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source: palm/trunk/SCRIPTS/mrun @ 1462

Last change on this file since 1462 was 1443, checked in by raasch, 10 years ago
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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 1443 2014-07-28 07:11:00Z suehring $
29	#
30	# 1442 2014-07-28 07:09:10Z raasch
31	# default queues for HLRN-III (lccrayb/lccrayh) defined
32	#
33	# 1422 2014-07-02 10:01:25Z kanani
34	# automatic restarts enabled for lccrayb,
35	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
36	#
37	# 1420 2014-06-10 06:24:14Z raasch
38	# -j1 option added to aprung command for lccrayf (CSC)
39	#
40	# 1402 2014-05-09 14:25:13Z raasch
41	# batch_job added to envpar-NAMELIST
42	#
43	# 1357 2014-04-11 15:02:03Z witha
44	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
45	# possible)
46	#
47	# 1320 2014-03-20 08:40:49Z raasch
48	# check namelist file set false by default
49	#
50	# 1304 2014-03-12 10:29:42Z raasch
51	# ulimit option changed from -Ss to -s
52	#
53	# bugfix: missing "fi" in r1289
54	#
55	# 1289 2014-03-04 07:12:34Z raasch
56	# comments translated to English
57	# necriam-, fimm-, ibmy-, and sgi-specific code removed
58	# export of variables for palm and interpret_config removed
59	#
60	# 1281 2014-02-01 07:55:49Z raasch
61	# rsync-copy restricted to Cray machines, since command is unavailable on some
62	# other systems
63	#
64	# 1279 2014-01-28 12:10:14Z raasch
65	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
66	# in order to remove annoying restrictions concerning the number of processors which
67	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
68	# restriction, one of the nodes will be filled with less than the given number of
69	# tasks per node. A respective warning is given.
70	#
71	# 1274 2014-01-09 13:14:54Z heinze
72	# adjustments for lccrayh
73	#
74	# 1272 2014-01-08 10:19:32Z witha
75	# small adjustment for lcflow
76	#
77	# 1270 2013-12-16 11:05:01Z fricke
78	# call of combine_plot_fields adjusted for lccrayb/lccrayh
79	#
80	# 1255 2013-11-07 14:43:35Z raasch
81	# further adjustments for lccrayb remote access
82	#
83	# 1241 2013-10-30 11:36:58Z heinze
84	# Enable use of nudging input and input of large scale forcing from
85	# external files
86	#
87	# 1229 2013-09-20 06:55:19Z raasch
88	# further adjustments for lccrayb
89	#
90	# 1224 2013-09-16 07:27:23Z raasch
91	# first adjustments for lccrayb
92	#
93	# 1210 2013-08-14 10:58:20Z raasch
94	# fftw support added
95	#
96	# 1201 2013-07-10 16:17:59Z witha
97	# adjustments for Forwind cluster (lcflow)
98	#
99	# 1199 2013-07-05 14:52:22Z raasch
100	# adjustments for CSC Helsinki (lccrayf),
101	# executables for batch jobs can be created in advance, in order to avoid calling
102	# the compiler within the batch job (only works if batch jobs are submitted on
103	# local host)
104	#
105	# 1190 2013-06-25 09:39:21Z heinze
106	# enable use of automatic restarts for ibmh
107	# use of cluster/express queue enabled (ibmh)
108	#
109	# 1124 2013-04-09 15:46:52Z raasch
110	# variable "memory" is exported via typeset option -x, because otherwise an unknown
111	# side effect may lead to data loss while getopts is reading the script-option arguments
112	#
113	# 1122 2013-04-09 08:37:16Z heinze
114	# Bugfix: change type of variable last_char
115	#
116	# 1119 2013-04-05 15:11:19Z raasch
117	# Bugfix for setting -T option for subjob
118	#
119	# 1108 2013-03-05 07:03:32Z raasch
120	# bugfix for coupled runs on lckyut/lckyuh
121	#
122	# 1106 2013-03-04 05:31:38Z raasch
123	# --stdin argument for mpiexec on lckyuh
124	# -y and -Y settings output to header
125	#
126	# 1103 2013-02-20 02:15:53Z raasch
127	# default script runs again under ksh, because of unsolved problems with read
128	# from stdin: when bash script is called from a ksh, message "read error: 0:
129	# Resource temporarily unavailable" appears and script does not stop,
130	# further bash compatibility adjustments,
131	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
132	# on lckyuh, but mrun does not terminate and issues a warning instead
133	#
134	# 1101 2013-02-17 10:20:21Z raasch
135	# script now running under bash instead of ksh, which required small adjustments
136	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
137	# read from stdin),
138	# cross compilername on lckyuh compute nodes replaced by real compiler name
139	#
140	# 1099 2013-02-10 01:47:43Z raasch
141	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
142	# and for Forwind cluster (lcflow)
143	# small further adjustments for lckyut
144	#
145	# 1094 2013-02-03 01:52:12Z raasch
146	# explicit ssh/scp port can be set in config file with environment variable
147	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
148	# decalpha parts (yonsei) removed
149	#
150	# 2013-02-02 07:06:13Z raasch
151	# adjustments for Kyushu-University computing center (lckyut - tatara)
152	#
153	# 1083 2013-01-04 10:22:09Z maronga
154	# bugfix in parameter file check (read %cpp_options was missing)
155	#
156	# 1069 2012-11-28 16:18:43Z maronga
157	# bugfix: coupling mode was always set to mpi2, typos removed
158	#
159	# 1058 2012-11-21 07:00:35Z raasch
160	# Intel inspector (inspxe) is given the number of PEs instead of the number of
161	# nodes
162	#
163	# 1046 2012-11-09 14:38:45Z maronga
164	# code put under GPL (PALM 3.9)
165	#
166	# 21/03/94 - Siggi - first version finished
167	# 03/03/94 - Siggi - script development started
168	#
169	#--------------------------------------------------------------------------------#
170	# mrun - script for running PALM jobs
171	#--------------------------------------------------------------------------------#
172
173
174
175	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
176
177	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
178	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
179	# (TOO MANY ARGUMENTS - PROBLEM)
180	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
181
182	AddFilenames=""
183	additional_conditions=""
184	add_source_path=""
185	afname=""
186	archive_save=true
187	archive_system=none
188	check_namelist_files=false
189	combine_plot_fields=true
190	compiler_name=""
191	cond1=""
192	cond2=""
193	config_file=.mrun.config
194	coupled_dist=""
195	coupled_mode="mpi1"
196	cpp_opts=""
197	cpp_options=""
198	cpumax=0
199	cpurest=0
200	create_executable_for_batch=false
201	delete_temporary_catalog=true
202	do_batch=false
203	do_compile=true
204	do_remote=false
205	do_stagein=true
206	do_stageout=true
207	do_trace=false
208	email_notification="none"
209	exclude=""
210	executable=""
211	execution_error=false
212	fftw_inc=""
213	fftw_lib=""
214	fftw_support=false
215	fname=test
216	fromhost=""
217	global_revision=""
218	group_number=none
219	host=""
220	host_file=""
221	hp=""
222	ignore_archive_error=false
223	input_list=""
224	interpreted_config_file=""
225	job_catalog="~/job_queue"
226	job_on_file=""
227	keep_data_from_previous_run=false
228	link_local_input=false
229	link_local_output=false
230	localhost_realname=$(hostname)
231	local_dvrserver_running=.FALSE.
232	locat=normal
233	mainprog=""
234	makefile=""
235	max_par_io_str=""
236	mc=$0
237	while [[ $(echo $mc \| grep -c "/") != 0 ]]
238	do
239	mc=`echo $mc \| cut -f2- -d"/"`
240	done
241	module_calls=""
242	mrun_script_name=$mc
243	netcdf_inc=""
244	netcdf_lib=""
245	netcdf_support=false
246	node_usage=default
247	numprocs=""
248	numprocs_atmos=0
249	numprocs_ocean=0
250	OOPT=""
251	openmp=false
252	output_list=""
253	package_list=""
254	queue=none
255	read_from_config=""
256	restart_run=false
257	if [[ `hostname` = rte10 ]]
258	then
259	return_addres=133.5.185.60
260	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
261	elif [[ `hostname` = climate0 ]]
262	then
263	return_addres=165.132.26.68
264	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
265	elif [[ `hostname` = urban00 ]]
266	then
267	return_addres=147.46.30.151
268	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
269	else
270	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
271	fi
272	return_password=""
273	return_username=$LOGNAME
274	remotecall=false
275	remote_username=""
276	run_coupled_model=false
277	run_mode=""
278	store_on_archive_system=false
279	dashes=" ----------------------------------------------------------------------------"
280	silent=false
281	source_list=""
282	source_path=SOURCE
283	tasks_per_node=""
284	threads_per_task=1
285	tmpcreate=false
286	tmp_data_catalog=""
287	transfer_problems=false
288	usern=$LOGNAME
289	use_openmp=false
290	version="MRUN 2.1 Rev$Rev: 1443 $"
291	working_directory=`pwd`
292	TOPT=""
293	XOPT=""
294	zeit=$( date \| cut -c 12-19 )
295
296	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
297	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
298	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
299	# SCRIPT-OPTION ARGUMENTS
300	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
301
302
303
304	# ERROR HANDLING IN CASE OF EXIT
305	trap 'rm -rf $working_directory/tmp_mrun
306	if [[ $locat != normal && $locat != control_c ]]
307	then
308
309	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
310	(( i = 0 ))
311	while (( i < iec ))
312	do
313	(( i = i + 1 ))
314	printf "\n *** Execution of ERROR-command:\n"
315	printf " >>> ${err_command[$i]}\n"
316	eval ${err_command[$i]}
317	done
318	if [[ -n $interpreted_config_file ]]
319	then
320	rm -rf $interpreted_config_file
321	fi
322	if [[ -n .mrun_environment ]]
323	then
324	rm -rf .mrun_environment
325	fi
326	if [[ $tmpcreate = true ]]
327	then
328	printf "\n *** Contents of \"$TEMPDIR\":\n"
329	ls -al; cd
330	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
331	fi
332	if [[ "$dvrserver_id" != "" ]]
333	then
334	echo "+++ killing dvrserver_id=$dvrserver_id"
335	kill $dvrserver_id
336	fi
337	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
338	then
339	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
340	fi
341	printf "\n\n+++ MRUN killed \n\n"
342	elif [[ $locat != control_c ]]
343	then
344	printf "\n\n --> all actions finished\n\n"
345	printf " Bye, bye $usern !!\n\n"
346	fi' exit
347
348
349	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
350	trap 'rm -rf $working_directory/tmp_mrun
351	rm -rf $working_directory/tmp_check_namelist_files
352	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
353	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
354	then
355	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
356	fi
357	if [[ "$dvrserver_id" != "" ]]
358	then
359	echo "+++ killing dvrserver_id=$dvrserver_id"
360	kill $dvrserver_id
361	fi
362	printf "\n+++ MRUN killed by \"^C\" \n\n"
363	locat=control_c
364	exit
365	' 2
366
367
368	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
369	# BEEN SET
370	if [[ "$PALM_BIN" = "" ]]
371	then
372	printf "\n +++ environment variable PALM_BIN has not been set"
373	printf "\n please set it to the directory where the PALM scripts are located"
374	locat=palm_bin; exit
375	fi
376	export PATH=$PALM_BIN:$PATH
377
378
379
380	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
381	# WHICH WILL BE USED TO START RESTART-JOBS
382	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
383	do
384	case $option in
385	(a) afname=$OPTARG;;
386	(A) store_on_archive_system=true; mc="$mc -A";;
387	(b) do_batch=true; mc="$mc -b";;
388	(B) delete_temporary_catalog=false; mc="$mc -B";;
389	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
390	(C) restart_run=true; mc="$mc -C";;
391	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
392	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
393	(F) job_on_file="-D"; mc="$mc -F";;
394	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
395	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
396	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
397	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
398	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
399	(I) ignore_archive_error=true; mc="$mc -I";;
400	(k) keep_data_from_previous_run=true; mc="$mc -k";;
401	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
402	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
403	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
404	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
405	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
406	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
407	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
408	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
409	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
410	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
411	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
412	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
413	(S) read_from_config=false; mc="$mc -S";;
414	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
415	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
416	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
417	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
418	(v) silent=true; mc="$mc -v";;
419	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
420	(x) do_trace=true;set -x; mc="$mc -x";;
421	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
422	(y) ocean_file_appendix=true; mc="$mc -y";;
423	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
424	(z) check_namelist_files=false; mc="$mc -z";;
425	(Z) combine_plot_fields=false; mc="$mc -Z";;
426	(\?) printf "\n +++ unknown option $OPTARG \n"
427	printf "\n --> type \"$0 ?\" for available options \n"
428	locat=parameter;exit;;
429	esac
430	done
431
432
433	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
434	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
435	(( to_shift = $OPTIND - 1 ))
436	shift $to_shift
437
438	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
439	if [[ "$1" = "?" ]]
440	then
441	(printf "\n *** mrun can be called as follows:\n"
442	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"
443	printf "\n Description of available options:\n"
444	printf "\n Option Description Default-Value"
445	printf "\n -a base name of input files equiv. -d"
446	printf "\n -A archiving when using file-attribute fl"
447	printf "\n -b batch-job on local machine ---"
448	printf "\n -B do not delete temporary directory at end ---"
449	printf "\n -c configuration file .mrun.config"
450	printf "\n -d base name of files attached to program test"
451	printf "\n -D preprocessor(cpp)-directives \"\" "
452	printf "\n -F create remote job file only ---"
453	printf "\n -h execution host $localhost_realname"
454	printf "\n -i INPUT control list \"\" "
455	printf "\n -I archiving errors of previous batch-jobs"
456	printf "\n will be ignored"
457	printf "\n -k keep data from previous run"
458	printf "\n -K additional conditions for controling"
459	printf "\n usage of conditional code and"
460	printf "\n env-variables in configuration file \"\" "
461	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
462	printf "\n -M Makefile name Makefile"
463	printf "\n -n node usage (shared/not_shared) depending on -h"
464	printf "\n -o OUTPUT control list \"\" "
465	printf "\n -O threads per openMP task ---"
466	printf "\n -p software package list \"\" "
467	printf "\n -q queue \"$queue\" "
468	printf "\n -r run control list (combines -i -o) \"\" "
469	printf "\n -s filenames of routines to be compiled \"\" "
470	printf "\n must end with .f, .f90, .F, or .c !"
