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source: palm/trunk/SCRIPTS/mrun @ 1442

Last change on this file since 1442 was 1442, checked in by raasch, 10 years ago
queues for lccrayb/lccrayh adjusted
Property svn:keywords set to `Id Rev`
File size: 175.4 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	# Default queues for HLRN-III (lccrayb/lccrayh) defined
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1442 2014-07-28 07:09:10Z raasch $
29	#
30	# 1422 2014-07-02 10:01:25Z kanani
31	# automatic restarts enabled for lccrayb,
32	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
33	#
34	# 1420 2014-06-10 06:24:14Z raasch
35	# -j1 option added to aprung command for lccrayf (CSC)
36	#
37	# 1402 2014-05-09 14:25:13Z raasch
38	# batch_job added to envpar-NAMELIST
39	#
40	# 1357 2014-04-11 15:02:03Z witha
41	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
42	# possible)
43	#
44	# 1320 2014-03-20 08:40:49Z raasch
45	# check namelist file set false by default
46	#
47	# 1304 2014-03-12 10:29:42Z raasch
48	# ulimit option changed from -Ss to -s
49	#
50	# bugfix: missing "fi" in r1289
51	#
52	# 1289 2014-03-04 07:12:34Z raasch
53	# comments translated to English
54	# necriam-, fimm-, ibmy-, and sgi-specific code removed
55	# export of variables for palm and interpret_config removed
56	#
57	# 1281 2014-02-01 07:55:49Z raasch
58	# rsync-copy restricted to Cray machines, since command is unavailable on some
59	# other systems
60	#
61	# 1279 2014-01-28 12:10:14Z raasch
62	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
63	# in order to remove annoying restrictions concerning the number of processors which
64	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
65	# restriction, one of the nodes will be filled with less than the given number of
66	# tasks per node. A respective warning is given.
67	#
68	# 1274 2014-01-09 13:14:54Z heinze
69	# adjustments for lccrayh
70	#
71	# 1272 2014-01-08 10:19:32Z witha
72	# small adjustment for lcflow
73	#
74	# 1270 2013-12-16 11:05:01Z fricke
75	# call of combine_plot_fields adjusted for lccrayb/lccrayh
76	#
77	# 1255 2013-11-07 14:43:35Z raasch
78	# further adjustments for lccrayb remote access
79	#
80	# 1241 2013-10-30 11:36:58Z heinze
81	# Enable use of nudging input and input of large scale forcing from
82	# external files
83	#
84	# 1229 2013-09-20 06:55:19Z raasch
85	# further adjustments for lccrayb
86	#
87	# 1224 2013-09-16 07:27:23Z raasch
88	# first adjustments for lccrayb
89	#
90	# 1210 2013-08-14 10:58:20Z raasch
91	# fftw support added
92	#
93	# 1201 2013-07-10 16:17:59Z witha
94	# adjustments for Forwind cluster (lcflow)
95	#
96	# 1199 2013-07-05 14:52:22Z raasch
97	# adjustments for CSC Helsinki (lccrayf),
98	# executables for batch jobs can be created in advance, in order to avoid calling
99	# the compiler within the batch job (only works if batch jobs are submitted on
100	# local host)
101	#
102	# 1190 2013-06-25 09:39:21Z heinze
103	# enable use of automatic restarts for ibmh
104	# use of cluster/express queue enabled (ibmh)
105	#
106	# 1124 2013-04-09 15:46:52Z raasch
107	# variable "memory" is exported via typeset option -x, because otherwise an unknown
108	# side effect may lead to data loss while getopts is reading the script-option arguments
109	#
110	# 1122 2013-04-09 08:37:16Z heinze
111	# Bugfix: change type of variable last_char
112	#
113	# 1119 2013-04-05 15:11:19Z raasch
114	# Bugfix for setting -T option for subjob
115	#
116	# 1108 2013-03-05 07:03:32Z raasch
117	# bugfix for coupled runs on lckyut/lckyuh
118	#
119	# 1106 2013-03-04 05:31:38Z raasch
120	# --stdin argument for mpiexec on lckyuh
121	# -y and -Y settings output to header
122	#
123	# 1103 2013-02-20 02:15:53Z raasch
124	# default script runs again under ksh, because of unsolved problems with read
125	# from stdin: when bash script is called from a ksh, message "read error: 0:
126	# Resource temporarily unavailable" appears and script does not stop,
127	# further bash compatibility adjustments,
128	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
129	# on lckyuh, but mrun does not terminate and issues a warning instead
130	#
131	# 1101 2013-02-17 10:20:21Z raasch
132	# script now running under bash instead of ksh, which required small adjustments
133	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
134	# read from stdin),
135	# cross compilername on lckyuh compute nodes replaced by real compiler name
136	#
137	# 1099 2013-02-10 01:47:43Z raasch
138	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
139	# and for Forwind cluster (lcflow)
140	# small further adjustments for lckyut
141	#
142	# 1094 2013-02-03 01:52:12Z raasch
143	# explicit ssh/scp port can be set in config file with environment variable
144	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
145	# decalpha parts (yonsei) removed
146	#
147	# 2013-02-02 07:06:13Z raasch
148	# adjustments for Kyushu-University computing center (lckyut - tatara)
149	#
150	# 1083 2013-01-04 10:22:09Z maronga
151	# bugfix in parameter file check (read %cpp_options was missing)
152	#
153	# 1069 2012-11-28 16:18:43Z maronga
154	# bugfix: coupling mode was always set to mpi2, typos removed
155	#
156	# 1058 2012-11-21 07:00:35Z raasch
157	# Intel inspector (inspxe) is given the number of PEs instead of the number of
158	# nodes
159	#
160	# 1046 2012-11-09 14:38:45Z maronga
161	# code put under GPL (PALM 3.9)
162	#
163	# 21/03/94 - Siggi - first version finished
164	# 03/03/94 - Siggi - script development started
165	#
166	#--------------------------------------------------------------------------------#
167	# mrun - script for running PALM jobs
168	#--------------------------------------------------------------------------------#
169
170
171
172	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
173
174	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
175	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
176	# (TOO MANY ARGUMENTS - PROBLEM)
177	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
178
179	AddFilenames=""
180	additional_conditions=""
181	add_source_path=""
182	afname=""
183	archive_save=true
184	archive_system=none
185	check_namelist_files=false
186	combine_plot_fields=true
187	compiler_name=""
188	cond1=""
189	cond2=""
190	config_file=.mrun.config
191	coupled_dist=""
192	coupled_mode="mpi1"
193	cpp_opts=""
194	cpp_options=""
195	cpumax=0
196	cpurest=0
197	create_executable_for_batch=false
198	delete_temporary_catalog=true
199	do_batch=false
200	do_compile=true
201	do_remote=false
202	do_stagein=true
203	do_stageout=true
204	do_trace=false
205	email_notification="none"
206	exclude=""
207	executable=""
208	execution_error=false
209	fftw_inc=""
210	fftw_lib=""
211	fftw_support=false
212	fname=test
213	fromhost=""
214	global_revision=""
215	group_number=none
216	host=""
217	host_file=""
218	hp=""
219	ignore_archive_error=false
220	input_list=""
221	interpreted_config_file=""
222	job_catalog="~/job_queue"
223	job_on_file=""
224	keep_data_from_previous_run=false
225	link_local_input=false
226	link_local_output=false
227	localhost_realname=$(hostname)
228	local_dvrserver_running=.FALSE.
229	locat=normal
230	mainprog=""
231	makefile=""
232	max_par_io_str=""
233	mc=$0
234	while [[ $(echo $mc \| grep -c "/") != 0 ]]
235	do
236	mc=`echo $mc \| cut -f2- -d"/"`
237	done
238	module_calls=""
239	mrun_script_name=$mc
240	netcdf_inc=""
241	netcdf_lib=""
242	netcdf_support=false
243	node_usage=default
244	numprocs=""
245	numprocs_atmos=0
246	numprocs_ocean=0
247	OOPT=""
248	openmp=false
249	output_list=""
250	package_list=""
251	queue=none
252	read_from_config=""
253	restart_run=false
254	if [[ `hostname` = rte10 ]]
255	then
256	return_addres=133.5.185.60
257	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
258	elif [[ `hostname` = climate0 ]]
259	then
260	return_addres=165.132.26.68
261	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
262	elif [[ `hostname` = urban00 ]]
263	then
264	return_addres=147.46.30.151
265	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
266	else
267	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
268	fi
269	return_password=""
270	return_username=$LOGNAME
271	remotecall=false
272	remote_username=""
273	run_coupled_model=false
274	run_mode=""
275	store_on_archive_system=false
276	dashes=" ----------------------------------------------------------------------------"
277	silent=false
278	source_list=""
279	source_path=SOURCE
280	tasks_per_node=""
281	threads_per_task=1
282	tmpcreate=false
283	tmp_data_catalog=""
284	transfer_problems=false
285	usern=$LOGNAME
286	use_openmp=false
287	version="MRUN 2.1 Rev$Rev: 1442 $"
288	working_directory=`pwd`
289	TOPT=""
290	XOPT=""
291	zeit=$( date \| cut -c 12-19 )
292
293	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
294	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
295	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
296	# SCRIPT-OPTION ARGUMENTS
297	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
298
299
300
301	# ERROR HANDLING IN CASE OF EXIT
302	trap 'rm -rf $working_directory/tmp_mrun
303	if [[ $locat != normal && $locat != control_c ]]
304	then
305
306	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
307	(( i = 0 ))
308	while (( i < iec ))
309	do
310	(( i = i + 1 ))
311	printf "\n *** Execution of ERROR-command:\n"
312	printf " >>> ${err_command[$i]}\n"
313	eval ${err_command[$i]}
314	done
315	if [[ -n $interpreted_config_file ]]
316	then
317	rm -rf $interpreted_config_file
318	fi
319	if [[ -n .mrun_environment ]]
320	then
321	rm -rf .mrun_environment
322	fi
323	if [[ $tmpcreate = true ]]
324	then
325	printf "\n *** Contents of \"$TEMPDIR\":\n"
326	ls -al; cd
327	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
328	fi
329	if [[ "$dvrserver_id" != "" ]]
330	then
331	echo "+++ killing dvrserver_id=$dvrserver_id"
332	kill $dvrserver_id
333	fi
334	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
335	then
336	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
337	fi
338	printf "\n\n+++ MRUN killed \n\n"
339	elif [[ $locat != control_c ]]
340	then
341	printf "\n\n --> all actions finished\n\n"
342	printf " Bye, bye $usern !!\n\n"
343	fi' exit
344
345
346	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
347	trap 'rm -rf $working_directory/tmp_mrun
348	rm -rf $working_directory/tmp_check_namelist_files
349	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
350	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
351	then
352	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
353	fi
354	if [[ "$dvrserver_id" != "" ]]
355	then
356	echo "+++ killing dvrserver_id=$dvrserver_id"
357	kill $dvrserver_id
358	fi
359	printf "\n+++ MRUN killed by \"^C\" \n\n"
360	locat=control_c
361	exit
362	' 2
363
364
365	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
366	# BEEN SET
367	if [[ "$PALM_BIN" = "" ]]
368	then
369	printf "\n +++ environment variable PALM_BIN has not been set"
370	printf "\n please set it to the directory where the PALM scripts are located"
371	locat=palm_bin; exit
372	fi
373	export PATH=$PALM_BIN:$PATH
374
375
376
377	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
378	# WHICH WILL BE USED TO START RESTART-JOBS
379	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
380	do
381	case $option in
382	(a) afname=$OPTARG;;
383	(A) store_on_archive_system=true; mc="$mc -A";;
384	(b) do_batch=true; mc="$mc -b";;
385	(B) delete_temporary_catalog=false; mc="$mc -B";;
386	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
387	(C) restart_run=true; mc="$mc -C";;
388	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
389	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
390	(F) job_on_file="-D"; mc="$mc -F";;
391	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
392	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
393	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
394	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
395	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
396	(I) ignore_archive_error=true; mc="$mc -I";;
397	(k) keep_data_from_previous_run=true; mc="$mc -k";;
398	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
399	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
400	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
401	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
402	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
403	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
404	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
405	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
406	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
407	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
408	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
409	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
410	(S) read_from_config=false; mc="$mc -S";;
411	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
412	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
413	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
414	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
415	(v) silent=true; mc="$mc -v";;
416	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
417	(x) do_trace=true;set -x; mc="$mc -x";;
418	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
419	(y) ocean_file_appendix=true; mc="$mc -y";;
420	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
421	(z) check_namelist_files=false; mc="$mc -z";;
422	(Z) combine_plot_fields=false; mc="$mc -Z";;
423	(\?) printf "\n +++ unknown option $OPTARG \n"
424	printf "\n --> type \"$0 ?\" for available options \n"
425	locat=parameter;exit;;
426	esac
427	done
428
429
430	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
431	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
432	(( to_shift = $OPTIND - 1 ))
433	shift $to_shift
434
435	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
436	if [[ "$1" = "?" ]]
437	then
438	(printf "\n *** mrun can be called as follows:\n"
439	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"
440	printf "\n Description of available options:\n"
441	printf "\n Option Description Default-Value"
442	printf "\n -a base name of input files equiv. -d"
443	printf "\n -A archiving when using file-attribute fl"
444	printf "\n -b batch-job on local machine ---"
445	printf "\n -B do not delete temporary directory at end ---"
446	printf "\n -c configuration file .mrun.config"
447	printf "\n -d base name of files attached to program test"
448	printf "\n -D preprocessor(cpp)-directives \"\" "
449	printf "\n -F create remote job file only ---"
450	printf "\n -h execution host $localhost_realname"
451	printf "\n -i INPUT control list \"\" "
452	printf "\n -I archiving errors of previous batch-jobs"
453	printf "\n will be ignored"
454	printf "\n -k keep data from previous run"
455	printf "\n -K additional conditions for controling"
456	printf "\n usage of conditional code and"
457	printf "\n env-variables in configuration file \"\" "
458	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
459	printf "\n -M Makefile name Makefile"
460	printf "\n -n node usage (shared/not_shared) depending on -h"
461	printf "\n -o OUTPUT control list \"\" "
462	printf "\n -O threads per openMP task ---"
463	printf "\n -p software package list \"\" "
464	printf "\n -q queue \"$queue\" "
465	printf "\n -r run control list (combines -i -o) \"\" "
466	printf "\n -s filenames of routines to be compiled \"\" "
467	printf "\n must end with .f, .f90, .F, or .c !"
