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source: palm/trunk/SCRIPTS/mrun @ 1346

Last change on this file since 1346 was 1328, checked in by maronga, 11 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1328 2014-03-21 11:00:33Z heinze $
29	#
30	# 1320 2014-03-20 08:40:49Z raasch
31	# check namelist file set false by default
32	#
33	# 1304 2014-03-12 10:29:42Z raasch
34	# ulimit option changed from -Ss to -s
35	#
36	# bugfix: missing "fi" in r1289
37	#
38	# 1289 2014-03-04 07:12:34Z raasch
39	# comments translated to English
40	# necriam-, fimm-, ibmy-, and sgi-specific code removed
41	# export of variables for palm and interpret_config removed
42	#
43	# 1281 2014-02-01 07:55:49Z raasch
44	# rsync-copy restricted to Cray machines, since command is unavailable on some
45	# other systems
46	#
47	# 1279 2014-01-28 12:10:14Z raasch
48	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
49	# in order to remove annoying restrictions concerning the number of processors which
50	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
51	# restriction, one of the nodes will be filled with less than the given number of
52	# tasks per node. A respective warning is given.
53	#
54	# 1274 2014-01-09 13:14:54Z heinze
55	# adjustments for lccrayh
56	#
57	# 1272 2014-01-08 10:19:32Z witha
58	# small adjustment for lcflow
59	#
60	# 1270 2013-12-16 11:05:01Z fricke
61	# call of combine_plot_fields adjusted for lccrayb/lccrayh
62	#
63	# 1255 2013-11-07 14:43:35Z raasch
64	# further adjustments for lccrayb remote access
65	#
66	# 1241 2013-10-30 11:36:58Z heinze
67	# Enable use of nudging input and input of large scale forcing from
68	# external files
69	#
70	# 1229 2013-09-20 06:55:19Z raasch
71	# further adjustments for lccrayb
72	#
73	# 1224 2013-09-16 07:27:23Z raasch
74	# first adjustments for lccrayb
75	#
76	# 1210 2013-08-14 10:58:20Z raasch
77	# fftw support added
78	#
79	# 1201 2013-07-10 16:17:59Z witha
80	# adjustments for Forwind cluster (lcflow)
81	#
82	# 1199 2013-07-05 14:52:22Z raasch
83	# adjustments for CSC Helsinki (lccrayf),
84	# executables for batch jobs can be created in advance, in order to avoid calling
85	# the compiler within the batch job (only works if batch jobs are submitted on
86	# local host)
87	#
88	# 1190 2013-06-25 09:39:21Z heinze
89	# enable use of automatic restarts for ibmh
90	# use of cluster/express queue enabled (ibmh)
91	#
92	# 1124 2013-04-09 15:46:52Z raasch
93	# variable "memory" is exported via typeset option -x, because otherwise an unknown
94	# side effect may lead to data loss while getopts is reading the script-option arguments
95	#
96	# 1122 2013-04-09 08:37:16Z heinze
97	# Bugfix: change type of variable last_char
98	#
99	# 1119 2013-04-05 15:11:19Z raasch
100	# Bugfix for setting -T option for subjob
101	#
102	# 1108 2013-03-05 07:03:32Z raasch
103	# bugfix for coupled runs on lckyut/lckyuh
104	#
105	# 1106 2013-03-04 05:31:38Z raasch
106	# --stdin argument for mpiexec on lckyuh
107	# -y and -Y settings output to header
108	#
109	# 1103 2013-02-20 02:15:53Z raasch
110	# default script runs again under ksh, because of unsolved problems with read
111	# from stdin: when bash script is called from a ksh, message "read error: 0:
112	# Resource temporarily unavailable" appears and script does not stop,
113	# further bash compatibility adjustments,
114	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
115	# on lckyuh, but mrun does not terminate and issues a warning instead
116	#
117	# 1101 2013-02-17 10:20:21Z raasch
118	# script now running under bash instead of ksh, which required small adjustments
119	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
120	# read from stdin),
121	# cross compilername on lckyuh compute nodes replaced by real compiler name
122	#
123	# 1099 2013-02-10 01:47:43Z raasch
124	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
125	# and for Forwind cluster (lcflow)
126	# small further adjustments for lckyut
127	#
128	# 1094 2013-02-03 01:52:12Z raasch
129	# explicit ssh/scp port can be set in config file with environment variable
130	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
131	# decalpha parts (yonsei) removed
132	#
133	# 2013-02-02 07:06:13Z raasch
134	# adjustments for Kyushu-University computing center (lckyut - tatara)
135	#
136	# 1083 2013-01-04 10:22:09Z maronga
137	# bugfix in parameter file check (read %cpp_options was missing)
138	#
139	# 1069 2012-11-28 16:18:43Z maronga
140	# bugfix: coupling mode was always set to mpi2, typos removed
141	#
142	# 1058 2012-11-21 07:00:35Z raasch
143	# Intel inspector (inspxe) is given the number of PEs instead of the number of
144	# nodes
145	#
146	# 1046 2012-11-09 14:38:45Z maronga
147	# code put under GPL (PALM 3.9)
148	#
149	# 21/03/94 - Siggi - first version finished
150	# 03/03/94 - Siggi - script development started
151	#
152	#--------------------------------------------------------------------------------#
153	# mrun - script for running PALM jobs
154	#--------------------------------------------------------------------------------#
155
156
157
158	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
159
160	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
161	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
162	# (TOO MANY ARGUMENTS - PROBLEM)
163	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
164
165	AddFilenames=""
166	additional_conditions=""
167	add_source_path=""
168	afname=""
169	archive_save=true
170	archive_system=none
171	check_namelist_files=false
172	combine_plot_fields=true
173	compiler_name=""
174	cond1=""
175	cond2=""
176	config_file=.mrun.config
177	coupled_dist=""
178	coupled_mode="mpi1"
179	cpp_opts=""
180	cpp_options=""
181	cpumax=0
182	cpurest=0
183	create_executable_for_batch=false
184	delete_temporary_catalog=true
185	do_batch=false
186	do_compile=true
187	do_remote=false
188	do_stagein=true
189	do_stageout=true
190	do_trace=false
191	email_notification="none"
192	exclude=""
193	executable=""
194	execution_error=false
195	fftw_inc=""
196	fftw_lib=""
197	fftw_support=false
198	fname=test
199	fromhost=""
200	global_revision=""
201	group_number=none
202	host=""
203	host_file=""
204	hp=""
205	ignore_archive_error=false
206	input_list=""
207	interpreted_config_file=""
208	job_catalog="~/job_queue"
209	job_on_file=""
210	keep_data_from_previous_run=false
211	link_local_input=false
212	link_local_output=false
213	localhost_realname=$(hostname)
214	local_dvrserver_running=.FALSE.
215	locat=normal
216	mainprog=""
217	makefile=""
218	max_par_io_str=""
219	mc=$0
220	while [[ $(echo $mc \| grep -c "/") != 0 ]]
221	do
222	mc=`echo $mc \| cut -f2- -d"/"`
223	done
224	module_calls=""
225	mrun_script_name=$mc
226	netcdf_inc=""
227	netcdf_lib=""
228	netcdf_support=false
229	node_usage=default
230	numprocs=""
231	numprocs_atmos=0
232	numprocs_ocean=0
233	OOPT=""
234	openmp=false
235	output_list=""
236	package_list=""
237	queue=none
238	read_from_config=""
239	restart_run=false
240	if [[ `hostname` = rte10 ]]
241	then
242	return_addres=133.5.185.60
243	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
244	elif [[ `hostname` = climate0 ]]
245	then
246	return_addres=165.132.26.68
247	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
248	elif [[ `hostname` = urban00 ]]
249	then
250	return_addres=147.46.30.151
251	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
252	else
253	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
254	fi
255	return_password=""
256	return_username=$LOGNAME
257	remotecall=false
258	remote_username=""
259	run_coupled_model=false
260	run_mode=""
261	store_on_archive_system=false
262	dashes=" ----------------------------------------------------------------------------"
263	silent=false
264	source_list=""
265	source_path=SOURCE
266	tasks_per_node=""
267	threads_per_task=1
268	tmpcreate=false
269	tmp_data_catalog=""
270	transfer_problems=false
271	usern=$LOGNAME
272	use_openmp=false
273	version="MRUN 2.1 Rev$Rev: 1328 $"
274	working_directory=`pwd`
275	TOPT=""
276	XOPT=""
277	zeit=$( date \| cut -c 12-19 )
278
279	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
280	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
281	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
282	# SCRIPT-OPTION ARGUMENTS
283	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
284
285
286
287	# ERROR HANDLING IN CASE OF EXIT
288	trap 'rm -rf $working_directory/tmp_mrun
289	if [[ $locat != normal && $locat != control_c ]]
290	then
291
292	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
293	(( i = 0 ))
294	while (( i < iec ))
295	do
296	(( i = i + 1 ))
297	printf "\n *** Execution of ERROR-command:\n"
298	printf " >>> ${err_command[$i]}\n"
299	eval ${err_command[$i]}
300	done
301	if [[ -n $interpreted_config_file ]]
302	then
303	rm -rf $interpreted_config_file
304	fi
305	if [[ -n .mrun_environment ]]
306	then
307	rm -rf .mrun_environment
308	fi
309	if [[ $tmpcreate = true ]]
310	then
311	printf "\n *** Contents of \"$TEMPDIR\":\n"
312	ls -al; cd
313	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
314	fi
315	if [[ "$dvrserver_id" != "" ]]
316	then
317	echo "+++ killing dvrserver_id=$dvrserver_id"
318	kill $dvrserver_id
319	fi
320	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
321	then
322	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
323	fi
324	printf "\n\n+++ MRUN killed \n\n"
325	elif [[ $locat != control_c ]]
326	then
327	printf "\n\n --> all actions finished\n\n"
328	printf " Bye, bye $usern !!\n\n"
329	fi' exit
330
331
332	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
333	trap 'rm -rf $working_directory/tmp_mrun
334	rm -rf $working_directory/tmp_check_namelist_files
335	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
336	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
337	then
338	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
339	fi
340	if [[ "$dvrserver_id" != "" ]]
341	then
342	echo "+++ killing dvrserver_id=$dvrserver_id"
343	kill $dvrserver_id
344	fi
345	printf "\n+++ MRUN killed by \"^C\" \n\n"
346	locat=control_c
347	exit
348	' 2
349
350
351	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
352	# BEEN SET
353	if [[ "$PALM_BIN" = "" ]]
354	then
355	printf "\n +++ environment variable PALM_BIN has not been set"
356	printf "\n please set it to the directory where the PALM scripts are located"
357	locat=palm_bin; exit
358	fi
359	export PATH=$PALM_BIN:$PATH
360
361
362
363	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
364	# WHICH WILL BE USED TO START RESTART-JOBS
365	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
366	do
367	case $option in
368	(a) afname=$OPTARG;;
369	(A) store_on_archive_system=true; mc="$mc -A";;
370	(b) do_batch=true; mc="$mc -b";;
371	(B) delete_temporary_catalog=false; mc="$mc -B";;
372	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
373	(C) restart_run=true; mc="$mc -C";;
374	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
375	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
376	(F) job_on_file="-D"; mc="$mc -F";;
377	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
378	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
379	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
380	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
381	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
382	(I) ignore_archive_error=true; mc="$mc -I";;
383	(k) keep_data_from_previous_run=true; mc="$mc -k";;
384	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
385	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
386	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
387	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
388	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
389	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
390	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
391	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
392	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
393	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
394	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
395	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
396	(S) read_from_config=false; mc="$mc -S";;
397	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
398	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
399	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
400	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
401	(v) silent=true; mc="$mc -v";;
402	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
403	(x) do_trace=true;set -x; mc="$mc -x";;
404	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
405	(y) ocean_file_appendix=true; mc="$mc -y";;
406	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
407	(z) check_namelist_files=false; mc="$mc -z";;
408	(Z) combine_plot_fields=false; mc="$mc -Z";;
409	(\?) printf "\n +++ unknown option $OPTARG \n"
410	printf "\n --> type \"$0 ?\" for available options \n"
411	locat=parameter;exit;;
412	esac
413	done
414
415
416	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
417	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
418	(( to_shift = $OPTIND - 1 ))
419	shift $to_shift
420
421	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
422	if [[ "$1" = "?" ]]
423	then
424	(printf "\n *** mrun can be called as follows:\n"
425	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"
426	printf "\n Description of available options:\n"
427	printf "\n Option Description Default-Value"
428	printf "\n -a base name of input files equiv. -d"
429	printf "\n -A archiving when using file-attribute fl"
430	printf "\n -b batch-job on local machine ---"
431	printf "\n -B do not delete temporary directory at end ---"
432	printf "\n -c configuration file .mrun.config"
433	printf "\n -d base name of files attached to program test"
434	printf "\n -D preprocessor(cpp)-directives \"\" "
435	printf "\n -F create remote job file only ---"
436	printf "\n -h execution host $localhost_realname"
437	printf "\n -i INPUT control list \"\" "
438	printf "\n -I archiving errors of previous batch-jobs"
439	printf "\n will be ignored"
440	printf "\n -k keep data from previous run"
441	printf "\n -K additional conditions for controling"
442	printf "\n usage of conditional code and"
443	printf "\n env-variables in configuration file \"\" "
444	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
445	printf "\n -M Makefile name Makefile"
446	printf "\n -n node usage (shared/not_shared) depending on -h"
447	printf "\n -o OUTPUT control list \"\" "
448	printf "\n -O threads per openMP task ---"
449	printf "\n -p software package list \"\" "
450	printf "\n -q queue \"$queue\" "
451	printf "\n -r run control list (combines -i -o) \"\" "
452	printf "\n -s filenames of routines to be compiled \"\" "
453	printf "\n must end with .f, .f90, .F, or .c !"
454	printf "\n use \"..\" for more than one file and wildcards"
455	printf "\n -s LM compiles all locally modified files"
456	printf "\n -S config file interpreted by shellscript ---"
457	printf "\n -t allowed cpu-time in seconds (batch) 0"
458	printf "\n -T tasks per node depending on -h"
459	printf "\n -u username on remote machine \"\" "
460	printf "\n -v no prompt for confirmation ---"
461	printf "\n -w maximum parallel io streams as given by -X"
462	printf "\n -x tracing of mrun for debug purposes ---"
463	printf "\n -X # of processors (on parallel machines) 1"
464	printf "\n -y add appendix \"_O\" to all local output"
465	printf "\n files (ocean precursor runs followed by"
466	printf "\n coupled atmosphere-ocean runs) ---"
467	printf "\n -Y run coupled model, \"#1 #2\" with"
468	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
469	printf "\n -z disable a priori parameter file check ---"
470	printf "\n -Z skip combine_plot_fields at the end of "
471	printf "\n the simulation ---"
472	printf "\n "
473	printf "\n Possible values of positional parameter <modus>:"
474	printf "\n \"?\" - this outline \n\n") \| more
475	exit
476	elif [[ "$1" != "" ]]
477	then
478	printf "\n +++ positional parameter $1 unknown \n"
479	locat=parameter; exit
480	fi
481
482
483
484	# SHORT STARTING MESSAGE
485	printf "\n*** $version "
486	printf "\n will be executed. Please wait ..."
