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source: palm/trunk/SCRIPTS/mrun @ 1312

Last change on this file since 1312 was 1310, checked in by raasch, 11 years ago
update of GPL copyright
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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 1310 2014-03-14 08:01:56Z heinze $
29	#
30	# 1304 2014-03-12 10:29:42Z raasch
31	# ulimit option changed from -Ss to -s
32	#
33	# bugfix: missing "fi" in r1289
34	#
35	# 1289 2014-03-04 07:12:34Z raasch
36	# comments translated to English
37	# necriam-, fimm-, ibmy-, and sgi-specific code removed
38	# export of variables for palm and interpret_config removed
39	#
40	# 1281 2014-02-01 07:55:49Z raasch
41	# rsync-copy restricted to Cray machines, since command is unavailable on some
42	# other systems
43	#
44	# 1279 2014-01-28 12:10:14Z raasch
45	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
46	# in order to remove annoying restrictions concerning the number of processors which
47	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
48	# restriction, one of the nodes will be filled with less than the given number of
49	# tasks per node. A respective warning is given.
50	#
51	# 1274 2014-01-09 13:14:54Z heinze
52	# adjustments for lccrayh
53	#
54	# 1272 2014-01-08 10:19:32Z witha
55	# small adjustment for lcflow
56	#
57	# 1270 2013-12-16 11:05:01Z fricke
58	# call of combine_plot_fields adjusted for lccrayb/lccrayh
59	#
60	# 1255 2013-11-07 14:43:35Z raasch
61	# further adjustments for lccrayb remote access
62	#
63	# 1241 2013-10-30 11:36:58Z heinze
64	# Enable use of nudging input and input of large scale forcing from
65	# external files
66	#
67	# 1229 2013-09-20 06:55:19Z raasch
68	# further adjustments for lccrayb
69	#
70	# 1224 2013-09-16 07:27:23Z raasch
71	# first adjustments for lccrayb
72	#
73	# 1210 2013-08-14 10:58:20Z raasch
74	# fftw support added
75	#
76	# 1201 2013-07-10 16:17:59Z witha
77	# adjustments for Forwind cluster (lcflow)
78	#
79	# 1199 2013-07-05 14:52:22Z raasch
80	# adjustments for CSC Helsinki (lccrayf),
81	# executables for batch jobs can be created in advance, in order to avoid calling
82	# the compiler within the batch job (only works if batch jobs are submitted on
83	# local host)
84	#
85	# 1190 2013-06-25 09:39:21Z heinze
86	# enable use of automatic restarts for ibmh
87	# use of cluster/express queue enabled (ibmh)
88	#
89	# 1124 2013-04-09 15:46:52Z raasch
90	# variable "memory" is exported via typeset option -x, because otherwise an unknown
91	# side effect may lead to data loss while getopts is reading the script-option arguments
92	#
93	# 1122 2013-04-09 08:37:16Z heinze
94	# Bugfix: change type of variable last_char
95	#
96	# 1119 2013-04-05 15:11:19Z raasch
97	# Bugfix for setting -T option for subjob
98	#
99	# 1108 2013-03-05 07:03:32Z raasch
100	# bugfix for coupled runs on lckyut/lckyuh
101	#
102	# 1106 2013-03-04 05:31:38Z raasch
103	# --stdin argument for mpiexec on lckyuh
104	# -y and -Y settings output to header
105	#
106	# 1103 2013-02-20 02:15:53Z raasch
107	# default script runs again under ksh, because of unsolved problems with read
108	# from stdin: when bash script is called from a ksh, message "read error: 0:
109	# Resource temporarily unavailable" appears and script does not stop,
110	# further bash compatibility adjustments,
111	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
112	# on lckyuh, but mrun does not terminate and issues a warning instead
113	#
114	# 1101 2013-02-17 10:20:21Z raasch
115	# script now running under bash instead of ksh, which required small adjustments
116	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
117	# read from stdin),
118	# cross compilername on lckyuh compute nodes replaced by real compiler name
119	#
120	# 1099 2013-02-10 01:47:43Z raasch
121	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
122	# and for Forwind cluster (lcflow)
123	# small further adjustments for lckyut
124	#
125	# 1094 2013-02-03 01:52:12Z raasch
126	# explicit ssh/scp port can be set in config file with environment variable
127	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
128	# decalpha parts (yonsei) removed
129	#
130	# 2013-02-02 07:06:13Z raasch
131	# adjustments for Kyushu-University computing center (lckyut - tatara)
132	#
133	# 1083 2013-01-04 10:22:09Z maronga
134	# bugfix in parameter file check (read %cpp_options was missing)
135	#
136	# 1069 2012-11-28 16:18:43Z maronga
137	# bugfix: coupling mode was always set to mpi2, typos removed
138	#
139	# 1058 2012-11-21 07:00:35Z raasch
140	# Intel inspector (inspxe) is given the number of PEs instead of the number of
141	# nodes
142	#
143	# 1046 2012-11-09 14:38:45Z maronga
144	# code put under GPL (PALM 3.9)
145	#
146	# 21/03/94 - Siggi - first version finished
147	# 03/03/94 - Siggi - script development started
148	#
149	#--------------------------------------------------------------------------------#
150	# mrun - script for running PALM jobs
151	#--------------------------------------------------------------------------------#
152
153
154
155	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
156
157	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
158	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
159	# (TOO MANY ARGUMENTS - PROBLEM)
160	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
161
162	AddFilenames=""
163	additional_conditions=""
164	add_source_path=""
165	afname=""
166	archive_save=true
167	archive_system=none
168	check_namelist_files=true
169	combine_plot_fields=true
170	compiler_name=""
171	cond1=""
172	cond2=""
173	config_file=.mrun.config
174	coupled_dist=""
175	coupled_mode="mpi1"
176	cpp_opts=""
177	cpp_options=""
178	cpumax=0
179	cpurest=0
180	create_executable_for_batch=false
181	delete_temporary_catalog=true
182	do_batch=false
183	do_compile=true
184	do_remote=false
185	do_stagein=true
186	do_stageout=true
187	do_trace=false
188	email_notification="none"
189	exclude=""
190	executable=""
191	execution_error=false
192	fftw_inc=""
193	fftw_lib=""
194	fftw_support=false
195	fname=test
196	fromhost=""
197	global_revision=""
198	group_number=none
199	host=""
200	host_file=""
201	hp=""
202	ignore_archive_error=false
203	input_list=""
204	interpreted_config_file=""
205	job_catalog="~/job_queue"
206	job_on_file=""
207	keep_data_from_previous_run=false
208	link_local_input=false
209	link_local_output=false
210	localhost_realname=$(hostname)
211	local_dvrserver_running=.FALSE.
212	locat=normal
213	mainprog=""
214	makefile=""
215	max_par_io_str=""
216	mc=$0
217	while [[ $(echo $mc \| grep -c "/") != 0 ]]
218	do
219	mc=`echo $mc \| cut -f2- -d"/"`
220	done
221	module_calls=""
222	mrun_script_name=$mc
223	netcdf_inc=""
224	netcdf_lib=""
225	netcdf_support=false
226	node_usage=default
227	numprocs=""
228	numprocs_atmos=0
229	numprocs_ocean=0
230	OOPT=""
231	openmp=false
232	output_list=""
233	package_list=""
234	queue=none
235	read_from_config=""
236	restart_run=false
237	if [[ `hostname` = rte10 ]]
238	then
239	return_addres=133.5.185.60
240	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
241	elif [[ `hostname` = climate0 ]]
242	then
243	return_addres=165.132.26.68
244	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
245	elif [[ `hostname` = urban00 ]]
246	then
247	return_addres=147.46.30.151
248	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
249	else
250	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
251	fi
252	return_password=""
253	return_username=$LOGNAME
254	remotecall=false
255	remote_username=""
256	run_coupled_model=false
257	run_mode=""
258	store_on_archive_system=false
259	dashes=" ----------------------------------------------------------------------------"
260	silent=false
261	source_list=""
262	source_path=SOURCE
263	tasks_per_node=""
264	threads_per_task=1
265	tmpcreate=false
266	tmp_data_catalog=""
267	transfer_problems=false
268	usern=$LOGNAME
269	use_openmp=false
270	version="MRUN 2.1 Rev$Rev: 1310 $"
271	working_directory=`pwd`
272	TOPT=""
273	XOPT=""
274	zeit=$( date \| cut -c 12-19 )
275
276	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
277	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
278	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
279	# SCRIPT-OPTION ARGUMENTS
280	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
281
282
283
284	# ERROR HANDLING IN CASE OF EXIT
285	trap 'rm -rf $working_directory/tmp_mrun
286	if [[ $locat != normal && $locat != control_c ]]
287	then
288
289	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
290	(( i = 0 ))
291	while (( i < iec ))
292	do
293	(( i = i + 1 ))
294	printf "\n *** Execution of ERROR-command:\n"
295	printf " >>> ${err_command[$i]}\n"
296	eval ${err_command[$i]}
297	done
298	if [[ -n $interpreted_config_file ]]
299	then
300	rm -rf $interpreted_config_file
301	fi
302	if [[ -n .mrun_environment ]]
303	then
304	rm -rf .mrun_environment
305	fi
306	if [[ $tmpcreate = true ]]
307	then
308	printf "\n *** Contents of \"$TEMPDIR\":\n"
309	ls -al; cd
310	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
311	fi
312	if [[ "$dvrserver_id" != "" ]]
313	then
314	echo "+++ killing dvrserver_id=$dvrserver_id"
315	kill $dvrserver_id
316	fi
317	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
318	then
319	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
320	fi
321	printf "\n\n+++ MRUN killed \n\n"
322	elif [[ $locat != control_c ]]
323	then
324	printf "\n\n --> all actions finished\n\n"
325	printf " Bye, bye $usern !!\n\n"
326	fi' exit
327
328
329	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
330	trap 'rm -rf $working_directory/tmp_mrun
331	rm -rf $working_directory/tmp_check_namelist_files
332	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
333	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
334	then
335	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
336	fi
337	if [[ "$dvrserver_id" != "" ]]
338	then
339	echo "+++ killing dvrserver_id=$dvrserver_id"
340	kill $dvrserver_id
341	fi
342	printf "\n+++ MRUN killed by \"^C\" \n\n"
343	locat=control_c
344	exit
345	' 2
346
347
348	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
349	# BEEN SET
350	if [[ "$PALM_BIN" = "" ]]
351	then
352	printf "\n +++ environment variable PALM_BIN has not been set"
353	printf "\n please set it to the directory where the PALM scripts are located"
354	locat=palm_bin; exit
355	fi
356	export PATH=$PALM_BIN:$PATH
357
358
359
360	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
361	# WHICH WILL BE USED TO START RESTART-JOBS
362	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
363	do
364	case $option in
365	(a) afname=$OPTARG;;
366	(A) store_on_archive_system=true; mc="$mc -A";;
367	(b) do_batch=true; mc="$mc -b";;
368	(B) delete_temporary_catalog=false; mc="$mc -B";;
369	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
370	(C) restart_run=true; mc="$mc -C";;
371	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
372	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
373	(F) job_on_file="-D"; mc="$mc -F";;
374	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
375	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
376	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
377	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
378	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
379	(I) ignore_archive_error=true; mc="$mc -I";;
380	(k) keep_data_from_previous_run=true; mc="$mc -k";;
381	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
382	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
383	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
384	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
385	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
386	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
387	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
388	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
389	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
390	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
391	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
392	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
393	(S) read_from_config=false; mc="$mc -S";;
394	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
395	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
396	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
397	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
398	(v) silent=true; mc="$mc -v";;
399	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
400	(x) do_trace=true;set -x; mc="$mc -x";;
401	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
402	(y) ocean_file_appendix=true; mc="$mc -y";;
403	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
404	(z) check_namelist_files=false; mc="$mc -z";;
405	(Z) combine_plot_fields=false; mc="$mc -Z";;
406	(\?) printf "\n +++ unknown option $OPTARG \n"
407	printf "\n --> type \"$0 ?\" for available options \n"
408	locat=parameter;exit;;
409	esac
410	done
411
412
413	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
414	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
415	(( to_shift = $OPTIND - 1 ))
416	shift $to_shift
417
418	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
419	if [[ "$1" = "?" ]]
420	then
421	(printf "\n *** mrun can be called as follows:\n"
422	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"
423	printf "\n Description of available options:\n"
424	printf "\n Option Description Default-Value"
425	printf "\n -a base name of input files equiv. -d"
426	printf "\n -A archiving when using file-attribute fl"
427	printf "\n -b batch-job on local machine ---"
428	printf "\n -B do not delete temporary directory at end ---"
429	printf "\n -c configuration file .mrun.config"
430	printf "\n -d base name of files attached to program test"
431	printf "\n -D preprocessor(cpp)-directives \"\" "
432	printf "\n -F create remote job file only ---"
433	printf "\n -h execution host $localhost_realname"
434	printf "\n -i INPUT control list \"\" "
435	printf "\n -I archiving errors of previous batch-jobs"
436	printf "\n will be ignored"
437	printf "\n -k keep data from previous run"
438	printf "\n -K additional conditions for controling"
439	printf "\n usage of conditional code and"
440	printf "\n env-variables in configuration file \"\" "
441	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
442	printf "\n -M Makefile name Makefile"
443	printf "\n -n node usage (shared/not_shared) depending on -h"
444	printf "\n -o OUTPUT control list \"\" "
445	printf "\n -O threads per openMP task ---"
446	printf "\n -p software package list \"\" "
447	printf "\n -q queue \"$queue\" "
448	printf "\n -r run control list (combines -i -o) \"\" "
449	printf "\n -s filenames of routines to be compiled \"\" "
450	printf "\n must end with .f, .f90, .F, or .c !"
451	printf "\n use \"..\" for more than one file and wildcards"
452	printf "\n -s LM compiles all locally modified files"
453	printf "\n -S config file interpreted by shellscript ---"
454	printf "\n -t allowed cpu-time in seconds (batch) 0"
455	printf "\n -T tasks per node depending on -h"
456	printf "\n -u username on remote machine \"\" "
457	printf "\n -v no prompt for confirmation ---"
458	printf "\n -w maximum parallel io streams as given by -X"
459	printf "\n -x tracing of mrun for debug purposes ---"
460	printf "\n -X # of processors (on parallel machines) 1"
461	printf "\n -y add appendix \"_O\" to all local output"
462	printf "\n files (ocean precursor runs followed by"
463	printf "\n coupled atmosphere-ocean runs) ---"
464	printf "\n -Y run coupled model, \"#1 #2\" with"
465	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
466	printf "\n -z disable a priori parameter file check ---"
467	printf "\n -Z skip combine_plot_fields at the end of "
468	printf "\n the simulation ---"
469	printf "\n "
470	printf "\n Possible values of positional parameter <modus>:"
471	printf "\n \"?\" - this outline \n\n") \| more
472	exit
473	elif [[ "$1" != "" ]]
474	then
475	printf "\n +++ positional parameter $1 unknown \n"
476	locat=parameter; exit
477	fi
478
479
480
481	# SHORT STARTING MESSAGE
482	printf "\n*** $version "
483	printf "\n will be executed. Please wait ..."