468	printf "\n use \"..\" for more than one file and wildcards"
469	printf "\n -s LM compiles all locally modified files"
470	printf "\n -S config file interpreted by shellscript ---"
471	printf "\n -t allowed cpu-time in seconds (batch) 0"
472	printf "\n -T tasks per node depending on -h"
473	printf "\n -u username on remote machine \"\" "
474	printf "\n -v no prompt for confirmation ---"
475	printf "\n -w maximum parallel io streams as given by -X"
476	printf "\n -x tracing of mrun for debug purposes ---"
477	printf "\n -X # of processors (on parallel machines) 1"
478	printf "\n -y add appendix \"_O\" to all local output"
479	printf "\n files (ocean precursor runs followed by"
480	printf "\n coupled atmosphere-ocean runs) ---"
481	printf "\n -Y run coupled model, \"#1 #2\" with"
482	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
483	printf "\n -z disable a priori parameter file check ---"
484	printf "\n -Z skip combine_plot_fields at the end of "
485	printf "\n the simulation ---"
486	printf "\n "
487	printf "\n Possible values of positional parameter <modus>:"
488	printf "\n \"?\" - this outline \n\n") \| more
489	exit
490	elif [[ "$1" != "" ]]
491	then
492	printf "\n +++ positional parameter $1 unknown \n"
493	locat=parameter; exit
494	fi
495
496
497
498	# SHORT STARTING MESSAGE
499	printf "\n*** $version "
500	printf "\n will be executed. Please wait ..."
501
502
503
504	# CHECK, IF CONFIGURATION FILE EXISTS
505	if [[ ! -f $config_file ]]
506	then
507	printf "\n\n +++ configuration file: "
508	printf "\n $config_file"
509	printf "\n does not exist"
510	locat=connect; exit
511	fi
512
513
514	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
515	line=""
516	grep "%host_identifier" $config_file > tmp_mrun
517	while read line
518	do
519	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
520	then
521	HOSTNAME=`echo $line \| cut -d" " -s -f2`
522	host_identifier=`echo $line \| cut -d" " -s -f3`
523	if [[ $localhost_realname = $HOSTNAME ]]
524	then
525	localhost=$host_identifier
526	break
527	fi
528	fi
529	done < tmp_mrun
530
531	if [[ "$localhost" = "" ]]
532	then
533	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
534	printf "\n for local host \"$localhost_realname\"."
535	printf "\n Please add line"
536	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
537	printf "\n to the configuration file."
538	locat=localhost; exit
539	fi
540
541
542	# SET HOST-SPECIFIC VARIABLES
543	case $localhost_realname in
544	(r1\|r2\|h01\|b01) archive_system=tivoli;;
545	(cs*) archive_system=ut;;
546	esac
547
548
549	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
550	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
551	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
552	[[ "$afname" = "" ]] && afname=$fname
553
554
555	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
556	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
557	# STATEMENTS IN THE CONFIGURATION FILE
558	if [[ "$run_mode" != "" ]]
559	then
560	input_list="$input_list $run_mode"
561	output_list="$output_list $run_mode"
562	fi
563
564
565	# ??? is this (and the respective option -H) really required ???
566	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
567	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
568	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
569	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
570	if [[ "$fromhost" = "" ]]
571	then
572	fromhost=$localhost
573	fi
574
575
576	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
577	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
578	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
579	# TO BE SUBMITTED (I.E. do_bacth=true)
580	if [[ -n $host && "$host" != $localhost ]]
581	then
582	do_batch=true
583	do_remote=true
584	case $host in
585	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
586	(*) printf "\n"
587	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
588	printf "\n is not available"
589	locat=nqs; (( iec = 0 )); exit;;
590	esac
591	else
592	host=$localhost
593	fi
594
595
596	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
597	if [[ -n $additional_conditions ]]
598	then
599	cond1=`echo $additional_conditions \| cut -d" " -f1`
600	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
601	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
602	if [[ -n $dummy ]]
603	then
604	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
605	locat=options; exit
606	fi
607	block=_$cond1
608	[[ -n $cond2 ]] && block=${block}_$cond2
609	fi
610
611
612	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
613	if [[ $run_coupled_model = true ]]
614	then
615
616	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
617	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
618
619	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
620	then
621
622	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
623	printf "\n PEs (total) : $numprocs"
624	printf "\n PEs (atmosphere): $numprocs_atmos"
625	printf "\n PEs (ocean) : $numprocs_ocean"
626	locat=coupling; exit
627
628	fi
629
630
631	# GET coupled_mode FROM THE CONFIG FILE
632	line=""
633	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
634	while read line
635	do
636	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
637	then
638	coupled_mode="mpi2"
639	fi
640	done < tmp_mrun
641
642	fi
643
644
645	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
646	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
647	then
648	if [[ $ignore_archive_error = false ]]
649	then
650	printf "\n +++ data archiving of previous run failed"
651	printf "\n see directory \~/job_queue on remote machine"
652	locat=archive; exit
653	else
654	printf "\n +++ warning: data archiving in a previous run failed"
655	printf "\n MRUN continues, trying to get backup copy"
656	fi
657	fi
658
659
660	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
661	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
662	mrun_memory=$memory
663	mrun_group_number=$group_number
664	mrun_cpumax=$cpumax
665	mrun_numprocs=$numprocs
666
667
668	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
669	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
670	if [[ "$read_from_config" = false ]]
671	then
672
673	[[ $silent = false ]] && printf "\n Reading the configuration file... "
674
675	# READ THE CONFIGURATION FILE LINE BY LINE
676	while read zeile
677	do
678	[[ $silent = false ]] && printf "."
679
680
681	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
682	eval zeile=\"$zeile\"
683
684
685	# INTERPRET THE LINE
686	if [[ "$(echo $zeile)" = "" ]]
687	then
688	# EMPTY LINE, NO ACTION
689	continue
690
691	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
692	then
693
694	# LINE IS A COMMENT LINE
695	true
696
697	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
698	then
699
700	# LINE DEFINES AN ENVIRONMENT-VARIABLE
701	zeile=$(echo $zeile \| cut -c2-)
702	var=`echo $zeile \| cut -d" " -f1`
703	value=`echo $zeile \| cut -d" " -s -f2`
704	for_host=`echo $zeile \| cut -d" " -s -f3`
705	for_cond1=`echo $zeile \| cut -d" " -s -f4`
706	for_cond2=`echo $zeile \| cut -d" " -s -f5`
707
708	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
709	then
710
711	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
712	# "::" IS REPLACED BY ":".
713	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
714
715
716	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
717	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
718	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
719	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
720	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
721	# CONFIGURATION-FILE.
722	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
723	then
724	eval $var=\$value
725
726	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
727	if [[ $do_trace = true ]]
728	then
729	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
730	fi
731	fi
732
733	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
734	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
735	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
736	# MUST HAVE TO BE STARTED
737	if [[ $var = host ]]
738	then
739	if [[ -n $host && "$host" != $localhost ]]
740	then
741	do_batch=true
742	do_remote=true
743	case $host in
744	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
745	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
746	printf "\n is not available"
747	locat=nqs; exit;;
748	esac
749	else
750	host=$localhost
751	fi
752	fi
753
754	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
755	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
756	# BY MRUN (E.G. subjob)
757	export $var
758	fi
759
760
761
762
763	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
764	then
765
766	# LINE DEFINES ERROR-COMMAND
767	(( iec = iec + 1 ))
768	zeile=$(echo $zeile \| cut -c4-)
769	err_command[$iec]="$zeile"
770
771	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
772	then
773
774	# LINE DEFINES INPUT-COMMAND
775	(( iic = iic + 1 ))
776	zeile=$(echo $zeile \| cut -c4-)
777	in_command[$iic]="$zeile"
778
779	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
780	then
781
782	# LINE DEFINES OUTPUT-COMMAND
783	(( ioc = ioc + 1 ))
784	zeile=$(echo $zeile \| cut -c4-)
785	out_command[$ioc]="$zeile"
786
787	else
788
789	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
790	# s2a: in/out - field
791	# s2b: loc - field (optional)
792	# s2c: tr/ar - field (optional)
793	s1=`echo $zeile \| cut -d" " -f1`
794	s2=`echo $zeile \| cut -d" " -s -f2`
795	s2a=$(echo $s2 \| cut -d":" -f1)
796	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
797	then
798	s2b=""
799	s2c=""
800	else
801	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
802	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
803	fi
804	s3=`echo $zeile \| cut -d" " -f3`
805	s4=`echo $zeile \| cut -d" " -s -f4`
806	s5=`echo $zeile \| cut -d" " -s -f5`
807	s6=`echo $zeile \| cut -d" " -s -f6`
808
809
810	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
811	# INPUT- OR OUTPUT-LIST.
812	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
813	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
814	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
815	# IS NOT CHECKED AND STORED.
816	IFSALT="$IFS"; IFS="$IFS:"
817	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
818	then
819	found=false
820	for actual in $input_list
821	do
822	for formal in $s3
823	do
824	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
825	done
826	done
827	if [[ $found = true ]]
828	then
829	(( iin = iin + 1 ))
830	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
831	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
832	extin[$iin]=$s6
833	fi
834	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
835	then
836	found=false
837	for actual in $output_list
838	do
839	for formal in $s3
840	do
841	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
842	done
843	done
844	if [[ $found = true ]]
845	then
846	(( iout = iout + 1 ))
847	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
848	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
849	fi
850	elif [[ "$s2a" != in && "$s2a" != out ]]
851	then
852	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
853	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
854	locat=connect; exit
855	fi
856	IFS="$IFSALT"
857	fi
858	done < $config_file
859
860	else
861
862
863	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
864	[[ $silent = false ]] && printf "..."
865	interpreted_config_file=.icf.$RANDOM
866
867
868
869	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
870	cat > .mrun_environment << %%END%%
871	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
872	config_file = '$config_file', do_remote = '$do_remote',
873	do_trace = '$do_trace', host = '$host',
874	input_list = '$input_list', icf = '$interpreted_config_file',
875	localhost = '$localhost', output_list = '$output_list' /
876
877	%%END%%
878
879	if [[ "$host" != $localhost ]]
880	then
881
882	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
883	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
884	if [[ $? != 0 ]]
885	then
886	printf "\n\n +++ no interpret_config found"
887	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
888	locat=interpret_config; exit
889	fi
890	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
891	$interpret_config_executable
892
893	else
894
895	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
896	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
897	then
898	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
899	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
900	locat=interpret_config; exit
901	else
902	interpret_config${block}.x
903	fi
904
905	fi
906	rm .mrun_environment
907
908
909	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
910	chmod u+x $interpreted_config_file
911	export PATH=$PATH:.
912	. $interpreted_config_file
913	rm $interpreted_config_file
914
915	fi
916
917
918	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
919	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
920	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
921	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
922	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
923	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
924	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
925
926
927	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
928	# FOR SOURCE-FILES TO BE COMPILED.
929	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
930	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
931	if [[ "$SOURCES_COMPLETE" = "" ]]
932	then
933
934	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
935	# HAS BEEN DEFINED
936	source_path=""
937	line=""
938	grep "%source_path" $config_file > tmp_mrun
939	while read line
940	do
941	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
942	then
943	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
944	then
945	global_source_path=`echo $line \| cut -d" " -f2`
946	fi
947	fi
948	done < tmp_mrun
949
950	line=""
951	found=false
952	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
953	while read line
954	do
955	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
956	then
957	if [[ $found = true ]]
958	then
959	printf "\n\n +++ more than one source path found in configuration file"
960	printf "\n for local host \"$localhost\" "
961	locat=source_path; exit
962	fi
963	source_path=`echo $line \| cut -d" " -f2`
964	found=true
965	fi
966	done < tmp_mrun
967	rm tmp_mrun
968
969	if [[ "$source_path" = "" ]]
970	then
971	if [[ "$global_source_path" != "" ]]
972	then
973	source_path=$global_source_path
974	else
975	printf "\n\n +++ no source path found in configuration file"
976	printf "\n for local host \"$localhost\" "
977	locat=source_path; exit
978	fi
979	fi
980	eval source_path=$source_path
981
982	if [[ ! -d $source_path ]]
983	then
984	printf "\n\n +++ source path \"$source_path\" on local host"
985	printf "\n \"$localhost\" does not exist"
986	locat=source_path; exit
987	fi
988
989	fi
990
991
992	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
993	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
994	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
995	then
996	global_revision=`svnversion $source_path 2>/dev/null`
997	global_revision="Rev: $global_revision"
998	fi
999
1000
1001	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1002	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1003	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1004	if [[ -n $host && "$host" != $localhost ]]
1005	then
1006	do_batch=true
1007	do_remote=true
1008	case $host in
1009	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1010	(*) printf "\n"
1011	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1012	printf "\n is not available"
1013	locat=nqs; (( iec = 0 )); exit;;
1014	esac
1015	else
1016	host=$localhost
1017	fi
1018
1019
1020	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1021	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1022	then
1023
1024	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1025	if [[ ! -n $numprocs ]]
1026	then
1027	printf "\n"
1028	printf "\n +++ option \"-K parallel\" requires additional specification"
1029	printf "\n of the number of processors to be used by"
1030	printf "\n mrun-option \"-X\" or by environment-variable"
1031	printf "\n \"numprocs\" in the configuration file"
1032	locat=numprocs; (( iec = 0 )); exit
1033	fi
1034
1035	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1036	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1037	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1038	then
1039	printf "\n"
1040	printf "\n +++ option \"-T\" (tasks per node) is missing"
1041	printf "\n set -T option or define tasks_per_node in the config file"
1042	locat=tasks_per_node; (( iec = 0 )); exit
1043	fi
1044
1045	if (( numprocs < tasks_per_node ))
1046	then
1047	printf "\n"
1048	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1049	printf "\n given values: -T $tasks_per_node -X $numprocs"
1050	locat=tasks_per_node; (( iec = 0 )); exit
1051	fi
1052
1053	if [[ $host != lcflow && $host != lcxt5m ]]
1054	then
1055	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1056	(( ival = $tasks_per_node ))
1057	(( pes = numprocs ))
1058	(( ii = pes / ival ))
1059	(( remaining_pes = pes - ii * ival ))
1060	if (( remaining_pes > 0 ))
1061	then
1062	printf "\n"
1063	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1064	printf "\n divisor of the total number of processors (option \"-X\")"
1065	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1066	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1067	(( nodes = nodes + 1 ))
1068	fi
1069	fi
1070
1071
1072	# SETTINGS FOR SUBJOB-COMMAND
1073	OOPT="-O $threads_per_task"
1074
1075	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1076	if [[ "$tasks_per_node" != "" ]]
1077	then
1078	TOPT="-T $tasks_per_node"
1079	fi
1080
1081	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1082	if [[ $node_usage = default ]]
1083	then
1084	if [[ $host = ibms ]]
1085	then
1086	node_usage=shared
1087	else
1088	node_usage=not_shared
1089	fi
1090	fi
1091
1092	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1093	then
1094	printf "\n"
1095	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1096	printf "\n \"shared\" or \"not_shared\""
1097	locat=tasks_per_node; (( iec = 0 )); exit
1098	fi
1099
1100	fi
1101
1102	# CHECK IF HOSTFILE EXISTS
1103	if [[ -n $hostfile ]]
1104	then
1105	if [[ ! -f $hostfile ]]
1106	then
1107	printf "\n"
1108	printf "\n +++ hostfile \"$hostfile\" does not exist"
1109	locat=hostfile; exit
1110	fi
1111	fi
1112
1113
1114	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1115	if [[ "$maximum_parallel_io_streams" = "" ]]
1116	then
1117	maximum_parallel_io_streams=$numprocs
1118	fi
1119
1120
1121	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1122	if [[ "$scp_port" != "" ]]
1123	then
1124	PORTOPT="-P $scp_port"
1125	SSH_PORTOPT="-p $scp_port"
1126	fi
1127
1128
1129	# SET DEFAULT-QUEUE, IF NOT GIVEN
1130	if [[ $queue = none ]]
1131	then
1132	case $host in
1133	(ibmh) queue=cluster;;
1134	(ibmkisti) queue=class.32plus;;
1135	(lccrayb) queue=mpp1q;;
1136	(lccrayh) queue=mpp1q;;
1137	(lckiaps) queue=normal;;
1138	(lckyoto) queue=ph;;
1139	(lckyuh) queue=fx-single;;
1140	(lckyut) queue=cx-single;;
1141	(lctit) queue=S;;
1142	(nech) queue=none;;
1143	(unics) queue=unics;;
1144	esac
1145	fi
1146
1147
1148	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1149	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1150	(( i = 0 ))
1151	while (( i < iin ))
1152	do
1153	(( i = i + 1 ))
1154	(( maxcycle = 0 ))
1155
1156	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1157	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1158	if [[ "${actionin[$i]}" = di ]]
1159	then
1160	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1161	# HOST ONLY
1162	eval filename=${pathin[$i]}/${endin[$i]}
1163	else
1164	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1165	# HOST ONLY
1166	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1167	fi
1168	eval pathname=${pathin[$i]}
1169
1170	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1171	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1172	then
1173	filename_input=$filename
1174	fi
1175
1176	# CHECK IF FILE EXISTS
1177	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1178	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1179	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1180	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1181	then
1182
1183	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1184	if [[ "${transin[$i]}" != "locopt" ]]
1185	then
1186	printf "\n\n +++ INPUT-file: "
1187	if [[ "${extin[$i]}" = "" ]]
1188	then
1189	printf "\n $filename"
1190	else
1191	printf "\n $filename.${extin[$i]}"
1192	fi
1193	printf "\n does not exist\n"
1194	locat=input; exit
1195	else
1196	transin[$i]="unavailable"
1197	fi
1198	else
1199
1200	# DETERMINE THE FILE'S CYCLE NUMBER
1201	ls -1 -d $filename > filelist 2>/dev/null
1202	ls -1 -d $filename.* >> filelist 2>/dev/null
1203	while read zeile
1204	do
1205	cycle=$(echo $zeile \| cut -f2 -d".")
1206	if [[ "$cycle" = "$zeile" ]]
1207	then
1208	(( icycle = 0 ))
1209	elif [[ "$cycle" = "${extin[$i]}" ]]
1210	then
1211	(( icycle = 0 ))
1212	else
1213	(( icycle = $cycle ))
1214	fi
1215	if (( icycle > maxcycle ))
1216	then
1217	(( maxcycle = icycle ))
1218	file_to_be_used=$zeile
1219	fi
1220	done <filelist
1221	rm filelist
1222
1223	# APPEND CYCLE NUMBER TO FILENAME
1224	if (( maxcycle > 0 ))
1225	then
1226	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1227	then
1228	filename=${filename}.$maxcycle.${extin[$i]}
1229	else
1230	filename=${filename}.$maxcycle
1231	fi
1232	else
1233	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1234	then
1235	filename=${filename}.${extin[$i]}
1236	fi
1237	fi
1238
1239	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1240	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1241	absnamein[$i]=$filename
1242	if (( maxcycle > 0 ))
1243	then
1244	if [[ "${actionin[$i]}" = di ]]
1245	then
1246	frelin[$i]=${endin[$i]}.$maxcycle
1247	else
1248	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1249	fi
1250	else
1251	if [[ "${actionin[$i]}" = di ]]
1252	then
1253	frelin[$i]=${endin[$i]}
1254	else
1255	frelin[$i]=${afname}${endin[$i]}
1256	fi
1257	fi
1258
1259	fi
1260	done
1261
1262	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1263	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1264	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1265	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1266	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1267	# REMOTE HOST)
1268	(( i = 0 ))
1269	while (( i < iout ))
1270	do
1271	(( i = i + 1 ))
1272	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1273	then
1274	if [[ "${actionout[$i]}" = tr ]]
1275	then
1276	actionout[$i]=""
1277	elif [[ "${actionout[$i]}" = trpe ]]
1278	then
1279	actionout[$i]=pe
1280	elif [[ "${actionout[$i]}" = tra ]]
1281	then
1282	actionout[$i]=a
1283	fi
1284	(( maxcycle = 0 ))
1285	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1286	eval catalogname=${pathout[$i]}
1287	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1288	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1289	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1290	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1291	then
1292
1293	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1294	if cat /dev/null > $filename
1295	then
1296	rm $filename
1297	else
1298
1299	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1300	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1301	if [[ ! -d $catalogname ]]
1302	then
1303	if mkdir -p $catalogname
1304	then
1305	printf "\n\n *** directory:"
1306	printf "\n $catalogname"
1307	printf "\n was created\n"
1308	else
1309	printf "\n\n +++ OUTPUT-file:"
1310	printf "\n $filename"
1311	printf "\n cannot be created, because directory does not exist"
1312	printf "\n and cannot be created either"
1313	printf "\n"
1314	locat=output ; exit
1315	fi 2>/dev/null
1316	else
1317	printf "\n\n +++ OUTPUT-file:"
1318	printf "\n $filename"
1319	printf "\n cannot be created, although directory exists"
1320	printf "\n"
1321	locat=output ; exit
1322	fi
1323	fi 2>/dev/null
1324	else
1325
1326	# DETERMINE THE CYCLE NUMBER
1327	ls -1 -d $filename > filelist 2>/dev/null
1328	ls -1 -d $filename.* >> filelist 2>/dev/null
1329	while read zeile
1330	do
1331	cycle=$(echo $zeile \| cut -f2 -d".")
1332	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1333	then
1334	(( icycle = 1 ))
1335	else
1336	(( icycle = $cycle + 1 ))
1337	fi
1338	if (( icycle > maxcycle ))
1339	then
1340	(( maxcycle = icycle ))
1341	fi
1342	done <filelist
1343	rm filelist
1344	fi
1345
1346	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1347	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1348	if [[ "${actionout[$i]}" != a ]]
1349	then
1350	if (( maxcycle > 0 ))
1351	then
1352	filename=${filename}.$maxcycle
1353	if cat /dev/null > $filename
1354	then
1355	rm $filename
1356	else
1357	printf "\n +++ OUTPUT-file:"
1358	printf "\n $filename"
1359	printf "\n cannot be created"
1360	locat=output ; exit
1361	fi
1362	fi
1363	else
1364	(( maxcycle = maxcycle - 1 ))
1365	if (( maxcycle > 0 ))
1366	then
1367	filename=${filename}.$maxcycle
1368	fi
1369	fi
1370
1371	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1372	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1373	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1374	pathout[$i]=$filename
1375	if (( maxcycle > 0 ))
1376	then
1377	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1378	else
1379	frelout[$i]=${fname}${endout[$i]}
1380	fi
1381
1382	fi
1383	done
1384
1385
1386	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1387	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1388	then
1389	if [[ "$dvr_inc" = "" ]]
1390	then
1391	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1392	printf "\n This is required for the dvrp_graphics package.\n"
1393	locat=dvr; exit
1394	fi
1395	if [[ "$dvr_lib" = "" ]]
1396	then
1397	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1398	printf "\n This is required for the dvrp_graphics package.\n"
1399	locat=dvr; exit
1400	fi
1401	fi
1402
1403
1404	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1405	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1406	if [[ "$mainprog" = "" && "$executable" = "" ]]
1407	then
1408	printf "\n +++ neither main program nor executable defined"
1409	locat=source; exit
1410	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1411	then
1412	printf "\n +++ main program as well as executable defined"
1413	locat=source; exit
1414	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1415	then
1416	do_compile=false
1417	fi
1418
1419
1420	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1421	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1422	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1423	then
1424	rm -rf SOURCES_FOR_RUN_$fname
1425	mkdir SOURCES_FOR_RUN_$fname
1426	fi
1427
1428
1429	# COLLECT ALL ROUTINES TO BE COMPILED
1430	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1431	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1432	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1433	then
1434
1435	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1436
1437	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1438	then
1439
1440	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1441	source_list=""
1442	cd $source_path
1443
1444
1445	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1446	if [[ ! -d .svn ]]
1447	then
1448	printf "\n\n +++ source directory"
1449	printf "\n \"$source_path\" "
1450	printf "\n is not under control of \"subversion\"."
1451	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1452	fi
1453
1454
1455	# LIST ALL MODIFIED SOURCE CODE FILES
1456	Filenames=""
1457	svn status > tmp_mrun
1458	while read line
1459	do
1460	firstc=`echo $line \| cut -c1`
1461	if [[ $firstc = M \|\| $firstc = "?" ]]
1462	then
1463	Name=`echo "$line" \| cut -c8-`
1464	extension=`echo $Name \| cut -d. -f2`
1465	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1466	then
1467	Filenames="$Filenames "$Name
1468	fi
1469	fi
1470	done < tmp_mrun
1471
1472
1473	# COPY FILES TO SOURCES_FOR_RUN_...
1474	for dateiname in $Filenames
1475	do
1476	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1477	source_list=$source_list"$dateiname "
1478	done
1479
1480	cd - > /dev/null
1481
1482
1483	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1484	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1485	elif [[ "$source_list" != "" && $restart_run != true ]]
1486	then
1487
1488	cd $source_path
1489
1490	for filename in $source_list
1491	do
1492
1493	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1494	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1495	then
1496	printf "\n +++ source code file: $filename"
1497	printf "\n must not contain (\"/\") "
1498	locat=source; exit
1499	fi
1500
1501	if [[ ! -f $filename ]]
1502	then
1503	printf "\n +++ source code file: $filename"
1504	printf "\n does not exist"
1505	locat=source; exit
1506	else
1507	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1508	fi
1509
1510	done
1511
1512	cd - > /dev/null
1513
1514	fi
1515
1516
1517	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1518	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1519	if [[ $restart_run != true ]]
1520	then
1521
1522	if [[ ! -f "$source_path/$mainprog" ]]
1523	then
1524	printf "\n\n +++ main program: $mainprog"
1525	printf "\n does not exist in source directory"
1526	printf "\n \"$source_path\"\n"
1527	locat=source; exit
1528	else
1529	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1530	then
1531	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1532	source_list=${mainprog}" $source_list"
1533	fi
1534	fi
1535	fi
1536
1537
1538	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1539	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1540	if [[ "$restart_run" != true ]]
1541	then
1542	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1543	if [[ ! -f $makefile ]]
1544	then
1545	printf "\n +++ file \"$makefile\" does not exist"
1546	locat=make; exit
1547	else
1548	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1549	fi
1550	fi
1551
1552
1553	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1554	if [[ $restart_run != true && "$add_source_path" != "" ]]
1555	then
1556
1557	# DOES THE DIRECTORY EXIST?
1558	if [[ ! -d $add_source_path ]]
1559	then
1560	printf "\n\n +++ WARNING: additional source code directory"
1561	printf "\n \"$add_source_path\" "
1562	printf "\n does not exist or is not a directory."
1563	printf "\n No source code will be used from this directory!\n"
1564	add_source_path=""
1565	if [[ $silent == false ]]
1566	then
1567	sleep 3
1568	fi
1569	else
1570
1571	cd $add_source_path
1572	found=false
1573
1574	Names=$(ls -1 *.f90 2>&1)
1575	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1576	Names=$(ls -1 *.F90 2>&1)
1577	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1578	Names=$(ls -1 *.F 2>&1)
1579	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1580	Names=$(ls -1 *.f 2>&1)
1581	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1582	Names=$(ls -1 *.c 2>&1)
1583	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1584
1585	cd - > /dev/null
1586	cd SOURCES_FOR_RUN_$fname
1587
1588	# COPY MAKEFILE IF EXISTING
1589	if [[ -f $add_source_path/Makefile ]]
1590	then
1591	printf "\n\n *** user Makefile from directory"
1592	printf "\n \"$add_source_path\" is used \n"
1593	if [[ $silent == false ]]
1594	then
1595	sleep 1
1596	fi
1597	cp $add_source_path/Makefile .
1598	fi
1599
1600	for dateiname in $AddFilenames
1601	do
1602	if [[ -f $dateiname ]]
1603	then
1604	printf "\n +++ source code file \"$dateiname\" found in additional"
1605	printf "\n source code directory \"$add_source_path\" "
1606	printf "\n but was also given with option \"-s\" which means that it should be taken"
1607	printf "\n from directory \"$source_path\"."
1608	locat=source; exit
1609	fi
1610
1611	cp $add_source_path/$dateiname .
1612	source_list="$source_list $dateiname"
1613
1614	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1615	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1616	then
1617	printf "\n\n +++ user file \"$dateiname\" "
1618	printf "\n is not listed in Makefile \n"
1619	locat=source; exit
1620	else
1621
1622	if [[ $found = false ]]
1623	then
1624	found=true
1625	printf "\n\n *** following user file(s) added to the"
1626	printf " files to be translated:\n "
1627	fi
1628	printf "$dateiname "
1629	if [[ $silent == false ]]
1630	then
1631	sleep 0.5
1632	fi
1633
1634	fi
1635	done
1636	[[ $found = true ]] && printf "\n"
1637	cd - > /dev/null
1638	fi
1639	fi
1640
1641
1642	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1643	# TO THE LIST OF FILES TO BE COMPILED
1644	if [[ $restart_run != true && -n $package_list ]]
1645	then
1646
1647	cd $source_path
1648
1649	for package in $package_list
1650	do
1651
1652	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1653
1654	# DETERMINE FILES BELONGING TO THE PACKAGE
1655	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1656	# THE NAME OF THE DIRECTORY
1657	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1658
1659
1660	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1661	# IF THEY ARE NOT ALREADY PART OF THE LIST
1662	for source_list_name in $package_source_list
1663	do
1664	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1665	then
1666
1667	# ONLY TAKE FILES WITH VALID SUFFIX
1668	ending=`echo $source_list_name \| cut -f2 -d.`
1669	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1670	then
1671	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1672	source_list="$source_list $source_list_name"
1673	fi
1674	fi
1675	done
1676	done
1677
1678	cd - > /dev/null
1679	fi
1680
1681	fi # do_compile=true
1682
1683
1684	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1685	# AND SET PRE-PROCESSOR DIRECTIVES
1686	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1687	then
1688
1689	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1690	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1691	then
1692	cpp_options="${cpp_options},-D__ibm=__ibm"
1693	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1694	then
1695	cpp_options="$cpp_options -D__nec"
1696	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1697	then
1698	cpp_options="$cpp_options -D__lc"
1699	else
1700	cpp_options="$cpp_options -D__$localhost"
1701	fi
1702
1703	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1704	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1705	then
1706	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1707	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1708	else
1709	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1710	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1711	fi
1712
1713	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1714	if [[ -n $package_list ]]
1715	then
1716	for package in $package_list
1717	do
1718	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1719	then
1720	if [[ $package != "dvrp_graphics+1PE" ]]
1721	then
1722	cpp_options="${cpp_options},-D__$package=__$package"
1723	else
1724	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1725	export use_seperate_pe_for_dvrp_output=true
1726	fi
1727	else
1728	if [[ $package != "dvrp_graphics+1PE" ]]
1729	then
1730	cpp_options="$cpp_options -D__$package"
1731	else
1732	cpp_options="$cpp_options -D__dvrp_graphics"
1733	export use_seperate_pe_for_dvrp_output=true
1734	fi
1735	fi
1736	done
1737	fi
1738
1739	# SET DIRECTIVES GIVEN BY OPTION -D
1740	if [[ -n $cpp_opts ]]
1741	then
1742	for popts in $cpp_opts
1743	do
1744	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1745	then
1746	cpp_options="${cpp_options},-D__$popts=__$popts"
1747	else
1748	cpp_options="$cpp_options -D__$popts"
1749	fi
1750	done
1751	fi
1752
1753	else
1754
1755
1756	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1757	if [[ $do_remote = false ]]
1758	then
1759	if [[ ! -f $executable ]]
1760	then
1761	printf "\n +++ executable file: $executable"
1762	printf "\n does not exist"
1763	locat=executable; exit
1764	fi
1765	fi
1766	fi
1767
1768
1769	# DETERMINE THE JOB MODE
1770	if [[ "$ENVIRONMENT" = BATCH ]]
1771	then
1772	batch_job=.TRUE.
1773	jobmo=BATCH
1774	else
1775	batch_job=.FALSE.
1776	jobmo=INTERACTIVE
1777	fi
1778
1779
1780	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1781	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1782	then
1783	printf "\n +++ no interactive runs allowed on host \"$host\" "
1784	printf "\n please submit batch job using mrun option \"-b\" \n"
1785	locat=normal; exit
1786	fi
1787
1788
1789	# CHECK, IF USER DEFINED A COMPILER
1790	if [[ "$compiler_name" = "" ]]
1791	then
1792
1793	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1794	locat=compiler_name; exit
1795
1796	fi
1797
1798
1799	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1800	kennung=$RANDOM
1801	if [[ "$tmp_user_catalog" = "" ]]
1802	then
1803	if [[ $localhost = ibmh ]]
1804	then
1805	tmp_user_catalog=$SCRATCH
1806	elif [[ $localhost = nech ]]
1807	then
1808	tmp_user_catalog=$WRKSHR
1809	else
1810	tmp_user_catalog=/tmp
1811	fi
1812	fi
1813	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1814
1815
1816	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1817	if [[ "$tmp_data_catalog" = "" ]]
1818	then
1819	if [[ $localhost = nech ]]
1820	then
1821	tmp_data_catalog=$WRKSHR/mrun_restart_data
1822	else
1823	tmp_data_catalog=/tmp/mrun_restart_data
1824	fi
1825	fi
1826
1827
1828	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1829	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1830	then
1831	eval fopts=\"$fopts\"
1832	eval lopts=\"$lopts\"
1833	fi
1834
1835
1836
1837	# DETERMINE COMPILE- AND LINK-OPTIONS
1838	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1839	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1840	ROPTS="$ropts"
1841	# 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 ]]
1842	# then
1843	XOPT="-X $numprocs"
1844	# fi
1845
1846
1847
1848	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1849	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1850	done=false
1851	while [[ $done = false ]]
1852	do
1853	cputime=$cpumax
1854	if (( $cputime == 0 ))
1855	then
1856	if [[ $do_batch = true ]]
1857	then
1858	printf "\n +++ cpu-time is undefined"
1859	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1860	printf "\n >>> "
1861	read cputime 1>/dev/null 2>&1
1862	else
1863	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1864	fi
1865	else
1866	done=true
1867	fi
1868	cpumax=$cputime
1869	done
1870
1871	(( minuten = cputime / 60 ))
1872	(( sekunden = cputime - minuten * 60 ))
1873
1874
1875	# CHECK THE MEMORY DEMAND
1876	if [[ $do_batch = true ]]
1877	then
1878	done=false
1879	while [[ $done = false ]]
1880	do
1881	if (( memory == 0 ))
1882	then
1883	printf "\n +++ memory demand is undefined"
1884	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1885	printf "\n >>> "
1886	read memory 1>/dev/null 2>&1
1887	else
1888	done=true
1889	fi
1890	done
1891	fi
1892
1893
1894	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1895	if [[ $do_remote = true && -z $remote_username ]]
1896	then
1897	while [[ -z $remote_username ]]
1898	do
1899	printf "\n +++ username on remote host \"$host\" is undefined"
1900	printf "\n >>> Please type username:"
1901	printf "\n >>> "
1902	read remote_username
1903	done
1904	mc="$mc -u$remote_username"
1905	fi
1906
1907	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1908	if [[ "$login_init_cmd" != "" ]]
1909	then
1910	export init_cmds="${login_init_cmd};"
1911	fi
1912
1913
1914	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1915	if [[ "$modules" != "" ]]
1916	then
1917	if [[ $host = lctit ]]
1918	then
1919	export module_calls=". $modules"
1920	else
1921	export module_calls="module load ${modules};"
1922	fi
1923	fi
1924
1925
1926
1927	# OUTPUT OF THE MRUN-HEADER
1928	calltime=$(date)
1929	printf "\n"
1930	printf "#------------------------------------------------------------------------# \n"
1931	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1932	printf "\| \| \n"
1933	spalte1="called on:"; spalte2=$localhost_realname
1934	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1935	if [[ $do_remote = true ]]
1936	then
1937	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1938	else
1939	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1940	fi
1941	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1942	if [[ -n $numprocs ]]
1943	then
1944	if [[ $run_coupled_model = false ]]
1945	then
1946	spalte1="number of PEs:"; spalte2=$numprocs
1947	else
1948	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1949	fi
1950	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1951	fi
1952	if [[ -n $tasks_per_node ]]
1953	then
1954	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1955	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1956	if (( remaining_pes > 0 ))
1957	then
1958	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1959	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1960	fi
1961	fi
1962	if [[ $maximum_parallel_io_streams != $numprocs ]]
1963	then
1964	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1965	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1966	fi
1967	if [[ $use_openmp = true ]]
1968	then
1969	spalte1="threads per task:"; spalte2="$threads_per_task"
1970	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1971	fi
1972	printf "\| \| \n"
1973	if [[ $do_compile = true ]]
1974	then
1975	if [[ "$mopts" != "" ]]
1976	then
1977	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	zeile=$(echo "$mopts" \| cut -c46-)
1980	while [[ "$zeile" != "" ]]
1981	do
1982	spalte1=""
1983	spalte2=$(echo "$zeile" \| cut -c-45)
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	zeile=$(echo "$zeile" \| cut -c46-)
1986	done
1987	fi
1988
1989	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1990	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1991	zeile=$(echo "$cpp_options" \| cut -c46-)
1992	while [[ "$zeile" != "" ]]
1993	do
1994	spalte1=""
1995	spalte2=$(echo "$zeile" \| cut -c-45)
1996	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1997	zeile=$(echo "$zeile" \| cut -c46-)
1998	done
1999
2000	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2001	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2002	zeile=$(echo "$fopts" \| cut -c46-)
2003	while [[ "$zeile" != "" ]]
2004	do
2005	spalte1=""
2006	spalte2=$(echo "$zeile" \| cut -c-45)
2007	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2008	zeile=$(echo "$zeile" \| cut -c46-)
2009	done
2010
2011	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2012	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2013	zeile=$(echo "$lopts" \| cut -c46-)
2014	while [[ "$zeile" != "" ]]
2015	do
2016	spalte1=""
2017	spalte2=$(echo "$zeile" \| cut -c-45)
2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2019	zeile=$(echo "$zeile" \| cut -c46-)
2020	done
2021
2022	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2023	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2024	zeile=$(echo "$modules" \| cut -c46-)
2025	while [[ "$zeile" != "" ]]
2026	do
2027	spalte1=""
2028	spalte2=$(echo "$zeile" \| cut -c-45)
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030	zeile=$(echo "$zeile" \| cut -c46-)
2031	done
2032
2033	spalte1="main program:"; spalte2=$mainprog
2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2035	else
2036	spalte1=executable:; spalte2=$executable
2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2038	fi
2039	printf "\| \| \n"
2040	spalte1="base name of files:"; spalte2=$fname
2041	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2042	if [[ $fname != $afname ]]
2043	then
2044	spalte1="base name of input files:"; spalte2=$afname
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046	fi
2047	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051
2052	if [[ "$ocean_file_appendix" = true ]]
2053	then
2054	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2055	fi
2056
2057	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2058	then
2059	spalte1="memory demand / PE":; spalte2="$memory MB"
2060	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2061	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2063	fi
2064
2065	if [[ $do_compile = true ]]
2066	then
2067	printf "\| \| \n"
2068	printf "\| Files to be compiled: \| \n"
2069	zeile=$source_list
2070	while [[ "$zeile" != "" ]]
2071	do
2072	linestart=$(echo $zeile \| cut -c-70)
2073	printf "\| %-70s \| \n" "$linestart"
2074	zeile=$(echo "$zeile" \| cut -c71-)
2075	done
2076	fi
2077	printf "#------------------------------------------------------------------------#"
2078
2079
2080
2081	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2082	if [[ $do_trace = true ]]
2083	then
2084	(( i = 0 ))
2085	while (( i < iin ))
2086	do
2087	(( i = i + 1 ))
2088	if (( i == 1 ))
2089	then
2090	printf "\n\n >>> INPUT-file assignments:\n"
2091	fi
2092	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2093	done
2094	(( i = 0 ))
2095	while (( i < iout ))
2096	do
2097	(( i = i + 1 ))
2098	if (( i == 1 ))
2099	then
2100	printf "\n\n >>> OUTPUT-file assignments:\n"
2101	fi
2102	printf "\n ${localout[$i]} : ${pathout[$i]}"
2103	done
2104	(( i = 0 ))
2105	while (( i < iic ))
2106	do
2107	(( i = i + 1 ))
2108	if (( i == 1 ))
2109	then
2110	printf "\n\n >>> INPUT-commands:\n"
2111	fi
2112	printf "\n ${in_command[$i]}"
2113	done
2114	(( i = 0 ))
2115	while (( i < ioc ))
2116	do
2117	(( i = i + 1 ))
2118	if (( i == 1 ))
2119	then
2120	printf "\n\n >>> OUTPUT-commands:\n"
2121	fi
2122	printf "\n ${out_command[$i]}"
2123	done
2124	fi
2125
2126
2127	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2128	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2129	then
2130	antwort=dummy
2131	printf "\n\n"
2132	printf " >>> everything o.k. (y/n) ? "
2133	while read antwort
2134	do
2135	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2136	then
2137	printf " >>> everything o.k. (y/n) ? "
2138	else
2139	break
2140	fi
2141	done
2142	if [[ $antwort = n \|\| $antwort = N ]]
2143	then
2144	locat=user_abort; (( iec = 0 )); exit
2145	fi
2146	if [[ $do_batch = true ]]
2147	then
2148	printf " >>> batch-job will be created and submitted"
2149	else
2150	printf " >>> MRUN will now continue to execute on this machine"
2151	fi
2152	fi
2153
2154
2155	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2156	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2157	check_depository="${working_directory}/trunk/UTIL"
2158	check_sources="${working_directory}/tmp_check_namelist_files"
2159	skip_check=false
2160
2161	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2162	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2163	then
2164	skip_check=true
2165	reason="run on remote host or parameter file check has not been compiled."
2166	fi
2167	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2168	then
2169	skip_check=true
2170	reason="parameter file check has not been compiled."
2171	fi
2172
2173	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2174	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2175	then
2176	skip_check=true
2177	reason="serial run."
2178	fi
2179
2180	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2181	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2182	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2183	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2184	if [[ $check_namelist_files == false ]]
2185	then
2186	skip_check=true
2187	reason="-z option set."
2188	fi
2189
2190	if [[ $fromhost != $localhost ]]
2191	then
2192	skip_check=true
2193	reason="submitting host is local host."
2194	fi
2195
2196	if [[ $run_coupled_model == true ]]
2197	then
2198	skip_check=true
2199	reason="coupled run."
2200	fi
2201
2202	if [[ $restart_run == true ]]
2203	then
2204	skip_check=true
2205	reason="restart run."
2206	fi
2207
2208	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2209	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2210	last_char=`echo $filename_input \| cut -c $last_char_int`
2211	if [[ "$last_char" == "f" ]]
2212	then
2213	skip_check=true
2214	reason="restart run."
2215	fi
2216
2217	if [[ $skip_check == false ]]
2218	then
2219	tmp_check=${working_directory}/tmp_check
2220
2221	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2222	# NOT NECESSARILY REQUIRED
2223	line=""
2224	found=false
2225	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2226	while read line1
2227	do
2228	line="$line1"
2229	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2230	then
2231	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2232	found=true
2233	fi
2234	done < $tmp_check
2235
2236	if [[ $found = false ]]
2237	then
2238	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2239	fi
2240
2241	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2242	# NOT NECESSARILY REQUIRED
2243	line=""
2244	found=false
2245	grep "NUDGING_DATA" $config_file > $tmp_check
2246	while read line1
2247	do
2248	line="$line1"
2249	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2250	then
2251	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2252	found=true
2253	fi
2254	done < $tmp_check
2255
2256	if [[ $found = false ]]
2257	then
2258	printf "\n +++ no NUDGING list entry found in the configuration file."
2259	fi
2260
2261	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2262	# NOT NECESSARILY REQUIRED
2263	line=""
2264	found=false
2265	grep "LSF_DATA" $config_file > $tmp_check
2266	while read line1
2267	do
2268	line="$line1"
2269	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2270	then
2271	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2272	found=true
2273	fi
2274	done < $tmp_check
2275
2276	if [[ $found = false ]]
2277	then
2278	printf "\n +++ no LSF list entry found in the configuration file."
2279	fi
2280
2281	rm -rf ${working_directory}/tmp_check
2282
2283	# CHECK IF THE P3DF FILE MUST BE CHECKED
2284	for item in $input_list
2285	do
2286	if [[ "$item" == "restart" ]]
2287	then
2288	check_restart=1
2289	else
2290	check_restart=0
2291	fi
2292	done
2293
2294	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2295	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2296	then
2297	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2298	locat=check_namelist; exit
2299	fi
2300
2301	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2302	if [[ $check_restart == 1 ]]
2303	then
2304
2305	filenamef="${filename_input}f"
2306	if [[ ! -f $filenamef ]]
2307	then
2308	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2309	check_restart=0
2310	answer=dummy
2311	printf "\n\n"
2312
2313	if [[ $silent == false ]]
2314	then
2315	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2316	do
2317	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2318	read answer
2319	done
2320	if [[ $answer = a \|\| $answer = A ]]
2321	then
2322	printf "\n +++ Aborting...."
2323	locat=normal; exit
2324	fi
2325	fi
2326	else
2327	check_restart=1
2328	fi
2329	fi
2330
2331	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2332	mkdir $check_sources
2333	cd $check_sources
2334
2335
2336	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2337	if [[ -d $add_source_path ]]
2338	then
2339	printf "\n\n *** copying files from $check_depository"
2340	cp $check_depository/check_namelist_files.tar ./
2341
2342	printf "\n\n *** untar of makefile and source files in $check_sources"
2343	tar -xf check_namelist_files.tar > /dev/null 2>&1
2344
2345	printf "\n\n *** adding user code."
2346	cp $add_source_path/* ./
2347	touch check_namelist_files.f90
2348
2349	# GET COMPILER OPTIONS AND PERFORM MAKE
2350	printf "\n\n *** compiling code if necessary...\n"
2351
2352	# workaround for batch jobs on local machine (lcxe6)
2353	if [[ $do_batch == true && $do_remote == false ]]
2354	then
2355	eval $init_cmds
2356	fi
2357
2358	# GET CHECK OPTIONS
2359	line=""
2360	found=false
2361
2362	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2363
2364	while read line1
2365	do
2366
2367	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2368	then
2369	line="$line1"
2370	fi
2371
2372	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2373	then
2374	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2375	line="$line "
2376	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'`
2377	found=true
2378	fi
2379
2380	done < $tmp_check
2381	copts_check="$copts_check -D__check -D__parallel"
2382
2383	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2384
2385	# GET MAKE OUTPUT
2386	if [[ $? != 0 ]]
2387	then
2388	printf "\n +++ error during make."
2389	answer=dummy
2390	printf "\n\n"
2391	if [[ $silent == false ]]
2392	then
2393	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2394	do
2395	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2396	read answer
2397	done
2398	if [[ $answer = a \|\| $answer = A ]]
2399	then
2400	printf "\n +++ Aborting..."
2401	rm -rf $check_sources
2402	locat=normal; exit
2403	else
2404	skip_check=true
2405	fi
2406	else
2407	skip_check=true
2408	fi
2409	fi
2410	else
2411	cp $PALM_BIN/check_namelist_files.x ./
2412	fi
2413
2414	cp $filename_input ./PARIN
2415	if [[ $check_restart == 1 ]]
2416	then
2417	cp $filenamef ./PARINF
2418	fi
2419
2420	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2421	then
2422	printf "\n *** adding topography data"
2423	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2424
2425	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2426	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2427	# WHICH REQUIRE SUFFICIENT MEMORY
2428	ulimit -s unlimited
2429	fi
2430
2431	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2432	then
2433	printf "\n *** adding nudging data"
2434	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2435	fi
2436
2437	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2438	then
2439	printf "\n *** adding large scale forcing data"
2440	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2441	fi
2442
2443	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2444	cat > ENVPAR << %%END%%
2445	&envpar run_identifier = '$fname', host = '$host',
2446	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2447	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2448	maximum_cpu_time_allowed = ${cpumax}.,
2449	revision = '$global_revision',
2450	local_dvrserver_running = $local_dvrserver_running /
2451
2452	%%END%%
2453
2454	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2455	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2456	then
2457	printf "\n +++ WARNING: check_namelist_files.x not found."
2458	answer=dummy
2459	printf "\n\n"
2460
2461	if [[ $silent == false ]]
2462	then
2463	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2464	do
2465	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2466	read answer
2467	done
2468	if [[ $answer = a \|\| $answer = A ]]
2469	then
2470	printf "\n +++ Aborting..."
2471	rm -rf $check_sources
2472	locat=normal; exit
2473	else
2474	printf "\n *** skipping parameter file check."
2475	fi
2476	fi
2477
2478	elif [[ $skip_check == false ]]
2479	then
2480	# STARTING THE PARAMETER FILE CHECK
2481	printf "\n\n *** starting parameter file check..."
2482
2483	# CHECKING THE P3D FILE
2484	printf "\n\n (1) checking $filename_input"
2485	echo "$numprocs 0 0" > VARIN
2486	errors=`./check_namelist_files.x < VARIN 2>&1`
2487
2488	check_error=false
2489	if [[ "$errors" == "" ]]
2490	then
2491	printf " --> o.k."
2492	else
2493	printf " --> failed."
2494	check_error=true
2495	printf "\n\n $errors"
2496	fi
2497
2498	# CHECKING THE PD3F FILE IF NECESSARY
2499	if [[ $check_restart == 1 && $check_error == false ]]
2500	then
2501	printf "\n\n (2) checking $filenamef"
2502
2503	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2504	# IN &INIPAR LIST
2505	found=false
2506	cat PARINF \| while read line
2507	do
2508	line=$(echo $line\|sed 's/ //g')
2509	if [[ $line == "&inipar" ]]
2510	then
2511	start_search=true
2512	fi
2513
2514	if [[ $start_search == true ]]
2515	then
2516	if [[ $line == "initializing_actions='read_restart_data'" ]]
2517	then
2518	found=true
2519	break
2520	fi
2521	fi
2522
2523	if [[ $line == "/" ]]
2524	then
2525	start_search=false
2526	fi
2527
2528	done
2529
2530	if [[ $found = false ]]
2531	then
2532	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2533	printf "\n in &inipar list in $fname$p3df_suffix."
2534	rm -rf $check_sources
2535	locat=check_namelist; exit
2536	fi
2537
2538	# READ max_user_pr FROM FILES
2539	if [[ -f parin_for_check ]]
2540	then
2541	read max_pr_user < parin_for_check
2542	else
2543	max_user_pr=0
2544	fi
2545
2546	echo "$numprocs 1 $max_pr_user" > VARIN
2547	errors=`./check_namelist_files.x < VARIN 2>&1`
2548
2549	if [[ "$errors" == "" ]]
2550	then
2551	printf " --> o.k."
2552	else
2553	printf " --> failed."
2554	check_error=true
2555	printf "\n\n $errors"
2556	fi
2557	fi
2558
2559	# REPORT ERRORS AND CONTINUE/EXIT
2560	if [[ $check_error == true ]]
2561	then
2562	printf "\n +++ errors found in the parameter file!\n"
2563	answer=dummy
2564	printf "\n\n"
2565
2566	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2567	do
2568	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2569	read answer
2570	done
2571
2572	if [[ $answer = a \|\| $answer = A ]]
2573	then
2574	printf "\n +++ Aborting..."
2575	rm -rf $check_sources
2576	locat=normal; exit
2577	fi
2578	else
2579	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2580	fi
2581	rm -rf $check_sources
2582	fi
2583	else
2584	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2585	fi
2586
2587	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2588	rm -rf $check_sources
2589	cd $working_directory
2590
2591
2592	# DETERMINE PATH FOR MAKE DEPOSITORY
2593	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2594	then
2595
2596	line=""
2597	grep "%depository_path" $config_file > tmp_mrun
2598	while read line
2599	do
2600	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2601	then
2602	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2603	then
2604	global_depository_path=`echo $line \| cut -d" " -s -f2`
2605	fi
2606	fi
2607	done < tmp_mrun
2608
2609	line=""
2610	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2611	while read line
2612	do
2613	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2614	then
2615	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2616	then
2617	local_depository_path=`echo $line \| cut -d" " -s -f2`
2618	fi
2619	fi
2620	done < tmp_mrun
2621
2622	if [[ "$local_depository_path" = "" ]]
2623	then
2624	if [[ "$global_depository_path" != "" ]]
2625	then
2626	local_depository_path=$global_depository_path
2627	else
2628	printf "\n\n +++ no depository path found in configuration file"
2629	printf "\n for local host \"$localhost\" "
2630	printf "\n please set \"\%depository_path\" in configuration file\n"
2631	locat=config_file; exit
2632	fi
2633	fi
2634	eval local_depository_path=$local_depository_path
2635	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2636	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2637
2638
2639	basename=`echo $mainprog \| cut -f1 -d"."`
2640	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2641	if [[ ! -f $make_depository ]]
2642	then
2643	printf "\n"
2644	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2645	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2646	fi
2647
2648	fi
2649
2650
2651	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2652	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2653	if [[ $do_batch = false ]]
2654	then
2655
2656
2657	# CREATE THE TEMPORARY WORKING DIRECTORY
2658	mkdir -p $TEMPDIR
2659	chmod go+rx $TEMPDIR
2660	tmpcreate=true
2661
2662
2663	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2664	# INTO THE TEMPORARY WORKING DIRECTORY
2665	if [[ $do_compile = true ]]
2666	then
2667
2668	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2669	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2670	if [[ $localhost = nech ]]
2671	then
2672	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2673	if mkdir -p $TEMPDIR_COMPILE
2674	then
2675	printf "\n *** \"$TEMPDIR_COMPILE\" "
2676	printf "\n is generated as temporary directory for cross compiling\n"
2677	else
2678	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2679	printf "\n needed for cross compilation failed"
2680	locat=compile
2681	exit
2682	fi
2683	else
2684	TEMPDIR_COMPILE=$TEMPDIR
2685	fi
2686
2687	cp $make_depository $TEMPDIR_COMPILE
2688	cd $TEMPDIR_COMPILE
2689	tar -xf $make_depository > /dev/null 2>&1
2690	cd - > /dev/null
2691
2692	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2693	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2694	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2695	then
2696	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2697	else
2698	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2699	fi
2700
2701	else
2702
2703	cp $executable ${TEMPDIR}/a.out
2704
2705	fi
2706
2707
2708	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2709	cd $TEMPDIR
2710	printf "\n *** changed to temporary directory: $TEMPDIR"
2711
2712
2713	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2714	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2715	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2716	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2717	(( i = 0 ))
2718	while (( i < iout ))
2719	do
2720	(( i = i + 1 ))
2721	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2722	then
2723	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2724	else
2725	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2726	fi
2727	done
2728
2729
2730	# IF REQUIRED, START WITH COMPILING
2731	if [[ $do_compile = true ]]
2732	then
2733
2734
2735	if [[ -f a.out ]]
2736	then
2737
2738	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2739	printf "\n\n\n *** executable a.out found"
2740	printf "\n no compilation required \n"
2741
2742	else
2743
2744	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2745	printf "\n\n\n *** compilation starts \n$dashes\n"
2746	printf " *** compilation with make using following options:\n"
2747	printf " make depository: $make_depository"
2748	if [[ "$mopts" != "" ]]
2749	then
2750	printf " make options: $mopts\n"
2751	fi
2752	printf " compilername: $compiler_name\n"
2753	printf " compiler options: $fopts\n"
2754	printf " preprocessor directives: $cpp_options \n"
2755	printf " linker options: $lopts \n"
2756	if [[ "$modules" != "" ]]
2757	then
2758	printf " modules to be load: $modules \n"
2759	fi
2760	printf " source code files: $source_list \n"
2761
2762	if [[ $localhost = nech ]]
2763	then
2764	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\" "
2765	cp $TEMPDIR_COMPILE/a.out .
2766	[[ $? != 0 ]] && compile_error=true
2767	rm -rf $TEMPDIR_COMPILE
2768	elif [[ $localhost = ibmh ]]
2769	then
2770	printf " compiler is called via ssh on \"plogin1\" \n"
2771	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\" "
2772	[[ ! -f a.out ]] && compile_error=true
2773	continue # STATUS=1, IF a.out EXISTS
2774	elif [[ $localhost = lcflow ]]
2775	then
2776	printf " compiler is called via ssh on \"flow\" \n"
2777	/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\" "
2778	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2779	[[ "$check_for_file" = "" ]] && compile_error=true
2780	continue # STATUS=1, IF a.out EXISTS
2781	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2782	then
2783	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2784	else
2785	[[ "$init_cmds" != "" ]] && eval $init_cmds
2786	[[ "$module_calls" != "" ]] && eval $module_calls
2787	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2788	fi
2789
2790	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2791	then
2792	printf "\n +++ error occured while compiling or linking"
2793	locat=compile
2794
2795	exit
2796	else
2797	printf "$dashes\n *** compilation finished \n"
2798	fi
2799
2800	fi
2801
2802	fi
2803
2804
2805	# PROVIDE THE INPUT FILES
2806	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2807	(( i = 0 ))
2808	while (( i < iin ))
2809	do
2810	(( i = i + 1 ))
2811	if (( i == 1 ))
2812	then
2813	printf "\n\n *** providing INPUT-files:\n$dashes"
2814	fi
2815
2816
2817	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2818	if [[ "${transin[$i]}" = unavailable ]]
2819	then
2820	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2821	then
2822	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2823	printf "\n is not available!"
2824	else
2825	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2826	printf "\n is not available!"
2827	fi
2828	continue
2829	fi
2830
2831	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2832	files_for_pes=false; datentyp=file
2833	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2834	then
2835	files_for_pes=true; datentyp=directory
2836	actionin[$i]=""
2837	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2838	then
2839	actionin[$i]=""
2840	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2841	then
2842	files_for_pes=true; datentyp=directory
2843	actionin[$i]="ar"
2844	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2845	then
2846	actionin[$i]="ar"
2847	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2848	then
2849	files_for_pes=true; datentyp=directory
2850	actionin[$i]="fl"
2851	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2852	then
2853	actionin[$i]="fl"
2854	fi
2855
2856	if [[ $files_for_pes = true ]]
2857	then
2858	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2859	else
2860	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2861	fi
2862
2863	# INPUT-FILE FOR A RESTART RUN.
2864	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2865	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2866	if [[ "${actionin[$i]}" = fl ]]
2867	then
2868	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2869	if [[ $files_for_pes = false ]]
2870	then
2871	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2872	then
2873	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2874	got_tmp[$i]=true
2875	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2876	then
2877	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2878	printf "\n *** trying to use backup copy in \"$WORK\" "
2879	cp $WORK/${frelin[$i]} ${localin[$i]}
2880	else
2881	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2882	printf "\n or \"$tmp_data_catalog\" does not exist!"
2883	printf "\n *** trying to get copy from archive"
2884	actionin[$i]=ar
2885	fi
2886	else
2887	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2888	then
2889	mkdir ${localin[$i]}
2890	cd $tmp_data_catalog/${frelin[$i]}
2891	for file in $(ls *)
2892	do
2893	ln $file $TEMPDIR/${localin[$i]}
2894	done
2895	cd $TEMPDIR
2896	got_tmp[$i]=true
2897	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2898	then
2899	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2900	printf "\n *** trying to use backup copy in \"$WORK\" "
2901	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2902	else
2903	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2904	printf "\n or \"$tmp_data_catalog\" does not exist!"
2905	printf "\n *** trying to get copy from archive"
2906	actionin[$i]=ar
2907	fi
2908	fi
2909	fi
2910
2911
2912	# FILE IS STORED ON THE ARCHIVE SYSTEM
2913	if [[ "${actionin[$i]}" = ar ]]
2914	then
2915
2916	if [[ $files_for_pes = false ]]
2917	then
2918	printf "\n file will be restored from archive-system ($archive_system)!"
2919	else
2920	printf "\n directory will be restored from archive-system ($archive_system)!"
2921	fi
2922
2923	file_restored=false
2924
2925	if [[ $archive_system = asterix ]]
2926	then
2927	do_stagein=true
2928	(( stagein_anz = 0 ))
2929	while [[ $do_stagein = true ]]
2930	do
2931	if [[ $files_for_pes = false ]]
2932	then
2933	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2934	else
2935	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2936	fi
2937	cat STAGEIN_OUTPUT
2938	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2939	then
2940	file_restored=true
2941	do_stagein=false
2942	else
2943	(( stagein_anz = stagein_anz + 1 ))
2944	if (( stagein_anz == 10 ))
2945	then
2946	printf "\n +++ stagein stoped after 10 tries"
2947	locat=stage
2948	exit
2949	fi
2950	printf "\n +++ restoring from archive failed, trying again:"
2951	sleep 900
2952	fi
2953	done
2954	elif [[ $archive_system = DMF ]]
2955	then
2956	if [[ $files_for_pes = false ]]
2957	then
2958	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2959	locat=DMF
2960	exit
2961	else
2962	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2963	cp -r $ARCHIVE/${frelin[$i]} $PWD
2964	file_restored=true
2965	fi
2966	elif [[ $archive_system = tivoli ]]
2967	then
2968	if [[ $files_for_pes = false ]]
2969	then
2970	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2971	else
2972	(( inode = 0 ))
2973	while (( inode < nodes ))
2974	do
2975	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2976	(( inode = inode + 1 ))
2977	done
2978	fi
2979	file_restored=true
2980	elif [[ $archive_system = ut ]]
2981	then
2982	if [[ $files_for_pes = false ]]
2983	then
2984	cp $UT/${frelin[$i]} .
2985	else
2986	(( inode = 0 ))
2987	while (( inode < nodes ))
2988	do
2989	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2990	(( inode = inode + 1 ))
2991	done
2992	fi
2993	file_restored=true
2994	else
2995	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2996	locat=rearchive
2997	exit
2998	fi
2999
3000	if [[ $file_restored = true ]]
3001	then
3002
3003	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3004	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3005	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3006	if [[ $files_for_pes = false ]]
3007	then
3008	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3009	else
3010	mkdir $tmp_data_catalog/${frelin[$i]}
3011	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3012	fi
3013	got_tmp[$i]=true
3014
3015	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3016	mv ${frelin[$i]} ${localin[$i]}
3017
3018	fi
3019	fi
3020
3021
3022	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3023	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3024	then
3025
3026	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3027	then
3028
3029	# FILE COPIES ARE PROVIDED FOR ALL CORES
3030	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3031	printf "\n file will be provided for $numprocs processors"
3032	mkdir ${localin[$i]}
3033	ival=$numprocs
3034	(( ii = 0 ))
3035	while (( ii <= ival-1 ))
3036	do
3037	if (( ii < 10 ))
3038	then
3039	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3040	elif (( ii < 100 ))
3041	then
3042	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3043	elif (( ii < 1000 ))
3044	then
3045	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3046	else
3047	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3048	fi
3049	(( ii = ii + 1 ))
3050	done
3051
3052	else
3053
3054	if [[ $files_for_pes = true ]]
3055	then
3056
3057	# PROVIDE FILES FOR EACH CORE
3058	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3059	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3060	printf "\n providing $numprocs files for the respective processors"
3061	mkdir ${localin[$i]}
3062	if [[ $link_local_input = true ]]
3063	then
3064	printf " using ln -f\n"
3065	cd ${absnamein[$i]}
3066	for file in $(ls *)
3067	do
3068	ln -f $file ${localin[$i]}
3069	done
3070	cd $TEMPDIR
3071	fi
3072
3073	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3074	if [[ ! -f "${localin[$i]}/_0000" ]]
3075	then
3076	if [[ $link_local_input = true ]]
3077	then
3078	printf " ln failed for .../_0000, using cp...\n"
3079	fi
3080	cp -r ${absnamein[$i]}/* ${localin[$i]}
3081	fi
3082
3083	else
3084
3085	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3086	if [[ $link_local_input = true ]]
3087	then
3088	printf " using ln -f\n"
3089	ln -f ${absnamein[$i]} ${localin[$i]}
3090	fi
3091	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3092	if [[ ! -f "${localin[$i]}" ]]
3093	then
3094	if [[ $link_local_input = true ]]
3095	then
3096	printf " ln failed, using cp...\n"
3097	fi
3098	cp ${absnamein[$i]} ${localin[$i]}
3099	fi
3100	fi
3101	fi
3102	fi
3103
3104	done
3105	if (( i != 0 ))
3106	then
3107	printf "\n$dashes\n *** all INPUT-files provided \n"
3108	fi
3109
3110
3111	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3112	(( i = 0 ))
3113	while (( i < iic ))
3114	do
3115	(( i = i + 1 ))
3116	if (( i == 1 ))
3117	then
3118	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3119	fi
3120	printf "\n >>> ${in_command[$i]}"
3121	eval ${in_command[$i]}
3122	if (( i == iic ))
3123	then
3124	printf "\n$dashes\n"
3125	fi
3126	done
3127
3128
3129	# SET THE REMAINING CPU-TIME
3130	cpurest=${cpumax}.
3131
3132
3133	# START DVR STREAMING SERVER
3134	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3135	then
3136	if [[ "$dvr_server" != "" ]]
3137	then
3138
3139	printf "\n\n *** preparing the dvr streaming server configuration file"
3140
3141	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3142	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3143	if [[ "$running_dvrserver_id" != "" ]]
3144	then
3145
3146	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3147	printf "\n This server is used instead starting a new one!"
3148	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3149
3150	else
3151
3152	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3153	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3154	then
3155	cp ${PALM_BIN}/.dvrserver.config .
3156
3157	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3158	user_id=`id -u`
3159	group_id=`id -g`
3160
3161	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3162	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3163	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3164	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3165	mv .dvrserver.3 .dvrserver.config
3166	rm .dvrserver.1 .dvrserver.2
3167
3168	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3169	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3170	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3171	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3172	local_dvrserver_running=.TRUE.
3173	else
3174	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3175	printf "\n \"$PALM_BIN\" "
3176	locat=dvr
3177	exit
3178	fi
3179
3180	fi
3181
3182	else
3183	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3184	fi
3185	fi
3186
3187
3188	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3189	# (FILE ENVPAR WILL BE READ BY PALM)
3190	cat > ENVPAR << %%END%%
3191	&envpar run_identifier = '$fname', host = '$localhost',
3192	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3193	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3194	maximum_cpu_time_allowed = ${cpumax}.,
3195	revision = '$global_revision',
3196	local_dvrserver_running = $local_dvrserver_running,
3197	batch_job = $batch_job /
3198
3199	%%END%%
3200
3201
3202	# STARTING THE EXECUTABLE
3203	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3204	PATH=$PATH:$TEMPDIR
3205
3206	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3207	if [[ "$mpi_debug" = true ]]
3208	then
3209	export MPI_CHECK_ARGS=1
3210	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3211	fi
3212
3213	if [[ "$totalview" = true ]]
3214	then
3215	printf "\n *** totalview debugger will be used"
3216	tv_opt="-tv"
3217	else
3218	tv_opt=""
3219	fi
3220
3221	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3222	then
3223	if [[ "$ENVIRONMENT" = BATCH ]]
3224	then
3225	continue
3226	fi
3227	if [[ $localhost = ibmh ]]
3228	then
3229
3230	# SETUP THE IBM MPI ENVIRONMENT
3231	export MP_SHARED_MEMORY=yes
3232	export AIXTHREADS_SCOPE=S
3233	export OMP_NUM_THREADS=$threads_per_task
3234	export AUTHSTATE=files
3235	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3236
3237	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3238	export MP_ADAPTER_USE=shared
3239	export MP_CPU_USE=multiple
3240	export MP_TIMEOUT=1200
3241
3242	unset MP_TASK_AFFINITY
3243
3244	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3245	#(( ii = 1 ))
3246	#while (( ii <= $numprocs ))
3247	#do
3248	# echo $localhost_realname >> hostfile
3249	# (( ii = ii + 1 ))
3250	#done
3251	#export MP_HOSTFILE=hostfile
3252
3253	if [[ "$LOADLBATCH" = yes ]]
3254	then
3255	totalview poe a.out $ROPTS
3256	else
3257	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3258	export TVDSVRLAUNCHCMD=ssh
3259	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3260	fi
3261
3262	fi # END DEBUG MODE
3263
3264	else
3265
3266	# NORMAL EXECUTION
3267	if [[ -n $numprocs ]]
3268	then
3269
3270	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3271	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3272	then
3273
3274	# SETUP THE IBM MPI ENVIRONMENT
3275	if [[ $host != ibmh && $host != ibmkisti ]]
3276	then
3277	export MP_SHARED_MEMORY=yes
3278	export AIXTHREAD_SCOPE=S
3279	export OMP_NUM_THREADS=$threads_per_task
3280	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3281	export AUTHSTATE=files
3282	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3283	# export MP_PRINTENV=yes
3284
3285	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3286	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3287	export MP_WAIT_MODE=poll
3288	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3289	fi
3290
3291	if [[ $host = ibmkisti ]]
3292	then
3293	export LANG=en_US
3294	export MP_SHARED_MEMORY=yes
3295	if [[ $threads_per_task = 1 ]]
3296	then
3297	export MP_SINGLE_THREAD=yes
3298	export MEMORY_AFFINITY=MCM
3299	else
3300	export OMP_NUM_THREADS=$threads_per_task
3301	fi
3302	fi
3303
3304	if [[ "$LOADLBATCH" = yes ]]
3305	then
3306	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3307	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3308	then
3309	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3310	else
3311	if [[ $run_coupled_model = false ]]
3312	then
3313	if [[ "$ocean_file_appendix" = true ]]
3314	then
3315	echo "precursor_ocean" > runfile_atmos
3316	else
3317	echo "precursor_atmos" > runfile_atmos
3318	fi
3319	else
3320	(( iia = $numprocs_atmos / $threads_per_task ))
3321	(( iio = $numprocs_ocean / $threads_per_task ))
3322	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3323	printf "\n using $coupled_mode coupling"
3324	printf "\n\n"
3325	echo "coupled_run $iia $iio" > runfile_atmos
3326	fi
3327	poe ./a.out $ROPTS < runfile_atmos
3328	fi
3329	else
3330	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3331	then
3332	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3333	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3334	then
3335	if [[ -f $hostfile ]]
3336	then
3337	cp $hostfile hostfile
3338	else
3339	(( ii = 1 ))
3340	while (( ii <= $numprocs ))
3341	do
3342	echo $localhost_realname >> hostfile
3343	(( ii = ii + 1 ))
3344	done
3345	fi
3346	export MP_HOSTFILE=hostfile
3347	if [[ $run_coupled_model = false ]]
3348	then
3349	if [[ "$ocean_file_appendix" = true ]]
3350	then
3351	echo "precursor_ocean" > runfile_atmos
3352	else
3353	echo "precursor_atmos" > runfile_atmos
3354	fi
3355	else
3356	(( iia = $numprocs_atmos / $threads_per_task ))
3357	(( iio = $numprocs_ocean / $threads_per_task ))
3358	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3359	printf "\n using $coupled_mode coupling"
3360	printf "\n\n"
3361	echo "coupled_run $iia $iio" > runfile_atmos
3362	fi
3363
3364	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3365
3366	else
3367	if [[ "$host_file" = "" ]]
3368	then
3369	printf "\n +++ no hostfile given in configuration file"
3370	locat=config_file
3371	exit
3372	else
3373	eval host_file=$host_file
3374	fi
3375	export MP_HOSTFILE=$host_file
3376	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3377	fi
3378	fi
3379	elif [[ $host = nech ]]
3380	then
3381	(( ii = nodes ))
3382	if [[ $ii = 1 ]]
3383	then
3384	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3385	export MPIPROGINF=YES
3386	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3387	echo "*** execution on single node with mpirun"
3388	mpirun -np $numprocs ./a.out $ROPTS
3389	else
3390	(( i = 0 ))
3391	while (( i < ii ))
3392	do
3393	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3394	(( i = i + 1 ))
3395	done
3396
3397	echo "#!/bin/sh" > mpi_exec_shell
3398	echo " " >> mpi_exec_shell
3399	echo "set -u" >> mpi_exec_shell
3400	echo "F_ERRCNT=0" >> mpi_exec_shell
3401	echo "MPIPROGINV=YES" >> mpi_exec_shell
3402	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3403	echo "cpurest=$cpurest" >> mpi_exec_shell
3404	echo "fname=$fname" >> mpi_exec_shell
3405	echo "localhost=$localhost" >> mpi_exec_shell
3406	echo "return_addres=$return_addres" >> mpi_exec_shell
3407	echo "return_username=$return_username" >> mpi_exec_shell
3408	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3409	echo "write_binary=$write_binary" >> mpi_exec_shell
3410	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3411	echo " " >> mpi_exec_shell
3412	echo "export F_ERRCNT" >> mpi_exec_shell
3413	echo "export MPIPROGINV" >> mpi_exec_shell
3414	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3415	echo "export cpurest" >> mpi_exec_shell
3416	echo "export fname" >> mpi_exec_shell
3417	echo "export localhost" >> mpi_exec_shell
3418	echo "export return_addres" >> mpi_exec_shell
3419	echo "export return_username" >> mpi_exec_shell
3420	echo "export tasks_per_node" >> mpi_exec_shell
3421	echo "export write_binary" >> mpi_exec_shell
3422	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3423	echo " " >> mpi_exec_shell
3424	echo "exec ./a.out" >> mpi_exec_shell
3425
3426	chmod u+x mpi_exec_shell
3427	export MPIPROGINF=YES
3428	mpirun -f multinode_config &
3429	wait
3430
3431	fi
3432	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3433	then
3434
3435	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3436	# DOES NOT EXIST
3437	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3438	then
3439	if [[ -f $hostfile ]]
3440	then
3441	cp $hostfile hostfile
3442	(( ii = $numprocs / $threads_per_task ))
3443	else
3444	(( ii = 1 ))
3445	while (( ii <= $numprocs / $threads_per_task ))
3446	do
3447	echo $localhost_realname >> hostfile
3448	(( ii = ii + 1 ))
3449	done
3450	fi
3451	eval zeile=\"`head -n $ii hostfile`\"
3452	printf "\n *** running on: $zeile"
3453	fi
3454
3455	(( ii = $numprocs / $threads_per_task ))
3456	export OMP_NUM_THREADS=$threads_per_task
3457
3458	if [[ $threads_per_task != 1 ]]
3459	then
3460	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3461	# MAY ABORT
3462	ulimit -s unlimited
3463	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3464	fi
3465	if [[ $run_coupled_model = false ]]
3466	then
3467	if [[ "$ocean_file_appendix" = true ]]
3468	then
3469	echo "precursor_ocean" > runfile_atmos
3470	else
3471	echo "precursor_atmos" > runfile_atmos
3472	fi
3473	printf "\n\n"
3474
3475	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3476	then
3477	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3478	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3479	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3480	elif [[ $host = lccrayf ]]
3481	then
3482	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3483	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3484	then
3485	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3486	elif [[ $host = lcflow ]]
3487	then
3488	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3489	elif [[ $host = lcsb ]]
3490	then
3491	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3492	elif [[ $host = lckiaps ]]
3493	then
3494	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3495	elif [[ $host = lckyu* ]]
3496	then
3497	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3498	else
3499	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3500	fi
3501	else
3502
3503	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3504	(( iia = $numprocs_atmos / $threads_per_task ))
3505	(( iio = $numprocs_ocean / $threads_per_task ))
3506	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3507	printf "\n using $coupled_mode coupling"
3508	printf "\n\n"
3509
3510	if [[ $coupled_mode = "mpi2" ]]
3511	then
3512	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3513	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3514
3515	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3516	then
3517
3518	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3519	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3520
3521	else
3522	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3523	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3524	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3525	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3526	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3527	fi
3528	wait
3529
3530	else
3531
3532	echo "coupled_run $iia $iio" > runfile_atmos
3533
3534	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3535	then
3536
3537	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3538
3539	elif [[ $host = lck \|\| $host = lckordi ]]
3540	then
3541
3542	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3543
3544	elif [[ $host = lckyu* ]]
3545	then
3546
3547	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3548
3549	fi
3550	wait
3551	fi
3552
3553	fi
3554
3555	elif [[ $host = lckyoto ]]
3556	then
3557	set -xv
3558	export P4_RSHCOMMAND=plesh
3559	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3560	if [[ "$ENVIRONMENT" = BATCH ]]
3561	then
3562	if [[ "$cond2" = fujitsu ]]
3563	then
3564	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3565	elif [[ "cond2" = pgi ]]
3566	then
3567	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3568	else
3569	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3570	fi
3571	else
3572	if [[ "$cond2" = "" ]]
3573	then
3574	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3575	else
3576	mpirun -np $numprocs ./a.out $ROPTS
3577	fi
3578	fi
3579	set +xv
3580
3581	elif [[ $host = lctit ]]
3582	then
3583	export OMP_NUM_THREADS=$threads_per_task
3584	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3585	if [[ "$threads_per_task" != 1 ]]
3586	then
3587	export MV2_ENABLE_AFFINITY=0
3588	fi
3589	echo "----- PBS_NODEFILE content:"
3590	cat $PBS_NODEFILE
3591	echo "-----"
3592	(( ii = $numprocs / $threads_per_task ))
3593	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3594	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3595	else
3596	mpprun -n $numprocs a.out $ROPTS
3597	fi
3598	else
3599	a.out $ROPTS
3600	fi
3601	fi
3602
3603	if [[ $? != 0 ]]
3604	then
3605
3606	# ABORT IN CASE OF RUNTIME ERRORS
3607	printf "\n +++ runtime error occured"
3608	locat=execution
3609	exit
3610
3611	else
3612
3613	printf "\n$dashes\n *** execution finished \n"
3614
3615	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3616	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3617	if [[ "$dvrserver_id" != "" ]]
3618	then
3619	kill $dvrserver_id
3620	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3621
3622	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3623	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3624	if [[ -d DATA_DVR ]]
3625	then
3626
3627	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3628	# DIRECTORY
3629	cp .dvrserver.config DATA_DVR
3630
3631	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3632	# SEQUENCE MODE DATA TOO)
3633	process_dvr_output -d DATA_DVR -f $fname -s
3634
3635	else
3636
3637	# PROCESS THE LOCAL OUTPUT
3638	process_dvr_output -l -d DATA_DVR -f $fname
3639
3640	fi
3641
3642	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3643	then
3644
3645	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3646	process_dvr_output -l -d DATA_DVR -f $fname
3647
3648	fi
3649	fi
3650
3651
3652
3653	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3654	# BY EACH CORE INTO ONE FILE
3655	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3656	then
3657	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3658	printf "\n 2d- and/or 3d-data may be incomplete!"
3659	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3660	elif [[ "$combine_plot_fields" == true ]]
3661	then
3662	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3663	then
3664	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3665	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3666	else
3667	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3668	combine_plot_fields${block}.x
3669	fi
3670	else
3671
3672	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3673	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3674	# ??? koennen wir das streichen ???
3675	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3676	fi
3677
3678
3679
3680	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3681	(( i = 0 ))
3682	while (( i < ioc ))
3683	do
3684	(( i = i + 1 ))
3685	if (( i == 1 ))
3686	then
3687	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3688	fi
3689	printf "\n >>> ${out_command[$i]}"
3690	eval ${out_command[$i]}
3691	if (( i == ioc ))
3692	then
3693	printf "\n$dashes\n"
3694	fi
3695	done
3696
3697
3698	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3699	if [[ $do_trace = true ]]
3700	then
3701	printf "\n\n"
3702	ls -al
3703	fi
3704
3705
3706
3707	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3708	(( i = 0 ))
3709	while (( i < iout ))
3710	do
3711	(( i = i + 1 ))
3712	if (( i == 1 ))
3713	then
3714	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3715	fi
3716
3717	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3718	files_for_pes=false; filetyp=file
3719	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3720	then
3721	files_for_pes=true; filetyp=directory
3722	actionout[$i]=""
3723	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3724	then
3725	actionout[$i]=""
3726	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3727	then
3728	files_for_pes=true; filetyp=directory
3729	actionout[$i]="ar"
3730	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3731	then
3732	actionout[$i]="ar"
3733	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3734	then
3735	files_for_pes=true; filetyp=directory
3736	actionout[$i]="fl"
3737	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3738	then
3739	actionout[$i]="fl"
3740	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3741	then
3742	files_for_pes=true; filetyp=directory
3743	actionout[$i]="tr"
3744	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3745	then
3746	actionout[$i]="tr"
3747	fi
3748
3749	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3750	then
3751	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3752	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3753	then
3754	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3755	else
3756
3757
3758	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3759	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3760	if [[ "${actionout[$i]}" = tr ]]
3761	then
3762	if [[ $localhost != $fromhost ]]
3763	then
3764	if [[ $files_for_pes = false ]]
3765	then
3766	cps=""
3767	cst=""
3768	else
3769	cps=-c
3770	cst="/"
3771	fi
3772	if [[ $localhost = nech ]]
3773	then
3774
3775	# TRANSFER IN SEPERATE JOB
3776	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3777	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3778	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3779	if [[ $files_for_pes = false ]]
3780	then
3781	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3782	else
3783	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3784	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3785	fi
3786
3787	echo "set -x" > transfer_${localout[$i]}
3788	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3789
3790	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3791	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3792	printf "\n or higher cycle\n"
3793	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3794
3795	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3796
3797	if [[ $localhost = nech ]]
3798	then
3799	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3800	else
3801	if [[ "$LOGNAME" = b323013 ]]
3802	then
3803	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3804	else
3805	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3806	fi
3807	fi
3808
3809	else
3810
3811	# TRANSFER WITHIN THIS JOB
3812	transfer_failed=false
3813	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3814	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3815	if [[ $localhost = lccrayb ]]
3816	then
3817	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3818	elif [[ $localhost = lccrayh ]]
3819	then
3820	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3821	else
3822	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3823	fi
3824	[[ $? != 0 ]] && transfer_failed=true
3825
3826	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3827	if [[ $transfer_failed = true ]]
3828	then
3829	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3830	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3831
3832	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3833	eval local_catalog=${pathout[$i]}
3834	if [[ ! -d $local_catalog ]]
3835	then
3836	printf " *** local directory does not exist. Trying to create:\n"
3837	printf " $local_catalog \n"
3838	mkdir -p $local_catalog
3839	fi
3840	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3841	transfer_problems=true
3842	fi
3843	fi
3844	else
3845
3846	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3847	actionout[$i]=""
3848	fi
3849	fi
3850
3851
3852	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3853	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3854	if [[ "${actionout[$i]}" = tra ]]
3855	then
3856	if [[ $localhost != $fromhost ]]
3857	then
3858	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3859	then
3860
3861	# TRANSFER IN SEPERATE JOB
3862	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3863	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3864	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3865	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3866
3867	echo "set -x" > transfer_${localout[$i]}
3868	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3869
3870	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3871	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3872	printf "\n or higher cycle\n"
3873	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3874
3875	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3876
3877	if [[ $localhost = nech ]]
3878	then
3879	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3880	else
3881	if [[ $LOGNAME = b323013 ]]
3882	then
3883	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3884	else
3885	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3886	fi
3887	fi
3888
3889	else
3890
3891	# TRANSFER WITHIN THIS JOB
3892	transfer_failed=false
3893	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3894	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3895	if [[ $localhost = lccrayb ]]
3896	then
3897	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3898	elif [[ $localhost = lccrayh ]]
3899	then
3900	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3901	else
3902	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3903	fi
3904	[[ $? != 0 ]] && transfer_failed=true
3905
3906	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3907	if [[ $transfer_failed = true ]]
3908	then
3909	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3910	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3911
3912	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3913	eval local_catalog=${pathout[$i]}
3914	if [[ ! -d $local_catalog ]]
3915	then
3916	printf " *** local directory does not exist. Trying to create:\n"
3917	printf " $local_catalog \n"
3918	mkdir -p $local_catalog
3919	fi
3920
3921	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3922	transfer_problems=true
3923	fi
3924	fi
3925	else
3926
3927	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3928	actionout[$i]=a
3929	fi
3930	fi
3931
3932
3933	# OUTPUT-FILE FOR A RESTART-RUN.
3934	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3935	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3936	# AS LAST ACTION, ARCHIVING IS INITIATED.
3937	if [[ "${actionout[$i]}" = fl ]]
3938	then
3939	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3940	chmod g+rx $tmp_data_catalog
3941	if [[ $files_for_pes = false ]]
3942	then
3943	printf "\n >>> OUTPUT: ${localout[$i]} to"
3944	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3945	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3946	else
3947	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3948	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3949	mkdir $tmp_data_catalog/${frelout[$i]}
3950	cd ${localout[$i]}
3951	for file in $(ls *)
3952	do
3953	ln -f $file $tmp_data_catalog/${frelout[$i]}
3954	done
3955	cd $TEMPDIR
3956	fi
3957
3958
3959	# CREATE AND SUBMIT ARCHIVING-JOB
3960	if [[ $store_on_archive_system = true ]]
3961	then
3962
3963	if [[ $archive_system = asterix ]]
3964	then
3965	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3966	if [[ $files_for_pes = false ]]
3967	then
3968	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3969	else
3970	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3971	fi
3972	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3973	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3974	echo "then" >> archive_${frelout[$i]}
3975	echo " do_stageout=false" >> archive_${frelout[$i]}
3976	echo "else" >> archive_${frelout[$i]}
3977	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3978	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3979	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3980	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3981	if [[ $files_for_pes = false ]]
3982	then
3983	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3984	else
3985	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3986	fi
3987	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3988	echo "fi" >> archive_${frelout[$i]}
3989	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3990	elif [[ $archive_system = DMF ]]
3991	then
3992	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3993	if [[ $files_for_pes = false ]]
3994	then
3995	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3996	locat=DMF
3997	exit
3998	else
3999	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4000	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4001	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4002	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4003	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4004	fi
4005	elif [[ $archive_system = tivoli ]]
4006	then
4007	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4008	if [[ $files_for_pes = false ]]
4009	then
4010	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4011	echo "set -x" >> archive_${frelout[$i]}
4012	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4013	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4014	else
4015
4016	echo "set -x" >> archive_${frelout[$i]}
4017	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4018	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4019	cd $tmp_data_catalog
4020	all_files=`ls -1 ${frelout[$i]}/*`
4021	cd - > /dev/null
4022	(( inode = 0 ))
4023	(( tp1 = tasks_per_node + 1 ))
4024	while (( inode < nodes ))
4025	do
4026	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4027	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4028	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4029	(( inode = inode + 1 ))
4030	done
4031	fi
4032	elif [[ $archive_system = ut ]]
4033	then
4034	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4035	if [[ $files_for_pes = false ]]
4036	then
4037	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4038	echo "set -x" >> archive_${frelout[$i]}
4039	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4040	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4041	else
4042
4043	echo "set -x" >> archive_${frelout[$i]}
4044	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4045	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4046	cd $tmp_data_catalog
4047	all_files=`ls -1 ${frelout[$i]}/*`
4048	cd - > /dev/null
4049	(( inode = 0 ))
4050	(( tp1 = tasks_per_node + 1 ))
4051	while (( inode < nodes ))
4052	do
4053	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4054	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4055	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4056	(( inode = inode + 1 ))
4057	done
4058	fi
4059	elif [[ $archive_system = none ]]
4060	then
4061	printf " +++ archiving on $localhost not available!\n"
4062	fi
4063
4064	if [[ $archive_system != none ]]
4065	then
4066	if [[ $localhost = nech ]]
4067	then
4068	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4069	fi
4070	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4071	fi
4072	else
4073	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4074	fi
4075
4076
4077	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4078	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4079	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4080	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4081	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4082	if [[ $files_for_pes = false ]]
4083	then
4084	cat /dev/null > ${pathout[$i]}
4085	else
4086	mkdir -p ${pathout[$i]}
4087	fi
4088
4089	fi
4090
4091
4092	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4093	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4094	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4095	if [[ "${actionout[$i]}" = ar ]]
4096	then
4097	if [[ $files_for_pes = false ]]
4098	then
4099	printf "\n >>> OUTPUT: ${localout[$i]} to"
4100	printf "\n ${pathout[$i]}"
4101	printf "\n File will be copied to archive-system ($archive_system) !\n"
4102	else
4103	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4104	printf "\n ${pathout[$i]}"
4105	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4106	fi
4107	mv ${localout[$i]} ${frelout[$i]}
4108
4109	file_saved=false
4110
4111	if [[ $archive_system = asterix ]]
4112	then
4113	do_stageout=true
4114	(( stageout_anz = 0 ))
4115	while [[ $do_stageout = true ]]
4116	do
4117	if [[ $files_for_pes = false ]]
4118	then
4119	stageout ${frelout[$i]} > STAGE_OUTPUT
4120	else
4121	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4122	fi
4123	cat STAGE_OUTPUT
4124	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4125	then
4126	file_saved=true
4127	do_stageout=false
4128	else
4129	if [[ $files_for_pes = false ]]
4130	then
4131	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4132	else
4133	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4134	fi
4135	(( stageout_anz = stageout_anz + 1 ))
4136	if (( stageout_anz == 10 ))
4137	then
4138	printf "\n +++ stoped after 10 unsuccessful tries!"
