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source: palm/trunk/SCRIPTS/mrun @ 2278

Last change on this file since 2278 was 2268, checked in by raasch, 7 years ago
bugfix for calculating cycle numbers for output files in r2261
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 2268 2017-06-09 10:34:09Z schwenkel $
[2268]	29	# bugfix for calculating cycle numbers for output files in r2261
	30	#
	31	# 2262 2017-06-08 14:52:23Z raasch
[2262]	32	# bugfix for r2261
	33	#
	34	# 2261 2017-06-08 14:25:57Z raasch
[2261]	35	# unified cycle numbers for output files are used,
	36	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
	37	# creation of file OUTPUT_FILE_CONNECTIONS removed,
	38	# archive feature completely removed from the script,
	39	# nech related parts completely removed
	40	#
	41	# 2257 2017-06-07 14:07:05Z witha
[2257]	42	# adjustments for lceddy, removed lcflow-specific code
	43	#
	44	# 2186 2017-03-21 05:36:31Z raasch
[1867]	45	#
[2186]	46	# 2185 2017-03-21 05:09:29Z raasch
	47	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
	48	#
[2150]	49	# 2148 2017-02-09 16:56:42Z scharf
	50	# changed allocation of resources for lcbullhh in srun command
	51	#
[2142]	52	# 2141 2017-02-06 10:19:32Z gronemeier
	53	# made check for existing files language independent
	54	#
[1945]	55	# 1944 2016-06-15 06:29:00Z raasch
	56	# adjustments for using HLRN ssh-keys
	57	#
[1941]	58	# 1940 2016-06-14 05:15:20Z raasch $
	59	# adjustments for lckiaps
	60	#
[1867]	61	# 1866 2016-04-15 06:50:59Z raasch
	62	# adjusted for lcocean
[1805]	63	#
[1842]	64	# 1841 2016-04-07 19:14:06Z raasch
	65	# script now running under bash
	66	#
[1805]	67	# 1804 2016-04-05 16:30:18Z maronga
[1779]	68	# test: implementing an execute mechanism where the execute command is given in the
	69	# configuration file
	70	# ROPTS removed from execution commands
	71	# Warnings about missing optional files or user code changed to informative messages
[1804]	72	# Removed parameter file check
[1305]	73	#
[1756]	74	# 1755 2016-02-22 13:53:39Z maronga
	75	# Minor bugfix to last commit
	76	#
[1754]	77	# 1753 2016-02-22 13:49:49Z maronga
	78	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
	79	#
[1623]	80	# 1622 2015-07-20 06:21:36Z heinze
	81	# bugfix for Mistral (lcbullhh)
	82	#
	83	# 1621 2015-07-17 11:39:33Z heinze
[1621]	84	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
[1200]	85	#
[1610]	86	# 1609 2015-07-03 15:37:58Z maronga
	87	# Modified the random number of the temporary working directory to match the
	88	# queuing system number on HLRN-III (lccray*).
	89	#
[1605]	90	# 1604 2015-06-23 15:48:03Z suehring
	91	# Enable coupled runs for lcmuk
	92	#
[1599]	93	# 1598 2015-05-29 06:45:40Z raasch
	94	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
	95	#
[1550]	96	# 1549 2015-01-30 14:26:16Z suehring
	97	# Enable interactive debug sessions with allinea debugger
	98	#
[1548]	99	# 1547 2015-01-29 15:09:12Z witha
	100	# adjustments for ForWind computing cluster (lcflow)
	101	#
[1492]	102	# 1491 2014-11-12 08:12:57Z heinze
	103	# correct setting of batch_job allowed for ibm-machines
	104	#
[1469]	105	# 1468 2014-09-24 14:06:57Z maronga
	106	# Typo removed (addres->address)
	107	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
	108	# Added support for restart runs (remote) for lcxe6
	109	#
[1443]	110	# 1442 2014-07-28 07:09:10Z raasch
	111	# default queues for HLRN-III (lccrayb/lccrayh) defined
	112	#
[1423]	113	# 1422 2014-07-02 10:01:25Z kanani
	114	# automatic restarts enabled for lccrayb,
	115	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
	116	#
[1421]	117	# 1420 2014-06-10 06:24:14Z raasch
	118	# -j1 option added to aprung command for lccrayf (CSC)
	119	#
[1403]	120	# 1402 2014-05-09 14:25:13Z raasch
	121	# batch_job added to envpar-NAMELIST
	122	#
[1358]	123	# 1357 2014-04-11 15:02:03Z witha
	124	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
	125	# possible)
	126	#
[1328]	127	# 1320 2014-03-20 08:40:49Z raasch
	128	# check namelist file set false by default
	129	#
[1305]	130	# 1304 2014-03-12 10:29:42Z raasch
	131	# ulimit option changed from -Ss to -s
	132	#
	133	# bugfix: missing "fi" in r1289
	134	#
[1290]	135	# 1289 2014-03-04 07:12:34Z raasch
	136	# comments translated to English
	137	# necriam-, fimm-, ibmy-, and sgi-specific code removed
	138	# export of variables for palm and interpret_config removed
	139	#
[1282]	140	# 1281 2014-02-01 07:55:49Z raasch
	141	# rsync-copy restricted to Cray machines, since command is unavailable on some
	142	# other systems
	143	#
[1280]	144	# 1279 2014-01-28 12:10:14Z raasch
	145	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
	146	# in order to remove annoying restrictions concerning the number of processors which
	147	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
	148	# restriction, one of the nodes will be filled with less than the given number of
	149	# tasks per node. A respective warning is given.
	150	#
[1275]	151	# 1274 2014-01-09 13:14:54Z heinze
	152	# adjustments for lccrayh
	153	#
[1273]	154	# 1272 2014-01-08 10:19:32Z witha
	155	# small adjustment for lcflow
	156	#
[1271]	157	# 1270 2013-12-16 11:05:01Z fricke
	158	# call of combine_plot_fields adjusted for lccrayb/lccrayh
	159	#
[1256]	160	# 1255 2013-11-07 14:43:35Z raasch
	161	# further adjustments for lccrayb remote access
	162	#
[1242]	163	# 1241 2013-10-30 11:36:58Z heinze
	164	# Enable use of nudging input and input of large scale forcing from
	165	# external files
	166	#
[1230]	167	# 1229 2013-09-20 06:55:19Z raasch
	168	# further adjustments for lccrayb
	169	#
[1225]	170	# 1224 2013-09-16 07:27:23Z raasch
	171	# first adjustments for lccrayb
	172	#
[1211]	173	# 1210 2013-08-14 10:58:20Z raasch
	174	# fftw support added
	175	#
[1203]	176	# 1201 2013-07-10 16:17:59Z witha
	177	# adjustments for Forwind cluster (lcflow)
	178	#
[1200]	179	# 1199 2013-07-05 14:52:22Z raasch
[1199]	180	# adjustments for CSC Helsinki (lccrayf),
	181	# executables for batch jobs can be created in advance, in order to avoid calling
	182	# the compiler within the batch job (only works if batch jobs are submitted on
	183	# local host)
[1104]	184	#
[1191]	185	# 1190 2013-06-25 09:39:21Z heinze
	186	# enable use of automatic restarts for ibmh
[1185]	187	# use of cluster/express queue enabled (ibmh)
[1104]	188	#
[1125]	189	# 1124 2013-04-09 15:46:52Z raasch
	190	# variable "memory" is exported via typeset option -x, because otherwise an unknown
	191	# side effect may lead to data loss while getopts is reading the script-option arguments
	192	#
[1123]	193	# 1122 2013-04-09 08:37:16Z heinze
	194	# Bugfix: change type of variable last_char
	195	#
[1121]	196	# 1119 2013-04-05 15:11:19Z raasch
	197	# Bugfix for setting -T option for subjob
	198	#
[1109]	199	# 1108 2013-03-05 07:03:32Z raasch
	200	# bugfix for coupled runs on lckyut/lckyuh
	201	#
[1107]	202	# 1106 2013-03-04 05:31:38Z raasch
	203	# --stdin argument for mpiexec on lckyuh
	204	# -y and -Y settings output to header
	205	#
[1104]	206	# 1103 2013-02-20 02:15:53Z raasch
[1103]	207	# default script runs again under ksh, because of unsolved problems with read
	208	# from stdin: when bash script is called from a ksh, message "read error: 0:
	209	# Resource temporarily unavailable" appears and script does not stop,
	210	# further bash compatibility adjustments,
	211	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
	212	# on lckyuh, but mrun does not terminate and issues a warning instead
[1046]	213	#
[1102]	214	# 1101 2013-02-17 10:20:21Z raasch
	215	# script now running under bash instead of ksh, which required small adjustments
	216	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
	217	# read from stdin),
	218	# cross compilername on lckyuh compute nodes replaced by real compiler name
	219	#
[1100]	220	# 1099 2013-02-10 01:47:43Z raasch
	221	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
	222	# and for Forwind cluster (lcflow)
	223	# small further adjustments for lckyut
	224	#
[1096]	225	# 1094 2013-02-03 01:52:12Z raasch
	226	# explicit ssh/scp port can be set in config file with environment variable
	227	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
	228	# decalpha parts (yonsei) removed
	229	#
[1091]	230	# 2013-02-02 07:06:13Z raasch
[1099]	231	# adjustments for Kyushu-University computing center (lckyut - tatara)
[1091]	232	#
[1084]	233	# 1083 2013-01-04 10:22:09Z maronga
	234	# bugfix in parameter file check (read %cpp_options was missing)
	235	#
[1070]	236	# 1069 2012-11-28 16:18:43Z maronga
	237	# bugfix: coupling mode was always set to mpi2, typos removed
	238	#
[1059]	239	# 1058 2012-11-21 07:00:35Z raasch
	240	# Intel inspector (inspxe) is given the number of PEs instead of the number of
	241	# nodes
	242	#
[1047]	243	# 1046 2012-11-09 14:38:45Z maronga
	244	# code put under GPL (PALM 3.9)
	245	#
[1090]	246	# 21/03/94 - Siggi - first version finished
	247	# 03/03/94 - Siggi - script development started
	248	#
[1059]	249	#--------------------------------------------------------------------------------#
[1090]	250	# mrun - script for running PALM jobs
	251	#--------------------------------------------------------------------------------#
[1]	252
[1047]	253
[1]	254
[1289]	255	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
[1]	256
[1289]	257	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	258	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
	259	# (TOO MANY ARGUMENTS - PROBLEM)
	260	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
[1]	261
	262	AddFilenames=""
	263	additional_conditions=""
	264	add_source_path=""
	265	afname=""
[1320]	266	check_namelist_files=false
[920]	267	combine_plot_fields=true
[1]	268	compiler_name=""
	269	cond1=""
	270	cond2=""
	271	config_file=.mrun.config
[206]	272	coupled_dist=""
	273	coupled_mode="mpi1"
[1]	274	cpp_opts=""
[82]	275	cpp_options=""
[1]	276	cpumax=0
	277	cpurest=0
[1199]	278	create_executable_for_batch=false
[1]	279	delete_temporary_catalog=true
	280	do_batch=false
	281	do_compile=true
	282	do_remote=false
	283	do_stagein=true
	284	do_stageout=true
	285	do_trace=false
[352]	286	email_notification="none"
[1]	287	exclude=""
	288	executable=""
[1779]	289	execute_command="none"
[1]	290	execution_error=false
[1210]	291	fftw_inc=""
	292	fftw_lib=""
	293	fftw_support=false
[1289]	294	fname=test
[1]	295	fromhost=""
[78]	296	global_revision=""
[122]	297	group_number=none
[1]	298	host=""
	299	host_file=""
	300	hp=""
	301	input_list=""
	302	interpreted_config_file=""
[164]	303	job_catalog="~/job_queue"
[1]	304	job_on_file=""
	305	keep_data_from_previous_run=false
[183]	306	link_local_input=false
[149]	307	link_local_output=false
[1]	308	localhost_realname=$(hostname)
[260]	309	local_dvrserver_running=.FALSE.