471	printf "\n use \"..\" for more than one file and wildcards"
472	printf "\n -s LM compiles all locally modified files"
473	printf "\n -S config file interpreted by shellscript ---"
474	printf "\n -t allowed cpu-time in seconds (batch) 0"
475	printf "\n -T tasks per node depending on -h"
476	printf "\n -u username on remote machine \"\" "
477	printf "\n -v no prompt for confirmation ---"
478	printf "\n -w maximum parallel io streams as given by -X"
479	printf "\n -x tracing of mrun for debug purposes ---"
480	printf "\n -X # of processors (on parallel machines) 1"
481	printf "\n -y add appendix \"_O\" to all local output"
482	printf "\n files (ocean precursor runs followed by"
483	printf "\n coupled atmosphere-ocean runs) ---"
484	printf "\n -Y run coupled model, \"#1 #2\" with"
485	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
486	printf "\n -z disable a priori parameter file check ---"
487	printf "\n -Z skip combine_plot_fields at the end of "
488	printf "\n the simulation ---"
489	printf "\n "
490	printf "\n Possible values of positional parameter <modus>:"
491	printf "\n \"?\" - this outline \n\n") \| more
492	exit
493	elif [[ "$1" != "" ]]
494	then
495	printf "\n +++ positional parameter $1 unknown \n"
496	locat=parameter; exit
497	fi
498
499
500
501	# SHORT STARTING MESSAGE
502	printf "\n*** $version "
503	printf "\n will be executed. Please wait ..."
504
505
506
507	# CHECK, IF CONFIGURATION FILE EXISTS
508	if [[ ! -f $config_file ]]
509	then
510	printf "\n\n +++ configuration file: "
511	printf "\n $config_file"
512	printf "\n does not exist"
513	locat=connect; exit
514	fi
515
516
517	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
518	line=""
519	grep "%host_identifier" $config_file > tmp_mrun
520	while read line
521	do
522	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
523	then
524	HOSTNAME=`echo $line \| cut -d" " -s -f2`
525	host_identifier=`echo $line \| cut -d" " -s -f3`
526	if [[ $localhost_realname = $HOSTNAME ]]
527	then
528	localhost=$host_identifier
529	break
530	fi
531	fi
532	done < tmp_mrun
533
534	if [[ "$localhost" = "" ]]
535	then
536	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
537	printf "\n for local host \"$localhost_realname\"."
538	printf "\n Please add line"
539	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
540	printf "\n to the configuration file."
541	locat=localhost; exit
542	fi
543
544
545	# SET HOST-SPECIFIC VARIABLES
546	case $localhost_realname in
547	(r1\|r2\|h01\|b01) archive_system=tivoli;;
548	(cs*) archive_system=ut;;
549	esac
550
551
552	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
553	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
554	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
555	[[ "$afname" = "" ]] && afname=$fname
556
557
558	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
559	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
560	# STATEMENTS IN THE CONFIGURATION FILE
561	if [[ "$run_mode" != "" ]]
562	then
563	input_list="$input_list $run_mode"
564	output_list="$output_list $run_mode"
565	fi
566
567
568	# ??? is this (and the respective option -H) really required ???
569	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
570	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
571	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
572	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
573	if [[ "$fromhost" = "" ]]
574	then
575	fromhost=$localhost
576	fi
577
578
579	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
580	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
581	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
582	# TO BE SUBMITTED (I.E. do_bacth=true)
583	if [[ -n $host && "$host" != $localhost ]]
584	then
585	do_batch=true
586	do_remote=true
587	case $host in
588	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
589	(*) printf "\n"
590	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
591	printf "\n is not available"
592	locat=nqs; (( iec = 0 )); exit;;
593	esac
594	else
595	host=$localhost
596	fi
597
598
599	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
600	if [[ -n $additional_conditions ]]
601	then
602	cond1=`echo $additional_conditions \| cut -d" " -f1`
603	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
604	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
605	if [[ -n $dummy ]]
606	then
607	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
608	locat=options; exit
609	fi
610	block=_$cond1
611	[[ -n $cond2 ]] && block=${block}_$cond2
612	fi
613
614
615	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
616	if [[ $run_coupled_model = true ]]
617	then
618
619	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
620	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
621
622	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
623	then
624
625	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
626	printf "\n PEs (total) : $numprocs"
627	printf "\n PEs (atmosphere): $numprocs_atmos"
628	printf "\n PEs (ocean) : $numprocs_ocean"
629	locat=coupling; exit
630
631	fi
632
633
634	# GET coupled_mode FROM THE CONFIG FILE
635	line=""
636	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
637	while read line
638	do
639	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
640	then
641	coupled_mode="mpi2"
642	fi
643	done < tmp_mrun
644
645	fi
646
647
648	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
649	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
650	then
651	if [[ $ignore_archive_error = false ]]
652	then
653	printf "\n +++ data archiving of previous run failed"
654	printf "\n see directory \~/job_queue on remote machine"
655	locat=archive; exit
656	else
657	printf "\n +++ warning: data archiving in a previous run failed"
658	printf "\n MRUN continues, trying to get backup copy"
659	fi
660	fi
661
662
663	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
664	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
665	mrun_memory=$memory
666	mrun_group_number=$group_number
667	mrun_cpumax=$cpumax
668	mrun_numprocs=$numprocs
669
670
671	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
672	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
673	if [[ "$read_from_config" = false ]]
674	then
675
676	[[ $silent = false ]] && printf "\n Reading the configuration file... "
677
678	# READ THE CONFIGURATION FILE LINE BY LINE
679	while read zeile
680	do
681	[[ $silent = false ]] && printf "."
682
683
684	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
685	eval zeile=\"$zeile\"
686
687
688	# INTERPRET THE LINE
689	if [[ "$(echo $zeile)" = "" ]]
690	then
691	# EMPTY LINE, NO ACTION
692	continue
693
694	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
695	then
696
697	# LINE IS A COMMENT LINE
698	true
699
700	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
701	then
702
703	# LINE DEFINES AN ENVIRONMENT-VARIABLE
704	zeile=$(echo $zeile \| cut -c2-)
705	var=`echo $zeile \| cut -d" " -f1`
706	value=`echo $zeile \| cut -d" " -s -f2`
707	for_host=`echo $zeile \| cut -d" " -s -f3`
708	for_cond1=`echo $zeile \| cut -d" " -s -f4`
709	for_cond2=`echo $zeile \| cut -d" " -s -f5`
710
711	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
712	then
713
714	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
715	# "::" IS REPLACED BY ":".
716	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
717
718
719	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
720	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
721	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
722	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
723	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
724	# CONFIGURATION-FILE.
725	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
726	then
727	eval $var=\$value
728
729	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
730	if [[ $do_trace = true ]]
731	then
732	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
733	fi
734	fi
735
736	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
737	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
738	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
739	# MUST HAVE TO BE STARTED
740	if [[ $var = host ]]
741	then
742	if [[ -n $host && "$host" != $localhost ]]
743	then
744	do_batch=true
745	do_remote=true
746	case $host in
747	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
748	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
749	printf "\n is not available"
750	locat=nqs; exit;;
751	esac
752	else
753	host=$localhost
754	fi
755	fi
756
757	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
758	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
759	# BY MRUN (E.G. subjob)
760	export $var
761	fi
762
763
764
765
766	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
767	then
768
769	# LINE DEFINES ERROR-COMMAND
770	(( iec = iec + 1 ))
771	zeile=$(echo $zeile \| cut -c4-)
772	err_command[$iec]="$zeile"
773
774	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
775	then
776
777	# LINE DEFINES INPUT-COMMAND
778	(( iic = iic + 1 ))
779	zeile=$(echo $zeile \| cut -c4-)
780	in_command[$iic]="$zeile"
781
782	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
783	then
784
785	# LINE DEFINES OUTPUT-COMMAND
786	(( ioc = ioc + 1 ))
787	zeile=$(echo $zeile \| cut -c4-)
788	out_command[$ioc]="$zeile"
789
790	else
791
792	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
793	# s2a: in/out - field
794	# s2b: loc - field (optional)
795	# s2c: tr/ar - field (optional)
796	s1=`echo $zeile \| cut -d" " -f1`
797	s2=`echo $zeile \| cut -d" " -s -f2`
798	s2a=$(echo $s2 \| cut -d":" -f1)
799	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
800	then
801	s2b=""
802	s2c=""
803	else
804	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
805	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
806	fi
807	s3=`echo $zeile \| cut -d" " -f3`
808	s4=`echo $zeile \| cut -d" " -s -f4`
809	s5=`echo $zeile \| cut -d" " -s -f5`
810	s6=`echo $zeile \| cut -d" " -s -f6`
811
812
813	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
814	# INPUT- OR OUTPUT-LIST.
815	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
816	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
817	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
818	# IS NOT CHECKED AND STORED.
819	IFSALT="$IFS"; IFS="$IFS:"
820	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
821	then
822	found=false
823	for actual in $input_list
824	do
825	for formal in $s3
826	do
827	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
828	done
829	done
830	if [[ $found = true ]]
831	then
832	(( iin = iin + 1 ))
833	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
834	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
835	extin[$iin]=$s6
836	fi
837	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
838	then
839	found=false
840	for actual in $output_list
841	do
842	for formal in $s3
843	do
844	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
845	done
846	done
847	if [[ $found = true ]]
848	then
849	(( iout = iout + 1 ))
850	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
851	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
852	fi
853	elif [[ "$s2a" != in && "$s2a" != out ]]
854	then
855	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
856	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
857	locat=connect; exit
858	fi
859	IFS="$IFSALT"
860	fi
861	done < $config_file
862
863	else
864
865
866	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
867	[[ $silent = false ]] && printf "..."
868	interpreted_config_file=.icf.$RANDOM
869
870
871
872	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
873	cat > .mrun_environment << %%END%%
874	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
875	config_file = '$config_file', do_remote = '$do_remote',
876	do_trace = '$do_trace', host = '$host',
877	input_list = '$input_list', icf = '$interpreted_config_file',
878	localhost = '$localhost', output_list = '$output_list' /
879
880	%%END%%
881
882	if [[ "$host" != $localhost ]]
883	then
884
885	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
886	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
887	if [[ $? != 0 ]]
888	then
889	printf "\n\n +++ no interpret_config found"
890	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
891	locat=interpret_config; exit
892	fi
893	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
894	$interpret_config_executable
895
896	else
897
898	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
899	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
900	then
901	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
902	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
903	locat=interpret_config; exit
904	else
905	interpret_config${block}.x
906	fi
907
908	fi
909	rm .mrun_environment
910
911
912	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
913	chmod u+x $interpreted_config_file
914	export PATH=$PATH:.
915	. $interpreted_config_file
916	rm $interpreted_config_file
917
918	fi
919
920
921	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
922	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
923	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
924	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
925	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
926	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
927	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
928
929
930	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
931	# FOR SOURCE-FILES TO BE COMPILED.
932	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
933	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
934	if [[ "$SOURCES_COMPLETE" = "" ]]
935	then
936
937	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
938	# HAS BEEN DEFINED
939	source_path=""
940	line=""
941	grep "%source_path" $config_file > tmp_mrun
942	while read line
943	do
944	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
945	then
946	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
947	then
948	global_source_path=`echo $line \| cut -d" " -f2`
949	fi
950	fi
951	done < tmp_mrun
952
953	line=""
954	found=false
955	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
956	while read line
957	do
958	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
959	then
960	if [[ $found = true ]]
961	then
962	printf "\n\n +++ more than one source path found in configuration file"
963	printf "\n for local host \"$localhost\" "
964	locat=source_path; exit
965	fi
966	source_path=`echo $line \| cut -d" " -f2`
967	found=true
968	fi
969	done < tmp_mrun
970	rm tmp_mrun
971
972	if [[ "$source_path" = "" ]]
973	then
974	if [[ "$global_source_path" != "" ]]
975	then
976	source_path=$global_source_path
977	else
978	printf "\n\n +++ no source path found in configuration file"
979	printf "\n for local host \"$localhost\" "
980	locat=source_path; exit
981	fi
982	fi
983	eval source_path=$source_path
984
985	if [[ ! -d $source_path ]]
986	then
987	printf "\n\n +++ source path \"$source_path\" on local host"
988	printf "\n \"$localhost\" does not exist"
989	locat=source_path; exit
990	fi
991
992	fi
993
994
995	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
996	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
997	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
998	then
999	global_revision=`svnversion $source_path 2>/dev/null`
1000	global_revision="Rev: $global_revision"
1001	fi
1002
1003
1004	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1005	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1006	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1007	if [[ -n $host && "$host" != $localhost ]]
1008	then
1009	do_batch=true
1010	do_remote=true
1011	case $host in
1012	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1013	(*) printf "\n"
1014	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1015	printf "\n is not available"
1016	locat=nqs; (( iec = 0 )); exit;;
1017	esac
1018	else
1019	host=$localhost
1020	fi
1021
1022
1023	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1024	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1025	then
1026
1027	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1028	if [[ ! -n $numprocs ]]
1029	then
1030	printf "\n"
1031	printf "\n +++ option \"-K parallel\" requires additional specification"
1032	printf "\n of the number of processors to be used by"
1033	printf "\n mrun-option \"-X\" or by environment-variable"
1034	printf "\n \"numprocs\" in the configuration file"
1035	locat=numprocs; (( iec = 0 )); exit
1036	fi
1037
1038	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1039	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1040	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1041	then
1042	printf "\n"
1043	printf "\n +++ option \"-T\" (tasks per node) is missing"
1044	printf "\n set -T option or define tasks_per_node in the config file"
1045	locat=tasks_per_node; (( iec = 0 )); exit
1046	fi
1047
1048	if (( numprocs < tasks_per_node ))
1049	then
1050	printf "\n"
1051	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1052	printf "\n given values: -T $tasks_per_node -X $numprocs"
1053	locat=tasks_per_node; (( iec = 0 )); exit
1054	fi
1055
1056	if [[ $host != lcflow && $host != lcxt5m ]]
1057	then
1058	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1059	(( ival = $tasks_per_node ))
1060	(( pes = numprocs ))
1061	(( ii = pes / ival ))
1062	(( remaining_pes = pes - ii * ival ))
1063	if (( remaining_pes > 0 ))
1064	then
1065	printf "\n"
1066	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1067	printf "\n divisor of the total number of processors (option \"-X\")"
1068	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1069	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1070	(( nodes = nodes + 1 ))
1071	fi
1072	fi
1073
1074
1075	# SETTINGS FOR SUBJOB-COMMAND
1076	OOPT="-O $threads_per_task"
1077
1078	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1079	if [[ "$tasks_per_node" != "" ]]
1080	then
1081	TOPT="-T $tasks_per_node"
1082	fi
1083
1084	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1085	if [[ $node_usage = default ]]
1086	then
1087	if [[ $host = ibms ]]
1088	then
1089	node_usage=shared
1090	else
1091	node_usage=not_shared
1092	fi
1093	fi
1094
1095	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1096	then
1097	printf "\n"
1098	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1099	printf "\n \"shared\" or \"not_shared\""
1100	locat=tasks_per_node; (( iec = 0 )); exit
1101	fi
1102
1103	fi
1104
1105	# CHECK IF HOSTFILE EXISTS
1106	if [[ -n $hostfile ]]
1107	then
1108	if [[ ! -f $hostfile ]]
1109	then
1110	printf "\n"
1111	printf "\n +++ hostfile \"$hostfile\" does not exist"
1112	locat=hostfile; exit
1113	fi
1114	fi
1115
1116
1117	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1118	if [[ "$maximum_parallel_io_streams" = "" ]]
1119	then
1120	maximum_parallel_io_streams=$numprocs
1121	fi
1122
1123
1124	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1125	if [[ "$scp_port" != "" ]]
1126	then
1127	PORTOPT="-P $scp_port"
1128	SSH_PORTOPT="-p $scp_port"
1129	fi
1130
1131
1132	# SET DEFAULT-QUEUE, IF NOT GIVEN
1133	if [[ $queue = none ]]
1134	then
1135	case $host in
1136	(ibmh) queue=cluster;;
1137	(ibmkisti) queue=class.32plus;;
1138	(lccrayb) queue=mpp1q;;
1139	(lccrayh) queue=mpp1q;;
1140	(lckiaps) queue=normal;;
1141	(lckyoto) queue=ph;;
1142	(lckyuh) queue=fx-single;;
1143	(lckyut) queue=cx-single;;
1144	(lctit) queue=S;;
1145	(nech) queue=none;;
1146	(unics) queue=unics;;
1147	esac
1148	fi
1149
1150
1151	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1152	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1153	(( i = 0 ))
1154	while (( i < iin ))
1155	do
1156	(( i = i + 1 ))
1157	(( maxcycle = 0 ))
1158
1159	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1160	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1161	if [[ "${actionin[$i]}" = di ]]
1162	then
1163	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1164	# HOST ONLY
1165	eval filename=${pathin[$i]}/${endin[$i]}
1166	else
1167	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1168	# HOST ONLY
1169	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1170	fi
1171	eval pathname=${pathin[$i]}
1172
1173	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1174	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1175	then
1176	filename_input=$filename
1177	fi
1178
1179	# CHECK IF FILE EXISTS
1180	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1181	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1182	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1183	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1184	then
1185
1186	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1187	if [[ "${transin[$i]}" != "locopt" ]]
1188	then
1189	printf "\n\n +++ INPUT-file: "
1190	if [[ "${extin[$i]}" = "" ]]
1191	then
1192	printf "\n $filename"
1193	else
1194	printf "\n $filename.${extin[$i]}"
1195	fi
1196	printf "\n does not exist\n"
1197	locat=input; exit
1198	else
1199	transin[$i]="unavailable"
1200	fi
1201	else
1202
1203	# DETERMINE THE FILE'S CYCLE NUMBER
1204	ls -1 -d $filename > filelist 2>/dev/null
1205	ls -1 -d $filename.* >> filelist 2>/dev/null
1206	while read zeile
1207	do
1208	cycle=$(echo $zeile \| cut -f2 -d".")
