Home

Context Navigation

source: palm/trunk/SCRIPTS/mrun @ 1598

Last change on this file since 1598 was 1598, checked in by raasch, 9 years ago
bugfix for creating hostfile in openmp-mode if run on one node
Property svn:keywords set to `Id Rev`
File size: 177.8 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	# bugfix for creating hostfile in openmp-mode if run on one node
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1598 2015-05-29 06:45:40Z raasch $
29	#
30	# 1549 2015-01-30 14:26:16Z suehring
31	# Enable interactive debug sessions with allinea debugger
32	#
33	# 1547 2015-01-29 15:09:12Z witha
34	# adjustments for ForWind computing cluster (lcflow)
35	#
36	# 1491 2014-11-12 08:12:57Z heinze
37	# correct setting of batch_job allowed for ibm-machines
38	#
39	# 1468 2014-09-24 14:06:57Z maronga
40	# Typo removed (addres->address)
41	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
42	# Added support for restart runs (remote) for lcxe6
43	#
44	# 1442 2014-07-28 07:09:10Z raasch
45	# default queues for HLRN-III (lccrayb/lccrayh) defined
46	#
47	# 1422 2014-07-02 10:01:25Z kanani
48	# automatic restarts enabled for lccrayb,
49	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
50	#
51	# 1420 2014-06-10 06:24:14Z raasch
52	# -j1 option added to aprung command for lccrayf (CSC)
53	#
54	# 1402 2014-05-09 14:25:13Z raasch
55	# batch_job added to envpar-NAMELIST
56	#
57	# 1357 2014-04-11 15:02:03Z witha
58	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
59	# possible)
60	#
61	# 1320 2014-03-20 08:40:49Z raasch
62	# check namelist file set false by default
63	#
64	# 1304 2014-03-12 10:29:42Z raasch
65	# ulimit option changed from -Ss to -s
66	#
67	# bugfix: missing "fi" in r1289
68	#
69	# 1289 2014-03-04 07:12:34Z raasch
70	# comments translated to English
71	# necriam-, fimm-, ibmy-, and sgi-specific code removed
72	# export of variables for palm and interpret_config removed
73	#
74	# 1281 2014-02-01 07:55:49Z raasch
75	# rsync-copy restricted to Cray machines, since command is unavailable on some
76	# other systems
77	#
78	# 1279 2014-01-28 12:10:14Z raasch
79	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
80	# in order to remove annoying restrictions concerning the number of processors which
81	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
82	# restriction, one of the nodes will be filled with less than the given number of
83	# tasks per node. A respective warning is given.
84	#
85	# 1274 2014-01-09 13:14:54Z heinze
86	# adjustments for lccrayh
87	#
88	# 1272 2014-01-08 10:19:32Z witha
89	# small adjustment for lcflow
90	#
91	# 1270 2013-12-16 11:05:01Z fricke
92	# call of combine_plot_fields adjusted for lccrayb/lccrayh
93	#
94	# 1255 2013-11-07 14:43:35Z raasch
95	# further adjustments for lccrayb remote access
96	#
97	# 1241 2013-10-30 11:36:58Z heinze
98	# Enable use of nudging input and input of large scale forcing from
99	# external files
100	#
101	# 1229 2013-09-20 06:55:19Z raasch
102	# further adjustments for lccrayb
103	#
104	# 1224 2013-09-16 07:27:23Z raasch
105	# first adjustments for lccrayb
106	#
107	# 1210 2013-08-14 10:58:20Z raasch
108	# fftw support added
109	#
110	# 1201 2013-07-10 16:17:59Z witha
111	# adjustments for Forwind cluster (lcflow)
112	#
113	# 1199 2013-07-05 14:52:22Z raasch
114	# adjustments for CSC Helsinki (lccrayf),
115	# executables for batch jobs can be created in advance, in order to avoid calling
116	# the compiler within the batch job (only works if batch jobs are submitted on
117	# local host)
118	#
119	# 1190 2013-06-25 09:39:21Z heinze
120	# enable use of automatic restarts for ibmh
121	# use of cluster/express queue enabled (ibmh)
122	#
123	# 1124 2013-04-09 15:46:52Z raasch
124	# variable "memory" is exported via typeset option -x, because otherwise an unknown
125	# side effect may lead to data loss while getopts is reading the script-option arguments
126	#
127	# 1122 2013-04-09 08:37:16Z heinze
128	# Bugfix: change type of variable last_char
129	#
130	# 1119 2013-04-05 15:11:19Z raasch
131	# Bugfix for setting -T option for subjob
132	#
133	# 1108 2013-03-05 07:03:32Z raasch
134	# bugfix for coupled runs on lckyut/lckyuh
135	#
136	# 1106 2013-03-04 05:31:38Z raasch
137	# --stdin argument for mpiexec on lckyuh
138	# -y and -Y settings output to header
139	#
140	# 1103 2013-02-20 02:15:53Z raasch
141	# default script runs again under ksh, because of unsolved problems with read
142	# from stdin: when bash script is called from a ksh, message "read error: 0:
143	# Resource temporarily unavailable" appears and script does not stop,
144	# further bash compatibility adjustments,
145	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
146	# on lckyuh, but mrun does not terminate and issues a warning instead
147	#
148	# 1101 2013-02-17 10:20:21Z raasch
149	# script now running under bash instead of ksh, which required small adjustments
150	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
151	# read from stdin),
152	# cross compilername on lckyuh compute nodes replaced by real compiler name
153	#
154	# 1099 2013-02-10 01:47:43Z raasch
155	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
156	# and for Forwind cluster (lcflow)
157	# small further adjustments for lckyut
158	#
159	# 1094 2013-02-03 01:52:12Z raasch
160	# explicit ssh/scp port can be set in config file with environment variable
161	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
162	# decalpha parts (yonsei) removed
163	#
164	# 2013-02-02 07:06:13Z raasch
165	# adjustments for Kyushu-University computing center (lckyut - tatara)
166	#
167	# 1083 2013-01-04 10:22:09Z maronga
168	# bugfix in parameter file check (read %cpp_options was missing)
169	#
170	# 1069 2012-11-28 16:18:43Z maronga
171	# bugfix: coupling mode was always set to mpi2, typos removed
172	#
173	# 1058 2012-11-21 07:00:35Z raasch
174	# Intel inspector (inspxe) is given the number of PEs instead of the number of
175	# nodes
176	#
177	# 1046 2012-11-09 14:38:45Z maronga
178	# code put under GPL (PALM 3.9)
179	#
180	# 21/03/94 - Siggi - first version finished
181	# 03/03/94 - Siggi - script development started
182	#
183	#--------------------------------------------------------------------------------#
184	# mrun - script for running PALM jobs
185	#--------------------------------------------------------------------------------#
186
187
188
189	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
190
191	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
192	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
193	# (TOO MANY ARGUMENTS - PROBLEM)
194	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
195
196	AddFilenames=""
197	additional_conditions=""
198	add_source_path=""
199	afname=""
200	archive_save=true
201	archive_system=none
202	check_namelist_files=false
203	combine_plot_fields=true
204	compiler_name=""
205	cond1=""
206	cond2=""
207	config_file=.mrun.config
208	coupled_dist=""
209	coupled_mode="mpi1"
210	cpp_opts=""
211	cpp_options=""
212	cpumax=0
213	cpurest=0
214	create_executable_for_batch=false
215	delete_temporary_catalog=true
216	do_batch=false
217	do_compile=true
218	do_remote=false
219	do_stagein=true
220	do_stageout=true
221	do_trace=false
222	email_notification="none"
223	exclude=""
224	executable=""
225	execution_error=false
226	fftw_inc=""
227	fftw_lib=""
228	fftw_support=false
229	fname=test
230	fromhost=""
231	global_revision=""
232	group_number=none
233	host=""
234	host_file=""
235	hp=""
236	ignore_archive_error=false
237	input_list=""
238	interpreted_config_file=""
239	job_catalog="~/job_queue"
240	job_on_file=""
241	keep_data_from_previous_run=false
242	link_local_input=false
243	link_local_output=false
244	localhost_realname=$(hostname)
245	local_dvrserver_running=.FALSE.
246	locat=normal
247	mainprog=""
248	makefile=""
249	max_par_io_str=""
250	mc=$0
251	while [[ $(echo $mc \| grep -c "/") != 0 ]]
252	do
253	mc=`echo $mc \| cut -f2- -d"/"`
254	done
255	module_calls=""
256	mrun_script_name=$mc
257	netcdf_inc=""
258	netcdf_lib=""
259	netcdf_support=false
260	node_usage=default
261	numprocs=""
262	numprocs_atmos=0
263	numprocs_ocean=0
264	OOPT=""
265	openmp=false
266	output_list=""
267	package_list=""
268	queue=none
269	read_from_config=""
270	restart_run=false
271	if [[ `hostname` = rte10 ]]
272	then
273	return_address=133.5.185.60
274	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
275	elif [[ `hostname` = climate0 ]]
276	then
277	return_address=165.132.26.68
278	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
279	elif [[ `hostname` = urban00 ]]
280	then
281	return_address=147.46.30.151
282	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
283	else
284	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
285	fi
286	return_password=""
287	return_username=$LOGNAME
288	remotecall=false
289	remote_username=""
290	run_coupled_model=false
291	run_mode=""
292	store_on_archive_system=false
293	dashes=" ----------------------------------------------------------------------------"
294	silent=false
295	source_list=""
296	source_path=SOURCE
297	tasks_per_node=""
298	threads_per_task=1
299	tmpcreate=false
300	tmp_data_catalog=""
301	transfer_problems=false
302	usern=$LOGNAME
303	use_openmp=false
304	version="MRUN 2.1 Rev$Rev: 1598 $"
305	working_directory=`pwd`
306	TOPT=""
307	XOPT=""
308	zeit=$( date \| cut -c 12-19 )
309
310	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
311	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
312	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
313	# SCRIPT-OPTION ARGUMENTS
314	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
315
316
317
318	# ERROR HANDLING IN CASE OF EXIT
319	trap 'rm -rf $working_directory/tmp_mrun
320	if [[ $locat != normal && $locat != control_c ]]
321	then
322
323	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
324	(( i = 0 ))
325	while (( i < iec ))
326	do
327	(( i = i + 1 ))
328	printf "\n *** Execution of ERROR-command:\n"
329	printf " >>> ${err_command[$i]}\n"
330	eval ${err_command[$i]}
331	done
332	if [[ -n $interpreted_config_file ]]
333	then
334	rm -rf $interpreted_config_file
335	fi
336	if [[ -n .mrun_environment ]]
337	then
338	rm -rf .mrun_environment
339	fi
340	if [[ $tmpcreate = true ]]
341	then
342	printf "\n *** Contents of \"$TEMPDIR\":\n"
343	ls -al; cd
344	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
345	fi
346	if [[ "$dvrserver_id" != "" ]]
347	then
348	echo "+++ killing dvrserver_id=$dvrserver_id"
349	kill $dvrserver_id
350	fi
351	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
352	then
353	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
354	fi
355	printf "\n\n+++ MRUN killed \n\n"
356	elif [[ $locat != control_c ]]
357	then
358	printf "\n\n --> all actions finished\n\n"
359	printf " Bye, bye $usern !!\n\n"
360	fi' exit
361
362
363	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
364	trap 'rm -rf $working_directory/tmp_mrun
365	rm -rf $working_directory/tmp_check_namelist_files
366	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
367	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
368	then
369	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
370	fi
371	if [[ "$dvrserver_id" != "" ]]
372	then
373	echo "+++ killing dvrserver_id=$dvrserver_id"
374	kill $dvrserver_id
375	fi
376	printf "\n+++ MRUN killed by \"^C\" \n\n"
377	locat=control_c
378	exit
379	' 2
380
381
382	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
383	# BEEN SET
384	if [[ "$PALM_BIN" = "" ]]
385	then
386	printf "\n +++ environment variable PALM_BIN has not been set"
387	printf "\n please set it to the directory where the PALM scripts are located"
388	locat=palm_bin; exit
389	fi
390	export PATH=$PALM_BIN:$PATH
391
392
393
394	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
395	# WHICH WILL BE USED TO START RESTART-JOBS
396	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
397	do
398	case $option in
399	(a) afname=$OPTARG;;
400	(A) store_on_archive_system=true; mc="$mc -A";;
401	(b) do_batch=true; mc="$mc -b";;
402	(B) delete_temporary_catalog=false; mc="$mc -B";;
403	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
404	(C) restart_run=true; mc="$mc -C";;
405	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
406	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
407	(F) job_on_file="-D"; mc="$mc -F";;
408	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
409	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
410	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
411	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
412	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
413	(I) ignore_archive_error=true; mc="$mc -I";;
414	(k) keep_data_from_previous_run=true; mc="$mc -k";;
415	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
416	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
417	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
418	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
419	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
420	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
421	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
422	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
423	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
424	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
425	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
426	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
427	(S) read_from_config=false; mc="$mc -S";;
428	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
429	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
430	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
431	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
432	(v) silent=true; mc="$mc -v";;
433	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
434	(x) do_trace=true;set -x; mc="$mc -x";;
435	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
436	(y) ocean_file_appendix=true; mc="$mc -y";;
437	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
438	(z) check_namelist_files=false; mc="$mc -z";;
439	(Z) combine_plot_fields=false; mc="$mc -Z";;
440	(\?) printf "\n +++ unknown option $OPTARG \n"
441	printf "\n --> type \"$0 ?\" for available options \n"
442	locat=parameter;exit;;
443	esac
444	done
445
446
447	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
448	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
449	(( to_shift = $OPTIND - 1 ))
450	shift $to_shift
451
452	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
453	if [[ "$1" = "?" ]]
454	then
455	(printf "\n *** mrun can be called as follows:\n"
456	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"
457	printf "\n Description of available options:\n"
458	printf "\n Option Description Default-Value"
459	printf "\n -a base name of input files equiv. -d"
460	printf "\n -A archiving when using file-attribute fl"
461	printf "\n -b batch-job on local machine ---"
462	printf "\n -B do not delete temporary directory at end ---"
463	printf "\n -c configuration file .mrun.config"
464	printf "\n -d base name of files attached to program test"
465	printf "\n -D preprocessor(cpp)-directives \"\" "
466	printf "\n -F create remote job file only ---"
467	printf "\n -h execution host $localhost_realname"
468	printf "\n -i INPUT control list \"\" "
469	printf "\n -I archiving errors of previous batch-jobs"
470	printf "\n will be ignored"
471	printf "\n -k keep data from previous run"
472	printf "\n -K additional conditions for controling"
473	printf "\n usage of conditional code and"
474	printf "\n env-variables in configuration file \"\" "
475	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
476	printf "\n -M Makefile name Makefile"
477	printf "\n -n node usage (shared/not_shared) depending on -h"
478	printf "\n -o OUTPUT control list \"\" "
479	printf "\n -O threads per openMP task ---"
480	printf "\n -p software package list \"\" "
481	printf "\n -q queue \"$queue\" "
482	printf "\n -r run control list (combines -i -o) \"\" "
483	printf "\n -s filenames of routines to be compiled \"\" "
484	printf "\n must end with .f, .f90, .F, or .c !"
