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source: palm/trunk/SCRIPTS/mrun @ 1612

Last change on this file since 1612 was 1610, checked in by maronga, 9 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 1610 2015-07-03 15:38:36Z maronga $
29	#
30	# 1609 2015-07-03 15:37:58Z maronga
31	# Modified the random number of the temporary working directory to match the
32	# queuing system number on HLRN-III (lccray*).
33	#
34	# 1604 2015-06-23 15:48:03Z suehring
35	# Enable coupled runs for lcmuk
36	#
37	# 1598 2015-05-29 06:45:40Z raasch
38	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
39	#
40	# 1549 2015-01-30 14:26:16Z suehring
41	# Enable interactive debug sessions with allinea debugger
42	#
43	# 1547 2015-01-29 15:09:12Z witha
44	# adjustments for ForWind computing cluster (lcflow)
45	#
46	# 1491 2014-11-12 08:12:57Z heinze
47	# correct setting of batch_job allowed for ibm-machines
48	#
49	# 1468 2014-09-24 14:06:57Z maronga
50	# Typo removed (addres->address)
51	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
52	# Added support for restart runs (remote) for lcxe6
53	#
54	# 1442 2014-07-28 07:09:10Z raasch
55	# default queues for HLRN-III (lccrayb/lccrayh) defined
56	#
57	# 1422 2014-07-02 10:01:25Z kanani
58	# automatic restarts enabled for lccrayb,
59	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
60	#
61	# 1420 2014-06-10 06:24:14Z raasch
62	# -j1 option added to aprung command for lccrayf (CSC)
63	#
64	# 1402 2014-05-09 14:25:13Z raasch
65	# batch_job added to envpar-NAMELIST
66	#
67	# 1357 2014-04-11 15:02:03Z witha
68	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
69	# possible)
70	#
71	# 1320 2014-03-20 08:40:49Z raasch
72	# check namelist file set false by default
73	#
74	# 1304 2014-03-12 10:29:42Z raasch
75	# ulimit option changed from -Ss to -s
76	#
77	# bugfix: missing "fi" in r1289
78	#
79	# 1289 2014-03-04 07:12:34Z raasch
80	# comments translated to English
81	# necriam-, fimm-, ibmy-, and sgi-specific code removed
82	# export of variables for palm and interpret_config removed
83	#
84	# 1281 2014-02-01 07:55:49Z raasch
85	# rsync-copy restricted to Cray machines, since command is unavailable on some
86	# other systems
87	#
88	# 1279 2014-01-28 12:10:14Z raasch
89	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
90	# in order to remove annoying restrictions concerning the number of processors which
91	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
92	# restriction, one of the nodes will be filled with less than the given number of
93	# tasks per node. A respective warning is given.
94	#
95	# 1274 2014-01-09 13:14:54Z heinze
96	# adjustments for lccrayh
97	#
98	# 1272 2014-01-08 10:19:32Z witha
99	# small adjustment for lcflow
100	#
101	# 1270 2013-12-16 11:05:01Z fricke
102	# call of combine_plot_fields adjusted for lccrayb/lccrayh
103	#
104	# 1255 2013-11-07 14:43:35Z raasch
105	# further adjustments for lccrayb remote access
106	#
107	# 1241 2013-10-30 11:36:58Z heinze
108	# Enable use of nudging input and input of large scale forcing from
109	# external files
110	#
111	# 1229 2013-09-20 06:55:19Z raasch
112	# further adjustments for lccrayb
113	#
114	# 1224 2013-09-16 07:27:23Z raasch
115	# first adjustments for lccrayb
116	#
117	# 1210 2013-08-14 10:58:20Z raasch
118	# fftw support added
119	#
120	# 1201 2013-07-10 16:17:59Z witha
121	# adjustments for Forwind cluster (lcflow)
122	#
123	# 1199 2013-07-05 14:52:22Z raasch
124	# adjustments for CSC Helsinki (lccrayf),
125	# executables for batch jobs can be created in advance, in order to avoid calling
126	# the compiler within the batch job (only works if batch jobs are submitted on
127	# local host)
128	#
129	# 1190 2013-06-25 09:39:21Z heinze
130	# enable use of automatic restarts for ibmh
131	# use of cluster/express queue enabled (ibmh)
132	#
133	# 1124 2013-04-09 15:46:52Z raasch
134	# variable "memory" is exported via typeset option -x, because otherwise an unknown
135	# side effect may lead to data loss while getopts is reading the script-option arguments
136	#
137	# 1122 2013-04-09 08:37:16Z heinze
138	# Bugfix: change type of variable last_char
139	#
140	# 1119 2013-04-05 15:11:19Z raasch
141	# Bugfix for setting -T option for subjob
142	#
143	# 1108 2013-03-05 07:03:32Z raasch
144	# bugfix for coupled runs on lckyut/lckyuh
145	#
146	# 1106 2013-03-04 05:31:38Z raasch
147	# --stdin argument for mpiexec on lckyuh
148	# -y and -Y settings output to header
149	#
150	# 1103 2013-02-20 02:15:53Z raasch
151	# default script runs again under ksh, because of unsolved problems with read
152	# from stdin: when bash script is called from a ksh, message "read error: 0:
153	# Resource temporarily unavailable" appears and script does not stop,
154	# further bash compatibility adjustments,
155	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
156	# on lckyuh, but mrun does not terminate and issues a warning instead
157	#
158	# 1101 2013-02-17 10:20:21Z raasch
159	# script now running under bash instead of ksh, which required small adjustments
160	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
161	# read from stdin),
162	# cross compilername on lckyuh compute nodes replaced by real compiler name
163	#
164	# 1099 2013-02-10 01:47:43Z raasch
165	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
166	# and for Forwind cluster (lcflow)
167	# small further adjustments for lckyut
168	#
169	# 1094 2013-02-03 01:52:12Z raasch
170	# explicit ssh/scp port can be set in config file with environment variable
171	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
172	# decalpha parts (yonsei) removed
173	#
174	# 2013-02-02 07:06:13Z raasch
175	# adjustments for Kyushu-University computing center (lckyut - tatara)
176	#
177	# 1083 2013-01-04 10:22:09Z maronga
178	# bugfix in parameter file check (read %cpp_options was missing)
179	#
180	# 1069 2012-11-28 16:18:43Z maronga
181	# bugfix: coupling mode was always set to mpi2, typos removed
182	#
183	# 1058 2012-11-21 07:00:35Z raasch
184	# Intel inspector (inspxe) is given the number of PEs instead of the number of
185	# nodes
186	#
187	# 1046 2012-11-09 14:38:45Z maronga
188	# code put under GPL (PALM 3.9)
189	#
190	# 21/03/94 - Siggi - first version finished
191	# 03/03/94 - Siggi - script development started
192	#
193	#--------------------------------------------------------------------------------#
194	# mrun - script for running PALM jobs
195	#--------------------------------------------------------------------------------#
196
197
198
199	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
200
201	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
202	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
203	# (TOO MANY ARGUMENTS - PROBLEM)
204	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
205
206	AddFilenames=""
207	additional_conditions=""
208	add_source_path=""
209	afname=""
210	archive_save=true
211	archive_system=none
212	check_namelist_files=false
213	combine_plot_fields=true
214	compiler_name=""
215	cond1=""
216	cond2=""
217	config_file=.mrun.config
218	coupled_dist=""
219	coupled_mode="mpi1"
220	cpp_opts=""
221	cpp_options=""
222	cpumax=0
223	cpurest=0
224	create_executable_for_batch=false
225	delete_temporary_catalog=true
226	do_batch=false
227	do_compile=true
228	do_remote=false
229	do_stagein=true
230	do_stageout=true
231	do_trace=false
232	email_notification="none"
233	exclude=""
234	executable=""
235	execution_error=false
236	fftw_inc=""
237	fftw_lib=""
238	fftw_support=false
239	fname=test
240	fromhost=""
241	global_revision=""
242	group_number=none
243	host=""
244	host_file=""
245	hp=""
246	ignore_archive_error=false
247	input_list=""
248	interpreted_config_file=""
249	job_catalog="~/job_queue"
250	job_on_file=""
251	keep_data_from_previous_run=false
252	link_local_input=false
253	link_local_output=false
254	localhost_realname=$(hostname)
255	local_dvrserver_running=.FALSE.
256	locat=normal
257	mainprog=""
258	makefile=""
259	max_par_io_str=""
260	mc=$0
261	while [[ $(echo $mc \| grep -c "/") != 0 ]]
262	do
263	mc=`echo $mc \| cut -f2- -d"/"`
264	done
265	module_calls=""
266	mrun_script_name=$mc
267	netcdf_inc=""
268	netcdf_lib=""
269	netcdf_support=false
270	node_usage=default
271	numprocs=""
272	numprocs_atmos=0
273	numprocs_ocean=0
274	OOPT=""
275	openmp=false
276	output_list=""
277	package_list=""
278	queue=none
279	read_from_config=""
280	restart_run=false
281	if [[ `hostname` = rte10 ]]
282	then
283	return_address=133.5.185.60
284	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
285	elif [[ `hostname` = climate0 ]]
286	then
287	return_address=165.132.26.68
288	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
289	elif [[ `hostname` = urban00 ]]
290	then
291	return_address=147.46.30.151
292	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
293	else
294	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
295	fi
296	return_password=""
297	return_username=$LOGNAME
298	remotecall=false
299	remote_username=""
300	run_coupled_model=false
301	run_mode=""
302	store_on_archive_system=false
303	dashes=" ----------------------------------------------------------------------------"
304	silent=false
305	source_list=""
306	source_path=SOURCE
307	tasks_per_node=""
308	threads_per_task=1
309	tmpcreate=false
310	tmp_data_catalog=""
311	transfer_problems=false
312	usern=$LOGNAME
313	use_openmp=false
314	version="MRUN 2.1 Rev$Rev: 1610 $"
315	working_directory=`pwd`
316	TOPT=""
317	XOPT=""
318	zeit=$( date \| cut -c 12-19 )
319
320	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
321	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
322	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
323	# SCRIPT-OPTION ARGUMENTS
324	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
325
326
327
328	# ERROR HANDLING IN CASE OF EXIT
329	trap 'rm -rf $working_directory/tmp_mrun
330	if [[ $locat != normal && $locat != control_c ]]
331	then
332
333	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
334	(( i = 0 ))
335	while (( i < iec ))
336	do
337	(( i = i + 1 ))
338	printf "\n *** Execution of ERROR-command:\n"
339	printf " >>> ${err_command[$i]}\n"
340	eval ${err_command[$i]}
341	done
342	if [[ -n $interpreted_config_file ]]
343	then
344	rm -rf $interpreted_config_file
345	fi
346	if [[ -n .mrun_environment ]]
347	then
348	rm -rf .mrun_environment
349	fi
350	if [[ $tmpcreate = true ]]
351	then
352	printf "\n *** Contents of \"$TEMPDIR\":\n"
353	ls -al; cd
354	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
355	fi
356	if [[ "$dvrserver_id" != "" ]]
357	then
358	echo "+++ killing dvrserver_id=$dvrserver_id"
359	kill $dvrserver_id
360	fi
361	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
362	then
363	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
364	fi
365	printf "\n\n+++ MRUN killed \n\n"
366	elif [[ $locat != control_c ]]
367	then
368	printf "\n\n --> all actions finished\n\n"
369	printf " Bye, bye $usern !!\n\n"
370	fi' exit
371
372
373	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
374	trap 'rm -rf $working_directory/tmp_mrun
375	rm -rf $working_directory/tmp_check_namelist_files
376	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
377	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
378	then
379	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
380	fi
381	if [[ "$dvrserver_id" != "" ]]
382	then
383	echo "+++ killing dvrserver_id=$dvrserver_id"
384	kill $dvrserver_id
385	fi
386	printf "\n+++ MRUN killed by \"^C\" \n\n"
387	locat=control_c
388	exit
389	' 2
390
391
392	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
393	# BEEN SET
394	if [[ "$PALM_BIN" = "" ]]
395	then
396	printf "\n +++ environment variable PALM_BIN has not been set"
397	printf "\n please set it to the directory where the PALM scripts are located"
398	locat=palm_bin; exit
399	fi
400	export PATH=$PALM_BIN:$PATH
401
402
403
404	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
405	# WHICH WILL BE USED TO START RESTART-JOBS
406	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
407	do
408	case $option in
409	(a) afname=$OPTARG;;
410	(A) store_on_archive_system=true; mc="$mc -A";;
411	(b) do_batch=true; mc="$mc -b";;
412	(B) delete_temporary_catalog=false; mc="$mc -B";;
413	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
414	(C) restart_run=true; mc="$mc -C";;
415	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
416	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
417	(F) job_on_file="-D"; mc="$mc -F";;
418	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
419	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
420	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
421	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
422	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
423	(I) ignore_archive_error=true; mc="$mc -I";;
424	(k) keep_data_from_previous_run=true; mc="$mc -k";;
425	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
426	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
427	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
428	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
429	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
430	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
431	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
432	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
433	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
434	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
435	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
436	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
437	(S) read_from_config=false; mc="$mc -S";;
438	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
439	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
440	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
441	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
442	(v) silent=true; mc="$mc -v";;
443	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
444	(x) do_trace=true;set -x; mc="$mc -x";;
445	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
446	(y) ocean_file_appendix=true; mc="$mc -y";;
447	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
448	(z) check_namelist_files=false; mc="$mc -z";;
449	(Z) combine_plot_fields=false; mc="$mc -Z";;
450	(\?) printf "\n +++ unknown option $OPTARG \n"
451	printf "\n --> type \"$0 ?\" for available options \n"
452	locat=parameter;exit;;
453	esac
454	done
455
456
457	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
458	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
459	(( to_shift = $OPTIND - 1 ))
460	shift $to_shift
461
462	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
463	if [[ "$1" = "?" ]]
464	then
465	(printf "\n *** mrun can be called as follows:\n"
466	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"
467	printf "\n Description of available options:\n"
468	printf "\n Option Description Default-Value"
469	printf "\n -a base name of input files equiv. -d"
470	printf "\n -A archiving when using file-attribute fl"
471	printf "\n -b batch-job on local machine ---"
472	printf "\n -B do not delete temporary directory at end ---"
473	printf "\n -c configuration file .mrun.config"
474	printf "\n -d base name of files attached to program test"
475	printf "\n -D preprocessor(cpp)-directives \"\" "
476	printf "\n -F create remote job file only ---"
477	printf "\n -h execution host $localhost_realname"
478	printf "\n -i INPUT control list \"\" "
479	printf "\n -I archiving errors of previous batch-jobs"
480	printf "\n will be ignored"
481	printf "\n -k keep data from previous run"
482	printf "\n -K additional conditions for controling"
483	printf "\n usage of conditional code and"
484	printf "\n env-variables in configuration file \"\" "
485	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
486	printf "\n -M Makefile name Makefile"
487	printf "\n -n node usage (shared/not_shared) depending on -h"
488	printf "\n -o OUTPUT control list \"\" "
489	printf "\n -O threads per openMP task ---"
490	printf "\n -p software package list \"\" "
491	printf "\n -q queue \"$queue\" "
492	printf "\n -r run control list (combines -i -o) \"\" "
493	printf "\n -s filenames of routines to be compiled \"\" "
494	printf "\n must end with .f, .f90, .F, or .c !"
