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source: palm/trunk/SCRIPTS/mrun @ 1520

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

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