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source: palm/trunk/SCRIPTS/mrun @ 2556

Last change on this file since 2556 was 2365, checked in by kanani, 7 years ago
Vertical nesting implemented (SadiqHuq?)
Property svn:keywords set to `Id Rev`
File size: 146.2 KB

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	# ------------------
[1805]	24	#
[2186]	25	#
[1805]	26	# Former revisions:
	27	# -----------------
	28	# $Id: mrun 2365 2017-08-21 14:59:59Z scharf $
[2365]	29	# Added lckea & lckeam. KIT/IMK-IFU Garmisch cluster. LRZ (SadiqHuq)
	30	# Vertical grid nesting: set vnested_mode. -N Procs for fine and coarse grid.
	31	#
	32	# 2303 2017-07-04 12:26:18Z raasch
[2303]	33	# bugfix: setting default value for write_binary
	34	#
	35	# 2298 2017-06-29 09:28:18Z raasch
[2298]	36	# write_binary in ENVPAR has type LOGICAL now,
	37	# MPI2 coupling removed
	38	#
	39	# 2297 2017-06-28 14:35:57Z scharf
[2295]	40	# adjustments for using lcgeohu (cirrus @ HUB)
	41	# cpp_opts removed
	42	#
	43	# 2290 2017-06-19 11:03:06Z raasch
[2290]	44	# further test output removed
	45	#
	46	# 2286 2017-06-15 13:31:57Z raasch
[2286]	47	# test output for cycle number removed
	48	#
	49	# 2268 2017-06-09 10:34:09Z raasch
[2268]	50	# bugfix for calculating cycle numbers for output files in r2261
	51	#
	52	# 2262 2017-06-08 14:52:23Z raasch
[2262]	53	# bugfix for r2261
	54	#
	55	# 2261 2017-06-08 14:25:57Z raasch
[2261]	56	# unified cycle numbers for output files are used,
	57	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
	58	# creation of file OUTPUT_FILE_CONNECTIONS removed,
	59	# archive feature completely removed from the script,
	60	# nech related parts completely removed
	61	#
	62	# 2257 2017-06-07 14:07:05Z witha
[2257]	63	# adjustments for lceddy, removed lcflow-specific code
	64	#
	65	# 2186 2017-03-21 05:36:31Z raasch
[1867]	66	#
[2186]	67	# 2185 2017-03-21 05:09:29Z raasch
	68	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
	69	#
[2150]	70	# 2148 2017-02-09 16:56:42Z scharf
	71	# changed allocation of resources for lcbullhh in srun command
	72	#
[2142]	73	# 2141 2017-02-06 10:19:32Z gronemeier
	74	# made check for existing files language independent
	75	#
[1945]	76	# 1944 2016-06-15 06:29:00Z raasch
	77	# adjustments for using HLRN ssh-keys
	78	#
[1941]	79	# 1940 2016-06-14 05:15:20Z raasch $
	80	# adjustments for lckiaps
	81	#
[1867]	82	# 1866 2016-04-15 06:50:59Z raasch
	83	# adjusted for lcocean
[1805]	84	#
[1842]	85	# 1841 2016-04-07 19:14:06Z raasch
	86	# script now running under bash
	87	#
[1805]	88	# 1804 2016-04-05 16:30:18Z maronga
[1779]	89	# test: implementing an execute mechanism where the execute command is given in the
	90	# configuration file
	91	# ROPTS removed from execution commands
	92	# Warnings about missing optional files or user code changed to informative messages
[1804]	93	# Removed parameter file check
[1305]	94	#
[1756]	95	# 1755 2016-02-22 13:53:39Z maronga
	96	# Minor bugfix to last commit
	97	#
[1754]	98	# 1753 2016-02-22 13:49:49Z maronga
	99	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
	100	#
[1623]	101	# 1622 2015-07-20 06:21:36Z heinze
	102	# bugfix for Mistral (lcbullhh)
	103	#
	104	# 1621 2015-07-17 11:39:33Z heinze
[1621]	105	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
[1200]	106	#
[1610]	107	# 1609 2015-07-03 15:37:58Z maronga
	108	# Modified the random number of the temporary working directory to match the
	109	# queuing system number on HLRN-III (lccray*).
	110	#
[1605]	111	# 1604 2015-06-23 15:48:03Z suehring
	112	# Enable coupled runs for lcmuk
	113	#
[1599]	114	# 1598 2015-05-29 06:45:40Z raasch
	115	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
	116	#
[1550]	117	# 1549 2015-01-30 14:26:16Z suehring
	118	# Enable interactive debug sessions with allinea debugger
	119	#
[1548]	120	# 1547 2015-01-29 15:09:12Z witha
	121	# adjustments for ForWind computing cluster (lcflow)
	122	#
[1492]	123	# 1491 2014-11-12 08:12:57Z heinze
	124	# correct setting of batch_job allowed for ibm-machines
	125	#
[1469]	126	# 1468 2014-09-24 14:06:57Z maronga
	127	# Typo removed (addres->address)
	128	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
	129	# Added support for restart runs (remote) for lcxe6
	130	#
[1443]	131	# 1442 2014-07-28 07:09:10Z raasch
	132	# default queues for HLRN-III (lccrayb/lccrayh) defined
	133	#
[1423]	134	# 1422 2014-07-02 10:01:25Z kanani
	135	# automatic restarts enabled for lccrayb,
	136	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
	137	#
[1421]	138	# 1420 2014-06-10 06:24:14Z raasch
	139	# -j1 option added to aprung command for lccrayf (CSC)
	140	#
[1403]	141	# 1402 2014-05-09 14:25:13Z raasch
	142	# batch_job added to envpar-NAMELIST
	143	#
[1358]	144	# 1357 2014-04-11 15:02:03Z witha
	145	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
	146	# possible)
	147	#
[1328]	148	# 1320 2014-03-20 08:40:49Z raasch
	149	# check namelist file set false by default
	150	#
[1305]	151	# 1304 2014-03-12 10:29:42Z raasch
	152	# ulimit option changed from -Ss to -s
	153	#
	154	# bugfix: missing "fi" in r1289
	155	#
[1290]	156	# 1289 2014-03-04 07:12:34Z raasch
	157	# comments translated to English
	158	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	159	# export of variables for palm and interpret_config removed
	160	#
[1282]	161	# 1281 2014-02-01 07:55:49Z raasch
	162	# rsync-copy restricted to Cray machines, since command is unavailable on some
	163	# other systems
	164	#
[1280]	165	# 1279 2014-01-28 12:10:14Z raasch
	166	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	167	# in order to remove annoying restrictions concerning the number of processors which
	168	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	169	# restriction, one of the nodes will be filled with less than the given number of
	170	# tasks per node. A respective warning is given.
	171	#
[1275]	172	# 1274 2014-01-09 13:14:54Z heinze
	173	# adjustments for lccrayh
	174	#
[1273]	175	# 1272 2014-01-08 10:19:32Z witha
	176	# small adjustment for lcflow
	177	#
[1271]	178	# 1270 2013-12-16 11:05:01Z fricke
	179	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	180	#
[1256]	181	# 1255 2013-11-07 14:43:35Z raasch
	182	# further adjustments for lccrayb remote access
	183	#
[1242]	184	# 1241 2013-10-30 11:36:58Z heinze
	185	# Enable use of nudging input and input of large scale forcing from
	186	# external files
	187	#
[1230]	188	# 1229 2013-09-20 06:55:19Z raasch
	189	# further adjustments for lccrayb
	190	#
[1225]	191	# 1224 2013-09-16 07:27:23Z raasch
	192	# first adjustments for lccrayb
	193	#
[1211]	194	# 1210 2013-08-14 10:58:20Z raasch
	195	# fftw support added
	196	#
[1203]	197	# 1201 2013-07-10 16:17:59Z witha
	198	# adjustments for Forwind cluster (lcflow)
	199	#
[1200]	200	# 1199 2013-07-05 14:52:22Z raasch
[1199]	201	# adjustments for CSC Helsinki (lccrayf),
	202	# executables for batch jobs can be created in advance, in order to avoid calling
	203	# the compiler within the batch job (only works if batch jobs are submitted on
	204	# local host)
[1104]	205	#
[1191]	206	# 1190 2013-06-25 09:39:21Z heinze
	207	# enable use of automatic restarts for ibmh
[1185]	208	# use of cluster/express queue enabled (ibmh)
[1104]	209	#
[1125]	210	# 1124 2013-04-09 15:46:52Z raasch
	211	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	212	# side effect may lead to data loss while getopts is reading the script-option arguments
	213	#
[1123]	214	# 1122 2013-04-09 08:37:16Z heinze
	215	# Bugfix: change type of variable last_char
	216	#
[1121]	217	# 1119 2013-04-05 15:11:19Z raasch
	218	# Bugfix for setting -T option for subjob
	219	#
[1109]	220	# 1108 2013-03-05 07:03:32Z raasch
	221	# bugfix for coupled runs on lckyut/lckyuh
	222	#
[1107]	223	# 1106 2013-03-04 05:31:38Z raasch
	224	# --stdin argument for mpiexec on lckyuh
	225	# -y and -Y settings output to header
	226	#
[1104]	227	# 1103 2013-02-20 02:15:53Z raasch
[1103]	228	# default script runs again under ksh, because of unsolved problems with read
	229	# from stdin: when bash script is called from a ksh, message "read error: 0:
	230	# Resource temporarily unavailable" appears and script does not stop,
	231	# further bash compatibility adjustments,
	232	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	233	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	234	#
[1102]	235	# 1101 2013-02-17 10:20:21Z raasch
	236	# script now running under bash instead of ksh, which required small adjustments
	237	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	238	# read from stdin),
	239	# cross compilername on lckyuh compute nodes replaced by real compiler name
	240	#
[1100]	241	# 1099 2013-02-10 01:47:43Z raasch
	242	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	243	# and for Forwind cluster (lcflow)
	244	# small further adjustments for lckyut
	245	#
[1096]	246	# 1094 2013-02-03 01:52:12Z raasch
	247	# explicit ssh/scp port can be set in config file with environment variable
	248	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	249	# decalpha parts (yonsei) removed
	250	#
[1091]	251	# 2013-02-02 07:06:13Z raasch
[1099]	252	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	253	#
[1084]	254	# 1083 2013-01-04 10:22:09Z maronga
	255	# bugfix in parameter file check (read %cpp_options was missing)
	256	#
[1070]	257	# 1069 2012-11-28 16:18:43Z maronga
	258	# bugfix: coupling mode was always set to mpi2, typos removed
	259	#
[1059]	260	# 1058 2012-11-21 07:00:35Z raasch
	261	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	262	# nodes
	263	#
[1047]	264	# 1046 2012-11-09 14:38:45Z maronga
	265	# code put under GPL (PALM 3.9)
	266	#
[1090]	267	# 21/03/94 - Siggi - first version finished
	268	# 03/03/94 - Siggi - script development started
	269	#
[1059]	270	#--------------------------------------------------------------------------------#
[1090]	271	# mrun - script for running PALM jobs
	272	#--------------------------------------------------------------------------------#
[1]	273
[1047]	274
[1]	275
[1289]	276	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	277
[1289]	278	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	279	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	280	# (TOO MANY ARGUMENTS - PROBLEM)
	281	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	282
	283	AddFilenames=""
	284	additional_conditions=""
	285	add_source_path=""
	286	afname=""
[1320]	287	check_namelist_files=false
[920]	288	combine_plot_fields=true
[1]	289	compiler_name=""
	290	cond1=""
	291	cond2=""
	292	config_file=.mrun.config
[206]	293	coupled_dist=""
[82]	294	cpp_options=""
[1]	295	cpumax=0
	296	cpurest=0
[1199]	297	create_executable_for_batch=false
[1]	298	delete_temporary_catalog=true
	299	do_batch=false
	300	do_compile=true
	301	do_remote=false
	302	do_stagein=true
	303	do_stageout=true
	304	do_trace=false
[352]	305	email_notification="none"
[1]	306	exclude=""
	307	executable=""
[1779]	308	execute_command="none"
[1]	309	execution_error=false
[1210]	310	fftw_inc=""
	311	fftw_lib=""
	312	fftw_support=false
[2297]	313	fname=test
[1]	314	fromhost=""
[78]	315	global_revision=""
[122]	316	group_number=none
[1]	317	host=""
	318	host_file=""
	319	hp=""
	320	input_list=""
	321	interpreted_config_file=""
[164]	322	job_catalog="~/job_queue"
[1]	323	job_on_file=""
	324	keep_data_from_previous_run=false
[183]	325	link_local_input=false
[149]	326	link_local_output=false
[1]	327	localhost_realname=$(hostname)
[260]	328	local_dvrserver_running=.FALSE.