487
488
489
490	# CHECK, IF CONFIGURATION FILE EXISTS
491	if [[ ! -f $config_file ]]
492	then
493	printf "\n\n +++ configuration file: "
494	printf "\n $config_file"
495	printf "\n does not exist"
496	locat=connect; exit
497	fi
498
499
500	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
501	line=""
502	grep "%host_identifier" $config_file > tmp_mrun
503	while read line
504	do
505	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
506	then
507	HOSTNAME=`echo $line \| cut -d" " -s -f2`
508	host_identifier=`echo $line \| cut -d" " -s -f3`
509	if [[ $localhost_realname = $HOSTNAME ]]
510	then
511	localhost=$host_identifier
512	break
513	fi
514	fi
515	done < tmp_mrun
516
517	if [[ "$localhost" = "" ]]
518	then
519	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
520	printf "\n for local host \"$localhost_realname\"."
521	printf "\n Please add line"
522	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
523	printf "\n to the configuration file."
524	locat=localhost; exit
525	fi
526
527
528	# SET HOST-SPECIFIC VARIABLES
529	case $localhost_realname in
530	(r1\|r2\|h01\|b01) archive_system=tivoli;;
531	(cs*) archive_system=ut;;
532	esac
533
534
535	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
536	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
537	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
538	[[ "$afname" = "" ]] && afname=$fname
539
540
541	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
542	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
543	# STATEMENTS IN THE CONFIGURATION FILE
544	if [[ "$run_mode" != "" ]]
545	then
546	input_list="$input_list $run_mode"
547	output_list="$output_list $run_mode"
548	fi
549
550
551	# ??? is this (and the respective option -H) really required ???
552	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
553	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
554	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
555	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
556	if [[ "$fromhost" = "" ]]
557	then
558	fromhost=$localhost
559	fi
560
561
562	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
563	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
564	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
565	# TO BE SUBMITTED (I.E. do_bacth=true)
566	if [[ -n $host && "$host" != $localhost ]]
567	then
568	do_batch=true
569	do_remote=true
570	case $host in
571	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
572	(*) printf "\n"
573	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
574	printf "\n is not available"
575	locat=nqs; (( iec = 0 )); exit;;
576	esac
577	else
578	host=$localhost
579	fi
580
581
582	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
583	if [[ -n $additional_conditions ]]
584	then
585	cond1=`echo $additional_conditions \| cut -d" " -f1`
586	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
587	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
588	if [[ -n $dummy ]]
589	then
590	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
591	locat=options; exit
592	fi
593	block=_$cond1
594	[[ -n $cond2 ]] && block=${block}_$cond2
595	fi
596
597
598	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
599	if [[ $run_coupled_model = true ]]
600	then
601
602	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
603	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
604
605	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
606	then
607
608	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
609	printf "\n PEs (total) : $numprocs"
610	printf "\n PEs (atmosphere): $numprocs_atmos"
611	printf "\n PEs (ocean) : $numprocs_ocean"
612	locat=coupling; exit
613
614	fi
615
616
617	# GET coupled_mode FROM THE CONFIG FILE
618	line=""
619	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
620	while read line
621	do
622	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
623	then
624	coupled_mode="mpi2"
625	fi
626	done < tmp_mrun
627
628	fi
629
630
631	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
632	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
633	then
634	if [[ $ignore_archive_error = false ]]
635	then
636	printf "\n +++ data archiving of previous run failed"
637	printf "\n see directory \~/job_queue on remote machine"
638	locat=archive; exit
639	else
640	printf "\n +++ warning: data archiving in a previous run failed"
641	printf "\n MRUN continues, trying to get backup copy"
642	fi
643	fi
644
645
646	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
647	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
648	mrun_memory=$memory
649	mrun_group_number=$group_number
650	mrun_cpumax=$cpumax
651	mrun_numprocs=$numprocs
652
653
654	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
655	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
656	if [[ "$read_from_config" = false ]]
657	then
658
659	[[ $silent = false ]] && printf "\n Reading the configuration file... "
660
661	# READ THE CONFIGURATION FILE LINE BY LINE
662	while read zeile
663	do
664	[[ $silent = false ]] && printf "."
665
666
667	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
668	eval zeile=\"$zeile\"
669
670
671	# INTERPRET THE LINE
672	if [[ "$(echo $zeile)" = "" ]]
673	then
674	# EMPTY LINE, NO ACTION
675	continue
676
677	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
678	then
679
680	# LINE IS A COMMENT LINE
681	true
682
683	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
684	then
685
686	# LINE DEFINES AN ENVIRONMENT-VARIABLE
687	zeile=$(echo $zeile \| cut -c2-)
688	var=`echo $zeile \| cut -d" " -f1`
689	value=`echo $zeile \| cut -d" " -s -f2`
690	for_host=`echo $zeile \| cut -d" " -s -f3`
691	for_cond1=`echo $zeile \| cut -d" " -s -f4`
692	for_cond2=`echo $zeile \| cut -d" " -s -f5`
693
694	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
695	then
696
697	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
698	# "::" IS REPLACED BY ":".
699	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
700
701
702	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
703	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
704	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
705	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
706	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
707	# CONFIGURATION-FILE.
708	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
709	then
710	eval $var=\$value
711
712	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
713	if [[ $do_trace = true ]]
714	then
715	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
716	fi
717	fi
718
719	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
720	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
721	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
722	# MUST HAVE TO BE STARTED
723	if [[ $var = host ]]
724	then
725	if [[ -n $host && "$host" != $localhost ]]
726	then
727	do_batch=true
728	do_remote=true
729	case $host in
730	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
731	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
732	printf "\n is not available"
733	locat=nqs; exit;;
734	esac
735	else
736	host=$localhost
737	fi
738	fi
739
740	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
741	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
742	# BY MRUN (E.G. subjob)
743	export $var
744	fi
745
746
747
748
749	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
750	then
751
752	# LINE DEFINES ERROR-COMMAND
753	(( iec = iec + 1 ))
754	zeile=$(echo $zeile \| cut -c4-)
755	err_command[$iec]="$zeile"
756
757	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
758	then
759
760	# LINE DEFINES INPUT-COMMAND
761	(( iic = iic + 1 ))
762	zeile=$(echo $zeile \| cut -c4-)
763	in_command[$iic]="$zeile"
764
765	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
766	then
767
768	# LINE DEFINES OUTPUT-COMMAND
769	(( ioc = ioc + 1 ))
770	zeile=$(echo $zeile \| cut -c4-)
771	out_command[$ioc]="$zeile"
772
773	else
774
775	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
776	# s2a: in/out - field
777	# s2b: loc - field (optional)
778	# s2c: tr/ar - field (optional)
779	s1=`echo $zeile \| cut -d" " -f1`
780	s2=`echo $zeile \| cut -d" " -s -f2`
781	s2a=$(echo $s2 \| cut -d":" -f1)
782	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
783	then
784	s2b=""
785	s2c=""
786	else
787	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
788	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
789	fi
790	s3=`echo $zeile \| cut -d" " -f3`
791	s4=`echo $zeile \| cut -d" " -s -f4`
792	s5=`echo $zeile \| cut -d" " -s -f5`
793	s6=`echo $zeile \| cut -d" " -s -f6`
794
795
796	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
797	# INPUT- OR OUTPUT-LIST.
798	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
799	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
800	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
801	# IS NOT CHECKED AND STORED.
802	IFSALT="$IFS"; IFS="$IFS:"
803	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
804	then
805	found=false
806	for actual in $input_list
807	do
808	for formal in $s3
809	do
810	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
811	done
812	done
813	if [[ $found = true ]]
814	then
815	(( iin = iin + 1 ))
816	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
817	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
818	extin[$iin]=$s6
819	fi
820	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
821	then
822	found=false
823	for actual in $output_list
824	do
825	for formal in $s3
826	do
827	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
828	done
829	done
830	if [[ $found = true ]]
831	then
832	(( iout = iout + 1 ))
833	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
834	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
835	fi
836	elif [[ "$s2a" != in && "$s2a" != out ]]
837	then
838	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
839	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
840	locat=connect; exit
841	fi
842	IFS="$IFSALT"
843	fi
844	done < $config_file
845
846	else
847
848
849	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
850	[[ $silent = false ]] && printf "..."
851	interpreted_config_file=.icf.$RANDOM
852
853
854
855	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
856	cat > .mrun_environment << %%END%%
857	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
858	config_file = '$config_file', do_remote = '$do_remote',
859	do_trace = '$do_trace', host = '$host',
860	input_list = '$input_list', icf = '$interpreted_config_file',
861	localhost = '$localhost', output_list = '$output_list' /
862
863	%%END%%
864
865	if [[ "$host" != $localhost ]]
866	then
867
868	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
869	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
870	if [[ $? != 0 ]]
871	then
872	printf "\n\n +++ no interpret_config found"
873	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
874	locat=interpret_config; exit
875	fi
876	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
877	$interpret_config_executable
878
879	else
880
881	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
882	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
883	then
884	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
885	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
886	locat=interpret_config; exit
887	else
888	interpret_config${block}.x
889	fi
890
891	fi
892	rm .mrun_environment
893
894
895	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
896	chmod u+x $interpreted_config_file
897	export PATH=$PATH:.
898	. $interpreted_config_file
899	rm $interpreted_config_file
900
901	fi
902
903
904	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
905	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
906	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
907	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
908	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
909	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
910	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
911
912
913	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
914	# FOR SOURCE-FILES TO BE COMPILED.
915	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
916	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
917	if [[ "$SOURCES_COMPLETE" = "" ]]
918	then
919
920	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
921	# HAS BEEN DEFINED
922	source_path=""
923	line=""
924	grep "%source_path" $config_file > tmp_mrun
925	while read line
926	do
927	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
928	then
929	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
930	then
931	global_source_path=`echo $line \| cut -d" " -f2`
932	fi
933	fi
934	done < tmp_mrun
935
936	line=""
937	found=false
938	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
939	while read line
940	do
941	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
942	then
943	if [[ $found = true ]]
944	then
945	printf "\n\n +++ more than one source path found in configuration file"
946	printf "\n for local host \"$localhost\" "
947	locat=source_path; exit
948	fi
949	source_path=`echo $line \| cut -d" " -f2`
950	found=true
951	fi
952	done < tmp_mrun
953	rm tmp_mrun
954
955	if [[ "$source_path" = "" ]]
956	then
957	if [[ "$global_source_path" != "" ]]
958	then
959	source_path=$global_source_path
960	else
961	printf "\n\n +++ no source path found in configuration file"
962	printf "\n for local host \"$localhost\" "
963	locat=source_path; exit
964	fi
965	fi
966	eval source_path=$source_path
967
968	if [[ ! -d $source_path ]]
969	then
970	printf "\n\n +++ source path \"$source_path\" on local host"
971	printf "\n \"$localhost\" does not exist"
972	locat=source_path; exit
973	fi
974
975	fi
976
977
978	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
979	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
980	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
981	then
982	global_revision=`svnversion $source_path 2>/dev/null`
983	global_revision="Rev: $global_revision"
984	fi
985
986
987	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
988	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
989	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
990	if [[ -n $host && "$host" != $localhost ]]
991	then
992	do_batch=true
993	do_remote=true
994	case $host in
995	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
996	(*) printf "\n"
997	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
998	printf "\n is not available"
999	locat=nqs; (( iec = 0 )); exit;;
1000	esac
1001	else
1002	host=$localhost
1003	fi
1004
1005
1006	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1007	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1008	then
1009
1010	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1011	if [[ ! -n $numprocs ]]
1012	then
1013	printf "\n"
1014	printf "\n +++ option \"-K parallel\" requires additional specification"
1015	printf "\n of the number of processors to be used by"
1016	printf "\n mrun-option \"-X\" or by environment-variable"
1017	printf "\n \"numprocs\" in the configuration file"
1018	locat=numprocs; (( iec = 0 )); exit
1019	fi
1020
1021	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1022	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1023	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1024	then
1025	printf "\n"
1026	printf "\n +++ option \"-T\" (tasks per node) is missing"
1027	printf "\n set -T option or define tasks_per_node in the config file"
1028	locat=tasks_per_node; (( iec = 0 )); exit
1029	fi
1030
1031	if (( numprocs < tasks_per_node ))
1032	then
1033	printf "\n"
1034	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1035	printf "\n given values: -T $tasks_per_node -X $numprocs"
1036	locat=tasks_per_node; (( iec = 0 )); exit
1037	fi
1038
1039	if [[ $host != lcflow && $host != lcxt5m ]]
1040	then
1041	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1042	(( ival = $tasks_per_node ))
1043	(( pes = numprocs ))
1044	(( ii = pes / ival ))
1045	(( remaining_pes = pes - ii * ival ))
1046	if (( remaining_pes > 0 ))
1047	then
1048	printf "\n"
1049	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1050	printf "\n divisor of the total number of processors (option \"-X\")"
1051	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1052	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1053	(( nodes = nodes + 1 ))
1054	fi
1055	fi
1056
1057
1058	# SETTINGS FOR SUBJOB-COMMAND
1059	OOPT="-O $threads_per_task"
1060
1061	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1062	if [[ "$tasks_per_node" != "" ]]
1063	then
1064	TOPT="-T $tasks_per_node"
1065	fi
1066
1067	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1068	if [[ $node_usage = default ]]
1069	then
1070	if [[ $host = ibms ]]
1071	then
1072	node_usage=shared
1073	else
1074	node_usage=not_shared
1075	fi
1076	fi
1077
1078	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1079	then
1080	printf "\n"
1081	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1082	printf "\n \"shared\" or \"not_shared\""
1083	locat=tasks_per_node; (( iec = 0 )); exit
1084	fi
1085
1086	fi
1087
1088	# CHECK IF HOSTFILE EXISTS
1089	if [[ -n $hostfile ]]
1090	then
1091	if [[ ! -f $hostfile ]]
1092	then
1093	printf "\n"
1094	printf "\n +++ hostfile \"$hostfile\" does not exist"
1095	locat=hostfile; exit
1096	fi
1097	fi
1098
1099
1100	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1101	if [[ "$maximum_parallel_io_streams" = "" ]]
1102	then
1103	maximum_parallel_io_streams=$numprocs
1104	fi
1105
1106
1107	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1108	if [[ "$scp_port" != "" ]]
1109	then
1110	PORTOPT="-P $scp_port"
1111	SSH_PORTOPT="-p $scp_port"
1112	fi
1113
1114
1115	# SET DEFAULT-QUEUE, IF NOT GIVEN
1116	if [[ $queue = none ]]
1117	then
1118	case $host in
1119	(ibmh) queue=cluster;;
1120	(ibmkisti) queue=class.32plus;;
1121	(lckiaps) queue=normal;;
1122	(lckyoto) queue=ph;;
1123	(lckyuh) queue=fx-single;;
1124	(lckyut) queue=cx-single;;
1125	(lctit) queue=S;;
1126	(nech) queue=none;;
1127	(unics) queue=unics;;
1128	esac
1129	fi
1130
1131
1132	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1133	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1134	(( i = 0 ))
1135	while (( i < iin ))
1136	do
1137	(( i = i + 1 ))
1138	(( maxcycle = 0 ))
1139
1140	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1141	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1142	if [[ "${actionin[$i]}" = di ]]
1143	then
1144	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1145	# HOST ONLY
1146	eval filename=${pathin[$i]}/${endin[$i]}
1147	else
1148	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1149	# HOST ONLY
1150	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1151	fi
1152	eval pathname=${pathin[$i]}
1153
1154	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1155	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1156	then
1157	filename_input=$filename
1158	fi
1159
1160	# CHECK IF FILE EXISTS
1161	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1162	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1163	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1164	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1165	then
1166
1167	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1168	if [[ "${transin[$i]}" != "locopt" ]]
1169	then
1170	printf "\n\n +++ INPUT-file: "
1171	if [[ "${extin[$i]}" = "" ]]
1172	then
1173	printf "\n $filename"
1174	else
1175	printf "\n $filename.${extin[$i]}"
1176	fi
1177	printf "\n does not exist\n"
1178	locat=input; exit
1179	else
1180	transin[$i]="unavailable"
1181	fi
1182	else
1183
1184	# DETERMINE THE FILE'S CYCLE NUMBER
1185	ls -1 -d $filename > filelist 2>/dev/null
1186	ls -1 -d $filename.* >> filelist 2>/dev/null
1187	while read zeile
1188	do
1189	cycle=$(echo $zeile \| cut -f2 -d".")