[1]	310	locat=normal
	311	mainprog=""
	312	makefile=""
[759]	313	max_par_io_str=""
[1]	314	mc=$0
	315	while [[ $(echo $mc \| grep -c "/") != 0 ]]
	316	do
	317	mc=`echo $mc \| cut -f2- -d"/"`
	318	done
[493]	319	module_calls=""
[1]	320	mrun_script_name=$mc
[82]	321	netcdf_inc=""
	322	netcdf_lib=""
[1]	323	netcdf_support=false
	324	node_usage=default
	325	numprocs=""
[206]	326	numprocs_atmos=0
	327	numprocs_ocean=0
[1]	328	OOPT=""
	329	openmp=false
	330	output_list=""
	331	package_list=""
	332	queue=none
	333	read_from_config=""
[5]	334	restart_run=false
[622]	335	if [[ `hostname` = rte10 ]]
[1]	336	then
[1468]	337	return_address=133.5.185.60
	338	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[693]	339	elif [[ `hostname` = climate0 ]]
	340	then
[1468]	341	return_address=165.132.26.68
	342	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1866]	343	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
	344	then
	345	return_address="schultzl-Latitude-E6540"
	346	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[1021]	347	elif [[ `hostname` = urban00 ]]
	348	then
[1468]	349	return_address=147.46.30.151
	350	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
[622]	351	else
[1468]	352	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
[1]	353	fi
	354	return_password=""
	355	return_username=$LOGNAME
	356	remotecall=false
	357	remote_username=""
[102]	358	run_coupled_model=false
[1]	359	run_mode=""
[1289]	360	dashes=" ----------------------------------------------------------------------------"
[1]	361	silent=false
	362	source_list=""
	363	source_path=SOURCE
	364	tasks_per_node=""
	365	threads_per_task=1
	366	tmpcreate=false
	367	tmp_data_catalog=""
	368	transfer_problems=false
	369	usern=$LOGNAME
[377]	370	use_openmp=false
[1289]	371	version="MRUN 2.1 Rev$Rev: 2268 $"
[1]	372	working_directory=`pwd`
	373	TOPT=""
	374	XOPT=""
	375	zeit=$( date \| cut -c 12-19 )
	376
[1124]	377	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
[1289]	378	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	379	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	380	# SCRIPT-OPTION ARGUMENTS
[2261]	381	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]	382
[1289]	383	# ERROR HANDLING IN CASE OF EXIT
[83]	384	trap 'rm -rf $working_directory/tmp_mrun
[1289]	385	if [[ $locat != normal && $locat != control_c ]]
[1]	386	then
	387
[1289]	388	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
[1]	389	(( i = 0 ))
	390	while (( i < iec ))
	391	do
	392	(( i = i + 1 ))
	393	printf "\n *** Execution of ERROR-command:\n"
	394	printf " >>> ${err_command[$i]}\n"
	395	eval ${err_command[$i]}
	396	done
[1101]	397	if [[ -n $interpreted_config_file ]]
	398	then
[1]	399	rm -rf $interpreted_config_file
	400	fi
[1101]	401	if [[ -n .mrun_environment ]]
	402	then
[71]	403	rm -rf .mrun_environment
	404	fi
[1]	405	if [[ $tmpcreate = true ]]
	406	then
[2147]	407	# printf "\n *** Contents of \"$TEMPDIR\":\n"
	408	# ls -al; cd
[1]	409	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	410	fi
[260]	411	if [[ "$dvrserver_id" != "" ]]
	412	then
	413	echo "+++ killing dvrserver_id=$dvrserver_id"
	414	kill $dvrserver_id
	415	fi
[1]	416	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	417	then
	418	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	419	fi
	420	printf "\n\n+++ MRUN killed \n\n"
	421	elif [[ $locat != control_c ]]
	422	then
	423	printf "\n\n --> all actions finished\n\n"
	424	printf " Bye, bye $usern !!\n\n"
	425	fi' exit
	426
	427
[1289]	428	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[83]	429	trap 'rm -rf $working_directory/tmp_mrun
[807]	430	rm -rf $working_directory/tmp_check_namelist_files
[69]	431	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
[1]	432	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
	433	then
	434	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
	435	fi
[260]	436	if [[ "$dvrserver_id" != "" ]]
	437	then
	438	echo "+++ killing dvrserver_id=$dvrserver_id"
	439	kill $dvrserver_id
	440	fi
[1]	441	printf "\n+++ MRUN killed by \"^C\" \n\n"
	442	locat=control_c
	443	exit
	444	' 2
	445
	446
[22]	447	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
	448	# BEEN SET
	449	if [[ "$PALM_BIN" = "" ]]
	450	then
	451	printf "\n +++ environment variable PALM_BIN has not been set"
	452	printf "\n please set it to the directory where the PALM scripts are located"
	453	locat=palm_bin; exit
	454	fi
[180]	455	export PATH=$PALM_BIN:$PATH
[22]	456
	457
[1]	458
[1289]	459	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
	460	# WHICH WILL BE USED TO START RESTART-JOBS
[2261]	461	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]	462	do
	463	case $option in
	464	(a) afname=$OPTARG;;
	465	(b) do_batch=true; mc="$mc -b";;
	466	(B) delete_temporary_catalog=false; mc="$mc -B";;
	467	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
[5]	468	(C) restart_run=true; mc="$mc -C";;
[1]	469	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
[79]	470	(F) job_on_file="-D"; mc="$mc -F";;
[122]	471	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
[78]	472	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
[1]	473	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
	474	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
	475	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
	476	(k) keep_data_from_previous_run=true; mc="$mc -k";;
[210]	477	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
[1]	478	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
	479	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
	480	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
	481	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
[622]	482	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
[1]	483	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
	484	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
	485	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
	486	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
[1468]	487	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
[1]	488	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
	489	(S) read_from_config=false; mc="$mc -S";;
	490	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
[759]	491	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
[1]	492	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
	493	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
	494	(v) silent=true; mc="$mc -v";;
[759]	495	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
[1]	496	(x) do_trace=true;set -x; mc="$mc -x";;
	497	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
[291]	498	(y) ocean_file_appendix=true; mc="$mc -y";;
[206]	499	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
[807]	500	(z) check_namelist_files=false; mc="$mc -z";;
[920]	501	(Z) combine_plot_fields=false; mc="$mc -Z";;
[1]	502	(\?) printf "\n +++ unknown option $OPTARG \n"
	503	printf "\n --> type \"$0 ?\" for available options \n"
	504	locat=parameter;exit;;
	505	esac
	506	done
	507
	508
[1289]	509	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	510	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
[1101]	511	(( to_shift = $OPTIND - 1 ))
	512	shift $to_shift
[1]	513
[1289]	514	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
[1]	515	if [[ "$1" = "?" ]]
	516	then
	517	(printf "\n *** mrun can be called as follows:\n"
[1804]	518	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]	519	printf "\n Description of available options:\n"
	520	printf "\n Option Description Default-Value"
	521	printf "\n -a base name of input files equiv. -d"
	522	printf "\n -b batch-job on local machine ---"
	523	printf "\n -B do not delete temporary directory at end ---"
	524	printf "\n -c configuration file .mrun.config"
	525	printf "\n -d base name of files attached to program test"
	526	printf "\n -D preprocessor(cpp)-directives \"\" "
	527	printf "\n -F create remote job file only ---"
	528	printf "\n -h execution host $localhost_realname"
	529	printf "\n -i INPUT control list \"\" "
	530	printf "\n -k keep data from previous run"
	531	printf "\n -K additional conditions for controling"
	532	printf "\n usage of conditional code and"
	533	printf "\n env-variables in configuration file \"\" "
	534	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	535	printf "\n -M Makefile name Makefile"
	536	printf "\n -n node usage (shared/not_shared) depending on -h"
	537	printf "\n -o OUTPUT control list \"\" "
[1304]	538	printf "\n -O threads per openMP task ---"
[1]	539	printf "\n -p software package list \"\" "
	540	printf "\n -q queue \"$queue\" "
	541	printf "\n -r run control list (combines -i -o) \"\" "
	542	printf "\n -s filenames of routines to be compiled \"\" "
	543	printf "\n must end with .f, .f90, .F, or .c !"
	544	printf "\n use \"..\" for more than one file and wildcards"
[837]	545	printf "\n -s LM compiles all locally modified files"
[1]	546	printf "\n -S config file interpreted by shellscript ---"
	547	printf "\n -t allowed cpu-time in seconds (batch) 0"
	548	printf "\n -T tasks per node depending on -h"
	549	printf "\n -u username on remote machine \"\" "
	550	printf "\n -v no prompt for confirmation ---"
[759]	551	printf "\n -w maximum parallel io streams as given by -X"
[1]	552	printf "\n -x tracing of mrun for debug purposes ---"
	553	printf "\n -X # of processors (on parallel machines) 1"
[291]	554	printf "\n -y add appendix \"_O\" to all local output"
	555	printf "\n files (ocean precursor runs followed by"
	556	printf "\n coupled atmosphere-ocean runs) ---"
[206]	557	printf "\n -Y run coupled model, \"#1 #2\" with"
	558	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
[920]	559	printf "\n -Z skip combine_plot_fields at the end of "
	560	printf "\n the simulation ---"
[1]	561	printf "\n "
	562	printf "\n Possible values of positional parameter <modus>:"
	563	printf "\n \"?\" - this outline \n\n") \| more
	564	exit
	565	elif [[ "$1" != "" ]]
	566	then
	567	printf "\n +++ positional parameter $1 unknown \n"
	568	locat=parameter; exit
	569	fi
	570
	571
	572
[1289]	573	# SHORT STARTING MESSAGE
[1]	574	printf "\n*** $version "
	575	printf "\n will be executed. Please wait ..."
	576
	577
[82]	578
[1289]	579	# CHECK, IF CONFIGURATION FILE EXISTS
[82]	580	if [[ ! -f $config_file ]]
	581	then
	582	printf "\n\n +++ configuration file: "
	583	printf "\n $config_file"
	584	printf "\n does not exist"
	585	locat=connect; exit
	586	fi
	587
	588
[1289]	589	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
[82]	590	line=""
	591	grep "%host_identifier" $config_file > tmp_mrun
	592	while read line
	593	do
[206]	594	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
[82]	595	then
	596	HOSTNAME=`echo $line \| cut -d" " -s -f2`
	597	host_identifier=`echo $line \| cut -d" " -s -f3`
[83]	598	if [[ $localhost_realname = $HOSTNAME ]]
[82]	599	then
	600	localhost=$host_identifier
	601	break
	602	fi
	603	fi
	604	done < tmp_mrun
	605
	606	if [[ "$localhost" = "" ]]
	607	then
	608	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
	609	printf "\n for local host \"$localhost_realname\"."
	610	printf "\n Please add line"
	611	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
	612	printf "\n to the configuration file."
	613	locat=localhost; exit
	614	fi
	615
	616
[1289]	617	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
	618	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
	619	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
[1]	620	[[ "$afname" = "" ]] && afname=$fname
	621
	622
[1289]	623	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
	624	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
	625	# STATEMENTS IN THE CONFIGURATION FILE
[1]	626	if [[ "$run_mode" != "" ]]
	627	then
	628	input_list="$input_list $run_mode"
	629	output_list="$output_list $run_mode"
	630	fi
	631
	632
[1289]	633	# ??? is this (and the respective option -H) really required ???
	634	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
	635	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
	636	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
	637	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
[1]	638	if [[ "$fromhost" = "" ]]
	639	then
	640	fromhost=$localhost
	641	fi
	642
	643
[1289]	644	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
	645	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
	646	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
[1609]	647	# TO BE SUBMITTED (I.E. do_batch=true)
[1]	648	if [[ -n $host && "$host" != $localhost ]]
	649	then
	650	do_batch=true
	651	do_remote=true
	652	case $host in
[2261]	653	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	654	(*) printf "\n"
[83]	655	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	656	printf "\n is not available"
[1]	657	locat=nqs; (( iec = 0 )); exit;;
	658	esac
	659	else
	660	host=$localhost
	661	fi
	662
	663
[1289]	664	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
[1]	665	if [[ -n $additional_conditions ]]
	666	then
[69]	667	cond1=`echo $additional_conditions \| cut -d" " -f1`
	668	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
	669	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
[1]	670	if [[ -n $dummy ]]
	671	then
	672	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
	673	locat=options; exit
	674	fi
[503]	675	block=_$cond1
	676	[[ -n $cond2 ]] && block=${block}_$cond2
[1]	677	fi
	678
	679
[1289]	680	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
[206]	681	if [[ $run_coupled_model = true ]]
	682	then
	683
[1289]	684	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	685	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	686
	687	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
[206]	688	then
	689
[1289]	690	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	691	printf "\n PEs (total) : $numprocs"
	692	printf "\n PEs (atmosphere): $numprocs_atmos"
	693	printf "\n PEs (ocean) : $numprocs_ocean"
	694	locat=coupling; exit
[206]	695
[1289]	696	fi
[206]	697
	698
	699	# GET coupled_mode FROM THE CONFIG FILE
	700	line=""
	701	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
	702	while read line
	703	do
[1779]	704	echo line=\"$line\"
	705	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
[206]	706	then
	707	coupled_mode="mpi2"
	708	fi
	709	done < tmp_mrun
	710
	711	fi
	712
[1289]	713	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
	714	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
[1099]	715	mrun_memory=$memory
	716	mrun_group_number=$group_number
	717	mrun_cpumax=$cpumax
	718	mrun_numprocs=$numprocs
[1]	719
[1099]	720
[1289]	721	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
[1468]	722	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
[1]	723	if [[ "$read_from_config" = false ]]
	724	then
	725	[[ $silent = false ]] && printf "\n Reading the configuration file... "
[1289]	726
	727	# READ THE CONFIGURATION FILE LINE BY LINE
[1]	728	while read zeile
	729	do
	730	[[ $silent = false ]] && printf "."
	731
	732
[1289]	733	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
[1]	734	eval zeile=\"$zeile\"
	735
	736
[1289]	737	# INTERPRET THE LINE
[21]	738	if [[ "$(echo $zeile)" = "" ]]
[1]	739	then
[1289]	740	# EMPTY LINE, NO ACTION
[21]	741	continue
[1]	742
[21]	743	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
	744	then
	745
[1289]	746	# LINE IS A COMMENT LINE
[1]	747	true
	748
	749	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
	750	then
	751
[1289]	752	# LINE DEFINES AN ENVIRONMENT-VARIABLE
[1]	753	zeile=$(echo $zeile \| cut -c2-)
[69]	754	var=`echo $zeile \| cut -d" " -f1`
	755	value=`echo $zeile \| cut -d" " -s -f2`
	756	for_host=`echo $zeile \| cut -d" " -s -f3`
	757	for_cond1=`echo $zeile \| cut -d" " -s -f4`
	758	for_cond2=`echo $zeile \| cut -d" " -s -f5`
[1]	759
	760	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
	761	then
	762
[1289]	763	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
	764	# "::" IS REPLACED BY ":".
[1]	765	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
	766
	767
[1289]	768	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	769	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	770	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	771	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	772	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	773	# CONFIGURATION-FILE.
[1]	774	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	775	then
	776	eval $var=\$value
	777
[1289]	778	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
[1]	779	if [[ $do_trace = true ]]
	780	then
	781	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	782	fi
	783	fi
	784
[1289]	785	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
	786	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
	787	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
	788	# MUST HAVE TO BE STARTED
[1]	789	if [[ $var = host ]]
	790	then
	791	if [[ -n $host && "$host" != $localhost ]]
	792	then
	793	do_batch=true
	794	do_remote=true
	795	case $host in
[2261]	796	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[83]	797	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	798	printf "\n is not available"
[1]	799	locat=nqs; exit;;
	800	esac
	801	else
	802	host=$localhost
	803	fi
	804	fi
	805
[1289]	806	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
	807	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
	808	# BY MRUN (E.G. subjob)
[1]	809	export $var
	810	fi
	811
	812
	813
	814
	815	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
	816	then
	817
[1289]	818	# LINE DEFINES ERROR-COMMAND
[1]	819	(( iec = iec + 1 ))
	820	zeile=$(echo $zeile \| cut -c4-)
	821	err_command[$iec]="$zeile"
	822
	823	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
	824	then
	825
[1289]	826	# LINE DEFINES INPUT-COMMAND
[1]	827	(( iic = iic + 1 ))
	828	zeile=$(echo $zeile \| cut -c4-)
	829	in_command[$iic]="$zeile"
	830
	831	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
	832	then
	833
[1289]	834	# LINE DEFINES OUTPUT-COMMAND
[1]	835	(( ioc = ioc + 1 ))
	836	zeile=$(echo $zeile \| cut -c4-)
	837	out_command[$ioc]="$zeile"
	838
	839	else
	840
[1289]	841	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	842	# s2a: in/out - field
	843	# s2b: loc - field (optional)
	844	# s2c: tr/ar - field (optional)
[69]	845	s1=`echo $zeile \| cut -d" " -f1`
	846	s2=`echo $zeile \| cut -d" " -s -f2`
[1]	847	s2a=$(echo $s2 \| cut -d":" -f1)
	848	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	849	then
	850	s2b=""
	851	s2c=""
	852	else
[69]	853	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	854	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
[1]	855	fi
[69]	856	s3=`echo $zeile \| cut -d" " -f3`
	857	s4=`echo $zeile \| cut -d" " -s -f4`
	858	s5=`echo $zeile \| cut -d" " -s -f5`
	859	s6=`echo $zeile \| cut -d" " -s -f6`
[1]	860
	861
[1289]	862	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	863	# INPUT- OR OUTPUT-LIST.
	864	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	865	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	866	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	867	# IS NOT CHECKED AND STORED.
[1]	868	IFSALT="$IFS"; IFS="$IFS:"
	869	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	870	then
	871	found=false
	872	for actual in $input_list
	873	do
	874	for formal in $s3
	875	do
	876	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	877	done
	878	done
	879	if [[ $found = true ]]
	880	then
	881	(( iin = iin + 1 ))
	882	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
	883	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
	884	extin[$iin]=$s6
	885	fi
	886	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
	887	then
	888	found=false
	889	for actual in $output_list
	890	do
	891	for formal in $s3
	892	do
	893	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	894	done
	895	done
	896	if [[ $found = true ]]
	897	then
	898	(( iout = iout + 1 ))
	899	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
	900	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
	901	fi
	902	elif [[ "$s2a" != in && "$s2a" != out ]]
	903	then
	904	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	905	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	906	locat=connect; exit
	907	fi
	908	IFS="$IFSALT"
	909	fi
	910	done < $config_file
	911
	912	else
	913
[1289]	914	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
[1]	915	[[ $silent = false ]] && printf "..."
