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source: palm/trunk/SCRIPTS/mrun @ 1423

Last change on this file since 1423 was 1423, checked in by kanani, 10 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1423 2014-07-02 10:07:30Z kanani $
29	#
30	# 1422 2014-07-02 10:01:25Z kanani
31	# automatic restarts enabled for lccrayb,
32	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
33	#
34	# 1420 2014-06-10 06:24:14Z raasch
35	# -j1 option added to aprung command for lccrayf (CSC)
36	#
37	# 1402 2014-05-09 14:25:13Z raasch
38	# batch_job added to envpar-NAMELIST
39	#
40	# 1357 2014-04-11 15:02:03Z witha
41	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
42	# possible)
43	#
44	# 1320 2014-03-20 08:40:49Z raasch
45	# check namelist file set false by default
46	#
47	# 1304 2014-03-12 10:29:42Z raasch
48	# ulimit option changed from -Ss to -s
49	#
50	# bugfix: missing "fi" in r1289
51	#
52	# 1289 2014-03-04 07:12:34Z raasch
53	# comments translated to English
54	# necriam-, fimm-, ibmy-, and sgi-specific code removed
55	# export of variables for palm and interpret_config removed
56	#
57	# 1281 2014-02-01 07:55:49Z raasch
58	# rsync-copy restricted to Cray machines, since command is unavailable on some
59	# other systems
60	#
61	# 1279 2014-01-28 12:10:14Z raasch
62	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
63	# in order to remove annoying restrictions concerning the number of processors which
64	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
65	# restriction, one of the nodes will be filled with less than the given number of
66	# tasks per node. A respective warning is given.
67	#
68	# 1274 2014-01-09 13:14:54Z heinze
69	# adjustments for lccrayh
70	#
71	# 1272 2014-01-08 10:19:32Z witha
72	# small adjustment for lcflow
73	#
74	# 1270 2013-12-16 11:05:01Z fricke
75	# call of combine_plot_fields adjusted for lccrayb/lccrayh
76	#
77	# 1255 2013-11-07 14:43:35Z raasch
78	# further adjustments for lccrayb remote access
79	#
80	# 1241 2013-10-30 11:36:58Z heinze
81	# Enable use of nudging input and input of large scale forcing from
82	# external files
83	#
84	# 1229 2013-09-20 06:55:19Z raasch
85	# further adjustments for lccrayb
86	#
87	# 1224 2013-09-16 07:27:23Z raasch
88	# first adjustments for lccrayb
89	#
90	# 1210 2013-08-14 10:58:20Z raasch
91	# fftw support added
92	#
93	# 1201 2013-07-10 16:17:59Z witha
94	# adjustments for Forwind cluster (lcflow)
95	#
96	# 1199 2013-07-05 14:52:22Z raasch
97	# adjustments for CSC Helsinki (lccrayf),
98	# executables for batch jobs can be created in advance, in order to avoid calling
99	# the compiler within the batch job (only works if batch jobs are submitted on
100	# local host)
101	#
102	# 1190 2013-06-25 09:39:21Z heinze
103	# enable use of automatic restarts for ibmh
104	# use of cluster/express queue enabled (ibmh)
105	#
106	# 1124 2013-04-09 15:46:52Z raasch
107	# variable "memory" is exported via typeset option -x, because otherwise an unknown
108	# side effect may lead to data loss while getopts is reading the script-option arguments
109	#
110	# 1122 2013-04-09 08:37:16Z heinze
111	# Bugfix: change type of variable last_char
112	#
113	# 1119 2013-04-05 15:11:19Z raasch
114	# Bugfix for setting -T option for subjob
115	#
116	# 1108 2013-03-05 07:03:32Z raasch
117	# bugfix for coupled runs on lckyut/lckyuh
118	#
119	# 1106 2013-03-04 05:31:38Z raasch
120	# --stdin argument for mpiexec on lckyuh
121	# -y and -Y settings output to header
122	#
123	# 1103 2013-02-20 02:15:53Z raasch
124	# default script runs again under ksh, because of unsolved problems with read
125	# from stdin: when bash script is called from a ksh, message "read error: 0:
126	# Resource temporarily unavailable" appears and script does not stop,
127	# further bash compatibility adjustments,
128	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
129	# on lckyuh, but mrun does not terminate and issues a warning instead
130	#
131	# 1101 2013-02-17 10:20:21Z raasch
132	# script now running under bash instead of ksh, which required small adjustments
133	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
134	# read from stdin),
135	# cross compilername on lckyuh compute nodes replaced by real compiler name
136	#
137	# 1099 2013-02-10 01:47:43Z raasch
138	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
139	# and for Forwind cluster (lcflow)
140	# small further adjustments for lckyut
141	#
142	# 1094 2013-02-03 01:52:12Z raasch
143	# explicit ssh/scp port can be set in config file with environment variable
144	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
145	# decalpha parts (yonsei) removed
146	#
147	# 2013-02-02 07:06:13Z raasch
148	# adjustments for Kyushu-University computing center (lckyut - tatara)
149	#
150	# 1083 2013-01-04 10:22:09Z maronga
151	# bugfix in parameter file check (read %cpp_options was missing)
152	#
153	# 1069 2012-11-28 16:18:43Z maronga
154	# bugfix: coupling mode was always set to mpi2, typos removed
155	#
156	# 1058 2012-11-21 07:00:35Z raasch
157	# Intel inspector (inspxe) is given the number of PEs instead of the number of
158	# nodes
159	#
160	# 1046 2012-11-09 14:38:45Z maronga
161	# code put under GPL (PALM 3.9)
162	#
163	# 21/03/94 - Siggi - first version finished
164	# 03/03/94 - Siggi - script development started
165	#
166	#--------------------------------------------------------------------------------#
167	# mrun - script for running PALM jobs
168	#--------------------------------------------------------------------------------#
169
170
171
172	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
173
174	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
175	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
176	# (TOO MANY ARGUMENTS - PROBLEM)
177	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
178
179	AddFilenames=""
180	additional_conditions=""
181	add_source_path=""
182	afname=""
183	archive_save=true
184	archive_system=none
185	check_namelist_files=false
186	combine_plot_fields=true
187	compiler_name=""
188	cond1=""
189	cond2=""
190	config_file=.mrun.config
191	coupled_dist=""
192	coupled_mode="mpi1"
193	cpp_opts=""
194	cpp_options=""
195	cpumax=0
196	cpurest=0
197	create_executable_for_batch=false
198	delete_temporary_catalog=true
199	do_batch=false
200	do_compile=true
201	do_remote=false
202	do_stagein=true
203	do_stageout=true
204	do_trace=false
205	email_notification="none"
206	exclude=""
207	executable=""
208	execution_error=false
209	fftw_inc=""
210	fftw_lib=""
211	fftw_support=false
212	fname=test
213	fromhost=""
214	global_revision=""
215	group_number=none
216	host=""
217	host_file=""
218	hp=""
219	ignore_archive_error=false
220	input_list=""
221	interpreted_config_file=""
222	job_catalog="~/job_queue"
223	job_on_file=""
224	keep_data_from_previous_run=false
225	link_local_input=false
226	link_local_output=false
227	localhost_realname=$(hostname)
228	local_dvrserver_running=.FALSE.
229	locat=normal
230	mainprog=""
231	makefile=""
232	max_par_io_str=""
233	mc=$0
234	while [[ $(echo $mc \| grep -c "/") != 0 ]]
235	do
236	mc=`echo $mc \| cut -f2- -d"/"`
237	done
238	module_calls=""
239	mrun_script_name=$mc
240	netcdf_inc=""
241	netcdf_lib=""
242	netcdf_support=false
243	node_usage=default
244	numprocs=""
245	numprocs_atmos=0
246	numprocs_ocean=0
247	OOPT=""
248	openmp=false
249	output_list=""
250	package_list=""
251	queue=none
252	read_from_config=""
253	restart_run=false
254	if [[ `hostname` = rte10 ]]
255	then
256	return_addres=133.5.185.60
257	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
258	elif [[ `hostname` = climate0 ]]
259	then
260	return_addres=165.132.26.68
261	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
262	elif [[ `hostname` = urban00 ]]
263	then
264	return_addres=147.46.30.151
265	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
266	else
267	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
268	fi
269	return_password=""
270	return_username=$LOGNAME
271	remotecall=false
272	remote_username=""
273	run_coupled_model=false
274	run_mode=""
275	store_on_archive_system=false
276	dashes=" ----------------------------------------------------------------------------"
277	silent=false
278	source_list=""
279	source_path=SOURCE
280	tasks_per_node=""
281	threads_per_task=1
282	tmpcreate=false
283	tmp_data_catalog=""
284	transfer_problems=false
285	usern=$LOGNAME
286	use_openmp=false
287	version="MRUN 2.1 Rev$Rev: 1423 $"
288	working_directory=`pwd`
289	TOPT=""
290	XOPT=""
291	zeit=$( date \| cut -c 12-19 )
292
293	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
294	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
295	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
296	# SCRIPT-OPTION ARGUMENTS
297	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
298
299
300
301	# ERROR HANDLING IN CASE OF EXIT
302	trap 'rm -rf $working_directory/tmp_mrun
303	if [[ $locat != normal && $locat != control_c ]]
304	then
305
306	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
307	(( i = 0 ))
308	while (( i < iec ))
309	do
310	(( i = i + 1 ))
311	printf "\n *** Execution of ERROR-command:\n"
312	printf " >>> ${err_command[$i]}\n"
313	eval ${err_command[$i]}
314	done
315	if [[ -n $interpreted_config_file ]]
316	then
317	rm -rf $interpreted_config_file
318	fi
319	if [[ -n .mrun_environment ]]
320	then
321	rm -rf .mrun_environment
322	fi
323	if [[ $tmpcreate = true ]]
324	then
325	printf "\n *** Contents of \"$TEMPDIR\":\n"
326	ls -al; cd
327	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
328	fi
329	if [[ "$dvrserver_id" != "" ]]
330	then
331	echo "+++ killing dvrserver_id=$dvrserver_id"
332	kill $dvrserver_id
333	fi
334	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
335	then
336	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
337	fi
338	printf "\n\n+++ MRUN killed \n\n"
339	elif [[ $locat != control_c ]]
340	then
341	printf "\n\n --> all actions finished\n\n"
342	printf " Bye, bye $usern !!\n\n"
343	fi' exit
344
345
346	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
347	trap 'rm -rf $working_directory/tmp_mrun
348	rm -rf $working_directory/tmp_check_namelist_files
349	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
350	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
351	then
352	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
353	fi
354	if [[ "$dvrserver_id" != "" ]]
355	then
356	echo "+++ killing dvrserver_id=$dvrserver_id"
357	kill $dvrserver_id
358	fi
359	printf "\n+++ MRUN killed by \"^C\" \n\n"
360	locat=control_c
361	exit
362	' 2
363
364
365	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
366	# BEEN SET
367	if [[ "$PALM_BIN" = "" ]]
368	then
369	printf "\n +++ environment variable PALM_BIN has not been set"
370	printf "\n please set it to the directory where the PALM scripts are located"
371	locat=palm_bin; exit
372	fi
373	export PATH=$PALM_BIN:$PATH
374
375
376
377	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
378	# WHICH WILL BE USED TO START RESTART-JOBS
379	while getopts :a:AbBc:Cd:D:Fg:G:h:H:i:IkK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
380	do
381	case $option in
382	(a) afname=$OPTARG;;
383	(A) store_on_archive_system=true; mc="$mc -A";;
384	(b) do_batch=true; mc="$mc -b";;
385	(B) delete_temporary_catalog=false; mc="$mc -B";;
386	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
387	(C) restart_run=true; mc="$mc -C";;
388	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
389	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
390	(F) job_on_file="-D"; mc="$mc -F";;
391	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
392	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
393	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
394	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
395	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
396	(I) ignore_archive_error=true; mc="$mc -I";;
397	(k) keep_data_from_previous_run=true; mc="$mc -k";;
398	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
399	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
400	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
401	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
402	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
403	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
404	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
405	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
406	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
407	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
408	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
409	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
410	(S) read_from_config=false; mc="$mc -S";;
411	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
412	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
413	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
414	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
415	(v) silent=true; mc="$mc -v";;
416	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
417	(x) do_trace=true;set -x; mc="$mc -x";;
418	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
419	(y) ocean_file_appendix=true; mc="$mc -y";;
420	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
421	(z) check_namelist_files=false; mc="$mc -z";;
422	(Z) combine_plot_fields=false; mc="$mc -Z";;
423	(\?) printf "\n +++ unknown option $OPTARG \n"
424	printf "\n --> type \"$0 ?\" for available options \n"
425	locat=parameter;exit;;
426	esac
427	done
428
429
430	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
431	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
432	(( to_shift = $OPTIND - 1 ))
433	shift $to_shift
434
435	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
436	if [[ "$1" = "?" ]]
437	then
438	(printf "\n *** mrun can be called as follows:\n"
439	printf "\n $mrun_script_name -b -c.. -d.. -D.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -z -Z <modus> \n"
440	printf "\n Description of available options:\n"
441	printf "\n Option Description Default-Value"
442	printf "\n -a base name of input files equiv. -d"
443	printf "\n -A archiving when using file-attribute fl"
444	printf "\n -b batch-job on local machine ---"
445	printf "\n -B do not delete temporary directory at end ---"
446	printf "\n -c configuration file .mrun.config"
447	printf "\n -d base name of files attached to program test"
448	printf "\n -D preprocessor(cpp)-directives \"\" "
449	printf "\n -F create remote job file only ---"
450	printf "\n -h execution host $localhost_realname"
451	printf "\n -i INPUT control list \"\" "
452	printf "\n -I archiving errors of previous batch-jobs"
453	printf "\n will be ignored"
454	printf "\n -k keep data from previous run"
455	printf "\n -K additional conditions for controling"
456	printf "\n usage of conditional code and"
457	printf "\n env-variables in configuration file \"\" "
458	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
459	printf "\n -M Makefile name Makefile"
460	printf "\n -n node usage (shared/not_shared) depending on -h"
461	printf "\n -o OUTPUT control list \"\" "
462	printf "\n -O threads per openMP task ---"
463	printf "\n -p software package list \"\" "
464	printf "\n -q queue \"$queue\" "
465	printf "\n -r run control list (combines -i -o) \"\" "
466	printf "\n -s filenames of routines to be compiled \"\" "
467	printf "\n must end with .f, .f90, .F, or .c !"