495	printf "\n use \"..\" for more than one file and wildcards"
496	printf "\n -s LM compiles all locally modified files"
497	printf "\n -S config file interpreted by shellscript ---"
498	printf "\n -t allowed cpu-time in seconds (batch) 0"
499	printf "\n -T tasks per node depending on -h"
500	printf "\n -u username on remote machine \"\" "
501	printf "\n -v no prompt for confirmation ---"
502	printf "\n -w maximum parallel io streams as given by -X"
503	printf "\n -x tracing of mrun for debug purposes ---"
504	printf "\n -X # of processors (on parallel machines) 1"
505	printf "\n -y add appendix \"_O\" to all local output"
506	printf "\n files (ocean precursor runs followed by"
507	printf "\n coupled atmosphere-ocean runs) ---"
508	printf "\n -Y run coupled model, \"#1 #2\" with"
509	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
510	printf "\n -z disable a priori parameter file check ---"
511	printf "\n -Z skip combine_plot_fields at the end of "
512	printf "\n the simulation ---"
513	printf "\n "
514	printf "\n Possible values of positional parameter <modus>:"
515	printf "\n \"?\" - this outline \n\n") \| more
516	exit
517	elif [[ "$1" != "" ]]
518	then
519	printf "\n +++ positional parameter $1 unknown \n"
520	locat=parameter; exit
521	fi
522
523
524
525	# SHORT STARTING MESSAGE
526	printf "\n*** $version "
527	printf "\n will be executed. Please wait ..."
528
529
530
531	# CHECK, IF CONFIGURATION FILE EXISTS
532	if [[ ! -f $config_file ]]
533	then
534	printf "\n\n +++ configuration file: "
535	printf "\n $config_file"
536	printf "\n does not exist"
537	locat=connect; exit
538	fi
539
540
541	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
542	line=""
543	grep "%host_identifier" $config_file > tmp_mrun
544	while read line
545	do
546	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
547	then
548	HOSTNAME=`echo $line \| cut -d" " -s -f2`
549	host_identifier=`echo $line \| cut -d" " -s -f3`
550	if [[ $localhost_realname = $HOSTNAME ]]
551	then
552	localhost=$host_identifier
553	break
554	fi
555	fi
556	done < tmp_mrun
557
558	if [[ "$localhost" = "" ]]
559	then
560	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
561	printf "\n for local host \"$localhost_realname\"."
562	printf "\n Please add line"
563	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
564	printf "\n to the configuration file."
565	locat=localhost; exit
566	fi
567
568
569	# SET HOST-SPECIFIC VARIABLES
570	case $localhost_realname in
571	(r1\|r2\|h01\|b01) archive_system=tivoli;;
572	(cs*) archive_system=ut;;
573	esac
574
575
576	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
577	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
578	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
579	[[ "$afname" = "" ]] && afname=$fname
580
581
582	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
583	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
584	# STATEMENTS IN THE CONFIGURATION FILE
585	if [[ "$run_mode" != "" ]]
586	then
587	input_list="$input_list $run_mode"
588	output_list="$output_list $run_mode"
589	fi
590
591
592	# ??? is this (and the respective option -H) really required ???
593	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
594	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
595	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
596	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
597	if [[ "$fromhost" = "" ]]
598	then
599	fromhost=$localhost
600	fi
601
602
603	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
604	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
605	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
606	# TO BE SUBMITTED (I.E. do_batch=true)
607	if [[ -n $host && "$host" != $localhost ]]
608	then
609	do_batch=true
610	do_remote=true
611	case $host in
612	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
613	(*) printf "\n"
614	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
615	printf "\n is not available"
616	locat=nqs; (( iec = 0 )); exit;;
617	esac
618	else
619	host=$localhost
620	fi
621
622
623	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
624	if [[ -n $additional_conditions ]]
625	then
626	cond1=`echo $additional_conditions \| cut -d" " -f1`
627	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
628	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
629	if [[ -n $dummy ]]
630	then
631	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
632	locat=options; exit
633	fi
634	block=_$cond1
635	[[ -n $cond2 ]] && block=${block}_$cond2
636	fi
637
638
639	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
640	if [[ $run_coupled_model = true ]]
641	then
642
643	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
644	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
645
646	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
647	then
648
649	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
650	printf "\n PEs (total) : $numprocs"
651	printf "\n PEs (atmosphere): $numprocs_atmos"
652	printf "\n PEs (ocean) : $numprocs_ocean"
653	locat=coupling; exit
654
655	fi
656
657
658	# GET coupled_mode FROM THE CONFIG FILE
659	line=""
660	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
661	while read line
662	do
663	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
664	then
665	coupled_mode="mpi2"
666	fi
667	done < tmp_mrun
668
669	fi
670
671
672	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
673	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
674	then
675	if [[ $ignore_archive_error = false ]]
676	then
677	printf "\n +++ data archiving of previous run failed"
678	printf "\n see directory \~/job_queue on remote machine"
679	locat=archive; exit
680	else
681	printf "\n +++ warning: data archiving in a previous run failed"
682	printf "\n MRUN continues, trying to get backup copy"
683	fi
684	fi
685
686
687	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
688	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
689	mrun_memory=$memory
690	mrun_group_number=$group_number
691	mrun_cpumax=$cpumax
692	mrun_numprocs=$numprocs
693
694
695	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
696	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
697	if [[ "$read_from_config" = false ]]
698	then
699
700	[[ $silent = false ]] && printf "\n Reading the configuration file... "
701
702	# READ THE CONFIGURATION FILE LINE BY LINE
703	while read zeile
704	do
705	[[ $silent = false ]] && printf "."
706
707
708	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
709	eval zeile=\"$zeile\"
710
711
712	# INTERPRET THE LINE
713	if [[ "$(echo $zeile)" = "" ]]
714	then
715	# EMPTY LINE, NO ACTION
716	continue
717
718	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
719	then
720
721	# LINE IS A COMMENT LINE
722	true
723
724	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
725	then
726
727	# LINE DEFINES AN ENVIRONMENT-VARIABLE
728	zeile=$(echo $zeile \| cut -c2-)
729	var=`echo $zeile \| cut -d" " -f1`
730	value=`echo $zeile \| cut -d" " -s -f2`
731	for_host=`echo $zeile \| cut -d" " -s -f3`
732	for_cond1=`echo $zeile \| cut -d" " -s -f4`
733	for_cond2=`echo $zeile \| cut -d" " -s -f5`
734
735	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
736	then
737
738	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
739	# "::" IS REPLACED BY ":".
740	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
741
742
743	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
744	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
745	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
746	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
747	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
748	# CONFIGURATION-FILE.
749	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
750	then
751	eval $var=\$value
752
753	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
754	if [[ $do_trace = true ]]
755	then
756	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
757	fi
758	fi
759
760	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
761	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
762	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
763	# MUST HAVE TO BE STARTED
764	if [[ $var = host ]]
765	then
766	if [[ -n $host && "$host" != $localhost ]]
767	then
768	do_batch=true
769	do_remote=true
770	case $host in
771	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
772	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
773	printf "\n is not available"
774	locat=nqs; exit;;
775	esac
776	else
777	host=$localhost
778	fi
779	fi
780
781	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
782	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
783	# BY MRUN (E.G. subjob)
784	export $var
785	fi
786
787
788
789
790	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
791	then
792
793	# LINE DEFINES ERROR-COMMAND
794	(( iec = iec + 1 ))
795	zeile=$(echo $zeile \| cut -c4-)
796	err_command[$iec]="$zeile"
797
798	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
799	then
800
801	# LINE DEFINES INPUT-COMMAND
802	(( iic = iic + 1 ))
803	zeile=$(echo $zeile \| cut -c4-)
804	in_command[$iic]="$zeile"
805
806	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
807	then
808
809	# LINE DEFINES OUTPUT-COMMAND
810	(( ioc = ioc + 1 ))
811	zeile=$(echo $zeile \| cut -c4-)
812	out_command[$ioc]="$zeile"
813
814	else
815
816	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
817	# s2a: in/out - field
818	# s2b: loc - field (optional)
819	# s2c: tr/ar - field (optional)
820	s1=`echo $zeile \| cut -d" " -f1`
821	s2=`echo $zeile \| cut -d" " -s -f2`
822	s2a=$(echo $s2 \| cut -d":" -f1)
823	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
824	then
825	s2b=""
826	s2c=""
827	else
828	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
829	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
830	fi
831	s3=`echo $zeile \| cut -d" " -f3`
832	s4=`echo $zeile \| cut -d" " -s -f4`
833	s5=`echo $zeile \| cut -d" " -s -f5`
834	s6=`echo $zeile \| cut -d" " -s -f6`
835
836
837	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
838	# INPUT- OR OUTPUT-LIST.
839	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
840	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
841	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
842	# IS NOT CHECKED AND STORED.
843	IFSALT="$IFS"; IFS="$IFS:"
844	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
845	then
846	found=false
847	for actual in $input_list
848	do
849	for formal in $s3
850	do
851	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
852	done
853	done
854	if [[ $found = true ]]
855	then
856	(( iin = iin + 1 ))
857	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
858	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
859	extin[$iin]=$s6
860	fi
861	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
862	then
863	found=false
864	for actual in $output_list
865	do
866	for formal in $s3
867	do
868	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
869	done
870	done
871	if [[ $found = true ]]
872	then
873	(( iout = iout + 1 ))
874	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
875	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
876	fi
877	elif [[ "$s2a" != in && "$s2a" != out ]]
878	then
879	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
880	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
881	locat=connect; exit
882	fi
883	IFS="$IFSALT"
884	fi
885	done < $config_file
886
887	else
888
889
890	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
891	[[ $silent = false ]] && printf "..."
892	interpreted_config_file=.icf.$RANDOM
893
894
895
896	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
897	cat > .mrun_environment << %%END%%
898	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
899	config_file = '$config_file', do_remote = '$do_remote',
900	do_trace = '$do_trace', host = '$host',
901	input_list = '$input_list', icf = '$interpreted_config_file',
902	localhost = '$localhost', output_list = '$output_list' /
903
904	%%END%%
905
906	if [[ "$host" != $localhost ]]
907	then
908
909	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
910	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
911	if [[ $? != 0 ]]
912	then
913	printf "\n\n +++ no interpret_config found"
914	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
915	locat=interpret_config; exit
916	fi
917	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
918	$interpret_config_executable
919
920	else
921
922	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
923	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
924	then
925	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
926	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
927	locat=interpret_config; exit
928	else
929	interpret_config${block}.x
930	fi
931
932	fi
933	rm .mrun_environment
934
935
936	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
937	chmod u+x $interpreted_config_file
938	export PATH=$PATH:.
939	. $interpreted_config_file
940	rm $interpreted_config_file
941
942	fi
943
944
945	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
946	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
947	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
948	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
949	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
950	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
951	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
952
953
954	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
955	# FOR SOURCE-FILES TO BE COMPILED.
956	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
957	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
958	if [[ "$SOURCES_COMPLETE" = "" ]]
959	then
960
961	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
962	# HAS BEEN DEFINED
963	source_path=""
964	line=""
965	grep "%source_path" $config_file > tmp_mrun
966	while read line
967	do
968	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
969	then
970	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
971	then
972	global_source_path=`echo $line \| cut -d" " -f2`
973	fi
974	fi
975	done < tmp_mrun
976
977	line=""
978	found=false
979	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
980	while read line
981	do
982	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
983	then
984	if [[ $found = true ]]
985	then
986	printf "\n\n +++ more than one source path found in configuration file"
987	printf "\n for local host \"$localhost\" "
988	locat=source_path; exit
989	fi
990	source_path=`echo $line \| cut -d" " -f2`
991	found=true
992	fi
993	done < tmp_mrun
994	rm tmp_mrun
995
996	if [[ "$source_path" = "" ]]
997	then
998	if [[ "$global_source_path" != "" ]]
999	then
1000	source_path=$global_source_path
1001	else
1002	printf "\n\n +++ no source path found in configuration file"
1003	printf "\n for local host \"$localhost\" "
1004	locat=source_path; exit
1005	fi
1006	fi
1007	eval source_path=$source_path
1008
1009	if [[ ! -d $source_path ]]
1010	then
1011	printf "\n\n +++ source path \"$source_path\" on local host"
1012	printf "\n \"$localhost\" does not exist"
1013	locat=source_path; exit
1014	fi
1015
1016	fi
1017
1018
1019	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1020	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1021	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1022	then
1023	global_revision=`svnversion $source_path 2>/dev/null`
1024	global_revision="Rev: $global_revision"
1025	fi
1026
1027
1028	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1029	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1030	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1031	if [[ -n $host && "$host" != $localhost ]]
1032	then
1033	do_batch=true
1034	do_remote=true
1035	case $host in
1036	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1037	(*) printf "\n"
1038	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1039	printf "\n is not available"
1040	locat=nqs; (( iec = 0 )); exit;;
1041	esac
1042	else
1043	host=$localhost
1044	fi
1045
1046
1047	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1048	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1049	then
1050
1051	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1052	if [[ ! -n $numprocs ]]
1053	then
1054	printf "\n"
1055	printf "\n +++ option \"-K parallel\" requires additional specification"
1056	printf "\n of the number of processors to be used by"
1057	printf "\n mrun-option \"-X\" or by environment-variable"
1058	printf "\n \"numprocs\" in the configuration file"
1059	locat=numprocs; (( iec = 0 )); exit
1060	fi
1061
1062	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1063	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1064	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1065	then
1066	printf "\n"
1067	printf "\n +++ option \"-T\" (tasks per node) is missing"
1068	printf "\n set -T option or define tasks_per_node in the config file"
1069	locat=tasks_per_node; (( iec = 0 )); exit
1070	fi
1071
1072	if (( numprocs < tasks_per_node ))
1073	then
1074	printf "\n"
1075	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1076	printf "\n given values: -T $tasks_per_node -X $numprocs"
1077	locat=tasks_per_node; (( iec = 0 )); exit
1078	fi
1079
1080	if [[ $host != lcflow && $host != lcxt5m ]]
1081	then
1082	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1083	(( ival = $tasks_per_node ))
1084	(( pes = numprocs ))
1085	(( ii = pes / ival ))
1086	(( remaining_pes = pes - ii * ival ))
1087	if (( remaining_pes > 0 ))
1088	then
1089	printf "\n"
1090	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1091	printf "\n divisor of the total number of processors (option \"-X\")"
1092	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1093	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1094	(( nodes = nodes + 1 ))
1095	fi
1096	fi
1097
1098
1099	# SETTINGS FOR SUBJOB-COMMAND
1100	OOPT="-O $threads_per_task"
1101
1102	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1103	if [[ "$tasks_per_node" != "" ]]
1104	then
1105	TOPT="-T $tasks_per_node"
1106	fi
1107
1108	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1109	if [[ $node_usage = default ]]
1110	then
1111	if [[ $host = ibms ]]
1112	then
1113	node_usage=shared
1114	else
1115	node_usage=not_shared
1116	fi
1117	fi
1118
1119	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1120	then
1121	printf "\n"
1122	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1123	printf "\n \"shared\" or \"not_shared\""
1124	locat=tasks_per_node; (( iec = 0 )); exit
1125	fi
1126
1127	fi
1128
1129	# CHECK IF HOSTFILE EXISTS
1130	if [[ -n $hostfile ]]
1131	then
1132	if [[ ! -f $hostfile ]]
1133	then
1134	printf "\n"
1135	printf "\n +++ hostfile \"$hostfile\" does not exist"
1136	locat=hostfile; exit
1137	fi
1138	fi
1139
1140
1141	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1142	if [[ "$maximum_parallel_io_streams" = "" ]]
1143	then
1144	maximum_parallel_io_streams=$numprocs
1145	fi
1146
1147
1148	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1149	if [[ "$scp_port" != "" ]]
1150	then
1151	PORTOPT="-P $scp_port"
1152	SSH_PORTOPT="-p $scp_port"
1153	fi
1154
1155
1156	# SET DEFAULT-QUEUE, IF NOT GIVEN
1157	if [[ $queue = none ]]
1158	then
1159	case $host in
1160	(ibmh) queue=cluster;;
1161	(ibmkisti) queue=class.32plus;;
1162	(lccrayb) queue=mpp1q;;
1163	(lccrayh) queue=mpp1q;;
1164	(lckiaps) queue=normal;;
1165	(lckyoto) queue=ph;;
1166	(lckyuh) queue=fx-single;;
1167	(lckyut) queue=cx-single;;
1168	(lctit) queue=S;;
1169	(nech) queue=none;;
1170	(unics) queue=unics;;
1171	esac
1172	fi
1173
1174
1175	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1176	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1177	(( i = 0 ))
1178	while (( i < iin ))
1179	do
1180	(( i = i + 1 ))
1181	(( maxcycle = 0 ))
1182
1183	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1184	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1185	if [[ "${actionin[$i]}" = di ]]
1186	then
1187	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1188	# HOST ONLY
1189	eval filename=${pathin[$i]}/${endin[$i]}
1190	else
1191	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1192	# HOST ONLY
1193	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1194	fi
1195	eval pathname=${pathin[$i]}
1196
1197	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1198	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1199	then
1200	filename_input=$filename
1201	fi
1202
1203	# CHECK IF FILE EXISTS
1204	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1205	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1206	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1207	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1208	then
1209
1210	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1211	if [[ "${transin[$i]}" != "locopt" ]]
1212	then
1213	printf "\n\n +++ INPUT-file: "
1214	if [[ "${extin[$i]}" = "" ]]
1215	then
1216	printf "\n $filename"
1217	else
1218	printf "\n $filename.${extin[$i]}"
1219	fi
1220	printf "\n does not exist\n"
1221	locat=input; exit
1222	else
1223	transin[$i]="unavailable"
1224	fi
1225	else
1226
1227	# DETERMINE THE FILE'S CYCLE NUMBER
1228	ls -1 -d $filename > filelist 2>/dev/null
1229	ls -1 -d $filename.* >> filelist 2>/dev/null
1230	while read zeile
1231	do
1232	cycle=$(echo $zeile \| cut -f2 -d".")
