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source: palm/trunk/SCRIPTS/mrun @ 1605

Last change on this file since 1605 was 1605, checked in by suehring, 9 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1605 2015-06-23 15:49:12Z suehring $
29	#
30	# 1604 2015-06-23 15:48:03Z suehring
31	# Enable coupled runs for lcmuk
32	#
33	# 1598 2015-05-29 06:45:40Z raasch
34	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
35	#
36	# 1549 2015-01-30 14:26:16Z suehring
37	# Enable interactive debug sessions with allinea debugger
38	#
39	# 1547 2015-01-29 15:09:12Z witha
40	# adjustments for ForWind computing cluster (lcflow)
41	#
42	# 1491 2014-11-12 08:12:57Z heinze
43	# correct setting of batch_job allowed for ibm-machines
44	#
45	# 1468 2014-09-24 14:06:57Z maronga
46	# Typo removed (addres->address)
47	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
48	# Added support for restart runs (remote) for lcxe6
49	#
50	# 1442 2014-07-28 07:09:10Z raasch
51	# default queues for HLRN-III (lccrayb/lccrayh) defined
52	#
53	# 1422 2014-07-02 10:01:25Z kanani
54	# automatic restarts enabled for lccrayb,
55	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
56	#
57	# 1420 2014-06-10 06:24:14Z raasch
58	# -j1 option added to aprung command for lccrayf (CSC)
59	#
60	# 1402 2014-05-09 14:25:13Z raasch
61	# batch_job added to envpar-NAMELIST
62	#
63	# 1357 2014-04-11 15:02:03Z witha
64	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
65	# possible)
66	#
67	# 1320 2014-03-20 08:40:49Z raasch
68	# check namelist file set false by default
69	#
70	# 1304 2014-03-12 10:29:42Z raasch
71	# ulimit option changed from -Ss to -s
72	#
73	# bugfix: missing "fi" in r1289
74	#
75	# 1289 2014-03-04 07:12:34Z raasch
76	# comments translated to English
77	# necriam-, fimm-, ibmy-, and sgi-specific code removed
78	# export of variables for palm and interpret_config removed
79	#
80	# 1281 2014-02-01 07:55:49Z raasch
81	# rsync-copy restricted to Cray machines, since command is unavailable on some
82	# other systems
83	#
84	# 1279 2014-01-28 12:10:14Z raasch
85	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
86	# in order to remove annoying restrictions concerning the number of processors which
87	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
88	# restriction, one of the nodes will be filled with less than the given number of
89	# tasks per node. A respective warning is given.
90	#
91	# 1274 2014-01-09 13:14:54Z heinze
92	# adjustments for lccrayh
93	#
94	# 1272 2014-01-08 10:19:32Z witha
95	# small adjustment for lcflow
96	#
97	# 1270 2013-12-16 11:05:01Z fricke
98	# call of combine_plot_fields adjusted for lccrayb/lccrayh
99	#
100	# 1255 2013-11-07 14:43:35Z raasch
101	# further adjustments for lccrayb remote access
102	#
103	# 1241 2013-10-30 11:36:58Z heinze
104	# Enable use of nudging input and input of large scale forcing from
105	# external files
106	#
107	# 1229 2013-09-20 06:55:19Z raasch
108	# further adjustments for lccrayb
109	#
110	# 1224 2013-09-16 07:27:23Z raasch
111	# first adjustments for lccrayb
112	#
113	# 1210 2013-08-14 10:58:20Z raasch
114	# fftw support added
115	#
116	# 1201 2013-07-10 16:17:59Z witha
117	# adjustments for Forwind cluster (lcflow)
118	#
119	# 1199 2013-07-05 14:52:22Z raasch
120	# adjustments for CSC Helsinki (lccrayf),
121	# executables for batch jobs can be created in advance, in order to avoid calling
122	# the compiler within the batch job (only works if batch jobs are submitted on
123	# local host)
124	#
125	# 1190 2013-06-25 09:39:21Z heinze
126	# enable use of automatic restarts for ibmh
127	# use of cluster/express queue enabled (ibmh)
128	#
129	# 1124 2013-04-09 15:46:52Z raasch
130	# variable "memory" is exported via typeset option -x, because otherwise an unknown
131	# side effect may lead to data loss while getopts is reading the script-option arguments
132	#
133	# 1122 2013-04-09 08:37:16Z heinze
134	# Bugfix: change type of variable last_char
135	#
136	# 1119 2013-04-05 15:11:19Z raasch
137	# Bugfix for setting -T option for subjob
138	#
139	# 1108 2013-03-05 07:03:32Z raasch
140	# bugfix for coupled runs on lckyut/lckyuh
141	#
142	# 1106 2013-03-04 05:31:38Z raasch
143	# --stdin argument for mpiexec on lckyuh
144	# -y and -Y settings output to header
145	#
146	# 1103 2013-02-20 02:15:53Z raasch
147	# default script runs again under ksh, because of unsolved problems with read
148	# from stdin: when bash script is called from a ksh, message "read error: 0:
149	# Resource temporarily unavailable" appears and script does not stop,
150	# further bash compatibility adjustments,
151	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
152	# on lckyuh, but mrun does not terminate and issues a warning instead
153	#
154	# 1101 2013-02-17 10:20:21Z raasch
155	# script now running under bash instead of ksh, which required small adjustments
156	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
157	# read from stdin),
158	# cross compilername on lckyuh compute nodes replaced by real compiler name
159	#
160	# 1099 2013-02-10 01:47:43Z raasch
161	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
162	# and for Forwind cluster (lcflow)
163	# small further adjustments for lckyut
164	#
165	# 1094 2013-02-03 01:52:12Z raasch
166	# explicit ssh/scp port can be set in config file with environment variable
167	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
168	# decalpha parts (yonsei) removed
169	#
170	# 2013-02-02 07:06:13Z raasch
171	# adjustments for Kyushu-University computing center (lckyut - tatara)
172	#
173	# 1083 2013-01-04 10:22:09Z maronga
174	# bugfix in parameter file check (read %cpp_options was missing)
175	#
176	# 1069 2012-11-28 16:18:43Z maronga
177	# bugfix: coupling mode was always set to mpi2, typos removed
178	#
179	# 1058 2012-11-21 07:00:35Z raasch
180	# Intel inspector (inspxe) is given the number of PEs instead of the number of
181	# nodes
182	#
183	# 1046 2012-11-09 14:38:45Z maronga
184	# code put under GPL (PALM 3.9)
185	#
186	# 21/03/94 - Siggi - first version finished
187	# 03/03/94 - Siggi - script development started
188	#
189	#--------------------------------------------------------------------------------#
190	# mrun - script for running PALM jobs
191	#--------------------------------------------------------------------------------#
192
193
194
195	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
196
197	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
198	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
199	# (TOO MANY ARGUMENTS - PROBLEM)
200	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
201
202	AddFilenames=""
203	additional_conditions=""
204	add_source_path=""
205	afname=""
206	archive_save=true
207	archive_system=none
208	check_namelist_files=false
209	combine_plot_fields=true
210	compiler_name=""
211	cond1=""
212	cond2=""
213	config_file=.mrun.config
214	coupled_dist=""
215	coupled_mode="mpi1"
216	cpp_opts=""
217	cpp_options=""
218	cpumax=0
219	cpurest=0
220	create_executable_for_batch=false
221	delete_temporary_catalog=true
222	do_batch=false
223	do_compile=true
224	do_remote=false
225	do_stagein=true
226	do_stageout=true
227	do_trace=false
228	email_notification="none"
229	exclude=""
230	executable=""
231	execution_error=false
232	fftw_inc=""
233	fftw_lib=""
234	fftw_support=false
235	fname=test
236	fromhost=""
237	global_revision=""
238	group_number=none
239	host=""
240	host_file=""
241	hp=""
242	ignore_archive_error=false
243	input_list=""
244	interpreted_config_file=""
245	job_catalog="~/job_queue"
246	job_on_file=""
247	keep_data_from_previous_run=false
248	link_local_input=false
249	link_local_output=false
250	localhost_realname=$(hostname)
251	local_dvrserver_running=.FALSE.
252	locat=normal
253	mainprog=""
254	makefile=""
255	max_par_io_str=""
256	mc=$0
257	while [[ $(echo $mc \| grep -c "/") != 0 ]]
258	do
259	mc=`echo $mc \| cut -f2- -d"/"`
260	done
261	module_calls=""
262	mrun_script_name=$mc
263	netcdf_inc=""
264	netcdf_lib=""
265	netcdf_support=false
266	node_usage=default
267	numprocs=""
268	numprocs_atmos=0
269	numprocs_ocean=0
270	OOPT=""
271	openmp=false
272	output_list=""
273	package_list=""
274	queue=none
275	read_from_config=""
276	restart_run=false
277	if [[ `hostname` = rte10 ]]
278	then
279	return_address=133.5.185.60
280	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
281	elif [[ `hostname` = climate0 ]]
282	then
283	return_address=165.132.26.68
284	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
285	elif [[ `hostname` = urban00 ]]
286	then
287	return_address=147.46.30.151
288	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
289	else
290	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
291	fi
292	return_password=""
293	return_username=$LOGNAME
294	remotecall=false
295	remote_username=""
296	run_coupled_model=false
297	run_mode=""
298	store_on_archive_system=false
299	dashes=" ----------------------------------------------------------------------------"
300	silent=false
301	source_list=""
302	source_path=SOURCE
303	tasks_per_node=""
304	threads_per_task=1
305	tmpcreate=false
306	tmp_data_catalog=""
307	transfer_problems=false
308	usern=$LOGNAME
309	use_openmp=false
310	version="MRUN 2.1 Rev$Rev: 1605 $"
311	working_directory=`pwd`
312	TOPT=""
313	XOPT=""
314	zeit=$( date \| cut -c 12-19 )
315
316	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
317	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
318	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
319	# SCRIPT-OPTION ARGUMENTS
320	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
321
322
323
324	# ERROR HANDLING IN CASE OF EXIT
325	trap 'rm -rf $working_directory/tmp_mrun
326	if [[ $locat != normal && $locat != control_c ]]
327	then
328
329	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
330	(( i = 0 ))
331	while (( i < iec ))
332	do
333	(( i = i + 1 ))
334	printf "\n *** Execution of ERROR-command:\n"
335	printf " >>> ${err_command[$i]}\n"
336	eval ${err_command[$i]}
337	done
338	if [[ -n $interpreted_config_file ]]
339	then
340	rm -rf $interpreted_config_file
341	fi
342	if [[ -n .mrun_environment ]]
343	then
344	rm -rf .mrun_environment
345	fi
346	if [[ $tmpcreate = true ]]
347	then
348	printf "\n *** Contents of \"$TEMPDIR\":\n"
349	ls -al; cd
350	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
351	fi
352	if [[ "$dvrserver_id" != "" ]]
353	then
354	echo "+++ killing dvrserver_id=$dvrserver_id"
355	kill $dvrserver_id
356	fi
357	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
358	then
359	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
360	fi
361	printf "\n\n+++ MRUN killed \n\n"
362	elif [[ $locat != control_c ]]
363	then
364	printf "\n\n --> all actions finished\n\n"
365	printf " Bye, bye $usern !!\n\n"
366	fi' exit
367
368
369	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
370	trap 'rm -rf $working_directory/tmp_mrun
371	rm -rf $working_directory/tmp_check_namelist_files
372	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
373	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
374	then
375	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
376	fi
377	if [[ "$dvrserver_id" != "" ]]
378	then
379	echo "+++ killing dvrserver_id=$dvrserver_id"
380	kill $dvrserver_id
381	fi
382	printf "\n+++ MRUN killed by \"^C\" \n\n"
383	locat=control_c
384	exit
385	' 2
386
387
388	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
389	# BEEN SET
390	if [[ "$PALM_BIN" = "" ]]
391	then
392	printf "\n +++ environment variable PALM_BIN has not been set"
393	printf "\n please set it to the directory where the PALM scripts are located"
394	locat=palm_bin; exit
395	fi
396	export PATH=$PALM_BIN:$PATH
397
398
399
400	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
401	# WHICH WILL BE USED TO START RESTART-JOBS
402	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
403	do
404	case $option in
405	(a) afname=$OPTARG;;
406	(A) store_on_archive_system=true; mc="$mc -A";;
407	(b) do_batch=true; mc="$mc -b";;
408	(B) delete_temporary_catalog=false; mc="$mc -B";;
409	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
410	(C) restart_run=true; mc="$mc -C";;
411	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
412	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
413	(F) job_on_file="-D"; mc="$mc -F";;
414	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
415	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
416	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
417	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
418	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
419	(I) ignore_archive_error=true; mc="$mc -I";;
420	(k) keep_data_from_previous_run=true; mc="$mc -k";;
421	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
422	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
423	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
424	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
425	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
426	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
427	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
428	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
429	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
430	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
431	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
432	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
433	(S) read_from_config=false; mc="$mc -S";;
434	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
435	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
436	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
437	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
438	(v) silent=true; mc="$mc -v";;
439	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
440	(x) do_trace=true;set -x; mc="$mc -x";;
441	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
442	(y) ocean_file_appendix=true; mc="$mc -y";;
443	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
444	(z) check_namelist_files=false; mc="$mc -z";;
445	(Z) combine_plot_fields=false; mc="$mc -Z";;
446	(\?) printf "\n +++ unknown option $OPTARG \n"
447	printf "\n --> type \"$0 ?\" for available options \n"
448	locat=parameter;exit;;
449	esac
450	done
451
452
453	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
454	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
455	(( to_shift = $OPTIND - 1 ))
456	shift $to_shift
457
458	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
459	if [[ "$1" = "?" ]]
460	then
461	(printf "\n *** mrun can be called as follows:\n"
462	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"
463	printf "\n Description of available options:\n"
464	printf "\n Option Description Default-Value"
465	printf "\n -a base name of input files equiv. -d"
466	printf "\n -A archiving when using file-attribute fl"
467	printf "\n -b batch-job on local machine ---"
468	printf "\n -B do not delete temporary directory at end ---"
469	printf "\n -c configuration file .mrun.config"
470	printf "\n -d base name of files attached to program test"
471	printf "\n -D preprocessor(cpp)-directives \"\" "
472	printf "\n -F create remote job file only ---"
473	printf "\n -h execution host $localhost_realname"
474	printf "\n -i INPUT control list \"\" "
475	printf "\n -I archiving errors of previous batch-jobs"
476	printf "\n will be ignored"
477	printf "\n -k keep data from previous run"
478	printf "\n -K additional conditions for controling"
479	printf "\n usage of conditional code and"
480	printf "\n env-variables in configuration file \"\" "
481	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
482	printf "\n -M Makefile name Makefile"
483	printf "\n -n node usage (shared/not_shared) depending on -h"
484	printf "\n -o OUTPUT control list \"\" "
485	printf "\n -O threads per openMP task ---"
486	printf "\n -p software package list \"\" "
487	printf "\n -q queue \"$queue\" "
488	printf "\n -r run control list (combines -i -o) \"\" "
489	printf "\n -s filenames of routines to be compiled \"\" "
490	printf "\n must end with .f, .f90, .F, or .c !"