1209	if [[ "$cycle" = "$zeile" ]]
1210	then
1211	(( icycle = 0 ))
1212	elif [[ "$cycle" = "${extin[$i]}" ]]
1213	then
1214	(( icycle = 0 ))
1215	else
1216	(( icycle = $cycle ))
1217	fi
1218	if (( icycle > maxcycle ))
1219	then
1220	(( maxcycle = icycle ))
1221	file_to_be_used=$zeile
1222	fi
1223	done <filelist
1224	rm filelist
1225
1226	# APPEND CYCLE NUMBER TO FILENAME
1227	if (( maxcycle > 0 ))
1228	then
1229	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1230	then
1231	filename=${filename}.$maxcycle.${extin[$i]}
1232	else
1233	filename=${filename}.$maxcycle
1234	fi
1235	else
1236	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1237	then
1238	filename=${filename}.${extin[$i]}
1239	fi
1240	fi
1241
1242	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1243	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1244	absnamein[$i]=$filename
1245	if (( maxcycle > 0 ))
1246	then
1247	if [[ "${actionin[$i]}" = di ]]
1248	then
1249	frelin[$i]=${endin[$i]}.$maxcycle
1250	else
1251	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1252	fi
1253	else
1254	if [[ "${actionin[$i]}" = di ]]
1255	then
1256	frelin[$i]=${endin[$i]}
1257	else
1258	frelin[$i]=${afname}${endin[$i]}
1259	fi
1260	fi
1261
1262	fi
1263	done
1264
1265	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1266	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1267	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1268	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1269	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1270	# REMOTE HOST)
1271	(( i = 0 ))
1272	while (( i < iout ))
1273	do
1274	(( i = i + 1 ))
1275	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1276	then
1277	if [[ "${actionout[$i]}" = tr ]]
1278	then
1279	actionout[$i]=""
1280	elif [[ "${actionout[$i]}" = trpe ]]
1281	then
1282	actionout[$i]=pe
1283	elif [[ "${actionout[$i]}" = tra ]]
1284	then
1285	actionout[$i]=a
1286	fi
1287	(( maxcycle = 0 ))
1288	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1289	eval catalogname=${pathout[$i]}
1290	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1291	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1292	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1293	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1294	then
1295
1296	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1297	if cat /dev/null > $filename
1298	then
1299	rm $filename
1300	else
1301
1302	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1303	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1304	if [[ ! -d $catalogname ]]
1305	then
1306	if mkdir -p $catalogname
1307	then
1308	printf "\n\n *** directory:"
1309	printf "\n $catalogname"
1310	printf "\n was created\n"
1311	else
1312	printf "\n\n +++ OUTPUT-file:"
1313	printf "\n $filename"
1314	printf "\n cannot be created, because directory does not exist"
1315	printf "\n and cannot be created either"
1316	printf "\n"
1317	locat=output ; exit
1318	fi 2>/dev/null
1319	else
1320	printf "\n\n +++ OUTPUT-file:"
1321	printf "\n $filename"
1322	printf "\n cannot be created, although directory exists"
1323	printf "\n"
1324	locat=output ; exit
1325	fi
1326	fi 2>/dev/null
1327	else
1328
1329	# DETERMINE THE CYCLE NUMBER
1330	ls -1 -d $filename > filelist 2>/dev/null
1331	ls -1 -d $filename.* >> filelist 2>/dev/null
1332	while read zeile
1333	do
1334	cycle=$(echo $zeile \| cut -f2 -d".")
1335	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1336	then
1337	(( icycle = 1 ))
1338	else
1339	(( icycle = $cycle + 1 ))
1340	fi
1341	if (( icycle > maxcycle ))
1342	then
1343	(( maxcycle = icycle ))
1344	fi
1345	done <filelist
1346	rm filelist
1347	fi
1348
1349	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1350	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1351	if [[ "${actionout[$i]}" != a ]]
1352	then
1353	if (( maxcycle > 0 ))
1354	then
1355	filename=${filename}.$maxcycle
1356	if cat /dev/null > $filename
1357	then
1358	rm $filename
1359	else
1360	printf "\n +++ OUTPUT-file:"
1361	printf "\n $filename"
1362	printf "\n cannot be created"
1363	locat=output ; exit
1364	fi
1365	fi
1366	else
1367	(( maxcycle = maxcycle - 1 ))
1368	if (( maxcycle > 0 ))
1369	then
1370	filename=${filename}.$maxcycle
1371	fi
1372	fi
1373
1374	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1375	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1376	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1377	pathout[$i]=$filename
1378	if (( maxcycle > 0 ))
1379	then
1380	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1381	else
1382	frelout[$i]=${fname}${endout[$i]}
1383	fi
1384
1385	fi
1386	done
1387
1388
1389	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1390	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1391	then
1392	if [[ "$dvr_inc" = "" ]]
1393	then
1394	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1395	printf "\n This is required for the dvrp_graphics package.\n"
1396	locat=dvr; exit
1397	fi
1398	if [[ "$dvr_lib" = "" ]]
1399	then
1400	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1401	printf "\n This is required for the dvrp_graphics package.\n"
1402	locat=dvr; exit
1403	fi
1404	fi
1405
1406
1407	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1408	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1409	if [[ "$mainprog" = "" && "$executable" = "" ]]
1410	then
1411	printf "\n +++ neither main program nor executable defined"
1412	locat=source; exit
1413	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1414	then
1415	printf "\n +++ main program as well as executable defined"
1416	locat=source; exit
1417	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1418	then
1419	do_compile=false
1420	fi
1421
1422
1423	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1424	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1425	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1426	then
1427	rm -rf SOURCES_FOR_RUN_$fname
1428	mkdir SOURCES_FOR_RUN_$fname
1429	fi
1430
1431
1432	# COLLECT ALL ROUTINES TO BE COMPILED
1433	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1434	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1435	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1436	then
1437
1438	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1439
1440	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1441	then
1442
1443	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1444	source_list=""
1445	cd $source_path
1446
1447
1448	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1449	if [[ ! -d .svn ]]
1450	then
1451	printf "\n\n +++ source directory"
1452	printf "\n \"$source_path\" "
1453	printf "\n is not under control of \"subversion\"."
1454	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1455	fi
1456
1457
1458	# LIST ALL MODIFIED SOURCE CODE FILES
1459	Filenames=""
1460	svn status > tmp_mrun
1461	while read line
1462	do
1463	firstc=`echo $line \| cut -c1`
1464	if [[ $firstc = M \|\| $firstc = "?" ]]
1465	then
1466	Name=`echo "$line" \| cut -c8-`
1467	extension=`echo $Name \| cut -d. -f2`
1468	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1469	then
1470	Filenames="$Filenames "$Name
1471	fi
1472	fi
1473	done < tmp_mrun
1474
1475
1476	# COPY FILES TO SOURCES_FOR_RUN_...
1477	for dateiname in $Filenames
1478	do
1479	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1480	source_list=$source_list"$dateiname "
1481	done
1482
1483	cd - > /dev/null
1484
1485
1486	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1487	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1488	elif [[ "$source_list" != "" && $restart_run != true ]]
1489	then
1490
1491	cd $source_path
1492
1493	for filename in $source_list
1494	do
1495
1496	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1497	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1498	then
1499	printf "\n +++ source code file: $filename"
1500	printf "\n must not contain (\"/\") "
1501	locat=source; exit
1502	fi
1503
1504	if [[ ! -f $filename ]]
1505	then
1506	printf "\n +++ source code file: $filename"
1507	printf "\n does not exist"
1508	locat=source; exit
1509	else
1510	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1511	fi
1512
1513	done
1514
1515	cd - > /dev/null
1516
1517	fi
1518
1519
1520	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1521	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1522	if [[ $restart_run != true ]]
1523	then
1524
1525	if [[ ! -f "$source_path/$mainprog" ]]
1526	then
1527	printf "\n\n +++ main program: $mainprog"
1528	printf "\n does not exist in source directory"
1529	printf "\n \"$source_path\"\n"
1530	locat=source; exit
1531	else
1532	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1533	then
1534	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1535	source_list=${mainprog}" $source_list"
1536	fi
1537	fi
1538	fi
1539
1540
1541	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1542	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1543	if [[ "$restart_run" != true ]]
1544	then
1545	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1546	if [[ ! -f $makefile ]]
1547	then
1548	printf "\n +++ file \"$makefile\" does not exist"
1549	locat=make; exit
1550	else
1551	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1552	fi
1553	fi
1554
1555
1556	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1557	if [[ $restart_run != true && "$add_source_path" != "" ]]
1558	then
1559
1560	# DOES THE DIRECTORY EXIST?
1561	if [[ ! -d $add_source_path ]]
1562	then
1563	printf "\n\n +++ WARNING: additional source code directory"
1564	printf "\n \"$add_source_path\" "
1565	printf "\n does not exist or is not a directory."
1566	printf "\n No source code will be used from this directory!\n"
1567	add_source_path=""
1568	if [[ $silent == false ]]
1569	then
1570	sleep 3
1571	fi
1572	else
1573
1574	cd $add_source_path
1575	found=false
1576
1577	Names=$(ls -1 *.f90 2>&1)
1578	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1579	Names=$(ls -1 *.F90 2>&1)
1580	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1581	Names=$(ls -1 *.F 2>&1)
1582	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1583	Names=$(ls -1 *.f 2>&1)
1584	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1585	Names=$(ls -1 *.c 2>&1)
1586	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1587
1588	cd - > /dev/null
1589	cd SOURCES_FOR_RUN_$fname
1590
1591	# COPY MAKEFILE IF EXISTING
1592	if [[ -f $add_source_path/Makefile ]]
1593	then
1594	printf "\n\n *** user Makefile from directory"
1595	printf "\n \"$add_source_path\" is used \n"
1596	if [[ $silent == false ]]
1597	then
1598	sleep 1
1599	fi
1600	cp $add_source_path/Makefile .
1601	fi
1602
1603	for dateiname in $AddFilenames
1604	do
1605	if [[ -f $dateiname ]]
1606	then
1607	printf "\n +++ source code file \"$dateiname\" found in additional"
1608	printf "\n source code directory \"$add_source_path\" "
1609	printf "\n but was also given with option \"-s\" which means that it should be taken"
1610	printf "\n from directory \"$source_path\"."
1611	locat=source; exit
1612	fi
1613
1614	cp $add_source_path/$dateiname .
1615	source_list="$source_list $dateiname"
1616
1617	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1618	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1619	then
1620	printf "\n\n +++ user file \"$dateiname\" "
1621	printf "\n is not listed in Makefile \n"
1622	locat=source; exit
1623	else
1624
1625	if [[ $found = false ]]
1626	then
1627	found=true
1628	printf "\n\n *** following user file(s) added to the"
1629	printf " files to be translated:\n "
1630	fi
1631	printf "$dateiname "
1632	if [[ $silent == false ]]
1633	then
1634	sleep 0.5
1635	fi
1636
1637	fi
1638	done
1639	[[ $found = true ]] && printf "\n"
1640	cd - > /dev/null
1641	fi
1642	fi
1643
1644
1645	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1646	# TO THE LIST OF FILES TO BE COMPILED
1647	if [[ $restart_run != true && -n $package_list ]]
1648	then
1649
1650	cd $source_path
1651
1652	for package in $package_list
1653	do
1654
1655	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1656
1657	# DETERMINE FILES BELONGING TO THE PACKAGE
1658	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1659	# THE NAME OF THE DIRECTORY
1660	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1661
1662
1663	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1664	# IF THEY ARE NOT ALREADY PART OF THE LIST
1665	for source_list_name in $package_source_list
1666	do
1667	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1668	then
1669
1670	# ONLY TAKE FILES WITH VALID SUFFIX
1671	ending=`echo $source_list_name \| cut -f2 -d.`
1672	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1673	then
1674	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1675	source_list="$source_list $source_list_name"
1676	fi
1677	fi
1678	done
1679	done
1680
1681	cd - > /dev/null
1682	fi
1683
1684	fi # do_compile=true
1685
1686
1687	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1688	# AND SET PRE-PROCESSOR DIRECTIVES
1689	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1690	then
1691
1692	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1693	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1694	then
1695	cpp_options="${cpp_options},-D__ibm=__ibm"
1696	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1697	then
1698	cpp_options="$cpp_options -D__nec"
1699	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1700	then
1701	cpp_options="$cpp_options -D__lc"
1702	else
1703	cpp_options="$cpp_options -D__$localhost"
1704	fi
1705
1706	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1707	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1708	then
1709	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1710	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1711	else
1712	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1713	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1714	fi
1715
1716	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1717	if [[ -n $package_list ]]
1718	then
1719	for package in $package_list
1720	do
1721	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1722	then
1723	if [[ $package != "dvrp_graphics+1PE" ]]
1724	then
1725	cpp_options="${cpp_options},-D__$package=__$package"
1726	else
1727	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1728	export use_seperate_pe_for_dvrp_output=true
1729	fi
1730	else
1731	if [[ $package != "dvrp_graphics+1PE" ]]
1732	then
1733	cpp_options="$cpp_options -D__$package"
1734	else
1735	cpp_options="$cpp_options -D__dvrp_graphics"
1736	export use_seperate_pe_for_dvrp_output=true
1737	fi
1738	fi
1739	done
1740	fi
1741
1742	# SET DIRECTIVES GIVEN BY OPTION -D
1743	if [[ -n $cpp_opts ]]
1744	then
1745	for popts in $cpp_opts
1746	do
1747	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1748	then
1749	cpp_options="${cpp_options},-D__$popts=__$popts"
1750	else
1751	cpp_options="$cpp_options -D__$popts"
1752	fi
1753	done
1754	fi
1755
1756	else
1757
1758
1759	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1760	if [[ $do_remote = false ]]
1761	then
1762	if [[ ! -f $executable ]]
1763	then
1764	printf "\n +++ executable file: $executable"
1765	printf "\n does not exist"
1766	locat=executable; exit
1767	fi
1768	fi
1769	fi
1770
1771
1772	# DETERMINE THE JOB MODE
1773	if [[ "$ENVIRONMENT" = BATCH ]]
1774	then
1775	batch_job=.TRUE.