1233	if [[ "$cycle" = "$zeile" ]]
1234	then
1235	(( icycle = 0 ))
1236	elif [[ "$cycle" = "${extin[$i]}" ]]
1237	then
1238	(( icycle = 0 ))
1239	else
1240	(( icycle = $cycle ))
1241	fi
1242	if (( icycle > maxcycle ))
1243	then
1244	(( maxcycle = icycle ))
1245	file_to_be_used=$zeile
1246	fi
1247	done <filelist
1248	rm filelist
1249
1250	# APPEND CYCLE NUMBER TO FILENAME
1251	if (( maxcycle > 0 ))
1252	then
1253	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1254	then
1255	filename=${filename}.$maxcycle.${extin[$i]}
1256	else
1257	filename=${filename}.$maxcycle
1258	fi
1259	else
1260	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1261	then
1262	filename=${filename}.${extin[$i]}
1263	fi
1264	fi
1265
1266	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1267	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1268	absnamein[$i]=$filename
1269	if (( maxcycle > 0 ))
1270	then
1271	if [[ "${actionin[$i]}" = di ]]
1272	then
1273	frelin[$i]=${endin[$i]}.$maxcycle
1274	else
1275	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1276	fi
1277	else
1278	if [[ "${actionin[$i]}" = di ]]
1279	then
1280	frelin[$i]=${endin[$i]}
1281	else
1282	frelin[$i]=${afname}${endin[$i]}
1283	fi
1284	fi
1285
1286	fi
1287	done
1288
1289	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1290	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1291	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1292	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1293	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1294	# REMOTE HOST)
1295	(( i = 0 ))
1296	while (( i < iout ))
1297	do
1298	(( i = i + 1 ))
1299	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1300	then
1301	if [[ "${actionout[$i]}" = tr ]]
1302	then
1303	actionout[$i]=""
1304	elif [[ "${actionout[$i]}" = trpe ]]
1305	then
1306	actionout[$i]=pe
1307	elif [[ "${actionout[$i]}" = tra ]]
1308	then
1309	actionout[$i]=a
1310	fi
1311	(( maxcycle = 0 ))
1312	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1313	eval catalogname=${pathout[$i]}
1314	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1315	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1316	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1317	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1318	then
1319
1320	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1321	if cat /dev/null > $filename
1322	then
1323	rm $filename
1324	else
1325
1326	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1327	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1328	if [[ ! -d $catalogname ]]
1329	then
1330	if mkdir -p $catalogname
1331	then
1332	printf "\n\n *** directory:"
1333	printf "\n $catalogname"
1334	printf "\n was created\n"
1335	else
1336	printf "\n\n +++ OUTPUT-file:"
1337	printf "\n $filename"
1338	printf "\n cannot be created, because directory does not exist"
1339	printf "\n and cannot be created either"
1340	printf "\n"
1341	locat=output ; exit
1342	fi 2>/dev/null
1343	else
1344	printf "\n\n +++ OUTPUT-file:"
1345	printf "\n $filename"
1346	printf "\n cannot be created, although directory exists"
1347	printf "\n"
1348	locat=output ; exit
1349	fi
1350	fi 2>/dev/null
1351	else
1352
1353	# DETERMINE THE CYCLE NUMBER
1354	ls -1 -d $filename > filelist 2>/dev/null
1355	ls -1 -d $filename.* >> filelist 2>/dev/null
1356	while read zeile
1357	do
1358	cycle=$(echo $zeile \| cut -f2 -d".")
1359	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1360	then
1361	(( icycle = 1 ))
1362	else
1363	(( icycle = $cycle + 1 ))
1364	fi
1365	if (( icycle > maxcycle ))
1366	then
1367	(( maxcycle = icycle ))
1368	fi
1369	done <filelist
1370	rm filelist
1371	fi
1372
1373	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1374	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1375	if [[ "${actionout[$i]}" != a ]]
1376	then
1377	if (( maxcycle > 0 ))
1378	then
1379	filename=${filename}.$maxcycle
1380	if cat /dev/null > $filename
1381	then
1382	rm $filename
1383	else
1384	printf "\n +++ OUTPUT-file:"
1385	printf "\n $filename"
1386	printf "\n cannot be created"
1387	locat=output ; exit
1388	fi
1389	fi
1390	else
1391	(( maxcycle = maxcycle - 1 ))
1392	if (( maxcycle > 0 ))
1393	then
1394	filename=${filename}.$maxcycle
1395	fi
1396	fi
1397
1398	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1399	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1400	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1401	pathout[$i]=$filename
1402	if (( maxcycle > 0 ))
1403	then
1404	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1405	else
1406	frelout[$i]=${fname}${endout[$i]}
1407	fi
1408
1409	fi
1410	done
1411
1412
1413	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1414	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1415	then
1416	if [[ "$dvr_inc" = "" ]]
1417	then
1418	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1419	printf "\n This is required for the dvrp_graphics package.\n"
1420	locat=dvr; exit
1421	fi
1422	if [[ "$dvr_lib" = "" ]]
1423	then
1424	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1425	printf "\n This is required for the dvrp_graphics package.\n"
1426	locat=dvr; exit
1427	fi
1428	fi
1429
1430
1431	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1432	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1433	if [[ "$mainprog" = "" && "$executable" = "" ]]
1434	then
1435	printf "\n +++ neither main program nor executable defined"
1436	locat=source; exit
1437	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1438	then
1439	printf "\n +++ main program as well as executable defined"
1440	locat=source; exit
1441	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1442	then
1443	do_compile=false
1444	fi
1445
1446
1447	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1448	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1449	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1450	then
1451	rm -rf SOURCES_FOR_RUN_$fname
1452	mkdir SOURCES_FOR_RUN_$fname
1453	fi
1454
1455
1456	# COLLECT ALL ROUTINES TO BE COMPILED
1457	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1458	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1459	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1460	then
1461
1462	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1463
1464	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1465	then
1466
1467	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1468	source_list=""
1469	cd $source_path
1470
1471
1472	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1473	if [[ ! -d .svn ]]
1474	then
1475	printf "\n\n +++ source directory"
1476	printf "\n \"$source_path\" "
1477	printf "\n is not under control of \"subversion\"."
1478	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1479	fi
1480
1481
1482	# LIST ALL MODIFIED SOURCE CODE FILES
1483	Filenames=""
1484	svn status > tmp_mrun
1485	while read line
1486	do
1487	firstc=`echo $line \| cut -c1`
1488	if [[ $firstc = M \|\| $firstc = "?" ]]
1489	then
1490	Name=`echo "$line" \| cut -c8-`
1491	extension=`echo $Name \| cut -d. -f2`
1492	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1493	then
1494	Filenames="$Filenames "$Name
1495	fi
1496	fi
1497	done < tmp_mrun
1498
1499
1500	# COPY FILES TO SOURCES_FOR_RUN_...
1501	for dateiname in $Filenames
1502	do
1503	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1504	source_list=$source_list"$dateiname "
1505	done
1506
1507	cd - > /dev/null
1508
1509
1510	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1511	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1512	elif [[ "$source_list" != "" && $restart_run != true ]]
1513	then
1514
1515	cd $source_path
1516
1517	for filename in $source_list
1518	do
1519
1520	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1521	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1522	then
1523	printf "\n +++ source code file: $filename"
1524	printf "\n must not contain (\"/\") "
1525	locat=source; exit
1526	fi
1527
1528	if [[ ! -f $filename ]]
1529	then
1530	printf "\n +++ source code file: $filename"
1531	printf "\n does not exist"
1532	locat=source; exit
1533	else
1534	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1535	fi
1536
1537	done
1538
1539	cd - > /dev/null
1540
1541	fi
1542
1543
1544	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1545	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1546	if [[ $restart_run != true ]]
1547	then
1548
1549	if [[ ! -f "$source_path/$mainprog" ]]
1550	then
1551	printf "\n\n +++ main program: $mainprog"
1552	printf "\n does not exist in source directory"
1553	printf "\n \"$source_path\"\n"
1554	locat=source; exit
1555	else
1556	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1557	then
1558	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1559	source_list=${mainprog}" $source_list"
1560	fi
1561	fi
1562	fi
1563
1564
1565	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1566	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1567	if [[ "$restart_run" != true ]]
1568	then
1569	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1570	if [[ ! -f $makefile ]]
1571	then
1572	printf "\n +++ file \"$makefile\" does not exist"
1573	locat=make; exit
1574	else
1575	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1576	fi
1577	fi
1578
1579
1580	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1581	if [[ $restart_run != true && "$add_source_path" != "" ]]
1582	then
1583
1584	# DOES THE DIRECTORY EXIST?
1585	if [[ ! -d $add_source_path ]]
1586	then
1587	printf "\n\n +++ WARNING: additional source code directory"
1588	printf "\n \"$add_source_path\" "
1589	printf "\n does not exist or is not a directory."
1590	printf "\n No source code will be used from this directory!\n"
1591	add_source_path=""
1592	if [[ $silent == false ]]
1593	then
1594	sleep 3
1595	fi
1596	else
1597
1598	cd $add_source_path
1599	found=false
1600
1601	Names=$(ls -1 *.f90 2>&1)
1602	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1603	Names=$(ls -1 *.F90 2>&1)
1604	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1605	Names=$(ls -1 *.F 2>&1)
1606	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1607	Names=$(ls -1 *.f 2>&1)
1608	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1609	Names=$(ls -1 *.c 2>&1)
1610	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1611
1612	cd - > /dev/null
1613	cd SOURCES_FOR_RUN_$fname
1614
1615	# COPY MAKEFILE IF EXISTING
1616	if [[ -f $add_source_path/Makefile ]]
1617	then
1618	printf "\n\n *** user Makefile from directory"
1619	printf "\n \"$add_source_path\" is used \n"
1620	if [[ $silent == false ]]
1621	then
1622	sleep 1
1623	fi
1624	cp $add_source_path/Makefile .
1625	fi
1626
1627	for dateiname in $AddFilenames
1628	do
1629	if [[ -f $dateiname ]]
1630	then
1631	printf "\n +++ source code file \"$dateiname\" found in additional"
1632	printf "\n source code directory \"$add_source_path\" "
1633	printf "\n but was also given with option \"-s\" which means that it should be taken"
1634	printf "\n from directory \"$source_path\"."
1635	locat=source; exit
1636	fi
1637
1638	cp $add_source_path/$dateiname .
1639	source_list="$source_list $dateiname"
1640
1641	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1642	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1643	then
1644	printf "\n\n +++ user file \"$dateiname\" "
1645	printf "\n is not listed in Makefile \n"
1646	locat=source; exit
1647	else
1648
1649	if [[ $found = false ]]
1650	then
1651	found=true
1652	printf "\n\n *** following user file(s) added to the"
1653	printf " files to be translated:\n "
1654	fi
1655	printf "$dateiname "
1656	if [[ $silent == false ]]
1657	then
1658	sleep 0.5
1659	fi
1660
1661	fi
1662	done
1663	[[ $found = true ]] && printf "\n"
1664	cd - > /dev/null
1665	fi
1666	fi
1667
1668
1669	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1670	# TO THE LIST OF FILES TO BE COMPILED
1671	if [[ $restart_run != true && -n $package_list ]]
1672	then
1673
1674	cd $source_path
1675
1676	for package in $package_list
1677	do
1678
1679	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1680
1681	# DETERMINE FILES BELONGING TO THE PACKAGE
1682	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1683	# THE NAME OF THE DIRECTORY
1684	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1685
1686
1687	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1688	# IF THEY ARE NOT ALREADY PART OF THE LIST
1689	for source_list_name in $package_source_list
1690	do
1691	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1692	then
1693
1694	# ONLY TAKE FILES WITH VALID SUFFIX
1695	ending=`echo $source_list_name \| cut -f2 -d.`
1696	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1697	then
1698	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1699	source_list="$source_list $source_list_name"
1700	fi
1701	fi
1702	done
1703	done
1704
1705	cd - > /dev/null
1706	fi
1707
1708	fi # do_compile=true
1709
1710
1711	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1712	# AND SET PRE-PROCESSOR DIRECTIVES
1713	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1714	then
1715
1716	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1717	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1718	then
1719	cpp_options="${cpp_options},-D__ibm=__ibm"
1720	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1721	then
1722	cpp_options="$cpp_options -D__nec"
1723	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1724	then
1725	cpp_options="$cpp_options -D__lc"
1726	else
1727	cpp_options="$cpp_options -D__$localhost"
1728	fi
1729
1730	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1731	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1732	then
1733	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1734	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1735	else
1736	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1737	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1738	fi
1739
1740	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1741	if [[ -n $package_list ]]
1742	then
1743	for package in $package_list
1744	do
1745	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1746	then
1747	if [[ $package != "dvrp_graphics+1PE" ]]
1748	then
1749	cpp_options="${cpp_options},-D__$package=__$package"
1750	else
1751	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1752	export use_seperate_pe_for_dvrp_output=true
1753	fi
1754	else
1755	if [[ $package != "dvrp_graphics+1PE" ]]
1756	then
1757	cpp_options="$cpp_options -D__$package"
1758	else
1759	cpp_options="$cpp_options -D__dvrp_graphics"
1760	export use_seperate_pe_for_dvrp_output=true
1761	fi
1762	fi
1763	done
1764	fi
1765
1766	# SET DIRECTIVES GIVEN BY OPTION -D
1767	if [[ -n $cpp_opts ]]
1768	then
1769	for popts in $cpp_opts
1770	do
1771	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1772	then
1773	cpp_options="${cpp_options},-D__$popts=__$popts"
1774	else
1775	cpp_options="$cpp_options -D__$popts"
1776	fi
1777	done
1778	fi
1779
1780	else
1781
1782
1783	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1784	if [[ $do_remote = false ]]
1785	then
1786	if [[ ! -f $executable ]]
1787	then
1788	printf "\n +++ executable file: $executable"
1789	printf "\n does not exist"
1790	locat=executable; exit
1791	fi
1792	fi
1793	fi
1794
1795
1796	# DETERMINE THE JOB MODE
1797	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1798	then
1799	if [[ "$LOADLBATCH" = yes ]]
1800	then
1801	batch_job=.TRUE.
1802	jobmo=BATCH
1803	else
1804	batch_job=.FALSE.
1805	jobmo=INTERACTIVE
1806	fi
1807	else
1808	if [[ "$ENVIRONMENT" = BATCH ]]
1809	then
1810	batch_job=.TRUE.
1811	jobmo=BATCH
1812	else
1813	batch_job=.FALSE.
1814	jobmo=INTERACTIVE
1815	fi
1816	fi
1817
1818	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1819	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1820	then
1821	printf "\n +++ no interactive runs allowed on host \"$host\" "
1822	printf "\n please submit batch job using mrun option \"-b\" \n"
1823	locat=normal; exit
1824	fi
1825
1826
1827	# CHECK, IF USER DEFINED A COMPILER
1828	if [[ "$compiler_name" = "" ]]
1829	then
1830
1831	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1832	locat=compiler_name; exit
1833
1834	fi
1835
1836
1837	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1838
1839	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1840	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1841	then
1842	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1843	else
1844	kennung=$RANDOM
1845	fi
1846
1847	if [[ "$tmp_user_catalog" = "" ]]
1848	then
1849	if [[ $localhost = ibmh ]]
1850	then
1851	tmp_user_catalog=$SCRATCH
1852	elif [[ $localhost = nech ]]
1853	then
1854	tmp_user_catalog=$WRKSHR
1855	else
1856	tmp_user_catalog=/tmp
1857	fi
1858	fi
1859	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1860
1861
1862	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1863	if [[ "$tmp_data_catalog" = "" ]]
1864	then
1865	if [[ $localhost = nech ]]
1866	then
1867	tmp_data_catalog=$WRKSHR/mrun_restart_data
1868	else
1869	tmp_data_catalog=/tmp/mrun_restart_data
1870	fi
1871	fi
1872
1873
1874	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1875	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1876	then
1877	eval fopts=\"$fopts\"
1878	eval lopts=\"$lopts\"
1879	fi
1880
1881
1882
1883	# DETERMINE COMPILE- AND LINK-OPTIONS
1884	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1885	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1886	ROPTS="$ropts"
1887	# 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 ]]
1888	# then
1889	XOPT="-X $numprocs"
1890	# fi
1891
1892
1893
1894	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1895	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1896	done=false
1897	while [[ $done = false ]]
1898	do
1899	cputime=$cpumax
1900	if (( $cputime == 0 ))
1901	then
1902	if [[ $do_batch = true ]]
1903	then
1904	printf "\n +++ cpu-time is undefined"
1905	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1906	printf "\n >>> "
1907	read cputime 1>/dev/null 2>&1
1908	else
1909	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1910	fi
1911	else
1912	done=true
1913	fi
1914	cpumax=$cputime
1915	done
1916
1917	(( minuten = cputime / 60 ))
1918	(( sekunden = cputime - minuten * 60 ))
1919
1920
1921	# CHECK THE MEMORY DEMAND
1922	if [[ $do_batch = true ]]
1923	then
1924	done=false
1925	while [[ $done = false ]]
1926	do
1927	if (( memory == 0 ))
1928	then
1929	printf "\n +++ memory demand is undefined"
1930	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1931	printf "\n >>> "
1932	read memory 1>/dev/null 2>&1
1933	else
1934	done=true
1935	fi
1936	done
1937	fi
1938
1939
1940	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1941	if [[ $do_remote = true && -z $remote_username ]]
1942	then
1943	while [[ -z $remote_username ]]
1944	do
1945	printf "\n +++ username on remote host \"$host\" is undefined"
1946	printf "\n >>> Please type username:"
1947	printf "\n >>> "
1948	read remote_username
1949	done
1950	mc="$mc -u$remote_username"
1951	fi
1952
1953	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1954	if [[ "$login_init_cmd" != "" ]]
1955	then
1956	export init_cmds="${login_init_cmd};"
1957	fi
1958
1959
1960	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1961	if [[ "$modules" != "" ]]
1962	then
1963	if [[ $host = lctit ]]
1964	then
1965	export module_calls=". $modules"
1966	else
1967	export module_calls="module load ${modules};"
1968	fi
1969	fi
1970
1971
1972
1973	# OUTPUT OF THE MRUN-HEADER
1974	calltime=$(date)
1975	printf "\n"
1976	printf "#------------------------------------------------------------------------# \n"
1977	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1978	printf "\| \| \n"
1979	spalte1="called on:"; spalte2=$localhost_realname
1980	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1981	if [[ $do_remote = true ]]
1982	then
1983	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1984	else
1985	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1986	fi
1987	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1988	if [[ -n $numprocs ]]
1989	then
1990	if [[ $run_coupled_model = false ]]
1991	then
1992	spalte1="number of PEs:"; spalte2=$numprocs
1993	else
1994	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1995	fi
1996	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1997	fi
1998	if [[ -n $tasks_per_node ]]
1999	then
2000	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2001	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2002	if (( remaining_pes > 0 ))
2003	then
2004	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2005	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2006	fi
2007	fi
2008	if [[ $maximum_parallel_io_streams != $numprocs ]]
2009	then
2010	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2012	fi
2013	if [[ $use_openmp = true ]]
2014	then
2015	spalte1="threads per task:"; spalte2="$threads_per_task"
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	fi
2018	printf "\| \| \n"
2019	if [[ $do_compile = true ]]
2020	then
2021	if [[ "$mopts" != "" ]]
2022	then
2023	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	zeile=$(echo "$mopts" \| cut -c46-)
2026	while [[ "$zeile" != "" ]]
2027	do
2028	spalte1=""
2029	spalte2=$(echo "$zeile" \| cut -c-45)
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	zeile=$(echo "$zeile" \| cut -c46-)
2032	done
2033	fi
2034
2035	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2036	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2037	zeile=$(echo "$cpp_options" \| cut -c46-)
2038	while [[ "$zeile" != "" ]]
2039	do
2040	spalte1=""
2041	spalte2=$(echo "$zeile" \| cut -c-45)
2042	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2043	zeile=$(echo "$zeile" \| cut -c46-)
2044	done
2045
2046	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2047	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2048	zeile=$(echo "$fopts" \| cut -c46-)
2049	while [[ "$zeile" != "" ]]
2050	do
2051	spalte1=""
2052	spalte2=$(echo "$zeile" \| cut -c-45)
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054	zeile=$(echo "$zeile" \| cut -c46-)
2055	done
2056
2057	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2058	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2059	zeile=$(echo "$lopts" \| cut -c46-)
2060	while [[ "$zeile" != "" ]]
2061	do
2062	spalte1=""
2063	spalte2=$(echo "$zeile" \| cut -c-45)
2064	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2065	zeile=$(echo "$zeile" \| cut -c46-)
2066	done
2067
2068	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2069	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2070	zeile=$(echo "$modules" \| cut -c46-)
2071	while [[ "$zeile" != "" ]]
2072	do
2073	spalte1=""
2074	spalte2=$(echo "$zeile" \| cut -c-45)
2075	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2076	zeile=$(echo "$zeile" \| cut -c46-)
2077	done
2078
2079	spalte1="main program:"; spalte2=$mainprog
2080	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2081	else
2082	spalte1=executable:; spalte2=$executable
2083	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2084	fi
2085	printf "\| \| \n"
2086	spalte1="base name of files:"; spalte2=$fname
2087	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2088	if [[ $fname != $afname ]]
2089	then
2090	spalte1="base name of input files:"; spalte2=$afname
2091	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2092	fi
2093	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2094	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2095	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2096	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2097
2098	if [[ "$ocean_file_appendix" = true ]]
2099	then
2100	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2101	fi
2102
2103	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2104	then
2105	spalte1="memory demand / PE":; spalte2="$memory MB"
2106	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2107	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2108	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2109	fi
2110
2111	if [[ $do_compile = true ]]
2112	then
2113	printf "\| \| \n"
2114	printf "\| Files to be compiled: \| \n"
2115	zeile=$source_list
2116	while [[ "$zeile" != "" ]]
2117	do
2118	linestart=$(echo $zeile \| cut -c-70)
2119	printf "\| %-70s \| \n" "$linestart"
2120	zeile=$(echo "$zeile" \| cut -c71-)
2121	done
2122	fi
2123	printf "#------------------------------------------------------------------------#"
2124
2125
2126
2127	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2128	if [[ $do_trace = true ]]
2129	then
2130	(( i = 0 ))
2131	while (( i < iin ))
2132	do
2133	(( i = i + 1 ))
2134	if (( i == 1 ))
2135	then
2136	printf "\n\n >>> INPUT-file assignments:\n"
2137	fi
2138	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2139	done
2140	(( i = 0 ))
2141	while (( i < iout ))
2142	do
2143	(( i = i + 1 ))
2144	if (( i == 1 ))
2145	then
2146	printf "\n\n >>> OUTPUT-file assignments:\n"
2147	fi
2148	printf "\n ${localout[$i]} : ${pathout[$i]}"
2149	done
2150	(( i = 0 ))
2151	while (( i < iic ))
2152	do
2153	(( i = i + 1 ))
2154	if (( i == 1 ))
2155	then
2156	printf "\n\n >>> INPUT-commands:\n"
2157	fi
2158	printf "\n ${in_command[$i]}"
2159	done
2160	(( i = 0 ))
2161	while (( i < ioc ))
2162	do
2163	(( i = i + 1 ))
2164	if (( i == 1 ))
2165	then
2166	printf "\n\n >>> OUTPUT-commands:\n"
2167	fi
2168	printf "\n ${out_command[$i]}"
2169	done
2170	fi
2171
2172
2173	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2174	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2175	then
2176	antwort=dummy
2177	printf "\n\n"
2178	printf " >>> everything o.k. (y/n) ? "
2179	while read antwort
2180	do
2181	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2182	then
2183	printf " >>> everything o.k. (y/n) ? "
2184	else
2185	break
2186	fi
2187	done
2188	if [[ $antwort = n \|\| $antwort = N ]]
2189	then
2190	locat=user_abort; (( iec = 0 )); exit
2191	fi
2192	if [[ $do_batch = true ]]
2193	then
2194	printf " >>> batch-job will be created and submitted"
2195	else
2196	printf " >>> MRUN will now continue to execute on this machine"
2197	fi
2198	fi
2199
2200
2201	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2202	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2203	check_depository="${working_directory}/trunk/UTIL"
2204	check_sources="${working_directory}/tmp_check_namelist_files"
2205	skip_check=false
2206
2207	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2208	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2209	then
2210	skip_check=true
2211	reason="run on remote host or parameter file check has not been compiled."
2212	fi
2213	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2214	then
2215	skip_check=true
2216	reason="parameter file check has not been compiled."
2217	fi
2218
2219	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2220	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2221	then
2222	skip_check=true
2223	reason="serial run."
2224	fi
2225
2226	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2227	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2228	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2229	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2230	if [[ $check_namelist_files == false ]]
2231	then
2232	skip_check=true
2233	reason="-z option set."
2234	fi
2235
2236	if [[ $fromhost != $localhost ]]
2237	then
2238	skip_check=true
2239	reason="submitting host is local host."
2240	fi
2241
2242	if [[ $run_coupled_model == true ]]
2243	then
2244	skip_check=true
2245	reason="coupled run."
2246	fi
2247
2248	if [[ $restart_run == true ]]
2249	then
2250	skip_check=true
2251	reason="restart run."
2252	fi
2253
2254	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2255	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2256	last_char=`echo $filename_input \| cut -c $last_char_int`
2257	if [[ "$last_char" == "f" ]]
2258	then
2259	skip_check=true
2260	reason="restart run."
2261	fi
2262
2263	if [[ $skip_check == false ]]
2264	then
2265	tmp_check=${working_directory}/tmp_check
2266
2267	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2268	# NOT NECESSARILY REQUIRED
2269	line=""
2270	found=false
2271	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2272	while read line1
2273	do
2274	line="$line1"
2275	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2276	then
2277	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2278	found=true
2279	fi
2280	done < $tmp_check
2281
2282	if [[ $found = false ]]
2283	then
2284	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2285	fi
2286
2287	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2288	# NOT NECESSARILY REQUIRED
2289	line=""
2290	found=false
2291	grep "NUDGING_DATA" $config_file > $tmp_check
2292	while read line1
2293	do
2294	line="$line1"
2295	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2296	then
2297	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2298	found=true
2299	fi
2300	done < $tmp_check
2301
2302	if [[ $found = false ]]
2303	then
2304	printf "\n +++ no NUDGING list entry found in the configuration file."
2305	fi
2306
2307	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2308	# NOT NECESSARILY REQUIRED
2309	line=""
2310	found=false
2311	grep "LSF_DATA" $config_file > $tmp_check
2312	while read line1
2313	do
2314	line="$line1"
2315	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2316	then
2317	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2318	found=true
2319	fi
2320	done < $tmp_check
2321
2322	if [[ $found = false ]]
2323	then
2324	printf "\n +++ no LSF list entry found in the configuration file."
2325	fi
2326
2327	rm -rf ${working_directory}/tmp_check
2328
2329	# CHECK IF THE P3DF FILE MUST BE CHECKED
2330	for item in $input_list
2331	do
2332	if [[ "$item" == "restart" ]]
2333	then
2334	check_restart=1
2335	else
2336	check_restart=0
2337	fi
2338	done
2339
2340	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2341	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2342	then
2343	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2344	locat=check_namelist; exit
2345	fi
2346
2347	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2348	if [[ $check_restart == 1 ]]
2349	then
2350
2351	filenamef="${filename_input}f"
2352	if [[ ! -f $filenamef ]]
2353	then
2354	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2355	check_restart=0
2356	answer=dummy
2357	printf "\n\n"
2358
2359	if [[ $silent == false ]]
2360	then
2361	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2362	do
2363	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2364	read answer
2365	done
2366	if [[ $answer = a \|\| $answer = A ]]
2367	then
2368	printf "\n +++ Aborting...."
2369	locat=normal; exit
2370	fi
2371	fi
2372	else
2373	check_restart=1
2374	fi
2375	fi
2376
2377	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2378	mkdir $check_sources
2379	cd $check_sources
2380
2381
2382	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2383	if [[ -d $add_source_path ]]
2384	then
2385	printf "\n\n *** copying files from $check_depository"
2386	cp $check_depository/check_namelist_files.tar ./
2387
2388	printf "\n\n *** untar of makefile and source files in $check_sources"
2389	tar -xf check_namelist_files.tar > /dev/null 2>&1
2390
2391	printf "\n\n *** adding user code."
2392	cp $add_source_path/* ./
2393	touch check_namelist_files.f90
2394
2395	# GET COMPILER OPTIONS AND PERFORM MAKE
2396	printf "\n\n *** compiling code if necessary...\n"
2397
2398	# workaround for batch jobs on local machine (lcxe6)
2399	if [[ $do_batch == true && $do_remote == false ]]
2400	then
2401	eval $init_cmds
2402	fi
2403
2404	# GET CHECK OPTIONS
2405	line=""
2406	found=false
2407
2408	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2409
2410	while read line1
2411	do
2412
2413	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2414	then
2415	line="$line1"
2416	fi
2417
2418	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2419	then
2420	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2421	line="$line "
2422	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'`
2423	found=true
2424	fi
2425
2426	done < $tmp_check
2427	copts_check="$copts_check -D__check -D__parallel"
2428
2429	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2430
2431	# GET MAKE OUTPUT
2432	if [[ $? != 0 ]]
2433	then
2434	printf "\n +++ error during make."
2435	answer=dummy
2436	printf "\n\n"
2437	if [[ $silent == false ]]
2438	then
2439	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2440	do
2441	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2442	read answer
2443	done
2444	if [[ $answer = a \|\| $answer = A ]]
2445	then
2446	printf "\n +++ Aborting..."
2447	rm -rf $check_sources
2448	locat=normal; exit
2449	else
2450	skip_check=true
2451	fi
2452	else
2453	skip_check=true
2454	fi
2455	fi
2456	else
2457	cp $PALM_BIN/check_namelist_files.x ./
2458	fi
2459
2460	cp $filename_input ./PARIN
2461	if [[ $check_restart == 1 ]]
2462	then
2463	cp $filenamef ./PARINF
2464	fi
2465
2466	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2467	then
2468	printf "\n *** adding topography data"
2469	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2470
2471	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2472	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2473	# WHICH REQUIRE SUFFICIENT MEMORY
2474	ulimit -s unlimited
2475	fi
2476
2477	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2478	then
2479	printf "\n *** adding nudging data"
2480	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2481	fi
2482
2483	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2484	then
2485	printf "\n *** adding large scale forcing data"
2486	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2487	fi
2488
2489	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2490	cat > ENVPAR << %%END%%
2491	&envpar run_identifier = '$fname', host = '$host',
2492	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2493	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2494	maximum_cpu_time_allowed = ${cpumax}.,
2495	revision = '$global_revision',
2496	local_dvrserver_running = $local_dvrserver_running /
2497
2498	%%END%%
2499
2500	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2501	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2502	then
2503	printf "\n +++ WARNING: check_namelist_files.x not found."
2504	answer=dummy
2505	printf "\n\n"
2506
2507	if [[ $silent == false ]]
2508	then
2509	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2510	do
2511	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2512	read answer
2513	done
2514	if [[ $answer = a \|\| $answer = A ]]
2515	then
2516	printf "\n +++ Aborting..."
2517	rm -rf $check_sources
2518	locat=normal; exit
2519	else
2520	printf "\n *** skipping parameter file check."
2521	fi
2522	fi
2523
2524	elif [[ $skip_check == false ]]
2525	then
2526	# STARTING THE PARAMETER FILE CHECK
2527	printf "\n\n *** starting parameter file check..."
2528
2529	# CHECKING THE P3D FILE
2530	printf "\n\n (1) checking $filename_input"
2531	echo "$numprocs 0 0" > VARIN
2532	errors=`./check_namelist_files.x < VARIN 2>&1`
2533
2534	check_error=false
2535	if [[ "$errors" == "" ]]
2536	then
2537	printf " --> o.k."
2538	else
2539	printf " --> failed."
2540	check_error=true
2541	printf "\n\n $errors"
2542	fi
2543
2544	# CHECKING THE PD3F FILE IF NECESSARY
2545	if [[ $check_restart == 1 && $check_error == false ]]
2546	then
2547	printf "\n\n (2) checking $filenamef"
2548
2549	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2550	# IN &INIPAR LIST
2551	found=false
2552	cat PARINF \| while read line
2553	do
2554	line=$(echo $line\|sed 's/ //g')
2555	if [[ $line == "&inipar" ]]
2556	then
2557	start_search=true
2558	fi
2559
2560	if [[ $start_search == true ]]
2561	then
2562	if [[ $line == "initializing_actions='read_restart_data'" ]]
2563	then
2564	found=true
2565	break
2566	fi
2567	fi
2568
2569	if [[ $line == "/" ]]
2570	then
2571	start_search=false
2572	fi
2573
2574	done
2575
2576	if [[ $found = false ]]
2577	then
2578	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2579	printf "\n in &inipar list in $fname$p3df_suffix."
2580	rm -rf $check_sources
2581	locat=check_namelist; exit
2582	fi
2583
2584	# READ max_user_pr FROM FILES
2585	if [[ -f parin_for_check ]]
2586	then
2587	read max_pr_user < parin_for_check
2588	else
2589	max_user_pr=0
2590	fi
2591
2592	echo "$numprocs 1 $max_pr_user" > VARIN
2593	errors=`./check_namelist_files.x < VARIN 2>&1`
2594
2595	if [[ "$errors" == "" ]]
2596	then
2597	printf " --> o.k."
2598	else
2599	printf " --> failed."
2600	check_error=true
2601	printf "\n\n $errors"
2602	fi
2603	fi
2604
2605	# REPORT ERRORS AND CONTINUE/EXIT
2606	if [[ $check_error == true ]]
2607	then
2608	printf "\n +++ errors found in the parameter file!\n"
2609	answer=dummy
2610	printf "\n\n"
2611
2612	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2613	do
2614	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2615	read answer
2616	done
2617
2618	if [[ $answer = a \|\| $answer = A ]]
2619	then
2620	printf "\n +++ Aborting..."
2621	rm -rf $check_sources
2622	locat=normal; exit
2623	fi
2624	else
2625	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2626	fi
2627	rm -rf $check_sources
2628	fi
2629	else
2630	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2631	fi
2632
2633	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2634	rm -rf $check_sources
2635	cd $working_directory
2636
2637
2638	# DETERMINE PATH FOR MAKE DEPOSITORY
2639	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2640	then
2641
2642	line=""
2643	grep "%depository_path" $config_file > tmp_mrun
2644	while read line
2645	do
2646	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2647	then
2648	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2649	then
2650	global_depository_path=`echo $line \| cut -d" " -s -f2`
2651	fi
2652	fi
2653	done < tmp_mrun
2654
2655	line=""
2656	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2657	while read line
2658	do
2659	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2660	then
2661	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2662	then
2663	local_depository_path=`echo $line \| cut -d" " -s -f2`
2664	fi
2665	fi
2666	done < tmp_mrun
2667
2668	if [[ "$local_depository_path" = "" ]]
2669	then
2670	if [[ "$global_depository_path" != "" ]]
2671	then
2672	local_depository_path=$global_depository_path
2673	else
2674	printf "\n\n +++ no depository path found in configuration file"
2675	printf "\n for local host \"$localhost\" "
2676	printf "\n please set \"\%depository_path\" in configuration file\n"
2677	locat=config_file; exit
2678	fi
2679	fi
2680	eval local_depository_path=$local_depository_path
2681	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2682	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2683
2684
2685	basename=`echo $mainprog \| cut -f1 -d"."`
2686	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2687	if [[ ! -f $make_depository ]]
2688	then
2689	printf "\n"
2690	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2691	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2692	fi
2693
2694	fi
2695
2696
2697	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2698	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2699	if [[ $do_batch = false ]]
2700	then
2701
2702
2703	# CREATE THE TEMPORARY WORKING DIRECTORY
2704	mkdir -p $TEMPDIR
2705	chmod go+rx $TEMPDIR
2706	tmpcreate=true
2707
2708
2709	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2710	# INTO THE TEMPORARY WORKING DIRECTORY
2711	if [[ $do_compile = true ]]
2712	then
2713
2714	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2715	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2716	if [[ $localhost = nech ]]
2717	then
2718	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2719	if mkdir -p $TEMPDIR_COMPILE
2720	then
2721	printf "\n *** \"$TEMPDIR_COMPILE\" "
2722	printf "\n is generated as temporary directory for cross compiling\n"
2723	else
2724	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2725	printf "\n needed for cross compilation failed"
2726	locat=compile
2727	exit
2728	fi
2729	else
2730	TEMPDIR_COMPILE=$TEMPDIR
2731	fi
2732
2733	cp $make_depository $TEMPDIR_COMPILE
2734	cd $TEMPDIR_COMPILE
2735	tar -xf $make_depository > /dev/null 2>&1
2736	cd - > /dev/null
2737
2738	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2739	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2740	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2741	then
2742	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2743	else
2744	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2745	fi
2746
2747	else
2748
2749	cp $executable ${TEMPDIR}/a.out
2750
2751	fi
2752
2753
2754	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2755	cd $TEMPDIR
2756	printf "\n *** changed to temporary directory: $TEMPDIR"
2757
2758
2759	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2760	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2761	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2762	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2763	(( i = 0 ))
2764	while (( i < iout ))
2765	do
2766	(( i = i + 1 ))
2767	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2768	then
2769	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2770	else
2771	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2772	fi
2773	done
2774
2775
2776	# IF REQUIRED, START WITH COMPILING
2777	if [[ $do_compile = true ]]
2778	then
2779
2780
2781	if [[ -f a.out ]]
2782	then
2783
2784	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2785	printf "\n\n\n *** executable a.out found"
2786	printf "\n no compilation required \n"
2787
2788	else
2789
2790	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2791	printf "\n\n\n *** compilation starts \n$dashes\n"
2792	printf " *** compilation with make using following options:\n"
2793	printf " make depository: $make_depository"
2794	if [[ "$mopts" != "" ]]
2795	then
2796	printf " make options: $mopts\n"
2797	fi
2798	printf " compilername: $compiler_name\n"
2799	printf " compiler options: $fopts\n"
2800	printf " preprocessor directives: $cpp_options \n"
2801	printf " linker options: $lopts \n"
2802	if [[ "$modules" != "" ]]
2803	then
2804	printf " modules to be load: $modules \n"
2805	fi
2806	printf " source code files: $source_list \n"
2807
2808	if [[ $localhost = nech ]]
2809	then
2810	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\" "
2811	cp $TEMPDIR_COMPILE/a.out .
2812	[[ $? != 0 ]] && compile_error=true
2813	rm -rf $TEMPDIR_COMPILE
2814	elif [[ $localhost = ibmh ]]
2815	then
2816	printf " compiler is called via ssh on \"plogin1\" \n"
2817	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\" "
2818	[[ ! -f a.out ]] && compile_error=true
2819	continue # STATUS=1, IF a.out EXISTS
2820	elif [[ $localhost = lcflow ]]
2821	then
2822	printf " compiler is called via ssh on \"flow\" \n"
2823	/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\" "
2824	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2825	[[ "$check_for_file" = "" ]] && compile_error=true
2826	continue # STATUS=1, IF a.out EXISTS
2827	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2828	then
2829	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2830	else
2831	[[ "$init_cmds" != "" ]] && eval $init_cmds
2832	[[ "$module_calls" != "" ]] && eval $module_calls
2833	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2834	fi
2835
2836	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2837	then
2838	printf "\n +++ error occured while compiling or linking"
2839	locat=compile
2840
2841	exit
2842	else
2843	printf "$dashes\n *** compilation finished \n"
2844	fi
2845
2846	fi
2847
2848	fi
2849
2850
2851	# PROVIDE THE INPUT FILES
2852	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2853	(( i = 0 ))
2854	while (( i < iin ))
2855	do
2856	(( i = i + 1 ))
2857	if (( i == 1 ))
2858	then
2859	printf "\n\n *** providing INPUT-files:\n$dashes"
2860	fi
2861
2862
2863	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2864	if [[ "${transin[$i]}" = unavailable ]]
2865	then
2866	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2867	then
2868	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2869	printf "\n is not available!"
2870	else
2871	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2872	printf "\n is not available!"
2873	fi
2874	continue
2875	fi
2876
2877	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2878	files_for_pes=false; datentyp=file
2879	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2880	then
2881	files_for_pes=true; datentyp=directory
2882	actionin[$i]=""
2883	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2884	then
2885	actionin[$i]=""
2886	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2887	then
2888	files_for_pes=true; datentyp=directory
2889	actionin[$i]="ar"
2890	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2891	then
2892	actionin[$i]="ar"
2893	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2894	then
2895	files_for_pes=true; datentyp=directory
2896	actionin[$i]="fl"
2897	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2898	then
2899	actionin[$i]="fl"
2900	fi
2901
2902	if [[ $files_for_pes = true ]]
2903	then
2904	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2905	else
2906	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2907	fi
2908
2909	# INPUT-FILE FOR A RESTART RUN.
2910	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2911	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2912	if [[ "${actionin[$i]}" = fl ]]
2913	then
2914	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2915	if [[ $files_for_pes = false ]]
2916	then
2917	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2918	then
2919	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2920	got_tmp[$i]=true
2921	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2922	then
2923	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2924	printf "\n *** trying to use backup copy in \"$WORK\" "
2925	cp $WORK/${frelin[$i]} ${localin[$i]}
2926	else
2927	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2928	printf "\n or \"$tmp_data_catalog\" does not exist!"
2929	printf "\n *** trying to get copy from archive"
2930	actionin[$i]=ar
2931	fi
2932	else
2933	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2934	then
2935	mkdir ${localin[$i]}
2936	cd $tmp_data_catalog/${frelin[$i]}
2937	for file in $(ls *)
2938	do
2939	ln $file $TEMPDIR/${localin[$i]}
2940	done
2941	cd $TEMPDIR
2942	got_tmp[$i]=true
2943	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2944	then
2945	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2946	printf "\n *** trying to use backup copy in \"$WORK\" "
2947	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2948	else
2949	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2950	printf "\n or \"$tmp_data_catalog\" does not exist!"
2951	printf "\n *** trying to get copy from archive"
2952	actionin[$i]=ar
2953	fi
2954	fi
2955	fi
2956
2957
2958	# FILE IS STORED ON THE ARCHIVE SYSTEM
2959	if [[ "${actionin[$i]}" = ar ]]
2960	then
2961
2962	if [[ $files_for_pes = false ]]
2963	then
2964	printf "\n file will be restored from archive-system ($archive_system)!"
2965	else
2966	printf "\n directory will be restored from archive-system ($archive_system)!"
