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source: palm/trunk/SCRIPTS/mrun @ 1291

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

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