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source: palm/trunk/SCRIPTS/mrun @ 1483

Last change on this file since 1483 was 1469, checked in by maronga, 10 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1469 2014-09-24 14:09:56Z raasch $
29	#
30	# 1468 2014-09-24 14:06:57Z maronga
31	# Typo removed (addres->address)
32	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
33	# Added support for restart runs (remote) for lcxe6
34	#
35	# 1442 2014-07-28 07:09:10Z raasch
36	# default queues for HLRN-III (lccrayb/lccrayh) defined
37	#
38	# 1422 2014-07-02 10:01:25Z kanani
39	# automatic restarts enabled for lccrayb,
40	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
41	#
42	# 1420 2014-06-10 06:24:14Z raasch
43	# -j1 option added to aprung command for lccrayf (CSC)
44	#
45	# 1402 2014-05-09 14:25:13Z raasch
46	# batch_job added to envpar-NAMELIST
47	#
48	# 1357 2014-04-11 15:02:03Z witha
49	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
50	# possible)
51	#
52	# 1320 2014-03-20 08:40:49Z raasch
53	# check namelist file set false by default
54	#
55	# 1304 2014-03-12 10:29:42Z raasch
56	# ulimit option changed from -Ss to -s
57	#
58	# bugfix: missing "fi" in r1289
59	#
60	# 1289 2014-03-04 07:12:34Z raasch
61	# comments translated to English
62	# necriam-, fimm-, ibmy-, and sgi-specific code removed
63	# export of variables for palm and interpret_config removed
64	#
65	# 1281 2014-02-01 07:55:49Z raasch
66	# rsync-copy restricted to Cray machines, since command is unavailable on some
67	# other systems
68	#
69	# 1279 2014-01-28 12:10:14Z raasch
70	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
71	# in order to remove annoying restrictions concerning the number of processors which
72	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
73	# restriction, one of the nodes will be filled with less than the given number of
74	# tasks per node. A respective warning is given.
75	#
76	# 1274 2014-01-09 13:14:54Z heinze
77	# adjustments for lccrayh
78	#
79	# 1272 2014-01-08 10:19:32Z witha
80	# small adjustment for lcflow
81	#
82	# 1270 2013-12-16 11:05:01Z fricke
83	# call of combine_plot_fields adjusted for lccrayb/lccrayh
84	#
85	# 1255 2013-11-07 14:43:35Z raasch
86	# further adjustments for lccrayb remote access
87	#
88	# 1241 2013-10-30 11:36:58Z heinze
89	# Enable use of nudging input and input of large scale forcing from
90	# external files
91	#
92	# 1229 2013-09-20 06:55:19Z raasch
93	# further adjustments for lccrayb
94	#
95	# 1224 2013-09-16 07:27:23Z raasch
96	# first adjustments for lccrayb
97	#
98	# 1210 2013-08-14 10:58:20Z raasch
99	# fftw support added
100	#
101	# 1201 2013-07-10 16:17:59Z witha
102	# adjustments for Forwind cluster (lcflow)
103	#
104	# 1199 2013-07-05 14:52:22Z raasch
105	# adjustments for CSC Helsinki (lccrayf),
106	# executables for batch jobs can be created in advance, in order to avoid calling
107	# the compiler within the batch job (only works if batch jobs are submitted on
108	# local host)
109	#
110	# 1190 2013-06-25 09:39:21Z heinze
111	# enable use of automatic restarts for ibmh
112	# use of cluster/express queue enabled (ibmh)
113	#
114	# 1124 2013-04-09 15:46:52Z raasch
115	# variable "memory" is exported via typeset option -x, because otherwise an unknown
116	# side effect may lead to data loss while getopts is reading the script-option arguments
117	#
118	# 1122 2013-04-09 08:37:16Z heinze
119	# Bugfix: change type of variable last_char
120	#
121	# 1119 2013-04-05 15:11:19Z raasch
122	# Bugfix for setting -T option for subjob
123	#
124	# 1108 2013-03-05 07:03:32Z raasch
125	# bugfix for coupled runs on lckyut/lckyuh
126	#
127	# 1106 2013-03-04 05:31:38Z raasch
128	# --stdin argument for mpiexec on lckyuh
129	# -y and -Y settings output to header
130	#
131	# 1103 2013-02-20 02:15:53Z raasch
132	# default script runs again under ksh, because of unsolved problems with read
133	# from stdin: when bash script is called from a ksh, message "read error: 0:
134	# Resource temporarily unavailable" appears and script does not stop,
135	# further bash compatibility adjustments,
136	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
137	# on lckyuh, but mrun does not terminate and issues a warning instead
138	#
139	# 1101 2013-02-17 10:20:21Z raasch
140	# script now running under bash instead of ksh, which required small adjustments
141	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
142	# read from stdin),
143	# cross compilername on lckyuh compute nodes replaced by real compiler name
144	#
145	# 1099 2013-02-10 01:47:43Z raasch
146	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
147	# and for Forwind cluster (lcflow)
148	# small further adjustments for lckyut
149	#
150	# 1094 2013-02-03 01:52:12Z raasch
151	# explicit ssh/scp port can be set in config file with environment variable
152	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
153	# decalpha parts (yonsei) removed
154	#
155	# 2013-02-02 07:06:13Z raasch
156	# adjustments for Kyushu-University computing center (lckyut - tatara)
157	#
158	# 1083 2013-01-04 10:22:09Z maronga
159	# bugfix in parameter file check (read %cpp_options was missing)
160	#
161	# 1069 2012-11-28 16:18:43Z maronga
162	# bugfix: coupling mode was always set to mpi2, typos removed
163	#
164	# 1058 2012-11-21 07:00:35Z raasch
165	# Intel inspector (inspxe) is given the number of PEs instead of the number of
166	# nodes
167	#
168	# 1046 2012-11-09 14:38:45Z maronga
169	# code put under GPL (PALM 3.9)
170	#
171	# 21/03/94 - Siggi - first version finished
172	# 03/03/94 - Siggi - script development started
173	#
174	#--------------------------------------------------------------------------------#
175	# mrun - script for running PALM jobs
176	#--------------------------------------------------------------------------------#
177
178
179
180	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
181
182	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
183	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
184	# (TOO MANY ARGUMENTS - PROBLEM)
185	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
186
187	AddFilenames=""
188	additional_conditions=""
189	add_source_path=""
190	afname=""
191	archive_save=true
192	archive_system=none
193	check_namelist_files=false
194	combine_plot_fields=true
195	compiler_name=""
196	cond1=""
197	cond2=""
198	config_file=.mrun.config
199	coupled_dist=""
200	coupled_mode="mpi1"
201	cpp_opts=""
202	cpp_options=""
203	cpumax=0
204	cpurest=0
205	create_executable_for_batch=false
206	delete_temporary_catalog=true
207	do_batch=false
208	do_compile=true
209	do_remote=false
210	do_stagein=true
211	do_stageout=true
212	do_trace=false
213	email_notification="none"
214	exclude=""
215	executable=""
216	execution_error=false
217	fftw_inc=""
218	fftw_lib=""
219	fftw_support=false
220	fname=test
221	fromhost=""
222	global_revision=""
223	group_number=none
224	host=""
225	host_file=""
226	hp=""
227	ignore_archive_error=false
228	input_list=""
229	interpreted_config_file=""
230	job_catalog="~/job_queue"
231	job_on_file=""
232	keep_data_from_previous_run=false
233	link_local_input=false
234	link_local_output=false
235	localhost_realname=$(hostname)
236	local_dvrserver_running=.FALSE.
237	locat=normal
238	mainprog=""
239	makefile=""
240	max_par_io_str=""
241	mc=$0
242	while [[ $(echo $mc \| grep -c "/") != 0 ]]
243	do
244	mc=`echo $mc \| cut -f2- -d"/"`
245	done
246	module_calls=""
247	mrun_script_name=$mc
248	netcdf_inc=""
249	netcdf_lib=""
250	netcdf_support=false
251	node_usage=default
252	numprocs=""
253	numprocs_atmos=0
254	numprocs_ocean=0
255	OOPT=""
256	openmp=false
257	output_list=""
258	package_list=""
259	queue=none
260	read_from_config=""
261	restart_run=false
262	if [[ `hostname` = rte10 ]]
263	then
264	return_address=133.5.185.60
265	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
266	elif [[ `hostname` = climate0 ]]
267	then
268	return_address=165.132.26.68
269	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
270	elif [[ `hostname` = urban00 ]]
271	then
272	return_address=147.46.30.151
273	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
274	else
275	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
276	fi
277	return_password=""
278	return_username=$LOGNAME
279	remotecall=false
280	remote_username=""
281	run_coupled_model=false
282	run_mode=""
283	store_on_archive_system=false
284	dashes=" ----------------------------------------------------------------------------"
285	silent=false
286	source_list=""
287	source_path=SOURCE
288	tasks_per_node=""
289	threads_per_task=1
290	tmpcreate=false
291	tmp_data_catalog=""
292	transfer_problems=false
293	usern=$LOGNAME
294	use_openmp=false
295	version="MRUN 2.1 Rev$Rev: 1469 $"
296	working_directory=`pwd`
297	TOPT=""
298	XOPT=""
299	zeit=$( date \| cut -c 12-19 )
300
301	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
302	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
303	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
304	# SCRIPT-OPTION ARGUMENTS
305	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
306
307
308
309	# ERROR HANDLING IN CASE OF EXIT
310	trap 'rm -rf $working_directory/tmp_mrun
311	if [[ $locat != normal && $locat != control_c ]]
312	then
313
314	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
315	(( i = 0 ))
316	while (( i < iec ))
317	do
318	(( i = i + 1 ))
319	printf "\n *** Execution of ERROR-command:\n"
320	printf " >>> ${err_command[$i]}\n"
321	eval ${err_command[$i]}
322	done
323	if [[ -n $interpreted_config_file ]]
324	then
325	rm -rf $interpreted_config_file
326	fi
327	if [[ -n .mrun_environment ]]
328	then
329	rm -rf .mrun_environment
330	fi
331	if [[ $tmpcreate = true ]]
332	then
333	printf "\n *** Contents of \"$TEMPDIR\":\n"
334	ls -al; cd
335	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
336	fi
337	if [[ "$dvrserver_id" != "" ]]
338	then
339	echo "+++ killing dvrserver_id=$dvrserver_id"
340	kill $dvrserver_id
341	fi
342	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
343	then
344	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
345	fi
346	printf "\n\n+++ MRUN killed \n\n"
347	elif [[ $locat != control_c ]]
348	then
349	printf "\n\n --> all actions finished\n\n"
350	printf " Bye, bye $usern !!\n\n"
351	fi' exit
352
353
354	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
355	trap 'rm -rf $working_directory/tmp_mrun
356	rm -rf $working_directory/tmp_check_namelist_files
357	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
358	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
359	then
360	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
361	fi
362	if [[ "$dvrserver_id" != "" ]]
363	then
364	echo "+++ killing dvrserver_id=$dvrserver_id"
365	kill $dvrserver_id
366	fi
367	printf "\n+++ MRUN killed by \"^C\" \n\n"
368	locat=control_c
369	exit
370	' 2
371
372
373	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
374	# BEEN SET
375	if [[ "$PALM_BIN" = "" ]]
376	then
377	printf "\n +++ environment variable PALM_BIN has not been set"
378	printf "\n please set it to the directory where the PALM scripts are located"
379	locat=palm_bin; exit
380	fi
381	export PATH=$PALM_BIN:$PATH
382
383
384
385	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
386	# WHICH WILL BE USED TO START RESTART-JOBS
387	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
388	do
389	case $option in
390	(a) afname=$OPTARG;;
391	(A) store_on_archive_system=true; mc="$mc -A";;
392	(b) do_batch=true; mc="$mc -b";;
393	(B) delete_temporary_catalog=false; mc="$mc -B";;
394	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
395	(C) restart_run=true; mc="$mc -C";;
396	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
397	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
398	(F) job_on_file="-D"; mc="$mc -F";;
399	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
400	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
401	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
402	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
403	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
404	(I) ignore_archive_error=true; mc="$mc -I";;
405	(k) keep_data_from_previous_run=true; mc="$mc -k";;
406	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
407	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
408	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
409	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
410	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
411	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
412	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
413	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
414	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
415	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
416	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
417	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
418	(S) read_from_config=false; mc="$mc -S";;
419	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
420	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
421	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
422	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
423	(v) silent=true; mc="$mc -v";;
424	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
425	(x) do_trace=true;set -x; mc="$mc -x";;
426	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
427	(y) ocean_file_appendix=true; mc="$mc -y";;
428	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
429	(z) check_namelist_files=false; mc="$mc -z";;
430	(Z) combine_plot_fields=false; mc="$mc -Z";;
431	(\?) printf "\n +++ unknown option $OPTARG \n"
432	printf "\n --> type \"$0 ?\" for available options \n"
433	locat=parameter;exit;;
434	esac
435	done
436
437
438	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
439	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
440	(( to_shift = $OPTIND - 1 ))
441	shift $to_shift
442
443	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
444	if [[ "$1" = "?" ]]
445	then
446	(printf "\n *** mrun can be called as follows:\n"
447	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"
448	printf "\n Description of available options:\n"
449	printf "\n Option Description Default-Value"
450	printf "\n -a base name of input files equiv. -d"
451	printf "\n -A archiving when using file-attribute fl"
452	printf "\n -b batch-job on local machine ---"
453	printf "\n -B do not delete temporary directory at end ---"
454	printf "\n -c configuration file .mrun.config"
455	printf "\n -d base name of files attached to program test"
456	printf "\n -D preprocessor(cpp)-directives \"\" "
457	printf "\n -F create remote job file only ---"
458	printf "\n -h execution host $localhost_realname"
459	printf "\n -i INPUT control list \"\" "
460	printf "\n -I archiving errors of previous batch-jobs"
461	printf "\n will be ignored"
462	printf "\n -k keep data from previous run"
463	printf "\n -K additional conditions for controling"
464	printf "\n usage of conditional code and"
465	printf "\n env-variables in configuration file \"\" "
466	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
467	printf "\n -M Makefile name Makefile"
468	printf "\n -n node usage (shared/not_shared) depending on -h"
469	printf "\n -o OUTPUT control list \"\" "
470	printf "\n -O threads per openMP task ---"
471	printf "\n -p software package list \"\" "
472	printf "\n -q queue \"$queue\" "
473	printf "\n -r run control list (combines -i -o) \"\" "
474	printf "\n -s filenames of routines to be compiled \"\" "
475	printf "\n must end with .f, .f90, .F, or .c !"