485	printf "\n use \"..\" for more than one file and wildcards"
486	printf "\n -s LM compiles all locally modified files"
487	printf "\n -S config file interpreted by shellscript ---"
488	printf "\n -t allowed cpu-time in seconds (batch) 0"
489	printf "\n -T tasks per node depending on -h"
490	printf "\n -u username on remote machine \"\" "
491	printf "\n -v no prompt for confirmation ---"
492	printf "\n -w maximum parallel io streams as given by -X"
493	printf "\n -x tracing of mrun for debug purposes ---"
494	printf "\n -X # of processors (on parallel machines) 1"
495	printf "\n -y add appendix \"_O\" to all local output"
496	printf "\n files (ocean precursor runs followed by"
497	printf "\n coupled atmosphere-ocean runs) ---"
498	printf "\n -Y run coupled model, \"#1 #2\" with"
499	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
500	printf "\n -z disable a priori parameter file check ---"
501	printf "\n -Z skip combine_plot_fields at the end of "
502	printf "\n the simulation ---"
503	printf "\n "
504	printf "\n Possible values of positional parameter <modus>:"
505	printf "\n \"?\" - this outline \n\n") \| more
506	exit
507	elif [[ "$1" != "" ]]
508	then
509	printf "\n +++ positional parameter $1 unknown \n"
510	locat=parameter; exit
511	fi
512
513
514
515	# SHORT STARTING MESSAGE
516	printf "\n*** $version "
517	printf "\n will be executed. Please wait ..."
518
519
520
521	# CHECK, IF CONFIGURATION FILE EXISTS
522	if [[ ! -f $config_file ]]
523	then
524	printf "\n\n +++ configuration file: "
525	printf "\n $config_file"
526	printf "\n does not exist"
527	locat=connect; exit
528	fi
529
530
531	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
532	line=""
533	grep "%host_identifier" $config_file > tmp_mrun
534	while read line
535	do
536	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
537	then
538	HOSTNAME=`echo $line \| cut -d" " -s -f2`
539	host_identifier=`echo $line \| cut -d" " -s -f3`
540	if [[ $localhost_realname = $HOSTNAME ]]
541	then
542	localhost=$host_identifier
543	break
544	fi
545	fi
546	done < tmp_mrun
547
548	if [[ "$localhost" = "" ]]
549	then
550	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
551	printf "\n for local host \"$localhost_realname\"."
552	printf "\n Please add line"
553	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
554	printf "\n to the configuration file."
555	locat=localhost; exit
556	fi
557
558
559	# SET HOST-SPECIFIC VARIABLES
560	case $localhost_realname in
561	(r1\|r2\|h01\|b01) archive_system=tivoli;;
562	(cs*) archive_system=ut;;
563	esac
564
565
566	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
567	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
568	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
569	[[ "$afname" = "" ]] && afname=$fname
570
571
572	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
573	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
574	# STATEMENTS IN THE CONFIGURATION FILE
575	if [[ "$run_mode" != "" ]]
576	then
577	input_list="$input_list $run_mode"
578	output_list="$output_list $run_mode"
579	fi
580
581
582	# ??? is this (and the respective option -H) really required ???
583	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
584	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
585	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
586	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
587	if [[ "$fromhost" = "" ]]
588	then
589	fromhost=$localhost
590	fi
591
592
593	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
594	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
595	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
596	# TO BE SUBMITTED (I.E. do_bacth=true)
597	if [[ -n $host && "$host" != $localhost ]]
598	then
599	do_batch=true
600	do_remote=true
601	case $host in
602	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
603	(*) printf "\n"
604	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
605	printf "\n is not available"
606	locat=nqs; (( iec = 0 )); exit;;
607	esac
608	else
609	host=$localhost
610	fi
611
612
613	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
614	if [[ -n $additional_conditions ]]
615	then
616	cond1=`echo $additional_conditions \| cut -d" " -f1`
617	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
618	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
619	if [[ -n $dummy ]]
620	then
621	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
622	locat=options; exit
623	fi
624	block=_$cond1
625	[[ -n $cond2 ]] && block=${block}_$cond2
626	fi
627
628
629	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
630	if [[ $run_coupled_model = true ]]
631	then
632
633	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
634	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
635
636	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
637	then
638
639	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
640	printf "\n PEs (total) : $numprocs"
641	printf "\n PEs (atmosphere): $numprocs_atmos"
642	printf "\n PEs (ocean) : $numprocs_ocean"
643	locat=coupling; exit
644
645	fi
646
647
648	# GET coupled_mode FROM THE CONFIG FILE
649	line=""
650	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
651	while read line
652	do
653	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
654	then
655	coupled_mode="mpi2"
656	fi
657	done < tmp_mrun
658
659	fi
660
661
662	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
663	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
664	then
665	if [[ $ignore_archive_error = false ]]
666	then
667	printf "\n +++ data archiving of previous run failed"
668	printf "\n see directory \~/job_queue on remote machine"
669	locat=archive; exit
670	else
671	printf "\n +++ warning: data archiving in a previous run failed"
672	printf "\n MRUN continues, trying to get backup copy"
673	fi
674	fi
675
676
677	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
678	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
679	mrun_memory=$memory
680	mrun_group_number=$group_number
681	mrun_cpumax=$cpumax
682	mrun_numprocs=$numprocs
683
684
685	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
686	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
687	if [[ "$read_from_config" = false ]]
688	then
689
690	[[ $silent = false ]] && printf "\n Reading the configuration file... "
691
692	# READ THE CONFIGURATION FILE LINE BY LINE
693	while read zeile
694	do
695	[[ $silent = false ]] && printf "."
696
697
698	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
699	eval zeile=\"$zeile\"
700
701
702	# INTERPRET THE LINE
703	if [[ "$(echo $zeile)" = "" ]]
704	then
705	# EMPTY LINE, NO ACTION
706	continue
707
708	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
709	then
710
711	# LINE IS A COMMENT LINE
712	true
713
714	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
715	then
716
717	# LINE DEFINES AN ENVIRONMENT-VARIABLE
718	zeile=$(echo $zeile \| cut -c2-)
719	var=`echo $zeile \| cut -d" " -f1`
720	value=`echo $zeile \| cut -d" " -s -f2`
721	for_host=`echo $zeile \| cut -d" " -s -f3`
722	for_cond1=`echo $zeile \| cut -d" " -s -f4`
723	for_cond2=`echo $zeile \| cut -d" " -s -f5`
724
725	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
726	then
727
728	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
729	# "::" IS REPLACED BY ":".
730	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
731
732
733	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
734	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
735	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
736	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
737	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
738	# CONFIGURATION-FILE.
739	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
740	then
741	eval $var=\$value
742
743	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
744	if [[ $do_trace = true ]]
745	then
746	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
747	fi
748	fi
749
750	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
751	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
752	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
753	# MUST HAVE TO BE STARTED
754	if [[ $var = host ]]
755	then
756	if [[ -n $host && "$host" != $localhost ]]
757	then
758	do_batch=true
759	do_remote=true
760	case $host in
761	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
762	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
763	printf "\n is not available"
764	locat=nqs; exit;;
765	esac
766	else
767	host=$localhost
768	fi
769	fi
770
771	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
772	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
773	# BY MRUN (E.G. subjob)
774	export $var
775	fi
776
777
778
779
780	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
781	then
782
783	# LINE DEFINES ERROR-COMMAND
784	(( iec = iec + 1 ))
785	zeile=$(echo $zeile \| cut -c4-)
786	err_command[$iec]="$zeile"
787
788	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
789	then
790
791	# LINE DEFINES INPUT-COMMAND
792	(( iic = iic + 1 ))
793	zeile=$(echo $zeile \| cut -c4-)
794	in_command[$iic]="$zeile"
795
796	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
797	then
798
799	# LINE DEFINES OUTPUT-COMMAND
800	(( ioc = ioc + 1 ))
801	zeile=$(echo $zeile \| cut -c4-)
802	out_command[$ioc]="$zeile"
803
804	else
805
806	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
807	# s2a: in/out - field
808	# s2b: loc - field (optional)
809	# s2c: tr/ar - field (optional)
810	s1=`echo $zeile \| cut -d" " -f1`
811	s2=`echo $zeile \| cut -d" " -s -f2`
812	s2a=$(echo $s2 \| cut -d":" -f1)
813	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
814	then
815	s2b=""
816	s2c=""
817	else
818	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
819	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
820	fi
821	s3=`echo $zeile \| cut -d" " -f3`
822	s4=`echo $zeile \| cut -d" " -s -f4`
823	s5=`echo $zeile \| cut -d" " -s -f5`
824	s6=`echo $zeile \| cut -d" " -s -f6`
825
826
827	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
828	# INPUT- OR OUTPUT-LIST.
829	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
830	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
831	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
832	# IS NOT CHECKED AND STORED.
833	IFSALT="$IFS"; IFS="$IFS:"
834	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
835	then
836	found=false
837	for actual in $input_list
838	do
839	for formal in $s3
840	do
841	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
842	done
843	done
844	if [[ $found = true ]]
845	then
846	(( iin = iin + 1 ))
847	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
848	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
849	extin[$iin]=$s6
850	fi
851	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
852	then
853	found=false
854	for actual in $output_list
855	do
856	for formal in $s3
857	do
858	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
859	done
860	done
861	if [[ $found = true ]]
862	then
863	(( iout = iout + 1 ))
864	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
865	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
866	fi
867	elif [[ "$s2a" != in && "$s2a" != out ]]
868	then
869	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
870	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
871	locat=connect; exit
872	fi
873	IFS="$IFSALT"
874	fi
875	done < $config_file
876
877	else
878
879
880	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
881	[[ $silent = false ]] && printf "..."
882	interpreted_config_file=.icf.$RANDOM
883
884
885
886	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
887	cat > .mrun_environment << %%END%%
888	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
889	config_file = '$config_file', do_remote = '$do_remote',
890	do_trace = '$do_trace', host = '$host',
891	input_list = '$input_list', icf = '$interpreted_config_file',
892	localhost = '$localhost', output_list = '$output_list' /
893
894	%%END%%
895
896	if [[ "$host" != $localhost ]]
897	then
898
899	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
900	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
901	if [[ $? != 0 ]]
902	then
903	printf "\n\n +++ no interpret_config found"
904	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
905	locat=interpret_config; exit
906	fi
907	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
908	$interpret_config_executable
909
910	else
911
912	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
913	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
914	then
915	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
916	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
917	locat=interpret_config; exit
918	else
919	interpret_config${block}.x
920	fi
921
922	fi
923	rm .mrun_environment
924
925
926	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
927	chmod u+x $interpreted_config_file
928	export PATH=$PATH:.
929	. $interpreted_config_file
930	rm $interpreted_config_file
931
932	fi
933
934
935	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
936	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
937	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
938	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
939	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
940	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
941	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
942
943
944	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
945	# FOR SOURCE-FILES TO BE COMPILED.
946	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
947	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
948	if [[ "$SOURCES_COMPLETE" = "" ]]
949	then
950
951	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
952	# HAS BEEN DEFINED
953	source_path=""
954	line=""
955	grep "%source_path" $config_file > tmp_mrun
956	while read line
957	do
958	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
959	then
960	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
961	then
962	global_source_path=`echo $line \| cut -d" " -f2`
963	fi
964	fi
965	done < tmp_mrun
966
967	line=""
968	found=false
969	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
970	while read line
971	do
972	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
973	then
974	if [[ $found = true ]]
975	then
976	printf "\n\n +++ more than one source path found in configuration file"
977	printf "\n for local host \"$localhost\" "
978	locat=source_path; exit
979	fi
980	source_path=`echo $line \| cut -d" " -f2`
981	found=true
982	fi
983	done < tmp_mrun
984	rm tmp_mrun
985
986	if [[ "$source_path" = "" ]]
987	then
988	if [[ "$global_source_path" != "" ]]
989	then
990	source_path=$global_source_path
991	else
992	printf "\n\n +++ no source path found in configuration file"
993	printf "\n for local host \"$localhost\" "
994	locat=source_path; exit
995	fi
996	fi
997	eval source_path=$source_path
998
999	if [[ ! -d $source_path ]]
1000	then
1001	printf "\n\n +++ source path \"$source_path\" on local host"
1002	printf "\n \"$localhost\" does not exist"
1003	locat=source_path; exit
1004	fi
1005
1006	fi
1007
1008
1009	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1010	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1011	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1012	then
1013	global_revision=`svnversion $source_path 2>/dev/null`
1014	global_revision="Rev: $global_revision"
1015	fi
1016
1017
1018	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1019	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1020	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1021	if [[ -n $host && "$host" != $localhost ]]
1022	then
1023	do_batch=true
1024	do_remote=true
1025	case $host in
1026	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1027	(*) printf "\n"
1028	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1029	printf "\n is not available"
1030	locat=nqs; (( iec = 0 )); exit;;
1031	esac
1032	else
1033	host=$localhost
1034	fi
1035
1036
1037	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1038	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1039	then
1040
1041	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1042	if [[ ! -n $numprocs ]]
1043	then
1044	printf "\n"
1045	printf "\n +++ option \"-K parallel\" requires additional specification"
1046	printf "\n of the number of processors to be used by"
1047	printf "\n mrun-option \"-X\" or by environment-variable"
1048	printf "\n \"numprocs\" in the configuration file"
1049	locat=numprocs; (( iec = 0 )); exit
1050	fi
1051
1052	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1053	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1054	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1055	then
1056	printf "\n"
1057	printf "\n +++ option \"-T\" (tasks per node) is missing"
1058	printf "\n set -T option or define tasks_per_node in the config file"
1059	locat=tasks_per_node; (( iec = 0 )); exit
1060	fi
1061
1062	if (( numprocs < tasks_per_node ))
1063	then
1064	printf "\n"
1065	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1066	printf "\n given values: -T $tasks_per_node -X $numprocs"
1067	locat=tasks_per_node; (( iec = 0 )); exit
1068	fi
1069
1070	if [[ $host != lcflow && $host != lcxt5m ]]
1071	then
1072	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1073	(( ival = $tasks_per_node ))
1074	(( pes = numprocs ))
1075	(( ii = pes / ival ))
1076	(( remaining_pes = pes - ii * ival ))
1077	if (( remaining_pes > 0 ))
1078	then
1079	printf "\n"
1080	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1081	printf "\n divisor of the total number of processors (option \"-X\")"
1082	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1083	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1084	(( nodes = nodes + 1 ))
1085	fi
1086	fi
1087
1088
1089	# SETTINGS FOR SUBJOB-COMMAND
1090	OOPT="-O $threads_per_task"
1091
1092	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1093	if [[ "$tasks_per_node" != "" ]]
1094	then
1095	TOPT="-T $tasks_per_node"
1096	fi
1097
1098	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1099	if [[ $node_usage = default ]]
1100	then
1101	if [[ $host = ibms ]]
1102	then
1103	node_usage=shared
1104	else
1105	node_usage=not_shared
1106	fi
1107	fi
1108
1109	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1110	then
1111	printf "\n"
1112	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1113	printf "\n \"shared\" or \"not_shared\""
1114	locat=tasks_per_node; (( iec = 0 )); exit
1115	fi
1116
1117	fi
1118
1119	# CHECK IF HOSTFILE EXISTS
1120	if [[ -n $hostfile ]]
1121	then
1122	if [[ ! -f $hostfile ]]
1123	then
1124	printf "\n"
1125	printf "\n +++ hostfile \"$hostfile\" does not exist"
1126	locat=hostfile; exit
1127	fi
1128	fi
1129
1130
1131	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1132	if [[ "$maximum_parallel_io_streams" = "" ]]
1133	then
1134	maximum_parallel_io_streams=$numprocs
1135	fi
1136
1137
1138	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1139	if [[ "$scp_port" != "" ]]
1140	then
1141	PORTOPT="-P $scp_port"
1142	SSH_PORTOPT="-p $scp_port"
1143	fi
1144
1145
1146	# SET DEFAULT-QUEUE, IF NOT GIVEN
1147	if [[ $queue = none ]]
1148	then
1149	case $host in
1150	(ibmh) queue=cluster;;
1151	(ibmkisti) queue=class.32plus;;
1152	(lccrayb) queue=mpp1q;;
1153	(lccrayh) queue=mpp1q;;
1154	(lckiaps) queue=normal;;
1155	(lckyoto) queue=ph;;
1156	(lckyuh) queue=fx-single;;
1157	(lckyut) queue=cx-single;;
1158	(lctit) queue=S;;
1159	(nech) queue=none;;
1160	(unics) queue=unics;;
1161	esac
1162	fi
1163
1164
1165	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1166	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1167	(( i = 0 ))
1168	while (( i < iin ))
1169	do
1170	(( i = i + 1 ))
1171	(( maxcycle = 0 ))
1172
1173	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1174	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1175	if [[ "${actionin[$i]}" = di ]]
1176	then
1177	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1178	# HOST ONLY
1179	eval filename=${pathin[$i]}/${endin[$i]}
1180	else
1181	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1182	# HOST ONLY
1183	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1184	fi
1185	eval pathname=${pathin[$i]}
1186
1187	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1188	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1189	then
1190	filename_input=$filename
1191	fi
1192
1193	# CHECK IF FILE EXISTS
1194	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1195	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1196	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1197	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1198	then
1199
1200	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1201	if [[ "${transin[$i]}" != "locopt" ]]
1202	then
1203	printf "\n\n +++ INPUT-file: "
1204	if [[ "${extin[$i]}" = "" ]]
1205	then
1206	printf "\n $filename"
1207	else
1208	printf "\n $filename.${extin[$i]}"
1209	fi
1210	printf "\n does not exist\n"
1211	locat=input; exit
1212	else
1213	transin[$i]="unavailable"
1214	fi
1215	else
1216
1217	# DETERMINE THE FILE'S CYCLE NUMBER
1218	ls -1 -d $filename > filelist 2>/dev/null
1219	ls -1 -d $filename.* >> filelist 2>/dev/null
1220	while read zeile
1221	do
1222	cycle=$(echo $zeile \| cut -f2 -d".")
