Home

Context Navigation

source: palm/trunk/SCRIPTS/mrun @ 1548

Last change on this file since 1548 was 1548, checked in by witha, 10 years ago
last commit documented
Property svn:keywords set to `Id Rev`
File size: 177.0 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 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1548 2015-01-29 15:11:41Z witha $
29	#
30	# 1547 2015-01-29 15:09:12Z witha
31	# adjustments for ForWind computing cluster (lcflow)
32	#
33	# 1491 2014-11-12 08:12:57Z heinze
34	# correct setting of batch_job allowed for ibm-machines
35	#
36	# 1468 2014-09-24 14:06:57Z maronga
37	# Typo removed (addres->address)
38	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
39	# Added support for restart runs (remote) for lcxe6
40	#
41	# 1442 2014-07-28 07:09:10Z raasch
42	# default queues for HLRN-III (lccrayb/lccrayh) defined
43	#
44	# 1422 2014-07-02 10:01:25Z kanani
45	# automatic restarts enabled for lccrayb,
46	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
47	#
48	# 1420 2014-06-10 06:24:14Z raasch
49	# -j1 option added to aprung command for lccrayf (CSC)
50	#
51	# 1402 2014-05-09 14:25:13Z raasch
52	# batch_job added to envpar-NAMELIST
53	#
54	# 1357 2014-04-11 15:02:03Z witha
55	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
56	# possible)
57	#
58	# 1320 2014-03-20 08:40:49Z raasch
59	# check namelist file set false by default
60	#
61	# 1304 2014-03-12 10:29:42Z raasch
62	# ulimit option changed from -Ss to -s
63	#
64	# bugfix: missing "fi" in r1289
65	#
66	# 1289 2014-03-04 07:12:34Z raasch
67	# comments translated to English
68	# necriam-, fimm-, ibmy-, and sgi-specific code removed
69	# export of variables for palm and interpret_config removed
70	#
71	# 1281 2014-02-01 07:55:49Z raasch
72	# rsync-copy restricted to Cray machines, since command is unavailable on some
73	# other systems
74	#
75	# 1279 2014-01-28 12:10:14Z raasch
76	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
77	# in order to remove annoying restrictions concerning the number of processors which
78	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
79	# restriction, one of the nodes will be filled with less than the given number of
80	# tasks per node. A respective warning is given.
81	#
82	# 1274 2014-01-09 13:14:54Z heinze
83	# adjustments for lccrayh
84	#
85	# 1272 2014-01-08 10:19:32Z witha
86	# small adjustment for lcflow
87	#
88	# 1270 2013-12-16 11:05:01Z fricke
89	# call of combine_plot_fields adjusted for lccrayb/lccrayh
90	#
91	# 1255 2013-11-07 14:43:35Z raasch
92	# further adjustments for lccrayb remote access
93	#
94	# 1241 2013-10-30 11:36:58Z heinze
95	# Enable use of nudging input and input of large scale forcing from
96	# external files
97	#
98	# 1229 2013-09-20 06:55:19Z raasch
99	# further adjustments for lccrayb
100	#
101	# 1224 2013-09-16 07:27:23Z raasch
102	# first adjustments for lccrayb
103	#
104	# 1210 2013-08-14 10:58:20Z raasch
105	# fftw support added
106	#
107	# 1201 2013-07-10 16:17:59Z witha
108	# adjustments for Forwind cluster (lcflow)
109	#
110	# 1199 2013-07-05 14:52:22Z raasch
111	# adjustments for CSC Helsinki (lccrayf),
112	# executables for batch jobs can be created in advance, in order to avoid calling
113	# the compiler within the batch job (only works if batch jobs are submitted on
114	# local host)
115	#
116	# 1190 2013-06-25 09:39:21Z heinze
117	# enable use of automatic restarts for ibmh
118	# use of cluster/express queue enabled (ibmh)
119	#
120	# 1124 2013-04-09 15:46:52Z raasch
121	# variable "memory" is exported via typeset option -x, because otherwise an unknown
122	# side effect may lead to data loss while getopts is reading the script-option arguments
123	#
124	# 1122 2013-04-09 08:37:16Z heinze
125	# Bugfix: change type of variable last_char
126	#
127	# 1119 2013-04-05 15:11:19Z raasch
128	# Bugfix for setting -T option for subjob
129	#
130	# 1108 2013-03-05 07:03:32Z raasch
131	# bugfix for coupled runs on lckyut/lckyuh
132	#
133	# 1106 2013-03-04 05:31:38Z raasch
134	# --stdin argument for mpiexec on lckyuh
135	# -y and -Y settings output to header
136	#
137	# 1103 2013-02-20 02:15:53Z raasch
138	# default script runs again under ksh, because of unsolved problems with read
139	# from stdin: when bash script is called from a ksh, message "read error: 0:
140	# Resource temporarily unavailable" appears and script does not stop,
141	# further bash compatibility adjustments,
142	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
143	# on lckyuh, but mrun does not terminate and issues a warning instead
144	#
145	# 1101 2013-02-17 10:20:21Z raasch
146	# script now running under bash instead of ksh, which required small adjustments
147	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
148	# read from stdin),
149	# cross compilername on lckyuh compute nodes replaced by real compiler name
150	#
151	# 1099 2013-02-10 01:47:43Z raasch
152	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
153	# and for Forwind cluster (lcflow)
154	# small further adjustments for lckyut
155	#
156	# 1094 2013-02-03 01:52:12Z raasch
157	# explicit ssh/scp port can be set in config file with environment variable
158	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
159	# decalpha parts (yonsei) removed
160	#
161	# 2013-02-02 07:06:13Z raasch
162	# adjustments for Kyushu-University computing center (lckyut - tatara)
163	#
164	# 1083 2013-01-04 10:22:09Z maronga
165	# bugfix in parameter file check (read %cpp_options was missing)
166	#
167	# 1069 2012-11-28 16:18:43Z maronga
168	# bugfix: coupling mode was always set to mpi2, typos removed
169	#
170	# 1058 2012-11-21 07:00:35Z raasch
171	# Intel inspector (inspxe) is given the number of PEs instead of the number of
172	# nodes
173	#
174	# 1046 2012-11-09 14:38:45Z maronga
175	# code put under GPL (PALM 3.9)
176	#
177	# 21/03/94 - Siggi - first version finished
178	# 03/03/94 - Siggi - script development started
179	#
180	#--------------------------------------------------------------------------------#
181	# mrun - script for running PALM jobs
182	#--------------------------------------------------------------------------------#
183
184
185
186	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
187
188	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
189	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
190	# (TOO MANY ARGUMENTS - PROBLEM)
191	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
192
193	AddFilenames=""
194	additional_conditions=""
195	add_source_path=""
196	afname=""
197	archive_save=true
198	archive_system=none
199	check_namelist_files=false
200	combine_plot_fields=true
201	compiler_name=""
202	cond1=""
203	cond2=""
204	config_file=.mrun.config
205	coupled_dist=""
206	coupled_mode="mpi1"
207	cpp_opts=""
208	cpp_options=""
209	cpumax=0
210	cpurest=0
211	create_executable_for_batch=false
212	delete_temporary_catalog=true
213	do_batch=false
214	do_compile=true
215	do_remote=false
216	do_stagein=true
217	do_stageout=true
218	do_trace=false
219	email_notification="none"
220	exclude=""
221	executable=""
222	execution_error=false
223	fftw_inc=""
224	fftw_lib=""
225	fftw_support=false
226	fname=test
227	fromhost=""
228	global_revision=""
229	group_number=none
230	host=""
231	host_file=""
232	hp=""
233	ignore_archive_error=false
234	input_list=""
235	interpreted_config_file=""
236	job_catalog="~/job_queue"
237	job_on_file=""
238	keep_data_from_previous_run=false
239	link_local_input=false
240	link_local_output=false
241	localhost_realname=$(hostname)
242	local_dvrserver_running=.FALSE.
243	locat=normal
244	mainprog=""
245	makefile=""
246	max_par_io_str=""
247	mc=$0
248	while [[ $(echo $mc \| grep -c "/") != 0 ]]
249	do
250	mc=`echo $mc \| cut -f2- -d"/"`
251	done
252	module_calls=""
253	mrun_script_name=$mc
254	netcdf_inc=""
255	netcdf_lib=""
256	netcdf_support=false
257	node_usage=default
258	numprocs=""
259	numprocs_atmos=0
260	numprocs_ocean=0
261	OOPT=""
262	openmp=false
263	output_list=""
264	package_list=""
265	queue=none
266	read_from_config=""
267	restart_run=false
268	if [[ `hostname` = rte10 ]]
269	then
270	return_address=133.5.185.60
271	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
272	elif [[ `hostname` = climate0 ]]
273	then
274	return_address=165.132.26.68
275	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
276	elif [[ `hostname` = urban00 ]]
277	then
278	return_address=147.46.30.151
279	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
280	else
281	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
282	fi
283	return_password=""
284	return_username=$LOGNAME
285	remotecall=false
286	remote_username=""
287	run_coupled_model=false
288	run_mode=""
289	store_on_archive_system=false
290	dashes=" ----------------------------------------------------------------------------"
291	silent=false
292	source_list=""
293	source_path=SOURCE
294	tasks_per_node=""
295	threads_per_task=1
296	tmpcreate=false
297	tmp_data_catalog=""
298	transfer_problems=false
299	usern=$LOGNAME
300	use_openmp=false
301	version="MRUN 2.1 Rev$Rev: 1548 $"
302	working_directory=`pwd`
303	TOPT=""
304	XOPT=""
305	zeit=$( date \| cut -c 12-19 )
306
307	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
308	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
309	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
310	# SCRIPT-OPTION ARGUMENTS
311	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
312
313
314
315	# ERROR HANDLING IN CASE OF EXIT
316	trap 'rm -rf $working_directory/tmp_mrun
317	if [[ $locat != normal && $locat != control_c ]]
318	then
319
320	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
321	(( i = 0 ))
322	while (( i < iec ))
323	do
324	(( i = i + 1 ))
325	printf "\n *** Execution of ERROR-command:\n"
326	printf " >>> ${err_command[$i]}\n"
327	eval ${err_command[$i]}
328	done
329	if [[ -n $interpreted_config_file ]]
330	then
331	rm -rf $interpreted_config_file
332	fi
333	if [[ -n .mrun_environment ]]
334	then
335	rm -rf .mrun_environment
336	fi
337	if [[ $tmpcreate = true ]]
338	then
339	printf "\n *** Contents of \"$TEMPDIR\":\n"
340	ls -al; cd
341	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
342	fi
343	if [[ "$dvrserver_id" != "" ]]
344	then
345	echo "+++ killing dvrserver_id=$dvrserver_id"
346	kill $dvrserver_id
347	fi
348	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
349	then
350	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
351	fi
352	printf "\n\n+++ MRUN killed \n\n"
353	elif [[ $locat != control_c ]]
354	then
355	printf "\n\n --> all actions finished\n\n"
356	printf " Bye, bye $usern !!\n\n"
357	fi' exit
358
359
360	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
361	trap 'rm -rf $working_directory/tmp_mrun
362	rm -rf $working_directory/tmp_check_namelist_files
363	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
364	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
365	then
366	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
367	fi
368	if [[ "$dvrserver_id" != "" ]]
369	then
370	echo "+++ killing dvrserver_id=$dvrserver_id"
371	kill $dvrserver_id
372	fi
373	printf "\n+++ MRUN killed by \"^C\" \n\n"
374	locat=control_c
375	exit
376	' 2
377
378
379	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
380	# BEEN SET
381	if [[ "$PALM_BIN" = "" ]]
382	then
383	printf "\n +++ environment variable PALM_BIN has not been set"
384	printf "\n please set it to the directory where the PALM scripts are located"
385	locat=palm_bin; exit
386	fi
387	export PATH=$PALM_BIN:$PATH
388
389
390
391	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
392	# WHICH WILL BE USED TO START RESTART-JOBS
393	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
394	do
395	case $option in
396	(a) afname=$OPTARG;;
397	(A) store_on_archive_system=true; mc="$mc -A";;
398	(b) do_batch=true; mc="$mc -b";;
399	(B) delete_temporary_catalog=false; mc="$mc -B";;
400	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
401	(C) restart_run=true; mc="$mc -C";;
402	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
403	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
404	(F) job_on_file="-D"; mc="$mc -F";;
405	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
406	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
407	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
408	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
409	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
410	(I) ignore_archive_error=true; mc="$mc -I";;
411	(k) keep_data_from_previous_run=true; mc="$mc -k";;
412	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
413	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
414	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
415	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
416	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
417	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
418	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
419	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
420	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
421	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
422	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
423	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
424	(S) read_from_config=false; mc="$mc -S";;
425	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
426	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
427	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
428	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
429	(v) silent=true; mc="$mc -v";;
430	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
431	(x) do_trace=true;set -x; mc="$mc -x";;
432	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
433	(y) ocean_file_appendix=true; mc="$mc -y";;
434	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
435	(z) check_namelist_files=false; mc="$mc -z";;
436	(Z) combine_plot_fields=false; mc="$mc -Z";;
437	(\?) printf "\n +++ unknown option $OPTARG \n"
438	printf "\n --> type \"$0 ?\" for available options \n"
439	locat=parameter;exit;;
440	esac
441	done
442
443
444	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
445	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
446	(( to_shift = $OPTIND - 1 ))
447	shift $to_shift
448
449	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
450	if [[ "$1" = "?" ]]
451	then
452	(printf "\n *** mrun can be called as follows:\n"
453	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"
454	printf "\n Description of available options:\n"
455	printf "\n Option Description Default-Value"
456	printf "\n -a base name of input files equiv. -d"
457	printf "\n -A archiving when using file-attribute fl"
458	printf "\n -b batch-job on local machine ---"
459	printf "\n -B do not delete temporary directory at end ---"
460	printf "\n -c configuration file .mrun.config"
461	printf "\n -d base name of files attached to program test"
462	printf "\n -D preprocessor(cpp)-directives \"\" "
463	printf "\n -F create remote job file only ---"
464	printf "\n -h execution host $localhost_realname"
465	printf "\n -i INPUT control list \"\" "
466	printf "\n -I archiving errors of previous batch-jobs"
467	printf "\n will be ignored"
468	printf "\n -k keep data from previous run"
469	printf "\n -K additional conditions for controling"
470	printf "\n usage of conditional code and"
471	printf "\n env-variables in configuration file \"\" "
472	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
473	printf "\n -M Makefile name Makefile"
474	printf "\n -n node usage (shared/not_shared) depending on -h"
475	printf "\n -o OUTPUT control list \"\" "
476	printf "\n -O threads per openMP task ---"
477	printf "\n -p software package list \"\" "
478	printf "\n -q queue \"$queue\" "
479	printf "\n -r run control list (combines -i -o) \"\" "
480	printf "\n -s filenames of routines to be compiled \"\" "
481	printf "\n must end with .f, .f90, .F, or .c !"