491	printf "\n use \"..\" for more than one file and wildcards"
492	printf "\n -s LM compiles all locally modified files"
493	printf "\n -S config file interpreted by shellscript ---"
494	printf "\n -t allowed cpu-time in seconds (batch) 0"
495	printf "\n -T tasks per node depending on -h"
496	printf "\n -u username on remote machine \"\" "
497	printf "\n -v no prompt for confirmation ---"
498	printf "\n -w maximum parallel io streams as given by -X"
499	printf "\n -x tracing of mrun for debug purposes ---"
500	printf "\n -X # of processors (on parallel machines) 1"
501	printf "\n -y add appendix \"_O\" to all local output"
502	printf "\n files (ocean precursor runs followed by"
503	printf "\n coupled atmosphere-ocean runs) ---"
504	printf "\n -Y run coupled model, \"#1 #2\" with"
505	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
506	printf "\n -z disable a priori parameter file check ---"
507	printf "\n -Z skip combine_plot_fields at the end of "
508	printf "\n the simulation ---"
509	printf "\n "
510	printf "\n Possible values of positional parameter <modus>:"
511	printf "\n \"?\" - this outline \n\n") \| more
512	exit
513	elif [[ "$1" != "" ]]
514	then
515	printf "\n +++ positional parameter $1 unknown \n"
516	locat=parameter; exit
517	fi
518
519
520
521	# SHORT STARTING MESSAGE
522	printf "\n*** $version "
523	printf "\n will be executed. Please wait ..."
524
525
526
527	# CHECK, IF CONFIGURATION FILE EXISTS
528	if [[ ! -f $config_file ]]
529	then
530	printf "\n\n +++ configuration file: "
531	printf "\n $config_file"
532	printf "\n does not exist"
533	locat=connect; exit
534	fi
535
536
537	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
538	line=""
539	grep "%host_identifier" $config_file > tmp_mrun
540	while read line
541	do
542	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
543	then
544	HOSTNAME=`echo $line \| cut -d" " -s -f2`
545	host_identifier=`echo $line \| cut -d" " -s -f3`
546	if [[ $localhost_realname = $HOSTNAME ]]
547	then
548	localhost=$host_identifier
549	break
550	fi
551	fi
552	done < tmp_mrun
553
554	if [[ "$localhost" = "" ]]
555	then
556	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
557	printf "\n for local host \"$localhost_realname\"."
558	printf "\n Please add line"
559	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
560	printf "\n to the configuration file."
561	locat=localhost; exit
562	fi
563
564
565	# SET HOST-SPECIFIC VARIABLES
566	case $localhost_realname in
567	(r1\|r2\|h01\|b01) archive_system=tivoli;;
568	(cs*) archive_system=ut;;
569	esac
570
571
572	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
573	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
574	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
575	[[ "$afname" = "" ]] && afname=$fname
576
577
578	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
579	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
580	# STATEMENTS IN THE CONFIGURATION FILE
581	if [[ "$run_mode" != "" ]]
582	then
583	input_list="$input_list $run_mode"
584	output_list="$output_list $run_mode"
585	fi
586
587
588	# ??? is this (and the respective option -H) really required ???
589	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
590	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
591	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
592	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
593	if [[ "$fromhost" = "" ]]
594	then
595	fromhost=$localhost
596	fi
597
598
599	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
600	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
601	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
602	# TO BE SUBMITTED (I.E. do_bacth=true)
603	if [[ -n $host && "$host" != $localhost ]]
604	then
605	do_batch=true
606	do_remote=true
607	case $host in
608	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
609	(*) printf "\n"
610	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
611	printf "\n is not available"
612	locat=nqs; (( iec = 0 )); exit;;
613	esac
614	else
615	host=$localhost
616	fi
617
618
619	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
620	if [[ -n $additional_conditions ]]
621	then
622	cond1=`echo $additional_conditions \| cut -d" " -f1`
623	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
624	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
625	if [[ -n $dummy ]]
626	then
627	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
628	locat=options; exit
629	fi
630	block=_$cond1
631	[[ -n $cond2 ]] && block=${block}_$cond2
632	fi
633
634
635	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
636	if [[ $run_coupled_model = true ]]
637	then
638
639	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
640	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
641
642	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
643	then
644
645	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
646	printf "\n PEs (total) : $numprocs"
647	printf "\n PEs (atmosphere): $numprocs_atmos"
648	printf "\n PEs (ocean) : $numprocs_ocean"
649	locat=coupling; exit
650
651	fi
652
653
654	# GET coupled_mode FROM THE CONFIG FILE
655	line=""
656	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
657	while read line
658	do
659	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
660	then
661	coupled_mode="mpi2"
662	fi
663	done < tmp_mrun
664
665	fi
666
667
668	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
669	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
670	then
671	if [[ $ignore_archive_error = false ]]
672	then
673	printf "\n +++ data archiving of previous run failed"
674	printf "\n see directory \~/job_queue on remote machine"
675	locat=archive; exit
676	else
677	printf "\n +++ warning: data archiving in a previous run failed"
678	printf "\n MRUN continues, trying to get backup copy"
679	fi
680	fi
681
682
683	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
684	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
685	mrun_memory=$memory
686	mrun_group_number=$group_number
687	mrun_cpumax=$cpumax
688	mrun_numprocs=$numprocs
689
690
691	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
692	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
693	if [[ "$read_from_config" = false ]]
694	then
695
696	[[ $silent = false ]] && printf "\n Reading the configuration file... "
697
698	# READ THE CONFIGURATION FILE LINE BY LINE
699	while read zeile
700	do
701	[[ $silent = false ]] && printf "."
702
703
704	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
705	eval zeile=\"$zeile\"
706
707
708	# INTERPRET THE LINE
709	if [[ "$(echo $zeile)" = "" ]]
710	then
711	# EMPTY LINE, NO ACTION
712	continue
713
714	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
715	then
716
717	# LINE IS A COMMENT LINE
718	true
719
720	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
721	then
722
723	# LINE DEFINES AN ENVIRONMENT-VARIABLE
724	zeile=$(echo $zeile \| cut -c2-)
725	var=`echo $zeile \| cut -d" " -f1`
726	value=`echo $zeile \| cut -d" " -s -f2`
727	for_host=`echo $zeile \| cut -d" " -s -f3`
728	for_cond1=`echo $zeile \| cut -d" " -s -f4`
729	for_cond2=`echo $zeile \| cut -d" " -s -f5`
730
731	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
732	then
733
734	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
735	# "::" IS REPLACED BY ":".
736	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
737
738
739	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
740	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
741	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
742	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
743	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
744	# CONFIGURATION-FILE.
745	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
746	then
747	eval $var=\$value
748
749	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
750	if [[ $do_trace = true ]]
751	then
752	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
753	fi
754	fi
755
756	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
757	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
758	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
759	# MUST HAVE TO BE STARTED
760	if [[ $var = host ]]
761	then
762	if [[ -n $host && "$host" != $localhost ]]
763	then
764	do_batch=true
765	do_remote=true
766	case $host in
767	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
768	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
769	printf "\n is not available"
770	locat=nqs; exit;;
771	esac
772	else
773	host=$localhost
774	fi
775	fi
776
777	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
778	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
779	# BY MRUN (E.G. subjob)
780	export $var
781	fi
782
783
784
785
786	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
787	then
788
789	# LINE DEFINES ERROR-COMMAND
790	(( iec = iec + 1 ))
791	zeile=$(echo $zeile \| cut -c4-)
792	err_command[$iec]="$zeile"
793
794	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
795	then
796
797	# LINE DEFINES INPUT-COMMAND
798	(( iic = iic + 1 ))
799	zeile=$(echo $zeile \| cut -c4-)
800	in_command[$iic]="$zeile"
801
802	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
803	then
804
805	# LINE DEFINES OUTPUT-COMMAND
806	(( ioc = ioc + 1 ))
807	zeile=$(echo $zeile \| cut -c4-)
808	out_command[$ioc]="$zeile"
809
810	else
811
812	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
813	# s2a: in/out - field
814	# s2b: loc - field (optional)
815	# s2c: tr/ar - field (optional)
816	s1=`echo $zeile \| cut -d" " -f1`
817	s2=`echo $zeile \| cut -d" " -s -f2`
818	s2a=$(echo $s2 \| cut -d":" -f1)
819	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
820	then
821	s2b=""
822	s2c=""
823	else
824	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
825	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
826	fi
827	s3=`echo $zeile \| cut -d" " -f3`
828	s4=`echo $zeile \| cut -d" " -s -f4`
829	s5=`echo $zeile \| cut -d" " -s -f5`
830	s6=`echo $zeile \| cut -d" " -s -f6`
831
832
833	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
834	# INPUT- OR OUTPUT-LIST.
835	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
836	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
837	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
838	# IS NOT CHECKED AND STORED.
839	IFSALT="$IFS"; IFS="$IFS:"
840	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
841	then
842	found=false
843	for actual in $input_list
844	do
845	for formal in $s3
846	do
847	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
848	done
849	done
850	if [[ $found = true ]]
851	then
852	(( iin = iin + 1 ))
853	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
854	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
855	extin[$iin]=$s6
856	fi
857	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
858	then
859	found=false
860	for actual in $output_list
861	do
862	for formal in $s3
863	do
864	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
865	done
866	done
867	if [[ $found = true ]]
868	then
869	(( iout = iout + 1 ))
870	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
871	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
872	fi
873	elif [[ "$s2a" != in && "$s2a" != out ]]
874	then
875	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
876	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
877	locat=connect; exit
878	fi
879	IFS="$IFSALT"
880	fi
881	done < $config_file
882
883	else
884
885
886	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
887	[[ $silent = false ]] && printf "..."
888	interpreted_config_file=.icf.$RANDOM
889
890
891
892	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
893	cat > .mrun_environment << %%END%%
894	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
895	config_file = '$config_file', do_remote = '$do_remote',
896	do_trace = '$do_trace', host = '$host',
897	input_list = '$input_list', icf = '$interpreted_config_file',
898	localhost = '$localhost', output_list = '$output_list' /
899
900	%%END%%
901
902	if [[ "$host" != $localhost ]]
903	then
904
905	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
906	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
907	if [[ $? != 0 ]]
908	then
909	printf "\n\n +++ no interpret_config found"
910	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
911	locat=interpret_config; exit
912	fi
913	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
914	$interpret_config_executable
915
916	else
917
918	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
919	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
920	then
921	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
922	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
923	locat=interpret_config; exit
924	else
925	interpret_config${block}.x
926	fi
927
928	fi
929	rm .mrun_environment
930
931
932	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
933	chmod u+x $interpreted_config_file
934	export PATH=$PATH:.
935	. $interpreted_config_file
936	rm $interpreted_config_file
937
938	fi
939
940
941	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
942	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
943	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
944	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
945	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
946	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
947	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
948
949
950	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
951	# FOR SOURCE-FILES TO BE COMPILED.
952	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
953	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
954	if [[ "$SOURCES_COMPLETE" = "" ]]
955	then
956
957	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
958	# HAS BEEN DEFINED
959	source_path=""
960	line=""
961	grep "%source_path" $config_file > tmp_mrun
962	while read line
963	do
964	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
965	then
966	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
967	then
968	global_source_path=`echo $line \| cut -d" " -f2`
969	fi
970	fi
971	done < tmp_mrun
972
973	line=""
974	found=false
975	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
976	while read line
977	do
978	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
979	then
980	if [[ $found = true ]]
981	then
982	printf "\n\n +++ more than one source path found in configuration file"
983	printf "\n for local host \"$localhost\" "
984	locat=source_path; exit
985	fi
986	source_path=`echo $line \| cut -d" " -f2`
987	found=true
988	fi
989	done < tmp_mrun
990	rm tmp_mrun
991
992	if [[ "$source_path" = "" ]]
993	then
994	if [[ "$global_source_path" != "" ]]
995	then
996	source_path=$global_source_path
997	else
998	printf "\n\n +++ no source path found in configuration file"
999	printf "\n for local host \"$localhost\" "
1000	locat=source_path; exit
1001	fi
1002	fi
1003	eval source_path=$source_path
1004
1005	if [[ ! -d $source_path ]]
1006	then
1007	printf "\n\n +++ source path \"$source_path\" on local host"
1008	printf "\n \"$localhost\" does not exist"
1009	locat=source_path; exit
1010	fi
1011
1012	fi
1013
1014
1015	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1016	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1017	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1018	then
1019	global_revision=`svnversion $source_path 2>/dev/null`
1020	global_revision="Rev: $global_revision"
1021	fi
1022
1023
1024	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1025	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1026	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1027	if [[ -n $host && "$host" != $localhost ]]
1028	then
1029	do_batch=true
1030	do_remote=true
1031	case $host in
1032	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1033	(*) printf "\n"
1034	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1035	printf "\n is not available"
1036	locat=nqs; (( iec = 0 )); exit;;
1037	esac
1038	else
1039	host=$localhost
1040	fi
1041
1042
1043	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1044	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1045	then
1046
1047	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1048	if [[ ! -n $numprocs ]]
1049	then
1050	printf "\n"
1051	printf "\n +++ option \"-K parallel\" requires additional specification"
1052	printf "\n of the number of processors to be used by"
1053	printf "\n mrun-option \"-X\" or by environment-variable"
1054	printf "\n \"numprocs\" in the configuration file"
1055	locat=numprocs; (( iec = 0 )); exit
1056	fi
1057
1058	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1059	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1060	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1061	then
1062	printf "\n"
1063	printf "\n +++ option \"-T\" (tasks per node) is missing"
1064	printf "\n set -T option or define tasks_per_node in the config file"
1065	locat=tasks_per_node; (( iec = 0 )); exit
1066	fi
1067
1068	if (( numprocs < tasks_per_node ))
1069	then
1070	printf "\n"
1071	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1072	printf "\n given values: -T $tasks_per_node -X $numprocs"
1073	locat=tasks_per_node; (( iec = 0 )); exit
1074	fi
1075
1076	if [[ $host != lcflow && $host != lcxt5m ]]
1077	then
1078	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1079	(( ival = $tasks_per_node ))
1080	(( pes = numprocs ))
1081	(( ii = pes / ival ))
1082	(( remaining_pes = pes - ii * ival ))
1083	if (( remaining_pes > 0 ))
1084	then
1085	printf "\n"
1086	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1087	printf "\n divisor of the total number of processors (option \"-X\")"
1088	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1089	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1090	(( nodes = nodes + 1 ))
1091	fi
1092	fi
1093
1094
1095	# SETTINGS FOR SUBJOB-COMMAND
1096	OOPT="-O $threads_per_task"
1097
1098	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1099	if [[ "$tasks_per_node" != "" ]]
1100	then
1101	TOPT="-T $tasks_per_node"
1102	fi
1103
1104	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1105	if [[ $node_usage = default ]]
1106	then
1107	if [[ $host = ibms ]]
1108	then
1109	node_usage=shared
1110	else
1111	node_usage=not_shared
1112	fi
1113	fi
1114
1115	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1116	then
1117	printf "\n"
1118	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1119	printf "\n \"shared\" or \"not_shared\""
1120	locat=tasks_per_node; (( iec = 0 )); exit
1121	fi
1122
1123	fi
1124
1125	# CHECK IF HOSTFILE EXISTS
1126	if [[ -n $hostfile ]]
1127	then
1128	if [[ ! -f $hostfile ]]
1129	then
1130	printf "\n"
1131	printf "\n +++ hostfile \"$hostfile\" does not exist"
1132	locat=hostfile; exit
1133	fi
1134	fi
1135
1136
1137	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1138	if [[ "$maximum_parallel_io_streams" = "" ]]
1139	then
1140	maximum_parallel_io_streams=$numprocs
1141	fi
1142
1143
1144	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1145	if [[ "$scp_port" != "" ]]
1146	then
1147	PORTOPT="-P $scp_port"
1148	SSH_PORTOPT="-p $scp_port"
1149	fi
1150
1151
1152	# SET DEFAULT-QUEUE, IF NOT GIVEN
1153	if [[ $queue = none ]]
1154	then
1155	case $host in
1156	(ibmh) queue=cluster;;
1157	(ibmkisti) queue=class.32plus;;
1158	(lccrayb) queue=mpp1q;;
1159	(lccrayh) queue=mpp1q;;
1160	(lckiaps) queue=normal;;
1161	(lckyoto) queue=ph;;
1162	(lckyuh) queue=fx-single;;
1163	(lckyut) queue=cx-single;;
1164	(lctit) queue=S;;
1165	(nech) queue=none;;
1166	(unics) queue=unics;;
1167	esac
1168	fi
1169
1170
1171	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1172	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1173	(( i = 0 ))
1174	while (( i < iin ))
1175	do
1176	(( i = i + 1 ))
1177	(( maxcycle = 0 ))
1178
1179	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1180	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1181	if [[ "${actionin[$i]}" = di ]]
1182	then
1183	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1184	# HOST ONLY
1185	eval filename=${pathin[$i]}/${endin[$i]}
1186	else
1187	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1188	# HOST ONLY
1189	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1190	fi
1191	eval pathname=${pathin[$i]}
1192
1193	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1194	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1195	then
1196	filename_input=$filename
1197	fi
1198
1199	# CHECK IF FILE EXISTS
1200	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1201	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1202	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1203	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1204	then
1205
1206	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1207	if [[ "${transin[$i]}" != "locopt" ]]
1208	then
1209	printf "\n\n +++ INPUT-file: "
1210	if [[ "${extin[$i]}" = "" ]]
1211	then
1212	printf "\n $filename"
1213	else
1214	printf "\n $filename.${extin[$i]}"
1215	fi
1216	printf "\n does not exist\n"
1217	locat=input; exit
1218	else
1219	transin[$i]="unavailable"
1220	fi
1221	else
1222
1223	# DETERMINE THE FILE'S CYCLE NUMBER
1224	ls -1 -d $filename > filelist 2>/dev/null
1225	ls -1 -d $filename.* >> filelist 2>/dev/null
1226	while read zeile
1227	do
1228	cycle=$(echo $zeile \| cut -f2 -d".")