1776	jobmo=BATCH
1777	else
1778	batch_job=.FALSE.
1779	jobmo=INTERACTIVE
1780	fi
1781
1782
1783	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1784	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1785	then
1786	printf "\n +++ no interactive runs allowed on host \"$host\" "
1787	printf "\n please submit batch job using mrun option \"-b\" \n"
1788	locat=normal; exit
1789	fi
1790
1791
1792	# CHECK, IF USER DEFINED A COMPILER
1793	if [[ "$compiler_name" = "" ]]
1794	then
1795
1796	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1797	locat=compiler_name; exit
1798
1799	fi
1800
1801
1802	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1803	kennung=$RANDOM
1804	if [[ "$tmp_user_catalog" = "" ]]
1805	then
1806	if [[ $localhost = ibmh ]]
1807	then
1808	tmp_user_catalog=$SCRATCH
1809	elif [[ $localhost = nech ]]
1810	then
1811	tmp_user_catalog=$WRKSHR
1812	else
1813	tmp_user_catalog=/tmp
1814	fi
1815	fi
1816	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1817
1818
1819	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1820	if [[ "$tmp_data_catalog" = "" ]]
1821	then
1822	if [[ $localhost = nech ]]
1823	then
1824	tmp_data_catalog=$WRKSHR/mrun_restart_data
1825	else
1826	tmp_data_catalog=/tmp/mrun_restart_data
1827	fi
1828	fi
1829
1830
1831	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1832	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1833	then
1834	eval fopts=\"$fopts\"
1835	eval lopts=\"$lopts\"
1836	fi
1837
1838
1839
1840	# DETERMINE COMPILE- AND LINK-OPTIONS
1841	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1842	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1843	ROPTS="$ropts"
1844	# 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 ]]
1845	# then
1846	XOPT="-X $numprocs"
1847	# fi
1848
1849
1850
1851	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1852	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1853	done=false
1854	while [[ $done = false ]]
1855	do
1856	cputime=$cpumax
1857	if (( $cputime == 0 ))
1858	then
1859	if [[ $do_batch = true ]]
1860	then
1861	printf "\n +++ cpu-time is undefined"
1862	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1863	printf "\n >>> "
1864	read cputime 1>/dev/null 2>&1
1865	else
1866	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1867	fi
1868	else
1869	done=true
1870	fi
1871	cpumax=$cputime
1872	done
1873
1874	(( minuten = cputime / 60 ))
1875	(( sekunden = cputime - minuten * 60 ))
1876
1877
1878	# CHECK THE MEMORY DEMAND
1879	if [[ $do_batch = true ]]
1880	then
1881	done=false
1882	while [[ $done = false ]]
1883	do
1884	if (( memory == 0 ))
1885	then
1886	printf "\n +++ memory demand is undefined"
1887	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1888	printf "\n >>> "
1889	read memory 1>/dev/null 2>&1
1890	else
1891	done=true
1892	fi
1893	done
1894	fi
1895
1896
1897	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1898	if [[ $do_remote = true && -z $remote_username ]]
1899	then
1900	while [[ -z $remote_username ]]
1901	do
1902	printf "\n +++ username on remote host \"$host\" is undefined"
1903	printf "\n >>> Please type username:"
1904	printf "\n >>> "
1905	read remote_username
1906	done
1907	mc="$mc -u$remote_username"
1908	fi
1909
1910	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1911	if [[ "$login_init_cmd" != "" ]]
1912	then
1913	export init_cmds="${login_init_cmd};"
1914	fi
1915
1916
1917	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1918	if [[ "$modules" != "" ]]
1919	then
1920	if [[ $host = lctit ]]
1921	then
1922	export module_calls=". $modules"
1923	else
1924	export module_calls="module load ${modules};"
1925	fi
1926	fi
1927
1928
1929
1930	# OUTPUT OF THE MRUN-HEADER
1931	calltime=$(date)
1932	printf "\n"
1933	printf "#------------------------------------------------------------------------# \n"
1934	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1935	printf "\| \| \n"
1936	spalte1="called on:"; spalte2=$localhost_realname
1937	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1938	if [[ $do_remote = true ]]
1939	then
1940	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1941	else
1942	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1943	fi
1944	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1945	if [[ -n $numprocs ]]
1946	then
1947	if [[ $run_coupled_model = false ]]
1948	then
1949	spalte1="number of PEs:"; spalte2=$numprocs
1950	else
1951	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1952	fi
1953	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1954	fi
1955	if [[ -n $tasks_per_node ]]
1956	then
1957	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1958	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1959	if (( remaining_pes > 0 ))
1960	then
1961	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1962	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1963	fi
1964	fi
1965	if [[ $maximum_parallel_io_streams != $numprocs ]]
1966	then
1967	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1968	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1969	fi
1970	if [[ $use_openmp = true ]]
1971	then
1972	spalte1="threads per task:"; spalte2="$threads_per_task"
1973	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1974	fi
1975	printf "\| \| \n"
1976	if [[ $do_compile = true ]]
1977	then
1978	if [[ "$mopts" != "" ]]
1979	then
1980	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1981	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1982	zeile=$(echo "$mopts" \| cut -c46-)
1983	while [[ "$zeile" != "" ]]
1984	do
1985	spalte1=""
1986	spalte2=$(echo "$zeile" \| cut -c-45)
1987	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1988	zeile=$(echo "$zeile" \| cut -c46-)
1989	done
1990	fi
1991
1992	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1993	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1994	zeile=$(echo "$cpp_options" \| cut -c46-)
1995	while [[ "$zeile" != "" ]]
1996	do
1997	spalte1=""
1998	spalte2=$(echo "$zeile" \| cut -c-45)
1999	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2000	zeile=$(echo "$zeile" \| cut -c46-)
2001	done
2002
2003	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2004	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2005	zeile=$(echo "$fopts" \| cut -c46-)
2006	while [[ "$zeile" != "" ]]
2007	do
2008	spalte1=""
2009	spalte2=$(echo "$zeile" \| cut -c-45)
2010	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2011	zeile=$(echo "$zeile" \| cut -c46-)
2012	done
2013
2014	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	zeile=$(echo "$lopts" \| cut -c46-)
2017	while [[ "$zeile" != "" ]]
2018	do
2019	spalte1=""
2020	spalte2=$(echo "$zeile" \| cut -c-45)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	zeile=$(echo "$zeile" \| cut -c46-)
2023	done
2024
2025	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2026	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2027	zeile=$(echo "$modules" \| cut -c46-)
2028	while [[ "$zeile" != "" ]]
2029	do
2030	spalte1=""
2031	spalte2=$(echo "$zeile" \| cut -c-45)
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033	zeile=$(echo "$zeile" \| cut -c46-)
2034	done
2035
2036	spalte1="main program:"; spalte2=$mainprog
2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2038	else
2039	spalte1=executable:; spalte2=$executable
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	fi
2042	printf "\| \| \n"
2043	spalte1="base name of files:"; spalte2=$fname
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	if [[ $fname != $afname ]]
2046	then
2047	spalte1="base name of input files:"; spalte2=$afname
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049	fi
2050	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2051	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2052	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054
2055	if [[ "$ocean_file_appendix" = true ]]
2056	then
2057	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2058	fi
2059
2060	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2061	then
2062	spalte1="memory demand / PE":; spalte2="$memory MB"
2063	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2064	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2065	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2066	fi
2067
2068	if [[ $do_compile = true ]]
2069	then
2070	printf "\| \| \n"
2071	printf "\| Files to be compiled: \| \n"
2072	zeile=$source_list
2073	while [[ "$zeile" != "" ]]
2074	do
2075	linestart=$(echo $zeile \| cut -c-70)
2076	printf "\| %-70s \| \n" "$linestart"
2077	zeile=$(echo "$zeile" \| cut -c71-)
2078	done
2079	fi
2080	printf "#------------------------------------------------------------------------#"
2081
2082
2083
2084	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2085	if [[ $do_trace = true ]]
2086	then
2087	(( i = 0 ))
2088	while (( i < iin ))
2089	do
2090	(( i = i + 1 ))
2091	if (( i == 1 ))
2092	then
2093	printf "\n\n >>> INPUT-file assignments:\n"
2094	fi
2095	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2096	done
2097	(( i = 0 ))
2098	while (( i < iout ))
2099	do
2100	(( i = i + 1 ))
2101	if (( i == 1 ))
2102	then
2103	printf "\n\n >>> OUTPUT-file assignments:\n"
2104	fi
2105	printf "\n ${localout[$i]} : ${pathout[$i]}"
2106	done
2107	(( i = 0 ))
2108	while (( i < iic ))
2109	do
2110	(( i = i + 1 ))
2111	if (( i == 1 ))
2112	then
2113	printf "\n\n >>> INPUT-commands:\n"
2114	fi
2115	printf "\n ${in_command[$i]}"
2116	done
2117	(( i = 0 ))
2118	while (( i < ioc ))
2119	do
2120	(( i = i + 1 ))
2121	if (( i == 1 ))
2122	then
2123	printf "\n\n >>> OUTPUT-commands:\n"
2124	fi
2125	printf "\n ${out_command[$i]}"
2126	done
2127	fi
2128
2129
2130	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2131	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2132	then
2133	antwort=dummy
2134	printf "\n\n"
2135	printf " >>> everything o.k. (y/n) ? "
2136	while read antwort
2137	do
2138	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2139	then
2140	printf " >>> everything o.k. (y/n) ? "
2141	else
2142	break
2143	fi
2144	done
2145	if [[ $antwort = n \|\| $antwort = N ]]
2146	then
2147	locat=user_abort; (( iec = 0 )); exit
2148	fi
2149	if [[ $do_batch = true ]]
2150	then
2151	printf " >>> batch-job will be created and submitted"
2152	else
2153	printf " >>> MRUN will now continue to execute on this machine"
2154	fi
2155	fi
2156
2157
2158	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2159	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2160	check_depository="${working_directory}/trunk/UTIL"
2161	check_sources="${working_directory}/tmp_check_namelist_files"
2162	skip_check=false
2163
2164	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2165	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2166	then
2167	skip_check=true
2168	reason="run on remote host or parameter file check has not been compiled."
2169	fi
2170	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2171	then
2172	skip_check=true
2173	reason="parameter file check has not been compiled."
2174	fi
2175
2176	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2177	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2178	then
2179	skip_check=true
2180	reason="serial run."
2181	fi
2182
2183	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2184	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2185	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2186	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2187	if [[ $check_namelist_files == false ]]
2188	then
2189	skip_check=true
2190	reason="-z option set."
2191	fi
2192
2193	if [[ $fromhost != $localhost ]]
2194	then
2195	skip_check=true
2196	reason="submitting host is local host."
2197	fi
2198
2199	if [[ $run_coupled_model == true ]]
2200	then
2201	skip_check=true
2202	reason="coupled run."
2203	fi
2204
2205	if [[ $restart_run == true ]]
2206	then
2207	skip_check=true
2208	reason="restart run."
2209	fi
2210
2211	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2212	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2213	last_char=`echo $filename_input \| cut -c $last_char_int`
2214	if [[ "$last_char" == "f" ]]
2215	then
2216	skip_check=true
2217	reason="restart run."
2218	fi
2219
2220	if [[ $skip_check == false ]]
2221	then
2222	tmp_check=${working_directory}/tmp_check
2223
2224	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2225	# NOT NECESSARILY REQUIRED
2226	line=""
2227	found=false
2228	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2229	while read line1
2230	do
2231	line="$line1"
2232	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2233	then
2234	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2235	found=true
2236	fi
2237	done < $tmp_check
2238
2239	if [[ $found = false ]]
2240	then
2241	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2242	fi
2243
2244	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2245	# NOT NECESSARILY REQUIRED
2246	line=""
2247	found=false
2248	grep "NUDGING_DATA" $config_file > $tmp_check
2249	while read line1
2250	do
2251	line="$line1"
2252	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2253	then
2254	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2255	found=true
2256	fi
2257	done < $tmp_check
2258
2259	if [[ $found = false ]]
2260	then
2261	printf "\n +++ no NUDGING list entry found in the configuration file."
2262	fi
2263
2264	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2265	# NOT NECESSARILY REQUIRED
2266	line=""
2267	found=false
2268	grep "LSF_DATA" $config_file > $tmp_check
2269	while read line1
2270	do
2271	line="$line1"
2272	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2273	then
2274	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2275	found=true
2276	fi
2277	done < $tmp_check
2278
2279	if [[ $found = false ]]
2280	then
2281	printf "\n +++ no LSF list entry found in the configuration file."
2282	fi
2283
2284	rm -rf ${working_directory}/tmp_check
2285
2286	# CHECK IF THE P3DF FILE MUST BE CHECKED
2287	for item in $input_list
2288	do
2289	if [[ "$item" == "restart" ]]
2290	then
2291	check_restart=1
2292	else
2293	check_restart=0
2294	fi
2295	done
2296
2297	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2298	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2299	then
2300	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2301	locat=check_namelist; exit
2302	fi
2303
2304	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2305	if [[ $check_restart == 1 ]]
2306	then
2307
2308	filenamef="${filename_input}f"
2309	if [[ ! -f $filenamef ]]
2310	then
2311	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2312	check_restart=0
2313	answer=dummy
2314	printf "\n\n"
2315
2316	if [[ $silent == false ]]
2317	then
2318	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2319	do
2320	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2321	read answer
2322	done
2323	if [[ $answer = a \|\| $answer = A ]]
2324	then
2325	printf "\n +++ Aborting...."
