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source: palm/trunk/SCRIPTS/mrun @ 1609

Last change on this file since 1609 was 1609, checked in by maronga, 9 years ago
minor changes in mrun and bugfix in poismg_fast
Property svn:keywords set to `Id Rev`
File size: 178.5 KB

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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	# Modified the random number of the temporary working directory to match the
25	# queuing system number on HLRN-III (lccray*).
26	#
27	# Former revisions:
28	# -----------------
29	# $Id: mrun 1609 2015-07-03 15:37:58Z maronga $
30	#
31	# 1604 2015-06-23 15:48:03Z suehring
32	# Enable coupled runs for lcmuk
33	#
34	# 1598 2015-05-29 06:45:40Z raasch
35	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
36	#
37	# 1549 2015-01-30 14:26:16Z suehring
38	# Enable interactive debug sessions with allinea debugger
39	#
40	# 1547 2015-01-29 15:09:12Z witha
41	# adjustments for ForWind computing cluster (lcflow)
42	#
43	# 1491 2014-11-12 08:12:57Z heinze
44	# correct setting of batch_job allowed for ibm-machines
45	#
46	# 1468 2014-09-24 14:06:57Z maronga
47	# Typo removed (addres->address)
48	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
49	# Added support for restart runs (remote) for lcxe6
50	#
51	# 1442 2014-07-28 07:09:10Z raasch
52	# default queues for HLRN-III (lccrayb/lccrayh) defined
53	#
54	# 1422 2014-07-02 10:01:25Z kanani
55	# automatic restarts enabled for lccrayb,
56	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
57	#
58	# 1420 2014-06-10 06:24:14Z raasch
59	# -j1 option added to aprung command for lccrayf (CSC)
60	#
61	# 1402 2014-05-09 14:25:13Z raasch
62	# batch_job added to envpar-NAMELIST
63	#
64	# 1357 2014-04-11 15:02:03Z witha
65	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
66	# possible)
67	#
68	# 1320 2014-03-20 08:40:49Z raasch
69	# check namelist file set false by default
70	#
71	# 1304 2014-03-12 10:29:42Z raasch
72	# ulimit option changed from -Ss to -s
73	#
74	# bugfix: missing "fi" in r1289
75	#
76	# 1289 2014-03-04 07:12:34Z raasch
77	# comments translated to English
78	# necriam-, fimm-, ibmy-, and sgi-specific code removed
79	# export of variables for palm and interpret_config removed
80	#
81	# 1281 2014-02-01 07:55:49Z raasch
82	# rsync-copy restricted to Cray machines, since command is unavailable on some
83	# other systems
84	#
85	# 1279 2014-01-28 12:10:14Z raasch
86	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
87	# in order to remove annoying restrictions concerning the number of processors which
88	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
89	# restriction, one of the nodes will be filled with less than the given number of
90	# tasks per node. A respective warning is given.
91	#
92	# 1274 2014-01-09 13:14:54Z heinze
93	# adjustments for lccrayh
94	#
95	# 1272 2014-01-08 10:19:32Z witha
96	# small adjustment for lcflow
97	#
98	# 1270 2013-12-16 11:05:01Z fricke
99	# call of combine_plot_fields adjusted for lccrayb/lccrayh
100	#
101	# 1255 2013-11-07 14:43:35Z raasch
102	# further adjustments for lccrayb remote access
103	#
104	# 1241 2013-10-30 11:36:58Z heinze
105	# Enable use of nudging input and input of large scale forcing from
106	# external files
107	#
108	# 1229 2013-09-20 06:55:19Z raasch
109	# further adjustments for lccrayb
110	#
111	# 1224 2013-09-16 07:27:23Z raasch
112	# first adjustments for lccrayb
113	#
114	# 1210 2013-08-14 10:58:20Z raasch
115	# fftw support added
116	#
117	# 1201 2013-07-10 16:17:59Z witha
118	# adjustments for Forwind cluster (lcflow)
119	#
120	# 1199 2013-07-05 14:52:22Z raasch
121	# adjustments for CSC Helsinki (lccrayf),
122	# executables for batch jobs can be created in advance, in order to avoid calling
123	# the compiler within the batch job (only works if batch jobs are submitted on
124	# local host)
125	#
126	# 1190 2013-06-25 09:39:21Z heinze
127	# enable use of automatic restarts for ibmh
128	# use of cluster/express queue enabled (ibmh)
129	#
130	# 1124 2013-04-09 15:46:52Z raasch
131	# variable "memory" is exported via typeset option -x, because otherwise an unknown
132	# side effect may lead to data loss while getopts is reading the script-option arguments
133	#
134	# 1122 2013-04-09 08:37:16Z heinze
135	# Bugfix: change type of variable last_char
136	#
137	# 1119 2013-04-05 15:11:19Z raasch
138	# Bugfix for setting -T option for subjob
139	#
140	# 1108 2013-03-05 07:03:32Z raasch
141	# bugfix for coupled runs on lckyut/lckyuh
142	#
143	# 1106 2013-03-04 05:31:38Z raasch
144	# --stdin argument for mpiexec on lckyuh
145	# -y and -Y settings output to header
146	#
147	# 1103 2013-02-20 02:15:53Z raasch
148	# default script runs again under ksh, because of unsolved problems with read
149	# from stdin: when bash script is called from a ksh, message "read error: 0:
150	# Resource temporarily unavailable" appears and script does not stop,
151	# further bash compatibility adjustments,
152	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
153	# on lckyuh, but mrun does not terminate and issues a warning instead
154	#
155	# 1101 2013-02-17 10:20:21Z raasch
156	# script now running under bash instead of ksh, which required small adjustments
157	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
158	# read from stdin),
159	# cross compilername on lckyuh compute nodes replaced by real compiler name
160	#
161	# 1099 2013-02-10 01:47:43Z raasch
162	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
163	# and for Forwind cluster (lcflow)
164	# small further adjustments for lckyut
165	#
166	# 1094 2013-02-03 01:52:12Z raasch
167	# explicit ssh/scp port can be set in config file with environment variable
168	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
169	# decalpha parts (yonsei) removed
170	#
171	# 2013-02-02 07:06:13Z raasch
172	# adjustments for Kyushu-University computing center (lckyut - tatara)
173	#
174	# 1083 2013-01-04 10:22:09Z maronga
175	# bugfix in parameter file check (read %cpp_options was missing)
176	#
177	# 1069 2012-11-28 16:18:43Z maronga
178	# bugfix: coupling mode was always set to mpi2, typos removed
179	#
180	# 1058 2012-11-21 07:00:35Z raasch
181	# Intel inspector (inspxe) is given the number of PEs instead of the number of
182	# nodes
183	#
184	# 1046 2012-11-09 14:38:45Z maronga
185	# code put under GPL (PALM 3.9)
186	#
187	# 21/03/94 - Siggi - first version finished
188	# 03/03/94 - Siggi - script development started
189	#
190	#--------------------------------------------------------------------------------#
191	# mrun - script for running PALM jobs
192	#--------------------------------------------------------------------------------#
193
194
195
196	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
197
198	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
199	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
200	# (TOO MANY ARGUMENTS - PROBLEM)
201	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
202
203	AddFilenames=""
204	additional_conditions=""
205	add_source_path=""
206	afname=""
207	archive_save=true
208	archive_system=none
209	check_namelist_files=false
210	combine_plot_fields=true
211	compiler_name=""
212	cond1=""
213	cond2=""
214	config_file=.mrun.config
215	coupled_dist=""
216	coupled_mode="mpi1"
217	cpp_opts=""
218	cpp_options=""
219	cpumax=0
220	cpurest=0
221	create_executable_for_batch=false
222	delete_temporary_catalog=true
223	do_batch=false
224	do_compile=true
225	do_remote=false
226	do_stagein=true
227	do_stageout=true
228	do_trace=false
229	email_notification="none"
230	exclude=""
231	executable=""
232	execution_error=false
233	fftw_inc=""
234	fftw_lib=""
235	fftw_support=false
236	fname=test
237	fromhost=""
238	global_revision=""
239	group_number=none
240	host=""
241	host_file=""
242	hp=""
243	ignore_archive_error=false
244	input_list=""
245	interpreted_config_file=""
246	job_catalog="~/job_queue"
247	job_on_file=""
248	keep_data_from_previous_run=false
249	link_local_input=false
250	link_local_output=false
251	localhost_realname=$(hostname)
252	local_dvrserver_running=.FALSE.
253	locat=normal
254	mainprog=""
255	makefile=""
256	max_par_io_str=""
257	mc=$0
258	while [[ $(echo $mc \| grep -c "/") != 0 ]]
259	do
260	mc=`echo $mc \| cut -f2- -d"/"`
261	done
262	module_calls=""
263	mrun_script_name=$mc
264	netcdf_inc=""
265	netcdf_lib=""
266	netcdf_support=false
267	node_usage=default
268	numprocs=""
269	numprocs_atmos=0
270	numprocs_ocean=0
271	OOPT=""
272	openmp=false
273	output_list=""
274	package_list=""
275	queue=none
276	read_from_config=""
277	restart_run=false
278	if [[ `hostname` = rte10 ]]
279	then
280	return_address=133.5.185.60
281	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
282	elif [[ `hostname` = climate0 ]]
283	then
284	return_address=165.132.26.68
285	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
286	elif [[ `hostname` = urban00 ]]
287	then
288	return_address=147.46.30.151
289	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
290	else
291	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
292	fi
293	return_password=""
294	return_username=$LOGNAME
295	remotecall=false
296	remote_username=""
297	run_coupled_model=false
298	run_mode=""
299	store_on_archive_system=false
300	dashes=" ----------------------------------------------------------------------------"
301	silent=false
302	source_list=""
303	source_path=SOURCE
304	tasks_per_node=""
305	threads_per_task=1
306	tmpcreate=false
307	tmp_data_catalog=""
308	transfer_problems=false
309	usern=$LOGNAME
310	use_openmp=false
311	version="MRUN 2.1 Rev$Rev: 1609 $"
312	working_directory=`pwd`
313	TOPT=""
314	XOPT=""
315	zeit=$( date \| cut -c 12-19 )
316
317	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
318	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
319	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
320	# SCRIPT-OPTION ARGUMENTS
321	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
322
323
324
325	# ERROR HANDLING IN CASE OF EXIT
326	trap 'rm -rf $working_directory/tmp_mrun
327	if [[ $locat != normal && $locat != control_c ]]
328	then
329
330	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
331	(( i = 0 ))
332	while (( i < iec ))
333	do
334	(( i = i + 1 ))
335	printf "\n *** Execution of ERROR-command:\n"
336	printf " >>> ${err_command[$i]}\n"
337	eval ${err_command[$i]}
338	done
339	if [[ -n $interpreted_config_file ]]
340	then
341	rm -rf $interpreted_config_file
342	fi
343	if [[ -n .mrun_environment ]]
344	then
345	rm -rf .mrun_environment
346	fi
347	if [[ $tmpcreate = true ]]
348	then
349	printf "\n *** Contents of \"$TEMPDIR\":\n"
350	ls -al; cd
351	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
352	fi
353	if [[ "$dvrserver_id" != "" ]]
354	then
355	echo "+++ killing dvrserver_id=$dvrserver_id"
356	kill $dvrserver_id
357	fi
358	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
359	then
360	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
361	fi
362	printf "\n\n+++ MRUN killed \n\n"
363	elif [[ $locat != control_c ]]
364	then
365	printf "\n\n --> all actions finished\n\n"
366	printf " Bye, bye $usern !!\n\n"
367	fi' exit
368
369
370	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
371	trap 'rm -rf $working_directory/tmp_mrun
372	rm -rf $working_directory/tmp_check_namelist_files
373	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
374	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
375	then
376	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
377	fi
378	if [[ "$dvrserver_id" != "" ]]
379	then
380	echo "+++ killing dvrserver_id=$dvrserver_id"
381	kill $dvrserver_id
382	fi
383	printf "\n+++ MRUN killed by \"^C\" \n\n"
384	locat=control_c
385	exit
386	' 2
387
388
389	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
390	# BEEN SET
391	if [[ "$PALM_BIN" = "" ]]
392	then
393	printf "\n +++ environment variable PALM_BIN has not been set"
394	printf "\n please set it to the directory where the PALM scripts are located"
395	locat=palm_bin; exit
396	fi
397	export PATH=$PALM_BIN:$PATH
398
399
400
401	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
402	# WHICH WILL BE USED TO START RESTART-JOBS
403	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
404	do
405	case $option in
406	(a) afname=$OPTARG;;
407	(A) store_on_archive_system=true; mc="$mc -A";;
408	(b) do_batch=true; mc="$mc -b";;
409	(B) delete_temporary_catalog=false; mc="$mc -B";;
410	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
411	(C) restart_run=true; mc="$mc -C";;
412	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
413	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
414	(F) job_on_file="-D"; mc="$mc -F";;
415	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
416	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
417	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
418	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
419	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
420	(I) ignore_archive_error=true; mc="$mc -I";;
421	(k) keep_data_from_previous_run=true; mc="$mc -k";;
422	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
423	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
424	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
425	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
426	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
427	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
428	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
429	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
430	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
431	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
432	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
433	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
434	(S) read_from_config=false; mc="$mc -S";;
435	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
436	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
437	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
438	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
439	(v) silent=true; mc="$mc -v";;
440	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
441	(x) do_trace=true;set -x; mc="$mc -x";;
442	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
443	(y) ocean_file_appendix=true; mc="$mc -y";;
444	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
445	(z) check_namelist_files=false; mc="$mc -z";;
446	(Z) combine_plot_fields=false; mc="$mc -Z";;
447	(\?) printf "\n +++ unknown option $OPTARG \n"
448	printf "\n --> type \"$0 ?\" for available options \n"
449	locat=parameter;exit;;
450	esac
451	done
452
453
454	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
455	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
456	(( to_shift = $OPTIND - 1 ))
457	shift $to_shift
458
459	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
460	if [[ "$1" = "?" ]]
461	then
462	(printf "\n *** mrun can be called as follows:\n"
463	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"
464	printf "\n Description of available options:\n"
465	printf "\n Option Description Default-Value"
466	printf "\n -a base name of input files equiv. -d"
467	printf "\n -A archiving when using file-attribute fl"
468	printf "\n -b batch-job on local machine ---"
469	printf "\n -B do not delete temporary directory at end ---"
470	printf "\n -c configuration file .mrun.config"
471	printf "\n -d base name of files attached to program test"
472	printf "\n -D preprocessor(cpp)-directives \"\" "
473	printf "\n -F create remote job file only ---"
474	printf "\n -h execution host $localhost_realname"
475	printf "\n -i INPUT control list \"\" "
476	printf "\n -I archiving errors of previous batch-jobs"
477	printf "\n will be ignored"
478	printf "\n -k keep data from previous run"
479	printf "\n -K additional conditions for controling"
480	printf "\n usage of conditional code and"
481	printf "\n env-variables in configuration file \"\" "
482	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
483	printf "\n -M Makefile name Makefile"
484	printf "\n -n node usage (shared/not_shared) depending on -h"
485	printf "\n -o OUTPUT control list \"\" "
486	printf "\n -O threads per openMP task ---"
487	printf "\n -p software package list \"\" "
488	printf "\n -q queue \"$queue\" "
489	printf "\n -r run control list (combines -i -o) \"\" "
490	printf "\n -s filenames of routines to be compiled \"\" "
491	printf "\n must end with .f, .f90, .F, or .c !"
492	printf "\n use \"..\" for more than one file and wildcards"
493	printf "\n -s LM compiles all locally modified files"
494	printf "\n -S config file interpreted by shellscript ---"
495	printf "\n -t allowed cpu-time in seconds (batch) 0"
496	printf "\n -T tasks per node depending on -h"
497	printf "\n -u username on remote machine \"\" "
498	printf "\n -v no prompt for confirmation ---"
499	printf "\n -w maximum parallel io streams as given by -X"
500	printf "\n -x tracing of mrun for debug purposes ---"
501	printf "\n -X # of processors (on parallel machines) 1"
502	printf "\n -y add appendix \"_O\" to all local output"
503	printf "\n files (ocean precursor runs followed by"
504	printf "\n coupled atmosphere-ocean runs) ---"
505	printf "\n -Y run coupled model, \"#1 #2\" with"
506	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
507	printf "\n -z disable a priori parameter file check ---"
508	printf "\n -Z skip combine_plot_fields at the end of "
509	printf "\n the simulation ---"
510	printf "\n "
511	printf "\n Possible values of positional parameter <modus>:"
512	printf "\n \"?\" - this outline \n\n") \| more
513	exit
514	elif [[ "$1" != "" ]]
515	then
516	printf "\n +++ positional parameter $1 unknown \n"
517	locat=parameter; exit
518	fi
519
520
521
522	# SHORT STARTING MESSAGE
523	printf "\n*** $version "
524	printf "\n will be executed. Please wait ..."
525
526
527
528	# CHECK, IF CONFIGURATION FILE EXISTS
529	if [[ ! -f $config_file ]]
530	then
531	printf "\n\n +++ configuration file: "
532	printf "\n $config_file"
533	printf "\n does not exist"
534	locat=connect; exit
535	fi
536
537
538	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
539	line=""
540	grep "%host_identifier" $config_file > tmp_mrun
541	while read line
542	do
543	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
544	then
545	HOSTNAME=`echo $line \| cut -d" " -s -f2`
546	host_identifier=`echo $line \| cut -d" " -s -f3`
547	if [[ $localhost_realname = $HOSTNAME ]]
548	then
549	localhost=$host_identifier
550	break
551	fi
552	fi
553	done < tmp_mrun
554
555	if [[ "$localhost" = "" ]]
556	then
557	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
558	printf "\n for local host \"$localhost_realname\"."
559	printf "\n Please add line"
560	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
561	printf "\n to the configuration file."
562	locat=localhost; exit
563	fi
564
565
566	# SET HOST-SPECIFIC VARIABLES
567	case $localhost_realname in
568	(r1\|r2\|h01\|b01) archive_system=tivoli;;
569	(cs*) archive_system=ut;;
570	esac
571
572
573	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
574	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
575	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
576	[[ "$afname" = "" ]] && afname=$fname
577
578
579	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
580	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
581	# STATEMENTS IN THE CONFIGURATION FILE
582	if [[ "$run_mode" != "" ]]
583	then
584	input_list="$input_list $run_mode"
585	output_list="$output_list $run_mode"
586	fi
587
588
589	# ??? is this (and the respective option -H) really required ???
590	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
591	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
592	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
593	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
594	if [[ "$fromhost" = "" ]]
595	then
596	fromhost=$localhost
597	fi
598
599
600	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
601	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
602	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
603	# TO BE SUBMITTED (I.E. do_batch=true)
604	if [[ -n $host && "$host" != $localhost ]]
605	then
606	do_batch=true
607	do_remote=true
608	case $host in
609	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
610	(*) printf "\n"
611	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
612	printf "\n is not available"
613	locat=nqs; (( iec = 0 )); exit;;
614	esac
615	else
616	host=$localhost
617	fi
618
619
620	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
621	if [[ -n $additional_conditions ]]
622	then
623	cond1=`echo $additional_conditions \| cut -d" " -f1`
624	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
625	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
626	if [[ -n $dummy ]]
627	then
628	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
629	locat=options; exit
630	fi
631	block=_$cond1
632	[[ -n $cond2 ]] && block=${block}_$cond2
633	fi
634
635
636	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
637	if [[ $run_coupled_model = true ]]
638	then
639
640	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
641	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
642
643	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
644	then
645
646	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
647	printf "\n PEs (total) : $numprocs"
648	printf "\n PEs (atmosphere): $numprocs_atmos"
649	printf "\n PEs (ocean) : $numprocs_ocean"
650	locat=coupling; exit
651
652	fi
653
654
655	# GET coupled_mode FROM THE CONFIG FILE
656	line=""
657	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
658	while read line
659	do
660	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
661	then
662	coupled_mode="mpi2"
663	fi
664	done < tmp_mrun
665
666	fi
667
668
669	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
670	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
671	then
672	if [[ $ignore_archive_error = false ]]
673	then
674	printf "\n +++ data archiving of previous run failed"
675	printf "\n see directory \~/job_queue on remote machine"
676	locat=archive; exit
677	else
678	printf "\n +++ warning: data archiving in a previous run failed"
679	printf "\n MRUN continues, trying to get backup copy"
680	fi
681	fi
682
683
684	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
685	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
686	mrun_memory=$memory
687	mrun_group_number=$group_number
688	mrun_cpumax=$cpumax
689	mrun_numprocs=$numprocs
690
691
692	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
693	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
694	if [[ "$read_from_config" = false ]]
695	then
696
697	[[ $silent = false ]] && printf "\n Reading the configuration file... "
698
699	# READ THE CONFIGURATION FILE LINE BY LINE
700	while read zeile
701	do
702	[[ $silent = false ]] && printf "."
703
704
705	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
706	eval zeile=\"$zeile\"
707
708
709	# INTERPRET THE LINE
710	if [[ "$(echo $zeile)" = "" ]]
711	then
712	# EMPTY LINE, NO ACTION
713	continue
714
715	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
716	then
717
718	# LINE IS A COMMENT LINE
719	true
720
721	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
722	then
723
724	# LINE DEFINES AN ENVIRONMENT-VARIABLE
725	zeile=$(echo $zeile \| cut -c2-)
726	var=`echo $zeile \| cut -d" " -f1`
727	value=`echo $zeile \| cut -d" " -s -f2`
728	for_host=`echo $zeile \| cut -d" " -s -f3`
729	for_cond1=`echo $zeile \| cut -d" " -s -f4`
730	for_cond2=`echo $zeile \| cut -d" " -s -f5`
731
732	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
733	then
734
735	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
736	# "::" IS REPLACED BY ":".
737	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
738
739
740	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
741	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
742	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
743	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
744	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
745	# CONFIGURATION-FILE.
746	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
747	then
748	eval $var=\$value
749
750	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
751	if [[ $do_trace = true ]]
752	then
753	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
754	fi
755	fi
756
757	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
758	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
759	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
760	# MUST HAVE TO BE STARTED
761	if [[ $var = host ]]
762	then
763	if [[ -n $host && "$host" != $localhost ]]
764	then
765	do_batch=true
766	do_remote=true
767	case $host in
768	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
769	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
770	printf "\n is not available"
771	locat=nqs; exit;;
772	esac
773	else
774	host=$localhost
775	fi
776	fi
777
778	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
779	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
780	# BY MRUN (E.G. subjob)
781	export $var
782	fi
783
784
785
786
787	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
788	then
789
790	# LINE DEFINES ERROR-COMMAND
791	(( iec = iec + 1 ))
792	zeile=$(echo $zeile \| cut -c4-)
793	err_command[$iec]="$zeile"
794
795	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
796	then
797
798	# LINE DEFINES INPUT-COMMAND
799	(( iic = iic + 1 ))
800	zeile=$(echo $zeile \| cut -c4-)
801	in_command[$iic]="$zeile"
802
803	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
804	then
805
806	# LINE DEFINES OUTPUT-COMMAND
807	(( ioc = ioc + 1 ))
808	zeile=$(echo $zeile \| cut -c4-)
809	out_command[$ioc]="$zeile"
810
811	else
812
813	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
814	# s2a: in/out - field
815	# s2b: loc - field (optional)
816	# s2c: tr/ar - field (optional)
817	s1=`echo $zeile \| cut -d" " -f1`
818	s2=`echo $zeile \| cut -d" " -s -f2`
819	s2a=$(echo $s2 \| cut -d":" -f1)
820	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
821	then
822	s2b=""
823	s2c=""
824	else
825	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
826	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
827	fi
828	s3=`echo $zeile \| cut -d" " -f3`
829	s4=`echo $zeile \| cut -d" " -s -f4`
830	s5=`echo $zeile \| cut -d" " -s -f5`
831	s6=`echo $zeile \| cut -d" " -s -f6`
832
833
834	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
835	# INPUT- OR OUTPUT-LIST.
836	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
837	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
838	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
839	# IS NOT CHECKED AND STORED.
840	IFSALT="$IFS"; IFS="$IFS:"
841	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
842	then
843	found=false
844	for actual in $input_list
845	do
846	for formal in $s3
847	do
848	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
849	done
850	done
851	if [[ $found = true ]]
852	then
853	(( iin = iin + 1 ))
854	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
855	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
856	extin[$iin]=$s6
857	fi
858	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
859	then
860	found=false
861	for actual in $output_list
862	do
863	for formal in $s3
864	do
865	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
866	done
867	done
868	if [[ $found = true ]]
869	then
870	(( iout = iout + 1 ))
871	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
872	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
873	fi
874	elif [[ "$s2a" != in && "$s2a" != out ]]
875	then
876	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
877	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
878	locat=connect; exit
879	fi
880	IFS="$IFSALT"
881	fi
882	done < $config_file
883
884	else
885
886
887	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
888	[[ $silent = false ]] && printf "..."
889	interpreted_config_file=.icf.$RANDOM
890
891
892
893	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
894	cat > .mrun_environment << %%END%%
895	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
896	config_file = '$config_file', do_remote = '$do_remote',
897	do_trace = '$do_trace', host = '$host',
898	input_list = '$input_list', icf = '$interpreted_config_file',
899	localhost = '$localhost', output_list = '$output_list' /
900
901	%%END%%
902
903	if [[ "$host" != $localhost ]]
904	then
905
906	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
907	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
908	if [[ $? != 0 ]]
909	then
910	printf "\n\n +++ no interpret_config found"
911	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
912	locat=interpret_config; exit
913	fi
914	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
915	$interpret_config_executable
916
917	else
918
919	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
920	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
921	then
922	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
923	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
924	locat=interpret_config; exit
925	else
926	interpret_config${block}.x
927	fi
928
929	fi
930	rm .mrun_environment
931
932
933	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
934	chmod u+x $interpreted_config_file
935	export PATH=$PATH:.
936	. $interpreted_config_file
937	rm $interpreted_config_file
938
939	fi
940
941
942	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
943	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
944	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
945	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
946	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
947	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
948	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
949
950
951	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
952	# FOR SOURCE-FILES TO BE COMPILED.
953	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
954	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
955	if [[ "$SOURCES_COMPLETE" = "" ]]
956	then
957
958	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
959	# HAS BEEN DEFINED
960	source_path=""
961	line=""
962	grep "%source_path" $config_file > tmp_mrun
963	while read line
964	do
965	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
966	then
967	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
968	then
969	global_source_path=`echo $line \| cut -d" " -f2`
970	fi
971	fi
972	done < tmp_mrun
973
974	line=""
975	found=false
976	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
977	while read line
978	do
979	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
980	then
981	if [[ $found = true ]]
982	then
983	printf "\n\n +++ more than one source path found in configuration file"
984	printf "\n for local host \"$localhost\" "
985	locat=source_path; exit
986	fi
987	source_path=`echo $line \| cut -d" " -f2`
988	found=true
989	fi
990	done < tmp_mrun
991	rm tmp_mrun
992
993	if [[ "$source_path" = "" ]]
994	then
995	if [[ "$global_source_path" != "" ]]
996	then
997	source_path=$global_source_path
998	else
999	printf "\n\n +++ no source path found in configuration file"
1000	printf "\n for local host \"$localhost\" "
1001	locat=source_path; exit
1002	fi
1003	fi
1004	eval source_path=$source_path
1005
1006	if [[ ! -d $source_path ]]
1007	then
1008	printf "\n\n +++ source path \"$source_path\" on local host"
1009	printf "\n \"$localhost\" does not exist"
1010	locat=source_path; exit
1011	fi
1012
1013	fi
1014
1015
1016	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1017	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1018	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1019	then
1020	global_revision=`svnversion $source_path 2>/dev/null`
1021	global_revision="Rev: $global_revision"
1022	fi
1023
1024
1025	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1026	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1027	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1028	if [[ -n $host && "$host" != $localhost ]]
1029	then
1030	do_batch=true
1031	do_remote=true
1032	case $host in
1033	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1034	(*) printf "\n"
1035	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1036	printf "\n is not available"
1037	locat=nqs; (( iec = 0 )); exit;;
1038	esac
1039	else
1040	host=$localhost
1041	fi
1042
1043
1044	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1045	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1046	then
1047
1048	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1049	if [[ ! -n $numprocs ]]
1050	then
1051	printf "\n"
1052	printf "\n +++ option \"-K parallel\" requires additional specification"
1053	printf "\n of the number of processors to be used by"
1054	printf "\n mrun-option \"-X\" or by environment-variable"
1055	printf "\n \"numprocs\" in the configuration file"
1056	locat=numprocs; (( iec = 0 )); exit
1057	fi
1058
1059	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1060	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1061	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1062	then
1063	printf "\n"
1064	printf "\n +++ option \"-T\" (tasks per node) is missing"
1065	printf "\n set -T option or define tasks_per_node in the config file"
1066	locat=tasks_per_node; (( iec = 0 )); exit
1067	fi
1068
1069	if (( numprocs < tasks_per_node ))
1070	then
1071	printf "\n"
1072	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1073	printf "\n given values: -T $tasks_per_node -X $numprocs"
1074	locat=tasks_per_node; (( iec = 0 )); exit
1075	fi
1076
1077	if [[ $host != lcflow && $host != lcxt5m ]]
1078	then
1079	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1080	(( ival = $tasks_per_node ))
1081	(( pes = numprocs ))
1082	(( ii = pes / ival ))
1083	(( remaining_pes = pes - ii * ival ))
1084	if (( remaining_pes > 0 ))
1085	then
1086	printf "\n"
1087	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1088	printf "\n divisor of the total number of processors (option \"-X\")"
1089	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1090	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1091	(( nodes = nodes + 1 ))
1092	fi
1093	fi
1094
1095
1096	# SETTINGS FOR SUBJOB-COMMAND
1097	OOPT="-O $threads_per_task"
1098
1099	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1100	if [[ "$tasks_per_node" != "" ]]
1101	then
1102	TOPT="-T $tasks_per_node"
1103	fi
1104
1105	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1106	if [[ $node_usage = default ]]
1107	then
1108	if [[ $host = ibms ]]
1109	then
1110	node_usage=shared
1111	else
1112	node_usage=not_shared
1113	fi
1114	fi
1115
1116	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1117	then
1118	printf "\n"
1119	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1120	printf "\n \"shared\" or \"not_shared\""
1121	locat=tasks_per_node; (( iec = 0 )); exit
1122	fi
1123
1124	fi
1125
1126	# CHECK IF HOSTFILE EXISTS
1127	if [[ -n $hostfile ]]
1128	then
1129	if [[ ! -f $hostfile ]]
1130	then
1131	printf "\n"
1132	printf "\n +++ hostfile \"$hostfile\" does not exist"
1133	locat=hostfile; exit
1134	fi
1135	fi
1136
1137
1138	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1139	if [[ "$maximum_parallel_io_streams" = "" ]]
1140	then
1141	maximum_parallel_io_streams=$numprocs
1142	fi
1143
1144
1145	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1146	if [[ "$scp_port" != "" ]]
1147	then
1148	PORTOPT="-P $scp_port"
1149	SSH_PORTOPT="-p $scp_port"
1150	fi
1151
1152
1153	# SET DEFAULT-QUEUE, IF NOT GIVEN
1154	if [[ $queue = none ]]
1155	then
1156	case $host in
1157	(ibmh) queue=cluster;;
1158	(ibmkisti) queue=class.32plus;;
1159	(lccrayb) queue=mpp1q;;
1160	(lccrayh) queue=mpp1q;;
1161	(lckiaps) queue=normal;;
1162	(lckyoto) queue=ph;;
1163	(lckyuh) queue=fx-single;;
1164	(lckyut) queue=cx-single;;
1165	(lctit) queue=S;;
1166	(nech) queue=none;;
1167	(unics) queue=unics;;
1168	esac
1169	fi
1170
1171
1172	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1173	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1174	(( i = 0 ))
1175	while (( i < iin ))
1176	do
1177	(( i = i + 1 ))
1178	(( maxcycle = 0 ))
1179
1180	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1181	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1182	if [[ "${actionin[$i]}" = di ]]
1183	then
1184	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1185	# HOST ONLY
1186	eval filename=${pathin[$i]}/${endin[$i]}
1187	else
1188	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1189	# HOST ONLY
1190	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1191	fi
1192	eval pathname=${pathin[$i]}
1193
1194	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1195	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1196	then
1197	filename_input=$filename
1198	fi
1199
1200	# CHECK IF FILE EXISTS
1201	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1202	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1203	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1204	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1205	then
1206
1207	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1208	if [[ "${transin[$i]}" != "locopt" ]]
1209	then
1210	printf "\n\n +++ INPUT-file: "
1211	if [[ "${extin[$i]}" = "" ]]
1212	then
1213	printf "\n $filename"
1214	else
1215	printf "\n $filename.${extin[$i]}"
1216	fi
1217	printf "\n does not exist\n"
1218	locat=input; exit
1219	else
1220	transin[$i]="unavailable"
1221	fi
1222	else
1223
1224	# DETERMINE THE FILE'S CYCLE NUMBER
1225	ls -1 -d $filename > filelist 2>/dev/null
1226	ls -1 -d $filename.* >> filelist 2>/dev/null
1227	while read zeile
1228	do
1229	cycle=$(echo $zeile \| cut -f2 -d".")