476	printf "\n use \"..\" for more than one file and wildcards"
477	printf "\n -s LM compiles all locally modified files"
478	printf "\n -S config file interpreted by shellscript ---"
479	printf "\n -t allowed cpu-time in seconds (batch) 0"
480	printf "\n -T tasks per node depending on -h"
481	printf "\n -u username on remote machine \"\" "
482	printf "\n -v no prompt for confirmation ---"
483	printf "\n -w maximum parallel io streams as given by -X"
484	printf "\n -x tracing of mrun for debug purposes ---"
485	printf "\n -X # of processors (on parallel machines) 1"
486	printf "\n -y add appendix \"_O\" to all local output"
487	printf "\n files (ocean precursor runs followed by"
488	printf "\n coupled atmosphere-ocean runs) ---"
489	printf "\n -Y run coupled model, \"#1 #2\" with"
490	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
491	printf "\n -z disable a priori parameter file check ---"
492	printf "\n -Z skip combine_plot_fields at the end of "
493	printf "\n the simulation ---"
494	printf "\n "
495	printf "\n Possible values of positional parameter <modus>:"
496	printf "\n \"?\" - this outline \n\n") \| more
497	exit
498	elif [[ "$1" != "" ]]
499	then
500	printf "\n +++ positional parameter $1 unknown \n"
501	locat=parameter; exit
502	fi
503
504
505
506	# SHORT STARTING MESSAGE
507	printf "\n*** $version "
508	printf "\n will be executed. Please wait ..."
509
510
511
512	# CHECK, IF CONFIGURATION FILE EXISTS
513	if [[ ! -f $config_file ]]
514	then
515	printf "\n\n +++ configuration file: "
516	printf "\n $config_file"
517	printf "\n does not exist"
518	locat=connect; exit
519	fi
520
521
522	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
523	line=""
524	grep "%host_identifier" $config_file > tmp_mrun
525	while read line
526	do
527	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
528	then
529	HOSTNAME=`echo $line \| cut -d" " -s -f2`
530	host_identifier=`echo $line \| cut -d" " -s -f3`
531	if [[ $localhost_realname = $HOSTNAME ]]
532	then
533	localhost=$host_identifier
534	break
535	fi
536	fi
537	done < tmp_mrun
538
539	if [[ "$localhost" = "" ]]
540	then
541	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
542	printf "\n for local host \"$localhost_realname\"."
543	printf "\n Please add line"
544	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
545	printf "\n to the configuration file."
546	locat=localhost; exit
547	fi
548
549
550	# SET HOST-SPECIFIC VARIABLES
551	case $localhost_realname in
552	(r1\|r2\|h01\|b01) archive_system=tivoli;;
553	(cs*) archive_system=ut;;
554	esac
555
556
557	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
558	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
559	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
560	[[ "$afname" = "" ]] && afname=$fname
561
562
563	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
564	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
565	# STATEMENTS IN THE CONFIGURATION FILE
566	if [[ "$run_mode" != "" ]]
567	then
568	input_list="$input_list $run_mode"
569	output_list="$output_list $run_mode"
570	fi
571
572
573	# ??? is this (and the respective option -H) really required ???
574	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
575	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
576	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
577	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
578	if [[ "$fromhost" = "" ]]
579	then
580	fromhost=$localhost
581	fi
582
583
584	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
585	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
586	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
587	# TO BE SUBMITTED (I.E. do_bacth=true)
588	if [[ -n $host && "$host" != $localhost ]]
589	then
590	do_batch=true
591	do_remote=true
592	case $host in
593	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
594	(*) printf "\n"
595	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
596	printf "\n is not available"
597	locat=nqs; (( iec = 0 )); exit;;
598	esac
599	else
600	host=$localhost
601	fi
602
603
604	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
605	if [[ -n $additional_conditions ]]
606	then
607	cond1=`echo $additional_conditions \| cut -d" " -f1`
608	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
609	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
610	if [[ -n $dummy ]]
611	then
612	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
613	locat=options; exit
614	fi
615	block=_$cond1
616	[[ -n $cond2 ]] && block=${block}_$cond2
617	fi
618
619
620	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
621	if [[ $run_coupled_model = true ]]
622	then
623
624	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
625	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
626
627	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
628	then
629
630	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
631	printf "\n PEs (total) : $numprocs"
632	printf "\n PEs (atmosphere): $numprocs_atmos"
633	printf "\n PEs (ocean) : $numprocs_ocean"
634	locat=coupling; exit
635
636	fi
637
638
639	# GET coupled_mode FROM THE CONFIG FILE
640	line=""
641	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
642	while read line
643	do
644	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
645	then
646	coupled_mode="mpi2"
647	fi
648	done < tmp_mrun
649
650	fi
651
652
653	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
654	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
655	then
656	if [[ $ignore_archive_error = false ]]
657	then
658	printf "\n +++ data archiving of previous run failed"
659	printf "\n see directory \~/job_queue on remote machine"
660	locat=archive; exit
661	else
662	printf "\n +++ warning: data archiving in a previous run failed"
663	printf "\n MRUN continues, trying to get backup copy"
664	fi
665	fi
666
667
668	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
669	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
670	mrun_memory=$memory
671	mrun_group_number=$group_number
672	mrun_cpumax=$cpumax
673	mrun_numprocs=$numprocs
674
675
676	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
677	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
678	if [[ "$read_from_config" = false ]]
679	then
680
681	[[ $silent = false ]] && printf "\n Reading the configuration file... "
682
683	# READ THE CONFIGURATION FILE LINE BY LINE
684	while read zeile
685	do
686	[[ $silent = false ]] && printf "."
687
688
689	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
690	eval zeile=\"$zeile\"
691
692
693	# INTERPRET THE LINE
694	if [[ "$(echo $zeile)" = "" ]]
695	then
696	# EMPTY LINE, NO ACTION
697	continue
698
699	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
700	then
701
702	# LINE IS A COMMENT LINE
703	true
704
705	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
706	then
707
708	# LINE DEFINES AN ENVIRONMENT-VARIABLE
709	zeile=$(echo $zeile \| cut -c2-)
710	var=`echo $zeile \| cut -d" " -f1`
711	value=`echo $zeile \| cut -d" " -s -f2`
712	for_host=`echo $zeile \| cut -d" " -s -f3`
713	for_cond1=`echo $zeile \| cut -d" " -s -f4`
714	for_cond2=`echo $zeile \| cut -d" " -s -f5`
715
716	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
717	then
718
719	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
720	# "::" IS REPLACED BY ":".
721	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
722
723
724	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
725	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
726	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
727	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
728	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
729	# CONFIGURATION-FILE.
730	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
731	then
732	eval $var=\$value
733
734	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
735	if [[ $do_trace = true ]]
736	then
737	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
738	fi
739	fi
740
741	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
742	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
743	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
744	# MUST HAVE TO BE STARTED
745	if [[ $var = host ]]
746	then
747	if [[ -n $host && "$host" != $localhost ]]
748	then
749	do_batch=true
750	do_remote=true
751	case $host in
752	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
753	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
754	printf "\n is not available"
755	locat=nqs; exit;;
756	esac
757	else
758	host=$localhost
759	fi
760	fi
761
762	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
763	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
764	# BY MRUN (E.G. subjob)
765	export $var
766	fi
767
768
769
770
771	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
772	then
773
774	# LINE DEFINES ERROR-COMMAND
775	(( iec = iec + 1 ))
776	zeile=$(echo $zeile \| cut -c4-)
777	err_command[$iec]="$zeile"
778
779	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
780	then
781
782	# LINE DEFINES INPUT-COMMAND
783	(( iic = iic + 1 ))
784	zeile=$(echo $zeile \| cut -c4-)
785	in_command[$iic]="$zeile"
786
787	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
788	then
789
790	# LINE DEFINES OUTPUT-COMMAND
791	(( ioc = ioc + 1 ))
792	zeile=$(echo $zeile \| cut -c4-)
793	out_command[$ioc]="$zeile"
794
795	else
796
797	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
798	# s2a: in/out - field
799	# s2b: loc - field (optional)
800	# s2c: tr/ar - field (optional)
801	s1=`echo $zeile \| cut -d" " -f1`
802	s2=`echo $zeile \| cut -d" " -s -f2`
803	s2a=$(echo $s2 \| cut -d":" -f1)
804	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
805	then
806	s2b=""
807	s2c=""
808	else
809	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
810	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
811	fi
812	s3=`echo $zeile \| cut -d" " -f3`
813	s4=`echo $zeile \| cut -d" " -s -f4`
814	s5=`echo $zeile \| cut -d" " -s -f5`
815	s6=`echo $zeile \| cut -d" " -s -f6`
816
817
818	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
819	# INPUT- OR OUTPUT-LIST.
820	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
821	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
822	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
823	# IS NOT CHECKED AND STORED.
824	IFSALT="$IFS"; IFS="$IFS:"
825	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
826	then
827	found=false
828	for actual in $input_list
829	do
830	for formal in $s3
831	do
832	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
833	done
834	done
835	if [[ $found = true ]]
836	then
837	(( iin = iin + 1 ))
838	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
839	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
840	extin[$iin]=$s6
841	fi
842	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
843	then
844	found=false
845	for actual in $output_list
846	do
847	for formal in $s3
848	do
849	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
850	done
851	done
852	if [[ $found = true ]]
853	then
854	(( iout = iout + 1 ))
855	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
856	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
857	fi
858	elif [[ "$s2a" != in && "$s2a" != out ]]
859	then
860	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
861	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
862	locat=connect; exit
863	fi
864	IFS="$IFSALT"
865	fi
866	done < $config_file
867
868	else
869
870
871	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
872	[[ $silent = false ]] && printf "..."
873	interpreted_config_file=.icf.$RANDOM
874
875
876
877	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
878	cat > .mrun_environment << %%END%%
879	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
880	config_file = '$config_file', do_remote = '$do_remote',
881	do_trace = '$do_trace', host = '$host',
882	input_list = '$input_list', icf = '$interpreted_config_file',
883	localhost = '$localhost', output_list = '$output_list' /
884
885	%%END%%
886
887	if [[ "$host" != $localhost ]]
888	then
889
890	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
891	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
892	if [[ $? != 0 ]]
893	then
894	printf "\n\n +++ no interpret_config found"
895	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
896	locat=interpret_config; exit
897	fi
898	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
899	$interpret_config_executable
900
901	else
902
903	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
904	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
905	then
906	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
907	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
908	locat=interpret_config; exit
909	else
910	interpret_config${block}.x
911	fi
912
913	fi
914	rm .mrun_environment
915
916
917	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
918	chmod u+x $interpreted_config_file
919	export PATH=$PATH:.
920	. $interpreted_config_file
921	rm $interpreted_config_file
922
923	fi
924
925
926	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
927	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
928	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
929	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
930	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
931	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
932	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
933
934
935	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
936	# FOR SOURCE-FILES TO BE COMPILED.
937	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
938	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
939	if [[ "$SOURCES_COMPLETE" = "" ]]
940	then
941
942	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
943	# HAS BEEN DEFINED
944	source_path=""
945	line=""
946	grep "%source_path" $config_file > tmp_mrun
947	while read line
948	do
949	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
950	then
951	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
952	then
953	global_source_path=`echo $line \| cut -d" " -f2`
954	fi
955	fi
956	done < tmp_mrun
957
958	line=""
959	found=false
960	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
961	while read line
962	do
963	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
964	then
965	if [[ $found = true ]]
966	then
967	printf "\n\n +++ more than one source path found in configuration file"
968	printf "\n for local host \"$localhost\" "
969	locat=source_path; exit
970	fi
971	source_path=`echo $line \| cut -d" " -f2`
972	found=true
973	fi
974	done < tmp_mrun
975	rm tmp_mrun
976
977	if [[ "$source_path" = "" ]]
978	then
979	if [[ "$global_source_path" != "" ]]
980	then
981	source_path=$global_source_path
982	else
983	printf "\n\n +++ no source path found in configuration file"
984	printf "\n for local host \"$localhost\" "
985	locat=source_path; exit
986	fi
987	fi
988	eval source_path=$source_path
989
990	if [[ ! -d $source_path ]]
991	then
992	printf "\n\n +++ source path \"$source_path\" on local host"
993	printf "\n \"$localhost\" does not exist"
994	locat=source_path; exit
995	fi
996
997	fi
998
999
1000	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1001	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1002	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1003	then
1004	global_revision=`svnversion $source_path 2>/dev/null`
1005	global_revision="Rev: $global_revision"
1006	fi
1007
1008
1009	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1010	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1011	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1012	if [[ -n $host && "$host" != $localhost ]]
1013	then
1014	do_batch=true
1015	do_remote=true
1016	case $host in
1017	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1018	(*) printf "\n"
1019	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1020	printf "\n is not available"
1021	locat=nqs; (( iec = 0 )); exit;;
1022	esac
1023	else
1024	host=$localhost
1025	fi
1026
1027
1028	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1029	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1030	then
1031
1032	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1033	if [[ ! -n $numprocs ]]
1034	then
1035	printf "\n"
1036	printf "\n +++ option \"-K parallel\" requires additional specification"
1037	printf "\n of the number of processors to be used by"
1038	printf "\n mrun-option \"-X\" or by environment-variable"
1039	printf "\n \"numprocs\" in the configuration file"
1040	locat=numprocs; (( iec = 0 )); exit
1041	fi
1042
1043	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1044	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1045	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1046	then
1047	printf "\n"
1048	printf "\n +++ option \"-T\" (tasks per node) is missing"
1049	printf "\n set -T option or define tasks_per_node in the config file"
1050	locat=tasks_per_node; (( iec = 0 )); exit
1051	fi
1052
1053	if (( numprocs < tasks_per_node ))
1054	then
1055	printf "\n"
1056	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1057	printf "\n given values: -T $tasks_per_node -X $numprocs"
1058	locat=tasks_per_node; (( iec = 0 )); exit
1059	fi
1060
1061	if [[ $host != lcflow && $host != lcxt5m ]]
1062	then
1063	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1064	(( ival = $tasks_per_node ))
1065	(( pes = numprocs ))
1066	(( ii = pes / ival ))
1067	(( remaining_pes = pes - ii * ival ))
1068	if (( remaining_pes > 0 ))
1069	then
1070	printf "\n"
1071	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1072	printf "\n divisor of the total number of processors (option \"-X\")"
1073	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1074	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1075	(( nodes = nodes + 1 ))
1076	fi
1077	fi
1078
1079
1080	# SETTINGS FOR SUBJOB-COMMAND
1081	OOPT="-O $threads_per_task"
1082
1083	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1084	if [[ "$tasks_per_node" != "" ]]
1085	then
1086	TOPT="-T $tasks_per_node"
1087	fi
1088
1089	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1090	if [[ $node_usage = default ]]
1091	then
1092	if [[ $host = ibms ]]
1093	then
1094	node_usage=shared
1095	else
1096	node_usage=not_shared
1097	fi
1098	fi
1099
1100	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1101	then
1102	printf "\n"
1103	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1104	printf "\n \"shared\" or \"not_shared\""
1105	locat=tasks_per_node; (( iec = 0 )); exit
1106	fi
1107
1108	fi
1109
1110	# CHECK IF HOSTFILE EXISTS
1111	if [[ -n $hostfile ]]
1112	then
1113	if [[ ! -f $hostfile ]]
1114	then
1115	printf "\n"
1116	printf "\n +++ hostfile \"$hostfile\" does not exist"
1117	locat=hostfile; exit
1118	fi
1119	fi
1120
1121
1122	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1123	if [[ "$maximum_parallel_io_streams" = "" ]]
1124	then
1125	maximum_parallel_io_streams=$numprocs
1126	fi
1127
1128
1129	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1130	if [[ "$scp_port" != "" ]]
1131	then
1132	PORTOPT="-P $scp_port"
1133	SSH_PORTOPT="-p $scp_port"
1134	fi
1135
1136
1137	# SET DEFAULT-QUEUE, IF NOT GIVEN
1138	if [[ $queue = none ]]
1139	then
1140	case $host in
1141	(ibmh) queue=cluster;;
1142	(ibmkisti) queue=class.32plus;;
1143	(lccrayb) queue=mpp1q;;
1144	(lccrayh) queue=mpp1q;;
1145	(lckiaps) queue=normal;;
1146	(lckyoto) queue=ph;;
1147	(lckyuh) queue=fx-single;;
1148	(lckyut) queue=cx-single;;
1149	(lctit) queue=S;;
1150	(nech) queue=none;;
1151	(unics) queue=unics;;
1152	esac
1153	fi
1154
1155
1156	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1157	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1158	(( i = 0 ))
1159	while (( i < iin ))
1160	do
1161	(( i = i + 1 ))
1162	(( maxcycle = 0 ))
1163
1164	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1165	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1166	if [[ "${actionin[$i]}" = di ]]
1167	then
1168	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1169	# HOST ONLY
1170	eval filename=${pathin[$i]}/${endin[$i]}
1171	else
1172	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1173	# HOST ONLY
1174	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1175	fi
1176	eval pathname=${pathin[$i]}
1177
1178	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1179	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1180	then
1181	filename_input=$filename
1182	fi
1183
1184	# CHECK IF FILE EXISTS
1185	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1186	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1187	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1188	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1189	then
1190
1191	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1192	if [[ "${transin[$i]}" != "locopt" ]]
1193	then
1194	printf "\n\n +++ INPUT-file: "
1195	if [[ "${extin[$i]}" = "" ]]
1196	then
1197	printf "\n $filename"
1198	else
1199	printf "\n $filename.${extin[$i]}"
1200	fi
1201	printf "\n does not exist\n"
1202	locat=input; exit
1203	else
1204	transin[$i]="unavailable"
1205	fi
1206	else
1207
1208	# DETERMINE THE FILE'S CYCLE NUMBER
1209	ls -1 -d $filename > filelist 2>/dev/null
1210	ls -1 -d $filename.* >> filelist 2>/dev/null
1211	while read zeile
1212	do
1213	cycle=$(echo $zeile \| cut -f2 -d".")
