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source: palm/trunk/SCRIPTS/mrun @ 1421

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

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