1223	if [[ "$cycle" = "$zeile" ]]
1224	then
1225	(( icycle = 0 ))
1226	elif [[ "$cycle" = "${extin[$i]}" ]]
1227	then
1228	(( icycle = 0 ))
1229	else
1230	(( icycle = $cycle ))
1231	fi
1232	if (( icycle > maxcycle ))
1233	then
1234	(( maxcycle = icycle ))
1235	file_to_be_used=$zeile
1236	fi
1237	done <filelist
1238	rm filelist
1239
1240	# APPEND CYCLE NUMBER TO FILENAME
1241	if (( maxcycle > 0 ))
1242	then
1243	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1244	then
1245	filename=${filename}.$maxcycle.${extin[$i]}
1246	else
1247	filename=${filename}.$maxcycle
1248	fi
1249	else
1250	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1251	then
1252	filename=${filename}.${extin[$i]}
1253	fi
1254	fi
1255
1256	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1257	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1258	absnamein[$i]=$filename
1259	if (( maxcycle > 0 ))
1260	then
1261	if [[ "${actionin[$i]}" = di ]]
1262	then
1263	frelin[$i]=${endin[$i]}.$maxcycle
1264	else
1265	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1266	fi
1267	else
1268	if [[ "${actionin[$i]}" = di ]]
1269	then
1270	frelin[$i]=${endin[$i]}
1271	else
1272	frelin[$i]=${afname}${endin[$i]}
1273	fi
1274	fi
1275
1276	fi
1277	done
1278
1279	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1280	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1281	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1282	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1283	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1284	# REMOTE HOST)
1285	(( i = 0 ))
1286	while (( i < iout ))
1287	do
1288	(( i = i + 1 ))
1289	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1290	then
1291	if [[ "${actionout[$i]}" = tr ]]
1292	then
1293	actionout[$i]=""
1294	elif [[ "${actionout[$i]}" = trpe ]]
1295	then
1296	actionout[$i]=pe
1297	elif [[ "${actionout[$i]}" = tra ]]
1298	then
1299	actionout[$i]=a
1300	fi
1301	(( maxcycle = 0 ))
1302	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1303	eval catalogname=${pathout[$i]}
1304	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1305	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1306	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1307	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1308	then
1309
1310	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1311	if cat /dev/null > $filename
1312	then
1313	rm $filename
1314	else
1315
1316	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1317	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1318	if [[ ! -d $catalogname ]]
1319	then
1320	if mkdir -p $catalogname
1321	then
1322	printf "\n\n *** directory:"
1323	printf "\n $catalogname"
1324	printf "\n was created\n"
1325	else
1326	printf "\n\n +++ OUTPUT-file:"
1327	printf "\n $filename"
1328	printf "\n cannot be created, because directory does not exist"
1329	printf "\n and cannot be created either"
1330	printf "\n"
1331	locat=output ; exit
1332	fi 2>/dev/null
1333	else
1334	printf "\n\n +++ OUTPUT-file:"
1335	printf "\n $filename"
1336	printf "\n cannot be created, although directory exists"
1337	printf "\n"
1338	locat=output ; exit
1339	fi
1340	fi 2>/dev/null
1341	else
1342
1343	# DETERMINE THE CYCLE NUMBER
1344	ls -1 -d $filename > filelist 2>/dev/null
1345	ls -1 -d $filename.* >> filelist 2>/dev/null
1346	while read zeile
1347	do
1348	cycle=$(echo $zeile \| cut -f2 -d".")
1349	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1350	then
1351	(( icycle = 1 ))
1352	else
1353	(( icycle = $cycle + 1 ))
1354	fi
1355	if (( icycle > maxcycle ))
1356	then
1357	(( maxcycle = icycle ))
1358	fi
1359	done <filelist
1360	rm filelist
1361	fi
1362
1363	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1364	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1365	if [[ "${actionout[$i]}" != a ]]
1366	then
1367	if (( maxcycle > 0 ))
1368	then
1369	filename=${filename}.$maxcycle
1370	if cat /dev/null > $filename
1371	then
1372	rm $filename
1373	else
1374	printf "\n +++ OUTPUT-file:"
1375	printf "\n $filename"
1376	printf "\n cannot be created"
1377	locat=output ; exit
1378	fi
1379	fi
1380	else
1381	(( maxcycle = maxcycle - 1 ))
1382	if (( maxcycle > 0 ))
1383	then
1384	filename=${filename}.$maxcycle
1385	fi
1386	fi
1387
1388	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1389	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1390	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1391	pathout[$i]=$filename
1392	if (( maxcycle > 0 ))
1393	then
1394	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1395	else
1396	frelout[$i]=${fname}${endout[$i]}
1397	fi
1398
1399	fi
1400	done
1401
1402
1403	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1404	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1405	then
1406	if [[ "$dvr_inc" = "" ]]
1407	then
1408	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1409	printf "\n This is required for the dvrp_graphics package.\n"
1410	locat=dvr; exit
1411	fi
1412	if [[ "$dvr_lib" = "" ]]
1413	then
1414	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1415	printf "\n This is required for the dvrp_graphics package.\n"
1416	locat=dvr; exit
1417	fi
1418	fi
1419
1420
1421	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1422	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1423	if [[ "$mainprog" = "" && "$executable" = "" ]]
1424	then
1425	printf "\n +++ neither main program nor executable defined"
1426	locat=source; exit
1427	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1428	then
1429	printf "\n +++ main program as well as executable defined"
1430	locat=source; exit
1431	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1432	then
1433	do_compile=false
1434	fi
1435
1436
1437	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1438	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1439	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1440	then
1441	rm -rf SOURCES_FOR_RUN_$fname
1442	mkdir SOURCES_FOR_RUN_$fname
1443	fi
1444
1445
1446	# COLLECT ALL ROUTINES TO BE COMPILED
1447	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1448	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1449	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1450	then
1451
1452	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1453
1454	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1455	then
1456
1457	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1458	source_list=""
1459	cd $source_path
1460
1461
1462	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1463	if [[ ! -d .svn ]]
1464	then
1465	printf "\n\n +++ source directory"
1466	printf "\n \"$source_path\" "
1467	printf "\n is not under control of \"subversion\"."
1468	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1469	fi
1470
1471
1472	# LIST ALL MODIFIED SOURCE CODE FILES
1473	Filenames=""
1474	svn status > tmp_mrun
1475	while read line
1476	do
1477	firstc=`echo $line \| cut -c1`
1478	if [[ $firstc = M \|\| $firstc = "?" ]]
1479	then
1480	Name=`echo "$line" \| cut -c8-`
1481	extension=`echo $Name \| cut -d. -f2`
1482	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1483	then
1484	Filenames="$Filenames "$Name
1485	fi
1486	fi
1487	done < tmp_mrun
1488
1489
1490	# COPY FILES TO SOURCES_FOR_RUN_...
1491	for dateiname in $Filenames
1492	do
1493	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1494	source_list=$source_list"$dateiname "
1495	done
1496
1497	cd - > /dev/null
1498
1499
1500	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1501	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1502	elif [[ "$source_list" != "" && $restart_run != true ]]
1503	then
1504
1505	cd $source_path
1506
1507	for filename in $source_list
1508	do
1509
1510	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1511	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1512	then
1513	printf "\n +++ source code file: $filename"
1514	printf "\n must not contain (\"/\") "
1515	locat=source; exit
1516	fi
1517
1518	if [[ ! -f $filename ]]
1519	then
1520	printf "\n +++ source code file: $filename"
1521	printf "\n does not exist"
1522	locat=source; exit
1523	else
1524	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1525	fi
1526
1527	done
1528
1529	cd - > /dev/null
1530
1531	fi
1532
1533
1534	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1535	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1536	if [[ $restart_run != true ]]
1537	then
1538
1539	if [[ ! -f "$source_path/$mainprog" ]]
1540	then
1541	printf "\n\n +++ main program: $mainprog"
1542	printf "\n does not exist in source directory"
1543	printf "\n \"$source_path\"\n"
1544	locat=source; exit
1545	else
1546	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1547	then
1548	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1549	source_list=${mainprog}" $source_list"
1550	fi
1551	fi
1552	fi
1553
1554
1555	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1556	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1557	if [[ "$restart_run" != true ]]
1558	then
1559	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1560	if [[ ! -f $makefile ]]
1561	then
1562	printf "\n +++ file \"$makefile\" does not exist"
1563	locat=make; exit
1564	else
1565	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1566	fi
1567	fi
1568
1569
1570	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1571	if [[ $restart_run != true && "$add_source_path" != "" ]]
1572	then
1573
1574	# DOES THE DIRECTORY EXIST?
1575	if [[ ! -d $add_source_path ]]
1576	then
1577	printf "\n\n +++ WARNING: additional source code directory"
1578	printf "\n \"$add_source_path\" "
1579	printf "\n does not exist or is not a directory."
1580	printf "\n No source code will be used from this directory!\n"
1581	add_source_path=""
1582	if [[ $silent == false ]]
1583	then
1584	sleep 3
1585	fi
1586	else
1587
1588	cd $add_source_path
1589	found=false
1590
1591	Names=$(ls -1 *.f90 2>&1)
1592	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1593	Names=$(ls -1 *.F90 2>&1)
1594	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1595	Names=$(ls -1 *.F 2>&1)
1596	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1597	Names=$(ls -1 *.f 2>&1)
1598	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1599	Names=$(ls -1 *.c 2>&1)
1600	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1601
1602	cd - > /dev/null
1603	cd SOURCES_FOR_RUN_$fname
1604
1605	# COPY MAKEFILE IF EXISTING
1606	if [[ -f $add_source_path/Makefile ]]
1607	then
1608	printf "\n\n *** user Makefile from directory"
1609	printf "\n \"$add_source_path\" is used \n"
1610	if [[ $silent == false ]]
1611	then
1612	sleep 1
1613	fi
1614	cp $add_source_path/Makefile .
1615	fi
1616
1617	for dateiname in $AddFilenames
1618	do
1619	if [[ -f $dateiname ]]
1620	then
1621	printf "\n +++ source code file \"$dateiname\" found in additional"
1622	printf "\n source code directory \"$add_source_path\" "
1623	printf "\n but was also given with option \"-s\" which means that it should be taken"
1624	printf "\n from directory \"$source_path\"."
1625	locat=source; exit
1626	fi
1627
1628	cp $add_source_path/$dateiname .
1629	source_list="$source_list $dateiname"
1630
1631	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1632	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1633	then
1634	printf "\n\n +++ user file \"$dateiname\" "
1635	printf "\n is not listed in Makefile \n"
1636	locat=source; exit
1637	else
1638
1639	if [[ $found = false ]]
1640	then
1641	found=true
1642	printf "\n\n *** following user file(s) added to the"
1643	printf " files to be translated:\n "
1644	fi
1645	printf "$dateiname "
1646	if [[ $silent == false ]]
1647	then
1648	sleep 0.5
1649	fi
1650
1651	fi
1652	done
1653	[[ $found = true ]] && printf "\n"
1654	cd - > /dev/null
1655	fi
1656	fi
1657
1658
1659	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1660	# TO THE LIST OF FILES TO BE COMPILED
1661	if [[ $restart_run != true && -n $package_list ]]
1662	then
1663
1664	cd $source_path
1665
1666	for package in $package_list
1667	do
1668
1669	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1670
1671	# DETERMINE FILES BELONGING TO THE PACKAGE
1672	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1673	# THE NAME OF THE DIRECTORY
1674	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1675
1676
1677	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1678	# IF THEY ARE NOT ALREADY PART OF THE LIST
1679	for source_list_name in $package_source_list
1680	do
1681	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1682	then
1683
1684	# ONLY TAKE FILES WITH VALID SUFFIX
1685	ending=`echo $source_list_name \| cut -f2 -d.`
1686	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1687	then
1688	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1689	source_list="$source_list $source_list_name"
1690	fi
1691	fi
1692	done
1693	done
1694
1695	cd - > /dev/null
1696	fi
1697
1698	fi # do_compile=true
1699
1700
1701	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1702	# AND SET PRE-PROCESSOR DIRECTIVES
1703	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1704	then
1705
1706	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1707	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1708	then
1709	cpp_options="${cpp_options},-D__ibm=__ibm"
1710	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1711	then
1712	cpp_options="$cpp_options -D__nec"
1713	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1714	then
1715	cpp_options="$cpp_options -D__lc"
1716	else
1717	cpp_options="$cpp_options -D__$localhost"
1718	fi
1719
1720	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1721	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1722	then
1723	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1724	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1725	else
1726	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1727	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1728	fi
1729
1730	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1731	if [[ -n $package_list ]]
1732	then
1733	for package in $package_list
1734	do
1735	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1736	then
1737	if [[ $package != "dvrp_graphics+1PE" ]]
1738	then
1739	cpp_options="${cpp_options},-D__$package=__$package"
1740	else
1741	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1742	export use_seperate_pe_for_dvrp_output=true
1743	fi
1744	else
1745	if [[ $package != "dvrp_graphics+1PE" ]]
1746	then
1747	cpp_options="$cpp_options -D__$package"
1748	else
1749	cpp_options="$cpp_options -D__dvrp_graphics"
1750	export use_seperate_pe_for_dvrp_output=true
1751	fi
1752	fi
1753	done
1754	fi
1755
1756	# SET DIRECTIVES GIVEN BY OPTION -D
1757	if [[ -n $cpp_opts ]]
1758	then
1759	for popts in $cpp_opts
1760	do
1761	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1762	then
1763	cpp_options="${cpp_options},-D__$popts=__$popts"
1764	else
1765	cpp_options="$cpp_options -D__$popts"
1766	fi
1767	done
1768	fi
1769
1770	else
1771
1772
1773	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1774	if [[ $do_remote = false ]]
1775	then
1776	if [[ ! -f $executable ]]
1777	then
1778	printf "\n +++ executable file: $executable"
1779	printf "\n does not exist"
1780	locat=executable; exit
1781	fi
1782	fi
1783	fi
1784
1785
1786	# DETERMINE THE JOB MODE
1787	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1788	then
1789	if [[ "$LOADLBATCH" = yes ]]
1790	then
1791	batch_job=.TRUE.