482	printf "\n use \"..\" for more than one file and wildcards"
483	printf "\n -s LM compiles all locally modified files"
484	printf "\n -S config file interpreted by shellscript ---"
485	printf "\n -t allowed cpu-time in seconds (batch) 0"
486	printf "\n -T tasks per node depending on -h"
487	printf "\n -u username on remote machine \"\" "
488	printf "\n -v no prompt for confirmation ---"
489	printf "\n -w maximum parallel io streams as given by -X"
490	printf "\n -x tracing of mrun for debug purposes ---"
491	printf "\n -X # of processors (on parallel machines) 1"
492	printf "\n -y add appendix \"_O\" to all local output"
493	printf "\n files (ocean precursor runs followed by"
494	printf "\n coupled atmosphere-ocean runs) ---"
495	printf "\n -Y run coupled model, \"#1 #2\" with"
496	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
497	printf "\n -z disable a priori parameter file check ---"
498	printf "\n -Z skip combine_plot_fields at the end of "
499	printf "\n the simulation ---"
500	printf "\n "
501	printf "\n Possible values of positional parameter <modus>:"
502	printf "\n \"?\" - this outline \n\n") \| more
503	exit
504	elif [[ "$1" != "" ]]
505	then
506	printf "\n +++ positional parameter $1 unknown \n"
507	locat=parameter; exit
508	fi
509
510
511
512	# SHORT STARTING MESSAGE
513	printf "\n*** $version "
514	printf "\n will be executed. Please wait ..."
515
516
517
518	# CHECK, IF CONFIGURATION FILE EXISTS
519	if [[ ! -f $config_file ]]
520	then
521	printf "\n\n +++ configuration file: "
522	printf "\n $config_file"
523	printf "\n does not exist"
524	locat=connect; exit
525	fi
526
527
528	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
529	line=""
530	grep "%host_identifier" $config_file > tmp_mrun
531	while read line
532	do
533	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
534	then
535	HOSTNAME=`echo $line \| cut -d" " -s -f2`
536	host_identifier=`echo $line \| cut -d" " -s -f3`
537	if [[ $localhost_realname = $HOSTNAME ]]
538	then
539	localhost=$host_identifier
540	break
541	fi
542	fi
543	done < tmp_mrun
544
545	if [[ "$localhost" = "" ]]
546	then
547	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
548	printf "\n for local host \"$localhost_realname\"."
549	printf "\n Please add line"
550	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
551	printf "\n to the configuration file."
552	locat=localhost; exit
553	fi
554
555
556	# SET HOST-SPECIFIC VARIABLES
557	case $localhost_realname in
558	(r1\|r2\|h01\|b01) archive_system=tivoli;;
559	(cs*) archive_system=ut;;
560	esac
561
562
563	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
564	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
565	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
566	[[ "$afname" = "" ]] && afname=$fname
567
568
569	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
570	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
571	# STATEMENTS IN THE CONFIGURATION FILE
572	if [[ "$run_mode" != "" ]]
573	then
574	input_list="$input_list $run_mode"
575	output_list="$output_list $run_mode"
576	fi
577
578
579	# ??? is this (and the respective option -H) really required ???
580	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
581	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
582	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
583	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
584	if [[ "$fromhost" = "" ]]
585	then
586	fromhost=$localhost
587	fi
588
589
590	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
591	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
592	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
593	# TO BE SUBMITTED (I.E. do_bacth=true)
594	if [[ -n $host && "$host" != $localhost ]]
595	then
596	do_batch=true
597	do_remote=true
598	case $host in
599	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
600	(*) printf "\n"
601	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
602	printf "\n is not available"
603	locat=nqs; (( iec = 0 )); exit;;
604	esac
605	else
606	host=$localhost
607	fi
608
609
610	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
611	if [[ -n $additional_conditions ]]
612	then
613	cond1=`echo $additional_conditions \| cut -d" " -f1`
614	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
615	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
616	if [[ -n $dummy ]]
617	then
618	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
619	locat=options; exit
620	fi
621	block=_$cond1
622	[[ -n $cond2 ]] && block=${block}_$cond2
623	fi
624
625
626	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
627	if [[ $run_coupled_model = true ]]
628	then
629
630	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
631	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
632
633	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
634	then
635
636	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
637	printf "\n PEs (total) : $numprocs"
638	printf "\n PEs (atmosphere): $numprocs_atmos"
639	printf "\n PEs (ocean) : $numprocs_ocean"
640	locat=coupling; exit
641
642	fi
643
644
645	# GET coupled_mode FROM THE CONFIG FILE
646	line=""
647	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
648	while read line
649	do
650	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
651	then
652	coupled_mode="mpi2"
653	fi
654	done < tmp_mrun
655
656	fi
657
658
659	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
660	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
661	then
662	if [[ $ignore_archive_error = false ]]
663	then
664	printf "\n +++ data archiving of previous run failed"
665	printf "\n see directory \~/job_queue on remote machine"
666	locat=archive; exit
667	else
668	printf "\n +++ warning: data archiving in a previous run failed"
669	printf "\n MRUN continues, trying to get backup copy"
670	fi
671	fi
672
673
674	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
675	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
676	mrun_memory=$memory
677	mrun_group_number=$group_number
678	mrun_cpumax=$cpumax
679	mrun_numprocs=$numprocs
680
681
682	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
683	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
684	if [[ "$read_from_config" = false ]]
685	then
686
687	[[ $silent = false ]] && printf "\n Reading the configuration file... "
688
689	# READ THE CONFIGURATION FILE LINE BY LINE
690	while read zeile
691	do
692	[[ $silent = false ]] && printf "."
693
694
695	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
696	eval zeile=\"$zeile\"
697
698
699	# INTERPRET THE LINE
700	if [[ "$(echo $zeile)" = "" ]]
701	then
702	# EMPTY LINE, NO ACTION
703	continue
704
705	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
706	then
707
708	# LINE IS A COMMENT LINE
709	true
710
711	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
712	then
713
714	# LINE DEFINES AN ENVIRONMENT-VARIABLE
715	zeile=$(echo $zeile \| cut -c2-)
716	var=`echo $zeile \| cut -d" " -f1`
717	value=`echo $zeile \| cut -d" " -s -f2`
718	for_host=`echo $zeile \| cut -d" " -s -f3`
719	for_cond1=`echo $zeile \| cut -d" " -s -f4`
720	for_cond2=`echo $zeile \| cut -d" " -s -f5`
721
722	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
723	then
724
725	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
726	# "::" IS REPLACED BY ":".
727	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
728
729
730	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
731	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
732	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
733	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
734	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
735	# CONFIGURATION-FILE.
736	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
737	then
738	eval $var=\$value
739
740	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
741	if [[ $do_trace = true ]]
742	then
743	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
744	fi
745	fi
746
747	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
748	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
749	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
750	# MUST HAVE TO BE STARTED
751	if [[ $var = host ]]
752	then
753	if [[ -n $host && "$host" != $localhost ]]
754	then
755	do_batch=true
756	do_remote=true
757	case $host in
758	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
759	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
760	printf "\n is not available"
761	locat=nqs; exit;;
762	esac
763	else
764	host=$localhost
765	fi
766	fi
767
768	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
769	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
770	# BY MRUN (E.G. subjob)
771	export $var
772	fi
773
774
775
776
777	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
778	then
779
780	# LINE DEFINES ERROR-COMMAND
781	(( iec = iec + 1 ))
782	zeile=$(echo $zeile \| cut -c4-)
783	err_command[$iec]="$zeile"
784
785	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
786	then
787
788	# LINE DEFINES INPUT-COMMAND
789	(( iic = iic + 1 ))
790	zeile=$(echo $zeile \| cut -c4-)
791	in_command[$iic]="$zeile"
792
793	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
794	then
795
796	# LINE DEFINES OUTPUT-COMMAND
797	(( ioc = ioc + 1 ))
798	zeile=$(echo $zeile \| cut -c4-)
799	out_command[$ioc]="$zeile"
800
801	else
802
803	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
804	# s2a: in/out - field
805	# s2b: loc - field (optional)
806	# s2c: tr/ar - field (optional)
807	s1=`echo $zeile \| cut -d" " -f1`
808	s2=`echo $zeile \| cut -d" " -s -f2`
809	s2a=$(echo $s2 \| cut -d":" -f1)
810	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
811	then
812	s2b=""
813	s2c=""
814	else
815	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
816	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
817	fi
818	s3=`echo $zeile \| cut -d" " -f3`
819	s4=`echo $zeile \| cut -d" " -s -f4`
820	s5=`echo $zeile \| cut -d" " -s -f5`
821	s6=`echo $zeile \| cut -d" " -s -f6`
822
823
824	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
825	# INPUT- OR OUTPUT-LIST.
826	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
827	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
828	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
829	# IS NOT CHECKED AND STORED.
830	IFSALT="$IFS"; IFS="$IFS:"
831	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
832	then
833	found=false
834	for actual in $input_list
835	do
836	for formal in $s3
837	do
838	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
839	done
840	done
841	if [[ $found = true ]]
842	then
843	(( iin = iin + 1 ))
844	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
845	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
846	extin[$iin]=$s6
847	fi
848	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
849	then
850	found=false
851	for actual in $output_list
852	do
853	for formal in $s3
854	do
855	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
856	done
857	done
858	if [[ $found = true ]]
859	then
860	(( iout = iout + 1 ))
861	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
862	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
863	fi
864	elif [[ "$s2a" != in && "$s2a" != out ]]
865	then
866	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
867	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
868	locat=connect; exit
869	fi
870	IFS="$IFSALT"
871	fi
872	done < $config_file
873
874	else
875
876
877	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
878	[[ $silent = false ]] && printf "..."
879	interpreted_config_file=.icf.$RANDOM
880
881
882
883	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
884	cat > .mrun_environment << %%END%%
885	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
886	config_file = '$config_file', do_remote = '$do_remote',
887	do_trace = '$do_trace', host = '$host',
888	input_list = '$input_list', icf = '$interpreted_config_file',
889	localhost = '$localhost', output_list = '$output_list' /
890
891	%%END%%
892
893	if [[ "$host" != $localhost ]]
894	then
895
896	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
897	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
898	if [[ $? != 0 ]]
899	then
900	printf "\n\n +++ no interpret_config found"
901	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
902	locat=interpret_config; exit
903	fi
904	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
905	$interpret_config_executable
906
907	else
908
909	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
910	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
911	then
912	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
913	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
914	locat=interpret_config; exit
915	else
916	interpret_config${block}.x
917	fi
918
919	fi
920	rm .mrun_environment
921
922
923	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
924	chmod u+x $interpreted_config_file
925	export PATH=$PATH:.
926	. $interpreted_config_file
927	rm $interpreted_config_file
928
929	fi
930
931
932	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
933	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
934	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
935	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
936	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
937	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
938	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
939
940
941	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
942	# FOR SOURCE-FILES TO BE COMPILED.
943	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
944	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
945	if [[ "$SOURCES_COMPLETE" = "" ]]
946	then
947
948	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
949	# HAS BEEN DEFINED
950	source_path=""
951	line=""
952	grep "%source_path" $config_file > tmp_mrun
953	while read line
954	do
955	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
956	then
957	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
958	then
959	global_source_path=`echo $line \| cut -d" " -f2`
960	fi
961	fi
962	done < tmp_mrun
963
964	line=""
965	found=false
966	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
967	while read line
968	do
969	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
970	then
971	if [[ $found = true ]]
972	then
973	printf "\n\n +++ more than one source path found in configuration file"
974	printf "\n for local host \"$localhost\" "
975	locat=source_path; exit
976	fi
977	source_path=`echo $line \| cut -d" " -f2`
978	found=true
979	fi
980	done < tmp_mrun
981	rm tmp_mrun
982
983	if [[ "$source_path" = "" ]]
984	then
985	if [[ "$global_source_path" != "" ]]
986	then
987	source_path=$global_source_path
988	else
989	printf "\n\n +++ no source path found in configuration file"
990	printf "\n for local host \"$localhost\" "
991	locat=source_path; exit
992	fi
993	fi
994	eval source_path=$source_path
995
996	if [[ ! -d $source_path ]]
997	then
998	printf "\n\n +++ source path \"$source_path\" on local host"
999	printf "\n \"$localhost\" does not exist"
1000	locat=source_path; exit
1001	fi
1002
1003	fi
1004
1005
1006	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1007	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1008	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1009	then
1010	global_revision=`svnversion $source_path 2>/dev/null`
1011	global_revision="Rev: $global_revision"
1012	fi
1013
1014
1015	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1016	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1017	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1018	if [[ -n $host && "$host" != $localhost ]]
1019	then
1020	do_batch=true
1021	do_remote=true
1022	case $host in
1023	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1024	(*) printf "\n"
1025	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1026	printf "\n is not available"
1027	locat=nqs; (( iec = 0 )); exit;;
1028	esac
1029	else
1030	host=$localhost
1031	fi
1032
1033
1034	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1035	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1036	then
1037
1038	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1039	if [[ ! -n $numprocs ]]
1040	then
1041	printf "\n"
1042	printf "\n +++ option \"-K parallel\" requires additional specification"
1043	printf "\n of the number of processors to be used by"
1044	printf "\n mrun-option \"-X\" or by environment-variable"
1045	printf "\n \"numprocs\" in the configuration file"
1046	locat=numprocs; (( iec = 0 )); exit
1047	fi
1048
1049	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1050	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1051	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1052	then
1053	printf "\n"
1054	printf "\n +++ option \"-T\" (tasks per node) is missing"
1055	printf "\n set -T option or define tasks_per_node in the config file"
1056	locat=tasks_per_node; (( iec = 0 )); exit
1057	fi
1058
1059	if (( numprocs < tasks_per_node ))
1060	then
1061	printf "\n"
1062	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1063	printf "\n given values: -T $tasks_per_node -X $numprocs"
1064	locat=tasks_per_node; (( iec = 0 )); exit
1065	fi
1066
1067	if [[ $host != lcflow && $host != lcxt5m ]]
1068	then
1069	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1070	(( ival = $tasks_per_node ))
1071	(( pes = numprocs ))
1072	(( ii = pes / ival ))
1073	(( remaining_pes = pes - ii * ival ))
1074	if (( remaining_pes > 0 ))
1075	then
1076	printf "\n"
1077	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1078	printf "\n divisor of the total number of processors (option \"-X\")"
1079	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1080	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1081	(( nodes = nodes + 1 ))
1082	fi
1083	fi
1084
1085
1086	# SETTINGS FOR SUBJOB-COMMAND
1087	OOPT="-O $threads_per_task"
1088
1089	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1090	if [[ "$tasks_per_node" != "" ]]
1091	then
1092	TOPT="-T $tasks_per_node"
1093	fi
1094
1095	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1096	if [[ $node_usage = default ]]
1097	then
1098	if [[ $host = ibms ]]
1099	then
1100	node_usage=shared
1101	else
1102	node_usage=not_shared
1103	fi
1104	fi
1105
1106	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1107	then
1108	printf "\n"
1109	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1110	printf "\n \"shared\" or \"not_shared\""
1111	locat=tasks_per_node; (( iec = 0 )); exit
1112	fi
1113
1114	fi
1115
1116	# CHECK IF HOSTFILE EXISTS
1117	if [[ -n $hostfile ]]
1118	then
1119	if [[ ! -f $hostfile ]]
1120	then
1121	printf "\n"
1122	printf "\n +++ hostfile \"$hostfile\" does not exist"
1123	locat=hostfile; exit
1124	fi
1125	fi
1126
1127
1128	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1129	if [[ "$maximum_parallel_io_streams" = "" ]]
1130	then
1131	maximum_parallel_io_streams=$numprocs
1132	fi
1133
1134
1135	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1136	if [[ "$scp_port" != "" ]]
1137	then
1138	PORTOPT="-P $scp_port"
1139	SSH_PORTOPT="-p $scp_port"
1140	fi
1141
1142
1143	# SET DEFAULT-QUEUE, IF NOT GIVEN
1144	if [[ $queue = none ]]
1145	then
1146	case $host in
1147	(ibmh) queue=cluster;;
1148	(ibmkisti) queue=class.32plus;;
1149	(lccrayb) queue=mpp1q;;
1150	(lccrayh) queue=mpp1q;;
1151	(lckiaps) queue=normal;;
1152	(lckyoto) queue=ph;;
1153	(lckyuh) queue=fx-single;;
1154	(lckyut) queue=cx-single;;
1155	(lctit) queue=S;;
1156	(nech) queue=none;;
1157	(unics) queue=unics;;
1158	esac
1159	fi
1160
1161
1162	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1163	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1164	(( i = 0 ))
1165	while (( i < iin ))
1166	do
1167	(( i = i + 1 ))
1168	(( maxcycle = 0 ))
1169
1170	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1171	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1172	if [[ "${actionin[$i]}" = di ]]
1173	then
1174	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1175	# HOST ONLY
1176	eval filename=${pathin[$i]}/${endin[$i]}
1177	else
1178	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1179	# HOST ONLY
1180	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1181	fi
1182	eval pathname=${pathin[$i]}
1183
1184	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1185	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1186	then
1187	filename_input=$filename
1188	fi
1189
1190	# CHECK IF FILE EXISTS
1191	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1192	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1193	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1194	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1195	then
1196
1197	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1198	if [[ "${transin[$i]}" != "locopt" ]]
1199	then
1200	printf "\n\n +++ INPUT-file: "
1201	if [[ "${extin[$i]}" = "" ]]
1202	then
1203	printf "\n $filename"
1204	else
1205	printf "\n $filename.${extin[$i]}"
1206	fi
1207	printf "\n does not exist\n"
1208	locat=input; exit
1209	else
1210	transin[$i]="unavailable"
1211	fi
1212	else
1213
1214	# DETERMINE THE FILE'S CYCLE NUMBER
1215	ls -1 -d $filename > filelist 2>/dev/null
1216	ls -1 -d $filename.* >> filelist 2>/dev/null
1217	while read zeile
1218	do
1219	cycle=$(echo $zeile \| cut -f2 -d".")
