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source: palm/trunk/SCRIPTS/mrun @ 2286

Last change on this file since 2286 was 2286, checked in by raasch, 7 years ago
test output for cycle number removed
Property svn:keywords set to `Id Rev`
File size: 142.4 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 2286 2017-06-15 13:31:57Z raasch $
[2286]	29	# test output for cycle number removed
	30	#
	31	# 2268 2017-06-09 10:34:09Z raasch
[2268]	32	# bugfix for calculating cycle numbers for output files in r2261
	33	#
	34	# 2262 2017-06-08 14:52:23Z raasch
[2262]	35	# bugfix for r2261
	36	#
	37	# 2261 2017-06-08 14:25:57Z raasch
[2261]	38	# unified cycle numbers for output files are used,
	39	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
	40	# creation of file OUTPUT_FILE_CONNECTIONS removed,
	41	# archive feature completely removed from the script,
	42	# nech related parts completely removed
	43	#
	44	# 2257 2017-06-07 14:07:05Z witha
[2257]	45	# adjustments for lceddy, removed lcflow-specific code
	46	#
	47	# 2186 2017-03-21 05:36:31Z raasch
[1867]	48	#
[2186]	49	# 2185 2017-03-21 05:09:29Z raasch
	50	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
	51	#
[2150]	52	# 2148 2017-02-09 16:56:42Z scharf
	53	# changed allocation of resources for lcbullhh in srun command
	54	#
[2142]	55	# 2141 2017-02-06 10:19:32Z gronemeier
	56	# made check for existing files language independent
	57	#
[1945]	58	# 1944 2016-06-15 06:29:00Z raasch
	59	# adjustments for using HLRN ssh-keys
	60	#
[1941]	61	# 1940 2016-06-14 05:15:20Z raasch $
	62	# adjustments for lckiaps
	63	#
[1867]	64	# 1866 2016-04-15 06:50:59Z raasch
	65	# adjusted for lcocean
[1805]	66	#
[1842]	67	# 1841 2016-04-07 19:14:06Z raasch
	68	# script now running under bash
	69	#
[1805]	70	# 1804 2016-04-05 16:30:18Z maronga
[1779]	71	# test: implementing an execute mechanism where the execute command is given in the
	72	# configuration file
	73	# ROPTS removed from execution commands
	74	# Warnings about missing optional files or user code changed to informative messages
[1804]	75	# Removed parameter file check
[1305]	76	#
[1756]	77	# 1755 2016-02-22 13:53:39Z maronga
	78	# Minor bugfix to last commit
	79	#
[1754]	80	# 1753 2016-02-22 13:49:49Z maronga
	81	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
	82	#
[1623]	83	# 1622 2015-07-20 06:21:36Z heinze
	84	# bugfix for Mistral (lcbullhh)
	85	#
	86	# 1621 2015-07-17 11:39:33Z heinze
[1621]	87	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
[1200]	88	#
[1610]	89	# 1609 2015-07-03 15:37:58Z maronga
	90	# Modified the random number of the temporary working directory to match the
	91	# queuing system number on HLRN-III (lccray*).
	92	#
[1605]	93	# 1604 2015-06-23 15:48:03Z suehring
	94	# Enable coupled runs for lcmuk
	95	#
[1599]	96	# 1598 2015-05-29 06:45:40Z raasch
	97	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
	98	#
[1550]	99	# 1549 2015-01-30 14:26:16Z suehring
	100	# Enable interactive debug sessions with allinea debugger
	101	#
[1548]	102	# 1547 2015-01-29 15:09:12Z witha
	103	# adjustments for ForWind computing cluster (lcflow)
	104	#
[1492]	105	# 1491 2014-11-12 08:12:57Z heinze
	106	# correct setting of batch_job allowed for ibm-machines
	107	#
[1469]	108	# 1468 2014-09-24 14:06:57Z maronga
	109	# Typo removed (addres->address)
	110	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
	111	# Added support for restart runs (remote) for lcxe6
	112	#
[1443]	113	# 1442 2014-07-28 07:09:10Z raasch
	114	# default queues for HLRN-III (lccrayb/lccrayh) defined
	115	#
[1423]	116	# 1422 2014-07-02 10:01:25Z kanani
	117	# automatic restarts enabled for lccrayb,
	118	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
	119	#
[1421]	120	# 1420 2014-06-10 06:24:14Z raasch
	121	# -j1 option added to aprung command for lccrayf (CSC)
	122	#
[1403]	123	# 1402 2014-05-09 14:25:13Z raasch
	124	# batch_job added to envpar-NAMELIST
	125	#
[1358]	126	# 1357 2014-04-11 15:02:03Z witha
	127	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
	128	# possible)
	129	#
[1328]	130	# 1320 2014-03-20 08:40:49Z raasch
	131	# check namelist file set false by default
	132	#
[1305]	133	# 1304 2014-03-12 10:29:42Z raasch
	134	# ulimit option changed from -Ss to -s
	135	#
	136	# bugfix: missing "fi" in r1289
	137	#
[1290]	138	# 1289 2014-03-04 07:12:34Z raasch
	139	# comments translated to English
	140	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	141	# export of variables for palm and interpret_config removed
	142	#
[1282]	143	# 1281 2014-02-01 07:55:49Z raasch
	144	# rsync-copy restricted to Cray machines, since command is unavailable on some
	145	# other systems
	146	#
[1280]	147	# 1279 2014-01-28 12:10:14Z raasch
	148	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	149	# in order to remove annoying restrictions concerning the number of processors which
	150	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	151	# restriction, one of the nodes will be filled with less than the given number of
	152	# tasks per node. A respective warning is given.
	153	#
[1275]	154	# 1274 2014-01-09 13:14:54Z heinze
	155	# adjustments for lccrayh
	156	#
[1273]	157	# 1272 2014-01-08 10:19:32Z witha
	158	# small adjustment for lcflow
	159	#
[1271]	160	# 1270 2013-12-16 11:05:01Z fricke
	161	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	162	#
[1256]	163	# 1255 2013-11-07 14:43:35Z raasch
	164	# further adjustments for lccrayb remote access
	165	#
[1242]	166	# 1241 2013-10-30 11:36:58Z heinze
	167	# Enable use of nudging input and input of large scale forcing from
	168	# external files
	169	#
[1230]	170	# 1229 2013-09-20 06:55:19Z raasch
	171	# further adjustments for lccrayb
	172	#
[1225]	173	# 1224 2013-09-16 07:27:23Z raasch
	174	# first adjustments for lccrayb
	175	#
[1211]	176	# 1210 2013-08-14 10:58:20Z raasch
	177	# fftw support added
	178	#
[1203]	179	# 1201 2013-07-10 16:17:59Z witha
	180	# adjustments for Forwind cluster (lcflow)
	181	#
[1200]	182	# 1199 2013-07-05 14:52:22Z raasch
[1199]	183	# adjustments for CSC Helsinki (lccrayf),
	184	# executables for batch jobs can be created in advance, in order to avoid calling
	185	# the compiler within the batch job (only works if batch jobs are submitted on
	186	# local host)
[1104]	187	#
[1191]	188	# 1190 2013-06-25 09:39:21Z heinze
	189	# enable use of automatic restarts for ibmh
[1185]	190	# use of cluster/express queue enabled (ibmh)
[1104]	191	#
[1125]	192	# 1124 2013-04-09 15:46:52Z raasch
	193	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	194	# side effect may lead to data loss while getopts is reading the script-option arguments
	195	#
[1123]	196	# 1122 2013-04-09 08:37:16Z heinze
	197	# Bugfix: change type of variable last_char
	198	#
[1121]	199	# 1119 2013-04-05 15:11:19Z raasch
	200	# Bugfix for setting -T option for subjob
	201	#
[1109]	202	# 1108 2013-03-05 07:03:32Z raasch
	203	# bugfix for coupled runs on lckyut/lckyuh
	204	#
[1107]	205	# 1106 2013-03-04 05:31:38Z raasch
	206	# --stdin argument for mpiexec on lckyuh
	207	# -y and -Y settings output to header
	208	#
[1104]	209	# 1103 2013-02-20 02:15:53Z raasch
[1103]	210	# default script runs again under ksh, because of unsolved problems with read
	211	# from stdin: when bash script is called from a ksh, message "read error: 0:
	212	# Resource temporarily unavailable" appears and script does not stop,
	213	# further bash compatibility adjustments,
	214	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	215	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	216	#
[1102]	217	# 1101 2013-02-17 10:20:21Z raasch
	218	# script now running under bash instead of ksh, which required small adjustments
	219	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	220	# read from stdin),
	221	# cross compilername on lckyuh compute nodes replaced by real compiler name
	222	#
[1100]	223	# 1099 2013-02-10 01:47:43Z raasch
	224	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	225	# and for Forwind cluster (lcflow)
	226	# small further adjustments for lckyut
	227	#
[1096]	228	# 1094 2013-02-03 01:52:12Z raasch
	229	# explicit ssh/scp port can be set in config file with environment variable
	230	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	231	# decalpha parts (yonsei) removed
	232	#
[1091]	233	# 2013-02-02 07:06:13Z raasch
[1099]	234	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	235	#
[1084]	236	# 1083 2013-01-04 10:22:09Z maronga
	237	# bugfix in parameter file check (read %cpp_options was missing)
	238	#
[1070]	239	# 1069 2012-11-28 16:18:43Z maronga
	240	# bugfix: coupling mode was always set to mpi2, typos removed
	241	#
[1059]	242	# 1058 2012-11-21 07:00:35Z raasch
	243	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	244	# nodes
	245	#
[1047]	246	# 1046 2012-11-09 14:38:45Z maronga
	247	# code put under GPL (PALM 3.9)
	248	#
[1090]	249	# 21/03/94 - Siggi - first version finished
	250	# 03/03/94 - Siggi - script development started
	251	#
[1059]	252	#--------------------------------------------------------------------------------#
[1090]	253	# mrun - script for running PALM jobs
	254	#--------------------------------------------------------------------------------#
[1]	255
[1047]	256
[1]	257
[1289]	258	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	259
[1289]	260	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	261	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	262	# (TOO MANY ARGUMENTS - PROBLEM)
	263	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	264
	265	AddFilenames=""
	266	additional_conditions=""
	267	add_source_path=""
	268	afname=""
[1320]	269	check_namelist_files=false
[920]	270	combine_plot_fields=true
[1]	271	compiler_name=""
	272	cond1=""
	273	cond2=""
	274	config_file=.mrun.config
[206]	275	coupled_dist=""
	276	coupled_mode="mpi1"
[1]	277	cpp_opts=""
[82]	278	cpp_options=""
[1]	279	cpumax=0
	280	cpurest=0
[1199]	281	create_executable_for_batch=false
[1]	282	delete_temporary_catalog=true
	283	do_batch=false
	284	do_compile=true
	285	do_remote=false
	286	do_stagein=true
	287	do_stageout=true
	288	do_trace=false
[352]	289	email_notification="none"
[1]	290	exclude=""
	291	executable=""
[1779]	292	execute_command="none"
[1]	293	execution_error=false
[1210]	294	fftw_inc=""
	295	fftw_lib=""
	296	fftw_support=false
[1289]	297	fname=test
[1]	298	fromhost=""
[78]	299	global_revision=""
[122]	300	group_number=none
[1]	301	host=""
	302	host_file=""
	303	hp=""
	304	input_list=""
	305	interpreted_config_file=""
[164]	306	job_catalog="~/job_queue"
[1]	307	job_on_file=""
	308	keep_data_from_previous_run=false
[183]	309	link_local_input=false
[149]	310	link_local_output=false
[1]	311	localhost_realname=$(hostname)
[260]	312	local_dvrserver_running=.FALSE.
[1]	313	locat=normal
	314	mainprog=""
	315	makefile=""
[759]	316	max_par_io_str=""
[1]	317	mc=$0
	318	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	319	do
	320	mc=`echo $mc \| cut -f2- -d"/"`
	321	done
[493]	322	module_calls=""
[1]	323	mrun_script_name=$mc
[82]	324	netcdf_inc=""
	325	netcdf_lib=""
[1]	326	netcdf_support=false
	327	node_usage=default
	328	numprocs=""
[206]	329	numprocs_atmos=0
	330	numprocs_ocean=0
[1]	331	OOPT=""
	332	openmp=false
	333	output_list=""
	334	package_list=""
	335	queue=none
	336	read_from_config=""
[5]	337	restart_run=false
[622]	338	if [[ `hostname` = rte10 ]]
[1]	339	then
[1468]	340	return_address=133.5.185.60
	341	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[693]	342	elif [[ `hostname` = climate0 ]]
	343	then
[1468]	344	return_address=165.132.26.68
	345	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1866]	346	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
	347	then
	348	return_address="schultzl-Latitude-E6540"
	349	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1021]	350	elif [[ `hostname` = urban00 ]]
	351	then
[1468]	352	return_address=147.46.30.151
	353	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[622]	354	else
[1468]	355	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	356	fi
	357	return_password=""
	358	return_username=$LOGNAME
	359	remotecall=false
	360	remote_username=""
[102]	361	run_coupled_model=false
[1]	362	run_mode=""
[1289]	363	dashes=" ----------------------------------------------------------------------------"
[1]	364	silent=false
	365	source_list=""
	366	source_path=SOURCE
	367	tasks_per_node=""
	368	threads_per_task=1
	369	tmpcreate=false
	370	tmp_data_catalog=""
	371	transfer_problems=false
	372	usern=$LOGNAME
[377]	373	use_openmp=false
[1289]	374	version="MRUN 2.1 Rev$Rev: 2286 $"
[1]	375	working_directory=`pwd`
	376	TOPT=""
	377	XOPT=""
	378	zeit=$( date \| cut -c 12-19 )
	379
[1124]	380	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	381	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	382	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	383	# SCRIPT-OPTION ARGUMENTS
[2261]	384	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]	385
[1289]	386	# ERROR HANDLING IN CASE OF EXIT
[83]	387	trap 'rm -rf $working_directory/tmp_mrun
[1289]	388	if [[ $locat != normal && $locat != control_c ]]
[1]	389	then
	390
[1289]	391	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	392	(( i = 0 ))
	393	while (( i < iec ))
	394	do
	395	(( i = i + 1 ))
	396	printf "\n *** Execution of ERROR-command:\n"
	397	printf " >>> ${err_command[$i]}\n"
	398	eval ${err_command[$i]}
	399	done
[1101]	400	if [[ -n $interpreted_config_file ]]
	401	then
[1]	402	rm -rf $interpreted_config_file
	403	fi
[1101]	404	if [[ -n .mrun_environment ]]
	405	then
[71]	406	rm -rf .mrun_environment
	407	fi
[1]	408	if [[ $tmpcreate = true ]]
	409	then
[2147]	410	# printf "\n *** Contents of \"$TEMPDIR\":\n"
	411	# ls -al; cd
[1]	412	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	413	fi
[260]	414	if [[ "$dvrserver_id" != "" ]]
	415	then
	416	echo "+++ killing dvrserver_id=$dvrserver_id"
	417	kill $dvrserver_id
	418	fi
[1]	419	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	420	then
	421	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	422	fi
	423	printf "\n\n+++ MRUN killed \n\n"
	424	elif [[ $locat != control_c ]]
	425	then
	426	printf "\n\n --> all actions finished\n\n"
	427	printf " Bye, bye $usern !!\n\n"
	428	fi' exit
	429
	430
[1289]	431	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	432	trap 'rm -rf $working_directory/tmp_mrun
[807]	433	rm -rf $working_directory/tmp_check_namelist_files
[69]	434	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	435	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	436	then
	437	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	438	fi
[260]	439	if [[ "$dvrserver_id" != "" ]]
	440	then
	441	echo "+++ killing dvrserver_id=$dvrserver_id"
	442	kill $dvrserver_id
	443	fi
[1]	444	printf "\n+++ MRUN killed by \"^C\" \n\n"
	445	locat=control_c
	446	exit
	447	' 2
	448
	449
[22]	450	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	451	# BEEN SET
	452	if [[ "$PALM_BIN" = "" ]]
	453	then
	454	printf "\n +++ environment variable PALM_BIN has not been set"
	455	printf "\n please set it to the directory where the PALM scripts are located"
	456	locat=palm_bin; exit
	457	fi
[180]	458	export PATH=$PALM_BIN:$PATH
[22]	459
	460
[1]	461
[1289]	462	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	463	# WHICH WILL BE USED TO START RESTART-JOBS
[2261]	464	while getopts :a:bBc:Cd:D: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]	465	do
	466	case $option in
	467	(a) afname=$OPTARG;;
	468	(b) do_batch=true; mc="$mc -b";;
	469	(B) delete_temporary_catalog=false; mc="$mc -B";;
	470	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	471	(C) restart_run=true; mc="$mc -C";;
[1]	472	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[79]	473	(F) job_on_file="-D"; mc="$mc -F";;
[122]	474	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	475	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	476	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	477	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	478	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	479	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	480	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	481	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	482	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	483	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
	484	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	485	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	486	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	487	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	488	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	489	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
[1468]	490	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
[1]	491	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	492	(S) read_from_config=false; mc="$mc -S";;
	493	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	494	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	495	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	496	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	497	(v) silent=true; mc="$mc -v";;
[759]	498	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	499	(x) do_trace=true;set -x; mc="$mc -x";;
	500	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	501	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	502	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	503	(z) check_namelist_files=false; mc="$mc -z";;
[920]	504	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	505	(\?) printf "\n +++ unknown option $OPTARG \n"
	506	printf "\n --> type \"$0 ?\" for available options \n"
	507	locat=parameter;exit;;
	508	esac
	509	done
	510
	511
[1289]	512	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	513	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	514	(( to_shift = $OPTIND - 1 ))
	515	shift $to_shift
[1]	516
[1289]	517	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	518	if [[ "$1" = "?" ]]
	519	then
	520	(printf "\n *** mrun can be called as follows:\n"
[1804]	521	printf "\n $mrun_script_name -b -c.. -d.. -D.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -Z <modus> \n"
[1]	522	printf "\n Description of available options:\n"
	523	printf "\n Option Description Default-Value"
	524	printf "\n -a base name of input files equiv. -d"
	525	printf "\n -b batch-job on local machine ---"
	526	printf "\n -B do not delete temporary directory at end ---"
	527	printf "\n -c configuration file .mrun.config"
	528	printf "\n -d base name of files attached to program test"
	529	printf "\n -D preprocessor(cpp)-directives \"\" "
	530	printf "\n -F create remote job file only ---"
	531	printf "\n -h execution host $localhost_realname"
	532	printf "\n -i INPUT control list \"\" "
	533	printf "\n -k keep data from previous run"
	534	printf "\n -K additional conditions for controling"
	535	printf "\n usage of conditional code and"
	536	printf "\n env-variables in configuration file \"\" "
	537	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	538	printf "\n -M Makefile name Makefile"
	539	printf "\n -n node usage (shared/not_shared) depending on -h"
	540	printf "\n -o OUTPUT control list \"\" "
[1304]	541	printf "\n -O threads per openMP task ---"
[1]	542	printf "\n -p software package list \"\" "
	543	printf "\n -q queue \"$queue\" "
	544	printf "\n -r run control list (combines -i -o) \"\" "
	545	printf "\n -s filenames of routines to be compiled \"\" "
	546	printf "\n must end with .f, .f90, .F, or .c !"
	547	printf "\n use \"..\" for more than one file and wildcards"
[837]	548	printf "\n -s LM compiles all locally modified files"
[1]	549	printf "\n -S config file interpreted by shellscript ---"
	550	printf "\n -t allowed cpu-time in seconds (batch) 0"
	551	printf "\n -T tasks per node depending on -h"
	552	printf "\n -u username on remote machine \"\" "
	553	printf "\n -v no prompt for confirmation ---"
[759]	554	printf "\n -w maximum parallel io streams as given by -X"
[1]	555	printf "\n -x tracing of mrun for debug purposes ---"
	556	printf "\n -X # of processors (on parallel machines) 1"
[291]	557	printf "\n -y add appendix \"_O\" to all local output"
	558	printf "\n files (ocean precursor runs followed by"
	559	printf "\n coupled atmosphere-ocean runs) ---"
[206]	560	printf "\n -Y run coupled model, \"#1 #2\" with"
	561	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	562	printf "\n -Z skip combine_plot_fields at the end of "
	563	printf "\n the simulation ---"
[1]	564	printf "\n "
	565	printf "\n Possible values of positional parameter <modus>:"
	566	printf "\n \"?\" - this outline \n\n") \| more
	567	exit
	568	elif [[ "$1" != "" ]]
	569	then
	570	printf "\n +++ positional parameter $1 unknown \n"
	571	locat=parameter; exit
	572	fi
	573
	574
	575
[1289]	576	# SHORT STARTING MESSAGE
[1]	577	printf "\n*** $version "
	578	printf "\n will be executed. Please wait ..."
	579
	580
[82]	581
[1289]	582	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	583	if [[ ! -f $config_file ]]
	584	then
	585	printf "\n\n +++ configuration file: "
	586	printf "\n $config_file"
	587	printf "\n does not exist"
	588	locat=connect; exit
	589	fi
	590
	591
[1289]	592	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	593	line=""
	594	grep "%host_identifier" $config_file > tmp_mrun
	595	while read line
	596	do
[206]	597	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	598	then
	599	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	600	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	601	if [[ $localhost_realname = $HOSTNAME ]]
[82]	602	then
	603	localhost=$host_identifier
	604	break
	605	fi
	606	fi
	607	done < tmp_mrun
	608
	609	if [[ "$localhost" = "" ]]
	610	then
	611	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	612	printf "\n for local host \"$localhost_realname\"."
	613	printf "\n Please add line"
	614	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	615	printf "\n to the configuration file."
	616	locat=localhost; exit
	617	fi
	618
	619
[1289]	620	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	621	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	622	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	623	[[ "$afname" = "" ]] && afname=$fname
	624
	625
[1289]	626	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	627	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	628	# STATEMENTS IN THE CONFIGURATION FILE
[1]	629	if [[ "$run_mode" != "" ]]
	630	then
	631	input_list="$input_list $run_mode"
	632	output_list="$output_list $run_mode"
	633	fi
	634
	635
[1289]	636	# ??? is this (and the respective option -H) really required ???
	637	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	638	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	639	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	640	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	641	if [[ "$fromhost" = "" ]]
	642	then
	643	fromhost=$localhost
	644	fi
	645
	646
[1289]	647	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	648	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	649	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
[1609]	650	# TO BE SUBMITTED (I.E. do_batch=true)
[1]	651	if [[ -n $host && "$host" != $localhost ]]
	652	then
	653	do_batch=true
	654	do_remote=true
	655	case $host in
[2261]	656	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	657	(*) printf "\n"
[83]	658	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	659	printf "\n is not available"
[1]	660	locat=nqs; (( iec = 0 )); exit;;
	661	esac
	662	else
	663	host=$localhost
	664	fi
	665
	666
[1289]	667	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	668	if [[ -n $additional_conditions ]]
	669	then
[69]	670	cond1=`echo $additional_conditions \| cut -d" " -f1`
	671	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	672	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	673	if [[ -n $dummy ]]
	674	then
	675	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	676	locat=options; exit
	677	fi
[503]	678	block=_$cond1
	679	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	680	fi
	681
	682
[1289]	683	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
[206]	684	if [[ $run_coupled_model = true ]]
	685	then
	686
[1289]	687	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	688	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	689
	690	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	691	then
	692
[1289]	693	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	694	printf "\n PEs (total) : $numprocs"
	695	printf "\n PEs (atmosphere): $numprocs_atmos"
	696	printf "\n PEs (ocean) : $numprocs_ocean"
	697	locat=coupling; exit
[206]	698
[1289]	699	fi
[206]	700
	701
	702	# GET coupled_mode FROM THE CONFIG FILE
	703	line=""
	704	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
	705	while read line
	706	do
[1779]	707	echo line=\"$line\"
	708	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
[206]	709	then
	710	coupled_mode="mpi2"
	711	fi
	712	done < tmp_mrun
	713
	714	fi
	715
[1289]	716	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	717	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	718	mrun_memory=$memory
	719	mrun_group_number=$group_number
	720	mrun_cpumax=$cpumax
	721	mrun_numprocs=$numprocs
[1]	722
[1099]	723
[1289]	724	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
[1468]	725	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
[1]	726	if [[ "$read_from_config" = false ]]
	727	then
	728	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	729
	730	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	731	while read zeile
	732	do
	733	[[ $silent = false ]] && printf "."
	734
	735
[1289]	736	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	737	eval zeile=\"$zeile\"
	738
	739
[1289]	740	# INTERPRET THE LINE
[21]	741	if [[ "$(echo $zeile)" = "" ]]
[1]	742	then
[1289]	743	# EMPTY LINE, NO ACTION
[21]	744	continue
[1]	745
[21]	746	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	747	then
	748
[1289]	749	# LINE IS A COMMENT LINE
[1]	750	true
	751
	752	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	753	then
	754
[1289]	755	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	756	zeile=$(echo $zeile \| cut -c2-)
[69]	757	var=`echo $zeile \| cut -d" " -f1`
	758	value=`echo $zeile \| cut -d" " -s -f2`
	759	for_host=`echo $zeile \| cut -d" " -s -f3`
	760	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	761	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	762
	763	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	764	then
	765
[1289]	766	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	767	# "::" IS REPLACED BY ":".
[1]	768	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	769
	770
[1289]	771	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	772	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	773	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	774	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	775	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	776	# CONFIGURATION-FILE.
[1]	777	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	778	then
	779	eval $var=\$value
	780
[1289]	781	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	782	if [[ $do_trace = true ]]
	783	then
	784	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	785	fi
	786	fi
	787
[1289]	788	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	789	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	790	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	791	# MUST HAVE TO BE STARTED
[1]	792	if [[ $var = host ]]
	793	then
	794	if [[ -n $host && "$host" != $localhost ]]
	795	then
	796	do_batch=true
	797	do_remote=true
	798	case $host in
[2261]	799	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[83]	800	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	801	printf "\n is not available"
[1]	802	locat=nqs; exit;;
	803	esac
	804	else
	805	host=$localhost
	806	fi
	807	fi
	808
[1289]	809	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	810	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	811	# BY MRUN (E.G. subjob)
[1]	812	export $var
	813	fi
	814
	815
	816
	817
	818	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	819	then
	820
[1289]	821	# LINE DEFINES ERROR-COMMAND
[1]	822	(( iec = iec + 1 ))
	823	zeile=$(echo $zeile \| cut -c4-)
	824	err_command[$iec]="$zeile"
	825
	826	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	827	then
	828
[1289]	829	# LINE DEFINES INPUT-COMMAND
[1]	830	(( iic = iic + 1 ))
	831	zeile=$(echo $zeile \| cut -c4-)
	832	in_command[$iic]="$zeile"
	833
	834	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	835	then
	836
[1289]	837	# LINE DEFINES OUTPUT-COMMAND
[1]	838	(( ioc = ioc + 1 ))
	839	zeile=$(echo $zeile \| cut -c4-)
	840	out_command[$ioc]="$zeile"
	841
	842	else
	843
[1289]	844	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	845	# s2a: in/out - field
	846	# s2b: loc - field (optional)
	847	# s2c: tr/ar - field (optional)
[69]	848	s1=`echo $zeile \| cut -d" " -f1`
	849	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	850	s2a=$(echo $s2 \| cut -d":" -f1)
	851	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	852	then
	853	s2b=""
	854	s2c=""
	855	else
[69]	856	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	857	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	858	fi
[69]	859	s3=`echo $zeile \| cut -d" " -f3`
	860	s4=`echo $zeile \| cut -d" " -s -f4`
	861	s5=`echo $zeile \| cut -d" " -s -f5`
	862	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	863
	864
[1289]	865	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	866	# INPUT- OR OUTPUT-LIST.
	867	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	868	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	869	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	870	# IS NOT CHECKED AND STORED.
[1]	871	IFSALT="$IFS"; IFS="$IFS:"
	872	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	873	then
	874	found=false
	875	for actual in $input_list
	876	do
	877	for formal in $s3
	878	do
	879	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	880	done
	881	done
	882	if [[ $found = true ]]
	883	then
	884	(( iin = iin + 1 ))
	885	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	886	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	887	extin[$iin]=$s6
	888	fi
	889	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	890	then
	891	found=false
	892	for actual in $output_list
	893	do
	894	for formal in $s3
	895	do
	896	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	897	done
	898	done
	899	if [[ $found = true ]]
	900	then
	901	(( iout = iout + 1 ))
	902	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	903	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	904	fi
	905	elif [[ "$s2a" != in && "$s2a" != out ]]
	906	then
	907	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	908	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	909	locat=connect; exit
	910	fi
	911	IFS="$IFSALT"
	912	fi
	913	done < $config_file
	914
	915	else
	916
[1289]	917	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	918	[[ $silent = false ]] && printf "..."
[1289]	919	interpreted_config_file=.icf.$RANDOM
[1]	920
	921
[1917]	922
[1289]	923	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[2261]	924	cat > .mrun_environment << EOF
[69]	925	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	926	config_file = '$config_file', do_remote = '$do_remote',
	927	do_trace = '$do_trace', host = '$host',
	928	input_list = '$input_list', icf = '$interpreted_config_file',
	929	localhost = '$localhost', output_list = '$output_list' /
	930
[2261]	931	EOF
[69]	932
[1289]	933	if [[ "$host" != $localhost ]]
[66]	934	then
[503]	935
[1289]	936	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	937	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	938	if [[ $? != 0 ]]
[503]	939	then
[1289]	940	printf "\n\n +++ no interpret_config found"
	941	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	942	locat=interpret_config; exit
	943	fi
	944	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	945	$interpret_config_executable
[503]	946
[1289]	947	else
[503]	948
[1289]	949	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	950	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	951	then
	952	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	953	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	954	locat=interpret_config; exit
[503]	955	else
[1289]	956	interpret_config${block}.x
	957	fi
[503]	958
[66]	959	fi
[71]	960	rm .mrun_environment
[1]	961
[1917]	962
[1289]	963	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	964	chmod u+x $interpreted_config_file
	965	export PATH=$PATH:.
	966	. $interpreted_config_file
[71]	967	rm $interpreted_config_file
[1]	968
[1099]	969	fi
[71]	970
[1917]	971
[1289]	972	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	973	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	974	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	975	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	976	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	977	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	978	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	979
	980
[1289]	981	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	982	# FOR SOURCE-FILES TO BE COMPILED.
	983	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	984	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	985	if [[ "$SOURCES_COMPLETE" = "" ]]
	986	then
	987
[1289]	988	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	989	# HAS BEEN DEFINED
[1]	990	source_path=""
	991	line=""
	992	grep "%source_path" $config_file > tmp_mrun
	993	while read line
	994	do
	995	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	996	then
	997	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	998	then
	999	global_source_path=`echo $line \| cut -d" " -f2`
	1000	fi
	1001	fi
	1002	done < tmp_mrun
	1003
	1004	line=""
	1005	found=false
	1006	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	1007	while read line
	1008	do
	1009	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1010	then
	1011	if [[ $found = true ]]
	1012	then
	1013	printf "\n\n +++ more than one source path found in configuration file"
	1014	printf "\n for local host \"$localhost\" "
	1015	locat=source_path; exit
	1016	fi
	1017	source_path=`echo $line \| cut -d" " -f2`
	1018	found=true
	1019	fi
	1020	done < tmp_mrun
	1021	rm tmp_mrun
	1022
	1023	if [[ "$source_path" = "" ]]
	1024	then
	1025	if [[ "$global_source_path" != "" ]]
	1026	then
	1027	source_path=$global_source_path
	1028	else
	1029	printf "\n\n +++ no source path found in configuration file"
	1030	printf "\n for local host \"$localhost\" "
	1031	locat=source_path; exit
	1032	fi
	1033	fi
	1034	eval source_path=$source_path
	1035
	1036	if [[ ! -d $source_path ]]
	1037	then
	1038	printf "\n\n +++ source path \"$source_path\" on local host"
	1039	printf "\n \"$localhost\" does not exist"
	1040	locat=source_path; exit
	1041	fi
	1042
	1043	fi
	1044
	1045
[1289]	1046	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1047	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1048	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	1049	then
	1050	global_revision=`svnversion $source_path 2>/dev/null`
	1051	global_revision="Rev: $global_revision"
	1052	fi
[1]	1053
[78]	1054
[1289]	1055	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	1056	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	1057	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	1058	if [[ -n $host && "$host" != $localhost ]]
	1059	then
	1060	do_batch=true
	1061	do_remote=true
	1062	case $host in
[2261]	1063	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	1064	(*) printf "\n"
[83]	1065	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	1066	printf "\n is not available"
[1]	1067	locat=nqs; (( iec = 0 )); exit;;
	1068	esac
	1069	else
	1070	host=$localhost
	1071	fi
	1072
	1073
[1620]	1074
[1289]	1075	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1076	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1077	then
	1078
[1289]	1079	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1080	if [[ ! -n $numprocs ]]
	1081	then
	1082	printf "\n"
	1083	printf "\n +++ option \"-K parallel\" requires additional specification"
	1084	printf "\n of the number of processors to be used by"
	1085	printf "\n mrun-option \"-X\" or by environment-variable"
	1086	printf "\n \"numprocs\" in the configuration file"
	1087	locat=numprocs; (( iec = 0 )); exit
	1088	fi
	1089
[1289]	1090	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1091	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2257]	1092	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
[1]	1093	then
[759]	1094	printf "\n"
	1095	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1096	printf "\n set -T option or define tasks_per_node in the config file"
	1097	locat=tasks_per_node; (( iec = 0 )); exit
	1098	fi
[1279]	1099
	1100	if (( numprocs < tasks_per_node ))
	1101	then
	1102	printf "\n"
	1103	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1104	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1105	locat=tasks_per_node; (( iec = 0 )); exit
	1106	fi
	1107
[2257]	1108	if [[ $host != lcxt5m ]]
[759]	1109	then
[1279]	1110	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1111	(( ival = $tasks_per_node ))
	1112	(( pes = numprocs ))
	1113	(( ii = pes / ival ))
[1279]	1114	(( remaining_pes = pes - ii * ival ))
	1115	if (( remaining_pes > 0 ))
[848]	1116	then
	1117	printf "\n"
[1279]	1118	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1119	printf "\n divisor of the total number of processors (option \"-X\")"
	1120	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1121	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1122	(( nodes = nodes + 1 ))
[848]	1123	fi
[1]	1124	fi
	1125
[759]	1126
[377]	1127	# SETTINGS FOR SUBJOB-COMMAND
[1]	1128	OOPT="-O $threads_per_task"
	1129
[1289]	1130	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1131	if [[ "$tasks_per_node" != "" ]]
	1132	then
[1119]	1133	TOPT="-T $tasks_per_node"
[1]	1134	fi
	1135
[1289]	1136	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1137	if [[ $node_usage = default ]]
	1138	then
	1139	if [[ $host = ibms ]]
	1140	then
	1141	node_usage=shared
	1142	else
	1143	node_usage=not_shared
	1144	fi
	1145	fi
[181]	1146
[635]	1147	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1148	then
	1149	printf "\n"
	1150	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1151	printf "\n \"shared\" or \"not_shared\""
	1152	locat=tasks_per_node; (( iec = 0 )); exit
	1153	fi
	1154
	1155	fi
	1156
[1289]	1157	# CHECK IF HOSTFILE EXISTS
[1]	1158	if [[ -n $hostfile ]]
	1159	then
	1160	if [[ ! -f $hostfile ]]
	1161	then
	1162	printf "\n"
	1163	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1164	locat=hostfile; exit
	1165	fi
	1166	fi
	1167
	1168
[1289]	1169	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1170	if [[ "$maximum_parallel_io_streams" = "" ]]
	1171	then
	1172	maximum_parallel_io_streams=$numprocs
	1173	fi
[1]	1174
[759]	1175
[1289]	1176	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1177	if [[ "$scp_port" != "" ]]
	1178	then
	1179	PORTOPT="-P $scp_port"
	1180	SSH_PORTOPT="-p $scp_port"
	1181	fi
	1182
	1183
[1944]	1184	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1185	# CONFIG-FILE
	1186	if [[ "$ssh_key" != "" ]]
	1187	then
	1188	ssh_key="-i $HOME/.ssh/$ssh_key"
	1189	fi
	1190
	1191
[1289]	1192	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1193	if [[ $queue = none ]]
	1194	then
	1195	case $host in
[1184]	1196	(ibmh) queue=cluster;;
[693]	1197	(ibmkisti) queue=class.32plus;;
[1620]	1198	(lcbullhh) queue=compute;;
[1442]	1199	(lccrayb) queue=mpp1q;;
	1200	(lccrayh) queue=mpp1q;;
[1040]	1201	(lckiaps) queue=normal;;
[440]	1202	(lckyoto) queue=ph;;
[1099]	1203	(lckyuh) queue=fx-single;;
	1204	(lckyut) queue=cx-single;;
[635]	1205	(lctit) queue=S;;
[1]	1206	(unics) queue=unics;;
	1207	esac
	1208	fi
	1209
	1210
[1289]	1211	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1212	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1213	(( i = 0 ))
	1214	while (( i < iin ))
	1215	do
	1216	(( i = i + 1 ))
	1217	(( maxcycle = 0 ))
	1218
[1289]	1219	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1220	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1221	if [[ "${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"
[2261]	1382	echo "### filename = $filename"
[1]	1383	else
	1384	printf "\n\n +++ OUTPUT-file:"
	1385	printf "\n $filename"
	1386	printf "\n cannot be created, because directory does not exist"
	1387	printf "\n and cannot be created either"
	1388	printf "\n"
	1389	locat=output ; exit
	1390	fi 2>/dev/null
	1391	else
	1392	printf "\n\n +++ OUTPUT-file:"
	1393	printf "\n $filename"
	1394	printf "\n cannot be created, although directory exists"
	1395	printf "\n"
	1396	locat=output ; exit
	1397	fi
	1398	fi 2>/dev/null
	1399	else
	1400
[1289]	1401	# DETERMINE THE CYCLE NUMBER
[1]	1402	ls -1 -d $filename > filelist 2>/dev/null
	1403	ls -1 -d $filename.* >> filelist 2>/dev/null
	1404	while read zeile
	1405	do
[2261]	1406
	1407	# filename without path (i.e. after the last "/")
	1408	basefilename=$(basename ${zeile})
	1409
	1410	# check if there is an extension
	1411	extension=${basefilename##*.}
[2268]	1412	if [[ "$extension" = "${extout[$i]}" ]]
[1]	1413	then
[2268]	1414	basefilename=${basefilename%.*}
[2261]	1415	fi
	1416
	1417	# check for an existing cycle number
	1418	cycle=${basefilename##*.}
	1419	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1420	then
	1421	(( icycle = $cycle + 1 ))
	1422	else
[1]	1423	(( icycle = 1 ))
	1424	fi
[2261]	1425
[1]	1426	if (( icycle > maxcycle ))
	1427	then
	1428	(( maxcycle = icycle ))
	1429	fi
[2261]	1430
[1]	1431	done <filelist
	1432	rm filelist
	1433	fi
	1434
[1289]	1435	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1436	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1437	if [[ "${actionout[$i]}" != a ]]
	1438	then
	1439	if (( maxcycle > 0 ))
	1440	then
[2261]	1441	filename_tmp=${filename}.$maxcycle
	1442	if cat /dev/null > $filename_tmp
[1]	1443	then
[2261]	1444	rm $filename_tmp
[1]	1445	else
	1446	printf "\n +++ OUTPUT-file:"
[2261]	1447	printf "\n $filename_tmp"
[1]	1448	printf "\n cannot be created"
	1449	locat=output ; exit
	1450	fi
	1451	fi
	1452	else
	1453	(( maxcycle = maxcycle - 1 ))
	1454	fi
	1455
[2261]	1456	(( cycnum[$i] = maxcycle ))
[1]	1457	pathout[$i]=$filename
	1458
	1459	fi
	1460	done
	1461
	1462
[1289]	1463	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1464	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1465	then
[260]	1466	if [[ "$dvr_inc" = "" ]]
[83]	1467	then
[260]	1468	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1469	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1470	locat=dvr; exit
[83]	1471	fi
[260]	1472	if [[ "$dvr_lib" = "" ]]
[83]	1473	then
[260]	1474	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1475	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1476	locat=dvr; exit
[83]	1477	fi
	1478	fi
	1479
	1480
[1289]	1481	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1482	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1483	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1484	then
	1485	printf "\n +++ neither main program nor executable defined"
	1486	locat=source; exit
	1487	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1488	then
	1489	printf "\n +++ main program as well as executable defined"
	1490	locat=source; exit
	1491	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1492	then
	1493	do_compile=false
	1494	fi
	1495
	1496
[1289]	1497	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1498	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1499	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1500	then
	1501	rm -rf SOURCES_FOR_RUN_$fname
	1502	mkdir SOURCES_FOR_RUN_$fname
	1503	fi
	1504
	1505
[1289]	1506	# COLLECT ALL ROUTINES TO BE COMPILED
	1507	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1508	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1509	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1510	then
	1511
[5]	1512	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1513
[838]	1514	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1515	then
	1516
[1289]	1517	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1518	source_list=""
	1519	cd $source_path
	1520
	1521
[1289]	1522	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1523	if [[ ! -d .svn ]]
	1524	then
	1525	printf "\n\n +++ source directory"
	1526	printf "\n \"$source_path\" "
	1527	printf "\n is not under control of \"subversion\"."