1214	if [[ "$cycle" = "$zeile" ]]
1215	then
1216	(( icycle = 0 ))
1217	elif [[ "$cycle" = "${extin[$i]}" ]]
1218	then
1219	(( icycle = 0 ))
1220	else
1221	(( icycle = $cycle ))
1222	fi
1223	if (( icycle > maxcycle ))
1224	then
1225	(( maxcycle = icycle ))
1226	file_to_be_used=$zeile
1227	fi
1228	done <filelist
1229	rm filelist
1230
1231	# APPEND CYCLE NUMBER TO FILENAME
1232	if (( maxcycle > 0 ))
1233	then
1234	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1235	then
1236	filename=${filename}.$maxcycle.${extin[$i]}
1237	else
1238	filename=${filename}.$maxcycle
1239	fi
1240	else
1241	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1242	then
1243	filename=${filename}.${extin[$i]}
1244	fi
1245	fi
1246
1247	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1248	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1249	absnamein[$i]=$filename
1250	if (( maxcycle > 0 ))
1251	then
1252	if [[ "${actionin[$i]}" = di ]]
1253	then
1254	frelin[$i]=${endin[$i]}.$maxcycle
1255	else
1256	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1257	fi
1258	else
1259	if [[ "${actionin[$i]}" = di ]]
1260	then
1261	frelin[$i]=${endin[$i]}
1262	else
1263	frelin[$i]=${afname}${endin[$i]}
1264	fi
1265	fi
1266
1267	fi
1268	done
1269
1270	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1271	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1272	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1273	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1274	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1275	# REMOTE HOST)
1276	(( i = 0 ))
1277	while (( i < iout ))
1278	do
1279	(( i = i + 1 ))
1280	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1281	then
1282	if [[ "${actionout[$i]}" = tr ]]
1283	then
1284	actionout[$i]=""
1285	elif [[ "${actionout[$i]}" = trpe ]]
1286	then
1287	actionout[$i]=pe
1288	elif [[ "${actionout[$i]}" = tra ]]
1289	then
1290	actionout[$i]=a
1291	fi
1292	(( maxcycle = 0 ))
1293	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1294	eval catalogname=${pathout[$i]}
1295	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1296	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1297	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1298	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1299	then
1300
1301	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1302	if cat /dev/null > $filename
1303	then
1304	rm $filename
1305	else
1306
1307	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1308	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1309	if [[ ! -d $catalogname ]]
1310	then
1311	if mkdir -p $catalogname
1312	then
1313	printf "\n\n *** directory:"
1314	printf "\n $catalogname"
1315	printf "\n was created\n"
1316	else
1317	printf "\n\n +++ OUTPUT-file:"
1318	printf "\n $filename"
1319	printf "\n cannot be created, because directory does not exist"
1320	printf "\n and cannot be created either"
1321	printf "\n"
1322	locat=output ; exit
1323	fi 2>/dev/null
1324	else
1325	printf "\n\n +++ OUTPUT-file:"
1326	printf "\n $filename"
1327	printf "\n cannot be created, although directory exists"
1328	printf "\n"
1329	locat=output ; exit
1330	fi
1331	fi 2>/dev/null
1332	else
1333
1334	# DETERMINE THE CYCLE NUMBER
1335	ls -1 -d $filename > filelist 2>/dev/null
1336	ls -1 -d $filename.* >> filelist 2>/dev/null
1337	while read zeile
1338	do
1339	cycle=$(echo $zeile \| cut -f2 -d".")
1340	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1341	then
1342	(( icycle = 1 ))
1343	else
1344	(( icycle = $cycle + 1 ))
1345	fi
1346	if (( icycle > maxcycle ))
1347	then
1348	(( maxcycle = icycle ))
1349	fi
1350	done <filelist
1351	rm filelist
1352	fi
1353
1354	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1355	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1356	if [[ "${actionout[$i]}" != a ]]
1357	then
1358	if (( maxcycle > 0 ))
1359	then
1360	filename=${filename}.$maxcycle
1361	if cat /dev/null > $filename
1362	then
1363	rm $filename
1364	else
1365	printf "\n +++ OUTPUT-file:"
1366	printf "\n $filename"
1367	printf "\n cannot be created"
1368	locat=output ; exit
1369	fi
1370	fi
1371	else
1372	(( maxcycle = maxcycle - 1 ))
1373	if (( maxcycle > 0 ))
1374	then
1375	filename=${filename}.$maxcycle
1376	fi
1377	fi
1378
1379	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1380	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1381	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1382	pathout[$i]=$filename
1383	if (( maxcycle > 0 ))
1384	then
1385	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1386	else
1387	frelout[$i]=${fname}${endout[$i]}
1388	fi
1389
1390	fi
1391	done
1392
1393
1394	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1395	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1396	then
1397	if [[ "$dvr_inc" = "" ]]
1398	then
1399	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1400	printf "\n This is required for the dvrp_graphics package.\n"
1401	locat=dvr; exit
1402	fi
1403	if [[ "$dvr_lib" = "" ]]
1404	then
1405	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1406	printf "\n This is required for the dvrp_graphics package.\n"
1407	locat=dvr; exit
1408	fi
1409	fi
1410
1411
1412	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1413	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1414	if [[ "$mainprog" = "" && "$executable" = "" ]]
1415	then
1416	printf "\n +++ neither main program nor executable defined"
1417	locat=source; exit
1418	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1419	then
1420	printf "\n +++ main program as well as executable defined"
1421	locat=source; exit
1422	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1423	then
1424	do_compile=false
1425	fi
1426
1427
1428	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1429	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1430	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1431	then
1432	rm -rf SOURCES_FOR_RUN_$fname
1433	mkdir SOURCES_FOR_RUN_$fname
1434	fi
1435
1436
1437	# COLLECT ALL ROUTINES TO BE COMPILED
1438	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1439	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1440	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1441	then
1442
1443	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1444
1445	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1446	then
1447
1448	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1449	source_list=""
1450	cd $source_path
1451
1452
1453	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1454	if [[ ! -d .svn ]]
1455	then
1456	printf "\n\n +++ source directory"
1457	printf "\n \"$source_path\" "
1458	printf "\n is not under control of \"subversion\"."
1459	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1460	fi
1461
1462
1463	# LIST ALL MODIFIED SOURCE CODE FILES
1464	Filenames=""
1465	svn status > tmp_mrun
1466	while read line
1467	do
1468	firstc=`echo $line \| cut -c1`
1469	if [[ $firstc = M \|\| $firstc = "?" ]]
1470	then
1471	Name=`echo "$line" \| cut -c8-`
1472	extension=`echo $Name \| cut -d. -f2`
1473	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1474	then
1475	Filenames="$Filenames "$Name
1476	fi
1477	fi
1478	done < tmp_mrun
1479
1480
1481	# COPY FILES TO SOURCES_FOR_RUN_...
1482	for dateiname in $Filenames
1483	do
1484	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1485	source_list=$source_list"$dateiname "
1486	done
1487
1488	cd - > /dev/null
1489
1490
1491	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1492	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1493	elif [[ "$source_list" != "" && $restart_run != true ]]
1494	then
1495
1496	cd $source_path
1497
1498	for filename in $source_list
1499	do
1500
1501	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1502	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1503	then
1504	printf "\n +++ source code file: $filename"
1505	printf "\n must not contain (\"/\") "
1506	locat=source; exit
1507	fi
1508
1509	if [[ ! -f $filename ]]
1510	then
1511	printf "\n +++ source code file: $filename"
1512	printf "\n does not exist"
1513	locat=source; exit
1514	else
1515	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1516	fi
1517
1518	done
1519
1520	cd - > /dev/null
1521
1522	fi
1523
1524
1525	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1526	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1527	if [[ $restart_run != true ]]
1528	then
1529
1530	if [[ ! -f "$source_path/$mainprog" ]]
1531	then
1532	printf "\n\n +++ main program: $mainprog"
1533	printf "\n does not exist in source directory"
1534	printf "\n \"$source_path\"\n"
1535	locat=source; exit
1536	else
1537	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1538	then
1539	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1540	source_list=${mainprog}" $source_list"
1541	fi
1542	fi
1543	fi
1544
1545
1546	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1547	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1548	if [[ "$restart_run" != true ]]
1549	then
1550	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1551	if [[ ! -f $makefile ]]
1552	then
1553	printf "\n +++ file \"$makefile\" does not exist"
1554	locat=make; exit
1555	else
1556	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1557	fi
1558	fi
1559
1560
1561	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1562	if [[ $restart_run != true && "$add_source_path" != "" ]]
1563	then
1564
1565	# DOES THE DIRECTORY EXIST?
1566	if [[ ! -d $add_source_path ]]
1567	then
1568	printf "\n\n +++ WARNING: additional source code directory"
1569	printf "\n \"$add_source_path\" "
1570	printf "\n does not exist or is not a directory."
1571	printf "\n No source code will be used from this directory!\n"
1572	add_source_path=""
1573	if [[ $silent == false ]]
1574	then
1575	sleep 3
1576	fi
1577	else
1578
1579	cd $add_source_path
1580	found=false
1581
1582	Names=$(ls -1 *.f90 2>&1)
1583	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1584	Names=$(ls -1 *.F90 2>&1)
1585	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1586	Names=$(ls -1 *.F 2>&1)
1587	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1588	Names=$(ls -1 *.f 2>&1)
1589	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1590	Names=$(ls -1 *.c 2>&1)
1591	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1592
1593	cd - > /dev/null
1594	cd SOURCES_FOR_RUN_$fname
1595
1596	# COPY MAKEFILE IF EXISTING
1597	if [[ -f $add_source_path/Makefile ]]
1598	then
1599	printf "\n\n *** user Makefile from directory"
1600	printf "\n \"$add_source_path\" is used \n"
1601	if [[ $silent == false ]]
1602	then
1603	sleep 1
1604	fi
1605	cp $add_source_path/Makefile .
1606	fi
1607
1608	for dateiname in $AddFilenames
1609	do
1610	if [[ -f $dateiname ]]
1611	then
1612	printf "\n +++ source code file \"$dateiname\" found in additional"
1613	printf "\n source code directory \"$add_source_path\" "
1614	printf "\n but was also given with option \"-s\" which means that it should be taken"
1615	printf "\n from directory \"$source_path\"."
1616	locat=source; exit
1617	fi
1618
1619	cp $add_source_path/$dateiname .
1620	source_list="$source_list $dateiname"
1621
1622	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1623	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1624	then
1625	printf "\n\n +++ user file \"$dateiname\" "
1626	printf "\n is not listed in Makefile \n"
1627	locat=source; exit
1628	else
1629
1630	if [[ $found = false ]]
1631	then
1632	found=true
1633	printf "\n\n *** following user file(s) added to the"
1634	printf " files to be translated:\n "
1635	fi
1636	printf "$dateiname "
1637	if [[ $silent == false ]]
1638	then
1639	sleep 0.5
1640	fi
1641
1642	fi
1643	done
1644	[[ $found = true ]] && printf "\n"
1645	cd - > /dev/null
1646	fi
1647	fi
1648
1649
1650	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1651	# TO THE LIST OF FILES TO BE COMPILED
1652	if [[ $restart_run != true && -n $package_list ]]
1653	then
1654
1655	cd $source_path
1656
1657	for package in $package_list
1658	do
1659
1660	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1661
1662	# DETERMINE FILES BELONGING TO THE PACKAGE
1663	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1664	# THE NAME OF THE DIRECTORY
1665	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1666
1667
1668	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1669	# IF THEY ARE NOT ALREADY PART OF THE LIST
1670	for source_list_name in $package_source_list
1671	do
1672	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1673	then
1674
1675	# ONLY TAKE FILES WITH VALID SUFFIX
1676	ending=`echo $source_list_name \| cut -f2 -d.`
1677	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1678	then
1679	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1680	source_list="$source_list $source_list_name"
1681	fi
1682	fi
1683	done
1684	done
1685
1686	cd - > /dev/null
1687	fi
1688
1689	fi # do_compile=true
1690
1691
1692	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1693	# AND SET PRE-PROCESSOR DIRECTIVES
1694	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1695	then
1696
1697	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1698	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1699	then
1700	cpp_options="${cpp_options},-D__ibm=__ibm"
1701	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1702	then
1703	cpp_options="$cpp_options -D__nec"
1704	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1705	then
1706	cpp_options="$cpp_options -D__lc"
1707	else
1708	cpp_options="$cpp_options -D__$localhost"
1709	fi
1710
1711	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1712	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1713	then
1714	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1715	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1716	else
1717	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1718	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1719	fi
1720
1721	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1722	if [[ -n $package_list ]]
1723	then
1724	for package in $package_list
1725	do
1726	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1727	then
1728	if [[ $package != "dvrp_graphics+1PE" ]]
1729	then
1730	cpp_options="${cpp_options},-D__$package=__$package"
1731	else
1732	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1733	export use_seperate_pe_for_dvrp_output=true
1734	fi
1735	else
1736	if [[ $package != "dvrp_graphics+1PE" ]]
1737	then
1738	cpp_options="$cpp_options -D__$package"
1739	else
1740	cpp_options="$cpp_options -D__dvrp_graphics"
1741	export use_seperate_pe_for_dvrp_output=true
1742	fi
1743	fi
1744	done
1745	fi
1746
1747	# SET DIRECTIVES GIVEN BY OPTION -D
1748	if [[ -n $cpp_opts ]]
1749	then
1750	for popts in $cpp_opts
1751	do
1752	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1753	then
1754	cpp_options="${cpp_options},-D__$popts=__$popts"
1755	else
1756	cpp_options="$cpp_options -D__$popts"
1757	fi
1758	done
1759	fi
1760
1761	else
1762
1763
1764	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1765	if [[ $do_remote = false ]]
1766	then
1767	if [[ ! -f $executable ]]
1768	then
1769	printf "\n +++ executable file: $executable"
1770	printf "\n does not exist"
1771	locat=executable; exit
1772	fi
1773	fi
1774	fi
1775
1776
1777	# DETERMINE THE JOB MODE
1778	if [[ "$ENVIRONMENT" = BATCH ]]
1779	then
1780	batch_job=.TRUE.