1190	if [[ "$cycle" = "$zeile" ]]
1191	then
1192	(( icycle = 0 ))
1193	elif [[ "$cycle" = "${extin[$i]}" ]]
1194	then
1195	(( icycle = 0 ))
1196	else
1197	(( icycle = $cycle ))
1198	fi
1199	if (( icycle > maxcycle ))
1200	then
1201	(( maxcycle = icycle ))
1202	file_to_be_used=$zeile
1203	fi
1204	done <filelist
1205	rm filelist
1206
1207	# APPEND CYCLE NUMBER TO FILENAME
1208	if (( maxcycle > 0 ))
1209	then
1210	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1211	then
1212	filename=${filename}.$maxcycle.${extin[$i]}
1213	else
1214	filename=${filename}.$maxcycle
1215	fi
1216	else
1217	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1218	then
1219	filename=${filename}.${extin[$i]}
1220	fi
1221	fi
1222
1223	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1224	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1225	absnamein[$i]=$filename
1226	if (( maxcycle > 0 ))
1227	then
1228	if [[ "${actionin[$i]}" = di ]]
1229	then
1230	frelin[$i]=${endin[$i]}.$maxcycle
1231	else
1232	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1233	fi
1234	else
1235	if [[ "${actionin[$i]}" = di ]]
1236	then
1237	frelin[$i]=${endin[$i]}
1238	else
1239	frelin[$i]=${afname}${endin[$i]}
1240	fi
1241	fi
1242
1243	fi
1244	done
1245
1246	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1247	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1248	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1249	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1250	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1251	# REMOTE HOST)
1252	(( i = 0 ))
1253	while (( i < iout ))
1254	do
1255	(( i = i + 1 ))
1256	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1257	then
1258	if [[ "${actionout[$i]}" = tr ]]
1259	then
1260	actionout[$i]=""
1261	elif [[ "${actionout[$i]}" = trpe ]]
1262	then
1263	actionout[$i]=pe
1264	elif [[ "${actionout[$i]}" = tra ]]
1265	then
1266	actionout[$i]=a
1267	fi
1268	(( maxcycle = 0 ))
1269	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1270	eval catalogname=${pathout[$i]}
1271	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1272	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1273	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1274	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1275	then
1276
1277	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1278	if cat /dev/null > $filename
1279	then
1280	rm $filename
1281	else
1282
1283	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1284	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1285	if [[ ! -d $catalogname ]]
1286	then
1287	if mkdir -p $catalogname
1288	then
1289	printf "\n\n *** directory:"
1290	printf "\n $catalogname"
1291	printf "\n was created\n"
1292	else
1293	printf "\n\n +++ OUTPUT-file:"
1294	printf "\n $filename"
1295	printf "\n cannot be created, because directory does not exist"
1296	printf "\n and cannot be created either"
1297	printf "\n"
1298	locat=output ; exit
1299	fi 2>/dev/null
1300	else
1301	printf "\n\n +++ OUTPUT-file:"
1302	printf "\n $filename"
1303	printf "\n cannot be created, although directory exists"
1304	printf "\n"
1305	locat=output ; exit
1306	fi
1307	fi 2>/dev/null
1308	else
1309
1310	# DETERMINE THE CYCLE NUMBER
1311	ls -1 -d $filename > filelist 2>/dev/null
1312	ls -1 -d $filename.* >> filelist 2>/dev/null
1313	while read zeile
1314	do
1315	cycle=$(echo $zeile \| cut -f2 -d".")
1316	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1317	then
1318	(( icycle = 1 ))
1319	else
1320	(( icycle = $cycle + 1 ))
1321	fi
1322	if (( icycle > maxcycle ))
1323	then
1324	(( maxcycle = icycle ))
1325	fi
1326	done <filelist
1327	rm filelist
1328	fi
1329
1330	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1331	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1332	if [[ "${actionout[$i]}" != a ]]
1333	then
1334	if (( maxcycle > 0 ))
1335	then
1336	filename=${filename}.$maxcycle
1337	if cat /dev/null > $filename
1338	then
1339	rm $filename
1340	else
1341	printf "\n +++ OUTPUT-file:"
1342	printf "\n $filename"
1343	printf "\n cannot be created"
1344	locat=output ; exit
1345	fi
1346	fi
1347	else
1348	(( maxcycle = maxcycle - 1 ))
1349	if (( maxcycle > 0 ))
1350	then
1351	filename=${filename}.$maxcycle
1352	fi
1353	fi
1354
1355	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1356	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1357	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1358	pathout[$i]=$filename
1359	if (( maxcycle > 0 ))
1360	then
1361	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1362	else
1363	frelout[$i]=${fname}${endout[$i]}
1364	fi
1365
1366	fi
1367	done
1368
1369
1370	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1371	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1372	then
1373	if [[ "$dvr_inc" = "" ]]
1374	then
1375	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1376	printf "\n This is required for the dvrp_graphics package.\n"
1377	locat=dvr; exit
1378	fi
1379	if [[ "$dvr_lib" = "" ]]
1380	then
1381	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1382	printf "\n This is required for the dvrp_graphics package.\n"
1383	locat=dvr; exit
1384	fi
1385	fi
1386
1387
1388	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1389	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1390	if [[ "$mainprog" = "" && "$executable" = "" ]]
1391	then
1392	printf "\n +++ neither main program nor executable defined"
1393	locat=source; exit
1394	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1395	then
1396	printf "\n +++ main program as well as executable defined"
1397	locat=source; exit
1398	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1399	then
1400	do_compile=false
1401	fi
1402
1403
1404	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1405	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1406	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1407	then
1408	rm -rf SOURCES_FOR_RUN_$fname
1409	mkdir SOURCES_FOR_RUN_$fname
1410	fi
1411
1412
1413	# COLLECT ALL ROUTINES TO BE COMPILED
1414	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1415	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1416	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1417	then
1418
1419	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1420
1421	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1422	then
1423
1424	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1425	source_list=""
1426	cd $source_path
1427
1428
1429	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1430	if [[ ! -d .svn ]]
1431	then
1432	printf "\n\n +++ source directory"
1433	printf "\n \"$source_path\" "
1434	printf "\n is not under control of \"subversion\"."
1435	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1436	fi
1437
1438
1439	# LIST ALL MODIFIED SOURCE CODE FILES
1440	Filenames=""
1441	svn status > tmp_mrun
1442	while read line
1443	do
1444	firstc=`echo $line \| cut -c1`
1445	if [[ $firstc = M \|\| $firstc = "?" ]]
1446	then
1447	Name=`echo "$line" \| cut -c8-`
1448	extension=`echo $Name \| cut -d. -f2`
1449	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1450	then
1451	Filenames="$Filenames "$Name
1452	fi
1453	fi
1454	done < tmp_mrun
1455
1456
1457	# COPY FILES TO SOURCES_FOR_RUN_...
1458	for dateiname in $Filenames
1459	do
1460	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1461	source_list=$source_list"$dateiname "
1462	done
1463
1464	cd - > /dev/null
1465
1466
1467	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1468	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1469	elif [[ "$source_list" != "" && $restart_run != true ]]
1470	then
1471
1472	cd $source_path
1473
1474	for filename in $source_list
1475	do
1476
1477	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1478	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1479	then
1480	printf "\n +++ source code file: $filename"
1481	printf "\n must not contain (\"/\") "
1482	locat=source; exit
1483	fi
1484
1485	if [[ ! -f $filename ]]
1486	then
1487	printf "\n +++ source code file: $filename"
1488	printf "\n does not exist"
1489	locat=source; exit
1490	else
1491	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1492	fi
1493
1494	done
1495
1496	cd - > /dev/null
1497
1498	fi
1499
1500
1501	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1502	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1503	if [[ $restart_run != true ]]
1504	then
1505
1506	if [[ ! -f "$source_path/$mainprog" ]]
1507	then
1508	printf "\n\n +++ main program: $mainprog"
1509	printf "\n does not exist in source directory"
1510	printf "\n \"$source_path\"\n"
1511	locat=source; exit
1512	else
1513	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1514	then
1515	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1516	source_list=${mainprog}" $source_list"
1517	fi
1518	fi
1519	fi
1520
1521
1522	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1523	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1524	if [[ "$restart_run" != true ]]
1525	then
1526	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1527	if [[ ! -f $makefile ]]
1528	then
1529	printf "\n +++ file \"$makefile\" does not exist"
1530	locat=make; exit
1531	else
1532	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1533	fi
1534	fi
1535
1536
1537	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1538	if [[ $restart_run != true && "$add_source_path" != "" ]]
1539	then
1540
1541	# DOES THE DIRECTORY EXIST?
1542	if [[ ! -d $add_source_path ]]
1543	then
1544	printf "\n\n +++ WARNING: additional source code directory"
1545	printf "\n \"$add_source_path\" "
1546	printf "\n does not exist or is not a directory."
1547	printf "\n No source code will be used from this directory!\n"
1548	add_source_path=""
1549	if [[ $silent == false ]]
1550	then
1551	sleep 3
1552	fi
1553	else
1554
1555	cd $add_source_path
1556	found=false
1557
1558	Names=$(ls -1 *.f90 2>&1)
1559	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1560	Names=$(ls -1 *.F90 2>&1)
1561	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1562	Names=$(ls -1 *.F 2>&1)
1563	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1564	Names=$(ls -1 *.f 2>&1)
1565	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1566	Names=$(ls -1 *.c 2>&1)
1567	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1568
1569	cd - > /dev/null
1570	cd SOURCES_FOR_RUN_$fname
1571
1572	# COPY MAKEFILE IF EXISTING
1573	if [[ -f $add_source_path/Makefile ]]
1574	then
1575	printf "\n\n *** user Makefile from directory"
1576	printf "\n \"$add_source_path\" is used \n"
1577	if [[ $silent == false ]]
1578	then
1579	sleep 1
1580	fi
1581	cp $add_source_path/Makefile .
1582	fi
1583
1584	for dateiname in $AddFilenames
1585	do
1586	if [[ -f $dateiname ]]
1587	then
1588	printf "\n +++ source code file \"$dateiname\" found in additional"
1589	printf "\n source code directory \"$add_source_path\" "
1590	printf "\n but was also given with option \"-s\" which means that it should be taken"
1591	printf "\n from directory \"$source_path\"."
1592	locat=source; exit
1593	fi
1594
1595	cp $add_source_path/$dateiname .