[306]	1528	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1529	fi
	1530
	1531
[1289]	1532	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1533	Filenames=""
[69]	1534	svn status > tmp_mrun
	1535	while read line
[5]	1536	do
	1537	firstc=`echo $line \| cut -c1`
	1538	if [[ $firstc = M \|\| $firstc = "?" ]]
	1539	then
	1540	Name=`echo "$line" \| cut -c8-`
	1541	extension=`echo $Name \| cut -d. -f2`
	1542	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1543	then
	1544	Filenames="$Filenames "$Name
	1545	fi
	1546	fi
[69]	1547	done < tmp_mrun
[5]	1548
	1549
[1289]	1550	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1551	for dateiname in $Filenames
	1552	do
	1553	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1554	source_list=$source_list"$dateiname "
	1555	done
	1556
	1557	cd - > /dev/null
	1558
	1559
[1289]	1560	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1561	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1562	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1563	then
	1564
	1565	cd $source_path
	1566
	1567	for filename in $source_list
	1568	do
	1569
[1289]	1570	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1571	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1572	then
	1573	printf "\n +++ source code file: $filename"
	1574	printf "\n must not contain (\"/\") "
	1575	locat=source; exit
	1576	fi
	1577
	1578	if [[ ! -f $filename ]]
	1579	then
	1580	printf "\n +++ source code file: $filename"
	1581	printf "\n does not exist"
	1582	locat=source; exit
	1583	else
	1584	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1585	fi
	1586
	1587	done
	1588
	1589	cd - > /dev/null
	1590
	1591	fi
	1592
	1593
[1289]	1594	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1595	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1596	if [[ $restart_run != true ]]
[1]	1597	then
	1598
	1599	if [[ ! -f "$source_path/$mainprog" ]]
	1600	then
	1601	printf "\n\n +++ main program: $mainprog"
	1602	printf "\n does not exist in source directory"
	1603	printf "\n \"$source_path\"\n"
	1604	locat=source; exit
	1605	else
	1606	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1607	then
	1608	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1609	source_list=${mainprog}" $source_list"
	1610	fi
	1611	fi
	1612	fi
	1613
	1614
[1289]	1615	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1616	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1617	if [[ "$restart_run" != true ]]
	1618	then
	1619	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1620	if [[ ! -f $makefile ]]
	1621	then
	1622	printf "\n +++ file \"$makefile\" does not exist"
	1623	locat=make; exit
	1624	else
	1625	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1626	fi
	1627	fi
	1628
	1629
[1289]	1630	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1631	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1632	then
	1633
[1289]	1634	# DOES THE DIRECTORY EXIST?
[1]	1635	if [[ ! -d $add_source_path ]]
	1636	then
[1779]	1637	printf "\n\n *** INFORMATIVE: additional source code directory"
[1]	1638	printf "\n \"$add_source_path\" "
	1639	printf "\n does not exist or is not a directory."
	1640	printf "\n No source code will be used from this directory!\n"
	1641	add_source_path=""
[931]	1642	if [[ $silent == false ]]
	1643	then
	1644	sleep 3
	1645	fi
[1]	1646	else
	1647
	1648	cd $add_source_path
[211]	1649	found=false
[1]	1650
	1651	Names=$(ls -1 *.f90 2>&1)
	1652	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1653	Names=$(ls -1 *.F90 2>&1)
	1654	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1655	Names=$(ls -1 *.F 2>&1)
	1656	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1657	Names=$(ls -1 *.f 2>&1)
	1658	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1659	Names=$(ls -1 *.c 2>&1)
	1660	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1661
	1662	cd - > /dev/null
	1663	cd SOURCES_FOR_RUN_$fname
	1664
[211]	1665	# COPY MAKEFILE IF EXISTING
	1666	if [[ -f $add_source_path/Makefile ]]
	1667	then
	1668	printf "\n\n *** user Makefile from directory"
	1669	printf "\n \"$add_source_path\" is used \n"
[931]	1670	if [[ $silent == false ]]
	1671	then
	1672	sleep 1
	1673	fi
[211]	1674	cp $add_source_path/Makefile .
	1675	fi
	1676
[1]	1677	for dateiname in $AddFilenames
	1678	do
	1679	if [[ -f $dateiname ]]
	1680	then
	1681	printf "\n +++ source code file \"$dateiname\" found in additional"
	1682	printf "\n source code directory \"$add_source_path\" "
[211]	1683	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1684	printf "\n from directory \"$source_path\"."
[1]	1685	locat=source; exit
	1686	fi
	1687
	1688	cp $add_source_path/$dateiname .
	1689	source_list="$source_list $dateiname"
	1690
[211]	1691	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1692	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1693	then
	1694	printf "\n\n +++ user file \"$dateiname\" "
	1695	printf "\n is not listed in Makefile \n"
	1696	locat=source; exit
	1697	else
	1698
	1699	if [[ $found = false ]]
[1]	1700	then
[211]	1701	found=true
	1702	printf "\n\n *** following user file(s) added to the"
	1703	printf " files to be translated:\n "
[1]	1704	fi
[211]	1705	printf "$dateiname "
[931]	1706	if [[ $silent == false ]]
	1707	then
	1708	sleep 0.5
	1709	fi
	1710
[1]	1711	fi
	1712	done
[211]	1713	[[ $found = true ]] && printf "\n"
[1]	1714	cd - > /dev/null
	1715	fi
	1716	fi
	1717
	1718
[1289]	1719	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1720	# TO THE LIST OF FILES TO BE COMPILED
[5]	1721	if [[ $restart_run != true && -n $package_list ]]
[1]	1722	then
	1723
	1724	cd $source_path
	1725
	1726	for package in $package_list
	1727	do
	1728
	1729	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1730
[1289]	1731	# DETERMINE FILES BELONGING TO THE PACKAGE
	1732	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1733	# THE NAME OF THE DIRECTORY
[1]	1734	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1735
	1736
[1289]	1737	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1738	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1739	for source_list_name in $package_source_list
	1740	do
	1741	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1742	then
	1743
[1289]	1744	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1745	ending=`echo $source_list_name \| cut -f2 -d.`
	1746	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1747	then
	1748	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1749	source_list="$source_list $source_list_name"
	1750	fi
	1751	fi
	1752	done
	1753	done
	1754
	1755	cd - > /dev/null
	1756	fi
	1757
	1758	fi # do_compile=true
	1759
	1760
[1289]	1761	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1762	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1763	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1764	then
	1765
[1289]	1766	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[1]	1767	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1768	then
[82]	1769	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1770	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1771	then
[82]	1772	cpp_options="$cpp_options -D__nec"
	1773	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1774	then
	1775	cpp_options="$cpp_options -D__lc"
[1]	1776	else
[82]	1777	cpp_options="$cpp_options -D__$localhost"
[1]	1778	fi
[83]	1779
[1289]	1780	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[1]	1781	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1782	then
[82]	1783	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1784	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1785	else
[82]	1786	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1787	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1788	fi
[83]	1789
[1289]	1790	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1791	if [[ -n $package_list ]]
	1792	then
	1793	for package in $package_list
	1794	do
	1795	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1796	then
	1797	if [[ $package != "dvrp_graphics+1PE" ]]
	1798	then
[82]	1799	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1800	else
[82]	1801	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1802	export use_seperate_pe_for_dvrp_output=true
	1803	fi
	1804	else
	1805	if [[ $package != "dvrp_graphics+1PE" ]]
	1806	then
[82]	1807	cpp_options="$cpp_options -D__$package"
[1]	1808	else
[82]	1809	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1810	export use_seperate_pe_for_dvrp_output=true
	1811	fi
	1812	fi
	1813	done
	1814	fi
[83]	1815
[1289]	1816	# SET DIRECTIVES GIVEN BY OPTION -D
[1]	1817	if [[ -n $cpp_opts ]]
	1818	then
	1819	for popts in $cpp_opts
	1820	do
[82]	1821	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1822	then
	1823	cpp_options="${cpp_options},-D__$popts=__$popts"
	1824	else
	1825	cpp_options="$cpp_options -D__$popts"
	1826	fi
[1]	1827	done
	1828	fi
	1829
	1830	else
	1831
	1832
[1289]	1833	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1834	if [[ $do_remote = false ]]
	1835	then
	1836	if [[ ! -f $executable ]]
	1837	then
	1838	printf "\n +++ executable file: $executable"
	1839	printf "\n does not exist"
	1840	locat=executable; exit
	1841	fi
	1842	fi
	1843	fi
	1844
	1845
[1289]	1846	# DETERMINE THE JOB MODE
[1491]	1847	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
[1]	1848	then
[1491]	1849	if [[ "$LOADLBATCH" = yes ]]
	1850	then
	1851	batch_job=.TRUE.
	1852	jobmo=BATCH
	1853	else
	1854	batch_job=.FALSE.
	1855	jobmo=INTERACTIVE
	1856	fi
[1]	1857	else
[2185]	1858	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
[1491]	1859	then
	1860	batch_job=.TRUE.
	1861	jobmo=BATCH
	1862	else
	1863	batch_job=.FALSE.
	1864	jobmo=INTERACTIVE
	1865	fi
[1]	1866	fi
	1867
[1289]	1868	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1869	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1870	then
	1871	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1872	printf "\n please submit batch job using mrun option \"-b\" \n"
	1873	locat=normal; exit
	1874	fi
	1875
	1876
[1289]	1877	# CHECK, IF USER DEFINED A COMPILER
[1]	1878	if [[ "$compiler_name" = "" ]]
	1879	then
[82]	1880
[220]	1881	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1882	locat=compiler_name; exit
	1883
[1]	1884	fi
	1885
	1886
[1289]	1887	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1609]	1888
	1889	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
	1890	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
	1891	then
	1892	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
[1755]	1893	if [[ "$kennung" = "" ]]
[1753]	1894	then
	1895	kennung=$RANDOM
	1896	fi
[1609]	1897	else
	1898	kennung=$RANDOM
	1899	fi
	1900
[1]	1901	if [[ "$tmp_user_catalog" = "" ]]
	1902	then
[312]	1903	if [[ $localhost = ibmh ]]
[1]	1904	then
[312]	1905	tmp_user_catalog=$SCRATCH
[1]	1906	else
	1907	tmp_user_catalog=/tmp
	1908	fi
	1909	fi
	1910	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1911
	1912
[1289]	1913	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1914	if [[ "$tmp_data_catalog" = "" ]]
	1915	then
[2261]	1916	tmp_data_catalog=/tmp/mrun_restart_data
[1]	1917	fi
	1918
	1919
[1289]	1920	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1921	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1922	then
	1923	eval fopts=\"$fopts\"
	1924	eval lopts=\"$lopts\"
	1925	fi
	1926
	1927
[1289]	1928	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1929	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1930	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1779]	1931	XOPT="-X $numprocs"
[1]	1932
	1933
[1289]	1934	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1935	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1936	done=false
	1937	while [[ $done = false ]]
	1938	do
	1939	cputime=$cpumax
	1940	if (( $cputime == 0 ))
	1941	then
[246]	1942	if [[ $do_batch = true ]]
	1943	then
	1944	printf "\n +++ cpu-time is undefined"
	1945	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1946	printf "\n >>> "
	1947	read cputime 1>/dev/null 2>&1
	1948	else
	1949	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1950	fi
[1]	1951	else
	1952	done=true
	1953	fi
	1954	cpumax=$cputime
	1955	done
	1956
	1957	(( minuten = cputime / 60 ))
	1958	(( sekunden = cputime - minuten * 60 ))
	1959
	1960
[1289]	1961	# CHECK THE MEMORY DEMAND
[1]	1962	if [[ $do_batch = true ]]
	1963	then
	1964	done=false
	1965	while [[ $done = false ]]
	1966	do
	1967	if (( memory == 0 ))
	1968	then
	1969	printf "\n +++ memory demand is undefined"
	1970	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1971	printf "\n >>> "
	1972	read memory 1>/dev/null 2>&1
	1973	else
	1974	done=true
	1975	fi
	1976	done
	1977	fi
	1978
	1979
[1289]	1980	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	1981	if [[ $do_remote = true && -z $remote_username ]]
	1982	then
	1983	while [[ -z $remote_username ]]
	1984	do
	1985	printf "\n +++ username on remote host \"$host\" is undefined"
	1986	printf "\n >>> Please type username:"
	1987	printf "\n >>> "
	1988	read remote_username
	1989	done
	1990	mc="$mc -u$remote_username"
	1991	fi
	1992
[892]	1993	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	1994	if [[ "$login_init_cmd" != "" ]]
	1995	then
	1996	export init_cmds="${login_init_cmd};"
	1997	fi
[221]	1998
[892]	1999
[1289]	2000	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	2001	if [[ "$modules" != "" ]]
	2002	then
[678]	2003	if [[ $host = lctit ]]
	2004	then
	2005	export module_calls=". $modules"
	2006	else