1229	if [[ "$cycle" = "$zeile" ]]
1230	then
1231	(( icycle = 0 ))
1232	elif [[ "$cycle" = "${extin[$i]}" ]]
1233	then
1234	(( icycle = 0 ))
1235	else
1236	(( icycle = $cycle ))
1237	fi
1238	if (( icycle > maxcycle ))
1239	then
1240	(( maxcycle = icycle ))
1241	file_to_be_used=$zeile
1242	fi
1243	done <filelist
1244	rm filelist
1245
1246	# APPEND CYCLE NUMBER TO FILENAME
1247	if (( maxcycle > 0 ))
1248	then
1249	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1250	then
1251	filename=${filename}.$maxcycle.${extin[$i]}
1252	else
1253	filename=${filename}.$maxcycle
1254	fi
1255	else
1256	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1257	then
1258	filename=${filename}.${extin[$i]}
1259	fi
1260	fi
1261
1262	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1263	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1264	absnamein[$i]=$filename
1265	if (( maxcycle > 0 ))
1266	then
1267	if [[ "${actionin[$i]}" = di ]]
1268	then
1269	frelin[$i]=${endin[$i]}.$maxcycle
1270	else
1271	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1272	fi
1273	else
1274	if [[ "${actionin[$i]}" = di ]]
1275	then
1276	frelin[$i]=${endin[$i]}
1277	else
1278	frelin[$i]=${afname}${endin[$i]}
1279	fi
1280	fi
1281
1282	fi
1283	done
1284
1285	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1286	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1287	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1288	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1289	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1290	# REMOTE HOST)
1291	(( i = 0 ))
1292	while (( i < iout ))
1293	do
1294	(( i = i + 1 ))
1295	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1296	then
1297	if [[ "${actionout[$i]}" = tr ]]
1298	then
1299	actionout[$i]=""
1300	elif [[ "${actionout[$i]}" = trpe ]]
1301	then
1302	actionout[$i]=pe
1303	elif [[ "${actionout[$i]}" = tra ]]
1304	then
1305	actionout[$i]=a
1306	fi
1307	(( maxcycle = 0 ))
1308	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1309	eval catalogname=${pathout[$i]}
1310	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1311	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1312	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1313	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1314	then
1315
1316	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1317	if cat /dev/null > $filename
1318	then
1319	rm $filename
1320	else
1321
1322	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1323	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1324	if [[ ! -d $catalogname ]]
1325	then
1326	if mkdir -p $catalogname
1327	then
1328	printf "\n\n *** directory:"
1329	printf "\n $catalogname"
1330	printf "\n was created\n"
1331	else
1332	printf "\n\n +++ OUTPUT-file:"
1333	printf "\n $filename"
1334	printf "\n cannot be created, because directory does not exist"
1335	printf "\n and cannot be created either"
1336	printf "\n"
1337	locat=output ; exit
1338	fi 2>/dev/null
1339	else
1340	printf "\n\n +++ OUTPUT-file:"
1341	printf "\n $filename"
1342	printf "\n cannot be created, although directory exists"
1343	printf "\n"
1344	locat=output ; exit
1345	fi
1346	fi 2>/dev/null
1347	else
1348
1349	# DETERMINE THE CYCLE NUMBER
1350	ls -1 -d $filename > filelist 2>/dev/null
1351	ls -1 -d $filename.* >> filelist 2>/dev/null
1352	while read zeile
1353	do
1354	cycle=$(echo $zeile \| cut -f2 -d".")
1355	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1356	then
1357	(( icycle = 1 ))
1358	else
1359	(( icycle = $cycle + 1 ))
1360	fi
1361	if (( icycle > maxcycle ))
1362	then
1363	(( maxcycle = icycle ))
1364	fi
1365	done <filelist
1366	rm filelist
1367	fi
1368
1369	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1370	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1371	if [[ "${actionout[$i]}" != a ]]
1372	then
1373	if (( maxcycle > 0 ))
1374	then
1375	filename=${filename}.$maxcycle
1376	if cat /dev/null > $filename
1377	then
1378	rm $filename
1379	else
1380	printf "\n +++ OUTPUT-file:"
1381	printf "\n $filename"
1382	printf "\n cannot be created"
1383	locat=output ; exit
1384	fi
1385	fi
1386	else
1387	(( maxcycle = maxcycle - 1 ))
1388	if (( maxcycle > 0 ))
1389	then
1390	filename=${filename}.$maxcycle
1391	fi
1392	fi
1393
1394	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1395	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1396	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1397	pathout[$i]=$filename
1398	if (( maxcycle > 0 ))
1399	then
1400	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1401	else
1402	frelout[$i]=${fname}${endout[$i]}
1403	fi
1404
1405	fi
1406	done
1407
1408
1409	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1410	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1411	then
1412	if [[ "$dvr_inc" = "" ]]
1413	then
1414	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1415	printf "\n This is required for the dvrp_graphics package.\n"
1416	locat=dvr; exit
1417	fi
1418	if [[ "$dvr_lib" = "" ]]
1419	then
1420	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1421	printf "\n This is required for the dvrp_graphics package.\n"
1422	locat=dvr; exit
1423	fi
1424	fi
1425
1426
1427	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1428	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1429	if [[ "$mainprog" = "" && "$executable" = "" ]]
1430	then
1431	printf "\n +++ neither main program nor executable defined"
1432	locat=source; exit
1433	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1434	then
1435	printf "\n +++ main program as well as executable defined"
1436	locat=source; exit
1437	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1438	then
1439	do_compile=false
1440	fi
1441
1442
1443	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1444	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1445	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1446	then
1447	rm -rf SOURCES_FOR_RUN_$fname
1448	mkdir SOURCES_FOR_RUN_$fname
1449	fi
1450
1451
1452	# COLLECT ALL ROUTINES TO BE COMPILED
1453	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1454	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1455	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1456	then
1457
1458	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1459
1460	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1461	then
1462
1463	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1464	source_list=""
1465	cd $source_path
1466
1467
1468	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1469	if [[ ! -d .svn ]]
1470	then
1471	printf "\n\n +++ source directory"
1472	printf "\n \"$source_path\" "
1473	printf "\n is not under control of \"subversion\"."
1474	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1475	fi
1476
1477
1478	# LIST ALL MODIFIED SOURCE CODE FILES
1479	Filenames=""
1480	svn status > tmp_mrun
1481	while read line
1482	do
1483	firstc=`echo $line \| cut -c1`
1484	if [[ $firstc = M \|\| $firstc = "?" ]]
1485	then
1486	Name=`echo "$line" \| cut -c8-`
1487	extension=`echo $Name \| cut -d. -f2`
1488	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1489	then
1490	Filenames="$Filenames "$Name
1491	fi
1492	fi
1493	done < tmp_mrun
1494
1495
1496	# COPY FILES TO SOURCES_FOR_RUN_...
1497	for dateiname in $Filenames
1498	do
1499	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1500	source_list=$source_list"$dateiname "
1501	done
1502
1503	cd - > /dev/null
1504
1505
1506	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1507	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1508	elif [[ "$source_list" != "" && $restart_run != true ]]
1509	then
1510
1511	cd $source_path
1512
1513	for filename in $source_list
1514	do
1515
1516	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1517	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1518	then
1519	printf "\n +++ source code file: $filename"
1520	printf "\n must not contain (\"/\") "
1521	locat=source; exit
1522	fi
1523
1524	if [[ ! -f $filename ]]
1525	then
1526	printf "\n +++ source code file: $filename"
1527	printf "\n does not exist"
1528	locat=source; exit
1529	else
1530	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1531	fi
1532
1533	done
1534
1535	cd - > /dev/null
1536
1537	fi
1538
1539
1540	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1541	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1542	if [[ $restart_run != true ]]
1543	then
1544
1545	if [[ ! -f "$source_path/$mainprog" ]]
1546	then
1547	printf "\n\n +++ main program: $mainprog"
1548	printf "\n does not exist in source directory"
1549	printf "\n \"$source_path\"\n"
1550	locat=source; exit
1551	else
1552	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1553	then
1554	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1555	source_list=${mainprog}" $source_list"
1556	fi
1557	fi
1558	fi
1559
1560
1561	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1562	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1563	if [[ "$restart_run" != true ]]
1564	then
1565	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1566	if [[ ! -f $makefile ]]
1567	then
1568	printf "\n +++ file \"$makefile\" does not exist"
1569	locat=make; exit
1570	else
1571	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1572	fi
1573	fi
1574
1575
1576	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1577	if [[ $restart_run != true && "$add_source_path" != "" ]]
1578	then
1579
1580	# DOES THE DIRECTORY EXIST?
1581	if [[ ! -d $add_source_path ]]
1582	then
1583	printf "\n\n +++ WARNING: additional source code directory"
1584	printf "\n \"$add_source_path\" "
1585	printf "\n does not exist or is not a directory."
1586	printf "\n No source code will be used from this directory!\n"
1587	add_source_path=""
1588	if [[ $silent == false ]]
1589	then
1590	sleep 3
1591	fi
1592	else
1593
1594	cd $add_source_path
1595	found=false
1596
1597	Names=$(ls -1 *.f90 2>&1)
1598	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1599	Names=$(ls -1 *.F90 2>&1)
1600	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1601	Names=$(ls -1 *.F 2>&1)
1602	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1603	Names=$(ls -1 *.f 2>&1)
1604	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1605	Names=$(ls -1 *.c 2>&1)
1606	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1607
1608	cd - > /dev/null
1609	cd SOURCES_FOR_RUN_$fname
1610
1611	# COPY MAKEFILE IF EXISTING
1612	if [[ -f $add_source_path/Makefile ]]
1613	then
1614	printf "\n\n *** user Makefile from directory"
1615	printf "\n \"$add_source_path\" is used \n"
1616	if [[ $silent == false ]]
1617	then
1618	sleep 1
1619	fi
1620	cp $add_source_path/Makefile .
1621	fi
1622
1623	for dateiname in $AddFilenames
1624	do
1625	if [[ -f $dateiname ]]
1626	then
1627	printf "\n +++ source code file \"$dateiname\" found in additional"
1628	printf "\n source code directory \"$add_source_path\" "
1629	printf "\n but was also given with option \"-s\" which means that it should be taken"
1630	printf "\n from directory \"$source_path\"."
1631	locat=source; exit
1632	fi
1633
1634	cp $add_source_path/$dateiname .
1635	source_list="$source_list $dateiname"
1636
1637	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1638	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1639	then
1640	printf "\n\n +++ user file \"$dateiname\" "
1641	printf "\n is not listed in Makefile \n"
1642	locat=source; exit
1643	else
1644
1645	if [[ $found = false ]]
1646	then
1647	found=true
1648	printf "\n\n *** following user file(s) added to the"
1649	printf " files to be translated:\n "
1650	fi
1651	printf "$dateiname "
1652	if [[ $silent == false ]]
1653	then
1654	sleep 0.5
1655	fi
1656
1657	fi
1658	done
1659	[[ $found = true ]] && printf "\n"
1660	cd - > /dev/null
1661	fi
1662	fi
1663
1664
1665	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1666	# TO THE LIST OF FILES TO BE COMPILED
1667	if [[ $restart_run != true && -n $package_list ]]
1668	then
1669
1670	cd $source_path
1671
1672	for package in $package_list
1673	do
1674
1675	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1676
1677	# DETERMINE FILES BELONGING TO THE PACKAGE
1678	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1679	# THE NAME OF THE DIRECTORY
1680	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1681
1682
1683	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1684	# IF THEY ARE NOT ALREADY PART OF THE LIST
1685	for source_list_name in $package_source_list
1686	do
1687	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1688	then
1689
1690	# ONLY TAKE FILES WITH VALID SUFFIX
1691	ending=`echo $source_list_name \| cut -f2 -d.`
1692	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1693	then
1694	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1695	source_list="$source_list $source_list_name"
1696	fi
1697	fi
1698	done
1699	done
1700
1701	cd - > /dev/null
1702	fi
1703
1704	fi # do_compile=true
1705
1706
1707	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1708	# AND SET PRE-PROCESSOR DIRECTIVES
1709	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1710	then
1711
1712	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1713	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1714	then
1715	cpp_options="${cpp_options},-D__ibm=__ibm"
1716	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1717	then
1718	cpp_options="$cpp_options -D__nec"
1719	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1720	then
1721	cpp_options="$cpp_options -D__lc"
1722	else
1723	cpp_options="$cpp_options -D__$localhost"
1724	fi
1725
1726	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1727	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1728	then
1729	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1730	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1731	else
1732	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1733	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1734	fi
1735
1736	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1737	if [[ -n $package_list ]]
1738	then
1739	for package in $package_list
1740	do
1741	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1742	then
1743	if [[ $package != "dvrp_graphics+1PE" ]]
1744	then
1745	cpp_options="${cpp_options},-D__$package=__$package"
1746	else
1747	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1748	export use_seperate_pe_for_dvrp_output=true
1749	fi
1750	else
1751	if [[ $package != "dvrp_graphics+1PE" ]]
1752	then
1753	cpp_options="$cpp_options -D__$package"
1754	else
1755	cpp_options="$cpp_options -D__dvrp_graphics"
1756	export use_seperate_pe_for_dvrp_output=true
1757	fi
1758	fi
1759	done
1760	fi
1761
1762	# SET DIRECTIVES GIVEN BY OPTION -D
1763	if [[ -n $cpp_opts ]]
1764	then
1765	for popts in $cpp_opts
1766	do
1767	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1768	then
1769	cpp_options="${cpp_options},-D__$popts=__$popts"
1770	else
1771	cpp_options="$cpp_options -D__$popts"
1772	fi
1773	done
1774	fi
1775
1776	else
1777
1778
1779	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1780	if [[ $do_remote = false ]]
1781	then
1782	if [[ ! -f $executable ]]
1783	then
1784	printf "\n +++ executable file: $executable"
1785	printf "\n does not exist"
1786	locat=executable; exit
1787	fi
1788	fi
1789	fi
1790
1791
1792	# DETERMINE THE JOB MODE
1793	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1794	then
1795	if [[ "$LOADLBATCH" = yes ]]
1796	then
1797	batch_job=.TRUE.