1596	source_list="$source_list $dateiname"
1597
1598	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1599	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1600	then
1601	printf "\n\n +++ user file \"$dateiname\" "
1602	printf "\n is not listed in Makefile \n"
1603	locat=source; exit
1604	else
1605
1606	if [[ $found = false ]]
1607	then
1608	found=true
1609	printf "\n\n *** following user file(s) added to the"
1610	printf " files to be translated:\n "
1611	fi
1612	printf "$dateiname "
1613	if [[ $silent == false ]]
1614	then
1615	sleep 0.5
1616	fi
1617
1618	fi
1619	done
1620	[[ $found = true ]] && printf "\n"
1621	cd - > /dev/null
1622	fi
1623	fi
1624
1625
1626	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1627	# TO THE LIST OF FILES TO BE COMPILED
1628	if [[ $restart_run != true && -n $package_list ]]
1629	then
1630
1631	cd $source_path
1632
1633	for package in $package_list
1634	do
1635
1636	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1637
1638	# DETERMINE FILES BELONGING TO THE PACKAGE
1639	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1640	# THE NAME OF THE DIRECTORY
1641	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1642
1643
1644	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1645	# IF THEY ARE NOT ALREADY PART OF THE LIST
1646	for source_list_name in $package_source_list
1647	do
1648	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1649	then
1650
1651	# ONLY TAKE FILES WITH VALID SUFFIX
1652	ending=`echo $source_list_name \| cut -f2 -d.`
1653	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1654	then
1655	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1656	source_list="$source_list $source_list_name"
1657	fi
1658	fi
1659	done
1660	done
1661
1662	cd - > /dev/null
1663	fi
1664
1665	fi # do_compile=true
1666
1667
1668	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1669	# AND SET PRE-PROCESSOR DIRECTIVES
1670	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1671	then
1672
1673	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1674	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1675	then
1676	cpp_options="${cpp_options},-D__ibm=__ibm"
1677	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1678	then
1679	cpp_options="$cpp_options -D__nec"
1680	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1681	then
1682	cpp_options="$cpp_options -D__lc"
1683	else
1684	cpp_options="$cpp_options -D__$localhost"
1685	fi
1686
1687	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1688	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1689	then
1690	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1691	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1692	else
1693	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1694	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1695	fi
1696
1697	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1698	if [[ -n $package_list ]]
1699	then
1700	for package in $package_list
1701	do
1702	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1703	then
1704	if [[ $package != "dvrp_graphics+1PE" ]]
1705	then
1706	cpp_options="${cpp_options},-D__$package=__$package"
1707	else
1708	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1709	export use_seperate_pe_for_dvrp_output=true
1710	fi
1711	else
1712	if [[ $package != "dvrp_graphics+1PE" ]]
1713	then
1714	cpp_options="$cpp_options -D__$package"
1715	else
1716	cpp_options="$cpp_options -D__dvrp_graphics"
1717	export use_seperate_pe_for_dvrp_output=true
1718	fi
1719	fi
1720	done
1721	fi
1722
1723	# SET DIRECTIVES GIVEN BY OPTION -D
1724	if [[ -n $cpp_opts ]]
1725	then
1726	for popts in $cpp_opts
1727	do
1728	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1729	then
1730	cpp_options="${cpp_options},-D__$popts=__$popts"
1731	else
1732	cpp_options="$cpp_options -D__$popts"
1733	fi
1734	done
1735	fi
1736
1737	else
1738
1739
1740	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1741	if [[ $do_remote = false ]]
1742	then
1743	if [[ ! -f $executable ]]
1744	then
1745	printf "\n +++ executable file: $executable"
1746	printf "\n does not exist"
1747	locat=executable; exit
1748	fi
1749	fi
1750	fi
1751
1752
1753	# DETERMINE THE JOB MODE
1754	if [[ "$ENVIRONMENT" = BATCH ]]
1755	then
1756	jobmo=BATCH
1757	else
1758	jobmo=INTERACTIVE
1759	fi
1760
1761
1762	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1763	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1764	then
1765	printf "\n +++ no interactive runs allowed on host \"$host\" "
1766	printf "\n please submit batch job using mrun option \"-b\" \n"
1767	locat=normal; exit
1768	fi
1769
1770
1771	# CHECK, IF USER DEFINED A COMPILER
1772	if [[ "$compiler_name" = "" ]]
1773	then
1774
1775	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1776	locat=compiler_name; exit
1777
1778	fi
1779
1780
1781	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1782	kennung=$RANDOM
1783	if [[ "$tmp_user_catalog" = "" ]]
1784	then
1785	if [[ $localhost = ibmh ]]
1786	then
1787	tmp_user_catalog=$SCRATCH
1788	elif [[ $localhost = nech ]]
1789	then
1790	tmp_user_catalog=$WRKSHR
1791	else
1792	tmp_user_catalog=/tmp
1793	fi
1794	fi
1795	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1796
1797
1798	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1799	if [[ "$tmp_data_catalog" = "" ]]
1800	then
1801	if [[ $localhost = nech ]]
1802	then
1803	tmp_data_catalog=$WRKSHR/mrun_restart_data
1804	else
1805	tmp_data_catalog=/tmp/mrun_restart_data
1806	fi
1807	fi
1808
1809
1810	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1811	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1812	then
1813	eval fopts=\"$fopts\"
1814	eval lopts=\"$lopts\"
1815	fi
1816
1817
1818
1819	# DETERMINE COMPILE- AND LINK-OPTIONS
1820	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1821	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1822	ROPTS="$ropts"
1823	# 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 ]]
1824	# then
1825	XOPT="-X $numprocs"
1826	# fi
1827
1828
1829
1830	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1831	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1832	done=false
1833	while [[ $done = false ]]
1834	do
1835	cputime=$cpumax
1836	if (( $cputime == 0 ))
1837	then
1838	if [[ $do_batch = true ]]
1839	then
1840	printf "\n +++ cpu-time is undefined"
1841	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1842	printf "\n >>> "
1843	read cputime 1>/dev/null 2>&1
1844	else
1845	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1846	fi
1847	else
1848	done=true
1849	fi
1850	cpumax=$cputime
1851	done
1852
1853	(( minuten = cputime / 60 ))
1854	(( sekunden = cputime - minuten * 60 ))
1855
1856
1857	# CHECK THE MEMORY DEMAND
1858	if [[ $do_batch = true ]]
1859	then
1860	done=false
1861	while [[ $done = false ]]
1862	do
1863	if (( memory == 0 ))
1864	then
1865	printf "\n +++ memory demand is undefined"
1866	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1867	printf "\n >>> "
1868	read memory 1>/dev/null 2>&1
1869	else
1870	done=true
1871	fi
1872	done
1873	fi
1874
1875
1876	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1877	if [[ $do_remote = true && -z $remote_username ]]
1878	then
1879	while [[ -z $remote_username ]]
1880	do
1881	printf "\n +++ username on remote host \"$host\" is undefined"
1882	printf "\n >>> Please type username:"
1883	printf "\n >>> "
1884	read remote_username
1885	done
1886	mc="$mc -u$remote_username"
1887	fi
1888
1889	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1890	if [[ "$login_init_cmd" != "" ]]
1891	then
1892	export init_cmds="${login_init_cmd};"
1893	fi
1894
1895
1896	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1897	if [[ "$modules" != "" ]]
1898	then
1899	if [[ $host = lctit ]]
1900	then
1901	export module_calls=". $modules"
1902	else
1903	export module_calls="module load ${modules};"
1904	fi
1905	fi
1906
1907
1908
1909	# OUTPUT OF THE MRUN-HEADER
1910	calltime=$(date)
1911	printf "\n"
1912	printf "#------------------------------------------------------------------------# \n"
1913	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1914	printf "\| \| \n"
1915	spalte1="called on:"; spalte2=$localhost_realname
1916	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1917	if [[ $do_remote = true ]]
1918	then
1919	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1920	else
1921	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1922	fi
1923	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1924	if [[ -n $numprocs ]]
1925	then
1926	if [[ $run_coupled_model = false ]]
1927	then
1928	spalte1="number of PEs:"; spalte2=$numprocs
1929	else
1930	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1931	fi
1932	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1933	fi
1934	if [[ -n $tasks_per_node ]]
1935	then
1936	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1937	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1938	if (( remaining_pes > 0 ))
1939	then
1940	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1941	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1942	fi
1943	fi
1944	if [[ $maximum_parallel_io_streams != $numprocs ]]
1945	then
1946	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1947	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1948	fi
1949	if [[ $use_openmp = true ]]
1950	then
1951	spalte1="threads per task:"; spalte2="$threads_per_task"
1952	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1953	fi
1954	printf "\| \| \n"
1955	if [[ $do_compile = true ]]
1956	then
1957	if [[ "$mopts" != "" ]]
1958	then
1959	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1960	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1961	zeile=$(echo "$mopts" \| cut -c46-)
1962	while [[ "$zeile" != "" ]]
1963	do
1964	spalte1=""
1965	spalte2=$(echo "$zeile" \| cut -c-45)
1966	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1967	zeile=$(echo "$zeile" \| cut -c46-)
1968	done
1969	fi
1970
1971	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1972	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1973	zeile=$(echo "$cpp_options" \| cut -c46-)
1974	while [[ "$zeile" != "" ]]
1975	do
1976	spalte1=""
1977	spalte2=$(echo "$zeile" \| cut -c-45)
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	zeile=$(echo "$zeile" \| cut -c46-)
1980	done
1981
1982	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1983	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1984	zeile=$(echo "$fopts" \| cut -c46-)
1985	while [[ "$zeile" != "" ]]
1986	do
1987	spalte1=""
1988	spalte2=$(echo "$zeile" \| cut -c-45)
1989	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1990	zeile=$(echo "$zeile" \| cut -c46-)
1991	done
1992
1993	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1995	zeile=$(echo "$lopts" \| cut -c46-)
1996	while [[ "$zeile" != "" ]]
1997	do
1998	spalte1=""
1999	spalte2=$(echo "$zeile" \| cut -c-45)
2000	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2001	zeile=$(echo "$zeile" \| cut -c46-)
2002	done
2003
2004	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2005	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2006	zeile=$(echo "$modules" \| cut -c46-)
2007	while [[ "$zeile" != "" ]]
2008	do
2009	spalte1=""
2010	spalte2=$(echo "$zeile" \| cut -c-45)
2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2012	zeile=$(echo "$zeile" \| cut -c46-)
2013	done
2014
2015	spalte1="main program:"; spalte2=$mainprog
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	else
2018	spalte1=executable:; spalte2=$executable
2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2020	fi
2021	printf "\| \| \n"
2022	spalte1="base name of files:"; spalte2=$fname
2023	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2024	if [[ $fname != $afname ]]
2025	then
2026	spalte1="base name of input files:"; spalte2=$afname
2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2028	fi
2029	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033
2034	if [[ "$ocean_file_appendix" = true ]]
2035	then
2036	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2037	fi
2038
2039	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2040	then
2041	spalte1="memory demand / PE":; spalte2="$memory MB"
2042	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2043	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	fi
2046
2047	if [[ $do_compile = true ]]
2048	then
2049	printf "\| \| \n"
2050	printf "\| Files to be compiled: \| \n"
2051	zeile=$source_list
2052	while [[ "$zeile" != "" ]]
2053	do
2054	linestart=$(echo $zeile \| cut -c-70)
2055	printf "\| %-70s \| \n" "$linestart"
2056	zeile=$(echo "$zeile" \| cut -c71-)
2057	done
2058	fi
2059	printf "#------------------------------------------------------------------------#"
2060
2061
2062
2063	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2064	if [[ $do_trace = true ]]
2065	then
2066	(( i = 0 ))
2067	while (( i < iin ))
2068	do
2069	(( i = i + 1 ))
2070	if (( i == 1 ))
2071	then
2072	printf "\n\n >>> INPUT-file assignments:\n"
2073	fi
2074	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2075	done
2076	(( i = 0 ))
2077	while (( i < iout ))
2078	do
2079	(( i = i + 1 ))
2080	if (( i == 1 ))
2081	then
2082	printf "\n\n >>> OUTPUT-file assignments:\n"
2083	fi
2084	printf "\n ${localout[$i]} : ${pathout[$i]}"
2085	done
2086	(( i = 0 ))
2087	while (( i < iic ))
2088	do
2089	(( i = i + 1 ))
2090	if (( i == 1 ))
2091	then
2092	printf "\n\n >>> INPUT-commands:\n"
2093	fi
2094	printf "\n ${in_command[$i]}"
2095	done
2096	(( i = 0 ))
2097	while (( i < ioc ))
2098	do
2099	(( i = i + 1 ))
2100	if (( i == 1 ))
2101	then
2102	printf "\n\n >>> OUTPUT-commands:\n"
2103	fi
2104	printf "\n ${out_command[$i]}"
2105	done
2106	fi
2107
2108
2109	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2110	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2111	then
2112	antwort=dummy
2113	printf "\n\n"
2114	printf " >>> everything o.k. (y/n) ? "
2115	while read antwort
2116	do
2117	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2118	then
2119	printf " >>> everything o.k. (y/n) ? "
2120	else
2121	break
2122	fi
2123	done
2124	if [[ $antwort = n \|\| $antwort = N ]]
2125	then
2126	locat=user_abort; (( iec = 0 )); exit
2127	fi
2128	if [[ $do_batch = true ]]
2129	then
2130	printf " >>> batch-job will be created and submitted"
2131	else
2132	printf " >>> MRUN will now continue to execute on this machine"
2133	fi
2134	fi
2135
2136
2137	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2138	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2139	check_depository="${working_directory}/trunk/UTIL"
2140	check_sources="${working_directory}/tmp_check_namelist_files"
2141	skip_check=false
2142
2143	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2144	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2145	then
2146	skip_check=true
2147	reason="run on remote host or parameter file check has not been compiled."
2148	fi
2149	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2150	then
2151	skip_check=true
2152	reason="parameter file check has not been compiled."
2153	fi
2154
2155	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2156	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2157	then
2158	skip_check=true
2159	reason="serial run."
2160	fi
2161
2162	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2163	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2164	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2165	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2166	if [[ $check_namelist_files == false ]]
2167	then
2168	skip_check=true
2169	reason="-z option set."
2170	fi
2171
2172	if [[ $fromhost != $localhost ]]
2173	then
2174	skip_check=true
2175	reason="submitting host is local host."
2176	fi
2177
2178	if [[ $run_coupled_model == true ]]
2179	then
2180	skip_check=true
2181	reason="coupled run."
2182	fi
2183
2184	if [[ $restart_run == true ]]
2185	then
2186	skip_check=true
2187	reason="restart run."
2188	fi
2189
2190	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2191	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2192	last_char=`echo $filename_input \| cut -c $last_char_int`
2193	if [[ "$last_char" == "f" ]]
2194	then
2195	skip_check=true
2196	reason="restart run."
2197	fi
2198
2199	if [[ $skip_check == false ]]
2200	then
2201	tmp_check=${working_directory}/tmp_check
2202
2203	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2204	# NOT NECESSARILY REQUIRED
2205	line=""
2206	found=false
2207	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2208	while read line1
2209	do
2210	line="$line1"
2211	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2212	then
2213	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2214	found=true
2215	fi
2216	done < $tmp_check
2217
2218	if [[ $found = false ]]
2219	then
2220	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2221	fi
2222
2223	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2224	# NOT NECESSARILY REQUIRED
2225	line=""
2226	found=false
2227	grep "NUDGING_DATA" $config_file > $tmp_check
2228	while read line1
2229	do
2230	line="$line1"
2231	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2232	then
2233	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2234	found=true
2235	fi
2236	done < $tmp_check
2237
2238	if [[ $found = false ]]
2239	then
2240	printf "\n +++ no NUDGING list entry found in the configuration file."
2241	fi
2242
2243	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2244	# NOT NECESSARILY REQUIRED
2245	line=""
2246	found=false
2247	grep "LSF_DATA" $config_file > $tmp_check
2248	while read line1
2249	do
2250	line="$line1"
2251	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2252	then
2253	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2254	found=true
2255	fi
2256	done < $tmp_check
2257
2258	if [[ $found = false ]]
2259	then
2260	printf "\n +++ no LSF list entry found in the configuration file."
2261	fi
2262
2263	rm -rf ${working_directory}/tmp_check
2264
2265	# CHECK IF THE P3DF FILE MUST BE CHECKED
2266	for item in $input_list
2267	do
2268	if [[ "$item" == "restart" ]]
2269	then
2270	check_restart=1
2271	else
2272	check_restart=0
2273	fi
2274	done
2275
2276	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2277	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2278	then
2279	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2280	locat=check_namelist; exit
2281	fi
2282
2283	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2284	if [[ $check_restart == 1 ]]
2285	then
2286
2287	filenamef="${filename_input}f"
2288	if [[ ! -f $filenamef ]]
2289	then
2290	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2291	check_restart=0
2292	answer=dummy
2293	printf "\n\n"
2294
2295	if [[ $silent == false ]]
2296	then
2297	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2298	do
2299	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2300	read answer
2301	done
2302	if [[ $answer = a \|\| $answer = A ]]
2303	then
2304	printf "\n +++ Aborting...."
2305	locat=normal; exit
2306	fi
2307	fi
2308	else
2309	check_restart=1
2310	fi
2311	fi
2312
2313	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2314	mkdir $check_sources
2315	cd $check_sources
2316
2317
2318	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2319	if [[ -d $add_source_path ]]
2320	then
2321	printf "\n\n *** copying files from $check_depository"
2322	cp $check_depository/check_namelist_files.tar ./
2323
2324	printf "\n\n *** untar of makefile and source files in $check_sources"
2325	tar -xf check_namelist_files.tar > /dev/null 2>&1
2326
2327	printf "\n\n *** adding user code."