2326	locat=normal; exit
2327	fi
2328	fi
2329	else
2330	check_restart=1
2331	fi
2332	fi
2333
2334	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2335	mkdir $check_sources
2336	cd $check_sources
2337
2338
2339	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2340	if [[ -d $add_source_path ]]
2341	then
2342	printf "\n\n *** copying files from $check_depository"
2343	cp $check_depository/check_namelist_files.tar ./
2344
2345	printf "\n\n *** untar of makefile and source files in $check_sources"
2346	tar -xf check_namelist_files.tar > /dev/null 2>&1
2347
2348	printf "\n\n *** adding user code."
2349	cp $add_source_path/* ./
2350	touch check_namelist_files.f90
2351
2352	# GET COMPILER OPTIONS AND PERFORM MAKE
2353	printf "\n\n *** compiling code if necessary...\n"
2354
2355	# workaround for batch jobs on local machine (lcxe6)
2356	if [[ $do_batch == true && $do_remote == false ]]
2357	then
2358	eval $init_cmds
2359	fi
2360
2361	# GET CHECK OPTIONS
2362	line=""
2363	found=false
2364
2365	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2366
2367	while read line1
2368	do
2369
2370	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2371	then
2372	line="$line1"
2373	fi
2374
2375	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2376	then
2377	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2378	line="$line "
2379	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'`
2380	found=true
2381	fi
2382
2383	done < $tmp_check
2384	copts_check="$copts_check -D__check -D__parallel"
2385
2386	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2387
2388	# GET MAKE OUTPUT
2389	if [[ $? != 0 ]]
2390	then
2391	printf "\n +++ error during make."
2392	answer=dummy
2393	printf "\n\n"
2394	if [[ $silent == false ]]
2395	then
2396	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2397	do
2398	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2399	read answer
2400	done
2401	if [[ $answer = a \|\| $answer = A ]]
2402	then
2403	printf "\n +++ Aborting..."
2404	rm -rf $check_sources
2405	locat=normal; exit
2406	else
2407	skip_check=true
2408	fi
2409	else
2410	skip_check=true
2411	fi
2412	fi
2413	else
2414	cp $PALM_BIN/check_namelist_files.x ./
2415	fi
2416
2417	cp $filename_input ./PARIN
2418	if [[ $check_restart == 1 ]]
2419	then
2420	cp $filenamef ./PARINF
2421	fi
2422
2423	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2424	then
2425	printf "\n *** adding topography data"
2426	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2427
2428	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2429	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2430	# WHICH REQUIRE SUFFICIENT MEMORY
2431	ulimit -s unlimited
2432	fi
2433
2434	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2435	then
2436	printf "\n *** adding nudging data"
2437	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2438	fi
2439
2440	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2441	then
2442	printf "\n *** adding large scale forcing data"
2443	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2444	fi
2445
2446	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2447	cat > ENVPAR << %%END%%
2448	&envpar run_identifier = '$fname', host = '$host',
2449	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2450	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2451	maximum_cpu_time_allowed = ${cpumax}.,
2452	revision = '$global_revision',
2453	local_dvrserver_running = $local_dvrserver_running /
2454
2455	%%END%%
2456
2457	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2458	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2459	then
2460	printf "\n +++ WARNING: check_namelist_files.x not found."
2461	answer=dummy
2462	printf "\n\n"
2463
2464	if [[ $silent == false ]]
2465	then
2466	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2467	do
2468	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2469	read answer
2470	done
2471	if [[ $answer = a \|\| $answer = A ]]
2472	then
2473	printf "\n +++ Aborting..."
2474	rm -rf $check_sources
2475	locat=normal; exit
2476	else
2477	printf "\n *** skipping parameter file check."
2478	fi
2479	fi
2480
2481	elif [[ $skip_check == false ]]
2482	then
2483	# STARTING THE PARAMETER FILE CHECK
2484	printf "\n\n *** starting parameter file check..."
2485
2486	# CHECKING THE P3D FILE
2487	printf "\n\n (1) checking $filename_input"
2488	echo "$numprocs 0 0" > VARIN
2489	errors=`./check_namelist_files.x < VARIN 2>&1`
2490
2491	check_error=false
2492	if [[ "$errors" == "" ]]
2493	then
2494	printf " --> o.k."
2495	else
2496	printf " --> failed."
2497	check_error=true
2498	printf "\n\n $errors"
2499	fi
2500
2501	# CHECKING THE PD3F FILE IF NECESSARY
2502	if [[ $check_restart == 1 && $check_error == false ]]
2503	then
2504	printf "\n\n (2) checking $filenamef"
2505
2506	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2507	# IN &INIPAR LIST
2508	found=false
2509	cat PARINF \| while read line
2510	do
2511	line=$(echo $line\|sed 's/ //g')
2512	if [[ $line == "&inipar" ]]
2513	then
2514	start_search=true
2515	fi
2516
2517	if [[ $start_search == true ]]
2518	then
2519	if [[ $line == "initializing_actions='read_restart_data'" ]]
2520	then
2521	found=true
2522	break
2523	fi
2524	fi
2525
2526	if [[ $line == "/" ]]
2527	then
2528	start_search=false
2529	fi
2530
2531	done
2532
2533	if [[ $found = false ]]
2534	then
2535	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2536	printf "\n in &inipar list in $fname$p3df_suffix."
2537	rm -rf $check_sources
2538	locat=check_namelist; exit
2539	fi
2540
2541	# READ max_user_pr FROM FILES
2542	if [[ -f parin_for_check ]]
2543	then
2544	read max_pr_user < parin_for_check
2545	else
2546	max_user_pr=0
2547	fi
2548
2549	echo "$numprocs 1 $max_pr_user" > VARIN
2550	errors=`./check_namelist_files.x < VARIN 2>&1`
2551
2552	if [[ "$errors" == "" ]]
2553	then
2554	printf " --> o.k."
2555	else
2556	printf " --> failed."
2557	check_error=true
2558	printf "\n\n $errors"
2559	fi
2560	fi
2561
2562	# REPORT ERRORS AND CONTINUE/EXIT
2563	if [[ $check_error == true ]]
2564	then
2565	printf "\n +++ errors found in the parameter file!\n"
2566	answer=dummy
2567	printf "\n\n"
2568
2569	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2570	do
2571	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2572	read answer
2573	done
2574
2575	if [[ $answer = a \|\| $answer = A ]]
2576	then
2577	printf "\n +++ Aborting..."
2578	rm -rf $check_sources
2579	locat=normal; exit
2580	fi
2581	else
2582	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2583	fi
2584	rm -rf $check_sources
2585	fi
2586	else
2587	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2588	fi
2589
2590	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2591	rm -rf $check_sources
2592	cd $working_directory
2593
2594
2595	# DETERMINE PATH FOR MAKE DEPOSITORY
2596	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2597	then
2598
2599	line=""
2600	grep "%depository_path" $config_file > tmp_mrun
2601	while read line
2602	do
2603	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2604	then
2605	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2606	then
2607	global_depository_path=`echo $line \| cut -d" " -s -f2`
2608	fi
2609	fi
2610	done < tmp_mrun
2611
2612	line=""
2613	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2614	while read line
2615	do
2616	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2617	then
2618	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2619	then
2620	local_depository_path=`echo $line \| cut -d" " -s -f2`
2621	fi
2622	fi
2623	done < tmp_mrun
2624
2625	if [[ "$local_depository_path" = "" ]]
2626	then
2627	if [[ "$global_depository_path" != "" ]]
2628	then
2629	local_depository_path=$global_depository_path
2630	else
2631	printf "\n\n +++ no depository path found in configuration file"
2632	printf "\n for local host \"$localhost\" "
2633	printf "\n please set \"\%depository_path\" in configuration file\n"
2634	locat=config_file; exit
2635	fi
2636	fi
2637	eval local_depository_path=$local_depository_path
2638	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2639	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2640
2641
2642	basename=`echo $mainprog \| cut -f1 -d"."`
2643	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2644	if [[ ! -f $make_depository ]]
2645	then
2646	printf "\n"
2647	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2648	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2649	fi
2650
2651	fi
2652
2653
2654	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2655	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2656	if [[ $do_batch = false ]]
2657	then
2658
2659
2660	# CREATE THE TEMPORARY WORKING DIRECTORY
2661	mkdir -p $TEMPDIR
2662	chmod go+rx $TEMPDIR
2663	tmpcreate=true
2664
2665
2666	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2667	# INTO THE TEMPORARY WORKING DIRECTORY
2668	if [[ $do_compile = true ]]
2669	then
2670
2671	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2672	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2673	if [[ $localhost = nech ]]
2674	then
2675	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2676	if mkdir -p $TEMPDIR_COMPILE
2677	then
2678	printf "\n *** \"$TEMPDIR_COMPILE\" "
2679	printf "\n is generated as temporary directory for cross compiling\n"
2680	else
2681	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2682	printf "\n needed for cross compilation failed"
2683	locat=compile
2684	exit
2685	fi
2686	else
2687	TEMPDIR_COMPILE=$TEMPDIR
2688	fi
2689
2690	cp $make_depository $TEMPDIR_COMPILE
2691	cd $TEMPDIR_COMPILE
2692	tar -xf $make_depository > /dev/null 2>&1
2693	cd - > /dev/null
2694
2695	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2696	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2697	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2698	then
2699	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2700	else
2701	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2702	fi
2703
2704	else
2705
2706	cp $executable ${TEMPDIR}/a.out
2707
2708	fi
2709
2710
2711	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2712	cd $TEMPDIR
2713	printf "\n *** changed to temporary directory: $TEMPDIR"
2714
2715
2716	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2717	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2718	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2719	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2720	(( i = 0 ))
2721	while (( i < iout ))
2722	do
2723	(( i = i + 1 ))
2724	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2725	then
2726	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2727	else
2728	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2729	fi
2730	done
2731
2732
2733	# IF REQUIRED, START WITH COMPILING
2734	if [[ $do_compile = true ]]
2735	then
2736
2737
2738	if [[ -f a.out ]]
2739	then
2740
2741	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2742	printf "\n\n\n *** executable a.out found"
2743	printf "\n no compilation required \n"
2744
2745	else
2746
2747	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2748	printf "\n\n\n *** compilation starts \n$dashes\n"
2749	printf " *** compilation with make using following options:\n"
2750	printf " make depository: $make_depository"
2751	if [[ "$mopts" != "" ]]
2752	then
2753	printf " make options: $mopts\n"
2754	fi
2755	printf " compilername: $compiler_name\n"
2756	printf " compiler options: $fopts\n"
2757	printf " preprocessor directives: $cpp_options \n"
2758	printf " linker options: $lopts \n"
2759	if [[ "$modules" != "" ]]
2760	then
2761	printf " modules to be load: $modules \n"
2762	fi
2763	printf " source code files: $source_list \n"
2764
2765	if [[ $localhost = nech ]]
2766	then
2767	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\" "
2768	cp $TEMPDIR_COMPILE/a.out .
2769	[[ $? != 0 ]] && compile_error=true
2770	rm -rf $TEMPDIR_COMPILE
2771	elif [[ $localhost = ibmh ]]
2772	then
2773	printf " compiler is called via ssh on \"plogin1\" \n"
2774	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\" "
2775	[[ ! -f a.out ]] && compile_error=true
2776	continue # STATUS=1, IF a.out EXISTS
2777	elif [[ $localhost = lcflow ]]
2778	then
2779	printf " compiler is called via ssh on \"flow\" \n"
2780	/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\" "
2781	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2782	[[ "$check_for_file" = "" ]] && compile_error=true
2783	continue # STATUS=1, IF a.out EXISTS
2784	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2785	then
2786	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2787	else
2788	[[ "$init_cmds" != "" ]] && eval $init_cmds
2789	[[ "$module_calls" != "" ]] && eval $module_calls
2790	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2791	fi
2792
2793	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2794	then
2795	printf "\n +++ error occured while compiling or linking"
2796	locat=compile
2797
2798	exit
2799	else
2800	printf "$dashes\n *** compilation finished \n"
2801	fi
2802
2803	fi
2804
2805	fi
2806
2807
2808	# PROVIDE THE INPUT FILES
2809	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2810	(( i = 0 ))
2811	while (( i < iin ))
2812	do
2813	(( i = i + 1 ))
2814	if (( i == 1 ))
2815	then
2816	printf "\n\n *** providing INPUT-files:\n$dashes"
2817	fi
2818
2819
2820	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2821	if [[ "${transin[$i]}" = unavailable ]]
2822	then
2823	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2824	then
2825	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2826	printf "\n is not available!"
2827	else
2828	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2829	printf "\n is not available!"
2830	fi
2831	continue
2832	fi
2833
2834	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2835	files_for_pes=false; datentyp=file
2836	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2837	then
2838	files_for_pes=true; datentyp=directory
2839	actionin[$i]=""
2840	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2841	then
2842	actionin[$i]=""
2843	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2844	then
2845	files_for_pes=true; datentyp=directory
2846	actionin[$i]="ar"
2847	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2848	then
2849	actionin[$i]="ar"
2850	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2851	then
2852	files_for_pes=true; datentyp=directory
2853	actionin[$i]="fl"
2854	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2855	then
2856	actionin[$i]="fl"
2857	fi
2858
2859	if [[ $files_for_pes = true ]]
2860	then
2861	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2862	else
2863	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2864	fi
2865
2866	# INPUT-FILE FOR A RESTART RUN.
2867	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2868	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2869	if [[ "${actionin[$i]}" = fl ]]
2870	then
2871	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2872	if [[ $files_for_pes = false ]]
2873	then
2874	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2875	then
2876	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2877	got_tmp[$i]=true
2878	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2879	then
2880	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2881	printf "\n *** trying to use backup copy in \"$WORK\" "
2882	cp $WORK/${frelin[$i]} ${localin[$i]}
2883	else
2884	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2885	printf "\n or \"$tmp_data_catalog\" does not exist!"
2886	printf "\n *** trying to get copy from archive"
2887	actionin[$i]=ar
2888	fi
2889	else
2890	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2891	then
2892	mkdir ${localin[$i]}
2893	cd $tmp_data_catalog/${frelin[$i]}
2894	for file in $(ls *)
2895	do
2896	ln $file $TEMPDIR/${localin[$i]}
2897	done
2898	cd $TEMPDIR
2899	got_tmp[$i]=true
2900	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2901	then
2902	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2903	printf "\n *** trying to use backup copy in \"$WORK\" "
2904	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2905	else
2906	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2907	printf "\n or \"$tmp_data_catalog\" does not exist!"
2908	printf "\n *** trying to get copy from archive"
2909	actionin[$i]=ar
2910	fi
2911	fi
2912	fi
2913
2914
2915	# FILE IS STORED ON THE ARCHIVE SYSTEM
2916	if [[ "${actionin[$i]}" = ar ]]
2917	then
2918
2919	if [[ $files_for_pes = false ]]
2920	then
2921	printf "\n file will be restored from archive-system ($archive_system)!"