484
485
486
487	# CHECK, IF CONFIGURATION FILE EXISTS
488	if [[ ! -f $config_file ]]
489	then
490	printf "\n\n +++ configuration file: "
491	printf "\n $config_file"
492	printf "\n does not exist"
493	locat=connect; exit
494	fi
495
496
497	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
498	line=""
499	grep "%host_identifier" $config_file > tmp_mrun
500	while read line
501	do
502	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
503	then
504	HOSTNAME=`echo $line \| cut -d" " -s -f2`
505	host_identifier=`echo $line \| cut -d" " -s -f3`
506	if [[ $localhost_realname = $HOSTNAME ]]
507	then
508	localhost=$host_identifier
509	break
510	fi
511	fi
512	done < tmp_mrun
513
514	if [[ "$localhost" = "" ]]
515	then
516	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
517	printf "\n for local host \"$localhost_realname\"."
518	printf "\n Please add line"
519	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
520	printf "\n to the configuration file."
521	locat=localhost; exit
522	fi
523
524
525	# SET HOST-SPECIFIC VARIABLES
526	case $localhost_realname in
527	(r1\|r2\|h01\|b01) archive_system=tivoli;;
528	(cs*) archive_system=ut;;
529	esac
530
531
532	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
533	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
534	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
535	[[ "$afname" = "" ]] && afname=$fname
536
537
538	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
539	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
540	# STATEMENTS IN THE CONFIGURATION FILE
541	if [[ "$run_mode" != "" ]]
542	then
543	input_list="$input_list $run_mode"
544	output_list="$output_list $run_mode"
545	fi
546
547
548	# ??? is this (and the respective option -H) really required ???
549	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
550	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
551	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
552	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
553	if [[ "$fromhost" = "" ]]
554	then
555	fromhost=$localhost
556	fi
557
558
559	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
560	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
561	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
562	# TO BE SUBMITTED (I.E. do_bacth=true)
563	if [[ -n $host && "$host" != $localhost ]]
564	then
565	do_batch=true
566	do_remote=true
567	case $host in
568	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
569	(*) printf "\n"
570	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
571	printf "\n is not available"
572	locat=nqs; (( iec = 0 )); exit;;
573	esac
574	else
575	host=$localhost
576	fi
577
578
579	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
580	if [[ -n $additional_conditions ]]
581	then
582	cond1=`echo $additional_conditions \| cut -d" " -f1`
583	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
584	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
585	if [[ -n $dummy ]]
586	then
587	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
588	locat=options; exit
589	fi
590	block=_$cond1
591	[[ -n $cond2 ]] && block=${block}_$cond2
592	fi
593
594
595	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
596	if [[ $run_coupled_model = true ]]
597	then
598
599	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
600	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
601
602	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
603	then
604
605	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
606	printf "\n PEs (total) : $numprocs"
607	printf "\n PEs (atmosphere): $numprocs_atmos"
608	printf "\n PEs (ocean) : $numprocs_ocean"
609	locat=coupling; exit
610
611	fi
612
613
614	# GET coupled_mode FROM THE CONFIG FILE
615	line=""
616	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
617	while read line
618	do
619	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
620	then
621	coupled_mode="mpi2"
622	fi
623	done < tmp_mrun
624
625	fi
626
627
628	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
629	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
630	then
631	if [[ $ignore_archive_error = false ]]
632	then
633	printf "\n +++ data archiving of previous run failed"
634	printf "\n see directory \~/job_queue on remote machine"
635	locat=archive; exit
636	else
637	printf "\n +++ warning: data archiving in a previous run failed"
638	printf "\n MRUN continues, trying to get backup copy"
639	fi
640	fi
641
642
643	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
644	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
645	mrun_memory=$memory
646	mrun_group_number=$group_number
647	mrun_cpumax=$cpumax
648	mrun_numprocs=$numprocs
649
650
651	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
652	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
653	if [[ "$read_from_config" = false ]]
654	then
655
656	[[ $silent = false ]] && printf "\n Reading the configuration file... "
657
658	# READ THE CONFIGURATION FILE LINE BY LINE
659	while read zeile
660	do
661	[[ $silent = false ]] && printf "."
662
663
664	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
665	eval zeile=\"$zeile\"
666
667
668	# INTERPRET THE LINE
669	if [[ "$(echo $zeile)" = "" ]]
670	then
671	# EMPTY LINE, NO ACTION
672	continue
673
674	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
675	then
676
677	# LINE IS A COMMENT LINE
678	true
679
680	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
681	then
682
683	# LINE DEFINES AN ENVIRONMENT-VARIABLE
684	zeile=$(echo $zeile \| cut -c2-)
685	var=`echo $zeile \| cut -d" " -f1`
686	value=`echo $zeile \| cut -d" " -s -f2`
687	for_host=`echo $zeile \| cut -d" " -s -f3`
688	for_cond1=`echo $zeile \| cut -d" " -s -f4`
689	for_cond2=`echo $zeile \| cut -d" " -s -f5`
690
691	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
692	then
693
694	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
695	# "::" IS REPLACED BY ":".
696	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
697
698
699	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
700	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
701	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
702	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
703	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
704	# CONFIGURATION-FILE.
705	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
706	then
707	eval $var=\$value
708
709	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
710	if [[ $do_trace = true ]]
711	then
712	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
713	fi
714	fi
715
716	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
717	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
718	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
719	# MUST HAVE TO BE STARTED
720	if [[ $var = host ]]
721	then
722	if [[ -n $host && "$host" != $localhost ]]
723	then
724	do_batch=true
725	do_remote=true
726	case $host in
727	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
728	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
729	printf "\n is not available"
730	locat=nqs; exit;;
731	esac
732	else
733	host=$localhost
734	fi
735	fi
736
737	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
738	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
739	# BY MRUN (E.G. subjob)
740	export $var
741	fi
742
743
744
745
746	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
747	then
748
749	# LINE DEFINES ERROR-COMMAND
750	(( iec = iec + 1 ))
751	zeile=$(echo $zeile \| cut -c4-)
752	err_command[$iec]="$zeile"
753
754	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
755	then
756
757	# LINE DEFINES INPUT-COMMAND
758	(( iic = iic + 1 ))
759	zeile=$(echo $zeile \| cut -c4-)
760	in_command[$iic]="$zeile"
761
762	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
763	then
764
765	# LINE DEFINES OUTPUT-COMMAND
766	(( ioc = ioc + 1 ))
767	zeile=$(echo $zeile \| cut -c4-)
768	out_command[$ioc]="$zeile"
769
770	else
771
772	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
773	# s2a: in/out - field
774	# s2b: loc - field (optional)
775	# s2c: tr/ar - field (optional)
776	s1=`echo $zeile \| cut -d" " -f1`
777	s2=`echo $zeile \| cut -d" " -s -f2`
778	s2a=$(echo $s2 \| cut -d":" -f1)
779	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
780	then
781	s2b=""
782	s2c=""
783	else
784	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
785	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
786	fi
787	s3=`echo $zeile \| cut -d" " -f3`
788	s4=`echo $zeile \| cut -d" " -s -f4`
789	s5=`echo $zeile \| cut -d" " -s -f5`
790	s6=`echo $zeile \| cut -d" " -s -f6`
791
792
793	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
794	# INPUT- OR OUTPUT-LIST.
795	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
796	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
797	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
798	# IS NOT CHECKED AND STORED.
799	IFSALT="$IFS"; IFS="$IFS:"
800	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
801	then
802	found=false
803	for actual in $input_list
804	do
805	for formal in $s3
806	do
807	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
808	done
809	done
810	if [[ $found = true ]]
811	then
812	(( iin = iin + 1 ))
813	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
814	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
815	extin[$iin]=$s6
816	fi
817	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
818	then
819	found=false
820	for actual in $output_list
821	do
822	for formal in $s3
823	do
824	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
825	done
826	done
827	if [[ $found = true ]]
828	then
829	(( iout = iout + 1 ))
830	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
831	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
832	fi
833	elif [[ "$s2a" != in && "$s2a" != out ]]
834	then
835	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
836	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
837	locat=connect; exit
838	fi
839	IFS="$IFSALT"
840	fi
841	done < $config_file
842
843	else
844
845
846	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
847	[[ $silent = false ]] && printf "..."
848	interpreted_config_file=.icf.$RANDOM
849
850
851
852	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
853	cat > .mrun_environment << %%END%%
854	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
855	config_file = '$config_file', do_remote = '$do_remote',
856	do_trace = '$do_trace', host = '$host',
857	input_list = '$input_list', icf = '$interpreted_config_file',
858	localhost = '$localhost', output_list = '$output_list' /
859
860	%%END%%
861
862	if [[ "$host" != $localhost ]]
863	then
864
865	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
866	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
867	if [[ $? != 0 ]]
868	then
869	printf "\n\n +++ no interpret_config found"
870	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
871	locat=interpret_config; exit
872	fi
873	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
874	$interpret_config_executable
875
876	else
877
878	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
879	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
880	then
881	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
882	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
883	locat=interpret_config; exit
884	else
885	interpret_config${block}.x
886	fi
887
888	fi
889	rm .mrun_environment
890
891
892	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
893	chmod u+x $interpreted_config_file
894	export PATH=$PATH:.
895	. $interpreted_config_file
896	rm $interpreted_config_file
897
898	fi
899
900
901	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
902	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
903	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
904	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
905	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
906	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
907	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
908
909
910	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
911	# FOR SOURCE-FILES TO BE COMPILED.
912	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
913	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
914	if [[ "$SOURCES_COMPLETE" = "" ]]
915	then
916
917	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
918	# HAS BEEN DEFINED
919	source_path=""
920	line=""
921	grep "%source_path" $config_file > tmp_mrun
922	while read line
923	do
924	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
925	then
926	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
927	then
928	global_source_path=`echo $line \| cut -d" " -f2`
929	fi
930	fi
931	done < tmp_mrun
932
933	line=""
934	found=false
935	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
936	while read line
937	do
938	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
939	then
940	if [[ $found = true ]]
941	then
942	printf "\n\n +++ more than one source path found in configuration file"
943	printf "\n for local host \"$localhost\" "
944	locat=source_path; exit
945	fi
946	source_path=`echo $line \| cut -d" " -f2`
947	found=true
948	fi
949	done < tmp_mrun
950	rm tmp_mrun
951
952	if [[ "$source_path" = "" ]]
953	then
954	if [[ "$global_source_path" != "" ]]
955	then
956	source_path=$global_source_path
957	else
958	printf "\n\n +++ no source path found in configuration file"
959	printf "\n for local host \"$localhost\" "
960	locat=source_path; exit
961	fi
962	fi
963	eval source_path=$source_path
964
965	if [[ ! -d $source_path ]]
966	then
967	printf "\n\n +++ source path \"$source_path\" on local host"
968	printf "\n \"$localhost\" does not exist"
969	locat=source_path; exit
970	fi
971
972	fi
973
974
975	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
976	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
977	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
978	then
979	global_revision=`svnversion $source_path 2>/dev/null`
980	global_revision="Rev: $global_revision"
981	fi
982
983
984	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
985	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
986	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
987	if [[ -n $host && "$host" != $localhost ]]
988	then
989	do_batch=true
990	do_remote=true
991	case $host in
992	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
993	(*) printf "\n"
994	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
995	printf "\n is not available"
996	locat=nqs; (( iec = 0 )); exit;;
997	esac
998	else
999	host=$localhost
1000	fi
1001
1002
1003	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1004	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1005	then
1006
1007	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1008	if [[ ! -n $numprocs ]]
1009	then
1010	printf "\n"
1011	printf "\n +++ option \"-K parallel\" requires additional specification"
1012	printf "\n of the number of processors to be used by"
1013	printf "\n mrun-option \"-X\" or by environment-variable"
1014	printf "\n \"numprocs\" in the configuration file"
1015	locat=numprocs; (( iec = 0 )); exit
1016	fi
1017
1018	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1019	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1020	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1021	then
1022	printf "\n"
1023	printf "\n +++ option \"-T\" (tasks per node) is missing"
1024	printf "\n set -T option or define tasks_per_node in the config file"
1025	locat=tasks_per_node; (( iec = 0 )); exit
1026	fi
1027
1028	if (( numprocs < tasks_per_node ))
1029	then
1030	printf "\n"
1031	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1032	printf "\n given values: -T $tasks_per_node -X $numprocs"
1033	locat=tasks_per_node; (( iec = 0 )); exit
1034	fi
1035
1036	if [[ $host != lcflow && $host != lcxt5m ]]
1037	then
1038	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1039	(( ival = $tasks_per_node ))
1040	(( pes = numprocs ))
1041	(( ii = pes / ival ))
1042	(( remaining_pes = pes - ii * ival ))
1043	if (( remaining_pes > 0 ))
1044	then
1045	printf "\n"
1046	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1047	printf "\n divisor of the total number of processors (option \"-X\")"
1048	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1049	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1050	(( nodes = nodes + 1 ))
1051	fi
1052	fi
1053
1054
1055	# SETTINGS FOR SUBJOB-COMMAND
1056	OOPT="-O $threads_per_task"
1057
1058	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1059	if [[ "$tasks_per_node" != "" ]]
1060	then
1061	TOPT="-T $tasks_per_node"
1062	fi
1063
1064	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1065	if [[ $node_usage = default ]]
1066	then
1067	if [[ $host = ibms ]]
1068	then
1069	node_usage=shared
1070	else
1071	node_usage=not_shared
1072	fi
1073	fi
1074
1075	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1076	then
1077	printf "\n"
1078	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1079	printf "\n \"shared\" or \"not_shared\""
1080	locat=tasks_per_node; (( iec = 0 )); exit
1081	fi
1082
1083	fi
1084
1085	# CHECK IF HOSTFILE EXISTS
1086	if [[ -n $hostfile ]]
1087	then
1088	if [[ ! -f $hostfile ]]
1089	then
1090	printf "\n"
1091	printf "\n +++ hostfile \"$hostfile\" does not exist"
1092	locat=hostfile; exit
1093	fi
1094	fi
1095
1096
1097	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1098	if [[ "$maximum_parallel_io_streams" = "" ]]
1099	then
1100	maximum_parallel_io_streams=$numprocs
1101	fi
1102
1103
1104	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1105	if [[ "$scp_port" != "" ]]
1106	then
1107	PORTOPT="-P $scp_port"
1108	SSH_PORTOPT="-p $scp_port"
1109	fi
1110
1111
1112	# SET DEFAULT-QUEUE, IF NOT GIVEN
1113	if [[ $queue = none ]]
1114	then
1115	case $host in
1116	(ibmh) queue=cluster;;
1117	(ibmkisti) queue=class.32plus;;
1118	(lckiaps) queue=normal;;
1119	(lckyoto) queue=ph;;
1120	(lckyuh) queue=fx-single;;
1121	(lckyut) queue=cx-single;;
1122	(lctit) queue=S;;
1123	(nech) queue=none;;
1124	(unics) queue=unics;;
1125	esac
1126	fi
1127
1128
1129	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1130	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1131	(( i = 0 ))
1132	while (( i < iin ))
1133	do
1134	(( i = i + 1 ))
1135	(( maxcycle = 0 ))
1136
1137	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1138	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1139	if [[ "${actionin[$i]}" = di ]]
1140	then
1141	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1142	# HOST ONLY
1143	eval filename=${pathin[$i]}/${endin[$i]}
1144	else
1145	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1146	# HOST ONLY
1147	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1148	fi
1149	eval pathname=${pathin[$i]}
1150
1151	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1152	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1153	then
1154	filename_input=$filename
1155	fi
1156
1157	# CHECK IF FILE EXISTS
1158	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1159	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1160	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1161	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1162	then
1163
1164	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1165	if [[ "${transin[$i]}" != "locopt" ]]
1166	then
1167	printf "\n\n +++ INPUT-file: "
1168	if [[ "${extin[$i]}" = "" ]]
1169	then
1170	printf "\n $filename"
1171	else
1172	printf "\n $filename.${extin[$i]}"
1173	fi
1174	printf "\n does not exist\n"
1175	locat=input; exit
1176	else
1177	transin[$i]="unavailable"
1178	fi
1179	else
1180
1181	# DETERMINE THE FILE'S CYCLE NUMBER
1182	ls -1 -d $filename > filelist 2>/dev/null
1183	ls -1 -d $filename.* >> filelist 2>/dev/null
1184	while read zeile
1185	do
1186	cycle=$(echo $zeile \| cut -f2 -d".")