1798	jobmo=BATCH
1799	else
1800	batch_job=.FALSE.
1801	jobmo=INTERACTIVE
1802	fi
1803	else
1804	if [[ "$ENVIRONMENT" = BATCH ]]
1805	then
1806	batch_job=.TRUE.
1807	jobmo=BATCH
1808	else
1809	batch_job=.FALSE.
1810	jobmo=INTERACTIVE
1811	fi
1812	fi
1813
1814	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1815	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1816	then
1817	printf "\n +++ no interactive runs allowed on host \"$host\" "
1818	printf "\n please submit batch job using mrun option \"-b\" \n"
1819	locat=normal; exit
1820	fi
1821
1822
1823	# CHECK, IF USER DEFINED A COMPILER
1824	if [[ "$compiler_name" = "" ]]
1825	then
1826
1827	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1828	locat=compiler_name; exit
1829
1830	fi
1831
1832
1833	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1834	kennung=$RANDOM
1835	if [[ "$tmp_user_catalog" = "" ]]
1836	then
1837	if [[ $localhost = ibmh ]]
1838	then
1839	tmp_user_catalog=$SCRATCH
1840	elif [[ $localhost = nech ]]
1841	then
1842	tmp_user_catalog=$WRKSHR
1843	else
1844	tmp_user_catalog=/tmp
1845	fi
1846	fi
1847	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1848
1849
1850	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1851	if [[ "$tmp_data_catalog" = "" ]]
1852	then
1853	if [[ $localhost = nech ]]
1854	then
1855	tmp_data_catalog=$WRKSHR/mrun_restart_data
1856	else
1857	tmp_data_catalog=/tmp/mrun_restart_data
1858	fi
1859	fi
1860
1861
1862	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1863	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1864	then
1865	eval fopts=\"$fopts\"
1866	eval lopts=\"$lopts\"
1867	fi
1868
1869
1870
1871	# DETERMINE COMPILE- AND LINK-OPTIONS
1872	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1873	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1874	ROPTS="$ropts"
1875	# 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 ]]
1876	# then
1877	XOPT="-X $numprocs"
1878	# fi
1879
1880
1881
1882	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1883	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1884	done=false
1885	while [[ $done = false ]]
1886	do
1887	cputime=$cpumax
1888	if (( $cputime == 0 ))
1889	then
1890	if [[ $do_batch = true ]]
1891	then
1892	printf "\n +++ cpu-time is undefined"
1893	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1894	printf "\n >>> "
1895	read cputime 1>/dev/null 2>&1
1896	else
1897	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1898	fi
1899	else
1900	done=true
1901	fi
1902	cpumax=$cputime
1903	done
1904
1905	(( minuten = cputime / 60 ))
1906	(( sekunden = cputime - minuten * 60 ))
1907
1908
1909	# CHECK THE MEMORY DEMAND
1910	if [[ $do_batch = true ]]
1911	then
1912	done=false
1913	while [[ $done = false ]]
1914	do
1915	if (( memory == 0 ))
1916	then
1917	printf "\n +++ memory demand is undefined"
1918	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1919	printf "\n >>> "
1920	read memory 1>/dev/null 2>&1
1921	else
1922	done=true
1923	fi
1924	done
1925	fi
1926
1927
1928	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1929	if [[ $do_remote = true && -z $remote_username ]]
1930	then
1931	while [[ -z $remote_username ]]
1932	do
1933	printf "\n +++ username on remote host \"$host\" is undefined"
1934	printf "\n >>> Please type username:"
1935	printf "\n >>> "
1936	read remote_username
1937	done
1938	mc="$mc -u$remote_username"
1939	fi
1940
1941	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1942	if [[ "$login_init_cmd" != "" ]]
1943	then
1944	export init_cmds="${login_init_cmd};"
1945	fi
1946
1947
1948	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1949	if [[ "$modules" != "" ]]
1950	then
1951	if [[ $host = lctit ]]
1952	then
1953	export module_calls=". $modules"
1954	else
1955	export module_calls="module load ${modules};"
1956	fi
1957	fi
1958
1959
1960
1961	# OUTPUT OF THE MRUN-HEADER
1962	calltime=$(date)
1963	printf "\n"
1964	printf "#------------------------------------------------------------------------# \n"
1965	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1966	printf "\| \| \n"
1967	spalte1="called on:"; spalte2=$localhost_realname
1968	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1969	if [[ $do_remote = true ]]
1970	then
1971	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1972	else
1973	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1974	fi
1975	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1976	if [[ -n $numprocs ]]
1977	then
1978	if [[ $run_coupled_model = false ]]
1979	then
1980	spalte1="number of PEs:"; spalte2=$numprocs
1981	else
1982	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1983	fi
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	fi
1986	if [[ -n $tasks_per_node ]]
1987	then
1988	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1989	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1990	if (( remaining_pes > 0 ))
1991	then
1992	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1993	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1994	fi
1995	fi
1996	if [[ $maximum_parallel_io_streams != $numprocs ]]
1997	then
1998	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1999	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2000	fi
2001	if [[ $use_openmp = true ]]
2002	then
2003	spalte1="threads per task:"; spalte2="$threads_per_task"
2004	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2005	fi
2006	printf "\| \| \n"
2007	if [[ $do_compile = true ]]
2008	then
2009	if [[ "$mopts" != "" ]]
2010	then
2011	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2012	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2013	zeile=$(echo "$mopts" \| cut -c46-)
2014	while [[ "$zeile" != "" ]]
2015	do
2016	spalte1=""
2017	spalte2=$(echo "$zeile" \| cut -c-45)
2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2019	zeile=$(echo "$zeile" \| cut -c46-)
2020	done
2021	fi
2022
2023	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	zeile=$(echo "$cpp_options" \| cut -c46-)
2026	while [[ "$zeile" != "" ]]
2027	do
2028	spalte1=""
2029	spalte2=$(echo "$zeile" \| cut -c-45)
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	zeile=$(echo "$zeile" \| cut -c46-)
2032	done
2033
2034	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2035	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2036	zeile=$(echo "$fopts" \| cut -c46-)
2037	while [[ "$zeile" != "" ]]
2038	do
2039	spalte1=""
2040	spalte2=$(echo "$zeile" \| cut -c-45)
2041	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2042	zeile=$(echo "$zeile" \| cut -c46-)
2043	done
2044
2045	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2046	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2047	zeile=$(echo "$lopts" \| cut -c46-)
2048	while [[ "$zeile" != "" ]]
2049	do
2050	spalte1=""
2051	spalte2=$(echo "$zeile" \| cut -c-45)
2052	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2053	zeile=$(echo "$zeile" \| cut -c46-)
2054	done
2055
2056	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2057	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2058	zeile=$(echo "$modules" \| cut -c46-)
2059	while [[ "$zeile" != "" ]]
2060	do
2061	spalte1=""
2062	spalte2=$(echo "$zeile" \| cut -c-45)
2063	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2064	zeile=$(echo "$zeile" \| cut -c46-)
2065	done
2066
2067	spalte1="main program:"; spalte2=$mainprog
2068	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2069	else
2070	spalte1=executable:; spalte2=$executable
2071	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2072	fi
2073	printf "\| \| \n"
2074	spalte1="base name of files:"; spalte2=$fname
2075	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2076	if [[ $fname != $afname ]]
2077	then
2078	spalte1="base name of input files:"; spalte2=$afname
2079	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2080	fi
2081	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2082	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2083	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085
2086	if [[ "$ocean_file_appendix" = true ]]
2087	then
2088	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2089	fi
2090
2091	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2092	then
2093	spalte1="memory demand / PE":; spalte2="$memory MB"
2094	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2095	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2096	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2097	fi
2098
2099	if [[ $do_compile = true ]]
2100	then
2101	printf "\| \| \n"
2102	printf "\| Files to be compiled: \| \n"
2103	zeile=$source_list
2104	while [[ "$zeile" != "" ]]
2105	do
2106	linestart=$(echo $zeile \| cut -c-70)
2107	printf "\| %-70s \| \n" "$linestart"
2108	zeile=$(echo "$zeile" \| cut -c71-)
2109	done
2110	fi
2111	printf "#------------------------------------------------------------------------#"
2112
2113
2114
2115	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2116	if [[ $do_trace = true ]]
2117	then
2118	(( i = 0 ))
2119	while (( i < iin ))
2120	do
2121	(( i = i + 1 ))
2122	if (( i == 1 ))
2123	then
2124	printf "\n\n >>> INPUT-file assignments:\n"
2125	fi
2126	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2127	done
2128	(( i = 0 ))
2129	while (( i < iout ))
2130	do
2131	(( i = i + 1 ))
2132	if (( i == 1 ))
2133	then
2134	printf "\n\n >>> OUTPUT-file assignments:\n"
2135	fi
2136	printf "\n ${localout[$i]} : ${pathout[$i]}"
2137	done
2138	(( i = 0 ))
2139	while (( i < iic ))
2140	do
2141	(( i = i + 1 ))
2142	if (( i == 1 ))
2143	then
2144	printf "\n\n >>> INPUT-commands:\n"
2145	fi
2146	printf "\n ${in_command[$i]}"
2147	done
2148	(( i = 0 ))
2149	while (( i < ioc ))
2150	do
2151	(( i = i + 1 ))
2152	if (( i == 1 ))
2153	then
2154	printf "\n\n >>> OUTPUT-commands:\n"
2155	fi
2156	printf "\n ${out_command[$i]}"
2157	done
2158	fi
2159
2160
2161	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2162	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2163	then
2164	antwort=dummy
2165	printf "\n\n"
2166	printf " >>> everything o.k. (y/n) ? "
2167	while read antwort
2168	do
2169	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2170	then
2171	printf " >>> everything o.k. (y/n) ? "
2172	else
2173	break
2174	fi
2175	done
2176	if [[ $antwort = n \|\| $antwort = N ]]
2177	then
2178	locat=user_abort; (( iec = 0 )); exit
2179	fi
2180	if [[ $do_batch = true ]]
2181	then
2182	printf " >>> batch-job will be created and submitted"
2183	else
2184	printf " >>> MRUN will now continue to execute on this machine"
2185	fi
2186	fi
2187
2188
2189	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2190	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2191	check_depository="${working_directory}/trunk/UTIL"
2192	check_sources="${working_directory}/tmp_check_namelist_files"
2193	skip_check=false
2194
2195	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2196	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2197	then
2198	skip_check=true
2199	reason="run on remote host or parameter file check has not been compiled."
2200	fi
2201	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2202	then
2203	skip_check=true
2204	reason="parameter file check has not been compiled."
2205	fi
2206
2207	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2208	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2209	then
2210	skip_check=true
2211	reason="serial run."
2212	fi
2213
2214	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2215	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2216	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2217	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2218	if [[ $check_namelist_files == false ]]
2219	then
2220	skip_check=true
2221	reason="-z option set."
2222	fi
2223
2224	if [[ $fromhost != $localhost ]]
2225	then
2226	skip_check=true
2227	reason="submitting host is local host."
2228	fi
2229
2230	if [[ $run_coupled_model == true ]]
2231	then
2232	skip_check=true
2233	reason="coupled run."
2234	fi
2235
2236	if [[ $restart_run == true ]]
2237	then
2238	skip_check=true
2239	reason="restart run."
2240	fi
2241
2242	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2243	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2244	last_char=`echo $filename_input \| cut -c $last_char_int`
2245	if [[ "$last_char" == "f" ]]
2246	then
2247	skip_check=true
2248	reason="restart run."
2249	fi
2250
2251	if [[ $skip_check == false ]]
2252	then
2253	tmp_check=${working_directory}/tmp_check
2254
2255	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2256	# NOT NECESSARILY REQUIRED
2257	line=""
2258	found=false
2259	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2260	while read line1
2261	do
2262	line="$line1"
2263	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2264	then
2265	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2266	found=true
2267	fi
2268	done < $tmp_check
2269
2270	if [[ $found = false ]]
2271	then
2272	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2273	fi
2274
2275	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2276	# NOT NECESSARILY REQUIRED
2277	line=""
2278	found=false
2279	grep "NUDGING_DATA" $config_file > $tmp_check
2280	while read line1
2281	do
2282	line="$line1"
2283	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2284	then
2285	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2286	found=true
2287	fi
2288	done < $tmp_check
2289
2290	if [[ $found = false ]]
2291	then
2292	printf "\n +++ no NUDGING list entry found in the configuration file."
2293	fi
2294
2295	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2296	# NOT NECESSARILY REQUIRED
2297	line=""
2298	found=false
2299	grep "LSF_DATA" $config_file > $tmp_check
2300	while read line1
2301	do
2302	line="$line1"
2303	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2304	then
2305	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2306	found=true
2307	fi
2308	done < $tmp_check
2309
2310	if [[ $found = false ]]
2311	then
2312	printf "\n +++ no LSF list entry found in the configuration file."
2313	fi
2314
2315	rm -rf ${working_directory}/tmp_check
2316
2317	# CHECK IF THE P3DF FILE MUST BE CHECKED
2318	for item in $input_list
2319	do
2320	if [[ "$item" == "restart" ]]
2321	then
2322	check_restart=1
2323	else
2324	check_restart=0
2325	fi
2326	done
2327
2328	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2329	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2330	then
2331	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2332	locat=check_namelist; exit
2333	fi
2334
2335	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2336	if [[ $check_restart == 1 ]]
2337	then
2338
2339	filenamef="${filename_input}f"
2340	if [[ ! -f $filenamef ]]
2341	then
2342	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2343	check_restart=0
2344	answer=dummy
2345	printf "\n\n"
2346
2347	if [[ $silent == false ]]
2348	then
2349	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2350	do
2351	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2352	read answer
2353	done
2354	if [[ $answer = a \|\| $answer = A ]]
2355	then
2356	printf "\n +++ Aborting...."