1230	if [[ "$cycle" = "$zeile" ]]
1231	then
1232	(( icycle = 0 ))
1233	elif [[ "$cycle" = "${extin[$i]}" ]]
1234	then
1235	(( icycle = 0 ))
1236	else
1237	(( icycle = $cycle ))
1238	fi
1239	if (( icycle > maxcycle ))
1240	then
1241	(( maxcycle = icycle ))
1242	file_to_be_used=$zeile
1243	fi
1244	done <filelist
1245	rm filelist
1246
1247	# APPEND CYCLE NUMBER TO FILENAME
1248	if (( maxcycle > 0 ))
1249	then
1250	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1251	then
1252	filename=${filename}.$maxcycle.${extin[$i]}
1253	else
1254	filename=${filename}.$maxcycle
1255	fi
1256	else
1257	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1258	then
1259	filename=${filename}.${extin[$i]}
1260	fi
1261	fi
1262
1263	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1264	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1265	absnamein[$i]=$filename
1266	if (( maxcycle > 0 ))
1267	then
1268	if [[ "${actionin[$i]}" = di ]]
1269	then
1270	frelin[$i]=${endin[$i]}.$maxcycle
1271	else
1272	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1273	fi
1274	else
1275	if [[ "${actionin[$i]}" = di ]]
1276	then
1277	frelin[$i]=${endin[$i]}
1278	else
1279	frelin[$i]=${afname}${endin[$i]}
1280	fi
1281	fi
1282
1283	fi
1284	done
1285
1286	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1287	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1288	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1289	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1290	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1291	# REMOTE HOST)
1292	(( i = 0 ))
1293	while (( i < iout ))
1294	do
1295	(( i = i + 1 ))
1296	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1297	then
1298	if [[ "${actionout[$i]}" = tr ]]
1299	then
1300	actionout[$i]=""
1301	elif [[ "${actionout[$i]}" = trpe ]]
1302	then
1303	actionout[$i]=pe
1304	elif [[ "${actionout[$i]}" = tra ]]
1305	then
1306	actionout[$i]=a
1307	fi
1308	(( maxcycle = 0 ))
1309	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1310	eval catalogname=${pathout[$i]}
1311	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1312	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1313	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1314	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1315	then
1316
1317	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1318	if cat /dev/null > $filename
1319	then
1320	rm $filename
1321	else
1322
1323	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1324	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1325	if [[ ! -d $catalogname ]]
1326	then
1327	if mkdir -p $catalogname
1328	then
1329	printf "\n\n *** directory:"
1330	printf "\n $catalogname"
1331	printf "\n was created\n"
1332	else
1333	printf "\n\n +++ OUTPUT-file:"
1334	printf "\n $filename"
1335	printf "\n cannot be created, because directory does not exist"
1336	printf "\n and cannot be created either"
1337	printf "\n"
1338	locat=output ; exit
1339	fi 2>/dev/null
1340	else
1341	printf "\n\n +++ OUTPUT-file:"
1342	printf "\n $filename"
1343	printf "\n cannot be created, although directory exists"
1344	printf "\n"
1345	locat=output ; exit
1346	fi
1347	fi 2>/dev/null
1348	else
1349
1350	# DETERMINE THE CYCLE NUMBER
1351	ls -1 -d $filename > filelist 2>/dev/null
1352	ls -1 -d $filename.* >> filelist 2>/dev/null
1353	while read zeile
1354	do
1355	cycle=$(echo $zeile \| cut -f2 -d".")
1356	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1357	then
1358	(( icycle = 1 ))
1359	else
1360	(( icycle = $cycle + 1 ))
1361	fi
1362	if (( icycle > maxcycle ))
1363	then
1364	(( maxcycle = icycle ))
1365	fi
1366	done <filelist
1367	rm filelist
1368	fi
1369
1370	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1371	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1372	if [[ "${actionout[$i]}" != a ]]
1373	then
1374	if (( maxcycle > 0 ))
1375	then
1376	filename=${filename}.$maxcycle
1377	if cat /dev/null > $filename
1378	then
1379	rm $filename
1380	else
1381	printf "\n +++ OUTPUT-file:"
1382	printf "\n $filename"
1383	printf "\n cannot be created"
1384	locat=output ; exit
1385	fi
1386	fi
1387	else
1388	(( maxcycle = maxcycle - 1 ))
1389	if (( maxcycle > 0 ))
1390	then
1391	filename=${filename}.$maxcycle
1392	fi
1393	fi
1394
1395	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1396	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1397	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1398	pathout[$i]=$filename
1399	if (( maxcycle > 0 ))
1400	then
1401	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1402	else
1403	frelout[$i]=${fname}${endout[$i]}
1404	fi
1405
1406	fi
1407	done
1408
1409
1410	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1411	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1412	then
1413	if [[ "$dvr_inc" = "" ]]
1414	then
1415	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1416	printf "\n This is required for the dvrp_graphics package.\n"
1417	locat=dvr; exit
1418	fi
1419	if [[ "$dvr_lib" = "" ]]
1420	then
1421	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1422	printf "\n This is required for the dvrp_graphics package.\n"
1423	locat=dvr; exit
1424	fi
1425	fi
1426
1427
1428	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1429	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1430	if [[ "$mainprog" = "" && "$executable" = "" ]]
1431	then
1432	printf "\n +++ neither main program nor executable defined"
1433	locat=source; exit
1434	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1435	then
1436	printf "\n +++ main program as well as executable defined"
1437	locat=source; exit
1438	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1439	then
1440	do_compile=false
1441	fi
1442
1443
1444	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1445	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1446	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1447	then
1448	rm -rf SOURCES_FOR_RUN_$fname
1449	mkdir SOURCES_FOR_RUN_$fname
1450	fi
1451
1452
1453	# COLLECT ALL ROUTINES TO BE COMPILED
1454	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1455	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1456	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1457	then
1458
1459	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1460
1461	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1462	then
1463
1464	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1465	source_list=""
1466	cd $source_path
1467
1468
1469	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1470	if [[ ! -d .svn ]]
1471	then
1472	printf "\n\n +++ source directory"
1473	printf "\n \"$source_path\" "
1474	printf "\n is not under control of \"subversion\"."
1475	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1476	fi
1477
1478
1479	# LIST ALL MODIFIED SOURCE CODE FILES
1480	Filenames=""
1481	svn status > tmp_mrun
1482	while read line
1483	do
1484	firstc=`echo $line \| cut -c1`
1485	if [[ $firstc = M \|\| $firstc = "?" ]]
1486	then
1487	Name=`echo "$line" \| cut -c8-`
1488	extension=`echo $Name \| cut -d. -f2`
1489	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1490	then
1491	Filenames="$Filenames "$Name
1492	fi
1493	fi
1494	done < tmp_mrun
1495
1496
1497	# COPY FILES TO SOURCES_FOR_RUN_...
1498	for dateiname in $Filenames
1499	do
1500	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1501	source_list=$source_list"$dateiname "
1502	done
1503
1504	cd - > /dev/null
1505
1506
1507	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1508	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1509	elif [[ "$source_list" != "" && $restart_run != true ]]
1510	then
1511
1512	cd $source_path
1513
1514	for filename in $source_list
1515	do
1516
1517	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1518	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1519	then
1520	printf "\n +++ source code file: $filename"
1521	printf "\n must not contain (\"/\") "
1522	locat=source; exit
1523	fi
1524
1525	if [[ ! -f $filename ]]
1526	then
1527	printf "\n +++ source code file: $filename"
1528	printf "\n does not exist"
1529	locat=source; exit
1530	else
1531	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1532	fi
1533
1534	done
1535
1536	cd - > /dev/null
1537
1538	fi
1539
1540
1541	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1542	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1543	if [[ $restart_run != true ]]
1544	then
1545
1546	if [[ ! -f "$source_path/$mainprog" ]]
1547	then
1548	printf "\n\n +++ main program: $mainprog"
1549	printf "\n does not exist in source directory"
1550	printf "\n \"$source_path\"\n"
1551	locat=source; exit
1552	else
1553	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1554	then
1555	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1556	source_list=${mainprog}" $source_list"
1557	fi
1558	fi
1559	fi
1560
1561
1562	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1563	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1564	if [[ "$restart_run" != true ]]
1565	then
1566	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1567	if [[ ! -f $makefile ]]
1568	then
1569	printf "\n +++ file \"$makefile\" does not exist"
1570	locat=make; exit
1571	else
1572	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1573	fi
1574	fi
1575
1576
1577	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1578	if [[ $restart_run != true && "$add_source_path" != "" ]]
1579	then
1580
1581	# DOES THE DIRECTORY EXIST?
1582	if [[ ! -d $add_source_path ]]
1583	then
1584	printf "\n\n +++ WARNING: additional source code directory"
1585	printf "\n \"$add_source_path\" "
1586	printf "\n does not exist or is not a directory."
1587	printf "\n No source code will be used from this directory!\n"
1588	add_source_path=""
1589	if [[ $silent == false ]]
1590	then
1591	sleep 3
1592	fi
1593	else
1594
1595	cd $add_source_path
1596	found=false
1597
1598	Names=$(ls -1 *.f90 2>&1)
1599	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1600	Names=$(ls -1 *.F90 2>&1)
1601	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1602	Names=$(ls -1 *.F 2>&1)
1603	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1604	Names=$(ls -1 *.f 2>&1)
1605	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1606	Names=$(ls -1 *.c 2>&1)
1607	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1608
1609	cd - > /dev/null
1610	cd SOURCES_FOR_RUN_$fname
1611
1612	# COPY MAKEFILE IF EXISTING
1613	if [[ -f $add_source_path/Makefile ]]
1614	then
1615	printf "\n\n *** user Makefile from directory"
1616	printf "\n \"$add_source_path\" is used \n"
1617	if [[ $silent == false ]]
1618	then
1619	sleep 1
1620	fi
1621	cp $add_source_path/Makefile .
1622	fi
1623
1624	for dateiname in $AddFilenames
1625	do
1626	if [[ -f $dateiname ]]
1627	then
1628	printf "\n +++ source code file \"$dateiname\" found in additional"
1629	printf "\n source code directory \"$add_source_path\" "
1630	printf "\n but was also given with option \"-s\" which means that it should be taken"
1631	printf "\n from directory \"$source_path\"."
1632	locat=source; exit
1633	fi
1634
1635	cp $add_source_path/$dateiname .
1636	source_list="$source_list $dateiname"
1637
1638	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1639	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1640	then
1641	printf "\n\n +++ user file \"$dateiname\" "
1642	printf "\n is not listed in Makefile \n"
1643	locat=source; exit
1644	else
1645
1646	if [[ $found = false ]]
1647	then
1648	found=true
1649	printf "\n\n *** following user file(s) added to the"
1650	printf " files to be translated:\n "
1651	fi
1652	printf "$dateiname "
1653	if [[ $silent == false ]]
1654	then
1655	sleep 0.5
1656	fi
1657
1658	fi
1659	done
1660	[[ $found = true ]] && printf "\n"
1661	cd - > /dev/null
1662	fi
1663	fi
1664
1665
1666	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1667	# TO THE LIST OF FILES TO BE COMPILED
1668	if [[ $restart_run != true && -n $package_list ]]
1669	then
1670
1671	cd $source_path
1672
1673	for package in $package_list
1674	do
1675
1676	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1677
1678	# DETERMINE FILES BELONGING TO THE PACKAGE
1679	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1680	# THE NAME OF THE DIRECTORY
1681	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1682
1683
1684	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1685	# IF THEY ARE NOT ALREADY PART OF THE LIST
1686	for source_list_name in $package_source_list
1687	do
1688	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1689	then
1690
1691	# ONLY TAKE FILES WITH VALID SUFFIX
1692	ending=`echo $source_list_name \| cut -f2 -d.`
1693	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1694	then
1695	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1696	source_list="$source_list $source_list_name"
1697	fi
1698	fi
1699	done
1700	done
1701
1702	cd - > /dev/null
1703	fi
1704
1705	fi # do_compile=true
1706
1707
1708	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1709	# AND SET PRE-PROCESSOR DIRECTIVES
1710	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1711	then
1712
1713	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1714	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1715	then
1716	cpp_options="${cpp_options},-D__ibm=__ibm"
1717	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1718	then
1719	cpp_options="$cpp_options -D__nec"
1720	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1721	then
1722	cpp_options="$cpp_options -D__lc"
1723	else
1724	cpp_options="$cpp_options -D__$localhost"
1725	fi
1726
1727	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1728	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1729	then
1730	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1731	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1732	else
1733	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1734	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1735	fi
1736
1737	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1738	if [[ -n $package_list ]]
1739	then
1740	for package in $package_list
1741	do
1742	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1743	then
1744	if [[ $package != "dvrp_graphics+1PE" ]]
1745	then
1746	cpp_options="${cpp_options},-D__$package=__$package"
1747	else
1748	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1749	export use_seperate_pe_for_dvrp_output=true
1750	fi
1751	else
1752	if [[ $package != "dvrp_graphics+1PE" ]]
1753	then
1754	cpp_options="$cpp_options -D__$package"
1755	else
1756	cpp_options="$cpp_options -D__dvrp_graphics"
1757	export use_seperate_pe_for_dvrp_output=true
1758	fi
1759	fi
1760	done
1761	fi
1762
1763	# SET DIRECTIVES GIVEN BY OPTION -D
1764	if [[ -n $cpp_opts ]]
1765	then
1766	for popts in $cpp_opts
1767	do
1768	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1769	then
1770	cpp_options="${cpp_options},-D__$popts=__$popts"
1771	else
1772	cpp_options="$cpp_options -D__$popts"
1773	fi
1774	done
1775	fi
1776
1777	else
1778
1779
1780	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1781	if [[ $do_remote = false ]]
1782	then
1783	if [[ ! -f $executable ]]
1784	then
1785	printf "\n +++ executable file: $executable"
1786	printf "\n does not exist"
1787	locat=executable; exit
1788	fi
1789	fi
1790	fi
1791
1792
1793	# DETERMINE THE JOB MODE
1794	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1795	then
1796	if [[ "$LOADLBATCH" = yes ]]
1797	then
1798	batch_job=.TRUE.