1220	if [[ "$cycle" = "$zeile" ]]
1221	then
1222	(( icycle = 0 ))
1223	elif [[ "$cycle" = "${extin[$i]}" ]]
1224	then
1225	(( icycle = 0 ))
1226	else
1227	(( icycle = $cycle ))
1228	fi
1229	if (( icycle > maxcycle ))
1230	then
1231	(( maxcycle = icycle ))
1232	file_to_be_used=$zeile
1233	fi
1234	done <filelist
1235	rm filelist
1236
1237	# APPEND CYCLE NUMBER TO FILENAME
1238	if (( maxcycle > 0 ))
1239	then
1240	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1241	then
1242	filename=${filename}.$maxcycle.${extin[$i]}
1243	else
1244	filename=${filename}.$maxcycle
1245	fi
1246	else
1247	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1248	then
1249	filename=${filename}.${extin[$i]}
1250	fi
1251	fi
1252
1253	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1254	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1255	absnamein[$i]=$filename
1256	if (( maxcycle > 0 ))
1257	then
1258	if [[ "${actionin[$i]}" = di ]]
1259	then
1260	frelin[$i]=${endin[$i]}.$maxcycle
1261	else
1262	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1263	fi
1264	else
1265	if [[ "${actionin[$i]}" = di ]]
1266	then
1267	frelin[$i]=${endin[$i]}
1268	else
1269	frelin[$i]=${afname}${endin[$i]}
1270	fi
1271	fi
1272
1273	fi
1274	done
1275
1276	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1277	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1278	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1279	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1280	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1281	# REMOTE HOST)
1282	(( i = 0 ))
1283	while (( i < iout ))
1284	do
1285	(( i = i + 1 ))
1286	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1287	then
1288	if [[ "${actionout[$i]}" = tr ]]
1289	then
1290	actionout[$i]=""
1291	elif [[ "${actionout[$i]}" = trpe ]]
1292	then
1293	actionout[$i]=pe
1294	elif [[ "${actionout[$i]}" = tra ]]
1295	then
1296	actionout[$i]=a
1297	fi
1298	(( maxcycle = 0 ))
1299	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1300	eval catalogname=${pathout[$i]}
1301	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1302	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1303	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1304	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1305	then
1306
1307	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1308	if cat /dev/null > $filename
1309	then
1310	rm $filename
1311	else
1312
1313	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1314	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1315	if [[ ! -d $catalogname ]]
1316	then
1317	if mkdir -p $catalogname
1318	then
1319	printf "\n\n *** directory:"
1320	printf "\n $catalogname"
1321	printf "\n was created\n"
1322	else
1323	printf "\n\n +++ OUTPUT-file:"
1324	printf "\n $filename"
1325	printf "\n cannot be created, because directory does not exist"
1326	printf "\n and cannot be created either"
1327	printf "\n"
1328	locat=output ; exit
1329	fi 2>/dev/null
1330	else
1331	printf "\n\n +++ OUTPUT-file:"
1332	printf "\n $filename"
1333	printf "\n cannot be created, although directory exists"
1334	printf "\n"
1335	locat=output ; exit
1336	fi
1337	fi 2>/dev/null
1338	else
1339
1340	# DETERMINE THE CYCLE NUMBER
1341	ls -1 -d $filename > filelist 2>/dev/null
1342	ls -1 -d $filename.* >> filelist 2>/dev/null
1343	while read zeile
1344	do
1345	cycle=$(echo $zeile \| cut -f2 -d".")
1346	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1347	then
1348	(( icycle = 1 ))
1349	else
1350	(( icycle = $cycle + 1 ))
1351	fi
1352	if (( icycle > maxcycle ))
1353	then
1354	(( maxcycle = icycle ))
1355	fi
1356	done <filelist
1357	rm filelist
1358	fi
1359
1360	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1361	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1362	if [[ "${actionout[$i]}" != a ]]
1363	then
1364	if (( maxcycle > 0 ))
1365	then
1366	filename=${filename}.$maxcycle
1367	if cat /dev/null > $filename
1368	then
1369	rm $filename
1370	else
1371	printf "\n +++ OUTPUT-file:"
1372	printf "\n $filename"
1373	printf "\n cannot be created"
1374	locat=output ; exit
1375	fi
1376	fi
1377	else
1378	(( maxcycle = maxcycle - 1 ))
1379	if (( maxcycle > 0 ))
1380	then
1381	filename=${filename}.$maxcycle
1382	fi
1383	fi
1384
1385	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1386	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1387	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1388	pathout[$i]=$filename
1389	if (( maxcycle > 0 ))
1390	then
1391	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1392	else
1393	frelout[$i]=${fname}${endout[$i]}
1394	fi
1395
1396	fi
1397	done
1398
1399
1400	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1401	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1402	then
1403	if [[ "$dvr_inc" = "" ]]
1404	then
1405	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1406	printf "\n This is required for the dvrp_graphics package.\n"
1407	locat=dvr; exit
1408	fi
1409	if [[ "$dvr_lib" = "" ]]
1410	then
1411	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1412	printf "\n This is required for the dvrp_graphics package.\n"
1413	locat=dvr; exit
1414	fi
1415	fi
1416
1417
1418	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1419	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1420	if [[ "$mainprog" = "" && "$executable" = "" ]]
1421	then
1422	printf "\n +++ neither main program nor executable defined"
1423	locat=source; exit
1424	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1425	then
1426	printf "\n +++ main program as well as executable defined"
1427	locat=source; exit
1428	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1429	then
1430	do_compile=false
1431	fi
1432
1433
1434	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1435	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1436	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1437	then
1438	rm -rf SOURCES_FOR_RUN_$fname
1439	mkdir SOURCES_FOR_RUN_$fname
1440	fi
1441
1442
1443	# COLLECT ALL ROUTINES TO BE COMPILED
1444	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1445	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1446	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1447	then
1448
1449	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1450
1451	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1452	then
1453
1454	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1455	source_list=""
1456	cd $source_path
1457
1458
1459	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1460	if [[ ! -d .svn ]]
1461	then
1462	printf "\n\n +++ source directory"
1463	printf "\n \"$source_path\" "
1464	printf "\n is not under control of \"subversion\"."
1465	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1466	fi
1467
1468
1469	# LIST ALL MODIFIED SOURCE CODE FILES
1470	Filenames=""
1471	svn status > tmp_mrun
1472	while read line
1473	do
1474	firstc=`echo $line \| cut -c1`
1475	if [[ $firstc = M \|\| $firstc = "?" ]]
1476	then
1477	Name=`echo "$line" \| cut -c8-`
1478	extension=`echo $Name \| cut -d. -f2`
1479	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1480	then
1481	Filenames="$Filenames "$Name
1482	fi
1483	fi
1484	done < tmp_mrun
1485
1486
1487	# COPY FILES TO SOURCES_FOR_RUN_...
1488	for dateiname in $Filenames
1489	do
1490	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1491	source_list=$source_list"$dateiname "
1492	done
1493
1494	cd - > /dev/null
1495
1496
1497	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1498	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1499	elif [[ "$source_list" != "" && $restart_run != true ]]
1500	then
1501
1502	cd $source_path
1503
1504	for filename in $source_list
1505	do
1506
1507	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1508	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1509	then
1510	printf "\n +++ source code file: $filename"
1511	printf "\n must not contain (\"/\") "
1512	locat=source; exit
1513	fi
1514
1515	if [[ ! -f $filename ]]
1516	then
1517	printf "\n +++ source code file: $filename"
1518	printf "\n does not exist"
1519	locat=source; exit
1520	else
1521	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1522	fi
1523
1524	done
1525
1526	cd - > /dev/null
1527
1528	fi
1529
1530
1531	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1532	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1533	if [[ $restart_run != true ]]
1534	then
1535
1536	if [[ ! -f "$source_path/$mainprog" ]]
1537	then
1538	printf "\n\n +++ main program: $mainprog"
1539	printf "\n does not exist in source directory"
1540	printf "\n \"$source_path\"\n"
1541	locat=source; exit
1542	else
1543	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1544	then
1545	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1546	source_list=${mainprog}" $source_list"
1547	fi
1548	fi
1549	fi
1550
1551
1552	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1553	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1554	if [[ "$restart_run" != true ]]
1555	then
1556	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1557	if [[ ! -f $makefile ]]
1558	then
1559	printf "\n +++ file \"$makefile\" does not exist"
1560	locat=make; exit
1561	else
1562	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1563	fi
1564	fi
1565
1566
1567	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1568	if [[ $restart_run != true && "$add_source_path" != "" ]]
1569	then
1570
1571	# DOES THE DIRECTORY EXIST?
1572	if [[ ! -d $add_source_path ]]
1573	then
1574	printf "\n\n +++ WARNING: additional source code directory"
1575	printf "\n \"$add_source_path\" "
1576	printf "\n does not exist or is not a directory."
1577	printf "\n No source code will be used from this directory!\n"
1578	add_source_path=""
1579	if [[ $silent == false ]]
1580	then
1581	sleep 3
1582	fi
1583	else
1584
1585	cd $add_source_path
1586	found=false
1587
1588	Names=$(ls -1 *.f90 2>&1)
1589	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1590	Names=$(ls -1 *.F90 2>&1)
1591	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1592	Names=$(ls -1 *.F 2>&1)
1593	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1594	Names=$(ls -1 *.f 2>&1)
1595	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1596	Names=$(ls -1 *.c 2>&1)
1597	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1598
1599	cd - > /dev/null
1600	cd SOURCES_FOR_RUN_$fname
1601
1602	# COPY MAKEFILE IF EXISTING
1603	if [[ -f $add_source_path/Makefile ]]
1604	then
1605	printf "\n\n *** user Makefile from directory"
1606	printf "\n \"$add_source_path\" is used \n"
1607	if [[ $silent == false ]]
1608	then
1609	sleep 1
1610	fi
1611	cp $add_source_path/Makefile .
1612	fi
1613
1614	for dateiname in $AddFilenames
1615	do
1616	if [[ -f $dateiname ]]
1617	then
1618	printf "\n +++ source code file \"$dateiname\" found in additional"
1619	printf "\n source code directory \"$add_source_path\" "
1620	printf "\n but was also given with option \"-s\" which means that it should be taken"
1621	printf "\n from directory \"$source_path\"."
1622	locat=source; exit
1623	fi
1624
1625	cp $add_source_path/$dateiname .
1626	source_list="$source_list $dateiname"
1627
1628	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1629	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1630	then
1631	printf "\n\n +++ user file \"$dateiname\" "
1632	printf "\n is not listed in Makefile \n"
1633	locat=source; exit
1634	else
1635
1636	if [[ $found = false ]]
1637	then
1638	found=true
1639	printf "\n\n *** following user file(s) added to the"
1640	printf " files to be translated:\n "
1641	fi
1642	printf "$dateiname "
1643	if [[ $silent == false ]]
1644	then
1645	sleep 0.5
1646	fi
1647
1648	fi
1649	done
1650	[[ $found = true ]] && printf "\n"
1651	cd - > /dev/null
1652	fi
1653	fi
1654
1655
1656	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1657	# TO THE LIST OF FILES TO BE COMPILED
1658	if [[ $restart_run != true && -n $package_list ]]
1659	then
1660
1661	cd $source_path
1662
1663	for package in $package_list
1664	do
1665
1666	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1667
1668	# DETERMINE FILES BELONGING TO THE PACKAGE
1669	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1670	# THE NAME OF THE DIRECTORY
1671	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1672
1673
1674	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1675	# IF THEY ARE NOT ALREADY PART OF THE LIST
1676	for source_list_name in $package_source_list
1677	do
1678	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1679	then
1680
1681	# ONLY TAKE FILES WITH VALID SUFFIX
1682	ending=`echo $source_list_name \| cut -f2 -d.`
1683	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1684	then
1685	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1686	source_list="$source_list $source_list_name"
1687	fi
1688	fi
1689	done
1690	done
1691
1692	cd - > /dev/null
1693	fi
1694
1695	fi # do_compile=true
1696
1697
1698	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1699	# AND SET PRE-PROCESSOR DIRECTIVES
1700	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1701	then
1702
1703	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1704	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1705	then
1706	cpp_options="${cpp_options},-D__ibm=__ibm"
1707	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1708	then
1709	cpp_options="$cpp_options -D__nec"
1710	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1711	then
1712	cpp_options="$cpp_options -D__lc"
1713	else
1714	cpp_options="$cpp_options -D__$localhost"
1715	fi
1716
1717	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1718	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1719	then
1720	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1721	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1722	else
1723	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1724	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1725	fi
1726
1727	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1728	if [[ -n $package_list ]]
1729	then
1730	for package in $package_list
1731	do
1732	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1733	then
1734	if [[ $package != "dvrp_graphics+1PE" ]]
1735	then
1736	cpp_options="${cpp_options},-D__$package=__$package"
1737	else
1738	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1739	export use_seperate_pe_for_dvrp_output=true
1740	fi
1741	else
1742	if [[ $package != "dvrp_graphics+1PE" ]]
1743	then
1744	cpp_options="$cpp_options -D__$package"
1745	else
1746	cpp_options="$cpp_options -D__dvrp_graphics"
1747	export use_seperate_pe_for_dvrp_output=true
1748	fi
1749	fi
1750	done
1751	fi
1752
1753	# SET DIRECTIVES GIVEN BY OPTION -D
1754	if [[ -n $cpp_opts ]]
1755	then
1756	for popts in $cpp_opts
1757	do
1758	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1759	then
1760	cpp_options="${cpp_options},-D__$popts=__$popts"
1761	else
1762	cpp_options="$cpp_options -D__$popts"
1763	fi
1764	done
1765	fi
1766
1767	else
1768
1769
1770	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1771	if [[ $do_remote = false ]]
1772	then
1773	if [[ ! -f $executable ]]
1774	then
1775	printf "\n +++ executable file: $executable"
1776	printf "\n does not exist"
1777	locat=executable; exit
1778	fi
1779	fi
1780	fi
1781
1782
1783	# DETERMINE THE JOB MODE
1784	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1785	then
1786	if [[ "$LOADLBATCH" = yes ]]
1787	then
1788	batch_job=.TRUE.