	2007	export module_calls="module load ${modules};"
	2008	fi
[493]	2009	fi
	2010
[1289]	2011	# OUTPUT OF THE MRUN-HEADER
[1]	2012	calltime=$(date)
	2013	printf "\n"
[1101]	2014	printf "#------------------------------------------------------------------------# \n"
	2015	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	2016	printf "\| \| \n"
[1]	2017	spalte1="called on:"; spalte2=$localhost_realname
[1101]	2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	2019	if [[ $do_remote = true ]]
[1]	2020	then
[1289]	2021	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	2022	else
[1289]	2023	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	2024	fi
[1101]	2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2026	if [[ -n $numprocs ]]
	2027	then
[1106]	2028	if [[ $run_coupled_model = false ]]
	2029	then
	2030	spalte1="number of PEs:"; spalte2=$numprocs
	2031	else
	2032	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	2033	fi
[1101]	2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2035	fi
	2036	if [[ -n $tasks_per_node ]]
	2037	then
	2038	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	2040	if (( remaining_pes > 0 ))
	2041	then
	2042	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	2043	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2044	fi
[1]	2045	fi
[759]	2046	if [[ $maximum_parallel_io_streams != $numprocs ]]
	2047	then
	2048	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	2049	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	2050	fi
[622]	2051	if [[ $use_openmp = true ]]
[1]	2052	then
	2053	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	2054	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2055	fi
[1101]	2056	printf "\| \| \n"
[1]	2057	if [[ $do_compile = true ]]
	2058	then
[475]	2059	if [[ "$mopts" != "" ]]
	2060	then
[1101]	2061	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2063	zeile=$(echo "$mopts" \| cut -c46-)
[475]	2064	while [[ "$zeile" != "" ]]
	2065	do
	2066	spalte1=""
[1101]	2067	spalte2=$(echo "$zeile" \| cut -c-45)
	2068	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2069	zeile=$(echo "$zeile" \| cut -c46-)
[475]	2070	done
	2071	fi
	2072
[1101]	2073	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	2074	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2075	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	2076	while [[ "$zeile" != "" ]]
	2077	do
	2078	spalte1=""
[1101]	2079	spalte2=$(echo "$zeile" \| cut -c-45)
	2080	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2081	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2082	done
	2083
[1101]	2084	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	2085	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2086	zeile=$(echo "$fopts" \| cut -c46-)
[1]	2087	while [[ "$zeile" != "" ]]
	2088	do
	2089	spalte1=""
[1101]	2090	spalte2=$(echo "$zeile" \| cut -c-45)
	2091	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2092	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2093	done
	2094
[1101]	2095	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	2096	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2097	zeile=$(echo "$lopts" \| cut -c46-)
[1]	2098	while [[ "$zeile" != "" ]]
	2099	do
	2100	spalte1=""
[1101]	2101	spalte2=$(echo "$zeile" \| cut -c-45)
	2102	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2103	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2104	done
	2105
[1101]	2106	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2107	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2108	zeile=$(echo "$modules" \| cut -c46-)
[493]	2109	while [[ "$zeile" != "" ]]
	2110	do
	2111	spalte1=""
[1101]	2112	spalte2=$(echo "$zeile" \| cut -c-45)
	2113	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2114	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2115	done
	2116
[1101]	2117	spalte1="main program:"; spalte2=$mainprog
	2118	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2119	else
	2120	spalte1=executable:; spalte2=$executable
[1101]	2121	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2122	fi
[1101]	2123	printf "\| \| \n"
	2124	spalte1="base name of files:"; spalte2=$fname
	2125	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2126	if [[ $fname != $afname ]]
	2127	then
[1101]	2128	spalte1="base name of input files:"; spalte2=$afname
	2129	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2130	fi
[1101]	2131	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2132	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2133	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2134	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2135
[1106]	2136	if [[ "$ocean_file_appendix" = true ]]
	2137	then
	2138	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2139	fi
	2140
[1]	2141	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2142	then
	2143	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2144	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2145	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2146	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2147	fi
	2148
	2149	if [[ $do_compile = true ]]
	2150	then
[1101]	2151	printf "\| \| \n"
	2152	printf "\| Files to be compiled: \| \n"
[1]	2153	zeile=$source_list
	2154	while [[ "$zeile" != "" ]]
	2155	do
[1101]	2156	linestart=$(echo $zeile \| cut -c-70)
	2157	printf "\| %-70s \| \n" "$linestart"
	2158	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2159	done
	2160	fi
[1101]	2161	printf "#------------------------------------------------------------------------#"
[1]	2162
	2163
	2164
[1289]	2165	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2166	if [[ $do_trace = true ]]
	2167	then
	2168	(( i = 0 ))
	2169	while (( i < iin ))
	2170	do
	2171	(( i = i + 1 ))
	2172	if (( i == 1 ))
	2173	then
	2174	printf "\n\n >>> INPUT-file assignments:\n"
	2175	fi
	2176	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2177	done
	2178	(( i = 0 ))
	2179	while (( i < iout ))
	2180	do
	2181	(( i = i + 1 ))
	2182	if (( i == 1 ))
	2183	then
	2184	printf "\n\n >>> OUTPUT-file assignments:\n"
	2185	fi
	2186	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2187	done
	2188	(( i = 0 ))
	2189	while (( i < iic ))
	2190	do
	2191	(( i = i + 1 ))
	2192	if (( i == 1 ))
	2193	then
	2194	printf "\n\n >>> INPUT-commands:\n"
	2195	fi
	2196	printf "\n ${in_command[$i]}"
	2197	done
	2198	(( i = 0 ))
	2199	while (( i < ioc ))
	2200	do
	2201	(( i = i + 1 ))
	2202	if (( i == 1 ))
	2203	then
	2204	printf "\n\n >>> OUTPUT-commands:\n"
	2205	fi
	2206	printf "\n ${out_command[$i]}"
	2207	done
	2208	fi
	2209
[1289]	2210	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2211	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2212	then
	2213	antwort=dummy
	2214	printf "\n\n"
[1101]	2215	printf " >>> everything o.k. (y/n) ? "
	2216	while read antwort
[1]	2217	do
[1101]	2218	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2219	then
	2220	printf " >>> everything o.k. (y/n) ? "
	2221	else
	2222	break
	2223	fi
[1]	2224	done
	2225	if [[ $antwort = n \|\| $antwort = N ]]
	2226	then
	2227	locat=user_abort; (( iec = 0 )); exit
	2228	fi
	2229	if [[ $do_batch = true ]]
	2230	then
	2231	printf " >>> batch-job will be created and submitted"
	2232	else
[1289]	2233	printf " >>> MRUN will now continue to execute on this machine"
[1]	2234	fi
	2235	fi
	2236
[1804]	2237
[1199]	2238	# DETERMINE PATH FOR MAKE DEPOSITORY
	2239	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2240	then
	2241
	2242	line=""
	2243	grep "%depository_path" $config_file > tmp_mrun
	2244	while read line
	2245	do
	2246	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2247	then
	2248	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2249	then
	2250	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2251	fi
	2252	fi
	2253	done < tmp_mrun
	2254
	2255	line=""
	2256	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2257	while read line
	2258	do
	2259	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2260	then
	2261	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2262	then
	2263	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2264	fi
	2265	fi
	2266	done < tmp_mrun
	2267
	2268	if [[ "$local_depository_path" = "" ]]
	2269	then
	2270	if [[ "$global_depository_path" != "" ]]
	2271	then
	2272	local_depository_path=$global_depository_path
	2273	else
	2274	printf "\n\n +++ no depository path found in configuration file"
	2275	printf "\n for local host \"$localhost\" "
	2276	printf "\n please set \"\%depository_path\" in configuration file\n"
	2277	locat=config_file; exit
	2278	fi
	2279	fi
	2280	eval local_depository_path=$local_depository_path
	2281	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2282	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2283
	2284
	2285	basename=`echo $mainprog \| cut -f1 -d"."`
	2286	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2287	if [[ ! -f $make_depository ]]
	2288	then
	2289	printf "\n"
	2290	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2291	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2292	fi
	2293
	2294	fi
	2295
	2296
[1289]	2297	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2298	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2299	if [[ $do_batch = false ]]
	2300	then
	2301
	2302
[1289]	2303	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2304	mkdir -p $TEMPDIR
	2305	chmod go+rx $TEMPDIR
	2306	tmpcreate=true
	2307
	2308
[1289]	2309	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2310	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2311	if [[ $do_compile = true ]]
	2312	then
	2313
[2261]	2314	TEMPDIR_COMPILE=$TEMPDIR
[1]	2315
[1199]	2316	cp $make_depository $TEMPDIR_COMPILE
	2317	cd $TEMPDIR_COMPILE
	2318	tar -xf $make_depository > /dev/null 2>&1
	2319	cd - > /dev/null
[1]	2320
[1255]	2321	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2322	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2323	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2324	then
	2325	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2326	else
	2327	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2328	fi
[82]	2329
[1]	2330	else
[475]	2331
[1]	2332	cp $executable ${TEMPDIR}/a.out
[475]	2333
[1]	2334	fi
	2335
	2336
[1289]	2337	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2338	cd $TEMPDIR
[1]	2339	printf "\n *** changed to temporary directory: $TEMPDIR"
	2340
	2341
[1289]	2342	# IF REQUIRED, START WITH COMPILING
[1]	2343	if [[ $do_compile = true ]]
	2344	then
	2345
	2346
[1199]	2347	if [[ -f a.out ]]
[475]	2348	then
[82]	2349
[1199]	2350	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2351	printf "\n\n\n *** executable a.out found"
	2352	printf "\n no compilation required \n"
	2353
[1]	2354	else
[807]	2355
[1199]	2356	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2357	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2358	printf " *** compilation with make using following options:\n"
	2359	printf " make depository: $make_depository"
	2360	if [[ "$mopts" != "" ]]
	2361	then
	2362	printf " make options: $mopts\n"
	2363	fi
	2364	printf " compilername: $compiler_name\n"
	2365	printf " compiler options: $fopts\n"
	2366	printf " preprocessor directives: $cpp_options \n"
	2367	printf " linker options: $lopts \n"
	2368	if [[ "$modules" != "" ]]
	2369	then
	2370	printf " modules to be load: $modules \n"
	2371	fi
	2372	printf " source code files: $source_list \n"
[1]	2373
[2261]	2374	if [[ $localhost = ibmh ]]
[1199]	2375	then
	2376	printf " compiler is called via ssh on \"plogin1\" \n"
	2377	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\" "
	2378	[[ ! -f a.out ]] && compile_error=true
[1289]	2379	continue # STATUS=1, IF a.out EXISTS
[1866]	2380	elif [[ $localhost = lcocean ]]
	2381	then
	2382	printf " compiler is called via ssh on \"ocean\" \n"
	2383	echo $PWD
	2384	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\" "
	2385	[[ ! -f a.out ]] && compile_error=true
	2386	continue # STATUS=1, IF a.out EXISTS
[1620]	2387	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2388	then
	2389	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2257]	2390	elif [[ $localhost = lceddy ]]
	2391	then
	2392	which mpifc
	2393	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[1199]	2394	else
	2395	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2396	[[ "$module_calls" != "" ]] && eval $module_calls
	2397	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2398	fi
[181]	2399
[1199]	2400	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2401	then
	2402	printf "\n +++ error occured while compiling or linking"
	2403	locat=compile
	2404
[181]	2405	exit
[1199]	2406	else
[1289]	2407	printf "$dashes\n *** compilation finished \n"
[1199]	2408	fi
	2409
[1]	2410	fi
[1199]	2411
[1]	2412	fi
	2413
	2414
[1289]	2415	# PROVIDE THE INPUT FILES
	2416	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2417	(( i = 0 ))
	2418	while (( i < iin ))
	2419	do
	2420	(( i = i + 1 ))
	2421	if (( i == 1 ))
	2422	then
[1289]	2423	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2424	fi
	2425
	2426
[1289]	2427	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2428	if [[ "${transin[$i]}" = unavailable ]]
	2429	then
	2430	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2431	then
[1779]	2432	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2433	printf "\n is not available!"
[1]	2434	else
[1779]	2435	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2436	printf "\n is not available!"
[1]	2437	fi
	2438	continue
	2439	fi
	2440
[1289]	2441	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2442	files_for_pes=false; datentyp=file
	2443	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2444	then
[2261]	2445	files_for_pes=true; datentyp=files
[1]	2446	actionin[$i]=""
	2447	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2448	then
	2449	actionin[$i]=""
[2261]	2450	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
[1]	2451	then
[2261]	2452	files_for_pes=true; datentyp=files
	2453	actionin[$i]="ln"
	2454	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
[1]	2455	then
[2261]	2456	actionin[$i]="ln"
[1]	2457	fi
	2458
	2459	if [[ $files_for_pes = true ]]
	2460	then
	2461	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2462	else
	2463	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2464	fi
	2465
[2261]	2466	# INPUT-FILES TO BE LINKED
	2467	if [[ "${actionin[$i]}" = ln ]]
[1]	2468	then
[2261]	2469
	2470	printf "\n $datentyp will be linked"
[1]	2471	if [[ $files_for_pes = false ]]
	2472	then
[2261]	2473	if [[ -f "${absnamein[$i]}" ]]
[1]	2474	then
[2261]	2475	ln ${absnamein[$i]} ${localin[$i]}
[1]	2476	got_tmp[$i]=true
	2477	fi
	2478	else
[2261]	2479	if [[ -d "${absnamein[$i]}" ]]
[1]	2480	then
	2481	mkdir ${localin[$i]}
[2261]	2482	cd ${absnamein[$i]}
[149]	2483	for file in $(ls *)
	2484	do
	2485	ln $file $TEMPDIR/${localin[$i]}
[2261]	2486	done >\|/dev/null 2>&1
[149]	2487	cd $TEMPDIR
[1]	2488	fi
	2489
[2261]	2490	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2491	if [[ ! -f "${localin[$i]}/_000000" ]]
[1]	2492	then
[2261]	2493	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2494	cp -r ${absnamein[$i]}/* ${localin[$i]}
[1]	2495	fi
	2496
	2497	got_tmp[$i]=true
	2498	fi
	2499	fi
	2500
[1289]	2501	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	2502	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	2503	then
	2504
	2505	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	2506	then
	2507
[1289]	2508	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2509	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	2510	printf "\n file will be provided for $numprocs processors"
	2511	mkdir ${localin[$i]}
	2512	ival=$numprocs
	2513	(( ii = 0 ))
	2514	while (( ii <= ival-1 ))
	2515	do
	2516	if (( ii < 10 ))
	2517	then
	2518	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2519	elif (( ii < 100 ))
	2520	then
	2521	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2522	elif (( ii < 1000 ))
	2523	then
	2524	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2525	else
	2526	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2527	fi
	2528	(( ii = ii + 1 ))
	2529	done
	2530
	2531	else
	2532
	2533	if [[ $files_for_pes = true ]]
	2534	then
	2535
[1289]	2536	# PROVIDE FILES FOR EACH CORE
	2537	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2538	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	2539	printf "\n providing $numprocs files for the respective processors"
	2540	mkdir ${localin[$i]}
[2261]	2541	if [[ $link_local_input = true ]]
	2542	then
	2543	printf " files will be linked\n"
	2544	cd ${absnamein[$i]}
	2545	for file in $(ls *)
	2546	do
	2547	ln -f $file ${localin[$i]}
	2548	done
	2549	cd $TEMPDIR
	2550	fi
[1289]	2551
	2552	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[2261]	2553	if [[ ! -f "${localin[$i]}/_000000" ]]
	2554	then
	2555	if [[ $link_local_input = true ]]
	2556	then
	2557	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2558	fi
	2559	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2560	fi
[1]	2561
	2562	else
[1289]	2563
	2564	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[2261]	2565	if [[ $link_local_input = true ]]
	2566	then
	2567	printf " file will be linked\n"
	2568	ln -f ${absnamein[$i]} ${localin[$i]}
	2569	fi
	2570	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	2571	if [[ ! -f "${localin[$i]}" ]]
[183]	2572	then
[2261]	2573	if [[ $link_local_input = true ]]
	2574	then
	2575	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2576	fi
	2577	cp ${absnamein[$i]} ${localin[$i]}
[183]	2578	fi
[1]	2579	fi
	2580	fi
	2581	fi
	2582
	2583	done
	2584	if (( i != 0 ))
	2585	then
[1289]	2586	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	2587	fi
	2588
	2589
[1289]	2590	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	2591	(( i = 0 ))
	2592	while (( i < iic ))
	2593	do
	2594	(( i = i + 1 ))
	2595	if (( i == 1 ))
	2596	then
[1289]	2597	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	2598	fi
	2599	printf "\n >>> ${in_command[$i]}"
	2600	eval ${in_command[$i]}
	2601	if (( i == iic ))
	2602	then
[1289]	2603	printf "\n$dashes\n"
[1]	2604	fi
	2605	done
	2606
	2607
[1289]	2608	# SET THE REMAINING CPU-TIME
[1]	2609	cpurest=${cpumax}.
	2610
	2611
[260]	2612	# START DVR STREAMING SERVER
	2613	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	2614	then
	2615	if [[ "$dvr_server" != "" ]]
	2616	then
	2617
	2618	printf "\n\n *** preparing the dvr streaming server configuration file"
	2619
[1289]	2620	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	2621	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	2622	if [[ "$running_dvrserver_id" != "" ]]
	2623	then
	2624
[261]	2625	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	2626	printf "\n This server is used instead starting a new one!"
[261]	2627	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	2628
	2629	else
	2630
	2631	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	2632	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	2633	then
	2634	cp ${PALM_BIN}/.dvrserver.config .
	2635
[1289]	2636	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	2637	user_id=`id -u`
	2638	group_id=`id -g`
[1289]	2639
	2640	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	2641	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	2642	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	2643	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	2644	mv .dvrserver.3 .dvrserver.config
	2645	rm .dvrserver.1 .dvrserver.2
	2646
[1289]	2647	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	2648	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	2649	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	2650	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	2651	local_dvrserver_running=.TRUE.
	2652	else
	2653	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	2654	printf "\n \"$PALM_BIN\" "
	2655	locat=dvr
	2656	exit
	2657	fi
	2658
	2659	fi
	2660
	2661	else
	2662	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	2663	fi
	2664	fi
	2665
	2666
[1289]	2667	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2668	# (FILE ENVPAR WILL BE READ BY PALM)
[2261]	2669	cat > ENVPAR << EOF
[260]	2670	&envpar run_identifier = '$fname', host = '$localhost',
	2671	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
[759]	2672	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	2673	maximum_cpu_time_allowed = ${cpumax}.,
	2674	revision = '$global_revision',
[1402]	2675	local_dvrserver_running = $local_dvrserver_running,
	2676	batch_job = $batch_job /
[260]	2677
[2261]	2678	EOF
[260]	2679
	2680
[1289]	2681	# STARTING THE EXECUTABLE
	2682	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	2683	PATH=$PATH:$TEMPDIR
	2684
[1779]	2685
	2686	if [[ $execute_command != "none" ]]
[359]	2687	then
	2688
[1779]	2689	printf "\n +++ branch still not realized"
	2690	locat=execution
	2691	exit
	2692
[693]	2693	else
	2694
[1779]	2695	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
	2696	if [[ "$mpi_debug" = true ]]
[1549]	2697	then
[1779]	2698	export MPI_CHECK_ARGS=1
	2699	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
[1549]	2700	fi
	2701
[1779]	2702	if [[ "$totalview" = true ]]
[1]	2703	then
[1779]	2704	printf "\n *** totalview debugger will be used"
	2705	tv_opt="-tv"
	2706	else
	2707	tv_opt=""
[1]	2708	fi
[1779]	2709
	2710	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
[1]	2711	then
	2712
[1779]	2713	#Interactive ALLINEA DEBUG seesion
	2714	if [[ "$ENVIRONMENT" != BATCH ]]
	2715	then
	2716	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2717	then
	2718	if [[ "$allinea" = true ]]
	2719	then
	2720	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
[1]	2721
[1779]	2722	ddt aprun -n $ii -N $tasks_per_node a.out
	2723	wait
	2724	fi
	2725	fi
	2726	fi
[1]	2727
[1779]	2728	if [[ $localhost = ibmh ]]
	2729	then
[1]	2730
[1779]	2731	# SETUP THE IBM MPI ENVIRONMENT
	2732	export MP_SHARED_MEMORY=yes
	2733	export AIXTHREADS_SCOPE=S
	2734	export OMP_NUM_THREADS=$threads_per_task
	2735	export AUTHSTATE=files
	2736	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
[1]	2737
[1779]	2738	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	2739	export MP_ADAPTER_USE=shared
	2740	export MP_CPU_USE=multiple
	2741	export MP_TIMEOUT=1200
[622]	2742
[1779]	2743	unset MP_TASK_AFFINITY
[1295]	2744
[1779]	2745	if [[ "$LOADLBATCH" = yes ]]
	2746	then
	2747	totalview poe a.out
	2748	else
	2749	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2750	export TVDSVRLAUNCHCMD=ssh
	2751	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2752	fi
[622]	2753
[1779]	2754	fi # END DEBUG MODE
[1289]	2755
[1779]	2756	else
	2757
	2758	# NORMAL EXECUTION
	2759	if [[ -n $numprocs ]]
[1]	2760	then
[1289]	2761
[1779]	2762	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	2763	if [[ $(echo $host \| cut -c1-3) = ibm ]]
[312]	2764	then
[1]	2765
[1779]	2766	# SETUP THE IBM MPI ENVIRONMENT
	2767	if [[ $host != ibmh && $host != ibmkisti ]]
[696]	2768	then
[1779]	2769	export MP_SHARED_MEMORY=yes
	2770	export AIXTHREAD_SCOPE=S
[696]	2771	export OMP_NUM_THREADS=$threads_per_task
[1779]	2772	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	2773	export AUTHSTATE=files
	2774	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	2775	# export MP_PRINTENV=yes
	2776
	2777	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	2778	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
	2779	export MP_WAIT_MODE=poll
	2780	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
[696]	2781	fi
[693]	2782
[1779]	2783	if [[ $host = ibmkisti ]]
[1]	2784	then
[1779]	2785	export LANG=en_US
	2786	export MP_SHARED_MEMORY=yes
	2787	if [[ $threads_per_task = 1 ]]
[343]	2788	then
[1779]	2789	export MP_SINGLE_THREAD=yes
	2790	export MEMORY_AFFINITY=MCM
[343]	2791	else
[1779]	2792	export OMP_NUM_THREADS=$threads_per_task
[343]	2793	fi
[1]	2794	fi
[1779]	2795
	2796	if [[ "$LOADLBATCH" = yes ]]
[1]	2797	then
[1779]	2798	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	2799	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
[1]	2800	then
[1779]	2801	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
[1]	2802	else
[1779]	2803	if [[ $run_coupled_model = false ]]
	2804	then
	2805	if [[ "$ocean_file_appendix" = true ]]
	2806	then
	2807	echo "precursor_ocean" > runfile_atmos
	2808	else
	2809	echo "precursor_atmos" > runfile_atmos
	2810	fi
	2811	else
	2812	(( iia = $numprocs_atmos / $threads_per_task ))
	2813	(( iio = $numprocs_ocean / $threads_per_task ))
	2814	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2815	printf "\n using $coupled_mode coupling"
	2816	printf "\n\n"
	2817	echo "coupled_run $iia $iio" > runfile_atmos
	2818	fi
	2819	poe ./a.out < runfile_atmos
[1]	2820	fi
[1779]	2821	else
	2822	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[331]	2823	then
[1779]	2824	poe a.out -procs $numprocs -nodes 1 -rmpool 0
	2825	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
	2826	then
	2827	if [[ -f $hostfile ]]
[331]	2828	then
[1779]	2829	cp $hostfile hostfile
[331]	2830	else
[1779]	2831	(( ii = 1 ))
	2832	while (( ii <= $numprocs ))
	2833	do
	2834	echo $localhost_realname >> hostfile
	2835	(( ii = ii + 1 ))
	2836	done
[331]	2837	fi
[1779]	2838	export MP_HOSTFILE=hostfile
	2839	if [[ $run_coupled_model = false ]]
	2840	then
	2841	if [[ "$ocean_file_appendix" = true ]]
	2842	then
	2843	echo "precursor_ocean" > runfile_atmos
	2844	else
	2845	echo "precursor_atmos" > runfile_atmos
	2846	fi
	2847	else
	2848	(( iia = $numprocs_atmos / $threads_per_task ))
	2849	(( iio = $numprocs_ocean / $threads_per_task ))
	2850	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2851	printf "\n using $coupled_mode coupling"
	2852	printf "\n\n"
	2853	echo "coupled_run $iia $iio" > runfile_atmos
	2854	fi
[331]	2855
[1779]	2856	poe ./a.out -procs $numprocs < runfile_atmos
[1289]	2857
[1]	2858	else
[1779]	2859	if [[ "$host_file" = "" ]]
	2860	then
	2861	printf "\n +++ no hostfile given in configuration file"
	2862	locat=config_file
	2863	exit
	2864	else
	2865	eval host_file=$host_file
	2866	fi
	2867	export MP_HOSTFILE=$host_file
	2868	poe a.out -procs $numprocs -tasks_per_node $numprocs
[1]	2869	fi
	2870	fi
[1779]	2871
	2872	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	2873	then
[1779]	2874
	2875	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	2876	# DOES NOT EXIST
[2257]	2877	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
[179]	2878	then
[1779]	2879	if [[ -f $hostfile ]]
[1598]	2880	then
[1779]	2881	cp $hostfile hostfile
	2882	(( ii = $numprocs / $threads_per_task ))
	2883	[[ $ii = 0 ]] && (( ii = 1 ))
	2884	else
	2885	(( ii = 1 ))
	2886	while (( ii <= $numprocs / $threads_per_task ))
	2887	do
	2888	echo $localhost_realname >> hostfile
	2889	(( ii = ii + 1 ))
	2890	done
	2891	if (( $numprocs / $threads_per_task == 0 ))
	2892	then
	2893	echo $localhost_realname >> hostfile
	2894	fi
[1598]	2895	fi
[1779]	2896	eval zeile=\"`head -n $ii hostfile`\"
	2897	printf "\n *** running on: $zeile"
[179]	2898	fi
	2899
[1779]	2900	(( ii = $numprocs / $threads_per_task ))
	2901	[[ $ii = 0 ]] && (( ii = 1 ))
	2902	export OMP_NUM_THREADS=$threads_per_task
[1289]	2903
[1779]	2904	if [[ $threads_per_task != 1 ]]
[291]	2905	then
[1779]	2906	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	2907	# MAY ABORT
	2908	ulimit -s unlimited
	2909	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[291]	2910	fi
[1779]	2911	if [[ $run_coupled_model = false ]]
[1224]	2912	then
[1779]	2913	if [[ "$ocean_file_appendix" = true ]]
	2914	then
	2915	echo "precursor_ocean" > runfile_atmos
	2916	else
	2917	echo "precursor_atmos" > runfile_atmos
	2918	fi
	2919	printf "\n\n"
[1622]	2920
[1779]	2921	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2922	then
	2923	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
	2924	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2925	elif [[ $host = lcbullhh ]]
	2926	then
	2927	export OMPI_MCA_pml=cm
	2928	export OMPI_MCA_mtl=mxm
	2929	export OMPI_MCA_coll=^ghc
	2930	export OMPI_MCA_mtl_mxm_np=0
	2931	export MXM_RDMA_PORTS=mlx5_0:1
	2932	export MXM_LOG_LEVEL=ERROR
	2933	export OMP_NUM_THREADS=$threads_per_task
	2934	export KMP_AFFINITY=verbose,granularity=core,compact,1
	2935	export KMP_STACKSIZE=64m
[1622]	2936
[2147]	2937	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
[1622]	2938
[1779]	2939	elif [[ $host = lccrayf ]]
	2940	then
	2941	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
	2942	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
	2943	then
[2257]	2944	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2945	elif [[ $host = lceddy ]]
[1779]	2946	then
[2257]	2947	echo $ii
	2948	echo $tasks_per_node
	2949	echo $nodes
	2950	mpirun -n $ii a.out < runfile_atmos
[1866]	2951	elif [[ $host = lcocean ]]
	2952	then
	2953	mpirun a.out $ROPTS < runfile_atmos
[1779]	2954	elif [[ $host = lcsb ]]
	2955	then
	2956	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
[2257]	2957
[1779]	2958	elif [[ $host = lckiaps ]]
	2959	then
[1940]	2960	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
[1779]	2961	elif [[ $host = lckyu* ]]
	2962	then
	2963	mpiexec -n $ii --stdin runfile_atmos ./a.out
	2964	else
	2965	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
	2966	fi
	2967
[164]	2968	else
	2969
[1779]	2970	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
	2971	(( iia = $numprocs_atmos / $threads_per_task ))
	2972	(( iio = $numprocs_ocean / $threads_per_task ))
	2973	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2974	printf "\n using $coupled_mode coupling"
	2975	printf "\n\n"
[164]	2976
[1779]	2977	if [[ $coupled_mode = "mpi2" ]]
[206]	2978	then
[1779]	2979	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
	2980	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
[197]	2981
[1779]	2982	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	2983	then
[206]	2984
[1779]	2985	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
	2986	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
	2987
	2988	else
	2989	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