2357	locat=normal; exit
2358	fi
2359	fi
2360	else
2361	check_restart=1
2362	fi
2363	fi
2364
2365	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2366	mkdir $check_sources
2367	cd $check_sources
2368
2369
2370	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2371	if [[ -d $add_source_path ]]
2372	then
2373	printf "\n\n *** copying files from $check_depository"
2374	cp $check_depository/check_namelist_files.tar ./
2375
2376	printf "\n\n *** untar of makefile and source files in $check_sources"
2377	tar -xf check_namelist_files.tar > /dev/null 2>&1
2378
2379	printf "\n\n *** adding user code."
2380	cp $add_source_path/* ./
2381	touch check_namelist_files.f90
2382
2383	# GET COMPILER OPTIONS AND PERFORM MAKE
2384	printf "\n\n *** compiling code if necessary...\n"
2385
2386	# workaround for batch jobs on local machine (lcxe6)
2387	if [[ $do_batch == true && $do_remote == false ]]
2388	then
2389	eval $init_cmds
2390	fi
2391
2392	# GET CHECK OPTIONS
2393	line=""
2394	found=false
2395
2396	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2397
2398	while read line1
2399	do
2400
2401	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2402	then
2403	line="$line1"
2404	fi
2405
2406	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2407	then
2408	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2409	line="$line "
2410	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'`
2411	found=true
2412	fi
2413
2414	done < $tmp_check
2415	copts_check="$copts_check -D__check -D__parallel"
2416
2417	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2418
2419	# GET MAKE OUTPUT
2420	if [[ $? != 0 ]]
2421	then
2422	printf "\n +++ error during make."
2423	answer=dummy
2424	printf "\n\n"
2425	if [[ $silent == false ]]
2426	then
2427	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2428	do
2429	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2430	read answer
2431	done
2432	if [[ $answer = a \|\| $answer = A ]]
2433	then
2434	printf "\n +++ Aborting..."
2435	rm -rf $check_sources
2436	locat=normal; exit
2437	else
2438	skip_check=true
2439	fi
2440	else
2441	skip_check=true
2442	fi
2443	fi
2444	else
2445	cp $PALM_BIN/check_namelist_files.x ./
2446	fi
2447
2448	cp $filename_input ./PARIN
2449	if [[ $check_restart == 1 ]]
2450	then
2451	cp $filenamef ./PARINF
2452	fi
2453
2454	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2455	then
2456	printf "\n *** adding topography data"
2457	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2458
2459	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2460	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2461	# WHICH REQUIRE SUFFICIENT MEMORY
2462	ulimit -s unlimited
2463	fi
2464
2465	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2466	then
2467	printf "\n *** adding nudging data"
2468	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2469	fi
2470
2471	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2472	then
2473	printf "\n *** adding large scale forcing data"
2474	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2475	fi
2476
2477	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2478	cat > ENVPAR << %%END%%
2479	&envpar run_identifier = '$fname', host = '$host',
2480	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2481	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2482	maximum_cpu_time_allowed = ${cpumax}.,
2483	revision = '$global_revision',
2484	local_dvrserver_running = $local_dvrserver_running /
2485
2486	%%END%%
2487
2488	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2489	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2490	then
2491	printf "\n +++ WARNING: check_namelist_files.x not found."
2492	answer=dummy
2493	printf "\n\n"
2494
2495	if [[ $silent == false ]]
2496	then
2497	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2498	do
2499	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2500	read answer
2501	done
2502	if [[ $answer = a \|\| $answer = A ]]
2503	then
2504	printf "\n +++ Aborting..."
2505	rm -rf $check_sources
2506	locat=normal; exit
2507	else
2508	printf "\n *** skipping parameter file check."
2509	fi
2510	fi
2511
2512	elif [[ $skip_check == false ]]
2513	then
2514	# STARTING THE PARAMETER FILE CHECK
2515	printf "\n\n *** starting parameter file check..."
2516
2517	# CHECKING THE P3D FILE
2518	printf "\n\n (1) checking $filename_input"
2519	echo "$numprocs 0 0" > VARIN
2520	errors=`./check_namelist_files.x < VARIN 2>&1`
2521
2522	check_error=false
2523	if [[ "$errors" == "" ]]
2524	then
2525	printf " --> o.k."
2526	else
2527	printf " --> failed."
2528	check_error=true
2529	printf "\n\n $errors"
2530	fi
2531
2532	# CHECKING THE PD3F FILE IF NECESSARY
2533	if [[ $check_restart == 1 && $check_error == false ]]
2534	then
2535	printf "\n\n (2) checking $filenamef"
2536
2537	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2538	# IN &INIPAR LIST
2539	found=false
2540	cat PARINF \| while read line
2541	do
2542	line=$(echo $line\|sed 's/ //g')
2543	if [[ $line == "&inipar" ]]
2544	then
2545	start_search=true
2546	fi
2547
2548	if [[ $start_search == true ]]
2549	then
2550	if [[ $line == "initializing_actions='read_restart_data'" ]]
2551	then
2552	found=true
2553	break
2554	fi
2555	fi
2556
2557	if [[ $line == "/" ]]
2558	then
2559	start_search=false
2560	fi
2561
2562	done
2563
2564	if [[ $found = false ]]
2565	then
2566	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2567	printf "\n in &inipar list in $fname$p3df_suffix."
2568	rm -rf $check_sources
2569	locat=check_namelist; exit
2570	fi
2571
2572	# READ max_user_pr FROM FILES
2573	if [[ -f parin_for_check ]]
2574	then
2575	read max_pr_user < parin_for_check
2576	else
2577	max_user_pr=0
2578	fi
2579
2580	echo "$numprocs 1 $max_pr_user" > VARIN
2581	errors=`./check_namelist_files.x < VARIN 2>&1`
2582
2583	if [[ "$errors" == "" ]]
2584	then
2585	printf " --> o.k."
2586	else
2587	printf " --> failed."
2588	check_error=true
2589	printf "\n\n $errors"
2590	fi
2591	fi
2592
2593	# REPORT ERRORS AND CONTINUE/EXIT
2594	if [[ $check_error == true ]]
2595	then
2596	printf "\n +++ errors found in the parameter file!\n"
2597	answer=dummy
2598	printf "\n\n"
2599
2600	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2601	do
2602	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2603	read answer
2604	done
2605
2606	if [[ $answer = a \|\| $answer = A ]]
2607	then
2608	printf "\n +++ Aborting..."
2609	rm -rf $check_sources
2610	locat=normal; exit
2611	fi
2612	else
2613	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2614	fi
2615	rm -rf $check_sources
2616	fi
2617	else
2618	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2619	fi
2620
2621	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2622	rm -rf $check_sources
2623	cd $working_directory
2624
2625
2626	# DETERMINE PATH FOR MAKE DEPOSITORY
2627	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2628	then
2629
2630	line=""
2631	grep "%depository_path" $config_file > tmp_mrun
2632	while read line
2633	do
2634	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2635	then
2636	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2637	then
2638	global_depository_path=`echo $line \| cut -d" " -s -f2`
2639	fi
2640	fi
2641	done < tmp_mrun
2642
2643	line=""
2644	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2645	while read line
2646	do
2647	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2648	then
2649	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2650	then
2651	local_depository_path=`echo $line \| cut -d" " -s -f2`
2652	fi
2653	fi
2654	done < tmp_mrun
2655
2656	if [[ "$local_depository_path" = "" ]]
2657	then
2658	if [[ "$global_depository_path" != "" ]]
2659	then
2660	local_depository_path=$global_depository_path
2661	else
2662	printf "\n\n +++ no depository path found in configuration file"
2663	printf "\n for local host \"$localhost\" "
2664	printf "\n please set \"\%depository_path\" in configuration file\n"
2665	locat=config_file; exit
2666	fi
2667	fi
2668	eval local_depository_path=$local_depository_path
2669	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2670	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2671
2672
2673	basename=`echo $mainprog \| cut -f1 -d"."`
2674	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2675	if [[ ! -f $make_depository ]]
2676	then
2677	printf "\n"
2678	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2679	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2680	fi
2681
2682	fi
2683
2684
2685	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2686	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2687	if [[ $do_batch = false ]]
2688	then
2689
2690
2691	# CREATE THE TEMPORARY WORKING DIRECTORY
2692	mkdir -p $TEMPDIR
2693	chmod go+rx $TEMPDIR
2694	tmpcreate=true
2695
2696
2697	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2698	# INTO THE TEMPORARY WORKING DIRECTORY
2699	if [[ $do_compile = true ]]
2700	then
2701
2702	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2703	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2704	if [[ $localhost = nech ]]
2705	then
2706	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2707	if mkdir -p $TEMPDIR_COMPILE
2708	then
2709	printf "\n *** \"$TEMPDIR_COMPILE\" "
2710	printf "\n is generated as temporary directory for cross compiling\n"
2711	else
2712	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2713	printf "\n needed for cross compilation failed"
2714	locat=compile
2715	exit
2716	fi
2717	else
2718	TEMPDIR_COMPILE=$TEMPDIR
2719	fi
2720
2721	cp $make_depository $TEMPDIR_COMPILE
2722	cd $TEMPDIR_COMPILE
2723	tar -xf $make_depository > /dev/null 2>&1
2724	cd - > /dev/null
2725
2726	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2727	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2728	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2729	then
2730	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2731	else
2732	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2733	fi
2734
2735	else
2736
2737	cp $executable ${TEMPDIR}/a.out
2738
2739	fi
2740
2741
2742	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2743	cd $TEMPDIR
2744	printf "\n *** changed to temporary directory: $TEMPDIR"
2745
2746
2747	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2748	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2749	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2750	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2751	(( i = 0 ))
2752	while (( i < iout ))
2753	do
2754	(( i = i + 1 ))
2755	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2756	then
2757	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2758	else
2759	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2760	fi
2761	done
2762
2763
2764	# IF REQUIRED, START WITH COMPILING
2765	if [[ $do_compile = true ]]
2766	then
2767
2768
2769	if [[ -f a.out ]]
2770	then
2771
2772	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2773	printf "\n\n\n *** executable a.out found"
2774	printf "\n no compilation required \n"
2775
2776	else
2777
2778	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2779	printf "\n\n\n *** compilation starts \n$dashes\n"
2780	printf " *** compilation with make using following options:\n"
2781	printf " make depository: $make_depository"
2782	if [[ "$mopts" != "" ]]
2783	then
2784	printf " make options: $mopts\n"
2785	fi
2786	printf " compilername: $compiler_name\n"
2787	printf " compiler options: $fopts\n"
2788	printf " preprocessor directives: $cpp_options \n"
2789	printf " linker options: $lopts \n"
2790	if [[ "$modules" != "" ]]
2791	then
2792	printf " modules to be load: $modules \n"
2793	fi
2794	printf " source code files: $source_list \n"
2795
2796	if [[ $localhost = nech ]]
2797	then
2798	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\" "
2799	cp $TEMPDIR_COMPILE/a.out .
2800	[[ $? != 0 ]] && compile_error=true
2801	rm -rf $TEMPDIR_COMPILE
2802	elif [[ $localhost = ibmh ]]
2803	then
2804	printf " compiler is called via ssh on \"plogin1\" \n"
2805	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\" "
2806	[[ ! -f a.out ]] && compile_error=true
2807	continue # STATUS=1, IF a.out EXISTS
2808	elif [[ $localhost = lcflow ]]
2809	then
2810	printf " compiler is called via ssh on \"flow\" \n"
2811	/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\" "
2812	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2813	[[ "$check_for_file" = "" ]] && compile_error=true
2814	continue # STATUS=1, IF a.out EXISTS
2815	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2816	then
2817	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2818	else
2819	[[ "$init_cmds" != "" ]] && eval $init_cmds
2820	[[ "$module_calls" != "" ]] && eval $module_calls
2821	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2822	fi
2823
2824	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2825	then
2826	printf "\n +++ error occured while compiling or linking"
2827	locat=compile
2828
2829	exit
2830	else
2831	printf "$dashes\n *** compilation finished \n"
2832	fi
2833
2834	fi
2835
2836	fi
2837
2838
2839	# PROVIDE THE INPUT FILES
2840	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2841	(( i = 0 ))
2842	while (( i < iin ))
2843	do
2844	(( i = i + 1 ))
2845	if (( i == 1 ))
2846	then
2847	printf "\n\n *** providing INPUT-files:\n$dashes"
2848	fi
2849
2850
2851	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2852	if [[ "${transin[$i]}" = unavailable ]]
2853	then
2854	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2855	then
2856	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2857	printf "\n is not available!"
2858	else
2859	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2860	printf "\n is not available!"
2861	fi
2862	continue
2863	fi
2864
2865	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2866	files_for_pes=false; datentyp=file
2867	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2868	then
2869	files_for_pes=true; datentyp=directory
2870	actionin[$i]=""
2871	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2872	then
2873	actionin[$i]=""
2874	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2875	then
2876	files_for_pes=true; datentyp=directory
2877	actionin[$i]="ar"
2878	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2879	then
2880	actionin[$i]="ar"
2881	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2882	then
2883	files_for_pes=true; datentyp=directory
2884	actionin[$i]="fl"
2885	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2886	then
2887	actionin[$i]="fl"
2888	fi
2889
2890	if [[ $files_for_pes = true ]]
2891	then
2892	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2893	else
2894	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2895	fi
2896
2897	# INPUT-FILE FOR A RESTART RUN.
2898	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2899	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2900	if [[ "${actionin[$i]}" = fl ]]
2901	then
2902	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2903	if [[ $files_for_pes = false ]]
2904	then
2905	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2906	then
2907	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2908	got_tmp[$i]=true
2909	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2910	then
2911	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2912	printf "\n *** trying to use backup copy in \"$WORK\" "
2913	cp $WORK/${frelin[$i]} ${localin[$i]}
2914	else
2915	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2916	printf "\n or \"$tmp_data_catalog\" does not exist!"
2917	printf "\n *** trying to get copy from archive"
2918	actionin[$i]=ar
2919	fi
2920	else
2921	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2922	then
2923	mkdir ${localin[$i]}
2924	cd $tmp_data_catalog/${frelin[$i]}
2925	for file in $(ls *)
2926	do
2927	ln $file $TEMPDIR/${localin[$i]}
2928	done
2929	cd $TEMPDIR
2930	got_tmp[$i]=true
2931	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2932	then
2933	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2934	printf "\n *** trying to use backup copy in \"$WORK\" "
2935	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2936	else
2937	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2938	printf "\n or \"$tmp_data_catalog\" does not exist!"
2939	printf "\n *** trying to get copy from archive"
2940	actionin[$i]=ar
2941	fi
2942	fi
2943	fi
2944
2945
2946	# FILE IS STORED ON THE ARCHIVE SYSTEM
2947	if [[ "${actionin[$i]}" = ar ]]
2948	then
2949
2950	if [[ $files_for_pes = false ]]
2951	then
2952	printf "\n file will be restored from archive-system ($archive_system)!"
2953	else
2954	printf "\n directory will be restored from archive-system ($archive_system)!"