2328	cp $add_source_path/* ./
2329	touch check_namelist_files.f90
2330
2331	# GET COMPILER OPTIONS AND PERFORM MAKE
2332	printf "\n\n *** compiling code if necessary...\n"
2333
2334	# workaround for batch jobs on local machine (lcxe6)
2335	if [[ $do_batch == true && $do_remote == false ]]
2336	then
2337	eval $init_cmds
2338	fi
2339
2340	# GET CHECK OPTIONS
2341	line=""
2342	found=false
2343
2344	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2345
2346	while read line1
2347	do
2348
2349	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2350	then
2351	line="$line1"
2352	fi
2353
2354	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2355	then
2356	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2357	line="$line "
2358	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'`
2359	found=true
2360	fi
2361
2362	done < $tmp_check
2363	copts_check="$copts_check -D__check -D__parallel"
2364
2365	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2366
2367	# GET MAKE OUTPUT
2368	if [[ $? != 0 ]]
2369	then
2370	printf "\n +++ error during make."
2371	answer=dummy
2372	printf "\n\n"
2373	if [[ $silent == false ]]
2374	then
2375	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2376	do
2377	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2378	read answer
2379	done
2380	if [[ $answer = a \|\| $answer = A ]]
2381	then
2382	printf "\n +++ Aborting..."
2383	rm -rf $check_sources
2384	locat=normal; exit
2385	else
2386	skip_check=true
2387	fi
2388	else
2389	skip_check=true
2390	fi
2391	fi
2392	else
2393	cp $PALM_BIN/check_namelist_files.x ./
2394	fi
2395
2396	cp $filename_input ./PARIN
2397	if [[ $check_restart == 1 ]]
2398	then
2399	cp $filenamef ./PARINF
2400	fi
2401
2402	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2403	then
2404	printf "\n *** adding topography data"
2405	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2406
2407	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2408	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2409	# WHICH REQUIRE SUFFICIENT MEMORY
2410	ulimit -s unlimited
2411	fi
2412
2413	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2414	then
2415	printf "\n *** adding nudging data"
2416	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2417	fi
2418
2419	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2420	then
2421	printf "\n *** adding large scale forcing data"
2422	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2423	fi
2424
2425	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2426	cat > ENVPAR << %%END%%
2427	&envpar run_identifier = '$fname', host = '$host',
2428	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2429	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2430	maximum_cpu_time_allowed = ${cpumax}.,
2431	revision = '$global_revision',
2432	local_dvrserver_running = $local_dvrserver_running /
2433
2434	%%END%%
2435
2436	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2437	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2438	then
2439	printf "\n +++ WARNING: check_namelist_files.x not found."
2440	answer=dummy
2441	printf "\n\n"
2442
2443	if [[ $silent == false ]]
2444	then
2445	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2446	do
2447	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2448	read answer
2449	done
2450	if [[ $answer = a \|\| $answer = A ]]
2451	then
2452	printf "\n +++ Aborting..."
2453	rm -rf $check_sources
2454	locat=normal; exit
2455	else
2456	printf "\n *** skipping parameter file check."
2457	fi
2458	fi
2459
2460	elif [[ $skip_check == false ]]
2461	then
2462	# STARTING THE PARAMETER FILE CHECK
2463	printf "\n\n *** starting parameter file check..."
2464
2465	# CHECKING THE P3D FILE
2466	printf "\n\n (1) checking $filename_input"
2467	echo "$numprocs 0 0" > VARIN
2468	errors=`./check_namelist_files.x < VARIN 2>&1`
2469
2470	check_error=false
2471	if [[ "$errors" == "" ]]
2472	then
2473	printf " --> o.k."
2474	else
2475	printf " --> failed."
2476	check_error=true
2477	printf "\n\n $errors"
2478	fi
2479
2480	# CHECKING THE PD3F FILE IF NECESSARY
2481	if [[ $check_restart == 1 && $check_error == false ]]
2482	then
2483	printf "\n\n (2) checking $filenamef"
2484
2485	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2486	# IN &INIPAR LIST
2487	found=false
2488	cat PARINF \| while read line
2489	do
2490	line=$(echo $line\|sed 's/ //g')
2491	if [[ $line == "&inipar" ]]
2492	then
2493	start_search=true
2494	fi
2495
2496	if [[ $start_search == true ]]
2497	then
2498	if [[ $line == "initializing_actions='read_restart_data'" ]]
2499	then
2500	found=true
2501	break
2502	fi
2503	fi
2504
2505	if [[ $line == "/" ]]
2506	then
2507	start_search=false
2508	fi
2509
2510	done
2511
2512	if [[ $found = false ]]
2513	then
2514	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2515	printf "\n in &inipar list in $fname$p3df_suffix."
2516	rm -rf $check_sources
2517	locat=check_namelist; exit
2518	fi
2519
2520	# READ max_user_pr FROM FILES
2521	if [[ -f parin_for_check ]]
2522	then
2523	read max_pr_user < parin_for_check
2524	else
2525	max_user_pr=0
2526	fi
2527
2528	echo "$numprocs 1 $max_pr_user" > VARIN
2529	errors=`./check_namelist_files.x < VARIN 2>&1`
2530
2531	if [[ "$errors" == "" ]]
2532	then
2533	printf " --> o.k."
2534	else
2535	printf " --> failed."
2536	check_error=true
2537	printf "\n\n $errors"
2538	fi
2539	fi
2540
2541	# REPORT ERRORS AND CONTINUE/EXIT
2542	if [[ $check_error == true ]]
2543	then
2544	printf "\n +++ errors found in the parameter file!\n"
2545	answer=dummy
2546	printf "\n\n"
2547
2548	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2549	do
2550	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2551	read answer
2552	done
2553
2554	if [[ $answer = a \|\| $answer = A ]]
2555	then
2556	printf "\n +++ Aborting..."
2557	rm -rf $check_sources
2558	locat=normal; exit
2559	fi
2560	else
2561	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2562	fi
2563	rm -rf $check_sources
2564	fi
2565	else
2566	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2567	fi
2568
2569	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2570	rm -rf $check_sources
2571	cd $working_directory
2572
2573
2574	# DETERMINE PATH FOR MAKE DEPOSITORY
2575	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2576	then
2577
2578	line=""
2579	grep "%depository_path" $config_file > tmp_mrun
2580	while read line
2581	do
2582	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2583	then
2584	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2585	then
2586	global_depository_path=`echo $line \| cut -d" " -s -f2`
2587	fi
2588	fi
2589	done < tmp_mrun
2590
2591	line=""
2592	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2593	while read line
2594	do
2595	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2596	then
2597	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2598	then
2599	local_depository_path=`echo $line \| cut -d" " -s -f2`
2600	fi
2601	fi
2602	done < tmp_mrun
2603
2604	if [[ "$local_depository_path" = "" ]]
2605	then
2606	if [[ "$global_depository_path" != "" ]]
2607	then
2608	local_depository_path=$global_depository_path
2609	else
2610	printf "\n\n +++ no depository path found in configuration file"
2611	printf "\n for local host \"$localhost\" "
2612	printf "\n please set \"\%depository_path\" in configuration file\n"
2613	locat=config_file; exit
2614	fi
2615	fi
2616	eval local_depository_path=$local_depository_path
2617	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2618	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2619
2620
2621	basename=`echo $mainprog \| cut -f1 -d"."`
2622	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2623	if [[ ! -f $make_depository ]]
2624	then
2625	printf "\n"
2626	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2627	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2628	fi
2629
2630	fi
2631
2632
2633	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2634	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2635	if [[ $do_batch = false ]]
2636	then
2637
2638
2639	# CREATE THE TEMPORARY WORKING DIRECTORY
2640	mkdir -p $TEMPDIR
2641	chmod go+rx $TEMPDIR
2642	tmpcreate=true
2643
2644
2645	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2646	# INTO THE TEMPORARY WORKING DIRECTORY
2647	if [[ $do_compile = true ]]
2648	then
2649
2650	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2651	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2652	if [[ $localhost = nech ]]
2653	then
2654	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2655	if mkdir -p $TEMPDIR_COMPILE
2656	then
2657	printf "\n *** \"$TEMPDIR_COMPILE\" "
2658	printf "\n is generated as temporary directory for cross compiling\n"
2659	else
2660	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2661	printf "\n needed for cross compilation failed"
2662	locat=compile
2663	exit
2664	fi
2665	else
2666	TEMPDIR_COMPILE=$TEMPDIR
2667	fi
2668
2669	cp $make_depository $TEMPDIR_COMPILE
2670	cd $TEMPDIR_COMPILE
2671	tar -xf $make_depository > /dev/null 2>&1
2672	cd - > /dev/null
2673
2674	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2675	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2676	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2677	then
2678	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2679	else
2680	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2681	fi
2682
2683	else
2684
2685	cp $executable ${TEMPDIR}/a.out
2686
2687	fi
2688
2689
2690	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2691	cd $TEMPDIR
2692	printf "\n *** changed to temporary directory: $TEMPDIR"
2693
2694
2695	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2696	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2697	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2698	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2699	(( i = 0 ))
2700	while (( i < iout ))
2701	do
2702	(( i = i + 1 ))
2703	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2704	then
2705	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2706	else
2707	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2708	fi
2709	done
2710
2711
2712	# IF REQUIRED, START WITH COMPILING
2713	if [[ $do_compile = true ]]
2714	then
2715
2716
2717	if [[ -f a.out ]]
2718	then
2719
2720	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2721	printf "\n\n\n *** executable a.out found"
2722	printf "\n no compilation required \n"
2723
2724	else
2725
2726	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2727	printf "\n\n\n *** compilation starts \n$dashes\n"
2728	printf " *** compilation with make using following options:\n"
2729	printf " make depository: $make_depository"
2730	if [[ "$mopts" != "" ]]
2731	then
2732	printf " make options: $mopts\n"
2733	fi
2734	printf " compilername: $compiler_name\n"
2735	printf " compiler options: $fopts\n"
2736	printf " preprocessor directives: $cpp_options \n"
2737	printf " linker options: $lopts \n"
2738	if [[ "$modules" != "" ]]
2739	then
2740	printf " modules to be load: $modules \n"
2741	fi
2742	printf " source code files: $source_list \n"
2743
2744	if [[ $localhost = nech ]]
2745	then
2746	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\" "
2747	cp $TEMPDIR_COMPILE/a.out .
2748	[[ $? != 0 ]] && compile_error=true
2749	rm -rf $TEMPDIR_COMPILE
2750	elif [[ $localhost = ibmh ]]
2751	then
2752	printf " compiler is called via ssh on \"plogin1\" \n"
2753	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\" "
2754	[[ ! -f a.out ]] && compile_error=true
2755	continue # STATUS=1, IF a.out EXISTS
2756	elif [[ $localhost = lcflow ]]
2757	then
2758	printf " compiler is called via ssh on \"flow\" \n"
2759	/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\" "
2760	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2761	[[ "$check_for_file" = "" ]] && compile_error=true
2762	continue # STATUS=1, IF a.out EXISTS
2763	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2764	then
2765	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2766	else
2767	[[ "$init_cmds" != "" ]] && eval $init_cmds
2768	[[ "$module_calls" != "" ]] && eval $module_calls
2769	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2770	fi
2771
2772	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2773	then
2774	printf "\n +++ error occured while compiling or linking"
2775	locat=compile
2776
2777	exit
2778	else
2779	printf "$dashes\n *** compilation finished \n"
2780	fi
2781
2782	fi
2783
2784	fi
2785
2786
2787	# PROVIDE THE INPUT FILES
2788	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2789	(( i = 0 ))
2790	while (( i < iin ))
2791	do
2792	(( i = i + 1 ))
2793	if (( i == 1 ))
2794	then
2795	printf "\n\n *** providing INPUT-files:\n$dashes"
2796	fi
2797
2798
2799	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2800	if [[ "${transin[$i]}" = unavailable ]]
2801	then
2802	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2803	then
2804	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2805	printf "\n is not available!"
2806	else
2807	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2808	printf "\n is not available!"
2809	fi
2810	continue
2811	fi
2812
2813	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2814	files_for_pes=false; datentyp=file
2815	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2816	then
2817	files_for_pes=true; datentyp=directory
2818	actionin[$i]=""
2819	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2820	then
2821	actionin[$i]=""
2822	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2823	then
2824	files_for_pes=true; datentyp=directory
2825	actionin[$i]="ar"
2826	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2827	then
2828	actionin[$i]="ar"
2829	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2830	then
2831	files_for_pes=true; datentyp=directory
2832	actionin[$i]="fl"
2833	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2834	then
2835	actionin[$i]="fl"
2836	fi
2837
2838	if [[ $files_for_pes = true ]]
2839	then
2840	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2841	else
2842	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2843	fi
2844
2845	# INPUT-FILE FOR A RESTART RUN.
2846	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2847	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2848	if [[ "${actionin[$i]}" = fl ]]
2849	then
2850	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2851	if [[ $files_for_pes = false ]]
2852	then
2853	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2854	then
2855	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2856	got_tmp[$i]=true
2857	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2858	then
2859	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2860	printf "\n *** trying to use backup copy in \"$WORK\" "
2861	cp $WORK/${frelin[$i]} ${localin[$i]}
2862	else
2863	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2864	printf "\n or \"$tmp_data_catalog\" does not exist!"
2865	printf "\n *** trying to get copy from archive"
2866	actionin[$i]=ar
2867	fi
2868	else
2869	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2870	then
2871	mkdir ${localin[$i]}
2872	cd $tmp_data_catalog/${frelin[$i]}
2873	for file in $(ls *)
2874	do
2875	ln $file $TEMPDIR/${localin[$i]}
2876	done
2877	cd $TEMPDIR
2878	got_tmp[$i]=true
2879	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2880	then
2881	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2882	printf "\n *** trying to use backup copy in \"$WORK\" "
2883	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2884	else
2885	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2886	printf "\n or \"$tmp_data_catalog\" does not exist!"
2887	printf "\n *** trying to get copy from archive"
2888	actionin[$i]=ar
2889	fi
2890	fi
2891	fi
2892
2893
2894	# FILE IS STORED ON THE ARCHIVE SYSTEM
2895	if [[ "${actionin[$i]}" = ar ]]
2896	then
2897
2898	if [[ $files_for_pes = false ]]
2899	then
2900	printf "\n file will be restored from archive-system ($archive_system)!"
2901	else
2902	printf "\n directory will be restored from archive-system ($archive_system)!"
