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source: palm/trunk/SCRIPTS/mrun @ 1604

Last change on this file since 1604 was 1604, checked in by suehring, 9 years ago
Enable coupled runs for lcmuk
Property svn:keywords set to `Id Rev`
File size: 178.1 KB

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

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