1187	if [[ "$cycle" = "$zeile" ]]
1188	then
1189	(( icycle = 0 ))
1190	elif [[ "$cycle" = "${extin[$i]}" ]]
1191	then
1192	(( icycle = 0 ))
1193	else
1194	(( icycle = $cycle ))
1195	fi
1196	if (( icycle > maxcycle ))
1197	then
1198	(( maxcycle = icycle ))
1199	file_to_be_used=$zeile
1200	fi
1201	done <filelist
1202	rm filelist
1203
1204	# APPEND CYCLE NUMBER TO FILENAME
1205	if (( maxcycle > 0 ))
1206	then
1207	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1208	then
1209	filename=${filename}.$maxcycle.${extin[$i]}
1210	else
1211	filename=${filename}.$maxcycle
1212	fi
1213	else
1214	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1215	then
1216	filename=${filename}.${extin[$i]}
1217	fi
1218	fi
1219
1220	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1221	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1222	absnamein[$i]=$filename
1223	if (( maxcycle > 0 ))
1224	then
1225	if [[ "${actionin[$i]}" = di ]]
1226	then
1227	frelin[$i]=${endin[$i]}.$maxcycle
1228	else
1229	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1230	fi
1231	else
1232	if [[ "${actionin[$i]}" = di ]]
1233	then
1234	frelin[$i]=${endin[$i]}
1235	else
1236	frelin[$i]=${afname}${endin[$i]}
1237	fi
1238	fi
1239
1240	fi
1241	done
1242
1243	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1244	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1245	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1246	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1247	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1248	# REMOTE HOST)
1249	(( i = 0 ))
1250	while (( i < iout ))
1251	do
1252	(( i = i + 1 ))
1253	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1254	then
1255	if [[ "${actionout[$i]}" = tr ]]
1256	then
1257	actionout[$i]=""
1258	elif [[ "${actionout[$i]}" = trpe ]]
1259	then
1260	actionout[$i]=pe
1261	elif [[ "${actionout[$i]}" = tra ]]
1262	then
1263	actionout[$i]=a
1264	fi
1265	(( maxcycle = 0 ))
1266	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1267	eval catalogname=${pathout[$i]}
1268	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1269	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1270	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1271	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1272	then
1273
1274	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1275	if cat /dev/null > $filename
1276	then
1277	rm $filename
1278	else
1279
1280	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1281	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1282	if [[ ! -d $catalogname ]]
1283	then
1284	if mkdir -p $catalogname
1285	then
1286	printf "\n\n *** directory:"
1287	printf "\n $catalogname"
1288	printf "\n was created\n"
1289	else
1290	printf "\n\n +++ OUTPUT-file:"
1291	printf "\n $filename"
1292	printf "\n cannot be created, because directory does not exist"
1293	printf "\n and cannot be created either"
1294	printf "\n"
1295	locat=output ; exit
1296	fi 2>/dev/null
1297	else
1298	printf "\n\n +++ OUTPUT-file:"
1299	printf "\n $filename"
1300	printf "\n cannot be created, although directory exists"
1301	printf "\n"
1302	locat=output ; exit
1303	fi
1304	fi 2>/dev/null
1305	else
1306
1307	# DETERMINE THE CYCLE NUMBER
1308	ls -1 -d $filename > filelist 2>/dev/null
1309	ls -1 -d $filename.* >> filelist 2>/dev/null
1310	while read zeile
1311	do
1312	cycle=$(echo $zeile \| cut -f2 -d".")
1313	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1314	then
1315	(( icycle = 1 ))
1316	else
1317	(( icycle = $cycle + 1 ))
1318	fi
1319	if (( icycle > maxcycle ))
1320	then
1321	(( maxcycle = icycle ))
1322	fi
1323	done <filelist
1324	rm filelist
1325	fi
1326
1327	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1328	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1329	if [[ "${actionout[$i]}" != a ]]
1330	then
1331	if (( maxcycle > 0 ))
1332	then
1333	filename=${filename}.$maxcycle
1334	if cat /dev/null > $filename
1335	then
1336	rm $filename
1337	else
1338	printf "\n +++ OUTPUT-file:"
1339	printf "\n $filename"
1340	printf "\n cannot be created"
1341	locat=output ; exit
1342	fi
1343	fi
1344	else
1345	(( maxcycle = maxcycle - 1 ))
1346	if (( maxcycle > 0 ))
1347	then
1348	filename=${filename}.$maxcycle
1349	fi
1350	fi
1351
1352	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1353	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1354	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1355	pathout[$i]=$filename
1356	if (( maxcycle > 0 ))
1357	then
1358	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1359	else
1360	frelout[$i]=${fname}${endout[$i]}
1361	fi
1362
1363	fi
1364	done
1365
1366
1367	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1368	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1369	then
1370	if [[ "$dvr_inc" = "" ]]
1371	then
1372	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1373	printf "\n This is required for the dvrp_graphics package.\n"
1374	locat=dvr; exit
1375	fi
1376	if [[ "$dvr_lib" = "" ]]
1377	then
1378	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1379	printf "\n This is required for the dvrp_graphics package.\n"
1380	locat=dvr; exit
1381	fi
1382	fi
1383
1384
1385	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1386	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1387	if [[ "$mainprog" = "" && "$executable" = "" ]]
1388	then
1389	printf "\n +++ neither main program nor executable defined"
1390	locat=source; exit
1391	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1392	then
1393	printf "\n +++ main program as well as executable defined"
1394	locat=source; exit
1395	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1396	then
1397	do_compile=false
1398	fi
1399
1400
1401	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1402	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1403	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1404	then
1405	rm -rf SOURCES_FOR_RUN_$fname
1406	mkdir SOURCES_FOR_RUN_$fname
1407	fi
1408
1409
1410	# COLLECT ALL ROUTINES TO BE COMPILED
1411	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1412	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1413	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1414	then
1415
1416	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1417
1418	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1419	then
1420
1421	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1422	source_list=""
1423	cd $source_path
1424
1425
1426	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1427	if [[ ! -d .svn ]]
1428	then
1429	printf "\n\n +++ source directory"
1430	printf "\n \"$source_path\" "
1431	printf "\n is not under control of \"subversion\"."
1432	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1433	fi
1434
1435
1436	# LIST ALL MODIFIED SOURCE CODE FILES
1437	Filenames=""
1438	svn status > tmp_mrun
1439	while read line
1440	do
1441	firstc=`echo $line \| cut -c1`
1442	if [[ $firstc = M \|\| $firstc = "?" ]]
1443	then
1444	Name=`echo "$line" \| cut -c8-`
1445	extension=`echo $Name \| cut -d. -f2`
1446	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1447	then
1448	Filenames="$Filenames "$Name
1449	fi
1450	fi
1451	done < tmp_mrun
1452
1453
1454	# COPY FILES TO SOURCES_FOR_RUN_...
1455	for dateiname in $Filenames
1456	do
1457	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1458	source_list=$source_list"$dateiname "
1459	done
1460
1461	cd - > /dev/null
1462
1463
1464	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1465	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1466	elif [[ "$source_list" != "" && $restart_run != true ]]
1467	then
1468
1469	cd $source_path
1470
1471	for filename in $source_list
1472	do
1473
1474	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1475	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1476	then
1477	printf "\n +++ source code file: $filename"
1478	printf "\n must not contain (\"/\") "
1479	locat=source; exit
1480	fi
1481
1482	if [[ ! -f $filename ]]
1483	then
1484	printf "\n +++ source code file: $filename"
1485	printf "\n does not exist"
1486	locat=source; exit
1487	else
1488	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1489	fi
1490
1491	done
1492
1493	cd - > /dev/null
1494
1495	fi
1496
1497
1498	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1499	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1500	if [[ $restart_run != true ]]
1501	then
1502
1503	if [[ ! -f "$source_path/$mainprog" ]]
1504	then
1505	printf "\n\n +++ main program: $mainprog"
1506	printf "\n does not exist in source directory"
1507	printf "\n \"$source_path\"\n"
1508	locat=source; exit
1509	else
1510	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1511	then
1512	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1513	source_list=${mainprog}" $source_list"
1514	fi
1515	fi
1516	fi
1517
1518
1519	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1520	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1521	if [[ "$restart_run" != true ]]
1522	then
1523	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1524	if [[ ! -f $makefile ]]
1525	then
1526	printf "\n +++ file \"$makefile\" does not exist"
1527	locat=make; exit
1528	else
1529	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1530	fi
1531	fi
1532
1533
1534	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1535	if [[ $restart_run != true && "$add_source_path" != "" ]]
1536	then
1537
1538	# DOES THE DIRECTORY EXIST?
1539	if [[ ! -d $add_source_path ]]
1540	then
1541	printf "\n\n +++ WARNING: additional source code directory"
1542	printf "\n \"$add_source_path\" "
1543	printf "\n does not exist or is not a directory."
1544	printf "\n No source code will be used from this directory!\n"
1545	add_source_path=""
1546	if [[ $silent == false ]]
1547	then
1548	sleep 3
1549	fi
1550	else
1551
1552	cd $add_source_path
1553	found=false
1554
1555	Names=$(ls -1 *.f90 2>&1)
1556	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1557	Names=$(ls -1 *.F90 2>&1)
1558	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1559	Names=$(ls -1 *.F 2>&1)
1560	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1561	Names=$(ls -1 *.f 2>&1)
1562	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1563	Names=$(ls -1 *.c 2>&1)
1564	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1565
1566	cd - > /dev/null
1567	cd SOURCES_FOR_RUN_$fname
1568
1569	# COPY MAKEFILE IF EXISTING
1570	if [[ -f $add_source_path/Makefile ]]
1571	then
1572	printf "\n\n *** user Makefile from directory"
1573	printf "\n \"$add_source_path\" is used \n"
1574	if [[ $silent == false ]]
1575	then
1576	sleep 1
1577	fi
1578	cp $add_source_path/Makefile .
1579	fi
1580
1581	for dateiname in $AddFilenames
1582	do
1583	if [[ -f $dateiname ]]
1584	then
1585	printf "\n +++ source code file \"$dateiname\" found in additional"
1586	printf "\n source code directory \"$add_source_path\" "
1587	printf "\n but was also given with option \"-s\" which means that it should be taken"
1588	printf "\n from directory \"$source_path\"."
1589	locat=source; exit
1590	fi
1591
1592	cp $add_source_path/$dateiname .