1792	jobmo=BATCH
1793	else
1794	batch_job=.FALSE.
1795	jobmo=INTERACTIVE
1796	fi
1797	else
1798	if [[ "$ENVIRONMENT" = BATCH ]]
1799	then
1800	batch_job=.TRUE.
1801	jobmo=BATCH
1802	else
1803	batch_job=.FALSE.
1804	jobmo=INTERACTIVE
1805	fi
1806	fi
1807
1808	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1809	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1810	then
1811	printf "\n +++ no interactive runs allowed on host \"$host\" "
1812	printf "\n please submit batch job using mrun option \"-b\" \n"
1813	locat=normal; exit
1814	fi
1815
1816
1817	# CHECK, IF USER DEFINED A COMPILER
1818	if [[ "$compiler_name" = "" ]]
1819	then
1820
1821	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1822	locat=compiler_name; exit
1823
1824	fi
1825
1826
1827	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1828	kennung=$RANDOM
1829	if [[ "$tmp_user_catalog" = "" ]]
1830	then
1831	if [[ $localhost = ibmh ]]
1832	then
1833	tmp_user_catalog=$SCRATCH
1834	elif [[ $localhost = nech ]]
1835	then
1836	tmp_user_catalog=$WRKSHR
1837	else
1838	tmp_user_catalog=/tmp
1839	fi
1840	fi
1841	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1842
1843
1844	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1845	if [[ "$tmp_data_catalog" = "" ]]
1846	then
1847	if [[ $localhost = nech ]]
1848	then
1849	tmp_data_catalog=$WRKSHR/mrun_restart_data
1850	else
1851	tmp_data_catalog=/tmp/mrun_restart_data
1852	fi
1853	fi
1854
1855
1856	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1857	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1858	then
1859	eval fopts=\"$fopts\"
1860	eval lopts=\"$lopts\"
1861	fi
1862
1863
1864
1865	# DETERMINE COMPILE- AND LINK-OPTIONS
1866	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1867	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1868	ROPTS="$ropts"
1869	# 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 ]]
1870	# then
1871	XOPT="-X $numprocs"
1872	# fi
1873
1874
1875
1876	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1877	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1878	done=false
1879	while [[ $done = false ]]
1880	do
1881	cputime=$cpumax
1882	if (( $cputime == 0 ))
1883	then
1884	if [[ $do_batch = true ]]
1885	then
1886	printf "\n +++ cpu-time is undefined"
1887	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1888	printf "\n >>> "
1889	read cputime 1>/dev/null 2>&1
1890	else
1891	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1892	fi
1893	else
1894	done=true
1895	fi
1896	cpumax=$cputime
1897	done
1898
1899	(( minuten = cputime / 60 ))
1900	(( sekunden = cputime - minuten * 60 ))
1901
1902
1903	# CHECK THE MEMORY DEMAND
1904	if [[ $do_batch = true ]]
1905	then
1906	done=false
1907	while [[ $done = false ]]
1908	do
1909	if (( memory == 0 ))
1910	then
1911	printf "\n +++ memory demand is undefined"
1912	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1913	printf "\n >>> "
1914	read memory 1>/dev/null 2>&1
1915	else
1916	done=true
1917	fi
1918	done
1919	fi
1920
1921
1922	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1923	if [[ $do_remote = true && -z $remote_username ]]
1924	then
1925	while [[ -z $remote_username ]]
1926	do
1927	printf "\n +++ username on remote host \"$host\" is undefined"
1928	printf "\n >>> Please type username:"
1929	printf "\n >>> "
1930	read remote_username
1931	done
1932	mc="$mc -u$remote_username"
1933	fi
1934
1935	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1936	if [[ "$login_init_cmd" != "" ]]
1937	then
1938	export init_cmds="${login_init_cmd};"
1939	fi
1940
1941
1942	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1943	if [[ "$modules" != "" ]]
1944	then
1945	if [[ $host = lctit ]]
1946	then
1947	export module_calls=". $modules"
1948	else
1949	export module_calls="module load ${modules};"
1950	fi
1951	fi
1952
1953
1954
1955	# OUTPUT OF THE MRUN-HEADER
1956	calltime=$(date)
1957	printf "\n"
1958	printf "#------------------------------------------------------------------------# \n"
1959	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1960	printf "\| \| \n"
1961	spalte1="called on:"; spalte2=$localhost_realname
1962	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1963	if [[ $do_remote = true ]]
1964	then
1965	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1966	else
1967	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1968	fi
1969	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1970	if [[ -n $numprocs ]]
1971	then
1972	if [[ $run_coupled_model = false ]]
1973	then
1974	spalte1="number of PEs:"; spalte2=$numprocs
1975	else
1976	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1977	fi
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	fi
1980	if [[ -n $tasks_per_node ]]
1981	then
1982	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1983	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1984	if (( remaining_pes > 0 ))
1985	then
1986	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1987	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1988	fi
1989	fi
1990	if [[ $maximum_parallel_io_streams != $numprocs ]]
1991	then
1992	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1993	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1994	fi
1995	if [[ $use_openmp = true ]]
1996	then
1997	spalte1="threads per task:"; spalte2="$threads_per_task"
1998	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1999	fi
2000	printf "\| \| \n"
2001	if [[ $do_compile = true ]]
2002	then
2003	if [[ "$mopts" != "" ]]
2004	then
2005	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2006	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2007	zeile=$(echo "$mopts" \| cut -c46-)
2008	while [[ "$zeile" != "" ]]
2009	do
2010	spalte1=""
2011	spalte2=$(echo "$zeile" \| cut -c-45)
2012	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2013	zeile=$(echo "$zeile" \| cut -c46-)
2014	done
2015	fi
2016
2017	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2019	zeile=$(echo "$cpp_options" \| cut -c46-)
2020	while [[ "$zeile" != "" ]]
2021	do
2022	spalte1=""
2023	spalte2=$(echo "$zeile" \| cut -c-45)
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	zeile=$(echo "$zeile" \| cut -c46-)
2026	done
2027
2028	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030	zeile=$(echo "$fopts" \| cut -c46-)
2031	while [[ "$zeile" != "" ]]
2032	do
2033	spalte1=""
2034	spalte2=$(echo "$zeile" \| cut -c-45)
2035	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2036	zeile=$(echo "$zeile" \| cut -c46-)
2037	done
2038
2039	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	zeile=$(echo "$lopts" \| cut -c46-)
2042	while [[ "$zeile" != "" ]]
2043	do
2044	spalte1=""
2045	spalte2=$(echo "$zeile" \| cut -c-45)
2046	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2047	zeile=$(echo "$zeile" \| cut -c46-)
2048	done
2049
2050	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2051	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2052	zeile=$(echo "$modules" \| cut -c46-)
2053	while [[ "$zeile" != "" ]]
2054	do
2055	spalte1=""
2056	spalte2=$(echo "$zeile" \| cut -c-45)
2057	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2058	zeile=$(echo "$zeile" \| cut -c46-)
2059	done
2060
2061	spalte1="main program:"; spalte2=$mainprog
2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2063	else
2064	spalte1=executable:; spalte2=$executable
2065	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2066	fi
2067	printf "\| \| \n"
2068	spalte1="base name of files:"; spalte2=$fname
2069	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2070	if [[ $fname != $afname ]]
2071	then
2072	spalte1="base name of input files:"; spalte2=$afname
2073	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2074	fi
2075	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2076	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2077	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2079
2080	if [[ "$ocean_file_appendix" = true ]]
2081	then
2082	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2083	fi
2084
2085	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2086	then
2087	spalte1="memory demand / PE":; spalte2="$memory MB"
2088	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2089	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2090	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2091	fi
2092
2093	if [[ $do_compile = true ]]
2094	then
2095	printf "\| \| \n"
2096	printf "\| Files to be compiled: \| \n"
2097	zeile=$source_list
2098	while [[ "$zeile" != "" ]]
2099	do
2100	linestart=$(echo $zeile \| cut -c-70)
2101	printf "\| %-70s \| \n" "$linestart"
2102	zeile=$(echo "$zeile" \| cut -c71-)
2103	done
2104	fi
2105	printf "#------------------------------------------------------------------------#"
2106
2107
2108
2109	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2110	if [[ $do_trace = true ]]
2111	then
2112	(( i = 0 ))
2113	while (( i < iin ))
2114	do
2115	(( i = i + 1 ))
2116	if (( i == 1 ))
2117	then
2118	printf "\n\n >>> INPUT-file assignments:\n"
2119	fi
2120	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2121	done
2122	(( i = 0 ))
2123	while (( i < iout ))
2124	do
2125	(( i = i + 1 ))
2126	if (( i == 1 ))
2127	then
2128	printf "\n\n >>> OUTPUT-file assignments:\n"
2129	fi
2130	printf "\n ${localout[$i]} : ${pathout[$i]}"
2131	done
2132	(( i = 0 ))
2133	while (( i < iic ))
2134	do
2135	(( i = i + 1 ))
2136	if (( i == 1 ))
2137	then
2138	printf "\n\n >>> INPUT-commands:\n"
2139	fi
2140	printf "\n ${in_command[$i]}"
2141	done
2142	(( i = 0 ))
2143	while (( i < ioc ))
2144	do
2145	(( i = i + 1 ))
2146	if (( i == 1 ))
2147	then
2148	printf "\n\n >>> OUTPUT-commands:\n"
2149	fi
2150	printf "\n ${out_command[$i]}"
2151	done
2152	fi
2153
2154
2155	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2156	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2157	then
2158	antwort=dummy
2159	printf "\n\n"
2160	printf " >>> everything o.k. (y/n) ? "
2161	while read antwort
2162	do
2163	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2164	then
2165	printf " >>> everything o.k. (y/n) ? "
2166	else
2167	break
2168	fi
2169	done
2170	if [[ $antwort = n \|\| $antwort = N ]]
2171	then
2172	locat=user_abort; (( iec = 0 )); exit
2173	fi
2174	if [[ $do_batch = true ]]
2175	then
2176	printf " >>> batch-job will be created and submitted"
2177	else
2178	printf " >>> MRUN will now continue to execute on this machine"
2179	fi
2180	fi
2181
2182
2183	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2184	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2185	check_depository="${working_directory}/trunk/UTIL"
2186	check_sources="${working_directory}/tmp_check_namelist_files"
2187	skip_check=false
2188
2189	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2190	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2191	then
2192	skip_check=true
2193	reason="run on remote host or parameter file check has not been compiled."
2194	fi
2195	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2196	then
2197	skip_check=true
2198	reason="parameter file check has not been compiled."
2199	fi
2200
2201	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2202	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2203	then
2204	skip_check=true
2205	reason="serial run."
2206	fi
2207
2208	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2209	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2210	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2211	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2212	if [[ $check_namelist_files == false ]]
2213	then
2214	skip_check=true
2215	reason="-z option set."
2216	fi
2217
2218	if [[ $fromhost != $localhost ]]
2219	then
2220	skip_check=true
2221	reason="submitting host is local host."
2222	fi
2223
2224	if [[ $run_coupled_model == true ]]
2225	then
2226	skip_check=true
2227	reason="coupled run."
2228	fi
2229
2230	if [[ $restart_run == true ]]
2231	then
2232	skip_check=true
2233	reason="restart run."
2234	fi
2235
2236	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2237	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2238	last_char=`echo $filename_input \| cut -c $last_char_int`
2239	if [[ "$last_char" == "f" ]]
2240	then
2241	skip_check=true
2242	reason="restart run."
2243	fi
2244
2245	if [[ $skip_check == false ]]
2246	then
2247	tmp_check=${working_directory}/tmp_check
2248
2249	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2250	# NOT NECESSARILY REQUIRED
2251	line=""
2252	found=false
2253	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2254	while read line1
2255	do
2256	line="$line1"
2257	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2258	then
2259	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2260	found=true
2261	fi
2262	done < $tmp_check
2263
2264	if [[ $found = false ]]
2265	then
2266	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2267	fi
2268
2269	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2270	# NOT NECESSARILY REQUIRED
2271	line=""
2272	found=false
2273	grep "NUDGING_DATA" $config_file > $tmp_check
2274	while read line1
2275	do
2276	line="$line1"
2277	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2278	then
2279	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2280	found=true
2281	fi
2282	done < $tmp_check
2283
2284	if [[ $found = false ]]
2285	then
2286	printf "\n +++ no NUDGING list entry found in the configuration file."
2287	fi
2288
2289	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2290	# NOT NECESSARILY REQUIRED
2291	line=""
2292	found=false
2293	grep "LSF_DATA" $config_file > $tmp_check
2294	while read line1
2295	do
2296	line="$line1"
2297	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2298	then
2299	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2300	found=true
2301	fi
2302	done < $tmp_check
2303
2304	if [[ $found = false ]]
2305	then
2306	printf "\n +++ no LSF list entry found in the configuration file."
2307	fi
2308
2309	rm -rf ${working_directory}/tmp_check
2310
2311	# CHECK IF THE P3DF FILE MUST BE CHECKED
2312	for item in $input_list
2313	do
2314	if [[ "$item" == "restart" ]]
2315	then
2316	check_restart=1
2317	else
2318	check_restart=0
2319	fi
2320	done
2321
2322	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2323	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2324	then
2325	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2326	locat=check_namelist; exit
2327	fi
2328
2329	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2330	if [[ $check_restart == 1 ]]
2331	then
2332
2333	filenamef="${filename_input}f"
2334	if [[ ! -f $filenamef ]]
2335	then
2336	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2337	check_restart=0
2338	answer=dummy
2339	printf "\n\n"
2340
2341	if [[ $silent == false ]]
2342	then
2343	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2344	do
2345	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2346	read answer
2347	done
2348	if [[ $answer = a \|\| $answer = A ]]
2349	then
2350	printf "\n +++ Aborting...."