468	printf "\n use \"..\" for more than one file and wildcards"
469	printf "\n -s LM compiles all locally modified files"
470	printf "\n -S config file interpreted by shellscript ---"
471	printf "\n -t allowed cpu-time in seconds (batch) 0"
472	printf "\n -T tasks per node depending on -h"
473	printf "\n -u username on remote machine \"\" "
474	printf "\n -v no prompt for confirmation ---"
475	printf "\n -w maximum parallel io streams as given by -X"
476	printf "\n -x tracing of mrun for debug purposes ---"
477	printf "\n -X # of processors (on parallel machines) 1"
478	printf "\n -y add appendix \"_O\" to all local output"
479	printf "\n files (ocean precursor runs followed by"
480	printf "\n coupled atmosphere-ocean runs) ---"
481	printf "\n -Y run coupled model, \"#1 #2\" with"
482	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
483	printf "\n -z disable a priori parameter file check ---"
484	printf "\n -Z skip combine_plot_fields at the end of "
485	printf "\n the simulation ---"
486	printf "\n "
487	printf "\n Possible values of positional parameter <modus>:"
488	printf "\n \"?\" - this outline \n\n") \| more
489	exit
490	elif [[ "$1" != "" ]]
491	then
492	printf "\n +++ positional parameter $1 unknown \n"
493	locat=parameter; exit
494	fi
495
496
497
498	# SHORT STARTING MESSAGE
499	printf "\n*** $version "
500	printf "\n will be executed. Please wait ..."
501
502
503
504	# CHECK, IF CONFIGURATION FILE EXISTS
505	if [[ ! -f $config_file ]]
506	then
507	printf "\n\n +++ configuration file: "
508	printf "\n $config_file"
509	printf "\n does not exist"
510	locat=connect; exit
511	fi
512
513
514	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
515	line=""
516	grep "%host_identifier" $config_file > tmp_mrun
517	while read line
518	do
519	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
520	then
521	HOSTNAME=`echo $line \| cut -d" " -s -f2`
522	host_identifier=`echo $line \| cut -d" " -s -f3`
523	if [[ $localhost_realname = $HOSTNAME ]]
524	then
525	localhost=$host_identifier
526	break
527	fi
528	fi
529	done < tmp_mrun
530
531	if [[ "$localhost" = "" ]]
532	then
533	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
534	printf "\n for local host \"$localhost_realname\"."
535	printf "\n Please add line"
536	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
537	printf "\n to the configuration file."
538	locat=localhost; exit
539	fi
540
541
542	# SET HOST-SPECIFIC VARIABLES
543	case $localhost_realname in
544	(r1\|r2\|h01\|b01) archive_system=tivoli;;
545	(cs*) archive_system=ut;;
546	esac
547
548
549	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
550	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
551	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
552	[[ "$afname" = "" ]] && afname=$fname
553
554
555	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
556	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
557	# STATEMENTS IN THE CONFIGURATION FILE
558	if [[ "$run_mode" != "" ]]
559	then
560	input_list="$input_list $run_mode"
561	output_list="$output_list $run_mode"
562	fi
563
564
565	# ??? is this (and the respective option -H) really required ???
566	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
567	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
568	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
569	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
570	if [[ "$fromhost" = "" ]]
571	then
572	fromhost=$localhost
573	fi
574
575
576	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
577	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
578	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
579	# TO BE SUBMITTED (I.E. do_bacth=true)
580	if [[ -n $host && "$host" != $localhost ]]
581	then
582	do_batch=true
583	do_remote=true
584	case $host in
585	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
586	(*) printf "\n"
587	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
588	printf "\n is not available"
589	locat=nqs; (( iec = 0 )); exit;;
590	esac
591	else
592	host=$localhost
593	fi
594
595
596	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
597	if [[ -n $additional_conditions ]]
598	then
599	cond1=`echo $additional_conditions \| cut -d" " -f1`
600	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
601	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
602	if [[ -n $dummy ]]
603	then
604	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
605	locat=options; exit
606	fi
607	block=_$cond1
608	[[ -n $cond2 ]] && block=${block}_$cond2
609	fi
610
611
612	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
613	if [[ $run_coupled_model = true ]]
614	then
615
616	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
617	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
618
619	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
620	then
621
622	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
623	printf "\n PEs (total) : $numprocs"
624	printf "\n PEs (atmosphere): $numprocs_atmos"
625	printf "\n PEs (ocean) : $numprocs_ocean"
626	locat=coupling; exit
627
628	fi
629
630
631	# GET coupled_mode FROM THE CONFIG FILE
632	line=""
633	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
634	while read line
635	do
636	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
637	then
638	coupled_mode="mpi2"
639	fi
640	done < tmp_mrun
641
642	fi
643
644
645	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
646	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
647	then
648	if [[ $ignore_archive_error = false ]]
649	then
650	printf "\n +++ data archiving of previous run failed"
651	printf "\n see directory \~/job_queue on remote machine"
652	locat=archive; exit
653	else
654	printf "\n +++ warning: data archiving in a previous run failed"
655	printf "\n MRUN continues, trying to get backup copy"
656	fi
657	fi
658
659
660	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
661	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
662	mrun_memory=$memory
663	mrun_group_number=$group_number
664	mrun_cpumax=$cpumax
665	mrun_numprocs=$numprocs
666
667
668	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
669	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
670	if [[ "$read_from_config" = false ]]
671	then
672
673	[[ $silent = false ]] && printf "\n Reading the configuration file... "
674
675	# READ THE CONFIGURATION FILE LINE BY LINE
676	while read zeile
677	do
678	[[ $silent = false ]] && printf "."
679
680
681	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
682	eval zeile=\"$zeile\"
683
684
685	# INTERPRET THE LINE
686	if [[ "$(echo $zeile)" = "" ]]
687	then
688	# EMPTY LINE, NO ACTION
689	continue
690
691	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
692	then
693
694	# LINE IS A COMMENT LINE
695	true
696
697	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
698	then
699
700	# LINE DEFINES AN ENVIRONMENT-VARIABLE
701	zeile=$(echo $zeile \| cut -c2-)
702	var=`echo $zeile \| cut -d" " -f1`
703	value=`echo $zeile \| cut -d" " -s -f2`
704	for_host=`echo $zeile \| cut -d" " -s -f3`
705	for_cond1=`echo $zeile \| cut -d" " -s -f4`
706	for_cond2=`echo $zeile \| cut -d" " -s -f5`
707
708	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
709	then
710
711	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
712	# "::" IS REPLACED BY ":".
713	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
714
715
716	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
717	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
718	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
719	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
720	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
721	# CONFIGURATION-FILE.
722	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
723	then
724	eval $var=\$value
725
726	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
727	if [[ $do_trace = true ]]
728	then
729	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
730	fi
731	fi
732
733	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
734	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
735	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
736	# MUST HAVE TO BE STARTED
737	if [[ $var = host ]]
738	then
739	if [[ -n $host && "$host" != $localhost ]]
740	then
741	do_batch=true
742	do_remote=true
743	case $host in
744	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
745	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
746	printf "\n is not available"
747	locat=nqs; exit;;
748	esac
749	else
750	host=$localhost
751	fi
752	fi
753
754	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
755	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
756	# BY MRUN (E.G. subjob)
757	export $var
758	fi
759
760
761
762
763	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
764	then
765
766	# LINE DEFINES ERROR-COMMAND
767	(( iec = iec + 1 ))
768	zeile=$(echo $zeile \| cut -c4-)
769	err_command[$iec]="$zeile"
770
771	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
772	then
773
774	# LINE DEFINES INPUT-COMMAND
775	(( iic = iic + 1 ))
776	zeile=$(echo $zeile \| cut -c4-)
777	in_command[$iic]="$zeile"
778
779	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
780	then
781
782	# LINE DEFINES OUTPUT-COMMAND
783	(( ioc = ioc + 1 ))
784	zeile=$(echo $zeile \| cut -c4-)
785	out_command[$ioc]="$zeile"
786
787	else
788
789	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
790	# s2a: in/out - field
791	# s2b: loc - field (optional)
792	# s2c: tr/ar - field (optional)
793	s1=`echo $zeile \| cut -d" " -f1`
794	s2=`echo $zeile \| cut -d" " -s -f2`
795	s2a=$(echo $s2 \| cut -d":" -f1)
796	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
797	then
798	s2b=""
799	s2c=""
800	else
801	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
802	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
803	fi
804	s3=`echo $zeile \| cut -d" " -f3`
805	s4=`echo $zeile \| cut -d" " -s -f4`
806	s5=`echo $zeile \| cut -d" " -s -f5`
807	s6=`echo $zeile \| cut -d" " -s -f6`
808
809
810	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
811	# INPUT- OR OUTPUT-LIST.
812	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
813	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
814	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
815	# IS NOT CHECKED AND STORED.
816	IFSALT="$IFS"; IFS="$IFS:"
817	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
818	then
819	found=false
820	for actual in $input_list
821	do
822	for formal in $s3
823	do
824	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
825	done
826	done
827	if [[ $found = true ]]
828	then
829	(( iin = iin + 1 ))
830	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
831	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
832	extin[$iin]=$s6
833	fi
834	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
835	then
836	found=false
837	for actual in $output_list
838	do
839	for formal in $s3
840	do
841	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
842	done
843	done
844	if [[ $found = true ]]
845	then
846	(( iout = iout + 1 ))
847	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
848	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
849	fi
850	elif [[ "$s2a" != in && "$s2a" != out ]]
851	then
852	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
853	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
854	locat=connect; exit
855	fi
856	IFS="$IFSALT"
857	fi
858	done < $config_file
859
860	else
861
862
863	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
864	[[ $silent = false ]] && printf "..."
865	interpreted_config_file=.icf.$RANDOM
866
867
868
869	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
870	cat > .mrun_environment << %%END%%
871	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
872	config_file = '$config_file', do_remote = '$do_remote',
873	do_trace = '$do_trace', host = '$host',
874	input_list = '$input_list', icf = '$interpreted_config_file',
875	localhost = '$localhost', output_list = '$output_list' /
876
877	%%END%%
878
879	if [[ "$host" != $localhost ]]
880	then
881
882	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
883	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
884	if [[ $? != 0 ]]
885	then
886	printf "\n\n +++ no interpret_config found"
887	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
888	locat=interpret_config; exit
889	fi
890	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
891	$interpret_config_executable
892
893	else
894
895	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
896	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
897	then
898	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
899	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
900	locat=interpret_config; exit
901	else
902	interpret_config${block}.x
903	fi
904
905	fi
906	rm .mrun_environment
907
908
909	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
910	chmod u+x $interpreted_config_file
911	export PATH=$PATH:.
912	. $interpreted_config_file
913	rm $interpreted_config_file
914
915	fi
916
917
918	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
919	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
920	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
921	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
922	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
923	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
924	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
925
926
927	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
928	# FOR SOURCE-FILES TO BE COMPILED.
929	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
930	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
931	if [[ "$SOURCES_COMPLETE" = "" ]]
932	then
933
934	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
935	# HAS BEEN DEFINED
936	source_path=""
937	line=""
938	grep "%source_path" $config_file > tmp_mrun
939	while read line
940	do
941	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
942	then
943	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
944	then
945	global_source_path=`echo $line \| cut -d" " -f2`
946	fi
947	fi
948	done < tmp_mrun
949
950	line=""
951	found=false
952	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
953	while read line
954	do
955	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
956	then
957	if [[ $found = true ]]
958	then
959	printf "\n\n +++ more than one source path found in configuration file"
960	printf "\n for local host \"$localhost\" "
961	locat=source_path; exit
962	fi
963	source_path=`echo $line \| cut -d" " -f2`
964	found=true
965	fi
966	done < tmp_mrun
967	rm tmp_mrun
968
969	if [[ "$source_path" = "" ]]
970	then
971	if [[ "$global_source_path" != "" ]]
972	then
973	source_path=$global_source_path
974	else
975	printf "\n\n +++ no source path found in configuration file"
976	printf "\n for local host \"$localhost\" "
977	locat=source_path; exit
978	fi
979	fi
980	eval source_path=$source_path
981
982	if [[ ! -d $source_path ]]
983	then
984	printf "\n\n +++ source path \"$source_path\" on local host"
985	printf "\n \"$localhost\" does not exist"
986	locat=source_path; exit
987	fi
988
989	fi
990
991
992	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
993	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
994	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
995	then
996	global_revision=`svnversion $source_path 2>/dev/null`
997	global_revision="Rev: $global_revision"
998	fi
999
1000
1001	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1002	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1003	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1004	if [[ -n $host && "$host" != $localhost ]]
1005	then
1006	do_batch=true
1007	do_remote=true
1008	case $host in
1009	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1010	(*) printf "\n"
1011	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1012	printf "\n is not available"
1013	locat=nqs; (( iec = 0 )); exit;;
1014	esac
1015	else
1016	host=$localhost
1017	fi
1018
1019
1020	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1021	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1022	then
1023
1024	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1025	if [[ ! -n $numprocs ]]
1026	then
1027	printf "\n"
1028	printf "\n +++ option \"-K parallel\" requires additional specification"
1029	printf "\n of the number of processors to be used by"
1030	printf "\n mrun-option \"-X\" or by environment-variable"
1031	printf "\n \"numprocs\" in the configuration file"
1032	locat=numprocs; (( iec = 0 )); exit
1033	fi
1034
1035	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1036	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1037	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1038	then
1039	printf "\n"
1040	printf "\n +++ option \"-T\" (tasks per node) is missing"
1041	printf "\n set -T option or define tasks_per_node in the config file"
1042	locat=tasks_per_node; (( iec = 0 )); exit
1043	fi
1044
1045	if (( numprocs < tasks_per_node ))
1046	then
1047	printf "\n"
1048	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1049	printf "\n given values: -T $tasks_per_node -X $numprocs"
1050	locat=tasks_per_node; (( iec = 0 )); exit
1051	fi
1052
1053	if [[ $host != lcflow && $host != lcxt5m ]]
1054	then
1055	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1056	(( ival = $tasks_per_node ))
1057	(( pes = numprocs ))
1058	(( ii = pes / ival ))
1059	(( remaining_pes = pes - ii * ival ))
1060	if (( remaining_pes > 0 ))
1061	then
1062	printf "\n"
1063	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1064	printf "\n divisor of the total number of processors (option \"-X\")"
1065	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1066	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1067	(( nodes = nodes + 1 ))
1068	fi
1069	fi
1070
1071
1072	# SETTINGS FOR SUBJOB-COMMAND
1073	OOPT="-O $threads_per_task"
1074
1075	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1076	if [[ "$tasks_per_node" != "" ]]
1077	then
1078	TOPT="-T $tasks_per_node"
1079	fi
1080
1081	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1082	if [[ $node_usage = default ]]
1083	then
1084	if [[ $host = ibms ]]
1085	then
1086	node_usage=shared
1087	else
1088	node_usage=not_shared
1089	fi
1090	fi
1091
1092	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1093	then
1094	printf "\n"
1095	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1096	printf "\n \"shared\" or \"not_shared\""
1097	locat=tasks_per_node; (( iec = 0 )); exit
1098	fi
1099
1100	fi
1101
1102	# CHECK IF HOSTFILE EXISTS
1103	if [[ -n $hostfile ]]
1104	then
1105	if [[ ! -f $hostfile ]]
1106	then
1107	printf "\n"
1108	printf "\n +++ hostfile \"$hostfile\" does not exist"
1109	locat=hostfile; exit
1110	fi
1111	fi
1112
1113
1114	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1115	if [[ "$maximum_parallel_io_streams" = "" ]]
1116	then
1117	maximum_parallel_io_streams=$numprocs
1118	fi
1119
1120
1121	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1122	if [[ "$scp_port" != "" ]]
1123	then
1124	PORTOPT="-P $scp_port"
1125	SSH_PORTOPT="-p $scp_port"
1126	fi
1127
1128
1129	# SET DEFAULT-QUEUE, IF NOT GIVEN
1130	if [[ $queue = none ]]
1131	then
1132	case $host in
1133	(ibmh) queue=cluster;;
1134	(ibmkisti) queue=class.32plus;;
1135	(lckiaps) queue=normal;;
1136	(lckyoto) queue=ph;;
1137	(lckyuh) queue=fx-single;;
1138	(lckyut) queue=cx-single;;
1139	(lctit) queue=S;;
1140	(nech) queue=none;;
1141	(unics) queue=unics;;
1142	esac
1143	fi
1144
1145
1146	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1147	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1148	(( i = 0 ))
1149	while (( i < iin ))
1150	do
1151	(( i = i + 1 ))
1152	(( maxcycle = 0 ))
1153
1154	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1155	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1156	if [[ "${actionin[$i]}" = di ]]
1157	then
1158	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1159	# HOST ONLY
1160	eval filename=${pathin[$i]}/${endin[$i]}
1161	else
1162	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1163	# HOST ONLY
1164	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1165	fi
1166	eval pathname=${pathin[$i]}
1167
1168	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1169	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1170	then
1171	filename_input=$filename
1172	fi
1173
1174	# CHECK IF FILE EXISTS
1175	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1176	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1177	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1178	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1179	then
1180
1181	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1182	if [[ "${transin[$i]}" != "locopt" ]]
1183	then
1184	printf "\n\n +++ INPUT-file: "
1185	if [[ "${extin[$i]}" = "" ]]
1186	then
1187	printf "\n $filename"
1188	else
1189	printf "\n $filename.${extin[$i]}"
1190	fi
1191	printf "\n does not exist\n"
1192	locat=input; exit
1193	else
1194	transin[$i]="unavailable"
1195	fi
1196	else
1197
1198	# DETERMINE THE FILE'S CYCLE NUMBER
1199	ls -1 -d $filename > filelist 2>/dev/null
1200	ls -1 -d $filename.* >> filelist 2>/dev/null
1201	while read zeile
1202	do
1203	cycle=$(echo $zeile \| cut -f2 -d".")