1799	jobmo=BATCH
1800	else
1801	batch_job=.FALSE.
1802	jobmo=INTERACTIVE
1803	fi
1804	else
1805	if [[ "$ENVIRONMENT" = BATCH ]]
1806	then
1807	batch_job=.TRUE.
1808	jobmo=BATCH
1809	else
1810	batch_job=.FALSE.
1811	jobmo=INTERACTIVE
1812	fi
1813	fi
1814
1815	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1816	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1817	then
1818	printf "\n +++ no interactive runs allowed on host \"$host\" "
1819	printf "\n please submit batch job using mrun option \"-b\" \n"
1820	locat=normal; exit
1821	fi
1822
1823
1824	# CHECK, IF USER DEFINED A COMPILER
1825	if [[ "$compiler_name" = "" ]]
1826	then
1827
1828	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1829	locat=compiler_name; exit
1830
1831	fi
1832
1833
1834	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1835
1836	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1837	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1838	then
1839	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1840	else
1841	kennung=$RANDOM
1842	fi
1843
1844	if [[ "$tmp_user_catalog" = "" ]]
1845	then
1846	if [[ $localhost = ibmh ]]
1847	then
1848	tmp_user_catalog=$SCRATCH
1849	elif [[ $localhost = nech ]]
1850	then
1851	tmp_user_catalog=$WRKSHR
1852	else
1853	tmp_user_catalog=/tmp
1854	fi
1855	fi
1856	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1857
1858
1859	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1860	if [[ "$tmp_data_catalog" = "" ]]
1861	then
1862	if [[ $localhost = nech ]]
1863	then
1864	tmp_data_catalog=$WRKSHR/mrun_restart_data
1865	else
1866	tmp_data_catalog=/tmp/mrun_restart_data
1867	fi
1868	fi
1869
1870
1871	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1872	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1873	then
1874	eval fopts=\"$fopts\"
1875	eval lopts=\"$lopts\"
1876	fi
1877
1878
1879
1880	# DETERMINE COMPILE- AND LINK-OPTIONS
1881	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1882	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1883	ROPTS="$ropts"
1884	# 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 ]]
1885	# then
1886	XOPT="-X $numprocs"
1887	# fi
1888
1889
1890
1891	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1892	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1893	done=false
1894	while [[ $done = false ]]
1895	do
1896	cputime=$cpumax
1897	if (( $cputime == 0 ))
1898	then
1899	if [[ $do_batch = true ]]
1900	then
1901	printf "\n +++ cpu-time is undefined"
1902	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1903	printf "\n >>> "
1904	read cputime 1>/dev/null 2>&1
1905	else
1906	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1907	fi
1908	else
1909	done=true
1910	fi
1911	cpumax=$cputime
1912	done
1913
1914	(( minuten = cputime / 60 ))
1915	(( sekunden = cputime - minuten * 60 ))
1916
1917
1918	# CHECK THE MEMORY DEMAND
1919	if [[ $do_batch = true ]]
1920	then
1921	done=false
1922	while [[ $done = false ]]
1923	do
1924	if (( memory == 0 ))
1925	then
1926	printf "\n +++ memory demand is undefined"
1927	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1928	printf "\n >>> "
1929	read memory 1>/dev/null 2>&1
1930	else
1931	done=true
1932	fi
1933	done
1934	fi
1935
1936
1937	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1938	if [[ $do_remote = true && -z $remote_username ]]
1939	then
1940	while [[ -z $remote_username ]]
1941	do
1942	printf "\n +++ username on remote host \"$host\" is undefined"
1943	printf "\n >>> Please type username:"
1944	printf "\n >>> "
1945	read remote_username
1946	done
1947	mc="$mc -u$remote_username"
1948	fi
1949
1950	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1951	if [[ "$login_init_cmd" != "" ]]
1952	then
1953	export init_cmds="${login_init_cmd};"
1954	fi
1955
1956
1957	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1958	if [[ "$modules" != "" ]]
1959	then
1960	if [[ $host = lctit ]]
1961	then
1962	export module_calls=". $modules"
1963	else
1964	export module_calls="module load ${modules};"
1965	fi
1966	fi
1967
1968
1969
1970	# OUTPUT OF THE MRUN-HEADER
1971	calltime=$(date)
1972	printf "\n"
1973	printf "#------------------------------------------------------------------------# \n"
1974	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1975	printf "\| \| \n"
1976	spalte1="called on:"; spalte2=$localhost_realname
1977	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1978	if [[ $do_remote = true ]]
1979	then
1980	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1981	else
1982	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1983	fi
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	if [[ -n $numprocs ]]
1986	then
1987	if [[ $run_coupled_model = false ]]
1988	then
1989	spalte1="number of PEs:"; spalte2=$numprocs
1990	else
1991	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1992	fi
1993	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1994	fi
1995	if [[ -n $tasks_per_node ]]
1996	then
1997	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1998	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1999	if (( remaining_pes > 0 ))
2000	then
2001	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2002	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2003	fi
2004	fi
2005	if [[ $maximum_parallel_io_streams != $numprocs ]]
2006	then
2007	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2008	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2009	fi
2010	if [[ $use_openmp = true ]]
2011	then
2012	spalte1="threads per task:"; spalte2="$threads_per_task"
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	fi
2015	printf "\| \| \n"
2016	if [[ $do_compile = true ]]
2017	then
2018	if [[ "$mopts" != "" ]]
2019	then
2020	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	zeile=$(echo "$mopts" \| cut -c46-)
2023	while [[ "$zeile" != "" ]]
2024	do
2025	spalte1=""
2026	spalte2=$(echo "$zeile" \| cut -c-45)
2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2028	zeile=$(echo "$zeile" \| cut -c46-)
2029	done
2030	fi
2031
2032	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	zeile=$(echo "$cpp_options" \| cut -c46-)
2035	while [[ "$zeile" != "" ]]
2036	do
2037	spalte1=""
2038	spalte2=$(echo "$zeile" \| cut -c-45)
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	zeile=$(echo "$zeile" \| cut -c46-)
2041	done
2042
2043	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	zeile=$(echo "$fopts" \| cut -c46-)
2046	while [[ "$zeile" != "" ]]
2047	do
2048	spalte1=""
2049	spalte2=$(echo "$zeile" \| cut -c-45)
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	zeile=$(echo "$zeile" \| cut -c46-)
2052	done
2053
2054	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2055	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2056	zeile=$(echo "$lopts" \| cut -c46-)
2057	while [[ "$zeile" != "" ]]
2058	do
2059	spalte1=""
2060	spalte2=$(echo "$zeile" \| cut -c-45)
2061	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2062	zeile=$(echo "$zeile" \| cut -c46-)
2063	done
2064
2065	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2066	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2067	zeile=$(echo "$modules" \| cut -c46-)
2068	while [[ "$zeile" != "" ]]
2069	do
2070	spalte1=""
2071	spalte2=$(echo "$zeile" \| cut -c-45)
2072	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2073	zeile=$(echo "$zeile" \| cut -c46-)
2074	done
2075
2076	spalte1="main program:"; spalte2=$mainprog
2077	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2078	else
2079	spalte1=executable:; spalte2=$executable
2080	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2081	fi
2082	printf "\| \| \n"
2083	spalte1="base name of files:"; spalte2=$fname
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085	if [[ $fname != $afname ]]
2086	then
2087	spalte1="base name of input files:"; spalte2=$afname
2088	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2089	fi
2090	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2091	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2092	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2093	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2094
2095	if [[ "$ocean_file_appendix" = true ]]
2096	then
2097	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2098	fi
2099
2100	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2101	then
2102	spalte1="memory demand / PE":; spalte2="$memory MB"
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2105	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2106	fi
2107
2108	if [[ $do_compile = true ]]
2109	then
2110	printf "\| \| \n"
2111	printf "\| Files to be compiled: \| \n"
2112	zeile=$source_list
2113	while [[ "$zeile" != "" ]]
2114	do
2115	linestart=$(echo $zeile \| cut -c-70)
2116	printf "\| %-70s \| \n" "$linestart"
2117	zeile=$(echo "$zeile" \| cut -c71-)
2118	done
2119	fi
2120	printf "#------------------------------------------------------------------------#"
2121
2122
2123
2124	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2125	if [[ $do_trace = true ]]
2126	then
2127	(( i = 0 ))
2128	while (( i < iin ))
2129	do
2130	(( i = i + 1 ))
2131	if (( i == 1 ))
2132	then
2133	printf "\n\n >>> INPUT-file assignments:\n"
2134	fi
2135	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2136	done
2137	(( i = 0 ))
2138	while (( i < iout ))
2139	do
2140	(( i = i + 1 ))
2141	if (( i == 1 ))
2142	then
2143	printf "\n\n >>> OUTPUT-file assignments:\n"
2144	fi
2145	printf "\n ${localout[$i]} : ${pathout[$i]}"
2146	done
2147	(( i = 0 ))
2148	while (( i < iic ))
2149	do
2150	(( i = i + 1 ))
2151	if (( i == 1 ))
2152	then
2153	printf "\n\n >>> INPUT-commands:\n"
2154	fi
2155	printf "\n ${in_command[$i]}"
2156	done
2157	(( i = 0 ))
2158	while (( i < ioc ))
2159	do
2160	(( i = i + 1 ))
2161	if (( i == 1 ))
2162	then
2163	printf "\n\n >>> OUTPUT-commands:\n"
2164	fi
2165	printf "\n ${out_command[$i]}"
2166	done
2167	fi
2168
2169
2170	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2171	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2172	then
2173	antwort=dummy
2174	printf "\n\n"
2175	printf " >>> everything o.k. (y/n) ? "
2176	while read antwort
2177	do
2178	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2179	then
2180	printf " >>> everything o.k. (y/n) ? "
2181	else
2182	break
2183	fi
2184	done
2185	if [[ $antwort = n \|\| $antwort = N ]]
2186	then
2187	locat=user_abort; (( iec = 0 )); exit
2188	fi
2189	if [[ $do_batch = true ]]
2190	then
2191	printf " >>> batch-job will be created and submitted"
2192	else
2193	printf " >>> MRUN will now continue to execute on this machine"
2194	fi
2195	fi
2196
2197
2198	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2199	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2200	check_depository="${working_directory}/trunk/UTIL"
2201	check_sources="${working_directory}/tmp_check_namelist_files"
2202	skip_check=false
2203
2204	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2205	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2206	then
2207	skip_check=true
2208	reason="run on remote host or parameter file check has not been compiled."
2209	fi
2210	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2211	then
2212	skip_check=true
2213	reason="parameter file check has not been compiled."
2214	fi
2215
2216	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2217	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2218	then
2219	skip_check=true
2220	reason="serial run."
2221	fi
2222
2223	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2224	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2225	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2226	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2227	if [[ $check_namelist_files == false ]]
2228	then
2229	skip_check=true
2230	reason="-z option set."
2231	fi
2232
2233	if [[ $fromhost != $localhost ]]
2234	then
2235	skip_check=true
2236	reason="submitting host is local host."
2237	fi
2238
2239	if [[ $run_coupled_model == true ]]
2240	then
2241	skip_check=true
2242	reason="coupled run."
2243	fi
2244
2245	if [[ $restart_run == true ]]
2246	then
2247	skip_check=true
2248	reason="restart run."
2249	fi
2250
2251	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2252	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2253	last_char=`echo $filename_input \| cut -c $last_char_int`
2254	if [[ "$last_char" == "f" ]]
2255	then
2256	skip_check=true
2257	reason="restart run."
2258	fi
2259
2260	if [[ $skip_check == false ]]
2261	then
2262	tmp_check=${working_directory}/tmp_check
2263
2264	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2265	# NOT NECESSARILY REQUIRED
2266	line=""
2267	found=false
2268	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2269	while read line1
2270	do
2271	line="$line1"
2272	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2273	then
2274	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2275	found=true
2276	fi
2277	done < $tmp_check
2278
2279	if [[ $found = false ]]
2280	then
2281	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2282	fi
2283
2284	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2285	# NOT NECESSARILY REQUIRED
2286	line=""
2287	found=false
2288	grep "NUDGING_DATA" $config_file > $tmp_check
2289	while read line1
2290	do
2291	line="$line1"
2292	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2293	then
2294	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2295	found=true
2296	fi
2297	done < $tmp_check
2298
2299	if [[ $found = false ]]
2300	then
2301	printf "\n +++ no NUDGING list entry found in the configuration file."
2302	fi
2303
2304	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2305	# NOT NECESSARILY REQUIRED
2306	line=""
2307	found=false
2308	grep "LSF_DATA" $config_file > $tmp_check
2309	while read line1
2310	do
2311	line="$line1"
2312	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2313	then
2314	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2315	found=true
2316	fi
2317	done < $tmp_check
2318
2319	if [[ $found = false ]]
2320	then
2321	printf "\n +++ no LSF list entry found in the configuration file."
2322	fi
2323
2324	rm -rf ${working_directory}/tmp_check
2325
2326	# CHECK IF THE P3DF FILE MUST BE CHECKED
2327	for item in $input_list
2328	do
2329	if [[ "$item" == "restart" ]]
2330	then
2331	check_restart=1
2332	else
2333	check_restart=0
2334	fi
2335	done
2336
2337	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2338	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2339	then
2340	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2341	locat=check_namelist; exit
2342	fi
2343
2344	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2345	if [[ $check_restart == 1 ]]
2346	then
2347
2348	filenamef="${filename_input}f"
2349	if [[ ! -f $filenamef ]]
2350	then
2351	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2352	check_restart=0
2353	answer=dummy
2354	printf "\n\n"
2355
2356	if [[ $silent == false ]]
2357	then
2358	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2359	do
2360	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2361	read answer
2362	done
2363	if [[ $answer = a \|\| $answer = A ]]
2364	then
2365	printf "\n +++ Aborting...."