2955	fi
2956
2957	file_restored=false
2958
2959	if [[ $archive_system = asterix ]]
2960	then
2961	do_stagein=true
2962	(( stagein_anz = 0 ))
2963	while [[ $do_stagein = true ]]
2964	do
2965	if [[ $files_for_pes = false ]]
2966	then
2967	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2968	else
2969	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2970	fi
2971	cat STAGEIN_OUTPUT
2972	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2973	then
2974	file_restored=true
2975	do_stagein=false
2976	else
2977	(( stagein_anz = stagein_anz + 1 ))
2978	if (( stagein_anz == 10 ))
2979	then
2980	printf "\n +++ stagein stoped after 10 tries"
2981	locat=stage
2982	exit
2983	fi
2984	printf "\n +++ restoring from archive failed, trying again:"
2985	sleep 900
2986	fi
2987	done
2988	elif [[ $archive_system = DMF ]]
2989	then
2990	if [[ $files_for_pes = false ]]
2991	then
2992	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2993	locat=DMF
2994	exit
2995	else
2996	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2997	cp -r $ARCHIVE/${frelin[$i]} $PWD
2998	file_restored=true
2999	fi
3000	elif [[ $archive_system = tivoli ]]
3001	then
3002	if [[ $files_for_pes = false ]]
3003	then
3004	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3005	else
3006	(( inode = 0 ))
3007	while (( inode < nodes ))
3008	do
3009	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3010	(( inode = inode + 1 ))
3011	done
3012	fi
3013	file_restored=true
3014	elif [[ $archive_system = ut ]]
3015	then
3016	if [[ $files_for_pes = false ]]
3017	then
3018	cp $UT/${frelin[$i]} .
3019	else
3020	(( inode = 0 ))
3021	while (( inode < nodes ))
3022	do
3023	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3024	(( inode = inode + 1 ))
3025	done
3026	fi
3027	file_restored=true
3028	else
3029	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3030	locat=rearchive
3031	exit
3032	fi
3033
3034	if [[ $file_restored = true ]]
3035	then
3036
3037	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3038	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3039	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3040	if [[ $files_for_pes = false ]]
3041	then
3042	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3043	else
3044	mkdir $tmp_data_catalog/${frelin[$i]}
3045	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3046	fi
3047	got_tmp[$i]=true
3048
3049	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3050	mv ${frelin[$i]} ${localin[$i]}
3051
3052	fi
3053	fi
3054
3055
3056	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3057	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3058	then
3059
3060	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3061	then
3062
3063	# FILE COPIES ARE PROVIDED FOR ALL CORES
3064	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3065	printf "\n file will be provided for $numprocs processors"
3066	mkdir ${localin[$i]}
3067	ival=$numprocs
3068	(( ii = 0 ))
3069	while (( ii <= ival-1 ))
3070	do
3071	if (( ii < 10 ))
3072	then
3073	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3074	elif (( ii < 100 ))
3075	then
3076	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3077	elif (( ii < 1000 ))
3078	then
3079	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3080	else
3081	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3082	fi
3083	(( ii = ii + 1 ))
3084	done
3085
3086	else
3087
3088	if [[ $files_for_pes = true ]]
3089	then
3090
3091	# PROVIDE FILES FOR EACH CORE
3092	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3093	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3094	printf "\n providing $numprocs files for the respective processors"
3095	mkdir ${localin[$i]}
3096	if [[ $link_local_input = true ]]
3097	then
3098	printf " using ln -f\n"
3099	cd ${absnamein[$i]}
3100	for file in $(ls *)
3101	do
3102	ln -f $file ${localin[$i]}
3103	done
3104	cd $TEMPDIR
3105	fi
3106
3107	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3108	if [[ ! -f "${localin[$i]}/_0000" ]]
3109	then
3110	if [[ $link_local_input = true ]]
3111	then
3112	printf " ln failed for .../_0000, using cp...\n"
3113	fi
3114	cp -r ${absnamein[$i]}/* ${localin[$i]}
3115	fi
3116
3117	else
3118
3119	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3120	if [[ $link_local_input = true ]]
3121	then
3122	printf " using ln -f\n"
3123	ln -f ${absnamein[$i]} ${localin[$i]}
3124	fi
3125	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3126	if [[ ! -f "${localin[$i]}" ]]
3127	then
3128	if [[ $link_local_input = true ]]
3129	then
3130	printf " ln failed, using cp...\n"
3131	fi
3132	cp ${absnamein[$i]} ${localin[$i]}
3133	fi
3134	fi
3135	fi
3136	fi
3137
3138	done
3139	if (( i != 0 ))
3140	then
3141	printf "\n$dashes\n *** all INPUT-files provided \n"
3142	fi
3143
3144
3145	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3146	(( i = 0 ))
3147	while (( i < iic ))
3148	do
3149	(( i = i + 1 ))
3150	if (( i == 1 ))
3151	then
3152	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3153	fi
3154	printf "\n >>> ${in_command[$i]}"
3155	eval ${in_command[$i]}
3156	if (( i == iic ))
3157	then
3158	printf "\n$dashes\n"
3159	fi
3160	done
3161
3162
3163	# SET THE REMAINING CPU-TIME
3164	cpurest=${cpumax}.
3165
3166
3167	# START DVR STREAMING SERVER
3168	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3169	then
3170	if [[ "$dvr_server" != "" ]]
3171	then
3172
3173	printf "\n\n *** preparing the dvr streaming server configuration file"
3174
3175	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3176	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3177	if [[ "$running_dvrserver_id" != "" ]]
3178	then
3179
3180	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3181	printf "\n This server is used instead starting a new one!"
3182	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3183
3184	else
3185
3186	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3187	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3188	then
3189	cp ${PALM_BIN}/.dvrserver.config .
3190
3191	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3192	user_id=`id -u`
3193	group_id=`id -g`
3194
3195	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3196	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3197	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3198	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3199	mv .dvrserver.3 .dvrserver.config
3200	rm .dvrserver.1 .dvrserver.2
3201
3202	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3203	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3204	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3205	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3206	local_dvrserver_running=.TRUE.
3207	else
3208	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3209	printf "\n \"$PALM_BIN\" "
3210	locat=dvr
3211	exit
3212	fi
3213
3214	fi
3215
3216	else
3217	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3218	fi
3219	fi
3220
3221
3222	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3223	# (FILE ENVPAR WILL BE READ BY PALM)
3224	cat > ENVPAR << %%END%%
3225	&envpar run_identifier = '$fname', host = '$localhost',
3226	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3227	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3228	maximum_cpu_time_allowed = ${cpumax}.,
3229	revision = '$global_revision',
3230	local_dvrserver_running = $local_dvrserver_running,
3231	batch_job = $batch_job /
3232
3233	%%END%%
3234
3235
3236	# STARTING THE EXECUTABLE
3237	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3238	PATH=$PATH:$TEMPDIR
3239
3240	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3241	if [[ "$mpi_debug" = true ]]
3242	then
3243	export MPI_CHECK_ARGS=1
3244	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3245	fi
3246
3247	if [[ "$totalview" = true ]]
3248	then
3249	printf "\n *** totalview debugger will be used"
3250	tv_opt="-tv"
3251	else
3252	tv_opt=""
3253	fi
3254
3255	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3256	then
3257
3258	#Interactive ALLINEA DEBUG seesion
3259	if [[ "$ENVIRONMENT" != BATCH ]]
3260	then
3261	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3262	then
3263	if [[ "$allinea" = true ]]
3264	then
3265	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3266
3267	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3268	wait
3269	fi
3270	fi
3271	fi
3272
3273	if [[ "$ENVIRONMENT" = BATCH ]]
3274	then
3275	continue
3276	fi
3277	if [[ $localhost = ibmh ]]
3278	then
3279
3280	# SETUP THE IBM MPI ENVIRONMENT
3281	export MP_SHARED_MEMORY=yes
3282	export AIXTHREADS_SCOPE=S
3283	export OMP_NUM_THREADS=$threads_per_task
3284	export AUTHSTATE=files
3285	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3286
3287	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3288	export MP_ADAPTER_USE=shared
3289	export MP_CPU_USE=multiple
3290	export MP_TIMEOUT=1200
3291
3292	unset MP_TASK_AFFINITY
3293
3294	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3295	#(( ii = 1 ))
3296	#while (( ii <= $numprocs ))
3297	#do
3298	# echo $localhost_realname >> hostfile
3299	# (( ii = ii + 1 ))
3300	#done
3301	#export MP_HOSTFILE=hostfile
3302
3303	if [[ "$LOADLBATCH" = yes ]]
3304	then
3305	totalview poe a.out $ROPTS
3306	else
3307	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3308	export TVDSVRLAUNCHCMD=ssh
3309	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3310	fi
3311
3312	fi # END DEBUG MODE
3313
3314	else
3315
3316	# NORMAL EXECUTION
3317	if [[ -n $numprocs ]]
3318	then
3319
3320	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3321	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3322	then
3323
3324	# SETUP THE IBM MPI ENVIRONMENT
3325	if [[ $host != ibmh && $host != ibmkisti ]]
3326	then
3327	export MP_SHARED_MEMORY=yes
3328	export AIXTHREAD_SCOPE=S
3329	export OMP_NUM_THREADS=$threads_per_task
3330	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3331	export AUTHSTATE=files
3332	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3333	# export MP_PRINTENV=yes
3334
3335	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3336	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3337	export MP_WAIT_MODE=poll
3338	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3339	fi
3340
3341	if [[ $host = ibmkisti ]]
3342	then
3343	export LANG=en_US
3344	export MP_SHARED_MEMORY=yes
3345	if [[ $threads_per_task = 1 ]]
3346	then
3347	export MP_SINGLE_THREAD=yes
3348	export MEMORY_AFFINITY=MCM
3349	else
3350	export OMP_NUM_THREADS=$threads_per_task
3351	fi
3352	fi
3353
3354	if [[ "$LOADLBATCH" = yes ]]
3355	then
3356	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3357	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3358	then
3359	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3360	else
3361	if [[ $run_coupled_model = false ]]
3362	then
3363	if [[ "$ocean_file_appendix" = true ]]
3364	then
3365	echo "precursor_ocean" > runfile_atmos
3366	else
3367	echo "precursor_atmos" > runfile_atmos
3368	fi
3369	else
3370	(( iia = $numprocs_atmos / $threads_per_task ))
3371	(( iio = $numprocs_ocean / $threads_per_task ))
3372	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3373	printf "\n using $coupled_mode coupling"
3374	printf "\n\n"
3375	echo "coupled_run $iia $iio" > runfile_atmos
3376	fi
3377	poe ./a.out $ROPTS < runfile_atmos
3378	fi
3379	else
3380	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3381	then
3382	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3383	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3384	then
3385	if [[ -f $hostfile ]]
3386	then
3387	cp $hostfile hostfile
3388	else
3389	(( ii = 1 ))
3390	while (( ii <= $numprocs ))
3391	do
3392	echo $localhost_realname >> hostfile
3393	(( ii = ii + 1 ))
3394	done
3395	fi
3396	export MP_HOSTFILE=hostfile
3397	if [[ $run_coupled_model = false ]]
3398	then
3399	if [[ "$ocean_file_appendix" = true ]]
3400	then
3401	echo "precursor_ocean" > runfile_atmos
3402	else
3403	echo "precursor_atmos" > runfile_atmos
3404	fi
3405	else
3406	(( iia = $numprocs_atmos / $threads_per_task ))
3407	(( iio = $numprocs_ocean / $threads_per_task ))
3408	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3409	printf "\n using $coupled_mode coupling"
3410	printf "\n\n"
3411	echo "coupled_run $iia $iio" > runfile_atmos
3412	fi
3413
3414	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3415
3416	else
3417	if [[ "$host_file" = "" ]]
3418	then
3419	printf "\n +++ no hostfile given in configuration file"
3420	locat=config_file
3421	exit
3422	else
3423	eval host_file=$host_file
3424	fi
3425	export MP_HOSTFILE=$host_file
3426	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3427	fi
3428	fi
3429	elif [[ $host = nech ]]
3430	then
3431	(( ii = nodes ))
3432	if [[ $ii = 1 ]]
3433	then
3434	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3435	export MPIPROGINF=YES
3436	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3437	echo "*** execution on single node with mpirun"
3438	mpirun -np $numprocs ./a.out $ROPTS
3439	else
3440	(( i = 0 ))
3441	while (( i < ii ))
3442	do
3443	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3444	(( i = i + 1 ))
3445	done
3446
3447	echo "#!/bin/sh" > mpi_exec_shell
3448	echo " " >> mpi_exec_shell
3449	echo "set -u" >> mpi_exec_shell
3450	echo "F_ERRCNT=0" >> mpi_exec_shell
3451	echo "MPIPROGINV=YES" >> mpi_exec_shell
3452	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3453	echo "cpurest=$cpurest" >> mpi_exec_shell
3454	echo "fname=$fname" >> mpi_exec_shell
3455	echo "localhost=$localhost" >> mpi_exec_shell
3456	echo "return_address=$return_address" >> mpi_exec_shell
3457	echo "return_username=$return_username" >> mpi_exec_shell
3458	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3459	echo "write_binary=$write_binary" >> mpi_exec_shell
3460	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3461	echo " " >> mpi_exec_shell
3462	echo "export F_ERRCNT" >> mpi_exec_shell
3463	echo "export MPIPROGINV" >> mpi_exec_shell
3464	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3465	echo "export cpurest" >> mpi_exec_shell
3466	echo "export fname" >> mpi_exec_shell
3467	echo "export localhost" >> mpi_exec_shell
3468	echo "export return_address" >> mpi_exec_shell
3469	echo "export return_username" >> mpi_exec_shell
3470	echo "export tasks_per_node" >> mpi_exec_shell
3471	echo "export write_binary" >> mpi_exec_shell
3472	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3473	echo " " >> mpi_exec_shell
3474	echo "exec ./a.out" >> mpi_exec_shell
3475
3476	chmod u+x mpi_exec_shell
3477	export MPIPROGINF=YES
3478	mpirun -f multinode_config &
3479	wait
3480
3481	fi
3482	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3483	then
3484
3485	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3486	# DOES NOT EXIST
3487	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3488	then
3489	if [[ -f $hostfile ]]
3490	then
3491	cp $hostfile hostfile
3492	(( ii = $numprocs / $threads_per_task ))
3493	[[ $ii = 0 ]] && (( ii = 1 ))
3494	else
3495	(( ii = 1 ))
3496	while (( ii <= $numprocs / $threads_per_task ))
3497	do
3498	echo $localhost_realname >> hostfile
3499	(( ii = ii + 1 ))
3500	done
3501	if (( $numprocs / $threads_per_task == 0 ))
3502	then
3503	echo $localhost_realname >> hostfile
3504	fi
3505	fi
3506	eval zeile=\"`head -n $ii hostfile`\"
3507	printf "\n *** running on: $zeile"
3508	fi
3509
3510	(( ii = $numprocs / $threads_per_task ))
3511	[[ $ii = 0 ]] && (( ii = 1 ))
3512	export OMP_NUM_THREADS=$threads_per_task
3513
3514	if [[ $threads_per_task != 1 ]]
3515	then
3516	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3517	# MAY ABORT
3518	ulimit -s unlimited
3519	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3520	fi
3521	if [[ $run_coupled_model = false ]]
3522	then
3523	if [[ "$ocean_file_appendix" = true ]]
3524	then
3525	echo "precursor_ocean" > runfile_atmos
3526	else
3527	echo "precursor_atmos" > runfile_atmos
3528	fi
3529	printf "\n\n"
3530
3531	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3532	then
3533	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3534	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3535	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3536	elif [[ $host = lccrayf ]]
3537	then
3538	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3539	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3540	then
3541	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3542	elif [[ $host = lcflow ]]
3543	then
3544	mpirun -np $ii a.out < runfile_atmos $ROPTS
3545	elif [[ $host = lcsb ]]
3546	then
3547	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3548	elif [[ $host = lckiaps ]]
3549	then
3550	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3551	elif [[ $host = lckyu* ]]
3552	then
3553	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3554	else
3555	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3556	fi
3557	else
3558
3559	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3560	(( iia = $numprocs_atmos / $threads_per_task ))
3561	(( iio = $numprocs_ocean / $threads_per_task ))
3562	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3563	printf "\n using $coupled_mode coupling"
3564	printf "\n\n"
3565
3566	if [[ $coupled_mode = "mpi2" ]]
3567	then
3568	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3569	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3570
3571	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3572	then
3573
3574	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3575	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3576
3577	else
3578	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3579	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3580	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3581	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3582	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3583	fi
3584	wait
3585
3586	else
3587
3588	echo "coupled_run $iia $iio" > runfile_atmos
3589
3590	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3591	then
3592
3593	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3594
3595	elif [[ $host = lck \|\| $host = lckordi ]]
3596	then
3597
3598	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3599
3600	elif [[ $host = lckyu* ]]
3601	then
3602
3603	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3604
3605	elif [[ $host = lcmuk ]]
3606	then
3607
3608	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3609
3610	fi
3611	wait
3612	fi
3613
3614	fi
3615
3616	elif [[ $host = lckyoto ]]
3617	then
3618	set -xv
3619	export P4_RSHCOMMAND=plesh
3620	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3621	if [[ "$ENVIRONMENT" = BATCH ]]
3622	then
3623	if [[ "$cond2" = fujitsu ]]
3624	then
3625	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3626	elif [[ "cond2" = pgi ]]
3627	then
3628	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3629	else
3630	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3631	fi
3632	else
3633	if [[ "$cond2" = "" ]]
3634	then
3635	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3636	else
3637	mpirun -np $numprocs ./a.out $ROPTS
3638	fi
3639	fi
3640	set +xv
3641
3642	elif [[ $host = lctit ]]
3643	then
3644	export OMP_NUM_THREADS=$threads_per_task
3645	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3646	if [[ "$threads_per_task" != 1 ]]
3647	then
3648	export MV2_ENABLE_AFFINITY=0
3649	fi
3650	echo "----- PBS_NODEFILE content:"
3651	cat $PBS_NODEFILE
3652	echo "-----"
3653	(( ii = $numprocs / $threads_per_task ))
3654	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3655	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3656	else
3657	mpprun -n $numprocs a.out $ROPTS
3658	fi
3659	else
3660	a.out $ROPTS
3661	fi
3662	fi
3663
3664	if [[ $? != 0 ]]
3665	then
3666
3667	# ABORT IN CASE OF RUNTIME ERRORS
3668	printf "\n +++ runtime error occured"
3669	locat=execution
3670	exit
3671
3672	else
3673
3674	printf "\n$dashes\n *** execution finished \n"
3675
3676	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3677	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3678	if [[ "$dvrserver_id" != "" ]]
3679	then
3680	kill $dvrserver_id
3681	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3682
3683	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3684	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3685	if [[ -d DATA_DVR ]]
3686	then
3687
3688	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3689	# DIRECTORY
3690	cp .dvrserver.config DATA_DVR
3691
3692	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3693	# SEQUENCE MODE DATA TOO)
3694	process_dvr_output -d DATA_DVR -f $fname -s
3695
3696	else
3697
3698	# PROCESS THE LOCAL OUTPUT
3699	process_dvr_output -l -d DATA_DVR -f $fname
3700
3701	fi
3702
3703	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3704	then
3705
3706	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3707	process_dvr_output -l -d DATA_DVR -f $fname
3708
3709	fi
3710	fi
3711
3712
3713
3714	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3715	# BY EACH CORE INTO ONE FILE
3716	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3717	then
3718	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3719	printf "\n 2d- and/or 3d-data may be incomplete!"