[1]	329	locat=normal
	330	mainprog=""
	331	makefile=""
[759]	332	max_par_io_str=""
[1]	333	mc=$0
	334	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	335	do
	336	mc=`echo $mc \| cut -f2- -d"/"`
	337	done
[493]	338	module_calls=""
[1]	339	mrun_script_name=$mc
[2365]	340	vnested_dist=""
	341	vnested_mode="vnested_twi"
[82]	342	netcdf_inc=""
	343	netcdf_lib=""
[1]	344	netcdf_support=false
	345	node_usage=default
	346	numprocs=""
[206]	347	numprocs_atmos=0
	348	numprocs_ocean=0
[2365]	349	numprocs_crse=0
	350	numprocs_fine=0
[1]	351	OOPT=""
	352	openmp=false
	353	output_list=""
	354	package_list=""
	355	queue=none
	356	read_from_config=""
[5]	357	restart_run=false
[622]	358	if [[ `hostname` = rte10 ]]
[1]	359	then
[1468]	360	return_address=133.5.185.60
	361	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[693]	362	elif [[ `hostname` = climate0 ]]
	363	then
[1468]	364	return_address=165.132.26.68
	365	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1866]	366	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
	367	then
	368	return_address="schultzl-Latitude-E6540"
	369	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1021]	370	elif [[ `hostname` = urban00 ]]
	371	then
[1468]	372	return_address=147.46.30.151
	373	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[622]	374	else
[1468]	375	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	376	fi
	377	return_password=""
	378	return_username=$LOGNAME
	379	remotecall=false
	380	remote_username=""
[102]	381	run_coupled_model=false
[1]	382	run_mode=""
[2365]	383	run_vnested_model=false
[1289]	384	dashes=" ----------------------------------------------------------------------------"
[1]	385	silent=false
	386	source_list=""
	387	source_path=SOURCE
	388	tasks_per_node=""
	389	threads_per_task=1
	390	tmpcreate=false
	391	tmp_data_catalog=""
	392	transfer_problems=false
	393	usern=$LOGNAME
[377]	394	use_openmp=false
[1289]	395	version="MRUN 2.1 Rev$Rev: 2365 $"
[1]	396	working_directory=`pwd`
[2303]	397	write_binary=false
[1]	398	TOPT=""
	399	XOPT=""
	400	zeit=$( date \| cut -c 12-19 )
	401
[1124]	402	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	403	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	404	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	405	# SCRIPT-OPTION ARGUMENTS
[2261]	406	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes run_number sekunden tp1
[1]	407
[1289]	408	# ERROR HANDLING IN CASE OF EXIT
[83]	409	trap 'rm -rf $working_directory/tmp_mrun
[1289]	410	if [[ $locat != normal && $locat != control_c ]]
[1]	411	then
	412
[1289]	413	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	414	(( i = 0 ))
	415	while (( i < iec ))
	416	do
	417	(( i = i + 1 ))
	418	printf "\n *** Execution of ERROR-command:\n"
	419	printf " >>> ${err_command[$i]}\n"
	420	eval ${err_command[$i]}
	421	done
[1101]	422	if [[ -n $interpreted_config_file ]]
	423	then
[1]	424	rm -rf $interpreted_config_file
	425	fi
[1101]	426	if [[ -n .mrun_environment ]]
	427	then
[71]	428	rm -rf .mrun_environment
	429	fi
[1]	430	if [[ $tmpcreate = true ]]
	431	then
[2147]	432	# printf "\n *** Contents of \"$TEMPDIR\":\n"
	433	# ls -al; cd
[1]	434	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	435	fi
[260]	436	if [[ "$dvrserver_id" != "" ]]
	437	then
	438	echo "+++ killing dvrserver_id=$dvrserver_id"
	439	kill $dvrserver_id
	440	fi
[1]	441	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	442	then
	443	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	444	fi
	445	printf "\n\n+++ MRUN killed \n\n"
	446	elif [[ $locat != control_c ]]
	447	then
	448	printf "\n\n --> all actions finished\n\n"
	449	printf " Bye, bye $usern !!\n\n"
	450	fi' exit
	451
	452
[1289]	453	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	454	trap 'rm -rf $working_directory/tmp_mrun
[807]	455	rm -rf $working_directory/tmp_check_namelist_files
[69]	456	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	457	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	458	then
	459	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	460	fi
[260]	461	if [[ "$dvrserver_id" != "" ]]
	462	then
	463	echo "+++ killing dvrserver_id=$dvrserver_id"
	464	kill $dvrserver_id
	465	fi
[1]	466	printf "\n+++ MRUN killed by \"^C\" \n\n"
	467	locat=control_c
	468	exit
	469	' 2
	470
	471
[22]	472	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	473	# BEEN SET
	474	if [[ "$PALM_BIN" = "" ]]
	475	then
	476	printf "\n +++ environment variable PALM_BIN has not been set"
	477	printf "\n please set it to the directory where the PALM scripts are located"
	478	locat=palm_bin; exit
	479	fi
[180]	480	export PATH=$PALM_BIN:$PATH
[22]	481
	482
[1]	483
[1289]	484	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	485	# WHICH WILL BE USED TO START RESTART-JOBS
[2365]	486	while getopts :a:bBc:Cd:Fg:G:h:H:i:kK:m:M:n:N:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
[1]	487	do
	488	case $option in
	489	(a) afname=$OPTARG;;
	490	(b) do_batch=true; mc="$mc -b";;
	491	(B) delete_temporary_catalog=false; mc="$mc -B";;
	492	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	493	(C) restart_run=true; mc="$mc -C";;
[1]	494	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[79]	495	(F) job_on_file="-D"; mc="$mc -F";;
[122]	496	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	497	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	498	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	499	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	500	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	501	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	502	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	503	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	504	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	505	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
[2365]	506	(N) run_vnested_model=true; vnested_dist=$OPTARG; mc="$mc -N'$OPTARG'";;
[1]	507	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	508	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	509	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	510	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	511	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	512	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
[1468]	513	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
[1]	514	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	515	(S) read_from_config=false; mc="$mc -S";;
	516	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	517	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	518	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	519	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	520	(v) silent=true; mc="$mc -v";;
[759]	521	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	522	(x) do_trace=true;set -x; mc="$mc -x";;
	523	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	524	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	525	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	526	(z) check_namelist_files=false; mc="$mc -z";;
[920]	527	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	528	(\?) printf "\n +++ unknown option $OPTARG \n"
	529	printf "\n --> type \"$0 ?\" for available options \n"
	530	locat=parameter;exit;;
	531	esac
	532	done
	533
	534
[1289]	535	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	536	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	537	(( to_shift = $OPTIND - 1 ))
	538	shift $to_shift
[1]	539
[1289]	540	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	541	if [[ "$1" = "?" ]]
	542	then
	543	(printf "\n *** mrun can be called as follows:\n"
[2295]	544	printf "\n $mrun_script_name -b -c.. -d.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -Z <modus> \n"
[1]	545	printf "\n Description of available options:\n"
	546	printf "\n Option Description Default-Value"
	547	printf "\n -a base name of input files equiv. -d"
	548	printf "\n -b batch-job on local machine ---"
	549	printf "\n -B do not delete temporary directory at end ---"
	550	printf "\n -c configuration file .mrun.config"
	551	printf "\n -d base name of files attached to program test"
	552	printf "\n -F create remote job file only ---"
	553	printf "\n -h execution host $localhost_realname"
	554	printf "\n -i INPUT control list \"\" "
	555	printf "\n -k keep data from previous run"
	556	printf "\n -K additional conditions for controling"
	557	printf "\n usage of conditional code and"
	558	printf "\n env-variables in configuration file \"\" "
	559	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	560	printf "\n -M Makefile name Makefile"
	561	printf "\n -n node usage (shared/not_shared) depending on -h"
[2365]	562	printf "\n -N Vertical grid nesting. Number of"
	563	printf "\n PE for Coarse and Fine grid"
[1]	564	printf "\n -o OUTPUT control list \"\" "
[1304]	565	printf "\n -O threads per openMP task ---"
[1]	566	printf "\n -p software package list \"\" "
	567	printf "\n -q queue \"$queue\" "
	568	printf "\n -r run control list (combines -i -o) \"\" "
	569	printf "\n -s filenames of routines to be compiled \"\" "
	570	printf "\n must end with .f, .f90, .F, or .c !"
	571	printf "\n use \"..\" for more than one file and wildcards"
[837]	572	printf "\n -s LM compiles all locally modified files"
[1]	573	printf "\n -S config file interpreted by shellscript ---"
	574	printf "\n -t allowed cpu-time in seconds (batch) 0"
	575	printf "\n -T tasks per node depending on -h"
	576	printf "\n -u username on remote machine \"\" "
	577	printf "\n -v no prompt for confirmation ---"
[759]	578	printf "\n -w maximum parallel io streams as given by -X"
[1]	579	printf "\n -x tracing of mrun for debug purposes ---"
	580	printf "\n -X # of processors (on parallel machines) 1"
[291]	581	printf "\n -y add appendix \"_O\" to all local output"
	582	printf "\n files (ocean precursor runs followed by"
	583	printf "\n coupled atmosphere-ocean runs) ---"
[206]	584	printf "\n -Y run coupled model, \"#1 #2\" with"
	585	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	586	printf "\n -Z skip combine_plot_fields at the end of "
	587	printf "\n the simulation ---"
[1]	588	printf "\n "
	589	printf "\n Possible values of positional parameter <modus>:"
	590	printf "\n \"?\" - this outline \n\n") \| more
	591	exit
	592	elif [[ "$1" != "" ]]
	593	then
	594	printf "\n +++ positional parameter $1 unknown \n"
	595	locat=parameter; exit
	596	fi
	597
	598
	599
[1289]	600	# SHORT STARTING MESSAGE
[1]	601	printf "\n*** $version "
	602	printf "\n will be executed. Please wait ..."
	603
	604
[82]	605
[1289]	606	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	607	if [[ ! -f $config_file ]]
	608	then
	609	printf "\n\n +++ configuration file: "
	610	printf "\n $config_file"
	611	printf "\n does not exist"
	612	locat=connect; exit
	613	fi
	614
	615
[1289]	616	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	617	line=""
	618	grep "%host_identifier" $config_file > tmp_mrun
	619	while read line
	620	do
[206]	621	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	622	then
	623	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	624	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	625	if [[ $localhost_realname = $HOSTNAME ]]
[82]	626	then
	627	localhost=$host_identifier
	628	break
	629	fi
	630	fi
	631	done < tmp_mrun
	632
	633	if [[ "$localhost" = "" ]]
	634	then
	635	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	636	printf "\n for local host \"$localhost_realname\"."
	637	printf "\n Please add line"
	638	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	639	printf "\n to the configuration file."
	640	locat=localhost; exit
	641	fi
	642
	643
[1289]	644	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	645	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	646	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	647	[[ "$afname" = "" ]] && afname=$fname
	648
	649
[1289]	650	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	651	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	652	# STATEMENTS IN THE CONFIGURATION FILE
[1]	653	if [[ "$run_mode" != "" ]]
	654	then
	655	input_list="$input_list $run_mode"
	656	output_list="$output_list $run_mode"
	657	fi
	658
	659
[1289]	660	# ??? is this (and the respective option -H) really required ???
	661	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	662	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	663	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	664	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	665	if [[ "$fromhost" = "" ]]
	666	then
	667	fromhost=$localhost
	668	fi
	669
	670
[1289]	671	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	672	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	673	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
[1609]	674	# TO BE SUBMITTED (I.E. do_batch=true)
[1]	675	if [[ -n $host && "$host" != $localhost ]]
	676	then
	677	do_batch=true
	678	do_remote=true
	679	case $host in
[2295]	680	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[1]	681	(*) printf "\n"
[83]	682	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	683	printf "\n is not available"
[1]	684	locat=nqs; (( iec = 0 )); exit;;
	685	esac
	686	else
	687	host=$localhost
	688	fi
	689
	690
[1289]	691	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	692	if [[ -n $additional_conditions ]]
	693	then
[69]	694	cond1=`echo $additional_conditions \| cut -d" " -f1`
	695	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	696	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	697	if [[ -n $dummy ]]
	698	then
	699	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	700	locat=options; exit
	701	fi
[503]	702	block=_$cond1
	703	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	704	fi
	705
	706
[2298]	707	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
[206]	708	if [[ $run_coupled_model = true ]]
	709	then
	710
[1289]	711	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	712	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	713
	714	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	715	then
	716
[1289]	717	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	718	printf "\n PEs (total) : $numprocs"
	719	printf "\n PEs (atmosphere): $numprocs_atmos"
	720	printf "\n PEs (ocean) : $numprocs_ocean"
	721	locat=coupling; exit
[206]	722
[1289]	723	fi
[206]	724
	725	fi
	726
[2365]	727	# NESTING (-N) selected and vnesting_mode specified
	728	if [[ $run_vnested_model = true ]]
	729	then
	730
	731	if [[ -n $vnested_dist ]]
	732	then
	733
	734	numprocs_crse=`echo $vnested_dist \| cut -d" " -s -f1`
	735	numprocs_fine=`echo $vnested_dist \| cut -d" " -s -f2`
	736
	737	if (( $numprocs_crse + $numprocs_fine != $numprocs ))
	738	then
	739
	740	printf "\n +++ number of processors does not fit to specification by \"-N\"."
	741	printf "\n PEs (total) : $numprocs"
	742	printf "\n PEs (Coarse) : $numprocs_crse"
	743	printf "\n PEs (Fine) : $numprocs_fine"
	744	locat=vnesting; exit
	745
	746	fi
	747
	748	else
	749
	750	printf "\n +++ "Specify PE for fine and coarse grid: -N "nCGPE nFGPE \"-N\"."
	751	locat=vnesting; exit
	752
	753	fi
	754	vnested_dist=`echo "$numprocs_crse $numprocs_fine"`
	755	fi
	756
[1289]	757	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	758	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	759	mrun_memory=$memory
	760	mrun_group_number=$group_number
	761	mrun_cpumax=$cpumax
	762	mrun_numprocs=$numprocs
[1]	763
[1099]	764
[1289]	765	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
[1468]	766	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
[1]	767	if [[ "$read_from_config" = false ]]
	768	then
	769	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	770
	771	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	772	while read zeile
	773	do
	774	[[ $silent = false ]] && printf "."
	775
	776
[1289]	777	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	778	eval zeile=\"$zeile\"
	779
	780
[1289]	781	# INTERPRET THE LINE
[21]	782	if [[ "$(echo $zeile)" = "" ]]
[1]	783	then
[1289]	784	# EMPTY LINE, NO ACTION
[21]	785	continue
[1]	786
[21]	787	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	788	then
	789
[1289]	790	# LINE IS A COMMENT LINE
[1]	791	true
	792
	793	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	794	then
	795
[1289]	796	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	797	zeile=$(echo $zeile \| cut -c2-)
[69]	798	var=`echo $zeile \| cut -d" " -f1`
	799	value=`echo $zeile \| cut -d" " -s -f2`
	800	for_host=`echo $zeile \| cut -d" " -s -f3`
	801	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	802	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	803
	804	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	805	then
	806
[1289]	807	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	808	# "::" IS REPLACED BY ":".
[1]	809	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	810
	811
[1289]	812	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	813	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	814	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	815	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	816	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	817	# CONFIGURATION-FILE.
[1]	818	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	819	then
	820	eval $var=\$value
	821
[1289]	822	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	823	if [[ $do_trace = true ]]
	824	then
	825	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	826	fi
	827	fi
	828
[1289]	829	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	830	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	831	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	832	# MUST HAVE TO BE STARTED
[1]	833	if [[ $var = host ]]
	834	then
	835	if [[ -n $host && "$host" != $localhost ]]
	836	then
	837	do_batch=true
	838	do_remote=true
	839	case $host in
[2295]	840	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[83]	841	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	842	printf "\n is not available"
[1]	843	locat=nqs; exit;;
	844	esac
	845	else
	846	host=$localhost
	847	fi
	848	fi
	849
[1289]	850	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	851	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	852	# BY MRUN (E.G. subjob)
[1]	853	export $var
	854	fi
	855
	856
	857
	858
	859	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	860	then
	861
[1289]	862	# LINE DEFINES ERROR-COMMAND
[1]	863	(( iec = iec + 1 ))
	864	zeile=$(echo $zeile \| cut -c4-)
	865	err_command[$iec]="$zeile"
	866
	867	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	868	then
	869
[1289]	870	# LINE DEFINES INPUT-COMMAND
[1]	871	(( iic = iic + 1 ))
	872	zeile=$(echo $zeile \| cut -c4-)
	873	in_command[$iic]="$zeile"
	874
	875	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	876	then
	877
[1289]	878	# LINE DEFINES OUTPUT-COMMAND
[1]	879	(( ioc = ioc + 1 ))
	880	zeile=$(echo $zeile \| cut -c4-)
	881	out_command[$ioc]="$zeile"
	882
	883	else
	884
[1289]	885	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	886	# s2a: in/out - field
	887	# s2b: loc - field (optional)
	888	# s2c: tr/ar - field (optional)
[69]	889	s1=`echo $zeile \| cut -d" " -f1`
	890	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	891	s2a=$(echo $s2 \| cut -d":" -f1)
	892	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	893	then
	894	s2b=""
	895	s2c=""
	896	else
[69]	897	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	898	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	899	fi
[69]	900	s3=`echo $zeile \| cut -d" " -f3`
	901	s4=`echo $zeile \| cut -d" " -s -f4`
	902	s5=`echo $zeile \| cut -d" " -s -f5`
	903	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	904
	905
[1289]	906	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	907	# INPUT- OR OUTPUT-LIST.
	908	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	909	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	910	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	911	# IS NOT CHECKED AND STORED.