2366	locat=normal; exit
2367	fi
2368	fi
2369	else
2370	check_restart=1
2371	fi
2372	fi
2373
2374	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2375	mkdir $check_sources
2376	cd $check_sources
2377
2378
2379	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2380	if [[ -d $add_source_path ]]
2381	then
2382	printf "\n\n *** copying files from $check_depository"
2383	cp $check_depository/check_namelist_files.tar ./
2384
2385	printf "\n\n *** untar of makefile and source files in $check_sources"
2386	tar -xf check_namelist_files.tar > /dev/null 2>&1
2387
2388	printf "\n\n *** adding user code."
2389	cp $add_source_path/* ./
2390	touch check_namelist_files.f90
2391
2392	# GET COMPILER OPTIONS AND PERFORM MAKE
2393	printf "\n\n *** compiling code if necessary...\n"
2394
2395	# workaround for batch jobs on local machine (lcxe6)
2396	if [[ $do_batch == true && $do_remote == false ]]
2397	then
2398	eval $init_cmds
2399	fi
2400
2401	# GET CHECK OPTIONS
2402	line=""
2403	found=false
2404
2405	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2406
2407	while read line1
2408	do
2409
2410	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2411	then
2412	line="$line1"
2413	fi
2414
2415	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2416	then
2417	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2418	line="$line "
2419	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'`
2420	found=true
2421	fi
2422
2423	done < $tmp_check
2424	copts_check="$copts_check -D__check -D__parallel"
2425
2426	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2427
2428	# GET MAKE OUTPUT
2429	if [[ $? != 0 ]]
2430	then
2431	printf "\n +++ error during make."
2432	answer=dummy
2433	printf "\n\n"
2434	if [[ $silent == false ]]
2435	then
2436	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2437	do
2438	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2439	read answer
2440	done
2441	if [[ $answer = a \|\| $answer = A ]]
2442	then
2443	printf "\n +++ Aborting..."
2444	rm -rf $check_sources
2445	locat=normal; exit
2446	else
2447	skip_check=true
2448	fi
2449	else
2450	skip_check=true
2451	fi
2452	fi
2453	else
2454	cp $PALM_BIN/check_namelist_files.x ./
2455	fi
2456
2457	cp $filename_input ./PARIN
2458	if [[ $check_restart == 1 ]]
2459	then
2460	cp $filenamef ./PARINF
2461	fi
2462
2463	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2464	then
2465	printf "\n *** adding topography data"
2466	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2467
2468	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2469	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2470	# WHICH REQUIRE SUFFICIENT MEMORY
2471	ulimit -s unlimited
2472	fi
2473
2474	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2475	then
2476	printf "\n *** adding nudging data"
2477	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2478	fi
2479
2480	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2481	then
2482	printf "\n *** adding large scale forcing data"
2483	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2484	fi
2485
2486	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2487	cat > ENVPAR << %%END%%
2488	&envpar run_identifier = '$fname', host = '$host',
2489	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2490	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2491	maximum_cpu_time_allowed = ${cpumax}.,
2492	revision = '$global_revision',
2493	local_dvrserver_running = $local_dvrserver_running /
2494
2495	%%END%%
2496
2497	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2498	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2499	then
2500	printf "\n +++ WARNING: check_namelist_files.x not found."
2501	answer=dummy
2502	printf "\n\n"
2503
2504	if [[ $silent == false ]]
2505	then
2506	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2507	do
2508	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2509	read answer
2510	done
2511	if [[ $answer = a \|\| $answer = A ]]
2512	then
2513	printf "\n +++ Aborting..."
2514	rm -rf $check_sources
2515	locat=normal; exit
2516	else
2517	printf "\n *** skipping parameter file check."
2518	fi
2519	fi
2520
2521	elif [[ $skip_check == false ]]
2522	then
2523	# STARTING THE PARAMETER FILE CHECK
2524	printf "\n\n *** starting parameter file check..."
2525
2526	# CHECKING THE P3D FILE
2527	printf "\n\n (1) checking $filename_input"
2528	echo "$numprocs 0 0" > VARIN
2529	errors=`./check_namelist_files.x < VARIN 2>&1`
2530
2531	check_error=false
2532	if [[ "$errors" == "" ]]
2533	then
2534	printf " --> o.k."
2535	else
2536	printf " --> failed."
2537	check_error=true
2538	printf "\n\n $errors"
2539	fi
2540
2541	# CHECKING THE PD3F FILE IF NECESSARY
2542	if [[ $check_restart == 1 && $check_error == false ]]
2543	then
2544	printf "\n\n (2) checking $filenamef"
2545
2546	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2547	# IN &INIPAR LIST
2548	found=false
2549	cat PARINF \| while read line
2550	do
2551	line=$(echo $line\|sed 's/ //g')
2552	if [[ $line == "&inipar" ]]
2553	then
2554	start_search=true
2555	fi
2556
2557	if [[ $start_search == true ]]
2558	then
2559	if [[ $line == "initializing_actions='read_restart_data'" ]]
2560	then
2561	found=true
2562	break
2563	fi
2564	fi
2565
2566	if [[ $line == "/" ]]
2567	then
2568	start_search=false
2569	fi
2570
2571	done
2572
2573	if [[ $found = false ]]
2574	then
2575	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2576	printf "\n in &inipar list in $fname$p3df_suffix."
2577	rm -rf $check_sources
2578	locat=check_namelist; exit
2579	fi
2580
2581	# READ max_user_pr FROM FILES
2582	if [[ -f parin_for_check ]]
2583	then
2584	read max_pr_user < parin_for_check
2585	else
2586	max_user_pr=0
2587	fi
2588
2589	echo "$numprocs 1 $max_pr_user" > VARIN
2590	errors=`./check_namelist_files.x < VARIN 2>&1`
2591
2592	if [[ "$errors" == "" ]]
2593	then
2594	printf " --> o.k."
2595	else
2596	printf " --> failed."
2597	check_error=true
2598	printf "\n\n $errors"
2599	fi
2600	fi
2601
2602	# REPORT ERRORS AND CONTINUE/EXIT
2603	if [[ $check_error == true ]]
2604	then
2605	printf "\n +++ errors found in the parameter file!\n"
2606	answer=dummy
2607	printf "\n\n"
2608
2609	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2610	do
2611	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2612	read answer
2613	done
2614
2615	if [[ $answer = a \|\| $answer = A ]]
2616	then
2617	printf "\n +++ Aborting..."
2618	rm -rf $check_sources
2619	locat=normal; exit
2620	fi
2621	else
2622	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2623	fi
2624	rm -rf $check_sources
2625	fi
2626	else
2627	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2628	fi
2629
2630	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2631	rm -rf $check_sources
2632	cd $working_directory
2633
2634
2635	# DETERMINE PATH FOR MAKE DEPOSITORY
2636	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2637	then
2638
2639	line=""
2640	grep "%depository_path" $config_file > tmp_mrun
2641	while read line
2642	do
2643	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2644	then
2645	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2646	then
2647	global_depository_path=`echo $line \| cut -d" " -s -f2`
2648	fi
2649	fi
2650	done < tmp_mrun
2651
2652	line=""
2653	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2654	while read line
2655	do
2656	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2657	then
2658	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2659	then
2660	local_depository_path=`echo $line \| cut -d" " -s -f2`
2661	fi
2662	fi
2663	done < tmp_mrun
2664
2665	if [[ "$local_depository_path" = "" ]]
2666	then
2667	if [[ "$global_depository_path" != "" ]]
2668	then
2669	local_depository_path=$global_depository_path
2670	else
2671	printf "\n\n +++ no depository path found in configuration file"
2672	printf "\n for local host \"$localhost\" "
2673	printf "\n please set \"\%depository_path\" in configuration file\n"
2674	locat=config_file; exit
2675	fi
2676	fi
2677	eval local_depository_path=$local_depository_path
2678	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2679	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2680
2681
2682	basename=`echo $mainprog \| cut -f1 -d"."`
2683	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2684	if [[ ! -f $make_depository ]]
2685	then
2686	printf "\n"
2687	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2688	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2689	fi
2690
2691	fi
2692
2693
2694	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2695	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2696	if [[ $do_batch = false ]]
2697	then
2698
2699
2700	# CREATE THE TEMPORARY WORKING DIRECTORY
2701	mkdir -p $TEMPDIR
2702	chmod go+rx $TEMPDIR
2703	tmpcreate=true
2704
2705
2706	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2707	# INTO THE TEMPORARY WORKING DIRECTORY
2708	if [[ $do_compile = true ]]
2709	then
2710
2711	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2712	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2713	if [[ $localhost = nech ]]
2714	then
2715	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2716	if mkdir -p $TEMPDIR_COMPILE
2717	then
2718	printf "\n *** \"$TEMPDIR_COMPILE\" "
2719	printf "\n is generated as temporary directory for cross compiling\n"
2720	else
2721	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2722	printf "\n needed for cross compilation failed"
2723	locat=compile
2724	exit
2725	fi
2726	else
2727	TEMPDIR_COMPILE=$TEMPDIR
2728	fi
2729
2730	cp $make_depository $TEMPDIR_COMPILE
2731	cd $TEMPDIR_COMPILE
2732	tar -xf $make_depository > /dev/null 2>&1
2733	cd - > /dev/null
2734
2735	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2736	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2737	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2738	then
2739	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2740	else
2741	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2742	fi
2743
2744	else
2745
2746	cp $executable ${TEMPDIR}/a.out
2747
2748	fi
2749
2750
2751	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2752	cd $TEMPDIR
2753	printf "\n *** changed to temporary directory: $TEMPDIR"
2754
2755
2756	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2757	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2758	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2759	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2760	(( i = 0 ))
2761	while (( i < iout ))
2762	do
2763	(( i = i + 1 ))
2764	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2765	then
2766	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2767	else
2768	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2769	fi
2770	done
2771
2772
2773	# IF REQUIRED, START WITH COMPILING
2774	if [[ $do_compile = true ]]
2775	then
2776
2777
2778	if [[ -f a.out ]]
2779	then
2780
2781	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2782	printf "\n\n\n *** executable a.out found"
2783	printf "\n no compilation required \n"
2784
2785	else
2786
2787	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2788	printf "\n\n\n *** compilation starts \n$dashes\n"
2789	printf " *** compilation with make using following options:\n"
2790	printf " make depository: $make_depository"
2791	if [[ "$mopts" != "" ]]
2792	then
2793	printf " make options: $mopts\n"
2794	fi
2795	printf " compilername: $compiler_name\n"
2796	printf " compiler options: $fopts\n"
2797	printf " preprocessor directives: $cpp_options \n"
2798	printf " linker options: $lopts \n"
2799	if [[ "$modules" != "" ]]
2800	then
2801	printf " modules to be load: $modules \n"
2802	fi
2803	printf " source code files: $source_list \n"
2804
2805	if [[ $localhost = nech ]]
2806	then
2807	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\" "
2808	cp $TEMPDIR_COMPILE/a.out .
2809	[[ $? != 0 ]] && compile_error=true
2810	rm -rf $TEMPDIR_COMPILE
2811	elif [[ $localhost = ibmh ]]
2812	then
2813	printf " compiler is called via ssh on \"plogin1\" \n"
2814	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\" "
2815	[[ ! -f a.out ]] && compile_error=true
2816	continue # STATUS=1, IF a.out EXISTS
2817	elif [[ $localhost = lcflow ]]
2818	then
2819	printf " compiler is called via ssh on \"flow\" \n"
2820	/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\" "
2821	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2822	[[ "$check_for_file" = "" ]] && compile_error=true
2823	continue # STATUS=1, IF a.out EXISTS
2824	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2825	then
2826	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2827	else
2828	[[ "$init_cmds" != "" ]] && eval $init_cmds
2829	[[ "$module_calls" != "" ]] && eval $module_calls
2830	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2831	fi
2832
2833	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2834	then
2835	printf "\n +++ error occured while compiling or linking"
2836	locat=compile
2837
2838	exit
2839	else
2840	printf "$dashes\n *** compilation finished \n"
2841	fi
2842
2843	fi
2844
2845	fi
2846
2847
2848	# PROVIDE THE INPUT FILES
2849	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2850	(( i = 0 ))
2851	while (( i < iin ))
2852	do
2853	(( i = i + 1 ))
2854	if (( i == 1 ))
2855	then
2856	printf "\n\n *** providing INPUT-files:\n$dashes"
2857	fi
2858
2859
2860	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2861	if [[ "${transin[$i]}" = unavailable ]]
2862	then
2863	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2864	then
2865	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2866	printf "\n is not available!"
2867	else
2868	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2869	printf "\n is not available!"
2870	fi
2871	continue
2872	fi
2873
2874	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2875	files_for_pes=false; datentyp=file
2876	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2877	then
2878	files_for_pes=true; datentyp=directory
2879	actionin[$i]=""
2880	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2881	then
2882	actionin[$i]=""
2883	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2884	then
2885	files_for_pes=true; datentyp=directory
2886	actionin[$i]="ar"
2887	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2888	then
2889	actionin[$i]="ar"
2890	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2891	then
2892	files_for_pes=true; datentyp=directory
2893	actionin[$i]="fl"
2894	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2895	then
2896	actionin[$i]="fl"
2897	fi
2898
2899	if [[ $files_for_pes = true ]]
2900	then
2901	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2902	else
2903	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2904	fi
2905
2906	# INPUT-FILE FOR A RESTART RUN.
2907	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2908	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2909	if [[ "${actionin[$i]}" = fl ]]
2910	then
2911	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2912	if [[ $files_for_pes = false ]]
2913	then
2914	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2915	then
2916	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2917	got_tmp[$i]=true
2918	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2919	then
2920	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2921	printf "\n *** trying to use backup copy in \"$WORK\" "
2922	cp $WORK/${frelin[$i]} ${localin[$i]}
2923	else
2924	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2925	printf "\n or \"$tmp_data_catalog\" does not exist!"
2926	printf "\n *** trying to get copy from archive"
2927	actionin[$i]=ar
2928	fi
2929	else
2930	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2931	then
2932	mkdir ${localin[$i]}
2933	cd $tmp_data_catalog/${frelin[$i]}
2934	for file in $(ls *)
2935	do
2936	ln $file $TEMPDIR/${localin[$i]}
2937	done
2938	cd $TEMPDIR
2939	got_tmp[$i]=true
2940	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2941	then
2942	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2943	printf "\n *** trying to use backup copy in \"$WORK\" "
2944	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2945	else
2946	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2947	printf "\n or \"$tmp_data_catalog\" does not exist!"
2948	printf "\n *** trying to get copy from archive"
2949	actionin[$i]=ar
2950	fi
2951	fi
2952	fi
2953
2954
2955	# FILE IS STORED ON THE ARCHIVE SYSTEM
2956	if [[ "${actionin[$i]}" = ar ]]
2957	then
2958
2959	if [[ $files_for_pes = false ]]
2960	then
2961	printf "\n file will be restored from archive-system ($archive_system)!"
2962	else
2963	printf "\n directory will be restored from archive-system ($archive_system)!"