1781	jobmo=BATCH
1782	else
1783	batch_job=.FALSE.
1784	jobmo=INTERACTIVE
1785	fi
1786
1787
1788	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1789	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1790	then
1791	printf "\n +++ no interactive runs allowed on host \"$host\" "
1792	printf "\n please submit batch job using mrun option \"-b\" \n"
1793	locat=normal; exit
1794	fi
1795
1796
1797	# CHECK, IF USER DEFINED A COMPILER
1798	if [[ "$compiler_name" = "" ]]
1799	then
1800
1801	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1802	locat=compiler_name; exit
1803
1804	fi
1805
1806
1807	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1808	kennung=$RANDOM
1809	if [[ "$tmp_user_catalog" = "" ]]
1810	then
1811	if [[ $localhost = ibmh ]]
1812	then
1813	tmp_user_catalog=$SCRATCH
1814	elif [[ $localhost = nech ]]
1815	then
1816	tmp_user_catalog=$WRKSHR
1817	else
1818	tmp_user_catalog=/tmp
1819	fi
1820	fi
1821	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1822
1823
1824	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1825	if [[ "$tmp_data_catalog" = "" ]]
1826	then
1827	if [[ $localhost = nech ]]
1828	then
1829	tmp_data_catalog=$WRKSHR/mrun_restart_data
1830	else
1831	tmp_data_catalog=/tmp/mrun_restart_data
1832	fi
1833	fi
1834
1835
1836	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1837	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1838	then
1839	eval fopts=\"$fopts\"
1840	eval lopts=\"$lopts\"
1841	fi
1842
1843
1844
1845	# DETERMINE COMPILE- AND LINK-OPTIONS
1846	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1847	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1848	ROPTS="$ropts"
1849	# 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 ]]
1850	# then
1851	XOPT="-X $numprocs"
1852	# fi
1853
1854
1855
1856	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1857	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1858	done=false
1859	while [[ $done = false ]]
1860	do
1861	cputime=$cpumax
1862	if (( $cputime == 0 ))
1863	then
1864	if [[ $do_batch = true ]]
1865	then
1866	printf "\n +++ cpu-time is undefined"
1867	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1868	printf "\n >>> "
1869	read cputime 1>/dev/null 2>&1
1870	else
1871	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1872	fi
1873	else
1874	done=true
1875	fi
1876	cpumax=$cputime
1877	done
1878
1879	(( minuten = cputime / 60 ))
1880	(( sekunden = cputime - minuten * 60 ))
1881
1882
1883	# CHECK THE MEMORY DEMAND
1884	if [[ $do_batch = true ]]
1885	then
1886	done=false
1887	while [[ $done = false ]]
1888	do
1889	if (( memory == 0 ))
1890	then
1891	printf "\n +++ memory demand is undefined"
1892	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1893	printf "\n >>> "
1894	read memory 1>/dev/null 2>&1
1895	else
1896	done=true
1897	fi
1898	done
1899	fi
1900
1901
1902	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1903	if [[ $do_remote = true && -z $remote_username ]]
1904	then
1905	while [[ -z $remote_username ]]
1906	do
1907	printf "\n +++ username on remote host \"$host\" is undefined"
1908	printf "\n >>> Please type username:"
1909	printf "\n >>> "
1910	read remote_username
1911	done
1912	mc="$mc -u$remote_username"
1913	fi
1914
1915	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1916	if [[ "$login_init_cmd" != "" ]]
1917	then
1918	export init_cmds="${login_init_cmd};"
1919	fi
1920
1921
1922	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1923	if [[ "$modules" != "" ]]
1924	then
1925	if [[ $host = lctit ]]
1926	then
1927	export module_calls=". $modules"
1928	else
1929	export module_calls="module load ${modules};"
1930	fi
1931	fi
1932
1933
1934
1935	# OUTPUT OF THE MRUN-HEADER
1936	calltime=$(date)
1937	printf "\n"
1938	printf "#------------------------------------------------------------------------# \n"
1939	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1940	printf "\| \| \n"
1941	spalte1="called on:"; spalte2=$localhost_realname
1942	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1943	if [[ $do_remote = true ]]
1944	then
1945	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1946	else
1947	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1948	fi
1949	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1950	if [[ -n $numprocs ]]
1951	then
1952	if [[ $run_coupled_model = false ]]
1953	then
1954	spalte1="number of PEs:"; spalte2=$numprocs
1955	else
1956	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1957	fi
1958	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1959	fi
1960	if [[ -n $tasks_per_node ]]
1961	then
1962	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1963	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1964	if (( remaining_pes > 0 ))
1965	then
1966	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1967	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1968	fi
1969	fi
1970	if [[ $maximum_parallel_io_streams != $numprocs ]]
1971	then
1972	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1973	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1974	fi
1975	if [[ $use_openmp = true ]]
1976	then
1977	spalte1="threads per task:"; spalte2="$threads_per_task"
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	fi
1980	printf "\| \| \n"
1981	if [[ $do_compile = true ]]
1982	then
1983	if [[ "$mopts" != "" ]]
1984	then
1985	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1986	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1987	zeile=$(echo "$mopts" \| cut -c46-)
1988	while [[ "$zeile" != "" ]]
1989	do
1990	spalte1=""
1991	spalte2=$(echo "$zeile" \| cut -c-45)
1992	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1993	zeile=$(echo "$zeile" \| cut -c46-)
1994	done
1995	fi
1996
1997	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1998	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1999	zeile=$(echo "$cpp_options" \| cut -c46-)
2000	while [[ "$zeile" != "" ]]
2001	do
2002	spalte1=""
2003	spalte2=$(echo "$zeile" \| cut -c-45)
2004	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2005	zeile=$(echo "$zeile" \| cut -c46-)
2006	done
2007
2008	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2009	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2010	zeile=$(echo "$fopts" \| cut -c46-)
2011	while [[ "$zeile" != "" ]]
2012	do
2013	spalte1=""
2014	spalte2=$(echo "$zeile" \| cut -c-45)
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	zeile=$(echo "$zeile" \| cut -c46-)
2017	done
2018
2019	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2020	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2021	zeile=$(echo "$lopts" \| cut -c46-)
2022	while [[ "$zeile" != "" ]]
2023	do
2024	spalte1=""
2025	spalte2=$(echo "$zeile" \| cut -c-45)
2026	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2027	zeile=$(echo "$zeile" \| cut -c46-)
2028	done
2029
2030	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2031	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2032	zeile=$(echo "$modules" \| cut -c46-)
2033	while [[ "$zeile" != "" ]]
2034	do
2035	spalte1=""
2036	spalte2=$(echo "$zeile" \| cut -c-45)
2037	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2038	zeile=$(echo "$zeile" \| cut -c46-)
2039	done
2040
2041	spalte1="main program:"; spalte2=$mainprog
2042	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2043	else
2044	spalte1=executable:; spalte2=$executable
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046	fi
2047	printf "\| \| \n"
2048	spalte1="base name of files:"; spalte2=$fname
2049	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2050	if [[ $fname != $afname ]]
2051	then
2052	spalte1="base name of input files:"; spalte2=$afname
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054	fi
2055	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2056	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2057	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2058	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2059
2060	if [[ "$ocean_file_appendix" = true ]]
2061	then
2062	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2063	fi
2064
2065	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2066	then
2067	spalte1="memory demand / PE":; spalte2="$memory MB"
2068	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2069	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	fi
2072
2073	if [[ $do_compile = true ]]
2074	then
2075	printf "\| \| \n"
2076	printf "\| Files to be compiled: \| \n"
2077	zeile=$source_list
2078	while [[ "$zeile" != "" ]]
2079	do
2080	linestart=$(echo $zeile \| cut -c-70)
2081	printf "\| %-70s \| \n" "$linestart"
2082	zeile=$(echo "$zeile" \| cut -c71-)
2083	done
2084	fi
2085	printf "#------------------------------------------------------------------------#"
2086
2087
2088
2089	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2090	if [[ $do_trace = true ]]
2091	then
2092	(( i = 0 ))
2093	while (( i < iin ))
2094	do
2095	(( i = i + 1 ))
2096	if (( i == 1 ))
2097	then
2098	printf "\n\n >>> INPUT-file assignments:\n"
2099	fi
2100	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2101	done
2102	(( i = 0 ))
2103	while (( i < iout ))
2104	do
2105	(( i = i + 1 ))
2106	if (( i == 1 ))
2107	then
2108	printf "\n\n >>> OUTPUT-file assignments:\n"
2109	fi
2110	printf "\n ${localout[$i]} : ${pathout[$i]}"
2111	done
2112	(( i = 0 ))
2113	while (( i < iic ))
2114	do
2115	(( i = i + 1 ))
2116	if (( i == 1 ))
2117	then
2118	printf "\n\n >>> INPUT-commands:\n"
2119	fi
2120	printf "\n ${in_command[$i]}"
2121	done
2122	(( i = 0 ))
2123	while (( i < ioc ))
2124	do
2125	(( i = i + 1 ))
2126	if (( i == 1 ))
2127	then
2128	printf "\n\n >>> OUTPUT-commands:\n"
2129	fi
2130	printf "\n ${out_command[$i]}"
2131	done
2132	fi
2133
2134
2135	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2136	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2137	then
2138	antwort=dummy
2139	printf "\n\n"
2140	printf " >>> everything o.k. (y/n) ? "
2141	while read antwort
2142	do
2143	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2144	then
2145	printf " >>> everything o.k. (y/n) ? "
2146	else
2147	break
2148	fi
2149	done
2150	if [[ $antwort = n \|\| $antwort = N ]]
2151	then
2152	locat=user_abort; (( iec = 0 )); exit
2153	fi
2154	if [[ $do_batch = true ]]
2155	then
2156	printf " >>> batch-job will be created and submitted"
2157	else
2158	printf " >>> MRUN will now continue to execute on this machine"
2159	fi
2160	fi
2161
2162
2163	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2164	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2165	check_depository="${working_directory}/trunk/UTIL"
2166	check_sources="${working_directory}/tmp_check_namelist_files"
2167	skip_check=false
2168
2169	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2170	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2171	then
2172	skip_check=true
2173	reason="run on remote host or parameter file check has not been compiled."
2174	fi
2175	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2176	then
2177	skip_check=true
2178	reason="parameter file check has not been compiled."
2179	fi
2180
2181	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2182	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2183	then
2184	skip_check=true
2185	reason="serial run."
2186	fi
2187
2188	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2189	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2190	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2191	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2192	if [[ $check_namelist_files == false ]]
2193	then
2194	skip_check=true
2195	reason="-z option set."
2196	fi
2197
2198	if [[ $fromhost != $localhost ]]
2199	then
2200	skip_check=true
2201	reason="submitting host is local host."
2202	fi
2203
2204	if [[ $run_coupled_model == true ]]
2205	then
2206	skip_check=true
2207	reason="coupled run."
2208	fi
2209
2210	if [[ $restart_run == true ]]
2211	then
2212	skip_check=true
2213	reason="restart run."
2214	fi
2215
2216	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2217	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2218	last_char=`echo $filename_input \| cut -c $last_char_int`
2219	if [[ "$last_char" == "f" ]]
2220	then
2221	skip_check=true
2222	reason="restart run."
2223	fi
2224
2225	if [[ $skip_check == false ]]
2226	then
2227	tmp_check=${working_directory}/tmp_check
2228
2229	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2230	# NOT NECESSARILY REQUIRED
2231	line=""
2232	found=false
2233	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2234	while read line1
2235	do
2236	line="$line1"
2237	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2238	then
2239	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2240	found=true
2241	fi
2242	done < $tmp_check
2243
2244	if [[ $found = false ]]
2245	then
2246	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2247	fi
2248
2249	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2250	# NOT NECESSARILY REQUIRED
2251	line=""
2252	found=false
2253	grep "NUDGING_DATA" $config_file > $tmp_check
2254	while read line1
2255	do
2256	line="$line1"
2257	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2258	then
2259	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2260	found=true
2261	fi
2262	done < $tmp_check
2263
2264	if [[ $found = false ]]
2265	then
2266	printf "\n +++ no NUDGING list entry found in the configuration file."
2267	fi
2268
2269	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2270	# NOT NECESSARILY REQUIRED
2271	line=""
2272	found=false
2273	grep "LSF_DATA" $config_file > $tmp_check
2274	while read line1
2275	do
2276	line="$line1"
2277	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2278	then
2279	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2280	found=true
2281	fi
2282	done < $tmp_check
2283
2284	if [[ $found = false ]]
2285	then
2286	printf "\n +++ no LSF list entry found in the configuration file."
2287	fi
2288
2289	rm -rf ${working_directory}/tmp_check
2290
2291	# CHECK IF THE P3DF FILE MUST BE CHECKED
2292	for item in $input_list
2293	do
2294	if [[ "$item" == "restart" ]]
2295	then
2296	check_restart=1
2297	else
2298	check_restart=0
2299	fi
2300	done
2301
2302	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2303	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2304	then
2305	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2306	locat=check_namelist; exit
2307	fi
2308
2309	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2310	if [[ $check_restart == 1 ]]
2311	then
2312
2313	filenamef="${filename_input}f"
2314	if [[ ! -f $filenamef ]]
2315	then
2316	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2317	check_restart=0
2318	answer=dummy
2319	printf "\n\n"
2320
2321	if [[ $silent == false ]]
2322	then
2323	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2324	do
2325	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2326	read answer
2327	done
2328	if [[ $answer = a \|\| $answer = A ]]
2329	then
2330	printf "\n +++ Aborting...."