1789	jobmo=BATCH
1790	else
1791	batch_job=.FALSE.
1792	jobmo=INTERACTIVE
1793	fi
1794	else
1795	if [[ "$ENVIRONMENT" = BATCH ]]
1796	then
1797	batch_job=.TRUE.
1798	jobmo=BATCH
1799	else
1800	batch_job=.FALSE.
1801	jobmo=INTERACTIVE
1802	fi
1803	fi
1804
1805	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1806	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1807	then
1808	printf "\n +++ no interactive runs allowed on host \"$host\" "
1809	printf "\n please submit batch job using mrun option \"-b\" \n"
1810	locat=normal; exit
1811	fi
1812
1813
1814	# CHECK, IF USER DEFINED A COMPILER
1815	if [[ "$compiler_name" = "" ]]
1816	then
1817
1818	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1819	locat=compiler_name; exit
1820
1821	fi
1822
1823
1824	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1825	kennung=$RANDOM
1826	if [[ "$tmp_user_catalog" = "" ]]
1827	then
1828	if [[ $localhost = ibmh ]]
1829	then
1830	tmp_user_catalog=$SCRATCH
1831	elif [[ $localhost = nech ]]
1832	then
1833	tmp_user_catalog=$WRKSHR
1834	else
1835	tmp_user_catalog=/tmp
1836	fi
1837	fi
1838	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1839
1840
1841	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1842	if [[ "$tmp_data_catalog" = "" ]]
1843	then
1844	if [[ $localhost = nech ]]
1845	then
1846	tmp_data_catalog=$WRKSHR/mrun_restart_data
1847	else
1848	tmp_data_catalog=/tmp/mrun_restart_data
1849	fi
1850	fi
1851
1852
1853	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1854	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1855	then
1856	eval fopts=\"$fopts\"
1857	eval lopts=\"$lopts\"
1858	fi
1859
1860
1861
1862	# DETERMINE COMPILE- AND LINK-OPTIONS
1863	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1864	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1865	ROPTS="$ropts"
1866	# 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 ]]
1867	# then
1868	XOPT="-X $numprocs"
1869	# fi
1870
1871
1872
1873	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1874	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1875	done=false
1876	while [[ $done = false ]]
1877	do
1878	cputime=$cpumax
1879	if (( $cputime == 0 ))
1880	then
1881	if [[ $do_batch = true ]]
1882	then
1883	printf "\n +++ cpu-time is undefined"
1884	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1885	printf "\n >>> "
1886	read cputime 1>/dev/null 2>&1
1887	else
1888	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1889	fi
1890	else
1891	done=true
1892	fi
1893	cpumax=$cputime
1894	done
1895
1896	(( minuten = cputime / 60 ))
1897	(( sekunden = cputime - minuten * 60 ))
1898
1899
1900	# CHECK THE MEMORY DEMAND
1901	if [[ $do_batch = true ]]
1902	then
1903	done=false
1904	while [[ $done = false ]]
1905	do
1906	if (( memory == 0 ))
1907	then
1908	printf "\n +++ memory demand is undefined"
1909	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1910	printf "\n >>> "
1911	read memory 1>/dev/null 2>&1
1912	else
1913	done=true
1914	fi
1915	done
1916	fi
1917
1918
1919	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1920	if [[ $do_remote = true && -z $remote_username ]]
1921	then
1922	while [[ -z $remote_username ]]
1923	do
1924	printf "\n +++ username on remote host \"$host\" is undefined"
1925	printf "\n >>> Please type username:"
1926	printf "\n >>> "
1927	read remote_username
1928	done
1929	mc="$mc -u$remote_username"
1930	fi
1931
1932	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1933	if [[ "$login_init_cmd" != "" ]]
1934	then
1935	export init_cmds="${login_init_cmd};"
1936	fi
1937
1938
1939	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1940	if [[ "$modules" != "" ]]
1941	then
1942	if [[ $host = lctit ]]
1943	then
1944	export module_calls=". $modules"
1945	else
1946	export module_calls="module load ${modules};"
1947	fi
1948	fi
1949
1950
1951
1952	# OUTPUT OF THE MRUN-HEADER
1953	calltime=$(date)
1954	printf "\n"
1955	printf "#------------------------------------------------------------------------# \n"
1956	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1957	printf "\| \| \n"
1958	spalte1="called on:"; spalte2=$localhost_realname
1959	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1960	if [[ $do_remote = true ]]
1961	then
1962	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1963	else
1964	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1965	fi
1966	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1967	if [[ -n $numprocs ]]
1968	then
1969	if [[ $run_coupled_model = false ]]
1970	then
1971	spalte1="number of PEs:"; spalte2=$numprocs
1972	else
1973	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1974	fi
1975	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1976	fi
1977	if [[ -n $tasks_per_node ]]
1978	then
1979	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1980	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1981	if (( remaining_pes > 0 ))
1982	then
1983	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	fi
1986	fi
1987	if [[ $maximum_parallel_io_streams != $numprocs ]]
1988	then
1989	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1990	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1991	fi
1992	if [[ $use_openmp = true ]]
1993	then
1994	spalte1="threads per task:"; spalte2="$threads_per_task"
1995	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1996	fi
1997	printf "\| \| \n"
1998	if [[ $do_compile = true ]]
1999	then
2000	if [[ "$mopts" != "" ]]
2001	then
2002	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2003	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2004	zeile=$(echo "$mopts" \| cut -c46-)
2005	while [[ "$zeile" != "" ]]
2006	do
2007	spalte1=""
2008	spalte2=$(echo "$zeile" \| cut -c-45)
2009	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2010	zeile=$(echo "$zeile" \| cut -c46-)
2011	done
2012	fi
2013
2014	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	zeile=$(echo "$cpp_options" \| cut -c46-)
2017	while [[ "$zeile" != "" ]]
2018	do
2019	spalte1=""
2020	spalte2=$(echo "$zeile" \| cut -c-45)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	zeile=$(echo "$zeile" \| cut -c46-)
2023	done
2024
2025	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2026	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2027	zeile=$(echo "$fopts" \| cut -c46-)
2028	while [[ "$zeile" != "" ]]
2029	do
2030	spalte1=""
2031	spalte2=$(echo "$zeile" \| cut -c-45)
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033	zeile=$(echo "$zeile" \| cut -c46-)
2034	done
2035
2036	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2038	zeile=$(echo "$lopts" \| cut -c46-)
2039	while [[ "$zeile" != "" ]]
2040	do
2041	spalte1=""
2042	spalte2=$(echo "$zeile" \| cut -c-45)
2043	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2044	zeile=$(echo "$zeile" \| cut -c46-)
2045	done
2046
2047	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049	zeile=$(echo "$modules" \| cut -c46-)
2050	while [[ "$zeile" != "" ]]
2051	do
2052	spalte1=""
2053	spalte2=$(echo "$zeile" \| cut -c-45)
2054	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2055	zeile=$(echo "$zeile" \| cut -c46-)
2056	done
2057
2058	spalte1="main program:"; spalte2=$mainprog
2059	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2060	else
2061	spalte1=executable:; spalte2=$executable
2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2063	fi
2064	printf "\| \| \n"
2065	spalte1="base name of files:"; spalte2=$fname
2066	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2067	if [[ $fname != $afname ]]
2068	then
2069	spalte1="base name of input files:"; spalte2=$afname
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	fi
2072	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2073	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2074	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2075	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2076
2077	if [[ "$ocean_file_appendix" = true ]]
2078	then
2079	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2080	fi
2081
2082	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2083	then
2084	spalte1="memory demand / PE":; spalte2="$memory MB"
2085	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2086	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2087	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2088	fi
2089
2090	if [[ $do_compile = true ]]
2091	then
2092	printf "\| \| \n"
2093	printf "\| Files to be compiled: \| \n"
2094	zeile=$source_list
2095	while [[ "$zeile" != "" ]]
2096	do
2097	linestart=$(echo $zeile \| cut -c-70)
2098	printf "\| %-70s \| \n" "$linestart"
2099	zeile=$(echo "$zeile" \| cut -c71-)
2100	done
2101	fi
2102	printf "#------------------------------------------------------------------------#"
2103
2104
2105
2106	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2107	if [[ $do_trace = true ]]
2108	then
2109	(( i = 0 ))
2110	while (( i < iin ))
2111	do
2112	(( i = i + 1 ))
2113	if (( i == 1 ))
2114	then
2115	printf "\n\n >>> INPUT-file assignments:\n"
2116	fi
2117	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2118	done
2119	(( i = 0 ))
2120	while (( i < iout ))
2121	do
2122	(( i = i + 1 ))
2123	if (( i == 1 ))
2124	then
2125	printf "\n\n >>> OUTPUT-file assignments:\n"
2126	fi
2127	printf "\n ${localout[$i]} : ${pathout[$i]}"
2128	done
2129	(( i = 0 ))
2130	while (( i < iic ))
2131	do
2132	(( i = i + 1 ))
2133	if (( i == 1 ))
2134	then
2135	printf "\n\n >>> INPUT-commands:\n"
2136	fi
2137	printf "\n ${in_command[$i]}"
2138	done
2139	(( i = 0 ))
2140	while (( i < ioc ))
2141	do
2142	(( i = i + 1 ))
2143	if (( i == 1 ))
2144	then
2145	printf "\n\n >>> OUTPUT-commands:\n"
2146	fi
2147	printf "\n ${out_command[$i]}"
2148	done
2149	fi
2150
2151
2152	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2153	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2154	then
2155	antwort=dummy
2156	printf "\n\n"
2157	printf " >>> everything o.k. (y/n) ? "
2158	while read antwort
2159	do
2160	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2161	then
2162	printf " >>> everything o.k. (y/n) ? "
2163	else
2164	break
2165	fi
2166	done
2167	if [[ $antwort = n \|\| $antwort = N ]]
2168	then
2169	locat=user_abort; (( iec = 0 )); exit
2170	fi
2171	if [[ $do_batch = true ]]
2172	then
2173	printf " >>> batch-job will be created and submitted"
2174	else
2175	printf " >>> MRUN will now continue to execute on this machine"
2176	fi
2177	fi
2178
2179
2180	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2181	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2182	check_depository="${working_directory}/trunk/UTIL"
2183	check_sources="${working_directory}/tmp_check_namelist_files"
2184	skip_check=false
2185
2186	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2187	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2188	then
2189	skip_check=true
2190	reason="run on remote host or parameter file check has not been compiled."
2191	fi
2192	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2193	then
2194	skip_check=true
2195	reason="parameter file check has not been compiled."
2196	fi
2197
2198	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2199	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2200	then
2201	skip_check=true
2202	reason="serial run."
2203	fi
2204
2205	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2206	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2207	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2208	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2209	if [[ $check_namelist_files == false ]]
2210	then
2211	skip_check=true
2212	reason="-z option set."
2213	fi
2214
2215	if [[ $fromhost != $localhost ]]
2216	then
2217	skip_check=true
2218	reason="submitting host is local host."
2219	fi
2220
2221	if [[ $run_coupled_model == true ]]
2222	then
2223	skip_check=true
2224	reason="coupled run."
2225	fi
2226
2227	if [[ $restart_run == true ]]
2228	then
2229	skip_check=true
2230	reason="restart run."
2231	fi
2232
2233	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2234	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2235	last_char=`echo $filename_input \| cut -c $last_char_int`
2236	if [[ "$last_char" == "f" ]]
2237	then
2238	skip_check=true
2239	reason="restart run."
2240	fi
2241
2242	if [[ $skip_check == false ]]
2243	then
2244	tmp_check=${working_directory}/tmp_check
2245
2246	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2247	# NOT NECESSARILY REQUIRED
2248	line=""
2249	found=false
2250	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2251	while read line1
2252	do
2253	line="$line1"
2254	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2255	then
2256	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2257	found=true
2258	fi
2259	done < $tmp_check
2260
2261	if [[ $found = false ]]
2262	then
2263	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2264	fi
2265
2266	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2267	# NOT NECESSARILY REQUIRED
2268	line=""
2269	found=false
2270	grep "NUDGING_DATA" $config_file > $tmp_check
2271	while read line1
2272	do
2273	line="$line1"
2274	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2275	then
2276	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2277	found=true
2278	fi
2279	done < $tmp_check
2280
2281	if [[ $found = false ]]
2282	then
2283	printf "\n +++ no NUDGING list entry found in the configuration file."
2284	fi
2285
2286	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2287	# NOT NECESSARILY REQUIRED
2288	line=""
2289	found=false
2290	grep "LSF_DATA" $config_file > $tmp_check
2291	while read line1
2292	do
2293	line="$line1"
2294	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2295	then
2296	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2297	found=true
2298	fi
2299	done < $tmp_check
2300
2301	if [[ $found = false ]]
2302	then
2303	printf "\n +++ no LSF list entry found in the configuration file."
2304	fi
2305
2306	rm -rf ${working_directory}/tmp_check
2307
2308	# CHECK IF THE P3DF FILE MUST BE CHECKED
2309	for item in $input_list
2310	do
2311	if [[ "$item" == "restart" ]]
2312	then
2313	check_restart=1
2314	else
2315	check_restart=0
2316	fi
2317	done
2318
2319	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2320	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2321	then
2322	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2323	locat=check_namelist; exit
2324	fi
2325
2326	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2327	if [[ $check_restart == 1 ]]
2328	then
2329
2330	filenamef="${filename_input}f"
2331	if [[ ! -f $filenamef ]]
2332	then
2333	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2334	check_restart=0
2335	answer=dummy
2336	printf "\n\n"
2337
2338	if [[ $silent == false ]]
2339	then
2340	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2341	do
2342	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2343	read answer
2344	done
2345	if [[ $answer = a \|\| $answer = A ]]
2346	then
2347	printf "\n +++ Aborting...."