[1289]	916	interpreted_config_file=.icf.$RANDOM
[1]	917
	918
[1917]	919
[1289]	920	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
[2261]	921	cat > .mrun_environment << EOF
[69]	922	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
	923	config_file = '$config_file', do_remote = '$do_remote',
	924	do_trace = '$do_trace', host = '$host',
	925	input_list = '$input_list', icf = '$interpreted_config_file',
	926	localhost = '$localhost', output_list = '$output_list' /
	927
[2261]	928	EOF
[69]	929
[1289]	930	if [[ "$host" != $localhost ]]
[66]	931	then
[503]	932
[1289]	933	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
	934	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
	935	if [[ $? != 0 ]]
[503]	936	then
[1289]	937	printf "\n\n +++ no interpret_config found"
	938	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
	939	locat=interpret_config; exit
	940	fi
	941	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
	942	$interpret_config_executable
[503]	943
[1289]	944	else
[503]	945
[1289]	946	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
	947	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
	948	then
	949	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
	950	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
	951	locat=interpret_config; exit
[503]	952	else
[1289]	953	interpret_config${block}.x
	954	fi
[503]	955
[66]	956	fi
[71]	957	rm .mrun_environment
[1]	958
[1917]	959
[1289]	960	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
[1]	961	chmod u+x $interpreted_config_file
	962	export PATH=$PATH:.
	963	. $interpreted_config_file
[71]	964	rm $interpreted_config_file
[1]	965
[1099]	966	fi
[71]	967
[1917]	968
[1289]	969	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[1099]	970	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
	971	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
	972	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
	973	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
	974	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	975	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
[1]	976
	977
[1289]	978	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
	979	# FOR SOURCE-FILES TO BE COMPILED.
	980	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
	981	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
[1]	982	if [[ "$SOURCES_COMPLETE" = "" ]]
	983	then
	984
[1289]	985	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
	986	# HAS BEEN DEFINED
[1]	987	source_path=""
	988	line=""
	989	grep "%source_path" $config_file > tmp_mrun
	990	while read line
	991	do
	992	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	993	then
	994	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
	995	then
	996	global_source_path=`echo $line \| cut -d" " -f2`
	997	fi
	998	fi
	999	done < tmp_mrun
	1000
	1001	line=""
	1002	found=false
	1003	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
	1004	while read line
	1005	do
	1006	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	1007	then
	1008	if [[ $found = true ]]
	1009	then
	1010	printf "\n\n +++ more than one source path found in configuration file"
	1011	printf "\n for local host \"$localhost\" "
	1012	locat=source_path; exit
	1013	fi
	1014	source_path=`echo $line \| cut -d" " -f2`
	1015	found=true
	1016	fi
	1017	done < tmp_mrun
	1018	rm tmp_mrun
	1019
	1020	if [[ "$source_path" = "" ]]
	1021	then
	1022	if [[ "$global_source_path" != "" ]]
	1023	then
	1024	source_path=$global_source_path
	1025	else
	1026	printf "\n\n +++ no source path found in configuration file"
	1027	printf "\n for local host \"$localhost\" "
	1028	locat=source_path; exit
	1029	fi
	1030	fi
	1031	eval source_path=$source_path
	1032
	1033	if [[ ! -d $source_path ]]
	1034	then
	1035	printf "\n\n +++ source path \"$source_path\" on local host"
	1036	printf "\n \"$localhost\" does not exist"
	1037	locat=source_path; exit
	1038	fi
	1039
	1040	fi
	1041
	1042
[1289]	1043	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1044	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1045	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
[78]	1046	then
	1047	global_revision=`svnversion $source_path 2>/dev/null`
	1048	global_revision="Rev: $global_revision"
	1049	fi
[1]	1050
[78]	1051
[1289]	1052	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
	1053	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
	1054	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
[1]	1055	if [[ -n $host && "$host" != $localhost ]]
	1056	then
	1057	do_batch=true
	1058	do_remote=true
	1059	case $host in
[2261]	1060	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
[1]	1061	(*) printf "\n"
[83]	1062	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
	1063	printf "\n is not available"
[1]	1064	locat=nqs; (( iec = 0 )); exit;;
	1065	esac
	1066	else
	1067	host=$localhost
	1068	fi
	1069
	1070
[1620]	1071
[1289]	1072	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
[1]	1073	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
	1074	then
	1075
[1289]	1076	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
[1]	1077	if [[ ! -n $numprocs ]]
	1078	then
	1079	printf "\n"
	1080	printf "\n +++ option \"-K parallel\" requires additional specification"
	1081	printf "\n of the number of processors to be used by"
	1082	printf "\n mrun-option \"-X\" or by environment-variable"
	1083	printf "\n \"numprocs\" in the configuration file"
	1084	locat=numprocs; (( iec = 0 )); exit
	1085	fi
	1086
[1289]	1087	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1088	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2257]	1089	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
[1]	1090	then
[759]	1091	printf "\n"
	1092	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1093	printf "\n set -T option or define tasks_per_node in the config file"
	1094	locat=tasks_per_node; (( iec = 0 )); exit
	1095	fi
[1279]	1096
	1097	if (( numprocs < tasks_per_node ))
	1098	then
	1099	printf "\n"
	1100	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
	1101	printf "\n given values: -T $tasks_per_node -X $numprocs"
	1102	locat=tasks_per_node; (( iec = 0 )); exit
	1103	fi
	1104
[2257]	1105	if [[ $host != lcxt5m ]]
[759]	1106	then
[1279]	1107	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
[848]	1108	(( ival = $tasks_per_node ))
	1109	(( pes = numprocs ))
	1110	(( ii = pes / ival ))
[1279]	1111	(( remaining_pes = pes - ii * ival ))
	1112	if (( remaining_pes > 0 ))
[848]	1113	then
	1114	printf "\n"
[1279]	1115	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
[848]	1116	printf "\n divisor of the total number of processors (option \"-X\")"
	1117	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
[1279]	1118	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
	1119	(( nodes = nodes + 1 ))
[848]	1120	fi
[1]	1121	fi
	1122
[759]	1123
[377]	1124	# SETTINGS FOR SUBJOB-COMMAND
[1]	1125	OOPT="-O $threads_per_task"
	1126
[1289]	1127	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
[1]	1128	if [[ "$tasks_per_node" != "" ]]
	1129	then
[1119]	1130	TOPT="-T $tasks_per_node"
[1]	1131	fi
	1132
[1289]	1133	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
[1]	1134	if [[ $node_usage = default ]]
	1135	then
	1136	if [[ $host = ibms ]]
	1137	then
	1138	node_usage=shared
	1139	else
	1140	node_usage=not_shared
	1141	fi
	1142	fi
[181]	1143
[635]	1144	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
[1]	1145	then
	1146	printf "\n"
	1147	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
	1148	printf "\n \"shared\" or \"not_shared\""
	1149	locat=tasks_per_node; (( iec = 0 )); exit
	1150	fi
	1151
	1152	fi
	1153
[1289]	1154	# CHECK IF HOSTFILE EXISTS
[1]	1155	if [[ -n $hostfile ]]
	1156	then
	1157	if [[ ! -f $hostfile ]]
	1158	then
	1159	printf "\n"
	1160	printf "\n +++ hostfile \"$hostfile\" does not exist"
	1161	locat=hostfile; exit
	1162	fi
	1163	fi
	1164
	1165
[1289]	1166	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
[759]	1167	if [[ "$maximum_parallel_io_streams" = "" ]]
	1168	then
	1169	maximum_parallel_io_streams=$numprocs
	1170	fi
[1]	1171
[759]	1172
[1289]	1173	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
[1094]	1174	if [[ "$scp_port" != "" ]]
	1175	then
	1176	PORTOPT="-P $scp_port"
	1177	SSH_PORTOPT="-p $scp_port"
	1178	fi
	1179
	1180
[1944]	1181	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1182	# CONFIG-FILE
	1183	if [[ "$ssh_key" != "" ]]
	1184	then
	1185	ssh_key="-i $HOME/.ssh/$ssh_key"
	1186	fi
	1187
	1188
[1289]	1189	# SET DEFAULT-QUEUE, IF NOT GIVEN
[1]	1190	if [[ $queue = none ]]
	1191	then
	1192	case $host in
[1184]	1193	(ibmh) queue=cluster;;
[693]	1194	(ibmkisti) queue=class.32plus;;
[1620]	1195	(lcbullhh) queue=compute;;
[1442]	1196	(lccrayb) queue=mpp1q;;
	1197	(lccrayh) queue=mpp1q;;
[1040]	1198	(lckiaps) queue=normal;;
[440]	1199	(lckyoto) queue=ph;;
[1099]	1200	(lckyuh) queue=fx-single;;
	1201	(lckyut) queue=cx-single;;
[635]	1202	(lctit) queue=S;;
[1]	1203	(unics) queue=unics;;
	1204	esac
	1205	fi
	1206
	1207
[1289]	1208	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1209	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
[1]	1210	(( i = 0 ))
	1211	while (( i < iin ))
	1212	do
	1213	(( i = i + 1 ))
	1214	(( maxcycle = 0 ))
	1215
[1289]	1216	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1217	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[1]	1218	if [[ "${actionin[$i]}" = di ]]
	1219	then
[1289]	1220	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1221	# HOST ONLY
[1]	1222	eval filename=${pathin[$i]}/${endin[$i]}
	1223	else
[1289]	1224	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
	1225	# HOST ONLY
[1]	1226	eval filename=${pathin[$i]}/${afname}${endin[$i]}
	1227	fi
[892]	1228	eval pathname=${pathin[$i]}
[1]	1229
[1289]	1230	# CHECK IF FILE EXISTS
[2141]	1231	if ! ls $filename* 1>/dev/null 2>&1
[1]	1232	then
[1289]	1233
	1234	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[1]	1235	if [[ "${transin[$i]}" != "locopt" ]]
	1236	then
	1237	printf "\n\n +++ INPUT-file: "
[2261]	1238	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
[1]	1239	then
	1240	printf "\n $filename"
	1241	else
	1242	printf "\n $filename.${extin[$i]}"
	1243	fi
	1244	printf "\n does not exist\n"
	1245	locat=input; exit
	1246	else
	1247	transin[$i]="unavailable"
	1248	fi
	1249	else
	1250
[1289]	1251	# DETERMINE THE FILE'S CYCLE NUMBER
[1]	1252	ls -1 -d $filename > filelist 2>/dev/null
	1253	ls -1 -d $filename.* >> filelist 2>/dev/null
	1254	while read zeile
	1255	do
[2261]	1256	# filename without path (i.e. after the last "/")
	1257	basefilename=$(basename ${zeile})
	1258
	1259	# check if there is an extension
	1260	extension=${basefilename##*.}
	1261	if [[ "$extension" = "$extin[$i]" ]]
	1262	then
	1263	basefilename=${basefilename&.*}
	1264	fi
	1265
	1266	# check for an existing cycle number
	1267	cycle=${basefilename##*.}
	1268	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1269	then
	1270	(( icycle = $cycle ))
	1271	else
	1272	(( icycle = 0 ))
	1273	fi
	1274
	1275	if (( icycle > maxcycle ))
	1276	then
	1277	(( maxcycle = icycle ))
	1278	fi
	1279
	1280	# cycle=$(echo $zeile \| cut -f2 -d".")
	1281	# if [[ "$cycle" = "$zeile" ]]
	1282	# then
	1283	# (( icycle = 0 ))
	1284	# elif [[ "$cycle" = "${extin[$i]}" ]]
	1285	# then
	1286	# (( icycle = 0 ))
	1287	# else
	1288	# (( icycle = $cycle ))
	1289	# fi
	1290	# if (( icycle > maxcycle ))
	1291	# then
	1292	# (( maxcycle = icycle ))
	1293	# fi
[1]	1294	done <filelist
	1295	rm filelist
	1296
[1289]	1297	# APPEND CYCLE NUMBER TO FILENAME
[1]	1298	if (( maxcycle > 0 ))
	1299	then
	1300	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1301	then
	1302	filename=${filename}.$maxcycle.${extin[$i]}
	1303	else
	1304	filename=${filename}.$maxcycle
	1305	fi
	1306	else
	1307	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
	1308	then
	1309	filename=${filename}.${extin[$i]}
	1310	fi
	1311	fi
	1312
[1289]	1313	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
[2261]	1314	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
[1]	1315	absnamein[$i]=$filename
	1316	if (( maxcycle > 0 ))
	1317	then
	1318	if [[ "${actionin[$i]}" = di ]]
	1319	then
	1320	frelin[$i]=${endin[$i]}.$maxcycle
	1321	else
	1322	frelin[$i]=${afname}${endin[$i]}.$maxcycle
	1323	fi
	1324	else
	1325	if [[ "${actionin[$i]}" = di ]]
	1326	then
	1327	frelin[$i]=${endin[$i]}
	1328	else
	1329	frelin[$i]=${afname}${endin[$i]}
	1330	fi
	1331	fi
	1332
	1333	fi
	1334	done
[920]	1335
[1289]	1336	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1337	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1338	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
	1339	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
	1340	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1341	# REMOTE HOST)
[1]	1342	(( i = 0 ))
	1343	while (( i < iout ))
	1344	do
	1345	(( i = i + 1 ))
	1346	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	1347	then
[260]	1348	if [[ "${actionout[$i]}" = tr ]]
[1]	1349	then
	1350	actionout[$i]=""
[260]	1351	elif [[ "${actionout[$i]}" = trpe ]]
	1352	then
	1353	actionout[$i]=pe
[1]	1354	elif [[ "${actionout[$i]}" = tra ]]
	1355	then
	1356	actionout[$i]=a
	1357	fi
	1358	(( maxcycle = 0 ))
	1359	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	1360	eval catalogname=${pathout[$i]}
[2141]	1361	if ! ls $filename* 1>/dev/null 2>&1
[1]	1362	then
	1363
[1289]	1364	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
[1]	1365	if cat /dev/null > $filename
	1366	then
	1367	rm $filename
	1368	else
	1369
[1289]	1370	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1371	# IF IT DOES NOT EXIST, TRY TO CREATE IT
[1]	1372	if [[ ! -d $catalogname ]]
	1373	then
	1374	if mkdir -p $catalogname
	1375	then
	1376	printf "\n\n *** directory:"
	1377	printf "\n $catalogname"
	1378	printf "\n was created\n"
[2261]	1379	echo "### filename = $filename"
[1]	1380	else
	1381	printf "\n\n +++ OUTPUT-file:"
	1382	printf "\n $filename"
	1383	printf "\n cannot be created, because directory does not exist"
	1384	printf "\n and cannot be created either"
	1385	printf "\n"
	1386	locat=output ; exit
	1387	fi 2>/dev/null
	1388	else
	1389	printf "\n\n +++ OUTPUT-file:"
	1390	printf "\n $filename"
	1391	printf "\n cannot be created, although directory exists"
	1392	printf "\n"
	1393	locat=output ; exit
	1394	fi
	1395	fi 2>/dev/null
	1396	else
	1397
[1289]	1398	# DETERMINE THE CYCLE NUMBER
[1]	1399	ls -1 -d $filename > filelist 2>/dev/null
	1400	ls -1 -d $filename.* >> filelist 2>/dev/null
	1401	while read zeile
	1402	do
[2261]	1403
	1404	# filename without path (i.e. after the last "/")
	1405	basefilename=$(basename ${zeile})
	1406
	1407	# check if there is an extension
	1408	extension=${basefilename##*.}
[2268]	1409	if [[ "$extension" = "${extout[$i]}" ]]
[1]	1410	then
[2268]	1411	basefilename=${basefilename%.*}
[2261]	1412	fi
	1413
	1414	# check for an existing cycle number
	1415	cycle=${basefilename##*.}
	1416	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1417	then
	1418	(( icycle = $cycle + 1 ))
	1419	else
[1]	1420	(( icycle = 1 ))
	1421	fi
[2261]	1422
[1]	1423	if (( icycle > maxcycle ))
	1424	then
	1425	(( maxcycle = icycle ))
	1426	fi
[2261]	1427
[1]	1428	done <filelist
	1429	rm filelist
	1430	fi
	1431
[1289]	1432	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
	1433	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
[1]	1434	if [[ "${actionout[$i]}" != a ]]
	1435	then
	1436	if (( maxcycle > 0 ))
	1437	then
[2261]	1438	filename_tmp=${filename}.$maxcycle
	1439	if cat /dev/null > $filename_tmp
[1]	1440	then
[2261]	1441	rm $filename_tmp
[1]	1442	else
	1443	printf "\n +++ OUTPUT-file:"
[2261]	1444	printf "\n $filename_tmp"
[1]	1445	printf "\n cannot be created"
	1446	locat=output ; exit
	1447	fi
	1448	fi
	1449	else
	1450	(( maxcycle = maxcycle - 1 ))
	1451	fi
	1452
[2261]	1453	(( cycnum[$i] = maxcycle ))
[2268]	1454	echo "### file \"$filename\" will get cycle ${cycnum[$i]}"
[1]	1455	pathout[$i]=$filename
	1456
	1457	fi
	1458	done
	1459
	1460
[1289]	1461	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
[83]	1462	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	1463	then
[260]	1464	if [[ "$dvr_inc" = "" ]]
[83]	1465	then
[260]	1466	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
[83]	1467	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1468	locat=dvr; exit
[83]	1469	fi
[260]	1470	if [[ "$dvr_lib" = "" ]]
[83]	1471	then
[260]	1472	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
[83]	1473	printf "\n This is required for the dvrp_graphics package.\n"
[260]	1474	locat=dvr; exit
[83]	1475	fi
	1476	fi
	1477
	1478
[1289]	1479	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
	1480	# EXECUTABLES DO NOT NEED TO BE COMPILED.