1204	if [[ "$cycle" = "$zeile" ]]
1205	then
1206	(( icycle = 0 ))
1207	elif [[ "$cycle" = "${extin[$i]}" ]]
1208	then
1209	(( icycle = 0 ))
1210	else
1211	(( icycle = $cycle ))
1212	fi
1213	if (( icycle > maxcycle ))
1214	then
1215	(( maxcycle = icycle ))
1216	file_to_be_used=$zeile
1217	fi
1218	done <filelist
1219	rm filelist
1220
1221	# APPEND CYCLE NUMBER TO FILENAME
1222	if (( maxcycle > 0 ))
1223	then
1224	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1225	then
1226	filename=${filename}.$maxcycle.${extin[$i]}
1227	else
1228	filename=${filename}.$maxcycle
1229	fi
1230	else
1231	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1232	then
1233	filename=${filename}.${extin[$i]}
1234	fi
1235	fi
1236
1237	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1238	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1239	absnamein[$i]=$filename
1240	if (( maxcycle > 0 ))
1241	then
1242	if [[ "${actionin[$i]}" = di ]]
1243	then
1244	frelin[$i]=${endin[$i]}.$maxcycle
1245	else
1246	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1247	fi
1248	else
1249	if [[ "${actionin[$i]}" = di ]]
1250	then
1251	frelin[$i]=${endin[$i]}
1252	else
1253	frelin[$i]=${afname}${endin[$i]}
1254	fi
1255	fi
1256
1257	fi
1258	done
1259
1260	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1261	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1262	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1263	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1264	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1265	# REMOTE HOST)
1266	(( i = 0 ))
1267	while (( i < iout ))
1268	do
1269	(( i = i + 1 ))
1270	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1271	then
1272	if [[ "${actionout[$i]}" = tr ]]
1273	then
1274	actionout[$i]=""
1275	elif [[ "${actionout[$i]}" = trpe ]]
1276	then
1277	actionout[$i]=pe
1278	elif [[ "${actionout[$i]}" = tra ]]
1279	then
1280	actionout[$i]=a
1281	fi
1282	(( maxcycle = 0 ))
1283	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1284	eval catalogname=${pathout[$i]}
1285	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1286	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1287	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1288	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1289	then
1290
1291	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1292	if cat /dev/null > $filename
1293	then
1294	rm $filename
1295	else
1296
1297	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1298	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1299	if [[ ! -d $catalogname ]]
1300	then
1301	if mkdir -p $catalogname
1302	then
1303	printf "\n\n *** directory:"
1304	printf "\n $catalogname"
1305	printf "\n was created\n"
1306	else
1307	printf "\n\n +++ OUTPUT-file:"
1308	printf "\n $filename"
1309	printf "\n cannot be created, because directory does not exist"
1310	printf "\n and cannot be created either"
1311	printf "\n"
1312	locat=output ; exit
1313	fi 2>/dev/null
1314	else
1315	printf "\n\n +++ OUTPUT-file:"
1316	printf "\n $filename"
1317	printf "\n cannot be created, although directory exists"
1318	printf "\n"
1319	locat=output ; exit
1320	fi
1321	fi 2>/dev/null
1322	else
1323
1324	# DETERMINE THE CYCLE NUMBER
1325	ls -1 -d $filename > filelist 2>/dev/null
1326	ls -1 -d $filename.* >> filelist 2>/dev/null
1327	while read zeile
1328	do
1329	cycle=$(echo $zeile \| cut -f2 -d".")
1330	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1331	then
1332	(( icycle = 1 ))
1333	else
1334	(( icycle = $cycle + 1 ))
1335	fi
1336	if (( icycle > maxcycle ))
1337	then
1338	(( maxcycle = icycle ))
1339	fi
1340	done <filelist
1341	rm filelist
1342	fi
1343
1344	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1345	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1346	if [[ "${actionout[$i]}" != a ]]
1347	then
1348	if (( maxcycle > 0 ))
1349	then
1350	filename=${filename}.$maxcycle
1351	if cat /dev/null > $filename
1352	then
1353	rm $filename
1354	else
1355	printf "\n +++ OUTPUT-file:"
1356	printf "\n $filename"
1357	printf "\n cannot be created"
1358	locat=output ; exit
1359	fi
1360	fi
1361	else
1362	(( maxcycle = maxcycle - 1 ))
1363	if (( maxcycle > 0 ))
1364	then
1365	filename=${filename}.$maxcycle
1366	fi
1367	fi
1368
1369	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1370	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1371	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1372	pathout[$i]=$filename
1373	if (( maxcycle > 0 ))
1374	then
1375	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1376	else
1377	frelout[$i]=${fname}${endout[$i]}
1378	fi
1379
1380	fi
1381	done
1382
1383
1384	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1385	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1386	then
1387	if [[ "$dvr_inc" = "" ]]
1388	then
1389	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1390	printf "\n This is required for the dvrp_graphics package.\n"
1391	locat=dvr; exit
1392	fi
1393	if [[ "$dvr_lib" = "" ]]
1394	then
1395	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1396	printf "\n This is required for the dvrp_graphics package.\n"
1397	locat=dvr; exit
1398	fi
1399	fi
1400
1401
1402	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1403	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1404	if [[ "$mainprog" = "" && "$executable" = "" ]]
1405	then
1406	printf "\n +++ neither main program nor executable defined"
1407	locat=source; exit
1408	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1409	then
1410	printf "\n +++ main program as well as executable defined"
1411	locat=source; exit
1412	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1413	then
1414	do_compile=false
1415	fi
1416
1417
1418	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1419	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1420	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1421	then
1422	rm -rf SOURCES_FOR_RUN_$fname
1423	mkdir SOURCES_FOR_RUN_$fname
1424	fi
1425
1426
1427	# COLLECT ALL ROUTINES TO BE COMPILED
1428	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1429	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1430	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1431	then
1432
1433	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1434
1435	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1436	then
1437
1438	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1439	source_list=""
1440	cd $source_path
1441
1442
1443	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1444	if [[ ! -d .svn ]]
1445	then
1446	printf "\n\n +++ source directory"
1447	printf "\n \"$source_path\" "
1448	printf "\n is not under control of \"subversion\"."
1449	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1450	fi
1451
1452
1453	# LIST ALL MODIFIED SOURCE CODE FILES
1454	Filenames=""
1455	svn status > tmp_mrun
1456	while read line
1457	do
1458	firstc=`echo $line \| cut -c1`
1459	if [[ $firstc = M \|\| $firstc = "?" ]]
1460	then
1461	Name=`echo "$line" \| cut -c8-`
1462	extension=`echo $Name \| cut -d. -f2`
1463	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1464	then
1465	Filenames="$Filenames "$Name
1466	fi
1467	fi
1468	done < tmp_mrun
1469
1470
1471	# COPY FILES TO SOURCES_FOR_RUN_...
1472	for dateiname in $Filenames
1473	do
1474	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1475	source_list=$source_list"$dateiname "
1476	done
1477
1478	cd - > /dev/null
1479
1480
1481	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1482	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1483	elif [[ "$source_list" != "" && $restart_run != true ]]
1484	then
1485
1486	cd $source_path
1487
1488	for filename in $source_list
1489	do
1490
1491	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1492	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1493	then
1494	printf "\n +++ source code file: $filename"
1495	printf "\n must not contain (\"/\") "
1496	locat=source; exit
1497	fi
1498
1499	if [[ ! -f $filename ]]
1500	then
1501	printf "\n +++ source code file: $filename"
1502	printf "\n does not exist"
1503	locat=source; exit
1504	else
1505	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1506	fi
1507
1508	done
1509
1510	cd - > /dev/null
1511
1512	fi
1513
1514
1515	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1516	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1517	if [[ $restart_run != true ]]
1518	then
1519
1520	if [[ ! -f "$source_path/$mainprog" ]]
1521	then
1522	printf "\n\n +++ main program: $mainprog"
1523	printf "\n does not exist in source directory"
1524	printf "\n \"$source_path\"\n"
1525	locat=source; exit
1526	else
1527	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1528	then
1529	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1530	source_list=${mainprog}" $source_list"
1531	fi
1532	fi
1533	fi
1534
1535
1536	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1537	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1538	if [[ "$restart_run" != true ]]
1539	then
1540	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1541	if [[ ! -f $makefile ]]
1542	then
1543	printf "\n +++ file \"$makefile\" does not exist"
1544	locat=make; exit
1545	else
1546	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1547	fi
1548	fi
1549
1550
1551	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1552	if [[ $restart_run != true && "$add_source_path" != "" ]]
1553	then
1554
1555	# DOES THE DIRECTORY EXIST?
1556	if [[ ! -d $add_source_path ]]
1557	then
1558	printf "\n\n +++ WARNING: additional source code directory"
1559	printf "\n \"$add_source_path\" "
1560	printf "\n does not exist or is not a directory."
1561	printf "\n No source code will be used from this directory!\n"
1562	add_source_path=""
1563	if [[ $silent == false ]]
1564	then
1565	sleep 3
1566	fi
1567	else
1568
1569	cd $add_source_path
1570	found=false
1571
1572	Names=$(ls -1 *.f90 2>&1)
1573	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1574	Names=$(ls -1 *.F90 2>&1)
1575	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1576	Names=$(ls -1 *.F 2>&1)
1577	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1578	Names=$(ls -1 *.f 2>&1)
1579	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1580	Names=$(ls -1 *.c 2>&1)
1581	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1582
1583	cd - > /dev/null
1584	cd SOURCES_FOR_RUN_$fname
1585
1586	# COPY MAKEFILE IF EXISTING
1587	if [[ -f $add_source_path/Makefile ]]
1588	then
1589	printf "\n\n *** user Makefile from directory"
1590	printf "\n \"$add_source_path\" is used \n"
1591	if [[ $silent == false ]]
1592	then
1593	sleep 1
1594	fi
1595	cp $add_source_path/Makefile .
1596	fi
1597
1598	for dateiname in $AddFilenames
1599	do
1600	if [[ -f $dateiname ]]
1601	then
1602	printf "\n +++ source code file \"$dateiname\" found in additional"
1603	printf "\n source code directory \"$add_source_path\" "
1604	printf "\n but was also given with option \"-s\" which means that it should be taken"
1605	printf "\n from directory \"$source_path\"."
1606	locat=source; exit
1607	fi
1608
1609	cp $add_source_path/$dateiname .
1610	source_list="$source_list $dateiname"
1611
1612	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1613	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1614	then
1615	printf "\n\n +++ user file \"$dateiname\" "
1616	printf "\n is not listed in Makefile \n"
1617	locat=source; exit
1618	else
1619
1620	if [[ $found = false ]]
1621	then
1622	found=true
1623	printf "\n\n *** following user file(s) added to the"
1624	printf " files to be translated:\n "
1625	fi
1626	printf "$dateiname "
1627	if [[ $silent == false ]]
1628	then
1629	sleep 0.5
1630	fi
1631
1632	fi
1633	done
1634	[[ $found = true ]] && printf "\n"
1635	cd - > /dev/null
1636	fi
1637	fi
1638
1639
1640	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1641	# TO THE LIST OF FILES TO BE COMPILED
1642	if [[ $restart_run != true && -n $package_list ]]
1643	then
1644
1645	cd $source_path
1646
1647	for package in $package_list
1648	do
1649
1650	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1651
1652	# DETERMINE FILES BELONGING TO THE PACKAGE
1653	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1654	# THE NAME OF THE DIRECTORY
1655	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1656
1657
1658	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1659	# IF THEY ARE NOT ALREADY PART OF THE LIST
1660	for source_list_name in $package_source_list
1661	do
1662	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1663	then
1664
1665	# ONLY TAKE FILES WITH VALID SUFFIX
1666	ending=`echo $source_list_name \| cut -f2 -d.`
1667	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1668	then
1669	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1670	source_list="$source_list $source_list_name"
1671	fi
1672	fi
1673	done
1674	done
1675
1676	cd - > /dev/null
1677	fi
1678
1679	fi # do_compile=true
1680
1681
1682	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1683	# AND SET PRE-PROCESSOR DIRECTIVES
1684	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1685	then
1686
1687	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1688	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1689	then
1690	cpp_options="${cpp_options},-D__ibm=__ibm"
1691	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1692	then
1693	cpp_options="$cpp_options -D__nec"
1694	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1695	then
1696	cpp_options="$cpp_options -D__lc"
1697	else
1698	cpp_options="$cpp_options -D__$localhost"
1699	fi
1700
1701	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1702	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1703	then
1704	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1705	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1706	else
1707	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1708	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1709	fi
1710
1711	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1712	if [[ -n $package_list ]]
1713	then
1714	for package in $package_list
1715	do
1716	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1717	then
1718	if [[ $package != "dvrp_graphics+1PE" ]]
1719	then
1720	cpp_options="${cpp_options},-D__$package=__$package"
1721	else
1722	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1723	export use_seperate_pe_for_dvrp_output=true
1724	fi
1725	else
1726	if [[ $package != "dvrp_graphics+1PE" ]]
1727	then
1728	cpp_options="$cpp_options -D__$package"
1729	else
1730	cpp_options="$cpp_options -D__dvrp_graphics"
1731	export use_seperate_pe_for_dvrp_output=true
1732	fi
1733	fi
1734	done
1735	fi
1736
1737	# SET DIRECTIVES GIVEN BY OPTION -D
1738	if [[ -n $cpp_opts ]]
1739	then
1740	for popts in $cpp_opts
1741	do
1742	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1743	then
1744	cpp_options="${cpp_options},-D__$popts=__$popts"
1745	else
1746	cpp_options="$cpp_options -D__$popts"
1747	fi
1748	done
1749	fi
1750
1751	else
1752
1753
1754	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1755	if [[ $do_remote = false ]]
1756	then
1757	if [[ ! -f $executable ]]
1758	then
1759	printf "\n +++ executable file: $executable"
1760	printf "\n does not exist"
1761	locat=executable; exit
1762	fi
1763	fi
1764	fi
1765
1766
1767	# DETERMINE THE JOB MODE
1768	if [[ "$ENVIRONMENT" = BATCH ]]
1769	then
1770	batch_job=.TRUE.