2348	locat=normal; exit
2349	fi
2350	fi
2351	else
2352	check_restart=1
2353	fi
2354	fi
2355
2356	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2357	mkdir $check_sources
2358	cd $check_sources
2359
2360
2361	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2362	if [[ -d $add_source_path ]]
2363	then
2364	printf "\n\n *** copying files from $check_depository"
2365	cp $check_depository/check_namelist_files.tar ./
2366
2367	printf "\n\n *** untar of makefile and source files in $check_sources"
2368	tar -xf check_namelist_files.tar > /dev/null 2>&1
2369
2370	printf "\n\n *** adding user code."
2371	cp $add_source_path/* ./
2372	touch check_namelist_files.f90
2373
2374	# GET COMPILER OPTIONS AND PERFORM MAKE
2375	printf "\n\n *** compiling code if necessary...\n"
2376
2377	# workaround for batch jobs on local machine (lcxe6)
2378	if [[ $do_batch == true && $do_remote == false ]]
2379	then
2380	eval $init_cmds
2381	fi
2382
2383	# GET CHECK OPTIONS
2384	line=""
2385	found=false
2386
2387	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2388
2389	while read line1
2390	do
2391
2392	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2393	then
2394	line="$line1"
2395	fi
2396
2397	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2398	then
2399	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2400	line="$line "
2401	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'`
2402	found=true
2403	fi
2404
2405	done < $tmp_check
2406	copts_check="$copts_check -D__check -D__parallel"
2407
2408	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2409
2410	# GET MAKE OUTPUT
2411	if [[ $? != 0 ]]
2412	then
2413	printf "\n +++ error during make."
2414	answer=dummy
2415	printf "\n\n"
2416	if [[ $silent == false ]]
2417	then
2418	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2419	do
2420	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2421	read answer
2422	done
2423	if [[ $answer = a \|\| $answer = A ]]
2424	then
2425	printf "\n +++ Aborting..."
2426	rm -rf $check_sources
2427	locat=normal; exit
2428	else
2429	skip_check=true
2430	fi
2431	else
2432	skip_check=true
2433	fi
2434	fi
2435	else
2436	cp $PALM_BIN/check_namelist_files.x ./
2437	fi
2438
2439	cp $filename_input ./PARIN
2440	if [[ $check_restart == 1 ]]
2441	then
2442	cp $filenamef ./PARINF
2443	fi
2444
2445	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2446	then
2447	printf "\n *** adding topography data"
2448	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2449
2450	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2451	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2452	# WHICH REQUIRE SUFFICIENT MEMORY
2453	ulimit -s unlimited
2454	fi
2455
2456	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2457	then
2458	printf "\n *** adding nudging data"
2459	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2460	fi
2461
2462	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2463	then
2464	printf "\n *** adding large scale forcing data"
2465	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2466	fi
2467
2468	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2469	cat > ENVPAR << %%END%%
2470	&envpar run_identifier = '$fname', host = '$host',
2471	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2472	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2473	maximum_cpu_time_allowed = ${cpumax}.,
2474	revision = '$global_revision',
2475	local_dvrserver_running = $local_dvrserver_running /
2476
2477	%%END%%
2478
2479	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2480	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2481	then
2482	printf "\n +++ WARNING: check_namelist_files.x not found."
2483	answer=dummy
2484	printf "\n\n"
2485
2486	if [[ $silent == false ]]
2487	then
2488	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2489	do
2490	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2491	read answer
2492	done
2493	if [[ $answer = a \|\| $answer = A ]]
2494	then
2495	printf "\n +++ Aborting..."
2496	rm -rf $check_sources
2497	locat=normal; exit
2498	else
2499	printf "\n *** skipping parameter file check."
2500	fi
2501	fi
2502
2503	elif [[ $skip_check == false ]]
2504	then
2505	# STARTING THE PARAMETER FILE CHECK
2506	printf "\n\n *** starting parameter file check..."
2507
2508	# CHECKING THE P3D FILE
2509	printf "\n\n (1) checking $filename_input"
2510	echo "$numprocs 0 0" > VARIN
2511	errors=`./check_namelist_files.x < VARIN 2>&1`
2512
2513	check_error=false
2514	if [[ "$errors" == "" ]]
2515	then
2516	printf " --> o.k."
2517	else
2518	printf " --> failed."
2519	check_error=true
2520	printf "\n\n $errors"
2521	fi
2522
2523	# CHECKING THE PD3F FILE IF NECESSARY
2524	if [[ $check_restart == 1 && $check_error == false ]]
2525	then
2526	printf "\n\n (2) checking $filenamef"
2527
2528	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2529	# IN &INIPAR LIST
2530	found=false
2531	cat PARINF \| while read line
2532	do
2533	line=$(echo $line\|sed 's/ //g')
2534	if [[ $line == "&inipar" ]]
2535	then
2536	start_search=true
2537	fi
2538
2539	if [[ $start_search == true ]]
2540	then
2541	if [[ $line == "initializing_actions='read_restart_data'" ]]
2542	then
2543	found=true
2544	break
2545	fi
2546	fi
2547
2548	if [[ $line == "/" ]]
2549	then
2550	start_search=false
2551	fi
2552
2553	done
2554
2555	if [[ $found = false ]]
2556	then
2557	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2558	printf "\n in &inipar list in $fname$p3df_suffix."
2559	rm -rf $check_sources
2560	locat=check_namelist; exit
2561	fi
2562
2563	# READ max_user_pr FROM FILES
2564	if [[ -f parin_for_check ]]
2565	then
2566	read max_pr_user < parin_for_check
2567	else
2568	max_user_pr=0
2569	fi
2570
2571	echo "$numprocs 1 $max_pr_user" > VARIN
2572	errors=`./check_namelist_files.x < VARIN 2>&1`
2573
2574	if [[ "$errors" == "" ]]
2575	then
2576	printf " --> o.k."
2577	else
2578	printf " --> failed."
2579	check_error=true
2580	printf "\n\n $errors"
2581	fi
2582	fi
2583
2584	# REPORT ERRORS AND CONTINUE/EXIT
2585	if [[ $check_error == true ]]
2586	then
2587	printf "\n +++ errors found in the parameter file!\n"
2588	answer=dummy
2589	printf "\n\n"
2590
2591	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2592	do
2593	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2594	read answer
2595	done
2596
2597	if [[ $answer = a \|\| $answer = A ]]
2598	then
2599	printf "\n +++ Aborting..."
2600	rm -rf $check_sources
2601	locat=normal; exit
2602	fi
2603	else
2604	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2605	fi
2606	rm -rf $check_sources
2607	fi
2608	else
2609	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2610	fi
2611
2612	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2613	rm -rf $check_sources
2614	cd $working_directory
2615
2616
2617	# DETERMINE PATH FOR MAKE DEPOSITORY
2618	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2619	then
2620
2621	line=""
2622	grep "%depository_path" $config_file > tmp_mrun
2623	while read line
2624	do
2625	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2626	then
2627	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2628	then
2629	global_depository_path=`echo $line \| cut -d" " -s -f2`
2630	fi
2631	fi
2632	done < tmp_mrun
2633
2634	line=""
2635	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2636	while read line
2637	do
2638	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2639	then
2640	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2641	then
2642	local_depository_path=`echo $line \| cut -d" " -s -f2`
2643	fi
2644	fi
2645	done < tmp_mrun
2646
2647	if [[ "$local_depository_path" = "" ]]
2648	then
2649	if [[ "$global_depository_path" != "" ]]
2650	then
2651	local_depository_path=$global_depository_path
2652	else
2653	printf "\n\n +++ no depository path found in configuration file"
2654	printf "\n for local host \"$localhost\" "
2655	printf "\n please set \"\%depository_path\" in configuration file\n"
2656	locat=config_file; exit
2657	fi
2658	fi
2659	eval local_depository_path=$local_depository_path
2660	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2661	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2662
2663
2664	basename=`echo $mainprog \| cut -f1 -d"."`
2665	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2666	if [[ ! -f $make_depository ]]
2667	then
2668	printf "\n"
2669	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2670	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2671	fi
2672
2673	fi
2674
2675
2676	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2677	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2678	if [[ $do_batch = false ]]
2679	then
2680
2681
2682	# CREATE THE TEMPORARY WORKING DIRECTORY
2683	mkdir -p $TEMPDIR
2684	chmod go+rx $TEMPDIR
2685	tmpcreate=true
2686
2687
2688	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2689	# INTO THE TEMPORARY WORKING DIRECTORY
2690	if [[ $do_compile = true ]]
2691	then
2692
2693	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2694	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2695	if [[ $localhost = nech ]]
2696	then
2697	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2698	if mkdir -p $TEMPDIR_COMPILE
2699	then
2700	printf "\n *** \"$TEMPDIR_COMPILE\" "
2701	printf "\n is generated as temporary directory for cross compiling\n"
2702	else
2703	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2704	printf "\n needed for cross compilation failed"
2705	locat=compile
2706	exit
2707	fi
2708	else
2709	TEMPDIR_COMPILE=$TEMPDIR
2710	fi
2711
2712	cp $make_depository $TEMPDIR_COMPILE
2713	cd $TEMPDIR_COMPILE
2714	tar -xf $make_depository > /dev/null 2>&1
2715	cd - > /dev/null
2716
2717	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2718	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2719	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2720	then
2721	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2722	else
2723	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2724	fi
2725
2726	else
2727
2728	cp $executable ${TEMPDIR}/a.out
2729
2730	fi
2731
2732
2733	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2734	cd $TEMPDIR
2735	printf "\n *** changed to temporary directory: $TEMPDIR"
2736
2737
2738	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2739	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2740	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2741	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2742	(( i = 0 ))
2743	while (( i < iout ))
2744	do
2745	(( i = i + 1 ))
2746	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2747	then
2748	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2749	else
2750	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2751	fi
2752	done
2753
2754
2755	# IF REQUIRED, START WITH COMPILING
2756	if [[ $do_compile = true ]]
2757	then
2758
2759
2760	if [[ -f a.out ]]
2761	then
2762
2763	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2764	printf "\n\n\n *** executable a.out found"
2765	printf "\n no compilation required \n"
2766
2767	else
2768
2769	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2770	printf "\n\n\n *** compilation starts \n$dashes\n"
2771	printf " *** compilation with make using following options:\n"
2772	printf " make depository: $make_depository"
2773	if [[ "$mopts" != "" ]]
2774	then
2775	printf " make options: $mopts\n"
2776	fi
2777	printf " compilername: $compiler_name\n"
2778	printf " compiler options: $fopts\n"
2779	printf " preprocessor directives: $cpp_options \n"
2780	printf " linker options: $lopts \n"
2781	if [[ "$modules" != "" ]]
2782	then
2783	printf " modules to be load: $modules \n"
2784	fi
2785	printf " source code files: $source_list \n"
2786
2787	if [[ $localhost = nech ]]
2788	then
2789	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\" "
2790	cp $TEMPDIR_COMPILE/a.out .
2791	[[ $? != 0 ]] && compile_error=true
2792	rm -rf $TEMPDIR_COMPILE
2793	elif [[ $localhost = ibmh ]]
2794	then
2795	printf " compiler is called via ssh on \"plogin1\" \n"
2796	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\" "
2797	[[ ! -f a.out ]] && compile_error=true
2798	continue # STATUS=1, IF a.out EXISTS
2799	elif [[ $localhost = lcflow ]]
2800	then
2801	printf " compiler is called via ssh on \"flow\" \n"
2802	/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\" "
2803	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2804	[[ "$check_for_file" = "" ]] && compile_error=true
2805	continue # STATUS=1, IF a.out EXISTS
2806	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2807	then
2808	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2809	else
2810	[[ "$init_cmds" != "" ]] && eval $init_cmds
2811	[[ "$module_calls" != "" ]] && eval $module_calls
2812	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2813	fi
2814
2815	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2816	then
2817	printf "\n +++ error occured while compiling or linking"
2818	locat=compile
2819
2820	exit
2821	else
2822	printf "$dashes\n *** compilation finished \n"
2823	fi
2824
2825	fi
2826
2827	fi
2828
2829
2830	# PROVIDE THE INPUT FILES
2831	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2832	(( i = 0 ))
2833	while (( i < iin ))
2834	do
2835	(( i = i + 1 ))
2836	if (( i == 1 ))
2837	then
2838	printf "\n\n *** providing INPUT-files:\n$dashes"
2839	fi
2840
2841
2842	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2843	if [[ "${transin[$i]}" = unavailable ]]
2844	then
2845	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2846	then
2847	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2848	printf "\n is not available!"
2849	else
2850	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2851	printf "\n is not available!"
2852	fi
2853	continue
2854	fi
2855
2856	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2857	files_for_pes=false; datentyp=file
2858	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2859	then
2860	files_for_pes=true; datentyp=directory
2861	actionin[$i]=""
2862	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2863	then
2864	actionin[$i]=""
2865	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2866	then
2867	files_for_pes=true; datentyp=directory
2868	actionin[$i]="ar"
2869	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2870	then
2871	actionin[$i]="ar"
2872	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2873	then
2874	files_for_pes=true; datentyp=directory
2875	actionin[$i]="fl"
2876	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2877	then
2878	actionin[$i]="fl"
2879	fi
2880
2881	if [[ $files_for_pes = true ]]
2882	then
2883	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2884	else
2885	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2886	fi
2887
2888	# INPUT-FILE FOR A RESTART RUN.
2889	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2890	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2891	if [[ "${actionin[$i]}" = fl ]]
2892	then
2893	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2894	if [[ $files_for_pes = false ]]
2895	then
2896	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2897	then
2898	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2899	got_tmp[$i]=true
2900	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2901	then
2902	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2903	printf "\n *** trying to use backup copy in \"$WORK\" "
2904	cp $WORK/${frelin[$i]} ${localin[$i]}
2905	else
2906	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2907	printf "\n or \"$tmp_data_catalog\" does not exist!"
2908	printf "\n *** trying to get copy from archive"
2909	actionin[$i]=ar
2910	fi
2911	else
2912	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2913	then
2914	mkdir ${localin[$i]}
2915	cd $tmp_data_catalog/${frelin[$i]}
2916	for file in $(ls *)
2917	do
2918	ln $file $TEMPDIR/${localin[$i]}
2919	done
2920	cd $TEMPDIR
2921	got_tmp[$i]=true
2922	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2923	then
2924	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2925	printf "\n *** trying to use backup copy in \"$WORK\" "
2926	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2927	else
2928	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2929	printf "\n or \"$tmp_data_catalog\" does not exist!"
2930	printf "\n *** trying to get copy from archive"
2931	actionin[$i]=ar
2932	fi
2933	fi
2934	fi
2935
2936
2937	# FILE IS STORED ON THE ARCHIVE SYSTEM
2938	if [[ "${actionin[$i]}" = ar ]]
2939	then
2940
2941	if [[ $files_for_pes = false ]]
2942	then
2943	printf "\n file will be restored from archive-system ($archive_system)!"