2351	locat=normal; exit
2352	fi
2353	fi
2354	else
2355	check_restart=1
2356	fi
2357	fi
2358
2359	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2360	mkdir $check_sources
2361	cd $check_sources
2362
2363
2364	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2365	if [[ -d $add_source_path ]]
2366	then
2367	printf "\n\n *** copying files from $check_depository"
2368	cp $check_depository/check_namelist_files.tar ./
2369
2370	printf "\n\n *** untar of makefile and source files in $check_sources"
2371	tar -xf check_namelist_files.tar > /dev/null 2>&1
2372
2373	printf "\n\n *** adding user code."
2374	cp $add_source_path/* ./
2375	touch check_namelist_files.f90
2376
2377	# GET COMPILER OPTIONS AND PERFORM MAKE
2378	printf "\n\n *** compiling code if necessary...\n"
2379
2380	# workaround for batch jobs on local machine (lcxe6)
2381	if [[ $do_batch == true && $do_remote == false ]]
2382	then
2383	eval $init_cmds
2384	fi
2385
2386	# GET CHECK OPTIONS
2387	line=""
2388	found=false
2389
2390	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2391
2392	while read line1
2393	do
2394
2395	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2396	then
2397	line="$line1"
2398	fi
2399
2400	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2401	then
2402	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2403	line="$line "
2404	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'`
2405	found=true
2406	fi
2407
2408	done < $tmp_check
2409	copts_check="$copts_check -D__check -D__parallel"
2410
2411	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2412
2413	# GET MAKE OUTPUT
2414	if [[ $? != 0 ]]
2415	then
2416	printf "\n +++ error during make."
2417	answer=dummy
2418	printf "\n\n"
2419	if [[ $silent == false ]]
2420	then
2421	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2422	do
2423	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2424	read answer
2425	done
2426	if [[ $answer = a \|\| $answer = A ]]
2427	then
2428	printf "\n +++ Aborting..."
2429	rm -rf $check_sources
2430	locat=normal; exit
2431	else
2432	skip_check=true
2433	fi
2434	else
2435	skip_check=true
2436	fi
2437	fi
2438	else
2439	cp $PALM_BIN/check_namelist_files.x ./
2440	fi
2441
2442	cp $filename_input ./PARIN
2443	if [[ $check_restart == 1 ]]
2444	then
2445	cp $filenamef ./PARINF
2446	fi
2447
2448	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2449	then
2450	printf "\n *** adding topography data"
2451	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2452
2453	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2454	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2455	# WHICH REQUIRE SUFFICIENT MEMORY
2456	ulimit -s unlimited
2457	fi
2458
2459	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2460	then
2461	printf "\n *** adding nudging data"
2462	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2463	fi
2464
2465	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2466	then
2467	printf "\n *** adding large scale forcing data"
2468	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2469	fi
2470
2471	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2472	cat > ENVPAR << %%END%%
2473	&envpar run_identifier = '$fname', host = '$host',
2474	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2475	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2476	maximum_cpu_time_allowed = ${cpumax}.,
2477	revision = '$global_revision',
2478	local_dvrserver_running = $local_dvrserver_running /
2479
2480	%%END%%
2481
2482	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2483	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2484	then
2485	printf "\n +++ WARNING: check_namelist_files.x not found."
2486	answer=dummy
2487	printf "\n\n"
2488
2489	if [[ $silent == false ]]
2490	then
2491	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2492	do
2493	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2494	read answer
2495	done
2496	if [[ $answer = a \|\| $answer = A ]]
2497	then
2498	printf "\n +++ Aborting..."
2499	rm -rf $check_sources
2500	locat=normal; exit
2501	else
2502	printf "\n *** skipping parameter file check."
2503	fi
2504	fi
2505
2506	elif [[ $skip_check == false ]]
2507	then
2508	# STARTING THE PARAMETER FILE CHECK
2509	printf "\n\n *** starting parameter file check..."
2510
2511	# CHECKING THE P3D FILE
2512	printf "\n\n (1) checking $filename_input"
2513	echo "$numprocs 0 0" > VARIN
2514	errors=`./check_namelist_files.x < VARIN 2>&1`
2515
2516	check_error=false
2517	if [[ "$errors" == "" ]]
2518	then
2519	printf " --> o.k."
2520	else
2521	printf " --> failed."
2522	check_error=true
2523	printf "\n\n $errors"
2524	fi
2525
2526	# CHECKING THE PD3F FILE IF NECESSARY
2527	if [[ $check_restart == 1 && $check_error == false ]]
2528	then
2529	printf "\n\n (2) checking $filenamef"
2530
2531	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2532	# IN &INIPAR LIST
2533	found=false
2534	cat PARINF \| while read line
2535	do
2536	line=$(echo $line\|sed 's/ //g')
2537	if [[ $line == "&inipar" ]]
2538	then
2539	start_search=true
2540	fi
2541
2542	if [[ $start_search == true ]]
2543	then
2544	if [[ $line == "initializing_actions='read_restart_data'" ]]
2545	then
2546	found=true
2547	break
2548	fi
2549	fi
2550
2551	if [[ $line == "/" ]]
2552	then
2553	start_search=false
2554	fi
2555
2556	done
2557
2558	if [[ $found = false ]]
2559	then
2560	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2561	printf "\n in &inipar list in $fname$p3df_suffix."
2562	rm -rf $check_sources
2563	locat=check_namelist; exit
2564	fi
2565
2566	# READ max_user_pr FROM FILES
2567	if [[ -f parin_for_check ]]
2568	then
2569	read max_pr_user < parin_for_check
2570	else
2571	max_user_pr=0
2572	fi
2573
2574	echo "$numprocs 1 $max_pr_user" > VARIN
2575	errors=`./check_namelist_files.x < VARIN 2>&1`
2576
2577	if [[ "$errors" == "" ]]
2578	then
2579	printf " --> o.k."
2580	else
2581	printf " --> failed."
2582	check_error=true
2583	printf "\n\n $errors"
2584	fi
2585	fi
2586
2587	# REPORT ERRORS AND CONTINUE/EXIT
2588	if [[ $check_error == true ]]
2589	then
2590	printf "\n +++ errors found in the parameter file!\n"
2591	answer=dummy
2592	printf "\n\n"
2593
2594	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2595	do
2596	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2597	read answer
2598	done
2599
2600	if [[ $answer = a \|\| $answer = A ]]
2601	then
2602	printf "\n +++ Aborting..."
2603	rm -rf $check_sources
2604	locat=normal; exit
2605	fi
2606	else
2607	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2608	fi
2609	rm -rf $check_sources
2610	fi
2611	else
2612	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2613	fi
2614
2615	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2616	rm -rf $check_sources
2617	cd $working_directory
2618
2619
2620	# DETERMINE PATH FOR MAKE DEPOSITORY
2621	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2622	then
2623
2624	line=""
2625	grep "%depository_path" $config_file > tmp_mrun
2626	while read line
2627	do
2628	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2629	then
2630	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2631	then
2632	global_depository_path=`echo $line \| cut -d" " -s -f2`
2633	fi
2634	fi
2635	done < tmp_mrun
2636
2637	line=""
2638	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2639	while read line
2640	do
2641	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2642	then
2643	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2644	then
2645	local_depository_path=`echo $line \| cut -d" " -s -f2`
2646	fi
2647	fi
2648	done < tmp_mrun
2649
2650	if [[ "$local_depository_path" = "" ]]
2651	then
2652	if [[ "$global_depository_path" != "" ]]
2653	then
2654	local_depository_path=$global_depository_path
2655	else
2656	printf "\n\n +++ no depository path found in configuration file"
2657	printf "\n for local host \"$localhost\" "
2658	printf "\n please set \"\%depository_path\" in configuration file\n"
2659	locat=config_file; exit
2660	fi
2661	fi
2662	eval local_depository_path=$local_depository_path
2663	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2664	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2665
2666
2667	basename=`echo $mainprog \| cut -f1 -d"."`
2668	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2669	if [[ ! -f $make_depository ]]
2670	then
2671	printf "\n"
2672	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2673	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2674	fi
2675
2676	fi
2677
2678
2679	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2680	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2681	if [[ $do_batch = false ]]
2682	then
2683
2684
2685	# CREATE THE TEMPORARY WORKING DIRECTORY
2686	mkdir -p $TEMPDIR
2687	chmod go+rx $TEMPDIR
2688	tmpcreate=true
2689
2690
2691	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2692	# INTO THE TEMPORARY WORKING DIRECTORY
2693	if [[ $do_compile = true ]]
2694	then
2695
2696	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2697	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2698	if [[ $localhost = nech ]]
2699	then
2700	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2701	if mkdir -p $TEMPDIR_COMPILE
2702	then
2703	printf "\n *** \"$TEMPDIR_COMPILE\" "
2704	printf "\n is generated as temporary directory for cross compiling\n"
2705	else
2706	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2707	printf "\n needed for cross compilation failed"
2708	locat=compile
2709	exit
2710	fi
2711	else
2712	TEMPDIR_COMPILE=$TEMPDIR
2713	fi
2714
2715	cp $make_depository $TEMPDIR_COMPILE
2716	cd $TEMPDIR_COMPILE
2717	tar -xf $make_depository > /dev/null 2>&1
2718	cd - > /dev/null
2719
2720	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2721	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2722	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2723	then
2724	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2725	else
2726	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2727	fi
2728
2729	else
2730
2731	cp $executable ${TEMPDIR}/a.out
2732
2733	fi
2734
2735
2736	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2737	cd $TEMPDIR
2738	printf "\n *** changed to temporary directory: $TEMPDIR"
2739
2740
2741	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2742	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2743	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2744	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2745	(( i = 0 ))
2746	while (( i < iout ))
2747	do
2748	(( i = i + 1 ))
2749	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2750	then
2751	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2752	else
2753	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2754	fi
2755	done
2756
2757
2758	# IF REQUIRED, START WITH COMPILING
2759	if [[ $do_compile = true ]]
2760	then
2761
2762
2763	if [[ -f a.out ]]
2764	then
2765
2766	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2767	printf "\n\n\n *** executable a.out found"
2768	printf "\n no compilation required \n"
2769
2770	else
2771
2772	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2773	printf "\n\n\n *** compilation starts \n$dashes\n"
2774	printf " *** compilation with make using following options:\n"
2775	printf " make depository: $make_depository"
2776	if [[ "$mopts" != "" ]]
2777	then
2778	printf " make options: $mopts\n"
2779	fi
2780	printf " compilername: $compiler_name\n"
2781	printf " compiler options: $fopts\n"
2782	printf " preprocessor directives: $cpp_options \n"
2783	printf " linker options: $lopts \n"
2784	if [[ "$modules" != "" ]]
2785	then
2786	printf " modules to be load: $modules \n"
2787	fi
2788	printf " source code files: $source_list \n"
2789
2790	if [[ $localhost = nech ]]
2791	then
2792	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\" "
2793	cp $TEMPDIR_COMPILE/a.out .
2794	[[ $? != 0 ]] && compile_error=true
2795	rm -rf $TEMPDIR_COMPILE
2796	elif [[ $localhost = ibmh ]]
2797	then
2798	printf " compiler is called via ssh on \"plogin1\" \n"
2799	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\" "
2800	[[ ! -f a.out ]] && compile_error=true
2801	continue # STATUS=1, IF a.out EXISTS
2802	elif [[ $localhost = lcflow ]]
2803	then
2804	printf " compiler is called via ssh on \"flow\" \n"
2805	/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\" "
2806	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2807	[[ "$check_for_file" = "" ]] && compile_error=true
2808	continue # STATUS=1, IF a.out EXISTS
2809	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2810	then
2811	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2812	else
2813	[[ "$init_cmds" != "" ]] && eval $init_cmds
2814	[[ "$module_calls" != "" ]] && eval $module_calls
2815	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2816	fi
2817
2818	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2819	then
2820	printf "\n +++ error occured while compiling or linking"
2821	locat=compile
2822
2823	exit
2824	else
2825	printf "$dashes\n *** compilation finished \n"
2826	fi
2827
2828	fi
2829
2830	fi
2831
2832
2833	# PROVIDE THE INPUT FILES
2834	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2835	(( i = 0 ))
2836	while (( i < iin ))
2837	do
2838	(( i = i + 1 ))
2839	if (( i == 1 ))
2840	then
2841	printf "\n\n *** providing INPUT-files:\n$dashes"
2842	fi
2843
2844
2845	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2846	if [[ "${transin[$i]}" = unavailable ]]
2847	then
2848	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2849	then
2850	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2851	printf "\n is not available!"
2852	else
2853	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2854	printf "\n is not available!"
2855	fi
2856	continue
2857	fi
2858
2859	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2860	files_for_pes=false; datentyp=file
2861	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2862	then
2863	files_for_pes=true; datentyp=directory
2864	actionin[$i]=""
2865	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2866	then
2867	actionin[$i]=""
2868	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2869	then
2870	files_for_pes=true; datentyp=directory
2871	actionin[$i]="ar"
2872	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2873	then
2874	actionin[$i]="ar"
2875	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2876	then
2877	files_for_pes=true; datentyp=directory
2878	actionin[$i]="fl"
2879	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2880	then
2881	actionin[$i]="fl"
2882	fi
2883
2884	if [[ $files_for_pes = true ]]
2885	then
2886	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2887	else
2888	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2889	fi
2890
2891	# INPUT-FILE FOR A RESTART RUN.
2892	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2893	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2894	if [[ "${actionin[$i]}" = fl ]]
2895	then
2896	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2897	if [[ $files_for_pes = false ]]
2898	then
2899	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2900	then
2901	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2902	got_tmp[$i]=true
2903	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2904	then
2905	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2906	printf "\n *** trying to use backup copy in \"$WORK\" "
2907	cp $WORK/${frelin[$i]} ${localin[$i]}
2908	else
2909	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2910	printf "\n or \"$tmp_data_catalog\" does not exist!"
2911	printf "\n *** trying to get copy from archive"
2912	actionin[$i]=ar
2913	fi
2914	else
2915	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2916	then
2917	mkdir ${localin[$i]}
2918	cd $tmp_data_catalog/${frelin[$i]}
2919	for file in $(ls *)
2920	do
2921	ln $file $TEMPDIR/${localin[$i]}
2922	done
2923	cd $TEMPDIR
2924	got_tmp[$i]=true
2925	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2926	then
2927	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2928	printf "\n *** trying to use backup copy in \"$WORK\" "
2929	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2930	else
2931	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2932	printf "\n or \"$tmp_data_catalog\" does not exist!"
2933	printf "\n *** trying to get copy from archive"
2934	actionin[$i]=ar
2935	fi
2936	fi
2937	fi
2938
2939
2940	# FILE IS STORED ON THE ARCHIVE SYSTEM
2941	if [[ "${actionin[$i]}" = ar ]]
2942	then
2943
2944	if [[ $files_for_pes = false ]]
2945	then
2946	printf "\n file will be restored from archive-system ($archive_system)!"
2947	else
2948	printf "\n directory will be restored from archive-system ($archive_system)!"