3720	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3721	elif [[ "$combine_plot_fields" == true ]]
3722	then
3723	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3724	then
3725	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3726	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3727	else
3728	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3729	combine_plot_fields${block}.x
3730	fi
3731	else
3732
3733	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3734	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3735	# ??? koennen wir das streichen ???
3736	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3737	fi
3738
3739
3740
3741	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3742	(( i = 0 ))
3743	while (( i < ioc ))
3744	do
3745	(( i = i + 1 ))
3746	if (( i == 1 ))
3747	then
3748	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3749	fi
3750	printf "\n >>> ${out_command[$i]}"
3751	eval ${out_command[$i]}
3752	if (( i == ioc ))
3753	then
3754	printf "\n$dashes\n"
3755	fi
3756	done
3757
3758
3759	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3760	if [[ $do_trace = true ]]
3761	then
3762	printf "\n\n"
3763	ls -al
3764	fi
3765
3766
3767
3768	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3769	(( i = 0 ))
3770	while (( i < iout ))
3771	do
3772	(( i = i + 1 ))
3773	if (( i == 1 ))
3774	then
3775	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3776	fi
3777
3778	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3779	files_for_pes=false; filetyp=file
3780	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3781	then
3782	files_for_pes=true; filetyp=directory
3783	actionout[$i]=""
3784	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3785	then
3786	actionout[$i]=""
3787	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3788	then
3789	files_for_pes=true; filetyp=directory
3790	actionout[$i]="ar"
3791	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3792	then
3793	actionout[$i]="ar"
3794	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3795	then
3796	files_for_pes=true; filetyp=directory
3797	actionout[$i]="fl"
3798	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3799	then
3800	actionout[$i]="fl"
3801	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3802	then
3803	files_for_pes=true; filetyp=directory
3804	actionout[$i]="tr"
3805	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3806	then
3807	actionout[$i]="tr"
3808	fi
3809
3810	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3811	then
3812	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3813	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3814	then
3815	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3816	else
3817
3818
3819	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3820	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3821	if [[ "${actionout[$i]}" = tr ]]
3822	then
3823	if [[ $localhost != $fromhost ]]
3824	then
3825	if [[ $files_for_pes = false ]]
3826	then
3827	cps=""
3828	cst=""
3829	else
3830	cps=-c
3831	cst="/"
3832	fi
3833	if [[ $localhost = nech ]]
3834	then
3835
3836	# TRANSFER IN SEPERATE JOB
3837	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3838	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3839	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3840	if [[ $files_for_pes = false ]]
3841	then
3842	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3843	else
3844	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3845	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3846	fi
3847
3848	echo "set -x" > transfer_${localout[$i]}
3849	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3850
3851	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3852	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3853	printf "\n or higher cycle\n"
3854	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]}
3855
3856	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3857
3858	if [[ $localhost = nech ]]
3859	then
3860	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3861	else
3862	if [[ "$LOGNAME" = b323013 ]]
3863	then
3864	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3865	else
3866	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3867	fi
3868	fi
3869
3870	else
3871
3872	# TRANSFER WITHIN THIS JOB
3873	transfer_failed=false
3874	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3875	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3876	if [[ $localhost = lccrayb ]]
3877	then
3878	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]}"
3879	elif [[ $localhost = lccrayh ]]
3880	then
3881	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]}"
3882	elif [[ $localhost = lcxe6 ]]
3883	then
3884	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]}"
3885	else
3886	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3887	fi
3888	[[ $? != 0 ]] && transfer_failed=true
3889
3890	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3891	if [[ $transfer_failed = true ]]
3892	then
3893	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3894	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3895
3896	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3897	eval local_catalog=${pathout[$i]}
3898	if [[ ! -d $local_catalog ]]
3899	then
3900	printf " *** local directory does not exist. Trying to create:\n"
3901	printf " $local_catalog \n"
3902	mkdir -p $local_catalog
3903	fi
3904	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3905	transfer_problems=true
3906	fi
3907	fi
3908	else
3909
3910	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3911	actionout[$i]=""
3912	fi
3913	fi
3914
3915
3916	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3917	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3918	if [[ "${actionout[$i]}" = tra ]]
3919	then
3920	if [[ $localhost != $fromhost ]]
3921	then
3922	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3923	then
3924
3925	# TRANSFER IN SEPERATE JOB
3926	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3927	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3928	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3929	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3930
3931	echo "set -x" > transfer_${localout[$i]}
3932	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3933
3934	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3935	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3936	printf "\n or higher cycle\n"
3937	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]}
3938
3939	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3940
3941	if [[ $localhost = nech ]]
3942	then
3943	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3944	else
3945	if [[ $LOGNAME = b323013 ]]
3946	then
3947	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3948	else
3949	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3950	fi
3951	fi
3952
3953	else
3954
3955	# TRANSFER WITHIN THIS JOB
3956	transfer_failed=false
3957	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3958	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3959	if [[ $localhost = lccrayb ]]
3960	then
3961	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]}"
3962	elif [[ $localhost = lccrayh ]]
3963	then
3964	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]}"
3965	elif [[ $localhost = lcxe6 ]]
3966	then
3967	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]}"
3968	else
3969	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3970	fi
3971	[[ $? != 0 ]] && transfer_failed=true
3972
3973	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3974	if [[ $transfer_failed = true ]]
3975	then
3976	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3977	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3978
3979	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3980	eval local_catalog=${pathout[$i]}
3981	if [[ ! -d $local_catalog ]]
3982	then
3983	printf " *** local directory does not exist. Trying to create:\n"
3984	printf " $local_catalog \n"
3985	mkdir -p $local_catalog
3986	fi
3987
3988	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3989	transfer_problems=true
3990	fi
3991	fi
3992	else
3993
3994	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3995	actionout[$i]=a
3996	fi
3997	fi
3998
3999
4000	# OUTPUT-FILE FOR A RESTART-RUN.
4001	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4002	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4003	# AS LAST ACTION, ARCHIVING IS INITIATED.
4004	if [[ "${actionout[$i]}" = fl ]]
4005	then
4006	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4007	chmod g+rx $tmp_data_catalog
4008	if [[ $files_for_pes = false ]]
4009	then
4010	printf "\n >>> OUTPUT: ${localout[$i]} to"
4011	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4012	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4013	else
4014	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4015	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4016	mkdir $tmp_data_catalog/${frelout[$i]}
4017	cd ${localout[$i]}
4018	for file in $(ls *)
4019	do
4020	ln -f $file $tmp_data_catalog/${frelout[$i]}
4021	done
4022	cd $TEMPDIR
4023	fi
4024
4025
4026	# CREATE AND SUBMIT ARCHIVING-JOB
4027	if [[ $store_on_archive_system = true ]]
4028	then
4029
4030	if [[ $archive_system = asterix ]]
4031	then
4032	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4033	if [[ $files_for_pes = false ]]
4034	then
4035	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4036	else
4037	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4038	fi
4039	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4040	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4041	echo "then" >> archive_${frelout[$i]}
4042	echo " do_stageout=false" >> archive_${frelout[$i]}
4043	echo "else" >> archive_${frelout[$i]}
4044	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4045	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4046	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4047	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4048	if [[ $files_for_pes = false ]]
4049	then
4050	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4051	else
4052	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4053	fi
4054	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4055	echo "fi" >> archive_${frelout[$i]}
4056	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4057	elif [[ $archive_system = DMF ]]
4058	then
4059	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4060	if [[ $files_for_pes = false ]]
4061	then
4062	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4063	locat=DMF
4064	exit
4065	else
4066	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4067	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4068	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4069	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4070	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4071	fi
4072	elif [[ $archive_system = tivoli ]]
4073	then
4074	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4075	if [[ $files_for_pes = false ]]
4076	then
4077	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4078	echo "set -x" >> archive_${frelout[$i]}
4079	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4080	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4081	else
4082
4083	echo "set -x" >> archive_${frelout[$i]}
4084	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4085	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4086	cd $tmp_data_catalog
4087	all_files=`ls -1 ${frelout[$i]}/*`
4088	cd - > /dev/null
4089	(( inode = 0 ))
4090	(( tp1 = tasks_per_node + 1 ))
4091	while (( inode < nodes ))
4092	do
4093	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4094	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4095	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4096	(( inode = inode + 1 ))
4097	done
4098	fi
4099	elif [[ $archive_system = ut ]]
4100	then
4101	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4102	if [[ $files_for_pes = false ]]
4103	then
4104	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4105	echo "set -x" >> archive_${frelout[$i]}
4106	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4107	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4108	else
4109
4110	echo "set -x" >> archive_${frelout[$i]}
4111	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4112	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4113	cd $tmp_data_catalog
4114	all_files=`ls -1 ${frelout[$i]}/*`
4115	cd - > /dev/null
4116	(( inode = 0 ))
4117	(( tp1 = tasks_per_node + 1 ))
4118	while (( inode < nodes ))
4119	do
4120	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4121	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4122	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4123	(( inode = inode + 1 ))
4124	done
4125	fi
4126	elif [[ $archive_system = none ]]
4127	then
4128	printf " +++ archiving on $localhost not available!\n"
4129	fi
4130
4131	if [[ $archive_system != none ]]
4132	then
4133	if [[ $localhost = nech ]]
4134	then
4135	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4136	fi
4137	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4138	fi
4139	else
4140	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4141	fi
4142
4143
4144	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4145	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4146	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4147	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4148	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4149	if [[ $files_for_pes = false ]]
4150	then
4151	cat /dev/null > ${pathout[$i]}
4152	else
4153	mkdir -p ${pathout[$i]}
4154	fi
4155
4156	fi
4157
4158
4159	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4160	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4161	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4162	if [[ "${actionout[$i]}" = ar ]]
4163	then
4164	if [[ $files_for_pes = false ]]
4165	then
4166	printf "\n >>> OUTPUT: ${localout[$i]} to"
4167	printf "\n ${pathout[$i]}"
4168	printf "\n File will be copied to archive-system ($archive_system) !\n"
4169	else
4170	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4171	printf "\n ${pathout[$i]}"
4172	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4173	fi
4174	mv ${localout[$i]} ${frelout[$i]}
4175
4176	file_saved=false
4177
4178	if [[ $archive_system = asterix ]]
4179	then
4180	do_stageout=true
4181	(( stageout_anz = 0 ))
4182	while [[ $do_stageout = true ]]
4183	do
4184	if [[ $files_for_pes = false ]]
4185	then
4186	stageout ${frelout[$i]} > STAGE_OUTPUT
4187	else
4188	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4189	fi
4190	cat STAGE_OUTPUT
4191	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4192	then
4193	file_saved=true
4194	do_stageout=false
4195	else
4196	if [[ $files_for_pes = false ]]
4197	then
4198	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4199	else
4200	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4201	fi
4202	(( stageout_anz = stageout_anz + 1 ))
4203	if (( stageout_anz == 10 ))
4204	then
4205	printf "\n +++ stoped after 10 unsuccessful tries!"