2964	fi
2965
2966	file_restored=false
2967
2968	if [[ $archive_system = asterix ]]
2969	then
2970	do_stagein=true
2971	(( stagein_anz = 0 ))
2972	while [[ $do_stagein = true ]]
2973	do
2974	if [[ $files_for_pes = false ]]
2975	then
2976	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2977	else
2978	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2979	fi
2980	cat STAGEIN_OUTPUT
2981	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2982	then
2983	file_restored=true
2984	do_stagein=false
2985	else
2986	(( stagein_anz = stagein_anz + 1 ))
2987	if (( stagein_anz == 10 ))
2988	then
2989	printf "\n +++ stagein stoped after 10 tries"
2990	locat=stage
2991	exit
2992	fi
2993	printf "\n +++ restoring from archive failed, trying again:"
2994	sleep 900
2995	fi
2996	done
2997	elif [[ $archive_system = DMF ]]
2998	then
2999	if [[ $files_for_pes = false ]]
3000	then
3001	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3002	locat=DMF
3003	exit
3004	else
3005	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3006	cp -r $ARCHIVE/${frelin[$i]} $PWD
3007	file_restored=true
3008	fi
3009	elif [[ $archive_system = tivoli ]]
3010	then
3011	if [[ $files_for_pes = false ]]
3012	then
3013	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3014	else
3015	(( inode = 0 ))
3016	while (( inode < nodes ))
3017	do
3018	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3019	(( inode = inode + 1 ))
3020	done
3021	fi
3022	file_restored=true
3023	elif [[ $archive_system = ut ]]
3024	then
3025	if [[ $files_for_pes = false ]]
3026	then
3027	cp $UT/${frelin[$i]} .
3028	else
3029	(( inode = 0 ))
3030	while (( inode < nodes ))
3031	do
3032	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3033	(( inode = inode + 1 ))
3034	done
3035	fi
3036	file_restored=true
3037	else
3038	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3039	locat=rearchive
3040	exit
3041	fi
3042
3043	if [[ $file_restored = true ]]
3044	then
3045
3046	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3047	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3048	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3049	if [[ $files_for_pes = false ]]
3050	then
3051	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3052	else
3053	mkdir $tmp_data_catalog/${frelin[$i]}
3054	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3055	fi
3056	got_tmp[$i]=true
3057
3058	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3059	mv ${frelin[$i]} ${localin[$i]}
3060
3061	fi
3062	fi
3063
3064
3065	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3066	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3067	then
3068
3069	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3070	then
3071
3072	# FILE COPIES ARE PROVIDED FOR ALL CORES
3073	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3074	printf "\n file will be provided for $numprocs processors"
3075	mkdir ${localin[$i]}
3076	ival=$numprocs
3077	(( ii = 0 ))
3078	while (( ii <= ival-1 ))
3079	do
3080	if (( ii < 10 ))
3081	then
3082	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3083	elif (( ii < 100 ))
3084	then
3085	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3086	elif (( ii < 1000 ))
3087	then
3088	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3089	else
3090	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3091	fi
3092	(( ii = ii + 1 ))
3093	done
3094
3095	else
3096
3097	if [[ $files_for_pes = true ]]
3098	then
3099
3100	# PROVIDE FILES FOR EACH CORE
3101	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3102	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3103	printf "\n providing $numprocs files for the respective processors"
3104	mkdir ${localin[$i]}
3105	if [[ $link_local_input = true ]]
3106	then
3107	printf " using ln -f\n"
3108	cd ${absnamein[$i]}
3109	for file in $(ls *)
3110	do
3111	ln -f $file ${localin[$i]}
3112	done
3113	cd $TEMPDIR
3114	fi
3115
3116	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3117	if [[ ! -f "${localin[$i]}/_0000" ]]
3118	then
3119	if [[ $link_local_input = true ]]
3120	then
3121	printf " ln failed for .../_0000, using cp...\n"
3122	fi
3123	cp -r ${absnamein[$i]}/* ${localin[$i]}
3124	fi
3125
3126	else
3127
3128	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3129	if [[ $link_local_input = true ]]
3130	then
3131	printf " using ln -f\n"
3132	ln -f ${absnamein[$i]} ${localin[$i]}
3133	fi
3134	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3135	if [[ ! -f "${localin[$i]}" ]]
3136	then
3137	if [[ $link_local_input = true ]]
3138	then
3139	printf " ln failed, using cp...\n"
3140	fi
3141	cp ${absnamein[$i]} ${localin[$i]}
3142	fi
3143	fi
3144	fi
3145	fi
3146
3147	done
3148	if (( i != 0 ))
3149	then
3150	printf "\n$dashes\n *** all INPUT-files provided \n"
3151	fi
3152
3153
3154	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3155	(( i = 0 ))
3156	while (( i < iic ))
3157	do
3158	(( i = i + 1 ))
3159	if (( i == 1 ))
3160	then
3161	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3162	fi
3163	printf "\n >>> ${in_command[$i]}"
3164	eval ${in_command[$i]}
3165	if (( i == iic ))
3166	then
3167	printf "\n$dashes\n"
3168	fi
3169	done
3170
3171
3172	# SET THE REMAINING CPU-TIME
3173	cpurest=${cpumax}.
3174
3175
3176	# START DVR STREAMING SERVER
3177	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3178	then
3179	if [[ "$dvr_server" != "" ]]
3180	then
3181
3182	printf "\n\n *** preparing the dvr streaming server configuration file"
3183
3184	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3185	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3186	if [[ "$running_dvrserver_id" != "" ]]
3187	then
3188
3189	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3190	printf "\n This server is used instead starting a new one!"
3191	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3192
3193	else
3194
3195	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3196	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3197	then
3198	cp ${PALM_BIN}/.dvrserver.config .
3199
3200	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3201	user_id=`id -u`
3202	group_id=`id -g`
3203
3204	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3205	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3206	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3207	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3208	mv .dvrserver.3 .dvrserver.config
3209	rm .dvrserver.1 .dvrserver.2
3210
3211	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3212	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3213	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3214	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3215	local_dvrserver_running=.TRUE.
3216	else
3217	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3218	printf "\n \"$PALM_BIN\" "
3219	locat=dvr
3220	exit
3221	fi
3222
3223	fi
3224
3225	else
3226	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3227	fi
3228	fi
3229
3230
3231	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3232	# (FILE ENVPAR WILL BE READ BY PALM)
3233	cat > ENVPAR << %%END%%
3234	&envpar run_identifier = '$fname', host = '$localhost',
3235	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3236	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3237	maximum_cpu_time_allowed = ${cpumax}.,
3238	revision = '$global_revision',
3239	local_dvrserver_running = $local_dvrserver_running,
3240	batch_job = $batch_job /
3241
3242	%%END%%
3243
3244
3245	# STARTING THE EXECUTABLE
3246	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3247	PATH=$PATH:$TEMPDIR
3248
3249	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3250	if [[ "$mpi_debug" = true ]]
3251	then
3252	export MPI_CHECK_ARGS=1
3253	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3254	fi
3255
3256	if [[ "$totalview" = true ]]
3257	then
3258	printf "\n *** totalview debugger will be used"
3259	tv_opt="-tv"
3260	else
3261	tv_opt=""
3262	fi
3263
3264	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3265	then
3266
3267	#Interactive ALLINEA DEBUG seesion
3268	if [[ "$ENVIRONMENT" != BATCH ]]
3269	then
3270	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3271	then
3272	if [[ "$allinea" = true ]]
3273	then
3274	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3275
3276	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3277	wait
3278	fi
3279	fi
3280	fi
3281
3282	if [[ "$ENVIRONMENT" = BATCH ]]
3283	then
3284	continue
3285	fi
3286	if [[ $localhost = ibmh ]]
3287	then
3288
3289	# SETUP THE IBM MPI ENVIRONMENT
3290	export MP_SHARED_MEMORY=yes
3291	export AIXTHREADS_SCOPE=S
3292	export OMP_NUM_THREADS=$threads_per_task
3293	export AUTHSTATE=files
3294	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3295
3296	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3297	export MP_ADAPTER_USE=shared
3298	export MP_CPU_USE=multiple
3299	export MP_TIMEOUT=1200
3300
3301	unset MP_TASK_AFFINITY
3302
3303	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3304	#(( ii = 1 ))
3305	#while (( ii <= $numprocs ))
3306	#do
3307	# echo $localhost_realname >> hostfile
3308	# (( ii = ii + 1 ))
3309	#done
3310	#export MP_HOSTFILE=hostfile
3311
3312	if [[ "$LOADLBATCH" = yes ]]
3313	then
3314	totalview poe a.out $ROPTS
3315	else
3316	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3317	export TVDSVRLAUNCHCMD=ssh
3318	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3319	fi
3320
3321	fi # END DEBUG MODE
3322
3323	else
3324
3325	# NORMAL EXECUTION
3326	if [[ -n $numprocs ]]
3327	then
3328
3329	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3330	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3331	then
3332
3333	# SETUP THE IBM MPI ENVIRONMENT
3334	if [[ $host != ibmh && $host != ibmkisti ]]
3335	then
3336	export MP_SHARED_MEMORY=yes
3337	export AIXTHREAD_SCOPE=S
3338	export OMP_NUM_THREADS=$threads_per_task
3339	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3340	export AUTHSTATE=files
3341	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3342	# export MP_PRINTENV=yes
3343
3344	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3345	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3346	export MP_WAIT_MODE=poll
3347	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3348	fi
3349
3350	if [[ $host = ibmkisti ]]
3351	then
3352	export LANG=en_US
3353	export MP_SHARED_MEMORY=yes
3354	if [[ $threads_per_task = 1 ]]
3355	then
3356	export MP_SINGLE_THREAD=yes
3357	export MEMORY_AFFINITY=MCM
3358	else
3359	export OMP_NUM_THREADS=$threads_per_task
3360	fi
3361	fi
3362
3363	if [[ "$LOADLBATCH" = yes ]]
3364	then
3365	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3366	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3367	then
3368	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3369	else
3370	if [[ $run_coupled_model = false ]]
3371	then
3372	if [[ "$ocean_file_appendix" = true ]]
3373	then
3374	echo "precursor_ocean" > runfile_atmos
3375	else
3376	echo "precursor_atmos" > runfile_atmos
3377	fi
3378	else
3379	(( iia = $numprocs_atmos / $threads_per_task ))
3380	(( iio = $numprocs_ocean / $threads_per_task ))
3381	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3382	printf "\n using $coupled_mode coupling"
3383	printf "\n\n"
3384	echo "coupled_run $iia $iio" > runfile_atmos
3385	fi
3386	poe ./a.out $ROPTS < runfile_atmos
3387	fi
3388	else
3389	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3390	then
3391	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3392	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3393	then
3394	if [[ -f $hostfile ]]
3395	then
3396	cp $hostfile hostfile
3397	else
3398	(( ii = 1 ))
3399	while (( ii <= $numprocs ))
3400	do
3401	echo $localhost_realname >> hostfile
3402	(( ii = ii + 1 ))
3403	done
3404	fi
3405	export MP_HOSTFILE=hostfile
3406	if [[ $run_coupled_model = false ]]
3407	then
3408	if [[ "$ocean_file_appendix" = true ]]
3409	then
3410	echo "precursor_ocean" > runfile_atmos
3411	else
3412	echo "precursor_atmos" > runfile_atmos
3413	fi
3414	else
3415	(( iia = $numprocs_atmos / $threads_per_task ))
3416	(( iio = $numprocs_ocean / $threads_per_task ))
3417	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3418	printf "\n using $coupled_mode coupling"
3419	printf "\n\n"
3420	echo "coupled_run $iia $iio" > runfile_atmos
3421	fi
3422
3423	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3424
3425	else
3426	if [[ "$host_file" = "" ]]
3427	then
3428	printf "\n +++ no hostfile given in configuration file"
3429	locat=config_file
3430	exit
3431	else
3432	eval host_file=$host_file
3433	fi
3434	export MP_HOSTFILE=$host_file
3435	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3436	fi
3437	fi
3438	elif [[ $host = nech ]]
3439	then
3440	(( ii = nodes ))
3441	if [[ $ii = 1 ]]
3442	then
3443	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3444	export MPIPROGINF=YES
3445	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3446	echo "*** execution on single node with mpirun"
3447	mpirun -np $numprocs ./a.out $ROPTS
3448	else
3449	(( i = 0 ))
3450	while (( i < ii ))
3451	do
3452	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3453	(( i = i + 1 ))
3454	done
3455
3456	echo "#!/bin/sh" > mpi_exec_shell
3457	echo " " >> mpi_exec_shell
3458	echo "set -u" >> mpi_exec_shell
3459	echo "F_ERRCNT=0" >> mpi_exec_shell
3460	echo "MPIPROGINV=YES" >> mpi_exec_shell
3461	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3462	echo "cpurest=$cpurest" >> mpi_exec_shell
3463	echo "fname=$fname" >> mpi_exec_shell
3464	echo "localhost=$localhost" >> mpi_exec_shell
3465	echo "return_address=$return_address" >> mpi_exec_shell
3466	echo "return_username=$return_username" >> mpi_exec_shell
3467	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3468	echo "write_binary=$write_binary" >> mpi_exec_shell
3469	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3470	echo " " >> mpi_exec_shell
3471	echo "export F_ERRCNT" >> mpi_exec_shell
3472	echo "export MPIPROGINV" >> mpi_exec_shell
3473	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3474	echo "export cpurest" >> mpi_exec_shell
3475	echo "export fname" >> mpi_exec_shell
3476	echo "export localhost" >> mpi_exec_shell
3477	echo "export return_address" >> mpi_exec_shell
3478	echo "export return_username" >> mpi_exec_shell
3479	echo "export tasks_per_node" >> mpi_exec_shell
3480	echo "export write_binary" >> mpi_exec_shell
3481	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3482	echo " " >> mpi_exec_shell
3483	echo "exec ./a.out" >> mpi_exec_shell
3484
3485	chmod u+x mpi_exec_shell
3486	export MPIPROGINF=YES
3487	mpirun -f multinode_config &
3488	wait
3489
3490	fi
3491	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3492	then
3493
3494	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3495	# DOES NOT EXIST
3496	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3497	then
3498	if [[ -f $hostfile ]]
3499	then
3500	cp $hostfile hostfile
3501	(( ii = $numprocs / $threads_per_task ))
3502	[[ $ii = 0 ]] && (( ii = 1 ))
3503	else
3504	(( ii = 1 ))
3505	while (( ii <= $numprocs / $threads_per_task ))
3506	do
3507	echo $localhost_realname >> hostfile
3508	(( ii = ii + 1 ))
3509	done
3510	if (( $numprocs / $threads_per_task == 0 ))
3511	then
3512	echo $localhost_realname >> hostfile
3513	fi
3514	fi
3515	eval zeile=\"`head -n $ii hostfile`\"
3516	printf "\n *** running on: $zeile"
3517	fi
3518
3519	(( ii = $numprocs / $threads_per_task ))
3520	[[ $ii = 0 ]] && (( ii = 1 ))
3521	export OMP_NUM_THREADS=$threads_per_task
3522
3523	if [[ $threads_per_task != 1 ]]
3524	then
3525	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3526	# MAY ABORT
3527	ulimit -s unlimited
3528	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3529	fi
3530	if [[ $run_coupled_model = false ]]
3531	then
3532	if [[ "$ocean_file_appendix" = true ]]
3533	then
3534	echo "precursor_ocean" > runfile_atmos
3535	else
3536	echo "precursor_atmos" > runfile_atmos
3537	fi
3538	printf "\n\n"
3539
3540	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3541	then
3542	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3543	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3544	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3545	elif [[ $host = lccrayf ]]
3546	then
3547	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3548	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3549	then
3550	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3551	elif [[ $host = lcflow ]]
3552	then
3553	mpirun -np $ii a.out < runfile_atmos $ROPTS
3554	elif [[ $host = lcsb ]]
3555	then
3556	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3557	elif [[ $host = lckiaps ]]
3558	then
3559	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3560	elif [[ $host = lckyu* ]]
3561	then
3562	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3563	else
3564	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3565	fi
3566	else
3567
3568	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3569	(( iia = $numprocs_atmos / $threads_per_task ))
3570	(( iio = $numprocs_ocean / $threads_per_task ))
3571	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3572	printf "\n using $coupled_mode coupling"
3573	printf "\n\n"
3574
3575	if [[ $coupled_mode = "mpi2" ]]
3576	then
3577	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3578	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3579
3580	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3581	then
3582
3583	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3584	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3585
3586	else
3587	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3588	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3589	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3590	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3591	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3592	fi
3593	wait
3594
3595	else
3596
3597	echo "coupled_run $iia $iio" > runfile_atmos
3598
3599	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3600	then
3601
3602	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3603
3604	elif [[ $host = lck \|\| $host = lckordi ]]
3605	then
3606
3607	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3608
3609	elif [[ $host = lckyu* ]]
3610	then
3611
3612	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3613
3614	elif [[ $host = lcmuk ]]
3615	then
3616
3617	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3618
3619	fi
3620	wait
3621	fi
3622
3623	fi
3624
3625	elif [[ $host = lckyoto ]]
3626	then
3627	set -xv
3628	export P4_RSHCOMMAND=plesh
3629	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3630	if [[ "$ENVIRONMENT" = BATCH ]]
3631	then
3632	if [[ "$cond2" = fujitsu ]]
3633	then
3634	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3635	elif [[ "cond2" = pgi ]]
3636	then
3637	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3638	else
3639	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3640	fi
3641	else
3642	if [[ "$cond2" = "" ]]
3643	then
3644	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3645	else
3646	mpirun -np $numprocs ./a.out $ROPTS
3647	fi
3648	fi
3649	set +xv
3650
3651	elif [[ $host = lctit ]]
3652	then
3653	export OMP_NUM_THREADS=$threads_per_task
3654	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3655	if [[ "$threads_per_task" != 1 ]]
3656	then
3657	export MV2_ENABLE_AFFINITY=0
3658	fi
3659	echo "----- PBS_NODEFILE content:"
3660	cat $PBS_NODEFILE
3661	echo "-----"
3662	(( ii = $numprocs / $threads_per_task ))
3663	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3664	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3665	else
3666	mpprun -n $numprocs a.out $ROPTS
3667	fi
3668	else
3669	a.out $ROPTS
3670	fi
3671	fi
3672
3673	if [[ $? != 0 ]]
3674	then
3675
3676	# ABORT IN CASE OF RUNTIME ERRORS
3677	printf "\n +++ runtime error occured"
3678	locat=execution
3679	exit
3680
3681	else
3682
3683	printf "\n$dashes\n *** execution finished \n"
3684
3685	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3686	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3687	if [[ "$dvrserver_id" != "" ]]
3688	then
3689	kill $dvrserver_id
3690	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3691
3692	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3693	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3694	if [[ -d DATA_DVR ]]
3695	then
3696
3697	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3698	# DIRECTORY
3699	cp .dvrserver.config DATA_DVR
3700
3701	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3702	# SEQUENCE MODE DATA TOO)
3703	process_dvr_output -d DATA_DVR -f $fname -s
3704
3705	else
3706
3707	# PROCESS THE LOCAL OUTPUT
3708	process_dvr_output -l -d DATA_DVR -f $fname
3709
3710	fi
3711
3712	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3713	then
3714
3715	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3716	process_dvr_output -l -d DATA_DVR -f $fname
3717
3718	fi
3719	fi
3720
3721
3722
3723	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3724	# BY EACH CORE INTO ONE FILE
3725	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3726	then
3727	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3728	printf "\n 2d- and/or 3d-data may be incomplete!"
3729	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3730	elif [[ "$combine_plot_fields" == true ]]
3731	then
3732	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3733	then
3734	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3735	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3736	else
3737	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3738	combine_plot_fields${block}.x
3739	fi
3740	else
3741
3742	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3743	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3744	# ??? koennen wir das streichen ???
3745	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3746	fi
3747
3748
3749
3750	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3751	(( i = 0 ))
3752	while (( i < ioc ))
3753	do
3754	(( i = i + 1 ))
3755	if (( i == 1 ))
3756	then
3757	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3758	fi
3759	printf "\n >>> ${out_command[$i]}"
3760	eval ${out_command[$i]}
3761	if (( i == ioc ))
3762	then
3763	printf "\n$dashes\n"
3764	fi
3765	done
3766
3767
3768	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3769	if [[ $do_trace = true ]]
3770	then
3771	printf "\n\n"
3772	ls -al
3773	fi
3774
3775
3776
3777	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3778	(( i = 0 ))
3779	while (( i < iout ))
3780	do
3781	(( i = i + 1 ))
3782	if (( i == 1 ))
3783	then
3784	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3785	fi
3786
3787	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3788	files_for_pes=false; filetyp=file
3789	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3790	then
3791	files_for_pes=true; filetyp=directory
3792	actionout[$i]=""
3793	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3794	then
3795	actionout[$i]=""
3796	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3797	then
3798	files_for_pes=true; filetyp=directory
3799	actionout[$i]="ar"
3800	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3801	then
3802	actionout[$i]="ar"
3803	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3804	then
3805	files_for_pes=true; filetyp=directory
3806	actionout[$i]="fl"
3807	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3808	then
3809	actionout[$i]="fl"
3810	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3811	then
3812	files_for_pes=true; filetyp=directory
3813	actionout[$i]="tr"
3814	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3815	then
3816	actionout[$i]="tr"
3817	fi
3818
3819	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3820	then
3821	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3822	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3823	then
3824	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3825	else
3826
3827
3828	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3829	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3830	if [[ "${actionout[$i]}" = tr ]]
3831	then
3832	if [[ $localhost != $fromhost ]]
3833	then
3834	if [[ $files_for_pes = false ]]
3835	then
3836	cps=""
3837	cst=""
3838	else
3839	cps=-c
3840	cst="/"
3841	fi
3842	if [[ $localhost = nech ]]
3843	then
3844
3845	# TRANSFER IN SEPERATE JOB
3846	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3847	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3848	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3849	if [[ $files_for_pes = false ]]
3850	then
3851	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3852	else
3853	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3854	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3855	fi
3856
3857	echo "set -x" > transfer_${localout[$i]}
3858	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3859
3860	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3861	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3862	printf "\n or higher cycle\n"
3863	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]}
3864
3865	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3866
3867	if [[ $localhost = nech ]]
3868	then
3869	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3870	else
3871	if [[ "$LOGNAME" = b323013 ]]
3872	then
3873	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3874	else
3875	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3876	fi
3877	fi
3878
3879	else
3880
3881	# TRANSFER WITHIN THIS JOB
3882	transfer_failed=false
3883	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3884	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3885	if [[ $localhost = lccrayb ]]
3886	then
3887	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]}"
3888	elif [[ $localhost = lccrayh ]]
3889	then
3890	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]}"
3891	elif [[ $localhost = lcxe6 ]]
3892	then
3893	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]}"
3894	else
3895	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3896	fi
3897	[[ $? != 0 ]] && transfer_failed=true
3898
3899	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3900	if [[ $transfer_failed = true ]]
3901	then
3902	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3903	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3904
3905	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3906	eval local_catalog=${pathout[$i]}
3907	if [[ ! -d $local_catalog ]]
3908	then
3909	printf " *** local directory does not exist. Trying to create:\n"
3910	printf " $local_catalog \n"
3911	mkdir -p $local_catalog
3912	fi
3913	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3914	transfer_problems=true
3915	fi
3916	fi
3917	else
3918
3919	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3920	actionout[$i]=""
3921	fi
3922	fi
3923
3924
3925	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3926	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3927	if [[ "${actionout[$i]}" = tra ]]
3928	then
3929	if [[ $localhost != $fromhost ]]
3930	then
3931	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3932	then
3933
3934	# TRANSFER IN SEPERATE JOB
3935	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3936	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3937	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3938	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3939
3940	echo "set -x" > transfer_${localout[$i]}
3941	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3942
3943	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3944	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3945	printf "\n or higher cycle\n"
3946	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]}
3947
3948	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3949
3950	if [[ $localhost = nech ]]
3951	then
3952	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3953	else
3954	if [[ $LOGNAME = b323013 ]]
3955	then
3956	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3957	else
3958	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3959	fi
3960	fi
3961
3962	else
3963
3964	# TRANSFER WITHIN THIS JOB
3965	transfer_failed=false
3966	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3967	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3968	if [[ $localhost = lccrayb ]]
3969	then
3970	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]}"
3971	elif [[ $localhost = lccrayh ]]
3972	then
3973	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]}"
3974	elif [[ $localhost = lcxe6 ]]
3975	then
3976	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]}"
3977	else
3978	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3979	fi
3980	[[ $? != 0 ]] && transfer_failed=true
3981
3982	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3983	if [[ $transfer_failed = true ]]
3984	then
3985	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3986	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3987
3988	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3989	eval local_catalog=${pathout[$i]}
3990	if [[ ! -d $local_catalog ]]
3991	then
3992	printf " *** local directory does not exist. Trying to create:\n"
3993	printf " $local_catalog \n"
3994	mkdir -p $local_catalog
3995	fi
3996
3997	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3998	transfer_problems=true
3999	fi
4000	fi
4001	else
4002
4003	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4004	actionout[$i]=a
4005	fi
4006	fi
4007
4008
4009	# OUTPUT-FILE FOR A RESTART-RUN.
4010	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4011	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4012	# AS LAST ACTION, ARCHIVING IS INITIATED.
4013	if [[ "${actionout[$i]}" = fl ]]
4014	then
4015	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4016	chmod g+rx $tmp_data_catalog
4017	if [[ $files_for_pes = false ]]
4018	then
4019	printf "\n >>> OUTPUT: ${localout[$i]} to"
4020	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4021	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4022	else
4023	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4024	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4025	mkdir $tmp_data_catalog/${frelout[$i]}
4026	cd ${localout[$i]}
4027	for file in $(ls *)
4028	do
4029	ln -f $file $tmp_data_catalog/${frelout[$i]}
4030	done
4031	cd $TEMPDIR
4032	fi
4033
4034
4035	# CREATE AND SUBMIT ARCHIVING-JOB
4036	if [[ $store_on_archive_system = true ]]
4037	then
4038
4039	if [[ $archive_system = asterix ]]
4040	then
4041	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4042	if [[ $files_for_pes = false ]]
4043	then
4044	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4045	else
4046	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4047	fi
4048	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4049	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4050	echo "then" >> archive_${frelout[$i]}
4051	echo " do_stageout=false" >> archive_${frelout[$i]}
4052	echo "else" >> archive_${frelout[$i]}
4053	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4054	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4055	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4056	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4057	if [[ $files_for_pes = false ]]
4058	then
4059	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4060	else
4061	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4062	fi
4063	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4064	echo "fi" >> archive_${frelout[$i]}
4065	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4066	elif [[ $archive_system = DMF ]]
4067	then
4068	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4069	if [[ $files_for_pes = false ]]
4070	then
4071	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4072	locat=DMF
4073	exit
4074	else
4075	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4076	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4077	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4078	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4079	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4080	fi
4081	elif [[ $archive_system = tivoli ]]
4082	then
4083	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4084	if [[ $files_for_pes = false ]]
4085	then
4086	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4087	echo "set -x" >> archive_${frelout[$i]}
4088	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4089	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4090	else
4091
4092	echo "set -x" >> archive_${frelout[$i]}
4093	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4094	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4095	cd $tmp_data_catalog
4096	all_files=`ls -1 ${frelout[$i]}/*`
4097	cd - > /dev/null
4098	(( inode = 0 ))
4099	(( tp1 = tasks_per_node + 1 ))
4100	while (( inode < nodes ))
4101	do
4102	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4103	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4104	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4105	(( inode = inode + 1 ))
4106	done
4107	fi
4108	elif [[ $archive_system = ut ]]
4109	then
4110	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4111	if [[ $files_for_pes = false ]]
4112	then
4113	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4114	echo "set -x" >> archive_${frelout[$i]}
4115	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4116	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4117	else
4118
4119	echo "set -x" >> archive_${frelout[$i]}
4120	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4121	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4122	cd $tmp_data_catalog
4123	all_files=`ls -1 ${frelout[$i]}/*`
4124	cd - > /dev/null
4125	(( inode = 0 ))
4126	(( tp1 = tasks_per_node + 1 ))
4127	while (( inode < nodes ))
4128	do
4129	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4130	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4131	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4132	(( inode = inode + 1 ))
4133	done
4134	fi
4135	elif [[ $archive_system = none ]]
4136	then
4137	printf " +++ archiving on $localhost not available!\n"
4138	fi
4139
4140	if [[ $archive_system != none ]]
4141	then
4142	if [[ $localhost = nech ]]
4143	then
4144	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4145	fi
4146	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4147	fi
4148	else
4149	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4150	fi
4151
4152
4153	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4154	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4155	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4156	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4157	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4158	if [[ $files_for_pes = false ]]
4159	then
4160	cat /dev/null > ${pathout[$i]}
4161	else
4162	mkdir -p ${pathout[$i]}
4163	fi
4164
4165	fi
4166
4167
4168	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4169	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4170	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4171	if [[ "${actionout[$i]}" = ar ]]
4172	then
4173	if [[ $files_for_pes = false ]]
4174	then
4175	printf "\n >>> OUTPUT: ${localout[$i]} to"
4176	printf "\n ${pathout[$i]}"
4177	printf "\n File will be copied to archive-system ($archive_system) !\n"
4178	else
4179	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4180	printf "\n ${pathout[$i]}"
4181	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4182	fi
4183	mv ${localout[$i]} ${frelout[$i]}
4184
4185	file_saved=false
4186
4187	if [[ $archive_system = asterix ]]
4188	then
4189	do_stageout=true
4190	(( stageout_anz = 0 ))
4191	while [[ $do_stageout = true ]]
4192	do
4193	if [[ $files_for_pes = false ]]
4194	then
4195	stageout ${frelout[$i]} > STAGE_OUTPUT
4196	else
4197	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4198	fi
4199	cat STAGE_OUTPUT
4200	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4201	then
4202	file_saved=true
4203	do_stageout=false
4204	else
4205	if [[ $files_for_pes = false ]]
4206	then
4207	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4208	else
4209	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4210	fi
4211	(( stageout_anz = stageout_anz + 1 ))
4212	if (( stageout_anz == 10 ))
4213	then
4214	printf "\n +++ stoped after 10 unsuccessful tries!"
4215	archive_save=false
4216	do_stageout=false
4217	else
4218	printf "\n *** new try to store on archive after 15 min:"
4219	sleep 900
4220	fi
4221	fi
4222	done
4223	elif [[ $archive_system = DMF ]]
4224	then
4225	if [[ $files_for_pes = false ]]
4226	then
4227	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4228	locat=DMF
4229	exit
4230	else
4231	rm -rf $ARCHIVE/${frelout[$i]}
4232	cp -r ${frelout[$i]} $ARCHIVE
4233	fi
4234	file_saved=true
4235	elif [[ $archive_system = tivoli ]]
4236	then
4237	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4238	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4239	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4240	# WHEN THE ARCHIVE-JOB IS EXECUTED
4241	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4242	chmod g+rx $tmp_data_catalog
4243	if [[ $files_for_pes = false ]]
4244	then
4245	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4246	else
4247	mkdir $tmp_data_catalog/${frelout[$i]}
4248	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4249	fi
4250
4251	# GENERATE AND SUBMIT BATCH-JOB
4252	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4253	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4254	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4255	if [[ $files_for_pes = false ]]
4256	then
4257	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4258	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4259	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4260	else
4261	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4262	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4263	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4264	fi
4265
4266	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4267	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4268	file_saved=true
4269
4270	elif [[ $archive_system = ut ]]
4271	then
4272	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4273	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4274	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4275	# WHEN THE ARCHIVE-JOB IS EXECUTED
4276	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4277	chmod g+rx $tmp_data_catalog
4278	if [[ $files_for_pes = false ]]
4279	then
4280	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4281	else
4282	mkdir $tmp_data_catalog/${frelout[$i]}
4283	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4284	fi
4285
4286	# GENERATE AND SUBMIT BATCH-JOB
4287	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4288	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4289	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4290	if [[ $files_for_pes = false ]]
4291	then
4292	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4293	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4294	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4295	else
4296	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4297	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4298	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4299	fi
4300
4301	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4302	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4303	file_saved=true
4304
4305	else
4306	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4307	archive_save=false
4308	fi
4309
4310	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4311	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4312	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4313	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4314	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4315	if [[ $file_saved = true ]]
4316	then
4317	if [[ $files_for_pes = false ]]
4318	then
4319	cat /dev/null > ${pathout[$i]}
4320	else
4321	mkdir -p ${pathout[$i]}
4322	fi
4323	fi
4324
4325	fi
4326
4327	# APPEND ON THIS MACHINE
4328	if [[ "${actionout[$i]}" = "a" ]]
4329	then
4330	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4331	then
4332	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4333	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4334	else
4335	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4336	cat ${localout[$i]} >> ${pathout[$i]}
4337	fi
4338	fi
4339
4340	# COPY ON THIS MACHINE
4341	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4342	# ON DIFFERENT FILE-SYSTEMS
4343	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4344	then
4345
4346	# COPY IN CASE OF RUNS ON SINGLE CORES
4347	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4348	then
4349	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4350	if [[ $link_local_output = true ]]
4351	then
4352	printf " using ln -f\n"
4353	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4354	fi
4355	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4356	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4357	then
4358	if [[ $link_local_output = true ]]
4359	then
4360	printf " ln failed, using cp...\n"
4361	fi
4362	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4363	fi
4364	else
4365	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4366	if [[ $link_local_output = true ]]
4367	then
4368	printf " using ln -f\n"
4369	ln -f ${localout[$i]} ${pathout[$i]}
4370	fi
4371	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4372	if [[ ! -f "${pathout[$i]}" ]]
4373	then
4374	if [[ $link_local_output = true ]]
4375	then
4376	printf " ln failed, using cp...\n"
4377	fi
4378	cp ${localout[$i]} ${pathout[$i]}
4379	fi
4380	fi
4381
4382	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4383	then
4384
4385	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4386	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4387	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4388	if [[ $link_local_output = true ]]
4389	then
4390	printf " using ln -f\n"
4391	mkdir ${pathout[$i]}
4392	cd ${localout[$i]}
4393	for file in $(ls *)
4394	do
4395	ln -f $file ${pathout[$i]}
4396	done
4397	cd $TEMPDIR
4398	fi
4399
4400	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4401	if [[ ! -f "${pathout[$i]}/_0000" ]]
4402	then
4403	if [[ $link_local_output = true ]]
4404	then
4405	printf " ln failed for .../_0000, using cp...\n"
4406	fi
4407	cp -r ${localout[$i]} ${pathout[$i]}
4408	fi
4409
4410	fi
4411	fi
4412	done
4413	if (( i != 0 ))
4414	then
4415	if [[ $transfer_problems = true ]]
4416	then
4417	printf "\n$dashes\n *** OUTPUT-files saved"
4418	printf "\n +++ WARNING: some data transfers failed! \n"
4419	else
4420	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4421	fi
4422	fi
4423
4424
4425	# IF REQUIRED, START A RESTART-JOB
4426	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4427	if [[ -f CONTINUE_RUN ]]
4428	then
4429
4430	if [[ $archive_save = true ]]
4431	then
4432
4433	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4434	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4435	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4436	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4437	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4438	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4439	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4440	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4441	then
4442	mc=`echo $mc \| sed 's/#/f/g'`
4443	fi
4444
4445
4446	# START THE RESTART-JOB
4447	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4448	echo " $mc"
4449	printf "\n$dashes\n"
4450	if [[ $localhost != $fromhost ]]
4451	then
4452
4453	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4454	then
4455	echo "*** ssh will be used to initiate restart-runs!"
4456	echo " return_address=\"$return_address\" "
4457	echo " return_username=\"$return_username\" "
4458	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4459	then
4460	if [[ $localhost = ibmh ]]
4461	then
4462	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\" "
4463	elif [[ $localhost = lccrayb ]]
4464	then
4465	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\" "
4466	elif [[ $localhost = lccrayh ]]
4467	then
4468	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\" "
4469	elif [[ $localhost = lcxe6 ]]
4470	then
4471	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\" "
4472	else
4473	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 "
4474	fi
4475	else
4476	if [[ $localhost = ibmkisti ]]
4477	then
4478	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\" "
4479	elif [[ $localhost = lcflow ]]
4480	then
4481	/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 "
4482	elif [[ $localhost = lccrayb ]]
4483	then
4484	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\" "
4485	elif [[ $localhost = lccrayh ]]
4486	then
4487	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\" "
4488	else
4489	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4490	fi
4491	fi
4492	else
4493	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4494	locat=restart; exit
4495	fi
4496
4497	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4498	if [[ $queue = special1q ]]
4499	then
4500	sleep 120
4501	else
4502	sleep 30
4503	fi
4504
4505	else
4506
4507	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4508	# USING SSH)
4509	cd $LOCAL_PWD
4510	if [[ $localhost = lckyuh ]]
4511	then
4512	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4513	printf "\n please restart job manually using command:\n"
4514	printf "\n \"$mc\" "
4515	else
4516	eval $mc # THE ' MUST BE EVALUATED
4517	fi
4518	cd - > /dev/null
4519	fi
4520	if [[ $localhost = lckyuh ]]
4521	then
4522	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4523	else
4524	printf "\n$dashes\n *** restart-run initiated \n"
4525	fi
4526
4527
4528	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4529	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4530	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4531	# MAY BE VERY HUGE)
4532	(( i = 0 ))
4533	while (( i < iin ))
4534	do
4535	(( i = i + 1 ))
4536	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4537	then
4538	rm -r $tmp_data_catalog/${frelin[$i]}
4539	fi
4540	done
4541
4542	else
4543
4544	printf "\n +++ no restart-run possible, since errors occured"
4545	printf "\n during the archive process"
4546	fi
4547
4548	fi
4549
4550
4551
4552	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4553	if [[ "$email_notification" != "none" ]]
4554	then
4555
4556	if [[ $localhost != $fromhost ]]
4557	then
4558	if [[ -f CONTINUE_RUN ]]
4559	then
4560	echo "PALM restart run necessary" > email_text
4561	echo "description header of actual run:" >> email_text
4562	cat CONTINUE_RUN >> email_text
4563	echo "mrun-command to restart:" >> email_text
4564	echo "$mc" >> email_text
4565	else
4566	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4567	fi
4568	mail $email_notification < email_text
4569	printf "\n *** email notification sent to \"$email_notification\" "
4570	fi
4571	fi
4572
4573
4574
4575	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4576	cd $HOME
4577	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4578
4579	else
4580
4581
4582	# PREPARING ACTIONS,
4583	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4584
4585	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4586	mrun_com="$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 $remote_username"
4587	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4588	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4589	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4590	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4591	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4592	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4593	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4594	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4595	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4596	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4597	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4598	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4599	if [[ $use_openmp = true ]]
4600	then
4601	mrun_com=${mrun_com}" -O $threads_per_task"
4602	fi
4603	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4604	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4605	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4606	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4607	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4608	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4609	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4610	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4611	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4612	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4613	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4614	if [[ $do_remote = true ]]
4615	then
4616	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4617	fi
4618
4619
4620	# CREATE EXECUTABLE FOR BATCH JOB
4621	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4622	then
4623
4624	printf "\n *** creating the executable for batch job\n"
4625
4626	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4627	if [[ $host != $localhost ]]
4628	then
4629	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4630	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4631	locat=create_executable; exit
4632	fi
4633
4634	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4635	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4636
4637	cp $make_depository .
4638	tar -xf $make_depository > /dev/null 2>&1
4639	cp ../* . > /dev/null 2>&1
4640
4641	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4642
4643	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4644	then
4645	printf "\n +++ error occured while compiling or linking"
4646	locat=compile
4647	exit
4648	fi
4649
4650	mv a.out ..
4651	cd - > /dev/null 2>&1
4652	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4653
4654	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4655
4656	fi
4657
4658
4659	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4660	jobfile=jobfile.$RANDOM
4661
4662
4663	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4664	echo "mkdir $TEMPDIR" >> $jobfile
4665	echo "cd $TEMPDIR" >> $jobfile
4666
4667
4668	# ACTIVATE ERROR-TRACEBACK
4669	if [[ $do_trace = true ]]
4670	then
4671	echo "set -x" >> $jobfile
4672	else
4673	echo "set +vx" >> $jobfile
4674	fi
4675
4676
4677	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4678	if [[ "$init_cmds" != "" ]]
4679	then
4680	echo "$init_cmds" >> $jobfile
4681	fi
4682	if [[ "$module_calls" != "" ]]
4683	then
4684	echo "$module_calls" >> $jobfile
4685	fi
4686
4687
4688	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4689	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4690	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4691	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4692	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4693	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4694	# QUEUEING-SYSTEMS
4695	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4696	then
4697
4698	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4699	if [[ $restart_run != true ]]
4700	then
4701	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4702	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4703	fi
4704
4705	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4706	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4707	echo "set -x" >> $jobfile
4708	if [[ $host = $localhost ]]
4709	then
4710
4711	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4712	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4713	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4714	then
4715	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4716	else
4717	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4718	fi
4719
4720	else
4721	if [[ $host = ibmkisti ]]
4722	then
4723	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4724	echo "localdir=\`pwd\`" >> $jobfile
4725	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4726	elif [[ $host = lccrayb ]]
4727	then
4728	echo "localdir=\`pwd\`" >> $jobfile
4729	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4730	elif [[ $host = lccrayh ]]
4731	then
4732	echo "localdir=\`pwd\`" >> $jobfile
4733	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4734
4735	else
4736	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4737	fi
4738	fi
4739	echo "export SOURCES_COMPLETE=true" >> $jobfile
4740
4741	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4742	# WORKING DIRECTORY OF THE JOB
4743	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4744	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4745	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4746	echo "execute_mrun=true" >> $jobfile
4747	echo " " >> $jobfile
4748
4749	else
4750
4751	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4752	if [[ $do_compile = true ]]
4753	then
4754
4755	source_catalog=SOURCES_FOR_RUN_$fname
4756
4757	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4758	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4759	echo "export SOURCES_COMPLETE=true" >> $jobfile
4760	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4761
4762	for filename in $source_list
4763	do
4764	# BACKSLASH IS USED FOR MASKING
4765	echo "cat > $filename << \"%END%\"" >> $jobfile
4766	cat $source_catalog/$filename >> $jobfile
4767	echo " " >> $jobfile
4768	echo "%END%" >> $jobfile
4769	echo " " >> $jobfile
4770	done
4771
4772	# BACKSLASH IS USED FOR MASKING
4773	echo "cat > Makefile << \"%END%\"" >> $jobfile
4774	cat $source_catalog/Makefile >> $jobfile
4775	echo " " >> $jobfile
4776	echo "%END%" >> $jobfile
4777	echo " " >> $jobfile
4778
4779	echo "cd - > /dev/null" >> $jobfile
4780
4781	fi
4782
4783
4784	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4785	# BACKSLASH IS USED FOR MASKING
4786	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4787	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4788	echo "cat > $config_file << \"%END%\"" >> $jobfile
4789	if [[ $host = lckyuh ]]
4790	then
4791	# NO CROSS-COMPILER ON COMPUTE NODE
4792	sed 's/frtpx/frt/g' $config_file >> $jobfile
4793	else
4794	sed 's/#$.*//g' $config_file >> $jobfile
4795	fi
4796	echo "%END%" >> $jobfile
4797	echo " " >> $jobfile
4798
4799
4800	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4801	# BACKSLASH IS USED FOR MASKING
4802	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4803	if [[ $host = lckyuh ]]
4804	then
4805	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4806	else
4807	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4808	fi
4809	echo "%END%" >> $jobfile
4810	echo "chmod u+x $mrun_script_name" >> $jobfile
4811	echo "execute_mrun=true" >> $jobfile
4812	echo " " >> $jobfile
4813
4814	fi
4815
4816
4817	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4818	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4819	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4820	if [[ $do_remote = true ]]
4821	then
4822	(( i = 0 ))
4823	while (( i < iin ))
4824	do
4825	(( i = i + 1 ))
4826	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4827	if [[ "${transin[$i]}" = job ]]
4828	then
4829	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4830	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4831	echo " " >> $jobfile
4832	echo "%END%" >> $jobfile
4833	else
4834	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4835	fi
4836
4837	# CHECK, IF FILE COULD BE CREATED
4838	echo "if [[ \$? = 1 ]]" >> $jobfile
4839	echo "then" >> $jobfile
4840	echo " echo \" \" " >> $jobfile
4841	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4842	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4843	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4844	echo " execute_mrun=false" >> $jobfile
4845	echo "fi" >> $jobfile
4846	done
4847	fi
4848
4849	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4850	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4851	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4852	echo "LOCAL_PWD=$working_directory" >> $jobfile
4853	echo "export LOCAL_PWD" >> $jobfile
4854
4855	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4856	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4857	echo "export LOCAL_MRUN_PATH" >> $jobfile
4858
4859	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4860	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4861	# then
4862	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4863	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4864	# fi
4865
4866	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4867	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4868	echo "set -x" >> $jobfile
4869	echo "queue=$queue" >> $jobfile
4870	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4871	echo 'ls -al; echo `pwd`' >> $jobfile
4872	echo "cd \$HOME" >> $jobfile
4873	echo "rm -rf $TEMPDIR" >> $jobfile
4874
4875
4876
4877
4878	# START THE JOB USING SUBJOB-COMMAND
4879	if [[ $silent = false ]]
4880	then
4881	printf "\n "
4882	else
4883	printf "\n\n"
4884	fi
4885
4886	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
4887	rm -rf $jobfile
4888
4889
4890	fi # END OF REMOTE-PART

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