2331	locat=normal; exit
2332	fi
2333	fi
2334	else
2335	check_restart=1
2336	fi
2337	fi
2338
2339	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2340	mkdir $check_sources
2341	cd $check_sources
2342
2343
2344	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2345	if [[ -d $add_source_path ]]
2346	then
2347	printf "\n\n *** copying files from $check_depository"
2348	cp $check_depository/check_namelist_files.tar ./
2349
2350	printf "\n\n *** untar of makefile and source files in $check_sources"
2351	tar -xf check_namelist_files.tar > /dev/null 2>&1
2352
2353	printf "\n\n *** adding user code."
2354	cp $add_source_path/* ./
2355	touch check_namelist_files.f90
2356
2357	# GET COMPILER OPTIONS AND PERFORM MAKE
2358	printf "\n\n *** compiling code if necessary...\n"
2359
2360	# workaround for batch jobs on local machine (lcxe6)
2361	if [[ $do_batch == true && $do_remote == false ]]
2362	then
2363	eval $init_cmds
2364	fi
2365
2366	# GET CHECK OPTIONS
2367	line=""
2368	found=false
2369
2370	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2371
2372	while read line1
2373	do
2374
2375	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2376	then
2377	line="$line1"
2378	fi
2379
2380	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2381	then
2382	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2383	line="$line "
2384	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'`
2385	found=true
2386	fi
2387
2388	done < $tmp_check
2389	copts_check="$copts_check -D__check -D__parallel"
2390
2391	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2392
2393	# GET MAKE OUTPUT
2394	if [[ $? != 0 ]]
2395	then
2396	printf "\n +++ error during make."
2397	answer=dummy
2398	printf "\n\n"
2399	if [[ $silent == false ]]
2400	then
2401	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2402	do
2403	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2404	read answer
2405	done
2406	if [[ $answer = a \|\| $answer = A ]]
2407	then
2408	printf "\n +++ Aborting..."
2409	rm -rf $check_sources
2410	locat=normal; exit
2411	else
2412	skip_check=true
2413	fi
2414	else
2415	skip_check=true
2416	fi
2417	fi
2418	else
2419	cp $PALM_BIN/check_namelist_files.x ./
2420	fi
2421
2422	cp $filename_input ./PARIN
2423	if [[ $check_restart == 1 ]]
2424	then
2425	cp $filenamef ./PARINF
2426	fi
2427
2428	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2429	then
2430	printf "\n *** adding topography data"
2431	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2432
2433	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2434	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2435	# WHICH REQUIRE SUFFICIENT MEMORY
2436	ulimit -s unlimited
2437	fi
2438
2439	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2440	then
2441	printf "\n *** adding nudging data"
2442	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2443	fi
2444
2445	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2446	then
2447	printf "\n *** adding large scale forcing data"
2448	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2449	fi
2450
2451	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2452	cat > ENVPAR << %%END%%
2453	&envpar run_identifier = '$fname', host = '$host',
2454	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2455	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2456	maximum_cpu_time_allowed = ${cpumax}.,
2457	revision = '$global_revision',
2458	local_dvrserver_running = $local_dvrserver_running /
2459
2460	%%END%%
2461
2462	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2463	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2464	then
2465	printf "\n +++ WARNING: check_namelist_files.x not found."
2466	answer=dummy
2467	printf "\n\n"
2468
2469	if [[ $silent == false ]]
2470	then
2471	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2472	do
2473	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2474	read answer
2475	done
2476	if [[ $answer = a \|\| $answer = A ]]
2477	then
2478	printf "\n +++ Aborting..."
2479	rm -rf $check_sources
2480	locat=normal; exit
2481	else
2482	printf "\n *** skipping parameter file check."
2483	fi
2484	fi
2485
2486	elif [[ $skip_check == false ]]
2487	then
2488	# STARTING THE PARAMETER FILE CHECK
2489	printf "\n\n *** starting parameter file check..."
2490
2491	# CHECKING THE P3D FILE
2492	printf "\n\n (1) checking $filename_input"
2493	echo "$numprocs 0 0" > VARIN
2494	errors=`./check_namelist_files.x < VARIN 2>&1`
2495
2496	check_error=false
2497	if [[ "$errors" == "" ]]
2498	then
2499	printf " --> o.k."
2500	else
2501	printf " --> failed."
2502	check_error=true
2503	printf "\n\n $errors"
2504	fi
2505
2506	# CHECKING THE PD3F FILE IF NECESSARY
2507	if [[ $check_restart == 1 && $check_error == false ]]
2508	then
2509	printf "\n\n (2) checking $filenamef"
2510
2511	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2512	# IN &INIPAR LIST
2513	found=false
2514	cat PARINF \| while read line
2515	do
2516	line=$(echo $line\|sed 's/ //g')
2517	if [[ $line == "&inipar" ]]
2518	then
2519	start_search=true
2520	fi
2521
2522	if [[ $start_search == true ]]
2523	then
2524	if [[ $line == "initializing_actions='read_restart_data'" ]]
2525	then
2526	found=true
2527	break
2528	fi
2529	fi
2530
2531	if [[ $line == "/" ]]
2532	then
2533	start_search=false
2534	fi
2535
2536	done
2537
2538	if [[ $found = false ]]
2539	then
2540	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2541	printf "\n in &inipar list in $fname$p3df_suffix."
2542	rm -rf $check_sources
2543	locat=check_namelist; exit
2544	fi
2545
2546	# READ max_user_pr FROM FILES
2547	if [[ -f parin_for_check ]]
2548	then
2549	read max_pr_user < parin_for_check
2550	else
2551	max_user_pr=0
2552	fi
2553
2554	echo "$numprocs 1 $max_pr_user" > VARIN
2555	errors=`./check_namelist_files.x < VARIN 2>&1`
2556
2557	if [[ "$errors" == "" ]]
2558	then
2559	printf " --> o.k."
2560	else
2561	printf " --> failed."
2562	check_error=true
2563	printf "\n\n $errors"
2564	fi
2565	fi
2566
2567	# REPORT ERRORS AND CONTINUE/EXIT
2568	if [[ $check_error == true ]]
2569	then
2570	printf "\n +++ errors found in the parameter file!\n"
2571	answer=dummy
2572	printf "\n\n"
2573
2574	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2575	do
2576	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2577	read answer
2578	done
2579
2580	if [[ $answer = a \|\| $answer = A ]]
2581	then
2582	printf "\n +++ Aborting..."
2583	rm -rf $check_sources
2584	locat=normal; exit
2585	fi
2586	else
2587	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2588	fi
2589	rm -rf $check_sources
2590	fi
2591	else
2592	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2593	fi
2594
2595	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2596	rm -rf $check_sources
2597	cd $working_directory
2598
2599
2600	# DETERMINE PATH FOR MAKE DEPOSITORY
2601	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2602	then
2603
2604	line=""
2605	grep "%depository_path" $config_file > tmp_mrun
2606	while read line
2607	do
2608	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2609	then
2610	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2611	then
2612	global_depository_path=`echo $line \| cut -d" " -s -f2`
2613	fi
2614	fi
2615	done < tmp_mrun
2616
2617	line=""
2618	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2619	while read line
2620	do
2621	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2622	then
2623	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2624	then
2625	local_depository_path=`echo $line \| cut -d" " -s -f2`
2626	fi
2627	fi
2628	done < tmp_mrun
2629
2630	if [[ "$local_depository_path" = "" ]]
2631	then
2632	if [[ "$global_depository_path" != "" ]]
2633	then
2634	local_depository_path=$global_depository_path
2635	else
2636	printf "\n\n +++ no depository path found in configuration file"
2637	printf "\n for local host \"$localhost\" "
2638	printf "\n please set \"\%depository_path\" in configuration file\n"
2639	locat=config_file; exit
2640	fi
2641	fi
2642	eval local_depository_path=$local_depository_path
2643	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2644	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2645
2646
2647	basename=`echo $mainprog \| cut -f1 -d"."`
2648	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2649	if [[ ! -f $make_depository ]]
2650	then
2651	printf "\n"
2652	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2653	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2654	fi
2655
2656	fi
2657
2658
2659	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2660	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2661	if [[ $do_batch = false ]]
2662	then
2663
2664
2665	# CREATE THE TEMPORARY WORKING DIRECTORY
2666	mkdir -p $TEMPDIR
2667	chmod go+rx $TEMPDIR
2668	tmpcreate=true
2669
2670
2671	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2672	# INTO THE TEMPORARY WORKING DIRECTORY
2673	if [[ $do_compile = true ]]
2674	then
2675
2676	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2677	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2678	if [[ $localhost = nech ]]
2679	then
2680	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2681	if mkdir -p $TEMPDIR_COMPILE
2682	then
2683	printf "\n *** \"$TEMPDIR_COMPILE\" "
2684	printf "\n is generated as temporary directory for cross compiling\n"
2685	else
2686	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2687	printf "\n needed for cross compilation failed"
2688	locat=compile
2689	exit
2690	fi
2691	else
2692	TEMPDIR_COMPILE=$TEMPDIR
2693	fi
2694
2695	cp $make_depository $TEMPDIR_COMPILE
2696	cd $TEMPDIR_COMPILE
2697	tar -xf $make_depository > /dev/null 2>&1
2698	cd - > /dev/null
2699
2700	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2701	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2702	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2703	then
2704	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2705	else
2706	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2707	fi
2708
2709	else
2710
2711	cp $executable ${TEMPDIR}/a.out
2712
2713	fi
2714
2715
2716	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2717	cd $TEMPDIR
2718	printf "\n *** changed to temporary directory: $TEMPDIR"
2719
2720
2721	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2722	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2723	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2724	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2725	(( i = 0 ))
2726	while (( i < iout ))
2727	do
2728	(( i = i + 1 ))
2729	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2730	then
2731	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2732	else
2733	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2734	fi
2735	done
2736
2737
2738	# IF REQUIRED, START WITH COMPILING
2739	if [[ $do_compile = true ]]
2740	then
2741
2742
2743	if [[ -f a.out ]]
2744	then
2745
2746	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2747	printf "\n\n\n *** executable a.out found"
2748	printf "\n no compilation required \n"
2749
2750	else
2751
2752	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2753	printf "\n\n\n *** compilation starts \n$dashes\n"
2754	printf " *** compilation with make using following options:\n"
2755	printf " make depository: $make_depository"
2756	if [[ "$mopts" != "" ]]
2757	then
2758	printf " make options: $mopts\n"
2759	fi
2760	printf " compilername: $compiler_name\n"
2761	printf " compiler options: $fopts\n"
2762	printf " preprocessor directives: $cpp_options \n"
2763	printf " linker options: $lopts \n"
2764	if [[ "$modules" != "" ]]
2765	then
2766	printf " modules to be load: $modules \n"
2767	fi
2768	printf " source code files: $source_list \n"
2769
2770	if [[ $localhost = nech ]]
2771	then
2772	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\" "
2773	cp $TEMPDIR_COMPILE/a.out .
2774	[[ $? != 0 ]] && compile_error=true
2775	rm -rf $TEMPDIR_COMPILE
2776	elif [[ $localhost = ibmh ]]
2777	then
2778	printf " compiler is called via ssh on \"plogin1\" \n"
2779	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\" "
2780	[[ ! -f a.out ]] && compile_error=true
2781	continue # STATUS=1, IF a.out EXISTS
2782	elif [[ $localhost = lcflow ]]
2783	then
2784	printf " compiler is called via ssh on \"flow\" \n"
2785	/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\" "
2786	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2787	[[ "$check_for_file" = "" ]] && compile_error=true
2788	continue # STATUS=1, IF a.out EXISTS
2789	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2790	then
2791	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2792	else
2793	[[ "$init_cmds" != "" ]] && eval $init_cmds
2794	[[ "$module_calls" != "" ]] && eval $module_calls
2795	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2796	fi
2797
2798	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2799	then
2800	printf "\n +++ error occured while compiling or linking"
2801	locat=compile
2802
2803	exit
2804	else
2805	printf "$dashes\n *** compilation finished \n"
2806	fi
2807
2808	fi
2809
2810	fi
2811
2812
2813	# PROVIDE THE INPUT FILES
2814	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2815	(( i = 0 ))
2816	while (( i < iin ))
2817	do
2818	(( i = i + 1 ))
2819	if (( i == 1 ))
2820	then
2821	printf "\n\n *** providing INPUT-files:\n$dashes"
2822	fi
2823
2824
2825	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2826	if [[ "${transin[$i]}" = unavailable ]]
2827	then
2828	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2829	then
2830	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2831	printf "\n is not available!"
2832	else
2833	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2834	printf "\n is not available!"
2835	fi
2836	continue
2837	fi
2838
2839	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2840	files_for_pes=false; datentyp=file
2841	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2842	then
2843	files_for_pes=true; datentyp=directory
2844	actionin[$i]=""
2845	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2846	then
2847	actionin[$i]=""
2848	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2849	then
2850	files_for_pes=true; datentyp=directory
2851	actionin[$i]="ar"
2852	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2853	then
2854	actionin[$i]="ar"
2855	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2856	then
2857	files_for_pes=true; datentyp=directory
2858	actionin[$i]="fl"
2859	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2860	then
2861	actionin[$i]="fl"
2862	fi
2863
2864	if [[ $files_for_pes = true ]]
2865	then
2866	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2867	else
2868	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2869	fi
2870
2871	# INPUT-FILE FOR A RESTART RUN.
2872	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2873	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2874	if [[ "${actionin[$i]}" = fl ]]
2875	then
2876	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2877	if [[ $files_for_pes = false ]]
2878	then
2879	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2880	then
2881	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2882	got_tmp[$i]=true
2883	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2884	then
2885	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2886	printf "\n *** trying to use backup copy in \"$WORK\" "
2887	cp $WORK/${frelin[$i]} ${localin[$i]}
2888	else
2889	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2890	printf "\n or \"$tmp_data_catalog\" does not exist!"
2891	printf "\n *** trying to get copy from archive"
2892	actionin[$i]=ar
2893	fi
2894	else
2895	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2896	then
2897	mkdir ${localin[$i]}
2898	cd $tmp_data_catalog/${frelin[$i]}
2899	for file in $(ls *)
2900	do
2901	ln $file $TEMPDIR/${localin[$i]}
2902	done
2903	cd $TEMPDIR
2904	got_tmp[$i]=true
2905	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2906	then
2907	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2908	printf "\n *** trying to use backup copy in \"$WORK\" "
2909	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2910	else
2911	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2912	printf "\n or \"$tmp_data_catalog\" does not exist!"
2913	printf "\n *** trying to get copy from archive"
2914	actionin[$i]=ar
2915	fi
2916	fi
2917	fi
2918
2919
2920	# FILE IS STORED ON THE ARCHIVE SYSTEM
2921	if [[ "${actionin[$i]}" = ar ]]
2922	then
2923
2924	if [[ $files_for_pes = false ]]
2925	then
2926	printf "\n file will be restored from archive-system ($archive_system)!"
2927	else
2928	printf "\n directory will be restored from archive-system ($archive_system)!"