1593	source_list="$source_list $dateiname"
1594
1595	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1596	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1597	then
1598	printf "\n\n +++ user file \"$dateiname\" "
1599	printf "\n is not listed in Makefile \n"
1600	locat=source; exit
1601	else
1602
1603	if [[ $found = false ]]
1604	then
1605	found=true
1606	printf "\n\n *** following user file(s) added to the"
1607	printf " files to be translated:\n "
1608	fi
1609	printf "$dateiname "
1610	if [[ $silent == false ]]
1611	then
1612	sleep 0.5
1613	fi
1614
1615	fi
1616	done
1617	[[ $found = true ]] && printf "\n"
1618	cd - > /dev/null
1619	fi
1620	fi
1621
1622
1623	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1624	# TO THE LIST OF FILES TO BE COMPILED
1625	if [[ $restart_run != true && -n $package_list ]]
1626	then
1627
1628	cd $source_path
1629
1630	for package in $package_list
1631	do
1632
1633	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1634
1635	# DETERMINE FILES BELONGING TO THE PACKAGE
1636	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1637	# THE NAME OF THE DIRECTORY
1638	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1639
1640
1641	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1642	# IF THEY ARE NOT ALREADY PART OF THE LIST
1643	for source_list_name in $package_source_list
1644	do
1645	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1646	then
1647
1648	# ONLY TAKE FILES WITH VALID SUFFIX
1649	ending=`echo $source_list_name \| cut -f2 -d.`
1650	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1651	then
1652	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1653	source_list="$source_list $source_list_name"
1654	fi
1655	fi
1656	done
1657	done
1658
1659	cd - > /dev/null
1660	fi
1661
1662	fi # do_compile=true
1663
1664
1665	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1666	# AND SET PRE-PROCESSOR DIRECTIVES
1667	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1668	then
1669
1670	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1671	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1672	then
1673	cpp_options="${cpp_options},-D__ibm=__ibm"
1674	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1675	then
1676	cpp_options="$cpp_options -D__nec"
1677	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1678	then
1679	cpp_options="$cpp_options -D__lc"
1680	else
1681	cpp_options="$cpp_options -D__$localhost"
1682	fi
1683
1684	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1685	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1686	then
1687	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1688	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1689	else
1690	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1691	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1692	fi
1693
1694	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1695	if [[ -n $package_list ]]
1696	then
1697	for package in $package_list
1698	do
1699	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1700	then
1701	if [[ $package != "dvrp_graphics+1PE" ]]
1702	then
1703	cpp_options="${cpp_options},-D__$package=__$package"
1704	else
1705	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1706	export use_seperate_pe_for_dvrp_output=true
1707	fi
1708	else
1709	if [[ $package != "dvrp_graphics+1PE" ]]
1710	then
1711	cpp_options="$cpp_options -D__$package"
1712	else
1713	cpp_options="$cpp_options -D__dvrp_graphics"
1714	export use_seperate_pe_for_dvrp_output=true
1715	fi
1716	fi
1717	done
1718	fi
1719
1720	# SET DIRECTIVES GIVEN BY OPTION -D
1721	if [[ -n $cpp_opts ]]
1722	then
1723	for popts in $cpp_opts
1724	do
1725	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1726	then
1727	cpp_options="${cpp_options},-D__$popts=__$popts"
1728	else
1729	cpp_options="$cpp_options -D__$popts"
1730	fi
1731	done
1732	fi
1733
1734	else
1735
1736
1737	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1738	if [[ $do_remote = false ]]
1739	then
1740	if [[ ! -f $executable ]]
1741	then
1742	printf "\n +++ executable file: $executable"
1743	printf "\n does not exist"
1744	locat=executable; exit
1745	fi
1746	fi
1747	fi
1748
1749
1750	# DETERMINE THE JOB MODE
1751	if [[ "$ENVIRONMENT" = BATCH ]]
1752	then
1753	jobmo=BATCH
1754	else
1755	jobmo=INTERACTIVE
1756	fi
1757
1758
1759	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1760	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1761	then
1762	printf "\n +++ no interactive runs allowed on host \"$host\" "
1763	printf "\n please submit batch job using mrun option \"-b\" \n"
1764	locat=normal; exit
1765	fi
1766
1767
1768	# CHECK, IF USER DEFINED A COMPILER
1769	if [[ "$compiler_name" = "" ]]
1770	then
1771
1772	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1773	locat=compiler_name; exit
1774
1775	fi
1776
1777
1778	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1779	kennung=$RANDOM
1780	if [[ "$tmp_user_catalog" = "" ]]
1781	then
1782	if [[ $localhost = ibmh ]]
1783	then
1784	tmp_user_catalog=$SCRATCH
1785	elif [[ $localhost = nech ]]
1786	then
1787	tmp_user_catalog=$WRKSHR
1788	else
1789	tmp_user_catalog=/tmp
1790	fi
1791	fi
1792	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1793
1794
1795	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1796	if [[ "$tmp_data_catalog" = "" ]]
1797	then
1798	if [[ $localhost = nech ]]
1799	then
1800	tmp_data_catalog=$WRKSHR/mrun_restart_data
1801	else
1802	tmp_data_catalog=/tmp/mrun_restart_data
1803	fi
1804	fi
1805
1806
1807	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1808	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1809	then
1810	eval fopts=\"$fopts\"
1811	eval lopts=\"$lopts\"
1812	fi
1813
1814
1815
1816	# DETERMINE COMPILE- AND LINK-OPTIONS
1817	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1818	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1819	ROPTS="$ropts"
1820	# 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 ]]
1821	# then
1822	XOPT="-X $numprocs"
1823	# fi
1824
1825
1826
1827	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1828	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1829	done=false
1830	while [[ $done = false ]]
1831	do
1832	cputime=$cpumax
1833	if (( $cputime == 0 ))
1834	then
1835	if [[ $do_batch = true ]]
1836	then
1837	printf "\n +++ cpu-time is undefined"
1838	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1839	printf "\n >>> "
1840	read cputime 1>/dev/null 2>&1
1841	else
1842	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1843	fi
1844	else
1845	done=true
1846	fi
1847	cpumax=$cputime
1848	done
1849
1850	(( minuten = cputime / 60 ))
1851	(( sekunden = cputime - minuten * 60 ))
1852
1853
1854	# CHECK THE MEMORY DEMAND
1855	if [[ $do_batch = true ]]
1856	then
1857	done=false
1858	while [[ $done = false ]]
1859	do
1860	if (( memory == 0 ))
1861	then
1862	printf "\n +++ memory demand is undefined"
1863	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1864	printf "\n >>> "
1865	read memory 1>/dev/null 2>&1
1866	else
1867	done=true
1868	fi
1869	done
1870	fi
1871
1872
1873	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1874	if [[ $do_remote = true && -z $remote_username ]]
1875	then
1876	while [[ -z $remote_username ]]
1877	do
1878	printf "\n +++ username on remote host \"$host\" is undefined"
1879	printf "\n >>> Please type username:"
1880	printf "\n >>> "
1881	read remote_username
1882	done
1883	mc="$mc -u$remote_username"
1884	fi
1885
1886	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1887	if [[ "$login_init_cmd" != "" ]]
1888	then
1889	export init_cmds="${login_init_cmd};"
1890	fi
1891
1892
1893	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1894	if [[ "$modules" != "" ]]
1895	then
1896	if [[ $host = lctit ]]
1897	then
1898	export module_calls=". $modules"
1899	else
1900	export module_calls="module load ${modules};"
1901	fi
1902	fi
1903
1904
1905
1906	# OUTPUT OF THE MRUN-HEADER
1907	calltime=$(date)
1908	printf "\n"
1909	printf "#------------------------------------------------------------------------# \n"
1910	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1911	printf "\| \| \n"
1912	spalte1="called on:"; spalte2=$localhost_realname
1913	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1914	if [[ $do_remote = true ]]
1915	then
1916	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1917	else
1918	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1919	fi
1920	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1921	if [[ -n $numprocs ]]
1922	then
1923	if [[ $run_coupled_model = false ]]
1924	then
1925	spalte1="number of PEs:"; spalte2=$numprocs
1926	else
1927	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1928	fi
1929	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1930	fi
1931	if [[ -n $tasks_per_node ]]
1932	then
1933	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1934	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1935	if (( remaining_pes > 0 ))
1936	then
1937	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1938	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1939	fi
1940	fi
1941	if [[ $maximum_parallel_io_streams != $numprocs ]]
1942	then
1943	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1944	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1945	fi
1946	if [[ $use_openmp = true ]]
1947	then
1948	spalte1="threads per task:"; spalte2="$threads_per_task"
1949	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1950	fi
1951	printf "\| \| \n"
1952	if [[ $do_compile = true ]]
1953	then
1954	if [[ "$mopts" != "" ]]
1955	then
1956	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1957	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1958	zeile=$(echo "$mopts" \| cut -c46-)
1959	while [[ "$zeile" != "" ]]
1960	do
1961	spalte1=""
1962	spalte2=$(echo "$zeile" \| cut -c-45)
1963	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1964	zeile=$(echo "$zeile" \| cut -c46-)
1965	done
1966	fi
1967
1968	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1969	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1970	zeile=$(echo "$cpp_options" \| cut -c46-)
1971	while [[ "$zeile" != "" ]]
1972	do
1973	spalte1=""
1974	spalte2=$(echo "$zeile" \| cut -c-45)
1975	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1976	zeile=$(echo "$zeile" \| cut -c46-)
1977	done
1978
1979	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1980	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1981	zeile=$(echo "$fopts" \| cut -c46-)
1982	while [[ "$zeile" != "" ]]
1983	do
1984	spalte1=""
1985	spalte2=$(echo "$zeile" \| cut -c-45)
1986	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1987	zeile=$(echo "$zeile" \| cut -c46-)
1988	done
1989
1990	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
1991	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1992	zeile=$(echo "$lopts" \| cut -c46-)
1993	while [[ "$zeile" != "" ]]
1994	do
1995	spalte1=""
1996	spalte2=$(echo "$zeile" \| cut -c-45)
1997	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1998	zeile=$(echo "$zeile" \| cut -c46-)
1999	done
2000
2001	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2002	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2003	zeile=$(echo "$modules" \| cut -c46-)
2004	while [[ "$zeile" != "" ]]
2005	do
2006	spalte1=""
2007	spalte2=$(echo "$zeile" \| cut -c-45)
2008	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2009	zeile=$(echo "$zeile" \| cut -c46-)
2010	done
2011
2012	spalte1="main program:"; spalte2=$mainprog
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	else
2015	spalte1=executable:; spalte2=$executable
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	fi
2018	printf "\| \| \n"
2019	spalte1="base name of files:"; spalte2=$fname
2020	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2021	if [[ $fname != $afname ]]
2022	then
2023	spalte1="base name of input files:"; spalte2=$afname
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	fi
2026	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2028	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030
2031	if [[ "$ocean_file_appendix" = true ]]
2032	then
2033	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2034	fi
2035
2036	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2037	then
2038	spalte1="memory demand / PE":; spalte2="$memory MB"
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2041	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2042	fi
2043
2044	if [[ $do_compile = true ]]
2045	then
2046	printf "\| \| \n"
2047	printf "\| Files to be compiled: \| \n"
2048	zeile=$source_list
2049	while [[ "$zeile" != "" ]]
2050	do
2051	linestart=$(echo $zeile \| cut -c-70)
2052	printf "\| %-70s \| \n" "$linestart"
2053	zeile=$(echo "$zeile" \| cut -c71-)
2054	done
2055	fi
2056	printf "#------------------------------------------------------------------------#"
2057
2058
2059
2060	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2061	if [[ $do_trace = true ]]
2062	then
2063	(( i = 0 ))
2064	while (( i < iin ))
2065	do
2066	(( i = i + 1 ))
2067	if (( i == 1 ))
2068	then
2069	printf "\n\n >>> INPUT-file assignments:\n"
2070	fi
2071	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2072	done
2073	(( i = 0 ))
2074	while (( i < iout ))
2075	do
2076	(( i = i + 1 ))
2077	if (( i == 1 ))
2078	then
2079	printf "\n\n >>> OUTPUT-file assignments:\n"
2080	fi
2081	printf "\n ${localout[$i]} : ${pathout[$i]}"
2082	done
2083	(( i = 0 ))
2084	while (( i < iic ))
2085	do
2086	(( i = i + 1 ))
2087	if (( i == 1 ))
2088	then
2089	printf "\n\n >>> INPUT-commands:\n"
2090	fi
2091	printf "\n ${in_command[$i]}"
2092	done
2093	(( i = 0 ))
2094	while (( i < ioc ))
2095	do
2096	(( i = i + 1 ))
2097	if (( i == 1 ))
2098	then
2099	printf "\n\n >>> OUTPUT-commands:\n"
2100	fi
2101	printf "\n ${out_command[$i]}"
2102	done
2103	fi
2104
2105
2106	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2107	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2108	then
2109	antwort=dummy
2110	printf "\n\n"
2111	printf " >>> everything o.k. (y/n) ? "
2112	while read antwort
2113	do
2114	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2115	then
2116	printf " >>> everything o.k. (y/n) ? "
2117	else
2118	break
2119	fi
2120	done
2121	if [[ $antwort = n \|\| $antwort = N ]]
2122	then
2123	locat=user_abort; (( iec = 0 )); exit
2124	fi
2125	if [[ $do_batch = true ]]
2126	then
2127	printf " >>> batch-job will be created and submitted"
2128	else
2129	printf " >>> MRUN will now continue to execute on this machine"
2130	fi
2131	fi
2132
2133
2134	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2135	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2136	check_depository="${working_directory}/trunk/UTIL"
2137	check_sources="${working_directory}/tmp_check_namelist_files"
2138	skip_check=false
2139
2140	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2141	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2142	then
2143	skip_check=true
2144	reason="run on remote host or parameter file check has not been compiled."
2145	fi
2146	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2147	then
2148	skip_check=true
2149	reason="parameter file check has not been compiled."
2150	fi
2151
2152	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2153	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2154	then
2155	skip_check=true
2156	reason="serial run."
2157	fi
2158
2159	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2160	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2161	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2162	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2163	if [[ $check_namelist_files == false ]]
2164	then
2165	skip_check=true
2166	reason="-z option set."
2167	fi
2168
2169	if [[ $fromhost != $localhost ]]
2170	then
2171	skip_check=true
2172	reason="submitting host is local host."
2173	fi
2174
2175	if [[ $run_coupled_model == true ]]
2176	then
2177	skip_check=true
2178	reason="coupled run."
2179	fi
2180
2181	if [[ $restart_run == true ]]
2182	then
2183	skip_check=true
2184	reason="restart run."
2185	fi
2186
2187	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2188	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2189	last_char=`echo $filename_input \| cut -c $last_char_int`
2190	if [[ "$last_char" == "f" ]]
2191	then
2192	skip_check=true
2193	reason="restart run."
2194	fi
2195
2196	if [[ $skip_check == false ]]
2197	then
2198	tmp_check=${working_directory}/tmp_check
2199
2200	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2201	# NOT NECESSARILY REQUIRED
2202	line=""
2203	found=false
2204	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2205	while read line1
2206	do
2207	line="$line1"
2208	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2209	then
2210	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2211	found=true
2212	fi
2213	done < $tmp_check
2214
2215	if [[ $found = false ]]
2216	then
2217	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2218	fi
2219
2220	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2221	# NOT NECESSARILY REQUIRED
2222	line=""
2223	found=false
2224	grep "NUDGING_DATA" $config_file > $tmp_check
2225	while read line1
2226	do
2227	line="$line1"
2228	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2229	then
2230	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2231	found=true
2232	fi
2233	done < $tmp_check
2234
2235	if [[ $found = false ]]
2236	then
2237	printf "\n +++ no NUDGING list entry found in the configuration file."
2238	fi
2239
2240	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2241	# NOT NECESSARILY REQUIRED
2242	line=""
2243	found=false
2244	grep "LSF_DATA" $config_file > $tmp_check
2245	while read line1
2246	do
2247	line="$line1"
2248	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2249	then
2250	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2251	found=true
2252	fi
2253	done < $tmp_check
2254
2255	if [[ $found = false ]]
2256	then
2257	printf "\n +++ no LSF list entry found in the configuration file."
2258	fi
2259
2260	rm -rf ${working_directory}/tmp_check
2261
2262	# CHECK IF THE P3DF FILE MUST BE CHECKED
2263	for item in $input_list
2264	do
2265	if [[ "$item" == "restart" ]]
2266	then
2267	check_restart=1
2268	else
2269	check_restart=0
2270	fi
2271	done
2272
2273	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2274	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2275	then
2276	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2277	locat=check_namelist; exit
2278	fi
2279
2280	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2281	if [[ $check_restart == 1 ]]
2282	then
2283
2284	filenamef="${filename_input}f"
2285	if [[ ! -f $filenamef ]]
2286	then
2287	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2288	check_restart=0
2289	answer=dummy
2290	printf "\n\n"
2291
2292	if [[ $silent == false ]]
2293	then
2294	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2295	do
2296	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2297	read answer
2298	done
2299	if [[ $answer = a \|\| $answer = A ]]
2300	then
2301	printf "\n +++ Aborting...."
2302	locat=normal; exit
2303	fi
2304	fi
2305	else
2306	check_restart=1
2307	fi
2308	fi
2309
2310	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2311	mkdir $check_sources
2312	cd $check_sources
2313
2314
2315	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2316	if [[ -d $add_source_path ]]
2317	then
2318	printf "\n\n *** copying files from $check_depository"
2319	cp $check_depository/check_namelist_files.tar ./
2320
2321	printf "\n\n *** untar of makefile and source files in $check_sources"
2322	tar -xf check_namelist_files.tar > /dev/null 2>&1
2323
2324	printf "\n\n *** adding user code."
2325	cp $add_source_path/* ./
2326	touch check_namelist_files.f90
2327
2328	# GET COMPILER OPTIONS AND PERFORM MAKE
2329	printf "\n\n *** compiling code if necessary...\n"
2330
2331	# workaround for batch jobs on local machine (lcxe6)
2332	if [[ $do_batch == true && $do_remote == false ]]
2333	then
2334	eval $init_cmds
2335	fi
2336
2337	# GET CHECK OPTIONS
2338	line=""
2339	found=false
2340
2341	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2342
2343	while read line1
2344	do
2345
2346	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2347	then
2348	line="$line1"
2349	fi
2350
2351	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2352	then
2353	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2354	line="$line "
2355	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'`
2356	found=true
2357	fi
2358
2359	done < $tmp_check
2360	copts_check="$copts_check -D__check -D__parallel"
2361
2362	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2363
2364	# GET MAKE OUTPUT
2365	if [[ $? != 0 ]]
2366	then
2367	printf "\n +++ error during make."
2368	answer=dummy
2369	printf "\n\n"
2370	if [[ $silent == false ]]
2371	then
2372	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2373	do
2374	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2375	read answer
2376	done
2377	if [[ $answer = a \|\| $answer = A ]]
2378	then
2379	printf "\n +++ Aborting..."
2380	rm -rf $check_sources
2381	locat=normal; exit
2382	else
2383	skip_check=true
2384	fi
2385	else
2386	skip_check=true
2387	fi
2388	fi
2389	else
2390	cp $PALM_BIN/check_namelist_files.x ./
2391	fi
2392
2393	cp $filename_input ./PARIN
2394	if [[ $check_restart == 1 ]]
2395	then
2396	cp $filenamef ./PARINF
2397	fi
2398
2399	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2400	then
2401	printf "\n *** adding topography data"
2402	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2403
2404	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2405	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2406	# WHICH REQUIRE SUFFICIENT MEMORY
2407	ulimit -s unlimited
2408	fi
2409
2410	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2411	then
2412	printf "\n *** adding nudging data"
2413	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2414	fi
2415
2416	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2417	then
2418	printf "\n *** adding large scale forcing data"
2419	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2420	fi
2421
2422	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2423	cat > ENVPAR << %%END%%
2424	&envpar run_identifier = '$fname', host = '$host',
2425	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2426	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2427	maximum_cpu_time_allowed = ${cpumax}.,
2428	revision = '$global_revision',
2429	local_dvrserver_running = $local_dvrserver_running /
2430
2431	%%END%%
2432
2433	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2434	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2435	then
2436	printf "\n +++ WARNING: check_namelist_files.x not found."
2437	answer=dummy
2438	printf "\n\n"
2439
2440	if [[ $silent == false ]]
2441	then
2442	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2443	do
2444	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2445	read answer
2446	done
2447	if [[ $answer = a \|\| $answer = A ]]
2448	then
2449	printf "\n +++ Aborting..."
2450	rm -rf $check_sources
2451	locat=normal; exit
2452	else
2453	printf "\n *** skipping parameter file check."
2454	fi
2455	fi
2456
2457	elif [[ $skip_check == false ]]
2458	then
2459	# STARTING THE PARAMETER FILE CHECK
2460	printf "\n\n *** starting parameter file check..."
2461
2462	# CHECKING THE P3D FILE
2463	printf "\n\n (1) checking $filename_input"
2464	echo "$numprocs 0 0" > VARIN
2465	errors=`./check_namelist_files.x < VARIN 2>&1`
2466
2467	check_error=false
2468	if [[ "$errors" == "" ]]
2469	then
2470	printf " --> o.k."
2471	else
2472	printf " --> failed."
2473	check_error=true
2474	printf "\n\n $errors"
2475	fi
2476
2477	# CHECKING THE PD3F FILE IF NECESSARY
2478	if [[ $check_restart == 1 && $check_error == false ]]
2479	then
2480	printf "\n\n (2) checking $filenamef"
2481
2482	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2483	# IN &INIPAR LIST
2484	found=false
2485	cat PARINF \| while read line
2486	do
2487	line=$(echo $line\|sed 's/ //g')
2488	if [[ $line == "&inipar" ]]
2489	then
2490	start_search=true
2491	fi
2492
2493	if [[ $start_search == true ]]
2494	then
2495	if [[ $line == "initializing_actions='read_restart_data'" ]]
2496	then
2497	found=true
2498	break
2499	fi
2500	fi
2501
2502	if [[ $line == "/" ]]
2503	then
2504	start_search=false
2505	fi
2506
2507	done
2508
2509	if [[ $found = false ]]
2510	then
2511	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2512	printf "\n in &inipar list in $fname$p3df_suffix."
2513	rm -rf $check_sources
2514	locat=check_namelist; exit
2515	fi
2516
2517	# READ max_user_pr FROM FILES
2518	if [[ -f parin_for_check ]]
2519	then
2520	read max_pr_user < parin_for_check
2521	else
2522	max_user_pr=0
2523	fi
2524
2525	echo "$numprocs 1 $max_pr_user" > VARIN
2526	errors=`./check_namelist_files.x < VARIN 2>&1`
2527
2528	if [[ "$errors" == "" ]]
2529	then
2530	printf " --> o.k."
2531	else
2532	printf " --> failed."
2533	check_error=true
2534	printf "\n\n $errors"
2535	fi
2536	fi
2537
2538	# REPORT ERRORS AND CONTINUE/EXIT
2539	if [[ $check_error == true ]]
2540	then
2541	printf "\n +++ errors found in the parameter file!\n"
2542	answer=dummy
2543	printf "\n\n"
2544
2545	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2546	do
2547	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2548	read answer
2549	done
2550
2551	if [[ $answer = a \|\| $answer = A ]]
2552	then
2553	printf "\n +++ Aborting..."
2554	rm -rf $check_sources
2555	locat=normal; exit
2556	fi
2557	else
2558	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2559	fi
2560	rm -rf $check_sources
2561	fi
2562	else
2563	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2564	fi
2565
2566	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2567	rm -rf $check_sources
2568	cd $working_directory
2569
2570
2571	# DETERMINE PATH FOR MAKE DEPOSITORY
2572	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2573	then
2574
2575	line=""
2576	grep "%depository_path" $config_file > tmp_mrun
2577	while read line
2578	do
2579	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2580	then
2581	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2582	then
2583	global_depository_path=`echo $line \| cut -d" " -s -f2`
2584	fi
2585	fi
2586	done < tmp_mrun
2587
2588	line=""
2589	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2590	while read line
2591	do
2592	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2593	then
2594	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2595	then
2596	local_depository_path=`echo $line \| cut -d" " -s -f2`
2597	fi
2598	fi
2599	done < tmp_mrun
2600
2601	if [[ "$local_depository_path" = "" ]]
2602	then
2603	if [[ "$global_depository_path" != "" ]]
2604	then
2605	local_depository_path=$global_depository_path
2606	else
2607	printf "\n\n +++ no depository path found in configuration file"
2608	printf "\n for local host \"$localhost\" "
2609	printf "\n please set \"\%depository_path\" in configuration file\n"
2610	locat=config_file; exit
2611	fi
2612	fi
2613	eval local_depository_path=$local_depository_path
2614	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2615	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2616
2617
2618	basename=`echo $mainprog \| cut -f1 -d"."`
2619	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2620	if [[ ! -f $make_depository ]]
2621	then
2622	printf "\n"
2623	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2624	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2625	fi
2626
2627	fi
2628
2629
2630	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2631	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2632	if [[ $do_batch = false ]]
2633	then
2634
2635
2636	# CREATE THE TEMPORARY WORKING DIRECTORY
2637	mkdir -p $TEMPDIR
2638	chmod go+rx $TEMPDIR
2639	tmpcreate=true
2640
2641
2642	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2643	# INTO THE TEMPORARY WORKING DIRECTORY
2644	if [[ $do_compile = true ]]
2645	then
2646
2647	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2648	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2649	if [[ $localhost = nech ]]
2650	then
2651	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2652	if mkdir -p $TEMPDIR_COMPILE
2653	then
2654	printf "\n *** \"$TEMPDIR_COMPILE\" "
2655	printf "\n is generated as temporary directory for cross compiling\n"
2656	else
2657	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2658	printf "\n needed for cross compilation failed"
2659	locat=compile
2660	exit
2661	fi
2662	else
2663	TEMPDIR_COMPILE=$TEMPDIR
2664	fi
2665
2666	cp $make_depository $TEMPDIR_COMPILE
2667	cd $TEMPDIR_COMPILE
2668	tar -xf $make_depository > /dev/null 2>&1
2669	cd - > /dev/null
2670
2671	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2672	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2673	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2674	then
2675	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2676	else
2677	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2678	fi
2679
2680	else
2681
2682	cp $executable ${TEMPDIR}/a.out
2683
2684	fi
2685
2686
2687	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2688	cd $TEMPDIR
2689	printf "\n *** changed to temporary directory: $TEMPDIR"
2690
2691
2692	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2693	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2694	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2695	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2696	(( i = 0 ))
2697	while (( i < iout ))
2698	do
2699	(( i = i + 1 ))
2700	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2701	then
2702	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2703	else
2704	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2705	fi
2706	done
2707
2708
2709	# IF REQUIRED, START WITH COMPILING
2710	if [[ $do_compile = true ]]
2711	then
2712
2713
2714	if [[ -f a.out ]]
2715	then
2716
2717	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2718	printf "\n\n\n *** executable a.out found"
2719	printf "\n no compilation required \n"
2720
2721	else
2722
2723	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2724	printf "\n\n\n *** compilation starts \n$dashes\n"
2725	printf " *** compilation with make using following options:\n"
2726	printf " make depository: $make_depository"
2727	if [[ "$mopts" != "" ]]
2728	then
2729	printf " make options: $mopts\n"
2730	fi
2731	printf " compilername: $compiler_name\n"
2732	printf " compiler options: $fopts\n"
2733	printf " preprocessor directives: $cpp_options \n"
2734	printf " linker options: $lopts \n"
2735	if [[ "$modules" != "" ]]
2736	then
2737	printf " modules to be load: $modules \n"
2738	fi
2739	printf " source code files: $source_list \n"
2740
2741	if [[ $localhost = nech ]]
2742	then
2743	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\" "
2744	cp $TEMPDIR_COMPILE/a.out .
2745	[[ $? != 0 ]] && compile_error=true
2746	rm -rf $TEMPDIR_COMPILE
2747	elif [[ $localhost = ibmh ]]
2748	then
2749	printf " compiler is called via ssh on \"plogin1\" \n"
2750	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\" "
2751	[[ ! -f a.out ]] && compile_error=true
2752	continue # STATUS=1, IF a.out EXISTS
2753	elif [[ $localhost = lcflow ]]
2754	then
2755	printf " compiler is called via ssh on \"flow\" \n"
2756	/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\" "
2757	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2758	[[ "$check_for_file" = "" ]] && compile_error=true
2759	continue # STATUS=1, IF a.out EXISTS
2760	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2761	then
2762	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2763	else
2764	[[ "$init_cmds" != "" ]] && eval $init_cmds
2765	[[ "$module_calls" != "" ]] && eval $module_calls
2766	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2767	fi
2768
2769	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2770	then
2771	printf "\n +++ error occured while compiling or linking"
2772	locat=compile
2773
2774	exit
2775	else
2776	printf "$dashes\n *** compilation finished \n"
2777	fi
2778
2779	fi
2780
2781	fi
2782
2783
2784	# PROVIDE THE INPUT FILES
2785	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2786	(( i = 0 ))
2787	while (( i < iin ))
2788	do
2789	(( i = i + 1 ))
2790	if (( i == 1 ))
2791	then
2792	printf "\n\n *** providing INPUT-files:\n$dashes"
2793	fi
2794
2795
2796	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2797	if [[ "${transin[$i]}" = unavailable ]]
2798	then
2799	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2800	then
2801	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2802	printf "\n is not available!"
2803	else
2804	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2805	printf "\n is not available!"
2806	fi
2807	continue
2808	fi
2809
2810	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2811	files_for_pes=false; datentyp=file
2812	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2813	then
2814	files_for_pes=true; datentyp=directory
2815	actionin[$i]=""
2816	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2817	then
2818	actionin[$i]=""
2819	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2820	then
2821	files_for_pes=true; datentyp=directory
2822	actionin[$i]="ar"
2823	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2824	then
2825	actionin[$i]="ar"
2826	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2827	then
2828	files_for_pes=true; datentyp=directory
2829	actionin[$i]="fl"
2830	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2831	then
2832	actionin[$i]="fl"
2833	fi
2834
2835	if [[ $files_for_pes = true ]]
2836	then
2837	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2838	else
2839	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2840	fi
2841
2842	# INPUT-FILE FOR A RESTART RUN.
2843	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2844	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2845	if [[ "${actionin[$i]}" = fl ]]
2846	then
2847	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2848	if [[ $files_for_pes = false ]]
2849	then
2850	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2851	then
2852	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2853	got_tmp[$i]=true
2854	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2855	then
2856	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2857	printf "\n *** trying to use backup copy in \"$WORK\" "
2858	cp $WORK/${frelin[$i]} ${localin[$i]}
2859	else
2860	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2861	printf "\n or \"$tmp_data_catalog\" does not exist!"
2862	printf "\n *** trying to get copy from archive"
2863	actionin[$i]=ar
2864	fi
2865	else
2866	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2867	then
2868	mkdir ${localin[$i]}
2869	cd $tmp_data_catalog/${frelin[$i]}
2870	for file in $(ls *)
2871	do
2872	ln $file $TEMPDIR/${localin[$i]}
2873	done
2874	cd $TEMPDIR
2875	got_tmp[$i]=true
2876	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2877	then
2878	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2879	printf "\n *** trying to use backup copy in \"$WORK\" "
2880	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2881	else
2882	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2883	printf "\n or \"$tmp_data_catalog\" does not exist!"
2884	printf "\n *** trying to get copy from archive"
2885	actionin[$i]=ar
2886	fi
2887	fi
2888	fi
2889
2890
2891	# FILE IS STORED ON THE ARCHIVE SYSTEM
2892	if [[ "${actionin[$i]}" = ar ]]
2893	then
2894
2895	if [[ $files_for_pes = false ]]
2896	then
2897	printf "\n file will be restored from archive-system ($archive_system)!"
2898	else
2899	printf "\n directory will be restored from archive-system ($archive_system)!"
2900	fi
2901
2902	file_restored=false
2903
2904	if [[ $archive_system = asterix ]]
2905	then
2906	do_stagein=true
2907	(( stagein_anz = 0 ))
2908	while [[ $do_stagein = true ]]
2909	do
2910	if [[ $files_for_pes = false ]]
2911	then
2912	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2913	else
2914	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2915	fi
2916	cat STAGEIN_OUTPUT
2917	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2918	then
2919	file_restored=true
2920	do_stagein=false
2921	else
2922	(( stagein_anz = stagein_anz + 1 ))
2923	if (( stagein_anz == 10 ))
2924	then
2925	printf "\n +++ stagein stoped after 10 tries"
2926	locat=stage
2927	exit
2928	fi
2929	printf "\n +++ restoring from archive failed, trying again:"
2930	sleep 900
2931	fi
2932	done
2933	elif [[ $archive_system = DMF ]]
2934	then
2935	if [[ $files_for_pes = false ]]
2936	then
2937	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2938	locat=DMF
2939	exit
2940	else
2941	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2942	cp -r $ARCHIVE/${frelin[$i]} $PWD
2943	file_restored=true
2944	fi
2945	elif [[ $archive_system = tivoli ]]
2946	then
2947	if [[ $files_for_pes = false ]]
2948	then
2949	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2950	else
2951	(( inode = 0 ))
2952	while (( inode < nodes ))
2953	do
2954	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2955	(( inode = inode + 1 ))
2956	done
2957	fi
2958	file_restored=true
2959	elif [[ $archive_system = ut ]]
2960	then
2961	if [[ $files_for_pes = false ]]
2962	then
2963	cp $UT/${frelin[$i]} .
2964	else
2965	(( inode = 0 ))
2966	while (( inode < nodes ))
2967	do
2968	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2969	(( inode = inode + 1 ))
2970	done
2971	fi
2972	file_restored=true
2973	else
2974	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2975	locat=rearchive
2976	exit
2977	fi
2978
2979	if [[ $file_restored = true ]]
2980	then
2981
2982	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2983	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2984	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2985	if [[ $files_for_pes = false ]]
2986	then
2987	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2988	else
2989	mkdir $tmp_data_catalog/${frelin[$i]}
2990	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2991	fi
2992	got_tmp[$i]=true
2993
2994	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2995	mv ${frelin[$i]} ${localin[$i]}
2996
2997	fi
2998	fi
2999
3000
3001	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3002	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3003	then
3004
3005	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3006	then
3007
3008	# FILE COPIES ARE PROVIDED FOR ALL CORES
3009	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3010	printf "\n file will be provided for $numprocs processors"
3011	mkdir ${localin[$i]}
3012	ival=$numprocs
3013	(( ii = 0 ))
3014	while (( ii <= ival-1 ))
3015	do
3016	if (( ii < 10 ))
3017	then
3018	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3019	elif (( ii < 100 ))
3020	then
3021	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3022	elif (( ii < 1000 ))
3023	then
3024	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3025	else
3026	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3027	fi
3028	(( ii = ii + 1 ))
3029	done
3030
3031	else
3032
3033	if [[ $files_for_pes = true ]]
3034	then
3035
3036	# PROVIDE FILES FOR EACH CORE
3037	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3038	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3039	printf "\n providing $numprocs files for the respective processors"
3040	mkdir ${localin[$i]}
3041	if [[ $link_local_input = true ]]
3042	then
3043	printf " using ln -f\n"
3044	cd ${absnamein[$i]}
3045	for file in $(ls *)
3046	do
3047	ln -f $file ${localin[$i]}
3048	done
3049	cd $TEMPDIR
3050	fi
3051
3052	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3053	if [[ ! -f "${localin[$i]}/_0000" ]]
3054	then
3055	if [[ $link_local_input = true ]]
3056	then
3057	printf " ln failed for .../_0000, using cp...\n"
3058	fi
3059	cp -r ${absnamein[$i]}/* ${localin[$i]}
3060	fi
3061
3062	else
3063
3064	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3065	if [[ $link_local_input = true ]]
3066	then
3067	printf " using ln -f\n"
3068	ln -f ${absnamein[$i]} ${localin[$i]}
3069	fi
3070	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3071	if [[ ! -f "${localin[$i]}" ]]
3072	then
3073	if [[ $link_local_input = true ]]
3074	then
3075	printf " ln failed, using cp...\n"
3076	fi
3077	cp ${absnamein[$i]} ${localin[$i]}
3078	fi
3079	fi
3080	fi
3081	fi
3082
3083	done
3084	if (( i != 0 ))
3085	then
3086	printf "\n$dashes\n *** all INPUT-files provided \n"
3087	fi
3088
3089
3090	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3091	(( i = 0 ))
3092	while (( i < iic ))
3093	do
3094	(( i = i + 1 ))
3095	if (( i == 1 ))
3096	then
3097	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3098	fi
3099	printf "\n >>> ${in_command[$i]}"
3100	eval ${in_command[$i]}
3101	if (( i == iic ))
3102	then
3103	printf "\n$dashes\n"
3104	fi
3105	done
3106
3107
3108	# SET THE REMAINING CPU-TIME
3109	cpurest=${cpumax}.
3110
3111
3112	# START DVR STREAMING SERVER
3113	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3114	then
3115	if [[ "$dvr_server" != "" ]]
3116	then
3117
3118	printf "\n\n *** preparing the dvr streaming server configuration file"
3119
3120	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3121	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3122	if [[ "$running_dvrserver_id" != "" ]]
3123	then
3124
3125	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3126	printf "\n This server is used instead starting a new one!"
3127	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3128
3129	else
3130
3131	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3132	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3133	then
3134	cp ${PALM_BIN}/.dvrserver.config .
3135
3136	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3137	user_id=`id -u`
3138	group_id=`id -g`
3139
3140	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3141	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3142	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3143	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3144	mv .dvrserver.3 .dvrserver.config
3145	rm .dvrserver.1 .dvrserver.2
3146
3147	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3148	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3149	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3150	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3151	local_dvrserver_running=.TRUE.
3152	else
3153	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3154	printf "\n \"$PALM_BIN\" "
3155	locat=dvr
3156	exit
3157	fi
3158
3159	fi
3160
3161	else
3162	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3163	fi
3164	fi
3165
3166
3167	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3168	# (FILE ENVPAR WILL BE READ BY PALM)
3169	cat > ENVPAR << %%END%%
3170	&envpar run_identifier = '$fname', host = '$localhost',
3171	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3172	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3173	maximum_cpu_time_allowed = ${cpumax}.,
3174	revision = '$global_revision',
3175	local_dvrserver_running = $local_dvrserver_running /
3176
3177	%%END%%
3178
3179
3180	# STARTING THE EXECUTABLE
3181	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3182	PATH=$PATH:$TEMPDIR
3183
3184	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3185	if [[ "$mpi_debug" = true ]]
3186	then
3187	export MPI_CHECK_ARGS=1
3188	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3189	fi
3190
3191	if [[ "$totalview" = true ]]
3192	then
3193	printf "\n *** totalview debugger will be used"
3194	tv_opt="-tv"
3195	else
3196	tv_opt=""
3197	fi
3198
3199	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3200	then
3201	if [[ "$ENVIRONMENT" = BATCH ]]
3202	then
3203	continue
3204	fi
3205	if [[ $localhost = ibmh ]]
3206	then
3207
3208	# SETUP THE IBM MPI ENVIRONMENT
3209	export MP_SHARED_MEMORY=yes
3210	export AIXTHREADS_SCOPE=S
3211	export OMP_NUM_THREADS=$threads_per_task
3212	export AUTHSTATE=files
3213	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3214
3215	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3216	export MP_ADAPTER_USE=shared
3217	export MP_CPU_USE=multiple
3218	export MP_TIMEOUT=1200
3219
3220	unset MP_TASK_AFFINITY
3221
3222	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3223	#(( ii = 1 ))
3224	#while (( ii <= $numprocs ))
3225	#do
3226	# echo $localhost_realname >> hostfile
3227	# (( ii = ii + 1 ))
3228	#done
3229	#export MP_HOSTFILE=hostfile
3230
3231	if [[ "$LOADLBATCH" = yes ]]
3232	then
3233	totalview poe a.out $ROPTS
3234	else
3235	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3236	export TVDSVRLAUNCHCMD=ssh
3237	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3238	fi
3239
3240	fi # END DEBUG MODE
3241
3242	else
3243
3244	# NORMAL EXECUTION
3245	if [[ -n $numprocs ]]
3246	then
3247
3248	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3249	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3250	then
3251
3252	# SETUP THE IBM MPI ENVIRONMENT
3253	if [[ $host != ibmh && $host != ibmkisti ]]
3254	then
3255	export MP_SHARED_MEMORY=yes
3256	export AIXTHREAD_SCOPE=S
3257	export OMP_NUM_THREADS=$threads_per_task
3258	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3259	export AUTHSTATE=files
3260	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3261	# export MP_PRINTENV=yes
3262
3263	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3264	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3265	export MP_WAIT_MODE=poll
3266	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3267	fi
3268
3269	if [[ $host = ibmkisti ]]
3270	then
3271	export LANG=en_US
3272	export MP_SHARED_MEMORY=yes
3273	if [[ $threads_per_task = 1 ]]
3274	then
3275	export MP_SINGLE_THREAD=yes
3276	export MEMORY_AFFINITY=MCM
3277	else
3278	export OMP_NUM_THREADS=$threads_per_task
3279	fi
3280	fi
3281
3282	if [[ "$LOADLBATCH" = yes ]]
3283	then
3284	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3285	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3286	then
3287	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3288	else
3289	if [[ $run_coupled_model = false ]]
3290	then
3291	if [[ "$ocean_file_appendix" = true ]]
3292	then
3293	echo "precursor_ocean" > runfile_atmos
3294	else
3295	echo "precursor_atmos" > runfile_atmos
3296	fi
3297	else
3298	(( iia = $numprocs_atmos / $threads_per_task ))
3299	(( iio = $numprocs_ocean / $threads_per_task ))
3300	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3301	printf "\n using $coupled_mode coupling"
3302	printf "\n\n"
3303	echo "coupled_run $iia $iio" > runfile_atmos
3304	fi
3305	poe ./a.out $ROPTS < runfile_atmos
3306	fi
3307	else
3308	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3309	then
3310	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3311	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3312	then
3313	if [[ -f $hostfile ]]
3314	then
3315	cp $hostfile hostfile
3316	else
3317	(( ii = 1 ))
3318	while (( ii <= $numprocs ))
3319	do
3320	echo $localhost_realname >> hostfile
3321	(( ii = ii + 1 ))
3322	done
3323	fi
3324	export MP_HOSTFILE=hostfile
3325	if [[ $run_coupled_model = false ]]
3326	then
3327	if [[ "$ocean_file_appendix" = true ]]
3328	then
3329	echo "precursor_ocean" > runfile_atmos
3330	else
3331	echo "precursor_atmos" > runfile_atmos
3332	fi
3333	else
3334	(( iia = $numprocs_atmos / $threads_per_task ))
3335	(( iio = $numprocs_ocean / $threads_per_task ))
3336	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3337	printf "\n using $coupled_mode coupling"
3338	printf "\n\n"
3339	echo "coupled_run $iia $iio" > runfile_atmos
3340	fi
3341
3342	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3343
3344	else
3345	if [[ "$host_file" = "" ]]
3346	then
3347	printf "\n +++ no hostfile given in configuration file"
3348	locat=config_file
3349	exit
3350	else
3351	eval host_file=$host_file
3352	fi
3353	export MP_HOSTFILE=$host_file
3354	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3355	fi
3356	fi
3357	elif [[ $host = nech ]]
3358	then
3359	(( ii = nodes ))
3360	if [[ $ii = 1 ]]
3361	then
3362	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3363	export MPIPROGINF=YES
3364	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3365	echo "*** execution on single node with mpirun"
3366	mpirun -np $numprocs ./a.out $ROPTS
3367	else
3368	(( i = 0 ))
3369	while (( i < ii ))
3370	do
3371	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3372	(( i = i + 1 ))
3373	done
3374
3375	echo "#!/bin/sh" > mpi_exec_shell
3376	echo " " >> mpi_exec_shell
3377	echo "set -u" >> mpi_exec_shell
3378	echo "F_ERRCNT=0" >> mpi_exec_shell
3379	echo "MPIPROGINV=YES" >> mpi_exec_shell
3380	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3381	echo "cpurest=$cpurest" >> mpi_exec_shell
3382	echo "fname=$fname" >> mpi_exec_shell
3383	echo "localhost=$localhost" >> mpi_exec_shell
3384	echo "return_addres=$return_addres" >> mpi_exec_shell
3385	echo "return_username=$return_username" >> mpi_exec_shell
3386	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3387	echo "write_binary=$write_binary" >> mpi_exec_shell
3388	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3389	echo " " >> mpi_exec_shell
3390	echo "export F_ERRCNT" >> mpi_exec_shell
3391	echo "export MPIPROGINV" >> mpi_exec_shell
3392	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3393	echo "export cpurest" >> mpi_exec_shell
3394	echo "export fname" >> mpi_exec_shell
3395	echo "export localhost" >> mpi_exec_shell
3396	echo "export return_addres" >> mpi_exec_shell
3397	echo "export return_username" >> mpi_exec_shell
3398	echo "export tasks_per_node" >> mpi_exec_shell
3399	echo "export write_binary" >> mpi_exec_shell
3400	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3401	echo " " >> mpi_exec_shell
3402	echo "exec ./a.out" >> mpi_exec_shell
3403
3404	chmod u+x mpi_exec_shell
3405	export MPIPROGINF=YES
3406	mpirun -f multinode_config &
3407	wait
3408
3409	fi
3410	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3411	then
3412
3413	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3414	# DOES NOT EXIST
3415	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3416	then
3417	if [[ -f $hostfile ]]
3418	then
3419	cp $hostfile hostfile
3420	(( ii = $numprocs / $threads_per_task ))
3421	else
3422	(( ii = 1 ))
3423	while (( ii <= $numprocs / $threads_per_task ))
3424	do
3425	echo $localhost_realname >> hostfile
3426	(( ii = ii + 1 ))
3427	done
3428	fi
3429	eval zeile=\"`head -n $ii hostfile`\"
3430	printf "\n *** running on: $zeile"
3431	fi
3432
3433	(( ii = $numprocs / $threads_per_task ))
3434	export OMP_NUM_THREADS=$threads_per_task
3435
3436	if [[ $threads_per_task != 1 ]]
3437	then
3438	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3439	# MAY ABORT
3440	ulimit -s unlimited
3441	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3442	fi
3443	if [[ $run_coupled_model = false ]]
3444	then
3445	if [[ "$ocean_file_appendix" = true ]]
3446	then
3447	echo "precursor_ocean" > runfile_atmos
3448	else
3449	echo "precursor_atmos" > runfile_atmos
3450	fi
3451	printf "\n\n"
3452
3453	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3454	then
3455	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3456	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3457	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3458	elif [[ $host = lccrayf ]]
3459	then
3460	aprun -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3461	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3462	then
3463	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3464	elif [[ $host = lcflow ]]
3465	then
3466	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3467	elif [[ $host = lcsb ]]
3468	then
3469	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3470	elif [[ $host = lckiaps ]]
3471	then
3472	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3473	elif [[ $host = lckyu* ]]
3474	then
3475	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3476	else
3477	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3478	fi
3479	else
3480
3481	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3482	(( iia = $numprocs_atmos / $threads_per_task ))
3483	(( iio = $numprocs_ocean / $threads_per_task ))
3484	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3485	printf "\n using $coupled_mode coupling"
3486	printf "\n\n"
3487
3488	if [[ $coupled_mode = "mpi2" ]]
3489	then
3490	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3491	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3492
3493	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3494	then
3495
3496	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3497	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3498
3499	else
3500	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3501	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3502	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3503	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3504	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3505	fi
3506	wait
3507
3508	else
3509
3510	echo "coupled_run $iia $iio" > runfile_atmos
3511
3512	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3513	then
3514
3515	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3516
3517	elif [[ $host = lck \|\| $host = lckordi ]]
3518	then
3519
3520	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3521
3522	elif [[ $host = lckyu* ]]
3523	then
3524
3525	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3526
3527	fi
3528	wait
3529	fi
3530
3531	fi
3532
3533	elif [[ $host = lckyoto ]]
3534	then
3535	set -xv
3536	export P4_RSHCOMMAND=plesh
3537	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3538	if [[ "$ENVIRONMENT" = BATCH ]]
3539	then
3540	if [[ "$cond2" = fujitsu ]]
3541	then
3542	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3543	elif [[ "cond2" = pgi ]]
3544	then
3545	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3546	else
3547	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3548	fi
3549	else
3550	if [[ "$cond2" = "" ]]
3551	then
3552	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3553	else
3554	mpirun -np $numprocs ./a.out $ROPTS
3555	fi
3556	fi
3557	set +xv
3558
3559	elif [[ $host = lctit ]]
3560	then
3561	export OMP_NUM_THREADS=$threads_per_task
3562	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3563	if [[ "$threads_per_task" != 1 ]]
3564	then
3565	export MV2_ENABLE_AFFINITY=0
3566	fi
3567	echo "----- PBS_NODEFILE content:"
3568	cat $PBS_NODEFILE
3569	echo "-----"
3570	(( ii = $numprocs / $threads_per_task ))
3571	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3572	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3573	else
3574	mpprun -n $numprocs a.out $ROPTS
3575	fi
3576	else
3577	a.out $ROPTS
3578	fi
3579	fi
3580
3581	if [[ $? != 0 ]]
3582	then
3583
3584	# ABORT IN CASE OF RUNTIME ERRORS
3585	printf "\n +++ runtime error occured"
3586	locat=execution
3587	exit
3588
3589	else
3590
3591	printf "\n$dashes\n *** execution finished \n"
3592
3593	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3594	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3595	if [[ "$dvrserver_id" != "" ]]
3596	then
3597	kill $dvrserver_id
3598	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3599
3600	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3601	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3602	if [[ -d DATA_DVR ]]
3603	then
3604
3605	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3606	# DIRECTORY
3607	cp .dvrserver.config DATA_DVR
3608
3609	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3610	# SEQUENCE MODE DATA TOO)
3611	process_dvr_output -d DATA_DVR -f $fname -s
3612
3613	else
3614
3615	# PROCESS THE LOCAL OUTPUT
3616	process_dvr_output -l -d DATA_DVR -f $fname
3617
3618	fi
3619
3620	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3621	then
3622
3623	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3624	process_dvr_output -l -d DATA_DVR -f $fname
3625
3626	fi
3627	fi
3628
3629
3630
3631	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3632	# BY EACH CORE INTO ONE FILE
3633	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3634	then
3635	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3636	printf "\n 2d- and/or 3d-data may be incomplete!"
3637	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3638	elif [[ "$combine_plot_fields" == true ]]
3639	then
3640	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3641	then
3642	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3643	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3644	else
3645	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3646	combine_plot_fields${block}.x
3647	fi
3648	else
3649
3650	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3651	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3652	# ??? koennen wir das streichen ???
3653	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3654	fi
3655
3656
3657
3658	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3659	(( i = 0 ))
3660	while (( i < ioc ))
3661	do
3662	(( i = i + 1 ))
3663	if (( i == 1 ))
3664	then
3665	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3666	fi
3667	printf "\n >>> ${out_command[$i]}"
3668	eval ${out_command[$i]}
3669	if (( i == ioc ))
3670	then
3671	printf "\n$dashes\n"
3672	fi
3673	done
3674
3675
3676	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3677	if [[ $do_trace = true ]]
3678	then
3679	printf "\n\n"
3680	ls -al
3681	fi
3682
3683
3684
3685	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3686	(( i = 0 ))
3687	while (( i < iout ))
3688	do
3689	(( i = i + 1 ))
3690	if (( i == 1 ))
3691	then
3692	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3693	fi
3694
3695	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3696	files_for_pes=false; filetyp=file
3697	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3698	then
3699	files_for_pes=true; filetyp=directory
3700	actionout[$i]=""
3701	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3702	then
3703	actionout[$i]=""
3704	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3705	then
3706	files_for_pes=true; filetyp=directory
3707	actionout[$i]="ar"
3708	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3709	then
3710	actionout[$i]="ar"
3711	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3712	then
3713	files_for_pes=true; filetyp=directory
3714	actionout[$i]="fl"
3715	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3716	then
3717	actionout[$i]="fl"
3718	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3719	then
3720	files_for_pes=true; filetyp=directory
3721	actionout[$i]="tr"
3722	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3723	then
3724	actionout[$i]="tr"
3725	fi
3726
3727	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3728	then
3729	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3730	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3731	then
3732	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3733	else
3734
3735
3736	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3737	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3738	if [[ "${actionout[$i]}" = tr ]]
3739	then
3740	if [[ $localhost != $fromhost ]]
3741	then
3742	if [[ $files_for_pes = false ]]
3743	then
3744	cps=""
3745	cst=""
3746	else
3747	cps=-c
3748	cst="/"
3749	fi
3750	if [[ $localhost = nech ]]
3751	then
3752
3753	# TRANSFER IN SEPERATE JOB
3754	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3755	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3756	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3757	if [[ $files_for_pes = false ]]
3758	then
3759	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3760	else
3761	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3762	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3763	fi
3764
3765	echo "set -x" > transfer_${localout[$i]}
3766	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3767
3768	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3769	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3770	printf "\n or higher cycle\n"
3771	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]}
3772
3773	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3774
3775	if [[ $localhost = nech ]]
3776	then
3777	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3778	else
3779	if [[ "$LOGNAME" = b323013 ]]
3780	then
3781	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3782	else
3783	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3784	fi
3785	fi
3786
3787	else
3788
3789	# TRANSFER WITHIN THIS JOB
3790	transfer_failed=false
3791	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3792	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3793	if [[ $localhost = lccrayb ]]
3794	then
3795	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]}"
3796	elif [[ $localhost = lccrayh ]]
3797	then
3798	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]}"
3799	else
3800	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3801	fi
3802	[[ $? != 0 ]] && transfer_failed=true
3803
3804	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3805	if [[ $transfer_failed = true ]]
3806	then
3807	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3808	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3809
3810	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3811	eval local_catalog=${pathout[$i]}
3812	if [[ ! -d $local_catalog ]]
3813	then
3814	printf " *** local directory does not exist. Trying to create:\n"
3815	printf " $local_catalog \n"
3816	mkdir -p $local_catalog
3817	fi
3818	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3819	transfer_problems=true
3820	fi
3821	fi
3822	else
3823
3824	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3825	actionout[$i]=""
3826	fi
3827	fi
3828
3829
3830	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3831	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3832	if [[ "${actionout[$i]}" = tra ]]
3833	then
3834	if [[ $localhost != $fromhost ]]
3835	then
3836	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3837	then
3838
3839	# TRANSFER IN SEPERATE JOB
3840	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3841	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3842	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3843	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3844
3845	echo "set -x" > transfer_${localout[$i]}
3846	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3847
3848	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3849	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3850	printf "\n or higher cycle\n"
3851	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]}
3852
3853	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3854
3855	if [[ $localhost = nech ]]
3856	then
3857	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3858	else
3859	if [[ $LOGNAME = b323013 ]]
3860	then
3861	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3862	else
3863	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3864	fi
3865	fi
3866
3867	else
3868
3869	# TRANSFER WITHIN THIS JOB
3870	transfer_failed=false
3871	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3872	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3873	if [[ $localhost = lccrayb ]]
3874	then
3875	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]}"
3876	elif [[ $localhost = lccrayh ]]
3877	then
3878	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]}"
3879	else
3880	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3881	fi
3882	[[ $? != 0 ]] && transfer_failed=true
3883
3884	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3885	if [[ $transfer_failed = true ]]
3886	then
3887	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3888	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3889
3890	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3891	eval local_catalog=${pathout[$i]}
3892	if [[ ! -d $local_catalog ]]
3893	then
3894	printf " *** local directory does not exist. Trying to create:\n"
3895	printf " $local_catalog \n"
3896	mkdir -p $local_catalog
3897	fi
3898
3899	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3900	transfer_problems=true
3901	fi
3902	fi
3903	else
3904
3905	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3906	actionout[$i]=a
3907	fi
3908	fi
3909
3910
3911	# OUTPUT-FILE FOR A RESTART-RUN.
3912	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3913	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3914	# AS LAST ACTION, ARCHIVING IS INITIATED.
3915	if [[ "${actionout[$i]}" = fl ]]
3916	then
3917	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3918	chmod g+rx $tmp_data_catalog
3919	if [[ $files_for_pes = false ]]
3920	then
3921	printf "\n >>> OUTPUT: ${localout[$i]} to"
3922	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3923	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3924	else
3925	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3926	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3927	mkdir $tmp_data_catalog/${frelout[$i]}
3928	cd ${localout[$i]}
3929	for file in $(ls *)
3930	do
3931	ln -f $file $tmp_data_catalog/${frelout[$i]}
3932	done
3933	cd $TEMPDIR
3934	fi
3935
3936
3937	# CREATE AND SUBMIT ARCHIVING-JOB
3938	if [[ $store_on_archive_system = true ]]
3939	then
3940
3941	if [[ $archive_system = asterix ]]
3942	then
3943	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3944	if [[ $files_for_pes = false ]]
3945	then
3946	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3947	else
3948	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3949	fi
3950	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3951	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3952	echo "then" >> archive_${frelout[$i]}
3953	echo " do_stageout=false" >> archive_${frelout[$i]}
3954	echo "else" >> archive_${frelout[$i]}
3955	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3956	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3957	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3958	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3959	if [[ $files_for_pes = false ]]
3960	then
3961	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3962	else
3963	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3964	fi
3965	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3966	echo "fi" >> archive_${frelout[$i]}
3967	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3968	elif [[ $archive_system = DMF ]]
3969	then
3970	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3971	if [[ $files_for_pes = false ]]
3972	then
3973	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3974	locat=DMF
3975	exit
3976	else
3977	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3978	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3979	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3980	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3981	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3982	fi
3983	elif [[ $archive_system = tivoli ]]
3984	then
3985	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3986	if [[ $files_for_pes = false ]]
3987	then
3988	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3989	echo "set -x" >> archive_${frelout[$i]}
3990	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3991	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3992	else
3993
3994	echo "set -x" >> archive_${frelout[$i]}
3995	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3996	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3997	cd $tmp_data_catalog
3998	all_files=`ls -1 ${frelout[$i]}/*`
3999	cd - > /dev/null
4000	(( inode = 0 ))
4001	(( tp1 = tasks_per_node + 1 ))
4002	while (( inode < nodes ))
4003	do
4004	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4005	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4006	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4007	(( inode = inode + 1 ))
4008	done
4009	fi
4010	elif [[ $archive_system = ut ]]
4011	then
4012	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4013	if [[ $files_for_pes = false ]]
4014	then
4015	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4016	echo "set -x" >> archive_${frelout[$i]}
4017	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4018	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4019	else
4020
4021	echo "set -x" >> archive_${frelout[$i]}
4022	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4023	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4024	cd $tmp_data_catalog
4025	all_files=`ls -1 ${frelout[$i]}/*`
4026	cd - > /dev/null
4027	(( inode = 0 ))
4028	(( tp1 = tasks_per_node + 1 ))
4029	while (( inode < nodes ))
4030	do
4031	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4032	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4033	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4034	(( inode = inode + 1 ))
4035	done
4036	fi
4037	elif [[ $archive_system = none ]]
4038	then
4039	printf " +++ archiving on $localhost not available!\n"
4040	fi
4041
4042	if [[ $archive_system != none ]]
4043	then
4044	if [[ $localhost = nech ]]
4045	then
4046	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4047	fi
4048	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4049	fi
4050	else
4051	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4052	fi
4053
4054
4055	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4056	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4057	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4058	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4059	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4060	if [[ $files_for_pes = false ]]
4061	then
4062	cat /dev/null > ${pathout[$i]}
4063	else
4064	mkdir -p ${pathout[$i]}
4065	fi
4066
4067	fi
4068
4069
4070	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4071	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4072	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4073	if [[ "${actionout[$i]}" = ar ]]
4074	then
4075	if [[ $files_for_pes = false ]]
4076	then
4077	printf "\n >>> OUTPUT: ${localout[$i]} to"
4078	printf "\n ${pathout[$i]}"
4079	printf "\n File will be copied to archive-system ($archive_system) !\n"
4080	else
4081	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4082	printf "\n ${pathout[$i]}"
4083	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4084	fi
4085	mv ${localout[$i]} ${frelout[$i]}
4086
4087	file_saved=false
4088
4089	if [[ $archive_system = asterix ]]
4090	then
4091	do_stageout=true
4092	(( stageout_anz = 0 ))
4093	while [[ $do_stageout = true ]]
4094	do
4095	if [[ $files_for_pes = false ]]
4096	then
4097	stageout ${frelout[$i]} > STAGE_OUTPUT
4098	else
4099	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4100	fi
4101	cat STAGE_OUTPUT
4102	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4103	then
4104	file_saved=true
4105	do_stageout=false
4106	else
4107	if [[ $files_for_pes = false ]]
4108	then
4109	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4110	else
4111	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4112	fi
4113	(( stageout_anz = stageout_anz + 1 ))
4114	if (( stageout_anz == 10 ))
4115	then
4116	printf "\n +++ stoped after 10 unsuccessful tries!"
4117	archive_save=false
4118	do_stageout=false
4119	else
4120	printf "\n *** new try to store on archive after 15 min:"
4121	sleep 900
4122	fi
4123	fi
4124	done
4125	elif [[ $archive_system = DMF ]]
4126	then
4127	if [[ $files_for_pes = false ]]
4128	then
4129	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4130	locat=DMF
4131	exit
4132	else
4133	rm -rf $ARCHIVE/${frelout[$i]}
4134	cp -r ${frelout[$i]} $ARCHIVE
4135	fi
4136	file_saved=true
4137	elif [[ $archive_system = tivoli ]]
4138	then
4139	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4140	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4141	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4142	# WHEN THE ARCHIVE-JOB IS EXECUTED
4143	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4144	chmod g+rx $tmp_data_catalog
4145	if [[ $files_for_pes = false ]]
4146	then
4147	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4148	else
4149	mkdir $tmp_data_catalog/${frelout[$i]}
4150	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4151	fi
4152
4153	# GENERATE AND SUBMIT BATCH-JOB
4154	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4155	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4156	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4157	if [[ $files_for_pes = false ]]
4158	then
4159	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4160	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4161	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4162	else
4163	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4164	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4165	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4166	fi
4167
4168	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4169	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4170	file_saved=true
4171
4172	elif [[ $archive_system = ut ]]
4173	then
4174	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4175	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4176	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4177	# WHEN THE ARCHIVE-JOB IS EXECUTED
4178	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4179	chmod g+rx $tmp_data_catalog
4180	if [[ $files_for_pes = false ]]
4181	then
4182	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4183	else
4184	mkdir $tmp_data_catalog/${frelout[$i]}
4185	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4186	fi
4187
4188	# GENERATE AND SUBMIT BATCH-JOB
4189	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4190	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4191	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4192	if [[ $files_for_pes = false ]]
4193	then
4194	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4195	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4196	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4197	else
4198	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4199	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4200	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4201	fi
4202
4203	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4204	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4205	file_saved=true
4206
4207	else
4208	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4209	archive_save=false
4210	fi
4211
4212	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4213	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4214	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4215	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4216	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4217	if [[ $file_saved = true ]]
4218	then
4219	if [[ $files_for_pes = false ]]
4220	then
4221	cat /dev/null > ${pathout[$i]}
4222	else
4223	mkdir -p ${pathout[$i]}
4224	fi
4225	fi
4226
4227	fi
4228
4229	# APPEND ON THIS MACHINE
4230	if [[ "${actionout[$i]}" = "a" ]]
4231	then
4232	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4233	then
4234	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4235	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4236	else
4237	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4238	cat ${localout[$i]} >> ${pathout[$i]}
4239	fi
4240	fi
4241
4242	# COPY ON THIS MACHINE
4243	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4244	# ON DIFFERENT FILE-SYSTEMS
4245	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4246	then
4247
4248	# COPY IN CASE OF RUNS ON SINGLE CORES
4249	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4250	then
4251	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4252	if [[ $link_local_output = true ]]
4253	then
4254	printf " using ln -f\n"
4255	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4256	fi
4257	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4258	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4259	then
4260	if [[ $link_local_output = true ]]
4261	then
4262	printf " ln failed, using cp...\n"
4263	fi
4264	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4265	fi
4266	else
4267	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4268	if [[ $link_local_output = true ]]
4269	then
4270	printf " using ln -f\n"
4271	ln -f ${localout[$i]} ${pathout[$i]}
4272	fi
4273	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4274	if [[ ! -f "${pathout[$i]}" ]]
4275	then
4276	if [[ $link_local_output = true ]]
4277	then
4278	printf " ln failed, using cp...\n"
4279	fi
4280	cp ${localout[$i]} ${pathout[$i]}
4281	fi
4282	fi
4283
4284	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4285	then
4286
4287	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4288	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4289	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4290	if [[ $link_local_output = true ]]
4291	then
4292	printf " using ln -f\n"
4293	mkdir ${pathout[$i]}
4294	cd ${localout[$i]}
4295	for file in $(ls *)
4296	do
4297	ln -f $file ${pathout[$i]}
4298	done
4299	cd $TEMPDIR
4300	fi
4301
4302	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4303	if [[ ! -f "${pathout[$i]}/_0000" ]]
4304	then
4305	if [[ $link_local_output = true ]]
4306	then
4307	printf " ln failed for .../_0000, using cp...\n"
4308	fi
4309	cp -r ${localout[$i]} ${pathout[$i]}
4310	fi
4311
4312	fi
4313	fi
4314	done
4315	if (( i != 0 ))
4316	then
4317	if [[ $transfer_problems = true ]]
4318	then
4319	printf "\n$dashes\n *** OUTPUT-files saved"
4320	printf "\n +++ WARNING: some data transfers failed! \n"
4321	else
4322	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4323	fi
4324	fi
4325
4326
4327	# IF REQUIRED, START A RESTART-JOB
4328	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4329	if [[ -f CONTINUE_RUN ]]
4330	then
4331
4332	if [[ $archive_save = true ]]
4333	then
4334
4335	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4336	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4337	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4338	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4339	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4340	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4341	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4342	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4343	then
4344	mc=`echo $mc \| sed 's/#/f/g'`
4345	fi
4346
4347
4348	# START THE RESTART-JOB
4349	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4350	echo " $mc"
4351	printf "\n$dashes\n"
4352	if [[ $localhost != $fromhost ]]
4353	then
4354
4355	if [[ $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4356	then
4357	echo "*** ssh will be used to initiate restart-runs!"
4358	echo " return_addres=\"$return_addres\" "
4359	echo " return_username=\"$return_username\" "
4360	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4361	then
4362	if [[ $localhost = ibmh ]]
4363	then
4364	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4365	elif [[ $localhost = lccrayb ]]
4366	then
4367	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4368	elif [[ $localhost = lccrayh ]]
4369	then
4370	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4371
4372	else
4373	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4374	fi
4375	else
4376	if [[ $localhost = ibmkisti ]]
4377	then
4378	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\" "
4379	elif [[ $localhost = lcflow ]]
4380	then
4381	/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 "
4382	elif [[ $localhost = lccrayb ]]
4383	then
4384	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\" "
4385	elif [[ $localhost = lccrayh ]]
4386	then
4387	ssh $usern@130.75.4.1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4388	else
4389	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4390	fi
4391	fi
4392	else
4393	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4394	locat=restart; exit
4395	fi
4396
4397	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4398	if [[ $queue = special1q ]]
4399	then
4400	sleep 120
4401	else
4402	sleep 30
4403	fi
4404
4405	else
4406
4407	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4408	# USING SSH)
4409	cd $LOCAL_PWD
4410	if [[ $localhost = lckyuh ]]
4411	then
4412	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4413	printf "\n please restart job manually using command:\n"
4414	printf "\n \"$mc\" "
4415	else
4416	eval $mc # THE ' MUST BE EVALUATED
4417	fi
4418	cd - > /dev/null
4419	fi
4420	if [[ $localhost = lckyuh ]]
4421	then
4422	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4423	else
4424	printf "\n$dashes\n *** restart-run initiated \n"
4425	fi
4426
4427
4428	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4429	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4430	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4431	# MAY BE VERY HUGE)
4432	(( i = 0 ))
4433	while (( i < iin ))
4434	do
4435	(( i = i + 1 ))
4436	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4437	then
4438	rm -r $tmp_data_catalog/${frelin[$i]}
4439	fi
4440	done
4441
4442	else
4443
4444	printf "\n +++ no restart-run possible, since errors occured"
4445	printf "\n during the archive process"
4446	fi
4447
4448	fi
4449
4450
4451
4452	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4453	if [[ "$email_notification" != "none" ]]
4454	then
4455
4456	if [[ $localhost != $fromhost ]]
4457	then
4458	if [[ -f CONTINUE_RUN ]]
4459	then
4460	echo "PALM restart run necessary" > email_text
4461	echo "description header of actual run:" >> email_text
4462	cat CONTINUE_RUN >> email_text
4463	echo "mrun-command to restart:" >> email_text
4464	echo "$mc" >> email_text
4465	else
4466	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4467	fi
4468	mail $email_notification < email_text
4469	printf "\n *** email notification sent to \"$email_notification\" "
4470	fi
4471	fi
4472
4473
4474
4475	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4476	cd $HOME
4477	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4478
4479	else
4480
4481
4482	# PREPARING ACTIONS,
4483	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4484
4485	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4486	mrun_com="$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 $remote_username"
4487	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4488	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4489	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4490	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4491	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4492	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4493	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4494	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4495	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4496	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4497	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4498	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4499	if [[ $use_openmp = true ]]
4500	then
4501	mrun_com=${mrun_com}" -O $threads_per_task"
4502	fi
4503	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4504	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4505	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4506	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4507	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4508	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4509	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4510	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4511	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4512	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4513	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4514	if [[ $do_remote = true ]]
4515	then
4516	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4517	fi
4518
4519
4520	# CREATE EXECUTABLE FOR BATCH JOB
4521	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4522	then
4523
4524	printf "\n *** creating the executable for batch job\n"
4525
4526	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4527	if [[ $host != $localhost ]]
4528	then
4529	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4530	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4531	locat=create_executable; exit
4532	fi
4533
4534	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4535	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4536
4537	cp $make_depository .
4538	tar -xf $make_depository > /dev/null 2>&1
4539	cp ../* . > /dev/null 2>&1
4540
4541	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4542
4543	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4544	then
4545	printf "\n +++ error occured while compiling or linking"
4546	locat=compile
4547	exit
4548	fi
4549
4550	mv a.out ..
4551	cd - > /dev/null 2>&1
4552	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4553
4554	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4555
4556	fi
4557
4558
4559	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4560	jobfile=jobfile.$RANDOM
4561
4562
4563	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4564	echo "mkdir $TEMPDIR" >> $jobfile
4565	echo "cd $TEMPDIR" >> $jobfile
4566
4567
4568	# ACTIVATE ERROR-TRACEBACK
4569	if [[ $do_trace = true ]]
4570	then
4571	echo "set -x" >> $jobfile
4572	else
4573	echo "set +vx" >> $jobfile
4574	fi
4575
4576
4577	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4578	if [[ "$init_cmds" != "" ]]
4579	then
4580	echo "$init_cmds" >> $jobfile
4581	fi
4582	if [[ "$module_calls" != "" ]]
4583	then
4584	echo "$module_calls" >> $jobfile
4585	fi
4586
4587
4588	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4589	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4590	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4591	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4592	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4593	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4594	# QUEUEING-SYSTEMS
4595	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4596	then
4597
4598	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4599	if [[ $restart_run != true ]]
4600	then
4601	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4602	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4603	fi
4604
4605	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4606	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4607	echo "set -x" >> $jobfile
4608	if [[ $host = $localhost ]]
4609	then
4610
4611	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4612	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4613	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4614	then
4615	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4616	else
4617	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4618	fi
4619
4620	else
4621	if [[ $host = ibmkisti ]]
4622	then
4623	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4624	echo "localdir=\`pwd\`" >> $jobfile
4625	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4626	elif [[ $host = lccrayb ]]
4627	then
4628	echo "localdir=\`pwd\`" >> $jobfile
4629	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4630	elif [[ $host = lccrayh ]]
4631	then
4632	echo "localdir=\`pwd\`" >> $jobfile
4633	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4634
4635	else
4636	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4637	fi
4638	fi
4639	echo "export SOURCES_COMPLETE=true" >> $jobfile
4640
4641	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4642	# WORKING DIRECTORY OF THE JOB
4643	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4644	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4645	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4646	echo "execute_mrun=true" >> $jobfile
4647	echo " " >> $jobfile
4648
4649	else
4650
4651	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4652	if [[ $do_compile = true ]]
4653	then
4654
4655	source_catalog=SOURCES_FOR_RUN_$fname
4656
4657	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4658	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4659	echo "export SOURCES_COMPLETE=true" >> $jobfile
4660	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4661
4662	for filename in $source_list
4663	do
4664	# BACKSLASH IS USED FOR MASKING
4665	echo "cat > $filename << \"%END%\"" >> $jobfile
4666	cat $source_catalog/$filename >> $jobfile
4667	echo " " >> $jobfile
4668	echo "%END%" >> $jobfile
4669	echo " " >> $jobfile
4670	done
4671
4672	# BACKSLASH IS USED FOR MASKING
4673	echo "cat > Makefile << \"%END%\"" >> $jobfile
4674	cat $source_catalog/Makefile >> $jobfile
4675	echo " " >> $jobfile
4676	echo "%END%" >> $jobfile
4677	echo " " >> $jobfile
4678
4679	echo "cd - > /dev/null" >> $jobfile
4680
4681	fi
4682
4683
4684	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4685	# BACKSLASH IS USED FOR MASKING
4686	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4687	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4688	echo "cat > $config_file << \"%END%\"" >> $jobfile
4689	if [[ $host = lckyuh ]]
4690	then
4691	# NO CROSS-COMPILER ON COMPUTE NODE
4692	sed 's/frtpx/frt/g' $config_file >> $jobfile
4693	else
4694	sed 's/#$.*//g' $config_file >> $jobfile
4695	fi
4696	echo "%END%" >> $jobfile
4697	echo " " >> $jobfile
4698
4699
4700	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4701	# BACKSLASH IS USED FOR MASKING
4702	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4703	if [[ $host = lckyuh ]]
4704	then
4705	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4706	else
4707	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4708	fi
4709	echo "%END%" >> $jobfile
4710	echo "chmod u+x $mrun_script_name" >> $jobfile
4711	echo "execute_mrun=true" >> $jobfile
4712	echo " " >> $jobfile
4713
4714	fi
4715
4716
4717	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4718	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4719	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4720	if [[ $do_remote = true ]]
4721	then
4722	(( i = 0 ))
4723	while (( i < iin ))
4724	do
4725	(( i = i + 1 ))
4726	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4727	if [[ "${transin[$i]}" = job ]]
4728	then
4729	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4730	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4731	echo " " >> $jobfile
4732	echo "%END%" >> $jobfile
4733	else
4734	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4735	fi
4736
4737	# CHECK, IF FILE COULD BE CREATED
4738	echo "if [[ \$? = 1 ]]" >> $jobfile
4739	echo "then" >> $jobfile
4740	echo " echo \" \" " >> $jobfile
4741	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4742	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4743	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4744	echo " execute_mrun=false" >> $jobfile
4745	echo "fi" >> $jobfile
4746	done
4747	fi
4748
4749	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4750	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4751	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4752	echo "LOCAL_PWD=$working_directory" >> $jobfile
4753	echo "export LOCAL_PWD" >> $jobfile
4754
4755	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4756	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4757	echo "export LOCAL_MRUN_PATH" >> $jobfile
4758
4759	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4760	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4761	then
4762	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4763	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4764	fi
4765
4766	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4767	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4768	echo "set -x" >> $jobfile
4769	echo "queue=$queue" >> $jobfile
4770	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4771	echo 'ls -al; echo `pwd`' >> $jobfile
4772	echo "cd \$HOME" >> $jobfile
4773	echo "rm -rf $TEMPDIR" >> $jobfile
4774
4775
4776
4777
4778	# START THE JOB USING SUBJOB-COMMAND
4779	if [[ $silent = false ]]
4780	then
4781	printf "\n "
4782	else
4783	printf "\n\n"
4784	fi
4785
4786	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
4787	rm -rf $jobfile
4788
4789
4790	fi # END OF REMOTE-PART

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