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source: palm/trunk/SCRIPTS/mrun @ 1650

Last change on this file since 1650 was 1649, checked in by knoop, 9 years ago
Latex lecture update for PALM seminar in Hong Kong
Property svn:keywords set to `Id Rev`
File size: 180.4 KB

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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
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	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1649 2015-09-15 16:34:42Z knoop $
29	#
30	# 1622 2015-07-20 06:21:36Z heinze
31	# bugfix for Mistral (lcbullhh)
32	#
33	# 1621 2015-07-17 11:39:33Z heinze
34	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
35	#
36	# 1609 2015-07-03 15:37:58Z maronga
37	# Modified the random number of the temporary working directory to match the
38	# queuing system number on HLRN-III (lccray*).
39	#
40	# 1604 2015-06-23 15:48:03Z suehring
41	# Enable coupled runs for lcmuk
42	#
43	# 1598 2015-05-29 06:45:40Z raasch
44	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
45	#
46	# 1549 2015-01-30 14:26:16Z suehring
47	# Enable interactive debug sessions with allinea debugger
48	#
49	# 1547 2015-01-29 15:09:12Z witha
50	# adjustments for ForWind computing cluster (lcflow)
51	#
52	# 1491 2014-11-12 08:12:57Z heinze
53	# correct setting of batch_job allowed for ibm-machines
54	#
55	# 1468 2014-09-24 14:06:57Z maronga
56	# Typo removed (addres->address)
57	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
58	# Added support for restart runs (remote) for lcxe6
59	#
60	# 1442 2014-07-28 07:09:10Z raasch
61	# default queues for HLRN-III (lccrayb/lccrayh) defined
62	#
63	# 1422 2014-07-02 10:01:25Z kanani
64	# automatic restarts enabled for lccrayb,
65	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
66	#
67	# 1420 2014-06-10 06:24:14Z raasch
68	# -j1 option added to aprung command for lccrayf (CSC)
69	#
70	# 1402 2014-05-09 14:25:13Z raasch
71	# batch_job added to envpar-NAMELIST
72	#
73	# 1357 2014-04-11 15:02:03Z witha
74	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
75	# possible)
76	#
77	# 1320 2014-03-20 08:40:49Z raasch
78	# check namelist file set false by default
79	#
80	# 1304 2014-03-12 10:29:42Z raasch
81	# ulimit option changed from -Ss to -s
82	#
83	# bugfix: missing "fi" in r1289
84	#
85	# 1289 2014-03-04 07:12:34Z raasch
86	# comments translated to English
87	# necriam-, fimm-, ibmy-, and sgi-specific code removed
88	# export of variables for palm and interpret_config removed
89	#
90	# 1281 2014-02-01 07:55:49Z raasch
91	# rsync-copy restricted to Cray machines, since command is unavailable on some
92	# other systems
93	#
94	# 1279 2014-01-28 12:10:14Z raasch
95	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
96	# in order to remove annoying restrictions concerning the number of processors which
97	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
98	# restriction, one of the nodes will be filled with less than the given number of
99	# tasks per node. A respective warning is given.
100	#
101	# 1274 2014-01-09 13:14:54Z heinze
102	# adjustments for lccrayh
103	#
104	# 1272 2014-01-08 10:19:32Z witha
105	# small adjustment for lcflow
106	#
107	# 1270 2013-12-16 11:05:01Z fricke
108	# call of combine_plot_fields adjusted for lccrayb/lccrayh
109	#
110	# 1255 2013-11-07 14:43:35Z raasch
111	# further adjustments for lccrayb remote access
112	#
113	# 1241 2013-10-30 11:36:58Z heinze
114	# Enable use of nudging input and input of large scale forcing from
115	# external files
116	#
117	# 1229 2013-09-20 06:55:19Z raasch
118	# further adjustments for lccrayb
119	#
120	# 1224 2013-09-16 07:27:23Z raasch
121	# first adjustments for lccrayb
122	#
123	# 1210 2013-08-14 10:58:20Z raasch
124	# fftw support added
125	#
126	# 1201 2013-07-10 16:17:59Z witha
127	# adjustments for Forwind cluster (lcflow)
128	#
129	# 1199 2013-07-05 14:52:22Z raasch
130	# adjustments for CSC Helsinki (lccrayf),
131	# executables for batch jobs can be created in advance, in order to avoid calling
132	# the compiler within the batch job (only works if batch jobs are submitted on
133	# local host)
134	#
135	# 1190 2013-06-25 09:39:21Z heinze
136	# enable use of automatic restarts for ibmh
137	# use of cluster/express queue enabled (ibmh)
138	#
139	# 1124 2013-04-09 15:46:52Z raasch
140	# variable "memory" is exported via typeset option -x, because otherwise an unknown
141	# side effect may lead to data loss while getopts is reading the script-option arguments
142	#
143	# 1122 2013-04-09 08:37:16Z heinze
144	# Bugfix: change type of variable last_char
145	#
146	# 1119 2013-04-05 15:11:19Z raasch
147	# Bugfix for setting -T option for subjob
148	#
149	# 1108 2013-03-05 07:03:32Z raasch
150	# bugfix for coupled runs on lckyut/lckyuh
151	#
152	# 1106 2013-03-04 05:31:38Z raasch
153	# --stdin argument for mpiexec on lckyuh
154	# -y and -Y settings output to header
155	#
156	# 1103 2013-02-20 02:15:53Z raasch
157	# default script runs again under ksh, because of unsolved problems with read
158	# from stdin: when bash script is called from a ksh, message "read error: 0:
159	# Resource temporarily unavailable" appears and script does not stop,
160	# further bash compatibility adjustments,
161	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
162	# on lckyuh, but mrun does not terminate and issues a warning instead
163	#
164	# 1101 2013-02-17 10:20:21Z raasch
165	# script now running under bash instead of ksh, which required small adjustments
166	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
167	# read from stdin),
168	# cross compilername on lckyuh compute nodes replaced by real compiler name
169	#
170	# 1099 2013-02-10 01:47:43Z raasch
171	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
172	# and for Forwind cluster (lcflow)
173	# small further adjustments for lckyut
174	#
175	# 1094 2013-02-03 01:52:12Z raasch
176	# explicit ssh/scp port can be set in config file with environment variable
177	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
178	# decalpha parts (yonsei) removed
179	#
180	# 2013-02-02 07:06:13Z raasch
181	# adjustments for Kyushu-University computing center (lckyut - tatara)
182	#
183	# 1083 2013-01-04 10:22:09Z maronga
184	# bugfix in parameter file check (read %cpp_options was missing)
185	#
186	# 1069 2012-11-28 16:18:43Z maronga
187	# bugfix: coupling mode was always set to mpi2, typos removed
188	#
189	# 1058 2012-11-21 07:00:35Z raasch
190	# Intel inspector (inspxe) is given the number of PEs instead of the number of
191	# nodes
192	#
193	# 1046 2012-11-09 14:38:45Z maronga
194	# code put under GPL (PALM 3.9)
195	#
196	# 21/03/94 - Siggi - first version finished
197	# 03/03/94 - Siggi - script development started
198	#
199	#--------------------------------------------------------------------------------#
200	# mrun - script for running PALM jobs
201	#--------------------------------------------------------------------------------#
202
203
204
205	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
206
207	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
208	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
209	# (TOO MANY ARGUMENTS - PROBLEM)
210	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
211
212	AddFilenames=""
213	additional_conditions=""
214	add_source_path=""
215	afname=""
216	archive_save=true
217	archive_system=none
218	check_namelist_files=false
219	combine_plot_fields=true
220	compiler_name=""
221	cond1=""
222	cond2=""
223	config_file=.mrun.config
224	coupled_dist=""
225	coupled_mode="mpi1"
226	cpp_opts=""
227	cpp_options=""
228	cpumax=0
229	cpurest=0
230	create_executable_for_batch=false
231	delete_temporary_catalog=true
232	do_batch=false
233	do_compile=true
234	do_remote=false
235	do_stagein=true
236	do_stageout=true
237	do_trace=false
238	email_notification="none"
239	exclude=""
240	executable=""
241	execution_error=false
242	fftw_inc=""
243	fftw_lib=""
244	fftw_support=false
245	fname=test
246	fromhost=""
247	global_revision=""
248	group_number=none
249	host=""
250	host_file=""
251	hp=""
252	ignore_archive_error=false
253	input_list=""
254	interpreted_config_file=""
255	job_catalog="~/job_queue"
256	job_on_file=""
257	keep_data_from_previous_run=false
258	link_local_input=false
259	link_local_output=false
260	localhost_realname=$(hostname)
261	local_dvrserver_running=.FALSE.
262	locat=normal
263	mainprog=""
264	makefile=""
265	max_par_io_str=""
266	mc=$0
267	while [[ $(echo $mc \| grep -c "/") != 0 ]]
268	do
269	mc=`echo $mc \| cut -f2- -d"/"`
270	done
271	module_calls=""
272	mrun_script_name=$mc
273	netcdf_inc=""
274	netcdf_lib=""
275	netcdf_support=false
276	node_usage=default
277	numprocs=""
278	numprocs_atmos=0
279	numprocs_ocean=0
280	OOPT=""
281	openmp=false
282	output_list=""
283	package_list=""
284	queue=none
285	read_from_config=""
286	restart_run=false
287	if [[ `hostname` = rte10 ]]
288	then
289	return_address=133.5.185.60
290	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
291	elif [[ `hostname` = climate0 ]]
292	then
293	return_address=165.132.26.68
294	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
295	elif [[ `hostname` = urban00 ]]
296	then
297	return_address=147.46.30.151
298	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
299	else
300	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
301	fi
302	return_password=""
303	return_username=$LOGNAME
304	remotecall=false
305	remote_username=""
306	run_coupled_model=false
307	run_mode=""
308	store_on_archive_system=false
309	dashes=" ----------------------------------------------------------------------------"
310	silent=false
311	source_list=""
312	source_path=SOURCE
313	tasks_per_node=""
314	threads_per_task=1
315	tmpcreate=false
316	tmp_data_catalog=""
317	transfer_problems=false
318	usern=$LOGNAME
319	use_openmp=false
320	version="MRUN 2.1 Rev$Rev: 1649 $"
321	working_directory=`pwd`
322	TOPT=""
323	XOPT=""
324	zeit=$( date \| cut -c 12-19 )
325
326	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
327	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
328	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
329	# SCRIPT-OPTION ARGUMENTS
330	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
331
332	# ERROR HANDLING IN CASE OF EXIT
333	trap 'rm -rf $working_directory/tmp_mrun
334	if [[ $locat != normal && $locat != control_c ]]
335	then
336
337	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
338	(( i = 0 ))
339	while (( i < iec ))
340	do
341	(( i = i + 1 ))
342	printf "\n *** Execution of ERROR-command:\n"
343	printf " >>> ${err_command[$i]}\n"
344	eval ${err_command[$i]}
345	done
346	if [[ -n $interpreted_config_file ]]
347	then
348	rm -rf $interpreted_config_file
349	fi
350	if [[ -n .mrun_environment ]]
351	then
352	rm -rf .mrun_environment
353	fi
354	if [[ $tmpcreate = true ]]
355	then
356	printf "\n *** Contents of \"$TEMPDIR\":\n"
357	ls -al; cd
358	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
359	fi
360	if [[ "$dvrserver_id" != "" ]]
361	then
362	echo "+++ killing dvrserver_id=$dvrserver_id"
363	kill $dvrserver_id
364	fi
365	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
366	then
367	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
368	fi
369	printf "\n\n+++ MRUN killed \n\n"
370	elif [[ $locat != control_c ]]
371	then
372	printf "\n\n --> all actions finished\n\n"
373	printf " Bye, bye $usern !!\n\n"
374	fi' exit
375
376
377	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
378	trap 'rm -rf $working_directory/tmp_mrun
379	rm -rf $working_directory/tmp_check_namelist_files
380	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
381	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
382	then
383	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
384	fi
385	if [[ "$dvrserver_id" != "" ]]
386	then
387	echo "+++ killing dvrserver_id=$dvrserver_id"
388	kill $dvrserver_id
389	fi
390	printf "\n+++ MRUN killed by \"^C\" \n\n"
391	locat=control_c
392	exit
393	' 2
394
395
396	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
397	# BEEN SET
398	if [[ "$PALM_BIN" = "" ]]
399	then
400	printf "\n +++ environment variable PALM_BIN has not been set"
401	printf "\n please set it to the directory where the PALM scripts are located"
402	locat=palm_bin; exit
403	fi
404	export PATH=$PALM_BIN:$PATH
405
406
407
408	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
409	# WHICH WILL BE USED TO START RESTART-JOBS
410	while getopts :a:AbBc:Cd:D:Fg:G:h:H:i:IkK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
411	do
412	case $option in
413	(a) afname=$OPTARG;;
414	(A) store_on_archive_system=true; mc="$mc -A";;
415	(b) do_batch=true; mc="$mc -b";;
416	(B) delete_temporary_catalog=false; mc="$mc -B";;
417	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
418	(C) restart_run=true; mc="$mc -C";;
419	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
420	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
421	(F) job_on_file="-D"; mc="$mc -F";;
422	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
423	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
424	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
425	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
426	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
427	(I) ignore_archive_error=true; mc="$mc -I";;
428	(k) keep_data_from_previous_run=true; mc="$mc -k";;
429	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
430	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
431	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
432	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
433	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
434	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
435	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
436	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
437	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
438	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
439	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
440	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
441	(S) read_from_config=false; mc="$mc -S";;
442	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
443	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
444	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
445	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
446	(v) silent=true; mc="$mc -v";;
447	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
448	(x) do_trace=true;set -x; mc="$mc -x";;
449	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
450	(y) ocean_file_appendix=true; mc="$mc -y";;
451	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
452	(z) check_namelist_files=false; mc="$mc -z";;
453	(Z) combine_plot_fields=false; mc="$mc -Z";;
454	(\?) printf "\n +++ unknown option $OPTARG \n"
455	printf "\n --> type \"$0 ?\" for available options \n"
456	locat=parameter;exit;;
457	esac
458	done
459
460
461	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
462	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
463	(( to_shift = $OPTIND - 1 ))
464	shift $to_shift
465
466	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
467	if [[ "$1" = "?" ]]
468	then
469	(printf "\n *** mrun can be called as follows:\n"
470	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 -Z <modus> \n"
471	printf "\n Description of available options:\n"
472	printf "\n Option Description Default-Value"
473	printf "\n -a base name of input files equiv. -d"
474	printf "\n -A archiving when using file-attribute fl"
475	printf "\n -b batch-job on local machine ---"
476	printf "\n -B do not delete temporary directory at end ---"
477	printf "\n -c configuration file .mrun.config"
478	printf "\n -d base name of files attached to program test"
479	printf "\n -D preprocessor(cpp)-directives \"\" "
480	printf "\n -F create remote job file only ---"
481	printf "\n -h execution host $localhost_realname"
482	printf "\n -i INPUT control list \"\" "
483	printf "\n -I archiving errors of previous batch-jobs"
484	printf "\n will be ignored"
485	printf "\n -k keep data from previous run"
486	printf "\n -K additional conditions for controling"
487	printf "\n usage of conditional code and"
488	printf "\n env-variables in configuration file \"\" "
489	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
490	printf "\n -M Makefile name Makefile"
491	printf "\n -n node usage (shared/not_shared) depending on -h"
492	printf "\n -o OUTPUT control list \"\" "
493	printf "\n -O threads per openMP task ---"
494	printf "\n -p software package list \"\" "
495	printf "\n -q queue \"$queue\" "
496	printf "\n -r run control list (combines -i -o) \"\" "
497	printf "\n -s filenames of routines to be compiled \"\" "
498	printf "\n must end with .f, .f90, .F, or .c !"