	2990	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
	2991	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
	2992	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
	2993	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
	2994	fi
	2995	wait
	2996
[206]	2997	else
	2998
[1779]	2999	echo "coupled_run $iia $iio" > runfile_atmos
[164]	3000
[1779]	3001	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	3002	then
[206]	3003
[1779]	3004	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
[206]	3005
[1779]	3006	elif [[ $host = lck \|\| $host = lckordi ]]
	3007	then
[206]	3008
[1779]	3009	mpiexec -n $ii ./a.out < runfile_atmos &
[1108]	3010
[1779]	3011	elif [[ $host = lckyu* ]]
	3012	then
[1108]	3013
[1779]	3014	mpiexec -n $ii --stdin runfile_atmos ./a.out
[1108]	3015
[1779]	3016	elif [[ $host = lcmuk ]]
	3017	then
[1108]	3018
[1779]	3019	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
[1604]	3020
[1779]	3021	fi
	3022	wait
	3023	fi
[1604]	3024
[164]	3025	fi
[102]	3026
[1779]	3027	elif [[ $host = lckyoto ]]
[440]	3028	then
[1779]	3029	set -xv
	3030	export P4_RSHCOMMAND=plesh
	3031	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3032	if [[ "$ENVIRONMENT" = BATCH ]]
[505]	3033	then
[1779]	3034	if [[ "$cond2" = fujitsu ]]
	3035	then
	3036	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
	3037	elif [[ "cond2" = pgi ]]
	3038	then
	3039	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
	3040	else
	3041	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
	3042	fi
[505]	3043	else
[1779]	3044	if [[ "$cond2" = "" ]]
	3045	then
	3046	mpiruni_rsh -np $numprocs ./a.out # for intel
	3047	else
	3048	mpirun -np $numprocs ./a.out
	3049	fi
[505]	3050	fi
[1779]	3051	set +xv
	3052
	3053	elif [[ $host = lctit ]]
	3054	then
	3055	export OMP_NUM_THREADS=$threads_per_task
	3056	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3057	if [[ "$threads_per_task" != 1 ]]
[505]	3058	then
[1779]	3059	export MV2_ENABLE_AFFINITY=0
[505]	3060	fi
[1779]	3061	echo "----- PBS_NODEFILE content:"
	3062	cat $PBS_NODEFILE
	3063	echo "-----"
	3064	(( ii = $numprocs / $threads_per_task ))
	3065	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
	3066	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
[1289]	3067
[1779]	3068	else
	3069	mpprun -n $numprocs a.out
[678]	3070	fi
[1]	3071	else
[1779]	3072	a.out
[1]	3073	fi
[1289]	3074
[1779]	3075	fi # end normal (non-debug) execution
	3076
	3077	fi # end explicit execute_command or host-specific execute actions
	3078
[1289]	3079	if [[ $? != 0 ]]
[1]	3080	then
	3081
[1289]	3082	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3083	printf "\n +++ runtime error occured"
	3084	locat=execution
	3085	exit
[1289]	3086
[1]	3087	else
[260]	3088
[1289]	3089	printf "\n$dashes\n *** execution finished \n"
	3090
	3091	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3092	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3093	if [[ "$dvrserver_id" != "" ]]
	3094	then
	3095	kill $dvrserver_id
	3096	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3097
[1289]	3098	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3099	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3100	if [[ -d DATA_DVR ]]
	3101	then
[261]	3102
[1289]	3103	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3104	# DIRECTORY
[262]	3105	cp .dvrserver.config DATA_DVR
	3106
[1289]	3107	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3108	# SEQUENCE MODE DATA TOO)
[262]	3109	process_dvr_output -d DATA_DVR -f $fname -s
	3110
	3111	else
	3112
[1289]	3113	# PROCESS THE LOCAL OUTPUT
[262]	3114	process_dvr_output -l -d DATA_DVR -f $fname
	3115
	3116	fi
	3117
	3118	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3119	then
	3120
[1289]	3121	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3122	process_dvr_output -l -d DATA_DVR -f $fname
	3123
[260]	3124	fi
[1]	3125	fi
	3126
	3127
	3128
[1289]	3129	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3130	# BY EACH CORE INTO ONE FILE
[920]	3131	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3132	then
	3133	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3134	printf "\n 2d- and/or 3d-data may be incomplete!"
	3135	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3136	elif [[ "$combine_plot_fields" == true ]]
	3137	then
[1270]	3138	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3139	then
	3140	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
[1779]	3141	aprun -n 1 -N 1 combine_plot_fields${block}.x
[1270]	3142	else
	3143	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3144	combine_plot_fields${block}.x
	3145	fi
[920]	3146	else
[1289]	3147
	3148	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3149	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3150	# ??? koennen wir das streichen ???
[920]	3151	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3152	fi
[503]	3153
	3154
	3155
[1289]	3156	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3157	(( i = 0 ))
	3158	while (( i < ioc ))
	3159	do
	3160	(( i = i + 1 ))
	3161	if (( i == 1 ))
	3162	then
[1289]	3163	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3164	fi
	3165	printf "\n >>> ${out_command[$i]}"
	3166	eval ${out_command[$i]}
	3167	if (( i == ioc ))
	3168	then
[1289]	3169	printf "\n$dashes\n"
[1]	3170	fi
	3171	done
	3172
	3173
[1289]	3174	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3175	if [[ $do_trace = true ]]
	3176	then
	3177	printf "\n\n"
	3178	ls -al
	3179	fi
[2261]	3180
[1]	3181
[1289]	3182	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3183	(( i = 0 ))
	3184	while (( i < iout ))
	3185	do
	3186	(( i = i + 1 ))
	3187	if (( i == 1 ))
	3188	then
[2261]	3189	printf "\n\n *** saving OUTPUT-files:"
	3190
	3191	# GET RUN NUMBER ASSIGNED BY PALM
	3192	if [[ -f RUN_NUMBER ]]
	3193	then
	3194	read run_number < RUN_NUMBER
	3195	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	3196	usecycle_option="-U $run_number"
	3197	else
	3198	run_number=0
	3199	usecycle_option=""
	3200	fi
	3201	printf "\n$dashes"
[1]	3202	fi
	3203
[2261]	3204	# ADD CYCLE NUMBER TO FILENAME
	3205	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	3206	then
	3207
	3208	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	3209	if [[ "${actionout[$i]}" != "a" ]]
	3210	then
	3211	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	3212	# WITH AN EXISTING CYCLE NUMBER
	3213	if (( run_number >= cycnum[$i] ))
	3214	then
	3215	(( cycnum[$i] = run_number ))
	3216	else
	3217	if (( run_number > 0 ))
	3218	then
	3219	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	3220	fi
	3221	fi
	3222	fi
	3223	if (( cycnum[$i] > 0 ))
	3224	then
	3225	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	3226	fi
	3227	fi
	3228
[1289]	3229	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3230	files_for_pes=false; filetyp=file
[2261]	3231	link_local_output=false
[1]	3232	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3233	then
	3234	files_for_pes=true; filetyp=directory
	3235	actionout[$i]=""
	3236	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3237	then
	3238	actionout[$i]=""
[2261]	3239	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
[1]	3240	then
	3241	files_for_pes=true; filetyp=directory
[2261]	3242	link_local_output=true
	3243	actionout[$i]=""
	3244	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
[1]	3245	then
[2261]	3246	link_local_output
	3247	actionout[$i]=""
[1]	3248	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3249	then
	3250	files_for_pes=true; filetyp=directory
	3251	actionout[$i]="tr"
	3252	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3253	then
	3254	actionout[$i]="tr"
	3255	fi
	3256
	3257	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3258	then
	3259	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3260	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3261	then
	3262	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3263	else
	3264
	3265
[1289]	3266	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3267	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3268	if [[ "${actionout[$i]}" = tr ]]
	3269	then
	3270	if [[ $localhost != $fromhost ]]
	3271	then
	3272	if [[ $files_for_pes = false ]]
	3273	then
	3274	cps=""
	3275	cst=""
	3276	else
	3277	cps=-c
	3278	cst="/"
	3279	fi
[2261]	3280
	3281	transfer_failed=false
	3282	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3283	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
	3284	if [[ $localhost = lccrayb ]]
[1]	3285	then
[2261]	3286	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]}"
	3287	elif [[ $localhost = lccrayh ]]
	3288	then
	3289	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]}"
	3290	elif [[ $localhost = lcbullhh ]]
	3291	then
	3292	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]}"
	3293	elif [[ $localhost = lcxe6 ]]
	3294	then
	3295	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]	3296	else
[2261]	3297	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3298	fi
	3299	[[ $? != 0 ]] && transfer_failed=true
[1]	3300
[2261]	3301	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	3302	if [[ $transfer_failed = true ]]
	3303	then
	3304	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
	3305	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
[1]	3306
[2261]	3307	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	3308	eval local_catalog=${pathout[$i]}
	3309	if [[ ! -d $local_catalog ]]
[1]	3310	then
[2261]	3311	printf " *** local directory does not exist. Trying to create:\n"
	3312	printf " $local_catalog \n"
	3313	mkdir -p $local_catalog
[1]	3314	fi
[2261]	3315	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3316	transfer_problems=true
[1]	3317	fi
[2261]	3318
[1]	3319	else
	3320
[1289]	3321	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3322	actionout[$i]=""
	3323	fi
	3324	fi
	3325
	3326
[1289]	3327	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3328	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3329	if [[ "${actionout[$i]}" = tra ]]
	3330	then
	3331	if [[ $localhost != $fromhost ]]
	3332	then
[2261]	3333	if [[ $localhost = ibmh ]]
[1]	3334	then
	3335
[1289]	3336	# TRANSFER IN SEPERATE JOB
	3337	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3338	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3339	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3340	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3341
	3342	echo "set -x" > transfer_${localout[$i]}
	3343	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3344
	3345	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3346	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3347	printf "\n or higher cycle\n"
[1468]	3348	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]	3349
[1]	3350	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3351
[2261]	3352	if [[ $LOGNAME = b323013 ]]
[1]	3353	then
[2261]	3354	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3355	else
[2261]	3356	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3357	fi
	3358
	3359	else
	3360
[1289]	3361	# TRANSFER WITHIN THIS JOB
[1]	3362	transfer_failed=false
[82]	3363	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3364	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3365	if [[ $localhost = lccrayb ]]
	3366	then
[2261]	3367	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]	3368	elif [[ $localhost = lccrayh ]]
	3369	then
[2261]	3370	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]	3371	elif [[ $localhost = lcxe6 ]]
	3372	then
[2261]	3373	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]	3374	else
[1468]	3375	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3376	fi
[82]	3377	[[ $? != 0 ]] && transfer_failed=true
[1]	3378
[1289]	3379	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3380	if [[ $transfer_failed = true ]]
	3381	then
[1289]	3382	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3383	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3384
[1289]	3385	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3386	eval local_catalog=${pathout[$i]}
	3387	if [[ ! -d $local_catalog ]]
	3388	then
	3389	printf " *** local directory does not exist. Trying to create:\n"
	3390	printf " $local_catalog \n"
	3391	mkdir -p $local_catalog
	3392	fi
	3393
	3394	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3395	transfer_problems=true
	3396	fi
	3397	fi
	3398	else
	3399
[1289]	3400	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3401	actionout[$i]=a
	3402	fi
	3403	fi
	3404
	3405
[1289]	3406	# APPEND ON THIS MACHINE
[1]	3407	if [[ "${actionout[$i]}" = "a" ]]
	3408	then
[741]	3409	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	3410	then
	3411	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	3412	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	3413	else
	3414	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	3415	cat ${localout[$i]} >> ${pathout[$i]}
	3416	fi
[1]	3417	fi
	3418
[1289]	3419	# COPY ON THIS MACHINE
	3420	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	3421	# ON DIFFERENT FILE-SYSTEMS
[1]	3422	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	3423	then
	3424
[1289]	3425	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	3426	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	3427	then
	3428	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[2261]	3429	if [[ $link_local_output = true ]]
	3430	then
	3431	printf " file will be linked\n"
	3432	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3433	fi
	3434	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3435	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
[149]	3436	then
[2261]	3437	if [[ $link_local_output = true ]]
	3438	then
	3439	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3440	fi
	3441	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3442	else
	3443	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
[149]	3444	fi
[1]	3445	else
	3446	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[2261]	3447	if [[ $link_local_output = true ]]
	3448	then
	3449	printf " file will be linked\n"
	3450	ln -f ${localout[$i]} ${pathout[$i]}
	3451	fi
	3452	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3453	if [[ ! -f "${pathout[$i]}" ]]
[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 ${localout[$i]} ${pathout[$i]}
	3460	else
	3461	printf "+++ no copy because file ${pathout[$i]} exists\n"
[149]	3462	fi
[1]	3463	fi
	3464
	3465	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	3466	then
	3467
[1289]	3468	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	3469	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	3470	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[2261]	3471	if [[ $link_local_output = true ]]
	3472	then
	3473	printf " files will be linked\n"
	3474	mkdir ${pathout[$i]}
	3475	cd ${localout[$i]}
	3476	for file in $(ls *)
	3477	do
	3478	ln -f $file ${pathout[$i]}
	3479	done >\|/dev/null 2>&1
	3480	cd $TEMPDIR
	3481	fi
[1289]	3482
	3483	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[2261]	3484	if [[ ! -f "${pathout[$i]}/_000000" ]]
[149]	3485	then
[2261]	3486	if [[ $link_local_output = true ]]
	3487	then
	3488	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3489	fi
	3490	cp -r ${localout[$i]}/* ${pathout[$i]}
	3491	fi
[1]	3492
	3493	fi
	3494	fi
	3495	done
	3496	if (( i != 0 ))
	3497	then
	3498	if [[ $transfer_problems = true ]]
	3499	then
[1289]	3500	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	3501	printf "\n +++ WARNING: some data transfers failed! \n"
	3502	else
[1289]	3503	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	3504	fi
	3505	fi
	3506
	3507
[1289]	3508	# IF REQUIRED, START A RESTART-JOB
	3509	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	3510	if [[ -f CONTINUE_RUN ]]
	3511	then
	3512
[2261]	3513	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	3514	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	3515	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	3516	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
	3517	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	3518	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	3519	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	3520	if [[ $(echo $mc \| grep -c "#") != 0 ]]
[1]	3521	then
[2261]	3522	mc=`echo $mc \| sed 's/#/f/g'`
	3523	fi
[1]	3524
	3525
[2261]	3526	# START THE RESTART-JOB
	3527	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
	3528	echo " $mc"
	3529	printf "\n$dashes\n"
	3530	if [[ $localhost != $fromhost ]]
	3531	then
[1]	3532
[2261]	3533	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
[1]	3534	then
[2261]	3535	echo "*** ssh will be used to initiate restart-runs!"
	3536	echo " return_address=\"$return_address\" "
	3537	echo " return_username=\"$return_username\" "
	3538	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
[1]	3539	then
[2261]	3540	if [[ $localhost = ibmh ]]
[1]	3541	then
[2261]	3542	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\" "
	3543	elif [[ $localhost = lcbullhh ]]
	3544	then
	3545	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\" "
	3546	elif [[ $localhost = lccrayb ]]
	3547	then
	3548	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\" "
	3549	elif [[ $localhost = lccrayh ]]
	3550	then
	3551	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\" "
	3552	elif [[ $localhost = lcxe6 ]]
	3553	then
	3554	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]	3555	else
[2261]	3556	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]	3557	fi
	3558	else
[2261]	3559	if [[ $localhost = ibmkisti ]]
	3560	then
	3561	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\" "
	3562	elif [[ $localhost = lceddy ]]
	3563	then
	3564	/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 "
	3565	elif [[ $localhost = lcocean ]]
	3566	then
	3567	/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 "
	3568	elif [[ $localhost = lccrayb ]]
	3569	then
	3570	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\" "
	3571	elif [[ $localhost = lccrayh ]]
	3572	then
	3573	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\" "
	3574	else
	3575	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	3576	fi
[1]	3577	fi
[2261]	3578	else
	3579	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	3580	locat=restart; exit
	3581	fi
[1]	3582
[2261]	3583	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	3584	if [[ $queue = special1q ]]
	3585	then
	3586	sleep 120
[1]	3587	else
[2261]	3588	sleep 30
	3589	fi
[1]	3590
[2261]	3591	else
	3592
	3593	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	3594	# USING SSH)
	3595	cd $LOCAL_PWD
[1103]	3596	if [[ $localhost = lckyuh ]]
	3597	then
[2261]	3598	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	3599	printf "\n please restart job manually using command:\n"
	3600	printf "\n \"$mc\" "
[1103]	3601	else
[2261]	3602	eval $mc # THE ' MUST BE EVALUATED
[1103]	3603	fi
[2261]	3604	cd - > /dev/null
	3605	fi
	3606	if [[ $localhost = lckyuh ]]
	3607	then
	3608	printf "\n$dashes\n *** restart-run to be initiated manually\n"
	3609	else
	3610	printf "\n$dashes\n *** restart-run initiated \n"
	3611	fi
[1]	3612
	3613
[2261]	3614	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	3615	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	3616	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	3617	# MAY BE VERY HUGE)
	3618	(( i = 0 ))
	3619	while (( i < iin ))
	3620	do
	3621	(( i = i + 1 ))
	3622	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	3623	then
	3624	rm -r ${absnamein[$i]}
	3625	fi
	3626	done
[1]	3627
	3628	fi
	3629
	3630
	3631
[1289]	3632	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	3633	if [[ "$email_notification" != "none" ]]
[1]	3634	then
	3635
	3636	if [[ $localhost != $fromhost ]]
	3637	then
	3638	if [[ -f CONTINUE_RUN ]]
	3639	then
	3640	echo "PALM restart run necessary" > email_text
	3641	echo "description header of actual run:" >> email_text
	3642	cat CONTINUE_RUN >> email_text
	3643	echo "mrun-command to restart:" >> email_text
	3644	echo "$mc" >> email_text
	3645	else
	3646	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	3647	fi
	3648	mail $email_notification < email_text
	3649	printf "\n *** email notification sent to \"$email_notification\" "
	3650	fi
	3651	fi
	3652
	3653
	3654
[1289]	3655	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	3656	cd $HOME
	3657	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	3658
	3659	else
	3660
[1289]	3661	# PREPARING ACTIONS,
	3662	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	3663
[1289]	3664	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[1468]	3665	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
[1]	3666	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
[79]	3667	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	3668	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	3669	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	3670	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	3671	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	3672	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	3673	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	3674	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	3675	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	3676	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	3677	if [[ $use_openmp = true ]]
	3678	then
[622]	3679	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	3680	fi
[759]	3681	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[1]	3682	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	3683	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	3684	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	3685	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	3686	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	3687	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[920]	3688	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	3689	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	3690	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	3691	if [[ $do_remote = true ]]
	3692	then
	3693	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	3694	fi
	3695
	3696
[1289]	3697	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	3698	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	3699	then
	3700
	3701	printf "\n *** creating the executable for batch job\n"
	3702
[1289]	3703	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	3704	if [[ $host != $localhost ]]
	3705	then
	3706	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	3707	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	3708	locat=create_executable; exit
	3709	fi
	3710
	3711	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3712	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3713
	3714	cp $make_depository .
	3715	tar -xf $make_depository > /dev/null 2>&1
	3716	cp ../* . > /dev/null 2>&1
	3717
	3718	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	3719
	3720	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	3721	then
	3722	printf "\n +++ error occured while compiling or linking"
	3723	locat=compile
	3724	exit
	3725	fi
	3726
	3727	mv a.out ..
	3728	cd - > /dev/null 2>&1
	3729	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3730
	3731	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	3732
	3733	fi
	3734
	3735
[1289]	3736	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	3737	jobfile=jobfile.$RANDOM
	3738
	3739
[1289]	3740	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	3741	echo "mkdir $TEMPDIR" >> $jobfile
	3742	echo "cd $TEMPDIR" >> $jobfile
	3743
	3744
[1289]	3745	# ACTIVATE ERROR-TRACEBACK
[1]	3746	if [[ $do_trace = true ]]
	3747	then
	3748	echo "set -x" >> $jobfile
	3749	else
	3750	echo "set +vx" >> $jobfile
	3751	fi
	3752
	3753
[1289]	3754	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	3755	if [[ "$init_cmds" != "" ]]
	3756	then
	3757	echo "$init_cmds" >> $jobfile
	3758	fi
	3759	if [[ "$module_calls" != "" ]]
	3760	then
	3761	echo "$module_calls" >> $jobfile
	3762	fi
	3763
	3764
[1289]	3765	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	3766	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	3767	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	3768	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	3769	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	3770	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	3771	# QUEUEING-SYSTEMS
[1866]	3772	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
[1]	3773	then
	3774
[1289]	3775	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	3776	if [[ $restart_run != true ]]
	3777	then
	3778	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	3779	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	3780	fi
[1]	3781
[1289]	3782	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	3783	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	3784	echo "set -x" >> $jobfile
[693]	3785	if [[ $host = $localhost ]]
	3786	then
[1199]	3787	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	3788	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	3789	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	3790	then
	3791	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3792	else
	3793	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3794	fi
[1199]	3795
[693]	3796	else
[1255]	3797	if [[ $host = ibmkisti ]]
[693]	3798	then
[1289]	3799	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	3800	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3801	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1620]	3802	elif [[ $host = lcbullhh ]]
	3803	then
	3804	echo "localdir=\`pwd\`" >> $jobfile
	3805	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	3806
[1255]	3807	elif [[ $host = lccrayb ]]
	3808	then
	3809	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3810	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3811	elif [[ $host = lccrayh ]]
	3812	then
	3813	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3814	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3815
[1255]	3816	else
[1468]	3817	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	3818	fi
	3819	fi
[193]	3820	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	3821
[1289]	3822	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	3823	# WORKING DIRECTORY OF THE JOB
[193]	3824	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	3825	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	3826	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	3827	echo "execute_mrun=true" >> $jobfile
	3828	echo " " >> $jobfile
	3829
[191]	3830	else
	3831
[1289]	3832	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	3833	if [[ $do_compile = true ]]
	3834	then
	3835
	3836	source_catalog=SOURCES_FOR_RUN_$fname
	3837
[1289]	3838	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	3839	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	3840	echo "export SOURCES_COMPLETE=true" >> $jobfile
	3841	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	3842
	3843	for filename in $source_list
	3844	do
[1289]	3845	# BACKSLASH IS USED FOR MASKING
[191]	3846	echo "cat > $filename << \"%END%\"" >> $jobfile
	3847	cat $source_catalog/$filename >> $jobfile
	3848	echo " " >> $jobfile
	3849	echo "%END%" >> $jobfile
	3850	echo " " >> $jobfile
	3851	done
	3852
[1289]	3853	# BACKSLASH IS USED FOR MASKING
[191]	3854	echo "cat > Makefile << \"%END%\"" >> $jobfile
	3855	cat $source_catalog/Makefile >> $jobfile
[1]	3856	echo " " >> $jobfile
	3857	echo "%END%" >> $jobfile
	3858	echo " " >> $jobfile
	3859
[191]	3860	echo "cd - > /dev/null" >> $jobfile
[1]	3861
[191]	3862	fi
[1]	3863
	3864
[1289]	3865	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	3866	# BACKSLASH IS USED FOR MASKING
	3867	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	3868	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	3869	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	3870	if [[ $host = lckyuh ]]
	3871	then
[1289]	3872	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	3873	sed 's/frtpx/frt/g' $config_file >> $jobfile
	3874	else
	3875	sed 's/#$.*//g' $config_file >> $jobfile
	3876	fi
[191]	3877	echo "%END%" >> $jobfile
	3878	echo " " >> $jobfile
[1]	3879
	3880
[1289]	3881	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	3882	# BACKSLASH IS USED FOR MASKING
[1101]	3883	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	3884	if [[ $host = lckyuh ]]
	3885	then
	3886	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	3887	else
	3888	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	3889	fi
[1101]	3890	echo "%END%" >> $jobfile
[191]	3891	echo "chmod u+x $mrun_script_name" >> $jobfile
	3892	echo "execute_mrun=true" >> $jobfile
	3893	echo " " >> $jobfile
[1]	3894
	3895	fi
	3896
[191]	3897
[1289]	3898	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	3899	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	3900	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	3901	if [[ $do_remote = true ]]
	3902	then
	3903	(( i = 0 ))
	3904	while (( i < iin ))
	3905	do
	3906	(( i = i + 1 ))
	3907	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	3908	if [[ "${transin[$i]}" = job ]]
	3909	then
	3910	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	3911	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	3912	echo " " >> $jobfile
	3913	echo "%END%" >> $jobfile
	3914	else
[1468]	3915	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	3916	fi
	3917
[1289]	3918	# CHECK, IF FILE COULD BE CREATED
[1]	3919	echo "if [[ \$? = 1 ]]" >> $jobfile
	3920	echo "then" >> $jobfile
	3921	echo " echo \" \" " >> $jobfile
	3922	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	3923	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	3924	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	3925	echo " execute_mrun=false" >> $jobfile
	3926	echo "fi" >> $jobfile
	3927	done
	3928	fi
	3929
[1289]	3930	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3931	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	3932	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	3933	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3934	echo "export LOCAL_PWD" >> $jobfile
	3935
[1289]	3936	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	3937	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	3938	echo "export LOCAL_MRUN_PATH" >> $jobfile
	3939
[2257]	3940	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
	3941	if [[ $host = lceddy \|\| $localhost = lceddy ]]
	3942	then
[1099]	3943	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	3944	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[2257]	3945	fi
[1]	3946
[1289]	3947	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	3948	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	3949	echo "set -x" >> $jobfile
	3950	echo "queue=$queue" >> $jobfile
[1]	3951	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	3952	echo 'ls -al; echo `pwd`' >> $jobfile
	3953	echo "cd \$HOME" >> $jobfile
	3954	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	3955
	3956
	3957
	3958
[1289]	3959	# START THE JOB USING SUBJOB-COMMAND
[1]	3960	if [[ $silent = false ]]
	3961	then
	3962	printf "\n "
	3963	else
	3964	printf "\n\n"
	3965	fi
	3966
[1094]	3967	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]	3968	rm -rf $jobfile
	3969
	3970
[1289]	3971	fi # END OF REMOTE-PART

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