2922	else
2923	printf "\n directory will be restored from archive-system ($archive_system)!"
2924	fi
2925
2926	file_restored=false
2927
2928	if [[ $archive_system = asterix ]]
2929	then
2930	do_stagein=true
2931	(( stagein_anz = 0 ))
2932	while [[ $do_stagein = true ]]
2933	do
2934	if [[ $files_for_pes = false ]]
2935	then
2936	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2937	else
2938	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2939	fi
2940	cat STAGEIN_OUTPUT
2941	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2942	then
2943	file_restored=true
2944	do_stagein=false
2945	else
2946	(( stagein_anz = stagein_anz + 1 ))
2947	if (( stagein_anz == 10 ))
2948	then
2949	printf "\n +++ stagein stoped after 10 tries"
2950	locat=stage
2951	exit
2952	fi
2953	printf "\n +++ restoring from archive failed, trying again:"
2954	sleep 900
2955	fi
2956	done
2957	elif [[ $archive_system = DMF ]]
2958	then
2959	if [[ $files_for_pes = false ]]
2960	then
2961	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2962	locat=DMF
2963	exit
2964	else
2965	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2966	cp -r $ARCHIVE/${frelin[$i]} $PWD
2967	file_restored=true
2968	fi
2969	elif [[ $archive_system = tivoli ]]
2970	then
2971	if [[ $files_for_pes = false ]]
2972	then
2973	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2974	else
2975	(( inode = 0 ))
2976	while (( inode < nodes ))
2977	do
2978	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2979	(( inode = inode + 1 ))
2980	done
2981	fi
2982	file_restored=true
2983	elif [[ $archive_system = ut ]]
2984	then
2985	if [[ $files_for_pes = false ]]
2986	then
2987	cp $UT/${frelin[$i]} .
2988	else
2989	(( inode = 0 ))
2990	while (( inode < nodes ))
2991	do
2992	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2993	(( inode = inode + 1 ))
2994	done
2995	fi
2996	file_restored=true
2997	else
2998	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2999	locat=rearchive
3000	exit
3001	fi
3002
3003	if [[ $file_restored = true ]]
3004	then
3005
3006	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3007	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3008	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3009	if [[ $files_for_pes = false ]]
3010	then
3011	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3012	else
3013	mkdir $tmp_data_catalog/${frelin[$i]}
3014	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3015	fi
3016	got_tmp[$i]=true
3017
3018	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3019	mv ${frelin[$i]} ${localin[$i]}
3020
3021	fi
3022	fi
3023
3024
3025	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3026	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3027	then
3028
3029	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3030	then
3031
3032	# FILE COPIES ARE PROVIDED FOR ALL CORES
3033	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3034	printf "\n file will be provided for $numprocs processors"
3035	mkdir ${localin[$i]}
3036	ival=$numprocs
3037	(( ii = 0 ))
3038	while (( ii <= ival-1 ))
3039	do
3040	if (( ii < 10 ))
3041	then
3042	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3043	elif (( ii < 100 ))
3044	then
3045	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3046	elif (( ii < 1000 ))
3047	then
3048	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3049	else
3050	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3051	fi
3052	(( ii = ii + 1 ))
3053	done
3054
3055	else
3056
3057	if [[ $files_for_pes = true ]]
3058	then
3059
3060	# PROVIDE FILES FOR EACH CORE
3061	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3062	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3063	printf "\n providing $numprocs files for the respective processors"
3064	mkdir ${localin[$i]}
3065	if [[ $link_local_input = true ]]
3066	then
3067	printf " using ln -f\n"
3068	cd ${absnamein[$i]}
3069	for file in $(ls *)
3070	do
3071	ln -f $file ${localin[$i]}
3072	done
3073	cd $TEMPDIR
3074	fi
3075
3076	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3077	if [[ ! -f "${localin[$i]}/_0000" ]]
3078	then
3079	if [[ $link_local_input = true ]]
3080	then
3081	printf " ln failed for .../_0000, using cp...\n"
3082	fi
3083	cp -r ${absnamein[$i]}/* ${localin[$i]}
3084	fi
3085
3086	else
3087
3088	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3089	if [[ $link_local_input = true ]]
3090	then
3091	printf " using ln -f\n"
3092	ln -f ${absnamein[$i]} ${localin[$i]}
3093	fi
3094	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3095	if [[ ! -f "${localin[$i]}" ]]
3096	then
3097	if [[ $link_local_input = true ]]
3098	then
3099	printf " ln failed, using cp...\n"
3100	fi
3101	cp ${absnamein[$i]} ${localin[$i]}
3102	fi
3103	fi
3104	fi
3105	fi
3106
3107	done
3108	if (( i != 0 ))
3109	then
3110	printf "\n$dashes\n *** all INPUT-files provided \n"
3111	fi
3112
3113
3114	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3115	(( i = 0 ))
3116	while (( i < iic ))
3117	do
3118	(( i = i + 1 ))
3119	if (( i == 1 ))
3120	then
3121	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3122	fi
3123	printf "\n >>> ${in_command[$i]}"
3124	eval ${in_command[$i]}
3125	if (( i == iic ))
3126	then
3127	printf "\n$dashes\n"
3128	fi
3129	done
3130
3131
3132	# SET THE REMAINING CPU-TIME
3133	cpurest=${cpumax}.
3134
3135
3136	# START DVR STREAMING SERVER
3137	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3138	then
3139	if [[ "$dvr_server" != "" ]]
3140	then
3141
3142	printf "\n\n *** preparing the dvr streaming server configuration file"
3143
3144	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3145	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3146	if [[ "$running_dvrserver_id" != "" ]]
3147	then
3148
3149	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3150	printf "\n This server is used instead starting a new one!"
3151	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3152
3153	else
3154
3155	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3156	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3157	then
3158	cp ${PALM_BIN}/.dvrserver.config .
3159
3160	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3161	user_id=`id -u`
3162	group_id=`id -g`
3163
3164	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3165	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3166	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3167	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3168	mv .dvrserver.3 .dvrserver.config
3169	rm .dvrserver.1 .dvrserver.2
3170
3171	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3172	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3173	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3174	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3175	local_dvrserver_running=.TRUE.
3176	else
3177	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3178	printf "\n \"$PALM_BIN\" "
3179	locat=dvr
3180	exit
3181	fi
3182
3183	fi
3184
3185	else
3186	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3187	fi
3188	fi
3189
3190
3191	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3192	# (FILE ENVPAR WILL BE READ BY PALM)
3193	cat > ENVPAR << %%END%%
3194	&envpar run_identifier = '$fname', host = '$localhost',
3195	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3196	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3197	maximum_cpu_time_allowed = ${cpumax}.,
3198	revision = '$global_revision',
3199	local_dvrserver_running = $local_dvrserver_running,
3200	batch_job = $batch_job /
3201
3202	%%END%%
3203
3204
3205	# STARTING THE EXECUTABLE
3206	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3207	PATH=$PATH:$TEMPDIR
3208
3209	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3210	if [[ "$mpi_debug" = true ]]
3211	then
3212	export MPI_CHECK_ARGS=1
3213	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3214	fi
3215
3216	if [[ "$totalview" = true ]]
3217	then
3218	printf "\n *** totalview debugger will be used"
3219	tv_opt="-tv"
3220	else
3221	tv_opt=""
3222	fi
3223
3224	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3225	then
3226	if [[ "$ENVIRONMENT" = BATCH ]]
3227	then
3228	continue
3229	fi
3230	if [[ $localhost = ibmh ]]
3231	then
3232
3233	# SETUP THE IBM MPI ENVIRONMENT
3234	export MP_SHARED_MEMORY=yes
3235	export AIXTHREADS_SCOPE=S
3236	export OMP_NUM_THREADS=$threads_per_task
3237	export AUTHSTATE=files
3238	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3239
3240	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3241	export MP_ADAPTER_USE=shared
3242	export MP_CPU_USE=multiple
3243	export MP_TIMEOUT=1200
3244
3245	unset MP_TASK_AFFINITY
3246
3247	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3248	#(( ii = 1 ))
3249	#while (( ii <= $numprocs ))
3250	#do
3251	# echo $localhost_realname >> hostfile
3252	# (( ii = ii + 1 ))
3253	#done
3254	#export MP_HOSTFILE=hostfile
3255
3256	if [[ "$LOADLBATCH" = yes ]]
3257	then
3258	totalview poe a.out $ROPTS
3259	else
3260	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3261	export TVDSVRLAUNCHCMD=ssh
3262	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3263	fi
3264
3265	fi # END DEBUG MODE
3266
3267	else
3268
3269	# NORMAL EXECUTION
3270	if [[ -n $numprocs ]]
3271	then
3272
3273	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3274	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3275	then
3276
3277	# SETUP THE IBM MPI ENVIRONMENT
3278	if [[ $host != ibmh && $host != ibmkisti ]]
3279	then
3280	export MP_SHARED_MEMORY=yes
3281	export AIXTHREAD_SCOPE=S
3282	export OMP_NUM_THREADS=$threads_per_task
3283	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3284	export AUTHSTATE=files
3285	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3286	# export MP_PRINTENV=yes
3287
3288	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3289	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3290	export MP_WAIT_MODE=poll
3291	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3292	fi
3293
3294	if [[ $host = ibmkisti ]]
3295	then
3296	export LANG=en_US
3297	export MP_SHARED_MEMORY=yes
3298	if [[ $threads_per_task = 1 ]]
3299	then
3300	export MP_SINGLE_THREAD=yes
3301	export MEMORY_AFFINITY=MCM
3302	else
3303	export OMP_NUM_THREADS=$threads_per_task
3304	fi
3305	fi
3306
3307	if [[ "$LOADLBATCH" = yes ]]
3308	then
3309	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3310	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3311	then
3312	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3313	else
3314	if [[ $run_coupled_model = false ]]
3315	then
3316	if [[ "$ocean_file_appendix" = true ]]
3317	then
3318	echo "precursor_ocean" > runfile_atmos
3319	else
3320	echo "precursor_atmos" > runfile_atmos
3321	fi
3322	else
3323	(( iia = $numprocs_atmos / $threads_per_task ))
3324	(( iio = $numprocs_ocean / $threads_per_task ))
3325	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3326	printf "\n using $coupled_mode coupling"
3327	printf "\n\n"
3328	echo "coupled_run $iia $iio" > runfile_atmos
3329	fi
3330	poe ./a.out $ROPTS < runfile_atmos
3331	fi
3332	else
3333	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3334	then
3335	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3336	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3337	then
3338	if [[ -f $hostfile ]]
3339	then
3340	cp $hostfile hostfile
3341	else
3342	(( ii = 1 ))
3343	while (( ii <= $numprocs ))
3344	do
3345	echo $localhost_realname >> hostfile
3346	(( ii = ii + 1 ))
3347	done
3348	fi
3349	export MP_HOSTFILE=hostfile
3350	if [[ $run_coupled_model = false ]]
3351	then
3352	if [[ "$ocean_file_appendix" = true ]]
3353	then
3354	echo "precursor_ocean" > runfile_atmos
3355	else
3356	echo "precursor_atmos" > runfile_atmos
3357	fi
3358	else
3359	(( iia = $numprocs_atmos / $threads_per_task ))
3360	(( iio = $numprocs_ocean / $threads_per_task ))
3361	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3362	printf "\n using $coupled_mode coupling"
3363	printf "\n\n"
3364	echo "coupled_run $iia $iio" > runfile_atmos
3365	fi
3366
3367	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3368
3369	else
3370	if [[ "$host_file" = "" ]]
3371	then
3372	printf "\n +++ no hostfile given in configuration file"
3373	locat=config_file
3374	exit
3375	else
3376	eval host_file=$host_file
3377	fi
3378	export MP_HOSTFILE=$host_file
3379	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3380	fi
3381	fi
3382	elif [[ $host = nech ]]
3383	then
3384	(( ii = nodes ))
3385	if [[ $ii = 1 ]]
3386	then
3387	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3388	export MPIPROGINF=YES
3389	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3390	echo "*** execution on single node with mpirun"
3391	mpirun -np $numprocs ./a.out $ROPTS
3392	else
3393	(( i = 0 ))
3394	while (( i < ii ))
3395	do
3396	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3397	(( i = i + 1 ))
3398	done
3399
3400	echo "#!/bin/sh" > mpi_exec_shell
3401	echo " " >> mpi_exec_shell
3402	echo "set -u" >> mpi_exec_shell
3403	echo "F_ERRCNT=0" >> mpi_exec_shell
3404	echo "MPIPROGINV=YES" >> mpi_exec_shell
3405	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3406	echo "cpurest=$cpurest" >> mpi_exec_shell
3407	echo "fname=$fname" >> mpi_exec_shell
3408	echo "localhost=$localhost" >> mpi_exec_shell
3409	echo "return_addres=$return_addres" >> mpi_exec_shell
3410	echo "return_username=$return_username" >> mpi_exec_shell
3411	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3412	echo "write_binary=$write_binary" >> mpi_exec_shell
3413	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3414	echo " " >> mpi_exec_shell
3415	echo "export F_ERRCNT" >> mpi_exec_shell
3416	echo "export MPIPROGINV" >> mpi_exec_shell
3417	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3418	echo "export cpurest" >> mpi_exec_shell
3419	echo "export fname" >> mpi_exec_shell
3420	echo "export localhost" >> mpi_exec_shell
3421	echo "export return_addres" >> mpi_exec_shell
3422	echo "export return_username" >> mpi_exec_shell
3423	echo "export tasks_per_node" >> mpi_exec_shell
3424	echo "export write_binary" >> mpi_exec_shell
3425	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3426	echo " " >> mpi_exec_shell
3427	echo "exec ./a.out" >> mpi_exec_shell
3428
3429	chmod u+x mpi_exec_shell
3430	export MPIPROGINF=YES
3431	mpirun -f multinode_config &
3432	wait
3433
3434	fi
3435	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3436	then
3437
3438	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3439	# DOES NOT EXIST
3440	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3441	then
3442	if [[ -f $hostfile ]]
3443	then
3444	cp $hostfile hostfile
3445	(( ii = $numprocs / $threads_per_task ))
3446	else
3447	(( ii = 1 ))
3448	while (( ii <= $numprocs / $threads_per_task ))
3449	do
3450	echo $localhost_realname >> hostfile
3451	(( ii = ii + 1 ))
3452	done
3453	fi
3454	eval zeile=\"`head -n $ii hostfile`\"
3455	printf "\n *** running on: $zeile"
3456	fi
3457
3458	(( ii = $numprocs / $threads_per_task ))
3459	export OMP_NUM_THREADS=$threads_per_task
3460
3461	if [[ $threads_per_task != 1 ]]
3462	then
3463	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3464	# MAY ABORT
3465	ulimit -s unlimited
3466	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3467	fi
3468	if [[ $run_coupled_model = false ]]
3469	then
3470	if [[ "$ocean_file_appendix" = true ]]
3471	then
3472	echo "precursor_ocean" > runfile_atmos
3473	else
3474	echo "precursor_atmos" > runfile_atmos
3475	fi
3476	printf "\n\n"
3477
3478	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3479	then
3480	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3481	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3482	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3483	elif [[ $host = lccrayf ]]
3484	then
3485	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3486	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3487	then
3488	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3489	elif [[ $host = lcflow ]]
3490	then
3491	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3492	elif [[ $host = lcsb ]]
3493	then
3494	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3495	elif [[ $host = lckiaps ]]
3496	then
3497	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3498	elif [[ $host = lckyu* ]]
3499	then
3500	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3501	else
3502	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3503	fi
3504	else
3505
3506	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3507	(( iia = $numprocs_atmos / $threads_per_task ))
3508	(( iio = $numprocs_ocean / $threads_per_task ))
3509	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3510	printf "\n using $coupled_mode coupling"
3511	printf "\n\n"
3512
3513	if [[ $coupled_mode = "mpi2" ]]
3514	then
3515	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3516	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3517
3518	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3519	then
3520
3521	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3522	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3523
3524	else
3525	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3526	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3527	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3528	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3529	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3530	fi
3531	wait
3532
3533	else
3534
3535	echo "coupled_run $iia $iio" > runfile_atmos
3536
3537	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3538	then
3539
3540	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3541
3542	elif [[ $host = lck \|\| $host = lckordi ]]
3543	then
3544
3545	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3546
3547	elif [[ $host = lckyu* ]]
3548	then
3549
3550	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3551
3552	fi
3553	wait
3554	fi
3555
3556	fi
3557
3558	elif [[ $host = lckyoto ]]
3559	then
3560	set -xv
3561	export P4_RSHCOMMAND=plesh
3562	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3563	if [[ "$ENVIRONMENT" = BATCH ]]
3564	then
3565	if [[ "$cond2" = fujitsu ]]
3566	then
3567	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3568	elif [[ "cond2" = pgi ]]
3569	then
3570	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3571	else
3572	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3573	fi
3574	else
3575	if [[ "$cond2" = "" ]]
3576	then
3577	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3578	else
3579	mpirun -np $numprocs ./a.out $ROPTS
3580	fi
3581	fi
3582	set +xv
3583
3584	elif [[ $host = lctit ]]
3585	then
3586	export OMP_NUM_THREADS=$threads_per_task
3587	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3588	if [[ "$threads_per_task" != 1 ]]
3589	then
3590	export MV2_ENABLE_AFFINITY=0
3591	fi
3592	echo "----- PBS_NODEFILE content:"
3593	cat $PBS_NODEFILE
3594	echo "-----"
3595	(( ii = $numprocs / $threads_per_task ))
3596	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3597	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3598	else
3599	mpprun -n $numprocs a.out $ROPTS
3600	fi
3601	else
3602	a.out $ROPTS
3603	fi
3604	fi
3605
3606	if [[ $? != 0 ]]
3607	then
3608
3609	# ABORT IN CASE OF RUNTIME ERRORS
3610	printf "\n +++ runtime error occured"
3611	locat=execution
3612	exit
3613
3614	else
3615
3616	printf "\n$dashes\n *** execution finished \n"
3617
3618	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3619	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3620	if [[ "$dvrserver_id" != "" ]]
3621	then
3622	kill $dvrserver_id
3623	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3624
3625	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3626	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3627	if [[ -d DATA_DVR ]]
3628	then
3629
3630	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3631	# DIRECTORY
3632	cp .dvrserver.config DATA_DVR
3633
3634	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3635	# SEQUENCE MODE DATA TOO)
3636	process_dvr_output -d DATA_DVR -f $fname -s
3637
3638	else
3639
3640	# PROCESS THE LOCAL OUTPUT
3641	process_dvr_output -l -d DATA_DVR -f $fname
3642
3643	fi
3644
3645	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3646	then
3647
3648	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3649	process_dvr_output -l -d DATA_DVR -f $fname
3650
3651	fi
3652	fi
3653
3654
3655
3656	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3657	# BY EACH CORE INTO ONE FILE
3658	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3659	then
3660	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3661	printf "\n 2d- and/or 3d-data may be incomplete!"