2903	fi
2904
2905	file_restored=false
2906
2907	if [[ $archive_system = asterix ]]
2908	then
2909	do_stagein=true
2910	(( stagein_anz = 0 ))
2911	while [[ $do_stagein = true ]]
2912	do
2913	if [[ $files_for_pes = false ]]
2914	then
2915	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2916	else
2917	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2918	fi
2919	cat STAGEIN_OUTPUT
2920	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2921	then
2922	file_restored=true
2923	do_stagein=false
2924	else
2925	(( stagein_anz = stagein_anz + 1 ))
2926	if (( stagein_anz == 10 ))
2927	then
2928	printf "\n +++ stagein stoped after 10 tries"
2929	locat=stage
2930	exit
2931	fi
2932	printf "\n +++ restoring from archive failed, trying again:"
2933	sleep 900
2934	fi
2935	done
2936	elif [[ $archive_system = DMF ]]
2937	then
2938	if [[ $files_for_pes = false ]]
2939	then
2940	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2941	locat=DMF
2942	exit
2943	else
2944	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2945	cp -r $ARCHIVE/${frelin[$i]} $PWD
2946	file_restored=true
2947	fi
2948	elif [[ $archive_system = tivoli ]]
2949	then
2950	if [[ $files_for_pes = false ]]
2951	then
2952	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2953	else
2954	(( inode = 0 ))
2955	while (( inode < nodes ))
2956	do
2957	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2958	(( inode = inode + 1 ))
2959	done
2960	fi
2961	file_restored=true
2962	elif [[ $archive_system = ut ]]
2963	then
2964	if [[ $files_for_pes = false ]]
2965	then
2966	cp $UT/${frelin[$i]} .
2967	else
2968	(( inode = 0 ))
2969	while (( inode < nodes ))
2970	do
2971	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2972	(( inode = inode + 1 ))
2973	done
2974	fi
2975	file_restored=true
2976	else
2977	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2978	locat=rearchive
2979	exit
2980	fi
2981
2982	if [[ $file_restored = true ]]
2983	then
2984
2985	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2986	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2987	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2988	if [[ $files_for_pes = false ]]
2989	then
2990	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2991	else
2992	mkdir $tmp_data_catalog/${frelin[$i]}
2993	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2994	fi
2995	got_tmp[$i]=true
2996
2997	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2998	mv ${frelin[$i]} ${localin[$i]}
2999
3000	fi
3001	fi
3002
3003
3004	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3005	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3006	then
3007
3008	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3009	then
3010
3011	# FILE COPIES ARE PROVIDED FOR ALL CORES
3012	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3013	printf "\n file will be provided for $numprocs processors"
3014	mkdir ${localin[$i]}
3015	ival=$numprocs
3016	(( ii = 0 ))
3017	while (( ii <= ival-1 ))
3018	do
3019	if (( ii < 10 ))
3020	then
3021	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3022	elif (( ii < 100 ))
3023	then
3024	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3025	elif (( ii < 1000 ))
3026	then
3027	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3028	else
3029	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3030	fi
3031	(( ii = ii + 1 ))
3032	done
3033
3034	else
3035
3036	if [[ $files_for_pes = true ]]
3037	then
3038
3039	# PROVIDE FILES FOR EACH CORE
3040	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3041	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3042	printf "\n providing $numprocs files for the respective processors"
3043	mkdir ${localin[$i]}
3044	if [[ $link_local_input = true ]]
3045	then
3046	printf " using ln -f\n"
3047	cd ${absnamein[$i]}
3048	for file in $(ls *)
3049	do
3050	ln -f $file ${localin[$i]}
3051	done
3052	cd $TEMPDIR
3053	fi
3054
3055	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3056	if [[ ! -f "${localin[$i]}/_0000" ]]
3057	then
3058	if [[ $link_local_input = true ]]
3059	then
3060	printf " ln failed for .../_0000, using cp...\n"
3061	fi
3062	cp -r ${absnamein[$i]}/* ${localin[$i]}
3063	fi
3064
3065	else
3066
3067	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3068	if [[ $link_local_input = true ]]
3069	then
3070	printf " using ln -f\n"
3071	ln -f ${absnamein[$i]} ${localin[$i]}
3072	fi
3073	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3074	if [[ ! -f "${localin[$i]}" ]]
3075	then
3076	if [[ $link_local_input = true ]]
3077	then
3078	printf " ln failed, using cp...\n"
3079	fi
3080	cp ${absnamein[$i]} ${localin[$i]}
3081	fi
3082	fi
3083	fi
3084	fi
3085
3086	done
3087	if (( i != 0 ))
3088	then
3089	printf "\n$dashes\n *** all INPUT-files provided \n"
3090	fi
3091
3092
3093	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3094	(( i = 0 ))
3095	while (( i < iic ))
3096	do
3097	(( i = i + 1 ))
3098	if (( i == 1 ))
3099	then
3100	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3101	fi
3102	printf "\n >>> ${in_command[$i]}"
3103	eval ${in_command[$i]}
3104	if (( i == iic ))
3105	then
3106	printf "\n$dashes\n"
3107	fi
3108	done
3109
3110
3111	# SET THE REMAINING CPU-TIME
3112	cpurest=${cpumax}.
3113
3114
3115	# START DVR STREAMING SERVER
3116	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3117	then
3118	if [[ "$dvr_server" != "" ]]
3119	then
3120
3121	printf "\n\n *** preparing the dvr streaming server configuration file"
3122
3123	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3124	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3125	if [[ "$running_dvrserver_id" != "" ]]
3126	then
3127
3128	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3129	printf "\n This server is used instead starting a new one!"
3130	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3131
3132	else
3133
3134	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3135	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3136	then
3137	cp ${PALM_BIN}/.dvrserver.config .
3138
3139	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3140	user_id=`id -u`
3141	group_id=`id -g`
3142
3143	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3144	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3145	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3146	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3147	mv .dvrserver.3 .dvrserver.config
3148	rm .dvrserver.1 .dvrserver.2
3149
3150	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3151	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3152	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3153	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3154	local_dvrserver_running=.TRUE.
3155	else
3156	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3157	printf "\n \"$PALM_BIN\" "
3158	locat=dvr
3159	exit
3160	fi
3161
3162	fi
3163
3164	else
3165	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3166	fi
3167	fi
3168
3169
3170	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3171	# (FILE ENVPAR WILL BE READ BY PALM)
3172	cat > ENVPAR << %%END%%
3173	&envpar run_identifier = '$fname', host = '$localhost',
3174	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3175	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3176	maximum_cpu_time_allowed = ${cpumax}.,
3177	revision = '$global_revision',
3178	local_dvrserver_running = $local_dvrserver_running /
3179
3180	%%END%%
3181
3182
3183	# STARTING THE EXECUTABLE
3184	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3185	PATH=$PATH:$TEMPDIR
3186
3187	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3188	if [[ "$mpi_debug" = true ]]
3189	then
3190	export MPI_CHECK_ARGS=1
3191	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3192	fi
3193
3194	if [[ "$totalview" = true ]]
3195	then
3196	printf "\n *** totalview debugger will be used"
3197	tv_opt="-tv"
3198	else
3199	tv_opt=""
3200	fi
3201
3202	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3203	then
3204	if [[ "$ENVIRONMENT" = BATCH ]]
3205	then
3206	continue
3207	fi
3208	if [[ $localhost = ibmh ]]
3209	then
3210
3211	# SETUP THE IBM MPI ENVIRONMENT
3212	export MP_SHARED_MEMORY=yes
3213	export AIXTHREADS_SCOPE=S
3214	export OMP_NUM_THREADS=$threads_per_task
3215	export AUTHSTATE=files
3216	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3217
3218	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3219	export MP_ADAPTER_USE=shared
3220	export MP_CPU_USE=multiple
3221	export MP_TIMEOUT=1200
3222
3223	unset MP_TASK_AFFINITY
3224
3225	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3226	#(( ii = 1 ))
3227	#while (( ii <= $numprocs ))
3228	#do
3229	# echo $localhost_realname >> hostfile
3230	# (( ii = ii + 1 ))
3231	#done
3232	#export MP_HOSTFILE=hostfile
3233
3234	if [[ "$LOADLBATCH" = yes ]]
3235	then
3236	totalview poe a.out $ROPTS
3237	else
3238	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3239	export TVDSVRLAUNCHCMD=ssh
3240	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3241	fi
3242
3243	fi # END DEBUG MODE
3244
3245	else
3246
3247	# NORMAL EXECUTION
3248	if [[ -n $numprocs ]]
3249	then
3250
3251	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3252	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3253	then
3254
3255	# SETUP THE IBM MPI ENVIRONMENT
3256	if [[ $host != ibmh && $host != ibmkisti ]]
3257	then
3258	export MP_SHARED_MEMORY=yes
3259	export AIXTHREAD_SCOPE=S
3260	export OMP_NUM_THREADS=$threads_per_task
3261	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3262	export AUTHSTATE=files
3263	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3264	# export MP_PRINTENV=yes
3265
3266	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3267	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3268	export MP_WAIT_MODE=poll
3269	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3270	fi
3271
3272	if [[ $host = ibmkisti ]]
3273	then
3274	export LANG=en_US
3275	export MP_SHARED_MEMORY=yes
3276	if [[ $threads_per_task = 1 ]]
3277	then
3278	export MP_SINGLE_THREAD=yes
3279	export MEMORY_AFFINITY=MCM
3280	else
3281	export OMP_NUM_THREADS=$threads_per_task
3282	fi
3283	fi
3284
3285	if [[ "$LOADLBATCH" = yes ]]
3286	then
3287	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3288	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3289	then
3290	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3291	else
3292	if [[ $run_coupled_model = false ]]
3293	then
3294	if [[ "$ocean_file_appendix" = true ]]
3295	then
3296	echo "precursor_ocean" > runfile_atmos
3297	else
3298	echo "precursor_atmos" > runfile_atmos
3299	fi
3300	else
3301	(( iia = $numprocs_atmos / $threads_per_task ))
3302	(( iio = $numprocs_ocean / $threads_per_task ))
3303	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3304	printf "\n using $coupled_mode coupling"
3305	printf "\n\n"
3306	echo "coupled_run $iia $iio" > runfile_atmos
3307	fi
3308	poe ./a.out $ROPTS < runfile_atmos
3309	fi
3310	else
3311	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3312	then
3313	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3314	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3315	then
3316	if [[ -f $hostfile ]]
3317	then
3318	cp $hostfile hostfile
3319	else
3320	(( ii = 1 ))
3321	while (( ii <= $numprocs ))
3322	do
3323	echo $localhost_realname >> hostfile
3324	(( ii = ii + 1 ))
3325	done
3326	fi
3327	export MP_HOSTFILE=hostfile
3328	if [[ $run_coupled_model = false ]]
3329	then
3330	if [[ "$ocean_file_appendix" = true ]]
3331	then
3332	echo "precursor_ocean" > runfile_atmos
3333	else
3334	echo "precursor_atmos" > runfile_atmos
3335	fi
3336	else
3337	(( iia = $numprocs_atmos / $threads_per_task ))
3338	(( iio = $numprocs_ocean / $threads_per_task ))
3339	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3340	printf "\n using $coupled_mode coupling"
3341	printf "\n\n"
3342	echo "coupled_run $iia $iio" > runfile_atmos
3343	fi
3344
3345	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3346
3347	else
3348	if [[ "$host_file" = "" ]]
3349	then
3350	printf "\n +++ no hostfile given in configuration file"
3351	locat=config_file
3352	exit
3353	else
3354	eval host_file=$host_file
3355	fi
3356	export MP_HOSTFILE=$host_file
3357	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3358	fi
3359	fi
3360	elif [[ $host = nech ]]
3361	then
3362	(( ii = nodes ))
3363	if [[ $ii = 1 ]]
3364	then
3365	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3366	export MPIPROGINF=YES
3367	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3368	echo "*** execution on single node with mpirun"
3369	mpirun -np $numprocs ./a.out $ROPTS
3370	else
3371	(( i = 0 ))
3372	while (( i < ii ))
3373	do
3374	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3375	(( i = i + 1 ))
3376	done
3377
3378	echo "#!/bin/sh" > mpi_exec_shell
3379	echo " " >> mpi_exec_shell
3380	echo "set -u" >> mpi_exec_shell
3381	echo "F_ERRCNT=0" >> mpi_exec_shell
3382	echo "MPIPROGINV=YES" >> mpi_exec_shell
3383	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3384	echo "cpurest=$cpurest" >> mpi_exec_shell
3385	echo "fname=$fname" >> mpi_exec_shell
3386	echo "localhost=$localhost" >> mpi_exec_shell
3387	echo "return_addres=$return_addres" >> mpi_exec_shell
3388	echo "return_username=$return_username" >> mpi_exec_shell
3389	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3390	echo "write_binary=$write_binary" >> mpi_exec_shell
3391	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3392	echo " " >> mpi_exec_shell
3393	echo "export F_ERRCNT" >> mpi_exec_shell
3394	echo "export MPIPROGINV" >> mpi_exec_shell
3395	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3396	echo "export cpurest" >> mpi_exec_shell
3397	echo "export fname" >> mpi_exec_shell
3398	echo "export localhost" >> mpi_exec_shell
3399	echo "export return_addres" >> mpi_exec_shell
3400	echo "export return_username" >> mpi_exec_shell
3401	echo "export tasks_per_node" >> mpi_exec_shell
3402	echo "export write_binary" >> mpi_exec_shell
3403	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3404	echo " " >> mpi_exec_shell
3405	echo "exec ./a.out" >> mpi_exec_shell
3406
3407	chmod u+x mpi_exec_shell
3408	export MPIPROGINF=YES
3409	mpirun -f multinode_config &
3410	wait
3411
3412	fi
3413	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3414	then
3415
3416	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3417	# DOES NOT EXIST
3418	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3419	then
3420	if [[ -f $hostfile ]]
3421	then
3422	cp $hostfile hostfile
3423	(( ii = $numprocs / $threads_per_task ))
3424	else
3425	(( ii = 1 ))
3426	while (( ii <= $numprocs / $threads_per_task ))
3427	do
3428	echo $localhost_realname >> hostfile
3429	(( ii = ii + 1 ))
3430	done
3431	fi
3432	eval zeile=\"`head -n $ii hostfile`\"
3433	printf "\n *** running on: $zeile"
3434	fi
3435
3436	(( ii = $numprocs / $threads_per_task ))
3437	export OMP_NUM_THREADS=$threads_per_task
3438
3439	if [[ $threads_per_task != 1 ]]
3440	then
3441	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3442	# MAY ABORT
3443	ulimit -s unlimited
3444	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3445	fi
3446	if [[ $run_coupled_model = false ]]
3447	then
3448	if [[ "$ocean_file_appendix" = true ]]
3449	then
3450	echo "precursor_ocean" > runfile_atmos
3451	else
3452	echo "precursor_atmos" > runfile_atmos
3453	fi
3454	printf "\n\n"
3455
3456	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3457	then
3458	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3459	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3460	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3461	elif [[ $host = lccrayf ]]
3462	then
3463	aprun -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3464	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3465	then
3466	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3467	elif [[ $host = lcflow ]]
3468	then
3469	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3470	elif [[ $host = lcsb ]]
3471	then
3472	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3473	elif [[ $host = lckiaps ]]
3474	then
3475	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3476	elif [[ $host = lckyu* ]]
3477	then
3478	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3479	else
3480	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3481	fi
3482	else
3483
3484	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3485	(( iia = $numprocs_atmos / $threads_per_task ))
3486	(( iio = $numprocs_ocean / $threads_per_task ))
3487	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3488	printf "\n using $coupled_mode coupling"
3489	printf "\n\n"
3490
3491	if [[ $coupled_mode = "mpi2" ]]
3492	then
3493	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3494	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3495
3496	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3497	then
3498
3499	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3500	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3501
3502	else
3503	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3504	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3505	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3506	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3507	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3508	fi
3509	wait
3510
3511	else
3512
3513	echo "coupled_run $iia $iio" > runfile_atmos
3514
3515	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3516	then
3517
3518	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3519
3520	elif [[ $host = lck \|\| $host = lckordi ]]
3521	then
3522
3523	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3524
3525	elif [[ $host = lckyu* ]]
3526	then
3527
3528	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3529
3530	fi
3531	wait
3532	fi
3533
3534	fi
3535
3536	elif [[ $host = lckyoto ]]
3537	then
3538	set -xv
3539	export P4_RSHCOMMAND=plesh
3540	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3541	if [[ "$ENVIRONMENT" = BATCH ]]
3542	then
3543	if [[ "$cond2" = fujitsu ]]
3544	then
3545	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3546	elif [[ "cond2" = pgi ]]
3547	then
3548	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3549	else
3550	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3551	fi
3552	else
3553	if [[ "$cond2" = "" ]]
3554	then
3555	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3556	else
3557	mpirun -np $numprocs ./a.out $ROPTS
3558	fi
3559	fi
3560	set +xv
3561
3562	elif [[ $host = lctit ]]
3563	then
3564	export OMP_NUM_THREADS=$threads_per_task
3565	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3566	if [[ "$threads_per_task" != 1 ]]
3567	then
3568	export MV2_ENABLE_AFFINITY=0
3569	fi
3570	echo "----- PBS_NODEFILE content:"
3571	cat $PBS_NODEFILE
3572	echo "-----"
3573	(( ii = $numprocs / $threads_per_task ))
3574	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3575	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3576	else
3577	mpprun -n $numprocs a.out $ROPTS
3578	fi
3579	else
3580	a.out $ROPTS
3581	fi
3582	fi
3583
3584	if [[ $? != 0 ]]
3585	then
3586
3587	# ABORT IN CASE OF RUNTIME ERRORS
3588	printf "\n +++ runtime error occured"
3589	locat=execution
3590	exit
3591
3592	else
3593
3594	printf "\n$dashes\n *** execution finished \n"
3595
3596	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3597	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3598	if [[ "$dvrserver_id" != "" ]]
3599	then
3600	kill $dvrserver_id
3601	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3602
3603	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3604	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3605	if [[ -d DATA_DVR ]]
3606	then
3607
3608	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3609	# DIRECTORY
3610	cp .dvrserver.config DATA_DVR
3611
3612	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3613	# SEQUENCE MODE DATA TOO)
3614	process_dvr_output -d DATA_DVR -f $fname -s
3615
3616	else
3617
3618	# PROCESS THE LOCAL OUTPUT
3619	process_dvr_output -l -d DATA_DVR -f $fname
3620
3621	fi
3622
3623	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3624	then
3625
3626	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3627	process_dvr_output -l -d DATA_DVR -f $fname
3628
3629	fi
3630	fi
3631
3632
3633
3634	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3635	# BY EACH CORE INTO ONE FILE
3636	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3637	then
3638	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3639	printf "\n 2d- and/or 3d-data may be incomplete!"