1771	jobmo=BATCH
1772	else
1773	batch_job=.FALSE.
1774	jobmo=INTERACTIVE
1775	fi
1776
1777
1778	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1779	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1780	then
1781	printf "\n +++ no interactive runs allowed on host \"$host\" "
1782	printf "\n please submit batch job using mrun option \"-b\" \n"
1783	locat=normal; exit
1784	fi
1785
1786
1787	# CHECK, IF USER DEFINED A COMPILER
1788	if [[ "$compiler_name" = "" ]]
1789	then
1790
1791	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1792	locat=compiler_name; exit
1793
1794	fi
1795
1796
1797	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1798	kennung=$RANDOM
1799	if [[ "$tmp_user_catalog" = "" ]]
1800	then
1801	if [[ $localhost = ibmh ]]
1802	then
1803	tmp_user_catalog=$SCRATCH
1804	elif [[ $localhost = nech ]]
1805	then
1806	tmp_user_catalog=$WRKSHR
1807	else
1808	tmp_user_catalog=/tmp
1809	fi
1810	fi
1811	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1812
1813
1814	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1815	if [[ "$tmp_data_catalog" = "" ]]
1816	then
1817	if [[ $localhost = nech ]]
1818	then
1819	tmp_data_catalog=$WRKSHR/mrun_restart_data
1820	else
1821	tmp_data_catalog=/tmp/mrun_restart_data
1822	fi
1823	fi
1824
1825
1826	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1827	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1828	then
1829	eval fopts=\"$fopts\"
1830	eval lopts=\"$lopts\"
1831	fi
1832
1833
1834
1835	# DETERMINE COMPILE- AND LINK-OPTIONS
1836	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1837	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1838	ROPTS="$ropts"
1839	# 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 ]]
1840	# then
1841	XOPT="-X $numprocs"
1842	# fi
1843
1844
1845
1846	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1847	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1848	done=false
1849	while [[ $done = false ]]
1850	do
1851	cputime=$cpumax
1852	if (( $cputime == 0 ))
1853	then
1854	if [[ $do_batch = true ]]
1855	then
1856	printf "\n +++ cpu-time is undefined"
1857	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1858	printf "\n >>> "
1859	read cputime 1>/dev/null 2>&1
1860	else
1861	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1862	fi
1863	else
1864	done=true
1865	fi
1866	cpumax=$cputime
1867	done
1868
1869	(( minuten = cputime / 60 ))
1870	(( sekunden = cputime - minuten * 60 ))
1871
1872
1873	# CHECK THE MEMORY DEMAND
1874	if [[ $do_batch = true ]]
1875	then
1876	done=false
1877	while [[ $done = false ]]
1878	do
1879	if (( memory == 0 ))
1880	then
1881	printf "\n +++ memory demand is undefined"
1882	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1883	printf "\n >>> "
1884	read memory 1>/dev/null 2>&1
1885	else
1886	done=true
1887	fi
1888	done
1889	fi
1890
1891
1892	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1893	if [[ $do_remote = true && -z $remote_username ]]
1894	then
1895	while [[ -z $remote_username ]]
1896	do
1897	printf "\n +++ username on remote host \"$host\" is undefined"
1898	printf "\n >>> Please type username:"
1899	printf "\n >>> "
1900	read remote_username
1901	done
1902	mc="$mc -u$remote_username"
1903	fi
1904
1905	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1906	if [[ "$login_init_cmd" != "" ]]
1907	then
1908	export init_cmds="${login_init_cmd};"
1909	fi
1910
1911
1912	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1913	if [[ "$modules" != "" ]]
1914	then
1915	if [[ $host = lctit ]]
1916	then
1917	export module_calls=". $modules"
1918	else
1919	export module_calls="module load ${modules};"
1920	fi
1921	fi
1922
1923
1924
1925	# OUTPUT OF THE MRUN-HEADER
1926	calltime=$(date)
1927	printf "\n"
1928	printf "#------------------------------------------------------------------------# \n"
1929	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1930	printf "\| \| \n"
1931	spalte1="called on:"; spalte2=$localhost_realname
1932	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1933	if [[ $do_remote = true ]]
1934	then
1935	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1936	else
1937	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1938	fi
1939	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1940	if [[ -n $numprocs ]]
1941	then
1942	if [[ $run_coupled_model = false ]]
1943	then
1944	spalte1="number of PEs:"; spalte2=$numprocs
1945	else
1946	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1947	fi
1948	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1949	fi
1950	if [[ -n $tasks_per_node ]]
1951	then
1952	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1953	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1954	if (( remaining_pes > 0 ))
1955	then
1956	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1957	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1958	fi
1959	fi
1960	if [[ $maximum_parallel_io_streams != $numprocs ]]
1961	then
1962	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1963	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1964	fi
1965	if [[ $use_openmp = true ]]
1966	then
1967	spalte1="threads per task:"; spalte2="$threads_per_task"
1968	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1969	fi
1970	printf "\| \| \n"
1971	if [[ $do_compile = true ]]
1972	then
1973	if [[ "$mopts" != "" ]]
1974	then
1975	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1976	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1977	zeile=$(echo "$mopts" \| 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 "$zeile" \| cut -c46-)
1984	done
1985	fi
1986
1987	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1988	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1989	zeile=$(echo "$cpp_options" \| cut -c46-)
1990	while [[ "$zeile" != "" ]]
1991	do
1992	spalte1=""
1993	spalte2=$(echo "$zeile" \| cut -c-45)
1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1995	zeile=$(echo "$zeile" \| cut -c46-)
1996	done
1997
1998	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1999	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2000	zeile=$(echo "$fopts" \| cut -c46-)
2001	while [[ "$zeile" != "" ]]
2002	do
2003	spalte1=""
2004	spalte2=$(echo "$zeile" \| cut -c-45)
2005	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2006	zeile=$(echo "$zeile" \| cut -c46-)
2007	done
2008
2009	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2010	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2011	zeile=$(echo "$lopts" \| cut -c46-)
2012	while [[ "$zeile" != "" ]]
2013	do
2014	spalte1=""
2015	spalte2=$(echo "$zeile" \| cut -c-45)
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	zeile=$(echo "$zeile" \| cut -c46-)
2018	done
2019
2020	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	zeile=$(echo "$modules" \| cut -c46-)
2023	while [[ "$zeile" != "" ]]
2024	do
2025	spalte1=""
2026	spalte2=$(echo "$zeile" \| cut -c-45)
2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2028	zeile=$(echo "$zeile" \| cut -c46-)
2029	done
2030
2031	spalte1="main program:"; spalte2=$mainprog
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033	else
2034	spalte1=executable:; spalte2=$executable
2035	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2036	fi
2037	printf "\| \| \n"
2038	spalte1="base name of files:"; spalte2=$fname
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	if [[ $fname != $afname ]]
2041	then
2042	spalte1="base name of input files:"; spalte2=$afname
2043	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2044	fi
2045	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2046	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2047	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049
2050	if [[ "$ocean_file_appendix" = true ]]
2051	then
2052	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2053	fi
2054
2055	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2056	then
2057	spalte1="memory demand / PE":; spalte2="$memory MB"
2058	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2059	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2060	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2061	fi
2062
2063	if [[ $do_compile = true ]]
2064	then
2065	printf "\| \| \n"
2066	printf "\| Files to be compiled: \| \n"
2067	zeile=$source_list
2068	while [[ "$zeile" != "" ]]
2069	do
2070	linestart=$(echo $zeile \| cut -c-70)
2071	printf "\| %-70s \| \n" "$linestart"
2072	zeile=$(echo "$zeile" \| cut -c71-)
2073	done
2074	fi
2075	printf "#------------------------------------------------------------------------#"
2076
2077
2078
2079	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2080	if [[ $do_trace = true ]]
2081	then
2082	(( i = 0 ))
2083	while (( i < iin ))
2084	do
2085	(( i = i + 1 ))
2086	if (( i == 1 ))
2087	then
2088	printf "\n\n >>> INPUT-file assignments:\n"
2089	fi
2090	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2091	done
2092	(( i = 0 ))
2093	while (( i < iout ))
2094	do
2095	(( i = i + 1 ))
2096	if (( i == 1 ))
2097	then
2098	printf "\n\n >>> OUTPUT-file assignments:\n"
2099	fi
2100	printf "\n ${localout[$i]} : ${pathout[$i]}"
2101	done
2102	(( i = 0 ))
2103	while (( i < iic ))
2104	do
2105	(( i = i + 1 ))
2106	if (( i == 1 ))
2107	then
2108	printf "\n\n >>> INPUT-commands:\n"
2109	fi
2110	printf "\n ${in_command[$i]}"
2111	done
2112	(( i = 0 ))
2113	while (( i < ioc ))
2114	do
2115	(( i = i + 1 ))
2116	if (( i == 1 ))
2117	then
2118	printf "\n\n >>> OUTPUT-commands:\n"
2119	fi
2120	printf "\n ${out_command[$i]}"
2121	done
2122	fi
2123
2124
2125	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2126	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2127	then
2128	antwort=dummy
2129	printf "\n\n"
2130	printf " >>> everything o.k. (y/n) ? "
2131	while read antwort
2132	do
2133	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2134	then
2135	printf " >>> everything o.k. (y/n) ? "
2136	else
2137	break
2138	fi
2139	done
2140	if [[ $antwort = n \|\| $antwort = N ]]
2141	then
2142	locat=user_abort; (( iec = 0 )); exit
2143	fi
2144	if [[ $do_batch = true ]]
2145	then
2146	printf " >>> batch-job will be created and submitted"
2147	else
2148	printf " >>> MRUN will now continue to execute on this machine"
2149	fi
2150	fi
2151
2152
2153	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2154	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2155	check_depository="${working_directory}/trunk/UTIL"
2156	check_sources="${working_directory}/tmp_check_namelist_files"
2157	skip_check=false
2158
2159	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2160	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2161	then
2162	skip_check=true
2163	reason="run on remote host or parameter file check has not been compiled."
2164	fi
2165	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2166	then
2167	skip_check=true
2168	reason="parameter file check has not been compiled."
2169	fi
2170
2171	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2172	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2173	then
2174	skip_check=true
2175	reason="serial run."
2176	fi
2177
2178	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2179	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2180	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2181	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2182	if [[ $check_namelist_files == false ]]
2183	then
2184	skip_check=true
2185	reason="-z option set."
2186	fi
2187
2188	if [[ $fromhost != $localhost ]]
2189	then
2190	skip_check=true
2191	reason="submitting host is local host."
2192	fi
2193
2194	if [[ $run_coupled_model == true ]]
2195	then
2196	skip_check=true
2197	reason="coupled run."
2198	fi
2199
2200	if [[ $restart_run == true ]]
2201	then
2202	skip_check=true
2203	reason="restart run."
2204	fi
2205
2206	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2207	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2208	last_char=`echo $filename_input \| cut -c $last_char_int`
2209	if [[ "$last_char" == "f" ]]
2210	then
2211	skip_check=true
2212	reason="restart run."
2213	fi
2214
2215	if [[ $skip_check == false ]]
2216	then
2217	tmp_check=${working_directory}/tmp_check
2218
2219	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2220	# NOT NECESSARILY REQUIRED
2221	line=""
2222	found=false
2223	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2224	while read line1
2225	do
2226	line="$line1"
2227	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2228	then
2229	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2230	found=true
2231	fi
2232	done < $tmp_check
2233
2234	if [[ $found = false ]]
2235	then
2236	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2237	fi
2238
2239	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2240	# NOT NECESSARILY REQUIRED
2241	line=""
2242	found=false
2243	grep "NUDGING_DATA" $config_file > $tmp_check
2244	while read line1
2245	do
2246	line="$line1"
2247	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2248	then
2249	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2250	found=true
2251	fi
2252	done < $tmp_check
2253
2254	if [[ $found = false ]]
2255	then
2256	printf "\n +++ no NUDGING list entry found in the configuration file."
2257	fi
2258
2259	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2260	# NOT NECESSARILY REQUIRED
2261	line=""
2262	found=false
2263	grep "LSF_DATA" $config_file > $tmp_check
2264	while read line1
2265	do
2266	line="$line1"
2267	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2268	then
2269	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2270	found=true
2271	fi
2272	done < $tmp_check
2273
2274	if [[ $found = false ]]
2275	then
2276	printf "\n +++ no LSF list entry found in the configuration file."
2277	fi
2278
2279	rm -rf ${working_directory}/tmp_check
2280
2281	# CHECK IF THE P3DF FILE MUST BE CHECKED
2282	for item in $input_list
2283	do
2284	if [[ "$item" == "restart" ]]
2285	then
2286	check_restart=1
2287	else
2288	check_restart=0
2289	fi
2290	done
2291
2292	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2293	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2294	then
2295	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2296	locat=check_namelist; exit
2297	fi
2298
2299	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2300	if [[ $check_restart == 1 ]]
2301	then
2302
2303	filenamef="${filename_input}f"
2304	if [[ ! -f $filenamef ]]
2305	then
2306	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2307	check_restart=0
2308	answer=dummy
2309	printf "\n\n"
2310
2311	if [[ $silent == false ]]
2312	then
2313	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2314	do
2315	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2316	read answer
2317	done
2318	if [[ $answer = a \|\| $answer = A ]]
2319	then
2320	printf "\n +++ Aborting...."
2321	locat=normal; exit
2322	fi
2323	fi
2324	else
2325	check_restart=1
2326	fi
2327	fi
2328
2329	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2330	mkdir $check_sources
2331	cd $check_sources
2332
2333
2334	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2335	if [[ -d $add_source_path ]]
2336	then
2337	printf "\n\n *** copying files from $check_depository"
2338	cp $check_depository/check_namelist_files.tar ./
2339
2340	printf "\n\n *** untar of makefile and source files in $check_sources"
2341	tar -xf check_namelist_files.tar > /dev/null 2>&1
2342
2343	printf "\n\n *** adding user code."
2344	cp $add_source_path/* ./
2345	touch check_namelist_files.f90
2346
2347	# GET COMPILER OPTIONS AND PERFORM MAKE
2348	printf "\n\n *** compiling code if necessary...\n"
2349
2350	# workaround for batch jobs on local machine (lcxe6)
2351	if [[ $do_batch == true && $do_remote == false ]]
2352	then
2353	eval $init_cmds
2354	fi
2355
2356	# GET CHECK OPTIONS
2357	line=""
2358	found=false
2359
2360	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2361
2362	while read line1
2363	do
2364
2365	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2366	then
2367	line="$line1"
2368	fi
2369
2370	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2371	then
2372	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2373	line="$line "
2374	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'`
2375	found=true
2376	fi
2377
2378	done < $tmp_check
2379	copts_check="$copts_check -D__check -D__parallel"
2380
2381	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2382
2383	# GET MAKE OUTPUT
2384	if [[ $? != 0 ]]
2385	then
2386	printf "\n +++ error during make."
2387	answer=dummy
2388	printf "\n\n"
2389	if [[ $silent == false ]]
2390	then
2391	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2392	do
2393	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2394	read answer
2395	done
2396	if [[ $answer = a \|\| $answer = A ]]
2397	then
2398	printf "\n +++ Aborting..."
2399	rm -rf $check_sources
2400	locat=normal; exit
2401	else
2402	skip_check=true
2403	fi
2404	else
2405	skip_check=true
2406	fi
2407	fi
2408	else
2409	cp $PALM_BIN/check_namelist_files.x ./
2410	fi
2411
2412	cp $filename_input ./PARIN
2413	if [[ $check_restart == 1 ]]
2414	then
2415	cp $filenamef ./PARINF
2416	fi
2417
2418	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2419	then
2420	printf "\n *** adding topography data"
2421	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2422
2423	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2424	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2425	# WHICH REQUIRE SUFFICIENT MEMORY
2426	ulimit -s unlimited
2427	fi
2428
2429	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2430	then
2431	printf "\n *** adding nudging data"
2432	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2433	fi
2434
2435	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2436	then
2437	printf "\n *** adding large scale forcing data"
2438	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2439	fi
2440
2441	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2442	cat > ENVPAR << %%END%%
2443	&envpar run_identifier = '$fname', host = '$host',
2444	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2445	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2446	maximum_cpu_time_allowed = ${cpumax}.,
2447	revision = '$global_revision',
2448	local_dvrserver_running = $local_dvrserver_running /
2449
2450	%%END%%
2451
2452	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2453	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2454	then
2455	printf "\n +++ WARNING: check_namelist_files.x not found."
2456	answer=dummy
2457	printf "\n\n"
2458
2459	if [[ $silent == false ]]
2460	then
2461	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2462	do
2463	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2464	read answer
2465	done
2466	if [[ $answer = a \|\| $answer = A ]]
2467	then
2468	printf "\n +++ Aborting..."
2469	rm -rf $check_sources
2470	locat=normal; exit
2471	else
2472	printf "\n *** skipping parameter file check."
2473	fi
2474	fi
2475
2476	elif [[ $skip_check == false ]]
2477	then
2478	# STARTING THE PARAMETER FILE CHECK
2479	printf "\n\n *** starting parameter file check..."
2480
2481	# CHECKING THE P3D FILE
2482	printf "\n\n (1) checking $filename_input"
2483	echo "$numprocs 0 0" > VARIN
2484	errors=`./check_namelist_files.x < VARIN 2>&1`
2485
2486	check_error=false
2487	if [[ "$errors" == "" ]]
2488	then
2489	printf " --> o.k."
2490	else
2491	printf " --> failed."
2492	check_error=true
2493	printf "\n\n $errors"
2494	fi
2495
2496	# CHECKING THE PD3F FILE IF NECESSARY
2497	if [[ $check_restart == 1 && $check_error == false ]]
2498	then
2499	printf "\n\n (2) checking $filenamef"
2500
2501	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2502	# IN &INIPAR LIST
2503	found=false
2504	cat PARINF \| while read line
2505	do
2506	line=$(echo $line\|sed 's/ //g')
2507	if [[ $line == "&inipar" ]]
2508	then
2509	start_search=true
2510	fi
2511
2512	if [[ $start_search == true ]]
2513	then
2514	if [[ $line == "initializing_actions='read_restart_data'" ]]
2515	then
2516	found=true
2517	break
2518	fi
2519	fi
2520
2521	if [[ $line == "/" ]]
2522	then
2523	start_search=false
2524	fi
2525
2526	done
2527
2528	if [[ $found = false ]]
2529	then
2530	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2531	printf "\n in &inipar list in $fname$p3df_suffix."
2532	rm -rf $check_sources
2533	locat=check_namelist; exit
2534	fi
2535
2536	# READ max_user_pr FROM FILES
2537	if [[ -f parin_for_check ]]
2538	then
2539	read max_pr_user < parin_for_check
2540	else
2541	max_user_pr=0
2542	fi
2543
2544	echo "$numprocs 1 $max_pr_user" > VARIN
2545	errors=`./check_namelist_files.x < VARIN 2>&1`
2546
2547	if [[ "$errors" == "" ]]
2548	then
2549	printf " --> o.k."
2550	else
2551	printf " --> failed."
2552	check_error=true
2553	printf "\n\n $errors"
2554	fi
2555	fi
2556
2557	# REPORT ERRORS AND CONTINUE/EXIT
2558	if [[ $check_error == true ]]
2559	then
2560	printf "\n +++ errors found in the parameter file!\n"
2561	answer=dummy
2562	printf "\n\n"
2563
2564	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2565	do
2566	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2567	read answer
2568	done
2569
2570	if [[ $answer = a \|\| $answer = A ]]
2571	then
2572	printf "\n +++ Aborting..."
2573	rm -rf $check_sources
2574	locat=normal; exit
2575	fi
2576	else
2577	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2578	fi
2579	rm -rf $check_sources
2580	fi
2581	else
2582	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2583	fi
2584
2585	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2586	rm -rf $check_sources
2587	cd $working_directory
2588
2589
2590	# DETERMINE PATH FOR MAKE DEPOSITORY
2591	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2592	then
2593
2594	line=""
2595	grep "%depository_path" $config_file > tmp_mrun
2596	while read line
2597	do
2598	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2599	then
2600	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2601	then
2602	global_depository_path=`echo $line \| cut -d" " -s -f2`
2603	fi
2604	fi
2605	done < tmp_mrun
2606
2607	line=""
2608	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2609	while read line
2610	do
2611	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2612	then
2613	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2614	then
2615	local_depository_path=`echo $line \| cut -d" " -s -f2`
2616	fi
2617	fi
2618	done < tmp_mrun
2619
2620	if [[ "$local_depository_path" = "" ]]
2621	then
2622	if [[ "$global_depository_path" != "" ]]
2623	then
2624	local_depository_path=$global_depository_path
2625	else
2626	printf "\n\n +++ no depository path found in configuration file"
2627	printf "\n for local host \"$localhost\" "
2628	printf "\n please set \"\%depository_path\" in configuration file\n"
2629	locat=config_file; exit
2630	fi
2631	fi
2632	eval local_depository_path=$local_depository_path
2633	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2634	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2635
2636
2637	basename=`echo $mainprog \| cut -f1 -d"."`
2638	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2639	if [[ ! -f $make_depository ]]
2640	then
2641	printf "\n"
2642	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2643	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2644	fi
2645
2646	fi
2647
2648
2649	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2650	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2651	if [[ $do_batch = false ]]
2652	then
2653
2654
2655	# CREATE THE TEMPORARY WORKING DIRECTORY
2656	mkdir -p $TEMPDIR
2657	chmod go+rx $TEMPDIR
2658	tmpcreate=true
2659
2660
2661	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2662	# INTO THE TEMPORARY WORKING DIRECTORY
2663	if [[ $do_compile = true ]]
2664	then
2665
2666	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2667	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2668	if [[ $localhost = nech ]]
2669	then
2670	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2671	if mkdir -p $TEMPDIR_COMPILE
2672	then
2673	printf "\n *** \"$TEMPDIR_COMPILE\" "
2674	printf "\n is generated as temporary directory for cross compiling\n"
2675	else
2676	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2677	printf "\n needed for cross compilation failed"
2678	locat=compile
2679	exit
2680	fi
2681	else
2682	TEMPDIR_COMPILE=$TEMPDIR
2683	fi
2684
2685	cp $make_depository $TEMPDIR_COMPILE
2686	cd $TEMPDIR_COMPILE
2687	tar -xf $make_depository > /dev/null 2>&1
2688	cd - > /dev/null
2689
2690	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2691	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2692	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2693	then
2694	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2695	else
2696	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2697	fi
2698
2699	else
2700
2701	cp $executable ${TEMPDIR}/a.out
2702
2703	fi
2704
2705
2706	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2707	cd $TEMPDIR
2708	printf "\n *** changed to temporary directory: $TEMPDIR"
2709
2710
2711	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2712	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2713	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2714	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2715	(( i = 0 ))
2716	while (( i < iout ))
2717	do
2718	(( i = i + 1 ))
2719	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2720	then
2721	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2722	else
2723	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2724	fi
2725	done
2726
2727
2728	# IF REQUIRED, START WITH COMPILING
2729	if [[ $do_compile = true ]]
2730	then
2731
2732
2733	if [[ -f a.out ]]
2734	then
2735
2736	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2737	printf "\n\n\n *** executable a.out found"
2738	printf "\n no compilation required \n"
2739
2740	else
2741
2742	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2743	printf "\n\n\n *** compilation starts \n$dashes\n"
2744	printf " *** compilation with make using following options:\n"
2745	printf " make depository: $make_depository"
2746	if [[ "$mopts" != "" ]]
2747	then
2748	printf " make options: $mopts\n"
2749	fi
2750	printf " compilername: $compiler_name\n"
2751	printf " compiler options: $fopts\n"
2752	printf " preprocessor directives: $cpp_options \n"
2753	printf " linker options: $lopts \n"
2754	if [[ "$modules" != "" ]]
2755	then
2756	printf " modules to be load: $modules \n"
2757	fi
2758	printf " source code files: $source_list \n"
2759
2760	if [[ $localhost = nech ]]
2761	then
2762	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\" "
2763	cp $TEMPDIR_COMPILE/a.out .
2764	[[ $? != 0 ]] && compile_error=true
2765	rm -rf $TEMPDIR_COMPILE
2766	elif [[ $localhost = ibmh ]]
2767	then
2768	printf " compiler is called via ssh on \"plogin1\" \n"
2769	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\" "
2770	[[ ! -f a.out ]] && compile_error=true
2771	continue # STATUS=1, IF a.out EXISTS
2772	elif [[ $localhost = lcflow ]]
2773	then
2774	printf " compiler is called via ssh on \"flow\" \n"
2775	/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\" "
2776	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2777	[[ "$check_for_file" = "" ]] && compile_error=true
2778	continue # STATUS=1, IF a.out EXISTS
2779	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2780	then
2781	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2782	else
2783	[[ "$init_cmds" != "" ]] && eval $init_cmds
2784	[[ "$module_calls" != "" ]] && eval $module_calls
2785	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2786	fi
2787
2788	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2789	then
2790	printf "\n +++ error occured while compiling or linking"
2791	locat=compile
2792
2793	exit
2794	else
2795	printf "$dashes\n *** compilation finished \n"
2796	fi
2797
2798	fi
2799
2800	fi
2801
2802
2803	# PROVIDE THE INPUT FILES
2804	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2805	(( i = 0 ))
2806	while (( i < iin ))
2807	do
2808	(( i = i + 1 ))
2809	if (( i == 1 ))
2810	then
2811	printf "\n\n *** providing INPUT-files:\n$dashes"
2812	fi
2813
2814
2815	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2816	if [[ "${transin[$i]}" = unavailable ]]
2817	then
2818	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2819	then
2820	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2821	printf "\n is not available!"
2822	else
2823	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2824	printf "\n is not available!"
2825	fi
2826	continue
2827	fi
2828
2829	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2830	files_for_pes=false; datentyp=file
2831	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2832	then
2833	files_for_pes=true; datentyp=directory
2834	actionin[$i]=""
2835	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2836	then
2837	actionin[$i]=""
2838	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2839	then
2840	files_for_pes=true; datentyp=directory
2841	actionin[$i]="ar"
2842	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2843	then
2844	actionin[$i]="ar"
2845	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2846	then
2847	files_for_pes=true; datentyp=directory
2848	actionin[$i]="fl"
2849	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2850	then
2851	actionin[$i]="fl"
2852	fi
2853
2854	if [[ $files_for_pes = true ]]
2855	then
2856	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2857	else
2858	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2859	fi
2860
2861	# INPUT-FILE FOR A RESTART RUN.
2862	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2863	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2864	if [[ "${actionin[$i]}" = fl ]]
2865	then
2866	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2867	if [[ $files_for_pes = false ]]
2868	then
2869	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2870	then
2871	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2872	got_tmp[$i]=true
2873	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2874	then
2875	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2876	printf "\n *** trying to use backup copy in \"$WORK\" "
2877	cp $WORK/${frelin[$i]} ${localin[$i]}
2878	else
2879	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2880	printf "\n or \"$tmp_data_catalog\" does not exist!"
2881	printf "\n *** trying to get copy from archive"
2882	actionin[$i]=ar
2883	fi
2884	else
2885	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2886	then
2887	mkdir ${localin[$i]}
2888	cd $tmp_data_catalog/${frelin[$i]}
2889	for file in $(ls *)
2890	do
2891	ln $file $TEMPDIR/${localin[$i]}
2892	done
2893	cd $TEMPDIR
2894	got_tmp[$i]=true
2895	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2896	then
2897	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2898	printf "\n *** trying to use backup copy in \"$WORK\" "
2899	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2900	else
2901	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2902	printf "\n or \"$tmp_data_catalog\" does not exist!"
2903	printf "\n *** trying to get copy from archive"
2904	actionin[$i]=ar
2905	fi
2906	fi
2907	fi
2908
2909
2910	# FILE IS STORED ON THE ARCHIVE SYSTEM
2911	if [[ "${actionin[$i]}" = ar ]]
2912	then
2913
2914	if [[ $files_for_pes = false ]]
2915	then
2916	printf "\n file will be restored from archive-system ($archive_system)!"
2917	else
2918	printf "\n directory will be restored from archive-system ($archive_system)!"
2919	fi
2920
2921	file_restored=false
2922
2923	if [[ $archive_system = asterix ]]
2924	then
2925	do_stagein=true
2926	(( stagein_anz = 0 ))
2927	while [[ $do_stagein = true ]]
2928	do
2929	if [[ $files_for_pes = false ]]
2930	then
2931	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2932	else
2933	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2934	fi
2935	cat STAGEIN_OUTPUT
2936	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2937	then
2938	file_restored=true
2939	do_stagein=false
2940	else
2941	(( stagein_anz = stagein_anz + 1 ))
2942	if (( stagein_anz == 10 ))
2943	then
2944	printf "\n +++ stagein stoped after 10 tries"
2945	locat=stage
2946	exit
2947	fi
2948	printf "\n +++ restoring from archive failed, trying again:"
2949	sleep 900
2950	fi
2951	done
2952	elif [[ $archive_system = DMF ]]
2953	then
2954	if [[ $files_for_pes = false ]]
2955	then
2956	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2957	locat=DMF
2958	exit
2959	else
2960	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2961	cp -r $ARCHIVE/${frelin[$i]} $PWD
2962	file_restored=true
2963	fi
2964	elif [[ $archive_system = tivoli ]]
2965	then
2966	if [[ $files_for_pes = false ]]
2967	then
2968	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2969	else
2970	(( inode = 0 ))
2971	while (( inode < nodes ))
2972	do
2973	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2974	(( inode = inode + 1 ))
2975	done
2976	fi
2977	file_restored=true
2978	elif [[ $archive_system = ut ]]
2979	then
2980	if [[ $files_for_pes = false ]]
2981	then
2982	cp $UT/${frelin[$i]} .
2983	else
2984	(( inode = 0 ))
2985	while (( inode < nodes ))
2986	do
2987	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2988	(( inode = inode + 1 ))
2989	done
2990	fi
2991	file_restored=true
2992	else
2993	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2994	locat=rearchive
2995	exit
2996	fi
2997
2998	if [[ $file_restored = true ]]
2999	then
3000
3001	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3002	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3003	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3004	if [[ $files_for_pes = false ]]
3005	then
3006	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3007	else
3008	mkdir $tmp_data_catalog/${frelin[$i]}
3009	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3010	fi
3011	got_tmp[$i]=true
3012
3013	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3014	mv ${frelin[$i]} ${localin[$i]}
3015
3016	fi
3017	fi
3018
3019
3020	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3021	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3022	then
3023
3024	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3025	then
3026
3027	# FILE COPIES ARE PROVIDED FOR ALL CORES
3028	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3029	printf "\n file will be provided for $numprocs processors"
3030	mkdir ${localin[$i]}
3031	ival=$numprocs
3032	(( ii = 0 ))
3033	while (( ii <= ival-1 ))
3034	do
3035	if (( ii < 10 ))
3036	then
3037	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3038	elif (( ii < 100 ))
3039	then
3040	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3041	elif (( ii < 1000 ))
3042	then
3043	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3044	else
3045	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3046	fi
3047	(( ii = ii + 1 ))
3048	done
3049
3050	else
3051
3052	if [[ $files_for_pes = true ]]
3053	then
3054
3055	# PROVIDE FILES FOR EACH CORE
3056	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3057	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3058	printf "\n providing $numprocs files for the respective processors"
3059	mkdir ${localin[$i]}
3060	if [[ $link_local_input = true ]]
3061	then
3062	printf " using ln -f\n"
3063	cd ${absnamein[$i]}
3064	for file in $(ls *)
3065	do
3066	ln -f $file ${localin[$i]}
3067	done
3068	cd $TEMPDIR
3069	fi
3070
3071	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3072	if [[ ! -f "${localin[$i]}/_0000" ]]
3073	then
3074	if [[ $link_local_input = true ]]
3075	then
3076	printf " ln failed for .../_0000, using cp...\n"
3077	fi
3078	cp -r ${absnamein[$i]}/* ${localin[$i]}
3079	fi
3080
3081	else
3082
3083	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3084	if [[ $link_local_input = true ]]
3085	then
3086	printf " using ln -f\n"
3087	ln -f ${absnamein[$i]} ${localin[$i]}
3088	fi
3089	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3090	if [[ ! -f "${localin[$i]}" ]]
3091	then
3092	if [[ $link_local_input = true ]]
3093	then
3094	printf " ln failed, using cp...\n"
3095	fi
3096	cp ${absnamein[$i]} ${localin[$i]}
3097	fi
3098	fi
3099	fi
3100	fi
3101
3102	done
3103	if (( i != 0 ))
3104	then
3105	printf "\n$dashes\n *** all INPUT-files provided \n"
3106	fi
3107
3108
3109	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3110	(( i = 0 ))
3111	while (( i < iic ))
3112	do
3113	(( i = i + 1 ))
3114	if (( i == 1 ))
3115	then
3116	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3117	fi
3118	printf "\n >>> ${in_command[$i]}"
3119	eval ${in_command[$i]}
3120	if (( i == iic ))
3121	then
3122	printf "\n$dashes\n"
3123	fi
3124	done
3125
3126
3127	# SET THE REMAINING CPU-TIME
3128	cpurest=${cpumax}.
3129
3130
3131	# START DVR STREAMING SERVER
3132	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3133	then
3134	if [[ "$dvr_server" != "" ]]
3135	then
3136
3137	printf "\n\n *** preparing the dvr streaming server configuration file"
3138
3139	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3140	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3141	if [[ "$running_dvrserver_id" != "" ]]
3142	then
3143
3144	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3145	printf "\n This server is used instead starting a new one!"
3146	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3147
3148	else
3149
3150	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3151	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3152	then
3153	cp ${PALM_BIN}/.dvrserver.config .
3154
3155	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3156	user_id=`id -u`
3157	group_id=`id -g`
3158
3159	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3160	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3161	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3162	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3163	mv .dvrserver.3 .dvrserver.config
3164	rm .dvrserver.1 .dvrserver.2
3165
3166	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3167	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3168	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3169	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3170	local_dvrserver_running=.TRUE.
3171	else
3172	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3173	printf "\n \"$PALM_BIN\" "
3174	locat=dvr
3175	exit
3176	fi
3177
3178	fi
3179
3180	else
3181	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3182	fi
3183	fi
3184
3185
3186	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3187	# (FILE ENVPAR WILL BE READ BY PALM)
3188	cat > ENVPAR << %%END%%
3189	&envpar run_identifier = '$fname', host = '$localhost',
3190	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3191	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3192	maximum_cpu_time_allowed = ${cpumax}.,
3193	revision = '$global_revision',
3194	local_dvrserver_running = $local_dvrserver_running,
3195	batch_job = $batch_job /
3196
3197	%%END%%
3198
3199
3200	# STARTING THE EXECUTABLE
3201	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3202	PATH=$PATH:$TEMPDIR
3203
3204	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3205	if [[ "$mpi_debug" = true ]]
3206	then
3207	export MPI_CHECK_ARGS=1
3208	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3209	fi
3210
3211	if [[ "$totalview" = true ]]
3212	then
3213	printf "\n *** totalview debugger will be used"
3214	tv_opt="-tv"
3215	else
3216	tv_opt=""
3217	fi
3218
3219	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3220	then
3221	if [[ "$ENVIRONMENT" = BATCH ]]
3222	then
3223	continue
3224	fi
3225	if [[ $localhost = ibmh ]]
3226	then
3227
3228	# SETUP THE IBM MPI ENVIRONMENT
3229	export MP_SHARED_MEMORY=yes
3230	export AIXTHREADS_SCOPE=S
3231	export OMP_NUM_THREADS=$threads_per_task
3232	export AUTHSTATE=files
3233	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3234
3235	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3236	export MP_ADAPTER_USE=shared
3237	export MP_CPU_USE=multiple
3238	export MP_TIMEOUT=1200
3239
3240	unset MP_TASK_AFFINITY
3241
3242	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3243	#(( ii = 1 ))
3244	#while (( ii <= $numprocs ))
3245	#do
3246	# echo $localhost_realname >> hostfile
3247	# (( ii = ii + 1 ))
3248	#done
3249	#export MP_HOSTFILE=hostfile
3250
3251	if [[ "$LOADLBATCH" = yes ]]
3252	then
3253	totalview poe a.out $ROPTS
3254	else
3255	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3256	export TVDSVRLAUNCHCMD=ssh
3257	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3258	fi
3259
3260	fi # END DEBUG MODE
3261
3262	else
3263
3264	# NORMAL EXECUTION
3265	if [[ -n $numprocs ]]
3266	then
3267
3268	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3269	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3270	then
3271
3272	# SETUP THE IBM MPI ENVIRONMENT
3273	if [[ $host != ibmh && $host != ibmkisti ]]
3274	then
3275	export MP_SHARED_MEMORY=yes
3276	export AIXTHREAD_SCOPE=S
3277	export OMP_NUM_THREADS=$threads_per_task
3278	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3279	export AUTHSTATE=files
3280	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3281	# export MP_PRINTENV=yes
3282
3283	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3284	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3285	export MP_WAIT_MODE=poll
3286	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3287	fi
3288
3289	if [[ $host = ibmkisti ]]
3290	then
3291	export LANG=en_US
3292	export MP_SHARED_MEMORY=yes
3293	if [[ $threads_per_task = 1 ]]
3294	then
3295	export MP_SINGLE_THREAD=yes
3296	export MEMORY_AFFINITY=MCM
3297	else
3298	export OMP_NUM_THREADS=$threads_per_task
3299	fi
3300	fi
3301
3302	if [[ "$LOADLBATCH" = yes ]]
3303	then
3304	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3305	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3306	then
3307	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3308	else
3309	if [[ $run_coupled_model = false ]]
3310	then
3311	if [[ "$ocean_file_appendix" = true ]]
3312	then
3313	echo "precursor_ocean" > runfile_atmos
3314	else
3315	echo "precursor_atmos" > runfile_atmos
3316	fi
3317	else
3318	(( iia = $numprocs_atmos / $threads_per_task ))
3319	(( iio = $numprocs_ocean / $threads_per_task ))
3320	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3321	printf "\n using $coupled_mode coupling"
3322	printf "\n\n"
3323	echo "coupled_run $iia $iio" > runfile_atmos
3324	fi
3325	poe ./a.out $ROPTS < runfile_atmos
3326	fi
3327	else
3328	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3329	then
3330	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3331	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3332	then
3333	if [[ -f $hostfile ]]
3334	then
3335	cp $hostfile hostfile
3336	else
3337	(( ii = 1 ))
3338	while (( ii <= $numprocs ))
3339	do
3340	echo $localhost_realname >> hostfile
3341	(( ii = ii + 1 ))
3342	done
3343	fi
3344	export MP_HOSTFILE=hostfile
3345	if [[ $run_coupled_model = false ]]
3346	then
3347	if [[ "$ocean_file_appendix" = true ]]
3348	then
3349	echo "precursor_ocean" > runfile_atmos
3350	else
3351	echo "precursor_atmos" > runfile_atmos
3352	fi
3353	else
3354	(( iia = $numprocs_atmos / $threads_per_task ))
3355	(( iio = $numprocs_ocean / $threads_per_task ))
3356	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3357	printf "\n using $coupled_mode coupling"
3358	printf "\n\n"
3359	echo "coupled_run $iia $iio" > runfile_atmos
3360	fi
3361
3362	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3363
3364	else
3365	if [[ "$host_file" = "" ]]
3366	then
3367	printf "\n +++ no hostfile given in configuration file"
3368	locat=config_file
3369	exit
3370	else
3371	eval host_file=$host_file
3372	fi
3373	export MP_HOSTFILE=$host_file
3374	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3375	fi
3376	fi
3377	elif [[ $host = nech ]]
3378	then
3379	(( ii = nodes ))
3380	if [[ $ii = 1 ]]
3381	then
3382	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3383	export MPIPROGINF=YES
3384	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3385	echo "*** execution on single node with mpirun"
3386	mpirun -np $numprocs ./a.out $ROPTS
3387	else
3388	(( i = 0 ))
3389	while (( i < ii ))
3390	do
3391	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3392	(( i = i + 1 ))
3393	done
3394
3395	echo "#!/bin/sh" > mpi_exec_shell
3396	echo " " >> mpi_exec_shell
3397	echo "set -u" >> mpi_exec_shell
3398	echo "F_ERRCNT=0" >> mpi_exec_shell
3399	echo "MPIPROGINV=YES" >> mpi_exec_shell
3400	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3401	echo "cpurest=$cpurest" >> mpi_exec_shell
3402	echo "fname=$fname" >> mpi_exec_shell
3403	echo "localhost=$localhost" >> mpi_exec_shell
3404	echo "return_addres=$return_addres" >> mpi_exec_shell
3405	echo "return_username=$return_username" >> mpi_exec_shell
3406	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3407	echo "write_binary=$write_binary" >> mpi_exec_shell
3408	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3409	echo " " >> mpi_exec_shell
3410	echo "export F_ERRCNT" >> mpi_exec_shell
3411	echo "export MPIPROGINV" >> mpi_exec_shell
3412	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3413	echo "export cpurest" >> mpi_exec_shell
3414	echo "export fname" >> mpi_exec_shell
3415	echo "export localhost" >> mpi_exec_shell
3416	echo "export return_addres" >> mpi_exec_shell
3417	echo "export return_username" >> mpi_exec_shell
3418	echo "export tasks_per_node" >> mpi_exec_shell
3419	echo "export write_binary" >> mpi_exec_shell
3420	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3421	echo " " >> mpi_exec_shell
3422	echo "exec ./a.out" >> mpi_exec_shell
3423
3424	chmod u+x mpi_exec_shell
3425	export MPIPROGINF=YES
3426	mpirun -f multinode_config &
3427	wait
3428
3429	fi
3430	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3431	then
3432
3433	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3434	# DOES NOT EXIST
3435	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3436	then
3437	if [[ -f $hostfile ]]
3438	then
3439	cp $hostfile hostfile
3440	(( ii = $numprocs / $threads_per_task ))
3441	else
3442	(( ii = 1 ))
3443	while (( ii <= $numprocs / $threads_per_task ))
3444	do
3445	echo $localhost_realname >> hostfile
3446	(( ii = ii + 1 ))
3447	done
3448	fi
3449	eval zeile=\"`head -n $ii hostfile`\"
3450	printf "\n *** running on: $zeile"
3451	fi
3452
3453	(( ii = $numprocs / $threads_per_task ))
3454	export OMP_NUM_THREADS=$threads_per_task
3455
3456	if [[ $threads_per_task != 1 ]]
3457	then
3458	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3459	# MAY ABORT
3460	ulimit -s unlimited
3461	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3462	fi
3463	if [[ $run_coupled_model = false ]]
3464	then
3465	if [[ "$ocean_file_appendix" = true ]]
3466	then
3467	echo "precursor_ocean" > runfile_atmos
3468	else
3469	echo "precursor_atmos" > runfile_atmos
3470	fi
3471	printf "\n\n"
3472
3473	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3474	then
3475	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3476	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3477	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3478	elif [[ $host = lccrayf ]]
3479	then
3480	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3481	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3482	then
3483	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3484	elif [[ $host = lcflow ]]
3485	then
3486	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3487	elif [[ $host = lcsb ]]
3488	then
3489	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3490	elif [[ $host = lckiaps ]]
3491	then
3492	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3493	elif [[ $host = lckyu* ]]
3494	then
3495	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3496	else
3497	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3498	fi
3499	else
3500
3501	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3502	(( iia = $numprocs_atmos / $threads_per_task ))
3503	(( iio = $numprocs_ocean / $threads_per_task ))
3504	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3505	printf "\n using $coupled_mode coupling"
3506	printf "\n\n"
3507
3508	if [[ $coupled_mode = "mpi2" ]]
3509	then
3510	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3511	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3512
3513	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3514	then
3515
3516	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3517	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3518
3519	else
3520	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3521	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3522	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3523	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3524	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3525	fi
3526	wait
3527
3528	else
3529
3530	echo "coupled_run $iia $iio" > runfile_atmos
3531
3532	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3533	then
3534
3535	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3536
3537	elif [[ $host = lck \|\| $host = lckordi ]]
3538	then
3539
3540	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3541
3542	elif [[ $host = lckyu* ]]
3543	then
3544
3545	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3546
3547	fi
3548	wait
3549	fi
3550
3551	fi
3552
3553	elif [[ $host = lckyoto ]]
3554	then
3555	set -xv
3556	export P4_RSHCOMMAND=plesh
3557	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3558	if [[ "$ENVIRONMENT" = BATCH ]]
3559	then
3560	if [[ "$cond2" = fujitsu ]]
3561	then
3562	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3563	elif [[ "cond2" = pgi ]]
3564	then
3565	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3566	else
3567	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3568	fi
3569	else
3570	if [[ "$cond2" = "" ]]
3571	then
3572	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3573	else
3574	mpirun -np $numprocs ./a.out $ROPTS
3575	fi
3576	fi
3577	set +xv
3578
3579	elif [[ $host = lctit ]]
3580	then
3581	export OMP_NUM_THREADS=$threads_per_task
3582	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3583	if [[ "$threads_per_task" != 1 ]]
3584	then
3585	export MV2_ENABLE_AFFINITY=0
3586	fi
3587	echo "----- PBS_NODEFILE content:"
3588	cat $PBS_NODEFILE
3589	echo "-----"
3590	(( ii = $numprocs / $threads_per_task ))
3591	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3592	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3593	else
3594	mpprun -n $numprocs a.out $ROPTS
3595	fi
3596	else
3597	a.out $ROPTS
3598	fi
3599	fi
3600
3601	if [[ $? != 0 ]]
3602	then
3603
3604	# ABORT IN CASE OF RUNTIME ERRORS
3605	printf "\n +++ runtime error occured"
3606	locat=execution
3607	exit
3608
3609	else
3610
3611	printf "\n$dashes\n *** execution finished \n"
3612
3613	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3614	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3615	if [[ "$dvrserver_id" != "" ]]
3616	then
3617	kill $dvrserver_id
3618	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3619
3620	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3621	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3622	if [[ -d DATA_DVR ]]
3623	then
3624
3625	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3626	# DIRECTORY
3627	cp .dvrserver.config DATA_DVR
3628
3629	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3630	# SEQUENCE MODE DATA TOO)
3631	process_dvr_output -d DATA_DVR -f $fname -s
3632
3633	else
3634
3635	# PROCESS THE LOCAL OUTPUT
3636	process_dvr_output -l -d DATA_DVR -f $fname
3637
3638	fi
3639
3640	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3641	then
3642
3643	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3644	process_dvr_output -l -d DATA_DVR -f $fname
3645
3646	fi
3647	fi
3648
3649
3650
3651	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3652	# BY EACH CORE INTO ONE FILE
3653	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3654	then
3655	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3656	printf "\n 2d- and/or 3d-data may be incomplete!"
