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source: palm/trunk/SCRIPTS/mrun @ 1403

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

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