499	printf "\n use \"..\" for more than one file and wildcards"
500	printf "\n -s LM compiles all locally modified files"
501	printf "\n -S config file interpreted by shellscript ---"
502	printf "\n -t allowed cpu-time in seconds (batch) 0"
503	printf "\n -T tasks per node depending on -h"
504	printf "\n -u username on remote machine \"\" "
505	printf "\n -v no prompt for confirmation ---"
506	printf "\n -w maximum parallel io streams as given by -X"
507	printf "\n -x tracing of mrun for debug purposes ---"
508	printf "\n -X # of processors (on parallel machines) 1"
509	printf "\n -y add appendix \"_O\" to all local output"
510	printf "\n files (ocean precursor runs followed by"
511	printf "\n coupled atmosphere-ocean runs) ---"
512	printf "\n -Y run coupled model, \"#1 #2\" with"
513	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
514	printf "\n -z disable a priori parameter file check ---"
515	printf "\n -Z skip combine_plot_fields at the end of "
516	printf "\n the simulation ---"
517	printf "\n "
518	printf "\n Possible values of positional parameter <modus>:"
519	printf "\n \"?\" - this outline \n\n") \| more
520	exit
521	elif [[ "$1" != "" ]]
522	then
523	printf "\n +++ positional parameter $1 unknown \n"
524	locat=parameter; exit
525	fi
526
527
528
529	# SHORT STARTING MESSAGE
530	printf "\n*** $version "
531	printf "\n will be executed. Please wait ..."
532
533
534
535	# CHECK, IF CONFIGURATION FILE EXISTS
536	if [[ ! -f $config_file ]]
537	then
538	printf "\n\n +++ configuration file: "
539	printf "\n $config_file"
540	printf "\n does not exist"
541	locat=connect; exit
542	fi
543
544
545	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
546	line=""
547	grep "%host_identifier" $config_file > tmp_mrun
548	while read line
549	do
550	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
551	then
552	HOSTNAME=`echo $line \| cut -d" " -s -f2`
553	host_identifier=`echo $line \| cut -d" " -s -f3`
554	if [[ $localhost_realname = $HOSTNAME ]]
555	then
556	localhost=$host_identifier
557	break
558	fi
559	fi
560	done < tmp_mrun
561
562	if [[ "$localhost" = "" ]]
563	then
564	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
565	printf "\n for local host \"$localhost_realname\"."
566	printf "\n Please add line"
567	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
568	printf "\n to the configuration file."
569	locat=localhost; exit
570	fi
571
572
573	# SET HOST-SPECIFIC VARIABLES
574	case $localhost_realname in
575	(r1\|r2\|h01\|b01) archive_system=tivoli;;
576	(cs*) archive_system=ut;;
577	esac
578
579
580	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
581	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
582	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
583	[[ "$afname" = "" ]] && afname=$fname
584
585
586	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
587	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
588	# STATEMENTS IN THE CONFIGURATION FILE
589	if [[ "$run_mode" != "" ]]
590	then
591	input_list="$input_list $run_mode"
592	output_list="$output_list $run_mode"
593	fi
594
595
596	# ??? is this (and the respective option -H) really required ???
597	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
598	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
599	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
600	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
601	if [[ "$fromhost" = "" ]]
602	then
603	fromhost=$localhost
604	fi
605
606
607	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
608	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
609	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
610	# TO BE SUBMITTED (I.E. do_batch=true)
611	if [[ -n $host && "$host" != $localhost ]]
612	then
613	do_batch=true
614	do_remote=true
615	case $host in
616	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
617	(*) printf "\n"
618	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
619	printf "\n is not available"
620	locat=nqs; (( iec = 0 )); exit;;
621	esac
622	else
623	host=$localhost
624	fi
625
626
627	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
628	if [[ -n $additional_conditions ]]
629	then
630	cond1=`echo $additional_conditions \| cut -d" " -f1`
631	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
632	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
633	if [[ -n $dummy ]]
634	then
635	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
636	locat=options; exit
637	fi
638	block=_$cond1
639	[[ -n $cond2 ]] && block=${block}_$cond2
640	fi
641
642
643	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
644	if [[ $run_coupled_model = true ]]
645	then
646
647	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
648	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
649
650	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
651	then
652
653	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
654	printf "\n PEs (total) : $numprocs"
655	printf "\n PEs (atmosphere): $numprocs_atmos"
656	printf "\n PEs (ocean) : $numprocs_ocean"
657	locat=coupling; exit
658
659	fi
660
661
662	# GET coupled_mode FROM THE CONFIG FILE
663	line=""
664	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
665	while read line
666	do
667	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
668	then
669	coupled_mode="mpi2"
670	fi
671	done < tmp_mrun
672
673	fi
674
675	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
676	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
677	then
678	if [[ $ignore_archive_error = false ]]
679	then
680	printf "\n +++ data archiving of previous run failed"
681	printf "\n see directory \~/job_queue on remote machine"
682	locat=archive; exit
683	else
684	printf "\n +++ warning: data archiving in a previous run failed"
685	printf "\n MRUN continues, trying to get backup copy"
686	fi
687	fi
688
689
690	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
691	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
692	mrun_memory=$memory
693	mrun_group_number=$group_number
694	mrun_cpumax=$cpumax
695	mrun_numprocs=$numprocs
696
697
698	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
699	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
700	if [[ "$read_from_config" = false ]]
701	then
702	[[ $silent = false ]] && printf "\n Reading the configuration file... "
703
704	# READ THE CONFIGURATION FILE LINE BY LINE
705	while read zeile
706	do
707	[[ $silent = false ]] && printf "."
708
709
710	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
711	eval zeile=\"$zeile\"
712
713
714	# INTERPRET THE LINE
715	if [[ "$(echo $zeile)" = "" ]]
716	then
717	# EMPTY LINE, NO ACTION
718	continue
719
720	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
721	then
722
723	# LINE IS A COMMENT LINE
724	true
725
726	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
727	then
728
729	# LINE DEFINES AN ENVIRONMENT-VARIABLE
730	zeile=$(echo $zeile \| cut -c2-)
731	var=`echo $zeile \| cut -d" " -f1`
732	value=`echo $zeile \| cut -d" " -s -f2`
733	for_host=`echo $zeile \| cut -d" " -s -f3`
734	for_cond1=`echo $zeile \| cut -d" " -s -f4`
735	for_cond2=`echo $zeile \| cut -d" " -s -f5`
736
737	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
738	then
739
740	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
741	# "::" IS REPLACED BY ":".
742	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
743
744
745	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
746	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
747	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
748	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
749	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
750	# CONFIGURATION-FILE.
751	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
752	then
753	eval $var=\$value
754
755	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
756	if [[ $do_trace = true ]]
757	then
758	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
759	fi
760	fi
761
762	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
763	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
764	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
765	# MUST HAVE TO BE STARTED
766	if [[ $var = host ]]
767	then
768	if [[ -n $host && "$host" != $localhost ]]
769	then
770	do_batch=true
771	do_remote=true
772	case $host in
773	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
774	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
775	printf "\n is not available"
776	locat=nqs; exit;;
777	esac
778	else
779	host=$localhost
780	fi
781	fi
782
783	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
784	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
785	# BY MRUN (E.G. subjob)
786	export $var
787	fi
788
789
790
791
792	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
793	then
794
795	# LINE DEFINES ERROR-COMMAND
796	(( iec = iec + 1 ))
797	zeile=$(echo $zeile \| cut -c4-)
798	err_command[$iec]="$zeile"
799
800	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
801	then
802
803	# LINE DEFINES INPUT-COMMAND
804	(( iic = iic + 1 ))
805	zeile=$(echo $zeile \| cut -c4-)
806	in_command[$iic]="$zeile"
807
808	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
809	then
810
811	# LINE DEFINES OUTPUT-COMMAND
812	(( ioc = ioc + 1 ))
813	zeile=$(echo $zeile \| cut -c4-)
814	out_command[$ioc]="$zeile"
815
816	else
817
818	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
819	# s2a: in/out - field
820	# s2b: loc - field (optional)
821	# s2c: tr/ar - field (optional)
822	s1=`echo $zeile \| cut -d" " -f1`
823	s2=`echo $zeile \| cut -d" " -s -f2`
824	s2a=$(echo $s2 \| cut -d":" -f1)
825	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
826	then
827	s2b=""
828	s2c=""
829	else
830	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
831	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
832	fi
833	s3=`echo $zeile \| cut -d" " -f3`
834	s4=`echo $zeile \| cut -d" " -s -f4`
835	s5=`echo $zeile \| cut -d" " -s -f5`
836	s6=`echo $zeile \| cut -d" " -s -f6`
837
838
839	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
840	# INPUT- OR OUTPUT-LIST.
841	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
842	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
843	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
844	# IS NOT CHECKED AND STORED.
845	IFSALT="$IFS"; IFS="$IFS:"
846	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
847	then
848	found=false
849	for actual in $input_list
850	do
851	for formal in $s3
852	do
853	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
854	done
855	done
856	if [[ $found = true ]]
857	then
858	(( iin = iin + 1 ))
859	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
860	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
861	extin[$iin]=$s6
862	fi
863	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
864	then
865	found=false
866	for actual in $output_list
867	do
868	for formal in $s3
869	do
870	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
871	done
872	done
873	if [[ $found = true ]]
874	then
875	(( iout = iout + 1 ))
876	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
877	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
878	fi
879	elif [[ "$s2a" != in && "$s2a" != out ]]
880	then
881	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
882	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
883	locat=connect; exit
884	fi
885	IFS="$IFSALT"
886	fi
887	done < $config_file
888
889	else
890
891	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
892	[[ $silent = false ]] && printf "..."
893	interpreted_config_file=.icf.$RANDOM
894
895
896
897	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
898	cat > .mrun_environment << %%END%%
899	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
900	config_file = '$config_file', do_remote = '$do_remote',
901	do_trace = '$do_trace', host = '$host',
902	input_list = '$input_list', icf = '$interpreted_config_file',
903	localhost = '$localhost', output_list = '$output_list' /
904
905	%%END%%
906
907	if [[ "$host" != $localhost ]]
908	then
909
910	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
911	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
912	if [[ $? != 0 ]]
913	then
914	printf "\n\n +++ no interpret_config found"
915	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
916	locat=interpret_config; exit
917	fi
918	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
919	$interpret_config_executable
920
921	else
922
923	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
924	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
925	then
926	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
927	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
928	locat=interpret_config; exit
929	else
930	interpret_config${block}.x
931	fi
932
933	fi
934	rm .mrun_environment
935
936
937	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
938	chmod u+x $interpreted_config_file
939	export PATH=$PATH:.
940	. $interpreted_config_file
941	rm $interpreted_config_file
942
943	fi
944
945
946	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
947	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
948	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
949	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
950	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
951	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
952	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
953
954
955	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
956	# FOR SOURCE-FILES TO BE COMPILED.
957	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
958	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
959	if [[ "$SOURCES_COMPLETE" = "" ]]
960	then
961
962	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
963	# HAS BEEN DEFINED
964	source_path=""
965	line=""
966	grep "%source_path" $config_file > tmp_mrun
967	while read line
968	do
969	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
970	then
971	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
972	then
973	global_source_path=`echo $line \| cut -d" " -f2`
974	fi
975	fi
976	done < tmp_mrun
977
978	line=""
979	found=false
980	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
981	while read line
982	do
983	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
984	then
985	if [[ $found = true ]]
986	then
987	printf "\n\n +++ more than one source path found in configuration file"
988	printf "\n for local host \"$localhost\" "
989	locat=source_path; exit
990	fi
991	source_path=`echo $line \| cut -d" " -f2`
992	found=true
993	fi
994	done < tmp_mrun
995	rm tmp_mrun
996
997	if [[ "$source_path" = "" ]]
998	then
999	if [[ "$global_source_path" != "" ]]
1000	then
1001	source_path=$global_source_path
1002	else
1003	printf "\n\n +++ no source path found in configuration file"
1004	printf "\n for local host \"$localhost\" "
1005	locat=source_path; exit
1006	fi
1007	fi
1008	eval source_path=$source_path
1009
1010	if [[ ! -d $source_path ]]
1011	then
1012	printf "\n\n +++ source path \"$source_path\" on local host"
1013	printf "\n \"$localhost\" does not exist"
1014	locat=source_path; exit
1015	fi
1016
1017	fi
1018
1019
1020	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1021	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1022	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1023	then
1024	global_revision=`svnversion $source_path 2>/dev/null`
1025	global_revision="Rev: $global_revision"
1026	fi
1027
1028
1029	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1030	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1031	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1032	if [[ -n $host && "$host" != $localhost ]]
1033	then
1034	do_batch=true
1035	do_remote=true
1036	case $host in
1037	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1038	(*) printf "\n"
1039	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1040	printf "\n is not available"
1041	locat=nqs; (( iec = 0 )); exit;;
1042	esac
1043	else
1044	host=$localhost
1045	fi
1046
1047
1048
1049	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1050	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1051	then
1052
1053	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1054	if [[ ! -n $numprocs ]]
1055	then
1056	printf "\n"
1057	printf "\n +++ option \"-K parallel\" requires additional specification"
1058	printf "\n of the number of processors to be used by"
1059	printf "\n mrun-option \"-X\" or by environment-variable"
1060	printf "\n \"numprocs\" in the configuration file"
1061	locat=numprocs; (( iec = 0 )); exit
1062	fi
1063
1064	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1065	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1066	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1067	then
1068	printf "\n"
1069	printf "\n +++ option \"-T\" (tasks per node) is missing"
1070	printf "\n set -T option or define tasks_per_node in the config file"
1071	locat=tasks_per_node; (( iec = 0 )); exit
1072	fi
1073
1074	if (( numprocs < tasks_per_node ))
1075	then
1076	printf "\n"
1077	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1078	printf "\n given values: -T $tasks_per_node -X $numprocs"
1079	locat=tasks_per_node; (( iec = 0 )); exit
1080	fi
1081
1082	if [[ $host != lcflow && $host != lcxt5m ]]
1083	then
1084	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1085	(( ival = $tasks_per_node ))
1086	(( pes = numprocs ))
1087	(( ii = pes / ival ))
1088	(( remaining_pes = pes - ii * ival ))
1089	if (( remaining_pes > 0 ))
1090	then
1091	printf "\n"
1092	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1093	printf "\n divisor of the total number of processors (option \"-X\")"
1094	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1095	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1096	(( nodes = nodes + 1 ))
1097	fi
1098	fi
1099
1100
1101	# SETTINGS FOR SUBJOB-COMMAND
1102	OOPT="-O $threads_per_task"
1103
1104	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1105	if [[ "$tasks_per_node" != "" ]]
1106	then
1107	TOPT="-T $tasks_per_node"
1108	fi
1109
1110	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1111	if [[ $node_usage = default ]]
1112	then
1113	if [[ $host = ibms ]]
1114	then
1115	node_usage=shared
1116	else
1117	node_usage=not_shared
1118	fi
1119	fi
1120
1121	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1122	then
1123	printf "\n"
1124	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1125	printf "\n \"shared\" or \"not_shared\""
1126	locat=tasks_per_node; (( iec = 0 )); exit
1127	fi
1128
1129	fi
1130
1131	# CHECK IF HOSTFILE EXISTS
1132	if [[ -n $hostfile ]]
1133	then
1134	if [[ ! -f $hostfile ]]
1135	then
1136	printf "\n"
1137	printf "\n +++ hostfile \"$hostfile\" does not exist"
1138	locat=hostfile; exit
1139	fi
1140	fi
1141
1142
1143	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1144	if [[ "$maximum_parallel_io_streams" = "" ]]
1145	then
1146	maximum_parallel_io_streams=$numprocs
1147	fi
1148
1149
1150	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1151	if [[ "$scp_port" != "" ]]
1152	then
1153	PORTOPT="-P $scp_port"
1154	SSH_PORTOPT="-p $scp_port"
1155	fi
1156
1157
1158	# SET DEFAULT-QUEUE, IF NOT GIVEN
1159	if [[ $queue = none ]]
1160	then
1161	case $host in
1162	(ibmh) queue=cluster;;
1163	(ibmkisti) queue=class.32plus;;
1164	(lcbullhh) queue=compute;;
1165	(lccrayb) queue=mpp1q;;
1166	(lccrayh) queue=mpp1q;;
1167	(lckiaps) queue=normal;;
1168	(lckyoto) queue=ph;;
1169	(lckyuh) queue=fx-single;;
1170	(lckyut) queue=cx-single;;
1171	(lctit) queue=S;;
1172	(nech) queue=none;;
1173	(unics) queue=unics;;
1174	esac
1175	fi
1176
1177
1178	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1179	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1180	(( i = 0 ))
1181	while (( i < iin ))
1182	do
1183	(( i = i + 1 ))
1184	(( maxcycle = 0 ))
1185
1186	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1187	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1188	if [[ "${actionin[$i]}" = di ]]
1189	then
1190	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1191	# HOST ONLY
1192	eval filename=${pathin[$i]}/${endin[$i]}
1193	else
1194	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1195	# HOST ONLY
1196	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1197	fi
1198	eval pathname=${pathin[$i]}
1199
1200	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1201	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1202	then
1203	filename_input=$filename
1204	fi
1205
1206	# CHECK IF FILE EXISTS
1207	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1208	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1209	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1210	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1211	then
1212
1213	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1214	if [[ "${transin[$i]}" != "locopt" ]]
1215	then
1216	printf "\n\n +++ INPUT-file: "
1217	if [[ "${extin[$i]}" = "" ]]
1218	then
1219	printf "\n $filename"
1220	else
1221	printf "\n $filename.${extin[$i]}"
1222	fi
1223	printf "\n does not exist\n"
1224	locat=input; exit
1225	else
1226	transin[$i]="unavailable"
1227	fi
1228	else
1229
1230	# DETERMINE THE FILE'S CYCLE NUMBER
1231	ls -1 -d $filename > filelist 2>/dev/null
1232	ls -1 -d $filename.* >> filelist 2>/dev/null
1233	while read zeile
1234	do
1235	cycle=$(echo $zeile \| cut -f2 -d".")