3640	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3641	elif [[ "$combine_plot_fields" == true ]]
3642	then
3643	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3644	then
3645	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3646	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3647	else
3648	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3649	combine_plot_fields${block}.x
3650	fi
3651	else
3652
3653	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3654	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3655	# ??? koennen wir das streichen ???
3656	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3657	fi
3658
3659
3660
3661	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3662	(( i = 0 ))
3663	while (( i < ioc ))
3664	do
3665	(( i = i + 1 ))
3666	if (( i == 1 ))
3667	then
3668	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3669	fi
3670	printf "\n >>> ${out_command[$i]}"
3671	eval ${out_command[$i]}
3672	if (( i == ioc ))
3673	then
3674	printf "\n$dashes\n"
3675	fi
3676	done
3677
3678
3679	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3680	if [[ $do_trace = true ]]
3681	then
3682	printf "\n\n"
3683	ls -al
3684	fi
3685
3686
3687
3688	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3689	(( i = 0 ))
3690	while (( i < iout ))
3691	do
3692	(( i = i + 1 ))
3693	if (( i == 1 ))
3694	then
3695	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3696	fi
3697
3698	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3699	files_for_pes=false; filetyp=file
3700	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3701	then
3702	files_for_pes=true; filetyp=directory
3703	actionout[$i]=""
3704	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3705	then
3706	actionout[$i]=""
3707	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3708	then
3709	files_for_pes=true; filetyp=directory
3710	actionout[$i]="ar"
3711	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3712	then
3713	actionout[$i]="ar"
3714	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3715	then
3716	files_for_pes=true; filetyp=directory
3717	actionout[$i]="fl"
3718	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3719	then
3720	actionout[$i]="fl"
3721	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3722	then
3723	files_for_pes=true; filetyp=directory
3724	actionout[$i]="tr"
3725	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3726	then
3727	actionout[$i]="tr"
3728	fi
3729
3730	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3731	then
3732	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3733	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3734	then
3735	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3736	else
3737
3738
3739	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3740	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3741	if [[ "${actionout[$i]}" = tr ]]
3742	then
3743	if [[ $localhost != $fromhost ]]
3744	then
3745	if [[ $files_for_pes = false ]]
3746	then
3747	cps=""
3748	cst=""
3749	else
3750	cps=-c
3751	cst="/"
3752	fi
3753	if [[ $localhost = nech ]]
3754	then
3755
3756	# TRANSFER IN SEPERATE JOB
3757	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3758	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3759	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3760	if [[ $files_for_pes = false ]]
3761	then
3762	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3763	else
3764	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3765	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3766	fi
3767
3768	echo "set -x" > transfer_${localout[$i]}
3769	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3770
3771	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3772	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3773	printf "\n or higher cycle\n"
3774	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]}
3775
3776	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3777
3778	if [[ $localhost = nech ]]
3779	then
3780	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3781	else
3782	if [[ "$LOGNAME" = b323013 ]]
3783	then
3784	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3785	else
3786	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3787	fi
3788	fi
3789
3790	else
3791
3792	# TRANSFER WITHIN THIS JOB
3793	transfer_failed=false
3794	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3795	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3796	if [[ $localhost = lccrayb ]]
3797	then
3798	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]}"
3799	elif [[ $localhost = lccrayh ]]
3800	then
3801	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]}"
3802	else
3803	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3804	fi
3805	[[ $? != 0 ]] && transfer_failed=true
3806
3807	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3808	if [[ $transfer_failed = true ]]
3809	then
3810	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3811	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3812
3813	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3814	eval local_catalog=${pathout[$i]}
3815	if [[ ! -d $local_catalog ]]
3816	then
3817	printf " *** local directory does not exist. Trying to create:\n"
3818	printf " $local_catalog \n"
3819	mkdir -p $local_catalog
3820	fi
3821	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3822	transfer_problems=true
3823	fi
3824	fi
3825	else
3826
3827	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3828	actionout[$i]=""
3829	fi
3830	fi
3831
3832
3833	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3834	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3835	if [[ "${actionout[$i]}" = tra ]]
3836	then
3837	if [[ $localhost != $fromhost ]]
3838	then
3839	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3840	then
3841
3842	# TRANSFER IN SEPERATE JOB
3843	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3844	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3845	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3846	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3847
3848	echo "set -x" > transfer_${localout[$i]}
3849	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3850
3851	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3852	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3853	printf "\n or higher cycle\n"
3854	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]}
3855
3856	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3857
3858	if [[ $localhost = nech ]]
3859	then
3860	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3861	else
3862	if [[ $LOGNAME = b323013 ]]
3863	then
3864	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3865	else
3866	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3867	fi
3868	fi
3869
3870	else
3871
3872	# TRANSFER WITHIN THIS JOB
3873	transfer_failed=false
3874	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3875	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3876	if [[ $localhost = lccrayb ]]
3877	then
3878	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]}"
3879	elif [[ $localhost = lccrayh ]]
3880	then
3881	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]}"
3882	else
3883	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3884	fi
3885	[[ $? != 0 ]] && transfer_failed=true
3886
3887	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3888	if [[ $transfer_failed = true ]]
3889	then
3890	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3891	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3892
3893	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3894	eval local_catalog=${pathout[$i]}
3895	if [[ ! -d $local_catalog ]]
3896	then
3897	printf " *** local directory does not exist. Trying to create:\n"
3898	printf " $local_catalog \n"
3899	mkdir -p $local_catalog
3900	fi
3901
3902	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3903	transfer_problems=true
3904	fi
3905	fi
3906	else
3907
3908	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3909	actionout[$i]=a
3910	fi
3911	fi
3912
3913
3914	# OUTPUT-FILE FOR A RESTART-RUN.
3915	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3916	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3917	# AS LAST ACTION, ARCHIVING IS INITIATED.
3918	if [[ "${actionout[$i]}" = fl ]]
3919	then
3920	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3921	chmod g+rx $tmp_data_catalog
3922	if [[ $files_for_pes = false ]]
3923	then
3924	printf "\n >>> OUTPUT: ${localout[$i]} to"
3925	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3926	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3927	else
3928	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3929	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3930	mkdir $tmp_data_catalog/${frelout[$i]}
3931	cd ${localout[$i]}
3932	for file in $(ls *)
3933	do
3934	ln -f $file $tmp_data_catalog/${frelout[$i]}
3935	done
3936	cd $TEMPDIR
3937	fi
3938
3939
3940	# CREATE AND SUBMIT ARCHIVING-JOB
3941	if [[ $store_on_archive_system = true ]]
3942	then
3943
3944	if [[ $archive_system = asterix ]]
3945	then
3946	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3947	if [[ $files_for_pes = false ]]
3948	then
3949	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3950	else
3951	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3952	fi
3953	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3954	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3955	echo "then" >> archive_${frelout[$i]}
3956	echo " do_stageout=false" >> archive_${frelout[$i]}
3957	echo "else" >> archive_${frelout[$i]}
3958	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3959	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3960	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3961	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3962	if [[ $files_for_pes = false ]]
3963	then
3964	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3965	else
3966	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3967	fi
3968	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3969	echo "fi" >> archive_${frelout[$i]}
3970	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3971	elif [[ $archive_system = DMF ]]
3972	then
3973	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3974	if [[ $files_for_pes = false ]]
3975	then
3976	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3977	locat=DMF
3978	exit
3979	else
3980	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3981	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3982	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3983	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3984	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3985	fi
3986	elif [[ $archive_system = tivoli ]]
3987	then
3988	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3989	if [[ $files_for_pes = false ]]
3990	then
3991	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3992	echo "set -x" >> archive_${frelout[$i]}
3993	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3994	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3995	else
3996
3997	echo "set -x" >> archive_${frelout[$i]}
3998	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3999	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4000	cd $tmp_data_catalog
4001	all_files=`ls -1 ${frelout[$i]}/*`
4002	cd - > /dev/null
4003	(( inode = 0 ))
4004	(( tp1 = tasks_per_node + 1 ))
4005	while (( inode < nodes ))
4006	do
4007	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4008	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4009	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4010	(( inode = inode + 1 ))
4011	done
4012	fi
4013	elif [[ $archive_system = ut ]]
4014	then
4015	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4016	if [[ $files_for_pes = false ]]
4017	then
4018	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4019	echo "set -x" >> archive_${frelout[$i]}
4020	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4021	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4022	else
4023
4024	echo "set -x" >> archive_${frelout[$i]}
4025	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4026	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4027	cd $tmp_data_catalog
4028	all_files=`ls -1 ${frelout[$i]}/*`
4029	cd - > /dev/null
4030	(( inode = 0 ))
4031	(( tp1 = tasks_per_node + 1 ))
4032	while (( inode < nodes ))
4033	do
4034	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4035	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4036	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4037	(( inode = inode + 1 ))
4038	done
4039	fi
4040	elif [[ $archive_system = none ]]
4041	then
4042	printf " +++ archiving on $localhost not available!\n"
4043	fi
4044
4045	if [[ $archive_system != none ]]
4046	then
4047	if [[ $localhost = nech ]]
4048	then
4049	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4050	fi
4051	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4052	fi
4053	else
4054	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4055	fi
4056
4057
4058	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4059	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4060	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4061	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4062	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4063	if [[ $files_for_pes = false ]]
4064	then
4065	cat /dev/null > ${pathout[$i]}
4066	else
4067	mkdir -p ${pathout[$i]}
4068	fi
4069
4070	fi
4071
4072
4073	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4074	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4075	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4076	if [[ "${actionout[$i]}" = ar ]]
4077	then
4078	if [[ $files_for_pes = false ]]
4079	then
4080	printf "\n >>> OUTPUT: ${localout[$i]} to"
4081	printf "\n ${pathout[$i]}"
4082	printf "\n File will be copied to archive-system ($archive_system) !\n"
4083	else
4084	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4085	printf "\n ${pathout[$i]}"
4086	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4087	fi
4088	mv ${localout[$i]} ${frelout[$i]}
4089
4090	file_saved=false
4091
4092	if [[ $archive_system = asterix ]]
4093	then
4094	do_stageout=true
4095	(( stageout_anz = 0 ))
4096	while [[ $do_stageout = true ]]
4097	do
4098	if [[ $files_for_pes = false ]]
4099	then
4100	stageout ${frelout[$i]} > STAGE_OUTPUT
4101	else
4102	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4103	fi
4104	cat STAGE_OUTPUT
4105	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4106	then
4107	file_saved=true
4108	do_stageout=false
4109	else
4110	if [[ $files_for_pes = false ]]
4111	then
4112	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4113	else
4114	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4115	fi
4116	(( stageout_anz = stageout_anz + 1 ))
4117	if (( stageout_anz == 10 ))
4118	then
4119	printf "\n +++ stoped after 10 unsuccessful tries!"