2967	fi
2968
2969	file_restored=false
2970
2971	if [[ $archive_system = asterix ]]
2972	then
2973	do_stagein=true
2974	(( stagein_anz = 0 ))
2975	while [[ $do_stagein = true ]]
2976	do
2977	if [[ $files_for_pes = false ]]
2978	then
2979	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2980	else
2981	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2982	fi
2983	cat STAGEIN_OUTPUT
2984	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2985	then
2986	file_restored=true
2987	do_stagein=false
2988	else
2989	(( stagein_anz = stagein_anz + 1 ))
2990	if (( stagein_anz == 10 ))
2991	then
2992	printf "\n +++ stagein stoped after 10 tries"
2993	locat=stage
2994	exit
2995	fi
2996	printf "\n +++ restoring from archive failed, trying again:"
2997	sleep 900
2998	fi
2999	done
3000	elif [[ $archive_system = DMF ]]
3001	then
3002	if [[ $files_for_pes = false ]]
3003	then
3004	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3005	locat=DMF
3006	exit
3007	else
3008	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3009	cp -r $ARCHIVE/${frelin[$i]} $PWD
3010	file_restored=true
3011	fi
3012	elif [[ $archive_system = tivoli ]]
3013	then
3014	if [[ $files_for_pes = false ]]
3015	then
3016	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3017	else
3018	(( inode = 0 ))
3019	while (( inode < nodes ))
3020	do
3021	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3022	(( inode = inode + 1 ))
3023	done
3024	fi
3025	file_restored=true
3026	elif [[ $archive_system = ut ]]
3027	then
3028	if [[ $files_for_pes = false ]]
3029	then
3030	cp $UT/${frelin[$i]} .
3031	else
3032	(( inode = 0 ))
3033	while (( inode < nodes ))
3034	do
3035	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3036	(( inode = inode + 1 ))
3037	done
3038	fi
3039	file_restored=true
3040	else
3041	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3042	locat=rearchive
3043	exit
3044	fi
3045
3046	if [[ $file_restored = true ]]
3047	then
3048
3049	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3050	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3051	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3052	if [[ $files_for_pes = false ]]
3053	then
3054	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3055	else
3056	mkdir $tmp_data_catalog/${frelin[$i]}
3057	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3058	fi
3059	got_tmp[$i]=true
3060
3061	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3062	mv ${frelin[$i]} ${localin[$i]}
3063
3064	fi
3065	fi
3066
3067
3068	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3069	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3070	then
3071
3072	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3073	then
3074
3075	# FILE COPIES ARE PROVIDED FOR ALL CORES
3076	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3077	printf "\n file will be provided for $numprocs processors"
3078	mkdir ${localin[$i]}
3079	ival=$numprocs
3080	(( ii = 0 ))
3081	while (( ii <= ival-1 ))
3082	do
3083	if (( ii < 10 ))
3084	then
3085	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3086	elif (( ii < 100 ))
3087	then
3088	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3089	elif (( ii < 1000 ))
3090	then
3091	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3092	else
3093	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3094	fi
3095	(( ii = ii + 1 ))
3096	done
3097
3098	else
3099
3100	if [[ $files_for_pes = true ]]
3101	then
3102
3103	# PROVIDE FILES FOR EACH CORE
3104	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3105	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3106	printf "\n providing $numprocs files for the respective processors"
3107	mkdir ${localin[$i]}
3108	if [[ $link_local_input = true ]]
3109	then
3110	printf " using ln -f\n"
3111	cd ${absnamein[$i]}
3112	for file in $(ls *)
3113	do
3114	ln -f $file ${localin[$i]}
3115	done
3116	cd $TEMPDIR
3117	fi
3118
3119	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3120	if [[ ! -f "${localin[$i]}/_0000" ]]
3121	then
3122	if [[ $link_local_input = true ]]
3123	then
3124	printf " ln failed for .../_0000, using cp...\n"
3125	fi
3126	cp -r ${absnamein[$i]}/* ${localin[$i]}
3127	fi
3128
3129	else
3130
3131	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3132	if [[ $link_local_input = true ]]
3133	then
3134	printf " using ln -f\n"
3135	ln -f ${absnamein[$i]} ${localin[$i]}
3136	fi
3137	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3138	if [[ ! -f "${localin[$i]}" ]]
3139	then
3140	if [[ $link_local_input = true ]]
3141	then
3142	printf " ln failed, using cp...\n"
3143	fi
3144	cp ${absnamein[$i]} ${localin[$i]}
3145	fi
3146	fi
3147	fi
3148	fi
3149
3150	done
3151	if (( i != 0 ))
3152	then
3153	printf "\n$dashes\n *** all INPUT-files provided \n"
3154	fi
3155
3156
3157	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3158	(( i = 0 ))
3159	while (( i < iic ))
3160	do
3161	(( i = i + 1 ))
3162	if (( i == 1 ))
3163	then
3164	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3165	fi
3166	printf "\n >>> ${in_command[$i]}"
3167	eval ${in_command[$i]}
3168	if (( i == iic ))
3169	then
3170	printf "\n$dashes\n"
3171	fi
3172	done
3173
3174
3175	# SET THE REMAINING CPU-TIME
3176	cpurest=${cpumax}.
3177
3178
3179	# START DVR STREAMING SERVER
3180	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3181	then
3182	if [[ "$dvr_server" != "" ]]
3183	then
3184
3185	printf "\n\n *** preparing the dvr streaming server configuration file"
3186
3187	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3188	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3189	if [[ "$running_dvrserver_id" != "" ]]
3190	then
3191
3192	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3193	printf "\n This server is used instead starting a new one!"
3194	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3195
3196	else
3197
3198	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3199	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3200	then
3201	cp ${PALM_BIN}/.dvrserver.config .
3202
3203	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3204	user_id=`id -u`
3205	group_id=`id -g`
3206
3207	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3208	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3209	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3210	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3211	mv .dvrserver.3 .dvrserver.config
3212	rm .dvrserver.1 .dvrserver.2
3213
3214	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3215	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3216	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3217	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3218	local_dvrserver_running=.TRUE.
3219	else
3220	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3221	printf "\n \"$PALM_BIN\" "
3222	locat=dvr
3223	exit
3224	fi
3225
3226	fi
3227
3228	else
3229	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3230	fi
3231	fi
3232
3233
3234	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3235	# (FILE ENVPAR WILL BE READ BY PALM)
3236	cat > ENVPAR << %%END%%
3237	&envpar run_identifier = '$fname', host = '$localhost',
3238	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3239	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3240	maximum_cpu_time_allowed = ${cpumax}.,
3241	revision = '$global_revision',
3242	local_dvrserver_running = $local_dvrserver_running,
3243	batch_job = $batch_job /
3244
3245	%%END%%
3246
3247
3248	# STARTING THE EXECUTABLE
3249	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3250	PATH=$PATH:$TEMPDIR
3251
3252	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3253	if [[ "$mpi_debug" = true ]]
3254	then
3255	export MPI_CHECK_ARGS=1
3256	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3257	fi
3258
3259	if [[ "$totalview" = true ]]
3260	then
3261	printf "\n *** totalview debugger will be used"
3262	tv_opt="-tv"
3263	else
3264	tv_opt=""
3265	fi
3266
3267	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3268	then
3269
3270	#Interactive ALLINEA DEBUG seesion
3271	if [[ "$ENVIRONMENT" != BATCH ]]
3272	then
3273	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3274	then
3275	if [[ "$allinea" = true ]]
3276	then
3277	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3278
3279	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3280	wait
3281	fi
3282	fi
3283	fi
3284
3285	if [[ "$ENVIRONMENT" = BATCH ]]
3286	then
3287	continue
3288	fi
3289	if [[ $localhost = ibmh ]]
3290	then
3291
3292	# SETUP THE IBM MPI ENVIRONMENT
3293	export MP_SHARED_MEMORY=yes
3294	export AIXTHREADS_SCOPE=S
3295	export OMP_NUM_THREADS=$threads_per_task
3296	export AUTHSTATE=files
3297	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3298
3299	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3300	export MP_ADAPTER_USE=shared
3301	export MP_CPU_USE=multiple
3302	export MP_TIMEOUT=1200
3303
3304	unset MP_TASK_AFFINITY
3305
3306	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3307	#(( ii = 1 ))
3308	#while (( ii <= $numprocs ))
3309	#do
3310	# echo $localhost_realname >> hostfile
3311	# (( ii = ii + 1 ))
3312	#done
3313	#export MP_HOSTFILE=hostfile
3314
3315	if [[ "$LOADLBATCH" = yes ]]
3316	then
3317	totalview poe a.out $ROPTS
3318	else
3319	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3320	export TVDSVRLAUNCHCMD=ssh
3321	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3322	fi
3323
3324	fi # END DEBUG MODE
3325
3326	else
3327
3328	# NORMAL EXECUTION
3329	if [[ -n $numprocs ]]
3330	then
3331
3332	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3333	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3334	then
3335
3336	# SETUP THE IBM MPI ENVIRONMENT
3337	if [[ $host != ibmh && $host != ibmkisti ]]
3338	then
3339	export MP_SHARED_MEMORY=yes
3340	export AIXTHREAD_SCOPE=S
3341	export OMP_NUM_THREADS=$threads_per_task
3342	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3343	export AUTHSTATE=files
3344	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3345	# export MP_PRINTENV=yes
3346
3347	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3348	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3349	export MP_WAIT_MODE=poll
3350	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3351	fi
3352
3353	if [[ $host = ibmkisti ]]
3354	then
3355	export LANG=en_US
3356	export MP_SHARED_MEMORY=yes
3357	if [[ $threads_per_task = 1 ]]
3358	then
3359	export MP_SINGLE_THREAD=yes
3360	export MEMORY_AFFINITY=MCM
3361	else
3362	export OMP_NUM_THREADS=$threads_per_task
3363	fi
3364	fi
3365
3366	if [[ "$LOADLBATCH" = yes ]]
3367	then
3368	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3369	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3370	then
3371	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3372	else
3373	if [[ $run_coupled_model = false ]]
3374	then
3375	if [[ "$ocean_file_appendix" = true ]]
3376	then
3377	echo "precursor_ocean" > runfile_atmos
3378	else
3379	echo "precursor_atmos" > runfile_atmos
3380	fi
3381	else
3382	(( iia = $numprocs_atmos / $threads_per_task ))
3383	(( iio = $numprocs_ocean / $threads_per_task ))
3384	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3385	printf "\n using $coupled_mode coupling"
3386	printf "\n\n"
3387	echo "coupled_run $iia $iio" > runfile_atmos
3388	fi
3389	poe ./a.out $ROPTS < runfile_atmos
3390	fi
3391	else
3392	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3393	then
3394	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3395	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3396	then
3397	if [[ -f $hostfile ]]
3398	then
3399	cp $hostfile hostfile
3400	else
3401	(( ii = 1 ))
3402	while (( ii <= $numprocs ))
3403	do
3404	echo $localhost_realname >> hostfile
3405	(( ii = ii + 1 ))
3406	done
3407	fi
3408	export MP_HOSTFILE=hostfile
3409	if [[ $run_coupled_model = false ]]
3410	then
3411	if [[ "$ocean_file_appendix" = true ]]
3412	then
3413	echo "precursor_ocean" > runfile_atmos
3414	else
3415	echo "precursor_atmos" > runfile_atmos
3416	fi
3417	else
3418	(( iia = $numprocs_atmos / $threads_per_task ))
3419	(( iio = $numprocs_ocean / $threads_per_task ))
3420	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3421	printf "\n using $coupled_mode coupling"
3422	printf "\n\n"
3423	echo "coupled_run $iia $iio" > runfile_atmos
3424	fi
3425
3426	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3427
3428	else
3429	if [[ "$host_file" = "" ]]
3430	then
3431	printf "\n +++ no hostfile given in configuration file"
3432	locat=config_file
3433	exit
3434	else
3435	eval host_file=$host_file
3436	fi
3437	export MP_HOSTFILE=$host_file
3438	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3439	fi
3440	fi
3441	elif [[ $host = nech ]]
3442	then
3443	(( ii = nodes ))
3444	if [[ $ii = 1 ]]
3445	then
3446	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3447	export MPIPROGINF=YES
3448	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3449	echo "*** execution on single node with mpirun"
3450	mpirun -np $numprocs ./a.out $ROPTS
3451	else
3452	(( i = 0 ))
3453	while (( i < ii ))
3454	do
3455	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3456	(( i = i + 1 ))
3457	done
3458
3459	echo "#!/bin/sh" > mpi_exec_shell
3460	echo " " >> mpi_exec_shell
3461	echo "set -u" >> mpi_exec_shell
3462	echo "F_ERRCNT=0" >> mpi_exec_shell
3463	echo "MPIPROGINV=YES" >> mpi_exec_shell
3464	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3465	echo "cpurest=$cpurest" >> mpi_exec_shell
3466	echo "fname=$fname" >> mpi_exec_shell
3467	echo "localhost=$localhost" >> mpi_exec_shell
3468	echo "return_address=$return_address" >> mpi_exec_shell
3469	echo "return_username=$return_username" >> mpi_exec_shell
3470	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3471	echo "write_binary=$write_binary" >> mpi_exec_shell
3472	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3473	echo " " >> mpi_exec_shell
3474	echo "export F_ERRCNT" >> mpi_exec_shell
3475	echo "export MPIPROGINV" >> mpi_exec_shell
3476	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3477	echo "export cpurest" >> mpi_exec_shell
3478	echo "export fname" >> mpi_exec_shell
3479	echo "export localhost" >> mpi_exec_shell
3480	echo "export return_address" >> mpi_exec_shell
3481	echo "export return_username" >> mpi_exec_shell
3482	echo "export tasks_per_node" >> mpi_exec_shell
3483	echo "export write_binary" >> mpi_exec_shell
3484	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3485	echo " " >> mpi_exec_shell
3486	echo "exec ./a.out" >> mpi_exec_shell
3487
3488	chmod u+x mpi_exec_shell
3489	export MPIPROGINF=YES
3490	mpirun -f multinode_config &
3491	wait
3492
3493	fi
3494	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3495	then
3496
3497	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3498	# DOES NOT EXIST
3499	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3500	then
3501	if [[ -f $hostfile ]]
3502	then
3503	cp $hostfile hostfile
3504	(( ii = $numprocs / $threads_per_task ))
3505	[[ $ii = 0 ]] && (( ii = 1 ))
3506	else
3507	(( ii = 1 ))
3508	while (( ii <= $numprocs / $threads_per_task ))
3509	do
3510	echo $localhost_realname >> hostfile
3511	(( ii = ii + 1 ))
3512	done
3513	if (( $numprocs / $threads_per_task == 0 ))
3514	then
3515	echo $localhost_realname >> hostfile
3516	fi
3517	fi
3518	eval zeile=\"`head -n $ii hostfile`\"
3519	printf "\n *** running on: $zeile"
3520	fi
3521
3522	(( ii = $numprocs / $threads_per_task ))
3523	[[ $ii = 0 ]] && (( ii = 1 ))
3524	export OMP_NUM_THREADS=$threads_per_task
3525
3526	if [[ $threads_per_task != 1 ]]
3527	then
3528	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3529	# MAY ABORT
3530	ulimit -s unlimited
3531	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3532	fi
3533	if [[ $run_coupled_model = false ]]
3534	then
3535	if [[ "$ocean_file_appendix" = true ]]
3536	then
3537	echo "precursor_ocean" > runfile_atmos
3538	else
3539	echo "precursor_atmos" > runfile_atmos
3540	fi
3541	printf "\n\n"
3542
3543	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3544	then
3545	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3546	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3547	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3548	elif [[ $host = lccrayf ]]
3549	then
3550	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3551	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3552	then
3553	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3554	elif [[ $host = lcflow ]]
3555	then
3556	mpirun -np $ii a.out < runfile_atmos $ROPTS
3557	elif [[ $host = lcsb ]]
3558	then
3559	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3560	elif [[ $host = lckiaps ]]
3561	then
3562	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3563	elif [[ $host = lckyu* ]]
3564	then
3565	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3566	else
3567	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3568	fi
3569	else
3570
3571	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3572	(( iia = $numprocs_atmos / $threads_per_task ))
3573	(( iio = $numprocs_ocean / $threads_per_task ))
3574	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3575	printf "\n using $coupled_mode coupling"
3576	printf "\n\n"
3577
3578	if [[ $coupled_mode = "mpi2" ]]
3579	then
3580	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3581	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3582
3583	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3584	then
3585
3586	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3587	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3588
3589	else
3590	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3591	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3592	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3593	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3594	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3595	fi
3596	wait
3597
3598	else
3599
3600	echo "coupled_run $iia $iio" > runfile_atmos
3601
3602	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3603	then
3604
3605	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3606
3607	elif [[ $host = lck \|\| $host = lckordi ]]
3608	then
3609
3610	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3611
3612	elif [[ $host = lckyu* ]]
3613	then
3614
3615	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3616
3617	elif [[ $host = lcmuk ]]
3618	then
3619
3620	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3621
3622	fi
3623	wait
3624	fi
3625
3626	fi
3627
3628	elif [[ $host = lckyoto ]]
3629	then
3630	set -xv
3631	export P4_RSHCOMMAND=plesh
3632	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3633	if [[ "$ENVIRONMENT" = BATCH ]]
3634	then
3635	if [[ "$cond2" = fujitsu ]]
3636	then
3637	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3638	elif [[ "cond2" = pgi ]]
3639	then
3640	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3641	else
3642	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3643	fi
3644	else
3645	if [[ "$cond2" = "" ]]
3646	then
3647	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3648	else
3649	mpirun -np $numprocs ./a.out $ROPTS
3650	fi
3651	fi
3652	set +xv
3653
3654	elif [[ $host = lctit ]]
3655	then
3656	export OMP_NUM_THREADS=$threads_per_task
3657	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3658	if [[ "$threads_per_task" != 1 ]]
3659	then
3660	export MV2_ENABLE_AFFINITY=0
3661	fi
3662	echo "----- PBS_NODEFILE content:"
3663	cat $PBS_NODEFILE
3664	echo "-----"
3665	(( ii = $numprocs / $threads_per_task ))
3666	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3667	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3668	else
3669	mpprun -n $numprocs a.out $ROPTS
3670	fi
3671	else
3672	a.out $ROPTS
3673	fi
3674	fi
3675
3676	if [[ $? != 0 ]]
3677	then
3678
3679	# ABORT IN CASE OF RUNTIME ERRORS
3680	printf "\n +++ runtime error occured"
3681	locat=execution
3682	exit
3683
3684	else
3685
3686	printf "\n$dashes\n *** execution finished \n"
3687
3688	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3689	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3690	if [[ "$dvrserver_id" != "" ]]
3691	then
3692	kill $dvrserver_id
3693	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3694
3695	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3696	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3697	if [[ -d DATA_DVR ]]
3698	then
3699
3700	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3701	# DIRECTORY
3702	cp .dvrserver.config DATA_DVR
3703
3704	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3705	# SEQUENCE MODE DATA TOO)
3706	process_dvr_output -d DATA_DVR -f $fname -s
3707
3708	else
3709
3710	# PROCESS THE LOCAL OUTPUT
3711	process_dvr_output -l -d DATA_DVR -f $fname
3712
3713	fi
3714
3715	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3716	then
3717
3718	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3719	process_dvr_output -l -d DATA_DVR -f $fname
3720
3721	fi
3722	fi
3723
3724
3725
3726	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3727	# BY EACH CORE INTO ONE FILE
3728	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3729	then
3730	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3731	printf "\n 2d- and/or 3d-data may be incomplete!"
3732	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3733	elif [[ "$combine_plot_fields" == true ]]
3734	then
3735	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3736	then
3737	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3738	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3739	else
3740	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3741	combine_plot_fields${block}.x
3742	fi
3743	else
3744
3745	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3746	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3747	# ??? koennen wir das streichen ???
3748	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3749	fi
3750
3751
3752
3753	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3754	(( i = 0 ))
3755	while (( i < ioc ))
3756	do
3757	(( i = i + 1 ))
3758	if (( i == 1 ))
3759	then
3760	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3761	fi
3762	printf "\n >>> ${out_command[$i]}"
3763	eval ${out_command[$i]}
3764	if (( i == ioc ))
3765	then
3766	printf "\n$dashes\n"
3767	fi
3768	done
3769
3770
3771	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3772	if [[ $do_trace = true ]]
3773	then
3774	printf "\n\n"
3775	ls -al
3776	fi
3777
3778
3779
3780	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3781	(( i = 0 ))
3782	while (( i < iout ))
3783	do
3784	(( i = i + 1 ))
3785	if (( i == 1 ))
3786	then
3787	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3788	fi
3789
3790	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3791	files_for_pes=false; filetyp=file
3792	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3793	then
3794	files_for_pes=true; filetyp=directory
3795	actionout[$i]=""
3796	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3797	then
3798	actionout[$i]=""
3799	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3800	then
3801	files_for_pes=true; filetyp=directory
3802	actionout[$i]="ar"
3803	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3804	then
3805	actionout[$i]="ar"
3806	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3807	then
3808	files_for_pes=true; filetyp=directory
3809	actionout[$i]="fl"
3810	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3811	then
3812	actionout[$i]="fl"
3813	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3814	then
3815	files_for_pes=true; filetyp=directory
3816	actionout[$i]="tr"
3817	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3818	then
3819	actionout[$i]="tr"
3820	fi
3821
3822	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3823	then
3824	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3825	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3826	then
3827	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3828	else
3829
3830
3831	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3832	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3833	if [[ "${actionout[$i]}" = tr ]]
3834	then
3835	if [[ $localhost != $fromhost ]]
3836	then
3837	if [[ $files_for_pes = false ]]
3838	then
3839	cps=""
3840	cst=""
3841	else
3842	cps=-c
3843	cst="/"
3844	fi
3845	if [[ $localhost = nech ]]
3846	then
3847
3848	# TRANSFER IN SEPERATE JOB
3849	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3850	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3851	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3852	if [[ $files_for_pes = false ]]
3853	then
3854	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3855	else
3856	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3857	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3858	fi
3859
3860	echo "set -x" > transfer_${localout[$i]}
3861	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3862
3863	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3864	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3865	printf "\n or higher cycle\n"
3866	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3867
3868	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3869
3870	if [[ $localhost = nech ]]
3871	then
3872	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3873	else
3874	if [[ "$LOGNAME" = b323013 ]]
3875	then
3876	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3877	else
3878	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3879	fi
3880	fi
3881
3882	else
3883
3884	# TRANSFER WITHIN THIS JOB
3885	transfer_failed=false
3886	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3887	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3888	if [[ $localhost = lccrayb ]]
3889	then
3890	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3891	elif [[ $localhost = lccrayh ]]
3892	then
3893	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3894	elif [[ $localhost = lcxe6 ]]
3895	then
3896	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3897	else
3898	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3899	fi
3900	[[ $? != 0 ]] && transfer_failed=true
3901
3902	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3903	if [[ $transfer_failed = true ]]
3904	then
3905	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3906	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3907
3908	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3909	eval local_catalog=${pathout[$i]}
3910	if [[ ! -d $local_catalog ]]
3911	then
3912	printf " *** local directory does not exist. Trying to create:\n"
3913	printf " $local_catalog \n"
3914	mkdir -p $local_catalog
3915	fi
3916	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3917	transfer_problems=true
3918	fi
3919	fi
3920	else
3921
3922	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3923	actionout[$i]=""
3924	fi
3925	fi
3926
3927
3928	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3929	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3930	if [[ "${actionout[$i]}" = tra ]]
3931	then
3932	if [[ $localhost != $fromhost ]]
3933	then
3934	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3935	then
3936
3937	# TRANSFER IN SEPERATE JOB
3938	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3939	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3940	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3941	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3942
3943	echo "set -x" > transfer_${localout[$i]}
3944	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3945
3946	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3947	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3948	printf "\n or higher cycle\n"
3949	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3950
3951	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3952
3953	if [[ $localhost = nech ]]
3954	then
3955	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3956	else
3957	if [[ $LOGNAME = b323013 ]]
3958	then
3959	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3960	else
3961	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3962	fi
3963	fi
3964
3965	else
3966
3967	# TRANSFER WITHIN THIS JOB
3968	transfer_failed=false
3969	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3970	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3971	if [[ $localhost = lccrayb ]]
3972	then
3973	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3974	elif [[ $localhost = lccrayh ]]
3975	then
3976	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3977	elif [[ $localhost = lcxe6 ]]
3978	then
3979	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3980	else
3981	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3982	fi
3983	[[ $? != 0 ]] && transfer_failed=true
3984
3985	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3986	if [[ $transfer_failed = true ]]
3987	then
3988	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3989	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3990
3991	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3992	eval local_catalog=${pathout[$i]}
3993	if [[ ! -d $local_catalog ]]
3994	then
3995	printf " *** local directory does not exist. Trying to create:\n"
3996	printf " $local_catalog \n"
3997	mkdir -p $local_catalog
3998	fi
3999
4000	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4001	transfer_problems=true
4002	fi
4003	fi
4004	else
4005
4006	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4007	actionout[$i]=a
4008	fi
4009	fi
4010
4011
4012	# OUTPUT-FILE FOR A RESTART-RUN.
4013	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4014	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4015	# AS LAST ACTION, ARCHIVING IS INITIATED.
4016	if [[ "${actionout[$i]}" = fl ]]
4017	then
4018	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4019	chmod g+rx $tmp_data_catalog
4020	if [[ $files_for_pes = false ]]
4021	then
4022	printf "\n >>> OUTPUT: ${localout[$i]} to"
4023	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4024	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4025	else
4026	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4027	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4028	mkdir $tmp_data_catalog/${frelout[$i]}
4029	cd ${localout[$i]}
4030	for file in $(ls *)
4031	do
4032	ln -f $file $tmp_data_catalog/${frelout[$i]}
4033	done
4034	cd $TEMPDIR
4035	fi
4036
4037
4038	# CREATE AND SUBMIT ARCHIVING-JOB
4039	if [[ $store_on_archive_system = true ]]
4040	then
4041
4042	if [[ $archive_system = asterix ]]
4043	then
4044	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4045	if [[ $files_for_pes = false ]]
4046	then
4047	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4048	else
4049	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4050	fi
4051	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4052	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4053	echo "then" >> archive_${frelout[$i]}
4054	echo " do_stageout=false" >> archive_${frelout[$i]}
4055	echo "else" >> archive_${frelout[$i]}
4056	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4057	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4058	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4059	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4060	if [[ $files_for_pes = false ]]
4061	then
4062	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4063	else
4064	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4065	fi
4066	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4067	echo "fi" >> archive_${frelout[$i]}
4068	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4069	elif [[ $archive_system = DMF ]]
4070	then
4071	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4072	if [[ $files_for_pes = false ]]
4073	then
4074	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4075	locat=DMF
4076	exit
4077	else
4078	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4079	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4080	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4081	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4082	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4083	fi
4084	elif [[ $archive_system = tivoli ]]
4085	then
4086	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4087	if [[ $files_for_pes = false ]]
4088	then
4089	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4090	echo "set -x" >> archive_${frelout[$i]}
4091	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4092	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4093	else
4094
4095	echo "set -x" >> archive_${frelout[$i]}
4096	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4097	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4098	cd $tmp_data_catalog
4099	all_files=`ls -1 ${frelout[$i]}/*`
4100	cd - > /dev/null
4101	(( inode = 0 ))
4102	(( tp1 = tasks_per_node + 1 ))
4103	while (( inode < nodes ))
4104	do
4105	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4106	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4107	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4108	(( inode = inode + 1 ))
4109	done
4110	fi
4111	elif [[ $archive_system = ut ]]
4112	then
4113	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4114	if [[ $files_for_pes = false ]]
4115	then
4116	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4117	echo "set -x" >> archive_${frelout[$i]}
4118	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4119	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4120	else
4121
4122	echo "set -x" >> archive_${frelout[$i]}
4123	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4124	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4125	cd $tmp_data_catalog
4126	all_files=`ls -1 ${frelout[$i]}/*`
4127	cd - > /dev/null
4128	(( inode = 0 ))
4129	(( tp1 = tasks_per_node + 1 ))
4130	while (( inode < nodes ))
4131	do
4132	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4133	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4134	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4135	(( inode = inode + 1 ))
4136	done
4137	fi
4138	elif [[ $archive_system = none ]]
4139	then
4140	printf " +++ archiving on $localhost not available!\n"
4141	fi
4142
4143	if [[ $archive_system != none ]]
4144	then
4145	if [[ $localhost = nech ]]
4146	then
4147	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4148	fi
4149	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4150	fi
4151	else
4152	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4153	fi
4154
4155
4156	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4157	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4158	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4159	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4160	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4161	if [[ $files_for_pes = false ]]
4162	then
4163	cat /dev/null > ${pathout[$i]}
4164	else
4165	mkdir -p ${pathout[$i]}
4166	fi
4167
4168	fi
4169
4170
4171	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4172	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4173	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4174	if [[ "${actionout[$i]}" = ar ]]
4175	then
4176	if [[ $files_for_pes = false ]]
4177	then
4178	printf "\n >>> OUTPUT: ${localout[$i]} to"
4179	printf "\n ${pathout[$i]}"
4180	printf "\n File will be copied to archive-system ($archive_system) !\n"
4181	else
4182	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4183	printf "\n ${pathout[$i]}"
4184	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4185	fi
4186	mv ${localout[$i]} ${frelout[$i]}
4187
4188	file_saved=false
4189
4190	if [[ $archive_system = asterix ]]
4191	then
4192	do_stageout=true
4193	(( stageout_anz = 0 ))
4194	while [[ $do_stageout = true ]]
4195	do
4196	if [[ $files_for_pes = false ]]
4197	then
4198	stageout ${frelout[$i]} > STAGE_OUTPUT
4199	else
4200	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4201	fi
4202	cat STAGE_OUTPUT
4203	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4204	then
4205	file_saved=true
4206	do_stageout=false
4207	else
4208	if [[ $files_for_pes = false ]]
4209	then
4210	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4211	else
4212	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4213	fi
4214	(( stageout_anz = stageout_anz + 1 ))
4215	if (( stageout_anz == 10 ))
4216	then
4217	printf "\n +++ stoped after 10 unsuccessful tries!"
4218	archive_save=false
4219	do_stageout=false
4220	else
4221	printf "\n *** new try to store on archive after 15 min:"
4222	sleep 900
4223	fi
4224	fi
4225	done
4226	elif [[ $archive_system = DMF ]]
4227	then
4228	if [[ $files_for_pes = false ]]
4229	then
4230	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4231	locat=DMF
4232	exit
4233	else
4234	rm -rf $ARCHIVE/${frelout[$i]}
4235	cp -r ${frelout[$i]} $ARCHIVE
4236	fi
4237	file_saved=true
4238	elif [[ $archive_system = tivoli ]]
4239	then
4240	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4241	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4242	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4243	# WHEN THE ARCHIVE-JOB IS EXECUTED
4244	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4245	chmod g+rx $tmp_data_catalog
4246	if [[ $files_for_pes = false ]]
4247	then
4248	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4249	else
4250	mkdir $tmp_data_catalog/${frelout[$i]}
4251	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4252	fi
4253
4254	# GENERATE AND SUBMIT BATCH-JOB
4255	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4256	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4257	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4258	if [[ $files_for_pes = false ]]
4259	then
4260	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4261	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4262	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4263	else
4264	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4265	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4266	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4267	fi
4268
4269	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4270	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4271	file_saved=true
4272
4273	elif [[ $archive_system = ut ]]
4274	then
4275	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4276	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4277	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4278	# WHEN THE ARCHIVE-JOB IS EXECUTED
4279	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4280	chmod g+rx $tmp_data_catalog
4281	if [[ $files_for_pes = false ]]
4282	then
4283	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4284	else
4285	mkdir $tmp_data_catalog/${frelout[$i]}
4286	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4287	fi
4288
4289	# GENERATE AND SUBMIT BATCH-JOB
4290	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4291	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4292	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4293	if [[ $files_for_pes = false ]]
4294	then
4295	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4296	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4297	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4298	else
4299	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4300	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4301	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4302	fi
4303
4304	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4305	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4306	file_saved=true
4307
4308	else
4309	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4310	archive_save=false
4311	fi
4312
4313	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4314	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4315	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4316	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4317	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4318	if [[ $file_saved = true ]]
4319	then
4320	if [[ $files_for_pes = false ]]
4321	then
4322	cat /dev/null > ${pathout[$i]}
4323	else
4324	mkdir -p ${pathout[$i]}
4325	fi
4326	fi
4327
4328	fi
4329
4330	# APPEND ON THIS MACHINE
4331	if [[ "${actionout[$i]}" = "a" ]]
4332	then
4333	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4334	then
4335	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4336	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4337	else
4338	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4339	cat ${localout[$i]} >> ${pathout[$i]}
4340	fi
4341	fi
4342
4343	# COPY ON THIS MACHINE
4344	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4345	# ON DIFFERENT FILE-SYSTEMS
4346	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4347	then
4348
4349	# COPY IN CASE OF RUNS ON SINGLE CORES
4350	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4351	then
4352	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4353	if [[ $link_local_output = true ]]
4354	then
4355	printf " using ln -f\n"
4356	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4357	fi
4358	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4359	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4360	then
4361	if [[ $link_local_output = true ]]
4362	then
4363	printf " ln failed, using cp...\n"
4364	fi
4365	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4366	fi
4367	else
4368	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4369	if [[ $link_local_output = true ]]
4370	then
4371	printf " using ln -f\n"
4372	ln -f ${localout[$i]} ${pathout[$i]}
4373	fi
4374	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4375	if [[ ! -f "${pathout[$i]}" ]]
4376	then
4377	if [[ $link_local_output = true ]]
4378	then
4379	printf " ln failed, using cp...\n"
4380	fi
4381	cp ${localout[$i]} ${pathout[$i]}
4382	fi
4383	fi
4384
4385	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4386	then
4387
4388	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4389	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4390	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4391	if [[ $link_local_output = true ]]
4392	then
4393	printf " using ln -f\n"
4394	mkdir ${pathout[$i]}
4395	cd ${localout[$i]}
4396	for file in $(ls *)
4397	do
4398	ln -f $file ${pathout[$i]}
4399	done
4400	cd $TEMPDIR
4401	fi
4402
4403	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4404	if [[ ! -f "${pathout[$i]}/_0000" ]]
4405	then
4406	if [[ $link_local_output = true ]]
4407	then
4408	printf " ln failed for .../_0000, using cp...\n"
4409	fi
4410	cp -r ${localout[$i]} ${pathout[$i]}
4411	fi
4412
4413	fi
4414	fi
4415	done
4416	if (( i != 0 ))
4417	then
4418	if [[ $transfer_problems = true ]]
4419	then
4420	printf "\n$dashes\n *** OUTPUT-files saved"
4421	printf "\n +++ WARNING: some data transfers failed! \n"
4422	else
4423	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4424	fi
4425	fi
4426
4427
4428	# IF REQUIRED, START A RESTART-JOB
4429	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4430	if [[ -f CONTINUE_RUN ]]
4431	then
4432
4433	if [[ $archive_save = true ]]
4434	then
4435
4436	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4437	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4438	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4439	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4440	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4441	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4442	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4443	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4444	then
4445	mc=`echo $mc \| sed 's/#/f/g'`
4446	fi
4447
4448
4449	# START THE RESTART-JOB
4450	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4451	echo " $mc"
4452	printf "\n$dashes\n"
4453	if [[ $localhost != $fromhost ]]
4454	then
4455
4456	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4457	then
4458	echo "*** ssh will be used to initiate restart-runs!"
4459	echo " return_address=\"$return_address\" "
4460	echo " return_username=\"$return_username\" "
4461	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4462	then
4463	if [[ $localhost = ibmh ]]
4464	then
4465	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4466	elif [[ $localhost = lccrayb ]]
4467	then
4468	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4469	elif [[ $localhost = lccrayh ]]
4470	then
4471	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4472	elif [[ $localhost = lcxe6 ]]
4473	then
4474	ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4475	else
4476	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4477	fi
4478	else
4479	if [[ $localhost = ibmkisti ]]
4480	then
4481	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4482	elif [[ $localhost = lcflow ]]
4483	then
4484	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4485	elif [[ $localhost = lccrayb ]]
4486	then
4487	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4488	elif [[ $localhost = lccrayh ]]
4489	then
4490	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4491	else
4492	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4493	fi
4494	fi
4495	else
4496	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4497	locat=restart; exit
4498	fi
4499
4500	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4501	if [[ $queue = special1q ]]
4502	then
4503	sleep 120
4504	else
4505	sleep 30
4506	fi
4507
4508	else
4509
4510	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4511	# USING SSH)
4512	cd $LOCAL_PWD
4513	if [[ $localhost = lckyuh ]]
4514	then
4515	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4516	printf "\n please restart job manually using command:\n"
4517	printf "\n \"$mc\" "
4518	else
4519	eval $mc # THE ' MUST BE EVALUATED
4520	fi
4521	cd - > /dev/null
4522	fi
4523	if [[ $localhost = lckyuh ]]
4524	then
4525	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4526	else
4527	printf "\n$dashes\n *** restart-run initiated \n"
4528	fi
4529
4530
4531	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4532	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4533	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4534	# MAY BE VERY HUGE)
4535	(( i = 0 ))
4536	while (( i < iin ))
4537	do
4538	(( i = i + 1 ))
4539	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4540	then
4541	rm -r $tmp_data_catalog/${frelin[$i]}
4542	fi
4543	done
4544
4545	else
4546
4547	printf "\n +++ no restart-run possible, since errors occured"
4548	printf "\n during the archive process"
4549	fi
4550
4551	fi
4552
4553
4554
4555	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4556	if [[ "$email_notification" != "none" ]]
4557	then
4558
4559	if [[ $localhost != $fromhost ]]
4560	then
4561	if [[ -f CONTINUE_RUN ]]
4562	then
4563	echo "PALM restart run necessary" > email_text
4564	echo "description header of actual run:" >> email_text
4565	cat CONTINUE_RUN >> email_text
4566	echo "mrun-command to restart:" >> email_text
4567	echo "$mc" >> email_text
4568	else
4569	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4570	fi
4571	mail $email_notification < email_text
4572	printf "\n *** email notification sent to \"$email_notification\" "
4573	fi
4574	fi
4575
4576
4577
4578	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4579	cd $HOME
4580	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4581
4582	else
4583
4584
4585	# PREPARING ACTIONS,
4586	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4587
4588	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4589	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
4590	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4591	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4592	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4593	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4594	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4595	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4596	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4597	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4598	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4599	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4600	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4601	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4602	if [[ $use_openmp = true ]]
4603	then
4604	mrun_com=${mrun_com}" -O $threads_per_task"
4605	fi
4606	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4607	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4608	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4609	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4610	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4611	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4612	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4613	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4614	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4615	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4616	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4617	if [[ $do_remote = true ]]
4618	then
4619	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4620	fi
4621
4622
4623	# CREATE EXECUTABLE FOR BATCH JOB
4624	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4625	then
4626
4627	printf "\n *** creating the executable for batch job\n"
4628
4629	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4630	if [[ $host != $localhost ]]
4631	then
4632	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4633	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4634	locat=create_executable; exit
4635	fi
4636
4637	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4638	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4639
4640	cp $make_depository .
4641	tar -xf $make_depository > /dev/null 2>&1
4642	cp ../* . > /dev/null 2>&1
4643
4644	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4645
4646	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4647	then
4648	printf "\n +++ error occured while compiling or linking"
4649	locat=compile
4650	exit
4651	fi
4652
4653	mv a.out ..
4654	cd - > /dev/null 2>&1
4655	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4656
4657	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4658
4659	fi
4660
4661
4662	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4663	jobfile=jobfile.$RANDOM
4664
4665
4666	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4667	echo "mkdir $TEMPDIR" >> $jobfile
4668	echo "cd $TEMPDIR" >> $jobfile
4669
4670
4671	# ACTIVATE ERROR-TRACEBACK
4672	if [[ $do_trace = true ]]
4673	then
4674	echo "set -x" >> $jobfile
4675	else
4676	echo "set +vx" >> $jobfile
4677	fi
4678
4679
4680	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4681	if [[ "$init_cmds" != "" ]]
4682	then
4683	echo "$init_cmds" >> $jobfile
4684	fi
4685	if [[ "$module_calls" != "" ]]
4686	then
4687	echo "$module_calls" >> $jobfile
4688	fi
4689
4690
4691	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4692	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4693	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4694	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4695	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4696	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4697	# QUEUEING-SYSTEMS
4698	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4699	then
4700
4701	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4702	if [[ $restart_run != true ]]
4703	then
4704	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4705	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4706	fi
4707
4708	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4709	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4710	echo "set -x" >> $jobfile
4711	if [[ $host = $localhost ]]
4712	then
4713
4714	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4715	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4716	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4717	then
4718	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4719	else
4720	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4721	fi
4722
4723	else
4724	if [[ $host = ibmkisti ]]
4725	then
4726	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4727	echo "localdir=\`pwd\`" >> $jobfile
4728	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4729	elif [[ $host = lccrayb ]]
4730	then
4731	echo "localdir=\`pwd\`" >> $jobfile
4732	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4733	elif [[ $host = lccrayh ]]
4734	then
4735	echo "localdir=\`pwd\`" >> $jobfile
4736	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4737
4738	else
4739	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4740	fi
4741	fi
4742	echo "export SOURCES_COMPLETE=true" >> $jobfile
4743
4744	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4745	# WORKING DIRECTORY OF THE JOB
4746	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4747	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4748	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4749	echo "execute_mrun=true" >> $jobfile
4750	echo " " >> $jobfile
4751
4752	else
4753
4754	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4755	if [[ $do_compile = true ]]
4756	then
4757
4758	source_catalog=SOURCES_FOR_RUN_$fname
4759
4760	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4761	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4762	echo "export SOURCES_COMPLETE=true" >> $jobfile
4763	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4764
4765	for filename in $source_list
4766	do
4767	# BACKSLASH IS USED FOR MASKING
4768	echo "cat > $filename << \"%END%\"" >> $jobfile
4769	cat $source_catalog/$filename >> $jobfile
4770	echo " " >> $jobfile
4771	echo "%END%" >> $jobfile
4772	echo " " >> $jobfile
4773	done
4774
4775	# BACKSLASH IS USED FOR MASKING
4776	echo "cat > Makefile << \"%END%\"" >> $jobfile
4777	cat $source_catalog/Makefile >> $jobfile
4778	echo " " >> $jobfile
4779	echo "%END%" >> $jobfile
4780	echo " " >> $jobfile
4781
4782	echo "cd - > /dev/null" >> $jobfile
4783
4784	fi
4785
4786
4787	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4788	# BACKSLASH IS USED FOR MASKING
4789	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4790	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4791	echo "cat > $config_file << \"%END%\"" >> $jobfile
4792	if [[ $host = lckyuh ]]
4793	then
4794	# NO CROSS-COMPILER ON COMPUTE NODE
4795	sed 's/frtpx/frt/g' $config_file >> $jobfile
4796	else
4797	sed 's/#$.*//g' $config_file >> $jobfile
4798	fi
4799	echo "%END%" >> $jobfile
4800	echo " " >> $jobfile
4801
4802
4803	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4804	# BACKSLASH IS USED FOR MASKING
4805	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4806	if [[ $host = lckyuh ]]
4807	then
4808	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4809	else
4810	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4811	fi
4812	echo "%END%" >> $jobfile
4813	echo "chmod u+x $mrun_script_name" >> $jobfile
4814	echo "execute_mrun=true" >> $jobfile
4815	echo " " >> $jobfile
4816
4817	fi
4818
4819
4820	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4821	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4822	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4823	if [[ $do_remote = true ]]
4824	then
4825	(( i = 0 ))
4826	while (( i < iin ))
4827	do
4828	(( i = i + 1 ))
4829	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4830	if [[ "${transin[$i]}" = job ]]
4831	then
4832	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4833	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4834	echo " " >> $jobfile
4835	echo "%END%" >> $jobfile
4836	else
4837	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4838	fi
4839
4840	# CHECK, IF FILE COULD BE CREATED
4841	echo "if [[ \$? = 1 ]]" >> $jobfile
4842	echo "then" >> $jobfile
4843	echo " echo \" \" " >> $jobfile
4844	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4845	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4846	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4847	echo " execute_mrun=false" >> $jobfile
4848	echo "fi" >> $jobfile
4849	done
4850	fi
4851
4852	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4853	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4854	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4855	echo "LOCAL_PWD=$working_directory" >> $jobfile
4856	echo "export LOCAL_PWD" >> $jobfile
4857
4858	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4859	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4860	echo "export LOCAL_MRUN_PATH" >> $jobfile
4861
4862	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4863	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4864	# then
4865	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4866	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4867	# fi
4868
4869	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4870	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4871	echo "set -x" >> $jobfile
4872	echo "queue=$queue" >> $jobfile
4873	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4874	echo 'ls -al; echo `pwd`' >> $jobfile
4875	echo "cd \$HOME" >> $jobfile
4876	echo "rm -rf $TEMPDIR" >> $jobfile
4877
4878
4879
4880
4881	# START THE JOB USING SUBJOB-COMMAND
4882	if [[ $silent = false ]]
4883	then
4884	printf "\n "
4885	else
4886	printf "\n\n"
4887	fi
4888
4889	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
4890	rm -rf $jobfile
4891
4892
4893	fi # END OF REMOTE-PART

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