3657	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3658	elif [[ "$combine_plot_fields" == true ]]
3659	then
3660	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3661	then
3662	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3663	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3664	else
3665	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3666	combine_plot_fields${block}.x
3667	fi
3668	else
3669
3670	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3671	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3672	# ??? koennen wir das streichen ???
3673	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3674	fi
3675
3676
3677
3678	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3679	(( i = 0 ))
3680	while (( i < ioc ))
3681	do
3682	(( i = i + 1 ))
3683	if (( i == 1 ))
3684	then
3685	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3686	fi
3687	printf "\n >>> ${out_command[$i]}"
3688	eval ${out_command[$i]}
3689	if (( i == ioc ))
3690	then
3691	printf "\n$dashes\n"
3692	fi
3693	done
3694
3695
3696	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3697	if [[ $do_trace = true ]]
3698	then
3699	printf "\n\n"
3700	ls -al
3701	fi
3702
3703
3704
3705	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3706	(( i = 0 ))
3707	while (( i < iout ))
3708	do
3709	(( i = i + 1 ))
3710	if (( i == 1 ))
3711	then
3712	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3713	fi
3714
3715	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3716	files_for_pes=false; filetyp=file
3717	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3718	then
3719	files_for_pes=true; filetyp=directory
3720	actionout[$i]=""
3721	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3722	then
3723	actionout[$i]=""
3724	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3725	then
3726	files_for_pes=true; filetyp=directory
3727	actionout[$i]="ar"
3728	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3729	then
3730	actionout[$i]="ar"
3731	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3732	then
3733	files_for_pes=true; filetyp=directory
3734	actionout[$i]="fl"
3735	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3736	then
3737	actionout[$i]="fl"
3738	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3739	then
3740	files_for_pes=true; filetyp=directory
3741	actionout[$i]="tr"
3742	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3743	then
3744	actionout[$i]="tr"
3745	fi
3746
3747	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3748	then
3749	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3750	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3751	then
3752	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3753	else
3754
3755
3756	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3757	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3758	if [[ "${actionout[$i]}" = tr ]]
3759	then
3760	if [[ $localhost != $fromhost ]]
3761	then
3762	if [[ $files_for_pes = false ]]
3763	then
3764	cps=""
3765	cst=""
3766	else
3767	cps=-c
3768	cst="/"
3769	fi
3770	if [[ $localhost = nech ]]
3771	then
3772
3773	# TRANSFER IN SEPERATE JOB
3774	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3775	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3776	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3777	if [[ $files_for_pes = false ]]
3778	then
3779	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3780	else
3781	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3782	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3783	fi
3784
3785	echo "set -x" > transfer_${localout[$i]}
3786	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3787
3788	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3789	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3790	printf "\n or higher cycle\n"
3791	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]}
3792
3793	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3794
3795	if [[ $localhost = nech ]]
3796	then
3797	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3798	else
3799	if [[ "$LOGNAME" = b323013 ]]
3800	then
3801	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3802	else
3803	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3804	fi
3805	fi
3806
3807	else
3808
3809	# TRANSFER WITHIN THIS JOB
3810	transfer_failed=false
3811	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3812	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3813	if [[ $localhost = lccrayb ]]
3814	then
3815	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]}"
3816	elif [[ $localhost = lccrayh ]]
3817	then
3818	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]}"
3819	else
3820	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3821	fi
3822	[[ $? != 0 ]] && transfer_failed=true
3823
3824	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3825	if [[ $transfer_failed = true ]]
3826	then
3827	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3828	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3829
3830	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3831	eval local_catalog=${pathout[$i]}
3832	if [[ ! -d $local_catalog ]]
3833	then
3834	printf " *** local directory does not exist. Trying to create:\n"
3835	printf " $local_catalog \n"
3836	mkdir -p $local_catalog
3837	fi
3838	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3839	transfer_problems=true
3840	fi
3841	fi
3842	else
3843
3844	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3845	actionout[$i]=""
3846	fi
3847	fi
3848
3849
3850	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3851	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3852	if [[ "${actionout[$i]}" = tra ]]
3853	then
3854	if [[ $localhost != $fromhost ]]
3855	then
3856	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3857	then
3858
3859	# TRANSFER IN SEPERATE JOB
3860	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3861	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3862	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3863	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3864
3865	echo "set -x" > transfer_${localout[$i]}
3866	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3867
3868	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3869	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3870	printf "\n or higher cycle\n"
3871	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]}
3872
3873	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3874
3875	if [[ $localhost = nech ]]
3876	then
3877	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3878	else
3879	if [[ $LOGNAME = b323013 ]]
3880	then
3881	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3882	else
3883	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3884	fi
3885	fi
3886
3887	else
3888
3889	# TRANSFER WITHIN THIS JOB
3890	transfer_failed=false
3891	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3892	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3893	if [[ $localhost = lccrayb ]]
3894	then
3895	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]}"
3896	elif [[ $localhost = lccrayh ]]
3897	then
3898	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]}"
3899	else
3900	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3901	fi
3902	[[ $? != 0 ]] && transfer_failed=true
3903
3904	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3905	if [[ $transfer_failed = true ]]
3906	then
3907	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3908	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3909
3910	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3911	eval local_catalog=${pathout[$i]}
3912	if [[ ! -d $local_catalog ]]
3913	then
3914	printf " *** local directory does not exist. Trying to create:\n"
3915	printf " $local_catalog \n"
3916	mkdir -p $local_catalog
3917	fi
3918
3919	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3920	transfer_problems=true
3921	fi
3922	fi
3923	else
3924
3925	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3926	actionout[$i]=a
3927	fi
3928	fi
3929
3930
3931	# OUTPUT-FILE FOR A RESTART-RUN.
3932	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3933	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3934	# AS LAST ACTION, ARCHIVING IS INITIATED.
3935	if [[ "${actionout[$i]}" = fl ]]
3936	then
3937	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3938	chmod g+rx $tmp_data_catalog
3939	if [[ $files_for_pes = false ]]
3940	then
3941	printf "\n >>> OUTPUT: ${localout[$i]} to"
3942	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3943	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3944	else
3945	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3946	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3947	mkdir $tmp_data_catalog/${frelout[$i]}
3948	cd ${localout[$i]}
3949	for file in $(ls *)
3950	do
3951	ln -f $file $tmp_data_catalog/${frelout[$i]}
3952	done
3953	cd $TEMPDIR
3954	fi
3955
3956
3957	# CREATE AND SUBMIT ARCHIVING-JOB
3958	if [[ $store_on_archive_system = true ]]
3959	then
3960
3961	if [[ $archive_system = asterix ]]
3962	then
3963	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3964	if [[ $files_for_pes = false ]]
3965	then
3966	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3967	else
3968	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3969	fi
3970	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3971	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3972	echo "then" >> archive_${frelout[$i]}
3973	echo " do_stageout=false" >> archive_${frelout[$i]}
3974	echo "else" >> archive_${frelout[$i]}
3975	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3976	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3977	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3978	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3979	if [[ $files_for_pes = false ]]
3980	then
3981	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3982	else
3983	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3984	fi
3985	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3986	echo "fi" >> archive_${frelout[$i]}
3987	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3988	elif [[ $archive_system = DMF ]]
3989	then
3990	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3991	if [[ $files_for_pes = false ]]
3992	then
3993	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3994	locat=DMF
3995	exit
3996	else
3997	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3998	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3999	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4000	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4001	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4002	fi
4003	elif [[ $archive_system = tivoli ]]
4004	then
4005	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4006	if [[ $files_for_pes = false ]]
4007	then
4008	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4009	echo "set -x" >> archive_${frelout[$i]}
4010	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4011	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4012	else
4013
4014	echo "set -x" >> archive_${frelout[$i]}
4015	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4016	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4017	cd $tmp_data_catalog
4018	all_files=`ls -1 ${frelout[$i]}/*`
4019	cd - > /dev/null
4020	(( inode = 0 ))
4021	(( tp1 = tasks_per_node + 1 ))
4022	while (( inode < nodes ))
4023	do
4024	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4025	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4026	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4027	(( inode = inode + 1 ))
4028	done
4029	fi
4030	elif [[ $archive_system = ut ]]
4031	then
4032	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4033	if [[ $files_for_pes = false ]]
4034	then
4035	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4036	echo "set -x" >> archive_${frelout[$i]}
4037	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4038	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4039	else
4040
4041	echo "set -x" >> archive_${frelout[$i]}
4042	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4043	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4044	cd $tmp_data_catalog
4045	all_files=`ls -1 ${frelout[$i]}/*`
4046	cd - > /dev/null
4047	(( inode = 0 ))
4048	(( tp1 = tasks_per_node + 1 ))
4049	while (( inode < nodes ))
4050	do
4051	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4052	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4053	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4054	(( inode = inode + 1 ))
4055	done
4056	fi
4057	elif [[ $archive_system = none ]]
4058	then
4059	printf " +++ archiving on $localhost not available!\n"
4060	fi
4061
4062	if [[ $archive_system != none ]]
4063	then
4064	if [[ $localhost = nech ]]
4065	then
4066	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4067	fi
4068	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4069	fi
4070	else
4071	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4072	fi
4073
4074
4075	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4076	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4077	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4078	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4079	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4080	if [[ $files_for_pes = false ]]
4081	then
4082	cat /dev/null > ${pathout[$i]}
4083	else
4084	mkdir -p ${pathout[$i]}
4085	fi
4086
4087	fi
4088
4089
4090	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4091	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4092	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4093	if [[ "${actionout[$i]}" = ar ]]
4094	then
4095	if [[ $files_for_pes = false ]]
4096	then
4097	printf "\n >>> OUTPUT: ${localout[$i]} to"
4098	printf "\n ${pathout[$i]}"
4099	printf "\n File will be copied to archive-system ($archive_system) !\n"
4100	else
4101	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4102	printf "\n ${pathout[$i]}"
4103	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4104	fi
4105	mv ${localout[$i]} ${frelout[$i]}
4106
4107	file_saved=false
4108
4109	if [[ $archive_system = asterix ]]
4110	then
4111	do_stageout=true
4112	(( stageout_anz = 0 ))
4113	while [[ $do_stageout = true ]]
4114	do
4115	if [[ $files_for_pes = false ]]
4116	then
4117	stageout ${frelout[$i]} > STAGE_OUTPUT
4118	else
4119	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4120	fi
4121	cat STAGE_OUTPUT
4122	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4123	then
4124	file_saved=true
4125	do_stageout=false
4126	else
4127	if [[ $files_for_pes = false ]]
4128	then
4129	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4130	else
4131	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4132	fi
4133	(( stageout_anz = stageout_anz + 1 ))
4134	if (( stageout_anz == 10 ))
4135	then
4136	printf "\n +++ stoped after 10 unsuccessful tries!"