[1]	1481	if [[ "$mainprog" = "" && "$executable" = "" ]]
	1482	then
	1483	printf "\n +++ neither main program nor executable defined"
	1484	locat=source; exit
	1485	elif [[ "$mainprog" != "" && "$executable" != "" ]]
	1486	then
	1487	printf "\n +++ main program as well as executable defined"
	1488	locat=source; exit
	1489	elif [[ "$mainprog" = "" && "$executable" != "" ]]
	1490	then
	1491	do_compile=false
	1492	fi
	1493
	1494
[1289]	1495	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
	1496	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
[193]	1497	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
[191]	1498	then
	1499	rm -rf SOURCES_FOR_RUN_$fname
	1500	mkdir SOURCES_FOR_RUN_$fname
	1501	fi
	1502
	1503
[1289]	1504	# COLLECT ALL ROUTINES TO BE COMPILED
	1505	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
	1506	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
[1]	1507	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
	1508	then
	1509
[5]	1510	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
[1]	1511
[838]	1512	if [[ "$source_list" = LOCALLY_MODIFIED ]]
[1]	1513	then
	1514
[1289]	1515	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
[5]	1516	source_list=""
	1517	cd $source_path
	1518
	1519
[1289]	1520	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
[5]	1521	if [[ ! -d .svn ]]
	1522	then
	1523	printf "\n\n +++ source directory"
	1524	printf "\n \"$source_path\" "
	1525	printf "\n is not under control of \"subversion\"."
[306]	1526	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
[5]	1527	fi
	1528
	1529
[1289]	1530	# LIST ALL MODIFIED SOURCE CODE FILES
[5]	1531	Filenames=""
[69]	1532	svn status > tmp_mrun
	1533	while read line
[5]	1534	do
	1535	firstc=`echo $line \| cut -c1`
	1536	if [[ $firstc = M \|\| $firstc = "?" ]]
	1537	then
	1538	Name=`echo "$line" \| cut -c8-`
	1539	extension=`echo $Name \| cut -d. -f2`
	1540	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	1541	then
	1542	Filenames="$Filenames "$Name
	1543	fi
	1544	fi
[69]	1545	done < tmp_mrun
[5]	1546
	1547
[1289]	1548	# COPY FILES TO SOURCES_FOR_RUN_...
[5]	1549	for dateiname in $Filenames
	1550	do
	1551	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
	1552	source_list=$source_list"$dateiname "
	1553	done
	1554
	1555	cd - > /dev/null
	1556
	1557
[1289]	1558	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	1559	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
[5]	1560	elif [[ "$source_list" != "" && $restart_run != true ]]
[1]	1561	then
	1562
	1563	cd $source_path
	1564
	1565	for filename in $source_list
	1566	do
	1567
[1289]	1568	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
[1103]	1569	if [[ $(echo $filename \| grep -c "/") != 0 ]]
[1]	1570	then
	1571	printf "\n +++ source code file: $filename"
	1572	printf "\n must not contain (\"/\") "
	1573	locat=source; exit
	1574	fi
	1575
	1576	if [[ ! -f $filename ]]
	1577	then
	1578	printf "\n +++ source code file: $filename"
	1579	printf "\n does not exist"
	1580	locat=source; exit
	1581	else
	1582	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
	1583	fi
	1584
	1585	done
	1586
	1587	cd - > /dev/null
	1588
	1589	fi
	1590
	1591
[1289]	1592	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
	1593	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
[5]	1594	if [[ $restart_run != true ]]
[1]	1595	then
	1596
	1597	if [[ ! -f "$source_path/$mainprog" ]]
	1598	then
	1599	printf "\n\n +++ main program: $mainprog"
	1600	printf "\n does not exist in source directory"
	1601	printf "\n \"$source_path\"\n"
	1602	locat=source; exit
	1603	else
	1604	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
	1605	then
	1606	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
	1607	source_list=${mainprog}" $source_list"
	1608	fi
	1609	fi
	1610	fi
	1611
	1612
[1289]	1613	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	1614	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
[211]	1615	if [[ "$restart_run" != true ]]
	1616	then
	1617	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	1618	if [[ ! -f $makefile ]]
	1619	then
	1620	printf "\n +++ file \"$makefile\" does not exist"
	1621	locat=make; exit
	1622	else
	1623	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
	1624	fi
	1625	fi
	1626
	1627
[1289]	1628	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[5]	1629	if [[ $restart_run != true && "$add_source_path" != "" ]]
[1]	1630	then
	1631
[1289]	1632	# DOES THE DIRECTORY EXIST?
[1]	1633	if [[ ! -d $add_source_path ]]
	1634	then
[1779]	1635	printf "\n\n *** INFORMATIVE: additional source code directory"
[1]	1636	printf "\n \"$add_source_path\" "
	1637	printf "\n does not exist or is not a directory."
	1638	printf "\n No source code will be used from this directory!\n"
	1639	add_source_path=""
[931]	1640	if [[ $silent == false ]]
	1641	then
	1642	sleep 3
	1643	fi
[1]	1644	else
	1645
	1646	cd $add_source_path
[211]	1647	found=false
[1]	1648
	1649	Names=$(ls -1 *.f90 2>&1)
	1650	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1651	Names=$(ls -1 *.F90 2>&1)
	1652	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1653	Names=$(ls -1 *.F 2>&1)
	1654	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1655	Names=$(ls -1 *.f 2>&1)
	1656	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1657	Names=$(ls -1 *.c 2>&1)
	1658	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1659
	1660	cd - > /dev/null
	1661	cd SOURCES_FOR_RUN_$fname
	1662
[211]	1663	# COPY MAKEFILE IF EXISTING
	1664	if [[ -f $add_source_path/Makefile ]]
	1665	then
	1666	printf "\n\n *** user Makefile from directory"
	1667	printf "\n \"$add_source_path\" is used \n"
[931]	1668	if [[ $silent == false ]]
	1669	then
	1670	sleep 1
	1671	fi
[211]	1672	cp $add_source_path/Makefile .
	1673	fi
	1674
[1]	1675	for dateiname in $AddFilenames
	1676	do
	1677	if [[ -f $dateiname ]]
	1678	then
	1679	printf "\n +++ source code file \"$dateiname\" found in additional"
	1680	printf "\n source code directory \"$add_source_path\" "
[211]	1681	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1682	printf "\n from directory \"$source_path\"."
[1]	1683	locat=source; exit
	1684	fi
	1685
	1686	cp $add_source_path/$dateiname .
	1687	source_list="$source_list $dateiname"
	1688
[211]	1689	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1690	if [[ $(grep -c $dateiname Makefile) = 0 ]]
	1691	then
	1692	printf "\n\n +++ user file \"$dateiname\" "
	1693	printf "\n is not listed in Makefile \n"
	1694	locat=source; exit
	1695	else
	1696
	1697	if [[ $found = false ]]
[1]	1698	then
[211]	1699	found=true
	1700	printf "\n\n *** following user file(s) added to the"
	1701	printf " files to be translated:\n "
[1]	1702	fi
[211]	1703	printf "$dateiname "
[931]	1704	if [[ $silent == false ]]
	1705	then
	1706	sleep 0.5
	1707	fi
	1708
[1]	1709	fi
	1710	done
[211]	1711	[[ $found = true ]] && printf "\n"
[1]	1712	cd - > /dev/null
	1713	fi
	1714	fi
	1715
	1716
[1289]	1717	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
	1718	# TO THE LIST OF FILES TO BE COMPILED
[5]	1719	if [[ $restart_run != true && -n $package_list ]]
[1]	1720	then
	1721
	1722	cd $source_path
	1723
	1724	for package in $package_list
	1725	do
	1726
	1727	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
	1728
[1289]	1729	# DETERMINE FILES BELONGING TO THE PACKAGE
	1730	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
	1731	# THE NAME OF THE DIRECTORY
[1]	1732	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
	1733
	1734
[1289]	1735	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
	1736	# IF THEY ARE NOT ALREADY PART OF THE LIST
[1]	1737	for source_list_name in $package_source_list
	1738	do
	1739	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
	1740	then
	1741
[1289]	1742	# ONLY TAKE FILES WITH VALID SUFFIX
[1]	1743	ending=`echo $source_list_name \| cut -f2 -d.`
	1744	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
	1745	then
	1746	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
	1747	source_list="$source_list $source_list_name"
	1748	fi
	1749	fi
	1750	done
	1751	done
	1752
	1753	cd - > /dev/null
	1754	fi
	1755
	1756	fi # do_compile=true
	1757
	1758
[1289]	1759	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
	1760	# AND SET PRE-PROCESSOR DIRECTIVES
[1199]	1761	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1762	then
	1763
[1289]	1764	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
[1]	1765	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1766	then
[82]	1767	cpp_options="${cpp_options},-D__ibm=__ibm"
[1]	1768	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
	1769	then
[82]	1770	cpp_options="$cpp_options -D__nec"
	1771	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
	1772	then
	1773	cpp_options="$cpp_options -D__lc"
[1]	1774	else
[82]	1775	cpp_options="$cpp_options -D__$localhost"
[1]	1776	fi
[83]	1777
[1289]	1778	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
[1]	1779	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1780	then
[82]	1781	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
	1782	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
[1]	1783	else
[82]	1784	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
	1785	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
[1]	1786	fi
[83]	1787
[1289]	1788	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
[1]	1789	if [[ -n $package_list ]]
	1790	then
	1791	for package in $package_list
	1792	do
	1793	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1794	then
	1795	if [[ $package != "dvrp_graphics+1PE" ]]
	1796	then
[82]	1797	cpp_options="${cpp_options},-D__$package=__$package"
[1]	1798	else
[82]	1799	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
[1]	1800	export use_seperate_pe_for_dvrp_output=true
	1801	fi
	1802	else
	1803	if [[ $package != "dvrp_graphics+1PE" ]]
	1804	then
[82]	1805	cpp_options="$cpp_options -D__$package"
[1]	1806	else
[82]	1807	cpp_options="$cpp_options -D__dvrp_graphics"
[1]	1808	export use_seperate_pe_for_dvrp_output=true
	1809	fi
	1810	fi
	1811	done
	1812	fi
[83]	1813
[1289]	1814	# SET DIRECTIVES GIVEN BY OPTION -D
[1]	1815	if [[ -n $cpp_opts ]]
	1816	then
	1817	for popts in $cpp_opts
	1818	do
[82]	1819	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
	1820	then
	1821	cpp_options="${cpp_options},-D__$popts=__$popts"
	1822	else
	1823	cpp_options="$cpp_options -D__$popts"
	1824	fi
[1]	1825	done
	1826	fi
	1827
	1828	else
	1829
	1830
[1289]	1831	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
[1]	1832	if [[ $do_remote = false ]]
	1833	then
	1834	if [[ ! -f $executable ]]
	1835	then
	1836	printf "\n +++ executable file: $executable"
	1837	printf "\n does not exist"
	1838	locat=executable; exit
	1839	fi
	1840	fi
	1841	fi
	1842
	1843
[1289]	1844	# DETERMINE THE JOB MODE
[1491]	1845	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
[1]	1846	then
[1491]	1847	if [[ "$LOADLBATCH" = yes ]]
	1848	then
	1849	batch_job=.TRUE.
	1850	jobmo=BATCH
	1851	else
	1852	batch_job=.FALSE.
	1853	jobmo=INTERACTIVE
	1854	fi
[1]	1855	else
[2185]	1856	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
[1491]	1857	then
	1858	batch_job=.TRUE.
	1859	jobmo=BATCH
	1860	else
	1861	batch_job=.FALSE.