2944	else
2945	printf "\n directory will be restored from archive-system ($archive_system)!"
2946	fi
2947
2948	file_restored=false
2949
2950	if [[ $archive_system = asterix ]]
2951	then
2952	do_stagein=true
2953	(( stagein_anz = 0 ))
2954	while [[ $do_stagein = true ]]
2955	do
2956	if [[ $files_for_pes = false ]]
2957	then
2958	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2959	else
2960	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2961	fi
2962	cat STAGEIN_OUTPUT
2963	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2964	then
2965	file_restored=true
2966	do_stagein=false
2967	else
2968	(( stagein_anz = stagein_anz + 1 ))
2969	if (( stagein_anz == 10 ))
2970	then
2971	printf "\n +++ stagein stoped after 10 tries"
2972	locat=stage
2973	exit
2974	fi
2975	printf "\n +++ restoring from archive failed, trying again:"
2976	sleep 900
2977	fi
2978	done
2979	elif [[ $archive_system = DMF ]]
2980	then
2981	if [[ $files_for_pes = false ]]
2982	then
2983	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2984	locat=DMF
2985	exit
2986	else
2987	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2988	cp -r $ARCHIVE/${frelin[$i]} $PWD
2989	file_restored=true
2990	fi
2991	elif [[ $archive_system = tivoli ]]
2992	then
2993	if [[ $files_for_pes = false ]]
2994	then
2995	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2996	else
2997	(( inode = 0 ))
2998	while (( inode < nodes ))
2999	do
3000	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3001	(( inode = inode + 1 ))
3002	done
3003	fi
3004	file_restored=true
3005	elif [[ $archive_system = ut ]]
3006	then
3007	if [[ $files_for_pes = false ]]
3008	then
3009	cp $UT/${frelin[$i]} .
3010	else
3011	(( inode = 0 ))
3012	while (( inode < nodes ))
3013	do
3014	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3015	(( inode = inode + 1 ))
3016	done
3017	fi
3018	file_restored=true
3019	else
3020	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3021	locat=rearchive
3022	exit
3023	fi
3024
3025	if [[ $file_restored = true ]]
3026	then
3027
3028	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3029	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3030	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3031	if [[ $files_for_pes = false ]]
3032	then
3033	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3034	else
3035	mkdir $tmp_data_catalog/${frelin[$i]}
3036	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3037	fi
3038	got_tmp[$i]=true
3039
3040	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3041	mv ${frelin[$i]} ${localin[$i]}
3042
3043	fi
3044	fi
3045
3046
3047	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3048	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3049	then
3050
3051	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3052	then
3053
3054	# FILE COPIES ARE PROVIDED FOR ALL CORES
3055	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3056	printf "\n file will be provided for $numprocs processors"
3057	mkdir ${localin[$i]}
3058	ival=$numprocs
3059	(( ii = 0 ))
3060	while (( ii <= ival-1 ))
3061	do
3062	if (( ii < 10 ))
3063	then
3064	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3065	elif (( ii < 100 ))
3066	then
3067	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3068	elif (( ii < 1000 ))
3069	then
3070	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3071	else
3072	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3073	fi
3074	(( ii = ii + 1 ))
3075	done
3076
3077	else
3078
3079	if [[ $files_for_pes = true ]]
3080	then
3081
3082	# PROVIDE FILES FOR EACH CORE
3083	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3084	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3085	printf "\n providing $numprocs files for the respective processors"
3086	mkdir ${localin[$i]}
3087	if [[ $link_local_input = true ]]
3088	then
3089	printf " using ln -f\n"
3090	cd ${absnamein[$i]}
3091	for file in $(ls *)
3092	do
3093	ln -f $file ${localin[$i]}
3094	done
3095	cd $TEMPDIR
3096	fi
3097
3098	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3099	if [[ ! -f "${localin[$i]}/_0000" ]]
3100	then
3101	if [[ $link_local_input = true ]]
3102	then
3103	printf " ln failed for .../_0000, using cp...\n"
3104	fi
3105	cp -r ${absnamein[$i]}/* ${localin[$i]}
3106	fi
3107
3108	else
3109
3110	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3111	if [[ $link_local_input = true ]]
3112	then
3113	printf " using ln -f\n"
3114	ln -f ${absnamein[$i]} ${localin[$i]}
3115	fi
3116	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3117	if [[ ! -f "${localin[$i]}" ]]
3118	then
3119	if [[ $link_local_input = true ]]
3120	then
3121	printf " ln failed, using cp...\n"
3122	fi
3123	cp ${absnamein[$i]} ${localin[$i]}
3124	fi
3125	fi
3126	fi
3127	fi
3128
3129	done
3130	if (( i != 0 ))
3131	then
3132	printf "\n$dashes\n *** all INPUT-files provided \n"
3133	fi
3134
3135
3136	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3137	(( i = 0 ))
3138	while (( i < iic ))
3139	do
3140	(( i = i + 1 ))
3141	if (( i == 1 ))
3142	then
3143	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3144	fi
3145	printf "\n >>> ${in_command[$i]}"
3146	eval ${in_command[$i]}
3147	if (( i == iic ))
3148	then
3149	printf "\n$dashes\n"
3150	fi
3151	done
3152
3153
3154	# SET THE REMAINING CPU-TIME
3155	cpurest=${cpumax}.
3156
3157
3158	# START DVR STREAMING SERVER
3159	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3160	then
3161	if [[ "$dvr_server" != "" ]]
3162	then
3163
3164	printf "\n\n *** preparing the dvr streaming server configuration file"
3165
3166	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3167	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3168	if [[ "$running_dvrserver_id" != "" ]]
3169	then
3170
3171	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3172	printf "\n This server is used instead starting a new one!"
3173	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3174
3175	else
3176
3177	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3178	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3179	then
3180	cp ${PALM_BIN}/.dvrserver.config .
3181
3182	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3183	user_id=`id -u`
3184	group_id=`id -g`
3185
3186	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3187	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3188	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3189	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3190	mv .dvrserver.3 .dvrserver.config
3191	rm .dvrserver.1 .dvrserver.2
3192
3193	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3194	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3195	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3196	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3197	local_dvrserver_running=.TRUE.
3198	else
3199	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3200	printf "\n \"$PALM_BIN\" "
3201	locat=dvr
3202	exit
3203	fi
3204
3205	fi
3206
3207	else
3208	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3209	fi
3210	fi
3211
3212
3213	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3214	# (FILE ENVPAR WILL BE READ BY PALM)
3215	cat > ENVPAR << %%END%%
3216	&envpar run_identifier = '$fname', host = '$localhost',
3217	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3218	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3219	maximum_cpu_time_allowed = ${cpumax}.,
3220	revision = '$global_revision',
3221	local_dvrserver_running = $local_dvrserver_running,
3222	batch_job = $batch_job /
3223
3224	%%END%%
3225
3226
3227	# STARTING THE EXECUTABLE
3228	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3229	PATH=$PATH:$TEMPDIR
3230
3231	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3232	if [[ "$mpi_debug" = true ]]
3233	then
3234	export MPI_CHECK_ARGS=1
3235	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3236	fi
3237
3238	if [[ "$totalview" = true ]]
3239	then
3240	printf "\n *** totalview debugger will be used"
3241	tv_opt="-tv"
3242	else
3243	tv_opt=""
3244	fi
3245
3246	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3247	then
3248	if [[ "$ENVIRONMENT" = BATCH ]]
3249	then
3250	continue
3251	fi
3252	if [[ $localhost = ibmh ]]
3253	then
3254
3255	# SETUP THE IBM MPI ENVIRONMENT
3256	export MP_SHARED_MEMORY=yes
3257	export AIXTHREADS_SCOPE=S
3258	export OMP_NUM_THREADS=$threads_per_task
3259	export AUTHSTATE=files
3260	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3261
3262	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3263	export MP_ADAPTER_USE=shared
3264	export MP_CPU_USE=multiple
3265	export MP_TIMEOUT=1200
3266
3267	unset MP_TASK_AFFINITY
3268
3269	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3270	#(( ii = 1 ))
3271	#while (( ii <= $numprocs ))
3272	#do
3273	# echo $localhost_realname >> hostfile
3274	# (( ii = ii + 1 ))
3275	#done
3276	#export MP_HOSTFILE=hostfile
3277
3278	if [[ "$LOADLBATCH" = yes ]]
3279	then
3280	totalview poe a.out $ROPTS
3281	else
3282	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3283	export TVDSVRLAUNCHCMD=ssh
3284	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3285	fi
3286
3287	fi # END DEBUG MODE
3288
3289	else
3290
3291	# NORMAL EXECUTION
3292	if [[ -n $numprocs ]]
3293	then
3294
3295	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3296	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3297	then
3298
3299	# SETUP THE IBM MPI ENVIRONMENT
3300	if [[ $host != ibmh && $host != ibmkisti ]]
3301	then
3302	export MP_SHARED_MEMORY=yes
3303	export AIXTHREAD_SCOPE=S
3304	export OMP_NUM_THREADS=$threads_per_task
3305	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3306	export AUTHSTATE=files
3307	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3308	# export MP_PRINTENV=yes
3309
3310	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3311	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3312	export MP_WAIT_MODE=poll
3313	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3314	fi
3315
3316	if [[ $host = ibmkisti ]]
3317	then
3318	export LANG=en_US
3319	export MP_SHARED_MEMORY=yes
3320	if [[ $threads_per_task = 1 ]]
3321	then
3322	export MP_SINGLE_THREAD=yes
3323	export MEMORY_AFFINITY=MCM
3324	else
3325	export OMP_NUM_THREADS=$threads_per_task
3326	fi
3327	fi
3328
3329	if [[ "$LOADLBATCH" = yes ]]
3330	then
3331	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3332	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3333	then
3334	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3335	else
3336	if [[ $run_coupled_model = false ]]
3337	then
3338	if [[ "$ocean_file_appendix" = true ]]
3339	then
3340	echo "precursor_ocean" > runfile_atmos
3341	else
3342	echo "precursor_atmos" > runfile_atmos
3343	fi
3344	else
3345	(( iia = $numprocs_atmos / $threads_per_task ))
3346	(( iio = $numprocs_ocean / $threads_per_task ))
3347	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3348	printf "\n using $coupled_mode coupling"
3349	printf "\n\n"
3350	echo "coupled_run $iia $iio" > runfile_atmos
3351	fi
3352	poe ./a.out $ROPTS < runfile_atmos
3353	fi
3354	else
3355	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3356	then
3357	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3358	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3359	then
3360	if [[ -f $hostfile ]]
3361	then
3362	cp $hostfile hostfile
3363	else
3364	(( ii = 1 ))
3365	while (( ii <= $numprocs ))
3366	do
3367	echo $localhost_realname >> hostfile
3368	(( ii = ii + 1 ))
3369	done
3370	fi
3371	export MP_HOSTFILE=hostfile
3372	if [[ $run_coupled_model = false ]]
3373	then
3374	if [[ "$ocean_file_appendix" = true ]]
3375	then
3376	echo "precursor_ocean" > runfile_atmos
3377	else
3378	echo "precursor_atmos" > runfile_atmos
3379	fi
3380	else
3381	(( iia = $numprocs_atmos / $threads_per_task ))
3382	(( iio = $numprocs_ocean / $threads_per_task ))
3383	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3384	printf "\n using $coupled_mode coupling"
3385	printf "\n\n"
3386	echo "coupled_run $iia $iio" > runfile_atmos
3387	fi
3388
3389	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3390
3391	else
3392	if [[ "$host_file" = "" ]]
3393	then
3394	printf "\n +++ no hostfile given in configuration file"
3395	locat=config_file
3396	exit
3397	else
3398	eval host_file=$host_file
3399	fi
3400	export MP_HOSTFILE=$host_file
3401	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3402	fi
3403	fi
3404	elif [[ $host = nech ]]
3405	then
3406	(( ii = nodes ))
3407	if [[ $ii = 1 ]]
3408	then
3409	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3410	export MPIPROGINF=YES
3411	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3412	echo "*** execution on single node with mpirun"
3413	mpirun -np $numprocs ./a.out $ROPTS
3414	else
3415	(( i = 0 ))
3416	while (( i < ii ))
3417	do
3418	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3419	(( i = i + 1 ))
3420	done
3421
3422	echo "#!/bin/sh" > mpi_exec_shell
3423	echo " " >> mpi_exec_shell
3424	echo "set -u" >> mpi_exec_shell
3425	echo "F_ERRCNT=0" >> mpi_exec_shell
3426	echo "MPIPROGINV=YES" >> mpi_exec_shell
3427	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3428	echo "cpurest=$cpurest" >> mpi_exec_shell
3429	echo "fname=$fname" >> mpi_exec_shell
3430	echo "localhost=$localhost" >> mpi_exec_shell
3431	echo "return_address=$return_address" >> mpi_exec_shell
3432	echo "return_username=$return_username" >> mpi_exec_shell
3433	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3434	echo "write_binary=$write_binary" >> mpi_exec_shell
3435	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3436	echo " " >> mpi_exec_shell
3437	echo "export F_ERRCNT" >> mpi_exec_shell
3438	echo "export MPIPROGINV" >> mpi_exec_shell
3439	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3440	echo "export cpurest" >> mpi_exec_shell
3441	echo "export fname" >> mpi_exec_shell
3442	echo "export localhost" >> mpi_exec_shell
3443	echo "export return_address" >> mpi_exec_shell
3444	echo "export return_username" >> mpi_exec_shell
3445	echo "export tasks_per_node" >> mpi_exec_shell
3446	echo "export write_binary" >> mpi_exec_shell
3447	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3448	echo " " >> mpi_exec_shell
3449	echo "exec ./a.out" >> mpi_exec_shell
3450
3451	chmod u+x mpi_exec_shell
3452	export MPIPROGINF=YES
3453	mpirun -f multinode_config &
3454	wait
3455
3456	fi
3457	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3458	then
3459
3460	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3461	# DOES NOT EXIST
3462	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3463	then
3464	if [[ -f $hostfile ]]
3465	then
3466	cp $hostfile hostfile
3467	(( ii = $numprocs / $threads_per_task ))
3468	else
3469	(( ii = 1 ))
3470	while (( ii <= $numprocs / $threads_per_task ))
3471	do
3472	echo $localhost_realname >> hostfile
3473	(( ii = ii + 1 ))
3474	done
3475	fi
3476	eval zeile=\"`head -n $ii hostfile`\"
3477	printf "\n *** running on: $zeile"
3478	fi
3479
3480	(( ii = $numprocs / $threads_per_task ))
3481	export OMP_NUM_THREADS=$threads_per_task
3482
3483	if [[ $threads_per_task != 1 ]]
3484	then
3485	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3486	# MAY ABORT
3487	ulimit -s unlimited
3488	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3489	fi
3490	if [[ $run_coupled_model = false ]]
3491	then
3492	if [[ "$ocean_file_appendix" = true ]]
3493	then
3494	echo "precursor_ocean" > runfile_atmos
3495	else
3496	echo "precursor_atmos" > runfile_atmos
3497	fi
3498	printf "\n\n"
3499
3500	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3501	then
3502	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3503	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3504	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3505	elif [[ $host = lccrayf ]]
3506	then
3507	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3508	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3509	then
3510	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3511	elif [[ $host = lcflow ]]
3512	then
3513	mpirun -np $ii a.out < runfile_atmos $ROPTS
3514	elif [[ $host = lcsb ]]
3515	then
3516	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3517	elif [[ $host = lckiaps ]]
3518	then
3519	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3520	elif [[ $host = lckyu* ]]
3521	then
3522	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3523	else
3524	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3525	fi
3526	else
3527
3528	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3529	(( iia = $numprocs_atmos / $threads_per_task ))
3530	(( iio = $numprocs_ocean / $threads_per_task ))
3531	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3532	printf "\n using $coupled_mode coupling"
3533	printf "\n\n"
3534
3535	if [[ $coupled_mode = "mpi2" ]]
3536	then
3537	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3538	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3539
3540	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3541	then
3542
3543	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3544	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3545
3546	else
3547	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3548	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3549	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3550	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3551	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3552	fi
3553	wait
3554
3555	else
3556
3557	echo "coupled_run $iia $iio" > runfile_atmos
3558
3559	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3560	then
3561
3562	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3563
3564	elif [[ $host = lck \|\| $host = lckordi ]]
3565	then
3566
3567	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3568
3569	elif [[ $host = lckyu* ]]
3570	then
3571
3572	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3573
3574	fi
3575	wait
3576	fi
3577
3578	fi
3579
3580	elif [[ $host = lckyoto ]]
3581	then
3582	set -xv
3583	export P4_RSHCOMMAND=plesh
3584	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3585	if [[ "$ENVIRONMENT" = BATCH ]]
3586	then
3587	if [[ "$cond2" = fujitsu ]]
3588	then
3589	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3590	elif [[ "cond2" = pgi ]]
3591	then
3592	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3593	else
3594	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3595	fi
3596	else
3597	if [[ "$cond2" = "" ]]
3598	then
3599	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3600	else
3601	mpirun -np $numprocs ./a.out $ROPTS
3602	fi
3603	fi
3604	set +xv
3605
3606	elif [[ $host = lctit ]]
3607	then
3608	export OMP_NUM_THREADS=$threads_per_task
3609	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3610	if [[ "$threads_per_task" != 1 ]]
3611	then
3612	export MV2_ENABLE_AFFINITY=0
3613	fi
3614	echo "----- PBS_NODEFILE content:"
3615	cat $PBS_NODEFILE
3616	echo "-----"
3617	(( ii = $numprocs / $threads_per_task ))
3618	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3619	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3620	else
3621	mpprun -n $numprocs a.out $ROPTS
3622	fi
3623	else
3624	a.out $ROPTS
3625	fi
3626	fi
3627
3628	if [[ $? != 0 ]]
3629	then
3630
3631	# ABORT IN CASE OF RUNTIME ERRORS
3632	printf "\n +++ runtime error occured"
3633	locat=execution
3634	exit
3635
3636	else
3637
3638	printf "\n$dashes\n *** execution finished \n"
3639
3640	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3641	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3642	if [[ "$dvrserver_id" != "" ]]
3643	then
3644	kill $dvrserver_id
3645	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3646
3647	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3648	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3649	if [[ -d DATA_DVR ]]
3650	then
3651
3652	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3653	# DIRECTORY
3654	cp .dvrserver.config DATA_DVR
3655
3656	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3657	# SEQUENCE MODE DATA TOO)
3658	process_dvr_output -d DATA_DVR -f $fname -s
3659
3660	else
3661
3662	# PROCESS THE LOCAL OUTPUT
3663	process_dvr_output -l -d DATA_DVR -f $fname
3664
3665	fi
3666
3667	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3668	then
3669
3670	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3671	process_dvr_output -l -d DATA_DVR -f $fname
3672
3673	fi
3674	fi
3675
3676
3677
3678	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3679	# BY EACH CORE INTO ONE FILE
3680	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3681	then
3682	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3683	printf "\n 2d- and/or 3d-data may be incomplete!"