2949	fi
2950
2951	file_restored=false
2952
2953	if [[ $archive_system = asterix ]]
2954	then
2955	do_stagein=true
2956	(( stagein_anz = 0 ))
2957	while [[ $do_stagein = true ]]
2958	do
2959	if [[ $files_for_pes = false ]]
2960	then
2961	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2962	else
2963	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2964	fi
2965	cat STAGEIN_OUTPUT
2966	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2967	then
2968	file_restored=true
2969	do_stagein=false
2970	else
2971	(( stagein_anz = stagein_anz + 1 ))
2972	if (( stagein_anz == 10 ))
2973	then
2974	printf "\n +++ stagein stoped after 10 tries"
2975	locat=stage
2976	exit
2977	fi
2978	printf "\n +++ restoring from archive failed, trying again:"
2979	sleep 900
2980	fi
2981	done
2982	elif [[ $archive_system = DMF ]]
2983	then
2984	if [[ $files_for_pes = false ]]
2985	then
2986	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2987	locat=DMF
2988	exit
2989	else
2990	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2991	cp -r $ARCHIVE/${frelin[$i]} $PWD
2992	file_restored=true
2993	fi
2994	elif [[ $archive_system = tivoli ]]
2995	then
2996	if [[ $files_for_pes = false ]]
2997	then
2998	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2999	else
3000	(( inode = 0 ))
3001	while (( inode < nodes ))
3002	do
3003	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3004	(( inode = inode + 1 ))
3005	done
3006	fi
3007	file_restored=true
3008	elif [[ $archive_system = ut ]]
3009	then
3010	if [[ $files_for_pes = false ]]
3011	then
3012	cp $UT/${frelin[$i]} .
3013	else
3014	(( inode = 0 ))
3015	while (( inode < nodes ))
3016	do
3017	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3018	(( inode = inode + 1 ))
3019	done
3020	fi
3021	file_restored=true
3022	else
3023	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3024	locat=rearchive
3025	exit
3026	fi
3027
3028	if [[ $file_restored = true ]]
3029	then
3030
3031	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3032	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3033	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3034	if [[ $files_for_pes = false ]]
3035	then
3036	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3037	else
3038	mkdir $tmp_data_catalog/${frelin[$i]}
3039	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3040	fi
3041	got_tmp[$i]=true
3042
3043	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3044	mv ${frelin[$i]} ${localin[$i]}
3045
3046	fi
3047	fi
3048
3049
3050	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3051	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3052	then
3053
3054	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3055	then
3056
3057	# FILE COPIES ARE PROVIDED FOR ALL CORES
3058	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3059	printf "\n file will be provided for $numprocs processors"
3060	mkdir ${localin[$i]}
3061	ival=$numprocs
3062	(( ii = 0 ))
3063	while (( ii <= ival-1 ))
3064	do
3065	if (( ii < 10 ))
3066	then
3067	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3068	elif (( ii < 100 ))
3069	then
3070	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3071	elif (( ii < 1000 ))
3072	then
3073	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3074	else
3075	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3076	fi
3077	(( ii = ii + 1 ))
3078	done
3079
3080	else
3081
3082	if [[ $files_for_pes = true ]]
3083	then
3084
3085	# PROVIDE FILES FOR EACH CORE
3086	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3087	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3088	printf "\n providing $numprocs files for the respective processors"
3089	mkdir ${localin[$i]}
3090	if [[ $link_local_input = true ]]
3091	then
3092	printf " using ln -f\n"
3093	cd ${absnamein[$i]}
3094	for file in $(ls *)
3095	do
3096	ln -f $file ${localin[$i]}
3097	done
3098	cd $TEMPDIR
3099	fi
3100
3101	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3102	if [[ ! -f "${localin[$i]}/_0000" ]]
3103	then
3104	if [[ $link_local_input = true ]]
3105	then
3106	printf " ln failed for .../_0000, using cp...\n"
3107	fi
3108	cp -r ${absnamein[$i]}/* ${localin[$i]}
3109	fi
3110
3111	else
3112
3113	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3114	if [[ $link_local_input = true ]]
3115	then
3116	printf " using ln -f\n"
3117	ln -f ${absnamein[$i]} ${localin[$i]}
3118	fi
3119	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3120	if [[ ! -f "${localin[$i]}" ]]
3121	then
3122	if [[ $link_local_input = true ]]
3123	then
3124	printf " ln failed, using cp...\n"
3125	fi
3126	cp ${absnamein[$i]} ${localin[$i]}
3127	fi
3128	fi
3129	fi
3130	fi
3131
3132	done
3133	if (( i != 0 ))
3134	then
3135	printf "\n$dashes\n *** all INPUT-files provided \n"
3136	fi
3137
3138
3139	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3140	(( i = 0 ))
3141	while (( i < iic ))
3142	do
3143	(( i = i + 1 ))
3144	if (( i == 1 ))
3145	then
3146	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3147	fi
3148	printf "\n >>> ${in_command[$i]}"
3149	eval ${in_command[$i]}
3150	if (( i == iic ))
3151	then
3152	printf "\n$dashes\n"
3153	fi
3154	done
3155
3156
3157	# SET THE REMAINING CPU-TIME
3158	cpurest=${cpumax}.
3159
3160
3161	# START DVR STREAMING SERVER
3162	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3163	then
3164	if [[ "$dvr_server" != "" ]]
3165	then
3166
3167	printf "\n\n *** preparing the dvr streaming server configuration file"
3168
3169	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3170	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3171	if [[ "$running_dvrserver_id" != "" ]]
3172	then
3173
3174	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3175	printf "\n This server is used instead starting a new one!"
3176	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3177
3178	else
3179
3180	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3181	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3182	then
3183	cp ${PALM_BIN}/.dvrserver.config .
3184
3185	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3186	user_id=`id -u`
3187	group_id=`id -g`
3188
3189	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3190	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3191	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3192	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3193	mv .dvrserver.3 .dvrserver.config
3194	rm .dvrserver.1 .dvrserver.2
3195
3196	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3197	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3198	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3199	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3200	local_dvrserver_running=.TRUE.
3201	else
3202	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3203	printf "\n \"$PALM_BIN\" "
3204	locat=dvr
3205	exit
3206	fi
3207
3208	fi
3209
3210	else
3211	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3212	fi
3213	fi
3214
3215
3216	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3217	# (FILE ENVPAR WILL BE READ BY PALM)
3218	cat > ENVPAR << %%END%%
3219	&envpar run_identifier = '$fname', host = '$localhost',
3220	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3221	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3222	maximum_cpu_time_allowed = ${cpumax}.,
3223	revision = '$global_revision',
3224	local_dvrserver_running = $local_dvrserver_running,
3225	batch_job = $batch_job /
3226
3227	%%END%%
3228
3229
3230	# STARTING THE EXECUTABLE
3231	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3232	PATH=$PATH:$TEMPDIR
3233
3234	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3235	if [[ "$mpi_debug" = true ]]
3236	then
3237	export MPI_CHECK_ARGS=1
3238	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3239	fi
3240
3241	if [[ "$totalview" = true ]]
3242	then
3243	printf "\n *** totalview debugger will be used"
3244	tv_opt="-tv"
3245	else
3246	tv_opt=""
3247	fi
3248
3249	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3250	then
3251
3252	#Interactive ALLINEA DEBUG seesion
3253	if [[ "$ENVIRONMENT" != BATCH ]]
3254	then
3255	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3256	then
3257	if [[ "$allinea" = true ]]
3258	then
3259	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3260
3261	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3262	wait
3263	fi
3264	fi
3265	fi
3266
3267	if [[ "$ENVIRONMENT" = BATCH ]]
3268	then
3269	continue
3270	fi
3271	if [[ $localhost = ibmh ]]
3272	then
3273
3274	# SETUP THE IBM MPI ENVIRONMENT
3275	export MP_SHARED_MEMORY=yes
3276	export AIXTHREADS_SCOPE=S
3277	export OMP_NUM_THREADS=$threads_per_task
3278	export AUTHSTATE=files
3279	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3280
3281	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3282	export MP_ADAPTER_USE=shared
3283	export MP_CPU_USE=multiple
3284	export MP_TIMEOUT=1200
3285
3286	unset MP_TASK_AFFINITY
3287
3288	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3289	#(( ii = 1 ))
3290	#while (( ii <= $numprocs ))
3291	#do
3292	# echo $localhost_realname >> hostfile
3293	# (( ii = ii + 1 ))
3294	#done
3295	#export MP_HOSTFILE=hostfile
3296
3297	if [[ "$LOADLBATCH" = yes ]]
3298	then
3299	totalview poe a.out $ROPTS
3300	else
3301	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3302	export TVDSVRLAUNCHCMD=ssh
3303	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3304	fi
3305
3306	fi # END DEBUG MODE
3307
3308	else
3309
3310	# NORMAL EXECUTION
3311	if [[ -n $numprocs ]]
3312	then
3313
3314	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3315	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3316	then
3317
3318	# SETUP THE IBM MPI ENVIRONMENT
3319	if [[ $host != ibmh && $host != ibmkisti ]]
3320	then
3321	export MP_SHARED_MEMORY=yes
3322	export AIXTHREAD_SCOPE=S
3323	export OMP_NUM_THREADS=$threads_per_task
3324	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3325	export AUTHSTATE=files
3326	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3327	# export MP_PRINTENV=yes
3328
3329	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3330	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3331	export MP_WAIT_MODE=poll
3332	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3333	fi
3334
3335	if [[ $host = ibmkisti ]]
3336	then
3337	export LANG=en_US
3338	export MP_SHARED_MEMORY=yes
3339	if [[ $threads_per_task = 1 ]]
3340	then
3341	export MP_SINGLE_THREAD=yes
3342	export MEMORY_AFFINITY=MCM
3343	else
3344	export OMP_NUM_THREADS=$threads_per_task
3345	fi
3346	fi
3347
3348	if [[ "$LOADLBATCH" = yes ]]
3349	then
3350	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3351	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3352	then
3353	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3354	else
3355	if [[ $run_coupled_model = false ]]
3356	then
3357	if [[ "$ocean_file_appendix" = true ]]
3358	then
3359	echo "precursor_ocean" > runfile_atmos
3360	else
3361	echo "precursor_atmos" > runfile_atmos
3362	fi
3363	else
3364	(( iia = $numprocs_atmos / $threads_per_task ))
3365	(( iio = $numprocs_ocean / $threads_per_task ))
3366	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3367	printf "\n using $coupled_mode coupling"
3368	printf "\n\n"
3369	echo "coupled_run $iia $iio" > runfile_atmos
3370	fi
3371	poe ./a.out $ROPTS < runfile_atmos
3372	fi
3373	else
3374	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3375	then
3376	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3377	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3378	then
3379	if [[ -f $hostfile ]]
3380	then
3381	cp $hostfile hostfile
3382	else
3383	(( ii = 1 ))
3384	while (( ii <= $numprocs ))
3385	do
3386	echo $localhost_realname >> hostfile
3387	(( ii = ii + 1 ))
3388	done
3389	fi
3390	export MP_HOSTFILE=hostfile
3391	if [[ $run_coupled_model = false ]]
3392	then
3393	if [[ "$ocean_file_appendix" = true ]]
3394	then
3395	echo "precursor_ocean" > runfile_atmos
3396	else
3397	echo "precursor_atmos" > runfile_atmos
3398	fi
3399	else
3400	(( iia = $numprocs_atmos / $threads_per_task ))
3401	(( iio = $numprocs_ocean / $threads_per_task ))
3402	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3403	printf "\n using $coupled_mode coupling"
3404	printf "\n\n"
3405	echo "coupled_run $iia $iio" > runfile_atmos
3406	fi
3407
3408	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3409
3410	else
3411	if [[ "$host_file" = "" ]]
3412	then
3413	printf "\n +++ no hostfile given in configuration file"
3414	locat=config_file
3415	exit
3416	else
3417	eval host_file=$host_file
3418	fi
3419	export MP_HOSTFILE=$host_file
3420	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3421	fi
3422	fi
3423	elif [[ $host = nech ]]
3424	then
3425	(( ii = nodes ))
3426	if [[ $ii = 1 ]]
3427	then
3428	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3429	export MPIPROGINF=YES
3430	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3431	echo "*** execution on single node with mpirun"
3432	mpirun -np $numprocs ./a.out $ROPTS
3433	else
3434	(( i = 0 ))
3435	while (( i < ii ))
3436	do
3437	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3438	(( i = i + 1 ))
3439	done
3440
3441	echo "#!/bin/sh" > mpi_exec_shell
3442	echo " " >> mpi_exec_shell
3443	echo "set -u" >> mpi_exec_shell
3444	echo "F_ERRCNT=0" >> mpi_exec_shell
3445	echo "MPIPROGINV=YES" >> mpi_exec_shell
3446	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3447	echo "cpurest=$cpurest" >> mpi_exec_shell
3448	echo "fname=$fname" >> mpi_exec_shell
3449	echo "localhost=$localhost" >> mpi_exec_shell
3450	echo "return_address=$return_address" >> mpi_exec_shell
3451	echo "return_username=$return_username" >> mpi_exec_shell
3452	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3453	echo "write_binary=$write_binary" >> mpi_exec_shell
3454	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3455	echo " " >> mpi_exec_shell
3456	echo "export F_ERRCNT" >> mpi_exec_shell
3457	echo "export MPIPROGINV" >> mpi_exec_shell
3458	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3459	echo "export cpurest" >> mpi_exec_shell
3460	echo "export fname" >> mpi_exec_shell
3461	echo "export localhost" >> mpi_exec_shell
3462	echo "export return_address" >> mpi_exec_shell
3463	echo "export return_username" >> mpi_exec_shell
3464	echo "export tasks_per_node" >> mpi_exec_shell
3465	echo "export write_binary" >> mpi_exec_shell
3466	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3467	echo " " >> mpi_exec_shell
3468	echo "exec ./a.out" >> mpi_exec_shell
3469
3470	chmod u+x mpi_exec_shell
3471	export MPIPROGINF=YES
3472	mpirun -f multinode_config &
3473	wait
3474
3475	fi
3476	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3477	then
3478
3479	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3480	# DOES NOT EXIST
3481	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3482	then
3483	if [[ -f $hostfile ]]
3484	then
3485	cp $hostfile hostfile
3486	(( ii = $numprocs / $threads_per_task ))
3487	[[ $ii = 0 ]] && (( ii = 1 ))
3488	else
3489	(( ii = 1 ))
3490	while (( ii <= $numprocs / $threads_per_task ))
3491	do
3492	echo $localhost_realname >> hostfile
3493	(( ii = ii + 1 ))
3494	done
3495	if (( $numprocs / $threads_per_task == 0 ))
3496	then
3497	echo $localhost_realname >> hostfile
3498	fi
3499	fi
3500	eval zeile=\"`head -n $ii hostfile`\"
3501	printf "\n *** running on: $zeile"
3502	fi
3503
3504	(( ii = $numprocs / $threads_per_task ))
3505	[[ $ii = 0 ]] && (( ii = 1 ))
3506	export OMP_NUM_THREADS=$threads_per_task
3507
3508	if [[ $threads_per_task != 1 ]]
3509	then
3510	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3511	# MAY ABORT
3512	ulimit -s unlimited
3513	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3514	fi
3515	if [[ $run_coupled_model = false ]]
3516	then
3517	if [[ "$ocean_file_appendix" = true ]]
3518	then
3519	echo "precursor_ocean" > runfile_atmos
3520	else
3521	echo "precursor_atmos" > runfile_atmos
3522	fi
3523	printf "\n\n"
3524
3525	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3526	then
3527	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3528	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3529	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3530	elif [[ $host = lccrayf ]]
3531	then
3532	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3533	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3534	then
3535	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3536	elif [[ $host = lcflow ]]
3537	then
3538	mpirun -np $ii a.out < runfile_atmos $ROPTS
3539	elif [[ $host = lcsb ]]
3540	then
3541	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3542	elif [[ $host = lckiaps ]]
3543	then
3544	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3545	elif [[ $host = lckyu* ]]
3546	then
3547	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3548	else
3549	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3550	fi
3551	else
3552
3553	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3554	(( iia = $numprocs_atmos / $threads_per_task ))
3555	(( iio = $numprocs_ocean / $threads_per_task ))
3556	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3557	printf "\n using $coupled_mode coupling"
3558	printf "\n\n"
3559
3560	if [[ $coupled_mode = "mpi2" ]]
3561	then
3562	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3563	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3564
3565	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3566	then
3567
3568	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3569	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3570
3571	else
3572	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3573	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3574	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3575	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3576	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3577	fi
3578	wait
3579
3580	else
3581
3582	echo "coupled_run $iia $iio" > runfile_atmos
3583
3584	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3585	then
3586
3587	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3588
3589	elif [[ $host = lck \|\| $host = lckordi ]]
3590	then
3591
3592	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3593
3594	elif [[ $host = lckyu* ]]
3595	then
3596
3597	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3598
3599	fi
3600	wait
3601	fi
3602
3603	fi
3604
3605	elif [[ $host = lckyoto ]]
3606	then
3607	set -xv
3608	export P4_RSHCOMMAND=plesh
3609	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3610	if [[ "$ENVIRONMENT" = BATCH ]]
3611	then
3612	if [[ "$cond2" = fujitsu ]]
3613	then
3614	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3615	elif [[ "cond2" = pgi ]]
3616	then
3617	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3618	else
3619	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3620	fi
3621	else
3622	if [[ "$cond2" = "" ]]
3623	then
3624	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3625	else
3626	mpirun -np $numprocs ./a.out $ROPTS
3627	fi
3628	fi
3629	set +xv
3630
3631	elif [[ $host = lctit ]]
3632	then
3633	export OMP_NUM_THREADS=$threads_per_task
3634	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3635	if [[ "$threads_per_task" != 1 ]]
3636	then
3637	export MV2_ENABLE_AFFINITY=0
3638	fi
3639	echo "----- PBS_NODEFILE content:"
3640	cat $PBS_NODEFILE
3641	echo "-----"
3642	(( ii = $numprocs / $threads_per_task ))
3643	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3644	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3645	else
3646	mpprun -n $numprocs a.out $ROPTS
3647	fi
3648	else
3649	a.out $ROPTS
3650	fi
3651	fi
3652
3653	if [[ $? != 0 ]]
3654	then
3655
3656	# ABORT IN CASE OF RUNTIME ERRORS
3657	printf "\n +++ runtime error occured"
3658	locat=execution
3659	exit
3660
3661	else
3662
3663	printf "\n$dashes\n *** execution finished \n"
3664
3665	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3666	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3667	if [[ "$dvrserver_id" != "" ]]
3668	then
3669	kill $dvrserver_id
3670	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3671
3672	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3673	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3674	if [[ -d DATA_DVR ]]
3675	then
3676
3677	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3678	# DIRECTORY
3679	cp .dvrserver.config DATA_DVR
3680
3681	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3682	# SEQUENCE MODE DATA TOO)
3683	process_dvr_output -d DATA_DVR -f $fname -s
3684
3685	else
3686
3687	# PROCESS THE LOCAL OUTPUT
3688	process_dvr_output -l -d DATA_DVR -f $fname
3689
3690	fi
3691
3692	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3693	then
3694
3695	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3696	process_dvr_output -l -d DATA_DVR -f $fname
3697
3698	fi
3699	fi
3700
3701
3702
3703	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3704	# BY EACH CORE INTO ONE FILE
3705	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3706	then
3707	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3708	printf "\n 2d- and/or 3d-data may be incomplete!"