	1862	jobmo=INTERACTIVE
	1863	fi
[1]	1864	fi
	1865
[1289]	1866	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
[635]	1867	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
	1868	then
	1869	printf "\n +++ no interactive runs allowed on host \"$host\" "
	1870	printf "\n please submit batch job using mrun option \"-b\" \n"
	1871	locat=normal; exit
	1872	fi
	1873
	1874
[1289]	1875	# CHECK, IF USER DEFINED A COMPILER
[1]	1876	if [[ "$compiler_name" = "" ]]
	1877	then
[82]	1878
[220]	1879	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
[82]	1880	locat=compiler_name; exit
	1881
[1]	1882	fi
	1883
	1884
[1289]	1885	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
[1609]	1886
	1887	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
	1888	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
	1889	then
	1890	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
[1755]	1891	if [[ "$kennung" = "" ]]
[1753]	1892	then
	1893	kennung=$RANDOM
	1894	fi
[1609]	1895	else
	1896	kennung=$RANDOM
	1897	fi
	1898
[1]	1899	if [[ "$tmp_user_catalog" = "" ]]
	1900	then
[312]	1901	if [[ $localhost = ibmh ]]
[1]	1902	then
[312]	1903	tmp_user_catalog=$SCRATCH
[1]	1904	else
	1905	tmp_user_catalog=/tmp
	1906	fi
	1907	fi
	1908	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
	1909
	1910
[1289]	1911	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
[1]	1912	if [[ "$tmp_data_catalog" = "" ]]
	1913	then
[2261]	1914	tmp_data_catalog=/tmp/mrun_restart_data
[1]	1915	fi
	1916
	1917
[1289]	1918	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
[1199]	1919	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
[1]	1920	then
	1921	eval fopts=\"$fopts\"
	1922	eval lopts=\"$lopts\"
	1923	fi
	1924
	1925
[1289]	1926	# DETERMINE COMPILE- AND LINK-OPTIONS
[1210]	1927	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
	1928	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
[1779]	1929	XOPT="-X $numprocs"
[1]	1930
	1931
[1289]	1932	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
	1933	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
[1]	1934	done=false
	1935	while [[ $done = false ]]
	1936	do
	1937	cputime=$cpumax
	1938	if (( $cputime == 0 ))
	1939	then
[246]	1940	if [[ $do_batch = true ]]
	1941	then
	1942	printf "\n +++ cpu-time is undefined"
	1943	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1944	printf "\n >>> "
	1945	read cputime 1>/dev/null 2>&1
	1946	else
	1947	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
	1948	fi
[1]	1949	else
	1950	done=true
	1951	fi
	1952	cpumax=$cputime
	1953	done
	1954
	1955	(( minuten = cputime / 60 ))
	1956	(( sekunden = cputime - minuten * 60 ))
	1957
	1958
[1289]	1959	# CHECK THE MEMORY DEMAND
[1]	1960	if [[ $do_batch = true ]]
	1961	then
	1962	done=false
	1963	while [[ $done = false ]]
	1964	do
	1965	if (( memory == 0 ))
	1966	then
	1967	printf "\n +++ memory demand is undefined"
	1968	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1969	printf "\n >>> "
	1970	read memory 1>/dev/null 2>&1
	1971	else
	1972	done=true
	1973	fi
	1974	done
	1975	fi
	1976
	1977
[1289]	1978	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
[1]	1979	if [[ $do_remote = true && -z $remote_username ]]
	1980	then
	1981	while [[ -z $remote_username ]]
	1982	do
	1983	printf "\n +++ username on remote host \"$host\" is undefined"
	1984	printf "\n >>> Please type username:"
	1985	printf "\n >>> "
	1986	read remote_username
	1987	done
	1988	mc="$mc -u$remote_username"
	1989	fi
	1990
[892]	1991	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
	1992	if [[ "$login_init_cmd" != "" ]]
	1993	then
	1994	export init_cmds="${login_init_cmd};"
	1995	fi
[221]	1996
[892]	1997
[1289]	1998	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
[493]	1999	if [[ "$modules" != "" ]]
	2000	then
[678]	2001	if [[ $host = lctit ]]
	2002	then
	2003	export module_calls=". $modules"
	2004	else
	2005	export module_calls="module load ${modules};"
	2006	fi
[493]	2007	fi
	2008
[1289]	2009	# OUTPUT OF THE MRUN-HEADER
[1]	2010	calltime=$(date)
	2011	printf "\n"
[1101]	2012	printf "#------------------------------------------------------------------------# \n"
	2013	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	2014	printf "\| \| \n"
[1]	2015	spalte1="called on:"; spalte2=$localhost_realname
[1101]	2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1289]	2017	if [[ $do_remote = true ]]
[1]	2018	then
[1289]	2019	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
[1]	2020	else
[1289]	2021	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
[1]	2022	fi
[1101]	2023	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2024	if [[ -n $numprocs ]]
	2025	then
[1106]	2026	if [[ $run_coupled_model = false ]]
	2027	then
	2028	spalte1="number of PEs:"; spalte2=$numprocs
	2029	else
	2030	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
	2031	fi
[1101]	2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2033	fi
	2034	if [[ -n $tasks_per_node ]]
	2035	then
	2036	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
[1101]	2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1279]	2038	if (( remaining_pes > 0 ))
	2039	then
	2040	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
	2041	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2042	fi
[1]	2043	fi
[759]	2044	if [[ $maximum_parallel_io_streams != $numprocs ]]
	2045	then
	2046	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
[1101]	2047	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[759]	2048	fi
[622]	2049	if [[ $use_openmp = true ]]
[1]	2050	then
	2051	spalte1="threads per task:"; spalte2="$threads_per_task"
[1101]	2052	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2053	fi
[1101]	2054	printf "\| \| \n"
[1]	2055	if [[ $do_compile = true ]]
	2056	then
[475]	2057	if [[ "$mopts" != "" ]]
	2058	then
[1101]	2059	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
	2060	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2061	zeile=$(echo "$mopts" \| cut -c46-)
[475]	2062	while [[ "$zeile" != "" ]]
	2063	do
	2064	spalte1=""
[1101]	2065	spalte2=$(echo "$zeile" \| cut -c-45)
	2066	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2067	zeile=$(echo "$zeile" \| cut -c46-)
[475]	2068	done
	2069	fi
	2070
[1101]	2071	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
	2072	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2073	zeile=$(echo "$cpp_options" \| cut -c46-)
[1]	2074	while [[ "$zeile" != "" ]]
	2075	do
	2076	spalte1=""
[1101]	2077	spalte2=$(echo "$zeile" \| cut -c-45)
	2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2079	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2080	done
	2081
[1101]	2082	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
	2083	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2084	zeile=$(echo "$fopts" \| cut -c46-)
[1]	2085	while [[ "$zeile" != "" ]]
	2086	do
	2087	spalte1=""
[1101]	2088	spalte2=$(echo "$zeile" \| cut -c-45)
	2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2090	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2091	done
	2092
[1101]	2093	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
	2094	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2095	zeile=$(echo "$lopts" \| cut -c46-)
[1]	2096	while [[ "$zeile" != "" ]]
	2097	do
	2098	spalte1=""
[1101]	2099	spalte2=$(echo "$zeile" \| cut -c-45)
	2100	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2101	zeile=$(echo "$zeile" \| cut -c46-)
[1]	2102	done
	2103
[1101]	2104	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
	2105	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2106	zeile=$(echo "$modules" \| cut -c46-)
[493]	2107	while [[ "$zeile" != "" ]]
	2108	do
	2109	spalte1=""
[1101]	2110	spalte2=$(echo "$zeile" \| cut -c-45)
	2111	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2112	zeile=$(echo "$zeile" \| cut -c46-)
[493]	2113	done
	2114
[1101]	2115	spalte1="main program:"; spalte2=$mainprog
	2116	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2117	else
	2118	spalte1=executable:; spalte2=$executable
[1101]	2119	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2120	fi
[1101]	2121	printf "\| \| \n"
	2122	spalte1="base name of files:"; spalte2=$fname
	2123	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2124	if [[ $fname != $afname ]]
	2125	then
[1101]	2126	spalte1="base name of input files:"; spalte2=$afname
	2127	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2128	fi
[1101]	2129	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
	2130	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
	2131	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
	2132	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2133
[1106]	2134	if [[ "$ocean_file_appendix" = true ]]
	2135	then
	2136	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	2137	fi
	2138
[1]	2139	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
	2140	then
	2141	spalte1="memory demand / PE":; spalte2="$memory MB"
[1101]	2142	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2143	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
[1101]	2144	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
[1]	2145	fi
	2146
	2147	if [[ $do_compile = true ]]
	2148	then
[1101]	2149	printf "\| \| \n"
	2150	printf "\| Files to be compiled: \| \n"
[1]	2151	zeile=$source_list
	2152	while [[ "$zeile" != "" ]]
	2153	do
[1101]	2154	linestart=$(echo $zeile \| cut -c-70)
	2155	printf "\| %-70s \| \n" "$linestart"
	2156	zeile=$(echo "$zeile" \| cut -c71-)
[1]	2157	done
	2158	fi
[1101]	2159	printf "#------------------------------------------------------------------------#"
[1]	2160
	2161
	2162
[1289]	2163	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
[1]	2164	if [[ $do_trace = true ]]
	2165	then
	2166	(( i = 0 ))
	2167	while (( i < iin ))
	2168	do
	2169	(( i = i + 1 ))
	2170	if (( i == 1 ))
	2171	then
	2172	printf "\n\n >>> INPUT-file assignments:\n"
	2173	fi
	2174	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	2175	done
	2176	(( i = 0 ))
	2177	while (( i < iout ))
	2178	do
	2179	(( i = i + 1 ))
	2180	if (( i == 1 ))
	2181	then
	2182	printf "\n\n >>> OUTPUT-file assignments:\n"
	2183	fi
	2184	printf "\n ${localout[$i]} : ${pathout[$i]}"
	2185	done
	2186	(( i = 0 ))
	2187	while (( i < iic ))
	2188	do
	2189	(( i = i + 1 ))
	2190	if (( i == 1 ))
	2191	then
	2192	printf "\n\n >>> INPUT-commands:\n"
	2193	fi
	2194	printf "\n ${in_command[$i]}"
	2195	done
	2196	(( i = 0 ))
	2197	while (( i < ioc ))
	2198	do
	2199	(( i = i + 1 ))
	2200	if (( i == 1 ))
	2201	then
	2202	printf "\n\n >>> OUTPUT-commands:\n"
	2203	fi
	2204	printf "\n ${out_command[$i]}"
	2205	done
	2206	fi
	2207
[1289]	2208	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
[1]	2209	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
	2210	then
	2211	antwort=dummy
	2212	printf "\n\n"
[1101]	2213	printf " >>> everything o.k. (y/n) ? "
	2214	while read antwort
[1]	2215	do
[1101]	2216	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	2217	then
	2218	printf " >>> everything o.k. (y/n) ? "
	2219	else
	2220	break
	2221	fi
[1]	2222	done
	2223	if [[ $antwort = n \|\| $antwort = N ]]
	2224	then
	2225	locat=user_abort; (( iec = 0 )); exit
	2226	fi
	2227	if [[ $do_batch = true ]]
	2228	then
	2229	printf " >>> batch-job will be created and submitted"
	2230	else
[1289]	2231	printf " >>> MRUN will now continue to execute on this machine"
[1]	2232	fi
	2233	fi
	2234
[1804]	2235
[1199]	2236	# DETERMINE PATH FOR MAKE DEPOSITORY
	2237	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
	2238	then
	2239
	2240	line=""
	2241	grep "%depository_path" $config_file > tmp_mrun
	2242	while read line
	2243	do
	2244	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2245	then
	2246	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
	2247	then
	2248	global_depository_path=`echo $line \| cut -d" " -s -f2`
	2249	fi
	2250	fi
	2251	done < tmp_mrun
	2252
	2253	line=""
	2254	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
	2255	while read line
	2256	do
	2257	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
	2258	then
	2259	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
	2260	then
	2261	local_depository_path=`echo $line \| cut -d" " -s -f2`
	2262	fi
	2263	fi
	2264	done < tmp_mrun
	2265
	2266	if [[ "$local_depository_path" = "" ]]
	2267	then
	2268	if [[ "$global_depository_path" != "" ]]
	2269	then
	2270	local_depository_path=$global_depository_path
	2271	else
	2272	printf "\n\n +++ no depository path found in configuration file"
	2273	printf "\n for local host \"$localhost\" "
	2274	printf "\n please set \"\%depository_path\" in configuration file\n"
	2275	locat=config_file; exit
	2276	fi
	2277	fi
	2278	eval local_depository_path=$local_depository_path
	2279	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
	2280	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
	2281
	2282
	2283	basename=`echo $mainprog \| cut -f1 -d"."`
	2284	eval make_depository=${local_depository_path}/${basename}_current_version.tar
	2285	if [[ ! -f $make_depository ]]
	2286	then
	2287	printf "\n"
	2288	printf "\n *** WARNING: make depository \"$make_depository\" not found"
	2289	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
	2290	fi
	2291
	2292	fi
	2293
	2294
[1289]	2295	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	2296	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
[1]	2297	if [[ $do_batch = false ]]
	2298	then
	2299
	2300
[1289]	2301	# CREATE THE TEMPORARY WORKING DIRECTORY
[1]	2302	mkdir -p $TEMPDIR
	2303	chmod go+rx $TEMPDIR
	2304	tmpcreate=true
	2305
	2306
[1289]	2307	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
	2308	# INTO THE TEMPORARY WORKING DIRECTORY
[1]	2309	if [[ $do_compile = true ]]
	2310	then
	2311
[2261]	2312	TEMPDIR_COMPILE=$TEMPDIR
[1]	2313
[1199]	2314	cp $make_depository $TEMPDIR_COMPILE
	2315	cd $TEMPDIR_COMPILE
	2316	tar -xf $make_depository > /dev/null 2>&1
	2317	cd - > /dev/null
[1]	2318
[1255]	2319	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	2320	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
[1281]	2321	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	2322	then
	2323	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2324	else
	2325	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
	2326	fi
[82]	2327
[1]	2328	else
[475]	2329
[1]	2330	cp $executable ${TEMPDIR}/a.out
[475]	2331
[1]	2332	fi
	2333
	2334
[1289]	2335	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
[475]	2336	cd $TEMPDIR
[1]	2337	printf "\n *** changed to temporary directory: $TEMPDIR"
	2338
	2339
[1289]	2340	# IF REQUIRED, START WITH COMPILING
[1]	2341	if [[ $do_compile = true ]]
	2342	then
	2343
	2344
[1199]	2345	if [[ -f a.out ]]
[475]	2346	then
[82]	2347
[1199]	2348	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
	2349	printf "\n\n\n *** executable a.out found"
	2350	printf "\n no compilation required \n"
	2351
[1]	2352	else
[807]	2353
[1199]	2354	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
[1289]	2355	printf "\n\n\n *** compilation starts \n$dashes\n"
[1199]	2356	printf " *** compilation with make using following options:\n"
	2357	printf " make depository: $make_depository"
	2358	if [[ "$mopts" != "" ]]
	2359	then
	2360	printf " make options: $mopts\n"
	2361	fi
	2362	printf " compilername: $compiler_name\n"
	2363	printf " compiler options: $fopts\n"
	2364	printf " preprocessor directives: $cpp_options \n"
	2365	printf " linker options: $lopts \n"
	2366	if [[ "$modules" != "" ]]
	2367	then
	2368	printf " modules to be load: $modules \n"
	2369	fi
	2370	printf " source code files: $source_list \n"
[1]	2371
[2261]	2372	if [[ $localhost = ibmh ]]
[1199]	2373	then
	2374	printf " compiler is called via ssh on \"plogin1\" \n"
	2375	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\" "
	2376	[[ ! -f a.out ]] && compile_error=true
[1289]	2377	continue # STATUS=1, IF a.out EXISTS
[1866]	2378	elif [[ $localhost = lcocean ]]
	2379	then
	2380	printf " compiler is called via ssh on \"ocean\" \n"
	2381	echo $PWD
	2382	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\" "
	2383	[[ ! -f a.out ]] && compile_error=true
	2384	continue # STATUS=1, IF a.out EXISTS
[1620]	2385	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
[1199]	2386	then
	2387	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[2257]	2388	elif [[ $localhost = lceddy ]]
	2389	then
	2390	which mpifc
	2391	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
[1199]	2392	else
	2393	[[ "$init_cmds" != "" ]] && eval $init_cmds
	2394	[[ "$module_calls" != "" ]] && eval $module_calls
	2395	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	2396	fi
[181]	2397
[1199]	2398	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	2399	then
	2400	printf "\n +++ error occured while compiling or linking"
	2401	locat=compile
	2402
[181]	2403	exit
[1199]	2404	else
[1289]	2405	printf "$dashes\n *** compilation finished \n"
[1199]	2406	fi
	2407
[1]	2408	fi
[1199]	2409
[1]	2410	fi
	2411
	2412
[1289]	2413	# PROVIDE THE INPUT FILES
	2414	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[1]	2415	(( i = 0 ))
	2416	while (( i < iin ))
	2417	do
	2418	(( i = i + 1 ))
	2419	if (( i == 1 ))
	2420	then
[1289]	2421	printf "\n\n *** providing INPUT-files:\n$dashes"
[1]	2422	fi
	2423
	2424
[1289]	2425	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[1]	2426	if [[ "${transin[$i]}" = unavailable ]]
	2427	then
	2428	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	2429	then
[1779]	2430	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
	2431	printf "\n is not available!"
[1]	2432	else
[1779]	2433	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
	2434	printf "\n is not available!"