4139	archive_save=false
4140	do_stageout=false
4141	else
4142	printf "\n *** new try to store on archive after 15 min:"
4143	sleep 900
4144	fi
4145	fi
4146	done
4147	elif [[ $archive_system = DMF ]]
4148	then
4149	if [[ $files_for_pes = false ]]
4150	then
4151	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4152	locat=DMF
4153	exit
4154	else
4155	rm -rf $ARCHIVE/${frelout[$i]}
4156	cp -r ${frelout[$i]} $ARCHIVE
4157	fi
4158	file_saved=true
4159	elif [[ $archive_system = tivoli ]]
4160	then
4161	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4162	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4163	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4164	# WHEN THE ARCHIVE-JOB IS EXECUTED
4165	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4166	chmod g+rx $tmp_data_catalog
4167	if [[ $files_for_pes = false ]]
4168	then
4169	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4170	else
4171	mkdir $tmp_data_catalog/${frelout[$i]}
4172	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4173	fi
4174
4175	# GENERATE AND SUBMIT BATCH-JOB
4176	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4177	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4178	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4179	if [[ $files_for_pes = false ]]
4180	then
4181	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4182	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4183	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4184	else
4185	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4186	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4187	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4188	fi
4189
4190	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4191	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4192	file_saved=true
4193
4194	elif [[ $archive_system = ut ]]
4195	then
4196	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4197	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4198	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4199	# WHEN THE ARCHIVE-JOB IS EXECUTED
4200	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4201	chmod g+rx $tmp_data_catalog
4202	if [[ $files_for_pes = false ]]
4203	then
4204	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4205	else
4206	mkdir $tmp_data_catalog/${frelout[$i]}
4207	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4208	fi
4209
4210	# GENERATE AND SUBMIT BATCH-JOB
4211	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4212	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4213	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4214	if [[ $files_for_pes = false ]]
4215	then
4216	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4217	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4218	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4219	else
4220	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4221	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4222	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4223	fi
4224
4225	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4226	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4227	file_saved=true
4228
4229	else
4230	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4231	archive_save=false
4232	fi
4233
4234	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4235	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4236	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4237	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4238	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4239	if [[ $file_saved = true ]]
4240	then
4241	if [[ $files_for_pes = false ]]
4242	then
4243	cat /dev/null > ${pathout[$i]}
4244	else
4245	mkdir -p ${pathout[$i]}
4246	fi
4247	fi
4248
4249	fi
4250
4251	# APPEND ON THIS MACHINE
4252	if [[ "${actionout[$i]}" = "a" ]]
4253	then
4254	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4255	then
4256	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4257	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4258	else
4259	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4260	cat ${localout[$i]} >> ${pathout[$i]}
4261	fi
4262	fi
4263
4264	# COPY ON THIS MACHINE
4265	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4266	# ON DIFFERENT FILE-SYSTEMS
4267	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4268	then
4269
4270	# COPY IN CASE OF RUNS ON SINGLE CORES
4271	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4272	then
4273	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4274	if [[ $link_local_output = true ]]
4275	then
4276	printf " using ln -f\n"
4277	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4278	fi
4279	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4280	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4281	then
4282	if [[ $link_local_output = true ]]
4283	then
4284	printf " ln failed, using cp...\n"
4285	fi
4286	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4287	fi
4288	else
4289	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4290	if [[ $link_local_output = true ]]
4291	then
4292	printf " using ln -f\n"
4293	ln -f ${localout[$i]} ${pathout[$i]}
4294	fi
4295	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4296	if [[ ! -f "${pathout[$i]}" ]]
4297	then
4298	if [[ $link_local_output = true ]]
4299	then
4300	printf " ln failed, using cp...\n"
4301	fi
4302	cp ${localout[$i]} ${pathout[$i]}
4303	fi
4304	fi
4305
4306	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4307	then
4308
4309	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4310	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4311	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4312	if [[ $link_local_output = true ]]
4313	then
4314	printf " using ln -f\n"
4315	mkdir ${pathout[$i]}
4316	cd ${localout[$i]}
4317	for file in $(ls *)
4318	do
4319	ln -f $file ${pathout[$i]}
4320	done
4321	cd $TEMPDIR
4322	fi
4323
4324	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4325	if [[ ! -f "${pathout[$i]}/_0000" ]]
4326	then
4327	if [[ $link_local_output = true ]]
4328	then
4329	printf " ln failed for .../_0000, using cp...\n"
4330	fi
4331	cp -r ${localout[$i]} ${pathout[$i]}
4332	fi
4333
4334	fi
4335	fi
4336	done
4337	if (( i != 0 ))
4338	then
4339	if [[ $transfer_problems = true ]]
4340	then
4341	printf "\n$dashes\n *** OUTPUT-files saved"
4342	printf "\n +++ WARNING: some data transfers failed! \n"
4343	else
4344	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4345	fi
4346	fi
4347
4348
4349	# IF REQUIRED, START A RESTART-JOB
4350	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4351	if [[ -f CONTINUE_RUN ]]
4352	then
4353
4354	if [[ $archive_save = true ]]
4355	then
4356
4357	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4358	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4359	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4360	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4361	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4362	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4363	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4364	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4365	then
4366	mc=`echo $mc \| sed 's/#/f/g'`
4367	fi
4368
4369
4370	# START THE RESTART-JOB
4371	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4372	echo " $mc"
4373	printf "\n$dashes\n"
4374	if [[ $localhost != $fromhost ]]
4375	then
4376
4377	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4378	then
4379	echo "*** ssh will be used to initiate restart-runs!"
4380	echo " return_addres=\"$return_addres\" "
4381	echo " return_username=\"$return_username\" "
4382	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4383	then
4384	if [[ $localhost = ibmh ]]
4385	then
4386	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4387	elif [[ $localhost = lccrayb ]]
4388	then
4389	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4390	elif [[ $localhost = lccrayh ]]
4391	then
4392	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4393
4394	else
4395	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4396	fi
4397	else
4398	if [[ $localhost = ibmkisti ]]
4399	then
4400	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4401	elif [[ $localhost = lcflow ]]
4402	then
4403	/usr/bin/ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4404	elif [[ $localhost = lccrayb ]]
4405	then
4406	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4407	elif [[ $localhost = lccrayh ]]
4408	then
4409	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4410	else
4411	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4412	fi
4413	fi
4414	else
4415	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4416	locat=restart; exit
4417	fi
4418
4419	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4420	if [[ $queue = special1q ]]
4421	then
4422	sleep 120
4423	else
4424	sleep 30
4425	fi
4426
4427	else
4428
4429	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4430	# USING SSH)
4431	cd $LOCAL_PWD
4432	if [[ $localhost = lckyuh ]]
4433	then
4434	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4435	printf "\n please restart job manually using command:\n"
4436	printf "\n \"$mc\" "
4437	else
4438	eval $mc # THE ' MUST BE EVALUATED
4439	fi
4440	cd - > /dev/null
4441	fi
4442	if [[ $localhost = lckyuh ]]
4443	then
4444	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4445	else
4446	printf "\n$dashes\n *** restart-run initiated \n"
4447	fi
4448
4449
4450	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4451	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4452	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4453	# MAY BE VERY HUGE)
4454	(( i = 0 ))
4455	while (( i < iin ))
4456	do
4457	(( i = i + 1 ))
4458	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4459	then
4460	rm -r $tmp_data_catalog/${frelin[$i]}
4461	fi
4462	done
4463
4464	else
4465
4466	printf "\n +++ no restart-run possible, since errors occured"
4467	printf "\n during the archive process"
4468	fi
4469
4470	fi
4471
4472
4473
4474	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4475	if [[ "$email_notification" != "none" ]]
4476	then
4477
4478	if [[ $localhost != $fromhost ]]
4479	then
4480	if [[ -f CONTINUE_RUN ]]
4481	then
4482	echo "PALM restart run necessary" > email_text
4483	echo "description header of actual run:" >> email_text
4484	cat CONTINUE_RUN >> email_text
4485	echo "mrun-command to restart:" >> email_text
4486	echo "$mc" >> email_text
4487	else
4488	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4489	fi
4490	mail $email_notification < email_text
4491	printf "\n *** email notification sent to \"$email_notification\" "
4492	fi
4493	fi
4494
4495
4496
4497	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4498	cd $HOME
4499	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4500
4501	else
4502
4503
4504	# PREPARING ACTIONS,
4505	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4506
4507	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4508	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_addres -U $return_username -u $remote_username"
4509	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4510	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4511	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4512	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4513	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4514	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4515	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4516	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4517	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4518	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4519	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4520	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4521	if [[ $use_openmp = true ]]
4522	then
4523	mrun_com=${mrun_com}" -O $threads_per_task"
4524	fi
4525	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4526	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4527	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4528	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4529	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4530	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4531	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4532	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4533	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4534	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4535	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4536	if [[ $do_remote = true ]]
4537	then
4538	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4539	fi
4540
4541
4542	# CREATE EXECUTABLE FOR BATCH JOB
4543	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4544	then
4545
4546	printf "\n *** creating the executable for batch job\n"
4547
4548	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4549	if [[ $host != $localhost ]]
4550	then
4551	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4552	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4553	locat=create_executable; exit
4554	fi
4555
4556	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4557	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4558
4559	cp $make_depository .
4560	tar -xf $make_depository > /dev/null 2>&1
4561	cp ../* . > /dev/null 2>&1
4562
4563	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4564
4565	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4566	then
4567	printf "\n +++ error occured while compiling or linking"
4568	locat=compile
4569	exit
4570	fi
4571
4572	mv a.out ..
4573	cd - > /dev/null 2>&1
4574	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4575
4576	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4577
4578	fi
4579
4580
4581	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4582	jobfile=jobfile.$RANDOM
4583
4584
4585	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4586	echo "mkdir $TEMPDIR" >> $jobfile
4587	echo "cd $TEMPDIR" >> $jobfile
4588
4589
4590	# ACTIVATE ERROR-TRACEBACK
4591	if [[ $do_trace = true ]]
4592	then
4593	echo "set -x" >> $jobfile
4594	else
4595	echo "set +vx" >> $jobfile
4596	fi
4597
4598
4599	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4600	if [[ "$init_cmds" != "" ]]
4601	then
4602	echo "$init_cmds" >> $jobfile
4603	fi
4604	if [[ "$module_calls" != "" ]]
4605	then
4606	echo "$module_calls" >> $jobfile
4607	fi
4608
4609
4610	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4611	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4612	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4613	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4614	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4615	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4616	# QUEUEING-SYSTEMS
4617	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4618	then
4619
4620	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4621	if [[ $restart_run != true ]]
4622	then
4623	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4624	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4625	fi
4626
4627	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4628	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4629	echo "set -x" >> $jobfile
4630	if [[ $host = $localhost ]]
4631	then
4632
4633	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4634	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4635	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4636	then
4637	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4638	else
4639	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4640	fi
4641
4642	else
4643	if [[ $host = ibmkisti ]]
4644	then
4645	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4646	echo "localdir=\`pwd\`" >> $jobfile
4647	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4648	elif [[ $host = lccrayb ]]
4649	then
4650	echo "localdir=\`pwd\`" >> $jobfile
4651	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4652	elif [[ $host = lccrayh ]]
4653	then
4654	echo "localdir=\`pwd\`" >> $jobfile
4655	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4656
4657	else
4658	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4659	fi
4660	fi
4661	echo "export SOURCES_COMPLETE=true" >> $jobfile
4662
4663	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4664	# WORKING DIRECTORY OF THE JOB
4665	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4666	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4667	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4668	echo "execute_mrun=true" >> $jobfile
4669	echo " " >> $jobfile
4670
4671	else
4672
4673	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4674	if [[ $do_compile = true ]]
4675	then
4676
4677	source_catalog=SOURCES_FOR_RUN_$fname
4678
4679	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4680	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4681	echo "export SOURCES_COMPLETE=true" >> $jobfile
4682	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4683
4684	for filename in $source_list
4685	do
4686	# BACKSLASH IS USED FOR MASKING
4687	echo "cat > $filename << \"%END%\"" >> $jobfile
4688	cat $source_catalog/$filename >> $jobfile
4689	echo " " >> $jobfile
4690	echo "%END%" >> $jobfile
4691	echo " " >> $jobfile
4692	done
4693
4694	# BACKSLASH IS USED FOR MASKING
4695	echo "cat > Makefile << \"%END%\"" >> $jobfile
4696	cat $source_catalog/Makefile >> $jobfile
4697	echo " " >> $jobfile
4698	echo "%END%" >> $jobfile
4699	echo " " >> $jobfile
4700
4701	echo "cd - > /dev/null" >> $jobfile
4702
4703	fi
4704
4705
4706	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4707	# BACKSLASH IS USED FOR MASKING
4708	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4709	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4710	echo "cat > $config_file << \"%END%\"" >> $jobfile
4711	if [[ $host = lckyuh ]]
4712	then
4713	# NO CROSS-COMPILER ON COMPUTE NODE
4714	sed 's/frtpx/frt/g' $config_file >> $jobfile
4715	else
4716	sed 's/#$.*//g' $config_file >> $jobfile
4717	fi
4718	echo "%END%" >> $jobfile
4719	echo " " >> $jobfile
4720
4721
4722	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4723	# BACKSLASH IS USED FOR MASKING
4724	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4725	if [[ $host = lckyuh ]]
4726	then
4727	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4728	else
4729	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4730	fi
4731	echo "%END%" >> $jobfile
4732	echo "chmod u+x $mrun_script_name" >> $jobfile
4733	echo "execute_mrun=true" >> $jobfile
4734	echo " " >> $jobfile
4735
4736	fi
4737
4738
4739	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4740	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4741	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4742	if [[ $do_remote = true ]]
4743	then
4744	(( i = 0 ))
4745	while (( i < iin ))
4746	do
4747	(( i = i + 1 ))
4748	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4749	if [[ "${transin[$i]}" = job ]]
4750	then
4751	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4752	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4753	echo " " >> $jobfile
4754	echo "%END%" >> $jobfile
4755	else
4756	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4757	fi
4758
4759	# CHECK, IF FILE COULD BE CREATED
4760	echo "if [[ \$? = 1 ]]" >> $jobfile
4761	echo "then" >> $jobfile
4762	echo " echo \" \" " >> $jobfile
4763	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4764	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4765	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4766	echo " execute_mrun=false" >> $jobfile
4767	echo "fi" >> $jobfile
4768	done
4769	fi
4770
4771	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4772	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4773	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4774	echo "LOCAL_PWD=$working_directory" >> $jobfile
4775	echo "export LOCAL_PWD" >> $jobfile
4776
4777	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4778	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4779	echo "export LOCAL_MRUN_PATH" >> $jobfile
4780
4781	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4782	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4783	then
4784	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4785	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4786	fi
4787
4788	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4789	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4790	echo "set -x" >> $jobfile
4791	echo "queue=$queue" >> $jobfile
4792	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4793	echo 'ls -al; echo `pwd`' >> $jobfile
4794	echo "cd \$HOME" >> $jobfile
4795	echo "rm -rf $TEMPDIR" >> $jobfile
4796
4797
4798
4799
4800	# START THE JOB USING SUBJOB-COMMAND
4801	if [[ $silent = false ]]
4802	then
4803	printf "\n "
4804	else
4805	printf "\n\n"
4806	fi
4807
4808	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
4809	rm -rf $jobfile
4810
4811
4812	fi # END OF REMOTE-PART

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