1236	if [[ "$cycle" = "$zeile" ]]
1237	then
1238	(( icycle = 0 ))
1239	elif [[ "$cycle" = "${extin[$i]}" ]]
1240	then
1241	(( icycle = 0 ))
1242	else
1243	(( icycle = $cycle ))
1244	fi
1245	if (( icycle > maxcycle ))
1246	then
1247	(( maxcycle = icycle ))
1248	file_to_be_used=$zeile
1249	fi
1250	done <filelist
1251	rm filelist
1252
1253	# APPEND CYCLE NUMBER TO FILENAME
1254	if (( maxcycle > 0 ))
1255	then
1256	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1257	then
1258	filename=${filename}.$maxcycle.${extin[$i]}
1259	else
1260	filename=${filename}.$maxcycle
1261	fi
1262	else
1263	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1264	then
1265	filename=${filename}.${extin[$i]}
1266	fi
1267	fi
1268
1269	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1270	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1271	absnamein[$i]=$filename
1272	if (( maxcycle > 0 ))
1273	then
1274	if [[ "${actionin[$i]}" = di ]]
1275	then
1276	frelin[$i]=${endin[$i]}.$maxcycle
1277	else
1278	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1279	fi
1280	else
1281	if [[ "${actionin[$i]}" = di ]]
1282	then
1283	frelin[$i]=${endin[$i]}
1284	else
1285	frelin[$i]=${afname}${endin[$i]}
1286	fi
1287	fi
1288
1289	fi
1290	done
1291
1292	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1293	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1294	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1295	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1296	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1297	# REMOTE HOST)
1298	(( i = 0 ))
1299	while (( i < iout ))
1300	do
1301	(( i = i + 1 ))
1302	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1303	then
1304	if [[ "${actionout[$i]}" = tr ]]
1305	then
1306	actionout[$i]=""
1307	elif [[ "${actionout[$i]}" = trpe ]]
1308	then
1309	actionout[$i]=pe
1310	elif [[ "${actionout[$i]}" = tra ]]
1311	then
1312	actionout[$i]=a
1313	fi
1314	(( maxcycle = 0 ))
1315	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1316	eval catalogname=${pathout[$i]}
1317	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1318	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1319	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1320	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1321	then
1322
1323	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1324	if cat /dev/null > $filename
1325	then
1326	rm $filename
1327	else
1328
1329	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1330	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1331	if [[ ! -d $catalogname ]]
1332	then
1333	if mkdir -p $catalogname
1334	then
1335	printf "\n\n *** directory:"
1336	printf "\n $catalogname"
1337	printf "\n was created\n"
1338	else
1339	printf "\n\n +++ OUTPUT-file:"
1340	printf "\n $filename"
1341	printf "\n cannot be created, because directory does not exist"
1342	printf "\n and cannot be created either"
1343	printf "\n"
1344	locat=output ; exit
1345	fi 2>/dev/null
1346	else
1347	printf "\n\n +++ OUTPUT-file:"
1348	printf "\n $filename"
1349	printf "\n cannot be created, although directory exists"
1350	printf "\n"
1351	locat=output ; exit
1352	fi
1353	fi 2>/dev/null
1354	else
1355
1356	# DETERMINE THE CYCLE NUMBER
1357	ls -1 -d $filename > filelist 2>/dev/null
1358	ls -1 -d $filename.* >> filelist 2>/dev/null
1359	while read zeile
1360	do
1361	cycle=$(echo $zeile \| cut -f2 -d".")
1362	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1363	then
1364	(( icycle = 1 ))
1365	else
1366	(( icycle = $cycle + 1 ))
1367	fi
1368	if (( icycle > maxcycle ))
1369	then
1370	(( maxcycle = icycle ))
1371	fi
1372	done <filelist
1373	rm filelist
1374	fi
1375
1376	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1377	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1378	if [[ "${actionout[$i]}" != a ]]
1379	then
1380	if (( maxcycle > 0 ))
1381	then
1382	filename=${filename}.$maxcycle
1383	if cat /dev/null > $filename
1384	then
1385	rm $filename
1386	else
1387	printf "\n +++ OUTPUT-file:"
1388	printf "\n $filename"
1389	printf "\n cannot be created"
1390	locat=output ; exit
1391	fi
1392	fi
1393	else
1394	(( maxcycle = maxcycle - 1 ))
1395	if (( maxcycle > 0 ))
1396	then
1397	filename=${filename}.$maxcycle
1398	fi
1399	fi
1400
1401	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1402	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1403	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1404	pathout[$i]=$filename
1405	if (( maxcycle > 0 ))
1406	then
1407	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1408	else
1409	frelout[$i]=${fname}${endout[$i]}
1410	fi
1411
1412	fi
1413	done
1414
1415
1416	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1417	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1418	then
1419	if [[ "$dvr_inc" = "" ]]
1420	then
1421	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1422	printf "\n This is required for the dvrp_graphics package.\n"
1423	locat=dvr; exit
1424	fi
1425	if [[ "$dvr_lib" = "" ]]
1426	then
1427	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1428	printf "\n This is required for the dvrp_graphics package.\n"
1429	locat=dvr; exit
1430	fi
1431	fi
1432
1433
1434	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1435	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1436	if [[ "$mainprog" = "" && "$executable" = "" ]]
1437	then
1438	printf "\n +++ neither main program nor executable defined"
1439	locat=source; exit
1440	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1441	then
1442	printf "\n +++ main program as well as executable defined"
1443	locat=source; exit
1444	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1445	then
1446	do_compile=false
1447	fi
1448
1449
1450	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1451	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1452	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1453	then
1454	rm -rf SOURCES_FOR_RUN_$fname
1455	mkdir SOURCES_FOR_RUN_$fname
1456	fi
1457
1458
1459	# COLLECT ALL ROUTINES TO BE COMPILED
1460	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1461	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1462	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1463	then
1464
1465	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1466
1467	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1468	then
1469
1470	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1471	source_list=""
1472	cd $source_path
1473
1474
1475	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1476	if [[ ! -d .svn ]]
1477	then
1478	printf "\n\n +++ source directory"
1479	printf "\n \"$source_path\" "
1480	printf "\n is not under control of \"subversion\"."
1481	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1482	fi
1483
1484
1485	# LIST ALL MODIFIED SOURCE CODE FILES
1486	Filenames=""
1487	svn status > tmp_mrun
1488	while read line
1489	do
1490	firstc=`echo $line \| cut -c1`
1491	if [[ $firstc = M \|\| $firstc = "?" ]]
1492	then
1493	Name=`echo "$line" \| cut -c8-`
1494	extension=`echo $Name \| cut -d. -f2`
1495	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1496	then
1497	Filenames="$Filenames "$Name
1498	fi
1499	fi
1500	done < tmp_mrun
1501
1502
1503	# COPY FILES TO SOURCES_FOR_RUN_...
1504	for dateiname in $Filenames
1505	do
1506	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1507	source_list=$source_list"$dateiname "
1508	done
1509
1510	cd - > /dev/null
1511
1512
1513	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1514	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1515	elif [[ "$source_list" != "" && $restart_run != true ]]
1516	then
1517
1518	cd $source_path
1519
1520	for filename in $source_list
1521	do
1522
1523	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1524	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1525	then
1526	printf "\n +++ source code file: $filename"
1527	printf "\n must not contain (\"/\") "
1528	locat=source; exit
1529	fi
1530
1531	if [[ ! -f $filename ]]
1532	then
1533	printf "\n +++ source code file: $filename"
1534	printf "\n does not exist"
1535	locat=source; exit
1536	else
1537	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1538	fi
1539
1540	done
1541
1542	cd - > /dev/null
1543
1544	fi
1545
1546
1547	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1548	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1549	if [[ $restart_run != true ]]
1550	then
1551
1552	if [[ ! -f "$source_path/$mainprog" ]]
1553	then
1554	printf "\n\n +++ main program: $mainprog"
1555	printf "\n does not exist in source directory"
1556	printf "\n \"$source_path\"\n"
1557	locat=source; exit
1558	else
1559	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1560	then
1561	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1562	source_list=${mainprog}" $source_list"
1563	fi
1564	fi
1565	fi
1566
1567
1568	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1569	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1570	if [[ "$restart_run" != true ]]
1571	then
1572	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1573	if [[ ! -f $makefile ]]
1574	then
1575	printf "\n +++ file \"$makefile\" does not exist"
1576	locat=make; exit
1577	else
1578	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1579	fi
1580	fi
1581
1582
1583	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1584	if [[ $restart_run != true && "$add_source_path" != "" ]]
1585	then
1586
1587	# DOES THE DIRECTORY EXIST?
1588	if [[ ! -d $add_source_path ]]
1589	then
1590	printf "\n\n +++ WARNING: additional source code directory"
1591	printf "\n \"$add_source_path\" "
1592	printf "\n does not exist or is not a directory."
1593	printf "\n No source code will be used from this directory!\n"
1594	add_source_path=""
1595	if [[ $silent == false ]]
1596	then
1597	sleep 3
1598	fi
1599	else
1600
1601	cd $add_source_path
1602	found=false
1603
1604	Names=$(ls -1 *.f90 2>&1)
1605	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1606	Names=$(ls -1 *.F90 2>&1)
1607	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1608	Names=$(ls -1 *.F 2>&1)
1609	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1610	Names=$(ls -1 *.f 2>&1)
1611	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1612	Names=$(ls -1 *.c 2>&1)
1613	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1614
1615	cd - > /dev/null
1616	cd SOURCES_FOR_RUN_$fname
1617
1618	# COPY MAKEFILE IF EXISTING
1619	if [[ -f $add_source_path/Makefile ]]
1620	then
1621	printf "\n\n *** user Makefile from directory"
1622	printf "\n \"$add_source_path\" is used \n"
1623	if [[ $silent == false ]]
1624	then
1625	sleep 1
1626	fi
1627	cp $add_source_path/Makefile .
1628	fi
1629
1630	for dateiname in $AddFilenames
1631	do
1632	if [[ -f $dateiname ]]
1633	then
1634	printf "\n +++ source code file \"$dateiname\" found in additional"
1635	printf "\n source code directory \"$add_source_path\" "
1636	printf "\n but was also given with option \"-s\" which means that it should be taken"
1637	printf "\n from directory \"$source_path\"."
1638	locat=source; exit
1639	fi
1640
1641	cp $add_source_path/$dateiname .
1642	source_list="$source_list $dateiname"
1643
1644	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1645	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1646	then
1647	printf "\n\n +++ user file \"$dateiname\" "
1648	printf "\n is not listed in Makefile \n"
1649	locat=source; exit
1650	else
1651
1652	if [[ $found = false ]]
1653	then
1654	found=true
1655	printf "\n\n *** following user file(s) added to the"
1656	printf " files to be translated:\n "
1657	fi
1658	printf "$dateiname "
1659	if [[ $silent == false ]]
1660	then
1661	sleep 0.5
1662	fi
1663
1664	fi
1665	done
1666	[[ $found = true ]] && printf "\n"
1667	cd - > /dev/null
1668	fi
1669	fi
1670
1671
1672	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1673	# TO THE LIST OF FILES TO BE COMPILED
1674	if [[ $restart_run != true && -n $package_list ]]
1675	then
1676
1677	cd $source_path
1678
1679	for package in $package_list
1680	do
1681
1682	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1683
1684	# DETERMINE FILES BELONGING TO THE PACKAGE
1685	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1686	# THE NAME OF THE DIRECTORY
1687	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1688
1689
1690	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1691	# IF THEY ARE NOT ALREADY PART OF THE LIST
1692	for source_list_name in $package_source_list
1693	do
1694	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1695	then
1696
1697	# ONLY TAKE FILES WITH VALID SUFFIX
1698	ending=`echo $source_list_name \| cut -f2 -d.`
1699	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1700	then
1701	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1702	source_list="$source_list $source_list_name"
1703	fi
1704	fi
1705	done
1706	done
1707
1708	cd - > /dev/null
1709	fi
1710
1711	fi # do_compile=true
1712
1713
1714	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1715	# AND SET PRE-PROCESSOR DIRECTIVES
1716	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1717	then
1718
1719	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1720	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1721	then
1722	cpp_options="${cpp_options},-D__ibm=__ibm"
1723	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1724	then
1725	cpp_options="$cpp_options -D__nec"
1726	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1727	then
1728	cpp_options="$cpp_options -D__lc"
1729	else
1730	cpp_options="$cpp_options -D__$localhost"
1731	fi
1732
1733	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1734	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1735	then
1736	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1737	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1738	else
1739	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1740	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1741	fi
1742
1743	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1744	if [[ -n $package_list ]]
1745	then
1746	for package in $package_list
1747	do
1748	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1749	then
1750	if [[ $package != "dvrp_graphics+1PE" ]]
1751	then
1752	cpp_options="${cpp_options},-D__$package=__$package"
1753	else
1754	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1755	export use_seperate_pe_for_dvrp_output=true
1756	fi
1757	else
1758	if [[ $package != "dvrp_graphics+1PE" ]]
1759	then
1760	cpp_options="$cpp_options -D__$package"
1761	else
1762	cpp_options="$cpp_options -D__dvrp_graphics"
1763	export use_seperate_pe_for_dvrp_output=true
1764	fi
1765	fi
1766	done
1767	fi
1768
1769	# SET DIRECTIVES GIVEN BY OPTION -D
1770	if [[ -n $cpp_opts ]]
1771	then
1772	for popts in $cpp_opts
1773	do
1774	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1775	then
1776	cpp_options="${cpp_options},-D__$popts=__$popts"
1777	else
1778	cpp_options="$cpp_options -D__$popts"
1779	fi
1780	done
1781	fi
1782
1783	else
1784
1785
1786	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1787	if [[ $do_remote = false ]]
1788	then
1789	if [[ ! -f $executable ]]
1790	then
1791	printf "\n +++ executable file: $executable"
1792	printf "\n does not exist"
1793	locat=executable; exit
1794	fi
1795	fi
1796	fi
1797
1798
1799	# DETERMINE THE JOB MODE
1800	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1801	then
1802	if [[ "$LOADLBATCH" = yes ]]
1803	then
1804	batch_job=.TRUE.
1805	jobmo=BATCH
1806	else
1807	batch_job=.FALSE.
1808	jobmo=INTERACTIVE
1809	fi
1810	else
1811	if [[ "$ENVIRONMENT" = BATCH ]]
1812	then
1813	batch_job=.TRUE.
1814	jobmo=BATCH
1815	else
1816	batch_job=.FALSE.
1817	jobmo=INTERACTIVE
1818	fi
1819	fi
1820
1821	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1822	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1823	then
1824	printf "\n +++ no interactive runs allowed on host \"$host\" "
1825	printf "\n please submit batch job using mrun option \"-b\" \n"
1826	locat=normal; exit
1827	fi
1828
1829
1830	# CHECK, IF USER DEFINED A COMPILER
1831	if [[ "$compiler_name" = "" ]]
1832	then
1833
1834	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1835	locat=compiler_name; exit
1836
1837	fi
1838
1839
1840	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1841
1842	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1843	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1844	then
1845	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1846	else
1847	kennung=$RANDOM
1848	fi
1849
1850	if [[ "$tmp_user_catalog" = "" ]]
1851	then
1852	if [[ $localhost = ibmh ]]
1853	then
1854	tmp_user_catalog=$SCRATCH
1855	elif [[ $localhost = nech ]]
1856	then
1857	tmp_user_catalog=$WRKSHR
1858	else
1859	tmp_user_catalog=/tmp
1860	fi
1861	fi
1862	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1863
1864
1865	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1866	if [[ "$tmp_data_catalog" = "" ]]
1867	then
1868	if [[ $localhost = nech ]]
1869	then
1870	tmp_data_catalog=$WRKSHR/mrun_restart_data
1871	else
1872	tmp_data_catalog=/tmp/mrun_restart_data
1873	fi
1874	fi
1875
1876
1877	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1878	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1879	then
1880	eval fopts=\"$fopts\"
1881	eval lopts=\"$lopts\"
1882	fi
1883
1884
1885
1886	# DETERMINE COMPILE- AND LINK-OPTIONS
1887	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1888	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1889	ROPTS="$ropts"
1890	# if [[ ( $(echo $host \| cut -c1-3) = nec \|\| $(echo $host \| cut -c1-3) = ibm \|\| $host = lckyoto \|\| $host = lctit \|\| $host = lcflow \|\| $host = lcxe6 \|\| $host = lcxt5m \|\| $host = lck \|\| $host = lckiaps \|\| $host = lckordi \|\| $host = lcsb \|\| $host ) && -n $numprocs ]]
1891	# then
1892	XOPT="-X $numprocs"
1893	# fi
1894
1895
1896
1897	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1898	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1899	done=false
1900	while [[ $done = false ]]
1901	do
1902	cputime=$cpumax
1903	if (( $cputime == 0 ))
1904	then
1905	if [[ $do_batch = true ]]
1906	then
1907	printf "\n +++ cpu-time is undefined"
1908	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1909	printf "\n >>> "
1910	read cputime 1>/dev/null 2>&1
1911	else
1912	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1913	fi
1914	else
1915	done=true
1916	fi
1917	cpumax=$cputime
1918	done
1919
1920	(( minuten = cputime / 60 ))
1921	(( sekunden = cputime - minuten * 60 ))
1922
1923
1924	# CHECK THE MEMORY DEMAND
1925	if [[ $do_batch = true ]]
1926	then
1927	done=false
1928	while [[ $done = false ]]
1929	do
1930	if (( memory == 0 ))
1931	then
1932	printf "\n +++ memory demand is undefined"
1933	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1934	printf "\n >>> "
1935	read memory 1>/dev/null 2>&1
1936	else
1937	done=true
1938	fi
1939	done
1940	fi
1941
1942
1943	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1944	if [[ $do_remote = true && -z $remote_username ]]
1945	then
1946	while [[ -z $remote_username ]]
1947	do
1948	printf "\n +++ username on remote host \"$host\" is undefined"
1949	printf "\n >>> Please type username:"
1950	printf "\n >>> "
1951	read remote_username
1952	done
1953	mc="$mc -u$remote_username"
1954	fi
1955
1956	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1957	if [[ "$login_init_cmd" != "" ]]
1958	then
1959	export init_cmds="${login_init_cmd};"
1960	fi
1961
1962
1963	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1964	if [[ "$modules" != "" ]]
1965	then
1966	if [[ $host = lctit ]]
1967	then
1968	export module_calls=". $modules"
1969	else
1970	export module_calls="module load ${modules};"
1971	fi
1972	fi
1973
1974	# OUTPUT OF THE MRUN-HEADER
1975	calltime=$(date)
1976	printf "\n"
1977	printf "#------------------------------------------------------------------------# \n"
1978	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1979	printf "\| \| \n"
1980	spalte1="called on:"; spalte2=$localhost_realname
1981	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1982	if [[ $do_remote = true ]]
1983	then
1984	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1985	else
1986	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1987	fi
1988	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1989	if [[ -n $numprocs ]]
1990	then
1991	if [[ $run_coupled_model = false ]]
1992	then
1993	spalte1="number of PEs:"; spalte2=$numprocs
1994	else
1995	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1996	fi
1997	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1998	fi
1999	if [[ -n $tasks_per_node ]]
2000	then
2001	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2002	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2003	if (( remaining_pes > 0 ))
2004	then
2005	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2006	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2007	fi
2008	fi
2009	if [[ $maximum_parallel_io_streams != $numprocs ]]
2010	then
2011	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2012	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2013	fi
2014	if [[ $use_openmp = true ]]
2015	then
2016	spalte1="threads per task:"; spalte2="$threads_per_task"
2017	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2018	fi
2019	printf "\| \| \n"
2020	if [[ $do_compile = true ]]
2021	then
2022	if [[ "$mopts" != "" ]]
2023	then
2024	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2026	zeile=$(echo "$mopts" \| cut -c46-)
2027	while [[ "$zeile" != "" ]]
2028	do
2029	spalte1=""
2030	spalte2=$(echo "$zeile" \| cut -c-45)
2031	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2032	zeile=$(echo "$zeile" \| cut -c46-)
2033	done
2034	fi
2035
2036	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2038	zeile=$(echo "$cpp_options" \| cut -c46-)
2039	while [[ "$zeile" != "" ]]
2040	do
2041	spalte1=""
2042	spalte2=$(echo "$zeile" \| cut -c-45)
2043	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2044	zeile=$(echo "$zeile" \| cut -c46-)
2045	done
2046
2047	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049	zeile=$(echo "$fopts" \| cut -c46-)
2050	while [[ "$zeile" != "" ]]
2051	do
2052	spalte1=""
2053	spalte2=$(echo "$zeile" \| cut -c-45)
2054	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2055	zeile=$(echo "$zeile" \| cut -c46-)
2056	done
2057
2058	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2059	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2060	zeile=$(echo "$lopts" \| cut -c46-)
2061	while [[ "$zeile" != "" ]]
2062	do
2063	spalte1=""
2064	spalte2=$(echo "$zeile" \| cut -c-45)
2065	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2066	zeile=$(echo "$zeile" \| cut -c46-)
2067	done
2068
2069	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	zeile=$(echo "$modules" \| cut -c46-)
2072	while [[ "$zeile" != "" ]]
2073	do
2074	spalte1=""
2075	spalte2=$(echo "$zeile" \| cut -c-45)
2076	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2077	zeile=$(echo "$zeile" \| cut -c46-)
2078	done
2079
2080	spalte1="main program:"; spalte2=$mainprog
2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2082	else
2083	spalte1=executable:; spalte2=$executable
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085	fi
2086	printf "\| \| \n"
2087	spalte1="base name of files:"; spalte2=$fname
2088	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2089	if [[ $fname != $afname ]]
2090	then
2091	spalte1="base name of input files:"; spalte2=$afname
2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2093	fi
2094	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2095	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2096	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098
2099	if [[ "$ocean_file_appendix" = true ]]
2100	then
2101	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2102	fi
2103
2104	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2105	then
2106	spalte1="memory demand / PE":; spalte2="$memory MB"
2107	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2108	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2109	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2110	fi
2111
2112	if [[ $do_compile = true ]]
2113	then
2114	printf "\| \| \n"
2115	printf "\| Files to be compiled: \| \n"
2116	zeile=$source_list
2117	while [[ "$zeile" != "" ]]
2118	do
2119	linestart=$(echo $zeile \| cut -c-70)
2120	printf "\| %-70s \| \n" "$linestart"
2121	zeile=$(echo "$zeile" \| cut -c71-)
2122	done
2123	fi
2124	printf "#------------------------------------------------------------------------#"
2125
2126
2127
2128	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2129	if [[ $do_trace = true ]]
2130	then
2131	(( i = 0 ))
2132	while (( i < iin ))
2133	do
2134	(( i = i + 1 ))
2135	if (( i == 1 ))
2136	then
2137	printf "\n\n >>> INPUT-file assignments:\n"
2138	fi
2139	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2140	done
2141	(( i = 0 ))
2142	while (( i < iout ))
2143	do
2144	(( i = i + 1 ))
2145	if (( i == 1 ))
2146	then
2147	printf "\n\n >>> OUTPUT-file assignments:\n"
2148	fi
2149	printf "\n ${localout[$i]} : ${pathout[$i]}"
2150	done
2151	(( i = 0 ))
2152	while (( i < iic ))
2153	do
2154	(( i = i + 1 ))
2155	if (( i == 1 ))
2156	then
2157	printf "\n\n >>> INPUT-commands:\n"
2158	fi
2159	printf "\n ${in_command[$i]}"
2160	done
2161	(( i = 0 ))
2162	while (( i < ioc ))
2163	do
2164	(( i = i + 1 ))
2165	if (( i == 1 ))
2166	then
2167	printf "\n\n >>> OUTPUT-commands:\n"
2168	fi
2169	printf "\n ${out_command[$i]}"
2170	done
2171	fi
2172
2173	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2174	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2175	then
2176	antwort=dummy
2177	printf "\n\n"
2178	printf " >>> everything o.k. (y/n) ? "
2179	while read antwort
2180	do
2181	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2182	then
2183	printf " >>> everything o.k. (y/n) ? "
2184	else
2185	break
2186	fi
2187	done
2188	if [[ $antwort = n \|\| $antwort = N ]]
2189	then
2190	locat=user_abort; (( iec = 0 )); exit
2191	fi
2192	if [[ $do_batch = true ]]
2193	then
2194	printf " >>> batch-job will be created and submitted"
2195	else
2196	printf " >>> MRUN will now continue to execute on this machine"
2197	fi
2198	fi
2199
2200
2201	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2202	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2203	check_depository="${working_directory}/trunk/UTIL"
2204	check_sources="${working_directory}/tmp_check_namelist_files"
2205	skip_check=false
2206
2207	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2208	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2209	then
2210	skip_check=true
2211	reason="run on remote host or parameter file check has not been compiled."
2212	fi
2213	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2214	then
2215	skip_check=true
2216	reason="parameter file check has not been compiled."
2217	fi
2218
2219	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2220	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2221	then
2222	skip_check=true
2223	reason="serial run."
2224	fi
2225
2226	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2227	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2228	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2229	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2230	if [[ $check_namelist_files == false ]]
2231	then
2232	skip_check=true
2233	reason="-z option set."
2234	fi
2235
2236	if [[ $fromhost != $localhost ]]
2237	then
2238	skip_check=true
2239	reason="submitting host is local host."
2240	fi
2241
2242	if [[ $run_coupled_model == true ]]
2243	then
2244	skip_check=true
2245	reason="coupled run."
2246	fi
2247
2248	if [[ $restart_run == true ]]
2249	then
2250	skip_check=true
2251	reason="restart run."
2252	fi
2253
2254	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2255	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2256	last_char=`echo $filename_input \| cut -c $last_char_int`
2257	if [[ "$last_char" == "f" ]]
2258	then
2259	skip_check=true
2260	reason="restart run."
2261	fi
2262
2263	if [[ $skip_check == false ]]
2264	then
2265	tmp_check=${working_directory}/tmp_check
2266
2267	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2268	# NOT NECESSARILY REQUIRED
2269	line=""
2270	found=false
2271	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2272	while read line1
2273	do
2274	line="$line1"
2275	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2276	then
2277	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2278	found=true
2279	fi
2280	done < $tmp_check
2281
2282	if [[ $found = false ]]
2283	then
2284	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2285	fi
2286
2287	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2288	# NOT NECESSARILY REQUIRED
2289	line=""
2290	found=false
2291	grep "NUDGING_DATA" $config_file > $tmp_check
2292	while read line1
2293	do
2294	line="$line1"
2295	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2296	then
2297	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2298	found=true
2299	fi
2300	done < $tmp_check
2301
2302	if [[ $found = false ]]
2303	then
2304	printf "\n +++ no NUDGING list entry found in the configuration file."
2305	fi
2306
2307	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2308	# NOT NECESSARILY REQUIRED
2309	line=""
2310	found=false
2311	grep "LSF_DATA" $config_file > $tmp_check
2312	while read line1
2313	do
2314	line="$line1"
2315	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2316	then
2317	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2318	found=true
2319	fi
2320	done < $tmp_check
2321
2322	if [[ $found = false ]]
2323	then
2324	printf "\n +++ no LSF list entry found in the configuration file."
2325	fi
2326
2327	rm -rf ${working_directory}/tmp_check
2328
2329	# CHECK IF THE P3DF FILE MUST BE CHECKED
2330	for item in $input_list
2331	do
2332	if [[ "$item" == "restart" ]]
2333	then
2334	check_restart=1
2335	else
2336	check_restart=0
2337	fi
2338	done
2339
2340	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2341	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2342	then
2343	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2344	locat=check_namelist; exit
2345	fi
2346
2347	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2348	if [[ $check_restart == 1 ]]
2349	then
2350
2351	filenamef="${filename_input}f"
2352	if [[ ! -f $filenamef ]]
2353	then
2354	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2355	check_restart=0
2356	answer=dummy
2357	printf "\n\n"
2358
2359	if [[ $silent == false ]]
2360	then
2361	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2362	do
2363	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2364	read answer
2365	done
2366	if [[ $answer = a \|\| $answer = A ]]
2367	then
2368	printf "\n +++ Aborting...."
2369	locat=normal; exit
2370	fi
2371	fi
2372	else
2373	check_restart=1
2374	fi
2375	fi
2376
2377	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2378	mkdir $check_sources
2379	cd $check_sources
2380
2381
2382	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2383	if [[ -d $add_source_path ]]
2384	then
2385	printf "\n\n *** copying files from $check_depository"
2386	cp $check_depository/check_namelist_files.tar ./
2387
2388	printf "\n\n *** untar of makefile and source files in $check_sources"
2389	tar -xf check_namelist_files.tar > /dev/null 2>&1
2390
2391	printf "\n\n *** adding user code."
2392	cp $add_source_path/* ./
2393	touch check_namelist_files.f90
2394
2395	# GET COMPILER OPTIONS AND PERFORM MAKE
2396	printf "\n\n *** compiling code if necessary...\n"
2397
2398	# workaround for batch jobs on local machine (lcxe6)
2399	if [[ $do_batch == true && $do_remote == false ]]
2400	then
2401	eval $init_cmds
2402	fi
2403
2404	# GET CHECK OPTIONS
2405	line=""
2406	found=false
2407
2408	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2409
2410	while read line1
2411	do
2412
2413	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2414	then
2415	line="$line1"
2416	fi
2417
2418	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2419	then
2420	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2421	line="$line "
2422	copts_check=`echo $line \| cut -d" " -s -f2 \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g' \| sed 's/-D[^ ]* //g' \| sed 's/ -D.*//g'`
2423	found=true
2424	fi
2425
2426	done < $tmp_check
2427	copts_check="$copts_check -D__check -D__parallel"
2428
2429	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2430
2431	# GET MAKE OUTPUT
2432	if [[ $? != 0 ]]
2433	then
2434	printf "\n +++ error during make."
2435	answer=dummy
2436	printf "\n\n"
2437	if [[ $silent == false ]]
2438	then
2439	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2440	do
2441	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2442	read answer
2443	done
2444	if [[ $answer = a \|\| $answer = A ]]
2445	then
2446	printf "\n +++ Aborting..."
2447	rm -rf $check_sources
2448	locat=normal; exit
2449	else
2450	skip_check=true
2451	fi
2452	else
2453	skip_check=true
2454	fi
2455	fi
2456	else
2457	cp $PALM_BIN/check_namelist_files.x ./
2458	fi
2459
2460	cp $filename_input ./PARIN
2461	if [[ $check_restart == 1 ]]
2462	then
2463	cp $filenamef ./PARINF
2464	fi
2465
2466	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2467	then
2468	printf "\n *** adding topography data"
2469	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2470
2471	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2472	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2473	# WHICH REQUIRE SUFFICIENT MEMORY
2474	ulimit -s unlimited
2475	fi
2476
2477	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2478	then
2479	printf "\n *** adding nudging data"
2480	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2481	fi
2482
2483	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2484	then
2485	printf "\n *** adding large scale forcing data"
2486	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2487	fi
2488
2489	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2490	cat > ENVPAR << %%END%%
2491	&envpar run_identifier = '$fname', host = '$host',
2492	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2493	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2494	maximum_cpu_time_allowed = ${cpumax}.,
2495	revision = '$global_revision',
2496	local_dvrserver_running = $local_dvrserver_running /
2497
2498	%%END%%
2499
2500	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2501	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2502	then
2503	printf "\n +++ WARNING: check_namelist_files.x not found."
2504	answer=dummy
2505	printf "\n\n"
2506
2507	if [[ $silent == false ]]
2508	then
2509	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2510	do
2511	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2512	read answer
2513	done
2514	if [[ $answer = a \|\| $answer = A ]]
2515	then
2516	printf "\n +++ Aborting..."
2517	rm -rf $check_sources
2518	locat=normal; exit
2519	else
2520	printf "\n *** skipping parameter file check."
2521	fi
2522	fi
2523
2524	elif [[ $skip_check == false ]]
2525	then
2526	# STARTING THE PARAMETER FILE CHECK
2527	printf "\n\n *** starting parameter file check..."
2528
2529	# CHECKING THE P3D FILE
2530	printf "\n\n (1) checking $filename_input"
2531	echo "$numprocs 0 0" > VARIN
2532	errors=`./check_namelist_files.x < VARIN 2>&1`
2533
2534	check_error=false
2535	if [[ "$errors" == "" ]]
2536	then
2537	printf " --> o.k."
2538	else
2539	printf " --> failed."
2540	check_error=true
2541	printf "\n\n $errors"
2542	fi
2543
2544	# CHECKING THE PD3F FILE IF NECESSARY
2545	if [[ $check_restart == 1 && $check_error == false ]]
2546	then
2547	printf "\n\n (2) checking $filenamef"
2548
2549	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2550	# IN &INIPAR LIST
2551	found=false
2552	cat PARINF \| while read line
2553	do
2554	line=$(echo $line\|sed 's/ //g')
2555	if [[ $line == "&inipar" ]]
2556	then
2557	start_search=true
2558	fi
2559
2560	if [[ $start_search == true ]]
2561	then
2562	if [[ $line == "initializing_actions='read_restart_data'" ]]
2563	then
2564	found=true
2565	break
2566	fi
2567	fi
2568
2569	if [[ $line == "/" ]]
2570	then
2571	start_search=false
2572	fi
2573
2574	done
2575
2576	if [[ $found = false ]]
2577	then
2578	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2579	printf "\n in &inipar list in $fname$p3df_suffix."
2580	rm -rf $check_sources
2581	locat=check_namelist; exit
2582	fi
2583
2584	# READ max_user_pr FROM FILES
2585	if [[ -f parin_for_check ]]
2586	then
2587	read max_pr_user < parin_for_check
2588	else
2589	max_user_pr=0
2590	fi
2591
2592	echo "$numprocs 1 $max_pr_user" > VARIN
2593	errors=`./check_namelist_files.x < VARIN 2>&1`
2594
2595	if [[ "$errors" == "" ]]
2596	then
2597	printf " --> o.k."
2598	else
2599	printf " --> failed."
2600	check_error=true
2601	printf "\n\n $errors"
2602	fi
2603	fi
2604
2605	# REPORT ERRORS AND CONTINUE/EXIT
2606	if [[ $check_error == true ]]
2607	then
2608	printf "\n +++ errors found in the parameter file!\n"
2609	answer=dummy
2610	printf "\n\n"
2611
2612	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2613	do
2614	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2615	read answer
2616	done
2617
2618	if [[ $answer = a \|\| $answer = A ]]
2619	then
2620	printf "\n +++ Aborting..."
2621	rm -rf $check_sources
2622	locat=normal; exit
2623	fi
2624	else
2625	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2626	fi
2627	rm -rf $check_sources
2628	fi
2629	else
2630	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2631	fi
2632
2633	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2634	rm -rf $check_sources
2635	cd $working_directory
2636
2637	# DETERMINE PATH FOR MAKE DEPOSITORY
2638	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2639	then
2640
2641	line=""
2642	grep "%depository_path" $config_file > tmp_mrun
2643	while read line
2644	do
2645	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2646	then
2647	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2648	then
2649	global_depository_path=`echo $line \| cut -d" " -s -f2`
2650	fi
2651	fi
2652	done < tmp_mrun
2653
2654	line=""
2655	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2656	while read line
2657	do
2658	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2659	then
2660	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2661	then
2662	local_depository_path=`echo $line \| cut -d" " -s -f2`
2663	fi
2664	fi
2665	done < tmp_mrun
2666
2667	if [[ "$local_depository_path" = "" ]]
2668	then
2669	if [[ "$global_depository_path" != "" ]]
2670	then
2671	local_depository_path=$global_depository_path
2672	else
2673	printf "\n\n +++ no depository path found in configuration file"
2674	printf "\n for local host \"$localhost\" "
2675	printf "\n please set \"\%depository_path\" in configuration file\n"
2676	locat=config_file; exit
2677	fi
2678	fi
2679	eval local_depository_path=$local_depository_path
2680	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2681	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2682
2683
2684	basename=`echo $mainprog \| cut -f1 -d"."`
2685	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2686	if [[ ! -f $make_depository ]]
2687	then
2688	printf "\n"
2689	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2690	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2691	fi
2692
2693	fi
2694
2695
2696	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2697	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2698	if [[ $do_batch = false ]]
2699	then
2700
2701
2702	# CREATE THE TEMPORARY WORKING DIRECTORY
2703	mkdir -p $TEMPDIR
2704	chmod go+rx $TEMPDIR
2705	tmpcreate=true
2706
2707
2708	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2709	# INTO THE TEMPORARY WORKING DIRECTORY
2710	if [[ $do_compile = true ]]
2711	then
2712
2713	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2714	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2715	if [[ $localhost = nech ]]
2716	then
2717	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2718	if mkdir -p $TEMPDIR_COMPILE
2719	then
2720	printf "\n *** \"$TEMPDIR_COMPILE\" "
2721	printf "\n is generated as temporary directory for cross compiling\n"
2722	else
2723	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2724	printf "\n needed for cross compilation failed"
2725	locat=compile
2726	exit
2727	fi
2728	else
2729	TEMPDIR_COMPILE=$TEMPDIR
2730	fi
2731
2732	cp $make_depository $TEMPDIR_COMPILE
2733	cd $TEMPDIR_COMPILE
2734	tar -xf $make_depository > /dev/null 2>&1
2735	cd - > /dev/null
2736
2737	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2738	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2739	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2740	then
2741	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2742	else
2743	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2744	fi
2745
2746	else
2747
2748	cp $executable ${TEMPDIR}/a.out
2749
2750	fi
2751
2752
2753	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2754	cd $TEMPDIR
2755	printf "\n *** changed to temporary directory: $TEMPDIR"
2756
2757
2758	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2759	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2760	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2761	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2762	(( i = 0 ))
2763	while (( i < iout ))
2764	do
2765	(( i = i + 1 ))
2766	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2767	then
2768	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2769	else
2770	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2771	fi
2772	done
2773
2774
2775	# IF REQUIRED, START WITH COMPILING
2776	if [[ $do_compile = true ]]
2777	then
2778
2779
2780	if [[ -f a.out ]]
2781	then
2782
2783	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2784	printf "\n\n\n *** executable a.out found"
2785	printf "\n no compilation required \n"
2786
2787	else
2788
2789	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2790	printf "\n\n\n *** compilation starts \n$dashes\n"
2791	printf " *** compilation with make using following options:\n"
2792	printf " make depository: $make_depository"
2793	if [[ "$mopts" != "" ]]
2794	then
2795	printf " make options: $mopts\n"
2796	fi
2797	printf " compilername: $compiler_name\n"
2798	printf " compiler options: $fopts\n"
2799	printf " preprocessor directives: $cpp_options \n"
2800	printf " linker options: $lopts \n"
2801	if [[ "$modules" != "" ]]
2802	then
2803	printf " modules to be load: $modules \n"
2804	fi
2805	printf " source code files: $source_list \n"
2806
2807	if [[ $localhost = nech ]]
2808	then
2809	ssh $SSH_PORTOPT 136.172.44.192 -l $usern "$init_cmds $module_calls cd \$HOME/work/${usern}.$kennung; sxmake $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
2810	cp $TEMPDIR_COMPILE/a.out .
2811	[[ $? != 0 ]] && compile_error=true
2812	rm -rf $TEMPDIR_COMPILE
2813	elif [[ $localhost = ibmh ]]
2814	then
2815	printf " compiler is called via ssh on \"plogin1\" \n"
2816	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\" "
2817	[[ ! -f a.out ]] && compile_error=true
2818	continue # STATUS=1, IF a.out EXISTS
2819	elif [[ $localhost = lcflow ]]
2820	then
2821	printf " compiler is called via ssh on \"flow\" \n"
2822	/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
2823	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2824	[[ "$check_for_file" = "" ]] && compile_error=true
2825	continue # STATUS=1, IF a.out EXISTS
2826	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2827	then
2828	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2829	else
2830	[[ "$init_cmds" != "" ]] && eval $init_cmds
2831	[[ "$module_calls" != "" ]] && eval $module_calls
2832	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2833	fi
2834
2835	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2836	then
2837	printf "\n +++ error occured while compiling or linking"
2838	locat=compile
2839
2840	exit
2841	else
2842	printf "$dashes\n *** compilation finished \n"
2843	fi
2844
2845	fi
2846
2847	fi
2848
2849
2850	# PROVIDE THE INPUT FILES
2851	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2852	(( i = 0 ))
2853	while (( i < iin ))
2854	do
2855	(( i = i + 1 ))
2856	if (( i == 1 ))
2857	then
2858	printf "\n\n *** providing INPUT-files:\n$dashes"
2859	fi
2860
2861
2862	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2863	if [[ "${transin[$i]}" = unavailable ]]
2864	then
2865	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2866	then
2867	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2868	printf "\n is not available!"
2869	else
2870	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2871	printf "\n is not available!"
2872	fi
2873	continue
2874	fi
2875
2876	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2877	files_for_pes=false; datentyp=file
2878	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2879	then
2880	files_for_pes=true; datentyp=directory
2881	actionin[$i]=""
2882	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2883	then
2884	actionin[$i]=""
2885	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2886	then
2887	files_for_pes=true; datentyp=directory
2888	actionin[$i]="ar"
2889	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2890	then
2891	actionin[$i]="ar"
2892	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2893	then
2894	files_for_pes=true; datentyp=directory
2895	actionin[$i]="fl"
2896	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2897	then
2898	actionin[$i]="fl"
2899	fi
2900
2901	if [[ $files_for_pes = true ]]
2902	then
2903	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2904	else
2905	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2906	fi
2907
2908	# INPUT-FILE FOR A RESTART RUN.
2909	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2910	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2911	if [[ "${actionin[$i]}" = fl ]]
2912	then
2913	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2914	if [[ $files_for_pes = false ]]
2915	then
2916	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2917	then
2918	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2919	got_tmp[$i]=true
2920	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2921	then
2922	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2923	printf "\n *** trying to use backup copy in \"$WORK\" "
2924	cp $WORK/${frelin[$i]} ${localin[$i]}
2925	else
2926	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2927	printf "\n or \"$tmp_data_catalog\" does not exist!"
2928	printf "\n *** trying to get copy from archive"
2929	actionin[$i]=ar
2930	fi
2931	else
2932	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2933	then
2934	mkdir ${localin[$i]}
2935	cd $tmp_data_catalog/${frelin[$i]}
2936	for file in $(ls *)
2937	do
2938	ln $file $TEMPDIR/${localin[$i]}
2939	done
2940	cd $TEMPDIR
2941	got_tmp[$i]=true
2942	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2943	then
2944	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2945	printf "\n *** trying to use backup copy in \"$WORK\" "
2946	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2947	else
2948	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2949	printf "\n or \"$tmp_data_catalog\" does not exist!"
2950	printf "\n *** trying to get copy from archive"
2951	actionin[$i]=ar
2952	fi
2953	fi
2954	fi
2955
2956
2957	# FILE IS STORED ON THE ARCHIVE SYSTEM
2958	if [[ "${actionin[$i]}" = ar ]]
2959	then
2960
2961	if [[ $files_for_pes = false ]]
2962	then
2963	printf "\n file will be restored from archive-system ($archive_system)!"
2964	else
2965	printf "\n directory will be restored from archive-system ($archive_system)!"
2966	fi
2967
2968	file_restored=false
2969
2970	if [[ $archive_system = asterix ]]
2971	then
2972	do_stagein=true
2973	(( stagein_anz = 0 ))
2974	while [[ $do_stagein = true ]]
2975	do
2976	if [[ $files_for_pes = false ]]
2977	then
2978	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2979	else
2980	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2981	fi
2982	cat STAGEIN_OUTPUT
2983	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2984	then
2985	file_restored=true
2986	do_stagein=false
2987	else
2988	(( stagein_anz = stagein_anz + 1 ))
2989	if (( stagein_anz == 10 ))
2990	then
2991	printf "\n +++ stagein stoped after 10 tries"
2992	locat=stage
2993	exit
2994	fi
2995	printf "\n +++ restoring from archive failed, trying again:"
2996	sleep 900
2997	fi
2998	done
2999	elif [[ $archive_system = DMF ]]
3000	then
3001	if [[ $files_for_pes = false ]]
3002	then
3003	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3004	locat=DMF
3005	exit
3006	else
3007	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3008	cp -r $ARCHIVE/${frelin[$i]} $PWD
3009	file_restored=true
3010	fi
3011	elif [[ $archive_system = tivoli ]]
3012	then
3013	if [[ $files_for_pes = false ]]
3014	then
3015	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3016	else
3017	(( inode = 0 ))
3018	while (( inode < nodes ))
3019	do
3020	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3021	(( inode = inode + 1 ))
3022	done
3023	fi
3024	file_restored=true
3025	elif [[ $archive_system = ut ]]
3026	then
3027	if [[ $files_for_pes = false ]]
3028	then
3029	cp $UT/${frelin[$i]} .
3030	else
3031	(( inode = 0 ))
3032	while (( inode < nodes ))
3033	do
3034	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3035	(( inode = inode + 1 ))
3036	done
3037	fi
3038	file_restored=true
3039	else
3040	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3041	locat=rearchive
3042	exit
3043	fi
3044
3045	if [[ $file_restored = true ]]
3046	then
3047
3048	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3049	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3050	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3051	if [[ $files_for_pes = false ]]
3052	then
3053	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3054	else
3055	mkdir $tmp_data_catalog/${frelin[$i]}
3056	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3057	fi
3058	got_tmp[$i]=true
3059
3060	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3061	mv ${frelin[$i]} ${localin[$i]}
3062
3063	fi
3064	fi
3065
3066
3067	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3068	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3069	then
3070
3071	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3072	then
3073
3074	# FILE COPIES ARE PROVIDED FOR ALL CORES
3075	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3076	printf "\n file will be provided for $numprocs processors"
3077	mkdir ${localin[$i]}
3078	ival=$numprocs
3079	(( ii = 0 ))
3080	while (( ii <= ival-1 ))
3081	do
3082	if (( ii < 10 ))
3083	then
3084	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3085	elif (( ii < 100 ))
3086	then
3087	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3088	elif (( ii < 1000 ))
3089	then
3090	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3091	else
3092	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3093	fi
3094	(( ii = ii + 1 ))
3095	done
3096
3097	else
3098
3099	if [[ $files_for_pes = true ]]
3100	then
3101
3102	# PROVIDE FILES FOR EACH CORE
3103	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3104	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3105	printf "\n providing $numprocs files for the respective processors"
3106	mkdir ${localin[$i]}
3107	if [[ $link_local_input = true ]]
3108	then
3109	printf " using ln -f\n"
3110	cd ${absnamein[$i]}
3111	for file in $(ls *)
3112	do
3113	ln -f $file ${localin[$i]}
3114	done
3115	cd $TEMPDIR
3116	fi
3117
3118	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3119	if [[ ! -f "${localin[$i]}/_0000" ]]
3120	then
3121	if [[ $link_local_input = true ]]
3122	then
3123	printf " ln failed for .../_0000, using cp...\n"
3124	fi
3125	cp -r ${absnamein[$i]}/* ${localin[$i]}
3126	fi
3127
3128	else
3129
3130	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3131	if [[ $link_local_input = true ]]
3132	then
3133	printf " using ln -f\n"
3134	ln -f ${absnamein[$i]} ${localin[$i]}
3135	fi
3136	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3137	if [[ ! -f "${localin[$i]}" ]]
3138	then
3139	if [[ $link_local_input = true ]]
3140	then
3141	printf " ln failed, using cp...\n"
3142	fi
3143	cp ${absnamein[$i]} ${localin[$i]}
3144	fi
3145	fi
3146	fi
3147	fi
3148
3149	done
3150	if (( i != 0 ))
3151	then
3152	printf "\n$dashes\n *** all INPUT-files provided \n"
3153	fi
3154
3155
3156	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3157	(( i = 0 ))
3158	while (( i < iic ))
3159	do
3160	(( i = i + 1 ))
3161	if (( i == 1 ))
3162	then
3163	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3164	fi
3165	printf "\n >>> ${in_command[$i]}"
3166	eval ${in_command[$i]}
3167	if (( i == iic ))
3168	then
3169	printf "\n$dashes\n"
3170	fi
3171	done
3172
3173
3174	# SET THE REMAINING CPU-TIME
3175	cpurest=${cpumax}.
3176
3177
3178	# START DVR STREAMING SERVER
3179	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3180	then
3181	if [[ "$dvr_server" != "" ]]
3182	then
3183
3184	printf "\n\n *** preparing the dvr streaming server configuration file"
3185
3186	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3187	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3188	if [[ "$running_dvrserver_id" != "" ]]
3189	then
3190
3191	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3192	printf "\n This server is used instead starting a new one!"
3193	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3194
3195	else
3196
3197	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3198	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3199	then
3200	cp ${PALM_BIN}/.dvrserver.config .
3201
3202	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3203	user_id=`id -u`
3204	group_id=`id -g`
3205
3206	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3207	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3208	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3209	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3210	mv .dvrserver.3 .dvrserver.config
3211	rm .dvrserver.1 .dvrserver.2
3212
3213	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3214	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3215	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3216	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3217	local_dvrserver_running=.TRUE.
3218	else
3219	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3220	printf "\n \"$PALM_BIN\" "
3221	locat=dvr
3222	exit
3223	fi
3224
3225	fi
3226
3227	else
3228	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3229	fi
3230	fi
3231
3232
3233	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3234	# (FILE ENVPAR WILL BE READ BY PALM)
3235	cat > ENVPAR << %%END%%
3236	&envpar run_identifier = '$fname', host = '$localhost',
3237	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3238	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3239	maximum_cpu_time_allowed = ${cpumax}.,
3240	revision = '$global_revision',
3241	local_dvrserver_running = $local_dvrserver_running,
3242	batch_job = $batch_job /
3243
3244	%%END%%
3245
3246
3247	# STARTING THE EXECUTABLE
3248	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3249	PATH=$PATH:$TEMPDIR
3250
3251	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3252	if [[ "$mpi_debug" = true ]]
3253	then
3254	export MPI_CHECK_ARGS=1
3255	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3256	fi
3257
3258	if [[ "$totalview" = true ]]
3259	then
3260	printf "\n *** totalview debugger will be used"
3261	tv_opt="-tv"
3262	else
3263	tv_opt=""
3264	fi
3265
3266	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3267	then
3268
3269	#Interactive ALLINEA DEBUG seesion
3270	if [[ "$ENVIRONMENT" != BATCH ]]
3271	then
3272	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3273	then
3274	if [[ "$allinea" = true ]]
3275	then
3276	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3277
3278	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3279	wait
3280	fi
3281	fi
3282	fi
3283
3284	if [[ "$ENVIRONMENT" = BATCH ]]
3285	then
3286	continue
3287	fi
3288	if [[ $localhost = ibmh ]]
3289	then
3290
3291	# SETUP THE IBM MPI ENVIRONMENT
3292	export MP_SHARED_MEMORY=yes
3293	export AIXTHREADS_SCOPE=S
3294	export OMP_NUM_THREADS=$threads_per_task
3295	export AUTHSTATE=files
3296	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3297
3298	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3299	export MP_ADAPTER_USE=shared
3300	export MP_CPU_USE=multiple
3301	export MP_TIMEOUT=1200
3302
3303	unset MP_TASK_AFFINITY
3304
3305	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3306	#(( ii = 1 ))
3307	#while (( ii <= $numprocs ))
3308	#do
3309	# echo $localhost_realname >> hostfile
3310	# (( ii = ii + 1 ))
3311	#done
3312	#export MP_HOSTFILE=hostfile
3313
3314	if [[ "$LOADLBATCH" = yes ]]
3315	then
3316	totalview poe a.out $ROPTS
3317	else
3318	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3319	export TVDSVRLAUNCHCMD=ssh
3320	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3321	fi
3322
3323	fi # END DEBUG MODE
3324
3325	else
3326
3327	# NORMAL EXECUTION
3328	if [[ -n $numprocs ]]
3329	then
3330
3331	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3332	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3333	then
3334
3335	# SETUP THE IBM MPI ENVIRONMENT
3336	if [[ $host != ibmh && $host != ibmkisti ]]
3337	then
3338	export MP_SHARED_MEMORY=yes
3339	export AIXTHREAD_SCOPE=S
3340	export OMP_NUM_THREADS=$threads_per_task
3341	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3342	export AUTHSTATE=files
3343	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3344	# export MP_PRINTENV=yes
3345
3346	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3347	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3348	export MP_WAIT_MODE=poll
3349	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3350	fi
3351
3352	if [[ $host = ibmkisti ]]
3353	then
3354	export LANG=en_US
3355	export MP_SHARED_MEMORY=yes
3356	if [[ $threads_per_task = 1 ]]
3357	then
3358	export MP_SINGLE_THREAD=yes
3359	export MEMORY_AFFINITY=MCM
3360	else
3361	export OMP_NUM_THREADS=$threads_per_task
3362	fi
3363	fi
3364
3365	if [[ "$LOADLBATCH" = yes ]]
3366	then
3367	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3368	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3369	then
3370	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3371	else
3372	if [[ $run_coupled_model = false ]]
3373	then
3374	if [[ "$ocean_file_appendix" = true ]]
3375	then
3376	echo "precursor_ocean" > runfile_atmos
3377	else
3378	echo "precursor_atmos" > runfile_atmos
3379	fi
3380	else
3381	(( iia = $numprocs_atmos / $threads_per_task ))
3382	(( iio = $numprocs_ocean / $threads_per_task ))
3383	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3384	printf "\n using $coupled_mode coupling"
3385	printf "\n\n"
3386	echo "coupled_run $iia $iio" > runfile_atmos
3387	fi
3388	poe ./a.out $ROPTS < runfile_atmos
3389	fi
3390	else
3391	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3392	then
3393	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3394	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3395	then
3396	if [[ -f $hostfile ]]
3397	then
3398	cp $hostfile hostfile
3399	else
3400	(( ii = 1 ))
3401	while (( ii <= $numprocs ))
3402	do
3403	echo $localhost_realname >> hostfile
3404	(( ii = ii + 1 ))
3405	done
3406	fi
3407	export MP_HOSTFILE=hostfile
3408	if [[ $run_coupled_model = false ]]
3409	then
3410	if [[ "$ocean_file_appendix" = true ]]
3411	then
3412	echo "precursor_ocean" > runfile_atmos
3413	else
3414	echo "precursor_atmos" > runfile_atmos
3415	fi
3416	else
3417	(( iia = $numprocs_atmos / $threads_per_task ))
3418	(( iio = $numprocs_ocean / $threads_per_task ))
3419	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3420	printf "\n using $coupled_mode coupling"
3421	printf "\n\n"
3422	echo "coupled_run $iia $iio" > runfile_atmos
3423	fi
3424
3425	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3426
3427	else
3428	if [[ "$host_file" = "" ]]
3429	then
3430	printf "\n +++ no hostfile given in configuration file"
3431	locat=config_file
3432	exit
3433	else
3434	eval host_file=$host_file
3435	fi
3436	export MP_HOSTFILE=$host_file
3437	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3438	fi
3439	fi
3440	elif [[ $host = nech ]]
3441	then
3442	(( ii = nodes ))
3443	if [[ $ii = 1 ]]
3444	then
3445	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3446	export MPIPROGINF=YES
3447	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3448	echo "*** execution on single node with mpirun"
3449	mpirun -np $numprocs ./a.out $ROPTS
3450	else
3451	(( i = 0 ))
3452	while (( i < ii ))
3453	do
3454	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3455	(( i = i + 1 ))
3456	done
3457
3458	echo "#!/bin/sh" > mpi_exec_shell
3459	echo " " >> mpi_exec_shell
3460	echo "set -u" >> mpi_exec_shell
3461	echo "F_ERRCNT=0" >> mpi_exec_shell
3462	echo "MPIPROGINV=YES" >> mpi_exec_shell
3463	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3464	echo "cpurest=$cpurest" >> mpi_exec_shell
3465	echo "fname=$fname" >> mpi_exec_shell
3466	echo "localhost=$localhost" >> mpi_exec_shell
3467	echo "return_address=$return_address" >> mpi_exec_shell
3468	echo "return_username=$return_username" >> mpi_exec_shell
3469	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3470	echo "write_binary=$write_binary" >> mpi_exec_shell
3471	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3472	echo " " >> mpi_exec_shell
3473	echo "export F_ERRCNT" >> mpi_exec_shell
3474	echo "export MPIPROGINV" >> mpi_exec_shell
3475	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3476	echo "export cpurest" >> mpi_exec_shell
3477	echo "export fname" >> mpi_exec_shell
3478	echo "export localhost" >> mpi_exec_shell
3479	echo "export return_address" >> mpi_exec_shell
3480	echo "export return_username" >> mpi_exec_shell
3481	echo "export tasks_per_node" >> mpi_exec_shell
3482	echo "export write_binary" >> mpi_exec_shell
3483	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3484	echo " " >> mpi_exec_shell
3485	echo "exec ./a.out" >> mpi_exec_shell
3486
3487	chmod u+x mpi_exec_shell
3488	export MPIPROGINF=YES
3489	mpirun -f multinode_config &
3490	wait
3491
3492	fi
3493	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3494	then
3495
3496	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3497	# DOES NOT EXIST
3498	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3499
3500	then
3501	if [[ -f $hostfile ]]
3502	then
3503	cp $hostfile hostfile
3504	(( ii = $numprocs / $threads_per_task ))
3505	[[ $ii = 0 ]] && (( ii = 1 ))
3506	else
3507	(( ii = 1 ))
3508	while (( ii <= $numprocs / $threads_per_task ))
3509	do
3510	echo $localhost_realname >> hostfile
3511	(( ii = ii + 1 ))
3512	done
3513	if (( $numprocs / $threads_per_task == 0 ))
3514	then
3515	echo $localhost_realname >> hostfile
3516	fi
3517	fi
3518	eval zeile=\"`head -n $ii hostfile`\"
3519	printf "\n *** running on: $zeile"
3520	fi
3521
3522	(( ii = $numprocs / $threads_per_task ))
3523	[[ $ii = 0 ]] && (( ii = 1 ))
3524	export OMP_NUM_THREADS=$threads_per_task
3525
3526	if [[ $threads_per_task != 1 ]]
3527	then
3528	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3529	# MAY ABORT
3530	ulimit -s unlimited
3531	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3532	fi
3533	if [[ $run_coupled_model = false ]]
3534	then
3535	if [[ "$ocean_file_appendix" = true ]]
3536	then
3537	echo "precursor_ocean" > runfile_atmos
3538	else
3539	echo "precursor_atmos" > runfile_atmos
3540	fi
3541	printf "\n\n"
3542
3543	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3544	then
3545	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3546	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3547	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3548
3549	elif [[ $host = lcbullhh ]]
3550	then
3551	export OMPI_MCA_pml=cm
3552	export OMPI_MCA_mtl=mxm
3553	export OMPI_MCA_coll=^ghc
3554	export OMPI_MCA_mtl_mxm_np=0
3555	export MXM_RDMA_PORTS=mlx5_0:1
3556	export MXM_LOG_LEVEL=ERROR
3557	export OMP_NUM_THREADS=$threads_per_task
3558	export KMP_AFFINITY=verbose,granularity=core,compact,1
3559	export KMP_STACKSIZE=64m
3560
3561	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out
3562
3563	elif [[ $host = lccrayf ]]
3564	then
3565	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3566	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3567	then
3568	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3569	elif [[ $host = lcflow ]]
3570	then
3571	mpirun -np $ii a.out < runfile_atmos $ROPTS
3572	elif [[ $host = lcsb ]]
3573	then
3574	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3575	elif [[ $host = lckiaps ]]
3576	then
3577	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3578	elif [[ $host = lckyu* ]]
3579	then
3580	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3581	else
3582	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3583	fi
3584	else
3585
3586	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3587	(( iia = $numprocs_atmos / $threads_per_task ))
3588	(( iio = $numprocs_ocean / $threads_per_task ))
3589	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3590	printf "\n using $coupled_mode coupling"
3591	printf "\n\n"
3592
3593	if [[ $coupled_mode = "mpi2" ]]
3594	then
3595	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3596	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3597
3598	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3599	then
3600
3601	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3602	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3603
3604	else
3605	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3606	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3607	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3608	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3609	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3610	fi
3611	wait
3612
3613	else
3614
3615	echo "coupled_run $iia $iio" > runfile_atmos
3616
3617	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3618	then
3619
3620	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3621
3622	elif [[ $host = lck \|\| $host = lckordi ]]
3623	then
3624
3625	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3626
3627	elif [[ $host = lckyu* ]]
3628	then
3629
3630	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3631
3632	elif [[ $host = lcmuk ]]
3633	then
3634
3635	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3636
3637	fi
3638	wait
3639	fi
3640
3641	fi
3642
3643	elif [[ $host = lckyoto ]]
3644	then
3645	set -xv
3646	export P4_RSHCOMMAND=plesh
3647	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3648	if [[ "$ENVIRONMENT" = BATCH ]]
3649	then
3650	if [[ "$cond2" = fujitsu ]]
3651	then
3652	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3653	elif [[ "cond2" = pgi ]]
3654	then
3655	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3656	else
3657	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3658	fi
3659	else
3660	if [[ "$cond2" = "" ]]
3661	then
3662	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3663	else
3664	mpirun -np $numprocs ./a.out $ROPTS
3665	fi
3666	fi
3667	set +xv
3668
3669	elif [[ $host = lctit ]]
3670	then
3671	export OMP_NUM_THREADS=$threads_per_task
3672	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3673	if [[ "$threads_per_task" != 1 ]]
3674	then
3675	export MV2_ENABLE_AFFINITY=0
3676	fi
3677	echo "----- PBS_NODEFILE content:"
3678	cat $PBS_NODEFILE
3679	echo "-----"
3680	(( ii = $numprocs / $threads_per_task ))
3681	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3682	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3683
3684	else
3685	mpprun -n $numprocs a.out $ROPTS
3686	fi
3687	else
3688	a.out $ROPTS
3689	fi
3690	fi
3691
3692	if [[ $? != 0 ]]
3693	then
3694
3695	# ABORT IN CASE OF RUNTIME ERRORS
3696	printf "\n +++ runtime error occured"
3697	locat=execution
3698	exit
3699
3700	else
3701
3702	printf "\n$dashes\n *** execution finished \n"
3703
3704	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3705	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3706	if [[ "$dvrserver_id" != "" ]]
3707	then
3708	kill $dvrserver_id
3709	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3710
3711	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3712	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3713	if [[ -d DATA_DVR ]]
3714	then
3715
3716	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3717	# DIRECTORY
3718	cp .dvrserver.config DATA_DVR
3719
3720	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3721	# SEQUENCE MODE DATA TOO)
3722	process_dvr_output -d DATA_DVR -f $fname -s
3723
3724	else
3725
3726	# PROCESS THE LOCAL OUTPUT
3727	process_dvr_output -l -d DATA_DVR -f $fname
3728
3729	fi
3730
3731	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3732	then
3733
3734	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3735	process_dvr_output -l -d DATA_DVR -f $fname
3736
3737	fi
3738	fi
3739
3740
3741
3742	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3743	# BY EACH CORE INTO ONE FILE
3744	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3745	then
3746	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3747	printf "\n 2d- and/or 3d-data may be incomplete!"