[1]	2435	fi
	2436	continue
	2437	fi
	2438
[1289]	2439	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	2440	files_for_pes=false; datentyp=file
	2441	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
	2442	then
[2261]	2443	files_for_pes=true; datentyp=files
[1]	2444	actionin[$i]=""
	2445	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
	2446	then
	2447	actionin[$i]=""
[2261]	2448	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
[1]	2449	then
[2261]	2450	files_for_pes=true; datentyp=files
	2451	actionin[$i]="ln"
	2452	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
[1]	2453	then
[2261]	2454	actionin[$i]="ln"
[1]	2455	fi
	2456
	2457	if [[ $files_for_pes = true ]]
	2458	then
	2459	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2460	else
	2461	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2462	fi
	2463
[2261]	2464	# INPUT-FILES TO BE LINKED
	2465	if [[ "${actionin[$i]}" = ln ]]
[1]	2466	then
[2261]	2467
	2468	printf "\n $datentyp will be linked"
[1]	2469	if [[ $files_for_pes = false ]]
	2470	then
[2261]	2471	if [[ -f "${absnamein[$i]}" ]]
[1]	2472	then
[2261]	2473	ln ${absnamein[$i]} ${localin[$i]}
[1]	2474	got_tmp[$i]=true
	2475	fi
	2476	else
[2261]	2477	if [[ -d "${absnamein[$i]}" ]]
[1]	2478	then
	2479	mkdir ${localin[$i]}
[2261]	2480	cd ${absnamein[$i]}
[149]	2481	for file in $(ls *)
	2482	do
	2483	ln $file $TEMPDIR/${localin[$i]}
[2261]	2484	done >\|/dev/null 2>&1
[149]	2485	cd $TEMPDIR
[1]	2486	fi
	2487
[2261]	2488	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2489	if [[ ! -f "${localin[$i]}/_000000" ]]
[1]	2490	then
[2261]	2491	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2492	cp -r ${absnamein[$i]}/* ${localin[$i]}
[1]	2493	fi
	2494
	2495	got_tmp[$i]=true
	2496	fi
	2497	fi
	2498
[1289]	2499	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[1]	2500	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	2501	then
	2502
	2503	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
	2504	then
	2505
[1289]	2506	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2507	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
[1]	2508	printf "\n file will be provided for $numprocs processors"
	2509	mkdir ${localin[$i]}
	2510	ival=$numprocs
	2511	(( ii = 0 ))
	2512	while (( ii <= ival-1 ))
	2513	do
	2514	if (( ii < 10 ))
	2515	then
	2516	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2517	elif (( ii < 100 ))
	2518	then
	2519	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2520	elif (( ii < 1000 ))
	2521	then
	2522	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2523	else
	2524	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2525	fi
	2526	(( ii = ii + 1 ))
	2527	done
	2528
	2529	else
	2530
	2531	if [[ $files_for_pes = true ]]
	2532	then
	2533
[1289]	2534	# PROVIDE FILES FOR EACH CORE
	2535	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2536	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
[1]	2537	printf "\n providing $numprocs files for the respective processors"
	2538	mkdir ${localin[$i]}
[2261]	2539	if [[ $link_local_input = true ]]
	2540	then
	2541	printf " files will be linked\n"
	2542	cd ${absnamein[$i]}
	2543	for file in $(ls *)
	2544	do
	2545	ln -f $file ${localin[$i]}
	2546	done
	2547	cd $TEMPDIR
	2548	fi
[1289]	2549
	2550	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
[2261]	2551	if [[ ! -f "${localin[$i]}/_000000" ]]
	2552	then
	2553	if [[ $link_local_input = true ]]
	2554	then
	2555	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2556	fi
	2557	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2558	fi
[1]	2559
	2560	else
[1289]	2561
	2562	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
[2261]	2563	if [[ $link_local_input = true ]]
	2564	then
	2565	printf " file will be linked\n"
	2566	ln -f ${absnamein[$i]} ${localin[$i]}
	2567	fi
	2568	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
	2569	if [[ ! -f "${localin[$i]}" ]]
[183]	2570	then
[2261]	2571	if [[ $link_local_input = true ]]
	2572	then
	2573	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2574	fi
	2575	cp ${absnamein[$i]} ${localin[$i]}
[183]	2576	fi
[1]	2577	fi
	2578	fi
	2579	fi
	2580
	2581	done
	2582	if (( i != 0 ))
	2583	then
[1289]	2584	printf "\n$dashes\n *** all INPUT-files provided \n"
[1]	2585	fi
	2586
	2587
[1289]	2588	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	2589	(( i = 0 ))
	2590	while (( i < iic ))
	2591	do
	2592	(( i = i + 1 ))
	2593	if (( i == 1 ))
	2594	then
[1289]	2595	printf "\n\n *** execution of INPUT-commands:\n$dashes"
[1]	2596	fi
	2597	printf "\n >>> ${in_command[$i]}"
	2598	eval ${in_command[$i]}
	2599	if (( i == iic ))
	2600	then
[1289]	2601	printf "\n$dashes\n"
[1]	2602	fi
	2603	done
	2604
	2605
[1289]	2606	# SET THE REMAINING CPU-TIME
[1]	2607	cpurest=${cpumax}.
	2608
	2609
[260]	2610	# START DVR STREAMING SERVER
	2611	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	2612	then
	2613	if [[ "$dvr_server" != "" ]]
	2614	then
	2615
	2616	printf "\n\n *** preparing the dvr streaming server configuration file"
	2617
[1289]	2618	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
[260]	2619	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
	2620	if [[ "$running_dvrserver_id" != "" ]]
	2621	then
	2622
[261]	2623	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
[260]	2624	printf "\n This server is used instead starting a new one!"
[261]	2625	printf "\n If required, script \"process_dvr_output\" has to be run manually."
[260]	2626
	2627	else
	2628
	2629	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
	2630	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
	2631	then
	2632	cp ${PALM_BIN}/.dvrserver.config .
	2633
[1289]	2634	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
[260]	2635	user_id=`id -u`
	2636	group_id=`id -g`
[1289]	2637
	2638	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
[260]	2639	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
	2640	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
	2641	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
	2642	mv .dvrserver.3 .dvrserver.config
	2643	rm .dvrserver.1 .dvrserver.2
	2644
[1289]	2645	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
[260]	2646	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
	2647	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
	2648	printf "\n *** streaming server with id=$dvrserver_id is started in background"
	2649	local_dvrserver_running=.TRUE.
	2650	else
	2651	printf "\n +++ missing file \".dvrserver.config\" in directory:"
	2652	printf "\n \"$PALM_BIN\" "
	2653	locat=dvr
	2654	exit
	2655	fi
	2656
	2657	fi
	2658
	2659	else
	2660	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
	2661	fi
	2662	fi
	2663
	2664
[1289]	2665	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2666	# (FILE ENVPAR WILL BE READ BY PALM)
[2261]	2667	cat > ENVPAR << EOF
[260]	2668	&envpar run_identifier = '$fname', host = '$localhost',
	2669	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
[759]	2670	maximum_parallel_io_streams = $maximum_parallel_io_streams,
[260]	2671	maximum_cpu_time_allowed = ${cpumax}.,
	2672	revision = '$global_revision',
[1402]	2673	local_dvrserver_running = $local_dvrserver_running,
	2674	batch_job = $batch_job /
[260]	2675
[2261]	2676	EOF
[260]	2677
	2678
[1289]	2679	# STARTING THE EXECUTABLE
	2680	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[1]	2681	PATH=$PATH:$TEMPDIR
	2682
[1779]	2683
	2684	if [[ $execute_command != "none" ]]
[359]	2685	then
	2686
[1779]	2687	printf "\n +++ branch still not realized"
	2688	locat=execution
	2689	exit
	2690
[693]	2691	else
	2692
[1779]	2693	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
	2694	if [[ "$mpi_debug" = true ]]
[1549]	2695	then
[1779]	2696	export MPI_CHECK_ARGS=1
	2697	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
[1549]	2698	fi
	2699
[1779]	2700	if [[ "$totalview" = true ]]
[1]	2701	then
[1779]	2702	printf "\n *** totalview debugger will be used"
	2703	tv_opt="-tv"
	2704	else
	2705	tv_opt=""
[1]	2706	fi
[1779]	2707
	2708	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
[1]	2709	then
	2710
[1779]	2711	#Interactive ALLINEA DEBUG seesion
	2712	if [[ "$ENVIRONMENT" != BATCH ]]
	2713	then
	2714	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2715	then
	2716	if [[ "$allinea" = true ]]
	2717	then
	2718	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
[1]	2719
[1779]	2720	ddt aprun -n $ii -N $tasks_per_node a.out
	2721	wait
	2722	fi
	2723	fi
	2724	fi
[1]	2725
[1779]	2726	if [[ $localhost = ibmh ]]
	2727	then
[1]	2728
[1779]	2729	# SETUP THE IBM MPI ENVIRONMENT
	2730	export MP_SHARED_MEMORY=yes
	2731	export AIXTHREADS_SCOPE=S
	2732	export OMP_NUM_THREADS=$threads_per_task
	2733	export AUTHSTATE=files
	2734	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
[1]	2735
[1779]	2736	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
	2737	export MP_ADAPTER_USE=shared
	2738	export MP_CPU_USE=multiple
	2739	export MP_TIMEOUT=1200
[622]	2740
[1779]	2741	unset MP_TASK_AFFINITY
[1295]	2742
[1779]	2743	if [[ "$LOADLBATCH" = yes ]]
	2744	then
	2745	totalview poe a.out
	2746	else
	2747	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2748	export TVDSVRLAUNCHCMD=ssh
	2749	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
	2750	fi
[622]	2751
[1779]	2752	fi # END DEBUG MODE
[1289]	2753
[1779]	2754	else
	2755
	2756	# NORMAL EXECUTION
	2757	if [[ -n $numprocs ]]
[1]	2758	then
[1289]	2759
[1779]	2760	# RUNNING THE PROGRAM ON PARALLEL MACHINES
	2761	if [[ $(echo $host \| cut -c1-3) = ibm ]]
[312]	2762	then
[1]	2763
[1779]	2764	# SETUP THE IBM MPI ENVIRONMENT
	2765	if [[ $host != ibmh && $host != ibmkisti ]]
[696]	2766	then
[1779]	2767	export MP_SHARED_MEMORY=yes
	2768	export AIXTHREAD_SCOPE=S
[696]	2769	export OMP_NUM_THREADS=$threads_per_task
[1779]	2770	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
	2771	export AUTHSTATE=files
	2772	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
	2773	# export MP_PRINTENV=yes
	2774
	2775	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
	2776	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
	2777	export MP_WAIT_MODE=poll
	2778	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
[696]	2779	fi
[693]	2780
[1779]	2781	if [[ $host = ibmkisti ]]
[1]	2782	then
[1779]	2783	export LANG=en_US
	2784	export MP_SHARED_MEMORY=yes
	2785	if [[ $threads_per_task = 1 ]]
[343]	2786	then
[1779]	2787	export MP_SINGLE_THREAD=yes
	2788	export MEMORY_AFFINITY=MCM
[343]	2789	else
[1779]	2790	export OMP_NUM_THREADS=$threads_per_task
[343]	2791	fi
[1]	2792	fi
[1779]	2793
	2794	if [[ "$LOADLBATCH" = yes ]]
[1]	2795	then
[1779]	2796	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
	2797	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
[1]	2798	then
[1779]	2799	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
[1]	2800	else
[1779]	2801	if [[ $run_coupled_model = false ]]
	2802	then
	2803	if [[ "$ocean_file_appendix" = true ]]
	2804	then
	2805	echo "precursor_ocean" > runfile_atmos
	2806	else
	2807	echo "precursor_atmos" > runfile_atmos
	2808	fi
	2809	else
	2810	(( iia = $numprocs_atmos / $threads_per_task ))
	2811	(( iio = $numprocs_ocean / $threads_per_task ))
	2812	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2813	printf "\n using $coupled_mode coupling"
	2814	printf "\n\n"
	2815	echo "coupled_run $iia $iio" > runfile_atmos
	2816	fi
	2817	poe ./a.out < runfile_atmos
[1]	2818	fi
[1779]	2819	else
	2820	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
[331]	2821	then
[1779]	2822	poe a.out -procs $numprocs -nodes 1 -rmpool 0
	2823	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
	2824	then
	2825	if [[ -f $hostfile ]]
[331]	2826	then
[1779]	2827	cp $hostfile hostfile
[331]	2828	else
[1779]	2829	(( ii = 1 ))
	2830	while (( ii <= $numprocs ))
	2831	do
	2832	echo $localhost_realname >> hostfile
	2833	(( ii = ii + 1 ))
	2834	done
[331]	2835	fi
[1779]	2836	export MP_HOSTFILE=hostfile
	2837	if [[ $run_coupled_model = false ]]
	2838	then
	2839	if [[ "$ocean_file_appendix" = true ]]
	2840	then
	2841	echo "precursor_ocean" > runfile_atmos
	2842	else
	2843	echo "precursor_atmos" > runfile_atmos
	2844	fi
	2845	else
	2846	(( iia = $numprocs_atmos / $threads_per_task ))
	2847	(( iio = $numprocs_ocean / $threads_per_task ))
	2848	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2849	printf "\n using $coupled_mode coupling"
	2850	printf "\n\n"
	2851	echo "coupled_run $iia $iio" > runfile_atmos
	2852	fi
[331]	2853
[1779]	2854	poe ./a.out -procs $numprocs < runfile_atmos
[1289]	2855
[1]	2856	else
[1779]	2857	if [[ "$host_file" = "" ]]
	2858	then
	2859	printf "\n +++ no hostfile given in configuration file"
	2860	locat=config_file
	2861	exit
	2862	else
	2863	eval host_file=$host_file
	2864	fi
	2865	export MP_HOSTFILE=$host_file
	2866	poe a.out -procs $numprocs -tasks_per_node $numprocs
[1]	2867	fi
	2868	fi
[1779]	2869
	2870	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
[1]	2871	then
[1779]	2872
	2873	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
	2874	# DOES NOT EXIST
[2257]	2875	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
[179]	2876	then
[1779]	2877	if [[ -f $hostfile ]]
[1598]	2878	then
[1779]	2879	cp $hostfile hostfile
	2880	(( ii = $numprocs / $threads_per_task ))
	2881	[[ $ii = 0 ]] && (( ii = 1 ))
	2882	else
	2883	(( ii = 1 ))
	2884	while (( ii <= $numprocs / $threads_per_task ))
	2885	do
	2886	echo $localhost_realname >> hostfile
	2887	(( ii = ii + 1 ))
	2888	done
	2889	if (( $numprocs / $threads_per_task == 0 ))
	2890	then
	2891	echo $localhost_realname >> hostfile
	2892	fi
[1598]	2893	fi
[1779]	2894	eval zeile=\"`head -n $ii hostfile`\"
	2895	printf "\n *** running on: $zeile"
[179]	2896	fi
	2897
[1779]	2898	(( ii = $numprocs / $threads_per_task ))
	2899	[[ $ii = 0 ]] && (( ii = 1 ))
	2900	export OMP_NUM_THREADS=$threads_per_task
[1289]	2901
[1779]	2902	if [[ $threads_per_task != 1 ]]
[291]	2903	then
[1779]	2904	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
	2905	# MAY ABORT
	2906	ulimit -s unlimited
	2907	printf "\n threads per task: $threads_per_task stacksize: unlimited"
[291]	2908	fi
[1779]	2909	if [[ $run_coupled_model = false ]]
[1224]	2910	then
[1779]	2911	if [[ "$ocean_file_appendix" = true ]]
	2912	then
	2913	echo "precursor_ocean" > runfile_atmos
	2914	else
	2915	echo "precursor_atmos" > runfile_atmos
	2916	fi
	2917	printf "\n\n"
[1622]	2918
[1779]	2919	if [[ $host = lccrayb \|\| $host = lccrayh ]]
	2920	then
	2921	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
	2922	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2923	elif [[ $host = lcbullhh ]]
	2924	then
	2925	export OMPI_MCA_pml=cm
	2926	export OMPI_MCA_mtl=mxm
	2927	export OMPI_MCA_coll=^ghc
	2928	export OMPI_MCA_mtl_mxm_np=0
	2929	export MXM_RDMA_PORTS=mlx5_0:1
	2930	export MXM_LOG_LEVEL=ERROR
	2931	export OMP_NUM_THREADS=$threads_per_task
	2932	export KMP_AFFINITY=verbose,granularity=core,compact,1
	2933	export KMP_STACKSIZE=64m
[1622]	2934
[2147]	2935	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
[1622]	2936
[1779]	2937	elif [[ $host = lccrayf ]]
	2938	then
	2939	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
	2940	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
	2941	then
[2257]	2942	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
	2943	elif [[ $host = lceddy ]]
[1779]	2944	then
[2257]	2945	echo $ii
	2946	echo $tasks_per_node
	2947	echo $nodes
	2948	mpirun -n $ii a.out < runfile_atmos
[1866]	2949	elif [[ $host = lcocean ]]
	2950	then
	2951	mpirun a.out $ROPTS < runfile_atmos
[1779]	2952	elif [[ $host = lcsb ]]
	2953	then
	2954	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
[2257]	2955
[1779]	2956	elif [[ $host = lckiaps ]]
	2957	then
[1940]	2958	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
[1779]	2959	elif [[ $host = lckyu* ]]
	2960	then
	2961	mpiexec -n $ii --stdin runfile_atmos ./a.out
	2962	else
	2963	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
	2964	fi
	2965
[164]	2966	else
	2967
[1779]	2968	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
	2969	(( iia = $numprocs_atmos / $threads_per_task ))
	2970	(( iio = $numprocs_ocean / $threads_per_task ))
	2971	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2972	printf "\n using $coupled_mode coupling"
	2973	printf "\n\n"
[164]	2974
[1779]	2975	if [[ $coupled_mode = "mpi2" ]]
[206]	2976	then
[1779]	2977	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
	2978	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
[197]	2979
[1779]	2980	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	2981	then
[206]	2982
[1779]	2983	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
	2984	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
	2985
	2986	else
	2987	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
	2988	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