3684	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3685	elif [[ "$combine_plot_fields" == true ]]
3686	then
3687	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3688	then
3689	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3690	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3691	else
3692	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3693	combine_plot_fields${block}.x
3694	fi
3695	else
3696
3697	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3698	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3699	# ??? koennen wir das streichen ???
3700	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3701	fi
3702
3703
3704
3705	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3706	(( i = 0 ))
3707	while (( i < ioc ))
3708	do
3709	(( i = i + 1 ))
3710	if (( i == 1 ))
3711	then
3712	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3713	fi
3714	printf "\n >>> ${out_command[$i]}"
3715	eval ${out_command[$i]}
3716	if (( i == ioc ))
3717	then
3718	printf "\n$dashes\n"
3719	fi
3720	done
3721
3722
3723	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3724	if [[ $do_trace = true ]]
3725	then
3726	printf "\n\n"
3727	ls -al
3728	fi
3729
3730
3731
3732	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3733	(( i = 0 ))
3734	while (( i < iout ))
3735	do
3736	(( i = i + 1 ))
3737	if (( i == 1 ))
3738	then
3739	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3740	fi
3741
3742	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3743	files_for_pes=false; filetyp=file
3744	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3745	then
3746	files_for_pes=true; filetyp=directory
3747	actionout[$i]=""
3748	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3749	then
3750	actionout[$i]=""
3751	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3752	then
3753	files_for_pes=true; filetyp=directory
3754	actionout[$i]="ar"
3755	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3756	then
3757	actionout[$i]="ar"
3758	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3759	then
3760	files_for_pes=true; filetyp=directory
3761	actionout[$i]="fl"
3762	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3763	then
3764	actionout[$i]="fl"
3765	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3766	then
3767	files_for_pes=true; filetyp=directory
3768	actionout[$i]="tr"
3769	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3770	then
3771	actionout[$i]="tr"
3772	fi
3773
3774	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3775	then
3776	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3777	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3778	then
3779	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3780	else
3781
3782
3783	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3784	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3785	if [[ "${actionout[$i]}" = tr ]]
3786	then
3787	if [[ $localhost != $fromhost ]]
3788	then
3789	if [[ $files_for_pes = false ]]
3790	then
3791	cps=""
3792	cst=""
3793	else
3794	cps=-c
3795	cst="/"
3796	fi
3797	if [[ $localhost = nech ]]
3798	then
3799
3800	# TRANSFER IN SEPERATE JOB
3801	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3802	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3803	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3804	if [[ $files_for_pes = false ]]
3805	then
3806	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3807	else
3808	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3809	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3810	fi
3811
3812	echo "set -x" > transfer_${localout[$i]}
3813	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3814
3815	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3816	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3817	printf "\n or higher cycle\n"
3818	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3819
3820	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3821
3822	if [[ $localhost = nech ]]
3823	then
3824	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3825	else
3826	if [[ "$LOGNAME" = b323013 ]]
3827	then
3828	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3829	else
3830	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3831	fi
3832	fi
3833
3834	else
3835
3836	# TRANSFER WITHIN THIS JOB
3837	transfer_failed=false
3838	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3839	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3840	if [[ $localhost = lccrayb ]]
3841	then
3842	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3843	elif [[ $localhost = lccrayh ]]
3844	then
3845	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3846	elif [[ $localhost = lcxe6 ]]
3847	then
3848	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3849	else
3850	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3851	fi
3852	[[ $? != 0 ]] && transfer_failed=true
3853
3854	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3855	if [[ $transfer_failed = true ]]
3856	then
3857	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3858	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3859
3860	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3861	eval local_catalog=${pathout[$i]}
3862	if [[ ! -d $local_catalog ]]
3863	then
3864	printf " *** local directory does not exist. Trying to create:\n"
3865	printf " $local_catalog \n"
3866	mkdir -p $local_catalog
3867	fi
3868	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3869	transfer_problems=true
3870	fi
3871	fi
3872	else
3873
3874	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3875	actionout[$i]=""
3876	fi
3877	fi
3878
3879
3880	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3881	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3882	if [[ "${actionout[$i]}" = tra ]]
3883	then
3884	if [[ $localhost != $fromhost ]]
3885	then
3886	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3887	then
3888
3889	# TRANSFER IN SEPERATE JOB
3890	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3891	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3892	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3893	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3894
3895	echo "set -x" > transfer_${localout[$i]}
3896	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3897
3898	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3899	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3900	printf "\n or higher cycle\n"
3901	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3902
3903	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3904
3905	if [[ $localhost = nech ]]
3906	then
3907	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3908	else
3909	if [[ $LOGNAME = b323013 ]]
3910	then
3911	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3912	else
3913	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3914	fi
3915	fi
3916
3917	else
3918
3919	# TRANSFER WITHIN THIS JOB
3920	transfer_failed=false
3921	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3922	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3923	if [[ $localhost = lccrayb ]]
3924	then
3925	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3926	elif [[ $localhost = lccrayh ]]
3927	then
3928	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3929	elif [[ $localhost = lcxe6 ]]
3930	then
3931	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3932	else
3933	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3934	fi
3935	[[ $? != 0 ]] && transfer_failed=true
3936
3937	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3938	if [[ $transfer_failed = true ]]
3939	then
3940	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3941	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3942
3943	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3944	eval local_catalog=${pathout[$i]}
3945	if [[ ! -d $local_catalog ]]
3946	then
3947	printf " *** local directory does not exist. Trying to create:\n"
3948	printf " $local_catalog \n"
3949	mkdir -p $local_catalog
3950	fi
3951
3952	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3953	transfer_problems=true
3954	fi
3955	fi
3956	else
3957
3958	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3959	actionout[$i]=a
3960	fi
3961	fi
3962
3963
3964	# OUTPUT-FILE FOR A RESTART-RUN.
3965	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3966	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3967	# AS LAST ACTION, ARCHIVING IS INITIATED.
3968	if [[ "${actionout[$i]}" = fl ]]
3969	then
3970	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3971	chmod g+rx $tmp_data_catalog
3972	if [[ $files_for_pes = false ]]
3973	then
3974	printf "\n >>> OUTPUT: ${localout[$i]} to"
3975	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3976	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3977	else
3978	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3979	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3980	mkdir $tmp_data_catalog/${frelout[$i]}
3981	cd ${localout[$i]}
3982	for file in $(ls *)
3983	do
3984	ln -f $file $tmp_data_catalog/${frelout[$i]}
3985	done
3986	cd $TEMPDIR
3987	fi
3988
3989
3990	# CREATE AND SUBMIT ARCHIVING-JOB
3991	if [[ $store_on_archive_system = true ]]
3992	then
3993
3994	if [[ $archive_system = asterix ]]
3995	then
3996	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3997	if [[ $files_for_pes = false ]]
3998	then
3999	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4000	else
4001	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4002	fi
4003	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4004	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4005	echo "then" >> archive_${frelout[$i]}
4006	echo " do_stageout=false" >> archive_${frelout[$i]}
4007	echo "else" >> archive_${frelout[$i]}
4008	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4009	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4010	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4011	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4012	if [[ $files_for_pes = false ]]
4013	then
4014	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4015	else
4016	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4017	fi
4018	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4019	echo "fi" >> archive_${frelout[$i]}
4020	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4021	elif [[ $archive_system = DMF ]]
4022	then
4023	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4024	if [[ $files_for_pes = false ]]
4025	then
4026	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4027	locat=DMF
4028	exit
4029	else
4030	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4031	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4032	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4033	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4034	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4035	fi
4036	elif [[ $archive_system = tivoli ]]
4037	then
4038	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4039	if [[ $files_for_pes = false ]]
4040	then
4041	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4042	echo "set -x" >> archive_${frelout[$i]}
4043	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4044	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4045	else
4046
4047	echo "set -x" >> archive_${frelout[$i]}
4048	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4049	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4050	cd $tmp_data_catalog
4051	all_files=`ls -1 ${frelout[$i]}/*`
4052	cd - > /dev/null
4053	(( inode = 0 ))
4054	(( tp1 = tasks_per_node + 1 ))
4055	while (( inode < nodes ))
4056	do
4057	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4058	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4059	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4060	(( inode = inode + 1 ))
4061	done
4062	fi
4063	elif [[ $archive_system = ut ]]
4064	then
4065	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4066	if [[ $files_for_pes = false ]]
4067	then
4068	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4069	echo "set -x" >> archive_${frelout[$i]}
4070	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4071	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4072	else
4073
4074	echo "set -x" >> archive_${frelout[$i]}
4075	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4076	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4077	cd $tmp_data_catalog
4078	all_files=`ls -1 ${frelout[$i]}/*`
4079	cd - > /dev/null
4080	(( inode = 0 ))
4081	(( tp1 = tasks_per_node + 1 ))
4082	while (( inode < nodes ))
4083	do
4084	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4085	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4086	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4087	(( inode = inode + 1 ))
4088	done
4089	fi
4090	elif [[ $archive_system = none ]]
4091	then
4092	printf " +++ archiving on $localhost not available!\n"
4093	fi
4094
4095	if [[ $archive_system != none ]]
4096	then
4097	if [[ $localhost = nech ]]
4098	then
4099	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4100	fi
4101	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4102	fi
4103	else
4104	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4105	fi
4106
4107
4108	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4109	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4110	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4111	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4112	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4113	if [[ $files_for_pes = false ]]
4114	then
4115	cat /dev/null > ${pathout[$i]}
4116	else
4117	mkdir -p ${pathout[$i]}
4118	fi
4119
4120	fi
4121
4122
4123	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4124	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4125	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4126	if [[ "${actionout[$i]}" = ar ]]
4127	then
4128	if [[ $files_for_pes = false ]]
4129	then
4130	printf "\n >>> OUTPUT: ${localout[$i]} to"
4131	printf "\n ${pathout[$i]}"
4132	printf "\n File will be copied to archive-system ($archive_system) !\n"
4133	else
4134	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4135	printf "\n ${pathout[$i]}"
4136	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4137	fi
4138	mv ${localout[$i]} ${frelout[$i]}
4139
4140	file_saved=false
4141
4142	if [[ $archive_system = asterix ]]
4143	then
4144	do_stageout=true
4145	(( stageout_anz = 0 ))
4146	while [[ $do_stageout = true ]]
4147	do
4148	if [[ $files_for_pes = false ]]
4149	then
4150	stageout ${frelout[$i]} > STAGE_OUTPUT
4151	else
4152	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4153	fi
4154	cat STAGE_OUTPUT
4155	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4156	then
4157	file_saved=true
4158	do_stageout=false
4159	else
4160	if [[ $files_for_pes = false ]]
4161	then
4162	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4163	else
4164	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4165	fi
4166	(( stageout_anz = stageout_anz + 1 ))
4167	if (( stageout_anz == 10 ))
4168	then
4169	printf "\n +++ stoped after 10 unsuccessful tries!"