3662	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3663	elif [[ "$combine_plot_fields" == true ]]
3664	then
3665	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3666	then
3667	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3668	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3669	else
3670	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3671	combine_plot_fields${block}.x
3672	fi
3673	else
3674
3675	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3676	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3677	# ??? koennen wir das streichen ???
3678	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3679	fi
3680
3681
3682
3683	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3684	(( i = 0 ))
3685	while (( i < ioc ))
3686	do
3687	(( i = i + 1 ))
3688	if (( i == 1 ))
3689	then
3690	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3691	fi
3692	printf "\n >>> ${out_command[$i]}"
3693	eval ${out_command[$i]}
3694	if (( i == ioc ))
3695	then
3696	printf "\n$dashes\n"
3697	fi
3698	done
3699
3700
3701	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3702	if [[ $do_trace = true ]]
3703	then
3704	printf "\n\n"
3705	ls -al
3706	fi
3707
3708
3709
3710	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3711	(( i = 0 ))
3712	while (( i < iout ))
3713	do
3714	(( i = i + 1 ))
3715	if (( i == 1 ))
3716	then
3717	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3718	fi
3719
3720	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3721	files_for_pes=false; filetyp=file
3722	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3723	then
3724	files_for_pes=true; filetyp=directory
3725	actionout[$i]=""
3726	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3727	then
3728	actionout[$i]=""
3729	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3730	then
3731	files_for_pes=true; filetyp=directory
3732	actionout[$i]="ar"
3733	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3734	then
3735	actionout[$i]="ar"
3736	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3737	then
3738	files_for_pes=true; filetyp=directory
3739	actionout[$i]="fl"
3740	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3741	then
3742	actionout[$i]="fl"
3743	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3744	then
3745	files_for_pes=true; filetyp=directory
3746	actionout[$i]="tr"
3747	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3748	then
3749	actionout[$i]="tr"
3750	fi
3751
3752	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3753	then
3754	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3755	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3756	then
3757	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3758	else
3759
3760
3761	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3762	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3763	if [[ "${actionout[$i]}" = tr ]]
3764	then
3765	if [[ $localhost != $fromhost ]]
3766	then
3767	if [[ $files_for_pes = false ]]
3768	then
3769	cps=""
3770	cst=""
3771	else
3772	cps=-c
3773	cst="/"
3774	fi
3775	if [[ $localhost = nech ]]
3776	then
3777
3778	# TRANSFER IN SEPERATE JOB
3779	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3780	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3781	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3782	if [[ $files_for_pes = false ]]
3783	then
3784	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3785	else
3786	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3787	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3788	fi
3789
3790	echo "set -x" > transfer_${localout[$i]}
3791	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3792
3793	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3794	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3795	printf "\n or higher cycle\n"
3796	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3797
3798	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3799
3800	if [[ $localhost = nech ]]
3801	then
3802	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3803	else
3804	if [[ "$LOGNAME" = b323013 ]]
3805	then
3806	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3807	else
3808	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3809	fi
3810	fi
3811
3812	else
3813
3814	# TRANSFER WITHIN THIS JOB
3815	transfer_failed=false
3816	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3817	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3818	if [[ $localhost = lccrayb ]]
3819	then
3820	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3821	elif [[ $localhost = lccrayh ]]
3822	then
3823	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3824	else
3825	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3826	fi
3827	[[ $? != 0 ]] && transfer_failed=true
3828
3829	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3830	if [[ $transfer_failed = true ]]
3831	then
3832	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3833	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3834
3835	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3836	eval local_catalog=${pathout[$i]}
3837	if [[ ! -d $local_catalog ]]
3838	then
3839	printf " *** local directory does not exist. Trying to create:\n"
3840	printf " $local_catalog \n"
3841	mkdir -p $local_catalog
3842	fi
3843	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3844	transfer_problems=true
3845	fi
3846	fi
3847	else
3848
3849	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3850	actionout[$i]=""
3851	fi
3852	fi
3853
3854
3855	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3856	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3857	if [[ "${actionout[$i]}" = tra ]]
3858	then
3859	if [[ $localhost != $fromhost ]]
3860	then
3861	if [[ $localhost = ibmh \|\| $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	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3869
3870	echo "set -x" > transfer_${localout[$i]}
3871	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3872
3873	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3874	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3875	printf "\n or higher cycle\n"
3876	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3877
3878	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3879
3880	if [[ $localhost = nech ]]
3881	then
3882	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3883	else
3884	if [[ $LOGNAME = b323013 ]]
3885	then
3886	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3887	else
3888	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3889	fi
3890	fi
3891
3892	else
3893
3894	# TRANSFER WITHIN THIS JOB
3895	transfer_failed=false
3896	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3897	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3898	if [[ $localhost = lccrayb ]]
3899	then
3900	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3901	elif [[ $localhost = lccrayh ]]
3902	then
3903	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3904	else
3905	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3906	fi
3907	[[ $? != 0 ]] && transfer_failed=true
3908
3909	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3910	if [[ $transfer_failed = true ]]
3911	then
3912	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3913	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3914
3915	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3916	eval local_catalog=${pathout[$i]}
3917	if [[ ! -d $local_catalog ]]
3918	then
3919	printf " *** local directory does not exist. Trying to create:\n"
3920	printf " $local_catalog \n"
3921	mkdir -p $local_catalog
3922	fi
3923
3924	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3925	transfer_problems=true
3926	fi
3927	fi
3928	else
3929
3930	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3931	actionout[$i]=a
3932	fi
3933	fi
3934
3935
3936	# OUTPUT-FILE FOR A RESTART-RUN.
3937	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3938	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3939	# AS LAST ACTION, ARCHIVING IS INITIATED.
3940	if [[ "${actionout[$i]}" = fl ]]
3941	then
3942	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3943	chmod g+rx $tmp_data_catalog
3944	if [[ $files_for_pes = false ]]
3945	then
3946	printf "\n >>> OUTPUT: ${localout[$i]} to"
3947	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3948	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3949	else
3950	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3951	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3952	mkdir $tmp_data_catalog/${frelout[$i]}
3953	cd ${localout[$i]}
3954	for file in $(ls *)
3955	do
3956	ln -f $file $tmp_data_catalog/${frelout[$i]}
3957	done
3958	cd $TEMPDIR
3959	fi
3960
3961
3962	# CREATE AND SUBMIT ARCHIVING-JOB
3963	if [[ $store_on_archive_system = true ]]
3964	then
3965
3966	if [[ $archive_system = asterix ]]
3967	then
3968	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3969	if [[ $files_for_pes = false ]]
3970	then
3971	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3972	else
3973	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3974	fi
3975	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3976	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3977	echo "then" >> archive_${frelout[$i]}
3978	echo " do_stageout=false" >> archive_${frelout[$i]}
3979	echo "else" >> archive_${frelout[$i]}
3980	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3981	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3982	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3983	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3984	if [[ $files_for_pes = false ]]
3985	then
3986	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3987	else
3988	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3989	fi
3990	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3991	echo "fi" >> archive_${frelout[$i]}
3992	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3993	elif [[ $archive_system = DMF ]]
3994	then
3995	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3996	if [[ $files_for_pes = false ]]
3997	then
3998	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3999	locat=DMF
4000	exit
4001	else
4002	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4003	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4004	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4005	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4006	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4007	fi
4008	elif [[ $archive_system = tivoli ]]
4009	then
4010	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4011	if [[ $files_for_pes = false ]]
4012	then
4013	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4014	echo "set -x" >> archive_${frelout[$i]}
4015	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4016	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4017	else
4018
4019	echo "set -x" >> archive_${frelout[$i]}
4020	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4021	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4022	cd $tmp_data_catalog
4023	all_files=`ls -1 ${frelout[$i]}/*`
4024	cd - > /dev/null
4025	(( inode = 0 ))
4026	(( tp1 = tasks_per_node + 1 ))
4027	while (( inode < nodes ))
4028	do
4029	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4030	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4031	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4032	(( inode = inode + 1 ))
4033	done
4034	fi
4035	elif [[ $archive_system = ut ]]
4036	then
4037	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4038	if [[ $files_for_pes = false ]]
4039	then
4040	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4041	echo "set -x" >> archive_${frelout[$i]}
4042	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4043	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4044	else
4045
4046	echo "set -x" >> archive_${frelout[$i]}
4047	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4048	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4049	cd $tmp_data_catalog
4050	all_files=`ls -1 ${frelout[$i]}/*`
4051	cd - > /dev/null
4052	(( inode = 0 ))
4053	(( tp1 = tasks_per_node + 1 ))
4054	while (( inode < nodes ))
4055	do
4056	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4057	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4058	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4059	(( inode = inode + 1 ))
4060	done
4061	fi
4062	elif [[ $archive_system = none ]]
4063	then
4064	printf " +++ archiving on $localhost not available!\n"
4065	fi
4066
4067	if [[ $archive_system != none ]]
4068	then
4069	if [[ $localhost = nech ]]
4070	then
4071	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4072	fi
4073	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4074	fi
4075	else
4076	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4077	fi
4078
4079
4080	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4081	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4082	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4083	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4084	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4085	if [[ $files_for_pes = false ]]
4086	then
4087	cat /dev/null > ${pathout[$i]}
4088	else
4089	mkdir -p ${pathout[$i]}
4090	fi
4091
4092	fi
4093
4094
4095	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4096	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4097	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4098	if [[ "${actionout[$i]}" = ar ]]
4099	then
4100	if [[ $files_for_pes = false ]]
4101	then
4102	printf "\n >>> OUTPUT: ${localout[$i]} to"
4103	printf "\n ${pathout[$i]}"
4104	printf "\n File will be copied to archive-system ($archive_system) !\n"
4105	else
4106	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4107	printf "\n ${pathout[$i]}"
4108	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4109	fi
4110	mv ${localout[$i]} ${frelout[$i]}
4111
4112	file_saved=false
4113
4114	if [[ $archive_system = asterix ]]
4115	then
4116	do_stageout=true
4117	(( stageout_anz = 0 ))
4118	while [[ $do_stageout = true ]]
4119	do
4120	if [[ $files_for_pes = false ]]
4121	then
4122	stageout ${frelout[$i]} > STAGE_OUTPUT
4123	else
4124	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4125	fi
4126	cat STAGE_OUTPUT
4127	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4128	then
4129	file_saved=true
4130	do_stageout=false
4131	else
4132	if [[ $files_for_pes = false ]]
4133	then
4134	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4135	else
4136	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4137	fi
4138	(( stageout_anz = stageout_anz + 1 ))
4139	if (( stageout_anz == 10 ))
4140	then
4141	printf "\n +++ stoped after 10 unsuccessful tries!"