2929	fi
2930
2931	file_restored=false
2932
2933	if [[ $archive_system = asterix ]]
2934	then
2935	do_stagein=true
2936	(( stagein_anz = 0 ))
2937	while [[ $do_stagein = true ]]
2938	do
2939	if [[ $files_for_pes = false ]]
2940	then
2941	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2942	else
2943	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2944	fi
2945	cat STAGEIN_OUTPUT
2946	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2947	then
2948	file_restored=true
2949	do_stagein=false
2950	else
2951	(( stagein_anz = stagein_anz + 1 ))
2952	if (( stagein_anz == 10 ))
2953	then
2954	printf "\n +++ stagein stoped after 10 tries"
2955	locat=stage
2956	exit
2957	fi
2958	printf "\n +++ restoring from archive failed, trying again:"
2959	sleep 900
2960	fi
2961	done
2962	elif [[ $archive_system = DMF ]]
2963	then
2964	if [[ $files_for_pes = false ]]
2965	then
2966	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2967	locat=DMF
2968	exit
2969	else
2970	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2971	cp -r $ARCHIVE/${frelin[$i]} $PWD
2972	file_restored=true
2973	fi
2974	elif [[ $archive_system = tivoli ]]
2975	then
2976	if [[ $files_for_pes = false ]]
2977	then
2978	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2979	else
2980	(( inode = 0 ))
2981	while (( inode < nodes ))
2982	do
2983	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2984	(( inode = inode + 1 ))
2985	done
2986	fi
2987	file_restored=true
2988	elif [[ $archive_system = ut ]]
2989	then
2990	if [[ $files_for_pes = false ]]
2991	then
2992	cp $UT/${frelin[$i]} .
2993	else
2994	(( inode = 0 ))
2995	while (( inode < nodes ))
2996	do
2997	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2998	(( inode = inode + 1 ))
2999	done
3000	fi
3001	file_restored=true
3002	else
3003	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3004	locat=rearchive
3005	exit
3006	fi
3007
3008	if [[ $file_restored = true ]]
3009	then
3010
3011	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3012	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3013	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3014	if [[ $files_for_pes = false ]]
3015	then
3016	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3017	else
3018	mkdir $tmp_data_catalog/${frelin[$i]}
3019	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3020	fi
3021	got_tmp[$i]=true
3022
3023	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3024	mv ${frelin[$i]} ${localin[$i]}
3025
3026	fi
3027	fi
3028
3029
3030	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3031	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3032	then
3033
3034	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3035	then
3036
3037	# FILE COPIES ARE PROVIDED FOR ALL CORES
3038	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3039	printf "\n file will be provided for $numprocs processors"
3040	mkdir ${localin[$i]}
3041	ival=$numprocs
3042	(( ii = 0 ))
3043	while (( ii <= ival-1 ))
3044	do
3045	if (( ii < 10 ))
3046	then
3047	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3048	elif (( ii < 100 ))
3049	then
3050	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3051	elif (( ii < 1000 ))
3052	then
3053	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3054	else
3055	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3056	fi
3057	(( ii = ii + 1 ))
3058	done
3059
3060	else
3061
3062	if [[ $files_for_pes = true ]]
3063	then
3064
3065	# PROVIDE FILES FOR EACH CORE
3066	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3067	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3068	printf "\n providing $numprocs files for the respective processors"
3069	mkdir ${localin[$i]}
3070	if [[ $link_local_input = true ]]
3071	then
3072	printf " using ln -f\n"
3073	cd ${absnamein[$i]}
3074	for file in $(ls *)
3075	do
3076	ln -f $file ${localin[$i]}
3077	done
3078	cd $TEMPDIR
3079	fi
3080
3081	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3082	if [[ ! -f "${localin[$i]}/_0000" ]]
3083	then
3084	if [[ $link_local_input = true ]]
3085	then
3086	printf " ln failed for .../_0000, using cp...\n"
3087	fi
3088	cp -r ${absnamein[$i]}/* ${localin[$i]}
3089	fi
3090
3091	else
3092
3093	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3094	if [[ $link_local_input = true ]]
3095	then
3096	printf " using ln -f\n"
3097	ln -f ${absnamein[$i]} ${localin[$i]}
3098	fi
3099	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3100	if [[ ! -f "${localin[$i]}" ]]
3101	then
3102	if [[ $link_local_input = true ]]
3103	then
3104	printf " ln failed, using cp...\n"
3105	fi
3106	cp ${absnamein[$i]} ${localin[$i]}
3107	fi
3108	fi
3109	fi
3110	fi
3111
3112	done
3113	if (( i != 0 ))
3114	then
3115	printf "\n$dashes\n *** all INPUT-files provided \n"
3116	fi
3117
3118
3119	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3120	(( i = 0 ))
3121	while (( i < iic ))
3122	do
3123	(( i = i + 1 ))
3124	if (( i == 1 ))
3125	then
3126	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3127	fi
3128	printf "\n >>> ${in_command[$i]}"
3129	eval ${in_command[$i]}
3130	if (( i == iic ))
3131	then
3132	printf "\n$dashes\n"
3133	fi
3134	done
3135
3136
3137	# SET THE REMAINING CPU-TIME
3138	cpurest=${cpumax}.
3139
3140
3141	# START DVR STREAMING SERVER
3142	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3143	then
3144	if [[ "$dvr_server" != "" ]]
3145	then
3146
3147	printf "\n\n *** preparing the dvr streaming server configuration file"
3148
3149	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3150	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3151	if [[ "$running_dvrserver_id" != "" ]]
3152	then
3153
3154	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3155	printf "\n This server is used instead starting a new one!"
3156	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3157
3158	else
3159
3160	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3161	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3162	then
3163	cp ${PALM_BIN}/.dvrserver.config .
3164
3165	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3166	user_id=`id -u`
3167	group_id=`id -g`
3168
3169	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3170	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3171	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3172	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3173	mv .dvrserver.3 .dvrserver.config
3174	rm .dvrserver.1 .dvrserver.2
3175
3176	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3177	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3178	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3179	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3180	local_dvrserver_running=.TRUE.
3181	else
3182	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3183	printf "\n \"$PALM_BIN\" "
3184	locat=dvr
3185	exit
3186	fi
3187
3188	fi
3189
3190	else
3191	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3192	fi
3193	fi
3194
3195
3196	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3197	# (FILE ENVPAR WILL BE READ BY PALM)
3198	cat > ENVPAR << %%END%%
3199	&envpar run_identifier = '$fname', host = '$localhost',
3200	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3201	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3202	maximum_cpu_time_allowed = ${cpumax}.,
3203	revision = '$global_revision',
3204	local_dvrserver_running = $local_dvrserver_running,
3205	batch_job = $batch_job /
3206
3207	%%END%%
3208
3209
3210	# STARTING THE EXECUTABLE
3211	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3212	PATH=$PATH:$TEMPDIR
3213
3214	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3215	if [[ "$mpi_debug" = true ]]
3216	then
3217	export MPI_CHECK_ARGS=1
3218	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3219	fi
3220
3221	if [[ "$totalview" = true ]]
3222	then
3223	printf "\n *** totalview debugger will be used"
3224	tv_opt="-tv"
3225	else
3226	tv_opt=""
3227	fi
3228
3229	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3230	then
3231	if [[ "$ENVIRONMENT" = BATCH ]]
3232	then
3233	continue
3234	fi
3235	if [[ $localhost = ibmh ]]
3236	then
3237
3238	# SETUP THE IBM MPI ENVIRONMENT
3239	export MP_SHARED_MEMORY=yes
3240	export AIXTHREADS_SCOPE=S
3241	export OMP_NUM_THREADS=$threads_per_task
3242	export AUTHSTATE=files
3243	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3244
3245	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3246	export MP_ADAPTER_USE=shared
3247	export MP_CPU_USE=multiple
3248	export MP_TIMEOUT=1200
3249
3250	unset MP_TASK_AFFINITY
3251
3252	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3253	#(( ii = 1 ))
3254	#while (( ii <= $numprocs ))
3255	#do
3256	# echo $localhost_realname >> hostfile
3257	# (( ii = ii + 1 ))
3258	#done
3259	#export MP_HOSTFILE=hostfile
3260
3261	if [[ "$LOADLBATCH" = yes ]]
3262	then
3263	totalview poe a.out $ROPTS
3264	else
3265	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3266	export TVDSVRLAUNCHCMD=ssh
3267	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3268	fi
3269
3270	fi # END DEBUG MODE
3271
3272	else
3273
3274	# NORMAL EXECUTION
3275	if [[ -n $numprocs ]]
3276	then
3277
3278	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3279	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3280	then
3281
3282	# SETUP THE IBM MPI ENVIRONMENT
3283	if [[ $host != ibmh && $host != ibmkisti ]]
3284	then
3285	export MP_SHARED_MEMORY=yes
3286	export AIXTHREAD_SCOPE=S
3287	export OMP_NUM_THREADS=$threads_per_task
3288	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3289	export AUTHSTATE=files
3290	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3291	# export MP_PRINTENV=yes
3292
3293	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3294	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3295	export MP_WAIT_MODE=poll
3296	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3297	fi
3298
3299	if [[ $host = ibmkisti ]]
3300	then
3301	export LANG=en_US
3302	export MP_SHARED_MEMORY=yes
3303	if [[ $threads_per_task = 1 ]]
3304	then
3305	export MP_SINGLE_THREAD=yes
3306	export MEMORY_AFFINITY=MCM
3307	else
3308	export OMP_NUM_THREADS=$threads_per_task
3309	fi
3310	fi
3311
3312	if [[ "$LOADLBATCH" = yes ]]
3313	then
3314	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3315	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3316	then
3317	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3318	else
3319	if [[ $run_coupled_model = false ]]
3320	then
3321	if [[ "$ocean_file_appendix" = true ]]
3322	then
3323	echo "precursor_ocean" > runfile_atmos
3324	else
3325	echo "precursor_atmos" > runfile_atmos
3326	fi
3327	else
3328	(( iia = $numprocs_atmos / $threads_per_task ))
3329	(( iio = $numprocs_ocean / $threads_per_task ))
3330	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3331	printf "\n using $coupled_mode coupling"
3332	printf "\n\n"
3333	echo "coupled_run $iia $iio" > runfile_atmos
3334	fi
3335	poe ./a.out $ROPTS < runfile_atmos
3336	fi
3337	else
3338	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3339	then
3340	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3341	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3342	then
3343	if [[ -f $hostfile ]]
3344	then
3345	cp $hostfile hostfile
3346	else
3347	(( ii = 1 ))
3348	while (( ii <= $numprocs ))
3349	do
3350	echo $localhost_realname >> hostfile
3351	(( ii = ii + 1 ))
3352	done
3353	fi
3354	export MP_HOSTFILE=hostfile
3355	if [[ $run_coupled_model = false ]]
3356	then
3357	if [[ "$ocean_file_appendix" = true ]]
3358	then
3359	echo "precursor_ocean" > runfile_atmos
3360	else
3361	echo "precursor_atmos" > runfile_atmos
3362	fi
3363	else
3364	(( iia = $numprocs_atmos / $threads_per_task ))
3365	(( iio = $numprocs_ocean / $threads_per_task ))
3366	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3367	printf "\n using $coupled_mode coupling"
3368	printf "\n\n"
3369	echo "coupled_run $iia $iio" > runfile_atmos
3370	fi
3371
3372	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3373
3374	else
3375	if [[ "$host_file" = "" ]]
3376	then
3377	printf "\n +++ no hostfile given in configuration file"
3378	locat=config_file
3379	exit
3380	else
3381	eval host_file=$host_file
3382	fi
3383	export MP_HOSTFILE=$host_file
3384	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3385	fi
3386	fi
3387	elif [[ $host = nech ]]
3388	then
3389	(( ii = nodes ))
3390	if [[ $ii = 1 ]]
3391	then
3392	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3393	export MPIPROGINF=YES
3394	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3395	echo "*** execution on single node with mpirun"
3396	mpirun -np $numprocs ./a.out $ROPTS
3397	else
3398	(( i = 0 ))
3399	while (( i < ii ))
3400	do
3401	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3402	(( i = i + 1 ))
3403	done
3404
3405	echo "#!/bin/sh" > mpi_exec_shell
3406	echo " " >> mpi_exec_shell
3407	echo "set -u" >> mpi_exec_shell
3408	echo "F_ERRCNT=0" >> mpi_exec_shell
3409	echo "MPIPROGINV=YES" >> mpi_exec_shell
3410	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3411	echo "cpurest=$cpurest" >> mpi_exec_shell
3412	echo "fname=$fname" >> mpi_exec_shell
3413	echo "localhost=$localhost" >> mpi_exec_shell
3414	echo "return_address=$return_address" >> mpi_exec_shell
3415	echo "return_username=$return_username" >> mpi_exec_shell
3416	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3417	echo "write_binary=$write_binary" >> mpi_exec_shell
3418	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3419	echo " " >> mpi_exec_shell
3420	echo "export F_ERRCNT" >> mpi_exec_shell
3421	echo "export MPIPROGINV" >> mpi_exec_shell
3422	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3423	echo "export cpurest" >> mpi_exec_shell
3424	echo "export fname" >> mpi_exec_shell
3425	echo "export localhost" >> mpi_exec_shell
3426	echo "export return_address" >> mpi_exec_shell
3427	echo "export return_username" >> mpi_exec_shell
3428	echo "export tasks_per_node" >> mpi_exec_shell
3429	echo "export write_binary" >> mpi_exec_shell
3430	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3431	echo " " >> mpi_exec_shell
3432	echo "exec ./a.out" >> mpi_exec_shell
3433
3434	chmod u+x mpi_exec_shell
3435	export MPIPROGINF=YES
3436	mpirun -f multinode_config &
3437	wait
3438
3439	fi
3440	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3441	then
3442
3443	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3444	# DOES NOT EXIST
3445	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3446	then
3447	if [[ -f $hostfile ]]
3448	then
3449	cp $hostfile hostfile
3450	(( ii = $numprocs / $threads_per_task ))
3451	else
3452	(( ii = 1 ))
3453	while (( ii <= $numprocs / $threads_per_task ))
3454	do
3455	echo $localhost_realname >> hostfile
3456	(( ii = ii + 1 ))
3457	done
3458	fi
3459	eval zeile=\"`head -n $ii hostfile`\"
3460	printf "\n *** running on: $zeile"
3461	fi
3462
3463	(( ii = $numprocs / $threads_per_task ))
3464	export OMP_NUM_THREADS=$threads_per_task
3465
3466	if [[ $threads_per_task != 1 ]]
3467	then
3468	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3469	# MAY ABORT
3470	ulimit -s unlimited
3471	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3472	fi
3473	if [[ $run_coupled_model = false ]]
3474	then
3475	if [[ "$ocean_file_appendix" = true ]]
3476	then
3477	echo "precursor_ocean" > runfile_atmos
3478	else
3479	echo "precursor_atmos" > runfile_atmos
3480	fi
3481	printf "\n\n"
3482
3483	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3484	then
3485	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3486	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3487	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3488	elif [[ $host = lccrayf ]]
3489	then
3490	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3491	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3492	then
3493	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3494	elif [[ $host = lcflow ]]
3495	then
3496	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3497	elif [[ $host = lcsb ]]
3498	then
3499	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3500	elif [[ $host = lckiaps ]]
3501	then
3502	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3503	elif [[ $host = lckyu* ]]
3504	then
3505	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3506	else
3507	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3508	fi
3509	else
3510
3511	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3512	(( iia = $numprocs_atmos / $threads_per_task ))
3513	(( iio = $numprocs_ocean / $threads_per_task ))
3514	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3515	printf "\n using $coupled_mode coupling"
3516	printf "\n\n"
3517
3518	if [[ $coupled_mode = "mpi2" ]]
3519	then
3520	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3521	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3522
3523	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3524	then
3525
3526	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3527	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3528
3529	else
3530	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3531	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3532	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3533	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3534	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3535	fi
3536	wait
3537
3538	else
3539
3540	echo "coupled_run $iia $iio" > runfile_atmos
3541
3542	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3543	then
3544
3545	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3546
3547	elif [[ $host = lck \|\| $host = lckordi ]]
3548	then
3549
3550	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3551
3552	elif [[ $host = lckyu* ]]
3553	then
3554
3555	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3556
3557	fi
3558	wait
3559	fi
3560
3561	fi
3562
3563	elif [[ $host = lckyoto ]]
3564	then
3565	set -xv
3566	export P4_RSHCOMMAND=plesh
3567	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3568	if [[ "$ENVIRONMENT" = BATCH ]]
3569	then
3570	if [[ "$cond2" = fujitsu ]]
3571	then
3572	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3573	elif [[ "cond2" = pgi ]]
3574	then
3575	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3576	else
3577	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3578	fi
3579	else
3580	if [[ "$cond2" = "" ]]
3581	then
3582	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3583	else
3584	mpirun -np $numprocs ./a.out $ROPTS
3585	fi
3586	fi
3587	set +xv
3588
3589	elif [[ $host = lctit ]]
3590	then
3591	export OMP_NUM_THREADS=$threads_per_task
3592	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3593	if [[ "$threads_per_task" != 1 ]]
3594	then
3595	export MV2_ENABLE_AFFINITY=0
3596	fi
3597	echo "----- PBS_NODEFILE content:"
3598	cat $PBS_NODEFILE
3599	echo "-----"
3600	(( ii = $numprocs / $threads_per_task ))
3601	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3602	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3603	else
3604	mpprun -n $numprocs a.out $ROPTS
3605	fi
3606	else
3607	a.out $ROPTS
3608	fi
3609	fi
3610
3611	if [[ $? != 0 ]]
3612	then
3613
3614	# ABORT IN CASE OF RUNTIME ERRORS
3615	printf "\n +++ runtime error occured"
3616	locat=execution
3617	exit
3618
3619	else
3620
3621	printf "\n$dashes\n *** execution finished \n"
3622
3623	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3624	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3625	if [[ "$dvrserver_id" != "" ]]
3626	then
3627	kill $dvrserver_id
3628	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3629
3630	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3631	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3632	if [[ -d DATA_DVR ]]
3633	then
3634
3635	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3636	# DIRECTORY
3637	cp .dvrserver.config DATA_DVR
3638
3639	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3640	# SEQUENCE MODE DATA TOO)
3641	process_dvr_output -d DATA_DVR -f $fname -s
3642
3643	else
3644
3645	# PROCESS THE LOCAL OUTPUT
3646	process_dvr_output -l -d DATA_DVR -f $fname
3647
3648	fi
3649
3650	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3651	then
3652
3653	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3654	process_dvr_output -l -d DATA_DVR -f $fname
3655
3656	fi
3657	fi
3658
3659
3660
3661	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3662	# BY EACH CORE INTO ONE FILE
3663	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3664	then
3665	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3666	printf "\n 2d- and/or 3d-data may be incomplete!"