4170	archive_save=false
4171	do_stageout=false
4172	else
4173	printf "\n *** new try to store on archive after 15 min:"
4174	sleep 900
4175	fi
4176	fi
4177	done
4178	elif [[ $archive_system = DMF ]]
4179	then
4180	if [[ $files_for_pes = false ]]
4181	then
4182	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4183	locat=DMF
4184	exit
4185	else
4186	rm -rf $ARCHIVE/${frelout[$i]}
4187	cp -r ${frelout[$i]} $ARCHIVE
4188	fi
4189	file_saved=true
4190	elif [[ $archive_system = tivoli ]]
4191	then
4192	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4193	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4194	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4195	# WHEN THE ARCHIVE-JOB IS EXECUTED
4196	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4197	chmod g+rx $tmp_data_catalog
4198	if [[ $files_for_pes = false ]]
4199	then
4200	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4201	else
4202	mkdir $tmp_data_catalog/${frelout[$i]}
4203	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4204	fi
4205
4206	# GENERATE AND SUBMIT BATCH-JOB
4207	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4208	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4209	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4210	if [[ $files_for_pes = false ]]
4211	then
4212	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4213	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4214	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4215	else
4216	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4217	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4218	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4219	fi
4220
4221	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4222	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4223	file_saved=true
4224
4225	elif [[ $archive_system = ut ]]
4226	then
4227	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4228	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4229	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4230	# WHEN THE ARCHIVE-JOB IS EXECUTED
4231	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4232	chmod g+rx $tmp_data_catalog
4233	if [[ $files_for_pes = false ]]
4234	then
4235	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4236	else
4237	mkdir $tmp_data_catalog/${frelout[$i]}
4238	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4239	fi
4240
4241	# GENERATE AND SUBMIT BATCH-JOB
4242	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4243	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4244	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4245	if [[ $files_for_pes = false ]]
4246	then
4247	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4248	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4249	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4250	else
4251	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4252	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4253	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4254	fi
4255
4256	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4257	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4258	file_saved=true
4259
4260	else
4261	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4262	archive_save=false
4263	fi
4264
4265	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4266	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4267	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4268	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4269	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4270	if [[ $file_saved = true ]]
4271	then
4272	if [[ $files_for_pes = false ]]
4273	then
4274	cat /dev/null > ${pathout[$i]}
4275	else
4276	mkdir -p ${pathout[$i]}
4277	fi
4278	fi
4279
4280	fi
4281
4282	# APPEND ON THIS MACHINE
4283	if [[ "${actionout[$i]}" = "a" ]]
4284	then
4285	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4286	then
4287	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4288	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4289	else
4290	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4291	cat ${localout[$i]} >> ${pathout[$i]}
4292	fi
4293	fi
4294
4295	# COPY ON THIS MACHINE
4296	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4297	# ON DIFFERENT FILE-SYSTEMS
4298	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4299	then
4300
4301	# COPY IN CASE OF RUNS ON SINGLE CORES
4302	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4303	then
4304	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4305	if [[ $link_local_output = true ]]
4306	then
4307	printf " using ln -f\n"
4308	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4309	fi
4310	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4311	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4312	then
4313	if [[ $link_local_output = true ]]
4314	then
4315	printf " ln failed, using cp...\n"
4316	fi
4317	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4318	fi
4319	else
4320	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4321	if [[ $link_local_output = true ]]
4322	then
4323	printf " using ln -f\n"
4324	ln -f ${localout[$i]} ${pathout[$i]}
4325	fi
4326	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4327	if [[ ! -f "${pathout[$i]}" ]]
4328	then
4329	if [[ $link_local_output = true ]]
4330	then
4331	printf " ln failed, using cp...\n"
4332	fi
4333	cp ${localout[$i]} ${pathout[$i]}
4334	fi
4335	fi
4336
4337	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4338	then
4339
4340	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4341	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4342	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4343	if [[ $link_local_output = true ]]
4344	then
4345	printf " using ln -f\n"
4346	mkdir ${pathout[$i]}
4347	cd ${localout[$i]}
4348	for file in $(ls *)
4349	do
4350	ln -f $file ${pathout[$i]}
4351	done
4352	cd $TEMPDIR
4353	fi
4354
4355	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4356	if [[ ! -f "${pathout[$i]}/_0000" ]]
4357	then
4358	if [[ $link_local_output = true ]]
4359	then
4360	printf " ln failed for .../_0000, using cp...\n"
4361	fi
4362	cp -r ${localout[$i]} ${pathout[$i]}
4363	fi
4364
4365	fi
4366	fi
4367	done
4368	if (( i != 0 ))
4369	then
4370	if [[ $transfer_problems = true ]]
4371	then
4372	printf "\n$dashes\n *** OUTPUT-files saved"
4373	printf "\n +++ WARNING: some data transfers failed! \n"
4374	else
4375	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4376	fi
4377	fi
4378
4379
4380	# IF REQUIRED, START A RESTART-JOB
4381	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4382	if [[ -f CONTINUE_RUN ]]
4383	then
4384
4385	if [[ $archive_save = true ]]
4386	then
4387
4388	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4389	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4390	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4391	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4392	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4393	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4394	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4395	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4396	then
4397	mc=`echo $mc \| sed 's/#/f/g'`
4398	fi
4399
4400
4401	# START THE RESTART-JOB
4402	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4403	echo " $mc"
4404	printf "\n$dashes\n"
4405	if [[ $localhost != $fromhost ]]
4406	then
4407
4408	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4409	then
4410	echo "*** ssh will be used to initiate restart-runs!"
4411	echo " return_address=\"$return_address\" "
4412	echo " return_username=\"$return_username\" "
4413	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4414	then
4415	if [[ $localhost = ibmh ]]
4416	then
4417	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4418	elif [[ $localhost = lccrayb ]]
4419	then
4420	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4421	elif [[ $localhost = lccrayh ]]
4422	then
4423	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4424	elif [[ $localhost = lcxe6 ]]
4425	then
4426	ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4427	else
4428	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4429	fi
4430	else
4431	if [[ $localhost = ibmkisti ]]
4432	then
4433	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4434	elif [[ $localhost = lcflow ]]
4435	then
4436	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4437	elif [[ $localhost = lccrayb ]]
4438	then
4439	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4440	elif [[ $localhost = lccrayh ]]
4441	then
4442	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4443	else
4444	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4445	fi
4446	fi
4447	else
4448	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4449	locat=restart; exit
4450	fi
4451
4452	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4453	if [[ $queue = special1q ]]
4454	then
4455	sleep 120
4456	else
4457	sleep 30
4458	fi
4459
4460	else
4461
4462	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4463	# USING SSH)
4464	cd $LOCAL_PWD
4465	if [[ $localhost = lckyuh ]]
4466	then
4467	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4468	printf "\n please restart job manually using command:\n"
4469	printf "\n \"$mc\" "
4470	else
4471	eval $mc # THE ' MUST BE EVALUATED
4472	fi
4473	cd - > /dev/null
4474	fi
4475	if [[ $localhost = lckyuh ]]
4476	then
4477	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4478	else
4479	printf "\n$dashes\n *** restart-run initiated \n"
4480	fi
4481
4482
4483	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4484	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4485	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4486	# MAY BE VERY HUGE)
4487	(( i = 0 ))
4488	while (( i < iin ))
4489	do
4490	(( i = i + 1 ))
4491	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4492	then
4493	rm -r $tmp_data_catalog/${frelin[$i]}
4494	fi
4495	done
4496
4497	else
4498
4499	printf "\n +++ no restart-run possible, since errors occured"
4500	printf "\n during the archive process"
4501	fi
4502
4503	fi
4504
4505
4506
4507	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4508	if [[ "$email_notification" != "none" ]]
4509	then
4510
4511	if [[ $localhost != $fromhost ]]
4512	then
4513	if [[ -f CONTINUE_RUN ]]
4514	then
4515	echo "PALM restart run necessary" > email_text
4516	echo "description header of actual run:" >> email_text
4517	cat CONTINUE_RUN >> email_text
4518	echo "mrun-command to restart:" >> email_text
4519	echo "$mc" >> email_text
4520	else
4521	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4522	fi
4523	mail $email_notification < email_text
4524	printf "\n *** email notification sent to \"$email_notification\" "
4525	fi
4526	fi
4527
4528
4529
4530	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4531	cd $HOME
4532	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4533
4534	else
4535
4536
4537	# PREPARING ACTIONS,
4538	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4539
4540	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4541	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
4542	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4543	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4544	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4545	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4546	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4547	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4548	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4549	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4550	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4551	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4552	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4553	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4554	if [[ $use_openmp = true ]]
4555	then
4556	mrun_com=${mrun_com}" -O $threads_per_task"
4557	fi
4558	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4559	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4560	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4561	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4562	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4563	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4564	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4565	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4566	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4567	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4568	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4569	if [[ $do_remote = true ]]
4570	then
4571	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4572	fi
4573
4574
4575	# CREATE EXECUTABLE FOR BATCH JOB
4576	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4577	then
4578
4579	printf "\n *** creating the executable for batch job\n"
4580
4581	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4582	if [[ $host != $localhost ]]
4583	then
4584	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4585	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4586	locat=create_executable; exit
4587	fi
4588
4589	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4590	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4591
4592	cp $make_depository .
4593	tar -xf $make_depository > /dev/null 2>&1
4594	cp ../* . > /dev/null 2>&1
4595
4596	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4597
4598	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4599	then
4600	printf "\n +++ error occured while compiling or linking"
4601	locat=compile
4602	exit
4603	fi
4604
4605	mv a.out ..
4606	cd - > /dev/null 2>&1
4607	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4608
4609	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4610
4611	fi
4612
4613
4614	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4615	jobfile=jobfile.$RANDOM
4616
4617
4618	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4619	echo "mkdir $TEMPDIR" >> $jobfile
4620	echo "cd $TEMPDIR" >> $jobfile
4621
4622
4623	# ACTIVATE ERROR-TRACEBACK
4624	if [[ $do_trace = true ]]
4625	then
4626	echo "set -x" >> $jobfile
4627	else
4628	echo "set +vx" >> $jobfile
4629	fi
4630
4631
4632	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4633	if [[ "$init_cmds" != "" ]]
4634	then
4635	echo "$init_cmds" >> $jobfile
4636	fi
4637	if [[ "$module_calls" != "" ]]
4638	then
4639	echo "$module_calls" >> $jobfile
4640	fi
4641
4642
4643	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4644	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4645	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4646	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4647	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4648	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4649	# QUEUEING-SYSTEMS
4650	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4651	then
4652
4653	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4654	if [[ $restart_run != true ]]
4655	then
4656	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4657	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4658	fi
4659
4660	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4661	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4662	echo "set -x" >> $jobfile
4663	if [[ $host = $localhost ]]
4664	then
4665
4666	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4667	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4668	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4669	then
4670	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4671	else
4672	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4673	fi
4674
4675	else
4676	if [[ $host = ibmkisti ]]
4677	then
4678	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4679	echo "localdir=\`pwd\`" >> $jobfile
4680	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4681	elif [[ $host = lccrayb ]]
4682	then
4683	echo "localdir=\`pwd\`" >> $jobfile
4684	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4685	elif [[ $host = lccrayh ]]
4686	then
4687	echo "localdir=\`pwd\`" >> $jobfile
4688	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4689
4690	else
4691	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4692	fi
4693	fi
4694	echo "export SOURCES_COMPLETE=true" >> $jobfile
4695
4696	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4697	# WORKING DIRECTORY OF THE JOB
4698	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4699	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4700	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4701	echo "execute_mrun=true" >> $jobfile
4702	echo " " >> $jobfile
4703
4704	else
4705
4706	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4707	if [[ $do_compile = true ]]
4708	then
4709
4710	source_catalog=SOURCES_FOR_RUN_$fname
4711
4712	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4713	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4714	echo "export SOURCES_COMPLETE=true" >> $jobfile
4715	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4716
4717	for filename in $source_list
4718	do
4719	# BACKSLASH IS USED FOR MASKING
4720	echo "cat > $filename << \"%END%\"" >> $jobfile
4721	cat $source_catalog/$filename >> $jobfile
4722	echo " " >> $jobfile
4723	echo "%END%" >> $jobfile
4724	echo " " >> $jobfile
4725	done
4726
4727	# BACKSLASH IS USED FOR MASKING
4728	echo "cat > Makefile << \"%END%\"" >> $jobfile
4729	cat $source_catalog/Makefile >> $jobfile
4730	echo " " >> $jobfile
4731	echo "%END%" >> $jobfile
4732	echo " " >> $jobfile
4733
4734	echo "cd - > /dev/null" >> $jobfile
4735
4736	fi
4737
4738
4739	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4740	# BACKSLASH IS USED FOR MASKING
4741	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4742	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4743	echo "cat > $config_file << \"%END%\"" >> $jobfile
4744	if [[ $host = lckyuh ]]
4745	then
4746	# NO CROSS-COMPILER ON COMPUTE NODE
4747	sed 's/frtpx/frt/g' $config_file >> $jobfile
4748	else
4749	sed 's/#$.*//g' $config_file >> $jobfile
4750	fi
4751	echo "%END%" >> $jobfile
4752	echo " " >> $jobfile
4753
4754
4755	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4756	# BACKSLASH IS USED FOR MASKING
4757	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4758	if [[ $host = lckyuh ]]
4759	then
4760	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4761	else
4762	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4763	fi
4764	echo "%END%" >> $jobfile
4765	echo "chmod u+x $mrun_script_name" >> $jobfile
4766	echo "execute_mrun=true" >> $jobfile
4767	echo " " >> $jobfile
4768
4769	fi
4770
4771
4772	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4773	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4774	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4775	if [[ $do_remote = true ]]
4776	then
4777	(( i = 0 ))
4778	while (( i < iin ))
4779	do
4780	(( i = i + 1 ))
4781	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4782	if [[ "${transin[$i]}" = job ]]
4783	then
4784	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4785	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4786	echo " " >> $jobfile
4787	echo "%END%" >> $jobfile
4788	else
4789	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4790	fi
4791
4792	# CHECK, IF FILE COULD BE CREATED
4793	echo "if [[ \$? = 1 ]]" >> $jobfile
4794	echo "then" >> $jobfile
4795	echo " echo \" \" " >> $jobfile
4796	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4797	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4798	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4799	echo " execute_mrun=false" >> $jobfile
4800	echo "fi" >> $jobfile
4801	done
4802	fi
4803
4804	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4805	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4806	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4807	echo "LOCAL_PWD=$working_directory" >> $jobfile
4808	echo "export LOCAL_PWD" >> $jobfile
4809
4810	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4811	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4812	echo "export LOCAL_MRUN_PATH" >> $jobfile
4813
4814	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4815	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4816	# then
4817	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4818	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4819	# fi
4820
4821	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4822	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4823	echo "set -x" >> $jobfile
4824	echo "queue=$queue" >> $jobfile
4825	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4826	echo 'ls -al; echo `pwd`' >> $jobfile
4827	echo "cd \$HOME" >> $jobfile
4828	echo "rm -rf $TEMPDIR" >> $jobfile
4829
4830
4831
4832
4833	# START THE JOB USING SUBJOB-COMMAND
4834	if [[ $silent = false ]]
4835	then
4836	printf "\n "
4837	else
4838	printf "\n\n"
4839	fi
4840
4841	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
4842	rm -rf $jobfile
4843
4844
4845	fi # END OF REMOTE-PART

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |