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source: palm/trunk/SCRIPTS/mrun @ 2311

Last change on this file since 2311 was 2303, checked in by raasch, 7 years ago
bugfix: setting default value for write_binary
Property svn:keywords set to `Id Rev`
File size: 141.4 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 2303 2017-07-04 12:26:18Z suehring $
[2303]	29	# bugfix: setting default value for write_binary
	30	#
	31	# 2298 2017-06-29 09:28:18Z raasch
[2298]	32	# write_binary in ENVPAR has type LOGICAL now,
	33	# MPI2 coupling removed
	34	#
	35	# 2297 2017-06-28 14:35:57Z scharf
[2295]	36	# adjustments for using lcgeohu (cirrus @ HUB)
	37	# cpp_opts removed
	38	#
	39	# 2290 2017-06-19 11:03:06Z raasch
[2290]	40	# further test output removed
	41	#
	42	# 2286 2017-06-15 13:31:57Z raasch
[2286]	43	# test output for cycle number removed
	44	#
	45	# 2268 2017-06-09 10:34:09Z raasch
[2268]	46	# bugfix for calculating cycle numbers for output files in r2261
	47	#
	48	# 2262 2017-06-08 14:52:23Z raasch
[2262]	49	# bugfix for r2261
	50	#
	51	# 2261 2017-06-08 14:25:57Z raasch
[2261]	52	# unified cycle numbers for output files are used,
	53	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
	54	# creation of file OUTPUT_FILE_CONNECTIONS removed,
	55	# archive feature completely removed from the script,
	56	# nech related parts completely removed
	57	#
	58	# 2257 2017-06-07 14:07:05Z witha
[2257]	59	# adjustments for lceddy, removed lcflow-specific code
	60	#
	61	# 2186 2017-03-21 05:36:31Z raasch
[1867]	62	#
[2186]	63	# 2185 2017-03-21 05:09:29Z raasch
	64	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
	65	#
[2150]	66	# 2148 2017-02-09 16:56:42Z scharf
	67	# changed allocation of resources for lcbullhh in srun command
	68	#
[2142]	69	# 2141 2017-02-06 10:19:32Z gronemeier
	70	# made check for existing files language independent
	71	#
[1945]	72	# 1944 2016-06-15 06:29:00Z raasch
	73	# adjustments for using HLRN ssh-keys
	74	#
[1941]	75	# 1940 2016-06-14 05:15:20Z raasch $
	76	# adjustments for lckiaps
	77	#
[1867]	78	# 1866 2016-04-15 06:50:59Z raasch
	79	# adjusted for lcocean
[1805]	80	#
[1842]	81	# 1841 2016-04-07 19:14:06Z raasch
	82	# script now running under bash
	83	#
[1805]	84	# 1804 2016-04-05 16:30:18Z maronga
[1779]	85	# test: implementing an execute mechanism where the execute command is given in the
	86	# configuration file
	87	# ROPTS removed from execution commands
	88	# Warnings about missing optional files or user code changed to informative messages
[1804]	89	# Removed parameter file check
[1305]	90	#
[1756]	91	# 1755 2016-02-22 13:53:39Z maronga
	92	# Minor bugfix to last commit
	93	#
[1754]	94	# 1753 2016-02-22 13:49:49Z maronga
	95	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
	96	#
[1623]	97	# 1622 2015-07-20 06:21:36Z heinze
	98	# bugfix for Mistral (lcbullhh)
	99	#
	100	# 1621 2015-07-17 11:39:33Z heinze
[1621]	101	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
[1200]	102	#
[1610]	103	# 1609 2015-07-03 15:37:58Z maronga
	104	# Modified the random number of the temporary working directory to match the
	105	# queuing system number on HLRN-III (lccray*).
	106	#
[1605]	107	# 1604 2015-06-23 15:48:03Z suehring
	108	# Enable coupled runs for lcmuk
	109	#
[1599]	110	# 1598 2015-05-29 06:45:40Z raasch
	111	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
	112	#
[1550]	113	# 1549 2015-01-30 14:26:16Z suehring
	114	# Enable interactive debug sessions with allinea debugger
	115	#
[1548]	116	# 1547 2015-01-29 15:09:12Z witha
	117	# adjustments for ForWind computing cluster (lcflow)
	118	#
[1492]	119	# 1491 2014-11-12 08:12:57Z heinze
	120	# correct setting of batch_job allowed for ibm-machines
	121	#
[1469]	122	# 1468 2014-09-24 14:06:57Z maronga
	123	# Typo removed (addres->address)
	124	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
	125	# Added support for restart runs (remote) for lcxe6
	126	#
[1443]	127	# 1442 2014-07-28 07:09:10Z raasch
	128	# default queues for HLRN-III (lccrayb/lccrayh) defined
	129	#
[1423]	130	# 1422 2014-07-02 10:01:25Z kanani
	131	# automatic restarts enabled for lccrayb,
	132	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
	133	#
[1421]	134	# 1420 2014-06-10 06:24:14Z raasch
	135	# -j1 option added to aprung command for lccrayf (CSC)
	136	#
[1403]	137	# 1402 2014-05-09 14:25:13Z raasch
	138	# batch_job added to envpar-NAMELIST
	139	#
[1358]	140	# 1357 2014-04-11 15:02:03Z witha
	141	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
	142	# possible)
	143	#
[1328]	144	# 1320 2014-03-20 08:40:49Z raasch
	145	# check namelist file set false by default
	146	#
[1305]	147	# 1304 2014-03-12 10:29:42Z raasch
	148	# ulimit option changed from -Ss to -s
	149	#
	150	# bugfix: missing "fi" in r1289
	151	#
[1290]	152	# 1289 2014-03-04 07:12:34Z raasch
	153	# comments translated to English
	154	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	155	# export of variables for palm and interpret_config removed
	156	#
[1282]	157	# 1281 2014-02-01 07:55:49Z raasch
	158	# rsync-copy restricted to Cray machines, since command is unavailable on some
	159	# other systems
	160	#
[1280]	161	# 1279 2014-01-28 12:10:14Z raasch
	162	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	163	# in order to remove annoying restrictions concerning the number of processors which
	164	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	165	# restriction, one of the nodes will be filled with less than the given number of
	166	# tasks per node. A respective warning is given.
	167	#
[1275]	168	# 1274 2014-01-09 13:14:54Z heinze
	169	# adjustments for lccrayh
	170	#
[1273]	171	# 1272 2014-01-08 10:19:32Z witha
	172	# small adjustment for lcflow
	173	#
[1271]	174	# 1270 2013-12-16 11:05:01Z fricke
	175	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	176	#
[1256]	177	# 1255 2013-11-07 14:43:35Z raasch
	178	# further adjustments for lccrayb remote access
	179	#
[1242]	180	# 1241 2013-10-30 11:36:58Z heinze
	181	# Enable use of nudging input and input of large scale forcing from
	182	# external files
	183	#
[1230]	184	# 1229 2013-09-20 06:55:19Z raasch
	185	# further adjustments for lccrayb
	186	#
[1225]	187	# 1224 2013-09-16 07:27:23Z raasch
	188	# first adjustments for lccrayb
	189	#
[1211]	190	# 1210 2013-08-14 10:58:20Z raasch
	191	# fftw support added
	192	#
[1203]	193	# 1201 2013-07-10 16:17:59Z witha
	194	# adjustments for Forwind cluster (lcflow)
	195	#
[1200]	196	# 1199 2013-07-05 14:52:22Z raasch
[1199]	197	# adjustments for CSC Helsinki (lccrayf),
	198	# executables for batch jobs can be created in advance, in order to avoid calling
	199	# the compiler within the batch job (only works if batch jobs are submitted on
	200	# local host)
[1104]	201	#
[1191]	202	# 1190 2013-06-25 09:39:21Z heinze
	203	# enable use of automatic restarts for ibmh
[1185]	204	# use of cluster/express queue enabled (ibmh)
[1104]	205	#
[1125]	206	# 1124 2013-04-09 15:46:52Z raasch
	207	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	208	# side effect may lead to data loss while getopts is reading the script-option arguments
	209	#
[1123]	210	# 1122 2013-04-09 08:37:16Z heinze
	211	# Bugfix: change type of variable last_char
	212	#
[1121]	213	# 1119 2013-04-05 15:11:19Z raasch
	214	# Bugfix for setting -T option for subjob
	215	#
[1109]	216	# 1108 2013-03-05 07:03:32Z raasch
	217	# bugfix for coupled runs on lckyut/lckyuh
	218	#
[1107]	219	# 1106 2013-03-04 05:31:38Z raasch
	220	# --stdin argument for mpiexec on lckyuh
	221	# -y and -Y settings output to header
	222	#
[1104]	223	# 1103 2013-02-20 02:15:53Z raasch
[1103]	224	# default script runs again under ksh, because of unsolved problems with read
	225	# from stdin: when bash script is called from a ksh, message "read error: 0:
	226	# Resource temporarily unavailable" appears and script does not stop,
	227	# further bash compatibility adjustments,
	228	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	229	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	230	#
[1102]	231	# 1101 2013-02-17 10:20:21Z raasch
	232	# script now running under bash instead of ksh, which required small adjustments
	233	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	234	# read from stdin),
	235	# cross compilername on lckyuh compute nodes replaced by real compiler name
	236	#
[1100]	237	# 1099 2013-02-10 01:47:43Z raasch
	238	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	239	# and for Forwind cluster (lcflow)
	240	# small further adjustments for lckyut
	241	#
[1096]	242	# 1094 2013-02-03 01:52:12Z raasch
	243	# explicit ssh/scp port can be set in config file with environment variable
	244	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	245	# decalpha parts (yonsei) removed
	246	#
[1091]	247	# 2013-02-02 07:06:13Z raasch
[1099]	248	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	249	#
[1084]	250	# 1083 2013-01-04 10:22:09Z maronga
	251	# bugfix in parameter file check (read %cpp_options was missing)
	252	#
[1070]	253	# 1069 2012-11-28 16:18:43Z maronga
	254	# bugfix: coupling mode was always set to mpi2, typos removed
	255	#
[1059]	256	# 1058 2012-11-21 07:00:35Z raasch
	257	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	258	# nodes
	259	#
[1047]	260	# 1046 2012-11-09 14:38:45Z maronga
	261	# code put under GPL (PALM 3.9)
	262	#
[1090]	263	# 21/03/94 - Siggi - first version finished
	264	# 03/03/94 - Siggi - script development started
	265	#
[1059]	266	#--------------------------------------------------------------------------------#
[1090]	267	# mrun - script for running PALM jobs
	268	#--------------------------------------------------------------------------------#
[1]	269
[1047]	270
[1]	271
[1289]	272	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	273
[1289]	274	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	275	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	276	# (TOO MANY ARGUMENTS - PROBLEM)
	277	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	278
	279	AddFilenames=""
	280	additional_conditions=""
	281	add_source_path=""
	282	afname=""
[1320]	283	check_namelist_files=false
[920]	284	combine_plot_fields=true
[1]	285	compiler_name=""
	286	cond1=""
	287	cond2=""
	288	config_file=.mrun.config
[206]	289	coupled_dist=""
[82]	290	cpp_options=""
[1]	291	cpumax=0
	292	cpurest=0
[1199]	293	create_executable_for_batch=false
[1]	294	delete_temporary_catalog=true
	295	do_batch=false
	296	do_compile=true
	297	do_remote=false
	298	do_stagein=true
	299	do_stageout=true
	300	do_trace=false
[352]	301	email_notification="none"
[1]	302	exclude=""
	303	executable=""
[1779]	304	execute_command="none"
[1]	305	execution_error=false
[1210]	306	fftw_inc=""
	307	fftw_lib=""
	308	fftw_support=false
[2297]	309	fname=test
[1]	310	fromhost=""
[78]	311	global_revision=""
[122]	312	group_number=none
[1]	313	host=""
	314	host_file=""
	315	hp=""
	316	input_list=""
	317	interpreted_config_file=""
[164]	318	job_catalog="~/job_queue"
[1]	319	job_on_file=""
	320	keep_data_from_previous_run=false
[183]	321	link_local_input=false
[149]	322	link_local_output=false
[1]	323	localhost_realname=$(hostname)
[260]	324	local_dvrserver_running=.FALSE.
[1]	325	locat=normal
	326	mainprog=""
	327	makefile=""
[759]	328	max_par_io_str=""
[1]	329	mc=$0
	330	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	331	do
	332	mc=`echo $mc \| cut -f2- -d"/"`
	333	done
[493]	334	module_calls=""
[1]	335	mrun_script_name=$mc
[82]	336	netcdf_inc=""
	337	netcdf_lib=""
[1]	338	netcdf_support=false
	339	node_usage=default
	340	numprocs=""
[206]	341	numprocs_atmos=0
	342	numprocs_ocean=0
[1]	343	OOPT=""
	344	openmp=false
	345	output_list=""
	346	package_list=""
	347	queue=none
	348	read_from_config=""
[5]	349	restart_run=false
[622]	350	if [[ `hostname` = rte10 ]]
[1]	351	then
[1468]	352	return_address=133.5.185.60
	353	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[693]	354	elif [[ `hostname` = climate0 ]]
	355	then
[1468]	356	return_address=165.132.26.68
	357	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1866]	358	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
	359	then
	360	return_address="schultzl-Latitude-E6540"
	361	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1021]	362	elif [[ `hostname` = urban00 ]]
	363	then
[1468]	364	return_address=147.46.30.151
	365	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[622]	366	else
[1468]	367	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	368	fi
	369	return_password=""
	370	return_username=$LOGNAME
	371	remotecall=false
	372	remote_username=""
[102]	373	run_coupled_model=false
[1]	374	run_mode=""
[1289]	375	dashes=" ----------------------------------------------------------------------------"
[1]	376	silent=false
	377	source_list=""
	378	source_path=SOURCE
	379	tasks_per_node=""
	380	threads_per_task=1
	381	tmpcreate=false
	382	tmp_data_catalog=""
	383	transfer_problems=false
	384	usern=$LOGNAME
[377]	385	use_openmp=false
[1289]	386	version="MRUN 2.1 Rev$Rev: 2303 $"
[1]	387	working_directory=`pwd`
[2303]	388	write_binary=false
[1]	389	TOPT=""
	390	XOPT=""
	391	zeit=$( date \| cut -c 12-19 )
	392
[1124]	393	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	394	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	395	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	396	# SCRIPT-OPTION ARGUMENTS
[2261]	397	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]	398
[1289]	399	# ERROR HANDLING IN CASE OF EXIT
[83]	400	trap 'rm -rf $working_directory/tmp_mrun
[1289]	401	if [[ $locat != normal && $locat != control_c ]]
[1]	402	then
	403
[1289]	404	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	405	(( i = 0 ))
	406	while (( i < iec ))
	407	do
	408	(( i = i + 1 ))
	409	printf "\n *** Execution of ERROR-command:\n"
	410	printf " >>> ${err_command[$i]}\n"
	411	eval ${err_command[$i]}
	412	done
[1101]	413	if [[ -n $interpreted_config_file ]]
	414	then
[1]	415	rm -rf $interpreted_config_file
	416	fi
[1101]	417	if [[ -n .mrun_environment ]]
	418	then
[71]	419	rm -rf .mrun_environment
	420	fi
[1]	421	if [[ $tmpcreate = true ]]
	422	then
[2147]	423	# printf "\n *** Contents of \"$TEMPDIR\":\n"
	424	# ls -al; cd
[1]	425	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	426	fi
[260]	427	if [[ "$dvrserver_id" != "" ]]
	428	then
	429	echo "+++ killing dvrserver_id=$dvrserver_id"
	430	kill $dvrserver_id
	431	fi
[1]	432	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	433	then
	434	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	435	fi
	436	printf "\n\n+++ MRUN killed \n\n"
	437	elif [[ $locat != control_c ]]
	438	then
	439	printf "\n\n --> all actions finished\n\n"
	440	printf " Bye, bye $usern !!\n\n"
	441	fi' exit
	442
	443
[1289]	444	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	445	trap 'rm -rf $working_directory/tmp_mrun
[807]	446	rm -rf $working_directory/tmp_check_namelist_files
[69]	447	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	448	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	449	then
	450	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	451	fi
[260]	452	if [[ "$dvrserver_id" != "" ]]
	453	then
	454	echo "+++ killing dvrserver_id=$dvrserver_id"
	455	kill $dvrserver_id
	456	fi
[1]	457	printf "\n+++ MRUN killed by \"^C\" \n\n"
	458	locat=control_c
	459	exit
	460	' 2
	461
	462
[22]	463	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	464	# BEEN SET
	465	if [[ "$PALM_BIN" = "" ]]
	466	then
	467	printf "\n +++ environment variable PALM_BIN has not been set"
	468	printf "\n please set it to the directory where the PALM scripts are located"
	469	locat=palm_bin; exit
	470	fi
[180]	471	export PATH=$PALM_BIN:$PATH
[22]	472
	473
[1]	474
[1289]	475	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	476	# WHICH WILL BE USED TO START RESTART-JOBS
[2295]	477	while getopts :a:bBc:Cd:Fg:G:h:H:i:kK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
[1]	478	do
	479	case $option in
	480	(a) afname=$OPTARG;;
	481	(b) do_batch=true; mc="$mc -b";;
	482	(B) delete_temporary_catalog=false; mc="$mc -B";;
	483	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	484	(C) restart_run=true; mc="$mc -C";;
[1]	485	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[79]	486	(F) job_on_file="-D"; mc="$mc -F";;
[122]	487	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	488	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	489	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	490	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	491	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	492	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	493	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	494	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	495	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	496	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
	497	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	498	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	499	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	500	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	501	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	502	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
[1468]	503	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
[1]	504	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	505	(S) read_from_config=false; mc="$mc -S";;
	506	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	507	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	508	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	509	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	510	(v) silent=true; mc="$mc -v";;
[759]	511	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	512	(x) do_trace=true;set -x; mc="$mc -x";;
	513	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	514	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	515	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	516	(z) check_namelist_files=false; mc="$mc -z";;
[920]	517	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	518	(\?) printf "\n +++ unknown option $OPTARG \n"
	519	printf "\n --> type \"$0 ?\" for available options \n"
	520	locat=parameter;exit;;
	521	esac
	522	done
	523
	524
[1289]	525	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	526	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	527	(( to_shift = $OPTIND - 1 ))
	528	shift $to_shift
[1]	529
[1289]	530	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	531	if [[ "$1" = "?" ]]
	532	then
	533	(printf "\n *** mrun can be called as follows:\n"
[2295]	534	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]	535	printf "\n Description of available options:\n"
	536	printf "\n Option Description Default-Value"
	537	printf "\n -a base name of input files equiv. -d"
	538	printf "\n -b batch-job on local machine ---"
	539	printf "\n -B do not delete temporary directory at end ---"
	540	printf "\n -c configuration file .mrun.config"
	541	printf "\n -d base name of files attached to program test"
	542	printf "\n -F create remote job file only ---"
	543	printf "\n -h execution host $localhost_realname"
	544	printf "\n -i INPUT control list \"\" "
	545	printf "\n -k keep data from previous run"
	546	printf "\n -K additional conditions for controling"
	547	printf "\n usage of conditional code and"
	548	printf "\n env-variables in configuration file \"\" "
	549	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	550	printf "\n -M Makefile name Makefile"
	551	printf "\n -n node usage (shared/not_shared) depending on -h"
	552	printf "\n -o OUTPUT control list \"\" "
[1304]	553	printf "\n -O threads per openMP task ---"
[1]	554	printf "\n -p software package list \"\" "
	555	printf "\n -q queue \"$queue\" "
	556	printf "\n -r run control list (combines -i -o) \"\" "
	557	printf "\n -s filenames of routines to be compiled \"\" "
	558	printf "\n must end with .f, .f90, .F, or .c !"
	559	printf "\n use \"..\" for more than one file and wildcards"
[837]	560	printf "\n -s LM compiles all locally modified files"
[1]	561	printf "\n -S config file interpreted by shellscript ---"
	562	printf "\n -t allowed cpu-time in seconds (batch) 0"
	563	printf "\n -T tasks per node depending on -h"
	564	printf "\n -u username on remote machine \"\" "
	565	printf "\n -v no prompt for confirmation ---"
[759]	566	printf "\n -w maximum parallel io streams as given by -X"
[1]	567	printf "\n -x tracing of mrun for debug purposes ---"
	568	printf "\n -X # of processors (on parallel machines) 1"
[291]	569	printf "\n -y add appendix \"_O\" to all local output"
	570	printf "\n files (ocean precursor runs followed by"
	571	printf "\n coupled atmosphere-ocean runs) ---"
[206]	572	printf "\n -Y run coupled model, \"#1 #2\" with"
	573	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	574	printf "\n -Z skip combine_plot_fields at the end of "
	575	printf "\n the simulation ---"
[1]	576	printf "\n "
	577	printf "\n Possible values of positional parameter <modus>:"
	578	printf "\n \"?\" - this outline \n\n") \| more
	579	exit
	580	elif [[ "$1" != "" ]]
	581	then
	582	printf "\n +++ positional parameter $1 unknown \n"
	583	locat=parameter; exit
	584	fi
	585
	586
	587
[1289]	588	# SHORT STARTING MESSAGE
[1]	589	printf "\n*** $version "
	590	printf "\n will be executed. Please wait ..."
	591
	592
[82]	593
[1289]	594	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	595	if [[ ! -f $config_file ]]
	596	then
	597	printf "\n\n +++ configuration file: "
	598	printf "\n $config_file"
	599	printf "\n does not exist"
	600	locat=connect; exit
	601	fi
	602
	603
[1289]	604	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	605	line=""
	606	grep "%host_identifier" $config_file > tmp_mrun
	607	while read line
	608	do
[206]	609	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	610	then
	611	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	612	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	613	if [[ $localhost_realname = $HOSTNAME ]]
[82]	614	then
	615	localhost=$host_identifier
	616	break
	617	fi
	618	fi
	619	done < tmp_mrun
	620
	621	if [[ "$localhost" = "" ]]
	622	then
	623	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	624	printf "\n for local host \"$localhost_realname\"."
	625	printf "\n Please add line"
	626	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	627	printf "\n to the configuration file."
	628	locat=localhost; exit
	629	fi
	630
	631
[1289]	632	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	633	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	634	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	635	[[ "$afname" = "" ]] && afname=$fname
	636
	637
[1289]	638	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	639	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	640	# STATEMENTS IN THE CONFIGURATION FILE
[1]	641	if [[ "$run_mode" != "" ]]
	642	then
	643	input_list="$input_list $run_mode"
	644	output_list="$output_list $run_mode"
	645	fi
	646
	647
[1289]	648	# ??? is this (and the respective option -H) really required ???
	649	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	650	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	651	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	652	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	653	if [[ "$fromhost" = "" ]]
	654	then
	655	fromhost=$localhost
	656	fi
	657
	658
[1289]	659	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	660	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	661	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
[1609]	662	# TO BE SUBMITTED (I.E. do_batch=true)
[1]	663	if [[ -n $host && "$host" != $localhost ]]
	664	then
	665	do_batch=true
	666	do_remote=true
	667	case $host in
[2295]	668	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[1]	669	(*) printf "\n"
[83]	670	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	671	printf "\n is not available"
[1]	672	locat=nqs; (( iec = 0 )); exit;;
	673	esac
	674	else
	675	host=$localhost
	676	fi
	677
	678
[1289]	679	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	680	if [[ -n $additional_conditions ]]
	681	then
[69]	682	cond1=`echo $additional_conditions \| cut -d" " -f1`
	683	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	684	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	685	if [[ -n $dummy ]]
	686	then
	687	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	688	locat=options; exit
	689	fi
[503]	690	block=_$cond1
	691	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	692	fi
	693
	694
[2298]	695	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
[206]	696	if [[ $run_coupled_model = true ]]
	697	then
	698
[1289]	699	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	700	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	701
	702	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	703	then
	704
[1289]	705	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	706	printf "\n PEs (total) : $numprocs"
	707	printf "\n PEs (atmosphere): $numprocs_atmos"
	708	printf "\n PEs (ocean) : $numprocs_ocean"
	709	locat=coupling; exit
[206]	710
[1289]	711	fi
[206]	712
	713	fi
	714
[1289]	715	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	716	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	717	mrun_memory=$memory
	718	mrun_group_number=$group_number
	719	mrun_cpumax=$cpumax
	720	mrun_numprocs=$numprocs
[1]	721
[1099]	722
[1289]	723	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
[1468]	724	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
[1]	725	if [[ "$read_from_config" = false ]]
	726	then
	727	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	728
	729	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	730	while read zeile
	731	do
	732	[[ $silent = false ]] && printf "."
	733
	734
[1289]	735	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	736	eval zeile=\"$zeile\"
	737
	738
[1289]	739	# INTERPRET THE LINE
[21]	740	if [[ "$(echo $zeile)" = "" ]]
[1]	741	then
[1289]	742	# EMPTY LINE, NO ACTION
[21]	743	continue
[1]	744
[21]	745	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	746	then
	747
[1289]	748	# LINE IS A COMMENT LINE
[1]	749	true
	750
	751	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	752	then
	753
[1289]	754	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	755	zeile=$(echo $zeile \| cut -c2-)
[69]	756	var=`echo $zeile \| cut -d" " -f1`
	757	value=`echo $zeile \| cut -d" " -s -f2`
	758	for_host=`echo $zeile \| cut -d" " -s -f3`
	759	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	760	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	761
	762	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	763	then
	764
[1289]	765	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	766	# "::" IS REPLACED BY ":".
[1]	767	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	768
	769
[1289]	770	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	771	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	772	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	773	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	774	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	775	# CONFIGURATION-FILE.
[1]	776	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	777	then
	778	eval $var=\$value
	779
[1289]	780	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	781	if [[ $do_trace = true ]]
	782	then
	783	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	784	fi
	785	fi
	786
[1289]	787	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	788	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	789	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	790	# MUST HAVE TO BE STARTED
[1]	791	if [[ $var = host ]]
	792	then
	793	if [[ -n $host && "$host" != $localhost ]]
	794	then
	795	do_batch=true
	796	do_remote=true
	797	case $host in
[2295]	798	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[83]	799	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	800	printf "\n is not available"
[1]	801	locat=nqs; exit;;
	802	esac
	803	else
	804	host=$localhost
	805	fi
	806	fi
	807
[1289]	808	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	809	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	810	# BY MRUN (E.G. subjob)
[1]	811	export $var
	812	fi
	813
	814
	815
	816
	817	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	818	then
	819
[1289]	820	# LINE DEFINES ERROR-COMMAND
[1]	821	(( iec = iec + 1 ))
	822	zeile=$(echo $zeile \| cut -c4-)
	823	err_command[$iec]="$zeile"
	824
	825	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	826	then
	827
[1289]	828	# LINE DEFINES INPUT-COMMAND
[1]	829	(( iic = iic + 1 ))
	830	zeile=$(echo $zeile \| cut -c4-)
	831	in_command[$iic]="$zeile"
	832
	833	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	834	then
	835
[1289]	836	# LINE DEFINES OUTPUT-COMMAND
[1]	837	(( ioc = ioc + 1 ))
	838	zeile=$(echo $zeile \| cut -c4-)
	839	out_command[$ioc]="$zeile"
	840
	841	else
	842
[1289]	843	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	844	# s2a: in/out - field
	845	# s2b: loc - field (optional)
	846	# s2c: tr/ar - field (optional)
[69]	847	s1=`echo $zeile \| cut -d" " -f1`
	848	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	849	s2a=$(echo $s2 \| cut -d":" -f1)
	850	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	851	then
	852	s2b=""
	853	s2c=""
	854	else
[69]	855	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	856	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	857	fi
[69]	858	s3=`echo $zeile \| cut -d" " -f3`
	859	s4=`echo $zeile \| cut -d" " -s -f4`
	860	s5=`echo $zeile \| cut -d" " -s -f5`
	861	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	862
	863
[1289]	864	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	865	# INPUT- OR OUTPUT-LIST.
	866	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	867	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	868	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	869	# IS NOT CHECKED AND STORED.
[1]	870	IFSALT="$IFS"; IFS="$IFS:"
	871	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	872	then
	873	found=false
	874	for actual in $input_list
	875	do
	876	for formal in $s3
	877	do
	878	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	879	done
	880	done
	881	if [[ $found = true ]]
	882	then
	883	(( iin = iin + 1 ))
	884	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	885	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	886	extin[$iin]=$s6
	887	fi
	888	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	889	then
	890	found=false
	891	for actual in $output_list
	892	do
	893	for formal in $s3
	894	do
	895	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	896	done
	897	done
	898	if [[ $found = true ]]
	899	then
	900	(( iout = iout + 1 ))
	901	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	902	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	903	fi
	904	elif [[ "$s2a" != in && "$s2a" != out ]]
	905	then
	906	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	907	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	908	locat=connect; exit
	909	fi
	910	IFS="$IFSALT"
	911	fi
	912	done < $config_file
	913
	914	else
	915
[1289]	916	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	917	[[ $silent = false ]] && printf "..."
[1289]	918	interpreted_config_file=.icf.$RANDOM
[1]	919
	920
[1917]	921
[1289]	922	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[2261]	923	cat > .mrun_environment << EOF
[69]	924	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	925	config_file = '$config_file', do_remote = '$do_remote',
	926	do_trace = '$do_trace', host = '$host',
	927	input_list = '$input_list', icf = '$interpreted_config_file',
	928	localhost = '$localhost', output_list = '$output_list' /
	929
[2261]	930	EOF
[69]	931
[1289]	932	if [[ "$host" != $localhost ]]
[66]	933	then
[503]	934
[1289]	935	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	936	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	937	if [[ $? != 0 ]]
[503]	938	then
[1289]	939	printf "\n\n +++ no interpret_config found"
	940	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	941	locat=interpret_config; exit
	942	fi
	943	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	944	$interpret_config_executable
[503]	945
[1289]	946	else
[503]	947
[1289]	948	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	949	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	950	then
	951	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	952	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	953	locat=interpret_config; exit
[503]	954	else
[1289]	955	interpret_config${block}.x
	956	fi
[503]	957
[66]	958	fi
[71]	959	rm .mrun_environment
[1]	960
[1917]	961
[1289]	962	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	963	chmod u+x $interpreted_config_file
	964	export PATH=$PATH:.
	965	. $interpreted_config_file
[71]	966	rm $interpreted_config_file
[1]	967
[1099]	968	fi
[71]	969
[1917]	970
[1289]	971	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	972	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	973	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	974	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	975	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	976	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	977	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	978
	979
[1289]	980	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	981	# FOR SOURCE-FILES TO BE COMPILED.
	982	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	983	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	984	if [[ "$SOURCES_COMPLETE" = "" ]]
	985	then
	986
[1289]	987	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	988	# HAS BEEN DEFINED
[1]	989	source_path=""
	990	line=""
	991	grep "%source_path" $config_file > tmp_mrun
	992	while read line
	993	do
	994	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	995	then
	996	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	997	then
	998	global_source_path=`echo $line \| cut -d" " -f2`
	999	fi
	1000	fi
	1001	done < tmp_mrun
	1002
	1003	line=""
	1004	found=false
	1005	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	1006	while read line
	1007	do
	1008	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1009	then
	1010	if [[ $found = true ]]
	1011	then
	1012	printf "\n\n +++ more than one source path found in configuration file"
	1013	printf "\n for local host \"$localhost\" "
	1014	locat=source_path; exit
	1015	fi
	1016	source_path=`echo $line \| cut -d" " -f2`
	1017	found=true
	1018	fi
	1019	done < tmp_mrun
	1020	rm tmp_mrun
	1021
	1022	if [[ "$source_path" = "" ]]
	1023	then
	1024	if [[ "$global_source_path" != "" ]]
	1025	then
	1026	source_path=$global_source_path
	1027	else
	1028	printf "\n\n +++ no source path found in configuration file"
	1029	printf "\n for local host \"$localhost\" "
	1030	locat=source_path; exit
	1031	fi
	1032	fi
	1033	eval source_path=$source_path
	1034
	1035	if [[ ! -d $source_path ]]
	1036	then
	1037	printf "\n\n +++ source path \"$source_path\" on local host"
	1038	printf "\n \"$localhost\" does not exist"
	1039	locat=source_path; exit
	1040	fi
	1041
	1042	fi
	1043
	1044
[1289]	1045	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1046	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1047	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	1048	then
	1049	global_revision=`svnversion $source_path 2>/dev/null`
	1050	global_revision="Rev: $global_revision"
	1051	fi
[1]	1052
[78]	1053
[1289]	1054	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	1055	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	1056	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	1057	if [[ -n $host && "$host" != $localhost ]]
	1058	then
	1059	do_batch=true
	1060	do_remote=true
	1061	case $host in
[2295]	1062	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
[1]	1063	(*) printf "\n"
[83]	1064	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	1065	printf "\n is not available"
[1]	1066	locat=nqs; (( iec = 0 )); exit;;
	1067	esac
	1068	else
	1069	host=$localhost
	1070	fi
	1071
	1072
[1620]	1073
[1289]	1074	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1075	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1076	then
	1077
[1289]	1078	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1079	if [[ ! -n $numprocs ]]
	1080	then
	1081	printf "\n"
	1082	printf "\n +++ option \"-K parallel\" requires additional specification"
	1083	printf "\n of the number of processors to be used by"
	1084	printf "\n mrun-option \"-X\" or by environment-variable"
	1085	printf "\n \"numprocs\" in the configuration file"
	1086	locat=numprocs; (( iec = 0 )); exit
	1087	fi
	1088
[1289]	1089	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1090	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2257]	1091	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
[1]	1092	then
[759]	1093	printf "\n"
	1094	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1095	printf "\n set -T option or define tasks_per_node in the config file"
	1096	locat=tasks_per_node; (( iec = 0 )); exit
	1097	fi
[1279]	1098
	1099	if (( numprocs < tasks_per_node ))
	1100	then
	1101	printf "\n"
	1102	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1103	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1104	locat=tasks_per_node; (( iec = 0 )); exit
	1105	fi
	1106
[2257]	1107	if [[ $host != lcxt5m ]]
[759]	1108	then
[1279]	1109	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1110	(( ival = $tasks_per_node ))
	1111	(( pes = numprocs ))
	1112	(( ii = pes / ival ))
[1279]	1113	(( remaining_pes = pes - ii * ival ))
	1114	if (( remaining_pes > 0 ))
[848]	1115	then
	1116	printf "\n"
[1279]	1117	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1118	printf "\n divisor of the total number of processors (option \"-X\")"
	1119	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1120	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1121	(( nodes = nodes + 1 ))
[848]	1122	fi
[1]	1123	fi
	1124
[759]	1125
[377]	1126	# SETTINGS FOR SUBJOB-COMMAND
[1]	1127	OOPT="-O $threads_per_task"
	1128
[1289]	1129	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1130	if [[ "$tasks_per_node" != "" ]]
	1131	then
[1119]	1132	TOPT="-T $tasks_per_node"
[1]	1133	fi
	1134
[1289]	1135	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1136	if [[ $node_usage = default ]]
	1137	then
	1138	if [[ $host = ibms ]]
	1139	then
	1140	node_usage=shared
	1141	else
	1142	node_usage=not_shared
	1143	fi
	1144	fi
[181]	1145
[635]	1146	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1147	then
	1148	printf "\n"
	1149	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1150	printf "\n \"shared\" or \"not_shared\""
	1151	locat=tasks_per_node; (( iec = 0 )); exit
	1152	fi
	1153
	1154	fi
	1155
[1289]	1156	# CHECK IF HOSTFILE EXISTS
[1]	1157	if [[ -n $hostfile ]]
	1158	then
	1159	if [[ ! -f $hostfile ]]
	1160	then
	1161	printf "\n"
	1162	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1163	locat=hostfile; exit
	1164	fi
	1165	fi
	1166
	1167
[1289]	1168	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1169	if [[ "$maximum_parallel_io_streams" = "" ]]
	1170	then
	1171	maximum_parallel_io_streams=$numprocs
	1172	fi
[1]	1173
[759]	1174
[1289]	1175	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1176	if [[ "$scp_port" != "" ]]
	1177	then
	1178	PORTOPT="-P $scp_port"
	1179	SSH_PORTOPT="-p $scp_port"
	1180	fi
	1181
	1182
[1944]	1183	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1184	# CONFIG-FILE
	1185	if [[ "$ssh_key" != "" ]]
	1186	then
	1187	ssh_key="-i $HOME/.ssh/$ssh_key"
	1188	fi
	1189
	1190
[1289]	1191	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1192	if [[ $queue = none ]]
	1193	then
	1194	case $host in
[1184]	1195	(ibmh) queue=cluster;;
[693]	1196	(ibmkisti) queue=class.32plus;;
[1620]	1197	(lcbullhh) queue=compute;;
[1442]	1198	(lccrayb) queue=mpp1q;;
	1199	(lccrayh) queue=mpp1q;;
[2295]	1200	(lcgeohu) queue=short;;
[1040]	1201	(lckiaps) queue=normal;;
[440]	1202	(lckyoto) queue=ph;;
[1099]	1203	(lckyuh) queue=fx-single;;
	1204	(lckyut) queue=cx-single;;
[635]	1205	(lctit) queue=S;;
[1]	1206	(unics) queue=unics;;
	1207	esac
	1208	fi
	1209
	1210
[1289]	1211	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1212	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1213	(( i = 0 ))
	1214	while (( i < iin ))
	1215	do
	1216	(( i = i + 1 ))
	1217	(( maxcycle = 0 ))
	1218
[1289]	1219	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1220	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1221	if [[ "${actionin[$i]}" = di ]]
	1222	then
[1289]	1223	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1224	# HOST ONLY
[1]	1225	eval filename=${pathin[$i]}/${endin[$i]}
	1226	else
[1289]	1227	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1228	# HOST ONLY
[1]	1229	eval filename=${pathin[$i]}/${afname}${endin[$i]}
	1230	fi
[892]	1231	eval pathname=${pathin[$i]}
[1]	1232
[1289]	1233	# CHECK IF FILE EXISTS
[2141]	1234	if ! ls $filename* 1>/dev/null 2>&1
[1]	1235	then
[1289]	1236
	1237	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[1]	1238	if [[ "${transin[$i]}" != "locopt" ]]
	1239	then
	1240	printf "\n\n +++ INPUT-file: "
[2261]	1241	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
[1]	1242	then
	1243	printf "\n $filename"
	1244	else
	1245	printf "\n $filename.${extin[$i]}"
	1246	fi
	1247	printf "\n does not exist\n"
	1248	locat=input; exit
	1249	else
	1250	transin[$i]="unavailable"
	1251	fi
	1252	else
	1253
[1289]	1254	# DETERMINE THE FILE'S CYCLE NUMBER
[1]	1255	ls -1 -d $filename > filelist 2>/dev/null
	1256	ls -1 -d $filename.* >> filelist 2>/dev/null
	1257	while read zeile
	1258	do
[2261]	1259	# filename without path (i.e. after the last "/")
	1260	basefilename=$(basename ${zeile})
	1261
	1262	# check if there is an extension
	1263	extension=${basefilename##*.}
	1264	if [[ "$extension" = "$extin[$i]" ]]
	1265	then
	1266	basefilename=${basefilename&.*}
	1267	fi
	1268
	1269	# check for an existing cycle number
	1270	cycle=${basefilename##*.}
	1271	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1272	then
	1273	(( icycle = $cycle ))
	1274	else
	1275	(( icycle = 0 ))
	1276	fi
	1277
	1278	if (( icycle > maxcycle ))
	1279	then
	1280	(( maxcycle = icycle ))
	1281	fi
	1282
	1283	# cycle=$(echo $zeile \| cut -f2 -d".")
	1284	# if [[ "$cycle" = "$zeile" ]]
	1285	# then
	1286	# (( icycle = 0 ))
	1287	# elif [[ "$cycle" = "${extin[$i]}" ]]
	1288	# then
	1289	# (( icycle = 0 ))
	1290	# else
	1291	# (( icycle = $cycle ))
	1292	# fi
	1293	# if (( icycle > maxcycle ))
	1294	# then
	1295	# (( maxcycle = icycle ))
	1296	# fi
[1]	1297	done <filelist
	1298	rm filelist
	1299
[1289]	1300	# APPEND CYCLE NUMBER TO FILENAME
[1]	1301	if (( maxcycle > 0 ))
	1302	then
	1303	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1304	then
	1305	filename=${filename}.$maxcycle.${extin[$i]}
	1306	else
	1307	filename=${filename}.$maxcycle
	1308	fi
	1309	else
	1310	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1311	then
	1312	filename=${filename}.${extin[$i]}
	1313	fi
	1314	fi
	1315
[1289]	1316	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
[2261]	1317	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
[1]	1318	absnamein[$i]=$filename
	1319	if (( maxcycle > 0 ))
	1320	then
	1321	if [[ "${actionin[$i]}" = di ]]
	1322	then
	1323	frelin[$i]=${endin[$i]}.$maxcycle
	1324	else
	1325	frelin[$i]=${afname}${endin[$i]}.$maxcycle
	1326	fi
	1327	else
	1328	if [[ "${actionin[$i]}" = di ]]
	1329	then
	1330	frelin[$i]=${endin[$i]}
	1331	else
	1332	frelin[$i]=${afname}${endin[$i]}
	1333	fi
	1334	fi
	1335
	1336	fi
	1337	done
[920]	1338
[1289]	1339	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1340	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1341	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1342	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1343	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1344	# REMOTE HOST)
[1]	1345	(( i = 0 ))
	1346	while (( i < iout ))
	1347	do
	1348	(( i = i + 1 ))
	1349	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1350	then
[260]	1351	if [[ "${actionout[$i]}" = tr ]]
[1]	1352	then
	1353	actionout[$i]=""
[260]	1354	elif [[ "${actionout[$i]}" = trpe ]]
	1355	then
	1356	actionout[$i]=pe
[1]	1357	elif [[ "${actionout[$i]}" = tra ]]
	1358	then
	1359	actionout[$i]=a
	1360	fi
	1361	(( maxcycle = 0 ))
	1362	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1363	eval catalogname=${pathout[$i]}
[2141]	1364	if ! ls $filename* 1>/dev/null 2>&1
[1]	1365	then
	1366
[1289]	1367	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
[1]	1368	if cat /dev/null > $filename
	1369	then
	1370	rm $filename
	1371	else
	1372
[1289]	1373	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1374	# IF IT DOES NOT EXIST, TRY TO CREATE IT
[1]	1375	if [[ ! -d $catalogname ]]
	1376	then
	1377	if mkdir -p $catalogname
	1378	then
	1379	printf "\n\n *** directory:"
	1380	printf "\n $catalogname"
	1381	printf "\n was created\n"
	1382	else
	1383	printf "\n\n +++ OUTPUT-file:"
	1384	printf "\n $filename"
	1385	printf "\n cannot be created, because directory does not exist"
	1386	printf "\n and cannot be created either"
	1387	printf "\n"
	1388	locat=output ; exit
	1389	fi 2>/dev/null
	1390	else
	1391	printf "\n\n +++ OUTPUT-file:"
	1392	printf "\n $filename"
	1393	printf "\n cannot be created, although directory exists"
	1394	printf "\n"
	1395	locat=output ; exit
	1396	fi
	1397	fi 2>/dev/null
	1398	else
	1399
[1289]	1400	# DETERMINE THE CYCLE NUMBER
[1]	1401	ls -1 -d $filename > filelist 2>/dev/null
	1402	ls -1 -d $filename.* >> filelist 2>/dev/null
	1403	while read zeile
	1404	do
[2261]	1405
	1406	# filename without path (i.e. after the last "/")
	1407	basefilename=$(basename ${zeile})
	1408
	1409	# check if there is an extension
	1410	extension=${basefilename##*.}
[2268]	1411	if [[ "$extension" = "${extout[$i]}" ]]
[1]	1412	then
[2268]	1413	basefilename=${basefilename%.*}
[2261]	1414	fi
	1415
	1416	# check for an existing cycle number
	1417	cycle=${basefilename##*.}
	1418	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1419	then
	1420	(( icycle = $cycle + 1 ))
	1421	else
[1]	1422	(( icycle = 1 ))
	1423	fi
[2261]	1424
[1]	1425	if (( icycle > maxcycle ))
	1426	then
	1427	(( maxcycle = icycle ))
	1428	fi
[2261]	1429
[1]	1430	done <filelist
	1431	rm filelist
	1432	fi
	1433
[1289]	1434	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1435	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1436	if [[ "${actionout[$i]}" != a ]]
	1437	then
	1438	if (( maxcycle > 0 ))
	1439	then
[2261]	1440	filename_tmp=${filename}.$maxcycle
	1441	if cat /dev/null > $filename_tmp
[1]	1442	then
[2261]	1443	rm $filename_tmp
[1]	1444	else
	1445	printf "\n +++ OUTPUT-file:"
[2261]	1446	printf "\n $filename_tmp"
[1]	1447	printf "\n cannot be created"
	1448	locat=output ; exit
	1449	fi
	1450	fi
	1451	else
	1452	(( maxcycle = maxcycle - 1 ))
	1453	fi
	1454
[2261]	1455	(( cycnum[$i] = maxcycle ))
[1]	1456	pathout[$i]=$filename
	1457
	1458	fi
	1459	done
	1460
	1461
[1289]	1462	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1463	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1464	then
[260]	1465	if [[ "$dvr_inc" = "" ]]
[83]	1466	then
[260]	1467	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1468	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1469	locat=dvr; exit
[83]	1470	fi
[260]	1471	if [[ "$dvr_lib" = "" ]]
[83]	1472	then
[260]	1473	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1474	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1475	locat=dvr; exit
[83]	1476	fi
	1477	fi
	1478
	1479
[1289]	1480	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1481	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1482	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1483	then
	1484	printf "\n +++ neither main program nor executable defined"
	1485	locat=source; exit
	1486	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1487	then
	1488	printf "\n +++ main program as well as executable defined"
	1489	locat=source; exit
	1490	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1491	then
	1492	do_compile=false
	1493	fi
	1494
	1495
[1289]	1496	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1497	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1498	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1499	then
	1500	rm -rf SOURCES_FOR_RUN_$fname
	1501	mkdir SOURCES_FOR_RUN_$fname
	1502	fi
	1503
	1504
[1289]	1505	# COLLECT ALL ROUTINES TO BE COMPILED
	1506	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1507	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1508	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1509	then
	1510
[5]	1511	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1512
[838]	1513	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1514	then
	1515
[1289]	1516	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1517	source_list=""
	1518	cd $source_path
	1519
	1520
[1289]	1521	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1522	if [[ ! -d .svn ]]
	1523	then
	1524	printf "\n\n +++ source directory"
	1525	printf "\n \"$source_path\" "
	1526	printf "\n is not under control of \"subversion\"."
[306]	1527	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1528	fi
	1529
	1530
[1289]	1531	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1532	Filenames=""
[69]	1533	svn status > tmp_mrun
	1534	while read line
[5]	1535	do
	1536	firstc=`echo $line \| cut -c1`
	1537	if [[ $firstc = M \|\| $firstc = "?" ]]
	1538	then
	1539	Name=`echo "$line" \| cut -c8-`
	1540	extension=`echo $Name \| cut -d. -f2`
	1541	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1542	then
	1543	Filenames="$Filenames "$Name
	1544	fi
	1545	fi
[69]	1546	done < tmp_mrun
[5]	1547
	1548
[1289]	1549	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1550	for dateiname in $Filenames
	1551	do
	1552	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1553	source_list=$source_list"$dateiname "
	1554	done
	1555
	1556	cd - > /dev/null
	1557
	1558
[1289]	1559	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1560	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1561	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1562	then
	1563
	1564	cd $source_path
	1565
	1566	for filename in $source_list
	1567	do
	1568
[1289]	1569	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1570	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1571	then
	1572	printf "\n +++ source code file: $filename"
	1573	printf "\n must not contain (\"/\") "
	1574	locat=source; exit
	1575	fi
	1576
	1577	if [[ ! -f $filename ]]
	1578	then
	1579	printf "\n +++ source code file: $filename"
	1580	printf "\n does not exist"
	1581	locat=source; exit
	1582	else
	1583	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1584	fi
	1585
	1586	done
	1587
	1588	cd - > /dev/null
	1589
	1590	fi
	1591
	1592
[1289]	1593	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1594	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1595	if [[ $restart_run != true ]]
[1]	1596	then
	1597
	1598	if [[ ! -f "$source_path/$mainprog" ]]
	1599	then
	1600	printf "\n\n +++ main program: $mainprog"
	1601	printf "\n does not exist in source directory"
	1602	printf "\n \"$source_path\"\n"
	1603	locat=source; exit
	1604	else
	1605	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1606	then
	1607	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1608	source_list=${mainprog}" $source_list"
	1609	fi
	1610	fi
	1611	fi
	1612
	1613
[1289]	1614	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1615	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1616	if [[ "$restart_run" != true ]]
	1617	then
	1618	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1619	if [[ ! -f $makefile ]]
	1620	then
	1621	printf "\n +++ file \"$makefile\" does not exist"
	1622	locat=make; exit
	1623	else
	1624	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1625	fi
	1626	fi
	1627
	1628
[1289]	1629	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1630	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1631	then
	1632
[1289]	1633	# DOES THE DIRECTORY EXIST?
[1]	1634	if [[ ! -d $add_source_path ]]
	1635	then
[1779]	1636	printf "\n\n *** INFORMATIVE: additional source code directory"
[1]	1637	printf "\n \"$add_source_path\" "
	1638	printf "\n does not exist or is not a directory."
	1639	printf "\n No source code will be used from this directory!\n"
	1640	add_source_path=""
[931]	1641	if [[ $silent == false ]]
	1642	then
	1643	sleep 3
	1644	fi
[1]	1645	else
	1646
	1647	cd $add_source_path
[211]	1648	found=false
[1]	1649
	1650	Names=$(ls -1 *.f90 2>&1)
	1651	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1652	Names=$(ls -1 *.F90 2>&1)
	1653	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1654	Names=$(ls -1 *.F 2>&1)
	1655	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1656	Names=$(ls -1 *.f 2>&1)
	1657	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1658	Names=$(ls -1 *.c 2>&1)
	1659	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1660
	1661	cd - > /dev/null
	1662	cd SOURCES_FOR_RUN_$fname
	1663
[211]	1664	# COPY MAKEFILE IF EXISTING
	1665	if [[ -f $add_source_path/Makefile ]]
	1666	then
	1667	printf "\n\n *** user Makefile from directory"
	1668	printf "\n \"$add_source_path\" is used \n"
[931]	1669	if [[ $silent == false ]]
	1670	then
	1671	sleep 1
	1672	fi
[211]	1673	cp $add_source_path/Makefile .
	1674	fi
	1675
[1]	1676	for dateiname in $AddFilenames
	1677	do
	1678	if [[ -f $dateiname ]]
	1679	then
	1680	printf "\n +++ source code file \"$dateiname\" found in additional"
	1681	printf "\n source code directory \"$add_source_path\" "
[211]	1682	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1683	printf "\n from directory \"$source_path\"."
[1]	1684	locat=source; exit
	1685	fi
	1686
	1687	cp $add_source_path/$dateiname .
	1688	source_list="$source_list $dateiname"
	1689
[211]	1690	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1691	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1692	then
	1693	printf "\n\n +++ user file \"$dateiname\" "
	1694	printf "\n is not listed in Makefile \n"
	1695	locat=source; exit
	1696	else
	1697
	1698	if [[ $found = false ]]
[1]	1699	then
[211]	1700	found=true
	1701	printf "\n\n *** following user file(s) added to the"
	1702	printf " files to be translated:\n "
[1]	1703	fi
[211]	1704	printf "$dateiname "
[931]	1705	if [[ $silent == false ]]
	1706	then
	1707	sleep 0.5
	1708	fi
	1709
[1]	1710	fi
	1711	done
[211]	1712	[[ $found = true ]] && printf "\n"
[1]	1713	cd - > /dev/null
	1714	fi
	1715	fi
	1716
	1717
[1289]	1718	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1719	# TO THE LIST OF FILES TO BE COMPILED
[5]	1720	if [[ $restart_run != true && -n $package_list ]]
[1]	1721	then
	1722
	1723	cd $source_path
	1724
	1725	for package in $package_list
	1726	do
	1727
	1728	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1729
[1289]	1730	# DETERMINE FILES BELONGING TO THE PACKAGE
	1731	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1732	# THE NAME OF THE DIRECTORY
[1]	1733	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1734
	1735
[1289]	1736	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1737	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1738	for source_list_name in $package_source_list
	1739	do
	1740	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1741	then
	1742
[1289]	1743	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1744	ending=`echo $source_list_name \| cut -f2 -d.`
	1745	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1746	then
	1747	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1748	source_list="$source_list $source_list_name"
	1749	fi
	1750	fi
	1751	done
	1752	done
	1753
	1754	cd - > /dev/null
	1755	fi
	1756
	1757	fi # do_compile=true
	1758
	1759
[1289]	1760	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1761	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1762	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1763	then
	1764
[1289]	1765	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[1]	1766	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1767	then
[82]	1768	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1769	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1770	then
[82]	1771	cpp_options="$cpp_options -D__nec"
	1772	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1773	then
	1774	cpp_options="$cpp_options -D__lc"
[1]	1775	else
[82]	1776	cpp_options="$cpp_options -D__$localhost"
[1]	1777	fi
[83]	1778
[1289]	1779	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[1]	1780	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1781	then
[82]	1782	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1783	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1784	else
[82]	1785	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1786	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1787	fi
[83]	1788
[1289]	1789	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1790	if [[ -n $package_list ]]
	1791	then
	1792	for package in $package_list
	1793	do
	1794	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1795	then
	1796	if [[ $package != "dvrp_graphics+1PE" ]]
	1797	then
[82]	1798	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1799	else
[82]	1800	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1801	export use_seperate_pe_for_dvrp_output=true
	1802	fi
	1803	else
	1804	if [[ $package != "dvrp_graphics+1PE" ]]
	1805	then
[82]	1806	cpp_options="$cpp_options -D__$package"
[1]	1807	else
[82]	1808	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1809	export use_seperate_pe_for_dvrp_output=true
	1810	fi
	1811	fi
	1812	done
	1813	fi
[83]	1814
[1]	1815	else
	1816
	1817
[1289]	1818	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1819	if [[ $do_remote = false ]]
	1820	then
	1821	if [[ ! -f $executable ]]
	1822	then
	1823	printf "\n +++ executable file: $executable"
	1824	printf "\n does not exist"
	1825	locat=executable; exit
	1826	fi
	1827	fi
	1828	fi
	1829
	1830
[1289]	1831	# DETERMINE THE JOB MODE
[1491]	1832	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
[1]	1833	then
[1491]	1834	if [[ "$LOADLBATCH" = yes ]]
	1835	then
	1836	batch_job=.TRUE.
	1837	jobmo=BATCH
	1838	else
	1839	batch_job=.FALSE.
	1840	jobmo=INTERACTIVE
	1841	fi
[1]	1842	else
[2185]	1843	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
[1491]	1844	then
	1845	batch_job=.TRUE.
	1846	jobmo=BATCH
	1847	else
	1848	batch_job=.FALSE.
	1849	jobmo=INTERACTIVE
	1850	fi
[1]	1851	fi
	1852
[1289]	1853	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1854	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1855	then
	1856	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1857	printf "\n please submit batch job using mrun option \"-b\" \n"
	1858	locat=normal; exit
	1859	fi
	1860
	1861
[1289]	1862	# CHECK, IF USER DEFINED A COMPILER
[1]	1863	if [[ "$compiler_name" = "" ]]
	1864	then
[82]	1865
[220]	1866	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1867	locat=compiler_name; exit
	1868
[1]	1869	fi
	1870
	1871
[1289]	1872	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1609]	1873
	1874	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
	1875	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
	1876	then
	1877	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
[1755]	1878	if [[ "$kennung" = "" ]]
[1753]	1879	then
	1880	kennung=$RANDOM
	1881	fi
[1609]	1882	else
	1883	kennung=$RANDOM
	1884	fi
	1885
[1]	1886	if [[ "$tmp_user_catalog" = "" ]]
	1887	then
[312]	1888	if [[ $localhost = ibmh ]]
[1]	1889	then
[312]	1890	tmp_user_catalog=$SCRATCH
[1]	1891	else
	1892	tmp_user_catalog=/tmp
	1893	fi
	1894	fi
	1895	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1896
	1897
[1289]	1898	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1899	if [[ "$tmp_data_catalog" = "" ]]
	1900	then
[2261]	1901	tmp_data_catalog=/tmp/mrun_restart_data
[1]	1902	fi
	1903
	1904
[1289]	1905	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1906	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1907	then
	1908	eval fopts=\"$fopts\"
	1909	eval lopts=\"$lopts\"
	1910	fi
	1911
	1912
[1289]	1913	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1914	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1915	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1779]	1916	XOPT="-X $numprocs"
[1]	1917
	1918
[1289]	1919	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1920	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1921	done=false
	1922	while [[ $done = false ]]
	1923	do
	1924	cputime=$cpumax
	1925	if (( $cputime == 0 ))
	1926	then
[246]	1927	if [[ $do_batch = true ]]
	1928	then
	1929	printf "\n +++ cpu-time is undefined"
	1930	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1931	printf "\n >>> "
	1932	read cputime 1>/dev/null 2>&1
	1933	else
	1934	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1935	fi
[1]	1936	else
	1937	done=true
	1938	fi
	1939	cpumax=$cputime
	1940	done
	1941
	1942	(( minuten = cputime / 60 ))
	1943	(( sekunden = cputime - minuten * 60 ))
	1944
	1945
[1289]	1946	# CHECK THE MEMORY DEMAND
[1]	1947	if [[ $do_batch = true ]]
	1948	then
	1949	done=false
	1950	while [[ $done = false ]]
	1951	do
	1952	if (( memory == 0 ))
	1953	then
	1954	printf "\n +++ memory demand is undefined"
	1955	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1956	printf "\n >>> "
	1957	read memory 1>/dev/null 2>&1
	1958	else
	1959	done=true
	1960	fi
	1961	done
	1962	fi
	1963
	1964
[1289]	1965	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	1966	if [[ $do_remote = true && -z $remote_username ]]
	1967	then
	1968	while [[ -z $remote_username ]]
	1969	do
	1970	printf "\n +++ username on remote host \"$host\" is undefined"
	1971	printf "\n >>> Please type username:"
	1972	printf "\n >>> "
	1973	read remote_username
	1974	done
	1975	mc="$mc -u$remote_username"
	1976	fi
	1977
[892]	1978	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	1979	if [[ "$login_init_cmd" != "" ]]
	1980	then
	1981	export init_cmds="${login_init_cmd};"
	1982	fi
[221]	1983
[892]	1984
[1289]	1985	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	1986	if [[ "$modules" != "" ]]
	1987	then
[678]	1988	if [[ $host = lctit ]]
	1989	then
	1990	export module_calls=". $modules"
	1991	else
	1992	export module_calls="module load ${modules};"
	1993	fi
[493]	1994	fi
	1995
[1289]	1996	# OUTPUT OF THE MRUN-HEADER
[1]	1997	calltime=$(date)
	1998	printf "\n"
[1101]	1999	printf "#------------------------------------------------------------------------# \n"
	2000	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	2001	printf "\| \| \n"
[1]	2002	spalte1="called on:"; spalte2=$localhost_realname
[1101]	2003	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	2004	if [[ $do_remote = true ]]
[1]	2005	then
[1289]	2006	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	2007	else
[1289]	2008	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	2009	fi
[1101]	2010	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2011	if [[ -n $numprocs ]]
	2012	then
[1106]	2013	if [[ $run_coupled_model = false ]]
	2014	then
	2015	spalte1="number of PEs:"; spalte2=$numprocs
	2016	else
	2017	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	2018	fi
[1101]	2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2020	fi
	2021	if [[ -n $tasks_per_node ]]
	2022	then
	2023	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	2025	if (( remaining_pes > 0 ))
	2026	then
	2027	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	2028	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2029	fi
[1]	2030	fi
[759]	2031	if [[ $maximum_parallel_io_streams != $numprocs ]]
	2032	then
	2033	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	2035	fi
[622]	2036	if [[ $use_openmp = true ]]
[1]	2037	then
	2038	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2040	fi
[1101]	2041	printf "\| \| \n"
[1]	2042	if [[ $do_compile = true ]]
	2043	then
[475]	2044	if [[ "$mopts" != "" ]]
	2045	then
[1101]	2046	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	2047	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2048	zeile=$(echo "$mopts" \| cut -c46-)
[475]	2049	while [[ "$zeile" != "" ]]
	2050	do
	2051	spalte1=""
[1101]	2052	spalte2=$(echo "$zeile" \| cut -c-45)
	2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2054	zeile=$(echo "$zeile" \| cut -c46-)
[475]	2055	done
	2056	fi
	2057
[1101]	2058	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	2059	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2060	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	2061	while [[ "$zeile" != "" ]]
	2062	do
	2063	spalte1=""
[1101]	2064	spalte2=$(echo "$zeile" \| cut -c-45)
	2065	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2066	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2067	done
	2068
[1101]	2069	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2071	zeile=$(echo "$fopts" \| cut -c46-)
[1]	2072	while [[ "$zeile" != "" ]]
	2073	do
	2074	spalte1=""
[1101]	2075	spalte2=$(echo "$zeile" \| cut -c-45)
	2076	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2077	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2078	done
	2079
[1101]	2080	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2082	zeile=$(echo "$lopts" \| cut -c46-)
[1]	2083	while [[ "$zeile" != "" ]]
	2084	do
	2085	spalte1=""
[1101]	2086	spalte2=$(echo "$zeile" \| cut -c-45)
	2087	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2088	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2089	done
	2090
[1101]	2091	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2093	zeile=$(echo "$modules" \| cut -c46-)
[493]	2094	while [[ "$zeile" != "" ]]
	2095	do
	2096	spalte1=""
[1101]	2097	spalte2=$(echo "$zeile" \| cut -c-45)
	2098	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2099	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2100	done
	2101
[1101]	2102	spalte1="main program:"; spalte2=$mainprog
	2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2104	else
	2105	spalte1=executable:; spalte2=$executable
[1101]	2106	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2107	fi
[1101]	2108	printf "\| \| \n"
	2109	spalte1="base name of files:"; spalte2=$fname
	2110	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2111	if [[ $fname != $afname ]]
	2112	then
[1101]	2113	spalte1="base name of input files:"; spalte2=$afname
	2114	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2115	fi
[1101]	2116	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2117	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2118	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2119	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2120
[1106]	2121	if [[ "$ocean_file_appendix" = true ]]
	2122	then
	2123	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2124	fi
	2125
[1]	2126	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2127	then
	2128	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2129	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2130	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2131	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2132	fi
	2133
	2134	if [[ $do_compile = true ]]
	2135	then
[1101]	2136	printf "\| \| \n"
	2137	printf "\| Files to be compiled: \| \n"
[1]	2138	zeile=$source_list
	2139	while [[ "$zeile" != "" ]]
	2140	do
[1101]	2141	linestart=$(echo $zeile \| cut -c-70)
	2142	printf "\| %-70s \| \n" "$linestart"
	2143	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2144	done
	2145	fi
[1101]	2146	printf "#------------------------------------------------------------------------#"
[1]	2147
	2148
	2149
[1289]	2150	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2151	if [[ $do_trace = true ]]
	2152	then
	2153	(( i = 0 ))
	2154	while (( i < iin ))
	2155	do
	2156	(( i = i + 1 ))
	2157	if (( i == 1 ))
	2158	then
	2159	printf "\n\n >>> INPUT-file assignments:\n"
	2160	fi
	2161	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2162	done
	2163	(( i = 0 ))
	2164	while (( i < iout ))
	2165	do
	2166	(( i = i + 1 ))
	2167	if (( i == 1 ))
	2168	then
	2169	printf "\n\n >>> OUTPUT-file assignments:\n"
	2170	fi
	2171	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2172	done
	2173	(( i = 0 ))
	2174	while (( i < iic ))
	2175	do
	2176	(( i = i + 1 ))
	2177	if (( i == 1 ))
	2178	then
	2179	printf "\n\n >>> INPUT-commands:\n"
	2180	fi
	2181	printf "\n ${in_command[$i]}"
	2182	done
	2183	(( i = 0 ))
	2184	while (( i < ioc ))
	2185	do
	2186	(( i = i + 1 ))
	2187	if (( i == 1 ))
	2188	then
	2189	printf "\n\n >>> OUTPUT-commands:\n"
	2190	fi
	2191	printf "\n ${out_command[$i]}"
	2192	done
	2193	fi
	2194
[1289]	2195	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2196	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2197	then
	2198	antwort=dummy
	2199	printf "\n\n"
[1101]	2200	printf " >>> everything o.k. (y/n) ? "
	2201	while read antwort
[1]	2202	do
[1101]	2203	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2204	then
	2205	printf " >>> everything o.k. (y/n) ? "
	2206	else
	2207	break
	2208	fi
[1]	2209	done
	2210	if [[ $antwort = n \|\| $antwort = N ]]
	2211	then
	2212	locat=user_abort; (( iec = 0 )); exit
	2213	fi
	2214	if [[ $do_batch = true ]]
	2215	then
	2216	printf " >>> batch-job will be created and submitted"
	2217	else
[1289]	2218	printf " >>> MRUN will now continue to execute on this machine"
[1]	2219	fi
	2220	fi
	2221
[1804]	2222
[1199]	2223	# DETERMINE PATH FOR MAKE DEPOSITORY
	2224	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2225	then
	2226
	2227	line=""
	2228	grep "%depository_path" $config_file > tmp_mrun
	2229	while read line
	2230	do
	2231	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2232	then
	2233	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2234	then
	2235	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2236	fi
	2237	fi
	2238	done < tmp_mrun
	2239
	2240	line=""
	2241	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2242	while read line
	2243	do
	2244	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2245	then
	2246	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2247	then
	2248	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2249	fi
	2250	fi
	2251	done < tmp_mrun
	2252
	2253	if [[ "$local_depository_path" = "" ]]
	2254	then
	2255	if [[ "$global_depository_path" != "" ]]
	2256	then
	2257	local_depository_path=$global_depository_path
	2258	else
	2259	printf "\n\n +++ no depository path found in configuration file"
	2260	printf "\n for local host \"$localhost\" "
	2261	printf "\n please set \"\%depository_path\" in configuration file\n"
	2262	locat=config_file; exit
	2263	fi
	2264	fi
	2265	eval local_depository_path=$local_depository_path
	2266	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2267	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2268
	2269
	2270	basename=`echo $mainprog \| cut -f1 -d"."`
	2271	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2272	if [[ ! -f $make_depository ]]
	2273	then
	2274	printf "\n"
	2275	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2276	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2277	fi
	2278
	2279	fi
	2280
	2281
[1289]	2282	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2283	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2284	if [[ $do_batch = false ]]
	2285	then
	2286
	2287
[1289]	2288	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2289	mkdir -p $TEMPDIR
	2290	chmod go+rx $TEMPDIR
	2291	tmpcreate=true
	2292
	2293
[1289]	2294	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2295	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2296	if [[ $do_compile = true ]]
	2297	then
	2298
[2261]	2299	TEMPDIR_COMPILE=$TEMPDIR
[1]	2300
[1199]	2301	cp $make_depository $TEMPDIR_COMPILE
	2302	cd $TEMPDIR_COMPILE
	2303	tar -xf $make_depository > /dev/null 2>&1
	2304	cd - > /dev/null
[1]	2305
[1255]	2306	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2307	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2308	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2309	then
	2310	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2311	else
	2312	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2313	fi
[82]	2314
[1]	2315	else
[475]	2316
[1]	2317	cp $executable ${TEMPDIR}/a.out
[475]	2318
[1]	2319	fi
	2320
	2321
[1289]	2322	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2323	cd $TEMPDIR
[1]	2324	printf "\n *** changed to temporary directory: $TEMPDIR"
	2325
	2326
[1289]	2327	# IF REQUIRED, START WITH COMPILING
[1]	2328	if [[ $do_compile = true ]]
	2329	then
	2330
	2331
[1199]	2332	if [[ -f a.out ]]
[475]	2333	then
[82]	2334
[1199]	2335	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2336	printf "\n\n\n *** executable a.out found"
	2337	printf "\n no compilation required \n"
	2338
[1]	2339	else
[807]	2340
[1199]	2341	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2342	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2343	printf " *** compilation with make using following options:\n"
	2344	printf " make depository: $make_depository"
	2345	if [[ "$mopts" != "" ]]
	2346	then
	2347	printf " make options: $mopts\n"
	2348	fi
	2349	printf " compilername: $compiler_name\n"
	2350	printf " compiler options: $fopts\n"
	2351	printf " preprocessor directives: $cpp_options \n"
	2352	printf " linker options: $lopts \n"
	2353	if [[ "$modules" != "" ]]
	2354	then
	2355	printf " modules to be load: $modules \n"
	2356	fi
	2357	printf " source code files: $source_list \n"
[1]	2358
[2261]	2359	if [[ $localhost = ibmh ]]
[1199]	2360	then
	2361	printf " compiler is called via ssh on \"plogin1\" \n"
	2362	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\" "
	2363	[[ ! -f a.out ]] && compile_error=true
[1289]	2364	continue # STATUS=1, IF a.out EXISTS
[1866]	2365	elif [[ $localhost = lcocean ]]
	2366	then
	2367	printf " compiler is called via ssh on \"ocean\" \n"
	2368	echo $PWD
	2369	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\" "
	2370	[[ ! -f a.out ]] && compile_error=true
	2371	continue # STATUS=1, IF a.out EXISTS
[1620]	2372	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2373	then
	2374	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2295]	2375	elif [[ $localhost = lceddy ]]
[2257]	2376	then
[2295]	2377	which mpifc
[2257]	2378	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2295]	2379	elif [[ $localhost = lcgeohu ]]
	2380	then
	2381	printf " compiler is called via ssh on \"cirrus\" \n"
	2382	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=\"$lopts\" "
	2383	# this check did not work. Although a.out exists, it sets compile_error to true!
	2384	# [[ ! -f a.out ]] && compile_error=true
	2385	continue # STATUS=1, IF a.out EXISTS
[1199]	2386	else
	2387	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2388	[[ "$module_calls" != "" ]] && eval $module_calls
	2389	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2390	fi
[181]	2391
[1199]	2392	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2393	then
	2394	printf "\n +++ error occured while compiling or linking"
	2395	locat=compile
	2396
[181]	2397	exit
[1199]	2398	else
[1289]	2399	printf "$dashes\n *** compilation finished \n"
[1199]	2400	fi
	2401
[1]	2402	fi
[1199]	2403
[1]	2404	fi
	2405
	2406
[1289]	2407	# PROVIDE THE INPUT FILES
	2408	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2409	(( i = 0 ))
	2410	while (( i < iin ))
	2411	do
	2412	(( i = i + 1 ))
	2413	if (( i == 1 ))
	2414	then
[1289]	2415	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2416	fi
	2417
	2418
[1289]	2419	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2420	if [[ "${transin[$i]}" = unavailable ]]
	2421	then
	2422	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2423	then
[1779]	2424	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2425	printf "\n is not available!"
[1]	2426	else
[1779]	2427	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2428	printf "\n is not available!"
[1]	2429	fi
	2430	continue
	2431	fi
	2432
[1289]	2433	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2434	files_for_pes=false; datentyp=file
	2435	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2436	then
[2261]	2437	files_for_pes=true; datentyp=files
[1]	2438	actionin[$i]=""
	2439	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2440	then
	2441	actionin[$i]=""
[2261]	2442	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
[1]	2443	then
[2261]	2444	files_for_pes=true; datentyp=files
	2445	actionin[$i]="ln"
	2446	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
[1]	2447	then
[2261]	2448	actionin[$i]="ln"
[1]	2449	fi
	2450
	2451	if [[ $files_for_pes = true ]]
	2452	then
	2453	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2454	else
	2455	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2456	fi
	2457
[2261]	2458	# INPUT-FILES TO BE LINKED
	2459	if [[ "${actionin[$i]}" = ln ]]
[1]	2460	then
[2261]	2461
	2462	printf "\n $datentyp will be linked"
[1]	2463	if [[ $files_for_pes = false ]]
	2464	then
[2261]	2465	if [[ -f "${absnamein[$i]}" ]]
[1]	2466	then
[2261]	2467	ln ${absnamein[$i]} ${localin[$i]}
[1]	2468	got_tmp[$i]=true
	2469	fi
	2470	else
[2261]	2471	if [[ -d "${absnamein[$i]}" ]]
[1]	2472	then
	2473	mkdir ${localin[$i]}
[2261]	2474	cd ${absnamein[$i]}
[149]	2475	for file in $(ls *)
	2476	do
	2477	ln $file $TEMPDIR/${localin[$i]}
[2261]	2478	done >\|/dev/null 2>&1
[149]	2479	cd $TEMPDIR
[1]	2480	fi
	2481
[2261]	2482	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2483	if [[ ! -f "${localin[$i]}/_000000" ]]
[1]	2484	then
[2261]	2485	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2486	cp -r ${absnamein[$i]}/* ${localin[$i]}
[1]	2487	fi
	2488
	2489	got_tmp[$i]=true
	2490	fi
	2491	fi
	2492
[1289]	2493	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	2494	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	2495	then
	2496
	2497	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	2498	then
	2499
[1289]	2500	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2501	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	2502	printf "\n file will be provided for $numprocs processors"
	2503	mkdir ${localin[$i]}
	2504	ival=$numprocs
	2505	(( ii = 0 ))
	2506	while (( ii <= ival-1 ))
	2507	do
	2508	if (( ii < 10 ))
	2509	then
	2510	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2511	elif (( ii < 100 ))
	2512	then
	2513	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2514	elif (( ii < 1000 ))
	2515	then
	2516	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2517	else
	2518	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2519	fi
	2520	(( ii = ii + 1 ))
	2521	done
	2522
	2523	else
	2524
	2525	if [[ $files_for_pes = true ]]
	2526	then
	2527
[1289]	2528	# PROVIDE FILES FOR EACH CORE
	2529	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2530	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	2531	printf "\n providing $numprocs files for the respective processors"
	2532	mkdir ${localin[$i]}
[2261]	2533	if [[ $link_local_input = true ]]
	2534	then
	2535	printf " files will be linked\n"
	2536	cd ${absnamein[$i]}
	2537	for file in $(ls *)
	2538	do
	2539	ln -f $file ${localin[$i]}
	2540	done
	2541	cd $TEMPDIR
	2542	fi
[1289]	2543
	2544	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[2261]	2545	if [[ ! -f "${localin[$i]}/_000000" ]]
	2546	then
	2547	if [[ $link_local_input = true ]]
	2548	then
	2549	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2550	fi
	2551	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2552	fi
[1]	2553
	2554	else
[1289]	2555
	2556	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[2261]	2557	if [[ $link_local_input = true ]]
	2558	then
	2559	printf " file will be linked\n"
	2560	ln -f ${absnamein[$i]} ${localin[$i]}
	2561	fi
	2562	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	2563	if [[ ! -f "${localin[$i]}" ]]
[183]	2564	then
[2261]	2565	if [[ $link_local_input = true ]]
	2566	then
	2567	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2568	fi
	2569	cp ${absnamein[$i]} ${localin[$i]}
[183]	2570	fi
[1]	2571	fi
	2572	fi
	2573	fi
	2574
	2575	done
	2576	if (( i != 0 ))
	2577	then
[1289]	2578	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	2579	fi
	2580
	2581
[1289]	2582	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	2583	(( i = 0 ))
	2584	while (( i < iic ))
	2585	do
	2586	(( i = i + 1 ))
	2587	if (( i == 1 ))
	2588	then
[1289]	2589	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	2590	fi
	2591	printf "\n >>> ${in_command[$i]}"
	2592	eval ${in_command[$i]}
	2593	if (( i == iic ))
	2594	then
[1289]	2595	printf "\n$dashes\n"
[1]	2596	fi
	2597	done
	2598
	2599
[1289]	2600	# SET THE REMAINING CPU-TIME
[1]	2601	cpurest=${cpumax}.
	2602
	2603
[260]	2604	# START DVR STREAMING SERVER
	2605	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	2606	then
	2607	if [[ "$dvr_server" != "" ]]
	2608	then
	2609
	2610	printf "\n\n *** preparing the dvr streaming server configuration file"
	2611
[1289]	2612	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	2613	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	2614	if [[ "$running_dvrserver_id" != "" ]]
	2615	then
	2616
[261]	2617	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	2618	printf "\n This server is used instead starting a new one!"
[261]	2619	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	2620
	2621	else
	2622
	2623	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	2624	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	2625	then
	2626	cp ${PALM_BIN}/.dvrserver.config .
	2627
[1289]	2628	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	2629	user_id=`id -u`
	2630	group_id=`id -g`
[1289]	2631
	2632	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	2633	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	2634	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	2635	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	2636	mv .dvrserver.3 .dvrserver.config
	2637	rm .dvrserver.1 .dvrserver.2
	2638
[1289]	2639	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	2640	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	2641	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	2642	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	2643	local_dvrserver_running=.TRUE.
	2644	else
	2645	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	2646	printf "\n \"$PALM_BIN\" "
	2647	locat=dvr
	2648	exit
	2649	fi
	2650
	2651	fi
	2652
	2653	else
	2654	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	2655	fi
	2656	fi
	2657
	2658
[1289]	2659	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2660	# (FILE ENVPAR WILL BE READ BY PALM)
[2261]	2661	cat > ENVPAR << EOF
[260]	2662	&envpar run_identifier = '$fname', host = '$localhost',
[2298]	2663	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
[759]	2664	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	2665	maximum_cpu_time_allowed = ${cpumax}.,
	2666	revision = '$global_revision',
[1402]	2667	local_dvrserver_running = $local_dvrserver_running,
	2668	batch_job = $batch_job /
[260]	2669
[2261]	2670	EOF
[260]	2671
	2672
[1289]	2673	# STARTING THE EXECUTABLE
	2674	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	2675	PATH=$PATH:$TEMPDIR
	2676
[1779]	2677
	2678	if [[ $execute_command != "none" ]]
[359]	2679	then
	2680
[1779]	2681	printf "\n +++ branch still not realized"
	2682	locat=execution
	2683	exit
	2684
[693]	2685	else
	2686
[1779]	2687	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
	2688	if [[ "$mpi_debug" = true ]]
[1549]	2689	then
[1779]	2690	export MPI_CHECK_ARGS=1
	2691	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
[1549]	2692	fi
	2693
[1779]	2694	if [[ "$totalview" = true ]]
[1]	2695	then
[1779]	2696	printf "\n *** totalview debugger will be used"
	2697	tv_opt="-tv"
	2698	else
	2699	tv_opt=""
[1]	2700	fi
[1779]	2701
	2702	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
[1]	2703	then
	2704
[1779]	2705	#Interactive ALLINEA DEBUG seesion
	2706	if [[ "$ENVIRONMENT" != BATCH ]]
	2707	then
	2708	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2709	then
	2710	if [[ "$allinea" = true ]]
	2711	then
	2712	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
[1]	2713
[1779]	2714	ddt aprun -n $ii -N $tasks_per_node a.out
	2715	wait
	2716	fi
	2717	fi
	2718	fi
[1]	2719
[1779]	2720	if [[ $localhost = ibmh ]]
	2721	then
[1]	2722
[1779]	2723	# SETUP THE IBM MPI ENVIRONMENT
	2724	export MP_SHARED_MEMORY=yes
	2725	export AIXTHREADS_SCOPE=S
	2726	export OMP_NUM_THREADS=$threads_per_task
	2727	export AUTHSTATE=files
	2728	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
[1]	2729
[1779]	2730	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	2731	export MP_ADAPTER_USE=shared
	2732	export MP_CPU_USE=multiple
	2733	export MP_TIMEOUT=1200
[622]	2734
[1779]	2735	unset MP_TASK_AFFINITY
[1295]	2736
[1779]	2737	if [[ "$LOADLBATCH" = yes ]]
	2738	then
	2739	totalview poe a.out
	2740	else
	2741	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2742	export TVDSVRLAUNCHCMD=ssh
	2743	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2744	fi
[622]	2745
[1779]	2746	fi # END DEBUG MODE
[1289]	2747
[1779]	2748	else
	2749
	2750	# NORMAL EXECUTION
	2751	if [[ -n $numprocs ]]
[1]	2752	then
[1289]	2753
[1779]	2754	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	2755	if [[ $(echo $host \| cut -c1-3) = ibm ]]
[312]	2756	then
[1]	2757
[1779]	2758	# SETUP THE IBM MPI ENVIRONMENT
	2759	if [[ $host != ibmh && $host != ibmkisti ]]
[696]	2760	then
[1779]	2761	export MP_SHARED_MEMORY=yes
	2762	export AIXTHREAD_SCOPE=S
[696]	2763	export OMP_NUM_THREADS=$threads_per_task
[1779]	2764	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	2765	export AUTHSTATE=files
	2766	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	2767	# export MP_PRINTENV=yes
	2768
	2769	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	2770	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
	2771	export MP_WAIT_MODE=poll
	2772	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
[696]	2773	fi
[693]	2774
[1779]	2775	if [[ $host = ibmkisti ]]
[1]	2776	then
[1779]	2777	export LANG=en_US
	2778	export MP_SHARED_MEMORY=yes
	2779	if [[ $threads_per_task = 1 ]]
[343]	2780	then
[1779]	2781	export MP_SINGLE_THREAD=yes
	2782	export MEMORY_AFFINITY=MCM
[343]	2783	else
[1779]	2784	export OMP_NUM_THREADS=$threads_per_task
[343]	2785	fi
[1]	2786	fi
[1779]	2787
	2788	if [[ "$LOADLBATCH" = yes ]]
[1]	2789	then
[1779]	2790	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	2791	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
[1]	2792	then
[1779]	2793	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
[1]	2794	else
[1779]	2795	if [[ $run_coupled_model = false ]]
	2796	then
	2797	if [[ "$ocean_file_appendix" = true ]]
	2798	then
	2799	echo "precursor_ocean" > runfile_atmos
	2800	else
	2801	echo "precursor_atmos" > runfile_atmos
	2802	fi
	2803	else
	2804	(( iia = $numprocs_atmos / $threads_per_task ))
	2805	(( iio = $numprocs_ocean / $threads_per_task ))
	2806	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2807	printf "\n\n"
	2808	echo "coupled_run $iia $iio" > runfile_atmos
	2809	fi
	2810	poe ./a.out < runfile_atmos
[1]	2811	fi
[1779]	2812	else
	2813	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[331]	2814	then
[1779]	2815	poe a.out -procs $numprocs -nodes 1 -rmpool 0
	2816	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
	2817	then
	2818	if [[ -f $hostfile ]]
[331]	2819	then
[1779]	2820	cp $hostfile hostfile
[331]	2821	else
[1779]	2822	(( ii = 1 ))
	2823	while (( ii <= $numprocs ))
	2824	do
	2825	echo $localhost_realname >> hostfile
	2826	(( ii = ii + 1 ))
	2827	done
[331]	2828	fi
[1779]	2829	export MP_HOSTFILE=hostfile
	2830	if [[ $run_coupled_model = false ]]
	2831	then
	2832	if [[ "$ocean_file_appendix" = true ]]
	2833	then
	2834	echo "precursor_ocean" > runfile_atmos
	2835	else
	2836	echo "precursor_atmos" > runfile_atmos
	2837	fi
	2838	else
	2839	(( iia = $numprocs_atmos / $threads_per_task ))
	2840	(( iio = $numprocs_ocean / $threads_per_task ))
	2841	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2842	printf "\n\n"
	2843	echo "coupled_run $iia $iio" > runfile_atmos
	2844	fi
[331]	2845
[1779]	2846	poe ./a.out -procs $numprocs < runfile_atmos
[1289]	2847
[1]	2848	else
[1779]	2849	if [[ "$host_file" = "" ]]
	2850	then
	2851	printf "\n +++ no hostfile given in configuration file"
	2852	locat=config_file
	2853	exit
	2854	else
	2855	eval host_file=$host_file
	2856	fi
	2857	export MP_HOSTFILE=$host_file
	2858	poe a.out -procs $numprocs -tasks_per_node $numprocs
[1]	2859	fi
	2860	fi
[1779]	2861
	2862	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	2863	then
[1779]	2864
	2865	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	2866	# DOES NOT EXIST
[2257]	2867	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
[179]	2868	then
[1779]	2869	if [[ -f $hostfile ]]
[1598]	2870	then
[1779]	2871	cp $hostfile hostfile
	2872	(( ii = $numprocs / $threads_per_task ))
	2873	[[ $ii = 0 ]] && (( ii = 1 ))
	2874	else
	2875	(( ii = 1 ))
	2876	while (( ii <= $numprocs / $threads_per_task ))
	2877	do
	2878	echo $localhost_realname >> hostfile
	2879	(( ii = ii + 1 ))
	2880	done
	2881	if (( $numprocs / $threads_per_task == 0 ))
	2882	then
	2883	echo $localhost_realname >> hostfile
	2884	fi
[1598]	2885	fi
[1779]	2886	eval zeile=\"`head -n $ii hostfile`\"
	2887	printf "\n *** running on: $zeile"
[179]	2888	fi
	2889
[1779]	2890	(( ii = $numprocs / $threads_per_task ))
	2891	[[ $ii = 0 ]] && (( ii = 1 ))
	2892	export OMP_NUM_THREADS=$threads_per_task
[1289]	2893
[1779]	2894	if [[ $threads_per_task != 1 ]]
[291]	2895	then
[1779]	2896	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	2897	# MAY ABORT
	2898	ulimit -s unlimited
	2899	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[291]	2900	fi
[1779]	2901	if [[ $run_coupled_model = false ]]
[1224]	2902	then
[1779]	2903	if [[ "$ocean_file_appendix" = true ]]
	2904	then
	2905	echo "precursor_ocean" > runfile_atmos
	2906	else
	2907	echo "precursor_atmos" > runfile_atmos
	2908	fi
	2909	printf "\n\n"
[1622]	2910
[1779]	2911	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2912	then
	2913	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
	2914	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2915	elif [[ $host = lcbullhh ]]
	2916	then
	2917	export OMPI_MCA_pml=cm
	2918	export OMPI_MCA_mtl=mxm
	2919	export OMPI_MCA_coll=^ghc
	2920	export OMPI_MCA_mtl_mxm_np=0
	2921	export MXM_RDMA_PORTS=mlx5_0:1
	2922	export MXM_LOG_LEVEL=ERROR
	2923	export OMP_NUM_THREADS=$threads_per_task
	2924	export KMP_AFFINITY=verbose,granularity=core,compact,1
	2925	export KMP_STACKSIZE=64m
[1622]	2926
[2147]	2927	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
[1622]	2928
[1779]	2929	elif [[ $host = lccrayf ]]
	2930	then
	2931	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
	2932	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
	2933	then
[2257]	2934	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2935	elif [[ $host = lceddy ]]
[1779]	2936	then
[2257]	2937	echo $ii
[2295]	2938	echo $tasks_per_node
	2939	echo $nodes
[2257]	2940	mpirun -n $ii a.out < runfile_atmos
[2295]	2941	elif [[ $host = lcgeohu ]]
	2942	then
	2943	srun -n $ii a.out < runfile_atmos
[1866]	2944	elif [[ $host = lcocean ]]
	2945	then
	2946	mpirun a.out $ROPTS < runfile_atmos
[1779]	2947	elif [[ $host = lcsb ]]
	2948	then
	2949	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
[2257]	2950
[1779]	2951	elif [[ $host = lckiaps ]]
	2952	then
[1940]	2953	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
[1779]	2954	elif [[ $host = lckyu* ]]
	2955	then
	2956	mpiexec -n $ii --stdin runfile_atmos ./a.out
	2957	else
	2958	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
	2959	fi
	2960
[164]	2961	else
	2962
[2298]	2963	# COUPLED RUN
[1779]	2964	(( iia = $numprocs_atmos / $threads_per_task ))
	2965	(( iio = $numprocs_ocean / $threads_per_task ))
	2966	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2967	printf "\n\n"
[164]	2968
[2298]	2969	echo "coupled_run $iia $iio" > runfile_atmos
	2970
	2971	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
[206]	2972	then
[197]	2973
[2298]	2974	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
[206]	2975
[2298]	2976	elif [[ $host = lck \|\| $host = lckordi ]]
	2977	then
[1779]	2978
[2298]	2979	mpiexec -n $ii ./a.out < runfile_atmos &
[1779]	2980
[2298]	2981	elif [[ $host = lckyu* ]]
	2982	then
[206]	2983
[2298]	2984	mpiexec -n $ii --stdin runfile_atmos ./a.out
[164]	2985
[2298]	2986	elif [[ $host = lcmuk ]]
	2987	then
[206]	2988
[2298]	2989	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
[206]	2990
[1779]	2991	fi
[2298]	2992	wait
[1604]	2993
[164]	2994	fi
[102]	2995
[1779]	2996	elif [[ $host = lckyoto ]]
[440]	2997	then
[1779]	2998	set -xv
	2999	export P4_RSHCOMMAND=plesh
	3000	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3001	if [[ "$ENVIRONMENT" = BATCH ]]
[505]	3002	then
[1779]	3003	if [[ "$cond2" = fujitsu ]]
	3004	then
	3005	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
	3006	elif [[ "cond2" = pgi ]]
	3007	then
	3008	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
	3009	else
	3010	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
	3011	fi
[505]	3012	else
[1779]	3013	if [[ "$cond2" = "" ]]
	3014	then
	3015	mpiruni_rsh -np $numprocs ./a.out # for intel
	3016	else
	3017	mpirun -np $numprocs ./a.out
	3018	fi
[505]	3019	fi
[1779]	3020	set +xv
	3021
	3022	elif [[ $host = lctit ]]
	3023	then
	3024	export OMP_NUM_THREADS=$threads_per_task
	3025	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3026	if [[ "$threads_per_task" != 1 ]]
[505]	3027	then
[1779]	3028	export MV2_ENABLE_AFFINITY=0
[505]	3029	fi
[1779]	3030	echo "----- PBS_NODEFILE content:"
	3031	cat $PBS_NODEFILE
	3032	echo "-----"
	3033	(( ii = $numprocs / $threads_per_task ))
	3034	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
	3035	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
[1289]	3036
[1779]	3037	else
	3038	mpprun -n $numprocs a.out
[678]	3039	fi
[1]	3040	else
[1779]	3041	a.out
[1]	3042	fi
[1289]	3043
[1779]	3044	fi # end normal (non-debug) execution
	3045
	3046	fi # end explicit execute_command or host-specific execute actions
	3047
[1289]	3048	if [[ $? != 0 ]]
[1]	3049	then
	3050
[1289]	3051	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3052	printf "\n +++ runtime error occured"
	3053	locat=execution
	3054	exit
[1289]	3055
[1]	3056	else
[260]	3057
[1289]	3058	printf "\n$dashes\n *** execution finished \n"
	3059
	3060	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3061	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3062	if [[ "$dvrserver_id" != "" ]]
	3063	then
	3064	kill $dvrserver_id
	3065	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3066
[1289]	3067	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3068	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3069	if [[ -d DATA_DVR ]]
	3070	then
[261]	3071
[1289]	3072	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3073	# DIRECTORY
[262]	3074	cp .dvrserver.config DATA_DVR
	3075
[1289]	3076	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3077	# SEQUENCE MODE DATA TOO)
[262]	3078	process_dvr_output -d DATA_DVR -f $fname -s
	3079
	3080	else
	3081
[1289]	3082	# PROCESS THE LOCAL OUTPUT
[262]	3083	process_dvr_output -l -d DATA_DVR -f $fname
	3084
	3085	fi
	3086
	3087	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3088	then
	3089
[1289]	3090	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3091	process_dvr_output -l -d DATA_DVR -f $fname
	3092
[260]	3093	fi
[1]	3094	fi
	3095
	3096
	3097
[1289]	3098	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3099	# BY EACH CORE INTO ONE FILE
[920]	3100	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3101	then
	3102	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3103	printf "\n 2d- and/or 3d-data may be incomplete!"
	3104	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3105	elif [[ "$combine_plot_fields" == true ]]
	3106	then
[1270]	3107	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3108	then
	3109	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
[1779]	3110	aprun -n 1 -N 1 combine_plot_fields${block}.x
[1270]	3111	else
	3112	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3113	combine_plot_fields${block}.x
	3114	fi
[920]	3115	else
[1289]	3116
	3117	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3118	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3119	# ??? koennen wir das streichen ???
[920]	3120	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3121	fi
[503]	3122
	3123
	3124
[1289]	3125	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3126	(( i = 0 ))
	3127	while (( i < ioc ))
	3128	do
	3129	(( i = i + 1 ))
	3130	if (( i == 1 ))
	3131	then
[1289]	3132	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3133	fi
	3134	printf "\n >>> ${out_command[$i]}"
	3135	eval ${out_command[$i]}
	3136	if (( i == ioc ))
	3137	then
[1289]	3138	printf "\n$dashes\n"
[1]	3139	fi
	3140	done
	3141
	3142
[1289]	3143	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3144	if [[ $do_trace = true ]]
	3145	then
	3146	printf "\n\n"
	3147	ls -al
	3148	fi
[2261]	3149
[1]	3150
[1289]	3151	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3152	(( i = 0 ))
	3153	while (( i < iout ))
	3154	do
	3155	(( i = i + 1 ))
	3156	if (( i == 1 ))
	3157	then
[2261]	3158	printf "\n\n *** saving OUTPUT-files:"
	3159
	3160	# GET RUN NUMBER ASSIGNED BY PALM
	3161	if [[ -f RUN_NUMBER ]]
	3162	then
	3163	read run_number < RUN_NUMBER
	3164	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	3165	usecycle_option="-U $run_number"
	3166	else
	3167	run_number=0
	3168	usecycle_option=""
	3169	fi
	3170	printf "\n$dashes"
[1]	3171	fi
	3172
[2261]	3173	# ADD CYCLE NUMBER TO FILENAME
	3174	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	3175	then
	3176
	3177	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	3178	if [[ "${actionout[$i]}" != "a" ]]
	3179	then
	3180	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	3181	# WITH AN EXISTING CYCLE NUMBER
	3182	if (( run_number >= cycnum[$i] ))
	3183	then
	3184	(( cycnum[$i] = run_number ))
	3185	else
	3186	if (( run_number > 0 ))
	3187	then
	3188	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	3189	fi
	3190	fi
	3191	fi
	3192	if (( cycnum[$i] > 0 ))
	3193	then
	3194	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	3195	fi
	3196	fi
	3197
[1289]	3198	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3199	files_for_pes=false; filetyp=file
[2261]	3200	link_local_output=false
[1]	3201	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3202	then
	3203	files_for_pes=true; filetyp=directory
	3204	actionout[$i]=""
	3205	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3206	then
	3207	actionout[$i]=""
[2261]	3208	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
[1]	3209	then
	3210	files_for_pes=true; filetyp=directory
[2261]	3211	link_local_output=true
	3212	actionout[$i]=""
	3213	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
[1]	3214	then
[2261]	3215	link_local_output
	3216	actionout[$i]=""
[1]	3217	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3218	then
	3219	files_for_pes=true; filetyp=directory
	3220	actionout[$i]="tr"
	3221	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3222	then
	3223	actionout[$i]="tr"
	3224	fi
	3225
	3226	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3227	then
	3228	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3229	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3230	then
	3231	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3232	else
	3233
	3234
[1289]	3235	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3236	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3237	if [[ "${actionout[$i]}" = tr ]]
	3238	then
	3239	if [[ $localhost != $fromhost ]]
	3240	then
	3241	if [[ $files_for_pes = false ]]
	3242	then
	3243	cps=""
	3244	cst=""
	3245	else
	3246	cps=-c
	3247	cst="/"
	3248	fi
[2261]	3249
	3250	transfer_failed=false
	3251	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3252	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
	3253	if [[ $localhost = lccrayb ]]
[1]	3254	then
[2261]	3255	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]}"
	3256	elif [[ $localhost = lccrayh ]]
	3257	then
	3258	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]}"
	3259	elif [[ $localhost = lcbullhh ]]
	3260	then
	3261	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]}"
	3262	elif [[ $localhost = lcxe6 ]]
	3263	then
	3264	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]	3265	else
[2261]	3266	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3267	fi
	3268	[[ $? != 0 ]] && transfer_failed=true
[1]	3269
[2261]	3270	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	3271	if [[ $transfer_failed = true ]]
	3272	then
	3273	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
	3274	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
[1]	3275
[2261]	3276	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	3277	eval local_catalog=${pathout[$i]}
	3278	if [[ ! -d $local_catalog ]]
[1]	3279	then
[2261]	3280	printf " *** local directory does not exist. Trying to create:\n"
	3281	printf " $local_catalog \n"
	3282	mkdir -p $local_catalog
[1]	3283	fi
[2261]	3284	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3285	transfer_problems=true
[1]	3286	fi
[2261]	3287
[1]	3288	else
	3289
[1289]	3290	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3291	actionout[$i]=""
	3292	fi
	3293	fi
	3294
	3295
[1289]	3296	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3297	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3298	if [[ "${actionout[$i]}" = tra ]]
	3299	then
	3300	if [[ $localhost != $fromhost ]]
	3301	then
[2261]	3302	if [[ $localhost = ibmh ]]
[1]	3303	then
	3304
[1289]	3305	# TRANSFER IN SEPERATE JOB
	3306	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3307	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3308	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3309	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3310
	3311	echo "set -x" > transfer_${localout[$i]}
	3312	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3313
	3314	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3315	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3316	printf "\n or higher cycle\n"
[1468]	3317	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]	3318
[1]	3319	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3320
[2261]	3321	if [[ $LOGNAME = b323013 ]]
[1]	3322	then
[2261]	3323	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3324	else
[2261]	3325	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3326	fi
	3327
	3328	else
	3329
[1289]	3330	# TRANSFER WITHIN THIS JOB
[1]	3331	transfer_failed=false
[82]	3332	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3333	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3334	if [[ $localhost = lccrayb ]]
	3335	then
[2261]	3336	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]	3337	elif [[ $localhost = lccrayh ]]
	3338	then
[2261]	3339	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]	3340	elif [[ $localhost = lcxe6 ]]
	3341	then
[2261]	3342	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]	3343	else
[1468]	3344	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3345	fi
[82]	3346	[[ $? != 0 ]] && transfer_failed=true
[1]	3347
[1289]	3348	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3349	if [[ $transfer_failed = true ]]
	3350	then
[1289]	3351	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3352	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3353
[1289]	3354	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3355	eval local_catalog=${pathout[$i]}
	3356	if [[ ! -d $local_catalog ]]
	3357	then
	3358	printf " *** local directory does not exist. Trying to create:\n"
	3359	printf " $local_catalog \n"
	3360	mkdir -p $local_catalog
	3361	fi
	3362
	3363	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3364	transfer_problems=true
	3365	fi
	3366	fi
	3367	else
	3368
[1289]	3369	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3370	actionout[$i]=a
	3371	fi
	3372	fi
	3373
	3374
[1289]	3375	# APPEND ON THIS MACHINE
[1]	3376	if [[ "${actionout[$i]}" = "a" ]]
	3377	then
[741]	3378	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	3379	then
	3380	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	3381	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	3382	else
	3383	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	3384	cat ${localout[$i]} >> ${pathout[$i]}
	3385	fi
[1]	3386	fi
	3387
[1289]	3388	# COPY ON THIS MACHINE
	3389	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	3390	# ON DIFFERENT FILE-SYSTEMS
[1]	3391	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	3392	then
	3393
[1289]	3394	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	3395	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	3396	then
	3397	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[2261]	3398	if [[ $link_local_output = true ]]
	3399	then
	3400	printf " file will be linked\n"
	3401	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3402	fi
	3403	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3404	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
[149]	3405	then
[2261]	3406	if [[ $link_local_output = true ]]
	3407	then
	3408	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3409	fi
	3410	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3411	else
	3412	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
[149]	3413	fi
[1]	3414	else
	3415	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[2261]	3416	if [[ $link_local_output = true ]]
	3417	then
	3418	printf " file will be linked\n"
	3419	ln -f ${localout[$i]} ${pathout[$i]}
	3420	fi
	3421	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3422	if [[ ! -f "${pathout[$i]}" ]]
[149]	3423	then
[2261]	3424	if [[ $link_local_output = true ]]
	3425	then
	3426	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3427	fi
	3428	cp ${localout[$i]} ${pathout[$i]}
	3429	else
	3430	printf "+++ no copy because file ${pathout[$i]} exists\n"
[149]	3431	fi
[1]	3432	fi
	3433
	3434	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	3435	then
	3436
[1289]	3437	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	3438	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	3439	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[2261]	3440	if [[ $link_local_output = true ]]
	3441	then
	3442	printf " files will be linked\n"
	3443	mkdir ${pathout[$i]}
	3444	cd ${localout[$i]}
	3445	for file in $(ls *)
	3446	do
	3447	ln -f $file ${pathout[$i]}
	3448	done >\|/dev/null 2>&1
	3449	cd $TEMPDIR
	3450	fi
[1289]	3451
	3452	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[2261]	3453	if [[ ! -f "${pathout[$i]}/_000000" ]]
[149]	3454	then
[2261]	3455	if [[ $link_local_output = true ]]
	3456	then
	3457	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3458	fi
	3459	cp -r ${localout[$i]}/* ${pathout[$i]}
	3460	fi
[1]	3461
	3462	fi
	3463	fi
	3464	done
	3465	if (( i != 0 ))
	3466	then
	3467	if [[ $transfer_problems = true ]]
	3468	then
[1289]	3469	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	3470	printf "\n +++ WARNING: some data transfers failed! \n"
	3471	else
[1289]	3472	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	3473	fi
	3474	fi
	3475
	3476
[1289]	3477	# IF REQUIRED, START A RESTART-JOB
	3478	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	3479	if [[ -f CONTINUE_RUN ]]
	3480	then
	3481
[2261]	3482	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	3483	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	3484	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	3485	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
	3486	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	3487	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	3488	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	3489	if [[ $(echo $mc \| grep -c "#") != 0 ]]
[1]	3490	then
[2261]	3491	mc=`echo $mc \| sed 's/#/f/g'`
	3492	fi
[1]	3493
	3494
[2261]	3495	# START THE RESTART-JOB
	3496	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
	3497	echo " $mc"
	3498	printf "\n$dashes\n"
	3499	if [[ $localhost != $fromhost ]]
	3500	then
[1]	3501
[2295]	3502	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 \|\| $localhost = lcgeohu ]]
[1]	3503	then
[2261]	3504	echo "*** ssh will be used to initiate restart-runs!"
	3505	echo " return_address=\"$return_address\" "
	3506	echo " return_username=\"$return_username\" "
	3507	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
[1]	3508	then
[2261]	3509	if [[ $localhost = ibmh ]]
[1]	3510	then
[2261]	3511	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\" "
	3512	elif [[ $localhost = lcbullhh ]]
	3513	then
	3514	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\" "
	3515	elif [[ $localhost = lccrayb ]]
	3516	then
	3517	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\" "
	3518	elif [[ $localhost = lccrayh ]]
	3519	then
	3520	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\" "
	3521	elif [[ $localhost = lcxe6 ]]
	3522	then
	3523	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]	3524	else
[2261]	3525	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]	3526	fi
	3527	else
[2261]	3528	if [[ $localhost = ibmkisti ]]
	3529	then
	3530	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\" "
	3531	elif [[ $localhost = lceddy ]]
	3532	then
	3533	/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 "
	3534	elif [[ $localhost = lcocean ]]
	3535	then
	3536	/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 "
	3537	elif [[ $localhost = lccrayb ]]
	3538	then
	3539	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\" "
	3540	elif [[ $localhost = lccrayh ]]
	3541	then
	3542	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]	3543	elif [[ $localhost = lccgeohu ]]
	3544	then
	3545	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]	3546	else
	3547	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	3548	fi
[1]	3549	fi
[2261]	3550	else
	3551	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	3552	locat=restart; exit
	3553	fi
[1]	3554
[2261]	3555	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	3556	if [[ $queue = special1q ]]
	3557	then
	3558	sleep 120
[1]	3559	else
[2261]	3560	sleep 30
	3561	fi
[1]	3562
[2261]	3563	else
	3564
	3565	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	3566	# USING SSH)
	3567	cd $LOCAL_PWD
[1103]	3568	if [[ $localhost = lckyuh ]]
	3569	then
[2261]	3570	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	3571	printf "\n please restart job manually using command:\n"
	3572	printf "\n \"$mc\" "
[1103]	3573	else
[2261]	3574	eval $mc # THE ' MUST BE EVALUATED
[1103]	3575	fi
[2261]	3576	cd - > /dev/null
	3577	fi
	3578	if [[ $localhost = lckyuh ]]
	3579	then
	3580	printf "\n$dashes\n *** restart-run to be initiated manually\n"
	3581	else
	3582	printf "\n$dashes\n *** restart-run initiated \n"
	3583	fi
[1]	3584
	3585
[2261]	3586	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	3587	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	3588	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	3589	# MAY BE VERY HUGE)
	3590	(( i = 0 ))
	3591	while (( i < iin ))
	3592	do
	3593	(( i = i + 1 ))
	3594	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	3595	then
	3596	rm -r ${absnamein[$i]}
	3597	fi
	3598	done
[1]	3599
	3600	fi
	3601
	3602
	3603
[1289]	3604	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	3605	if [[ "$email_notification" != "none" ]]
[1]	3606	then
	3607
	3608	if [[ $localhost != $fromhost ]]
	3609	then
	3610	if [[ -f CONTINUE_RUN ]]
	3611	then
	3612	echo "PALM restart run necessary" > email_text
	3613	echo "description header of actual run:" >> email_text
	3614	cat CONTINUE_RUN >> email_text
	3615	echo "mrun-command to restart:" >> email_text
	3616	echo "$mc" >> email_text
	3617	else
	3618	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	3619	fi
	3620	mail $email_notification < email_text
	3621	printf "\n *** email notification sent to \"$email_notification\" "
	3622	fi
	3623	fi
	3624
	3625
	3626
[1289]	3627	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	3628	cd $HOME
	3629	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	3630
	3631	else
	3632
[1289]	3633	# PREPARING ACTIONS,
	3634	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	3635
[1289]	3636	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[1468]	3637	mrun_com="$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 $remote_username"
[79]	3638	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	3639	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	3640	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	3641	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	3642	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	3643	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	3644	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	3645	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	3646	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	3647	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	3648	if [[ $use_openmp = true ]]
	3649	then
[622]	3650	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	3651	fi
[759]	3652	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[1]	3653	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	3654	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	3655	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	3656	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	3657	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	3658	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[920]	3659	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	3660	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	3661	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	3662	if [[ $do_remote = true ]]
	3663	then
	3664	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	3665	fi
	3666
	3667
[1289]	3668	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	3669	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	3670	then
	3671
	3672	printf "\n *** creating the executable for batch job\n"
	3673
[1289]	3674	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	3675	if [[ $host != $localhost ]]
	3676	then
	3677	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	3678	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	3679	locat=create_executable; exit
	3680	fi
	3681
	3682	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3683	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3684
	3685	cp $make_depository .
	3686	tar -xf $make_depository > /dev/null 2>&1
	3687	cp ../* . > /dev/null 2>&1
	3688
	3689	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	3690
	3691	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	3692	then
	3693	printf "\n +++ error occured while compiling or linking"
	3694	locat=compile
	3695	exit
	3696	fi
	3697
	3698	mv a.out ..
	3699	cd - > /dev/null 2>&1
	3700	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3701
	3702	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	3703
	3704	fi
	3705
	3706
[1289]	3707	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	3708	jobfile=jobfile.$RANDOM
	3709
	3710
[1289]	3711	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	3712	echo "mkdir $TEMPDIR" >> $jobfile
	3713	echo "cd $TEMPDIR" >> $jobfile
	3714
	3715
[1289]	3716	# ACTIVATE ERROR-TRACEBACK
[1]	3717	if [[ $do_trace = true ]]
	3718	then
	3719	echo "set -x" >> $jobfile
	3720	else
	3721	echo "set +vx" >> $jobfile
	3722	fi
	3723
	3724
[1289]	3725	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	3726	if [[ "$init_cmds" != "" ]]
	3727	then
	3728	echo "$init_cmds" >> $jobfile
	3729	fi
	3730	if [[ "$module_calls" != "" ]]
	3731	then
	3732	echo "$module_calls" >> $jobfile
	3733	fi
	3734
	3735
[1289]	3736	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	3737	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	3738	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	3739	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	3740	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	3741	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	3742	# QUEUEING-SYSTEMS
[2295]	3743	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean \|\| $host = lcgeohu ]]
[1]	3744	then
	3745
[1289]	3746	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	3747	if [[ $restart_run != true ]]
	3748	then
	3749	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	3750	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	3751	fi
[1]	3752
[1289]	3753	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	3754	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	3755	echo "set -x" >> $jobfile
[693]	3756	if [[ $host = $localhost ]]
	3757	then
[1199]	3758	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	3759	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	3760	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	3761	then
	3762	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3763	else
	3764	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3765	fi
[1199]	3766
[693]	3767	else
[1255]	3768	if [[ $host = ibmkisti ]]
[693]	3769	then
[1289]	3770	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	3771	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3772	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1620]	3773	elif [[ $host = lcbullhh ]]
	3774	then
	3775	echo "localdir=\`pwd\`" >> $jobfile
	3776	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	3777
[1255]	3778	elif [[ $host = lccrayb ]]
	3779	then
	3780	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3781	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3782	elif [[ $host = lccrayh ]]
	3783	then
	3784	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3785	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3786
[1255]	3787	else
[1468]	3788	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	3789	fi
	3790	fi
[193]	3791	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	3792
[1289]	3793	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	3794	# WORKING DIRECTORY OF THE JOB
[193]	3795	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	3796	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	3797	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	3798	echo "execute_mrun=true" >> $jobfile
	3799	echo " " >> $jobfile
	3800
[191]	3801	else
	3802
[1289]	3803	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	3804	if [[ $do_compile = true ]]
	3805	then
	3806
	3807	source_catalog=SOURCES_FOR_RUN_$fname
	3808
[1289]	3809	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	3810	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	3811	echo "export SOURCES_COMPLETE=true" >> $jobfile
	3812	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	3813
	3814	for filename in $source_list
	3815	do
[1289]	3816	# BACKSLASH IS USED FOR MASKING
[191]	3817	echo "cat > $filename << \"%END%\"" >> $jobfile
	3818	cat $source_catalog/$filename >> $jobfile
	3819	echo " " >> $jobfile
	3820	echo "%END%" >> $jobfile
	3821	echo " " >> $jobfile
	3822	done
	3823
[1289]	3824	# BACKSLASH IS USED FOR MASKING
[191]	3825	echo "cat > Makefile << \"%END%\"" >> $jobfile
	3826	cat $source_catalog/Makefile >> $jobfile
[1]	3827	echo " " >> $jobfile
	3828	echo "%END%" >> $jobfile
	3829	echo " " >> $jobfile
	3830
[191]	3831	echo "cd - > /dev/null" >> $jobfile
[1]	3832
[191]	3833	fi
[1]	3834
	3835
[1289]	3836	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	3837	# BACKSLASH IS USED FOR MASKING
	3838	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	3839	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	3840	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	3841	if [[ $host = lckyuh ]]
	3842	then
[1289]	3843	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	3844	sed 's/frtpx/frt/g' $config_file >> $jobfile
	3845	else
	3846	sed 's/#$.*//g' $config_file >> $jobfile
	3847	fi
[191]	3848	echo "%END%" >> $jobfile
	3849	echo " " >> $jobfile
[1]	3850
	3851
[1289]	3852	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	3853	# BACKSLASH IS USED FOR MASKING
[1101]	3854	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	3855	if [[ $host = lckyuh ]]
	3856	then
	3857	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	3858	else
	3859	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	3860	fi
[1101]	3861	echo "%END%" >> $jobfile
[191]	3862	echo "chmod u+x $mrun_script_name" >> $jobfile
	3863	echo "execute_mrun=true" >> $jobfile
	3864	echo " " >> $jobfile
[1]	3865
	3866	fi
	3867
[191]	3868
[1289]	3869	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	3870	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	3871	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	3872	if [[ $do_remote = true ]]
	3873	then
	3874	(( i = 0 ))
	3875	while (( i < iin ))
	3876	do
	3877	(( i = i + 1 ))
	3878	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	3879	if [[ "${transin[$i]}" = job ]]
	3880	then
	3881	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	3882	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	3883	echo " " >> $jobfile
	3884	echo "%END%" >> $jobfile
	3885	else
[1468]	3886	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	3887	fi
	3888
[1289]	3889	# CHECK, IF FILE COULD BE CREATED
[1]	3890	echo "if [[ \$? = 1 ]]" >> $jobfile
	3891	echo "then" >> $jobfile
	3892	echo " echo \" \" " >> $jobfile
	3893	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	3894	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	3895	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	3896	echo " execute_mrun=false" >> $jobfile
	3897	echo "fi" >> $jobfile
	3898	done
	3899	fi
	3900
[1289]	3901	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3902	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	3903	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	3904	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3905	echo "export LOCAL_PWD" >> $jobfile
	3906
[1289]	3907	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	3908	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	3909	echo "export LOCAL_MRUN_PATH" >> $jobfile
	3910
[2257]	3911	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
	3912	if [[ $host = lceddy \|\| $localhost = lceddy ]]
	3913	then
[1099]	3914	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	3915	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[2257]	3916	fi
[1]	3917
[1289]	3918	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	3919	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	3920	echo "set -x" >> $jobfile
	3921	echo "queue=$queue" >> $jobfile
[1]	3922	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	3923	echo 'ls -al; echo `pwd`' >> $jobfile
	3924	echo "cd \$HOME" >> $jobfile
	3925	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	3926
	3927
	3928
	3929
[1289]	3930	# START THE JOB USING SUBJOB-COMMAND
[1]	3931	if [[ $silent = false ]]
	3932	then
	3933	printf "\n "
	3934	else
	3935	printf "\n\n"
	3936	fi
	3937
[1094]	3938	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]	3939	rm -rf $jobfile
	3940
	3941
[1289]	3942	fi # END OF REMOTE-PART

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