550	cd $source_path
	1551
	1552	for filename in $source_list
	1553	do
	1554
[1289]	1555	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1556	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1557	then
	1558	printf "\n +++ source code file: $filename"
	1559	printf "\n must not contain (\"/\") "
	1560	locat=source; exit
	1561	fi
	1562
	1563	if [[ ! -f $filename ]]
	1564	then
	1565	printf "\n +++ source code file: $filename"
	1566	printf "\n does not exist"
	1567	locat=source; exit
	1568	else
	1569	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1570	fi
	1571
	1572	done
	1573
	1574	cd - > /dev/null
	1575
	1576	fi
	1577
	1578
[1289]	1579	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1580	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1581	if [[ $restart_run != true ]]
[1]	1582	then
	1583
	1584	if [[ ! -f "$source_path/$mainprog" ]]
	1585	then
	1586	printf "\n\n +++ main program: $mainprog"
	1587	printf "\n does not exist in source directory"
	1588	printf "\n \"$source_path\"\n"
	1589	locat=source; exit
	1590	else
	1591	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1592	then
	1593	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1594	source_list=${mainprog}" $source_list"
	1595	fi
	1596	fi
	1597	fi
	1598
	1599
[1289]	1600	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1601	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1602	if [[ "$restart_run" != true ]]
	1603	then
	1604	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1605	if [[ ! -f $makefile ]]
	1606	then
	1607	printf "\n +++ file \"$makefile\" does not exist"
	1608	locat=make; exit
	1609	else
	1610	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1611	fi
	1612	fi
	1613
	1614
[1289]	1615	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1616	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1617	then
	1618
[1289]	1619	# DOES THE DIRECTORY EXIST?
[1]	1620	if [[ ! -d $add_source_path ]]
	1621	then
[1779]	1622	printf "\n\n *** INFORMATIVE: additional source code directory"
[1]	1623	printf "\n \"$add_source_path\" "
	1624	printf "\n does not exist or is not a directory."
	1625	printf "\n No source code will be used from this directory!\n"
	1626	add_source_path=""
[931]	1627	if [[ $silent == false ]]
	1628	then
	1629	sleep 3
	1630	fi
[1]	1631	else
	1632
	1633	cd $add_source_path
[211]	1634	found=false
[1]	1635
	1636	Names=$(ls -1 *.f90 2>&1)
	1637	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1638	Names=$(ls -1 *.F90 2>&1)
	1639	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1640	Names=$(ls -1 *.F 2>&1)
	1641	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1642	Names=$(ls -1 *.f 2>&1)
	1643	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1644	Names=$(ls -1 *.c 2>&1)
	1645	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1646
	1647	cd - > /dev/null
	1648	cd SOURCES_FOR_RUN_$fname
	1649
[211]	1650	# COPY MAKEFILE IF EXISTING
	1651	if [[ -f $add_source_path/Makefile ]]
	1652	then
	1653	printf "\n\n *** user Makefile from directory"
	1654	printf "\n \"$add_source_path\" is used \n"
[931]	1655	if [[ $silent == false ]]
	1656	then
	1657	sleep 1
	1658	fi
[211]	1659	cp $add_source_path/Makefile .
	1660	fi
	1661
[1]	1662	for dateiname in $AddFilenames
	1663	do
	1664	if [[ -f $dateiname ]]
	1665	then
	1666	printf "\n +++ source code file \"$dateiname\" found in additional"
	1667	printf "\n source code directory \"$add_source_path\" "
[211]	1668	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1669	printf "\n from directory \"$source_path\"."
[1]	1670	locat=source; exit
	1671	fi
	1672
	1673	cp $add_source_path/$dateiname .
	1674	source_list="$source_list $dateiname"
	1675
[211]	1676	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1677	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1678	then
	1679	printf "\n\n +++ user file \"$dateiname\" "
	1680	printf "\n is not listed in Makefile \n"
	1681	locat=source; exit
	1682	else
	1683
	1684	if [[ $found = false ]]
[1]	1685	then
[211]	1686	found=true
	1687	printf "\n\n *** following user file(s) added to the"
	1688	printf " files to be translated:\n "
[1]	1689	fi
[211]	1690	printf "$dateiname "
[931]	1691	if [[ $silent == false ]]
	1692	then
	1693	sleep 0.5
	1694	fi
	1695
[1]	1696	fi
	1697	done
[211]	1698	[[ $found = true ]] && printf "\n"
[1]	1699	cd - > /dev/null
	1700	fi
	1701	fi
	1702
	1703
[1289]	1704	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1705	# TO THE LIST OF FILES TO BE COMPILED
[5]	1706	if [[ $restart_run != true && -n $package_list ]]
[1]	1707	then
	1708
	1709	cd $source_path
	1710
	1711	for package in $package_list
	1712	do
	1713
	1714	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1715
[1289]	1716	# DETERMINE FILES BELONGING TO THE PACKAGE
	1717	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1718	# THE NAME OF THE DIRECTORY
[1]	1719	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1720
	1721
[1289]	1722	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1723	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1724	for source_list_name in $package_source_list
	1725	do
	1726	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1727	then
	1728
[1289]	1729	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1730	ending=`echo $source_list_name \| cut -f2 -d.`
	1731	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1732	then
	1733	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1734	source_list="$source_list $source_list_name"
	1735	fi
	1736	fi
	1737	done
	1738	done
	1739
	1740	cd - > /dev/null
	1741	fi
	1742
	1743	fi # do_compile=true
	1744
	1745
[1289]	1746	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1747	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1748	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1749	then
	1750
[1289]	1751	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[1]	1752	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1753	then
[82]	1754	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1755	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1756	then
[82]	1757	cpp_options="$cpp_options -D__nec"
	1758	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1759	then
	1760	cpp_options="$cpp_options -D__lc"
[1]	1761	else
[82]	1762	cpp_options="$cpp_options -D__$localhost"
[1]	1763	fi
[83]	1764
[1289]	1765	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[1]	1766	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1767	then
[82]	1768	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1769	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1770	else
[82]	1771	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1772	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1773	fi
[83]	1774
[1289]	1775	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1776	if [[ -n $package_list ]]
	1777	then
	1778	for package in $package_list
	1779	do
	1780	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1781	then
	1782	if [[ $package != "dvrp_graphics+1PE" ]]
	1783	then
[82]	1784	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1785	else
[82]	1786	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1787	export use_seperate_pe_for_dvrp_output=true
	1788	fi
	1789	else
	1790	if [[ $package != "dvrp_graphics+1PE" ]]
	1791	then
[82]	1792	cpp_options="$cpp_options -D__$package"
[1]	1793	else
[82]	1794	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1795	export use_seperate_pe_for_dvrp_output=true
	1796	fi
	1797	fi
	1798	done
	1799	fi
[83]	1800
[1289]	1801	# SET DIRECTIVES GIVEN BY OPTION -D
[1]	1802	if [[ -n $cpp_opts ]]
	1803	then
	1804	for popts in $cpp_opts
	1805	do
[82]	1806	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1807	then
	1808	cpp_options="${cpp_options},-D__$popts=__$popts"
	1809	else
	1810	cpp_options="$cpp_options -D__$popts"
	1811	fi
[1]	1812	done
	1813	fi
	1814
	1815	else
	1816
	1817
[1289]	1818	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1819	if [[ $do_remote = false ]]
	1820	then
	1821	if [[ ! -f $executable ]]
	1822	then
	1823	printf "\n +++ executable file: $executable"
	1824	printf "\n does not exist"
	1825	locat=executable; exit
	1826	fi
	1827	fi
	1828	fi
	1829
	1830
[1289]	1831	# DETERMINE THE JOB MODE
[1491]	1832	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
[1]	1833	then
[1491]	1834	if [[ "$LOADLBATCH" = yes ]]
	1835	then
	1836	batch_job=.TRUE.
	1837	jobmo=BATCH
	1838	else
	1839	batch_job=.FALSE.
	1840	jobmo=INTERACTIVE
	1841	fi
[1]	1842	else
[1491]	1843	if [[ "$ENVIRONMENT" = BATCH ]]
	1844	then
	1845	batch_job=.TRUE.
	1846	jobmo=BATCH
	1847	else
	1848	batch_job=.FALSE.
	1849	jobmo=INTERACTIVE
	1850	fi
[1]	1851	fi
	1852
[1289]	1853	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1854	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1855	then
	1856	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1857	printf "\n please submit batch job using mrun option \"-b\" \n"
	1858	locat=normal; exit
	1859	fi
	1860
	1861
[1289]	1862	# CHECK, IF USER DEFINED A COMPILER
[1]	1863	if [[ "$compiler_name" = "" ]]
	1864	then
[82]	1865
[220]	1866	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1867	locat=compiler_name; exit
	1868
[1]	1869	fi
	1870
	1871
[1289]	1872	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1609]	1873
	1874	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
	1875	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
	1876	then
	1877	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
[1755]	1878	if [[ "$kennung" = "" ]]
[1753]	1879	then
	1880	kennung=$RANDOM
	1881	fi
[1609]	1882	else
	1883	kennung=$RANDOM
	1884	fi
	1885
[1]	1886	if [[ "$tmp_user_catalog" = "" ]]
	1887	then
[312]	1888	if [[ $localhost = ibmh ]]
[1]	1889	then
[312]	1890	tmp_user_catalog=$SCRATCH
[1]	1891	elif [[ $localhost = nech ]]
	1892	then
	1893	tmp_user_catalog=$WRKSHR
	1894	else
	1895	tmp_user_catalog=/tmp
	1896	fi
	1897	fi
	1898	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1899
	1900
[1289]	1901	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1902	if [[ "$tmp_data_catalog" = "" ]]
	1903	then
[622]	1904	if [[ $localhost = nech ]]
[1]	1905	then
	1906	tmp_data_catalog=$WRKSHR/mrun_restart_data
	1907	else
	1908	tmp_data_catalog=/tmp/mrun_restart_data
	1909	fi
	1910	fi
	1911
	1912
[1289]	1913	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1914	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1915	then
	1916	eval fopts=\"$fopts\"
	1917	eval lopts=\"$lopts\"
	1918	fi
	1919
	1920
[1289]	1921	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1922	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1923	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1779]	1924	XOPT="-X $numprocs"
[1]	1925
	1926
[1289]	1927	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1928	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1929	done=false
	1930	while [[ $done = false ]]
	1931	do
	1932	cputime=$cpumax
	1933	if (( $cputime == 0 ))
	1934	then
[246]	1935	if [[ $do_batch = true ]]
	1936	then
	1937	printf "\n +++ cpu-time is undefined"
	1938	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1939	printf "\n >>> "
	1940	read cputime 1>/dev/null 2>&1
	1941	else
	1942	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1943	fi
[1]	1944	else
	1945	done=true
	1946	fi
	1947	cpumax=$cputime
	1948	done
	1949
	1950	(( minuten = cputime / 60 ))
	1951	(( sekunden = cputime - minuten * 60 ))
	1952
	1953
[1289]	1954	# CHECK THE MEMORY DEMAND
[1]	1955	if [[ $do_batch = true ]]
	1956	then
	1957	done=false
	1958	while [[ $done = false ]]
	1959	do
	1960	if (( memory == 0 ))
	1961	then
	1962	printf "\n +++ memory demand is undefined"
	1963	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1964	printf "\n >>> "
	1965	read memory 1>/dev/null 2>&1
	1966	else
	1967	done=true
	1968	fi
	1969	done
	1970	fi
	1971
	1972
[1289]	1973	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	1974	if [[ $do_remote = true && -z $remote_username ]]
	1975	then
	1976	while [[ -z $remote_username ]]
	1977	do
	1978	printf "\n +++ username on remote host \"$host\" is undefined"
	1979	printf "\n >>> Please type username:"
	1980	printf "\n >>> "
	1981	read remote_username
	1982	done
	1983	mc="$mc -u$remote_username"
	1984	fi
	1985
[892]	1986	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	1987	if [[ "$login_init_cmd" != "" ]]
	1988	then
	1989	export init_cmds="${login_init_cmd};"
	1990	fi
[221]	1991
[892]	1992
[1289]	1993	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	1994	if [[ "$modules" != "" ]]
	1995	then
[678]	1996	if [[ $host = lctit ]]
	1997	then
	1998	export module_calls=". $modules"
	1999	else
	2000	export module_calls="module load ${modules};"
	2001	fi
[493]	2002	fi
	2003
[1289]	2004	# OUTPUT OF THE MRUN-HEADER
[1]	2005	calltime=$(date)
	2006	printf "\n"
[1101]	2007	printf "#------------------------------------------------------------------------# \n"
	2008	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	2009	printf "\| \| \n"
[1]	2010	spalte1="called on:"; spalte2=$localhost_realname
[1101]	2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	2012	if [[ $do_remote = true ]]
[1]	2013	then
[1289]	2014	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	2015	else
[1289]	2016	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	2017	fi
[1101]	2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2019	if [[ -n $numprocs ]]
	2020	then
[1106]	2021	if [[ $run_coupled_model = false ]]
	2022	then
	2023	spalte1="number of PEs:"; spalte2=$numprocs
	2024	else
	2025	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	2026	fi
[1101]	2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2028	fi
	2029	if [[ -n $tasks_per_node ]]
	2030	then
	2031	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	2033	if (( remaining_pes > 0 ))
	2034	then
	2035	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	2036	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2037	fi
[1]	2038	fi
[759]	2039	if [[ $maximum_parallel_io_streams != $numprocs ]]
	2040	then
	2041	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	2042	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	2043	fi
[622]	2044	if [[ $use_openmp = true ]]
[1]	2045	then
	2046	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	2047	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2048	fi
[1101]	2049	printf "\| \| \n"
[1]	2050	if [[ $do_compile = true ]]
	2051	then
[475]	2052	if [[ "$mopts" != "" ]]
	2053	then
[1101]	2054	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	2055	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2056	zeile=$(echo "$mopts" \| cut -c46-)
[475]	2057	while [[ "$zeile" != "" ]]
	2058	do
	2059	spalte1=""
[1101]	2060	spalte2=$(echo "$zeile" \| cut -c-45)
	2061	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2062	zeile=$(echo "$zeile" \| cut -c46-)
[475]	2063	done
	2064	fi
	2065
[1101]	2066	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	2067	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2068	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	2069	while [[ "$zeile" != "" ]]
	2070	do
	2071	spalte1=""
[1101]	2072	spalte2=$(echo "$zeile" \| cut -c-45)
	2073	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2074	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2075	done
	2076
[1101]	2077	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2079	zeile=$(echo "$fopts" \| cut -c46-)
[1]	2080	while [[ "$zeile" != "" ]]
	2081	do
	2082	spalte1=""
[1101]	2083	spalte2=$(echo "$zeile" \| cut -c-45)
	2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2085	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2086	done
	2087
[1101]	2088	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2090	zeile=$(echo "$lopts" \| cut -c46-)
[1]	2091	while [[ "$zeile" != "" ]]
	2092	do
	2093	spalte1=""
[1101]	2094	spalte2=$(echo "$zeile" \| cut -c-45)
	2095	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2096	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2097	done
	2098
[1101]	2099	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2100	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2101	zeile=$(echo "$modules" \| cut -c46-)
[493]	2102	while [[ "$zeile" != "" ]]
	2103	do
	2104	spalte1=""
[1101]	2105	spalte2=$(echo "$zeile" \| cut -c-45)
	2106	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2107	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2108	done
	2109
[1101]	2110	spalte1="main program:"; spalte2=$mainprog
	2111	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2112	else
	2113	spalte1=executable:; spalte2=$executable
[1101]	2114	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2115	fi
[1101]	2116	printf "\| \| \n"
	2117	spalte1="base name of files:"; spalte2=$fname
	2118	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2119	if [[ $fname != $afname ]]
	2120	then
[1101]	2121	spalte1="base name of input files:"; spalte2=$afname
	2122	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2123	fi
[1101]	2124	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2125	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2126	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2127	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2128
[1106]	2129	if [[ "$ocean_file_appendix" = true ]]
	2130	then
	2131	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2132	fi
	2133
[1]	2134	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2135	then
	2136	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2137	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2138	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2139	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2140	fi
	2141
	2142	if [[ $do_compile = true ]]
	2143	then
[1101]	2144	printf "\| \| \n"
	2145	printf "\| Files to be compiled: \| \n"
[1]	2146	zeile=$source_list
	2147	while [[ "$zeile" != "" ]]
	2148	do
[1101]	2149	linestart=$(echo $zeile \| cut -c-70)
	2150	printf "\| %-70s \| \n" "$linestart"
	2151	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2152	done
	2153	fi
[1101]	2154	printf "#------------------------------------------------------------------------#"
[1]	2155
	2156
	2157
[1289]	2158	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2159	if [[ $do_trace = true ]]
	2160	then
	2161	(( i = 0 ))
	2162	while (( i < iin ))
	2163	do
	2164	(( i = i + 1 ))
	2165	if (( i == 1 ))
	2166	then
	2167	printf "\n\n >>> INPUT-file assignments:\n"
	2168	fi
	2169	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2170	done
	2171	(( i = 0 ))
	2172	while (( i < iout ))
	2173	do
	2174	(( i = i + 1 ))
	2175	if (( i == 1 ))
	2176	then
	2177	printf "\n\n >>> OUTPUT-file assignments:\n"
	2178	fi
	2179	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2180	done
	2181	(( i = 0 ))
	2182	while (( i < iic ))
	2183	do
	2184	(( i = i + 1 ))
	2185	if (( i == 1 ))
	2186	then
	2187	printf "\n\n >>> INPUT-commands:\n"
	2188	fi
	2189	printf "\n ${in_command[$i]}"
	2190	done
	2191	(( i = 0 ))
	2192	while (( i < ioc ))
	2193	do
	2194	(( i = i + 1 ))
	2195	if (( i == 1 ))
	2196	then
	2197	printf "\n\n >>> OUTPUT-commands:\n"
	2198	fi
	2199	printf "\n ${out_command[$i]}"
	2200	done
	2201	fi
	2202
[1289]	2203	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2204	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2205	then
	2206	antwort=dummy
	2207	printf "\n\n"
[1101]	2208	printf " >>> everything o.k. (y/n) ? "
	2209	while read antwort
[1]	2210	do
[1101]	2211	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2212	then
	2213	printf " >>> everything o.k. (y/n) ? "
	2214	else
	2215	break
	2216	fi
[1]	2217	done
	2218	if [[ $antwort = n \|\| $antwort = N ]]
	2219	then
	2220	locat=user_abort; (( iec = 0 )); exit
	2221	fi
	2222	if [[ $do_batch = true ]]
	2223	then
	2224	printf " >>> batch-job will be created and submitted"
	2225	else
[1289]	2226	printf " >>> MRUN will now continue to execute on this machine"
[1]	2227	fi
	2228	fi
	2229
[1804]	2230
[1199]	2231	# DETERMINE PATH FOR MAKE DEPOSITORY
	2232	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2233	then
	2234
	2235	line=""
	2236	grep "%depository_path" $config_file > tmp_mrun
	2237	while read line
	2238	do
	2239	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2240	then
	2241	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2242	then
	2243	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2244	fi
	2245	fi
	2246	done < tmp_mrun
	2247
	2248	line=""
	2249	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2250	while read line
	2251	do
	2252	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2253	then
	2254	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2255	then
	2256	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2257	fi
	2258	fi
	2259	done < tmp_mrun
	2260
	2261	if [[ "$local_depository_path" = "" ]]
	2262	then
	2263	if [[ "$global_depository_path" != "" ]]
	2264	then
	2265	local_depository_path=$global_depository_path
	2266	else
	2267	printf "\n\n +++ no depository path found in configuration file"
	2268	printf "\n for local host \"$localhost\" "
	2269	printf "\n please set \"\%depository_path\" in configuration file\n"
	2270	locat=config_file; exit
	2271	fi
	2272	fi
	2273	eval local_depository_path=$local_depository_path
	2274	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2275	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2276
	2277
	2278	basename=`echo $mainprog \| cut -f1 -d"."`
	2279	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2280	if [[ ! -f $make_depository ]]
	2281	then
	2282	printf "\n"
	2283	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2284	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2285	fi
	2286
	2287	fi
	2288
	2289
[1289]	2290	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2291	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2292	if [[ $do_batch = false ]]
	2293	then
	2294
	2295
[1289]	2296	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2297	mkdir -p $TEMPDIR
	2298	chmod go+rx $TEMPDIR
	2299	tmpcreate=true
	2300
	2301
[1289]	2302	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2303	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2304	if [[ $do_compile = true ]]
	2305	then
	2306
	2307	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
	2308	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
	2309	if [[ $localhost = nech ]]
	2310	then
	2311	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
	2312	if mkdir -p $TEMPDIR_COMPILE
	2313	then
	2314	printf "\n *** \"$TEMPDIR_COMPILE\" "
	2315	printf "\n is generated as temporary directory for cross compiling\n"
	2316	else
	2317	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
	2318	printf "\n needed for cross compilation failed"
	2319	locat=compile
	2320	exit
	2321	fi
	2322	else
	2323	TEMPDIR_COMPILE=$TEMPDIR
	2324	fi
	2325
[1199]	2326	cp $make_depository $TEMPDIR_COMPILE
	2327	cd $TEMPDIR_COMPILE
	2328	tar -xf $make_depository > /dev/null 2>&1
	2329	cd - > /dev/null
[1]	2330
[1255]	2331	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2332	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2333	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2334	then
	2335	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2336	else
	2337	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2338	fi
[82]	2339
[1]	2340	else
[475]	2341
[1]	2342	cp $executable ${TEMPDIR}/a.out
[475]	2343
[1]	2344	fi
	2345
	2346
[1289]	2347	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2348	cd $TEMPDIR
[1]	2349	printf "\n *** changed to temporary directory: $TEMPDIR"
	2350
	2351
[1289]	2352	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
	2353	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
	2354	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
	2355	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
[1]	2356	(( i = 0 ))
	2357	while (( i < iout ))
	2358	do
	2359	(( i = i + 1 ))
	2360	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
	2361	then
	2362	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
	2363	else
	2364	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
	2365	fi
	2366	done
	2367
	2368
[1289]	2369	# IF REQUIRED, START WITH COMPILING
[1]	2370	if [[ $do_compile = true ]]
	2371	then
	2372
	2373
[1199]	2374	if [[ -f a.out ]]
[475]	2375	then
[82]	2376
[1199]	2377	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2378	printf "\n\n\n *** executable a.out found"
	2379	printf "\n no compilation required \n"
	2380
[1]	2381	else
[807]	2382
[1199]	2383	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2384	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2385	printf " *** compilation with make using following options:\n"
	2386	printf " make depository: $make_depository"
	2387	if [[ "$mopts" != "" ]]
	2388	then
	2389	printf " make options: $mopts\n"
	2390	fi
	2391	printf " compilername: $compiler_name\n"
	2392	printf " compiler options: $fopts\n"
	2393	printf " preprocessor directives: $cpp_options \n"
	2394	printf " linker options: $lopts \n"
	2395	if [[ "$modules" != "" ]]
	2396	then
	2397	printf " modules to be load: $modules \n"
	2398	fi
	2399	printf " source code files: $source_list \n"
[1]	2400
[1199]	2401	if [[ $localhost = nech ]]
	2402	then
	2403	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\" "
	2404	cp $TEMPDIR_COMPILE/a.out .
	2405	[[ $? != 0 ]] && compile_error=true
	2406	rm -rf $TEMPDIR_COMPILE
	2407	elif [[ $localhost = ibmh ]]
	2408	then
	2409	printf " compiler is called via ssh on \"plogin1\" \n"
	2410	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\" "
	2411	[[ ! -f a.out ]] && compile_error=true
[1289]	2412	continue # STATUS=1, IF a.out EXISTS
[1866]	2413	elif [[ $localhost = lcocean ]]
	2414	then
	2415	printf " compiler is called via ssh on \"ocean\" \n"
	2416	echo $PWD
	2417	ssh $SSH_PORTOPT ocean -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\" "
	2418	[[ ! -f a.out ]] && compile_error=true
	2419	continue # STATUS=1, IF a.out EXISTS
[1199]	2420	elif [[ $localhost = lcflow ]]
	2421	then
	2422	printf " compiler is called via ssh on \"flow\" \n"
[1201]	2423	/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]	2424	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
	2425	[[ "$check_for_file" = "" ]] && compile_error=true
[1289]	2426	continue # STATUS=1, IF a.out EXISTS
[1620]	2427	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2428	then
	2429	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2430	else
	2431	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2432	[[ "$module_calls" != "" ]] && eval $module_calls
	2433	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2434	fi
[181]	2435
[1199]	2436	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2437	then
	2438	printf "\n +++ error occured while compiling or linking"
	2439	locat=compile
	2440
[181]	2441	exit
[1199]	2442	else
[1289]	2443	printf "$dashes\n *** compilation finished \n"
[1199]	2444	fi
	2445
[1]	2446	fi
[1199]	2447
[1]	2448	fi
	2449
	2450
[1289]	2451	# PROVIDE THE INPUT FILES
	2452	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2453	(( i = 0 ))
	2454	while (( i < iin ))
	2455	do
	2456	(( i = i + 1 ))
	2457	if (( i == 1 ))
	2458	then
[1289]	2459	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2460	fi
	2461
	2462
[1289]	2463	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2464	if [[ "${transin[$i]}" = unavailable ]]
	2465	then
	2466	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2467	then
[1779]	2468	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2469	printf "\n is not available!"
[1]	2470	else
[1779]	2471	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2472	printf "\n is not available!"
[1]	2473	fi
	2474	continue
	2475	fi
	2476
[1289]	2477	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2478	files_for_pes=false; datentyp=file
	2479	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2480	then
	2481	files_for_pes=true; datentyp=directory
	2482	actionin[$i]=""
	2483	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2484	then
	2485	actionin[$i]=""
	2486	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
	2487	then
	2488	files_for_pes=true; datentyp=directory
	2489	actionin[$i]="ar"
	2490	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
	2491	then
	2492	actionin[$i]="ar"
	2493	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
	2494	then
	2495	files_for_pes=true; datentyp=directory
	2496	actionin[$i]="fl"
	2497	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
	2498	then
	2499	actionin[$i]="fl"
	2500	fi
	2501
	2502	if [[ $files_for_pes = true ]]
	2503	then
	2504	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2505	else
	2506	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2507	fi
	2508
[1289]	2509	# INPUT-FILE FOR A RESTART RUN.
	2510	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
	2511	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
[1]	2512	if [[ "${actionin[$i]}" = fl ]]
	2513	then
	2514	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
	2515	if [[ $files_for_pes = false ]]
	2516	then
	2517	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
	2518	then
	2519	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
	2520	got_tmp[$i]=true
	2521	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
	2522	then
	2523	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
	2524	printf "\n *** trying to use backup copy in \"$WORK\" "
	2525	cp $WORK/${frelin[$i]} ${localin[$i]}
	2526	else
	2527	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
	2528	printf "\n or \"$tmp_data_catalog\" does not exist!"
	2529	printf "\n *** trying to get copy from archive"
	2530	actionin[$i]=ar
	2531	fi
	2532	else
	2533	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
	2534	then
	2535	mkdir ${localin[$i]}
[149]	2536	cd $tmp_data_catalog/${frelin[$i]}
	2537	for file in $(ls *)
	2538	do
	2539	ln $file $TEMPDIR/${localin[$i]}
	2540	done
	2541	cd $TEMPDIR
[1]	2542	got_tmp[$i]=true
	2543	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
	2544	then
	2545	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
	2546	printf "\n *** trying to use backup copy in \"$WORK\" "
	2547	cp -r $WORK/${frelin[$i]} ${localin[$i]}
	2548	else
	2549	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
	2550	printf "\n or \"$tmp_data_catalog\" does not exist!"
	2551	printf "\n *** trying to get copy from archive"
	2552	actionin[$i]=ar
	2553	fi
	2554	fi
	2555	fi
	2556
	2557
[1289]	2558	# FILE IS STORED ON THE ARCHIVE SYSTEM
[1]	2559	if [[ "${actionin[$i]}" = ar ]]
	2560	then
	2561
	2562	if [[ $files_for_pes = false ]]
	2563	then
	2564	printf "\n file will be restored from archive-system ($archive_system)!"
	2565	else
	2566	printf "\n directory will be restored from archive-system ($archive_system)!"
	2567	fi
	2568
	2569	file_restored=false
	2570
	2571	if [[ $archive_system = asterix ]]
	2572	then
	2573	do_stagein=true
	2574	(( stagein_anz = 0 ))
	2575	while [[ $do_stagein = true ]]
	2576	do
	2577	if [[ $files_for_pes = false ]]
	2578	then
	2579	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
	2580	else
	2581	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
	2582	fi
	2583	cat STAGEIN_OUTPUT
	2584	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
	2585	then
	2586	file_restored=true
	2587	do_stagein=false
	2588	else
	2589	(( stagein_anz = stagein_anz + 1 ))
	2590	if (( stagein_anz == 10 ))
	2591	then
	2592	printf "\n +++ stagein stoped after 10 tries"
	2593	locat=stage
	2594	exit
	2595	fi
	2596	printf "\n +++ restoring from archive failed, trying again:"
	2597	sleep 900
	2598	fi
	2599	done
	2600	elif [[ $archive_system = DMF ]]
	2601	then
	2602	if [[ $files_for_pes = false ]]
	2603	then
	2604	printf "\n +++ restoring of single files impossible with $archive_system !\n"
	2605	locat=DMF
	2606	exit
	2607	else
	2608	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
	2609	cp -r $ARCHIVE/${frelin[$i]} $PWD
	2610	file_restored=true
	2611	fi
	2612	elif [[ $archive_system = tivoli ]]
	2613	then
	2614	if [[ $files_for_pes = false ]]
	2615	then
[1289]	2616	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
[1]	2617	else
	2618	(( inode = 0 ))
	2619	while (( inode < nodes ))
	2620	do
[1289]	2621	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
[1]	2622	(( inode = inode + 1 ))
	2623	done
	2624	fi
	2625	file_restored=true
	2626	elif [[ $archive_system = ut ]]
	2627	then
	2628	if [[ $files_for_pes = false ]]
	2629	then
	2630	cp $UT/${frelin[$i]} .
	2631	else
	2632	(( inode = 0 ))
	2633	while (( inode < nodes ))
	2634	do
	2635	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
	2636	(( inode = inode + 1 ))
	2637	done
	2638	fi
	2639	file_restored=true
	2640	else
	2641	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
	2642	locat=rearchive
	2643	exit
	2644	fi
	2645
	2646	if [[ $file_restored = true ]]
	2647	then
	2648
[1289]	2649	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
	2650	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
[1]	2651	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
	2652	if [[ $files_for_pes = false ]]
	2653	then
	2654	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
	2655	else
	2656	mkdir $tmp_data_catalog/${frelin[$i]}
	2657	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
	2658	fi
	2659	got_tmp[$i]=true
	2660
[1289]	2661	# PROVIDE THE FILE UNDER ITS LOCAL NAME
[1]	2662	mv ${frelin[$i]} ${localin[$i]}
	2663
	2664	fi
	2665	fi
	2666
	2667
[1289]	2668	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	2669	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	2670	then
	2671
	2672	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	2673	then
	2674
[1289]	2675	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2676	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	2677	printf "\n file will be provided for $numprocs processors"
	2678	mkdir ${localin[$i]}
	2679	ival=$numprocs
	2680	(( ii = 0 ))
	2681	while (( ii <= ival-1 ))
	2682	do
	2683	if (( ii < 10 ))
	2684	then
	2685	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2686	elif (( ii < 100 ))
	2687	then
	2688	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2689	elif (( ii < 1000 ))
	2690	then
	2691	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2692	else
	2693	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2694	fi
	2695	(( ii = ii + 1 ))
	2696	done
	2697
	2698	else
	2699
	2700	if [[ $files_for_pes = true ]]
	2701	then
	2702
[1289]	2703	# PROVIDE FILES FOR EACH CORE
	2704	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2705	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	2706	printf "\n providing $numprocs files for the respective processors"
	2707	mkdir ${localin[$i]}
[183]	2708	if [[ $link_local_input = true ]]
	2709	then
	2710	printf " using ln -f\n"
	2711	cd ${absnamein[$i]}
	2712	for file in $(ls *)
	2713	do
	2714	ln -f $file ${localin[$i]}
	2715	done
	2716	cd $TEMPDIR
	2717	fi
[1289]	2718
	2719	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[183]	2720	if [[ ! -f "${localin[$i]}/_0000" ]]
	2721	then
	2722	if [[ $link_local_input = true ]]
	2723	then
	2724	printf " ln failed for .../_0000, using cp...\n"
	2725	fi
	2726	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2727	fi
[1]	2728
	2729	else
[1289]	2730
	2731	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[183]	2732	if [[ $link_local_input = true ]]
	2733	then
	2734	printf " using ln -f\n"
	2735	ln -f ${absnamein[$i]} ${localin[$i]}
	2736	fi
	2737	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	2738	if [[ ! -f "${localin[$i]}" ]]
	2739	then
	2740	if [[ $link_local_input = true ]]
	2741	then
	2742	printf " ln failed, using cp...\n"
	2743	fi
	2744	cp ${absnamein[$i]} ${localin[$i]}
	2745	fi
[1]	2746	fi
	2747	fi
	2748	fi
	2749
	2750	done
	2751	if (( i != 0 ))
	2752	then
[1289]	2753	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	2754	fi
	2755
	2756
[1289]	2757	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	2758	(( i = 0 ))
	2759	while (( i < iic ))
	2760	do
	2761	(( i = i + 1 ))
	2762	if (( i == 1 ))
	2763	then
[1289]	2764	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	2765	fi
	2766	printf "\n >>> ${in_command[$i]}"
	2767	eval ${in_command[$i]}
	2768	if (( i == iic ))
	2769	then
[1289]	2770	printf "\n$dashes\n"
[1]	2771	fi
	2772	done
	2773
	2774
[1289]	2775	# SET THE REMAINING CPU-TIME
[1]	2776	cpurest=${cpumax}.
	2777
	2778
[260]	2779	# START DVR STREAMING SERVER
	2780	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	2781	then
	2782	if [[ "$dvr_server" != "" ]]
	2783	then
	2784
	2785	printf "\n\n *** preparing the dvr streaming server configuration file"
	2786
[1289]	2787	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	2788	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	2789	if [[ "$running_dvrserver_id" != "" ]]
	2790	then
	2791
[261]	2792	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	2793	printf "\n This server is used instead starting a new one!"
[261]	2794	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	2795
	2796	else
	2797
	2798	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	2799	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	2800	then
	2801	cp ${PALM_BIN}/.dvrserver.config .
	2802
[1289]	2803	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	2804	user_id=`id -u`
	2805	group_id=`id -g`
[1289]	2806
	2807	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	2808	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	2809	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	2810	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	2811	mv .dvrserver.3 .dvrserver.config
	2812	rm .dvrserver.1 .dvrserver.2
	2813
[1289]	2814	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	2815	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	2816	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	2817	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	2818	local_dvrserver_running=.TRUE.
	2819	else
	2820	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	2821	printf "\n \"$PALM_BIN\" "
	2822	locat=dvr
	2823	exit
	2824	fi
	2825
	2826	fi
	2827
	2828	else
	2829	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	2830	fi
	2831	fi
	2832
	2833
[1289]	2834	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2835	# (FILE ENVPAR WILL BE READ BY PALM)
[260]	2836	cat > ENVPAR << %%END%%
	2837	&envpar run_identifier = '$fname', host = '$localhost',
	2838	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
[759]	2839	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	2840	maximum_cpu_time_allowed = ${cpumax}.,
	2841	revision = '$global_revision',
[1402]	2842	local_dvrserver_running = $local_dvrserver_running,
	2843	batch_job = $batch_job /
[260]	2844
	2845	%%END%%
	2846
	2847
[1289]	2848	# STARTING THE EXECUTABLE
	2849	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	2850	PATH=$PATH:$TEMPDIR
	2851
[1779]	2852
	2853	if [[ $execute_command != "none" ]]
[359]	2854	then
	2855
[1779]	2856	printf "\n +++ branch still not realized"
	2857	locat=execution
	2858	exit
	2859
[693]	2860	else
	2861
[1779]	2862	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
	2863	if [[ "$mpi_debug" = true ]]
[1549]	2864	then
[1779]	2865	export MPI_CHECK_ARGS=1
	2866	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
[1549]	2867	fi
	2868
[1779]	2869	if [[ "$totalview" = true ]]
[1]	2870	then
[1779]	2871	printf "\n *** totalview debugger will be used"
	2872	tv_opt="-tv"
	2873	else
	2874	tv_opt=""
[1]	2875	fi
[1779]	2876
	2877	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
[1]	2878	then
	2879
[1779]	2880	#Interactive ALLINEA DEBUG seesion
	2881	if [[ "$ENVIRONMENT" != BATCH ]]
	2882	then
	2883	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2884	then
	2885	if [[ "$allinea" = true ]]
	2886	then
	2887	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
[1]	2888
[1779]	2889	ddt aprun -n $ii -N $tasks_per_node a.out
	2890	wait
	2891	fi
	2892	fi
	2893	fi
[1]	2894
[1779]	2895	if [[ $localhost = ibmh ]]
	2896	then
[1]	2897
[1779]	2898	# SETUP THE IBM MPI ENVIRONMENT
	2899	export MP_SHARED_MEMORY=yes
	2900	export AIXTHREADS_SCOPE=S
	2901	export OMP_NUM_THREADS=$threads_per_task
	2902	export AUTHSTATE=files
	2903	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
[1]	2904
[1779]	2905	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	2906	export MP_ADAPTER_USE=shared
	2907	export MP_CPU_USE=multiple
	2908	export MP_TIMEOUT=1200
[622]	2909
[1779]	2910	unset MP_TASK_AFFINITY
[1295]	2911
[1779]	2912	if [[ "$LOADLBATCH" = yes ]]
	2913	then
	2914	totalview poe a.out
	2915	else
	2916	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2917	export TVDSVRLAUNCHCMD=ssh
	2918	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2919	fi
[622]	2920
[1779]	2921	fi # END DEBUG MODE
[1289]	2922
[1779]	2923	else
	2924
	2925	# NORMAL EXECUTION
	2926	if [[ -n $numprocs ]]
[1]	2927	then
[1289]	2928
[1779]	2929	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	2930	if [[ $(echo $host \| cut -c1-3) = ibm ]]
[312]	2931	then
[1]	2932
[1779]	2933	# SETUP THE IBM MPI ENVIRONMENT
	2934	if [[ $host != ibmh && $host != ibmkisti ]]
[696]	2935	then
[1779]	2936	export MP_SHARED_MEMORY=yes
	2937	export AIXTHREAD_SCOPE=S
[696]	2938	export OMP_NUM_THREADS=$threads_per_task
[1779]	2939	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	2940	export AUTHSTATE=files
	2941	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	2942	# export MP_PRINTENV=yes
	2943
	2944	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	2945	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
	2946	export MP_WAIT_MODE=poll
	2947	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
[696]	2948	fi
[693]	2949
[1779]	2950	if [[ $host = ibmkisti ]]
[1]	2951	then
[1779]	2952	export LANG=en_US
	2953	export MP_SHARED_MEMORY=yes
	2954	if [[ $threads_per_task = 1 ]]
[343]	2955	then
[1779]	2956	export MP_SINGLE_THREAD=yes
	2957	export MEMORY_AFFINITY=MCM
[343]	2958	else
[1779]	2959	export OMP_NUM_THREADS=$threads_per_task
[343]	2960	fi
[1]	2961	fi
[1779]	2962
	2963	if [[ "$LOADLBATCH" = yes ]]
[1]	2964	then
[1779]	2965	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	2966	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
[1]	2967	then
[1779]	2968	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
[1]	2969	else
[1779]	2970	if [[ $run_coupled_model = false ]]
	2971	then
	2972	if [[ "$ocean_file_appendix" = true ]]
	2973	then
	2974	echo "precursor_ocean" > runfile_atmos
	2975	else
	2976	echo "precursor_atmos" > runfile_atmos
	2977	fi
	2978	else
	2979	(( iia = $numprocs_atmos / $threads_per_task ))
	2980	(( iio = $numprocs_ocean / $threads_per_task ))
	2981	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2982	printf "\n using $coupled_mode coupling"
	2983	printf "\n\n"
	2984	echo "coupled_run $iia $iio" > runfile_atmos
	2985	fi
	2986	poe ./a.out < runfile_atmos
[1]	2987	fi
[1779]	2988	else
	2989	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[331]	2990	then
[1779]	2991	poe a.out -procs $numprocs -nodes 1 -rmpool 0
	2992	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
	2993	then
	2994	if [[ -f $hostfile ]]
[331]	2995	then
[1779]	2996	cp $hostfile hostfile
[331]	2997	else
[1779]	2998	(( ii = 1 ))
	2999	while (( ii <= $numprocs ))
	3000	do
	3001	echo $localhost_realname >> hostfile
	3002	(( ii = ii + 1 ))
	3003	done
[331]	3004	fi
[1779]	3005	export MP_HOSTFILE=hostfile
	3006	if [[ $run_coupled_model = false ]]
	3007	then
	3008	if [[ "$ocean_file_appendix" = true ]]
	3009	then
	3010	echo "precursor_ocean" > runfile_atmos
	3011	else
	3012	echo "precursor_atmos" > runfile_atmos
	3013	fi
	3014	else
	3015	(( iia = $numprocs_atmos / $threads_per_task ))
	3016	(( iio = $numprocs_ocean / $threads_per_task ))
	3017	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3018	printf "\n using $coupled_mode coupling"
	3019	printf "\n\n"
	3020	echo "coupled_run $iia $iio" > runfile_atmos
	3021	fi
[331]	3022
[1779]	3023	poe ./a.out -procs $numprocs < runfile_atmos
[1289]	3024
[1]	3025	else
[1779]	3026	if [[ "$host_file" = "" ]]
	3027	then
	3028	printf "\n +++ no hostfile given in configuration file"
	3029	locat=config_file
	3030	exit
	3031	else
	3032	eval host_file=$host_file
	3033	fi
	3034	export MP_HOSTFILE=$host_file
	3035	poe a.out -procs $numprocs -tasks_per_node $numprocs
[1]	3036	fi
	3037	fi
[1779]	3038
	3039	elif [[ $host = nech ]] # running on NEC machines
[1]	3040	then
	3041
[1779]	3042	(( ii = nodes ))
	3043	if [[ $ii = 1 ]]
	3044	then
	3045	export F_ERRCNT=0 # acceptable number of errors before program is stopped
	3046	export MPIPROGINF=YES
	3047	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
	3048	echo "*** execution on single node with mpirun"
	3049	mpirun -np $numprocs ./a.out
	3050	else
	3051	(( i = 0 ))
	3052	while (( i < ii ))
	3053	do
	3054	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
	3055	(( i = i + 1 ))
	3056	done
[1]	3057
[1779]	3058	echo "#!/bin/sh" > mpi_exec_shell
	3059	echo " " >> mpi_exec_shell
	3060	echo "set -u" >> mpi_exec_shell
	3061	echo "F_ERRCNT=0" >> mpi_exec_shell
	3062	echo "MPIPROGINV=YES" >> mpi_exec_shell
	3063	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
	3064	echo "cpurest=$cpurest" >> mpi_exec_shell
	3065	echo "fname=$fname" >> mpi_exec_shell
	3066	echo "localhost=$localhost" >> mpi_exec_shell
	3067	echo "return_address=$return_address" >> mpi_exec_shell
	3068	echo "return_username=$return_username" >> mpi_exec_shell
	3069	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
	3070	echo "write_binary=$write_binary" >> mpi_exec_shell
	3071	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
	3072	echo " " >> mpi_exec_shell
	3073	echo "export F_ERRCNT" >> mpi_exec_shell
	3074	echo "export MPIPROGINV" >> mpi_exec_shell
	3075	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
	3076	echo "export cpurest" >> mpi_exec_shell
	3077	echo "export fname" >> mpi_exec_shell
	3078	echo "export localhost" >> mpi_exec_shell
	3079	echo "export return_address" >> mpi_exec_shell
	3080	echo "export return_username" >> mpi_exec_shell
	3081	echo "export tasks_per_node" >> mpi_exec_shell
	3082	echo "export write_binary" >> mpi_exec_shell
	3083	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
	3084	echo " " >> mpi_exec_shell
	3085	echo "exec ./a.out" >> mpi_exec_shell
[1]	3086
[1779]	3087	chmod u+x mpi_exec_shell
	3088	export MPIPROGINF=YES
	3089	mpirun -f multinode_config &
	3090	wait
[1]	3091
[1779]	3092	fi
[1622]	3093
[1779]	3094	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	3095	then
[1779]	3096
	3097	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	3098	# DOES NOT EXIST
[1866]	3099	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]
[179]	3100	then
[1779]	3101	if [[ -f $hostfile ]]
[1598]	3102	then
[1779]	3103	cp $hostfile hostfile
	3104	(( ii = $numprocs / $threads_per_task ))
	3105	[[ $ii = 0 ]] && (( ii = 1 ))
	3106	else
	3107	(( ii = 1 ))
	3108	while (( ii <= $numprocs / $threads_per_task ))
	3109	do
	3110	echo $localhost_realname >> hostfile
	3111	(( ii = ii + 1 ))
	3112	done
	3113	if (( $numprocs / $threads_per_task == 0 ))
	3114	then
	3115	echo $localhost_realname >> hostfile
	3116	fi
[1598]	3117	fi
[1779]	3118	eval zeile=\"`head -n $ii hostfile`\"
	3119	printf "\n *** running on: $zeile"
[179]	3120	fi
	3121
[1779]	3122	(( ii = $numprocs / $threads_per_task ))
	3123	[[ $ii = 0 ]] && (( ii = 1 ))
	3124	export OMP_NUM_THREADS=$threads_per_task
[1289]	3125
[1779]	3126	if [[ $threads_per_task != 1 ]]
[291]	3127	then
[1779]	3128	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	3129	# MAY ABORT
	3130	ulimit -s unlimited
	3131	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[291]	3132	fi
[1779]	3133	if [[ $run_coupled_model = false ]]
[1224]	3134	then
[1779]	3135	if [[ "$ocean_file_appendix" = true ]]
	3136	then
	3137	echo "precursor_ocean" > runfile_atmos
	3138	else
	3139	echo "precursor_atmos" > runfile_atmos
	3140	fi
	3141	printf "\n\n"
[1622]	3142
[1779]	3143	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	3144	then
	3145	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
	3146	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	3147	elif [[ $host = lcbullhh ]]
	3148	then
	3149	export OMPI_MCA_pml=cm
	3150	export OMPI_MCA_mtl=mxm
	3151	export OMPI_MCA_coll=^ghc
	3152	export OMPI_MCA_mtl_mxm_np=0
	3153	export MXM_RDMA_PORTS=mlx5_0:1
	3154	export MXM_LOG_LEVEL=ERROR
	3155	export OMP_NUM_THREADS=$threads_per_task
	3156	export KMP_AFFINITY=verbose,granularity=core,compact,1
	3157	export KMP_STACKSIZE=64m
[1622]	3158
[1779]	3159	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
[1622]	3160
[1779]	3161	elif [[ $host = lccrayf ]]
	3162	then
	3163	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
	3164	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
	3165	then
	3166	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	3167	elif [[ $host = lcflow ]]
	3168	then
	3169	mpirun -np $ii a.out < runfile_atmos
[1866]	3170	elif [[ $host = lcocean ]]
	3171	then
	3172	mpirun a.out $ROPTS < runfile_atmos
[1779]	3173	elif [[ $host = lcsb ]]
	3174	then
	3175	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
	3176	elif [[ $host = lckiaps ]]
	3177	then
[1940]	3178	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
[1779]	3179	elif [[ $host = lckyu* ]]
	3180	then
	3181	mpiexec -n $ii --stdin runfile_atmos ./a.out
	3182	else
	3183	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
	3184	fi
	3185
[164]	3186	else
	3187
[1779]	3188	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
	3189	(( iia = $numprocs_atmos / $threads_per_task ))
	3190	(( iio = $numprocs_ocean / $threads_per_task ))
	3191	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3192	printf "\n using $coupled_mode coupling"
	3193	printf "\n\n"
[164]	3194
[1779]	3195	if [[ $coupled_mode = "mpi2" ]]
[206]	3196	then
[1779]	3197	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
	3198	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
[197]	3199
[1779]	3200	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	3201	then
[206]	3202
[1779]	3203	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
	3204	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
	3205
	3206	else
	3207	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
	3208	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
	3209	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
	3210	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
	3211	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
	3212	fi
	3213	wait
	3214
[206]	3215	else
	3216
[1779]	3217	echo "coupled_run $iia $iio" > runfile_atmos
[164]	3218
[1779]	3219	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	3220	then
[206]	3221
[1779]	3222	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
[206]	3223
[1779]	3224	elif [[ $host = lck \|\| $host = lckordi ]]
	3225	then
[206]	3226
[1779]	3227	mpiexec -n $ii ./a.out < runfile_atmos &
[1108]	3228
[1779]	3229	elif [[ $host = lckyu* ]]
	3230	then
[1108]	3231
[1779]	3232	mpiexec -n $ii --stdin runfile_atmos ./a.out
[1108]	3233
[1779]	3234	elif [[ $host = lcmuk ]]
	3235	then
[1108]	3236
[1779]	3237	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
[1604]	3238
[1779]	3239	fi
	3240	wait
	3241	fi
[1604]	3242
[164]	3243	fi
[102]	3244
[1779]	3245	elif [[ $host = lckyoto ]]
[440]	3246	then
[1779]	3247	set -xv
	3248	export P4_RSHCOMMAND=plesh
	3249	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3250	if [[ "$ENVIRONMENT" = BATCH ]]
[505]	3251	then
[1779]	3252	if [[ "$cond2" = fujitsu ]]
	3253	then
	3254	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
	3255	elif [[ "cond2" = pgi ]]
	3256	then
	3257	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
	3258	else
	3259	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
	3260	fi
[505]	3261	else
[1779]	3262	if [[ "$cond2" = "" ]]
	3263	then
	3264	mpiruni_rsh -np $numprocs ./a.out # for intel
	3265	else
	3266	mpirun -np $numprocs ./a.out
	3267	fi
[505]	3268	fi
[1779]	3269	set +xv
	3270
	3271	elif [[ $host = lctit ]]
	3272	then
	3273	export OMP_NUM_THREADS=$threads_per_task
	3274	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3275	if [[ "$threads_per_task" != 1 ]]
[505]	3276	then
[1779]	3277	export MV2_ENABLE_AFFINITY=0
[505]	3278	fi
[1779]	3279	echo "----- PBS_NODEFILE content:"
	3280	cat $PBS_NODEFILE
	3281	echo "-----"
	3282	(( ii = $numprocs / $threads_per_task ))
	3283	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
	3284	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
[1289]	3285
[1779]	3286	else
	3287	mpprun -n $numprocs a.out
[678]	3288	fi
[1]	3289	else
[1779]	3290	a.out
[1]	3291	fi
[1289]	3292
[1779]	3293	fi # end normal (non-debug) execution
	3294
	3295	fi # end explicit execute_command or host-specific execute actions
	3296
[1289]	3297	if [[ $? != 0 ]]
[1]	3298	then
	3299
[1289]	3300	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3301	printf "\n +++ runtime error occured"
	3302	locat=execution
	3303	exit
[1289]	3304
[1]	3305	else
[260]	3306
[1289]	3307	printf "\n$dashes\n *** execution finished \n"
	3308
	3309	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3310	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3311	if [[ "$dvrserver_id" != "" ]]
	3312	then
	3313	kill $dvrserver_id
	3314	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3315
[1289]	3316	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3317	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3318	if [[ -d DATA_DVR ]]
	3319	then
[261]	3320
[1289]	3321	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3322	# DIRECTORY
[262]	3323	cp .dvrserver.config DATA_DVR
	3324
[1289]	3325	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3326	# SEQUENCE MODE DATA TOO)
[262]	3327	process_dvr_output -d DATA_DVR -f $fname -s
	3328
	3329	else
	3330
[1289]	3331	# PROCESS THE LOCAL OUTPUT
[262]	3332	process_dvr_output -l -d DATA_DVR -f $fname
	3333
	3334	fi
	3335
	3336	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3337	then
	3338
[1289]	3339	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3340	process_dvr_output -l -d DATA_DVR -f $fname
	3341
[260]	3342	fi
[1]	3343	fi
	3344
	3345
	3346
[1289]	3347	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3348	# BY EACH CORE INTO ONE FILE
[920]	3349	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3350	then
	3351	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3352	printf "\n 2d- and/or 3d-data may be incomplete!"
	3353	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3354	elif [[ "$combine_plot_fields" == true ]]
	3355	then
[1270]	3356	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3357	then
	3358	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
[1779]	3359	aprun -n 1 -N 1 combine_plot_fields${block}.x
[1270]	3360	else
	3361	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3362	combine_plot_fields${block}.x
	3363	fi
[920]	3364	else
[1289]	3365
	3366	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3367	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3368	# ??? koennen wir das streichen ???
[920]	3369	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3370	fi
[503]	3371
	3372
	3373
[1289]	3374	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3375	(( i = 0 ))
	3376	while (( i < ioc ))
	3377	do
	3378	(( i = i + 1 ))
	3379	if (( i == 1 ))
	3380	then
[1289]	3381	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3382	fi
	3383	printf "\n >>> ${out_command[$i]}"
	3384	eval ${out_command[$i]}
	3385	if (( i == ioc ))
	3386	then
[1289]	3387	printf "\n$dashes\n"
[1]	3388	fi
	3389	done
	3390
	3391
[1289]	3392	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3393	if [[ $do_trace = true ]]
	3394	then
	3395	printf "\n\n"
	3396	ls -al
	3397	fi
	3398
	3399
	3400
[1289]	3401	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3402	(( i = 0 ))
	3403	while (( i < iout ))
	3404	do
	3405	(( i = i + 1 ))
	3406	if (( i == 1 ))
	3407	then
[1289]	3408	printf "\n\n *** saving OUTPUT-files:\n$dashes"
[1]	3409	fi
	3410
[1289]	3411	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3412	files_for_pes=false; filetyp=file
	3413	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3414	then
	3415	files_for_pes=true; filetyp=directory
	3416	actionout[$i]=""
	3417	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3418	then
	3419	actionout[$i]=""
	3420	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
	3421	then
	3422	files_for_pes=true; filetyp=directory
	3423	actionout[$i]="ar"
	3424	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
	3425	then
	3426	actionout[$i]="ar"
	3427	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
	3428	then
	3429	files_for_pes=true; filetyp=directory
	3430	actionout[$i]="fl"
	3431	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
	3432	then
	3433	actionout[$i]="fl"
	3434	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3435	then
	3436	files_for_pes=true; filetyp=directory
	3437	actionout[$i]="tr"
	3438	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3439	then
	3440	actionout[$i]="tr"
	3441	fi
	3442
	3443	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3444	then
	3445	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3446	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3447	then
	3448	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3449	else
	3450
	3451
[1289]	3452	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3453	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3454	if [[ "${actionout[$i]}" = tr ]]
	3455	then
	3456	if [[ $localhost != $fromhost ]]
	3457	then
	3458	if [[ $files_for_pes = false ]]
	3459	then
	3460	cps=""
	3461	cst=""
	3462	else
	3463	cps=-c
	3464	cst="/"
	3465	fi
[622]	3466	if [[ $localhost = nech ]]
[1]	3467	then
	3468
[1289]	3469	# TRANSFER IN SEPERATE JOB
	3470	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3471	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3472	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3473	if [[ $files_for_pes = false ]]
	3474	then
	3475	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3476	else
	3477	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
	3478	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
	3479	fi
	3480
	3481	echo "set -x" > transfer_${localout[$i]}
	3482	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3483
	3484	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
	3485	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
	3486	printf "\n or higher cycle\n"
[1468]	3487	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
[82]	3488
[1]	3489	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3490
	3491	if [[ $localhost = nech ]]
	3492	then
[1094]	3493	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
[1]	3494	else
	3495	if [[ "$LOGNAME" = b323013 ]]
	3496	then
[1094]	3497	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3498	else
[1094]	3499	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3500	fi
	3501	fi
	3502
	3503	else
	3504
[1289]	3505	# TRANSFER WITHIN THIS JOB
[1]	3506	transfer_failed=false
[82]	3507	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3508	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
[1255]	3509	if [[ $localhost = lccrayb ]]
	3510	then
[1468]	3511	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1274]	3512	elif [[ $localhost = lccrayh ]]
	3513	then
[1468]	3514	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1620]	3515	elif [[ $localhost = lcbullhh ]]
	3516	then
	3517	ssh $usern@mlogin101 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1468]	3518	elif [[ $localhost = lcxe6 ]]
	3519	then
	3520	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1255]	3521	else
[1468]	3522	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3523	fi
[82]	3524	[[ $? != 0 ]] && transfer_failed=true
[1]	3525
[1289]	3526	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3527	if [[ $transfer_failed = true ]]
	3528	then
[1289]	3529	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3530	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3531
[1289]	3532	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3533	eval local_catalog=${pathout[$i]}
	3534	if [[ ! -d $local_catalog ]]
	3535	then
	3536	printf " *** local directory does not exist. Trying to create:\n"
	3537	printf " $local_catalog \n"
	3538	mkdir -p $local_catalog
	3539	fi
	3540	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3541	transfer_problems=true
	3542	fi
	3543	fi
	3544	else
	3545
[1289]	3546	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3547	actionout[$i]=""
	3548	fi
	3549	fi
	3550
	3551
[1289]	3552	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3553	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3554	if [[ "${actionout[$i]}" = tra ]]
	3555	then
	3556	if [[ $localhost != $fromhost ]]
	3557	then
[622]	3558	if [[ $localhost = ibmh \|\| $localhost = nech ]]
[1]	3559	then
	3560
[1289]	3561	# TRANSFER IN SEPERATE JOB
	3562	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3563	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3564	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3565	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3566
	3567	echo "set -x" > transfer_${localout[$i]}
	3568	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3569
	3570	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3571	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3572	printf "\n or higher cycle\n"
[1468]	3573	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
[82]	3574
[1]	3575	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3576
	3577	if [[ $localhost = nech ]]
	3578	then
[1094]	3579	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
[1]	3580	else
	3581	if [[ $LOGNAME = b323013 ]]
	3582	then
[1094]	3583	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3584	else
[1094]	3585	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3586	fi
	3587	fi
	3588
	3589	else
	3590
[1289]	3591	# TRANSFER WITHIN THIS JOB
[1]	3592	transfer_failed=false
[82]	3593	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3594	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3595	if [[ $localhost = lccrayb ]]
	3596	then
[1468]	3597	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1274]	3598	elif [[ $localhost = lccrayh ]]
	3599	then
[1468]	3600	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
	3601	elif [[ $localhost = lcxe6 ]]
	3602	then
	3603	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1255]	3604	else
[1468]	3605	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3606	fi
[82]	3607	[[ $? != 0 ]] && transfer_failed=true
[1]	3608
[1289]	3609	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3610	if [[ $transfer_failed = true ]]
	3611	then
[1289]	3612	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3613	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3614
[1289]	3615	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3616	eval local_catalog=${pathout[$i]}
	3617	if [[ ! -d $local_catalog ]]
	3618	then
	3619	printf " *** local directory does not exist. Trying to create:\n"
	3620	printf " $local_catalog \n"
	3621	mkdir -p $local_catalog
	3622	fi
	3623
	3624	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3625	transfer_problems=true
	3626	fi
	3627	fi
	3628	else
	3629
[1289]	3630	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3631	actionout[$i]=a
	3632	fi
	3633	fi
	3634
	3635
[1289]	3636	# OUTPUT-FILE FOR A RESTART-RUN.
	3637	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
	3638	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
	3639	# AS LAST ACTION, ARCHIVING IS INITIATED.
[1]	3640	if [[ "${actionout[$i]}" = fl ]]
	3641	then
	3642	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	3643	chmod g+rx $tmp_data_catalog
	3644	if [[ $files_for_pes = false ]]
	3645	then
	3646	printf "\n >>> OUTPUT: ${localout[$i]} to"
	3647	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
	3648	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
	3649	else
	3650	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
	3651	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
	3652	mkdir $tmp_data_catalog/${frelout[$i]}
[149]	3653	cd ${localout[$i]}
	3654	for file in $(ls *)
	3655	do
	3656	ln -f $file $tmp_data_catalog/${frelout[$i]}
	3657	done
	3658	cd $TEMPDIR
[1]	3659	fi
	3660
	3661
[1289]	3662	# CREATE AND SUBMIT ARCHIVING-JOB
[1]	3663	if [[ $store_on_archive_system = true ]]
	3664	then
	3665
	3666	if [[ $archive_system = asterix ]]
	3667	then
	3668	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3669	if [[ $files_for_pes = false ]]
	3670	then
	3671	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3672	else
	3673	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3674	fi
	3675	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3676	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
	3677	echo "then" >> archive_${frelout[$i]}
	3678	echo " do_stageout=false" >> archive_${frelout[$i]}
	3679	echo "else" >> archive_${frelout[$i]}
	3680	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
	3681	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
	3682	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
	3683	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
	3684	if [[ $files_for_pes = false ]]
	3685	then
	3686	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
	3687	else
	3688	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
	3689	fi
	3690	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
	3691	echo "fi" >> archive_${frelout[$i]}
	3692	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
	3693	elif [[ $archive_system = DMF ]]
	3694	then
	3695	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3696	if [[ $files_for_pes = false ]]
	3697	then
	3698	printf "\n +++ archiving of single files impossible with $archive_system !\n"
	3699	locat=DMF
	3700	exit
	3701	else
[1289]	3702	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
[1]	3703	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
	3704	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
	3705	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
	3706	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
	3707	fi
	3708	elif [[ $archive_system = tivoli ]]
	3709	then
	3710	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3711	if [[ $files_for_pes = false ]]
	3712	then
[1289]	3713	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
[1]	3714	echo "set -x" >> archive_${frelout[$i]}
	3715	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3716	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3717	else
	3718
	3719	echo "set -x" >> archive_${frelout[$i]}
	3720	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
	3721	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3722	cd $tmp_data_catalog
	3723	all_files=`ls -1 ${frelout[$i]}/*`
	3724	cd - > /dev/null
	3725	(( inode = 0 ))
	3726	(( tp1 = tasks_per_node + 1 ))
	3727	while (( inode < nodes ))
	3728	do
	3729	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
	3730	all_files=`echo $all_files \| cut -d" " -f$tp1-`
[1289]	3731	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
[1]	3732	(( inode = inode + 1 ))
	3733	done
	3734	fi
	3735	elif [[ $archive_system = ut ]]
	3736	then
	3737	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
	3738	if [[ $files_for_pes = false ]]
	3739	then
[1289]	3740	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
[1]	3741	echo "set -x" >> archive_${frelout[$i]}
	3742	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	3743	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	3744	else
	3745
	3746	echo "set -x" >> archive_${frelout[$i]}
	3747	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
	3748	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
	3749	cd $tmp_data_catalog
	3750	all_files=`ls -1 ${frelout[$i]}/*`
	3751	cd - > /dev/null
	3752	(( inode = 0 ))
	3753	(( tp1 = tasks_per_node + 1 ))
	3754	while (( inode < nodes ))
	3755	do
	3756	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
	3757	all_files=`echo $all_files \| cut -d" " -f$tp1-`
	3758	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
	3759	(( inode = inode + 1 ))
	3760	done
	3761	fi
	3762	elif [[ $archive_system = none ]]
	3763	then
	3764	printf " +++ archiving on $localhost not available!\n"
	3765	fi
	3766
	3767	if [[ $archive_system != none ]]
	3768	then
[1289]	3769	if [[ $localhost = nech ]]
[1]	3770	then
[1094]	3771	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
[1]	3772	fi
	3773	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	3774	fi
	3775	else
[399]	3776	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
[1]	3777	fi
	3778
	3779
[1289]	3780	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
	3781	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
	3782	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
	3783	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
	3784	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
[1]	3785	if [[ $files_for_pes = false ]]
	3786	then
	3787	cat /dev/null > ${pathout[$i]}
	3788	else
	3789	mkdir -p ${pathout[$i]}
	3790	fi
	3791
	3792	fi
	3793
	3794
[1289]	3795	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
	3796	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
	3797	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
[1]	3798	if [[ "${actionout[$i]}" = ar ]]
	3799	then
	3800	if [[ $files_for_pes = false ]]
	3801	then
	3802	printf "\n >>> OUTPUT: ${localout[$i]} to"
	3803	printf "\n ${pathout[$i]}"
	3804	printf "\n File will be copied to archive-system ($archive_system) !\n"
	3805	else
	3806	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	3807	printf "\n ${pathout[$i]}"
	3808	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
	3809	fi
	3810	mv ${localout[$i]} ${frelout[$i]}
	3811
	3812	file_saved=false
	3813
	3814	if [[ $archive_system = asterix ]]
	3815	then
	3816	do_stageout=true
	3817	(( stageout_anz = 0 ))
	3818	while [[ $do_stageout = true ]]
	3819	do
	3820	if [[ $files_for_pes = false ]]
	3821	then
	3822	stageout ${frelout[$i]} > STAGE_OUTPUT
	3823	else
	3824	stageout -t ${frelout[$i]} > STAGE_OUTPUT
	3825	fi
	3826	cat STAGE_OUTPUT
	3827	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
	3828	then
	3829	file_saved=true
	3830	do_stageout=false
	3831	else
	3832	if [[ $files_for_pes = false ]]
	3833	then
	3834	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
	3835	else
	3836	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
	3837	fi
	3838	(( stageout_anz = stageout_anz + 1 ))
	3839	if (( stageout_anz == 10 ))
	3840	then
	3841	printf "\n +++ stoped after 10 unsuccessful tries!"
	3842	archive_save=false
	3843	do_stageout=false
	3844	else
	3845	printf "\n *** new try to store on archive after 15 min:"
	3846	sleep 900
	3847	fi
	3848	fi
	3849	done
	3850	elif [[ $archive_system = DMF ]]
	3851	then
	3852	if [[ $files_for_pes = false ]]
	3853	then
	3854	printf "\n +++ archiving of single files impossible on $archive_system!\n"
	3855	locat=DMF
	3856	exit
	3857	else
	3858	rm -rf $ARCHIVE/${frelout[$i]}
	3859	cp -r ${frelout[$i]} $ARCHIVE
	3860	fi
	3861	file_saved=true
	3862	elif [[ $archive_system = tivoli ]]
	3863	then
[1289]	3864	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
	3865	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
	3866	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
	3867	# WHEN THE ARCHIVE-JOB IS EXECUTED
[1]	3868	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	3869	chmod g+rx $tmp_data_catalog
	3870	if [[ $files_for_pes = false ]]
	3871	then
	3872	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
	3873	else
	3874	mkdir $tmp_data_catalog/${frelout[$i]}
	3875	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
	3876	fi
	3877
[1289]	3878	# GENERATE AND SUBMIT BATCH-JOB
	3879	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
	3880	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
[1]	3881	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
	3882	if [[ $files_for_pes = false ]]
	3883	then
	3884	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3885	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
	3886	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	3887	else
	3888	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
	3889	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
	3890	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	3891	fi
	3892
[1094]	3893	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
[1]	3894	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	3895	file_saved=true
	3896
	3897	elif [[ $archive_system = ut ]]
	3898	then
[1289]	3899	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
	3900	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
	3901	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
	3902	# WHEN THE ARCHIVE-JOB IS EXECUTED
[1]	3903	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
	3904	chmod g+rx $tmp_data_catalog
	3905	if [[ $files_for_pes = false ]]
	3906	then
	3907	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
	3908	else
	3909	mkdir $tmp_data_catalog/${frelout[$i]}
	3910	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
	3911	fi
	3912
[1289]	3913	# GENERATE AND SUBMIT BATCH-JOB
	3914	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
	3915	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
[1]	3916	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
	3917	if [[ $files_for_pes = false ]]
	3918	then
	3919	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	3920	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
	3921	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	3922	else
	3923	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
	3924	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
	3925	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
	3926	fi
	3927
[1094]	3928	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
[1]	3929	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
	3930	file_saved=true
	3931
	3932	else
	3933	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
	3934	archive_save=false
	3935	fi
[1289]	3936
	3937	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
	3938	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
	3939	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
	3940	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
	3941	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
[1]	3942	if [[ $file_saved = true ]]
	3943	then
	3944	if [[ $files_for_pes = false ]]
	3945	then
	3946	cat /dev/null > ${pathout[$i]}
	3947	else
	3948	mkdir -p ${pathout[$i]}
	3949	fi
	3950	fi
[1289]	3951
[1]	3952	fi
	3953
[1289]	3954	# APPEND ON THIS MACHINE
[1]	3955	if [[ "${actionout[$i]}" = "a" ]]
	3956	then
[741]	3957	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	3958	then
	3959	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	3960	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	3961	else
	3962	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	3963	cat ${localout[$i]} >> ${pathout[$i]}
	3964	fi
[1]	3965	fi
	3966
[1289]	3967	# COPY ON THIS MACHINE
	3968	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	3969	# ON DIFFERENT FILE-SYSTEMS
[1]	3970	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	3971	then
	3972
[1289]	3973	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	3974	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	3975	then
	3976	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[149]	3977	if [[ $link_local_output = true ]]
	3978	then
	3979	printf " using ln -f\n"
	3980	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3981	fi
	3982	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3983	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	3984	then
	3985	if [[ $link_local_output = true ]]
	3986	then
	3987	printf " ln failed, using cp...\n"
	3988	fi
	3989	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3990	fi
[1]	3991	else
	3992	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[149]	3993	if [[ $link_local_output = true ]]
	3994	then
	3995	printf " using ln -f\n"
	3996	ln -f ${localout[$i]} ${pathout[$i]}
	3997	fi
	3998	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3999	if [[ ! -f "${pathout[$i]}" ]]
	4000	then
	4001	if [[ $link_local_output = true ]]
	4002	then
	4003	printf " ln failed, using cp...\n"
	4004	fi
	4005	cp ${localout[$i]} ${pathout[$i]}
	4006	fi
[1]	4007	fi
	4008
	4009	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	4010	then
	4011
[1289]	4012	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	4013	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	4014	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[149]	4015	if [[ $link_local_output = true ]]
	4016	then
	4017	printf " using ln -f\n"
	4018	mkdir ${pathout[$i]}
	4019	cd ${localout[$i]}
	4020	for file in $(ls *)
	4021	do
	4022	ln -f $file ${pathout[$i]}
	4023	done
	4024	cd $TEMPDIR
	4025	fi
[1289]	4026
	4027	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[149]	4028	if [[ ! -f "${pathout[$i]}/_0000" ]]
	4029	then
	4030	if [[ $link_local_output = true ]]
	4031	then
	4032	printf " ln failed for .../_0000, using cp...\n"
	4033	fi
	4034	cp -r ${localout[$i]} ${pathout[$i]}
	4035	fi
[1]	4036
	4037	fi
	4038	fi
	4039	done
	4040	if (( i != 0 ))
	4041	then
	4042	if [[ $transfer_problems = true ]]
	4043	then
[1289]	4044	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	4045	printf "\n +++ WARNING: some data transfers failed! \n"
	4046	else
[1289]	4047	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	4048	fi
	4049	fi
	4050
	4051
[1289]	4052	# IF REQUIRED, START A RESTART-JOB
	4053	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	4054	if [[ -f CONTINUE_RUN ]]
	4055	then
	4056
	4057	if [[ $archive_save = true ]]
	4058	then
	4059
[1289]	4060	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	4061	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	4062	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	4063	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
[1]	4064	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	4065	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	4066	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	4067	if [[ $(echo $mc \| grep -c "#") != 0 ]]
	4068	then
	4069	mc=`echo $mc \| sed 's/#/f/g'`
	4070	fi
	4071
	4072
[1289]	4073	# START THE RESTART-JOB
[1468]	4074	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
[1]	4075	echo " $mc"
[1289]	4076	printf "\n$dashes\n"
[1]	4077	if [[ $localhost != $fromhost ]]
	4078	then
	4079
[1620]	4080	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
[1]	4081	then
	4082	echo "*** ssh will be used to initiate restart-runs!"