3709	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3710	elif [[ "$combine_plot_fields" == true ]]
3711	then
3712	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3713	then
3714	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3715	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3716	else
3717	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3718	combine_plot_fields${block}.x
3719	fi
3720	else
3721
3722	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3723	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3724	# ??? koennen wir das streichen ???
3725	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3726	fi
3727
3728
3729
3730	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3731	(( i = 0 ))
3732	while (( i < ioc ))
3733	do
3734	(( i = i + 1 ))
3735	if (( i == 1 ))
3736	then
3737	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3738	fi
3739	printf "\n >>> ${out_command[$i]}"
3740	eval ${out_command[$i]}
3741	if (( i == ioc ))
3742	then
3743	printf "\n$dashes\n"
3744	fi
3745	done
3746
3747
3748	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3749	if [[ $do_trace = true ]]
3750	then
3751	printf "\n\n"
3752	ls -al
3753	fi
3754
3755
3756
3757	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3758	(( i = 0 ))
3759	while (( i < iout ))
3760	do
3761	(( i = i + 1 ))
3762	if (( i == 1 ))
3763	then
3764	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3765	fi
3766
3767	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3768	files_for_pes=false; filetyp=file
3769	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3770	then
3771	files_for_pes=true; filetyp=directory
3772	actionout[$i]=""
3773	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3774	then
3775	actionout[$i]=""
3776	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3777	then
3778	files_for_pes=true; filetyp=directory
3779	actionout[$i]="ar"
3780	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3781	then
3782	actionout[$i]="ar"
3783	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3784	then
3785	files_for_pes=true; filetyp=directory
3786	actionout[$i]="fl"
3787	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3788	then
3789	actionout[$i]="fl"
3790	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3791	then
3792	files_for_pes=true; filetyp=directory
3793	actionout[$i]="tr"
3794	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3795	then
3796	actionout[$i]="tr"
3797	fi
3798
3799	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3800	then
3801	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3802	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3803	then
3804	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3805	else
3806
3807
3808	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3809	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3810	if [[ "${actionout[$i]}" = tr ]]
3811	then
3812	if [[ $localhost != $fromhost ]]
3813	then
3814	if [[ $files_for_pes = false ]]
3815	then
3816	cps=""
3817	cst=""
3818	else
3819	cps=-c
3820	cst="/"
3821	fi
3822	if [[ $localhost = nech ]]
3823	then
3824
3825	# TRANSFER IN SEPERATE JOB
3826	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3827	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3828	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3829	if [[ $files_for_pes = false ]]
3830	then
3831	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3832	else
3833	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3834	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3835	fi
3836
3837	echo "set -x" > transfer_${localout[$i]}
3838	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3839
3840	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3841	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3842	printf "\n or higher cycle\n"
3843	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]}
3844
3845	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3846
3847	if [[ $localhost = nech ]]
3848	then
3849	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3850	else
3851	if [[ "$LOGNAME" = b323013 ]]
3852	then
3853	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3854	else
3855	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3856	fi
3857	fi
3858
3859	else
3860
3861	# TRANSFER WITHIN THIS JOB
3862	transfer_failed=false
3863	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3864	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3865	if [[ $localhost = lccrayb ]]
3866	then
3867	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]}"
3868	elif [[ $localhost = lccrayh ]]
3869	then
3870	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]}"
3871	elif [[ $localhost = lcxe6 ]]
3872	then
3873	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]}"
3874	else
3875	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3876	fi
3877	[[ $? != 0 ]] && transfer_failed=true
3878
3879	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3880	if [[ $transfer_failed = true ]]
3881	then
3882	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3883	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3884
3885	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3886	eval local_catalog=${pathout[$i]}
3887	if [[ ! -d $local_catalog ]]
3888	then
3889	printf " *** local directory does not exist. Trying to create:\n"
3890	printf " $local_catalog \n"
3891	mkdir -p $local_catalog
3892	fi
3893	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3894	transfer_problems=true
3895	fi
3896	fi
3897	else
3898
3899	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3900	actionout[$i]=""
3901	fi
3902	fi
3903
3904
3905	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3906	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3907	if [[ "${actionout[$i]}" = tra ]]
3908	then
3909	if [[ $localhost != $fromhost ]]
3910	then
3911	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3912	then
3913
3914	# TRANSFER IN SEPERATE JOB
3915	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3916	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3917	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3918	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3919
3920	echo "set -x" > transfer_${localout[$i]}
3921	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3922
3923	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3924	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3925	printf "\n or higher cycle\n"
3926	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]}
3927
3928	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3929
3930	if [[ $localhost = nech ]]
3931	then
3932	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3933	else
3934	if [[ $LOGNAME = b323013 ]]
3935	then
3936	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3937	else
3938	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3939	fi
3940	fi
3941
3942	else
3943
3944	# TRANSFER WITHIN THIS JOB
3945	transfer_failed=false
3946	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3947	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3948	if [[ $localhost = lccrayb ]]
3949	then
3950	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]}"
3951	elif [[ $localhost = lccrayh ]]
3952	then
3953	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]}"
3954	elif [[ $localhost = lcxe6 ]]
3955	then
3956	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]}"
3957	else
3958	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3959	fi
3960	[[ $? != 0 ]] && transfer_failed=true
3961
3962	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3963	if [[ $transfer_failed = true ]]
3964	then
3965	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3966	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3967
3968	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3969	eval local_catalog=${pathout[$i]}
3970	if [[ ! -d $local_catalog ]]
3971	then
3972	printf " *** local directory does not exist. Trying to create:\n"
3973	printf " $local_catalog \n"
3974	mkdir -p $local_catalog
3975	fi
3976
3977	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3978	transfer_problems=true
3979	fi
3980	fi
3981	else
3982
3983	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3984	actionout[$i]=a
3985	fi
3986	fi
3987
3988
3989	# OUTPUT-FILE FOR A RESTART-RUN.
3990	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3991	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3992	# AS LAST ACTION, ARCHIVING IS INITIATED.
3993	if [[ "${actionout[$i]}" = fl ]]
3994	then
3995	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3996	chmod g+rx $tmp_data_catalog
3997	if [[ $files_for_pes = false ]]
3998	then
3999	printf "\n >>> OUTPUT: ${localout[$i]} to"
4000	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4001	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4002	else
4003	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4004	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4005	mkdir $tmp_data_catalog/${frelout[$i]}
4006	cd ${localout[$i]}
4007	for file in $(ls *)
4008	do
4009	ln -f $file $tmp_data_catalog/${frelout[$i]}
4010	done
4011	cd $TEMPDIR
4012	fi
4013
4014
4015	# CREATE AND SUBMIT ARCHIVING-JOB
4016	if [[ $store_on_archive_system = true ]]
4017	then
4018
4019	if [[ $archive_system = asterix ]]
4020	then
4021	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4022	if [[ $files_for_pes = false ]]
4023	then
4024	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4025	else
4026	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4027	fi
4028	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4029	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4030	echo "then" >> archive_${frelout[$i]}
4031	echo " do_stageout=false" >> archive_${frelout[$i]}
4032	echo "else" >> archive_${frelout[$i]}
4033	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4034	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4035	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4036	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4037	if [[ $files_for_pes = false ]]
4038	then
4039	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4040	else
4041	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4042	fi
4043	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4044	echo "fi" >> archive_${frelout[$i]}
4045	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4046	elif [[ $archive_system = DMF ]]
4047	then
4048	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4049	if [[ $files_for_pes = false ]]
4050	then
4051	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4052	locat=DMF
4053	exit
4054	else
4055	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4056	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4057	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4058	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4059	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4060	fi
4061	elif [[ $archive_system = tivoli ]]
4062	then
4063	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4064	if [[ $files_for_pes = false ]]
4065	then
4066	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4067	echo "set -x" >> archive_${frelout[$i]}
4068	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4069	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4070	else
4071
4072	echo "set -x" >> archive_${frelout[$i]}
4073	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4074	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4075	cd $tmp_data_catalog
4076	all_files=`ls -1 ${frelout[$i]}/*`
4077	cd - > /dev/null
4078	(( inode = 0 ))
4079	(( tp1 = tasks_per_node + 1 ))
4080	while (( inode < nodes ))
4081	do
4082	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4083	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4084	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4085	(( inode = inode + 1 ))
4086	done
4087	fi
4088	elif [[ $archive_system = ut ]]
4089	then
4090	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4091	if [[ $files_for_pes = false ]]
4092	then
4093	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4094	echo "set -x" >> archive_${frelout[$i]}
4095	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4096	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4097	else
4098
4099	echo "set -x" >> archive_${frelout[$i]}
4100	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4101	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4102	cd $tmp_data_catalog
4103	all_files=`ls -1 ${frelout[$i]}/*`
4104	cd - > /dev/null
4105	(( inode = 0 ))
4106	(( tp1 = tasks_per_node + 1 ))
4107	while (( inode < nodes ))
4108	do
4109	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4110	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4111	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4112	(( inode = inode + 1 ))
4113	done
4114	fi
4115	elif [[ $archive_system = none ]]
4116	then
4117	printf " +++ archiving on $localhost not available!\n"
4118	fi
4119
4120	if [[ $archive_system != none ]]
4121	then
4122	if [[ $localhost = nech ]]
4123	then
4124	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4125	fi
4126	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4127	fi
4128	else
4129	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4130	fi
4131
4132
4133	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4134	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4135	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4136	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4137	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4138	if [[ $files_for_pes = false ]]
4139	then
4140	cat /dev/null > ${pathout[$i]}
4141	else
4142	mkdir -p ${pathout[$i]}
4143	fi
4144
4145	fi
4146
4147
4148	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4149	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4150	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4151	if [[ "${actionout[$i]}" = ar ]]
4152	then
4153	if [[ $files_for_pes = false ]]
4154	then
4155	printf "\n >>> OUTPUT: ${localout[$i]} to"
4156	printf "\n ${pathout[$i]}"
4157	printf "\n File will be copied to archive-system ($archive_system) !\n"
4158	else
4159	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4160	printf "\n ${pathout[$i]}"
4161	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4162	fi
4163	mv ${localout[$i]} ${frelout[$i]}
4164
4165	file_saved=false
4166
4167	if [[ $archive_system = asterix ]]
4168	then
4169	do_stageout=true
4170	(( stageout_anz = 0 ))
4171	while [[ $do_stageout = true ]]
4172	do
4173	if [[ $files_for_pes = false ]]
4174	then
4175	stageout ${frelout[$i]} > STAGE_OUTPUT
4176	else
4177	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4178	fi
4179	cat STAGE_OUTPUT
4180	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4181	then
4182	file_saved=true
4183	do_stageout=false
4184	else
4185	if [[ $files_for_pes = false ]]
4186	then
4187	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4188	else
4189	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4190	fi
4191	(( stageout_anz = stageout_anz + 1 ))
4192	if (( stageout_anz == 10 ))
4193	then
4194	printf "\n +++ stoped after 10 unsuccessful tries!"