4120	archive_save=false
4121	do_stageout=false
4122	else
4123	printf "\n *** new try to store on archive after 15 min:"
4124	sleep 900
4125	fi
4126	fi
4127	done
4128	elif [[ $archive_system = DMF ]]
4129	then
4130	if [[ $files_for_pes = false ]]
4131	then
4132	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4133	locat=DMF
4134	exit
4135	else
4136	rm -rf $ARCHIVE/${frelout[$i]}
4137	cp -r ${frelout[$i]} $ARCHIVE
4138	fi
4139	file_saved=true
4140	elif [[ $archive_system = tivoli ]]
4141	then
4142	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4143	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4144	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4145	# WHEN THE ARCHIVE-JOB IS EXECUTED
4146	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4147	chmod g+rx $tmp_data_catalog
4148	if [[ $files_for_pes = false ]]
4149	then
4150	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4151	else
4152	mkdir $tmp_data_catalog/${frelout[$i]}
4153	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4154	fi
4155
4156	# GENERATE AND SUBMIT BATCH-JOB
4157	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4158	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4159	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4160	if [[ $files_for_pes = false ]]
4161	then
4162	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4163	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4164	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4165	else
4166	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4167	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4168	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4169	fi
4170
4171	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4172	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4173	file_saved=true
4174
4175	elif [[ $archive_system = ut ]]
4176	then
4177	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4178	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4179	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4180	# WHEN THE ARCHIVE-JOB IS EXECUTED
4181	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4182	chmod g+rx $tmp_data_catalog
4183	if [[ $files_for_pes = false ]]
4184	then
4185	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4186	else
4187	mkdir $tmp_data_catalog/${frelout[$i]}
4188	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4189	fi
4190
4191	# GENERATE AND SUBMIT BATCH-JOB
4192	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4193	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4194	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4195	if [[ $files_for_pes = false ]]
4196	then
4197	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4198	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4199	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4200	else
4201	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4202	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4203	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4204	fi
4205
4206	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4207	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4208	file_saved=true
4209
4210	else
4211	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4212	archive_save=false
4213	fi
4214
4215	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4216	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4217	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4218	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4219	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4220	if [[ $file_saved = true ]]
4221	then
4222	if [[ $files_for_pes = false ]]
4223	then
4224	cat /dev/null > ${pathout[$i]}
4225	else
4226	mkdir -p ${pathout[$i]}
4227	fi
4228	fi
4229
4230	fi
4231
4232	# APPEND ON THIS MACHINE
4233	if [[ "${actionout[$i]}" = "a" ]]
4234	then
4235	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4236	then
4237	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4238	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4239	else
4240	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4241	cat ${localout[$i]} >> ${pathout[$i]}
4242	fi
4243	fi
4244
4245	# COPY ON THIS MACHINE
4246	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4247	# ON DIFFERENT FILE-SYSTEMS
4248	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4249	then
4250
4251	# COPY IN CASE OF RUNS ON SINGLE CORES
4252	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4253	then
4254	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4255	if [[ $link_local_output = true ]]
4256	then
4257	printf " using ln -f\n"
4258	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4259	fi
4260	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4261	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4262	then
4263	if [[ $link_local_output = true ]]
4264	then
4265	printf " ln failed, using cp...\n"
4266	fi
4267	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4268	fi
4269	else
4270	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4271	if [[ $link_local_output = true ]]
4272	then
4273	printf " using ln -f\n"
4274	ln -f ${localout[$i]} ${pathout[$i]}
4275	fi
4276	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4277	if [[ ! -f "${pathout[$i]}" ]]
4278	then
4279	if [[ $link_local_output = true ]]
4280	then
4281	printf " ln failed, using cp...\n"
4282	fi
4283	cp ${localout[$i]} ${pathout[$i]}
4284	fi
4285	fi
4286
4287	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4288	then
4289
4290	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4291	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4292	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4293	if [[ $link_local_output = true ]]
4294	then
4295	printf " using ln -f\n"
4296	mkdir ${pathout[$i]}
4297	cd ${localout[$i]}
4298	for file in $(ls *)
4299	do
4300	ln -f $file ${pathout[$i]}
4301	done
4302	cd $TEMPDIR
4303	fi
4304
4305	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4306	if [[ ! -f "${pathout[$i]}/_0000" ]]
4307	then
4308	if [[ $link_local_output = true ]]
4309	then
4310	printf " ln failed for .../_0000, using cp...\n"
4311	fi
4312	cp -r ${localout[$i]} ${pathout[$i]}
4313	fi
4314
4315	fi
4316	fi
4317	done
4318	if (( i != 0 ))
4319	then
4320	if [[ $transfer_problems = true ]]
4321	then
4322	printf "\n$dashes\n *** OUTPUT-files saved"
4323	printf "\n +++ WARNING: some data transfers failed! \n"
4324	else
4325	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4326	fi
4327	fi
4328
4329
4330	# IF REQUIRED, START A RESTART-JOB
4331	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4332	if [[ -f CONTINUE_RUN ]]
4333	then
4334
4335	if [[ $archive_save = true ]]
4336	then
4337
4338	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4339	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4340	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4341	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4342	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4343	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4344	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4345	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4346	then
4347	mc=`echo $mc \| sed 's/#/f/g'`
4348	fi
4349
4350
4351	# START THE RESTART-JOB
4352	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4353	echo " $mc"
4354	printf "\n$dashes\n"
4355	if [[ $localhost != $fromhost ]]
4356	then
4357
4358	if [[ $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4359	then
4360	echo "*** ssh will be used to initiate restart-runs!"
4361	echo " return_addres=\"$return_addres\" "
4362	echo " return_username=\"$return_username\" "
4363	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4364	then
4365	if [[ $localhost = ibmh ]]
4366	then
4367	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\" "
4368	elif [[ $localhost = lccrayb ]]
4369	then
4370	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\" "
4371	elif [[ $localhost = lccrayh ]]
4372	then
4373	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\" "
4374
4375	else
4376	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 "
4377	fi
4378	else
4379	if [[ $localhost = ibmkisti ]]
4380	then
4381	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\" "
4382	elif [[ $localhost = lcflow ]]
4383	then
4384	/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 "
4385	elif [[ $localhost = lccrayb ]]
4386	then
4387	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\" "
4388	elif [[ $localhost = lccrayh ]]
4389	then
4390	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\" "
4391	else
4392	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4393	fi
4394	fi
4395	else
4396	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4397	locat=restart; exit
4398	fi
4399
4400	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4401	if [[ $queue = special1q ]]
4402	then
4403	sleep 120
4404	else
4405	sleep 30
4406	fi
4407
4408	else
4409
4410	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4411	# USING SSH)
4412	cd $LOCAL_PWD
4413	if [[ $localhost = lckyuh ]]
4414	then
4415	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4416	printf "\n please restart job manually using command:\n"
4417	printf "\n \"$mc\" "
4418	else
4419	eval $mc # THE ' MUST BE EVALUATED
4420	fi
4421	cd - > /dev/null
4422	fi
4423	if [[ $localhost = lckyuh ]]
4424	then
4425	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4426	else
4427	printf "\n$dashes\n *** restart-run initiated \n"
4428	fi
4429
4430
4431	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4432	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4433	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4434	# MAY BE VERY HUGE)
4435	(( i = 0 ))
4436	while (( i < iin ))
4437	do
4438	(( i = i + 1 ))
4439	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4440	then
4441	rm -r $tmp_data_catalog/${frelin[$i]}
4442	fi
4443	done
4444
4445	else
4446
4447	printf "\n +++ no restart-run possible, since errors occured"
4448	printf "\n during the archive process"
4449	fi
4450
4451	fi
4452
4453
4454
4455	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4456	if [[ "$email_notification" != "none" ]]
4457	then
4458
4459	if [[ $localhost != $fromhost ]]
4460	then
4461	if [[ -f CONTINUE_RUN ]]
4462	then
4463	echo "PALM restart run necessary" > email_text
4464	echo "description header of actual run:" >> email_text
4465	cat CONTINUE_RUN >> email_text
4466	echo "mrun-command to restart:" >> email_text
4467	echo "$mc" >> email_text
4468	else
4469	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4470	fi
4471	mail $email_notification < email_text
4472	printf "\n *** email notification sent to \"$email_notification\" "
4473	fi
4474	fi
4475
4476
4477
4478	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4479	cd $HOME
4480	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4481
4482	else
4483
4484
4485	# PREPARING ACTIONS,
4486	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4487
4488	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4489	mrun_com="$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 $remote_username"
4490	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4491	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4492	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4493	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4494	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4495	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4496	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4497	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4498	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4499	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4500	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4501	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4502	if [[ $use_openmp = true ]]
4503	then
4504	mrun_com=${mrun_com}" -O $threads_per_task"
4505	fi
4506	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4507	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4508	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4509	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4510	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4511	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4512	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4513	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4514	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4515	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4516	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4517	if [[ $do_remote = true ]]
4518	then
4519	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4520	fi
4521
4522
4523	# CREATE EXECUTABLE FOR BATCH JOB
4524	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4525	then
4526
4527	printf "\n *** creating the executable for batch job\n"
4528
4529	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4530	if [[ $host != $localhost ]]
4531	then
4532	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4533	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4534	locat=create_executable; exit
4535	fi
4536
4537	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4538	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4539
4540	cp $make_depository .
4541	tar -xf $make_depository > /dev/null 2>&1
4542	cp ../* . > /dev/null 2>&1
4543
4544	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4545
4546	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4547	then
4548	printf "\n +++ error occured while compiling or linking"
4549	locat=compile
4550	exit
4551	fi
4552
4553	mv a.out ..
4554	cd - > /dev/null 2>&1
4555	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4556
4557	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4558
4559	fi
4560
4561
4562	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4563	jobfile=jobfile.$RANDOM
4564
4565
4566	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4567	echo "mkdir $TEMPDIR" >> $jobfile
4568	echo "cd $TEMPDIR" >> $jobfile
4569
4570
4571	# ACTIVATE ERROR-TRACEBACK
4572	if [[ $do_trace = true ]]
4573	then
4574	echo "set -x" >> $jobfile
4575	else
4576	echo "set +vx" >> $jobfile
4577	fi
4578
4579
4580	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4581	if [[ "$init_cmds" != "" ]]
4582	then
4583	echo "$init_cmds" >> $jobfile
4584	fi
4585	if [[ "$module_calls" != "" ]]
4586	then
4587	echo "$module_calls" >> $jobfile
4588	fi
4589
4590
4591	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4592	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4593	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4594	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4595	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4596	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4597	# QUEUEING-SYSTEMS
4598	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4599	then
4600
4601	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4602	if [[ $restart_run != true ]]
4603	then
4604	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4605	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4606	fi
4607
4608	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4609	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4610	echo "set -x" >> $jobfile
4611	if [[ $host = $localhost ]]
4612	then
4613
4614	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4615	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4616	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4617	then
4618	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4619	else
4620	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4621	fi
4622
4623	else
4624	if [[ $host = ibmkisti ]]
4625	then
4626	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4627	echo "localdir=\`pwd\`" >> $jobfile
4628	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4629	elif [[ $host = lccrayb ]]
4630	then
4631	echo "localdir=\`pwd\`" >> $jobfile
4632	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4633	elif [[ $host = lccrayh ]]
4634	then
4635	echo "localdir=\`pwd\`" >> $jobfile
4636	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4637
4638	else
4639	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4640	fi
4641	fi
4642	echo "export SOURCES_COMPLETE=true" >> $jobfile
4643
4644	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4645	# WORKING DIRECTORY OF THE JOB
4646	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4647	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4648	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4649	echo "execute_mrun=true" >> $jobfile
4650	echo " " >> $jobfile
4651
4652	else
4653
4654	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4655	if [[ $do_compile = true ]]
4656	then
4657
4658	source_catalog=SOURCES_FOR_RUN_$fname
4659
4660	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4661	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4662	echo "export SOURCES_COMPLETE=true" >> $jobfile
4663	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4664
4665	for filename in $source_list
4666	do
4667	# BACKSLASH IS USED FOR MASKING
4668	echo "cat > $filename << \"%END%\"" >> $jobfile
4669	cat $source_catalog/$filename >> $jobfile
4670	echo " " >> $jobfile
4671	echo "%END%" >> $jobfile
4672	echo " " >> $jobfile
4673	done
4674
4675	# BACKSLASH IS USED FOR MASKING
4676	echo "cat > Makefile << \"%END%\"" >> $jobfile
4677	cat $source_catalog/Makefile >> $jobfile
4678	echo " " >> $jobfile
4679	echo "%END%" >> $jobfile
4680	echo " " >> $jobfile
4681
4682	echo "cd - > /dev/null" >> $jobfile
4683
4684	fi
4685
4686
4687	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4688	# BACKSLASH IS USED FOR MASKING
4689	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4690	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4691	echo "cat > $config_file << \"%END%\"" >> $jobfile
4692	if [[ $host = lckyuh ]]
4693	then
4694	# NO CROSS-COMPILER ON COMPUTE NODE
4695	sed 's/frtpx/frt/g' $config_file >> $jobfile
4696	else
4697	sed 's/#$.*//g' $config_file >> $jobfile
4698	fi
4699	echo "%END%" >> $jobfile
4700	echo " " >> $jobfile
4701
4702
4703	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4704	# BACKSLASH IS USED FOR MASKING
4705	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4706	if [[ $host = lckyuh ]]
4707	then
4708	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4709	else
4710	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4711	fi
4712	echo "%END%" >> $jobfile
4713	echo "chmod u+x $mrun_script_name" >> $jobfile
4714	echo "execute_mrun=true" >> $jobfile
4715	echo " " >> $jobfile
4716
4717	fi
4718
4719
4720	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4721	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4722	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4723	if [[ $do_remote = true ]]
4724	then
4725	(( i = 0 ))
4726	while (( i < iin ))
4727	do
4728	(( i = i + 1 ))
4729	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4730	if [[ "${transin[$i]}" = job ]]
4731	then
4732	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4733	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4734	echo " " >> $jobfile
4735	echo "%END%" >> $jobfile
4736	else
4737	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4738	fi
4739
4740	# CHECK, IF FILE COULD BE CREATED
4741	echo "if [[ \$? = 1 ]]" >> $jobfile
4742	echo "then" >> $jobfile
4743	echo " echo \" \" " >> $jobfile
4744	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4745	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4746	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4747	echo " execute_mrun=false" >> $jobfile
4748	echo "fi" >> $jobfile
4749	done
4750	fi
4751
4752	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4753	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4754	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4755	echo "LOCAL_PWD=$working_directory" >> $jobfile
4756	echo "export LOCAL_PWD" >> $jobfile
4757
4758	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4759	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4760	echo "export LOCAL_MRUN_PATH" >> $jobfile
4761
4762	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4763	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4764	then
4765	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4766	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4767	fi
4768
4769	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4770	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4771	echo "set -x" >> $jobfile
4772	echo "queue=$queue" >> $jobfile
4773	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4774	echo 'ls -al; echo `pwd`' >> $jobfile
4775	echo "cd \$HOME" >> $jobfile
4776	echo "rm -rf $TEMPDIR" >> $jobfile
4777
4778
4779
4780
4781	# START THE JOB USING SUBJOB-COMMAND
4782	if [[ $silent = false ]]
4783	then
4784	printf "\n "
4785	else
4786	printf "\n\n"
4787	fi
4788
4789	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
4790	rm -rf $jobfile
4791
4792
4793	fi # END OF REMOTE-PART

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