3667	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3668	elif [[ "$combine_plot_fields" == true ]]
3669	then
3670	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3671	then
3672	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3673	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3674	else
3675	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3676	combine_plot_fields${block}.x
3677	fi
3678	else
3679
3680	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3681	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3682	# ??? koennen wir das streichen ???
3683	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3684	fi
3685
3686
3687
3688	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3689	(( i = 0 ))
3690	while (( i < ioc ))
3691	do
3692	(( i = i + 1 ))
3693	if (( i == 1 ))
3694	then
3695	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3696	fi
3697	printf "\n >>> ${out_command[$i]}"
3698	eval ${out_command[$i]}
3699	if (( i == ioc ))
3700	then
3701	printf "\n$dashes\n"
3702	fi
3703	done
3704
3705
3706	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3707	if [[ $do_trace = true ]]
3708	then
3709	printf "\n\n"
3710	ls -al
3711	fi
3712
3713
3714
3715	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3716	(( i = 0 ))
3717	while (( i < iout ))
3718	do
3719	(( i = i + 1 ))
3720	if (( i == 1 ))
3721	then
3722	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3723	fi
3724
3725	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3726	files_for_pes=false; filetyp=file
3727	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3728	then
3729	files_for_pes=true; filetyp=directory
3730	actionout[$i]=""
3731	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3732	then
3733	actionout[$i]=""
3734	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3735	then
3736	files_for_pes=true; filetyp=directory
3737	actionout[$i]="ar"
3738	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3739	then
3740	actionout[$i]="ar"
3741	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3742	then
3743	files_for_pes=true; filetyp=directory
3744	actionout[$i]="fl"
3745	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3746	then
3747	actionout[$i]="fl"
3748	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3749	then
3750	files_for_pes=true; filetyp=directory
3751	actionout[$i]="tr"
3752	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3753	then
3754	actionout[$i]="tr"
3755	fi
3756
3757	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3758	then
3759	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3760	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3761	then
3762	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3763	else
3764
3765
3766	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3767	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3768	if [[ "${actionout[$i]}" = tr ]]
3769	then
3770	if [[ $localhost != $fromhost ]]
3771	then
3772	if [[ $files_for_pes = false ]]
3773	then
3774	cps=""
3775	cst=""
3776	else
3777	cps=-c
3778	cst="/"
3779	fi
3780	if [[ $localhost = nech ]]
3781	then
3782
3783	# TRANSFER IN SEPERATE JOB
3784	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3785	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3786	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3787	if [[ $files_for_pes = false ]]
3788	then
3789	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3790	else
3791	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3792	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3793	fi
3794
3795	echo "set -x" > transfer_${localout[$i]}
3796	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3797
3798	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3799	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3800	printf "\n or higher cycle\n"
3801	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3802
3803	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3804
3805	if [[ $localhost = nech ]]
3806	then
3807	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3808	else
3809	if [[ "$LOGNAME" = b323013 ]]
3810	then
3811	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3812	else
3813	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3814	fi
3815	fi
3816
3817	else
3818
3819	# TRANSFER WITHIN THIS JOB
3820	transfer_failed=false
3821	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3822	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3823	if [[ $localhost = lccrayb ]]
3824	then
3825	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3826	elif [[ $localhost = lccrayh ]]
3827	then
3828	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3829	elif [[ $localhost = lcxe6 ]]
3830	then
3831	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3832	else
3833	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3834	fi
3835	[[ $? != 0 ]] && transfer_failed=true
3836
3837	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3838	if [[ $transfer_failed = true ]]
3839	then
3840	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3841	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3842
3843	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3844	eval local_catalog=${pathout[$i]}
3845	if [[ ! -d $local_catalog ]]
3846	then
3847	printf " *** local directory does not exist. Trying to create:\n"
3848	printf " $local_catalog \n"
3849	mkdir -p $local_catalog
3850	fi
3851	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3852	transfer_problems=true
3853	fi
3854	fi
3855	else
3856
3857	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3858	actionout[$i]=""
3859	fi
3860	fi
3861
3862
3863	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3864	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3865	if [[ "${actionout[$i]}" = tra ]]
3866	then
3867	if [[ $localhost != $fromhost ]]
3868	then
3869	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3870	then
3871
3872	# TRANSFER IN SEPERATE JOB
3873	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3874	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3875	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3876	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3877
3878	echo "set -x" > transfer_${localout[$i]}
3879	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3880
3881	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3882	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3883	printf "\n or higher cycle\n"
3884	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3885
3886	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3887
3888	if [[ $localhost = nech ]]
3889	then
3890	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3891	else
3892	if [[ $LOGNAME = b323013 ]]
3893	then
3894	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3895	else
3896	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3897	fi
3898	fi
3899
3900	else
3901
3902	# TRANSFER WITHIN THIS JOB
3903	transfer_failed=false
3904	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3905	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3906	if [[ $localhost = lccrayb ]]
3907	then
3908	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3909	elif [[ $localhost = lccrayh ]]
3910	then
3911	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3912	elif [[ $localhost = lcxe6 ]]
3913	then
3914	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3915	else
3916	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3917	fi
3918	[[ $? != 0 ]] && transfer_failed=true
3919
3920	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3921	if [[ $transfer_failed = true ]]
3922	then
3923	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3924	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3925
3926	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3927	eval local_catalog=${pathout[$i]}
3928	if [[ ! -d $local_catalog ]]
3929	then
3930	printf " *** local directory does not exist. Trying to create:\n"
3931	printf " $local_catalog \n"
3932	mkdir -p $local_catalog
3933	fi
3934
3935	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3936	transfer_problems=true
3937	fi
3938	fi
3939	else
3940
3941	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3942	actionout[$i]=a
3943	fi
3944	fi
3945
3946
3947	# OUTPUT-FILE FOR A RESTART-RUN.
3948	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3949	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3950	# AS LAST ACTION, ARCHIVING IS INITIATED.
3951	if [[ "${actionout[$i]}" = fl ]]
3952	then
3953	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3954	chmod g+rx $tmp_data_catalog
3955	if [[ $files_for_pes = false ]]
3956	then
3957	printf "\n >>> OUTPUT: ${localout[$i]} to"
3958	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3959	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3960	else
3961	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3962	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3963	mkdir $tmp_data_catalog/${frelout[$i]}
3964	cd ${localout[$i]}
3965	for file in $(ls *)
3966	do
3967	ln -f $file $tmp_data_catalog/${frelout[$i]}
3968	done
3969	cd $TEMPDIR
3970	fi
3971
3972
3973	# CREATE AND SUBMIT ARCHIVING-JOB
3974	if [[ $store_on_archive_system = true ]]
3975	then
3976
3977	if [[ $archive_system = asterix ]]
3978	then
3979	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3980	if [[ $files_for_pes = false ]]
3981	then
3982	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3983	else
3984	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3985	fi
3986	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3987	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3988	echo "then" >> archive_${frelout[$i]}
3989	echo " do_stageout=false" >> archive_${frelout[$i]}
3990	echo "else" >> archive_${frelout[$i]}
3991	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3992	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3993	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3994	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3995	if [[ $files_for_pes = false ]]
3996	then
3997	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3998	else
3999	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4000	fi
4001	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4002	echo "fi" >> archive_${frelout[$i]}
4003	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4004	elif [[ $archive_system = DMF ]]
4005	then
4006	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4007	if [[ $files_for_pes = false ]]
4008	then
4009	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4010	locat=DMF
4011	exit
4012	else
4013	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4014	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4015	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4016	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4017	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4018	fi
4019	elif [[ $archive_system = tivoli ]]
4020	then
4021	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4022	if [[ $files_for_pes = false ]]
4023	then
4024	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4025	echo "set -x" >> archive_${frelout[$i]}
4026	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4027	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4028	else
4029
4030	echo "set -x" >> archive_${frelout[$i]}
4031	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4032	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4033	cd $tmp_data_catalog
4034	all_files=`ls -1 ${frelout[$i]}/*`
4035	cd - > /dev/null
4036	(( inode = 0 ))
4037	(( tp1 = tasks_per_node + 1 ))
4038	while (( inode < nodes ))
4039	do
4040	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4041	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4042	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4043	(( inode = inode + 1 ))
4044	done
4045	fi
4046	elif [[ $archive_system = ut ]]
4047	then
4048	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4049	if [[ $files_for_pes = false ]]
4050	then
4051	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4052	echo "set -x" >> archive_${frelout[$i]}
4053	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4054	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4055	else
4056
4057	echo "set -x" >> archive_${frelout[$i]}
4058	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4059	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4060	cd $tmp_data_catalog
4061	all_files=`ls -1 ${frelout[$i]}/*`
4062	cd - > /dev/null
4063	(( inode = 0 ))
4064	(( tp1 = tasks_per_node + 1 ))
4065	while (( inode < nodes ))
4066	do
4067	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4068	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4069	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4070	(( inode = inode + 1 ))
4071	done
4072	fi
4073	elif [[ $archive_system = none ]]
4074	then
4075	printf " +++ archiving on $localhost not available!\n"
4076	fi
4077
4078	if [[ $archive_system != none ]]
4079	then
4080	if [[ $localhost = nech ]]
4081	then
4082	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4083	fi
4084	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4085	fi
4086	else
4087	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4088	fi
4089
4090
4091	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4092	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4093	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4094	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4095	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4096	if [[ $files_for_pes = false ]]
4097	then
4098	cat /dev/null > ${pathout[$i]}
4099	else
4100	mkdir -p ${pathout[$i]}
4101	fi
4102
4103	fi
4104
4105
4106	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4107	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4108	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4109	if [[ "${actionout[$i]}" = ar ]]
4110	then
4111	if [[ $files_for_pes = false ]]
4112	then
4113	printf "\n >>> OUTPUT: ${localout[$i]} to"
4114	printf "\n ${pathout[$i]}"
4115	printf "\n File will be copied to archive-system ($archive_system) !\n"
4116	else
4117	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4118	printf "\n ${pathout[$i]}"
4119	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4120	fi
4121	mv ${localout[$i]} ${frelout[$i]}
4122
4123	file_saved=false
4124
4125	if [[ $archive_system = asterix ]]
4126	then
4127	do_stageout=true
4128	(( stageout_anz = 0 ))
4129	while [[ $do_stageout = true ]]
4130	do
4131	if [[ $files_for_pes = false ]]
4132	then
4133	stageout ${frelout[$i]} > STAGE_OUTPUT
4134	else
4135	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4136	fi
4137	cat STAGE_OUTPUT
4138	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4139	then
4140	file_saved=true
4141	do_stageout=false
4142	else
4143	if [[ $files_for_pes = false ]]
4144	then
4145	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4146	else
4147	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4148	fi
4149	(( stageout_anz = stageout_anz + 1 ))
4150	if (( stageout_anz == 10 ))
4151	then
4152	printf "\n +++ stoped after 10 unsuccessful tries!"