	2989	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
	2990	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
	2991	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
	2992	fi
	2993	wait
	2994
[206]	2995	else
	2996
[1779]	2997	echo "coupled_run $iia $iio" > runfile_atmos
[164]	2998
[1779]	2999	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
	3000	then
[206]	3001
[1779]	3002	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
[206]	3003
[1779]	3004	elif [[ $host = lck \|\| $host = lckordi ]]
	3005	then
[206]	3006
[1779]	3007	mpiexec -n $ii ./a.out < runfile_atmos &
[1108]	3008
[1779]	3009	elif [[ $host = lckyu* ]]
	3010	then
[1108]	3011
[1779]	3012	mpiexec -n $ii --stdin runfile_atmos ./a.out
[1108]	3013
[1779]	3014	elif [[ $host = lcmuk ]]
	3015	then
[1108]	3016
[1779]	3017	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
[1604]	3018
[1779]	3019	fi
	3020	wait
	3021	fi
[1604]	3022
[164]	3023	fi
[102]	3024
[1779]	3025	elif [[ $host = lckyoto ]]
[440]	3026	then
[1779]	3027	set -xv
	3028	export P4_RSHCOMMAND=plesh
	3029	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
	3030	if [[ "$ENVIRONMENT" = BATCH ]]
[505]	3031	then
[1779]	3032	if [[ "$cond2" = fujitsu ]]
	3033	then
	3034	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
	3035	elif [[ "cond2" = pgi ]]
	3036	then
	3037	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
	3038	else
	3039	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
	3040	fi
[505]	3041	else
[1779]	3042	if [[ "$cond2" = "" ]]
	3043	then
	3044	mpiruni_rsh -np $numprocs ./a.out # for intel
	3045	else
	3046	mpirun -np $numprocs ./a.out
	3047	fi
[505]	3048	fi
[1779]	3049	set +xv
	3050
	3051	elif [[ $host = lctit ]]
	3052	then
	3053	export OMP_NUM_THREADS=$threads_per_task
	3054	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
	3055	if [[ "$threads_per_task" != 1 ]]
[505]	3056	then
[1779]	3057	export MV2_ENABLE_AFFINITY=0
[505]	3058	fi
[1779]	3059	echo "----- PBS_NODEFILE content:"
	3060	cat $PBS_NODEFILE
	3061	echo "-----"
	3062	(( ii = $numprocs / $threads_per_task ))
	3063	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
	3064	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
[1289]	3065
[1779]	3066	else
	3067	mpprun -n $numprocs a.out
[678]	3068	fi
[1]	3069	else
[1779]	3070	a.out
[1]	3071	fi
[1289]	3072
[1779]	3073	fi # end normal (non-debug) execution
	3074
	3075	fi # end explicit execute_command or host-specific execute actions
	3076
[1289]	3077	if [[ $? != 0 ]]
[1]	3078	then
	3079
[1289]	3080	# ABORT IN CASE OF RUNTIME ERRORS
[1]	3081	printf "\n +++ runtime error occured"
	3082	locat=execution
	3083	exit
[1289]	3084
[1]	3085	else
[260]	3086
[1289]	3087	printf "\n$dashes\n *** execution finished \n"
	3088
	3089	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
	3090	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
[260]	3091	if [[ "$dvrserver_id" != "" ]]
	3092	then
	3093	kill $dvrserver_id
	3094	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
[261]	3095
[1289]	3096	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
	3097	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
[262]	3098	if [[ -d DATA_DVR ]]
	3099	then
[261]	3100
[1289]	3101	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
	3102	# DIRECTORY
[262]	3103	cp .dvrserver.config DATA_DVR
	3104
[1289]	3105	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
	3106	# SEQUENCE MODE DATA TOO)
[262]	3107	process_dvr_output -d DATA_DVR -f $fname -s
	3108
	3109	else
	3110
[1289]	3111	# PROCESS THE LOCAL OUTPUT
[262]	3112	process_dvr_output -l -d DATA_DVR -f $fname
	3113
	3114	fi
	3115
	3116	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
	3117	then
	3118
[1289]	3119	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
[262]	3120	process_dvr_output -l -d DATA_DVR -f $fname
	3121
[260]	3122	fi
[1]	3123	fi
	3124
	3125
	3126
[1289]	3127	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	3128	# BY EACH CORE INTO ONE FILE
[920]	3129	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
	3130	then
	3131	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
	3132	printf "\n 2d- and/or 3d-data may be incomplete!"
	3133	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
	3134	elif [[ "$combine_plot_fields" == true ]]
	3135	then
[1270]	3136	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
	3137	then
	3138	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
[1779]	3139	aprun -n 1 -N 1 combine_plot_fields${block}.x
[1270]	3140	else
	3141	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
	3142	combine_plot_fields${block}.x
	3143	fi
[920]	3144	else
[1289]	3145
	3146	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
	3147	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
	3148	# ??? koennen wir das streichen ???
[920]	3149	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	3150	fi
[503]	3151
	3152
	3153
[1289]	3154	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
[1]	3155	(( i = 0 ))
	3156	while (( i < ioc ))
	3157	do
	3158	(( i = i + 1 ))
	3159	if (( i == 1 ))
	3160	then
[1289]	3161	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
[1]	3162	fi
	3163	printf "\n >>> ${out_command[$i]}"
	3164	eval ${out_command[$i]}
	3165	if (( i == ioc ))
	3166	then
[1289]	3167	printf "\n$dashes\n"
[1]	3168	fi
	3169	done
	3170
	3171
[1289]	3172	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
[1]	3173	if [[ $do_trace = true ]]
	3174	then
	3175	printf "\n\n"
	3176	ls -al
	3177	fi
[2261]	3178
[1]	3179
[1289]	3180	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
[1]	3181	(( i = 0 ))
	3182	while (( i < iout ))
	3183	do
	3184	(( i = i + 1 ))
	3185	if (( i == 1 ))
	3186	then
[2261]	3187	printf "\n\n *** saving OUTPUT-files:"
	3188
	3189	# GET RUN NUMBER ASSIGNED BY PALM
	3190	if [[ -f RUN_NUMBER ]]
	3191	then
	3192	read run_number < RUN_NUMBER
	3193	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	3194	usecycle_option="-U $run_number"
	3195	else
	3196	run_number=0
	3197	usecycle_option=""
	3198	fi
	3199	printf "\n$dashes"
[1]	3200	fi
	3201
[2261]	3202	# ADD CYCLE NUMBER TO FILENAME
	3203	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	3204	then
	3205
	3206	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
	3207	if [[ "${actionout[$i]}" != "a" ]]
	3208	then
	3209	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	3210	# WITH AN EXISTING CYCLE NUMBER
	3211	if (( run_number >= cycnum[$i] ))
	3212	then
	3213	(( cycnum[$i] = run_number ))
	3214	else
	3215	if (( run_number > 0 ))
	3216	then
	3217	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	3218	fi
	3219	fi
	3220	fi
	3221	if (( cycnum[$i] > 0 ))
	3222	then
	3223	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
	3224	fi
	3225	fi
	3226
[1289]	3227	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
[1]	3228	files_for_pes=false; filetyp=file
[2261]	3229	link_local_output=false
[1]	3230	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
	3231	then
	3232	files_for_pes=true; filetyp=directory
	3233	actionout[$i]=""
	3234	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
	3235	then
	3236	actionout[$i]=""
[2261]	3237	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
[1]	3238	then
	3239	files_for_pes=true; filetyp=directory
[2261]	3240	link_local_output=true
	3241	actionout[$i]=""
	3242	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
[1]	3243	then
[2261]	3244	link_local_output
	3245	actionout[$i]=""
[1]	3246	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
	3247	then
	3248	files_for_pes=true; filetyp=directory
	3249	actionout[$i]="tr"
	3250	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
	3251	then
	3252	actionout[$i]="tr"
	3253	fi
	3254
	3255	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
	3256	then
	3257	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
[260]	3258	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
[1]	3259	then
	3260	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	3261	else
	3262
	3263
[1289]	3264	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3265	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3266	if [[ "${actionout[$i]}" = tr ]]
	3267	then
	3268	if [[ $localhost != $fromhost ]]
	3269	then
	3270	if [[ $files_for_pes = false ]]
	3271	then
	3272	cps=""
	3273	cst=""
	3274	else
	3275	cps=-c
	3276	cst="/"
	3277	fi
[2261]	3278
	3279	transfer_failed=false
	3280	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
	3281	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
	3282	if [[ $localhost = lccrayb ]]
[1]	3283	then
[2261]	3284	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]}"
	3285	elif [[ $localhost = lccrayh ]]
	3286	then
	3287	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]}"
	3288	elif [[ $localhost = lcbullhh ]]
	3289	then
	3290	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]}"
	3291	elif [[ $localhost = lcxe6 ]]
	3292	then
	3293	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]	3294	else
[2261]	3295	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
	3296	fi
	3297	[[ $? != 0 ]] && transfer_failed=true
[1]	3298
[2261]	3299	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	3300	if [[ $transfer_failed = true ]]
	3301	then
	3302	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
	3303	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
[1]	3304
[2261]	3305	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	3306	eval local_catalog=${pathout[$i]}
	3307	if [[ ! -d $local_catalog ]]
[1]	3308	then
[2261]	3309	printf " *** local directory does not exist. Trying to create:\n"
	3310	printf " $local_catalog \n"
	3311	mkdir -p $local_catalog
[1]	3312	fi
[2261]	3313	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3314	transfer_problems=true
[1]	3315	fi
[2261]	3316
[1]	3317	else
	3318
[1289]	3319	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
[1]	3320	actionout[$i]=""
	3321	fi
	3322	fi
	3323
	3324
[1289]	3325	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	3326	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
[1]	3327	if [[ "${actionout[$i]}" = tra ]]
	3328	then
	3329	if [[ $localhost != $fromhost ]]
	3330	then
[2261]	3331	if [[ $localhost = ibmh ]]
[1]	3332	then
	3333
[1289]	3334	# TRANSFER IN SEPERATE JOB
	3335	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
[1]	3336	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
	3337	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
	3338	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
	3339
	3340	echo "set -x" > transfer_${localout[$i]}
	3341	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
[82]	3342
	3343	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
	3344	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
	3345	printf "\n or higher cycle\n"
[1468]	3346	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]	3347
[1]	3348	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
	3349
[2261]	3350	if [[ $LOGNAME = b323013 ]]
[1]	3351	then
[2261]	3352	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3353	else
[2261]	3354	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
[1]	3355	fi
	3356
	3357	else
	3358
[1289]	3359	# TRANSFER WITHIN THIS JOB
[1]	3360	transfer_failed=false
[82]	3361	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
	3362	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
[1255]	3363	if [[ $localhost = lccrayb ]]
	3364	then
[2261]	3365	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]	3366	elif [[ $localhost = lccrayh ]]
	3367	then
[2261]	3368	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]	3369	elif [[ $localhost = lcxe6 ]]
	3370	then
[2261]	3371	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]	3372	else
[1468]	3373	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
[1255]	3374	fi
[82]	3375	[[ $? != 0 ]] && transfer_failed=true
[1]	3376
[1289]	3377	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
[1]	3378	if [[ $transfer_failed = true ]]
	3379	then
[1289]	3380	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[1]	3381	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
	3382
[1289]	3383	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
[1]	3384	eval local_catalog=${pathout[$i]}
	3385	if [[ ! -d $local_catalog ]]
	3386	then
	3387	printf " *** local directory does not exist. Trying to create:\n"
	3388	printf " $local_catalog \n"
	3389	mkdir -p $local_catalog
	3390	fi
	3391
	3392	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
	3393	transfer_problems=true
	3394	fi
	3395	fi
	3396	else
	3397
[1289]	3398	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
[1]	3399	actionout[$i]=a
	3400	fi
	3401	fi
	3402
	3403
[1289]	3404	# APPEND ON THIS MACHINE
[1]	3405	if [[ "${actionout[$i]}" = "a" ]]
	3406	then
[741]	3407	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	3408	then
	3409	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
	3410	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	3411	else
	3412	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
	3413	cat ${localout[$i]} >> ${pathout[$i]}
	3414	fi
[1]	3415	fi
	3416
[1289]	3417	# COPY ON THIS MACHINE
	3418	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	3419	# ON DIFFERENT FILE-SYSTEMS
[1]	3420	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
	3421	then
	3422
[1289]	3423	# COPY IN CASE OF RUNS ON SINGLE CORES
[5]	3424	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
[1]	3425	then
	3426	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
[2261]	3427	if [[ $link_local_output = true ]]
	3428	then
	3429	printf " file will be linked\n"
	3430	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3431	fi
	3432	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3433	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
[149]	3434	then
[2261]	3435	if [[ $link_local_output = true ]]
	3436	then
	3437	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3438	fi
	3439	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	3440	else
	3441	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
[149]	3442	fi
[1]	3443	else
	3444	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
[2261]	3445	if [[ $link_local_output = true ]]
	3446	then
	3447	printf " file will be linked\n"
	3448	ln -f ${localout[$i]} ${pathout[$i]}
	3449	fi
	3450	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	3451	if [[ ! -f "${pathout[$i]}" ]]
[149]	3452	then
[2261]	3453	if [[ $link_local_output = true ]]
	3454	then
	3455	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3456	fi
	3457	cp ${localout[$i]} ${pathout[$i]}
	3458	else
	3459	printf "+++ no copy because file ${pathout[$i]} exists\n"
[149]	3460	fi
[1]	3461	fi
	3462
	3463	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
	3464	then
	3465
[1289]	3466	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	3467	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
[1]	3468	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
[2261]	3469	if [[ $link_local_output = true ]]
	3470	then
	3471	printf " files will be linked\n"
	3472	mkdir ${pathout[$i]}
	3473	cd ${localout[$i]}
	3474	for file in $(ls *)
	3475	do
	3476	ln -f $file ${pathout[$i]}
	3477	done >\|/dev/null 2>&1
	3478	cd $TEMPDIR
	3479	fi
[1289]	3480
	3481	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
[2261]	3482	if [[ ! -f "${pathout[$i]}/_000000" ]]
[149]	3483	then
[2261]	3484	if [[ $link_local_output = true ]]
	3485	then
	3486	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	3487	fi
	3488	cp -r ${localout[$i]}/* ${pathout[$i]}
	3489	fi
[1]	3490
	3491	fi
	3492	fi
	3493	done
	3494	if (( i != 0 ))
	3495	then
	3496	if [[ $transfer_problems = true ]]
	3497	then
[1289]	3498	printf "\n$dashes\n *** OUTPUT-files saved"
[1]	3499	printf "\n +++ WARNING: some data transfers failed! \n"
	3500	else
[1289]	3501	printf "\n$dashes\n *** all OUTPUT-files saved \n"
[1]	3502	fi
	3503	fi
	3504
	3505
[1289]	3506	# IF REQUIRED, START A RESTART-JOB
	3507	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
[1]	3508	if [[ -f CONTINUE_RUN ]]
	3509	then
	3510
[2261]	3511	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
	3512	# -C TELLS MRUN THAT IT IS A RESTART-RUN
	3513	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	3514	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
	3515	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
	3516	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
	3517	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
	3518	if [[ $(echo $mc \| grep -c "#") != 0 ]]
[1]	3519	then
[2261]	3520	mc=`echo $mc \| sed 's/#/f/g'`
	3521	fi
[1]	3522
	3523
[2261]	3524	# START THE RESTART-JOB
	3525	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
	3526	echo " $mc"
	3527	printf "\n$dashes\n"
	3528	if [[ $localhost != $fromhost ]]
	3529	then
[1]	3530
[2261]	3531	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
[1]	3532	then
[2261]	3533	echo "*** ssh will be used to initiate restart-runs!"
	3534	echo " return_address=\"$return_address\" "
	3535	echo " return_username=\"$return_username\" "
	3536	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
[1]	3537	then
[2261]	3538	if [[ $localhost = ibmh ]]
[1]	3539	then
[2261]	3540	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\" "
	3541	elif [[ $localhost = lcbullhh ]]
	3542	then
	3543	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\" "
	3544	elif [[ $localhost = lccrayb ]]
	3545	then
	3546	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\" "
	3547	elif [[ $localhost = lccrayh ]]
	3548	then
	3549	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\" "
	3550	elif [[ $localhost = lcxe6 ]]
	3551	then
	3552	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]	3553	else
[2261]	3554	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	fi
	3556	else
[2261]	3557	if [[ $localhost = ibmkisti ]]
	3558	then
	3559	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\" "
	3560	elif [[ $localhost = lceddy ]]
	3561	then
	3562	/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 "
	3563	elif [[ $localhost = lcocean ]]
	3564	then
	3565	/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 "
	3566	elif [[ $localhost = lccrayb ]]
	3567	then
	3568	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\" "
	3569	elif [[ $localhost = lccrayh ]]
	3570	then
	3571	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\" "
	3572	else
	3573	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
	3574	fi
[1]	3575	fi
[2261]	3576	else
	3577	printf "\n +++ no restart mechanism available for host \"$localhost\" "
	3578	locat=restart; exit
	3579	fi
[1]	3580
[2261]	3581	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	3582	if [[ $queue = special1q ]]
	3583	then
	3584	sleep 120
[1]	3585	else
[2261]	3586	sleep 30
	3587	fi
[1]	3588
[2261]	3589	else
	3590
	3591	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
	3592	# USING SSH)
	3593	cd $LOCAL_PWD
[1103]	3594	if [[ $localhost = lckyuh ]]
	3595	then
[2261]	3596	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
	3597	printf "\n please restart job manually using command:\n"
	3598	printf "\n \"$mc\" "
[1103]	3599	else
[2261]	3600	eval $mc # THE ' MUST BE EVALUATED
[1103]	3601	fi
[2261]	3602	cd - > /dev/null
	3603	fi
	3604	if [[ $localhost = lckyuh ]]
	3605	then
	3606	printf "\n$dashes\n *** restart-run to be initiated manually\n"
	3607	else
	3608	printf "\n$dashes\n *** restart-run initiated \n"
	3609	fi
[1]	3610
	3611
[2261]	3612	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	3613	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	3614	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	3615	# MAY BE VERY HUGE)
	3616	(( i = 0 ))
	3617	while (( i < iin ))
	3618	do
	3619	(( i = i + 1 ))
	3620	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	3621	then
	3622	rm -r ${absnamein[$i]}
	3623	fi
	3624	done
[1]	3625
	3626	fi
	3627
	3628
	3629
[1289]	3630	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
[352]	3631	if [[ "$email_notification" != "none" ]]
[1]	3632	then
	3633
	3634	if [[ $localhost != $fromhost ]]
	3635	then
	3636	if [[ -f CONTINUE_RUN ]]
	3637	then
	3638	echo "PALM restart run necessary" > email_text
	3639	echo "description header of actual run:" >> email_text
	3640	cat CONTINUE_RUN >> email_text
	3641	echo "mrun-command to restart:" >> email_text
	3642	echo "$mc" >> email_text
	3643	else
	3644	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
	3645	fi
	3646	mail $email_notification < email_text
	3647	printf "\n *** email notification sent to \"$email_notification\" "
	3648	fi
	3649	fi
	3650
	3651
	3652
[1289]	3653	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
[1]	3654	cd $HOME
	3655	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
	3656
	3657	else
	3658
[1289]	3659	# PREPARING ACTIONS,
	3660	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
[1]	3661
[1289]	3662	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
[1468]	3663	mrun_com="$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 $remote_username"
[1]	3664	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
[79]	3665	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
[123]	3666	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
[1]	3667	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
	3668	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
	3669	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
	3670	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
	3671	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
	3672	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
	3673	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
	3674	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
	3675	if [[ $use_openmp = true ]]
	3676	then
[622]	3677	mrun_com=${mrun_com}" -O $threads_per_task"
[1]	3678	fi
[759]	3679	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
[1]	3680	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
	3681	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
	3682	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
[127]	3683	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
[291]	3684	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
[206]	3685	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
[920]	3686	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
	3687	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
[759]	3688	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
[1]	3689	if [[ $do_remote = true ]]
	3690	then
	3691	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
	3692	fi
	3693
	3694
[1289]	3695	# CREATE EXECUTABLE FOR BATCH JOB
[1199]	3696	if [[ $create_executable_for_batch = true && $restart_run != true ]]
	3697	then
	3698
	3699	printf "\n *** creating the executable for batch job\n"
	3700
[1289]	3701	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
[1199]	3702	if [[ $host != $localhost ]]
	3703	then
	3704	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
	3705	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
	3706	locat=create_executable; exit
	3707	fi
	3708
	3709	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3710	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3711
	3712	cp $make_depository .
	3713	tar -xf $make_depository > /dev/null 2>&1
	3714	cp ../* . > /dev/null 2>&1
	3715
	3716	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
	3717
	3718	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
	3719	then
	3720	printf "\n +++ error occured while compiling or linking"
	3721	locat=compile
	3722	exit
	3723	fi
	3724
	3725	mv a.out ..
	3726	cd - > /dev/null 2>&1
	3727	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
	3728
	3729	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
	3730
	3731	fi
	3732
	3733
[1289]	3734	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[1]	3735	jobfile=jobfile.$RANDOM
	3736
	3737
[1289]	3738	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[1]	3739	echo "mkdir $TEMPDIR" >> $jobfile
	3740	echo "cd $TEMPDIR" >> $jobfile
	3741
	3742
[1289]	3743	# ACTIVATE ERROR-TRACEBACK
[1]	3744	if [[ $do_trace = true ]]
	3745	then
	3746	echo "set -x" >> $jobfile
	3747	else
	3748	echo "set +vx" >> $jobfile
	3749	fi
	3750
	3751
[1289]	3752	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
[1043]	3753	if [[ "$init_cmds" != "" ]]
	3754	then
	3755	echo "$init_cmds" >> $jobfile
	3756	fi
	3757	if [[ "$module_calls" != "" ]]
	3758	then
	3759	echo "$module_calls" >> $jobfile
	3760	fi
	3761
	3762
[1289]	3763	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
	3764	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
	3765	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
	3766	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
	3767	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
	3768	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
	3769	# QUEUEING-SYSTEMS
[1866]	3770	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
[1]	3771	then
	3772
[1289]	3773	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
[191]	3774	if [[ $restart_run != true ]]
	3775	then
	3776	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
	3777	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
	3778	fi
[1]	3779
[1289]	3780	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
	3781	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
[193]	3782	echo "set -x" >> $jobfile
[693]	3783	if [[ $host = $localhost ]]
	3784	then
[1199]	3785	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
	3786	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
[1281]	3787	if [[ $(echo $host \| cut -c1-6) = lccray ]]
	3788	then
	3789	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3790	else
	3791	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
	3792	fi
[1199]	3793
[693]	3794	else
[1255]	3795	if [[ $host = ibmkisti ]]
[693]	3796	then
[1289]	3797	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
[693]	3798	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3799	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1620]	3800	elif [[ $host = lcbullhh ]]
	3801	then
	3802	echo "localdir=\`pwd\`" >> $jobfile
	3803	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
	3804
[1255]	3805	elif [[ $host = lccrayb ]]
	3806	then
	3807	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3808	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3809	elif [[ $host = lccrayh ]]
	3810	then
	3811	echo "localdir=\`pwd\`" >> $jobfile
[1468]	3812	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
[1274]	3813
[1255]	3814	else
[1468]	3815	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
[693]	3816	fi
	3817	fi
[193]	3818	echo "export SOURCES_COMPLETE=true" >> $jobfile
[1]	3819
[1289]	3820	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
	3821	# WORKING DIRECTORY OF THE JOB
[193]	3822	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
	3823	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
[1199]	3824	echo "chmod u+rwx $mrun_script_name" >> $jobfile
[193]	3825	echo "execute_mrun=true" >> $jobfile
	3826	echo " " >> $jobfile
	3827
[191]	3828	else
	3829
[1289]	3830	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
[191]	3831	if [[ $do_compile = true ]]
	3832	then
	3833
	3834	source_catalog=SOURCES_FOR_RUN_$fname
	3835
[1289]	3836	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
[191]	3837	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
	3838	echo "export SOURCES_COMPLETE=true" >> $jobfile
	3839	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
	3840
	3841	for filename in $source_list
	3842	do
[1289]	3843	# BACKSLASH IS USED FOR MASKING
[191]	3844	echo "cat > $filename << \"%END%\"" >> $jobfile
	3845	cat $source_catalog/$filename >> $jobfile
	3846	echo " " >> $jobfile
	3847	echo "%END%" >> $jobfile
	3848	echo " " >> $jobfile
	3849	done
	3850
[1289]	3851	# BACKSLASH IS USED FOR MASKING
[191]	3852	echo "cat > Makefile << \"%END%\"" >> $jobfile
	3853	cat $source_catalog/Makefile >> $jobfile
[1]	3854	echo " " >> $jobfile
	3855	echo "%END%" >> $jobfile
	3856	echo " " >> $jobfile
	3857
[191]	3858	echo "cd - > /dev/null" >> $jobfile
[1]	3859
[191]	3860	fi
[1]	3861
	3862
[1289]	3863	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
	3864	# BACKSLASH IS USED FOR MASKING
	3865	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
	3866	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
[191]	3867	echo "cat > $config_file << \"%END%\"" >> $jobfile
[1101]	3868	if [[ $host = lckyuh ]]
	3869	then
[1289]	3870	# NO CROSS-COMPILER ON COMPUTE NODE
[1101]	3871	sed 's/frtpx/frt/g' $config_file >> $jobfile
	3872	else
	3873	sed 's/#$.*//g' $config_file >> $jobfile
	3874	fi
[191]	3875	echo "%END%" >> $jobfile
	3876	echo " " >> $jobfile
[1]	3877
	3878
[1289]	3879	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
	3880	# BACKSLASH IS USED FOR MASKING
[1101]	3881	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
[1103]	3882	if [[ $host = lckyuh ]]
	3883	then
	3884	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
	3885	else
	3886	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
	3887	fi
[1101]	3888	echo "%END%" >> $jobfile
[191]	3889	echo "chmod u+x $mrun_script_name" >> $jobfile
	3890	echo "execute_mrun=true" >> $jobfile
	3891	echo " " >> $jobfile
[1]	3892
	3893	fi
	3894
[191]	3895
[1289]	3896	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
	3897	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
	3898	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
[1]	3899	if [[ $do_remote = true ]]
	3900	then
	3901	(( i = 0 ))
	3902	while (( i < iin ))
	3903	do
	3904	(( i = i + 1 ))
	3905	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
	3906	if [[ "${transin[$i]}" = job ]]
	3907	then
	3908	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
	3909	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
	3910	echo " " >> $jobfile
	3911	echo "%END%" >> $jobfile
	3912	else
[1468]	3913	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
[1]	3914	fi
	3915
[1289]	3916	# CHECK, IF FILE COULD BE CREATED
[1]	3917	echo "if [[ \$? = 1 ]]" >> $jobfile
	3918	echo "then" >> $jobfile
	3919	echo " echo \" \" " >> $jobfile
	3920	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
	3921	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
	3922	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
	3923	echo " execute_mrun=false" >> $jobfile
	3924	echo "fi" >> $jobfile
	3925	done
	3926	fi
	3927
[1289]	3928	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	3929	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
	3930	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
[1]	3931	echo "LOCAL_PWD=$working_directory" >> $jobfile
	3932	echo "export LOCAL_PWD" >> $jobfile
	3933
[1289]	3934	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
[22]	3935	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
[1]	3936	echo "export LOCAL_MRUN_PATH" >> $jobfile
	3937
[2257]	3938	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
	3939	if [[ $host = lceddy \|\| $localhost = lceddy ]]
	3940	then
[1099]	3941	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
	3942	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
[2257]	3943	fi
[1]	3944
[1289]	3945	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
	3946	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
[1101]	3947	echo "set -x" >> $jobfile
	3948	echo "queue=$queue" >> $jobfile
[1]	3949	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
[1101]	3950	echo 'ls -al; echo `pwd`' >> $jobfile
	3951	echo "cd \$HOME" >> $jobfile
	3952	echo "rm -rf $TEMPDIR" >> $jobfile
[1]	3953
	3954
	3955
	3956
[1289]	3957	# START THE JOB USING SUBJOB-COMMAND
[1]	3958	if [[ $silent = false ]]
	3959	then
	3960	printf "\n "
	3961	else
	3962	printf "\n\n"
	3963	fi
	3964
[1094]	3965	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]	3966	rm -rf $jobfile
	3967
	3968
[1289]	3969	fi # END OF REMOTE-PART

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