4206	archive_save=false
4207	do_stageout=false
4208	else
4209	printf "\n *** new try to store on archive after 15 min:"
4210	sleep 900
4211	fi
4212	fi
4213	done
4214	elif [[ $archive_system = DMF ]]
4215	then
4216	if [[ $files_for_pes = false ]]
4217	then
4218	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4219	locat=DMF
4220	exit
4221	else
4222	rm -rf $ARCHIVE/${frelout[$i]}
4223	cp -r ${frelout[$i]} $ARCHIVE
4224	fi
4225	file_saved=true
4226	elif [[ $archive_system = tivoli ]]
4227	then
4228	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4229	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4230	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4231	# WHEN THE ARCHIVE-JOB IS EXECUTED
4232	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4233	chmod g+rx $tmp_data_catalog
4234	if [[ $files_for_pes = false ]]
4235	then
4236	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4237	else
4238	mkdir $tmp_data_catalog/${frelout[$i]}
4239	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4240	fi
4241
4242	# GENERATE AND SUBMIT BATCH-JOB
4243	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4244	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4245	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4246	if [[ $files_for_pes = false ]]
4247	then
4248	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4249	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4250	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4251	else
4252	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4253	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4254	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4255	fi
4256
4257	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4258	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4259	file_saved=true
4260
4261	elif [[ $archive_system = ut ]]
4262	then
4263	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4264	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4265	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4266	# WHEN THE ARCHIVE-JOB IS EXECUTED
4267	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4268	chmod g+rx $tmp_data_catalog
4269	if [[ $files_for_pes = false ]]
4270	then
4271	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4272	else
4273	mkdir $tmp_data_catalog/${frelout[$i]}
4274	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4275	fi
4276
4277	# GENERATE AND SUBMIT BATCH-JOB
4278	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4279	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4280	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4281	if [[ $files_for_pes = false ]]
4282	then
4283	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4284	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4285	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4286	else
4287	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4288	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4289	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4290	fi
4291
4292	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4293	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4294	file_saved=true
4295
4296	else
4297	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4298	archive_save=false
4299	fi
4300
4301	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4302	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4303	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4304	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4305	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4306	if [[ $file_saved = true ]]
4307	then
4308	if [[ $files_for_pes = false ]]
4309	then
4310	cat /dev/null > ${pathout[$i]}
4311	else
4312	mkdir -p ${pathout[$i]}
4313	fi
4314	fi
4315
4316	fi
4317
4318	# APPEND ON THIS MACHINE
4319	if [[ "${actionout[$i]}" = "a" ]]
4320	then
4321	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4322	then
4323	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4324	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4325	else
4326	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4327	cat ${localout[$i]} >> ${pathout[$i]}
4328	fi
4329	fi
4330
4331	# COPY ON THIS MACHINE
4332	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4333	# ON DIFFERENT FILE-SYSTEMS
4334	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4335	then
4336
4337	# COPY IN CASE OF RUNS ON SINGLE CORES
4338	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4339	then
4340	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4341	if [[ $link_local_output = true ]]
4342	then
4343	printf " using ln -f\n"
4344	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4345	fi
4346	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4347	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4348	then
4349	if [[ $link_local_output = true ]]
4350	then
4351	printf " ln failed, using cp...\n"
4352	fi
4353	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4354	fi
4355	else
4356	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4357	if [[ $link_local_output = true ]]
4358	then
4359	printf " using ln -f\n"
4360	ln -f ${localout[$i]} ${pathout[$i]}
4361	fi
4362	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4363	if [[ ! -f "${pathout[$i]}" ]]
4364	then
4365	if [[ $link_local_output = true ]]
4366	then
4367	printf " ln failed, using cp...\n"
4368	fi
4369	cp ${localout[$i]} ${pathout[$i]}
4370	fi
4371	fi
4372
4373	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4374	then
4375
4376	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4377	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4378	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4379	if [[ $link_local_output = true ]]
4380	then
4381	printf " using ln -f\n"
4382	mkdir ${pathout[$i]}
4383	cd ${localout[$i]}
4384	for file in $(ls *)
4385	do
4386	ln -f $file ${pathout[$i]}
4387	done
4388	cd $TEMPDIR
4389	fi
4390
4391	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4392	if [[ ! -f "${pathout[$i]}/_0000" ]]
4393	then
4394	if [[ $link_local_output = true ]]
4395	then
4396	printf " ln failed for .../_0000, using cp...\n"
4397	fi
4398	cp -r ${localout[$i]} ${pathout[$i]}
4399	fi
4400
4401	fi
4402	fi
4403	done
4404	if (( i != 0 ))
4405	then
4406	if [[ $transfer_problems = true ]]
4407	then
4408	printf "\n$dashes\n *** OUTPUT-files saved"
4409	printf "\n +++ WARNING: some data transfers failed! \n"
4410	else
4411	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4412	fi
4413	fi
4414
4415
4416	# IF REQUIRED, START A RESTART-JOB
4417	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4418	if [[ -f CONTINUE_RUN ]]
4419	then
4420
4421	if [[ $archive_save = true ]]
4422	then
4423
4424	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4425	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4426	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4427	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4428	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4429	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4430	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4431	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4432	then
4433	mc=`echo $mc \| sed 's/#/f/g'`
4434	fi
4435
4436
4437	# START THE RESTART-JOB
4438	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4439	echo " $mc"
4440	printf "\n$dashes\n"
4441	if [[ $localhost != $fromhost ]]
4442	then
4443
4444	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4445	then
4446	echo "*** ssh will be used to initiate restart-runs!"
4447	echo " return_address=\"$return_address\" "
4448	echo " return_username=\"$return_username\" "
4449	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4450	then
4451	if [[ $localhost = ibmh ]]
4452	then
4453	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\" "
4454	elif [[ $localhost = lccrayb ]]
4455	then
4456	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\" "
4457	elif [[ $localhost = lccrayh ]]
4458	then
4459	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\" "
4460	elif [[ $localhost = lcxe6 ]]
4461	then
4462	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\" "
4463	else
4464	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 "
4465	fi
4466	else
4467	if [[ $localhost = ibmkisti ]]
4468	then
4469	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\" "
4470	elif [[ $localhost = lcflow ]]
4471	then
4472	/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 "
4473	elif [[ $localhost = lccrayb ]]
4474	then
4475	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\" "
4476	elif [[ $localhost = lccrayh ]]
4477	then
4478	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\" "
4479	else
4480	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4481	fi
4482	fi
4483	else
4484	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4485	locat=restart; exit
4486	fi
4487
4488	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4489	if [[ $queue = special1q ]]
4490	then
4491	sleep 120
4492	else
4493	sleep 30
4494	fi
4495
4496	else
4497
4498	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4499	# USING SSH)
4500	cd $LOCAL_PWD
4501	if [[ $localhost = lckyuh ]]
4502	then
4503	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4504	printf "\n please restart job manually using command:\n"
4505	printf "\n \"$mc\" "
4506	else
4507	eval $mc # THE ' MUST BE EVALUATED
4508	fi
4509	cd - > /dev/null
4510	fi
4511	if [[ $localhost = lckyuh ]]
4512	then
4513	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4514	else
4515	printf "\n$dashes\n *** restart-run initiated \n"
4516	fi
4517
4518
4519	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4520	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4521	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4522	# MAY BE VERY HUGE)
4523	(( i = 0 ))
4524	while (( i < iin ))
4525	do
4526	(( i = i + 1 ))
4527	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4528	then
4529	rm -r $tmp_data_catalog/${frelin[$i]}
4530	fi
4531	done
4532
4533	else
4534
4535	printf "\n +++ no restart-run possible, since errors occured"
4536	printf "\n during the archive process"
4537	fi
4538
4539	fi
4540
4541
4542
4543	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4544	if [[ "$email_notification" != "none" ]]
4545	then
4546
4547	if [[ $localhost != $fromhost ]]
4548	then
4549	if [[ -f CONTINUE_RUN ]]
4550	then
4551	echo "PALM restart run necessary" > email_text
4552	echo "description header of actual run:" >> email_text
4553	cat CONTINUE_RUN >> email_text
4554	echo "mrun-command to restart:" >> email_text
4555	echo "$mc" >> email_text
4556	else
4557	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4558	fi
4559	mail $email_notification < email_text
4560	printf "\n *** email notification sent to \"$email_notification\" "
4561	fi
4562	fi
4563
4564
4565
4566	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4567	cd $HOME
4568	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4569
4570	else
4571
4572
4573	# PREPARING ACTIONS,
4574	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4575
4576	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4577	mrun_com="$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 $remote_username"
4578	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4579	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4580	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4581	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4582	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4583	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4584	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4585	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4586	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4587	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4588	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4589	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4590	if [[ $use_openmp = true ]]
4591	then
4592	mrun_com=${mrun_com}" -O $threads_per_task"
4593	fi
4594	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4595	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4596	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4597	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4598	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4599	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4600	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4601	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4602	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4603	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4604	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4605	if [[ $do_remote = true ]]
4606	then
4607	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4608	fi
4609
4610
4611	# CREATE EXECUTABLE FOR BATCH JOB
4612	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4613	then
4614
4615	printf "\n *** creating the executable for batch job\n"
4616
4617	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4618	if [[ $host != $localhost ]]
4619	then
4620	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4621	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4622	locat=create_executable; exit
4623	fi
4624
4625	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4626	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4627
4628	cp $make_depository .
4629	tar -xf $make_depository > /dev/null 2>&1
4630	cp ../* . > /dev/null 2>&1
4631
4632	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4633
4634	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4635	then
4636	printf "\n +++ error occured while compiling or linking"
4637	locat=compile
4638	exit
4639	fi
4640
4641	mv a.out ..
4642	cd - > /dev/null 2>&1
4643	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4644
4645	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4646
4647	fi
4648
4649
4650	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4651	jobfile=jobfile.$RANDOM
4652
4653
4654	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4655	echo "mkdir $TEMPDIR" >> $jobfile
4656	echo "cd $TEMPDIR" >> $jobfile
4657
4658
4659	# ACTIVATE ERROR-TRACEBACK
4660	if [[ $do_trace = true ]]
4661	then
4662	echo "set -x" >> $jobfile
4663	else
4664	echo "set +vx" >> $jobfile
4665	fi
4666
4667
4668	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4669	if [[ "$init_cmds" != "" ]]
4670	then
4671	echo "$init_cmds" >> $jobfile
4672	fi
4673	if [[ "$module_calls" != "" ]]
4674	then
4675	echo "$module_calls" >> $jobfile
4676	fi
4677
4678
4679	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4680	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4681	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4682	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4683	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4684	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4685	# QUEUEING-SYSTEMS
4686	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4687	then
4688
4689	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4690	if [[ $restart_run != true ]]
4691	then
4692	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4693	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4694	fi
4695
4696	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4697	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4698	echo "set -x" >> $jobfile
4699	if [[ $host = $localhost ]]
4700	then
4701
4702	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4703	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4704	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4705	then
4706	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4707	else
4708	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4709	fi
4710
4711	else
4712	if [[ $host = ibmkisti ]]
4713	then
4714	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4715	echo "localdir=\`pwd\`" >> $jobfile
4716	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4717	elif [[ $host = lccrayb ]]
4718	then
4719	echo "localdir=\`pwd\`" >> $jobfile
4720	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4721	elif [[ $host = lccrayh ]]
4722	then
4723	echo "localdir=\`pwd\`" >> $jobfile
4724	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4725
4726	else
4727	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4728	fi
4729	fi
4730	echo "export SOURCES_COMPLETE=true" >> $jobfile
4731
4732	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4733	# WORKING DIRECTORY OF THE JOB
4734	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4735	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4736	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4737	echo "execute_mrun=true" >> $jobfile
4738	echo " " >> $jobfile
4739
4740	else
4741
4742	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4743	if [[ $do_compile = true ]]
4744	then
4745
4746	source_catalog=SOURCES_FOR_RUN_$fname
4747
4748	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4749	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4750	echo "export SOURCES_COMPLETE=true" >> $jobfile
4751	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4752
4753	for filename in $source_list
4754	do
4755	# BACKSLASH IS USED FOR MASKING
4756	echo "cat > $filename << \"%END%\"" >> $jobfile
4757	cat $source_catalog/$filename >> $jobfile
4758	echo " " >> $jobfile
4759	echo "%END%" >> $jobfile
4760	echo " " >> $jobfile
4761	done
4762
4763	# BACKSLASH IS USED FOR MASKING
4764	echo "cat > Makefile << \"%END%\"" >> $jobfile
4765	cat $source_catalog/Makefile >> $jobfile
4766	echo " " >> $jobfile
4767	echo "%END%" >> $jobfile
4768	echo " " >> $jobfile
4769
4770	echo "cd - > /dev/null" >> $jobfile
4771
4772	fi
4773
4774
4775	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4776	# BACKSLASH IS USED FOR MASKING
4777	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4778	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4779	echo "cat > $config_file << \"%END%\"" >> $jobfile
4780	if [[ $host = lckyuh ]]
4781	then
4782	# NO CROSS-COMPILER ON COMPUTE NODE
4783	sed 's/frtpx/frt/g' $config_file >> $jobfile
4784	else
4785	sed 's/#$.*//g' $config_file >> $jobfile
4786	fi
4787	echo "%END%" >> $jobfile
4788	echo " " >> $jobfile
4789
4790
4791	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4792	# BACKSLASH IS USED FOR MASKING
4793	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4794	if [[ $host = lckyuh ]]
4795	then
4796	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4797	else
4798	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4799	fi
4800	echo "%END%" >> $jobfile
4801	echo "chmod u+x $mrun_script_name" >> $jobfile
4802	echo "execute_mrun=true" >> $jobfile
4803	echo " " >> $jobfile
4804
4805	fi
4806
4807
4808	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4809	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4810	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4811	if [[ $do_remote = true ]]
4812	then
4813	(( i = 0 ))
4814	while (( i < iin ))
4815	do
4816	(( i = i + 1 ))
4817	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4818	if [[ "${transin[$i]}" = job ]]
4819	then
4820	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4821	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4822	echo " " >> $jobfile
4823	echo "%END%" >> $jobfile
4824	else
4825	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4826	fi
4827
4828	# CHECK, IF FILE COULD BE CREATED
4829	echo "if [[ \$? = 1 ]]" >> $jobfile
4830	echo "then" >> $jobfile
4831	echo " echo \" \" " >> $jobfile
4832	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4833	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4834	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4835	echo " execute_mrun=false" >> $jobfile
4836	echo "fi" >> $jobfile
4837	done
4838	fi
4839
4840	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4841	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4842	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4843	echo "LOCAL_PWD=$working_directory" >> $jobfile
4844	echo "export LOCAL_PWD" >> $jobfile
4845
4846	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4847	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4848	echo "export LOCAL_MRUN_PATH" >> $jobfile
4849
4850	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4851	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4852	# then
4853	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4854	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4855	# fi
4856
4857	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4858	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4859	echo "set -x" >> $jobfile
4860	echo "queue=$queue" >> $jobfile
4861	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4862	echo 'ls -al; echo `pwd`' >> $jobfile
4863	echo "cd \$HOME" >> $jobfile
4864	echo "rm -rf $TEMPDIR" >> $jobfile
4865
4866
4867
4868
4869	# START THE JOB USING SUBJOB-COMMAND
4870	if [[ $silent = false ]]
4871	then
4872	printf "\n "
4873	else
4874	printf "\n\n"
4875	fi
4876
4877	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
4878	rm -rf $jobfile
4879
4880
4881	fi # END OF REMOTE-PART

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