[1]	912	IFSALT="$IFS"; IFS="$IFS:"
	913	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	914	then
	915	found=false
	916	for actual in $input_list
	917	do
	918	for formal in $s3
	919	do
	920	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	921	done
	922	done
	923	if [[ $found = true ]]
	924	then
	925	(( iin = iin + 1 ))
	926	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	927	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	928	extin[$iin]=$s6
	929	fi
	930	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	931	then
	932	found=false
	933	for actual in $output_list
	934	do
	935	for formal in $s3
	936	do
	937	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	938	done
	939	done
	940	if [[ $found = true ]]
	941	then
	942	(( iout = iout + 1 ))
	943	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	944	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	945	fi
	946	elif [[ "$s2a" != in && "$s2a" != out ]]
	947	then
	948	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	949	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	950	locat=connect; exit
	951	fi
	952	IFS="$IFSALT"
	953	fi
	954	done < $config_file
	955
	956	else
	957
[1289]	958	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	959	[[ $silent = false ]] && printf "..."
[1289]	960	interpreted_config_file=.icf.$RANDOM
[1]	961
	962
[1917]	963
[1289]	964	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[2261]	965	cat > .mrun_environment << EOF
[69]	966	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	967	config_file = '$config_file', do_remote = '$do_remote',
	968	do_trace = '$do_trace', host = '$host',
	969	input_list = '$input_list', icf = '$interpreted_config_file',
	970	localhost = '$localhost', output_list = '$output_list' /
	971
[2261]	972	EOF
[69]	973
[1289]	974	if [[ "$host" != $localhost ]]
[66]	975	then
[503]	976
[1289]	977	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	978	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	979	if [[ $? != 0 ]]
[503]	980	then
[1289]	981	printf "\n\n +++ no interpret_config found"
	982	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	983	locat=interpret_config; exit
	984	fi
	985	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	986	$interpret_config_executable
[503]	987
[1289]	988	else
[503]	989
[1289]	990	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	991	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	992	then
	993	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	994	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	995	locat=interpret_config; exit
[503]	996	else
[1289]	997	interpret_config${block}.x
	998	fi
[503]	999
[66]	1000	fi
[71]	1001	rm .mrun_environment
[1]	1002
[1917]	1003
[1289]	1004	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	1005	chmod u+x $interpreted_config_file
	1006	export PATH=$PATH:.
	1007	. $interpreted_config_file
[71]	1008	rm $interpreted_config_file
[1]	1009
[1099]	1010	fi
[71]	1011
[1917]	1012
[1289]	1013	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	1014	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	1015	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	1016	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	1017	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	1018	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	1019	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	1020
	1021
[1289]	1022	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	1023	# FOR SOURCE-FILES TO BE COMPILED.
	1024	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	1025	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	1026	if [[ "$SOURCES_COMPLETE" = "" ]]
	1027	then
	1028
[1289]	1029	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	1030	# HAS BEEN DEFINED
[1]	1031	source_path=""
	1032	line=""
	1033	grep "%source_path" $config_file > tmp_mrun
	1034	while read line
	1035	do
	1036	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1037	then
	1038	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	1039	then
	1040	global_source_path=`echo $line \| cut -d" " -f2`
	1041	fi
	1042	fi
	1043	done < tmp_mrun
	1044
	1045	line=""
	1046	found=false
	1047	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	1048	while read line
	1049	do
	1050	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1051	then
	1052	if [[ $found = true ]]
	1053	then
	1054	printf "\n\n +++ more than one source path found in configuration file"
	1055	printf "\n for local host \"$localhost\" "
	1056	locat=source_path; exit
	1057	fi
	1058	source_path=`echo $line \| cut -d" " -f2`
	1059	found=true
	1060	fi
	1061	done < tmp_mrun
	1062	rm tmp_mrun
	1063
	1064	if [[ "$source_path" = "" ]]
	1065	then
	1066	if [[ "$global_source_path" != "" ]]
	1067	then
	1068	source_path=$global_source_path
	1069	else
	1070	printf "\n\n +++ no source path found in configuration file"
	1071	printf "\n for local host \"$localhost\" "
	1072	locat=source_path; exit
	1073	fi
	1074	fi
	1075	eval source_path=$source_path
	1076
	1077	if [[ ! -d $source_path ]]
	1078	then
	1079	printf "\n\n +++ source path \"$source_path\" on local host"
	1080	printf "\n \"$localhost\" does not exist"
	1081	locat=source_path; exit
	1082	fi
	1083
	1084	fi
	1085
	1086
[1289]	1087	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1088	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1089	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	1090	then
	1091	global_revision=`svnversion $source_path 2>/dev/null`
	1092	global_revision="Rev: $global_revision"
	1093	fi
[1]	1094
[78]	1095
[1289]	1096	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	1097	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	1098	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	1099	if [[ -n $host && "$host" != $localhost ]]
	1100	then
	1101	do_batch=true
	1102	do_remote=true
	1103	case $host in
[2295]	1104	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[1]	1105	(*) printf "\n"
[83]	1106	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	1107	printf "\n is not available"
[1]	1108	locat=nqs; (( iec = 0 )); exit;;
	1109	esac
	1110	else
	1111	host=$localhost
	1112	fi
	1113
	1114
[1620]	1115
[1289]	1116	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1117	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1118	then
	1119
[1289]	1120	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1121	if [[ ! -n $numprocs ]]
	1122	then
	1123	printf "\n"
	1124	printf "\n +++ option \"-K parallel\" requires additional specification"
	1125	printf "\n of the number of processors to be used by"
	1126	printf "\n mrun-option \"-X\" or by environment-variable"
	1127	printf "\n \"numprocs\" in the configuration file"
	1128	locat=numprocs; (( iec = 0 )); exit
	1129	fi
	1130
[1289]	1131	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1132	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2257]	1133	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
[1]	1134	then
[759]	1135	printf "\n"
	1136	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1137	printf "\n set -T option or define tasks_per_node in the config file"
	1138	locat=tasks_per_node; (( iec = 0 )); exit
	1139	fi
[1279]	1140
	1141	if (( numprocs < tasks_per_node ))
	1142	then
	1143	printf "\n"
	1144	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1145	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1146	locat=tasks_per_node; (( iec = 0 )); exit
	1147	fi
	1148
[2257]	1149	if [[ $host != lcxt5m ]]
[759]	1150	then
[1279]	1151	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1152	(( ival = $tasks_per_node ))
	1153	(( pes = numprocs ))
	1154	(( ii = pes / ival ))
[1279]	1155	(( remaining_pes = pes - ii * ival ))
	1156	if (( remaining_pes > 0 ))
[848]	1157	then
	1158	printf "\n"
[1279]	1159	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1160	printf "\n divisor of the total number of processors (option \"-X\")"
	1161	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1162	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1163	(( nodes = nodes + 1 ))
[848]	1164	fi
[1]	1165	fi
	1166
[759]	1167
[377]	1168	# SETTINGS FOR SUBJOB-COMMAND
[1]	1169	OOPT="-O $threads_per_task"
	1170
[1289]	1171	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1172	if [[ "$tasks_per_node" != "" ]]
	1173	then
[1119]	1174	TOPT="-T $tasks_per_node"
[1]	1175	fi
	1176
[1289]	1177	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1178	if [[ $node_usage = default ]]
	1179	then
	1180	if [[ $host = ibms ]]
	1181	then
	1182	node_usage=shared
	1183	else
	1184	node_usage=not_shared
	1185	fi
	1186	fi
[181]	1187
[635]	1188	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1189	then
	1190	printf "\n"
	1191	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1192	printf "\n \"shared\" or \"not_shared\""
	1193	locat=tasks_per_node; (( iec = 0 )); exit
	1194	fi
	1195
	1196	fi
	1197
[1289]	1198	# CHECK IF HOSTFILE EXISTS
[1]	1199	if [[ -n $hostfile ]]
	1200	then
	1201	if [[ ! -f $hostfile ]]
	1202	then
	1203	printf "\n"
	1204	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1205	locat=hostfile; exit
	1206	fi
	1207	fi
	1208
	1209
[1289]	1210	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1211	if [[ "$maximum_parallel_io_streams" = "" ]]
	1212	then
	1213	maximum_parallel_io_streams=$numprocs
	1214	fi
[1]	1215
[759]	1216
[1289]	1217	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1218	if [[ "$scp_port" != "" ]]
	1219	then
	1220	PORTOPT="-P $scp_port"
	1221	SSH_PORTOPT="-p $scp_port"
	1222	fi
	1223
	1224
[1944]	1225	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1226	# CONFIG-FILE
	1227	if [[ "$ssh_key" != "" ]]
	1228	then
	1229	ssh_key="-i $HOME/.ssh/$ssh_key"
	1230	fi
	1231
	1232
[1289]	1233	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1234	if [[ $queue = none ]]
	1235	then
	1236	case $host in
[1184]	1237	(ibmh) queue=cluster;;
[693]	1238	(ibmkisti) queue=class.32plus;;
[2365]	1239	(ibmmuc*) queue=test;;
	1240	(lcbwuni) queue=develop;;
[1620]	1241	(lcbullhh) queue=compute;;
[1442]	1242	(lccrayb) queue=mpp1q;;
	1243	(lccrayh) queue=mpp1q;;
[2295]	1244	(lcgeohu) queue=short;;
[1040]	1245	(lckiaps) queue=normal;;
[440]	1246	(lckyoto) queue=ph;;
[1099]	1247	(lckyuh) queue=fx-single;;
	1248	(lckyut) queue=cx-single;;
[2365]	1249	(lclrz) queue=mpp2;;
[635]	1250	(lctit) queue=S;;
[1]	1251	(unics) queue=unics;;
	1252	esac
	1253	fi
	1254
	1255
[1289]	1256	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1257	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1258	(( i = 0 ))
	1259	while (( i < iin ))
	1260	do
	1261	(( i = i + 1 ))
	1262	(( maxcycle = 0 ))
	1263
[1289]	1264	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1265	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1266	if [[ "${actionin[$i]}" = di ]]
	1267	then
[1289]	1268	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1269	# HOST ONLY
[1]	1270	eval filename=${pathin[$i]}/${endin[$i]}
	1271	else
[1289]	1272	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1273	# HOST ONLY
[1]	1274	eval filename=${pathin[$i]}/${afname}${endin[$i]}
	1275	fi
[892]	1276	eval pathname=${pathin[$i]}
[1]	1277
[1289]	1278	# CHECK IF FILE EXISTS
[2141]	1279	if ! ls $filename* 1>/dev/null 2>&1
[1]	1280	then
[1289]	1281
	1282	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[1]	1283	if [[ "${transin[$i]}" != "locopt" ]]
	1284	then
	1285	printf "\n\n +++ INPUT-file: "
[2261]	1286	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
[1]	1287	then
	1288	printf "\n $filename"
	1289	else
	1290	printf "\n $filename.${extin[$i]}"
	1291	fi
	1292	printf "\n does not exist\n"
	1293	locat=input; exit
	1294	else
	1295	transin[$i]="unavailable"
	1296	fi
	1297	else
	1298
[1289]	1299	# DETERMINE THE FILE'S CYCLE NUMBER
[1]	1300	ls -1 -d $filename > filelist 2>/dev/null
	1301	ls -1 -d $filename.* >> filelist 2>/dev/null
	1302	while read zeile
	1303	do
[2261]	1304	# filename without path (i.e. after the last "/")
	1305	basefilename=$(basename ${zeile})
	1306
	1307	# check if there is an extension
	1308	extension=${basefilename##*.}
	1309	if [[ "$extension" = "$extin[$i]" ]]
	1310	then
	1311	basefilename=${basefilename&.*}
	1312	fi
	1313
	1314	# check for an existing cycle number
	1315	cycle=${basefilename##*.}
	1316	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1317	then
	1318	(( icycle = $cycle ))
	1319	else
	1320	(( icycle = 0 ))
	1321	fi
	1322
	1323	if (( icycle > maxcycle ))
	1324	then
	1325	(( maxcycle = icycle ))
	1326	fi
	1327
	1328	# cycle=$(echo $zeile \| cut -f2 -d".")
	1329	# if [[ "$cycle" = "$zeile" ]]
	1330	# then
	1331	# (( icycle = 0 ))
	1332	# elif [[ "$cycle" = "${extin[$i]}" ]]
	1333	# then
	1334	# (( icycle = 0 ))
	1335	# else
	1336	# (( icycle = $cycle ))
	1337	# fi
	1338	# if (( icycle > maxcycle ))
	1339	# then
	1340	# (( maxcycle = icycle ))
	1341	# fi
[1]	1342	done <filelist
	1343	rm filelist
	1344
[1289]	1345	# APPEND CYCLE NUMBER TO FILENAME
[1]	1346	if (( maxcycle > 0 ))
	1347	then
	1348	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1349	then
	1350	filename=${filename}.$maxcycle.${extin[$i]}
	1351	else
	1352	filename=${filename}.$maxcycle
	1353	fi
	1354	else
	1355	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1356	then
	1357	filename=${filename}.${extin[$i]}
	1358	fi
	1359	fi
	1360
[1289]	1361	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
[2261]	1362	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
[1]	1363	absnamein[$i]=$filename
	1364	if (( maxcycle > 0 ))
	1365	then
	1366	if [[ "${actionin[$i]}" = di ]]
	1367	then
	1368	frelin[$i]=${endin[$i]}.$maxcycle
	1369	else
	1370	frelin[$i]=${afname}${endin[$i]}.$maxcycle
	1371	fi
	1372	else
	1373	if [[ "${actionin[$i]}" = di ]]
	1374	then
	1375	frelin[$i]=${endin[$i]}
	1376	else
	1377	frelin[$i]=${afname}${endin[$i]}
	1378	fi
	1379	fi
	1380
	1381	fi
	1382	done
[920]	1383
[1289]	1384	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1385	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1386	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1387	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1388	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1389	# REMOTE HOST)
[1]	1390	(( i = 0 ))
	1391	while (( i < iout ))
	1392	do
	1393	(( i = i + 1 ))
	1394	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1395	then
[260]	1396	if [[ "${actionout[$i]}" = tr ]]
[1]	1397	then
	1398	actionout[$i]=""
[260]	1399	elif [[ "${actionout[$i]}" = trpe ]]
	1400	then
	1401	actionout[$i]=pe
[1]	1402	elif [[ "${actionout[$i]}" = tra ]]
	1403	then
	1404	actionout[$i]=a
	1405	fi
	1406	(( maxcycle = 0 ))
	1407	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1408	eval catalogname=${pathout[$i]}
[2141]	1409	if ! ls $filename* 1>/dev/null 2>&1
[1]	1410	then
	1411
[1289]	1412	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
[1]	1413	if cat /dev/null > $filename
	1414	then
	1415	rm $filename
	1416	else
	1417
[1289]	1418	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1419	# IF IT DOES NOT EXIST, TRY TO CREATE IT
[1]	1420	if [[ ! -d $catalogname ]]
	1421	then
	1422	if mkdir -p $catalogname
	1423	then
	1424	printf "\n\n *** directory:"
	1425	printf "\n $catalogname"
	1426	printf "\n was created\n"
	1427	else
	1428	printf "\n\n +++ OUTPUT-file:"
	1429	printf "\n $filename"
	1430	printf "\n cannot be created, because directory does not exist"
	1431	printf "\n and cannot be created either"
	1432	printf "\n"
	1433	locat=output ; exit
	1434	fi 2>/dev/null
	1435	else
	1436	printf "\n\n +++ OUTPUT-file:"
	1437	printf "\n $filename"
	1438	printf "\n cannot be created, although directory exists"
	1439	printf "\n"
	1440	locat=output ; exit
	1441	fi
	1442	fi 2>/dev/null
	1443	else
	1444
[1289]	1445	# DETERMINE THE CYCLE NUMBER
[1]	1446	ls -1 -d $filename > filelist 2>/dev/null
	1447	ls -1 -d $filename.* >> filelist 2>/dev/null
	1448	while read zeile
	1449	do
[2261]	1450
	1451	# filename without path (i.e. after the last "/")
	1452	basefilename=$(basename ${zeile})
	1453
	1454	# check if there is an extension
	1455	extension=${basefilename##*.}
[2268]	1456	if [[ "$extension" = "${extout[$i]}" ]]
[1]	1457	then
[2268]	1458	basefilename=${basefilename%.*}
[2261]	1459	fi
	1460
	1461	# check for an existing cycle number
	1462	cycle=${basefilename##*.}
	1463	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1464	then
	1465	(( icycle = $cycle + 1 ))
	1466	else
[1]	1467	(( icycle = 1 ))
	1468	fi
[2261]	1469
[1]	1470	if (( icycle > maxcycle ))
	1471	then
	1472	(( maxcycle = icycle ))
	1473	fi
[2261]	1474
[1]	1475	done <filelist
	1476	rm filelist
	1477	fi
	1478
[1289]	1479	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1480	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1481	if [[ "${actionout[$i]}" != a ]]
	1482	then
	1483	if (( maxcycle > 0 ))
	1484	then
[2261]	1485	filename_tmp=${filename}.$maxcycle
	1486	if cat /dev/null > $filename_tmp
[1]	1487	then
[2261]	1488	rm $filename_tmp
[1]	1489	else
	1490	printf "\n +++ OUTPUT-file:"
[2261]	1491	printf "\n $filename_tmp"
[1]	1492	printf "\n cannot be created"
	1493	locat=output ; exit
	1494	fi
	1495	fi
	1496	else
	1497	(( maxcycle = maxcycle - 1 ))
	1498	fi
	1499
[2261]	1500	(( cycnum[$i] = maxcycle ))
[1]	1501	pathout[$i]=$filename
	1502
	1503	fi
	1504	done
	1505
	1506
[1289]	1507	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1508	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1509	then
[260]	1510	if [[ "$dvr_inc" = "" ]]
[83]	1511	then
[260]	1512	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1513	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1514	locat=dvr; exit
[83]	1515	fi
[260]	1516	if [[ "$dvr_lib" = "" ]]
[83]	1517	then
[260]	1518	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1519	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1520	locat=dvr; exit
[83]	1521	fi
	1522	fi
	1523
	1524
[1289]	1525	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1526	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1527	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1528	then
	1529	printf "\n +++ neither main program nor executable defined"
	1530	locat=source; exit
	1531	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1532	then
	1533	printf "\n +++ main program as well as executable defined"
	1534	locat=source; exit
	1535	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1536	then
	1537	do_compile=false
	1538	fi
	1539
	1540
[1289]	1541	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1542	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1543	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1544	then
	1545	rm -rf SOURCES_FOR_RUN_$fname
	1546	mkdir SOURCES_FOR_RUN_$fname
	1547	fi
	1548
	1549
[1289]	1550	# COLLECT ALL ROUTINES TO BE COMPILED
	1551	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1552	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1553	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1554	then
	1555
[5]	1556	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1557
[838]	1558	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1559	then
	1560
[1289]	1561	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1562	source_list=""
	1563	cd $source_path
	1564
	1565
[1289]	1566	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1567	if [[ ! -d .svn ]]
	1568	then
	1569	printf "\n\n +++ source directory"
	1570	printf "\n \"$source_path\" "
	1571	printf "\n is not under control of \"subversion\"."
[306]	1572	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1573	fi
	1574
	1575
[1289]	1576	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1577	Filenames=""
[69]	1578	svn status > tmp_mrun
	1579	while read line
[5]	1580	do
	1581	firstc=`echo $line \| cut -c1`
	1582	if [[ $firstc = M \|\| $firstc = "?" ]]
	1583	then
	1584	Name=`echo "$line" \| cut -c8-`
	1585	extension=`echo $Name \| cut -d. -f2`
	1586	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1587	then
	1588	Filenames="$Filenames "$Name
	1589	fi
	1590	fi
[69]	1591	done < tmp_mrun
[5]	1592
	1593
[1289]	1594	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1595	for dateiname in $Filenames
	1596	do
	1597	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1598	source_list=$source_list"$dateiname "
	1599	done
	1600
	1601	cd - > /dev/null
	1602
	1603
[1289]	1604	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1605	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1606	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1607	then
	1608
	1609	cd $source_path
	1610
	1611	for filename in $source_list
	1612	do
	1613
[1289]	1614	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1615	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1616	then
	1617	printf "\n +++ source code file: $filename"
	1618	printf "\n must not contain (\"/\") "
	1619	locat=source; exit
	1620	fi
	1621
	1622	if [[ ! -f $filename ]]
	1623	then
	1624	printf "\n +++ source code file: $filename"
	1625	printf "\n does not exist"
	1626	locat=source; exit
	1627	else
	1628	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1629	fi
	1630
	1631	done
	1632
	1633	cd - > /dev/null
	1634
	1635	fi
	1636
	1637
[1289]	1638	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1639	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1640	if [[ $restart_run != true ]]
[1]	1641	then
	1642
	1643	if [[ ! -f "$source_path/$mainprog" ]]
	1644	then
	1645	printf "\n\n +++ main program: $mainprog"
	1646	printf "\n does not exist in source directory"
	1647	printf "\n \"$source_path\"\n"
	1648	locat=source; exit
	1649	else
	1650	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1651	then
	1652	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1653	source_list=${mainprog}" $source_list"
	1654	fi
	1655	fi
	1656	fi
	1657
	1658
[1289]	1659	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1660	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1661	if [[ "$restart_run" != true ]]
	1662	then
	1663	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1664	if [[ ! -f $makefile ]]
	1665	then
	1666	printf "\n +++ file \"$makefile\" does not exist"
	1667	locat=make; exit
	1668	else
	1669	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1670	fi
	1671	fi
	1672
	1673
[1289]	1674	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1675	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1676	then
	1677
[1289]	1678	# DOES THE DIRECTORY EXIST?
[1]	1679	if [[ ! -d $add_source_path ]]
	1680	then
[1779]	1681	printf "\n\n *** INFORMATIVE: additional source code directory"
[1]	1682	printf "\n \"$add_source_path\" "
	1683	printf "\n does not exist or is not a directory."
	1684	printf "\n No source code will be used from this directory!\n"
	1685	add_source_path=""
[931]	1686	if [[ $silent == false ]]
	1687	then
	1688	sleep 3
	1689	fi
[1]	1690	else
	1691
	1692	cd $add_source_path
[211]	1693	found=false
[1]	1694
	1695	Names=$(ls -1 *.f90 2>&1)
	1696	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1697	Names=$(ls -1 *.F90 2>&1)
	1698	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1699	Names=$(ls -1 *.F 2>&1)
	1700	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1701	Names=$(ls -1 *.f 2>&1)
	1702	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1703	Names=$(ls -1 *.c 2>&1)
	1704	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1705
	1706	cd - > /dev/null
	1707	cd SOURCES_FOR_RUN_$fname
	1708
[211]	1709	# COPY MAKEFILE IF EXISTING
	1710	if [[ -f $add_source_path/Makefile ]]
	1711	then
	1712	printf "\n\n *** user Makefile from directory"
	1713	printf "\n \"$add_source_path\" is used \n"
[931]	1714	if [[ $silent == false ]]
	1715	then
	1716	sleep 1
	1717	fi
[211]	1718	cp $add_source_path/Makefile .
	1719	fi
	1720
[1]	1721	for dateiname in $AddFilenames
	1722	do
	1723	if [[ -f $dateiname ]]
	1724	then
	1725	printf "\n +++ source code file \"$dateiname\" found in additional"
	1726	printf "\n source code directory \"$add_source_path\" "
[211]	1727	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1728	printf "\n from directory \"$source_path\"."
[1]	1729	locat=source; exit
	1730	fi
	1731
	1732	cp $add_source_path/$dateiname .
	1733	source_list="$source_list $dateiname"
	1734
[211]	1735	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1736	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1737	then
	1738	printf "\n\n +++ user file \"$dateiname\" "
	1739	printf "\n is not listed in Makefile \n"
	1740	locat=source; exit
	1741	else
	1742
	1743	if [[ $found = false ]]
[1]	1744	then
[211]	1745	found=true
	1746	printf "\n\n *** following user file(s) added to the"
	1747	printf " files to be translated:\n "
[1]	1748	fi
[211]	1749	printf "$dateiname "
[931]	1750	if [[ $silent == false ]]
	1751	then
	1752	sleep 0.5
	1753	fi
	1754
[1]	1755	fi
	1756	done
[211]	1757	[[ $found = true ]] && printf "\n"
[1]	1758	cd - > /dev/null
	1759	fi
	1760	fi
	1761
	1762
[1289]	1763	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1764	# TO THE LIST OF FILES TO BE COMPILED
[5]	1765	if [[ $restart_run != true && -n $package_list ]]
[1]	1766	then
	1767
	1768	cd $source_path
	1769
	1770	for package in $package_list
	1771	do
	1772
	1773	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1774
[1289]	1775	# DETERMINE FILES BELONGING TO THE PACKAGE
	1776	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1777	# THE NAME OF THE DIRECTORY
[1]	1778	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1779
	1780
[1289]	1781	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1782	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1783	for source_list_name in $package_source_list
	1784	do
	1785	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1786	then
	1787
[1289]	1788	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1789	ending=`echo $source_list_name \| cut -f2 -d.`
	1790	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1791	then
	1792	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1793	source_list="$source_list $source_list_name"
	1794	fi
	1795	fi
	1796	done
	1797	done
	1798
	1799	cd - > /dev/null
	1800	fi
	1801
	1802	fi # do_compile=true
	1803
	1804
[1289]	1805	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1806	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1807	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1808	then
	1809
[1289]	1810	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[2365]	1811	if [[ $(echo $localhost \| cut -c1-3) = ibm && $localhost != ibmmuc* ]]
[1]	1812	then
[82]	1813	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1814	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1815	then
[82]	1816	cpp_options="$cpp_options -D__nec"
	1817	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1818	then
	1819	cpp_options="$cpp_options -D__lc"
[1]	1820	else
[82]	1821	cpp_options="$cpp_options -D__$localhost"
[1]	1822	fi
[83]	1823
[1289]	1824	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[2365]	1825	if [[ $(echo $localhost \| cut -c1-3) = ibm && $localhost != ibmmuc ]]
[1]	1826	then
[82]	1827	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1828	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1829	else
[82]	1830	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1831	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1832	fi
[83]	1833
[1289]	1834	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1835	if [[ -n $package_list ]]
	1836	then
	1837	for package in $package_list
	1838	do
	1839	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1840	then
	1841	if [[ $package != "dvrp_graphics+1PE" ]]
	1842	then
[82]	1843	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1844	else
[82]	1845	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1846	export use_seperate_pe_for_dvrp_output=true
	1847	fi
	1848	else
	1849	if [[ $package != "dvrp_graphics+1PE" ]]
	1850	then
[82]	1851	cpp_options="$cpp_options -D__$package"
[1]	1852	else
[82]	1853	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1854	export use_seperate_pe_for_dvrp_output=true
	1855	fi
	1856	fi
	1857	done
	1858	fi
[83]	1859
[1]	1860	else
	1861
	1862
[1289]	1863	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1864	if [[ $do_remote = false ]]
	1865	then
	1866	if [[ ! -f $executable ]]
	1867	then
	1868	printf "\n +++ executable file: $executable"
	1869	printf "\n does not exist"
	1870	locat=executable; exit
	1871	fi
	1872	fi
	1873	fi
	1874
	1875
[1289]	1876	# DETERMINE THE JOB MODE
[1491]	1877	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
[1]	1878	then
[1491]	1879	if [[ "$LOADLBATCH" = yes ]]
	1880	then
	1881	batch_job=.TRUE.
	1882	jobmo=BATCH
	1883	else
	1884	batch_job=.FALSE.
	1885	jobmo=INTERACTIVE
	1886	fi
[1]	1887	else
[2185]	1888	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
[1491]	1889	then
	1890	batch_job=.TRUE.
	1891	jobmo=BATCH
	1892	else
	1893	batch_job=.FALSE.
	1894	jobmo=INTERACTIVE
	1895	fi
[1]	1896	fi
	1897
[1289]	1898	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1899	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1900	then
	1901	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1902	printf "\n please submit batch job using mrun option \"-b\" \n"
	1903	locat=normal; exit
	1904	fi
	1905
	1906
[1289]	1907	# CHECK, IF USER DEFINED A COMPILER
[1]	1908	if [[ "$compiler_name" = "" ]]
	1909	then
[82]	1910
[220]	1911	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1912	locat=compiler_name; exit
	1913
[1]	1914	fi
	1915
	1916
[1289]	1917	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1609]	1918
	1919	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
	1920	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
	1921	then
	1922	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
[1755]	1923	if [[ "$kennung" = "" ]]
[1753]	1924	then
	1925	kennung=$RANDOM
	1926	fi
[1609]	1927	else
	1928	kennung=$RANDOM
	1929	fi
	1930
[1]	1931	if [[ "$tmp_user_catalog" = "" ]]
	1932	then
[312]	1933	if [[ $localhost = ibmh ]]
[1]	1934	then
[312]	1935	tmp_user_catalog=$SCRATCH
[1]	1936	else
	1937	tmp_user_catalog=/tmp
	1938	fi
	1939	fi
	1940
[2365]	1941	if [[ $localhost = ibmmuc* ]]
	1942	then
	1943	TEMPDIR=$tmp_user_catalog/${USER}.$kennung
	1944	else
	1945	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1946	fi
[1]	1947
[1289]	1948	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1949	if [[ "$tmp_data_catalog" = "" ]]
	1950	then
[2261]	1951	tmp_data_catalog=/tmp/mrun_restart_data
[1]	1952	fi
	1953
	1954
[1289]	1955	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1956	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1957	then
	1958	eval fopts=\"$fopts\"
	1959	eval lopts=\"$lopts\"
	1960	fi
	1961
	1962
[1289]	1963	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1964	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1965	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1779]	1966	XOPT="-X $numprocs"
[1]	1967
	1968
[1289]	1969	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1970	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1971	done=false
	1972	while [[ $done = false ]]
	1973	do
	1974	cputime=$cpumax
	1975	if (( $cputime == 0 ))
	1976	then
[246]	1977	if [[ $do_batch = true ]]
	1978	then
	1979	printf "\n +++ cpu-time is undefined"
	1980	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1981	printf "\n >>> "
	1982	read cputime 1>/dev/null 2>&1
	1983	else
	1984	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1985	fi
[1]	1986	else
	1987	done=true
	1988	fi
	1989	cpumax=$cputime
	1990	done
	1991
	1992	(( minuten = cputime / 60 ))
	1993	(( sekunden = cputime - minuten * 60 ))
	1994
	1995
[1289]	1996	# CHECK THE MEMORY DEMAND
[1]	1997	if [[ $do_batch = true ]]
	1998	then
	1999	done=false
	2000	while [[ $done = false ]]
	2001	do
	2002	if (( memory == 0 ))
	2003	then
	2004	printf "\n +++ memory demand is undefined"
	2005	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	2006	printf "\n >>> "
	2007	read memory 1>/dev/null 2>&1
	2008	else
	2009	done=true
	2010	fi
	2011	done
	2012	fi
	2013
	2014
[1289]	2015	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	2016	if [[ $do_remote = true && -z $remote_username ]]
	2017	then
	2018	while [[ -z $remote_username ]]
	2019	do
	2020	printf "\n +++ username on remote host \"$host\" is undefined"
	2021	printf "\n >>> Please type username:"
	2022	printf "\n >>> "
	2023	read remote_username
	2024	done
	2025	mc="$mc -u$remote_username"
	2026	fi
	2027
[892]	2028	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	2029	if [[ "$login_init_cmd" != "" ]]
	2030	then
	2031	export init_cmds="${login_init_cmd};"
	2032	fi
[221]	2033
[892]	2034
[1289]	2035	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	2036	if [[ "$modules" != "" ]]
	2037	then
[678]	2038	if [[ $host = lctit ]]
	2039	then
	2040	export module_calls=". $modules"
	2041	else
	2042	export module_calls="module load ${modules};"
	2043	fi
[493]	2044	fi
	2045
[1289]	2046	# OUTPUT OF THE MRUN-HEADER
[1]	2047	calltime=$(date)
	2048	printf "\n"
[1101]	2049	printf "#------------------------------------------------------------------------# \n"
	2050	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	2051	printf "\| \| \n"
[1]	2052	spalte1="called on:"; spalte2=$localhost_realname
[1101]	2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	2054	if [[ $do_remote = true ]]
[1]	2055	then
[1289]	2056	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	2057	else
[1289]	2058	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	2059	fi
[1101]	2060	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2061	if [[ -n $numprocs ]]
	2062	then
[1106]	2063	if [[ $run_coupled_model = false ]]
	2064	then
	2065	spalte1="number of PEs:"; spalte2=$numprocs
	2066	else
	2067	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	2068	fi
[1101]	2069	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2070	fi
	2071	if [[ -n $tasks_per_node ]]
	2072	then
	2073	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	2074	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	2075	if (( remaining_pes > 0 ))
	2076	then
	2077	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2079	fi
[1]	2080	fi
[759]	2081	if [[ $maximum_parallel_io_streams != $numprocs ]]
	2082	then
	2083	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	2085	fi
[622]	2086	if [[ $use_openmp = true ]]
[1]	2087	then
	2088	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2090	fi
[1101]	2091	printf "\| \| \n"
[1]	2092	if [[ $do_compile = true ]]
	2093	then
[475]	2094	if [[ "$mopts" != "" ]]
	2095	then
[1101]	2096	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2098	zeile=$(echo "$mopts" \| cut -c46-)
[475]	2099	while [[ "$zeile" != "" ]]
	2100	do
	2101	spalte1=""
[1101]	2102	spalte2=$(echo "$zeile" \| cut -c-45)
	2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2104	zeile=$(echo "$zeile" \| cut -c46-)
[475]	2105	done
	2106	fi
	2107
[1101]	2108	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	2109	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2110	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	2111	while [[ "$zeile" != "" ]]
	2112	do
	2113	spalte1=""
[1101]	2114	spalte2=$(echo "$zeile" \| cut -c-45)
	2115	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2116	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2117	done
	2118
[1101]	2119	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	2120	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2121	zeile=$(echo "$fopts" \| cut -c46-)
[1]	2122	while [[ "$zeile" != "" ]]
	2123	do
	2124	spalte1=""
[1101]	2125	spalte2=$(echo "$zeile" \| cut -c-45)
	2126	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2127	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2128	done
	2129
[1101]	2130	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	2131	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2132	zeile=$(echo "$lopts" \| cut -c46-)
[1]	2133	while [[ "$zeile" != "" ]]
	2134	do
	2135	spalte1=""
[1101]	2136	spalte2=$(echo "$zeile" \| cut -c-45)
	2137	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2138	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2139	done
	2140
[1101]	2141	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2142	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2143	zeile=$(echo "$modules" \| cut -c46-)
[493]	2144	while [[ "$zeile" != "" ]]
	2145	do
	2146	spalte1=""
[1101]	2147	spalte2=$(echo "$zeile" \| cut -c-45)
	2148	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2149	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2150	done
	2151
[1101]	2152	spalte1="main program:"; spalte2=$mainprog
	2153	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2154	else
	2155	spalte1=executable:; spalte2=$executable
[1101]	2156	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2157	fi
[1101]	2158	printf "\| \| \n"
	2159	spalte1="base name of files:"; spalte2=$fname
	2160	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2161	if [[ $fname != $afname ]]
	2162	then
[1101]	2163	spalte1="base name of input files:"; spalte2=$afname
	2164	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2165	fi
[1101]	2166	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2167	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2168	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2169	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2170
[1106]	2171	if [[ "$ocean_file_appendix" = true ]]
	2172	then
	2173	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2174	fi
	2175
[1]	2176	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2177	then
	2178	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2179	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2180	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2181	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2182	fi
	2183
	2184	if [[ $do_compile = true ]]
	2185	then
[1101]	2186	printf "\| \| \n"
	2187	printf "\| Files to be compiled: \| \n"
[1]	2188	zeile=$source_list
	2189	while [[ "$zeile" != "" ]]
	2190	do
[1101]	2191	linestart=$(echo $zeile \| cut -c-70)
	2192	printf "\| %-70s \| \n" "$linestart"
	2193	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2194	done
	2195	fi
[1101]	2196	printf "#------------------------------------------------------------------------#"
[1]	2197
	2198
	2199
[1289]	2200	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2201	if [[ $do_trace = true ]]
	2202	then
	2203	(( i = 0 ))
	2204	while (( i < iin ))
	2205	do
	2206	(( i = i + 1 ))
	2207	if (( i == 1 ))
	2208	then
	2209	printf "\n\n >>> INPUT-file assignments:\n"
	2210	fi
	2211	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2212	done
	2213	(( i = 0 ))
	2214	while (( i < iout ))
	2215	do
	2216	(( i = i + 1 ))
	2217	if (( i == 1 ))
	2218	then
	2219	printf "\n\n >>> OUTPUT-file assignments:\n"
	2220	fi
	2221	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2222	done
	2223	(( i = 0 ))
	2224	while (( i < iic ))
	2225	do
	2226	(( i = i + 1 ))
	2227	if (( i == 1 ))
	2228	then
	2229	printf "\n\n >>> INPUT-commands:\n"
	2230	fi
	2231	printf "\n ${in_command[$i]}"
	2232	done
	2233	(( i = 0 ))
	2234	while (( i < ioc ))
	2235	do
	2236	(( i = i + 1 ))
	2237	if (( i == 1 ))
	2238	then
	2239	printf "\n\n >>> OUTPUT-commands:\n"
	2240	fi
	2241	printf "\n ${out_command[$i]}"
	2242	done
	2243	fi
	2244
[1289]	2245	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2246	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2247	then
	2248	antwort=dummy
	2249	printf "\n\n"
[1101]	2250	printf " >>> everything o.k. (y/n) ? "
	2251	while read antwort
[1]	2252	do
[1101]	2253	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2254	then
	2255	printf " >>> everything o.k. (y/n) ? "
	2256	else
	2257	break
	2258	fi
[1]	2259	done
	2260	if [[ $antwort = n \|\| $antwort = N ]]
	2261	then
	2262	locat=user_abort; (( iec = 0 )); exit
	2263	fi
	2264	if [[ $do_batch = true ]]
	2265	then
	2266	printf " >>> batch-job will be created and submitted"
	2267	else
[1289]	2268	printf " >>> MRUN will now continue to execute on this machine"
[1]	2269	fi
	2270	fi
	2271
[1804]	2272
[1199]	2273	# DETERMINE PATH FOR MAKE DEPOSITORY
	2274	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2275	then
	2276
	2277	line=""
	2278	grep "%depository_path" $config_file > tmp_mrun
	2279	while read line
	2280	do
	2281	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2282	then
	2283	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2284	then
	2285	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2286	fi
	2287	fi
	2288	done < tmp_mrun
	2289
	2290	line=""
	2291	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2292	while read line
	2293	do
	2294	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2295	then
	2296	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2297	then
	2298	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2299	fi
	2300	fi
	2301	done < tmp_mrun
	2302
	2303	if [[ "$local_depository_path" = "" ]]
	2304	then
	2305	if [[ "$global_depository_path" != "" ]]
	2306	then
	2307	local_depository_path=$global_depository_path
	2308	else
	2309	printf "\n\n +++ no depository path found in configuration file"
	2310	printf "\n for local host \"$localhost\" "
	2311	printf "\n please set \"\%depository_path\" in configuration file\n"
	2312	locat=config_file; exit
	2313	fi
	2314	fi
	2315	eval local_depository_path=$local_depository_path
	2316	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2317	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2318
	2319
	2320	basename=`echo $mainprog \| cut -f1 -d"."`
	2321	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2322	if [[ ! -f $make_depository ]]
	2323	then
	2324	printf "\n"
	2325	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2326	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2327	fi
	2328
	2329	fi
	2330
	2331
[1289]	2332	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2333	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2334	if [[ $do_batch = false ]]
	2335	then
	2336
	2337
[1289]	2338	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2339	mkdir -p $TEMPDIR
	2340	chmod go+rx $TEMPDIR
	2341	tmpcreate=true
	2342
	2343
[1289]	2344	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2345	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2346	if [[ $do_compile = true ]]
	2347	then
	2348
[2261]	2349	TEMPDIR_COMPILE=$TEMPDIR
[1]	2350
[1199]	2351	cp $make_depository $TEMPDIR_COMPILE
	2352	cd $TEMPDIR_COMPILE
	2353	tar -xf $make_depository > /dev/null 2>&1
	2354	cd - > /dev/null
[1]	2355
[1255]	2356	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2357	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2358	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2359	then
	2360	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2361	else
	2362	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2363	fi
[82]	2364
[1]	2365	else
[475]	2366
[1]	2367	cp $executable ${TEMPDIR}/a.out
[475]	2368
[1]	2369	fi
	2370
	2371
[1289]	2372	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2373	cd $TEMPDIR
[1]	2374	printf "\n *** changed to temporary directory: $TEMPDIR"
	2375
	2376
[1289]	2377	# IF REQUIRED, START WITH COMPILING
[1]	2378	if [[ $do_compile = true ]]
	2379	then
	2380
	2381
[1199]	2382	if [[ -f a.out ]]
[475]	2383	then
[82]	2384
[1199]	2385	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2386	printf "\n\n\n *** executable a.out found"
	2387	printf "\n no compilation required \n"
	2388
[1]	2389	else
[807]	2390
[1199]	2391	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2392	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2393	printf " *** compilation with make using following options:\n"
	2394	printf " make depository: $make_depository"
	2395	if [[ "$mopts" != "" ]]
	2396	then
	2397	printf " make options: $mopts\n"
	2398	fi
	2399	printf " compilername: $compiler_name\n"
	2400	printf " compiler options: $fopts\n"
	2401	printf " preprocessor directives: $cpp_options \n"
	2402	printf " linker options: $lopts \n"
	2403	if [[ "$modules" != "" ]]
	2404	then
	2405	printf " modules to be load: $modules \n"
	2406	fi
	2407	printf " source code files: $source_list \n"
[1]	2408
[2261]	2409	if [[ $localhost = ibmh ]]
[1199]	2410	then
	2411	printf " compiler is called via ssh on \"plogin1\" \n"
	2412	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\" "
	2413	[[ ! -f a.out ]] && compile_error=true
[1289]	2414	continue # STATUS=1, IF a.out EXISTS
[1866]	2415	elif [[ $localhost = lcocean ]]
	2416	then
	2417	printf " compiler is called via ssh on \"ocean\" \n"
	2418	echo $PWD
	2419	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\" "
	2420	[[ ! -f a.out ]] && compile_error=true
	2421	continue # STATUS=1, IF a.out EXISTS
[1620]	2422	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2423	then
	2424	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2295]	2425	elif [[ $localhost = lceddy ]]
[2257]	2426	then
[2295]	2427	which mpifc
[2257]	2428	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2295]	2429	elif [[ $localhost = lcgeohu ]]
	2430	then
	2431	printf " compiler is called via ssh on \"cirrus\" \n"
	2432	ssh $SSH_PORTOPT cirrus.geo.hu-berlin.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=\"$lopts\" "
	2433	# this check did not work. Although a.out exists, it sets compile_error to true!
	2434	# [[ ! -f a.out ]] && compile_error=true
	2435	continue # STATUS=1, IF a.out EXISTS
[1199]	2436	else
	2437	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2438	[[ "$module_calls" != "" ]] && eval $module_calls
	2439	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2440	fi
[181]	2441
[1199]	2442	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2443	then
	2444	printf "\n +++ error occured while compiling or linking"
	2445	locat=compile
	2446
[181]	2447	exit
[1199]	2448	else
[1289]	2449	printf "$dashes\n *** compilation finished \n"
[1199]	2450	fi
	2451
[1]	2452	fi
[1199]	2453
[1]	2454	fi
	2455
	2456
[1289]	2457	# PROVIDE THE INPUT FILES
	2458	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2459	(( i = 0 ))
	2460	while (( i < iin ))
	2461	do
	2462	(( i = i + 1 ))
	2463	if (( i == 1 ))
	2464	then
[1289]	2465	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2466	fi
	2467
	2468
[1289]	2469	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2470	if [[ "${transin[$i]}" = unavailable ]]
	2471	then
	2472	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2473	then
[1779]	2474	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2475	printf "\n is not available!"
[1]	2476	else
[1779]	2477	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2478	printf "\n is not available!"
[1]	2479	fi
	2480	continue
	2481	fi
	2482
[1289]	2483	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2484	files_for_pes=false; datentyp=file
	2485	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2486	then
[2261]	2487	files_for_pes=true; datentyp=files
[1]	2488	actionin[$i]=""
	2489	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2490	then
	2491	actionin[$i]=""
[2261]	2492	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
[1]	2493	then
[2261]	2494	files_for_pes=true; datentyp=files
	2495	actionin[$i]="ln"
	2496	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
[1]	2497	then
[2261]	2498	actionin[$i]="ln"
[1]	2499	fi
	2500
	2501	if [[ $files_for_pes = true ]]
	2502	then
	2503	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2504	else
	2505	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2506	fi
	2507
[2261]	2508	# INPUT-FILES TO BE LINKED
	2509	if [[ "${actionin[$i]}" = ln ]]
[1]	2510	then
[2261]	2511
	2512	printf "\n $datentyp will be linked"
[1]	2513	if [[ $files_for_pes = false ]]
	2514	then
[2261]	2515	if [[ -f "${absnamein[$i]}" ]]
[1]	2516	then
[2261]	2517	ln ${absnamein[$i]} ${localin[$i]}
[1]	2518	got_tmp[$i]=true
	2519	fi
	2520	else
[2261]	2521	if [[ -d "${absnamein[$i]}" ]]
[1]	2522	then
	2523	mkdir ${localin[$i]}
[2261]	2524	cd ${absnamein[$i]}
[149]	2525	for file in $(ls *)
	2526	do
	2527	ln $file $TEMPDIR/${localin[$i]}
[2261]	2528	done >\|/dev/null 2>&1
[149]	2529	cd $TEMPDIR
[1]	2530	fi
	2531
[2261]	2532	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2533	if [[ ! -f "${localin[$i]}/_000000" ]]
[1]	2534	then
[2261]	2535	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2536	cp -r ${absnamein[$i]}/* ${localin[$i]}
[1]	2537	fi
	2538
	2539	got_tmp[$i]=true
	2540	fi
	2541	fi
	2542
[1289]	2543	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	2544	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	2545	then
	2546
	2547	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	2548	then
	2549
[1289]	2550	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2551	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	2552	printf "\n file will be provided for $numprocs processors"
	2553	mkdir ${localin[$i]}
	2554	ival=$numprocs
	2555	(( ii = 0 ))
	2556	while (( ii <= ival-1 ))
	2557	do
	2558	if (( ii < 10 ))
	2559	then
	2560	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2561	elif (( ii < 100 ))
	2562	then
	2563	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2564	elif (( ii < 1000 ))
	2565	then
	2566	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2567	else
	2568	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2569	fi
	2570	(( ii = ii + 1 ))
	2571	done
	2572
	2573	else
	2574
	2575	if [[ $files_for_pes = true ]]
	2576	then
	2577
[1289]	2578	# PROVIDE FILES FOR EACH CORE
	2579	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2580	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	2581	printf "\n providing $numprocs files for the respective processors"
	2582	mkdir ${localin[$i]}
[2261]	2583	if [[ $link_local_input = true ]]
	2584	then
	2585	printf " files will be linked\n"
	2586	cd ${absnamein[$i]}
	2587	for file in $(ls *)
	2588	do
	2589	ln -f $file ${localin[$i]}
	2590	done
	2591	cd $TEMPDIR
	2592	fi
[1289]	2593
	2594	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[2261]	2595	if [[ ! -f "${localin[$i]}/_000000" ]]
	2596	then
	2597	if [[ $link_local_input = true ]]
	2598	then
	2599	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2600	fi
	2601	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2602	fi
[1]	2603
	2604	else
[1289]	2605
	2606	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[2261]	2607	if [[ $link_local_input = true ]]
	2608	then
	2609	printf " file will be linked\n"
	2610	ln -f ${absnamein[$i]} ${localin[$i]}
	2611	fi
	2612	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	2613	if [[ ! -f "${localin[$i]}" ]]
[183]	2614	then
[2261]	2615	if [[ $link_local_input = true ]]
	2616	then
	2617	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2618	fi
	2619	cp ${absnamein[$i]} ${localin[$i]}
[183]	2620	fi
[1]	2621	fi
	2622	fi
	2623	fi
	2624
	2625	done
	2626	if (( i != 0 ))
	2627	then
[1289]	2628	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	2629	fi
	2630
	2631
[1289]	2632	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	2633	(( i = 0 ))
	2634	while (( i < iic ))
	2635	do
	2636	(( i = i + 1 ))
	2637	if (( i == 1 ))
	2638	then
[1289]	2639	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	2640	fi
	2641	printf "\n >>> ${in_command[$i]}"
	2642	eval ${in_command[$i]}
	2643	if (( i == iic ))
	2644	then
[1289]	2645	printf "\n$dashes\n"
[1]	2646	fi
	2647	done
	2648
	2649
[1289]	2650	# SET THE REMAINING CPU-TIME
[1]	2651	cpurest=${cpumax}.
	2652
	2653
[260]	2654	# START DVR STREAMING SERVER
	2655	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	2656	then
	2657	if [[ "$dvr_server" != "" ]]
	2658	then
	2659
	2660	printf "\n\n *** preparing the dvr streaming server configuration file"
	2661
[1289]	2662	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	2663	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	2664	if [[ "$running_dvrserver_id" != "" ]]
	2665	then
	2666
[261]	2667	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	2668	printf "\n This server is used instead starting a new one!"
[261]	2669	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	2670
	2671	else
	2672
	2673	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	2674	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	2675	then
	2676	cp ${PALM_BIN}/.dvrserver.config .
	2677
[1289]	2678	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	2679	user_id=`id -u`
	2680	group_id=`id -g`
[1289]	2681
	2682	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	2683	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	2684	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	2685	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	2686	mv .dvrserver.3 .dvrserver.config
	2687	rm .dvrserver.1 .dvrserver.2
	2688
[1289]	2689	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	2690	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	2691	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	2692	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	2693	local_dvrserver_running=.TRUE.
	2694	else
	2695	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	2696	printf "\n \"$PALM_BIN\" "
	2697	locat=dvr
	2698	exit
	2699	fi
	2700
	2701	fi
	2702
	2703	else
	2704	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	2705	fi
	2706	fi
	2707
	2708
[1289]	2709	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2710	# (FILE ENVPAR WILL BE READ BY PALM)
[2261]	2711	cat > ENVPAR << EOF
[260]	2712	&envpar run_identifier = '$fname', host = '$localhost',
[2298]	2713	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
[759]	2714	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	2715	maximum_cpu_time_allowed = ${cpumax}.,
	2716	revision = '$global_revision',
[1402]	2717	local_dvrserver_running = $local_dvrserver_running,
	2718	batch_job = $batch_job /
[260]	2719
[2261]	2720	EOF
[260]	2721
	2722
[1289]	2723	# STARTING THE EXECUTABLE
	2724	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	2725	PATH=$PATH:$TEMPDIR
	2726
[1779]	2727
	2728	if [[ $execute_command != "none" ]]
[359]	2729	then
	2730
[1779]	2731	printf "\n +++ branch still not realized"
	2732	locat=execution
	2733	exit
	2734
[693]	2735	else
	2736
[1779]	2737	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
	2738	if [[ "$mpi_debug" = true ]]
[1549]	2739	then
[1779]	2740	export MPI_CHECK_ARGS=1
	2741	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
[1549]	2742	fi
	2743
[1779]	2744	if [[ "$totalview" = true ]]
[1]	2745	then
[1779]	2746	printf "\n *** totalview debugger will be used"
	2747	tv_opt="-tv"
	2748	else
	2749	tv_opt=""
[1]	2750	fi
[1779]	2751
	2752	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
[1]	2753	then
	2754
[1779]	2755	#Interactive ALLINEA DEBUG seesion
	2756	if [[ "$ENVIRONMENT" != BATCH ]]
	2757	then
	2758	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2759	then
	2760	if [[ "$allinea" = true ]]
	2761	then
	2762	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
[1]	2763
[1779]	2764	ddt aprun -n $ii -N $tasks_per_node a.out
	2765	wait
	2766	fi
	2767	fi
	2768	fi
[1]	2769
[1779]	2770	if [[ $localhost = ibmh ]]
	2771	then
[1]	2772
[1779]	2773	# SETUP THE IBM MPI ENVIRONMENT
	2774	export MP_SHARED_MEMORY=yes
	2775	export AIXTHREADS_SCOPE=S
	2776	export OMP_NUM_THREADS=$threads_per_task
	2777	export AUTHSTATE=files
	2778	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
[1]	2779
[1779]	2780	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	2781	export MP_ADAPTER_USE=shared
	2782	export MP_CPU_USE=multiple
	2783	export MP_TIMEOUT=1200
[622]	2784
[1779]	2785	unset MP_TASK_AFFINITY
[1295]	2786
[1779]	2787	if [[ "$LOADLBATCH" = yes ]]
	2788	then
	2789	totalview poe a.out
	2790	else
	2791	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2792	export TVDSVRLAUNCHCMD=ssh
	2793	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2794	fi
[622]	2795
[1779]	2796	fi # END DEBUG MODE
[1289]	2797
[1779]	2798	else
	2799
	2800	# NORMAL EXECUTION
	2801	if [[ -n $numprocs ]]
[1]	2802	then
[1289]	2803
[1779]	2804	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	2805	if [[ $(echo $host \| cut -c1-3) = ibm ]]
[312]	2806	then
[1]	2807
[1779]	2808	# SETUP THE IBM MPI ENVIRONMENT
	2809	if [[ $host != ibmh && $host != ibmkisti ]]
[696]	2810	then
[1779]	2811	export MP_SHARED_MEMORY=yes
	2812	export AIXTHREAD_SCOPE=S
[696]	2813	export OMP_NUM_THREADS=$threads_per_task
[1779]	2814	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	2815	export AUTHSTATE=files
	2816	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	2817	# export MP_PRINTENV=yes
	2818
	2819	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	2820	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
	2821	export MP_WAIT_MODE=poll
	2822	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
[696]	2823	fi
[693]	2824
[1779]	2825	if [[ $host = ibmkisti ]]
[1]	2826	then
[1779]	2827	export LANG=en_US
	2828	export MP_SHARED_MEMORY=yes
	2829	if [[ $threads_per_task = 1 ]]
[343]	2830	then
[1779]	2831	export MP_SINGLE_THREAD=yes
	2832	export MEMORY_AFFINITY=MCM
[343]	2833	else
[1779]	2834	export OMP_NUM_THREADS=$threads_per_task
[343]	2835	fi
[1]	2836	fi
[1779]	2837
	2838	if [[ "$LOADLBATCH" = yes ]]
[1]	2839	then
[1779]	2840	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	2841	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
[1]	2842	then
[1779]	2843	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
[2365]	2844	elif [[ $localhost = ibmmuc* ]]
	2845	then
	2846	ulimit -c unlimited # only for debgingg
	2847	echo $MP_NODES > ~/job_queue/hostfile.$kennung
	2848	echo $MP_PROCS >> ~/job_queue/hostfile.$kennung
	2849	cat $LOADL_HOSTFILE >> ~/job_queue/hostfile.$kennung
	2850	export MP_NODES=$nodes
	2851	export MP_PROCS=$numprocs
	2852	# export MPI_SINGLE_THREAD=no # LRZ NetCDF
	2853	# export MP_TASKS_PER_NODE=$tasks_per_node
	2854	echo "Resource Info: "
	2855	echo "numprocs: " $numprocs " MP_PROCS " $MP_PROCS
	2856	echo "nodes: " $nodes " MP_NODES " $MP_NODES
	2857	echo "tasks_per_node: " $tasks_per_node
	2858	echo "threads_per_task: " $threads_per_task
	2859	export OMP_NUM_THREADS=1
	2860	source /lrz/sys/share/modules/init/bash
	2861	module li
	2862	echo "runfile_atmos"
	2863
	2864	if [[ $run_vnested_model = true ]]
	2865	then
	2866
	2867	printf "\n Nested run ($numprocs_crse Coarse, $numprocs_fine Fine)"
	2868	printf "\n using $nested_mode nesting"
	2869	printf "\n\n"
	2870
	2871	echo "$vnested_mode $numprocs_crse $numprocs_fine" > runfile_atmos
	2872
	2873	poe ./a.out < runfile_atmos
	2874	# mpiexec -n $numprocs ./a.out < runfile_atmos
	2875	else
	2876	echo "precursor_atmos" > runfile_atmos
	2877	poe ./a.out -proc $numprocs -nodes $nodes < runfile_atmos
	2878	# mpiexec -n $numprocs ./a.out < runfile_atmos
	2879
	2880	fi
[1]	2881	else
[1779]	2882	if [[ $run_coupled_model = false ]]
	2883	then
	2884	if [[ "$ocean_file_appendix" = true ]]
	2885	then
	2886	echo "precursor_ocean" > runfile_atmos
	2887	else
	2888	echo "precursor_atmos" > runfile_atmos
	2889	fi
	2890	else
	2891	(( iia = $numprocs_atmos / $threads_per_task ))
	2892	(( iio = $numprocs_ocean / $threads_per_task ))
	2893	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2894	printf "\n\n"
	2895	echo "coupled_run $iia $iio" > runfile_atmos
	2896	fi
	2897	poe ./a.out < runfile_atmos
[1]	2898	fi
[1779]	2899	else
	2900	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[331]	2901	then
[1779]	2902	poe a.out -procs $numprocs -nodes 1 -rmpool 0
	2903	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
	2904	then
	2905	if [[ -f $hostfile ]]
[331]	2906	then
[1779]	2907	cp $hostfile hostfile
[331]	2908	else
[1779]	2909	(( ii = 1 ))
	2910	while (( ii <= $numprocs ))
	2911	do
	2912	echo $localhost_realname >> hostfile
	2913	(( ii = ii + 1 ))
	2914	done
[331]	2915	fi
[1779]	2916	export MP_HOSTFILE=hostfile
	2917	if [[ $run_coupled_model = false ]]
	2918	then
	2919	if [[ "$ocean_file_appendix" = true ]]
	2920	then
	2921	echo "precursor_ocean" > runfile_atmos
	2922	else
	2923	echo "precursor_atmos" > runfile_atmos
	2924	fi
	2925	else
	2926	(( iia = $numprocs_atmos / $threads_per_task ))
	2927	(( iio = $numprocs_ocean / $threads_per_task ))
	2928	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2929	printf "\n\n"
	2930	echo "coupled_run $iia $iio" > runfile_atmos
	2931	fi
[331]	2932
[1779]	2933	poe ./a.out -procs $numprocs < runfile_atmos
[1289]	2934
[1]	2935	else
[1779]	2936	if [[ "$host_file" = "" ]]
	2937	then
	2938	printf "\n +++ no hostfile given in configuration file"
	2939	locat=config_file
	2940	exit
	2941	else
	2942	eval host_file=$host_file
	2943	fi
	2944	export MP_HOSTFILE=$host_file
	2945	poe a.out -procs $numprocs -tasks_per_node $numprocs
[1]	2946	fi
	2947	fi
[1779]	2948
	2949	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	2950	then
[1779]	2951
	2952	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	2953	# DOES NOT EXIST
[2257]	2954	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
[179]	2955	then
[1779]	2956	if [[ -f $hostfile ]]
[1598]	2957	then
[1779]	2958	cp $hostfile hostfile
	2959	(( ii = $numprocs / $threads_per_task ))
	2960	[[ $ii = 0 ]] && (( ii = 1 ))
	2961	else
	2962	(( ii = 1 ))
	2963	while (( ii <= $numprocs / $threads_per_task ))
	2964	do
	2965	echo $localhost_realname >> hostfile
	2966	(( ii = ii + 1 ))
	2967	done
	2968	if (( $numprocs / $threads_per_task == 0 ))
	2969	then
	2970	echo $localhost_realname >> hostfile
	2971	fi
[1598]	2972	fi
[1779]	2973	eval zeile=\"`head -n $ii hostfile`\"
	2974	printf "\n *** running on: $zeile"
[179]	2975	fi
	2976
[1779]	2977	(( ii = $numprocs / $threads_per_task ))
	2978	[[ $ii = 0 ]] && (( ii = 1 ))
	2979	export OMP_NUM_THREADS=$threads_per_task
[1289]	2980
[1779]	2981	if [[ $threads_per_task != 1 ]]
[291]	2982	then
[1779]	2983	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	2984	# MAY ABORT
	2985	ulimit -s unlimited
	2986	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[291]	2987	fi
[2365]	2988	if [[ $run_coupled_model = false && $run_vnested_model = false ]]
[1224]	2989	then
[1779]	2990	if [[ "$ocean_file_appendix" = true ]]
	2991	then
	2992	echo "precursor_ocean" > runfile_atmos
	2993	else
	2994	echo "precursor_atmos" > runfile_atmos
	2995	fi
	2996	printf "\n\n"
[1622]	2997
[1779]	2998	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2999	then
	3000	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
	3001	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	3002	elif [[ $host = lcbullhh ]]
	3003	then
	3004	export OMPI_MCA_pml=cm
	3005	export OMPI_MCA_mtl=mxm
	3006	export OMPI_MCA_coll=^ghc
	3007	export OMPI_MCA_mtl_mxm_np=0
	3008	export MXM_RDMA_PORTS=mlx5_0:1
	3009	export MXM_LOG_LEVEL=ERROR
	3010	export OMP_NUM_THREADS=$threads_per_task
	3011	export KMP_AFFINITY=verbose,granularity=core,compact,1
	3012	export KMP_STACKSIZE=64m
[1622]	3013
[2147]	3014	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
[1622]	3015
[1779]	3016	elif [[ $host = lccrayf ]]
	3017	then
	3018	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
	3019	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
	3020	then
[2257]	3021	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	3022	elif [[ $host = lceddy ]]
[1779]	3023	then
[2257]	3024	echo $ii
[2295]	3025	echo $tasks_per_node
	3026	echo $nodes
[2257]	3027	mpirun -n $ii a.out < runfile_atmos
[2295]	3028	elif [[ $host = lcgeohu ]]
	3029	then
	3030	srun -n $ii a.out < runfile_atmos
[1866]	3031	elif [[ $host = lcocean ]]
	3032	then
	3033	mpirun a.out $ROPTS < runfile_atmos
[1779]	3034	elif [[ $host = lcsb ]]
	3035	then
	3036	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
[2365]	3037	elif [[ $host = lclrz \|\| $host = lcbwuni ]]
	3038	then
	3039	mpiexec -n $ii a.out < runfile_atmos $ROPTeS
	3040	elif [[ $host = lckea* ]]
	3041	then
	3042	srun -n $ii a.out < runfile_atmos $ROPTeS
[1779]	3043	elif [[ $host = lckiaps ]]
	3044	then
[1940]	3045	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
[1779]	3046	elif [[ $host = lckyu* ]]
	3047	then
	3048	mpiexec -n $ii --stdin runfile_atmos ./a.out
	3049	else
	3050	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
	3051	fi
	3052
[2365]	3053	elif [[ $run_coupled_model = true ]]
	3054	then
[2298]	3055	# COUPLED RUN
[1779]	3056	(( iia = $numprocs_atmos / $threads_per_task ))
	3057	(( iio = $numprocs_ocean / $threads_per_task ))
	3058	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	3059	printf "\n\n"
[164]	3060
[2298]	3061	echo "coupled_run $iia $iio" > runfile_atmos
	3062
	3063	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
[206]	3064	then
[197]	3065
[2298]	3066	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
[206]	3067
[2298]	3068	elif [[ $host = lck \|\| $host = lckordi ]]
	3069	then
[1779]	3070
[2298]	3071	mpiexec -n $ii ./a.out < runfile_atmos &
[1779]	3072
[2298]	3073	elif [[ $host = lckyu* ]]
	3074	then
[206]	3075
[2298]	3076	mpiexec -n $ii --stdin runfile_atmos ./a.out
[164]	3077
[2298]	3078	elif [[ $host = lcmuk ]]
	3079	then
[206]	3080
[2298]	3081	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
[206]	3082
[1779]	3083	fi
[2298]	3084	wait
[1604]	3085
[2365]	3086
	3087	elif [[ $run_vnested_model = true ]]
	3088	then
	3089	printf "\n Vertical Nested run ($numprocs_crse Coarse, $numprocs_fine Fine)"
	3090	printf "\n using $vnested_mode vnesting"
	3091	printf "\n\n"
	3092
	3093	echo "$vnested_mode $numprocs_crse $numprocs_fine" > runfile_atmos
	3094
	3095	if [[ $host = lcbwuni \|\| $host = lclrz* ]]
	3096	then
	3097	mpiexec -n $ii a.out < runfile_atmos $ROPTeS
	3098	elif [[ $host = lckea* ]]
	3099	then
	3100	srun -n $ii a.out < runfile_atmos $ROPTeS
	3101	else
	3102	mpirun -np $numprocs ./a.out $ROPTS < runfile_atmos
	3103	fi
	3104	wait
[164]	3105	fi
[102]	3106
[1779]	3107	elif [[ $host = lckyoto ]]
[440]	3108	then
[1779]	3109	set -xv
	3110	export P4_RSHCOMMAND=plesh
	3111	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3112	if [[ "$ENVIRONMENT" = BATCH ]]
[505]	3113	then
[1779]	3114	if [[ "$cond2" = fujitsu ]]
	3115	then
	3116	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
	3117	elif [[ "cond2" = pgi ]]
	3118	then
	3119	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
	3120	else
	3121	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
	3122	fi
[505]	3123	else
[1779]	3124	if [[ "$cond2" = "" ]]
	3125	then
	3126	mpiruni_rsh -np $numprocs ./a.out # for intel
	3127	else
	3128	mpirun -np $numprocs ./a.out
	3129	fi
[505]	3130	fi
[1779]	3131	set +xv
	3132
	3133	elif [[ $host = lctit ]]
	3134	then
	3135	export OMP_NUM_THREADS=$threads_per_task
	3136	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3137	if [[ "$threads_per_task" != 1 ]]
[505]	3138	then
[1779]	3139	export MV2_ENABLE_AFFINITY=0
[505]	3140	fi
[1779]	3141	echo "----- PBS_NODEFILE content:"
	3142	cat $PBS_NODEFILE
	3143	echo "-----"
	3144	(( ii = $numprocs / $threads_per_task ))
	3145	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
	3146	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
[1289]	3147
[1779]	3148	else
	3149	mpprun -n $numprocs a.out
[678]	3150	fi
[1]	3151	else
[1779]	3152	a.out
[1]	3153	fi
[1289]	3154
[1779]	3155	fi # end normal (non-debug) execution
	3156
	3157	fi # end explicit execute_command or host-specific execute actions
	3158
[1289]	3159	if [[ $? != 0 ]]
[1]	3160	then
	3161
[1289]	3162	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3163	printf "\n +++ runtime error occured"
	3164	locat=execution
	3165	exit
[1289]	3166
[1]	3167	else
[260]	3168
[1289]	3169	printf "\n$dashes\n *** execution finished \n"
	3170
	3171	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3172	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3173	if [[ "$dvrserver_id" != "" ]]
	3174	then
	3175	kill $dvrserver_id
	3176	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3177
[1289]	3178	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3179	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3180	if [[ -d DATA_DVR ]]
	3181	then
[261]	3182
[1289]	3183	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3184	# DIRECTORY
[262]	3185	cp .dvrserver.config DATA_DVR
	3186
[1289]	3187	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3188	# SEQUENCE MODE DATA TOO)
[262]	3189	process_dvr_output -d DATA_DVR -f $fname -s
	3190
	3191	else
	3192
[1289]	3193	# PROCESS THE LOCAL OUTPUT
[262]	3194	process_dvr_output -l -d DATA_DVR -f $fname
	3195
	3196	fi
	3197
	3198	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3199	then
	3200
[1289]	3201	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3202	process_dvr_output -l -d DATA_DVR -f $fname
	3203
[260]	3204	fi
[1]	3205	fi
	3206
	3207
	3208
[1289]	3209	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3210	# BY EACH CORE INTO ONE FILE
[920]	3211	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3212	then
	3213	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3214	printf "\n 2d- and/or 3d-data may be incomplete!"
	3215	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3216	elif [[ "$combine_plot_fields" == true ]]
	3217	then
[1270]	3218	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3219	then
	3220	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
[1779]	3221	aprun -n 1 -N 1 combine_plot_fields${block}.x
[1270]	3222	else
	3223	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3224	combine_plot_fields${block}.x
	3225	fi
[920]	3226	else
[1289]	3227
	3228	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3229	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3230	# ??? koennen wir das streichen ???
[920]	3231	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3232	fi
[503]	3233
	3234
	3235
[1289]	3236	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3237	(( i = 0 ))
	3238	while (( i < ioc ))
	3239	do
	3240	(( i = i + 1 ))
	3241	if (( i == 1 ))
	3242	then
[1289]	3243	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3244	fi
	3245	printf "\n >>> ${out_command[$i]}"
	3246	eval ${out_command[$i]}
	3247	if (( i == ioc ))
	3248	then
[1289]	3249	printf "\n$dashes\n"
[1]	3250	fi
	3251	done
	3252
	3253
[1289]	3254	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3255	if [[ $do_trace = true ]]
	3256	then
	3257	printf "\n\n"
	3258	ls -al
	3259	fi
[2261]	3260
[1]	3261
[1289]	3262	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3263	(( i = 0 ))
	3264	while (( i < iout ))
	3265	do
	3266	(( i = i + 1 ))
	3267	if (( i == 1 ))
	3268	then
[2261]	3269	printf "\n\n *** saving OUTPUT-files:"
	3270
	3271	# GET RUN NUMBER ASSIGNED BY PALM
	3272	if [[ -f RUN_NUMBER ]]
	3273	then
	3274	read run_number < RUN_NUMBER
	3275	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	3276	usecycle_option="-U $run_number"
	3277	else
	3278	run_number=0
	3279	usecycle_option=""
	3280	fi
	3281	printf "\n$dashes"
[1]	3282	fi
	3283
[2261]	3284	# ADD CYCLE NUMBER TO FILENAME
	3285	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	3286	then
	3287
	3288	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	3289	if [[ "${actionout[$i]}" != "a" ]]
	3290	then
	3291	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	3292	# WITH AN EXISTING CYCLE NUMBER
	3293	if (( run_number >= cycnum[$i] ))
	3294	then
	3295	(( cycnum[$i] = run_number ))
	3296	else
	3297	if (( run_number > 0 ))
	3298	then
	3299	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	3300	fi
	3301	fi
	3302	fi
	3303	if (( cycnum[$i] > 0 ))
	3304	then
	3305	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	3306	fi
	3307	fi
	3308
[1289]	3309	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3310	files_for_pes=false; filetyp=file
[2261]	3311	link_local_output=false
[1]	3312	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3313	then
	3314	files_for_pes=true; filetyp=directory
	3315	actionout[$i]=""
	3316	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3317	then
	3318	actionout[$i]=""
[2261]	3319	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
[1]	3320	then
	3321	files_for_pes=true; filetyp=directory
[2261]	3322	link_local_output=true
	3323	actionout[$i]=""
	3324	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
[1]	3325	then
[2261]	3326	link_local_output
	3327	actionout[$i]=""
[1]	3328	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3329	then
	3330	files_for_pes=true; filetyp=directory
	3331	actionout[$i]="tr"
	3332	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3333	then
	3334	actionout[$i]="tr"
	3335	fi
	3336
	3337	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3338	then
	3339	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3340	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3341	then
	3342	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3343	else
	3344
	3345
[1289]	3346	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3347	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3348	if [[ "${actionout[$i]}" = tr ]]
	3349	then
	3350	if [[ $localhost != $fromhost ]]
	3351	then
	3352	if [[ $files_for_pes = false ]]
	3353	then
	3354	cps=""
	3355	cst=""
	3356	else
	3357	cps=-c
	3358	cst="/"
	3359	fi
[2261]	3360
	3361	transfer_failed=false
	3362	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3363	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
	3364	if [[ $localhost = lccrayb ]]
[1]	3365	then
[2261]	3366	ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
	3367	elif [[ $localhost = lccrayh ]]
	3368	then
	3369	ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
	3370	elif [[ $localhost = lcbullhh ]]
	3371	then
	3372	ssh $usern@mlogin101 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
	3373	elif [[ $localhost = lcxe6 ]]
	3374	then
	3375	ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1]	3376	else
[2261]	3377	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3378	fi
	3379	[[ $? != 0 ]] && transfer_failed=true
[1]	3380
[2261]	3381	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	3382	if [[ $transfer_failed = true ]]
	3383	then
	3384	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
	3385	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
[1]	3386
[2261]	3387	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	3388	eval local_catalog=${pathout[$i]}
	3389	if [[ ! -d $local_catalog ]]
[1]	3390	then
[2261]	3391	printf " *** local directory does not exist. Trying to create:\n"
	3392	printf " $local_catalog \n"
	3393	mkdir -p $local_catalog
[1]	3394	fi
[2261]	3395	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3396	transfer_problems=true
[1]	3397	fi
[2261]	3398
[1]	3399	else
	3400
[1289]	3401	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3402	actionout[$i]=""
	3403	fi
	3404	fi
	3405
	3406
[1289]	3407	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3408	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3409	if [[ "${actionout[$i]}" = tra ]]
	3410	then
	3411	if [[ $localhost != $fromhost ]]
	3412	then
[2261]	3413	if [[ $localhost = ibmh ]]
[1]	3414	then
	3415
[1289]	3416	# TRANSFER IN SEPERATE JOB
	3417	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3418	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3419	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3420	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3421
	3422	echo "set -x" > transfer_${localout[$i]}
	3423	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3424
	3425	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3426	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3427	printf "\n or higher cycle\n"
[1468]	3428	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]	3429
[1]	3430	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3431
[2261]	3432	if [[ $LOGNAME = b323013 ]]
[1]	3433	then
[2261]	3434	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3435	else
[2261]	3436	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3437	fi
	3438
	3439	else
	3440
[1289]	3441	# TRANSFER WITHIN THIS JOB
[1]	3442	transfer_failed=false
[82]	3443	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3444	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3445	if [[ $localhost = lccrayb ]]
	3446	then
[2261]	3447	ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1274]	3448	elif [[ $localhost = lccrayh ]]
	3449	then
[2261]	3450	ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1468]	3451	elif [[ $localhost = lcxe6 ]]
	3452	then
[2261]	3453	ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
[1255]	3454	else
[1468]	3455	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3456	fi
[82]	3457	[[ $? != 0 ]] && transfer_failed=true
[1]	3458
[1289]	3459	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3460	if [[ $transfer_failed = true ]]
	3461	then
[1289]	3462	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3463	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3464
[1289]	3465	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3466	eval local_catalog=${pathout[$i]}
	3467	if [[ ! -d $local_catalog ]]
	3468	then
	3469	printf " *** local directory does not exist. Trying to create:\n"
	3470	printf " $local_catalog \n"
	3471	mkdir -p $local_catalog
	3472	fi
	3473
	3474	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3475	transfer_problems=true
	3476	fi
	3477	fi
	3478	else
	3479
[1289]	3480	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3481	actionout[$i]=a
	3482	fi
	3483	fi
	3484
	3485
[1289]	3486	# APPEND ON THIS MACHINE
[1]	3487	if [[ "${actionout[$i]}" = "a" ]]
	3488	then
[741]	3489	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	3490	then
	3491	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	3492	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	3493	else
	3494	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	3495	cat ${localout[$i]} >> ${pathout[$i]}
	3496	fi
[1]	3497	fi
	3498
[1289]	3499	# COPY ON THIS MACHINE
	3500	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	3501	# ON DIFFERENT FILE-SYSTEMS
[1]	3502	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	3503	then
	3504
[1289]	3505	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	3506	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	3507	then
	3508	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[2261]	3509	if [[ $link_local_output = true ]]
	3510	then
	3511	printf " file will be linked\n"
	3512	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3513	fi
	3514	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3515	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
[149]	3516	then
[2261]	3517	if [[ $link_local_output = true ]]
	3518	then
	3519	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3520	fi
	3521	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3522	else
	3523	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
[149]	3524	fi
[1]	3525	else
	3526	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[2261]	3527	if [[ $link_local_output = true ]]
	3528	then
	3529	printf " file will be linked\n"
	3530	ln -f ${localout[$i]} ${pathout[$i]}
	3531	fi
	3532	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3533	if [[ ! -f "${pathout[$i]}" ]]
[149]	3534	then
[2261]	3535	if [[ $link_local_output = true ]]
	3536	then
	3537	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3538	fi
	3539	cp ${localout[$i]} ${pathout[$i]}
	3540	else
	3541	printf "+++ no copy because file ${pathout[$i]} exists\n"
[149]	3542	fi
[1]	3543	fi
	3544
	3545	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	3546	then
	3547
[1289]	3548	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	3549	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	3550	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[2261]	3551	if [[ $link_local_output = true ]]
	3552	then
	3553	printf " files will be linked\n"
	3554	mkdir ${pathout[$i]}
	3555	cd ${localout[$i]}
	3556	for file in $(ls *)
	3557	do
	3558	ln -f $file ${pathout[$i]}
	3559	done >\|/dev/null 2>&1
	3560	cd $TEMPDIR
	3561	fi
[1289]	3562
	3563	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[2261]	3564	if [[ ! -f "${pathout[$i]}/_000000" ]]
[149]	3565	then
[2261]	3566	if [[ $link_local_output = true ]]
	3567	then
	3568	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3569	fi
	3570	cp -r ${localout[$i]}/* ${pathout[$i]}
	3571	fi
[1]	3572
	3573	fi
	3574	fi
	3575	done
	3576	if (( i != 0 ))
	3577	then
	3578	if [[ $transfer_problems = true ]]
	3579	then
[1289]	3580	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	3581	printf "\n +++ WARNING: some data transfers failed! \n"
	3582	else
[1289]	3583	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	3584	fi
	3585	fi
	3586
	3587
[1289]	3588	# IF REQUIRED, START A RESTART-JOB
	3589	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	3590	if [[ -f CONTINUE_RUN ]]
	3591	then
	3592
[2261]	3593	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	3594	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	3595	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	3596	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
	3597	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	3598	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	3599	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	3600	if [[ $(echo $mc \| grep -c "#") != 0 ]]
[1]	3601	then
[2261]	3602	mc=`echo $mc \| sed 's/#/f/g'`
	3603	fi
[1]	3604
	3605
[2261]	3606	# START THE RESTART-JOB
	3607	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
	3608	echo " $mc"
	3609	printf "\n$dashes\n"
	3610	if [[ $localhost != $fromhost ]]
	3611	then
[1]	3612
[2295]	3613	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 \|\| $localhost = lcgeohu ]]
[1]	3614	then
[2261]	3615	echo "*** ssh will be used to initiate restart-runs!"