3748	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3749	elif [[ "$combine_plot_fields" == true ]]
3750	then
3751	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3752	then
3753	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3754	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3755	else
3756	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3757	combine_plot_fields${block}.x
3758	fi
3759	else
3760
3761	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3762	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3763	# ??? koennen wir das streichen ???
3764	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3765	fi
3766
3767
3768
3769	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3770	(( i = 0 ))
3771	while (( i < ioc ))
3772	do
3773	(( i = i + 1 ))
3774	if (( i == 1 ))
3775	then
3776	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3777	fi
3778	printf "\n >>> ${out_command[$i]}"
3779	eval ${out_command[$i]}
3780	if (( i == ioc ))
3781	then
3782	printf "\n$dashes\n"
3783	fi
3784	done
3785
3786
3787	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3788	if [[ $do_trace = true ]]
3789	then
3790	printf "\n\n"
3791	ls -al
3792	fi
3793
3794
3795
3796	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3797	(( i = 0 ))
3798	while (( i < iout ))
3799	do
3800	(( i = i + 1 ))
3801	if (( i == 1 ))
3802	then
3803	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3804	fi
3805
3806	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3807	files_for_pes=false; filetyp=file
3808	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3809	then
3810	files_for_pes=true; filetyp=directory
3811	actionout[$i]=""
3812	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3813	then
3814	actionout[$i]=""
3815	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3816	then
3817	files_for_pes=true; filetyp=directory
3818	actionout[$i]="ar"
3819	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3820	then
3821	actionout[$i]="ar"
3822	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3823	then
3824	files_for_pes=true; filetyp=directory
3825	actionout[$i]="fl"
3826	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3827	then
3828	actionout[$i]="fl"
3829	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3830	then
3831	files_for_pes=true; filetyp=directory
3832	actionout[$i]="tr"
3833	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3834	then
3835	actionout[$i]="tr"
3836	fi
3837
3838	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3839	then
3840	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3841	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3842	then
3843	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3844	else
3845
3846
3847	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3848	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3849	if [[ "${actionout[$i]}" = tr ]]
3850	then
3851	if [[ $localhost != $fromhost ]]
3852	then
3853	if [[ $files_for_pes = false ]]
3854	then
3855	cps=""
3856	cst=""
3857	else
3858	cps=-c
3859	cst="/"
3860	fi
3861	if [[ $localhost = nech ]]
3862	then
3863
3864	# TRANSFER IN SEPERATE JOB
3865	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3866	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3867	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3868	if [[ $files_for_pes = false ]]
3869	then
3870	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3871	else
3872	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3873	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3874	fi
3875
3876	echo "set -x" > transfer_${localout[$i]}
3877	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3878
3879	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3880	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3881	printf "\n or higher cycle\n"
3882	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3883
3884	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3885
3886	if [[ $localhost = nech ]]
3887	then
3888	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3889	else
3890	if [[ "$LOGNAME" = b323013 ]]
3891	then
3892	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3893	else
3894	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3895	fi
3896	fi
3897
3898	else
3899
3900	# TRANSFER WITHIN THIS JOB
3901	transfer_failed=false
3902	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3903	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3904	if [[ $localhost = lccrayb ]]
3905	then
3906	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3907	elif [[ $localhost = lccrayh ]]
3908	then
3909	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3910	elif [[ $localhost = lcbullhh ]]
3911	then
3912	ssh $usern@mlogin101 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3913	elif [[ $localhost = lcxe6 ]]
3914	then
3915	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3916	else
3917	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3918	fi
3919	[[ $? != 0 ]] && transfer_failed=true
3920
3921	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3922	if [[ $transfer_failed = true ]]
3923	then
3924	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3925	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3926
3927	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3928	eval local_catalog=${pathout[$i]}
3929	if [[ ! -d $local_catalog ]]
3930	then
3931	printf " *** local directory does not exist. Trying to create:\n"
3932	printf " $local_catalog \n"
3933	mkdir -p $local_catalog
3934	fi
3935	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3936	transfer_problems=true
3937	fi
3938	fi
3939	else
3940
3941	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3942	actionout[$i]=""
3943	fi
3944	fi
3945
3946
3947	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3948	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3949	if [[ "${actionout[$i]}" = tra ]]
3950	then
3951	if [[ $localhost != $fromhost ]]
3952	then
3953	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3954	then
3955
3956	# TRANSFER IN SEPERATE JOB
3957	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3958	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3959	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3960	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3961
3962	echo "set -x" > transfer_${localout[$i]}
3963	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3964
3965	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3966	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3967	printf "\n or higher cycle\n"
3968	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]}
3969
3970	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3971
3972	if [[ $localhost = nech ]]
3973	then
3974	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3975	else
3976	if [[ $LOGNAME = b323013 ]]
3977	then
3978	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3979	else
3980	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3981	fi
3982	fi
3983
3984	else
3985
3986	# TRANSFER WITHIN THIS JOB
3987	transfer_failed=false
3988	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3989	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3990	if [[ $localhost = lccrayb ]]
3991	then
3992	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3993	elif [[ $localhost = lccrayh ]]
3994	then
3995	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3996	elif [[ $localhost = lcxe6 ]]
3997	then
3998	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3999	else
4000	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
4001	fi
4002	[[ $? != 0 ]] && transfer_failed=true
4003
4004	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
4005	if [[ $transfer_failed = true ]]
4006	then
4007	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4008	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4009
4010	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4011	eval local_catalog=${pathout[$i]}
4012	if [[ ! -d $local_catalog ]]
4013	then
4014	printf " *** local directory does not exist. Trying to create:\n"
4015	printf " $local_catalog \n"
4016	mkdir -p $local_catalog
4017	fi
4018
4019	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4020	transfer_problems=true
4021	fi
4022	fi
4023	else
4024
4025	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4026	actionout[$i]=a
4027	fi
4028	fi
4029
4030
4031	# OUTPUT-FILE FOR A RESTART-RUN.
4032	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4033	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4034	# AS LAST ACTION, ARCHIVING IS INITIATED.
4035	if [[ "${actionout[$i]}" = fl ]]
4036	then
4037	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4038	chmod g+rx $tmp_data_catalog
4039	if [[ $files_for_pes = false ]]
4040	then
4041	printf "\n >>> OUTPUT: ${localout[$i]} to"
4042	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4043	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4044	else
4045	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4046	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4047	mkdir $tmp_data_catalog/${frelout[$i]}
4048	cd ${localout[$i]}
4049	for file in $(ls *)
4050	do
4051	ln -f $file $tmp_data_catalog/${frelout[$i]}
4052	done
4053	cd $TEMPDIR
4054	fi
4055
4056
4057	# CREATE AND SUBMIT ARCHIVING-JOB
4058	if [[ $store_on_archive_system = true ]]
4059	then
4060
4061	if [[ $archive_system = asterix ]]
4062	then
4063	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4064	if [[ $files_for_pes = false ]]
4065	then
4066	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4067	else
4068	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4069	fi
4070	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4071	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4072	echo "then" >> archive_${frelout[$i]}
4073	echo " do_stageout=false" >> archive_${frelout[$i]}
4074	echo "else" >> archive_${frelout[$i]}
4075	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4076	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4077	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4078	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4079	if [[ $files_for_pes = false ]]
4080	then
4081	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4082	else
4083	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4084	fi
4085	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4086	echo "fi" >> archive_${frelout[$i]}
4087	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4088	elif [[ $archive_system = DMF ]]
4089	then
4090	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4091	if [[ $files_for_pes = false ]]
4092	then
4093	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4094	locat=DMF
4095	exit
4096	else
4097	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4098	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4099	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4100	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4101	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4102	fi
4103	elif [[ $archive_system = tivoli ]]
4104	then
4105	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4106	if [[ $files_for_pes = false ]]
4107	then
4108	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4109	echo "set -x" >> archive_${frelout[$i]}
4110	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4111	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4112	else
4113
4114	echo "set -x" >> archive_${frelout[$i]}
4115	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4116	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4117	cd $tmp_data_catalog
4118	all_files=`ls -1 ${frelout[$i]}/*`
4119	cd - > /dev/null
4120	(( inode = 0 ))
4121	(( tp1 = tasks_per_node + 1 ))
4122	while (( inode < nodes ))
4123	do
4124	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4125	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4126	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4127	(( inode = inode + 1 ))
4128	done
4129	fi
4130	elif [[ $archive_system = ut ]]
4131	then
4132	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4133	if [[ $files_for_pes = false ]]
4134	then
4135	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4136	echo "set -x" >> archive_${frelout[$i]}
4137	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4138	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4139	else
4140
4141	echo "set -x" >> archive_${frelout[$i]}
4142	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4143	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4144	cd $tmp_data_catalog
4145	all_files=`ls -1 ${frelout[$i]}/*`
4146	cd - > /dev/null
4147	(( inode = 0 ))
4148	(( tp1 = tasks_per_node + 1 ))
4149	while (( inode < nodes ))
4150	do
4151	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4152	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4153	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4154	(( inode = inode + 1 ))
4155	done
4156	fi
4157	elif [[ $archive_system = none ]]
4158	then
4159	printf " +++ archiving on $localhost not available!\n"
4160	fi
4161
4162	if [[ $archive_system != none ]]
4163	then
4164	if [[ $localhost = nech ]]
4165	then
4166	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4167	fi
4168	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4169	fi
4170	else
4171	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4172	fi
4173
4174
4175	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4176	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4177	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4178	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4179	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4180	if [[ $files_for_pes = false ]]
4181	then
4182	cat /dev/null > ${pathout[$i]}
4183	else
4184	mkdir -p ${pathout[$i]}
4185	fi
4186
4187	fi
4188
4189
4190	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4191	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4192	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4193	if [[ "${actionout[$i]}" = ar ]]
4194	then
4195	if [[ $files_for_pes = false ]]
4196	then
4197	printf "\n >>> OUTPUT: ${localout[$i]} to"
4198	printf "\n ${pathout[$i]}"
4199	printf "\n File will be copied to archive-system ($archive_system) !\n"
4200	else
4201	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4202	printf "\n ${pathout[$i]}"
4203	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4204	fi
4205	mv ${localout[$i]} ${frelout[$i]}
4206
4207	file_saved=false
4208
4209	if [[ $archive_system = asterix ]]
4210	then
4211	do_stageout=true
4212	(( stageout_anz = 0 ))
4213	while [[ $do_stageout = true ]]
4214	do
4215	if [[ $files_for_pes = false ]]
4216	then
4217	stageout ${frelout[$i]} > STAGE_OUTPUT
4218	else
4219	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4220	fi
4221	cat STAGE_OUTPUT
4222	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4223	then
4224	file_saved=true
4225	do_stageout=false
4226	else
4227	if [[ $files_for_pes = false ]]
4228	then
4229	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4230	else
4231	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4232	fi
4233	(( stageout_anz = stageout_anz + 1 ))
4234	if (( stageout_anz == 10 ))
4235	then
4236	printf "\n +++ stoped after 10 unsuccessful tries!"