4137	archive_save=false
4138	do_stageout=false
4139	else
4140	printf "\n *** new try to store on archive after 15 min:"
4141	sleep 900
4142	fi
4143	fi
4144	done
4145	elif [[ $archive_system = DMF ]]
4146	then
4147	if [[ $files_for_pes = false ]]
4148	then
4149	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4150	locat=DMF
4151	exit
4152	else
4153	rm -rf $ARCHIVE/${frelout[$i]}
4154	cp -r ${frelout[$i]} $ARCHIVE
4155	fi
4156	file_saved=true
4157	elif [[ $archive_system = tivoli ]]
4158	then
4159	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4160	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4161	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4162	# WHEN THE ARCHIVE-JOB IS EXECUTED
4163	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4164	chmod g+rx $tmp_data_catalog
4165	if [[ $files_for_pes = false ]]
4166	then
4167	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4168	else
4169	mkdir $tmp_data_catalog/${frelout[$i]}
4170	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4171	fi
4172
4173	# GENERATE AND SUBMIT BATCH-JOB
4174	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4175	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4176	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4177	if [[ $files_for_pes = false ]]
4178	then
4179	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4180	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4181	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4182	else
4183	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4184	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4185	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4186	fi
4187
4188	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4189	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4190	file_saved=true
4191
4192	elif [[ $archive_system = ut ]]
4193	then
4194	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4195	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4196	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4197	# WHEN THE ARCHIVE-JOB IS EXECUTED
4198	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4199	chmod g+rx $tmp_data_catalog
4200	if [[ $files_for_pes = false ]]
4201	then
4202	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4203	else
4204	mkdir $tmp_data_catalog/${frelout[$i]}
4205	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4206	fi
4207
4208	# GENERATE AND SUBMIT BATCH-JOB
4209	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4210	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4211	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4212	if [[ $files_for_pes = false ]]
4213	then
4214	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4215	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4216	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4217	else
4218	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4219	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4220	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4221	fi
4222
4223	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4224	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4225	file_saved=true
4226
4227	else
4228	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4229	archive_save=false
4230	fi
4231
4232	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4233	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4234	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4235	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4236	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4237	if [[ $file_saved = true ]]
4238	then
4239	if [[ $files_for_pes = false ]]
4240	then
4241	cat /dev/null > ${pathout[$i]}
4242	else
4243	mkdir -p ${pathout[$i]}
4244	fi
4245	fi
4246
4247	fi
4248
4249	# APPEND ON THIS MACHINE
4250	if [[ "${actionout[$i]}" = "a" ]]
4251	then
4252	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4253	then
4254	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4255	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4256	else
4257	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4258	cat ${localout[$i]} >> ${pathout[$i]}
4259	fi
4260	fi
4261
4262	# COPY ON THIS MACHINE
4263	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4264	# ON DIFFERENT FILE-SYSTEMS
4265	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4266	then
4267
4268	# COPY IN CASE OF RUNS ON SINGLE CORES
4269	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4270	then
4271	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4272	if [[ $link_local_output = true ]]
4273	then
4274	printf " using ln -f\n"
4275	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4276	fi
4277	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4278	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4279	then
4280	if [[ $link_local_output = true ]]
4281	then
4282	printf " ln failed, using cp...\n"
4283	fi
4284	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4285	fi
4286	else
4287	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4288	if [[ $link_local_output = true ]]
4289	then
4290	printf " using ln -f\n"
4291	ln -f ${localout[$i]} ${pathout[$i]}
4292	fi
4293	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4294	if [[ ! -f "${pathout[$i]}" ]]
4295	then
4296	if [[ $link_local_output = true ]]
4297	then
4298	printf " ln failed, using cp...\n"
4299	fi
4300	cp ${localout[$i]} ${pathout[$i]}
4301	fi
4302	fi
4303
4304	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4305	then
4306
4307	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4308	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4309	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4310	if [[ $link_local_output = true ]]
4311	then
4312	printf " using ln -f\n"
4313	mkdir ${pathout[$i]}
4314	cd ${localout[$i]}
4315	for file in $(ls *)
4316	do
4317	ln -f $file ${pathout[$i]}
4318	done
4319	cd $TEMPDIR
4320	fi
4321
4322	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4323	if [[ ! -f "${pathout[$i]}/_0000" ]]
4324	then
4325	if [[ $link_local_output = true ]]
4326	then
4327	printf " ln failed for .../_0000, using cp...\n"
4328	fi
4329	cp -r ${localout[$i]} ${pathout[$i]}
4330	fi
4331
4332	fi
4333	fi
4334	done
4335	if (( i != 0 ))
4336	then
4337	if [[ $transfer_problems = true ]]
4338	then
4339	printf "\n$dashes\n *** OUTPUT-files saved"
4340	printf "\n +++ WARNING: some data transfers failed! \n"
4341	else
4342	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4343	fi
4344	fi
4345
4346
4347	# IF REQUIRED, START A RESTART-JOB
4348	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4349	if [[ -f CONTINUE_RUN ]]
4350	then
4351
4352	if [[ $archive_save = true ]]
4353	then
4354
4355	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4356	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4357	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4358	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4359	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4360	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4361	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4362	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4363	then
4364	mc=`echo $mc \| sed 's/#/f/g'`
4365	fi
4366
4367
4368	# START THE RESTART-JOB
4369	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4370	echo " $mc"
4371	printf "\n$dashes\n"
4372	if [[ $localhost != $fromhost ]]
4373	then
4374
4375	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4376	then
4377	echo "*** ssh will be used to initiate restart-runs!"
4378	echo " return_addres=\"$return_addres\" "
4379	echo " return_username=\"$return_username\" "
4380	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4381	then
4382	if [[ $localhost = ibmh ]]
4383	then
4384	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4385	elif [[ $localhost = lccrayb ]]
4386	then
4387	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4388	elif [[ $localhost = lccrayh ]]
4389	then
4390	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4391
4392	else
4393	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4394	fi
4395	else
4396	if [[ $localhost = ibmkisti ]]
4397	then
4398	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\" "
4399	elif [[ $localhost = lcflow ]]
4400	then
4401	/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 "
4402	elif [[ $localhost = lccrayb ]]
4403	then
4404	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\" "
4405	elif [[ $localhost = lccrayh ]]
4406	then
4407	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\" "
4408	else
4409	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4410	fi
4411	fi
4412	else
4413	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4414	locat=restart; exit
4415	fi
4416
4417	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4418	if [[ $queue = special1q ]]
4419	then
4420	sleep 120
4421	else
4422	sleep 30
4423	fi
4424
4425	else
4426
4427	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4428	# USING SSH)
4429	cd $LOCAL_PWD
4430	if [[ $localhost = lckyuh ]]
4431	then
4432	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4433	printf "\n please restart job manually using command:\n"
4434	printf "\n \"$mc\" "
4435	else
4436	eval $mc # THE ' MUST BE EVALUATED
4437	fi
4438	cd - > /dev/null
4439	fi
4440	if [[ $localhost = lckyuh ]]
4441	then
4442	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4443	else
4444	printf "\n$dashes\n *** restart-run initiated \n"
4445	fi
4446
4447
4448	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4449	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4450	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4451	# MAY BE VERY HUGE)
4452	(( i = 0 ))
4453	while (( i < iin ))
4454	do
4455	(( i = i + 1 ))
4456	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4457	then
4458	rm -r $tmp_data_catalog/${frelin[$i]}
4459	fi
4460	done
4461
4462	else
4463
4464	printf "\n +++ no restart-run possible, since errors occured"
4465	printf "\n during the archive process"
4466	fi
4467
4468	fi
4469
4470
4471
4472	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4473	if [[ "$email_notification" != "none" ]]
4474	then
4475
4476	if [[ $localhost != $fromhost ]]
4477	then
4478	if [[ -f CONTINUE_RUN ]]
4479	then
4480	echo "PALM restart run necessary" > email_text
4481	echo "description header of actual run:" >> email_text
4482	cat CONTINUE_RUN >> email_text
4483	echo "mrun-command to restart:" >> email_text
4484	echo "$mc" >> email_text
4485	else
4486	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4487	fi
4488	mail $email_notification < email_text
4489	printf "\n *** email notification sent to \"$email_notification\" "
4490	fi
4491	fi
4492
4493
4494
4495	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4496	cd $HOME
4497	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4498
4499	else
4500
4501
4502	# PREPARING ACTIONS,
4503	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4504
4505	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4506	mrun_com="$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 $remote_username"
4507	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4508	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4509	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4510	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4511	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4512	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4513	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4514	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4515	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4516	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4517	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4518	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4519	if [[ $use_openmp = true ]]
4520	then
4521	mrun_com=${mrun_com}" -O $threads_per_task"
4522	fi
4523	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4524	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4525	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4526	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4527	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4528	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4529	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4530	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4531	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4532	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4533	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4534	if [[ $do_remote = true ]]
4535	then
4536	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4537	fi
4538
4539
4540	# CREATE EXECUTABLE FOR BATCH JOB
4541	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4542	then
4543
4544	printf "\n *** creating the executable for batch job\n"
4545
4546	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4547	if [[ $host != $localhost ]]
4548	then
4549	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4550	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4551	locat=create_executable; exit
4552	fi
4553
4554	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4555	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4556
4557	cp $make_depository .
4558	tar -xf $make_depository > /dev/null 2>&1
4559	cp ../* . > /dev/null 2>&1
4560
4561	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4562
4563	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4564	then
4565	printf "\n +++ error occured while compiling or linking"
4566	locat=compile
4567	exit
4568	fi
4569
4570	mv a.out ..
4571	cd - > /dev/null 2>&1
4572	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4573
4574	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4575
4576	fi
4577
4578
4579	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4580	jobfile=jobfile.$RANDOM
4581
4582
4583	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4584	echo "mkdir $TEMPDIR" >> $jobfile
4585	echo "cd $TEMPDIR" >> $jobfile
4586
4587
4588	# ACTIVATE ERROR-TRACEBACK
4589	if [[ $do_trace = true ]]
4590	then
4591	echo "set -x" >> $jobfile
4592	else
4593	echo "set +vx" >> $jobfile
4594	fi
4595
4596
4597	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4598	if [[ "$init_cmds" != "" ]]
4599	then
4600	echo "$init_cmds" >> $jobfile
4601	fi
4602	if [[ "$module_calls" != "" ]]
4603	then
4604	echo "$module_calls" >> $jobfile
4605	fi
4606
4607
4608	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4609	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4610	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4611	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4612	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4613	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4614	# QUEUEING-SYSTEMS
4615	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4616	then
4617
4618	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4619	if [[ $restart_run != true ]]
4620	then
4621	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4622	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4623	fi
4624
4625	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4626	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4627	echo "set -x" >> $jobfile
4628	if [[ $host = $localhost ]]
4629	then
4630
4631	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4632	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4633	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4634	then
4635	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4636	else
4637	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4638	fi
4639
4640	else
4641	if [[ $host = ibmkisti ]]
4642	then
4643	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4644	echo "localdir=\`pwd\`" >> $jobfile
4645	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4646	elif [[ $host = lccrayb ]]
4647	then
4648	echo "localdir=\`pwd\`" >> $jobfile
4649	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4650	elif [[ $host = lccrayh ]]
4651	then
4652	echo "localdir=\`pwd\`" >> $jobfile
4653	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4654
4655	else
4656	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4657	fi
4658	fi
4659	echo "export SOURCES_COMPLETE=true" >> $jobfile
4660
4661	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4662	# WORKING DIRECTORY OF THE JOB
4663	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4664	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4665	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4666	echo "execute_mrun=true" >> $jobfile
4667	echo " " >> $jobfile
4668
4669	else
4670
4671	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4672	if [[ $do_compile = true ]]
4673	then
4674
4675	source_catalog=SOURCES_FOR_RUN_$fname
4676
4677	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4678	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4679	echo "export SOURCES_COMPLETE=true" >> $jobfile
4680	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4681
4682	for filename in $source_list
4683	do
4684	# BACKSLASH IS USED FOR MASKING
4685	echo "cat > $filename << \"%END%\"" >> $jobfile
4686	cat $source_catalog/$filename >> $jobfile
4687	echo " " >> $jobfile
4688	echo "%END%" >> $jobfile
4689	echo " " >> $jobfile
4690	done
4691
4692	# BACKSLASH IS USED FOR MASKING
4693	echo "cat > Makefile << \"%END%\"" >> $jobfile
4694	cat $source_catalog/Makefile >> $jobfile
4695	echo " " >> $jobfile
4696	echo "%END%" >> $jobfile
4697	echo " " >> $jobfile
4698
4699	echo "cd - > /dev/null" >> $jobfile
4700
4701	fi
4702
4703
4704	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4705	# BACKSLASH IS USED FOR MASKING
4706	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4707	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4708	echo "cat > $config_file << \"%END%\"" >> $jobfile
4709	if [[ $host = lckyuh ]]
4710	then
4711	# NO CROSS-COMPILER ON COMPUTE NODE
4712	sed 's/frtpx/frt/g' $config_file >> $jobfile
4713	else
4714	sed 's/#$.*//g' $config_file >> $jobfile
4715	fi
4716	echo "%END%" >> $jobfile
4717	echo " " >> $jobfile
4718
4719
4720	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4721	# BACKSLASH IS USED FOR MASKING
4722	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4723	if [[ $host = lckyuh ]]
4724	then
4725	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4726	else
4727	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4728	fi
4729	echo "%END%" >> $jobfile
4730	echo "chmod u+x $mrun_script_name" >> $jobfile
4731	echo "execute_mrun=true" >> $jobfile
4732	echo " " >> $jobfile
4733
4734	fi
4735
4736
4737	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4738	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4739	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4740	if [[ $do_remote = true ]]
4741	then
4742	(( i = 0 ))
4743	while (( i < iin ))
4744	do
4745	(( i = i + 1 ))
4746	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4747	if [[ "${transin[$i]}" = job ]]
4748	then
4749	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4750	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4751	echo " " >> $jobfile
4752	echo "%END%" >> $jobfile
4753	else
4754	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4755	fi
4756
4757	# CHECK, IF FILE COULD BE CREATED
4758	echo "if [[ \$? = 1 ]]" >> $jobfile
4759	echo "then" >> $jobfile
4760	echo " echo \" \" " >> $jobfile
4761	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4762	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4763	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4764	echo " execute_mrun=false" >> $jobfile
4765	echo "fi" >> $jobfile
4766	done
4767	fi
4768
4769	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4770	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4771	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4772	echo "LOCAL_PWD=$working_directory" >> $jobfile
4773	echo "export LOCAL_PWD" >> $jobfile
4774
4775	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4776	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4777	echo "export LOCAL_MRUN_PATH" >> $jobfile
4778
4779	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4780	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4781	then
4782	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4783	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4784	fi
4785
4786	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4787	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4788	echo "set -x" >> $jobfile
4789	echo "queue=$queue" >> $jobfile
4790	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4791	echo 'ls -al; echo `pwd`' >> $jobfile
4792	echo "cd \$HOME" >> $jobfile
4793	echo "rm -rf $TEMPDIR" >> $jobfile
4794
4795
4796
4797
4798	# START THE JOB USING SUBJOB-COMMAND
4799	if [[ $silent = false ]]
4800	then
4801	printf "\n "
4802	else
4803	printf "\n\n"
4804	fi
4805
4806	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
4807	rm -rf $jobfile
4808
4809
4810	fi # END OF REMOTE-PART

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