4195	archive_save=false
4196	do_stageout=false
4197	else
4198	printf "\n *** new try to store on archive after 15 min:"
4199	sleep 900
4200	fi
4201	fi
4202	done
4203	elif [[ $archive_system = DMF ]]
4204	then
4205	if [[ $files_for_pes = false ]]
4206	then
4207	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4208	locat=DMF
4209	exit
4210	else
4211	rm -rf $ARCHIVE/${frelout[$i]}
4212	cp -r ${frelout[$i]} $ARCHIVE
4213	fi
4214	file_saved=true
4215	elif [[ $archive_system = tivoli ]]
4216	then
4217	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4218	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4219	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4220	# WHEN THE ARCHIVE-JOB IS EXECUTED
4221	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4222	chmod g+rx $tmp_data_catalog
4223	if [[ $files_for_pes = false ]]
4224	then
4225	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4226	else
4227	mkdir $tmp_data_catalog/${frelout[$i]}
4228	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4229	fi
4230
4231	# GENERATE AND SUBMIT BATCH-JOB
4232	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4233	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4234	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4235	if [[ $files_for_pes = false ]]
4236	then
4237	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4238	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4239	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4240	else
4241	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4242	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4243	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4244	fi
4245
4246	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4247	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4248	file_saved=true
4249
4250	elif [[ $archive_system = ut ]]
4251	then
4252	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4253	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4254	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4255	# WHEN THE ARCHIVE-JOB IS EXECUTED
4256	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4257	chmod g+rx $tmp_data_catalog
4258	if [[ $files_for_pes = false ]]
4259	then
4260	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4261	else
4262	mkdir $tmp_data_catalog/${frelout[$i]}
4263	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4264	fi
4265
4266	# GENERATE AND SUBMIT BATCH-JOB
4267	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4268	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4269	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4270	if [[ $files_for_pes = false ]]
4271	then
4272	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4273	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4274	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4275	else
4276	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4277	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4278	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4279	fi
4280
4281	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4282	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4283	file_saved=true
4284
4285	else
4286	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4287	archive_save=false
4288	fi
4289
4290	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4291	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4292	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4293	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4294	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4295	if [[ $file_saved = true ]]
4296	then
4297	if [[ $files_for_pes = false ]]
4298	then
4299	cat /dev/null > ${pathout[$i]}
4300	else
4301	mkdir -p ${pathout[$i]}
4302	fi
4303	fi
4304
4305	fi
4306
4307	# APPEND ON THIS MACHINE
4308	if [[ "${actionout[$i]}" = "a" ]]
4309	then
4310	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4311	then
4312	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4313	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4314	else
4315	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4316	cat ${localout[$i]} >> ${pathout[$i]}
4317	fi
4318	fi
4319
4320	# COPY ON THIS MACHINE
4321	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4322	# ON DIFFERENT FILE-SYSTEMS
4323	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4324	then
4325
4326	# COPY IN CASE OF RUNS ON SINGLE CORES
4327	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4328	then
4329	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4330	if [[ $link_local_output = true ]]
4331	then
4332	printf " using ln -f\n"
4333	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4334	fi
4335	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4336	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4337	then
4338	if [[ $link_local_output = true ]]
4339	then
4340	printf " ln failed, using cp...\n"
4341	fi
4342	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4343	fi
4344	else
4345	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4346	if [[ $link_local_output = true ]]
4347	then
4348	printf " using ln -f\n"
4349	ln -f ${localout[$i]} ${pathout[$i]}
4350	fi
4351	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4352	if [[ ! -f "${pathout[$i]}" ]]
4353	then
4354	if [[ $link_local_output = true ]]
4355	then
4356	printf " ln failed, using cp...\n"
4357	fi
4358	cp ${localout[$i]} ${pathout[$i]}
4359	fi
4360	fi
4361
4362	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4363	then
4364
4365	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4366	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4367	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4368	if [[ $link_local_output = true ]]
4369	then
4370	printf " using ln -f\n"
4371	mkdir ${pathout[$i]}
4372	cd ${localout[$i]}
4373	for file in $(ls *)
4374	do
4375	ln -f $file ${pathout[$i]}
4376	done
4377	cd $TEMPDIR
4378	fi
4379
4380	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4381	if [[ ! -f "${pathout[$i]}/_0000" ]]
4382	then
4383	if [[ $link_local_output = true ]]
4384	then
4385	printf " ln failed for .../_0000, using cp...\n"
4386	fi
4387	cp -r ${localout[$i]} ${pathout[$i]}
4388	fi
4389
4390	fi
4391	fi
4392	done
4393	if (( i != 0 ))
4394	then
4395	if [[ $transfer_problems = true ]]
4396	then
4397	printf "\n$dashes\n *** OUTPUT-files saved"
4398	printf "\n +++ WARNING: some data transfers failed! \n"
4399	else
4400	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4401	fi
4402	fi
4403
4404
4405	# IF REQUIRED, START A RESTART-JOB
4406	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4407	if [[ -f CONTINUE_RUN ]]
4408	then
4409
4410	if [[ $archive_save = true ]]
4411	then
4412
4413	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4414	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4415	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4416	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4417	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4418	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4419	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4420	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4421	then
4422	mc=`echo $mc \| sed 's/#/f/g'`
4423	fi
4424
4425
4426	# START THE RESTART-JOB
4427	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4428	echo " $mc"
4429	printf "\n$dashes\n"
4430	if [[ $localhost != $fromhost ]]
4431	then
4432
4433	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4434	then
4435	echo "*** ssh will be used to initiate restart-runs!"
4436	echo " return_address=\"$return_address\" "
4437	echo " return_username=\"$return_username\" "
4438	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4439	then
4440	if [[ $localhost = ibmh ]]
4441	then
4442	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\" "
4443	elif [[ $localhost = lccrayb ]]
4444	then
4445	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\" "
4446	elif [[ $localhost = lccrayh ]]
4447	then
4448	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\" "
4449	elif [[ $localhost = lcxe6 ]]
4450	then
4451	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\" "
4452	else
4453	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	fi
4455	else
4456	if [[ $localhost = ibmkisti ]]
4457	then
4458	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\" "
4459	elif [[ $localhost = lcflow ]]
4460	then
4461	/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 "
4462	elif [[ $localhost = lccrayb ]]
4463	then
4464	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\" "
4465	elif [[ $localhost = lccrayh ]]
4466	then
4467	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\" "
4468	else
4469	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4470	fi
4471	fi
4472	else
4473	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4474	locat=restart; exit
4475	fi
4476
4477	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4478	if [[ $queue = special1q ]]
4479	then
4480	sleep 120
4481	else
4482	sleep 30
4483	fi
4484
4485	else
4486
4487	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4488	# USING SSH)
4489	cd $LOCAL_PWD
4490	if [[ $localhost = lckyuh ]]
4491	then
4492	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4493	printf "\n please restart job manually using command:\n"
4494	printf "\n \"$mc\" "
4495	else
4496	eval $mc # THE ' MUST BE EVALUATED
4497	fi
4498	cd - > /dev/null
4499	fi
4500	if [[ $localhost = lckyuh ]]
4501	then
4502	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4503	else
4504	printf "\n$dashes\n *** restart-run initiated \n"
4505	fi
4506
4507
4508	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4509	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4510	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4511	# MAY BE VERY HUGE)
4512	(( i = 0 ))
4513	while (( i < iin ))
4514	do
4515	(( i = i + 1 ))
4516	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4517	then
4518	rm -r $tmp_data_catalog/${frelin[$i]}
4519	fi
4520	done
4521
4522	else
4523
4524	printf "\n +++ no restart-run possible, since errors occured"
4525	printf "\n during the archive process"
4526	fi
4527
4528	fi
4529
4530
4531
4532	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4533	if [[ "$email_notification" != "none" ]]
4534	then
4535
4536	if [[ $localhost != $fromhost ]]
4537	then
4538	if [[ -f CONTINUE_RUN ]]
4539	then
4540	echo "PALM restart run necessary" > email_text
4541	echo "description header of actual run:" >> email_text
4542	cat CONTINUE_RUN >> email_text
4543	echo "mrun-command to restart:" >> email_text
4544	echo "$mc" >> email_text
4545	else
4546	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4547	fi
4548	mail $email_notification < email_text
4549	printf "\n *** email notification sent to \"$email_notification\" "
4550	fi
4551	fi
4552
4553
4554
4555	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4556	cd $HOME
4557	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4558
4559	else
4560
4561
4562	# PREPARING ACTIONS,
4563	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4564
4565	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4566	mrun_com="$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 $remote_username"
4567	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4568	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4569	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4570	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4571	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4572	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4573	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4574	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4575	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4576	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4577	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4578	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4579	if [[ $use_openmp = true ]]
4580	then
4581	mrun_com=${mrun_com}" -O $threads_per_task"
4582	fi
4583	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4584	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4585	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4586	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4587	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4588	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4589	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4590	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4591	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4592	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4593	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4594	if [[ $do_remote = true ]]
4595	then
4596	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4597	fi
4598
4599
4600	# CREATE EXECUTABLE FOR BATCH JOB
4601	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4602	then
4603
4604	printf "\n *** creating the executable for batch job\n"
4605
4606	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4607	if [[ $host != $localhost ]]
4608	then
4609	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4610	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4611	locat=create_executable; exit
4612	fi
4613
4614	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4615	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4616
4617	cp $make_depository .
4618	tar -xf $make_depository > /dev/null 2>&1
4619	cp ../* . > /dev/null 2>&1
4620
4621	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4622
4623	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4624	then
4625	printf "\n +++ error occured while compiling or linking"
4626	locat=compile
4627	exit
4628	fi
4629
4630	mv a.out ..
4631	cd - > /dev/null 2>&1
4632	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4633
4634	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4635
4636	fi
4637
4638
4639	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4640	jobfile=jobfile.$RANDOM
4641
4642
4643	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4644	echo "mkdir $TEMPDIR" >> $jobfile
4645	echo "cd $TEMPDIR" >> $jobfile
4646
4647
4648	# ACTIVATE ERROR-TRACEBACK
4649	if [[ $do_trace = true ]]
4650	then
4651	echo "set -x" >> $jobfile
4652	else
4653	echo "set +vx" >> $jobfile
4654	fi
4655
4656
4657	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4658	if [[ "$init_cmds" != "" ]]
4659	then
4660	echo "$init_cmds" >> $jobfile
4661	fi
4662	if [[ "$module_calls" != "" ]]
4663	then
4664	echo "$module_calls" >> $jobfile
4665	fi
4666
4667
4668	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4669	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4670	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4671	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4672	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4673	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4674	# QUEUEING-SYSTEMS
4675	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4676	then
4677
4678	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4679	if [[ $restart_run != true ]]
4680	then
4681	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4682	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4683	fi
4684
4685	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4686	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4687	echo "set -x" >> $jobfile
4688	if [[ $host = $localhost ]]
4689	then
4690
4691	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4692	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4693	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4694	then
4695	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4696	else
4697	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4698	fi
4699
4700	else
4701	if [[ $host = ibmkisti ]]
4702	then
4703	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4704	echo "localdir=\`pwd\`" >> $jobfile
4705	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4706	elif [[ $host = lccrayb ]]
4707	then
4708	echo "localdir=\`pwd\`" >> $jobfile
4709	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4710	elif [[ $host = lccrayh ]]
4711	then
4712	echo "localdir=\`pwd\`" >> $jobfile
4713	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4714
4715	else
4716	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4717	fi
4718	fi
4719	echo "export SOURCES_COMPLETE=true" >> $jobfile
4720
4721	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4722	# WORKING DIRECTORY OF THE JOB
4723	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4724	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4725	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4726	echo "execute_mrun=true" >> $jobfile
4727	echo " " >> $jobfile
4728
4729	else
4730
4731	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4732	if [[ $do_compile = true ]]
4733	then
4734
4735	source_catalog=SOURCES_FOR_RUN_$fname
4736
4737	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4738	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4739	echo "export SOURCES_COMPLETE=true" >> $jobfile
4740	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4741
4742	for filename in $source_list
4743	do
4744	# BACKSLASH IS USED FOR MASKING
4745	echo "cat > $filename << \"%END%\"" >> $jobfile
4746	cat $source_catalog/$filename >> $jobfile
4747	echo " " >> $jobfile
4748	echo "%END%" >> $jobfile
4749	echo " " >> $jobfile
4750	done
4751
4752	# BACKSLASH IS USED FOR MASKING
4753	echo "cat > Makefile << \"%END%\"" >> $jobfile
4754	cat $source_catalog/Makefile >> $jobfile
4755	echo " " >> $jobfile
4756	echo "%END%" >> $jobfile
4757	echo " " >> $jobfile
4758
4759	echo "cd - > /dev/null" >> $jobfile
4760
4761	fi
4762
4763
4764	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4765	# BACKSLASH IS USED FOR MASKING
4766	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4767	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4768	echo "cat > $config_file << \"%END%\"" >> $jobfile
4769	if [[ $host = lckyuh ]]
4770	then
4771	# NO CROSS-COMPILER ON COMPUTE NODE
4772	sed 's/frtpx/frt/g' $config_file >> $jobfile
4773	else
4774	sed 's/#$.*//g' $config_file >> $jobfile
4775	fi
4776	echo "%END%" >> $jobfile
4777	echo " " >> $jobfile
4778
4779
4780	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4781	# BACKSLASH IS USED FOR MASKING
4782	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4783	if [[ $host = lckyuh ]]
4784	then
4785	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4786	else
4787	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4788	fi
4789	echo "%END%" >> $jobfile
4790	echo "chmod u+x $mrun_script_name" >> $jobfile
4791	echo "execute_mrun=true" >> $jobfile
4792	echo " " >> $jobfile
4793
4794	fi
4795
4796
4797	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4798	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4799	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4800	if [[ $do_remote = true ]]
4801	then
4802	(( i = 0 ))
4803	while (( i < iin ))
4804	do
4805	(( i = i + 1 ))
4806	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4807	if [[ "${transin[$i]}" = job ]]
4808	then
4809	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4810	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4811	echo " " >> $jobfile
4812	echo "%END%" >> $jobfile
4813	else
4814	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4815	fi
4816
4817	# CHECK, IF FILE COULD BE CREATED
4818	echo "if [[ \$? = 1 ]]" >> $jobfile
4819	echo "then" >> $jobfile
4820	echo " echo \" \" " >> $jobfile
4821	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4822	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4823	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4824	echo " execute_mrun=false" >> $jobfile
4825	echo "fi" >> $jobfile
4826	done
4827	fi
4828
4829	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4830	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4831	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4832	echo "LOCAL_PWD=$working_directory" >> $jobfile
4833	echo "export LOCAL_PWD" >> $jobfile
4834
4835	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4836	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4837	echo "export LOCAL_MRUN_PATH" >> $jobfile
4838
4839	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4840	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4841	# then
4842	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4843	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4844	# fi
4845
4846	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4847	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4848	echo "set -x" >> $jobfile
4849	echo "queue=$queue" >> $jobfile
4850	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4851	echo 'ls -al; echo `pwd`' >> $jobfile
4852	echo "cd \$HOME" >> $jobfile
4853	echo "rm -rf $TEMPDIR" >> $jobfile
4854
4855
4856
4857
4858	# START THE JOB USING SUBJOB-COMMAND
4859	if [[ $silent = false ]]
4860	then
4861	printf "\n "
4862	else
4863	printf "\n\n"
4864	fi
4865
4866	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
4867	rm -rf $jobfile
4868
4869
4870	fi # END OF REMOTE-PART

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |