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source: palm/trunk/SCRIPTS/mrun @ 1401

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

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