4142	archive_save=false
4143	do_stageout=false
4144	else
4145	printf "\n *** new try to store on archive after 15 min:"
4146	sleep 900
4147	fi
4148	fi
4149	done
4150	elif [[ $archive_system = DMF ]]
4151	then
4152	if [[ $files_for_pes = false ]]
4153	then
4154	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4155	locat=DMF
4156	exit
4157	else
4158	rm -rf $ARCHIVE/${frelout[$i]}
4159	cp -r ${frelout[$i]} $ARCHIVE
4160	fi
4161	file_saved=true
4162	elif [[ $archive_system = tivoli ]]
4163	then
4164	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4165	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4166	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4167	# WHEN THE ARCHIVE-JOB IS EXECUTED
4168	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4169	chmod g+rx $tmp_data_catalog
4170	if [[ $files_for_pes = false ]]
4171	then
4172	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4173	else
4174	mkdir $tmp_data_catalog/${frelout[$i]}
4175	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4176	fi
4177
4178	# GENERATE AND SUBMIT BATCH-JOB
4179	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4180	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4181	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4182	if [[ $files_for_pes = false ]]
4183	then
4184	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4185	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4186	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4187	else
4188	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4189	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4190	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4191	fi
4192
4193	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4194	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4195	file_saved=true
4196
4197	elif [[ $archive_system = ut ]]
4198	then
4199	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4200	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4201	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4202	# WHEN THE ARCHIVE-JOB IS EXECUTED
4203	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4204	chmod g+rx $tmp_data_catalog
4205	if [[ $files_for_pes = false ]]
4206	then
4207	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4208	else
4209	mkdir $tmp_data_catalog/${frelout[$i]}
4210	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4211	fi
4212
4213	# GENERATE AND SUBMIT BATCH-JOB
4214	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4215	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4216	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4217	if [[ $files_for_pes = false ]]
4218	then
4219	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4220	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4221	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4222	else
4223	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4224	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4225	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4226	fi
4227
4228	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4229	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4230	file_saved=true
4231
4232	else
4233	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4234	archive_save=false
4235	fi
4236
4237	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4238	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4239	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4240	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4241	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4242	if [[ $file_saved = true ]]
4243	then
4244	if [[ $files_for_pes = false ]]
4245	then
4246	cat /dev/null > ${pathout[$i]}
4247	else
4248	mkdir -p ${pathout[$i]}
4249	fi
4250	fi
4251
4252	fi
4253
4254	# APPEND ON THIS MACHINE
4255	if [[ "${actionout[$i]}" = "a" ]]
4256	then
4257	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4258	then
4259	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4260	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4261	else
4262	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4263	cat ${localout[$i]} >> ${pathout[$i]}
4264	fi
4265	fi
4266
4267	# COPY ON THIS MACHINE
4268	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4269	# ON DIFFERENT FILE-SYSTEMS
4270	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4271	then
4272
4273	# COPY IN CASE OF RUNS ON SINGLE CORES
4274	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4275	then
4276	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4277	if [[ $link_local_output = true ]]
4278	then
4279	printf " using ln -f\n"
4280	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4281	fi
4282	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4283	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4284	then
4285	if [[ $link_local_output = true ]]
4286	then
4287	printf " ln failed, using cp...\n"
4288	fi
4289	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4290	fi
4291	else
4292	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4293	if [[ $link_local_output = true ]]
4294	then
4295	printf " using ln -f\n"
4296	ln -f ${localout[$i]} ${pathout[$i]}
4297	fi
4298	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4299	if [[ ! -f "${pathout[$i]}" ]]
4300	then
4301	if [[ $link_local_output = true ]]
4302	then
4303	printf " ln failed, using cp...\n"
4304	fi
4305	cp ${localout[$i]} ${pathout[$i]}
4306	fi
4307	fi
4308
4309	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4310	then
4311
4312	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4313	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4314	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4315	if [[ $link_local_output = true ]]
4316	then
4317	printf " using ln -f\n"
4318	mkdir ${pathout[$i]}
4319	cd ${localout[$i]}
4320	for file in $(ls *)
4321	do
4322	ln -f $file ${pathout[$i]}
4323	done
4324	cd $TEMPDIR
4325	fi
4326
4327	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4328	if [[ ! -f "${pathout[$i]}/_0000" ]]
4329	then
4330	if [[ $link_local_output = true ]]
4331	then
4332	printf " ln failed for .../_0000, using cp...\n"
4333	fi
4334	cp -r ${localout[$i]} ${pathout[$i]}
4335	fi
4336
4337	fi
4338	fi
4339	done
4340	if (( i != 0 ))
4341	then
4342	if [[ $transfer_problems = true ]]
4343	then
4344	printf "\n$dashes\n *** OUTPUT-files saved"
4345	printf "\n +++ WARNING: some data transfers failed! \n"
4346	else
4347	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4348	fi
4349	fi
4350
4351
4352	# IF REQUIRED, START A RESTART-JOB
4353	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4354	if [[ -f CONTINUE_RUN ]]
4355	then
4356
4357	if [[ $archive_save = true ]]
4358	then
4359
4360	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4361	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4362	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4363	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4364	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4365	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4366	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4367	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4368	then
4369	mc=`echo $mc \| sed 's/#/f/g'`
4370	fi
4371
4372
4373	# START THE RESTART-JOB
4374	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4375	echo " $mc"
4376	printf "\n$dashes\n"
4377	if [[ $localhost != $fromhost ]]
4378	then
4379
4380	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4381	then
4382	echo "*** ssh will be used to initiate restart-runs!"
4383	echo " return_addres=\"$return_addres\" "
4384	echo " return_username=\"$return_username\" "
4385	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4386	then
4387	if [[ $localhost = ibmh ]]
4388	then
4389	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4390	elif [[ $localhost = lccrayb ]]
4391	then
4392	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4393	elif [[ $localhost = lccrayh ]]
4394	then
4395	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4396
4397	else
4398	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4399	fi
4400	else
4401	if [[ $localhost = ibmkisti ]]
4402	then
4403	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4404	elif [[ $localhost = lcflow ]]
4405	then
4406	/usr/bin/ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4407	elif [[ $localhost = lccrayb ]]
4408	then
4409	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4410	elif [[ $localhost = lccrayh ]]
4411	then
4412	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4413	else
4414	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4415	fi
4416	fi
4417	else
4418	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4419	locat=restart; exit
4420	fi
4421
4422	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4423	if [[ $queue = special1q ]]
4424	then
4425	sleep 120
4426	else
4427	sleep 30
4428	fi
4429
4430	else
4431
4432	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4433	# USING SSH)
4434	cd $LOCAL_PWD
4435	if [[ $localhost = lckyuh ]]
4436	then
4437	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4438	printf "\n please restart job manually using command:\n"
4439	printf "\n \"$mc\" "
4440	else
4441	eval $mc # THE ' MUST BE EVALUATED
4442	fi
4443	cd - > /dev/null
4444	fi
4445	if [[ $localhost = lckyuh ]]
4446	then
4447	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4448	else
4449	printf "\n$dashes\n *** restart-run initiated \n"
4450	fi
4451
4452
4453	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4454	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4455	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4456	# MAY BE VERY HUGE)
4457	(( i = 0 ))
4458	while (( i < iin ))
4459	do
4460	(( i = i + 1 ))
4461	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4462	then
4463	rm -r $tmp_data_catalog/${frelin[$i]}
4464	fi
4465	done
4466
4467	else
4468
4469	printf "\n +++ no restart-run possible, since errors occured"
4470	printf "\n during the archive process"
4471	fi
4472
4473	fi
4474
4475
4476
4477	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4478	if [[ "$email_notification" != "none" ]]
4479	then
4480
4481	if [[ $localhost != $fromhost ]]
4482	then
4483	if [[ -f CONTINUE_RUN ]]
4484	then
4485	echo "PALM restart run necessary" > email_text
4486	echo "description header of actual run:" >> email_text
4487	cat CONTINUE_RUN >> email_text
4488	echo "mrun-command to restart:" >> email_text
4489	echo "$mc" >> email_text
4490	else
4491	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4492	fi
4493	mail $email_notification < email_text
4494	printf "\n *** email notification sent to \"$email_notification\" "
4495	fi
4496	fi
4497
4498
4499
4500	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4501	cd $HOME
4502	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4503
4504	else
4505
4506
4507	# PREPARING ACTIONS,
4508	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4509
4510	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4511	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_addres -U $return_username -u $remote_username"
4512	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4513	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4514	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4515	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4516	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4517	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4518	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4519	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4520	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4521	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4522	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4523	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4524	if [[ $use_openmp = true ]]
4525	then
4526	mrun_com=${mrun_com}" -O $threads_per_task"
4527	fi
4528	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4529	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4530	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4531	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4532	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4533	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4534	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4535	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4536	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4537	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4538	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4539	if [[ $do_remote = true ]]
4540	then
4541	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4542	fi
4543
4544
4545	# CREATE EXECUTABLE FOR BATCH JOB
4546	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4547	then
4548
4549	printf "\n *** creating the executable for batch job\n"
4550
4551	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4552	if [[ $host != $localhost ]]
4553	then
4554	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4555	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4556	locat=create_executable; exit
4557	fi
4558
4559	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4560	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4561
4562	cp $make_depository .
4563	tar -xf $make_depository > /dev/null 2>&1
4564	cp ../* . > /dev/null 2>&1
4565
4566	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4567
4568	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4569	then
4570	printf "\n +++ error occured while compiling or linking"
4571	locat=compile
4572	exit
4573	fi
4574
4575	mv a.out ..
4576	cd - > /dev/null 2>&1
4577	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4578
4579	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4580
4581	fi
4582
4583
4584	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4585	jobfile=jobfile.$RANDOM
4586
4587
4588	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4589	echo "mkdir $TEMPDIR" >> $jobfile
4590	echo "cd $TEMPDIR" >> $jobfile
4591
4592
4593	# ACTIVATE ERROR-TRACEBACK
4594	if [[ $do_trace = true ]]
4595	then
4596	echo "set -x" >> $jobfile
4597	else
4598	echo "set +vx" >> $jobfile
4599	fi
4600
4601
4602	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4603	if [[ "$init_cmds" != "" ]]
4604	then
4605	echo "$init_cmds" >> $jobfile
4606	fi
4607	if [[ "$module_calls" != "" ]]
4608	then
4609	echo "$module_calls" >> $jobfile
4610	fi
4611
4612
4613	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4614	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4615	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4616	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4617	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4618	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4619	# QUEUEING-SYSTEMS
4620	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4621	then
4622
4623	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4624	if [[ $restart_run != true ]]
4625	then
4626	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4627	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4628	fi
4629
4630	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4631	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4632	echo "set -x" >> $jobfile
4633	if [[ $host = $localhost ]]
4634	then
4635
4636	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4637	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4638	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4639	then
4640	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4641	else
4642	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4643	fi
4644
4645	else
4646	if [[ $host = ibmkisti ]]
4647	then
4648	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4649	echo "localdir=\`pwd\`" >> $jobfile
4650	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4651	elif [[ $host = lccrayb ]]
4652	then
4653	echo "localdir=\`pwd\`" >> $jobfile
4654	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4655	elif [[ $host = lccrayh ]]
4656	then
4657	echo "localdir=\`pwd\`" >> $jobfile
4658	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4659
4660	else
4661	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4662	fi
4663	fi
4664	echo "export SOURCES_COMPLETE=true" >> $jobfile
4665
4666	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4667	# WORKING DIRECTORY OF THE JOB
4668	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4669	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4670	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4671	echo "execute_mrun=true" >> $jobfile
4672	echo " " >> $jobfile
4673
4674	else
4675
4676	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4677	if [[ $do_compile = true ]]
4678	then
4679
4680	source_catalog=SOURCES_FOR_RUN_$fname
4681
4682	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4683	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4684	echo "export SOURCES_COMPLETE=true" >> $jobfile
4685	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4686
4687	for filename in $source_list
4688	do
4689	# BACKSLASH IS USED FOR MASKING
4690	echo "cat > $filename << \"%END%\"" >> $jobfile
4691	cat $source_catalog/$filename >> $jobfile
4692	echo " " >> $jobfile
4693	echo "%END%" >> $jobfile
4694	echo " " >> $jobfile
4695	done
4696
4697	# BACKSLASH IS USED FOR MASKING
4698	echo "cat > Makefile << \"%END%\"" >> $jobfile
4699	cat $source_catalog/Makefile >> $jobfile
4700	echo " " >> $jobfile
4701	echo "%END%" >> $jobfile
4702	echo " " >> $jobfile
4703
4704	echo "cd - > /dev/null" >> $jobfile
4705
4706	fi
4707
4708
4709	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4710	# BACKSLASH IS USED FOR MASKING
4711	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4712	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4713	echo "cat > $config_file << \"%END%\"" >> $jobfile
4714	if [[ $host = lckyuh ]]
4715	then
4716	# NO CROSS-COMPILER ON COMPUTE NODE
4717	sed 's/frtpx/frt/g' $config_file >> $jobfile
4718	else
4719	sed 's/#$.*//g' $config_file >> $jobfile
4720	fi
4721	echo "%END%" >> $jobfile
4722	echo " " >> $jobfile
4723
4724
4725	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4726	# BACKSLASH IS USED FOR MASKING
4727	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4728	if [[ $host = lckyuh ]]
4729	then
4730	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4731	else
4732	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4733	fi
4734	echo "%END%" >> $jobfile
4735	echo "chmod u+x $mrun_script_name" >> $jobfile
4736	echo "execute_mrun=true" >> $jobfile
4737	echo " " >> $jobfile
4738
4739	fi
4740
4741
4742	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4743	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4744	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4745	if [[ $do_remote = true ]]
4746	then
4747	(( i = 0 ))
4748	while (( i < iin ))
4749	do
4750	(( i = i + 1 ))
4751	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4752	if [[ "${transin[$i]}" = job ]]
4753	then
4754	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4755	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4756	echo " " >> $jobfile
4757	echo "%END%" >> $jobfile
4758	else
4759	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4760	fi
4761
4762	# CHECK, IF FILE COULD BE CREATED
4763	echo "if [[ \$? = 1 ]]" >> $jobfile
4764	echo "then" >> $jobfile
4765	echo " echo \" \" " >> $jobfile
4766	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4767	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4768	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4769	echo " execute_mrun=false" >> $jobfile
4770	echo "fi" >> $jobfile
4771	done
4772	fi
4773
4774	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4775	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4776	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4777	echo "LOCAL_PWD=$working_directory" >> $jobfile
4778	echo "export LOCAL_PWD" >> $jobfile
4779
4780	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4781	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4782	echo "export LOCAL_MRUN_PATH" >> $jobfile
4783
4784	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4785	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4786	then
4787	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4788	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4789	fi
4790
4791	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4792	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4793	echo "set -x" >> $jobfile
4794	echo "queue=$queue" >> $jobfile
4795	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4796	echo 'ls -al; echo `pwd`' >> $jobfile
4797	echo "cd \$HOME" >> $jobfile
4798	echo "rm -rf $TEMPDIR" >> $jobfile
4799
4800
4801
4802
4803	# START THE JOB USING SUBJOB-COMMAND
4804	if [[ $silent = false ]]
4805	then
4806	printf "\n "
4807	else
4808	printf "\n\n"
4809	fi
4810
4811	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
4812	rm -rf $jobfile
4813
4814
4815	fi # END OF REMOTE-PART

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