4237	archive_save=false
4238	do_stageout=false
4239	else
4240	printf "\n *** new try to store on archive after 15 min:"
4241	sleep 900
4242	fi
4243	fi
4244	done
4245	elif [[ $archive_system = DMF ]]
4246	then
4247	if [[ $files_for_pes = false ]]
4248	then
4249	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4250	locat=DMF
4251	exit
4252	else
4253	rm -rf $ARCHIVE/${frelout[$i]}
4254	cp -r ${frelout[$i]} $ARCHIVE
4255	fi
4256	file_saved=true
4257	elif [[ $archive_system = tivoli ]]
4258	then
4259	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4260	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4261	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4262	# WHEN THE ARCHIVE-JOB IS EXECUTED
4263	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4264	chmod g+rx $tmp_data_catalog
4265	if [[ $files_for_pes = false ]]
4266	then
4267	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4268	else
4269	mkdir $tmp_data_catalog/${frelout[$i]}
4270	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4271	fi
4272
4273	# GENERATE AND SUBMIT BATCH-JOB
4274	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4275	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4276	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4277	if [[ $files_for_pes = false ]]
4278	then
4279	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4280	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4281	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4282	else
4283	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4284	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4285	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4286	fi
4287
4288	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4289	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4290	file_saved=true
4291
4292	elif [[ $archive_system = ut ]]
4293	then
4294	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4295	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4296	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4297	# WHEN THE ARCHIVE-JOB IS EXECUTED
4298	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4299	chmod g+rx $tmp_data_catalog
4300	if [[ $files_for_pes = false ]]
4301	then
4302	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4303	else
4304	mkdir $tmp_data_catalog/${frelout[$i]}
4305	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4306	fi
4307
4308	# GENERATE AND SUBMIT BATCH-JOB
4309	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4310	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4311	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4312	if [[ $files_for_pes = false ]]
4313	then
4314	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4315	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4316	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4317	else
4318	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4319	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4320	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4321	fi
4322
4323	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4324	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4325	file_saved=true
4326
4327	else
4328	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4329	archive_save=false
4330	fi
4331
4332	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4333	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4334	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4335	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4336	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4337	if [[ $file_saved = true ]]
4338	then
4339	if [[ $files_for_pes = false ]]
4340	then
4341	cat /dev/null > ${pathout[$i]}
4342	else
4343	mkdir -p ${pathout[$i]}
4344	fi
4345	fi
4346
4347	fi
4348
4349	# APPEND ON THIS MACHINE
4350	if [[ "${actionout[$i]}" = "a" ]]
4351	then
4352	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4353	then
4354	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4355	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4356	else
4357	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4358	cat ${localout[$i]} >> ${pathout[$i]}
4359	fi
4360	fi
4361
4362	# COPY ON THIS MACHINE
4363	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4364	# ON DIFFERENT FILE-SYSTEMS
4365	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4366	then
4367
4368	# COPY IN CASE OF RUNS ON SINGLE CORES
4369	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4370	then
4371	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4372	if [[ $link_local_output = true ]]
4373	then
4374	printf " using ln -f\n"
4375	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4376	fi
4377	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4378	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4379	then
4380	if [[ $link_local_output = true ]]
4381	then
4382	printf " ln failed, using cp...\n"
4383	fi
4384	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4385	fi
4386	else
4387	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4388	if [[ $link_local_output = true ]]
4389	then
4390	printf " using ln -f\n"
4391	ln -f ${localout[$i]} ${pathout[$i]}
4392	fi
4393	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4394	if [[ ! -f "${pathout[$i]}" ]]
4395	then
4396	if [[ $link_local_output = true ]]
4397	then
4398	printf " ln failed, using cp...\n"
4399	fi
4400	cp ${localout[$i]} ${pathout[$i]}
4401	fi
4402	fi
4403
4404	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4405	then
4406
4407	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4408	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4409	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4410	if [[ $link_local_output = true ]]
4411	then
4412	printf " using ln -f\n"
4413	mkdir ${pathout[$i]}
4414	cd ${localout[$i]}
4415	for file in $(ls *)
4416	do
4417	ln -f $file ${pathout[$i]}
4418	done
4419	cd $TEMPDIR
4420	fi
4421
4422	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4423	if [[ ! -f "${pathout[$i]}/_0000" ]]
4424	then
4425	if [[ $link_local_output = true ]]
4426	then
4427	printf " ln failed for .../_0000, using cp...\n"
4428	fi
4429	cp -r ${localout[$i]} ${pathout[$i]}
4430	fi
4431
4432	fi
4433	fi
4434	done
4435	if (( i != 0 ))
4436	then
4437	if [[ $transfer_problems = true ]]
4438	then
4439	printf "\n$dashes\n *** OUTPUT-files saved"
4440	printf "\n +++ WARNING: some data transfers failed! \n"
4441	else
4442	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4443	fi
4444	fi
4445
4446
4447	# IF REQUIRED, START A RESTART-JOB
4448	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4449	if [[ -f CONTINUE_RUN ]]
4450	then
4451
4452	if [[ $archive_save = true ]]
4453	then
4454
4455	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4456	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4457	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4458	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4459	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4460	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4461	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4462	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4463	then
4464	mc=`echo $mc \| sed 's/#/f/g'`
4465	fi
4466
4467
4468	# START THE RESTART-JOB
4469	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4470	echo " $mc"
4471	printf "\n$dashes\n"
4472	if [[ $localhost != $fromhost ]]
4473	then
4474
4475	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4476	then
4477	echo "*** ssh will be used to initiate restart-runs!"
4478	echo " return_address=\"$return_address\" "
4479	echo " return_username=\"$return_username\" "
4480	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4481	then
4482	if [[ $localhost = ibmh ]]
4483	then
4484	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\" "
4485	elif [[ $localhost = lcbullhh ]]
4486	then
4487	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\" "
4488	elif [[ $localhost = lccrayb ]]
4489	then
4490	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\" "
4491	elif [[ $localhost = lccrayh ]]
4492	then
4493	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\" "
4494	elif [[ $localhost = lcxe6 ]]
4495	then
4496	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\" "
4497	else
4498	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 "
4499	fi
4500	else
4501	if [[ $localhost = ibmkisti ]]
4502	then
4503	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\" "
4504	elif [[ $localhost = lcflow ]]
4505	then
4506	/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 "
4507	elif [[ $localhost = lccrayb ]]
4508	then
4509	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\" "
4510	elif [[ $localhost = lccrayh ]]
4511	then
4512	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\" "
4513	else
4514	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4515	fi
4516	fi
4517	else
4518	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4519	locat=restart; exit
4520	fi
4521
4522	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4523	if [[ $queue = special1q ]]
4524	then
4525	sleep 120
4526	else
4527	sleep 30
4528	fi
4529
4530	else
4531
4532	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4533	# USING SSH)
4534	cd $LOCAL_PWD
4535	if [[ $localhost = lckyuh ]]
4536	then
4537	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4538	printf "\n please restart job manually using command:\n"
4539	printf "\n \"$mc\" "
4540	else
4541	eval $mc # THE ' MUST BE EVALUATED
4542	fi
4543	cd - > /dev/null
4544	fi
4545	if [[ $localhost = lckyuh ]]
4546	then
4547	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4548	else
4549	printf "\n$dashes\n *** restart-run initiated \n"
4550	fi
4551
4552
4553	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4554	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4555	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4556	# MAY BE VERY HUGE)
4557	(( i = 0 ))
4558	while (( i < iin ))
4559	do
4560	(( i = i + 1 ))
4561	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4562	then
4563	rm -r $tmp_data_catalog/${frelin[$i]}
4564	fi
4565	done
4566
4567	else
4568
4569	printf "\n +++ no restart-run possible, since errors occured"
4570	printf "\n during the archive process"
4571	fi
4572
4573	fi
4574
4575
4576
4577	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4578	if [[ "$email_notification" != "none" ]]
4579	then
4580
4581	if [[ $localhost != $fromhost ]]
4582	then
4583	if [[ -f CONTINUE_RUN ]]
4584	then
4585	echo "PALM restart run necessary" > email_text
4586	echo "description header of actual run:" >> email_text
4587	cat CONTINUE_RUN >> email_text
4588	echo "mrun-command to restart:" >> email_text
4589	echo "$mc" >> email_text
4590	else
4591	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4592	fi
4593	mail $email_notification < email_text
4594	printf "\n *** email notification sent to \"$email_notification\" "
4595	fi
4596	fi
4597
4598
4599
4600	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4601	cd $HOME
4602	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4603
4604	else
4605
4606	# PREPARING ACTIONS,
4607	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4608
4609	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4610	mrun_com="$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 $remote_username"
4611	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4612	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4613	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4614	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4615	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4616	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4617	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4618	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4619	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4620	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4621	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4622	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4623	if [[ $use_openmp = true ]]
4624	then
4625	mrun_com=${mrun_com}" -O $threads_per_task"
4626	fi
4627	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4628	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4629	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4630	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4631	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4632	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4633	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4634	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4635	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4636	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4637	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4638	if [[ $do_remote = true ]]
4639	then
4640	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4641	fi
4642
4643
4644	# CREATE EXECUTABLE FOR BATCH JOB
4645	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4646	then
4647
4648	printf "\n *** creating the executable for batch job\n"
4649
4650	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4651	if [[ $host != $localhost ]]
4652	then
4653	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4654	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4655	locat=create_executable; exit
4656	fi
4657
4658	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4659	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4660
4661	cp $make_depository .
4662	tar -xf $make_depository > /dev/null 2>&1
4663	cp ../* . > /dev/null 2>&1
4664
4665	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4666
4667	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4668	then
4669	printf "\n +++ error occured while compiling or linking"
4670	locat=compile
4671	exit
4672	fi
4673
4674	mv a.out ..
4675	cd - > /dev/null 2>&1
4676	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4677
4678	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4679
4680	fi
4681
4682
4683	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4684	jobfile=jobfile.$RANDOM
4685
4686
4687	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4688	echo "mkdir $TEMPDIR" >> $jobfile
4689	echo "cd $TEMPDIR" >> $jobfile
4690
4691
4692	# ACTIVATE ERROR-TRACEBACK
4693	if [[ $do_trace = true ]]
4694	then
4695	echo "set -x" >> $jobfile
4696	else
4697	echo "set +vx" >> $jobfile
4698	fi
4699
4700
4701	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4702	if [[ "$init_cmds" != "" ]]
4703	then
4704	echo "$init_cmds" >> $jobfile
4705	fi
4706	if [[ "$module_calls" != "" ]]
4707	then
4708	echo "$module_calls" >> $jobfile
4709	fi
4710
4711
4712	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4713	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4714	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4715	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4716	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4717	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4718	# QUEUEING-SYSTEMS
4719	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4720	then
4721
4722	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4723	if [[ $restart_run != true ]]
4724	then
4725	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4726	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4727	fi
4728
4729	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4730	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4731	echo "set -x" >> $jobfile
4732	if [[ $host = $localhost ]]
4733	then
4734	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4735	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4736	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4737	then
4738	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4739	else
4740	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4741	fi
4742
4743	else
4744	if [[ $host = ibmkisti ]]
4745	then
4746	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4747	echo "localdir=\`pwd\`" >> $jobfile
4748	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4749	elif [[ $host = lcbullhh ]]
4750	then
4751	echo "localdir=\`pwd\`" >> $jobfile
4752	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4753
4754	elif [[ $host = lccrayb ]]
4755	then
4756	echo "localdir=\`pwd\`" >> $jobfile
4757	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4758	elif [[ $host = lccrayh ]]
4759	then
4760	echo "localdir=\`pwd\`" >> $jobfile
4761	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4762
4763	else
4764	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4765	fi
4766	fi
4767	echo "export SOURCES_COMPLETE=true" >> $jobfile
4768
4769	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4770	# WORKING DIRECTORY OF THE JOB
4771	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4772	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4773	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4774	echo "execute_mrun=true" >> $jobfile
4775	echo " " >> $jobfile
4776
4777	else
4778
4779	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4780	if [[ $do_compile = true ]]
4781	then
4782
4783	source_catalog=SOURCES_FOR_RUN_$fname
4784
4785	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4786	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4787	echo "export SOURCES_COMPLETE=true" >> $jobfile
4788	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4789
4790	for filename in $source_list
4791	do
4792	# BACKSLASH IS USED FOR MASKING
4793	echo "cat > $filename << \"%END%\"" >> $jobfile
4794	cat $source_catalog/$filename >> $jobfile
4795	echo " " >> $jobfile
4796	echo "%END%" >> $jobfile
4797	echo " " >> $jobfile
4798	done
4799
4800	# BACKSLASH IS USED FOR MASKING
4801	echo "cat > Makefile << \"%END%\"" >> $jobfile
4802	cat $source_catalog/Makefile >> $jobfile
4803	echo " " >> $jobfile
4804	echo "%END%" >> $jobfile
4805	echo " " >> $jobfile
4806
4807	echo "cd - > /dev/null" >> $jobfile
4808
4809	fi
4810
4811
4812	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4813	# BACKSLASH IS USED FOR MASKING
4814	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4815	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4816	echo "cat > $config_file << \"%END%\"" >> $jobfile
4817	if [[ $host = lckyuh ]]
4818	then
4819	# NO CROSS-COMPILER ON COMPUTE NODE
4820	sed 's/frtpx/frt/g' $config_file >> $jobfile
4821	else
4822	sed 's/#$.*//g' $config_file >> $jobfile
4823	fi
4824	echo "%END%" >> $jobfile
4825	echo " " >> $jobfile
4826
4827
4828	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4829	# BACKSLASH IS USED FOR MASKING
4830	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4831	if [[ $host = lckyuh ]]
4832	then
4833	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4834	else
4835	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4836	fi
4837	echo "%END%" >> $jobfile
4838	echo "chmod u+x $mrun_script_name" >> $jobfile
4839	echo "execute_mrun=true" >> $jobfile
4840	echo " " >> $jobfile
4841
4842	fi
4843
4844
4845	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4846	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4847	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4848	if [[ $do_remote = true ]]
4849	then
4850	(( i = 0 ))
4851	while (( i < iin ))
4852	do
4853	(( i = i + 1 ))
4854	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4855	if [[ "${transin[$i]}" = job ]]
4856	then
4857	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4858	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4859	echo " " >> $jobfile
4860	echo "%END%" >> $jobfile
4861	else
4862	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4863	fi
4864
4865	# CHECK, IF FILE COULD BE CREATED
4866	echo "if [[ \$? = 1 ]]" >> $jobfile
4867	echo "then" >> $jobfile
4868	echo " echo \" \" " >> $jobfile
4869	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4870	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4871	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4872	echo " execute_mrun=false" >> $jobfile
4873	echo "fi" >> $jobfile
4874	done
4875	fi
4876
4877	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4878	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4879	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4880	echo "LOCAL_PWD=$working_directory" >> $jobfile
4881	echo "export LOCAL_PWD" >> $jobfile
4882
4883	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4884	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4885	echo "export LOCAL_MRUN_PATH" >> $jobfile
4886
4887	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4888	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4889	# then
4890	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4891	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4892	# fi
4893
4894	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4895	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4896	echo "set -x" >> $jobfile
4897	echo "queue=$queue" >> $jobfile
4898	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4899	echo 'ls -al; echo `pwd`' >> $jobfile
4900	echo "cd \$HOME" >> $jobfile
4901	echo "rm -rf $TEMPDIR" >> $jobfile
4902
4903
4904
4905
4906	# START THE JOB USING SUBJOB-COMMAND
4907	if [[ $silent = false ]]
4908	then
4909	printf "\n "
4910	else
4911	printf "\n\n"
4912	fi
4913
4914	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
4915	rm -rf $jobfile
4916
4917
4918	fi # END OF REMOTE-PART

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