	3616	echo " return_address=\"$return_address\" "
	3617	echo " return_username=\"$return_username\" "
	3618	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
[1]	3619	then
[2261]	3620	if [[ $localhost = ibmh ]]
[1]	3621	then
[2261]	3622	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\" "
	3623	elif [[ $localhost = lcbullhh ]]
	3624	then
	3625	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\" "
	3626	elif [[ $localhost = lccrayb ]]
	3627	then
	3628	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\" "
	3629	elif [[ $localhost = lccrayh ]]
	3630	then
	3631	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\" "
	3632	elif [[ $localhost = lcxe6 ]]
	3633	then
	3634	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\" "
[1]	3635	else
[2261]	3636	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 "
[1]	3637	fi
	3638	else
[2261]	3639	if [[ $localhost = ibmkisti ]]
	3640	then
	3641	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\" "
	3642	elif [[ $localhost = lceddy ]]
	3643	then
	3644	/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 "
	3645	elif [[ $localhost = lcocean ]]
	3646	then
	3647	/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 "
	3648	elif [[ $localhost = lccrayb ]]
	3649	then
	3650	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\" "
	3651	elif [[ $localhost = lccrayh ]]
	3652	then
	3653	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\" "
[2295]	3654	elif [[ $localhost = lccgeohu ]]
	3655	then
	3656	ssh $usern@cirrus.geo.hu-berlin.de "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
[2261]	3657	else
	3658	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	3659	fi
[1]	3660	fi
[2261]	3661	else
	3662	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	3663	locat=restart; exit
	3664	fi
[1]	3665
[2261]	3666	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	3667	if [[ $queue = special1q ]]
	3668	then
	3669	sleep 120
[1]	3670	else
[2261]	3671	sleep 30
	3672	fi
[1]	3673
[2261]	3674	else
	3675
	3676	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	3677	# USING SSH)
	3678	cd $LOCAL_PWD
[1103]	3679	if [[ $localhost = lckyuh ]]
	3680	then
[2261]	3681	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	3682	printf "\n please restart job manually using command:\n"
	3683	printf "\n \"$mc\" "
[1103]	3684	else
[2261]	3685	eval $mc # THE ' MUST BE EVALUATED
[1103]	3686	fi
[2261]	3687	cd - > /dev/null
	3688	fi
	3689	if [[ $localhost = lckyuh ]]
	3690	then
	3691	printf "\n$dashes\n *** restart-run to be initiated manually\n"
	3692	else
	3693	printf "\n$dashes\n *** restart-run initiated \n"
	3694	fi
[1]	3695
	3696
[2261]	3697	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	3698	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	3699	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	3700	# MAY BE VERY HUGE)
	3701	(( i = 0 ))
	3702	while (( i < iin ))
	3703	do
	3704	(( i = i + 1 ))
	3705	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	3706	then
	3707	rm -r ${absnamein[$i]}
	3708	fi
	3709	done
[1]	3710
	3711	fi
	3712
	3713
	3714
[1289]	3715	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	3716	if [[ "$email_notification" != "none" ]]
[1]	3717	then
	3718
	3719	if [[ $localhost != $fromhost ]]
	3720	then
	3721	if [[ -f CONTINUE_RUN ]]
	3722	then
	3723	echo "PALM restart run necessary" > email_text
	3724	echo "description header of actual run:" >> email_text
	3725	cat CONTINUE_RUN >> email_text
	3726	echo "mrun-command to restart:" >> email_text
	3727	echo "$mc" >> email_text
	3728	else
	3729	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	3730	fi
	3731	mail $email_notification < email_text
	3732	printf "\n *** email notification sent to \"$email_notification\" "
	3733	fi
	3734	fi
	3735
	3736
	3737
[1289]	3738	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	3739	cd $HOME
	3740	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	3741
	3742	else
	3743
[1289]	3744	# PREPARING ACTIONS,
	3745	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	3746
[1289]	3747	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[1468]	3748	mrun_com="$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 $remote_username"
[79]	3749	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	3750	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	3751	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	3752	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	3753	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	3754	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	3755	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	3756	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	3757	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	3758	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	3759	if [[ $use_openmp = true ]]
	3760	then
[622]	3761	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	3762	fi
[759]	3763	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[1]	3764	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	3765	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	3766	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	3767	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	3768	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	3769	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[2365]	3770	[[ $run_vnested_model = true ]] && mrun_com=${mrun_com}" -N \"$vnested_dist\""
[920]	3771	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	3772	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	3773	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	3774	if [[ $do_remote = true ]]
	3775	then
	3776	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	3777	fi
	3778
	3779
[1289]	3780	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	3781	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	3782	then
	3783
	3784	printf "\n *** creating the executable for batch job\n"
	3785
[1289]	3786	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	3787	if [[ $host != $localhost ]]
	3788	then
	3789	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	3790	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	3791	locat=create_executable; exit
	3792	fi
	3793
	3794	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3795	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3796
	3797	cp $make_depository .
	3798	tar -xf $make_depository > /dev/null 2>&1
	3799	cp ../* . > /dev/null 2>&1
	3800
	3801	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	3802
	3803	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	3804	then
	3805	printf "\n +++ error occured while compiling or linking"
	3806	locat=compile
	3807	exit
	3808	fi
	3809
	3810	mv a.out ..
	3811	cd - > /dev/null 2>&1
	3812	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3813
	3814	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	3815
	3816	fi
	3817
	3818
[1289]	3819	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	3820	jobfile=jobfile.$RANDOM
	3821
	3822
[1289]	3823	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	3824	echo "mkdir $TEMPDIR" >> $jobfile
	3825	echo "cd $TEMPDIR" >> $jobfile
	3826
	3827
[1289]	3828	# ACTIVATE ERROR-TRACEBACK
[1]	3829	if [[ $do_trace = true ]]
	3830	then
	3831	echo "set -x" >> $jobfile
	3832	else
	3833	echo "set +vx" >> $jobfile
	3834	fi
	3835
	3836
[1289]	3837	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	3838	if [[ "$init_cmds" != "" ]]
	3839	then
	3840	echo "$init_cmds" >> $jobfile
	3841	fi
	3842	if [[ "$module_calls" != "" ]]
	3843	then
	3844	echo "$module_calls" >> $jobfile
	3845	fi
	3846
	3847
[1289]	3848	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	3849	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	3850	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	3851	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	3852	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	3853	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	3854	# QUEUEING-SYSTEMS
[2295]	3855	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean \|\| $host = lcgeohu ]]
[1]	3856	then
	3857
[1289]	3858	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	3859	if [[ $restart_run != true ]]
	3860	then
	3861	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	3862	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	3863	fi
[1]	3864
[1289]	3865	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	3866	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	3867	echo "set -x" >> $jobfile
[693]	3868	if [[ $host = $localhost ]]
	3869	then
[1199]	3870	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	3871	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	3872	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	3873	then
	3874	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3875	else
	3876	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3877	fi
[1199]	3878
[693]	3879	else
[1255]	3880	if [[ $host = ibmkisti ]]
[693]	3881	then
[1289]	3882	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	3883	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3884	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1620]	3885	elif [[ $host = lcbullhh ]]
	3886	then
	3887	echo "localdir=\`pwd\`" >> $jobfile
	3888	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	3889
[1255]	3890	elif [[ $host = lccrayb ]]
	3891	then
	3892	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3893	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3894	elif [[ $host = lccrayh ]]
	3895	then
	3896	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3897	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3898
[1255]	3899	else
[1468]	3900	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	3901	fi
	3902	fi
[193]	3903	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	3904
[1289]	3905	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	3906	# WORKING DIRECTORY OF THE JOB
[193]	3907	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	3908	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	3909	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	3910	echo "execute_mrun=true" >> $jobfile
	3911	echo " " >> $jobfile
	3912
[191]	3913	else
	3914
[1289]	3915	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	3916	if [[ $do_compile = true ]]
	3917	then
	3918
	3919	source_catalog=SOURCES_FOR_RUN_$fname
	3920
[1289]	3921	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	3922	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	3923	echo "export SOURCES_COMPLETE=true" >> $jobfile
	3924	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	3925
	3926	for filename in $source_list
	3927	do
[1289]	3928	# BACKSLASH IS USED FOR MASKING
[191]	3929	echo "cat > $filename << \"%END%\"" >> $jobfile
	3930	cat $source_catalog/$filename >> $jobfile
	3931	echo " " >> $jobfile
	3932	echo "%END%" >> $jobfile
	3933	echo " " >> $jobfile
	3934	done
	3935
[1289]	3936	# BACKSLASH IS USED FOR MASKING
[191]	3937	echo "cat > Makefile << \"%END%\"" >> $jobfile
	3938	cat $source_catalog/Makefile >> $jobfile
[1]	3939	echo " " >> $jobfile
	3940	echo "%END%" >> $jobfile
	3941	echo " " >> $jobfile
	3942
[191]	3943	echo "cd - > /dev/null" >> $jobfile
[1]	3944
[191]	3945	fi
[1]	3946
	3947
[1289]	3948	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	3949	# BACKSLASH IS USED FOR MASKING
	3950	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	3951	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	3952	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	3953	if [[ $host = lckyuh ]]
	3954	then
[1289]	3955	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	3956	sed 's/frtpx/frt/g' $config_file >> $jobfile
	3957	else
	3958	sed 's/#$.*//g' $config_file >> $jobfile
	3959	fi
[191]	3960	echo "%END%" >> $jobfile
	3961	echo " " >> $jobfile
[1]	3962
	3963
[1289]	3964	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	3965	# BACKSLASH IS USED FOR MASKING
[1101]	3966	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	3967	if [[ $host = lckyuh ]]
	3968	then
	3969	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	3970	else
	3971	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	3972	fi
[1101]	3973	echo "%END%" >> $jobfile
[191]	3974	echo "chmod u+x $mrun_script_name" >> $jobfile
	3975	echo "execute_mrun=true" >> $jobfile
	3976	echo " " >> $jobfile
[1]	3977
	3978	fi
	3979
[191]	3980
[1289]	3981	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	3982	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	3983	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	3984	if [[ $do_remote = true ]]
	3985	then
	3986	(( i = 0 ))
	3987	while (( i < iin ))
	3988	do
	3989	(( i = i + 1 ))
	3990	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	3991	if [[ "${transin[$i]}" = job ]]
	3992	then
	3993	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	3994	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	3995	echo " " >> $jobfile
	3996	echo "%END%" >> $jobfile
	3997	else
[1468]	3998	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	3999	fi
	4000
[1289]	4001	# CHECK, IF FILE COULD BE CREATED
[1]	4002	echo "if [[ \$? = 1 ]]" >> $jobfile
	4003	echo "then" >> $jobfile
	4004	echo " echo \" \" " >> $jobfile
	4005	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	4006	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	4007	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	4008	echo " execute_mrun=false" >> $jobfile
	4009	echo "fi" >> $jobfile
	4010	done
	4011	fi
	4012
[1289]	4013	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	4014	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	4015	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	4016	echo "LOCAL_PWD=$working_directory" >> $jobfile
	4017	echo "export LOCAL_PWD" >> $jobfile
	4018
[1289]	4019	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	4020	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	4021	echo "export LOCAL_MRUN_PATH" >> $jobfile
	4022
[2257]	4023	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
	4024	if [[ $host = lceddy \|\| $localhost = lceddy ]]
	4025	then
[1099]	4026	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	4027	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[2257]	4028	fi
[1]	4029
[1289]	4030	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	4031	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	4032	echo "set -x" >> $jobfile
	4033	echo "queue=$queue" >> $jobfile
[1]	4034	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	4035	echo 'ls -al; echo `pwd`' >> $jobfile
	4036	echo "cd \$HOME" >> $jobfile
	4037	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	4038
	4039
	4040
	4041
[1289]	4042	# START THE JOB USING SUBJOB-COMMAND
[1]	4043	if [[ $silent = false ]]
	4044	then
	4045	printf "\n "
	4046	else
	4047	printf "\n\n"
	4048	fi
	4049
[1094]	4050	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]	4051	rm -rf $jobfile
	4052
	4053
[1289]	4054	fi # END OF REMOTE-PART

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