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source: palm/trunk/SCRIPTS/mrun @ 1304

Last change on this file since 1304 was 1304, checked in by raasch, 10 years ago
openmp bugfix + bugfix for single core MPI runs ulimit option in mrun changed from -Ss to -s
Property svn:keywords set to `Id Rev`
File size: 174.5 KB

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

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