4153	archive_save=false
4154	do_stageout=false
4155	else
4156	printf "\n *** new try to store on archive after 15 min:"
4157	sleep 900
4158	fi
4159	fi
4160	done
4161	elif [[ $archive_system = DMF ]]
4162	then
4163	if [[ $files_for_pes = false ]]
4164	then
4165	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4166	locat=DMF
4167	exit
4168	else
4169	rm -rf $ARCHIVE/${frelout[$i]}
4170	cp -r ${frelout[$i]} $ARCHIVE
4171	fi
4172	file_saved=true
4173	elif [[ $archive_system = tivoli ]]
4174	then
4175	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4176	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4177	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4178	# WHEN THE ARCHIVE-JOB IS EXECUTED
4179	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4180	chmod g+rx $tmp_data_catalog
4181	if [[ $files_for_pes = false ]]
4182	then
4183	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4184	else
4185	mkdir $tmp_data_catalog/${frelout[$i]}
4186	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4187	fi
4188
4189	# GENERATE AND SUBMIT BATCH-JOB
4190	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4191	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4192	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4193	if [[ $files_for_pes = false ]]
4194	then
4195	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4196	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4197	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4198	else
4199	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4200	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4201	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4202	fi
4203
4204	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4205	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4206	file_saved=true
4207
4208	elif [[ $archive_system = ut ]]
4209	then
4210	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4211	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4212	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4213	# WHEN THE ARCHIVE-JOB IS EXECUTED
4214	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4215	chmod g+rx $tmp_data_catalog
4216	if [[ $files_for_pes = false ]]
4217	then
4218	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4219	else
4220	mkdir $tmp_data_catalog/${frelout[$i]}
4221	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4222	fi
4223
4224	# GENERATE AND SUBMIT BATCH-JOB
4225	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4226	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4227	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4228	if [[ $files_for_pes = false ]]
4229	then
4230	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4231	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4232	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4233	else
4234	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4235	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4236	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4237	fi
4238
4239	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4240	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4241	file_saved=true
4242
4243	else
4244	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4245	archive_save=false
4246	fi
4247
4248	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4249	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4250	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4251	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4252	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4253	if [[ $file_saved = true ]]
4254	then
4255	if [[ $files_for_pes = false ]]
4256	then
4257	cat /dev/null > ${pathout[$i]}
4258	else
4259	mkdir -p ${pathout[$i]}
4260	fi
4261	fi
4262
4263	fi
4264
4265	# APPEND ON THIS MACHINE
4266	if [[ "${actionout[$i]}" = "a" ]]
4267	then
4268	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4269	then
4270	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4271	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4272	else
4273	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4274	cat ${localout[$i]} >> ${pathout[$i]}
4275	fi
4276	fi
4277
4278	# COPY ON THIS MACHINE
4279	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4280	# ON DIFFERENT FILE-SYSTEMS
4281	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4282	then
4283
4284	# COPY IN CASE OF RUNS ON SINGLE CORES
4285	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4286	then
4287	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4288	if [[ $link_local_output = true ]]
4289	then
4290	printf " using ln -f\n"
4291	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4292	fi
4293	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4294	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4295	then
4296	if [[ $link_local_output = true ]]
4297	then
4298	printf " ln failed, using cp...\n"
4299	fi
4300	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4301	fi
4302	else
4303	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4304	if [[ $link_local_output = true ]]
4305	then
4306	printf " using ln -f\n"
4307	ln -f ${localout[$i]} ${pathout[$i]}
4308	fi
4309	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4310	if [[ ! -f "${pathout[$i]}" ]]
4311	then
4312	if [[ $link_local_output = true ]]
4313	then
4314	printf " ln failed, using cp...\n"
4315	fi
4316	cp ${localout[$i]} ${pathout[$i]}
4317	fi
4318	fi
4319
4320	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4321	then
4322
4323	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4324	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4325	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4326	if [[ $link_local_output = true ]]
4327	then
4328	printf " using ln -f\n"
4329	mkdir ${pathout[$i]}
4330	cd ${localout[$i]}
4331	for file in $(ls *)
4332	do
4333	ln -f $file ${pathout[$i]}
4334	done
4335	cd $TEMPDIR
4336	fi
4337
4338	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4339	if [[ ! -f "${pathout[$i]}/_0000" ]]
4340	then
4341	if [[ $link_local_output = true ]]
4342	then
4343	printf " ln failed for .../_0000, using cp...\n"
4344	fi
4345	cp -r ${localout[$i]} ${pathout[$i]}
4346	fi
4347
4348	fi
4349	fi
4350	done
4351	if (( i != 0 ))
4352	then
4353	if [[ $transfer_problems = true ]]
4354	then
4355	printf "\n$dashes\n *** OUTPUT-files saved"
4356	printf "\n +++ WARNING: some data transfers failed! \n"
4357	else
4358	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4359	fi
4360	fi
4361
4362
4363	# IF REQUIRED, START A RESTART-JOB
4364	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4365	if [[ -f CONTINUE_RUN ]]
4366	then
4367
4368	if [[ $archive_save = true ]]
4369	then
4370
4371	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4372	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4373	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4374	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4375	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4376	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4377	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4378	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4379	then
4380	mc=`echo $mc \| sed 's/#/f/g'`
4381	fi
4382
4383
4384	# START THE RESTART-JOB
4385	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4386	echo " $mc"
4387	printf "\n$dashes\n"
4388	if [[ $localhost != $fromhost ]]
4389	then
4390
4391	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4392	then
4393	echo "*** ssh will be used to initiate restart-runs!"
4394	echo " return_address=\"$return_address\" "
4395	echo " return_username=\"$return_username\" "
4396	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4397	then
4398	if [[ $localhost = ibmh ]]
4399	then
4400	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4401	elif [[ $localhost = lccrayb ]]
4402	then
4403	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4404	elif [[ $localhost = lccrayh ]]
4405	then
4406	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4407	elif [[ $localhost = lcxe6 ]]
4408	then
4409	ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4410	else
4411	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4412	fi
4413	else
4414	if [[ $localhost = ibmkisti ]]
4415	then
4416	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4417	elif [[ $localhost = lcflow ]]
4418	then
4419	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4420	elif [[ $localhost = lccrayb ]]
4421	then
4422	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4423	elif [[ $localhost = lccrayh ]]
4424	then
4425	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4426	else
4427	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4428	fi
4429	fi
4430	else
4431	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4432	locat=restart; exit
4433	fi
4434
4435	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4436	if [[ $queue = special1q ]]
4437	then
4438	sleep 120
4439	else
4440	sleep 30
4441	fi
4442
4443	else
4444
4445	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4446	# USING SSH)
4447	cd $LOCAL_PWD
4448	if [[ $localhost = lckyuh ]]
4449	then
4450	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4451	printf "\n please restart job manually using command:\n"
4452	printf "\n \"$mc\" "
4453	else
4454	eval $mc # THE ' MUST BE EVALUATED
4455	fi
4456	cd - > /dev/null
4457	fi
4458	if [[ $localhost = lckyuh ]]
4459	then
4460	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4461	else
4462	printf "\n$dashes\n *** restart-run initiated \n"
4463	fi
4464
4465
4466	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4467	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4468	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4469	# MAY BE VERY HUGE)
4470	(( i = 0 ))
4471	while (( i < iin ))
4472	do
4473	(( i = i + 1 ))
4474	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4475	then
4476	rm -r $tmp_data_catalog/${frelin[$i]}
4477	fi
4478	done
4479
4480	else
4481
4482	printf "\n +++ no restart-run possible, since errors occured"
4483	printf "\n during the archive process"
4484	fi
4485
4486	fi
4487
4488
4489
4490	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4491	if [[ "$email_notification" != "none" ]]
4492	then
4493
4494	if [[ $localhost != $fromhost ]]
4495	then
4496	if [[ -f CONTINUE_RUN ]]
4497	then
4498	echo "PALM restart run necessary" > email_text
4499	echo "description header of actual run:" >> email_text
4500	cat CONTINUE_RUN >> email_text
4501	echo "mrun-command to restart:" >> email_text
4502	echo "$mc" >> email_text
4503	else
4504	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4505	fi
4506	mail $email_notification < email_text
4507	printf "\n *** email notification sent to \"$email_notification\" "
4508	fi
4509	fi
4510
4511
4512
4513	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4514	cd $HOME
4515	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4516
4517	else
4518
4519
4520	# PREPARING ACTIONS,
4521	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4522
4523	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4524	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
4525	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4526	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4527	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4528	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4529	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4530	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4531	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4532	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4533	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4534	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4535	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4536	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4537	if [[ $use_openmp = true ]]
4538	then
4539	mrun_com=${mrun_com}" -O $threads_per_task"
4540	fi
4541	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4542	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4543	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4544	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4545	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4546	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4547	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4548	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4549	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4550	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4551	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4552	if [[ $do_remote = true ]]
4553	then
4554	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4555	fi
4556
4557
4558	# CREATE EXECUTABLE FOR BATCH JOB
4559	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4560	then
4561
4562	printf "\n *** creating the executable for batch job\n"
4563
4564	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4565	if [[ $host != $localhost ]]
4566	then
4567	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4568	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4569	locat=create_executable; exit
4570	fi
4571
4572	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4573	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4574
4575	cp $make_depository .
4576	tar -xf $make_depository > /dev/null 2>&1
4577	cp ../* . > /dev/null 2>&1
4578
4579	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4580
4581	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4582	then
4583	printf "\n +++ error occured while compiling or linking"
4584	locat=compile
4585	exit
4586	fi
4587
4588	mv a.out ..
4589	cd - > /dev/null 2>&1
4590	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4591
4592	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4593
4594	fi
4595
4596
4597	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4598	jobfile=jobfile.$RANDOM
4599
4600
4601	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4602	echo "mkdir $TEMPDIR" >> $jobfile
4603	echo "cd $TEMPDIR" >> $jobfile
4604
4605
4606	# ACTIVATE ERROR-TRACEBACK
4607	if [[ $do_trace = true ]]
4608	then
4609	echo "set -x" >> $jobfile
4610	else
4611	echo "set +vx" >> $jobfile
4612	fi
4613
4614
4615	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4616	if [[ "$init_cmds" != "" ]]
4617	then
4618	echo "$init_cmds" >> $jobfile
4619	fi
4620	if [[ "$module_calls" != "" ]]
4621	then
4622	echo "$module_calls" >> $jobfile
4623	fi
4624
4625
4626	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4627	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4628	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4629	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4630	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4631	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4632	# QUEUEING-SYSTEMS
4633	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4634	then
4635
4636	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4637	if [[ $restart_run != true ]]
4638	then
4639	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4640	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4641	fi
4642
4643	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4644	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4645	echo "set -x" >> $jobfile
4646	if [[ $host = $localhost ]]
4647	then
4648
4649	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4650	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4651	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4652	then
4653	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4654	else
4655	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4656	fi
4657
4658	else
4659	if [[ $host = ibmkisti ]]
4660	then
4661	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4662	echo "localdir=\`pwd\`" >> $jobfile
4663	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4664	elif [[ $host = lccrayb ]]
4665	then
4666	echo "localdir=\`pwd\`" >> $jobfile
4667	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4668	elif [[ $host = lccrayh ]]
4669	then
4670	echo "localdir=\`pwd\`" >> $jobfile
4671	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4672
4673	else
4674	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4675	fi
4676	fi
4677	echo "export SOURCES_COMPLETE=true" >> $jobfile
4678
4679	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4680	# WORKING DIRECTORY OF THE JOB
4681	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4682	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4683	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4684	echo "execute_mrun=true" >> $jobfile
4685	echo " " >> $jobfile
4686
4687	else
4688
4689	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4690	if [[ $do_compile = true ]]
4691	then
4692
4693	source_catalog=SOURCES_FOR_RUN_$fname
4694
4695	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4696	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4697	echo "export SOURCES_COMPLETE=true" >> $jobfile
4698	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4699
4700	for filename in $source_list
4701	do
4702	# BACKSLASH IS USED FOR MASKING
4703	echo "cat > $filename << \"%END%\"" >> $jobfile
4704	cat $source_catalog/$filename >> $jobfile
4705	echo " " >> $jobfile
4706	echo "%END%" >> $jobfile
4707	echo " " >> $jobfile
4708	done
4709
4710	# BACKSLASH IS USED FOR MASKING
4711	echo "cat > Makefile << \"%END%\"" >> $jobfile
4712	cat $source_catalog/Makefile >> $jobfile
4713	echo " " >> $jobfile
4714	echo "%END%" >> $jobfile
4715	echo " " >> $jobfile
4716
4717	echo "cd - > /dev/null" >> $jobfile
4718
4719	fi
4720
4721
4722	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4723	# BACKSLASH IS USED FOR MASKING
4724	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4725	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4726	echo "cat > $config_file << \"%END%\"" >> $jobfile
4727	if [[ $host = lckyuh ]]
4728	then
4729	# NO CROSS-COMPILER ON COMPUTE NODE
4730	sed 's/frtpx/frt/g' $config_file >> $jobfile
4731	else
4732	sed 's/#$.*//g' $config_file >> $jobfile
4733	fi
4734	echo "%END%" >> $jobfile
4735	echo " " >> $jobfile
4736
4737
4738	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4739	# BACKSLASH IS USED FOR MASKING
4740	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4741	if [[ $host = lckyuh ]]
4742	then
4743	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4744	else
4745	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4746	fi
4747	echo "%END%" >> $jobfile
4748	echo "chmod u+x $mrun_script_name" >> $jobfile
4749	echo "execute_mrun=true" >> $jobfile
4750	echo " " >> $jobfile
4751
4752	fi
4753
4754
4755	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4756	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4757	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4758	if [[ $do_remote = true ]]
4759	then
4760	(( i = 0 ))
4761	while (( i < iin ))
4762	do
4763	(( i = i + 1 ))
4764	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4765	if [[ "${transin[$i]}" = job ]]
4766	then
4767	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4768	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4769	echo " " >> $jobfile
4770	echo "%END%" >> $jobfile
4771	else
4772	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4773	fi
4774
4775	# CHECK, IF FILE COULD BE CREATED
4776	echo "if [[ \$? = 1 ]]" >> $jobfile
4777	echo "then" >> $jobfile
4778	echo " echo \" \" " >> $jobfile
4779	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4780	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4781	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4782	echo " execute_mrun=false" >> $jobfile
4783	echo "fi" >> $jobfile
4784	done
4785	fi
4786
4787	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4788	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4789	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4790	echo "LOCAL_PWD=$working_directory" >> $jobfile
4791	echo "export LOCAL_PWD" >> $jobfile
4792
4793	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4794	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4795	echo "export LOCAL_MRUN_PATH" >> $jobfile
4796
4797	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4798	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4799	then
4800	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4801	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4802	fi
4803
4804	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4805	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4806	echo "set -x" >> $jobfile
4807	echo "queue=$queue" >> $jobfile
4808	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4809	echo 'ls -al; echo `pwd`' >> $jobfile
4810	echo "cd \$HOME" >> $jobfile
4811	echo "rm -rf $TEMPDIR" >> $jobfile
4812
4813
4814
4815
4816	# START THE JOB USING SUBJOB-COMMAND
4817	if [[ $silent = false ]]
4818	then
4819	printf "\n "
4820	else
4821	printf "\n\n"
4822	fi
4823
4824	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
4825	rm -rf $jobfile
4826
4827
4828	fi # END OF REMOTE-PART

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