[1468]	4083	echo " return_address=\"$return_address\" "
[1]	4084	echo " return_username=\"$return_username\" "
[1468]	4085	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
[1]	4086	then
[1190]	4087	if [[ $localhost = ibmh ]]
	4088	then
[1468]	4089	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1620]	4090	elif [[ $localhost = lcbullhh ]]
	4091	then
	4092	ssh $SSH_PORTOPT $usern@mlogin101 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1255]	4093	elif [[ $localhost = lccrayb ]]
	4094	then
[1468]	4095	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1274]	4096	elif [[ $localhost = lccrayh ]]
	4097	then
[1468]	4098	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
	4099	elif [[ $localhost = lcxe6 ]]
	4100	then
	4101	ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1190]	4102	else
[1468]	4103	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
[1190]	4104	fi
[1]	4105	else
[693]	4106	if [[ $localhost = ibmkisti ]]
	4107	then
[1468]	4108	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1255]	4109	elif [[ $localhost = lcflow ]]
	4110	then
[1468]	4111	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
[1866]	4112	elif [[ $localhost = lcocean ]]
	4113	then
	4114	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
[1255]	4115	elif [[ $localhost = lccrayb ]]
	4116	then
[1468]	4117	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[1274]	4118	elif [[ $localhost = lccrayh ]]
	4119	then
[1468]	4120	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[693]	4121	else
[1468]	4122	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
[693]	4123	fi
[1]	4124	fi
	4125	else
	4126	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	4127	locat=restart; exit
	4128	fi
	4129
[1289]	4130	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
[399]	4131	if [[ $queue = special1q ]]
	4132	then
	4133	sleep 120
	4134	else
	4135	sleep 30
	4136	fi
[1]	4137
	4138	else
	4139
[1289]	4140	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	4141	# USING SSH)
[1]	4142	cd $LOCAL_PWD
[1289]	4143	if [[ $localhost = lckyuh ]]
[108]	4144	then
[1103]	4145	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	4146	printf "\n please restart job manually using command:\n"
	4147	printf "\n \"$mc\" "
[108]	4148	else
[1289]	4149	eval $mc # THE ' MUST BE EVALUATED
[108]	4150	fi
[1]	4151	cd - > /dev/null
	4152	fi
[1103]	4153	if [[ $localhost = lckyuh ]]
	4154	then
[1289]	4155	printf "\n$dashes\n *** restart-run to be initiated manually\n"
[1103]	4156	else
[1289]	4157	printf "\n$dashes\n *** restart-run initiated \n"
[1103]	4158	fi
[1]	4159
	4160
[1289]	4161	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	4162	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	4163	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	4164	# MAY BE VERY HUGE)
[1]	4165	(( i = 0 ))
	4166	while (( i < iin ))
	4167	do
	4168	(( i = i + 1 ))
	4169	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	4170	then
	4171	rm -r $tmp_data_catalog/${frelin[$i]}
	4172	fi
	4173	done
	4174
	4175	else
	4176
	4177	printf "\n +++ no restart-run possible, since errors occured"
	4178	printf "\n during the archive process"
	4179	fi
	4180
	4181	fi
	4182
	4183
	4184
[1289]	4185	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	4186	if [[ "$email_notification" != "none" ]]
[1]	4187	then
	4188
	4189	if [[ $localhost != $fromhost ]]
	4190	then
	4191	if [[ -f CONTINUE_RUN ]]
	4192	then
	4193	echo "PALM restart run necessary" > email_text
	4194	echo "description header of actual run:" >> email_text
	4195	cat CONTINUE_RUN >> email_text
	4196	echo "mrun-command to restart:" >> email_text
	4197	echo "$mc" >> email_text
	4198	else
	4199	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	4200	fi
	4201	mail $email_notification < email_text
	4202	printf "\n *** email notification sent to \"$email_notification\" "
	4203	fi
	4204	fi
	4205
	4206
	4207
[1289]	4208	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	4209	cd $HOME
	4210	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	4211
	4212	else
	4213
[1289]	4214	# PREPARING ACTIONS,
	4215	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	4216
[1289]	4217	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[1468]	4218	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
[1]	4219	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
[79]	4220	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	4221	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	4222	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	4223	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	4224	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
	4225	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	4226	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	4227	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	4228	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	4229	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	4230	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	4231	if [[ $use_openmp = true ]]
	4232	then
[622]	4233	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	4234	fi
[759]	4235	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[397]	4236	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
[1]	4237	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	4238	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	4239	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	4240	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	4241	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	4242	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[920]	4243	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	4244	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	4245	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	4246	if [[ $do_remote = true ]]
	4247	then
	4248	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	4249	fi
	4250
	4251
[1289]	4252	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	4253	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	4254	then
	4255
	4256	printf "\n *** creating the executable for batch job\n"
	4257
[1289]	4258	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	4259	if [[ $host != $localhost ]]
	4260	then
	4261	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	4262	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	4263	locat=create_executable; exit
	4264	fi
	4265
	4266	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4267	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4268
	4269	cp $make_depository .
	4270	tar -xf $make_depository > /dev/null 2>&1
	4271	cp ../* . > /dev/null 2>&1
	4272
	4273	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	4274
	4275	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	4276	then
	4277	printf "\n +++ error occured while compiling or linking"
	4278	locat=compile
	4279	exit
	4280	fi
	4281
	4282	mv a.out ..
	4283	cd - > /dev/null 2>&1
	4284	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	4285
	4286	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	4287
	4288	fi
	4289
	4290
[1289]	4291	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	4292	jobfile=jobfile.$RANDOM
	4293
	4294
[1289]	4295	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	4296	echo "mkdir $TEMPDIR" >> $jobfile
	4297	echo "cd $TEMPDIR" >> $jobfile
	4298
	4299
[1289]	4300	# ACTIVATE ERROR-TRACEBACK
[1]	4301	if [[ $do_trace = true ]]
	4302	then
	4303	echo "set -x" >> $jobfile
	4304	else
	4305	echo "set +vx" >> $jobfile
	4306	fi
	4307
	4308
[1289]	4309	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	4310	if [[ "$init_cmds" != "" ]]
	4311	then
	4312	echo "$init_cmds" >> $jobfile
	4313	fi
	4314	if [[ "$module_calls" != "" ]]
	4315	then
	4316	echo "$module_calls" >> $jobfile
	4317	fi
	4318
	4319
[1289]	4320	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	4321	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	4322	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	4323	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	4324	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	4325	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	4326	# QUEUEING-SYSTEMS
[1866]	4327	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
[1]	4328	then
	4329
[1289]	4330	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	4331	if [[ $restart_run != true ]]
	4332	then
	4333	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	4334	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	4335	fi
[1]	4336
[1289]	4337	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	4338	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	4339	echo "set -x" >> $jobfile
[693]	4340	if [[ $host = $localhost ]]
	4341	then
[1199]	4342	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	4343	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	4344	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	4345	then
	4346	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	4347	else
	4348	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	4349	fi
[1199]	4350
[693]	4351	else
[1255]	4352	if [[ $host = ibmkisti ]]
[693]	4353	then
[1289]	4354	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	4355	echo "localdir=\`pwd\`" >> $jobfile
[1468]	4356	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1620]	4357	elif [[ $host = lcbullhh ]]
	4358	then
	4359	echo "localdir=\`pwd\`" >> $jobfile
	4360	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	4361
[1255]	4362	elif [[ $host = lccrayb ]]
	4363	then
	4364	echo "localdir=\`pwd\`" >> $jobfile
[1468]	4365	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	4366	elif [[ $host = lccrayh ]]
	4367	then
	4368	echo "localdir=\`pwd\`" >> $jobfile
[1468]	4369	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	4370
[1255]	4371	else
[1468]	4372	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	4373	fi
	4374	fi
[193]	4375	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	4376
[1289]	4377	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	4378	# WORKING DIRECTORY OF THE JOB
[193]	4379	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	4380	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	4381	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	4382	echo "execute_mrun=true" >> $jobfile
	4383	echo " " >> $jobfile
	4384
[191]	4385	else
	4386
[1289]	4387	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	4388	if [[ $do_compile = true ]]
	4389	then
	4390
	4391	source_catalog=SOURCES_FOR_RUN_$fname
	4392
[1289]	4393	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	4394	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	4395	echo "export SOURCES_COMPLETE=true" >> $jobfile
	4396	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	4397
	4398	for filename in $source_list
	4399	do
[1289]	4400	# BACKSLASH IS USED FOR MASKING
[191]	4401	echo "cat > $filename << \"%END%\"" >> $jobfile
	4402	cat $source_catalog/$filename >> $jobfile
	4403	echo " " >> $jobfile
	4404	echo "%END%" >> $jobfile
	4405	echo " " >> $jobfile
	4406	done
	4407
[1289]	4408	# BACKSLASH IS USED FOR MASKING
[191]	4409	echo "cat > Makefile << \"%END%\"" >> $jobfile
	4410	cat $source_catalog/Makefile >> $jobfile
[1]	4411	echo " " >> $jobfile
	4412	echo "%END%" >> $jobfile
	4413	echo " " >> $jobfile
	4414
[191]	4415	echo "cd - > /dev/null" >> $jobfile
[1]	4416
[191]	4417	fi
[1]	4418
	4419
[1289]	4420	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	4421	# BACKSLASH IS USED FOR MASKING
	4422	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	4423	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	4424	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	4425	if [[ $host = lckyuh ]]
	4426	then
[1289]	4427	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	4428	sed 's/frtpx/frt/g' $config_file >> $jobfile
	4429	else
	4430	sed 's/#$.*//g' $config_file >> $jobfile
	4431	fi
[191]	4432	echo "%END%" >> $jobfile
	4433	echo " " >> $jobfile
[1]	4434
	4435
[1289]	4436	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	4437	# BACKSLASH IS USED FOR MASKING
[1101]	4438	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	4439	if [[ $host = lckyuh ]]
	4440	then
	4441	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	4442	else
	4443	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	4444	fi
[1101]	4445	echo "%END%" >> $jobfile
[191]	4446	echo "chmod u+x $mrun_script_name" >> $jobfile
	4447	echo "execute_mrun=true" >> $jobfile
	4448	echo " " >> $jobfile
[1]	4449
	4450	fi
	4451
[191]	4452
[1289]	4453	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	4454	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	4455	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	4456	if [[ $do_remote = true ]]
	4457	then
	4458	(( i = 0 ))
	4459	while (( i < iin ))
	4460	do
	4461	(( i = i + 1 ))
	4462	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	4463	if [[ "${transin[$i]}" = job ]]
	4464	then
	4465	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	4466	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	4467	echo " " >> $jobfile
	4468	echo "%END%" >> $jobfile
	4469	else
[1468]	4470	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	4471	fi
	4472
[1289]	4473	# CHECK, IF FILE COULD BE CREATED
[1]	4474	echo "if [[ \$? = 1 ]]" >> $jobfile
	4475	echo "then" >> $jobfile
	4476	echo " echo \" \" " >> $jobfile
	4477	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	4478	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	4479	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	4480	echo " execute_mrun=false" >> $jobfile
	4481	echo "fi" >> $jobfile
	4482	done
	4483	fi
	4484
[1289]	4485	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	4486	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	4487	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	4488	echo "LOCAL_PWD=$working_directory" >> $jobfile
	4489	echo "export LOCAL_PWD" >> $jobfile
	4490
[1289]	4491	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	4492	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	4493	echo "export LOCAL_MRUN_PATH" >> $jobfile
	4494
[1289]	4495	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
[1547]	4496	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
	4497	# then
[1099]	4498	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	4499	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[1547]	4500	# fi
[1]	4501
[1289]	4502	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	4503	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	4504	echo "set -x" >> $jobfile
	4505	echo "queue=$queue" >> $jobfile
[1]	4506	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	4507	echo 'ls -al; echo `pwd`' >> $jobfile
	4508	echo "cd \$HOME" >> $jobfile
	4509	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	4510
	4511
	4512
	4513
[1289]	4514	# START THE JOB USING SUBJOB-COMMAND
[1]	4515	if [[ $silent = false ]]
	4516	then
	4517	printf "\n "
	4518	else
	4519	printf "\n\n"
	4520	fi
	4521
[1094]	4522	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]	4523	rm -rf $jobfile
	4524
	4525
[1289]	4526	fi # END OF REMOTE-PART

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