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source: palm/trunk/SCRIPTS/mrun @ 1620

Last change on this file since 1620 was 1620, checked in by heinze, 9 years ago
adjustments for Mistral at DKRZ Hamburg (lcbullhh)
Property svn:keywords set to `Id Rev`
File size: 180.2 KB

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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1620 2015-07-17 11:37:41Z heinze $
29	#
30	# 1609 2015-07-03 15:37:58Z maronga
31	# Modified the random number of the temporary working directory to match the
32	# queuing system number on HLRN-III (lccray*).
33	#
34	# 1604 2015-06-23 15:48:03Z suehring
35	# Enable coupled runs for lcmuk
36	#
37	# 1598 2015-05-29 06:45:40Z raasch
38	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
39	#
40	# 1549 2015-01-30 14:26:16Z suehring
41	# Enable interactive debug sessions with allinea debugger
42	#
43	# 1547 2015-01-29 15:09:12Z witha
44	# adjustments for ForWind computing cluster (lcflow)
45	#
46	# 1491 2014-11-12 08:12:57Z heinze
47	# correct setting of batch_job allowed for ibm-machines
48	#
49	# 1468 2014-09-24 14:06:57Z maronga
50	# Typo removed (addres->address)
51	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
52	# Added support for restart runs (remote) for lcxe6
53	#
54	# 1442 2014-07-28 07:09:10Z raasch
55	# default queues for HLRN-III (lccrayb/lccrayh) defined
56	#
57	# 1422 2014-07-02 10:01:25Z kanani
58	# automatic restarts enabled for lccrayb,
59	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
60	#
61	# 1420 2014-06-10 06:24:14Z raasch
62	# -j1 option added to aprung command for lccrayf (CSC)
63	#
64	# 1402 2014-05-09 14:25:13Z raasch
65	# batch_job added to envpar-NAMELIST
66	#
67	# 1357 2014-04-11 15:02:03Z witha
68	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
69	# possible)
70	#
71	# 1320 2014-03-20 08:40:49Z raasch
72	# check namelist file set false by default
73	#
74	# 1304 2014-03-12 10:29:42Z raasch
75	# ulimit option changed from -Ss to -s
76	#
77	# bugfix: missing "fi" in r1289
78	#
79	# 1289 2014-03-04 07:12:34Z raasch
80	# comments translated to English
81	# necriam-, fimm-, ibmy-, and sgi-specific code removed
82	# export of variables for palm and interpret_config removed
83	#
84	# 1281 2014-02-01 07:55:49Z raasch
85	# rsync-copy restricted to Cray machines, since command is unavailable on some
86	# other systems
87	#
88	# 1279 2014-01-28 12:10:14Z raasch
89	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
90	# in order to remove annoying restrictions concerning the number of processors which
91	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
92	# restriction, one of the nodes will be filled with less than the given number of
93	# tasks per node. A respective warning is given.
94	#
95	# 1274 2014-01-09 13:14:54Z heinze
96	# adjustments for lccrayh
97	#
98	# 1272 2014-01-08 10:19:32Z witha
99	# small adjustment for lcflow
100	#
101	# 1270 2013-12-16 11:05:01Z fricke
102	# call of combine_plot_fields adjusted for lccrayb/lccrayh
103	#
104	# 1255 2013-11-07 14:43:35Z raasch
105	# further adjustments for lccrayb remote access
106	#
107	# 1241 2013-10-30 11:36:58Z heinze
108	# Enable use of nudging input and input of large scale forcing from
109	# external files
110	#
111	# 1229 2013-09-20 06:55:19Z raasch
112	# further adjustments for lccrayb
113	#
114	# 1224 2013-09-16 07:27:23Z raasch
115	# first adjustments for lccrayb
116	#
117	# 1210 2013-08-14 10:58:20Z raasch
118	# fftw support added
119	#
120	# 1201 2013-07-10 16:17:59Z witha
121	# adjustments for Forwind cluster (lcflow)
122	#
123	# 1199 2013-07-05 14:52:22Z raasch
124	# adjustments for CSC Helsinki (lccrayf),
125	# executables for batch jobs can be created in advance, in order to avoid calling
126	# the compiler within the batch job (only works if batch jobs are submitted on
127	# local host)
128	#
129	# 1190 2013-06-25 09:39:21Z heinze
130	# enable use of automatic restarts for ibmh
131	# use of cluster/express queue enabled (ibmh)
132	#
133	# 1124 2013-04-09 15:46:52Z raasch
134	# variable "memory" is exported via typeset option -x, because otherwise an unknown
135	# side effect may lead to data loss while getopts is reading the script-option arguments
136	#
137	# 1122 2013-04-09 08:37:16Z heinze
138	# Bugfix: change type of variable last_char
139	#
140	# 1119 2013-04-05 15:11:19Z raasch
141	# Bugfix for setting -T option for subjob
142	#
143	# 1108 2013-03-05 07:03:32Z raasch
144	# bugfix for coupled runs on lckyut/lckyuh
145	#
146	# 1106 2013-03-04 05:31:38Z raasch
147	# --stdin argument for mpiexec on lckyuh
148	# -y and -Y settings output to header
149	#
150	# 1103 2013-02-20 02:15:53Z raasch
151	# default script runs again under ksh, because of unsolved problems with read
152	# from stdin: when bash script is called from a ksh, message "read error: 0:
153	# Resource temporarily unavailable" appears and script does not stop,
154	# further bash compatibility adjustments,
155	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
156	# on lckyuh, but mrun does not terminate and issues a warning instead
157	#
158	# 1101 2013-02-17 10:20:21Z raasch
159	# script now running under bash instead of ksh, which required small adjustments
160	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
161	# read from stdin),
162	# cross compilername on lckyuh compute nodes replaced by real compiler name
163	#
164	# 1099 2013-02-10 01:47:43Z raasch
165	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
166	# and for Forwind cluster (lcflow)
167	# small further adjustments for lckyut
168	#
169	# 1094 2013-02-03 01:52:12Z raasch
170	# explicit ssh/scp port can be set in config file with environment variable
171	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
172	# decalpha parts (yonsei) removed
173	#
174	# 2013-02-02 07:06:13Z raasch
175	# adjustments for Kyushu-University computing center (lckyut - tatara)
176	#
177	# 1083 2013-01-04 10:22:09Z maronga
178	# bugfix in parameter file check (read %cpp_options was missing)
179	#
180	# 1069 2012-11-28 16:18:43Z maronga
181	# bugfix: coupling mode was always set to mpi2, typos removed
182	#
183	# 1058 2012-11-21 07:00:35Z raasch
184	# Intel inspector (inspxe) is given the number of PEs instead of the number of
185	# nodes
186	#
187	# 1046 2012-11-09 14:38:45Z maronga
188	# code put under GPL (PALM 3.9)
189	#
190	# 21/03/94 - Siggi - first version finished
191	# 03/03/94 - Siggi - script development started
192	#
193	#--------------------------------------------------------------------------------#
194	# mrun - script for running PALM jobs
195	#--------------------------------------------------------------------------------#
196
197
198
199	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
200
201	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
202	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
203	# (TOO MANY ARGUMENTS - PROBLEM)
204	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
205
206	AddFilenames=""
207	additional_conditions=""
208	add_source_path=""
209	afname=""
210	archive_save=true
211	archive_system=none
212	check_namelist_files=false
213	combine_plot_fields=true
214	compiler_name=""
215	cond1=""
216	cond2=""
217	config_file=.mrun.config
218	coupled_dist=""
219	coupled_mode="mpi1"
220	cpp_opts=""
221	cpp_options=""
222	cpumax=0
223	cpurest=0
224	create_executable_for_batch=false
225	delete_temporary_catalog=true
226	do_batch=false
227	do_compile=true
228	do_remote=false
229	do_stagein=true
230	do_stageout=true
231	do_trace=false
232	email_notification="none"
233	exclude=""
234	executable=""
235	execution_error=false
236	fftw_inc=""
237	fftw_lib=""
238	fftw_support=false
239	fname=test
240	fromhost=""
241	global_revision=""
242	group_number=none
243	host=""
244	host_file=""
245	hp=""
246	ignore_archive_error=false
247	input_list=""
248	interpreted_config_file=""
249	job_catalog="~/job_queue"
250	job_on_file=""
251	keep_data_from_previous_run=false
252	link_local_input=false
253	link_local_output=false
254	localhost_realname=$(hostname)
255	local_dvrserver_running=.FALSE.
256	locat=normal
257	mainprog=""
258	makefile=""
259	max_par_io_str=""
260	mc=$0
261	while [[ $(echo $mc \| grep -c "/") != 0 ]]
262	do
263	mc=`echo $mc \| cut -f2- -d"/"`
264	done
265	module_calls=""
266	mrun_script_name=$mc
267	netcdf_inc=""
268	netcdf_lib=""
269	netcdf_support=false
270	node_usage=default
271	numprocs=""
272	numprocs_atmos=0
273	numprocs_ocean=0
274	OOPT=""
275	openmp=false
276	output_list=""
277	package_list=""
278	queue=none
279	read_from_config=""
280	restart_run=false
281	if [[ `hostname` = rte10 ]]
282	then
283	return_address=133.5.185.60
284	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
285	elif [[ `hostname` = climate0 ]]
286	then
287	return_address=165.132.26.68
288	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
289	elif [[ `hostname` = urban00 ]]
290	then
291	return_address=147.46.30.151
292	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
293	else
294	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
295	fi
296	return_password=""
297	return_username=$LOGNAME
298	remotecall=false
299	remote_username=""
300	run_coupled_model=false
301	run_mode=""
302	store_on_archive_system=false
303	dashes=" ----------------------------------------------------------------------------"
304	silent=false
305	source_list=""
306	source_path=SOURCE
307	tasks_per_node=""
308	threads_per_task=1
309	tmpcreate=false
310	tmp_data_catalog=""
311	transfer_problems=false
312	usern=$LOGNAME
313	use_openmp=false
314	version="MRUN 2.1 Rev$Rev: 1620 $"
315	working_directory=`pwd`
316	TOPT=""
317	XOPT=""
318	zeit=$( date \| cut -c 12-19 )
319
320	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
321	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
322	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
323	# SCRIPT-OPTION ARGUMENTS
324	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
325
326	# ERROR HANDLING IN CASE OF EXIT
327	trap 'rm -rf $working_directory/tmp_mrun
328	if [[ $locat != normal && $locat != control_c ]]
329	then
330
331	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
332	(( i = 0 ))
333	while (( i < iec ))
334	do
335	(( i = i + 1 ))
336	printf "\n *** Execution of ERROR-command:\n"
337	printf " >>> ${err_command[$i]}\n"
338	eval ${err_command[$i]}
339	done
340	if [[ -n $interpreted_config_file ]]
341	then
342	rm -rf $interpreted_config_file
343	fi
344	if [[ -n .mrun_environment ]]
345	then
346	rm -rf .mrun_environment
347	fi
348	if [[ $tmpcreate = true ]]
349	then
350	printf "\n *** Contents of \"$TEMPDIR\":\n"
351	ls -al; cd
352	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
353	fi
354	if [[ "$dvrserver_id" != "" ]]
355	then
356	echo "+++ killing dvrserver_id=$dvrserver_id"
357	kill $dvrserver_id
358	fi
359	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
360	then
361	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
362	fi
363	printf "\n\n+++ MRUN killed \n\n"
364	elif [[ $locat != control_c ]]
365	then
366	printf "\n\n --> all actions finished\n\n"
367	printf " Bye, bye $usern !!\n\n"
368	fi' exit
369
370
371	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
372	trap 'rm -rf $working_directory/tmp_mrun
373	rm -rf $working_directory/tmp_check_namelist_files
374	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
375	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
376	then
377	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
378	fi
379	if [[ "$dvrserver_id" != "" ]]
380	then
381	echo "+++ killing dvrserver_id=$dvrserver_id"
382	kill $dvrserver_id
383	fi
384	printf "\n+++ MRUN killed by \"^C\" \n\n"
385	locat=control_c
386	exit
387	' 2
388
389
390	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
391	# BEEN SET
392	if [[ "$PALM_BIN" = "" ]]
393	then
394	printf "\n +++ environment variable PALM_BIN has not been set"
395	printf "\n please set it to the directory where the PALM scripts are located"
396	locat=palm_bin; exit
397	fi
398	export PATH=$PALM_BIN:$PATH
399
400
401
402	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
403	# WHICH WILL BE USED TO START RESTART-JOBS
404	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
405	do
406	case $option in
407	(a) afname=$OPTARG;;
408	(A) store_on_archive_system=true; mc="$mc -A";;
409	(b) do_batch=true; mc="$mc -b";;
410	(B) delete_temporary_catalog=false; mc="$mc -B";;
411	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
412	(C) restart_run=true; mc="$mc -C";;
413	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
414	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
415	(F) job_on_file="-D"; mc="$mc -F";;
416	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
417	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
418	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
419	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
420	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
421	(I) ignore_archive_error=true; mc="$mc -I";;
422	(k) keep_data_from_previous_run=true; mc="$mc -k";;
423	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
424	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
425	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
426	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
427	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
428	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
429	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
430	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
431	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
432	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
433	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
434	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
435	(S) read_from_config=false; mc="$mc -S";;
436	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
437	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
438	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
439	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
440	(v) silent=true; mc="$mc -v";;
441	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
442	(x) do_trace=true;set -x; mc="$mc -x";;
443	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
444	(y) ocean_file_appendix=true; mc="$mc -y";;
445	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
446	(z) check_namelist_files=false; mc="$mc -z";;
447	(Z) combine_plot_fields=false; mc="$mc -Z";;
448	(\?) printf "\n +++ unknown option $OPTARG \n"
449	printf "\n --> type \"$0 ?\" for available options \n"
450	locat=parameter;exit;;
451	esac
452	done
453
454
455	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
456	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
457	(( to_shift = $OPTIND - 1 ))
458	shift $to_shift
459
460	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
461	if [[ "$1" = "?" ]]
462	then
463	(printf "\n *** mrun can be called as follows:\n"
464	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"
465	printf "\n Description of available options:\n"
466	printf "\n Option Description Default-Value"
467	printf "\n -a base name of input files equiv. -d"
468	printf "\n -A archiving when using file-attribute fl"
469	printf "\n -b batch-job on local machine ---"
470	printf "\n -B do not delete temporary directory at end ---"
471	printf "\n -c configuration file .mrun.config"
472	printf "\n -d base name of files attached to program test"
473	printf "\n -D preprocessor(cpp)-directives \"\" "
474	printf "\n -F create remote job file only ---"
475	printf "\n -h execution host $localhost_realname"
476	printf "\n -i INPUT control list \"\" "
477	printf "\n -I archiving errors of previous batch-jobs"
478	printf "\n will be ignored"
479	printf "\n -k keep data from previous run"
480	printf "\n -K additional conditions for controling"
481	printf "\n usage of conditional code and"
482	printf "\n env-variables in configuration file \"\" "
483	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
484	printf "\n -M Makefile name Makefile"
485	printf "\n -n node usage (shared/not_shared) depending on -h"
486	printf "\n -o OUTPUT control list \"\" "
487	printf "\n -O threads per openMP task ---"
488	printf "\n -p software package list \"\" "
489	printf "\n -q queue \"$queue\" "
490	printf "\n -r run control list (combines -i -o) \"\" "
491	printf "\n -s filenames of routines to be compiled \"\" "
492	printf "\n must end with .f, .f90, .F, or .c !"
493	printf "\n use \"..\" for more than one file and wildcards"
494	printf "\n -s LM compiles all locally modified files"
495	printf "\n -S config file interpreted by shellscript ---"
496	printf "\n -t allowed cpu-time in seconds (batch) 0"
497	printf "\n -T tasks per node depending on -h"
498	printf "\n -u username on remote machine \"\" "
499	printf "\n -v no prompt for confirmation ---"
500	printf "\n -w maximum parallel io streams as given by -X"
501	printf "\n -x tracing of mrun for debug purposes ---"
502	printf "\n -X # of processors (on parallel machines) 1"
503	printf "\n -y add appendix \"_O\" to all local output"
504	printf "\n files (ocean precursor runs followed by"
505	printf "\n coupled atmosphere-ocean runs) ---"
506	printf "\n -Y run coupled model, \"#1 #2\" with"
507	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
508	printf "\n -z disable a priori parameter file check ---"
509	printf "\n -Z skip combine_plot_fields at the end of "
510	printf "\n the simulation ---"
511	printf "\n "
512	printf "\n Possible values of positional parameter <modus>:"
513	printf "\n \"?\" - this outline \n\n") \| more
514	exit
515	elif [[ "$1" != "" ]]
516	then
517	printf "\n +++ positional parameter $1 unknown \n"
518	locat=parameter; exit
519	fi
520
521
522
523	# SHORT STARTING MESSAGE
524	printf "\n*** $version "
525	printf "\n will be executed. Please wait ..."
526
527
528
529	# CHECK, IF CONFIGURATION FILE EXISTS
530	if [[ ! -f $config_file ]]
531	then
532	printf "\n\n +++ configuration file: "
533	printf "\n $config_file"
534	printf "\n does not exist"
535	locat=connect; exit
536	fi
537
538
539	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
540	line=""
541	grep "%host_identifier" $config_file > tmp_mrun
542	while read line
543	do
544	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
545	then
546	HOSTNAME=`echo $line \| cut -d" " -s -f2`
547	host_identifier=`echo $line \| cut -d" " -s -f3`
548	if [[ $localhost_realname = $HOSTNAME ]]
549	then
550	localhost=$host_identifier
551	break
552	fi
553	fi
554	done < tmp_mrun
555
556	if [[ "$localhost" = "" ]]
557	then
558	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
559	printf "\n for local host \"$localhost_realname\"."
560	printf "\n Please add line"
561	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
562	printf "\n to the configuration file."
563	locat=localhost; exit
564	fi
565
566
567	# SET HOST-SPECIFIC VARIABLES
568	case $localhost_realname in
569	(r1\|r2\|h01\|b01) archive_system=tivoli;;
570	(cs*) archive_system=ut;;
571	esac
572
573
574	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
575	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
576	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
577	[[ "$afname" = "" ]] && afname=$fname
578
579
580	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
581	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
582	# STATEMENTS IN THE CONFIGURATION FILE
583	if [[ "$run_mode" != "" ]]
584	then
585	input_list="$input_list $run_mode"
586	output_list="$output_list $run_mode"
587	fi
588
589
590	# ??? is this (and the respective option -H) really required ???
591	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
592	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
593	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
594	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
595	if [[ "$fromhost" = "" ]]
596	then
597	fromhost=$localhost
598	fi
599
600
601	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
602	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
603	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
604	# TO BE SUBMITTED (I.E. do_batch=true)
605	if [[ -n $host && "$host" != $localhost ]]
606	then
607	do_batch=true
608	do_remote=true
609	case $host in
610	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
611	(*) printf "\n"
612	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
613	printf "\n is not available"
614	locat=nqs; (( iec = 0 )); exit;;
615	esac
616	else
617	host=$localhost
618	fi
619
620
621	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
622	if [[ -n $additional_conditions ]]
623	then
624	cond1=`echo $additional_conditions \| cut -d" " -f1`
625	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
626	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
627	if [[ -n $dummy ]]
628	then
629	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
630	locat=options; exit
631	fi
632	block=_$cond1
633	[[ -n $cond2 ]] && block=${block}_$cond2
634	fi
635
636
637	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
638	if [[ $run_coupled_model = true ]]
639	then
640
641	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
642	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
643
644	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
645	then
646
647	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
648	printf "\n PEs (total) : $numprocs"
649	printf "\n PEs (atmosphere): $numprocs_atmos"
650	printf "\n PEs (ocean) : $numprocs_ocean"
651	locat=coupling; exit
652
653	fi
654
655
656	# GET coupled_mode FROM THE CONFIG FILE
657	line=""
658	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
659	while read line
660	do
661	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
662	then
663	coupled_mode="mpi2"
664	fi
665	done < tmp_mrun
666
667	fi
668
669	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
670	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
671	then
672	if [[ $ignore_archive_error = false ]]
673	then
674	printf "\n +++ data archiving of previous run failed"
675	printf "\n see directory \~/job_queue on remote machine"
676	locat=archive; exit
677	else
678	printf "\n +++ warning: data archiving in a previous run failed"
679	printf "\n MRUN continues, trying to get backup copy"
680	fi
681	fi
682
683
684	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
685	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
686	mrun_memory=$memory
687	mrun_group_number=$group_number
688	mrun_cpumax=$cpumax
689	mrun_numprocs=$numprocs
690
691
692	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
693	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
694	if [[ "$read_from_config" = false ]]
695	then
696	[[ $silent = false ]] && printf "\n Reading the configuration file... "
697
698	# READ THE CONFIGURATION FILE LINE BY LINE
699	while read zeile
700	do
701	[[ $silent = false ]] && printf "."
702
703
704	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
705	eval zeile=\"$zeile\"
706
707
708	# INTERPRET THE LINE
709	if [[ "$(echo $zeile)" = "" ]]
710	then
711	# EMPTY LINE, NO ACTION
712	continue
713
714	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
715	then
716
717	# LINE IS A COMMENT LINE
718	true
719
720	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
721	then
722
723	# LINE DEFINES AN ENVIRONMENT-VARIABLE
724	zeile=$(echo $zeile \| cut -c2-)
725	var=`echo $zeile \| cut -d" " -f1`
726	value=`echo $zeile \| cut -d" " -s -f2`
727	for_host=`echo $zeile \| cut -d" " -s -f3`
728	for_cond1=`echo $zeile \| cut -d" " -s -f4`
729	for_cond2=`echo $zeile \| cut -d" " -s -f5`
730
731	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
732	then
733
734	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
735	# "::" IS REPLACED BY ":".
736	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
737
738
739	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
740	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
741	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
742	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
743	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
744	# CONFIGURATION-FILE.
745	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
746	then
747	eval $var=\$value
748
749	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
750	if [[ $do_trace = true ]]
751	then
752	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
753	fi
754	fi
755
756	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
757	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
758	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
759	# MUST HAVE TO BE STARTED
760	if [[ $var = host ]]
761	then
762	if [[ -n $host && "$host" != $localhost ]]
763	then
764	do_batch=true
765	do_remote=true
766	case $host in
767	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
768	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
769	printf "\n is not available"
770	locat=nqs; exit;;
771	esac
772	else
773	host=$localhost
774	fi
775	fi
776
777	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
778	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
779	# BY MRUN (E.G. subjob)
780	export $var
781	fi
782
783
784
785
786	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
787	then
788
789	# LINE DEFINES ERROR-COMMAND
790	(( iec = iec + 1 ))
791	zeile=$(echo $zeile \| cut -c4-)
792	err_command[$iec]="$zeile"
793
794	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
795	then
796
797	# LINE DEFINES INPUT-COMMAND
798	(( iic = iic + 1 ))
799	zeile=$(echo $zeile \| cut -c4-)
800	in_command[$iic]="$zeile"
801
802	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
803	then
804
805	# LINE DEFINES OUTPUT-COMMAND
806	(( ioc = ioc + 1 ))
807	zeile=$(echo $zeile \| cut -c4-)
808	out_command[$ioc]="$zeile"
809
810	else
811
812	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
813	# s2a: in/out - field
814	# s2b: loc - field (optional)
815	# s2c: tr/ar - field (optional)
816	s1=`echo $zeile \| cut -d" " -f1`
817	s2=`echo $zeile \| cut -d" " -s -f2`
818	s2a=$(echo $s2 \| cut -d":" -f1)
819	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
820	then
821	s2b=""
822	s2c=""
823	else
824	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
825	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
826	fi
827	s3=`echo $zeile \| cut -d" " -f3`
828	s4=`echo $zeile \| cut -d" " -s -f4`
829	s5=`echo $zeile \| cut -d" " -s -f5`
830	s6=`echo $zeile \| cut -d" " -s -f6`
831
832
833	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
834	# INPUT- OR OUTPUT-LIST.
835	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
836	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
837	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
838	# IS NOT CHECKED AND STORED.
839	IFSALT="$IFS"; IFS="$IFS:"
840	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
841	then
842	found=false
843	for actual in $input_list
844	do
845	for formal in $s3
846	do
847	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
848	done
849	done
850	if [[ $found = true ]]
851	then
852	(( iin = iin + 1 ))
853	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
854	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
855	extin[$iin]=$s6
856	fi
857	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
858	then
859	found=false
860	for actual in $output_list
861	do
862	for formal in $s3
863	do
864	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
865	done
866	done
867	if [[ $found = true ]]
868	then
869	(( iout = iout + 1 ))
870	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
871	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
872	fi
873	elif [[ "$s2a" != in && "$s2a" != out ]]
874	then
875	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
876	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
877	locat=connect; exit
878	fi
879	IFS="$IFSALT"
880	fi
881	done < $config_file
882
883	else
884
885	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
886	[[ $silent = false ]] && printf "..."
887	interpreted_config_file=.icf.$RANDOM
888
889
890
891	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
892	cat > .mrun_environment << %%END%%
893	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
894	config_file = '$config_file', do_remote = '$do_remote',
895	do_trace = '$do_trace', host = '$host',
896	input_list = '$input_list', icf = '$interpreted_config_file',
897	localhost = '$localhost', output_list = '$output_list' /
898
899	%%END%%
900
901	if [[ "$host" != $localhost ]]
902	then
903
904	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
905	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
906	if [[ $? != 0 ]]
907	then
908	printf "\n\n +++ no interpret_config found"
909	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
910	locat=interpret_config; exit
911	fi
912	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
913	$interpret_config_executable
914
915	else
916
917	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
918	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
919	then
920	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
921	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
922	locat=interpret_config; exit
923	else
924	interpret_config${block}.x
925	fi
926
927	fi
928	rm .mrun_environment
929
930
931	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
932	chmod u+x $interpreted_config_file
933	export PATH=$PATH:.
934	. $interpreted_config_file
935	rm $interpreted_config_file
936
937	fi
938
939
940	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
941	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
942	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
943	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
944	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
945	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
946	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
947
948
949	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
950	# FOR SOURCE-FILES TO BE COMPILED.
951	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
952	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
953	if [[ "$SOURCES_COMPLETE" = "" ]]
954	then
955
956	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
957	# HAS BEEN DEFINED
958	source_path=""
959	line=""
960	grep "%source_path" $config_file > tmp_mrun
961	while read line
962	do
963	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
964	then
965	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
966	then
967	global_source_path=`echo $line \| cut -d" " -f2`
968	fi
969	fi
970	done < tmp_mrun
971
972	line=""
973	found=false
974	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
975	while read line
976	do
977	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
978	then
979	if [[ $found = true ]]
980	then
981	printf "\n\n +++ more than one source path found in configuration file"
982	printf "\n for local host \"$localhost\" "
983	locat=source_path; exit
984	fi
985	source_path=`echo $line \| cut -d" " -f2`
986	found=true
987	fi
988	done < tmp_mrun
989	rm tmp_mrun
990
991	if [[ "$source_path" = "" ]]
992	then
993	if [[ "$global_source_path" != "" ]]
994	then
995	source_path=$global_source_path
996	else
997	printf "\n\n +++ no source path found in configuration file"
998	printf "\n for local host \"$localhost\" "
999	locat=source_path; exit
1000	fi
1001	fi
1002	eval source_path=$source_path
1003
1004	if [[ ! -d $source_path ]]
1005	then
1006	printf "\n\n +++ source path \"$source_path\" on local host"
1007	printf "\n \"$localhost\" does not exist"
1008	locat=source_path; exit
1009	fi
1010
1011	fi
1012
1013
1014	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1015	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1016	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1017	then
1018	global_revision=`svnversion $source_path 2>/dev/null`
1019	global_revision="Rev: $global_revision"
1020	fi
1021
1022
1023	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1024	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1025	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1026	if [[ -n $host && "$host" != $localhost ]]
1027	then
1028	do_batch=true
1029	do_remote=true
1030	case $host in
1031	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1032	(*) printf "\n"
1033	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1034	printf "\n is not available"
1035	locat=nqs; (( iec = 0 )); exit;;
1036	esac
1037	else
1038	host=$localhost
1039	fi
1040
1041
1042
1043	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1044	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1045	then
1046
1047	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1048	if [[ ! -n $numprocs ]]
1049	then
1050	printf "\n"
1051	printf "\n +++ option \"-K parallel\" requires additional specification"
1052	printf "\n of the number of processors to be used by"
1053	printf "\n mrun-option \"-X\" or by environment-variable"
1054	printf "\n \"numprocs\" in the configuration file"
1055	locat=numprocs; (( iec = 0 )); exit
1056	fi
1057
1058	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1059	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1060	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1061	then
1062	printf "\n"
1063	printf "\n +++ option \"-T\" (tasks per node) is missing"
1064	printf "\n set -T option or define tasks_per_node in the config file"
1065	locat=tasks_per_node; (( iec = 0 )); exit
1066	fi
1067
1068	if (( numprocs < tasks_per_node ))
1069	then
1070	printf "\n"
1071	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1072	printf "\n given values: -T $tasks_per_node -X $numprocs"
1073	locat=tasks_per_node; (( iec = 0 )); exit
1074	fi
1075
1076	if [[ $host != lcflow && $host != lcxt5m ]]
1077	then
1078	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1079	(( ival = $tasks_per_node ))
1080	(( pes = numprocs ))
1081	(( ii = pes / ival ))
1082	(( remaining_pes = pes - ii * ival ))
1083	if (( remaining_pes > 0 ))
1084	then
1085	printf "\n"
1086	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1087	printf "\n divisor of the total number of processors (option \"-X\")"
1088	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1089	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1090	(( nodes = nodes + 1 ))
1091	fi
1092	fi
1093
1094
1095	# SETTINGS FOR SUBJOB-COMMAND
1096	OOPT="-O $threads_per_task"
1097
1098	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1099	if [[ "$tasks_per_node" != "" ]]
1100	then
1101	TOPT="-T $tasks_per_node"
1102	fi
1103
1104	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1105	if [[ $node_usage = default ]]
1106	then
1107	if [[ $host = ibms ]]
1108	then
1109	node_usage=shared
1110	else
1111	node_usage=not_shared
1112	fi
1113	fi
1114
1115	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1116	then
1117	printf "\n"
1118	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1119	printf "\n \"shared\" or \"not_shared\""
1120	locat=tasks_per_node; (( iec = 0 )); exit
1121	fi
1122
1123	fi
1124
1125	# CHECK IF HOSTFILE EXISTS
1126	if [[ -n $hostfile ]]
1127	then
1128	if [[ ! -f $hostfile ]]
1129	then
1130	printf "\n"
1131	printf "\n +++ hostfile \"$hostfile\" does not exist"
1132	locat=hostfile; exit
1133	fi
1134	fi
1135
1136
1137	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1138	if [[ "$maximum_parallel_io_streams" = "" ]]
1139	then
1140	maximum_parallel_io_streams=$numprocs
1141	fi
1142
1143
1144	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1145	if [[ "$scp_port" != "" ]]
1146	then
1147	PORTOPT="-P $scp_port"
1148	SSH_PORTOPT="-p $scp_port"
1149	fi
1150
1151
1152	# SET DEFAULT-QUEUE, IF NOT GIVEN
1153	if [[ $queue = none ]]
1154	then
1155	case $host in
1156	(ibmh) queue=cluster;;
1157	(ibmkisti) queue=class.32plus;;
1158	(lcbullhh) queue=compute;;
1159	(lccrayb) queue=mpp1q;;
1160	(lccrayh) queue=mpp1q;;
1161	(lckiaps) queue=normal;;
1162	(lckyoto) queue=ph;;
1163	(lckyuh) queue=fx-single;;
1164	(lckyut) queue=cx-single;;
1165	(lctit) queue=S;;
1166	(nech) queue=none;;
1167	(unics) queue=unics;;
1168	esac
1169	fi
1170
1171
1172	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1173	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1174	(( i = 0 ))
1175	while (( i < iin ))
1176	do
1177	(( i = i + 1 ))
1178	(( maxcycle = 0 ))
1179
1180	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1181	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1182	if [[ "${actionin[$i]}" = di ]]
1183	then
1184	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1185	# HOST ONLY
1186	eval filename=${pathin[$i]}/${endin[$i]}
1187	else
1188	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1189	# HOST ONLY
1190	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1191	fi
1192	eval pathname=${pathin[$i]}
1193
1194	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1195	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1196	then
1197	filename_input=$filename
1198	fi
1199
1200	# CHECK IF FILE EXISTS
1201	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1202	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1203	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1204	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1205	then
1206
1207	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1208	if [[ "${transin[$i]}" != "locopt" ]]
1209	then
1210	printf "\n\n +++ INPUT-file: "
1211	if [[ "${extin[$i]}" = "" ]]
1212	then
1213	printf "\n $filename"
1214	else
1215	printf "\n $filename.${extin[$i]}"
1216	fi
1217	printf "\n does not exist\n"
1218	locat=input; exit
1219	else
1220	transin[$i]="unavailable"
1221	fi
1222	else
1223
1224	# DETERMINE THE FILE'S CYCLE NUMBER
1225	ls -1 -d $filename > filelist 2>/dev/null
1226	ls -1 -d $filename.* >> filelist 2>/dev/null
1227	while read zeile
1228	do
1229	cycle=$(echo $zeile \| cut -f2 -d".")
1230	if [[ "$cycle" = "$zeile" ]]
1231	then
1232	(( icycle = 0 ))
1233	elif [[ "$cycle" = "${extin[$i]}" ]]
1234	then
1235	(( icycle = 0 ))
1236	else
1237	(( icycle = $cycle ))
1238	fi
1239	if (( icycle > maxcycle ))
1240	then
1241	(( maxcycle = icycle ))
1242	file_to_be_used=$zeile
1243	fi
1244	done <filelist
1245	rm filelist
1246
1247	# APPEND CYCLE NUMBER TO FILENAME
1248	if (( maxcycle > 0 ))
1249	then
1250	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1251	then
1252	filename=${filename}.$maxcycle.${extin[$i]}
1253	else
1254	filename=${filename}.$maxcycle
1255	fi
1256	else
1257	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1258	then
1259	filename=${filename}.${extin[$i]}
1260	fi
1261	fi
1262
1263	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1264	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1265	absnamein[$i]=$filename
1266	if (( maxcycle > 0 ))
1267	then
1268	if [[ "${actionin[$i]}" = di ]]
1269	then
1270	frelin[$i]=${endin[$i]}.$maxcycle
1271	else
1272	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1273	fi
1274	else
1275	if [[ "${actionin[$i]}" = di ]]
1276	then
1277	frelin[$i]=${endin[$i]}
1278	else
1279	frelin[$i]=${afname}${endin[$i]}
1280	fi
1281	fi
1282
1283	fi
1284	done
1285
1286	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1287	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1288	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1289	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1290	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1291	# REMOTE HOST)
1292	(( i = 0 ))
1293	while (( i < iout ))
1294	do
1295	(( i = i + 1 ))
1296	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1297	then
1298	if [[ "${actionout[$i]}" = tr ]]
1299	then
1300	actionout[$i]=""
1301	elif [[ "${actionout[$i]}" = trpe ]]
1302	then
1303	actionout[$i]=pe
1304	elif [[ "${actionout[$i]}" = tra ]]
1305	then
1306	actionout[$i]=a
1307	fi
1308	(( maxcycle = 0 ))
1309	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1310	eval catalogname=${pathout[$i]}
1311	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1312	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1313	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1314	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1315	then
1316
1317	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1318	if cat /dev/null > $filename
1319	then
1320	rm $filename
1321	else
1322
1323	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1324	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1325	if [[ ! -d $catalogname ]]
1326	then
1327	if mkdir -p $catalogname
1328	then
1329	printf "\n\n *** directory:"
1330	printf "\n $catalogname"
1331	printf "\n was created\n"
1332	else
1333	printf "\n\n +++ OUTPUT-file:"
1334	printf "\n $filename"
1335	printf "\n cannot be created, because directory does not exist"
1336	printf "\n and cannot be created either"
1337	printf "\n"
1338	locat=output ; exit
1339	fi 2>/dev/null
1340	else
1341	printf "\n\n +++ OUTPUT-file:"
1342	printf "\n $filename"
1343	printf "\n cannot be created, although directory exists"
1344	printf "\n"
1345	locat=output ; exit
1346	fi
1347	fi 2>/dev/null
1348	else
1349
1350	# DETERMINE THE CYCLE NUMBER
1351	ls -1 -d $filename > filelist 2>/dev/null
1352	ls -1 -d $filename.* >> filelist 2>/dev/null
1353	while read zeile
1354	do
1355	cycle=$(echo $zeile \| cut -f2 -d".")
1356	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1357	then
1358	(( icycle = 1 ))
1359	else
1360	(( icycle = $cycle + 1 ))
1361	fi
1362	if (( icycle > maxcycle ))
1363	then
1364	(( maxcycle = icycle ))
1365	fi
1366	done <filelist
1367	rm filelist
1368	fi
1369
1370	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1371	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1372	if [[ "${actionout[$i]}" != a ]]
1373	then
1374	if (( maxcycle > 0 ))
1375	then
1376	filename=${filename}.$maxcycle
1377	if cat /dev/null > $filename
1378	then
1379	rm $filename
1380	else
1381	printf "\n +++ OUTPUT-file:"
1382	printf "\n $filename"
1383	printf "\n cannot be created"
1384	locat=output ; exit
1385	fi
1386	fi
1387	else
1388	(( maxcycle = maxcycle - 1 ))
1389	if (( maxcycle > 0 ))
1390	then
1391	filename=${filename}.$maxcycle
1392	fi
1393	fi
1394
1395	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1396	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1397	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1398	pathout[$i]=$filename
1399	if (( maxcycle > 0 ))
1400	then
1401	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1402	else
1403	frelout[$i]=${fname}${endout[$i]}
1404	fi
1405
1406	fi
1407	done
1408
1409
1410	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1411	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1412	then
1413	if [[ "$dvr_inc" = "" ]]
1414	then
1415	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1416	printf "\n This is required for the dvrp_graphics package.\n"
1417	locat=dvr; exit
1418	fi
1419	if [[ "$dvr_lib" = "" ]]
1420	then
1421	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1422	printf "\n This is required for the dvrp_graphics package.\n"
1423	locat=dvr; exit
1424	fi
1425	fi
1426
1427
1428	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1429	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1430	if [[ "$mainprog" = "" && "$executable" = "" ]]
1431	then
1432	printf "\n +++ neither main program nor executable defined"
1433	locat=source; exit
1434	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1435	then
1436	printf "\n +++ main program as well as executable defined"
1437	locat=source; exit
1438	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1439	then
1440	do_compile=false
1441	fi
1442
1443
1444	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1445	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1446	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1447	then
1448	rm -rf SOURCES_FOR_RUN_$fname
1449	mkdir SOURCES_FOR_RUN_$fname
1450	fi
1451
1452
1453	# COLLECT ALL ROUTINES TO BE COMPILED
1454	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1455	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1456	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1457	then
1458
1459	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1460
1461	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1462	then
1463
1464	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1465	source_list=""
1466	cd $source_path
1467
1468
1469	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1470	if [[ ! -d .svn ]]
1471	then
1472	printf "\n\n +++ source directory"
1473	printf "\n \"$source_path\" "
1474	printf "\n is not under control of \"subversion\"."
1475	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1476	fi
1477
1478
1479	# LIST ALL MODIFIED SOURCE CODE FILES
1480	Filenames=""
1481	svn status > tmp_mrun
1482	while read line
1483	do
1484	firstc=`echo $line \| cut -c1`
1485	if [[ $firstc = M \|\| $firstc = "?" ]]
1486	then
1487	Name=`echo "$line" \| cut -c8-`
1488	extension=`echo $Name \| cut -d. -f2`
1489	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1490	then
1491	Filenames="$Filenames "$Name
1492	fi
1493	fi
1494	done < tmp_mrun
1495
1496
1497	# COPY FILES TO SOURCES_FOR_RUN_...
1498	for dateiname in $Filenames
1499	do
1500	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1501	source_list=$source_list"$dateiname "
1502	done
1503
1504	cd - > /dev/null
1505
1506
1507	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1508	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1509	elif [[ "$source_list" != "" && $restart_run != true ]]
1510	then
1511
1512	cd $source_path
1513
1514	for filename in $source_list
1515	do
1516
1517	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1518	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1519	then
1520	printf "\n +++ source code file: $filename"
1521	printf "\n must not contain (\"/\") "
1522	locat=source; exit
1523	fi
1524
1525	if [[ ! -f $filename ]]
1526	then
1527	printf "\n +++ source code file: $filename"
1528	printf "\n does not exist"
1529	locat=source; exit
1530	else
1531	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1532	fi
1533
1534	done
1535
1536	cd - > /dev/null
1537
1538	fi
1539
1540
1541	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1542	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1543	if [[ $restart_run != true ]]
1544	then
1545
1546	if [[ ! -f "$source_path/$mainprog" ]]
1547	then
1548	printf "\n\n +++ main program: $mainprog"
1549	printf "\n does not exist in source directory"
1550	printf "\n \"$source_path\"\n"
1551	locat=source; exit
1552	else
1553	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1554	then
1555	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1556	source_list=${mainprog}" $source_list"
1557	fi
1558	fi
1559	fi
1560
1561
1562	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1563	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1564	if [[ "$restart_run" != true ]]
1565	then
1566	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1567	if [[ ! -f $makefile ]]
1568	then
1569	printf "\n +++ file \"$makefile\" does not exist"
1570	locat=make; exit
1571	else
1572	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1573	fi
1574	fi
1575
1576
1577	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1578	if [[ $restart_run != true && "$add_source_path" != "" ]]
1579	then
1580
1581	# DOES THE DIRECTORY EXIST?
1582	if [[ ! -d $add_source_path ]]
1583	then
1584	printf "\n\n +++ WARNING: additional source code directory"
1585	printf "\n \"$add_source_path\" "
1586	printf "\n does not exist or is not a directory."
1587	printf "\n No source code will be used from this directory!\n"
1588	add_source_path=""
1589	if [[ $silent == false ]]
1590	then
1591	sleep 3
1592	fi
1593	else
1594
1595	cd $add_source_path
1596	found=false
1597
1598	Names=$(ls -1 *.f90 2>&1)
1599	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1600	Names=$(ls -1 *.F90 2>&1)
1601	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1602	Names=$(ls -1 *.F 2>&1)
1603	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1604	Names=$(ls -1 *.f 2>&1)
1605	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1606	Names=$(ls -1 *.c 2>&1)
1607	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1608
1609	cd - > /dev/null
1610	cd SOURCES_FOR_RUN_$fname
1611
1612	# COPY MAKEFILE IF EXISTING
1613	if [[ -f $add_source_path/Makefile ]]
1614	then
1615	printf "\n\n *** user Makefile from directory"
1616	printf "\n \"$add_source_path\" is used \n"
1617	if [[ $silent == false ]]
1618	then
1619	sleep 1
1620	fi
1621	cp $add_source_path/Makefile .
1622	fi
1623
1624	for dateiname in $AddFilenames
1625	do
1626	if [[ -f $dateiname ]]
1627	then
1628	printf "\n +++ source code file \"$dateiname\" found in additional"
1629	printf "\n source code directory \"$add_source_path\" "
1630	printf "\n but was also given with option \"-s\" which means that it should be taken"
1631	printf "\n from directory \"$source_path\"."
1632	locat=source; exit
1633	fi
1634
1635	cp $add_source_path/$dateiname .
1636	source_list="$source_list $dateiname"
1637
1638	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1639	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1640	then
1641	printf "\n\n +++ user file \"$dateiname\" "
1642	printf "\n is not listed in Makefile \n"
1643	locat=source; exit
1644	else
1645
1646	if [[ $found = false ]]
1647	then
1648	found=true
1649	printf "\n\n *** following user file(s) added to the"
1650	printf " files to be translated:\n "
1651	fi
1652	printf "$dateiname "
1653	if [[ $silent == false ]]
1654	then
1655	sleep 0.5
1656	fi
1657
1658	fi
1659	done
1660	[[ $found = true ]] && printf "\n"
1661	cd - > /dev/null
1662	fi
1663	fi
1664
1665
1666	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1667	# TO THE LIST OF FILES TO BE COMPILED
1668	if [[ $restart_run != true && -n $package_list ]]
1669	then
1670
1671	cd $source_path
1672
1673	for package in $package_list
1674	do
1675
1676	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1677
1678	# DETERMINE FILES BELONGING TO THE PACKAGE
1679	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1680	# THE NAME OF THE DIRECTORY
1681	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1682
1683
1684	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1685	# IF THEY ARE NOT ALREADY PART OF THE LIST
1686	for source_list_name in $package_source_list
1687	do
1688	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1689	then
1690
1691	# ONLY TAKE FILES WITH VALID SUFFIX
1692	ending=`echo $source_list_name \| cut -f2 -d.`
1693	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1694	then
1695	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1696	source_list="$source_list $source_list_name"
1697	fi
1698	fi
1699	done
1700	done
1701
1702	cd - > /dev/null
1703	fi
1704
1705	fi # do_compile=true
1706
1707
1708	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1709	# AND SET PRE-PROCESSOR DIRECTIVES
1710	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1711	then
1712
1713	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1714	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1715	then
1716	cpp_options="${cpp_options},-D__ibm=__ibm"
1717	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1718	then
1719	cpp_options="$cpp_options -D__nec"
1720	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1721	then
1722	cpp_options="$cpp_options -D__lc"
1723	else
1724	cpp_options="$cpp_options -D__$localhost"
1725	fi
1726
1727	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1728	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1729	then
1730	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1731	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1732	else
1733	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1734	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1735	fi
1736
1737	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1738	if [[ -n $package_list ]]
1739	then
1740	for package in $package_list
1741	do
1742	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1743	then
1744	if [[ $package != "dvrp_graphics+1PE" ]]
1745	then
1746	cpp_options="${cpp_options},-D__$package=__$package"
1747	else
1748	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1749	export use_seperate_pe_for_dvrp_output=true
1750	fi
1751	else
1752	if [[ $package != "dvrp_graphics+1PE" ]]
1753	then
1754	cpp_options="$cpp_options -D__$package"
1755	else
1756	cpp_options="$cpp_options -D__dvrp_graphics"
1757	export use_seperate_pe_for_dvrp_output=true
1758	fi
1759	fi
1760	done
1761	fi
1762
1763	# SET DIRECTIVES GIVEN BY OPTION -D
1764	if [[ -n $cpp_opts ]]
1765	then
1766	for popts in $cpp_opts
1767	do
1768	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1769	then
1770	cpp_options="${cpp_options},-D__$popts=__$popts"
1771	else
1772	cpp_options="$cpp_options -D__$popts"
1773	fi
1774	done
1775	fi
1776
1777	else
1778
1779
1780	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1781	if [[ $do_remote = false ]]
1782	then
1783	if [[ ! -f $executable ]]
1784	then
1785	printf "\n +++ executable file: $executable"
1786	printf "\n does not exist"
1787	locat=executable; exit
1788	fi
1789	fi
1790	fi
1791
1792
1793	# DETERMINE THE JOB MODE
1794	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1795	then
1796	if [[ "$LOADLBATCH" = yes ]]
1797	then
1798	batch_job=.TRUE.
1799	jobmo=BATCH
1800	else
1801	batch_job=.FALSE.
1802	jobmo=INTERACTIVE
1803	fi
1804	else
1805	if [[ "$ENVIRONMENT" = BATCH ]]
1806	then
1807	batch_job=.TRUE.
1808	jobmo=BATCH
1809	else
1810	batch_job=.FALSE.
1811	jobmo=INTERACTIVE
1812	fi
1813	fi
1814
1815	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1816	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1817	then
1818	printf "\n +++ no interactive runs allowed on host \"$host\" "
1819	printf "\n please submit batch job using mrun option \"-b\" \n"
1820	locat=normal; exit
1821	fi
1822
1823
1824	# CHECK, IF USER DEFINED A COMPILER
1825	if [[ "$compiler_name" = "" ]]
1826	then
1827
1828	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1829	locat=compiler_name; exit
1830
1831	fi
1832
1833
1834	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1835
1836	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1837	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1838	then
1839	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1840	else
1841	kennung=$RANDOM
1842	fi
1843
1844	if [[ "$tmp_user_catalog" = "" ]]
1845	then
1846	if [[ $localhost = ibmh ]]
1847	then
1848	tmp_user_catalog=$SCRATCH
1849	elif [[ $localhost = nech ]]
1850	then
1851	tmp_user_catalog=$WRKSHR
1852	else
1853	tmp_user_catalog=/tmp
1854	fi
1855	fi
1856	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1857
1858
1859	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1860	if [[ "$tmp_data_catalog" = "" ]]
1861	then
1862	if [[ $localhost = nech ]]
1863	then
1864	tmp_data_catalog=$WRKSHR/mrun_restart_data
1865	else
1866	tmp_data_catalog=/tmp/mrun_restart_data
1867	fi
1868	fi
1869
1870
1871	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1872	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1873	then
1874	eval fopts=\"$fopts\"
1875	eval lopts=\"$lopts\"
1876	fi
1877
1878
1879
1880	# DETERMINE COMPILE- AND LINK-OPTIONS
1881	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1882	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1883	ROPTS="$ropts"
1884	# 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 ]]
1885	# then
1886	XOPT="-X $numprocs"
1887	# fi
1888
1889
1890
1891	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1892	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1893	done=false
1894	while [[ $done = false ]]
1895	do
1896	cputime=$cpumax
1897	if (( $cputime == 0 ))
1898	then
1899	if [[ $do_batch = true ]]
1900	then
1901	printf "\n +++ cpu-time is undefined"
1902	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1903	printf "\n >>> "
1904	read cputime 1>/dev/null 2>&1
1905	else
1906	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1907	fi
1908	else
1909	done=true
1910	fi
1911	cpumax=$cputime
1912	done
1913
1914	(( minuten = cputime / 60 ))
1915	(( sekunden = cputime - minuten * 60 ))
1916
1917
1918	# CHECK THE MEMORY DEMAND
1919	if [[ $do_batch = true ]]
1920	then
1921	done=false
1922	while [[ $done = false ]]
1923	do
1924	if (( memory == 0 ))
1925	then
1926	printf "\n +++ memory demand is undefined"
1927	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1928	printf "\n >>> "
1929	read memory 1>/dev/null 2>&1
1930	else
1931	done=true
1932	fi
1933	done
1934	fi
1935
1936
1937	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1938	if [[ $do_remote = true && -z $remote_username ]]
1939	then
1940	while [[ -z $remote_username ]]
1941	do
1942	printf "\n +++ username on remote host \"$host\" is undefined"
1943	printf "\n >>> Please type username:"
1944	printf "\n >>> "
1945	read remote_username
1946	done
1947	mc="$mc -u$remote_username"
1948	fi
1949
1950	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1951	if [[ "$login_init_cmd" != "" ]]
1952	then
1953	export init_cmds="${login_init_cmd};"
1954	fi
1955
1956
1957	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1958	if [[ "$modules" != "" ]]
1959	then
1960	if [[ $host = lctit ]]
1961	then
1962	export module_calls=". $modules"
1963	else
1964	export module_calls="module load ${modules};"
1965	fi
1966	fi
1967
1968
1969
1970	# OUTPUT OF THE MRUN-HEADER
1971	calltime=$(date)
1972	printf "\n"
1973	printf "#------------------------------------------------------------------------# \n"
1974	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1975	printf "\| \| \n"
1976	spalte1="called on:"; spalte2=$localhost_realname
1977	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1978	if [[ $do_remote = true ]]
1979	then
1980	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1981	else
1982	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1983	fi
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	if [[ -n $numprocs ]]
1986	then
1987	if [[ $run_coupled_model = false ]]
1988	then
1989	spalte1="number of PEs:"; spalte2=$numprocs
1990	else
1991	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1992	fi
1993	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1994	fi
1995	if [[ -n $tasks_per_node ]]
1996	then
1997	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1998	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1999	if (( remaining_pes > 0 ))
2000	then
2001	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2002	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2003	fi
2004	fi
2005	if [[ $maximum_parallel_io_streams != $numprocs ]]
2006	then
2007	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2008	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2009	fi
2010	if [[ $use_openmp = true ]]
2011	then
2012	spalte1="threads per task:"; spalte2="$threads_per_task"
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	fi
2015	printf "\| \| \n"
2016	if [[ $do_compile = true ]]
2017	then
2018	if [[ "$mopts" != "" ]]
2019	then
2020	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	zeile=$(echo "$mopts" \| cut -c46-)
2023	while [[ "$zeile" != "" ]]
2024	do
2025	spalte1=""
2026	spalte2=$(echo "$zeile" \| cut -c-45)
2027	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2028	zeile=$(echo "$zeile" \| cut -c46-)
2029	done
2030	fi
2031
2032	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	zeile=$(echo "$cpp_options" \| cut -c46-)
2035	while [[ "$zeile" != "" ]]
2036	do
2037	spalte1=""
2038	spalte2=$(echo "$zeile" \| cut -c-45)
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	zeile=$(echo "$zeile" \| cut -c46-)
2041	done
2042
2043	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	zeile=$(echo "$fopts" \| cut -c46-)
2046	while [[ "$zeile" != "" ]]
2047	do
2048	spalte1=""
2049	spalte2=$(echo "$zeile" \| cut -c-45)
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	zeile=$(echo "$zeile" \| cut -c46-)
2052	done
2053
2054	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2055	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2056	zeile=$(echo "$lopts" \| cut -c46-)
2057	while [[ "$zeile" != "" ]]
2058	do
2059	spalte1=""
2060	spalte2=$(echo "$zeile" \| cut -c-45)
2061	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2062	zeile=$(echo "$zeile" \| cut -c46-)
2063	done
2064
2065	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2066	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2067	zeile=$(echo "$modules" \| cut -c46-)
2068	while [[ "$zeile" != "" ]]
2069	do
2070	spalte1=""
2071	spalte2=$(echo "$zeile" \| cut -c-45)
2072	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2073	zeile=$(echo "$zeile" \| cut -c46-)
2074	done
2075
2076	spalte1="main program:"; spalte2=$mainprog
2077	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2078	else
2079	spalte1=executable:; spalte2=$executable
2080	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2081	fi
2082	printf "\| \| \n"
2083	spalte1="base name of files:"; spalte2=$fname
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085	if [[ $fname != $afname ]]
2086	then
2087	spalte1="base name of input files:"; spalte2=$afname
2088	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2089	fi
2090	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2091	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2092	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2093	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2094
2095	if [[ "$ocean_file_appendix" = true ]]
2096	then
2097	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2098	fi
2099
2100	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2101	then
2102	spalte1="memory demand / PE":; spalte2="$memory MB"
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2105	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2106	fi
2107
2108	if [[ $do_compile = true ]]
2109	then
2110	printf "\| \| \n"
2111	printf "\| Files to be compiled: \| \n"
2112	zeile=$source_list
2113	while [[ "$zeile" != "" ]]
2114	do
2115	linestart=$(echo $zeile \| cut -c-70)
2116	printf "\| %-70s \| \n" "$linestart"
2117	zeile=$(echo "$zeile" \| cut -c71-)
2118	done
2119	fi
2120	printf "#------------------------------------------------------------------------#"
2121
2122
2123
2124	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2125	if [[ $do_trace = true ]]
2126	then
2127	(( i = 0 ))
2128	while (( i < iin ))
2129	do
2130	(( i = i + 1 ))
2131	if (( i == 1 ))
2132	then
2133	printf "\n\n >>> INPUT-file assignments:\n"
2134	fi
2135	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2136	done
2137	(( i = 0 ))
2138	while (( i < iout ))
2139	do
2140	(( i = i + 1 ))
2141	if (( i == 1 ))
2142	then
2143	printf "\n\n >>> OUTPUT-file assignments:\n"
2144	fi
2145	printf "\n ${localout[$i]} : ${pathout[$i]}"
2146	done
2147	(( i = 0 ))
2148	while (( i < iic ))
2149	do
2150	(( i = i + 1 ))
2151	if (( i == 1 ))
2152	then
2153	printf "\n\n >>> INPUT-commands:\n"
2154	fi
2155	printf "\n ${in_command[$i]}"
2156	done
2157	(( i = 0 ))
2158	while (( i < ioc ))
2159	do
2160	(( i = i + 1 ))
2161	if (( i == 1 ))
2162	then
2163	printf "\n\n >>> OUTPUT-commands:\n"
2164	fi
2165	printf "\n ${out_command[$i]}"
2166	done
2167	fi
2168
2169	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2170	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2171	then
2172	antwort=dummy
2173	printf "\n\n"
2174	printf " >>> everything o.k. (y/n) ? "
2175	while read antwort
2176	do
2177	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2178	then
2179	printf " >>> everything o.k. (y/n) ? "
2180	else
2181	break
2182	fi
2183	done
2184	if [[ $antwort = n \|\| $antwort = N ]]
2185	then
2186	locat=user_abort; (( iec = 0 )); exit
2187	fi
2188	if [[ $do_batch = true ]]
2189	then
2190	printf " >>> batch-job will be created and submitted"
2191	else
2192	printf " >>> MRUN will now continue to execute on this machine"
2193	fi
2194	fi
2195
2196
2197	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2198	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2199	check_depository="${working_directory}/trunk/UTIL"
2200	check_sources="${working_directory}/tmp_check_namelist_files"
2201	skip_check=false
2202
2203	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2204	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2205	then
2206	skip_check=true
2207	reason="run on remote host or parameter file check has not been compiled."
2208	fi
2209	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2210	then
2211	skip_check=true
2212	reason="parameter file check has not been compiled."
2213	fi
2214
2215	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2216	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2217	then
2218	skip_check=true
2219	reason="serial run."
2220	fi
2221
2222	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2223	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2224	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2225	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2226	if [[ $check_namelist_files == false ]]
2227	then
2228	skip_check=true
2229	reason="-z option set."
2230	fi
2231
2232	if [[ $fromhost != $localhost ]]
2233	then
2234	skip_check=true
2235	reason="submitting host is local host."
2236	fi
2237
2238	if [[ $run_coupled_model == true ]]
2239	then
2240	skip_check=true
2241	reason="coupled run."
2242	fi
2243
2244	if [[ $restart_run == true ]]
2245	then
2246	skip_check=true
2247	reason="restart run."
2248	fi
2249
2250	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2251	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2252	last_char=`echo $filename_input \| cut -c $last_char_int`
2253	if [[ "$last_char" == "f" ]]
2254	then
2255	skip_check=true
2256	reason="restart run."
2257	fi
2258
2259	if [[ $skip_check == false ]]
2260	then
2261	tmp_check=${working_directory}/tmp_check
2262
2263	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2264	# NOT NECESSARILY REQUIRED
2265	line=""
2266	found=false
2267	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2268	while read line1
2269	do
2270	line="$line1"
2271	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2272	then
2273	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2274	found=true
2275	fi
2276	done < $tmp_check
2277
2278	if [[ $found = false ]]
2279	then
2280	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2281	fi
2282
2283	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2284	# NOT NECESSARILY REQUIRED
2285	line=""
2286	found=false
2287	grep "NUDGING_DATA" $config_file > $tmp_check
2288	while read line1
2289	do
2290	line="$line1"
2291	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2292	then
2293	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2294	found=true
2295	fi
2296	done < $tmp_check
2297
2298	if [[ $found = false ]]
2299	then
2300	printf "\n +++ no NUDGING list entry found in the configuration file."
2301	fi
2302
2303	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2304	# NOT NECESSARILY REQUIRED
2305	line=""
2306	found=false
2307	grep "LSF_DATA" $config_file > $tmp_check
2308	while read line1
2309	do
2310	line="$line1"
2311	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2312	then
2313	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2314	found=true
2315	fi
2316	done < $tmp_check
2317
2318	if [[ $found = false ]]
2319	then
2320	printf "\n +++ no LSF list entry found in the configuration file."
2321	fi
2322
2323	rm -rf ${working_directory}/tmp_check
2324
2325	# CHECK IF THE P3DF FILE MUST BE CHECKED
2326	for item in $input_list
2327	do
2328	if [[ "$item" == "restart" ]]
2329	then
2330	check_restart=1
2331	else
2332	check_restart=0
2333	fi
2334	done
2335
2336	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2337	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2338	then
2339	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2340	locat=check_namelist; exit
2341	fi
2342
2343	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2344	if [[ $check_restart == 1 ]]
2345	then
2346
2347	filenamef="${filename_input}f"
2348	if [[ ! -f $filenamef ]]
2349	then
2350	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2351	check_restart=0
2352	answer=dummy
2353	printf "\n\n"
2354
2355	if [[ $silent == false ]]
2356	then
2357	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2358	do
2359	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2360	read answer
2361	done
2362	if [[ $answer = a \|\| $answer = A ]]
2363	then
2364	printf "\n +++ Aborting...."
2365	locat=normal; exit
2366	fi
2367	fi
2368	else
2369	check_restart=1
2370	fi
2371	fi
2372
2373	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2374	mkdir $check_sources
2375	cd $check_sources
2376
2377
2378	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2379	if [[ -d $add_source_path ]]
2380	then
2381	printf "\n\n *** copying files from $check_depository"
2382	cp $check_depository/check_namelist_files.tar ./
2383
2384	printf "\n\n *** untar of makefile and source files in $check_sources"
2385	tar -xf check_namelist_files.tar > /dev/null 2>&1
2386
2387	printf "\n\n *** adding user code."
2388	cp $add_source_path/* ./
2389	touch check_namelist_files.f90
2390
2391	# GET COMPILER OPTIONS AND PERFORM MAKE
2392	printf "\n\n *** compiling code if necessary...\n"
2393
2394	# workaround for batch jobs on local machine (lcxe6)
2395	if [[ $do_batch == true && $do_remote == false ]]
2396	then
2397	eval $init_cmds
2398	fi
2399
2400	# GET CHECK OPTIONS
2401	line=""
2402	found=false
2403
2404	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2405
2406	while read line1
2407	do
2408
2409	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2410	then
2411	line="$line1"
2412	fi
2413
2414	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2415	then
2416	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2417	line="$line "
2418	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'`
2419	found=true
2420	fi
2421
2422	done < $tmp_check
2423	copts_check="$copts_check -D__check -D__parallel"
2424
2425	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2426
2427	# GET MAKE OUTPUT
2428	if [[ $? != 0 ]]
2429	then
2430	printf "\n +++ error during make."
2431	answer=dummy
2432	printf "\n\n"
2433	if [[ $silent == false ]]
2434	then
2435	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2436	do
2437	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2438	read answer
2439	done
2440	if [[ $answer = a \|\| $answer = A ]]
2441	then
2442	printf "\n +++ Aborting..."
2443	rm -rf $check_sources
2444	locat=normal; exit
2445	else
2446	skip_check=true
2447	fi
2448	else
2449	skip_check=true
2450	fi
2451	fi
2452	else
2453	cp $PALM_BIN/check_namelist_files.x ./
2454	fi
2455
2456	cp $filename_input ./PARIN
2457	if [[ $check_restart == 1 ]]
2458	then
2459	cp $filenamef ./PARINF
2460	fi
2461
2462	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2463	then
2464	printf "\n *** adding topography data"
2465	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2466
2467	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2468	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2469	# WHICH REQUIRE SUFFICIENT MEMORY
2470	ulimit -s unlimited
2471	fi
2472
2473	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2474	then
2475	printf "\n *** adding nudging data"
2476	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2477	fi
2478
2479	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2480	then
2481	printf "\n *** adding large scale forcing data"
2482	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2483	fi
2484
2485	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2486	cat > ENVPAR << %%END%%
2487	&envpar run_identifier = '$fname', host = '$host',
2488	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2489	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2490	maximum_cpu_time_allowed = ${cpumax}.,
2491	revision = '$global_revision',
2492	local_dvrserver_running = $local_dvrserver_running /
2493
2494	%%END%%
2495
2496	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2497	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2498	then
2499	printf "\n +++ WARNING: check_namelist_files.x not found."
2500	answer=dummy
2501	printf "\n\n"
2502
2503	if [[ $silent == false ]]
2504	then
2505	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2506	do
2507	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2508	read answer
2509	done
2510	if [[ $answer = a \|\| $answer = A ]]
2511	then
2512	printf "\n +++ Aborting..."
2513	rm -rf $check_sources
2514	locat=normal; exit
2515	else
2516	printf "\n *** skipping parameter file check."
2517	fi
2518	fi
2519
2520	elif [[ $skip_check == false ]]
2521	then
2522	# STARTING THE PARAMETER FILE CHECK
2523	printf "\n\n *** starting parameter file check..."
2524
2525	# CHECKING THE P3D FILE
2526	printf "\n\n (1) checking $filename_input"
2527	echo "$numprocs 0 0" > VARIN
2528	errors=`./check_namelist_files.x < VARIN 2>&1`
2529
2530	check_error=false
2531	if [[ "$errors" == "" ]]
2532	then
2533	printf " --> o.k."
2534	else
2535	printf " --> failed."
2536	check_error=true
2537	printf "\n\n $errors"
2538	fi
2539
2540	# CHECKING THE PD3F FILE IF NECESSARY
2541	if [[ $check_restart == 1 && $check_error == false ]]
2542	then
2543	printf "\n\n (2) checking $filenamef"
2544
2545	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2546	# IN &INIPAR LIST
2547	found=false
2548	cat PARINF \| while read line
2549	do
2550	line=$(echo $line\|sed 's/ //g')
2551	if [[ $line == "&inipar" ]]
2552	then
2553	start_search=true
2554	fi
2555
2556	if [[ $start_search == true ]]
2557	then
2558	if [[ $line == "initializing_actions='read_restart_data'" ]]
2559	then
2560	found=true
2561	break
2562	fi
2563	fi
2564
2565	if [[ $line == "/" ]]
2566	then
2567	start_search=false
2568	fi
2569
2570	done
2571
2572	if [[ $found = false ]]
2573	then
2574	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2575	printf "\n in &inipar list in $fname$p3df_suffix."
2576	rm -rf $check_sources
2577	locat=check_namelist; exit
2578	fi
2579
2580	# READ max_user_pr FROM FILES
2581	if [[ -f parin_for_check ]]
2582	then
2583	read max_pr_user < parin_for_check
2584	else
2585	max_user_pr=0
2586	fi
2587
2588	echo "$numprocs 1 $max_pr_user" > VARIN
2589	errors=`./check_namelist_files.x < VARIN 2>&1`
2590
2591	if [[ "$errors" == "" ]]
2592	then
2593	printf " --> o.k."
2594	else
2595	printf " --> failed."
2596	check_error=true
2597	printf "\n\n $errors"
2598	fi
2599	fi
2600
2601	# REPORT ERRORS AND CONTINUE/EXIT
2602	if [[ $check_error == true ]]
2603	then
2604	printf "\n +++ errors found in the parameter file!\n"
2605	answer=dummy
2606	printf "\n\n"
2607
2608	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2609	do
2610	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2611	read answer
2612	done
2613
2614	if [[ $answer = a \|\| $answer = A ]]
2615	then
2616	printf "\n +++ Aborting..."
2617	rm -rf $check_sources
2618	locat=normal; exit
2619	fi
2620	else
2621	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2622	fi
2623	rm -rf $check_sources
2624	fi
2625	else
2626	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2627	fi
2628
2629	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2630	rm -rf $check_sources
2631	cd $working_directory
2632
2633	# DETERMINE PATH FOR MAKE DEPOSITORY
2634	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2635	then
2636
2637	line=""
2638	grep "%depository_path" $config_file > tmp_mrun
2639	while read line
2640	do
2641	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2642	then
2643	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2644	then
2645	global_depository_path=`echo $line \| cut -d" " -s -f2`
2646	fi
2647	fi
2648	done < tmp_mrun
2649
2650	line=""
2651	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2652	while read line
2653	do
2654	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2655	then
2656	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2657	then
2658	local_depository_path=`echo $line \| cut -d" " -s -f2`
2659	fi
2660	fi
2661	done < tmp_mrun
2662
2663	if [[ "$local_depository_path" = "" ]]
2664	then
2665	if [[ "$global_depository_path" != "" ]]
2666	then
2667	local_depository_path=$global_depository_path
2668	else
2669	printf "\n\n +++ no depository path found in configuration file"
2670	printf "\n for local host \"$localhost\" "
2671	printf "\n please set \"\%depository_path\" in configuration file\n"
2672	locat=config_file; exit
2673	fi
2674	fi
2675	eval local_depository_path=$local_depository_path
2676	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2677	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2678
2679
2680	basename=`echo $mainprog \| cut -f1 -d"."`
2681	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2682	if [[ ! -f $make_depository ]]
2683	then
2684	printf "\n"
2685	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2686	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2687	fi
2688
2689	fi
2690
2691
2692	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2693	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2694	if [[ $do_batch = false ]]
2695	then
2696
2697
2698	# CREATE THE TEMPORARY WORKING DIRECTORY
2699	mkdir -p $TEMPDIR
2700	chmod go+rx $TEMPDIR
2701	tmpcreate=true
2702
2703
2704	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2705	# INTO THE TEMPORARY WORKING DIRECTORY
2706	if [[ $do_compile = true ]]
2707	then
2708
2709	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2710	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2711	if [[ $localhost = nech ]]
2712	then
2713	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2714	if mkdir -p $TEMPDIR_COMPILE
2715	then
2716	printf "\n *** \"$TEMPDIR_COMPILE\" "
2717	printf "\n is generated as temporary directory for cross compiling\n"
2718	else
2719	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2720	printf "\n needed for cross compilation failed"
2721	locat=compile
2722	exit
2723	fi
2724	else
2725	TEMPDIR_COMPILE=$TEMPDIR
2726	fi
2727
2728	cp $make_depository $TEMPDIR_COMPILE
2729	cd $TEMPDIR_COMPILE
2730	tar -xf $make_depository > /dev/null 2>&1
2731	cd - > /dev/null
2732
2733	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2734	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2735	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2736	then
2737	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2738	else
2739	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2740	fi
2741
2742	else
2743
2744	cp $executable ${TEMPDIR}/a.out
2745
2746	fi
2747
2748
2749	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2750	cd $TEMPDIR
2751	printf "\n *** changed to temporary directory: $TEMPDIR"
2752
2753
2754	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2755	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2756	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2757	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2758	(( i = 0 ))
2759	while (( i < iout ))
2760	do
2761	(( i = i + 1 ))
2762	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2763	then
2764	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2765	else
2766	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2767	fi
2768	done
2769
2770
2771	# IF REQUIRED, START WITH COMPILING
2772	if [[ $do_compile = true ]]
2773	then
2774
2775
2776	if [[ -f a.out ]]
2777	then
2778
2779	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2780	printf "\n\n\n *** executable a.out found"
2781	printf "\n no compilation required \n"
2782
2783	else
2784
2785	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2786	printf "\n\n\n *** compilation starts \n$dashes\n"
2787	printf " *** compilation with make using following options:\n"
2788	printf " make depository: $make_depository"
2789	if [[ "$mopts" != "" ]]
2790	then
2791	printf " make options: $mopts\n"
2792	fi
2793	printf " compilername: $compiler_name\n"
2794	printf " compiler options: $fopts\n"
2795	printf " preprocessor directives: $cpp_options \n"
2796	printf " linker options: $lopts \n"
2797	if [[ "$modules" != "" ]]
2798	then
2799	printf " modules to be load: $modules \n"
2800	fi
2801	printf " source code files: $source_list \n"
2802
2803	if [[ $localhost = nech ]]
2804	then
2805	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\" "
2806	cp $TEMPDIR_COMPILE/a.out .
2807	[[ $? != 0 ]] && compile_error=true
2808	rm -rf $TEMPDIR_COMPILE
2809	elif [[ $localhost = ibmh ]]
2810	then
2811	printf " compiler is called via ssh on \"plogin1\" \n"
2812	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\" "
2813	[[ ! -f a.out ]] && compile_error=true
2814	continue # STATUS=1, IF a.out EXISTS
2815	elif [[ $localhost = lcflow ]]
2816	then
2817	printf " compiler is called via ssh on \"flow\" \n"
2818	/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\" "
2819	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2820	[[ "$check_for_file" = "" ]] && compile_error=true
2821	continue # STATUS=1, IF a.out EXISTS
2822	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2823	then
2824	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2825	else
2826	[[ "$init_cmds" != "" ]] && eval $init_cmds
2827	[[ "$module_calls" != "" ]] && eval $module_calls
2828	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2829	fi
2830
2831	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2832	then
2833	printf "\n +++ error occured while compiling or linking"
2834	locat=compile
2835
2836	exit
2837	else
2838	printf "$dashes\n *** compilation finished \n"
2839	fi
2840
2841	fi
2842
2843	fi
2844
2845
2846	# PROVIDE THE INPUT FILES
2847	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2848	(( i = 0 ))
2849	while (( i < iin ))
2850	do
2851	(( i = i + 1 ))
2852	if (( i == 1 ))
2853	then
2854	printf "\n\n *** providing INPUT-files:\n$dashes"
2855	fi
2856
2857
2858	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2859	if [[ "${transin[$i]}" = unavailable ]]
2860	then
2861	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2862	then
2863	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2864	printf "\n is not available!"
2865	else
2866	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2867	printf "\n is not available!"
2868	fi
2869	continue
2870	fi
2871
2872	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2873	files_for_pes=false; datentyp=file
2874	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2875	then
2876	files_for_pes=true; datentyp=directory
2877	actionin[$i]=""
2878	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2879	then
2880	actionin[$i]=""
2881	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2882	then
2883	files_for_pes=true; datentyp=directory
2884	actionin[$i]="ar"
2885	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2886	then
2887	actionin[$i]="ar"
2888	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2889	then
2890	files_for_pes=true; datentyp=directory
2891	actionin[$i]="fl"
2892	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2893	then
2894	actionin[$i]="fl"
2895	fi
2896
2897	if [[ $files_for_pes = true ]]
2898	then
2899	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2900	else
2901	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2902	fi
2903
2904	# INPUT-FILE FOR A RESTART RUN.
2905	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2906	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2907	if [[ "${actionin[$i]}" = fl ]]
2908	then
2909	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2910	if [[ $files_for_pes = false ]]
2911	then
2912	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2913	then
2914	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2915	got_tmp[$i]=true
2916	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2917	then
2918	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2919	printf "\n *** trying to use backup copy in \"$WORK\" "
2920	cp $WORK/${frelin[$i]} ${localin[$i]}
2921	else
2922	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2923	printf "\n or \"$tmp_data_catalog\" does not exist!"
2924	printf "\n *** trying to get copy from archive"
2925	actionin[$i]=ar
2926	fi
2927	else
2928	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2929	then
2930	mkdir ${localin[$i]}
2931	cd $tmp_data_catalog/${frelin[$i]}
2932	for file in $(ls *)
2933	do
2934	ln $file $TEMPDIR/${localin[$i]}
2935	done
2936	cd $TEMPDIR
2937	got_tmp[$i]=true
2938	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2939	then
2940	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2941	printf "\n *** trying to use backup copy in \"$WORK\" "
2942	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2943	else
2944	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2945	printf "\n or \"$tmp_data_catalog\" does not exist!"
2946	printf "\n *** trying to get copy from archive"
2947	actionin[$i]=ar
2948	fi
2949	fi
2950	fi
2951
2952
2953	# FILE IS STORED ON THE ARCHIVE SYSTEM
2954	if [[ "${actionin[$i]}" = ar ]]
2955	then
2956
2957	if [[ $files_for_pes = false ]]
2958	then
2959	printf "\n file will be restored from archive-system ($archive_system)!"
2960	else
2961	printf "\n directory will be restored from archive-system ($archive_system)!"
2962	fi
2963
2964	file_restored=false
2965
2966	if [[ $archive_system = asterix ]]
2967	then
2968	do_stagein=true
2969	(( stagein_anz = 0 ))
2970	while [[ $do_stagein = true ]]
2971	do
2972	if [[ $files_for_pes = false ]]
2973	then
2974	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2975	else
2976	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2977	fi
2978	cat STAGEIN_OUTPUT
2979	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2980	then
2981	file_restored=true
2982	do_stagein=false
2983	else
2984	(( stagein_anz = stagein_anz + 1 ))
2985	if (( stagein_anz == 10 ))
2986	then
2987	printf "\n +++ stagein stoped after 10 tries"
2988	locat=stage
2989	exit
2990	fi
2991	printf "\n +++ restoring from archive failed, trying again:"
2992	sleep 900
2993	fi
2994	done
2995	elif [[ $archive_system = DMF ]]
2996	then
2997	if [[ $files_for_pes = false ]]
2998	then
2999	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3000	locat=DMF
3001	exit
3002	else
3003	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3004	cp -r $ARCHIVE/${frelin[$i]} $PWD
3005	file_restored=true
3006	fi
3007	elif [[ $archive_system = tivoli ]]
3008	then
3009	if [[ $files_for_pes = false ]]
3010	then
3011	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3012	else
3013	(( inode = 0 ))
3014	while (( inode < nodes ))
3015	do
3016	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3017	(( inode = inode + 1 ))
3018	done
3019	fi
3020	file_restored=true
3021	elif [[ $archive_system = ut ]]
3022	then
3023	if [[ $files_for_pes = false ]]
3024	then
3025	cp $UT/${frelin[$i]} .
3026	else
3027	(( inode = 0 ))
3028	while (( inode < nodes ))
3029	do
3030	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3031	(( inode = inode + 1 ))
3032	done
3033	fi
3034	file_restored=true
3035	else
3036	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3037	locat=rearchive
3038	exit
3039	fi
3040
3041	if [[ $file_restored = true ]]
3042	then
3043
3044	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3045	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3046	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3047	if [[ $files_for_pes = false ]]
3048	then
3049	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3050	else
3051	mkdir $tmp_data_catalog/${frelin[$i]}
3052	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3053	fi
3054	got_tmp[$i]=true
3055
3056	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3057	mv ${frelin[$i]} ${localin[$i]}
3058
3059	fi
3060	fi
3061
3062
3063	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3064	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3065	then
3066
3067	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3068	then
3069
3070	# FILE COPIES ARE PROVIDED FOR ALL CORES
3071	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3072	printf "\n file will be provided for $numprocs processors"
3073	mkdir ${localin[$i]}
3074	ival=$numprocs
3075	(( ii = 0 ))
3076	while (( ii <= ival-1 ))
3077	do
3078	if (( ii < 10 ))
3079	then
3080	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3081	elif (( ii < 100 ))
3082	then
3083	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3084	elif (( ii < 1000 ))
3085	then
3086	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3087	else
3088	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3089	fi
3090	(( ii = ii + 1 ))
3091	done
3092
3093	else
3094
3095	if [[ $files_for_pes = true ]]
3096	then
3097
3098	# PROVIDE FILES FOR EACH CORE
3099	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3100	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3101	printf "\n providing $numprocs files for the respective processors"
3102	mkdir ${localin[$i]}
3103	if [[ $link_local_input = true ]]
3104	then
3105	printf " using ln -f\n"
3106	cd ${absnamein[$i]}
3107	for file in $(ls *)
3108	do
3109	ln -f $file ${localin[$i]}
3110	done
3111	cd $TEMPDIR
3112	fi
3113
3114	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3115	if [[ ! -f "${localin[$i]}/_0000" ]]
3116	then
3117	if [[ $link_local_input = true ]]
3118	then
3119	printf " ln failed for .../_0000, using cp...\n"
3120	fi
3121	cp -r ${absnamein[$i]}/* ${localin[$i]}
3122	fi
3123
3124	else
3125
3126	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3127	if [[ $link_local_input = true ]]
3128	then
3129	printf " using ln -f\n"
3130	ln -f ${absnamein[$i]} ${localin[$i]}
3131	fi
3132	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3133	if [[ ! -f "${localin[$i]}" ]]
3134	then
3135	if [[ $link_local_input = true ]]
3136	then
3137	printf " ln failed, using cp...\n"
3138	fi
3139	cp ${absnamein[$i]} ${localin[$i]}
3140	fi
3141	fi
3142	fi
3143	fi
3144
3145	done
3146	if (( i != 0 ))
3147	then
3148	printf "\n$dashes\n *** all INPUT-files provided \n"
3149	fi
3150
3151
3152	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3153	(( i = 0 ))
3154	while (( i < iic ))
3155	do
3156	(( i = i + 1 ))
3157	if (( i == 1 ))
3158	then
3159	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3160	fi
3161	printf "\n >>> ${in_command[$i]}"
3162	eval ${in_command[$i]}
3163	if (( i == iic ))
3164	then
3165	printf "\n$dashes\n"
3166	fi
3167	done
3168
3169
3170	# SET THE REMAINING CPU-TIME
3171	cpurest=${cpumax}.
3172
3173
3174	# START DVR STREAMING SERVER
3175	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3176	then
3177	if [[ "$dvr_server" != "" ]]
3178	then
3179
3180	printf "\n\n *** preparing the dvr streaming server configuration file"
3181
3182	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3183	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3184	if [[ "$running_dvrserver_id" != "" ]]
3185	then
3186
3187	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3188	printf "\n This server is used instead starting a new one!"
3189	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3190
3191	else
3192
3193	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3194	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3195	then
3196	cp ${PALM_BIN}/.dvrserver.config .
3197
3198	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3199	user_id=`id -u`
3200	group_id=`id -g`
3201
3202	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3203	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3204	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3205	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3206	mv .dvrserver.3 .dvrserver.config
3207	rm .dvrserver.1 .dvrserver.2
3208
3209	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3210	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3211	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3212	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3213	local_dvrserver_running=.TRUE.
3214	else
3215	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3216	printf "\n \"$PALM_BIN\" "
3217	locat=dvr
3218	exit
3219	fi
3220
3221	fi
3222
3223	else
3224	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3225	fi
3226	fi
3227
3228
3229	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3230	# (FILE ENVPAR WILL BE READ BY PALM)
3231	cat > ENVPAR << %%END%%
3232	&envpar run_identifier = '$fname', host = '$localhost',
3233	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3234	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3235	maximum_cpu_time_allowed = ${cpumax}.,
3236	revision = '$global_revision',
3237	local_dvrserver_running = $local_dvrserver_running,
3238	batch_job = $batch_job /
3239
3240	%%END%%
3241
3242
3243	# STARTING THE EXECUTABLE
3244	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3245	PATH=$PATH:$TEMPDIR
3246
3247	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3248	if [[ "$mpi_debug" = true ]]
3249	then
3250	export MPI_CHECK_ARGS=1
3251	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3252	fi
3253
3254	if [[ "$totalview" = true ]]
3255	then
3256	printf "\n *** totalview debugger will be used"
3257	tv_opt="-tv"
3258	else
3259	tv_opt=""
3260	fi
3261
3262	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3263	then
3264
3265	#Interactive ALLINEA DEBUG seesion
3266	if [[ "$ENVIRONMENT" != BATCH ]]
3267	then
3268	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3269	then
3270	if [[ "$allinea" = true ]]
3271	then
3272	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3273
3274	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3275	wait
3276	fi
3277	fi
3278	fi
3279
3280	if [[ "$ENVIRONMENT" = BATCH ]]
3281	then
3282	continue
3283	fi
3284	if [[ $localhost = ibmh ]]
3285	then
3286
3287	# SETUP THE IBM MPI ENVIRONMENT
3288	export MP_SHARED_MEMORY=yes
3289	export AIXTHREADS_SCOPE=S
3290	export OMP_NUM_THREADS=$threads_per_task
3291	export AUTHSTATE=files
3292	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3293
3294	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3295	export MP_ADAPTER_USE=shared
3296	export MP_CPU_USE=multiple
3297	export MP_TIMEOUT=1200
3298
3299	unset MP_TASK_AFFINITY
3300
3301	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3302	#(( ii = 1 ))
3303	#while (( ii <= $numprocs ))
3304	#do
3305	# echo $localhost_realname >> hostfile
3306	# (( ii = ii + 1 ))
3307	#done
3308	#export MP_HOSTFILE=hostfile
3309
3310	if [[ "$LOADLBATCH" = yes ]]
3311	then
3312	totalview poe a.out $ROPTS
3313	else
3314	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3315	export TVDSVRLAUNCHCMD=ssh
3316	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3317	fi
3318
3319	fi # END DEBUG MODE
3320
3321	else
3322
3323	# NORMAL EXECUTION
3324	if [[ -n $numprocs ]]
3325	then
3326
3327	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3328	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3329	then
3330
3331	# SETUP THE IBM MPI ENVIRONMENT
3332	if [[ $host != ibmh && $host != ibmkisti ]]
3333	then
3334	export MP_SHARED_MEMORY=yes
3335	export AIXTHREAD_SCOPE=S
3336	export OMP_NUM_THREADS=$threads_per_task
3337	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3338	export AUTHSTATE=files
3339	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3340	# export MP_PRINTENV=yes
3341
3342	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3343	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3344	export MP_WAIT_MODE=poll
3345	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3346	fi
3347
3348	if [[ $host = ibmkisti ]]
3349	then
3350	export LANG=en_US
3351	export MP_SHARED_MEMORY=yes
3352	if [[ $threads_per_task = 1 ]]
3353	then
3354	export MP_SINGLE_THREAD=yes
3355	export MEMORY_AFFINITY=MCM
3356	else
3357	export OMP_NUM_THREADS=$threads_per_task
3358	fi
3359	fi
3360
3361	if [[ "$LOADLBATCH" = yes ]]
3362	then
3363	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3364	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3365	then
3366	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3367	else
3368	if [[ $run_coupled_model = false ]]
3369	then
3370	if [[ "$ocean_file_appendix" = true ]]
3371	then
3372	echo "precursor_ocean" > runfile_atmos
3373	else
3374	echo "precursor_atmos" > runfile_atmos
3375	fi
3376	else
3377	(( iia = $numprocs_atmos / $threads_per_task ))
3378	(( iio = $numprocs_ocean / $threads_per_task ))
3379	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3380	printf "\n using $coupled_mode coupling"
3381	printf "\n\n"
3382	echo "coupled_run $iia $iio" > runfile_atmos
3383	fi
3384	poe ./a.out $ROPTS < runfile_atmos
3385	fi
3386	else
3387	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3388	then
3389	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3390	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3391	then
3392	if [[ -f $hostfile ]]
3393	then
3394	cp $hostfile hostfile
3395	else
3396	(( ii = 1 ))
3397	while (( ii <= $numprocs ))
3398	do
3399	echo $localhost_realname >> hostfile
3400	(( ii = ii + 1 ))
3401	done
3402	fi
3403	export MP_HOSTFILE=hostfile
3404	if [[ $run_coupled_model = false ]]
3405	then
3406	if [[ "$ocean_file_appendix" = true ]]
3407	then
3408	echo "precursor_ocean" > runfile_atmos
3409	else
3410	echo "precursor_atmos" > runfile_atmos
3411	fi
3412	else
3413	(( iia = $numprocs_atmos / $threads_per_task ))
3414	(( iio = $numprocs_ocean / $threads_per_task ))
3415	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3416	printf "\n using $coupled_mode coupling"
3417	printf "\n\n"
3418	echo "coupled_run $iia $iio" > runfile_atmos
3419	fi
3420
3421	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3422
3423	else
3424	if [[ "$host_file" = "" ]]
3425	then
3426	printf "\n +++ no hostfile given in configuration file"
3427	locat=config_file
3428	exit
3429	else
3430	eval host_file=$host_file
3431	fi
3432	export MP_HOSTFILE=$host_file
3433	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3434	fi
3435	fi
3436	elif [[ $host = nech ]]
3437	then
3438	(( ii = nodes ))
3439	if [[ $ii = 1 ]]
3440	then
3441	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3442	export MPIPROGINF=YES
3443	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3444	echo "*** execution on single node with mpirun"
3445	mpirun -np $numprocs ./a.out $ROPTS
3446	else
3447	(( i = 0 ))
3448	while (( i < ii ))
3449	do
3450	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3451	(( i = i + 1 ))
3452	done
3453
3454	echo "#!/bin/sh" > mpi_exec_shell
3455	echo " " >> mpi_exec_shell
3456	echo "set -u" >> mpi_exec_shell
3457	echo "F_ERRCNT=0" >> mpi_exec_shell
3458	echo "MPIPROGINV=YES" >> mpi_exec_shell
3459	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3460	echo "cpurest=$cpurest" >> mpi_exec_shell
3461	echo "fname=$fname" >> mpi_exec_shell
3462	echo "localhost=$localhost" >> mpi_exec_shell
3463	echo "return_address=$return_address" >> mpi_exec_shell
3464	echo "return_username=$return_username" >> mpi_exec_shell
3465	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3466	echo "write_binary=$write_binary" >> mpi_exec_shell
3467	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3468	echo " " >> mpi_exec_shell
3469	echo "export F_ERRCNT" >> mpi_exec_shell
3470	echo "export MPIPROGINV" >> mpi_exec_shell
3471	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3472	echo "export cpurest" >> mpi_exec_shell
3473	echo "export fname" >> mpi_exec_shell
3474	echo "export localhost" >> mpi_exec_shell
3475	echo "export return_address" >> mpi_exec_shell
3476	echo "export return_username" >> mpi_exec_shell
3477	echo "export tasks_per_node" >> mpi_exec_shell
3478	echo "export write_binary" >> mpi_exec_shell
3479	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3480	echo " " >> mpi_exec_shell
3481	echo "exec ./a.out" >> mpi_exec_shell
3482
3483	chmod u+x mpi_exec_shell
3484	export MPIPROGINF=YES
3485	mpirun -f multinode_config &
3486	wait
3487
3488	fi
3489	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3490	then
3491
3492	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3493	# DOES NOT EXIST
3494	if [[ $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3495	then
3496	if [[ -f $hostfile ]]
3497	then
3498	cp $hostfile hostfile
3499	(( ii = $numprocs / $threads_per_task ))
3500	[[ $ii = 0 ]] && (( ii = 1 ))
3501	else
3502	(( ii = 1 ))
3503	while (( ii <= $numprocs / $threads_per_task ))
3504	do
3505	echo $localhost_realname >> hostfile
3506	(( ii = ii + 1 ))
3507	done
3508	if (( $numprocs / $threads_per_task == 0 ))
3509	then
3510	echo $localhost_realname >> hostfile
3511	fi
3512	fi
3513	eval zeile=\"`head -n $ii hostfile`\"
3514	printf "\n *** running on: $zeile"
3515	fi
3516
3517	(( ii = $numprocs / $threads_per_task ))
3518	[[ $ii = 0 ]] && (( ii = 1 ))
3519	export OMP_NUM_THREADS=$threads_per_task
3520
3521	if [[ $threads_per_task != 1 ]]
3522	then
3523	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3524	# MAY ABORT
3525	ulimit -s unlimited
3526	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3527	fi
3528	if [[ $run_coupled_model = false ]]
3529	then
3530	if [[ "$ocean_file_appendix" = true ]]
3531	then
3532	echo "precursor_ocean" > runfile_atmos
3533	else
3534	echo "precursor_atmos" > runfile_atmos
3535	fi
3536	printf "\n\n"
3537
3538	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3539	then
3540	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3541	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3542	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3543	elif [[ $host = lccrayf ]]
3544	then
3545	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3546	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3547	then
3548	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3549	elif [[ $host = lcflow ]]
3550	then
3551	mpirun -np $ii a.out < runfile_atmos $ROPTS
3552	elif [[ $host = lcsb ]]
3553	then
3554	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3555	elif [[ $host = lckiaps ]]
3556	then
3557	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3558	elif [[ $host = lckyu* ]]
3559	then
3560	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3561	else
3562	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3563	fi
3564	else
3565
3566	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3567	(( iia = $numprocs_atmos / $threads_per_task ))
3568	(( iio = $numprocs_ocean / $threads_per_task ))
3569	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3570	printf "\n using $coupled_mode coupling"
3571	printf "\n\n"
3572
3573	if [[ $coupled_mode = "mpi2" ]]
3574	then
3575	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3576	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3577
3578	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3579	then
3580
3581	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3582	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3583
3584	else
3585	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3586	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3587	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3588	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3589	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3590	fi
3591	wait
3592
3593	else
3594
3595	echo "coupled_run $iia $iio" > runfile_atmos
3596
3597	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3598	then
3599
3600	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3601
3602	elif [[ $host = lck \|\| $host = lckordi ]]
3603	then
3604
3605	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3606
3607	elif [[ $host = lckyu* ]]
3608	then
3609
3610	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3611
3612	elif [[ $host = lcmuk ]]
3613	then
3614
3615	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3616
3617	fi
3618	wait
3619	fi
3620
3621	fi
3622
3623	elif [[ $host = lckyoto ]]
3624	then
3625	set -xv
3626	export P4_RSHCOMMAND=plesh
3627	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3628	if [[ "$ENVIRONMENT" = BATCH ]]
3629	then
3630	if [[ "$cond2" = fujitsu ]]
3631	then
3632	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3633	elif [[ "cond2" = pgi ]]
3634	then
3635	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3636	else
3637	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3638	fi
3639	else
3640	if [[ "$cond2" = "" ]]
3641	then
3642	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3643	else
3644	mpirun -np $numprocs ./a.out $ROPTS
3645	fi
3646	fi
3647	set +xv
3648
3649	elif [[ $host = lctit ]]
3650	then
3651	export OMP_NUM_THREADS=$threads_per_task
3652	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3653	if [[ "$threads_per_task" != 1 ]]
3654	then
3655	export MV2_ENABLE_AFFINITY=0
3656	fi
3657	echo "----- PBS_NODEFILE content:"
3658	cat $PBS_NODEFILE
3659	echo "-----"
3660	(( ii = $numprocs / $threads_per_task ))
3661	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3662	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3663
3664	elif [[ $host = lcbullhh ]]
3665	then
3666	export OMPI_MCA_pml=cm
3667	export OMPI_MCA_mtl=mxm
3668	export OMPI_MCA_coll=^ghc
3669	export OMPI_MCA_mtl_mxm_np=0
3670	export MXM_RDMA_PORTS=mlx5_0:1
3671	export MXM_LOG_LEVEL=ERROR
3672	export OMP_NUM_THREADS=$threads_per_task
3673	export KMP_AFFINITY=verbose,granularity=core,compact,1
3674	export KMP_STACKSIZE=64m
3675
3676	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out
3677	else
3678	mpprun -n $numprocs a.out $ROPTS
3679	fi
3680	else
3681	a.out $ROPTS
3682	fi
3683	fi
3684
3685	if [[ $? != 0 ]]
3686	then
3687
3688	# ABORT IN CASE OF RUNTIME ERRORS
3689	printf "\n +++ runtime error occured"
3690	locat=execution
3691	exit
3692
3693	else
3694
3695	printf "\n$dashes\n *** execution finished \n"
3696
3697	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3698	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3699	if [[ "$dvrserver_id" != "" ]]
3700	then
3701	kill $dvrserver_id
3702	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3703
3704	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3705	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3706	if [[ -d DATA_DVR ]]
3707	then
3708
3709	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3710	# DIRECTORY
3711	cp .dvrserver.config DATA_DVR
3712
3713	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3714	# SEQUENCE MODE DATA TOO)
3715	process_dvr_output -d DATA_DVR -f $fname -s
3716
3717	else
3718
3719	# PROCESS THE LOCAL OUTPUT
3720	process_dvr_output -l -d DATA_DVR -f $fname
3721
3722	fi
3723
3724	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3725	then
3726
3727	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3728	process_dvr_output -l -d DATA_DVR -f $fname
3729
3730	fi
3731	fi
3732
3733
3734
3735	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3736	# BY EACH CORE INTO ONE FILE
3737	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3738	then
3739	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3740	printf "\n 2d- and/or 3d-data may be incomplete!"
3741	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3742	elif [[ "$combine_plot_fields" == true ]]
3743	then
3744	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3745	then
3746	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3747	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3748	else
3749	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3750	combine_plot_fields${block}.x
3751	fi
3752	else
3753
3754	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3755	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3756	# ??? koennen wir das streichen ???
3757	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3758	fi
3759
3760
3761
3762	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3763	(( i = 0 ))
3764	while (( i < ioc ))
3765	do
3766	(( i = i + 1 ))
3767	if (( i == 1 ))
3768	then
3769	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3770	fi
3771	printf "\n >>> ${out_command[$i]}"
3772	eval ${out_command[$i]}
3773	if (( i == ioc ))
3774	then
3775	printf "\n$dashes\n"
3776	fi
3777	done
3778
3779
3780	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3781	if [[ $do_trace = true ]]
3782	then
3783	printf "\n\n"
3784	ls -al
3785	fi
3786
3787
3788
3789	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3790	(( i = 0 ))
3791	while (( i < iout ))
3792	do
3793	(( i = i + 1 ))
3794	if (( i == 1 ))
3795	then
3796	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3797	fi
3798
3799	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3800	files_for_pes=false; filetyp=file
3801	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3802	then
3803	files_for_pes=true; filetyp=directory
3804	actionout[$i]=""
3805	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3806	then
3807	actionout[$i]=""
3808	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3809	then
3810	files_for_pes=true; filetyp=directory
3811	actionout[$i]="ar"
3812	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3813	then
3814	actionout[$i]="ar"
3815	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3816	then
3817	files_for_pes=true; filetyp=directory
3818	actionout[$i]="fl"
3819	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3820	then
3821	actionout[$i]="fl"
3822	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3823	then
3824	files_for_pes=true; filetyp=directory
3825	actionout[$i]="tr"
3826	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3827	then
3828	actionout[$i]="tr"
3829	fi
3830
3831	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3832	then
3833	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3834	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3835	then
3836	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3837	else
3838
3839
3840	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3841	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3842	if [[ "${actionout[$i]}" = tr ]]
3843	then
3844	if [[ $localhost != $fromhost ]]
3845	then
3846	if [[ $files_for_pes = false ]]
3847	then
3848	cps=""
3849	cst=""
3850	else
3851	cps=-c
3852	cst="/"
3853	fi
3854	if [[ $localhost = nech ]]
3855	then
3856
3857	# TRANSFER IN SEPERATE JOB
3858	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3859	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3860	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3861	if [[ $files_for_pes = false ]]
3862	then
3863	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3864	else
3865	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3866	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3867	fi
3868
3869	echo "set -x" > transfer_${localout[$i]}
3870	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3871
3872	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3873	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3874	printf "\n or higher cycle\n"
3875	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]}
3876
3877	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3878
3879	if [[ $localhost = nech ]]
3880	then
3881	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3882	else
3883	if [[ "$LOGNAME" = b323013 ]]
3884	then
3885	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3886	else
3887	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3888	fi
3889	fi
3890
3891	else
3892
3893	# TRANSFER WITHIN THIS JOB
3894	transfer_failed=false
3895	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3896	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3897	if [[ $localhost = lccrayb ]]
3898	then
3899	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]}"
3900	elif [[ $localhost = lccrayh ]]
3901	then
3902	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]}"
3903	elif [[ $localhost = lcbullhh ]]
3904	then
3905	ssh $usern@mlogin101 ". \\$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]}"
3906	elif [[ $localhost = lcxe6 ]]
3907	then
3908	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]}"
3909	else
3910	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3911	fi
3912	[[ $? != 0 ]] && transfer_failed=true
3913
3914	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3915	if [[ $transfer_failed = true ]]
3916	then
3917	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3918	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3919
3920	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3921	eval local_catalog=${pathout[$i]}
3922	if [[ ! -d $local_catalog ]]
3923	then
3924	printf " *** local directory does not exist. Trying to create:\n"
3925	printf " $local_catalog \n"
3926	mkdir -p $local_catalog
3927	fi
3928	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3929	transfer_problems=true
3930	fi
3931	fi
3932	else
3933
3934	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3935	actionout[$i]=""
3936	fi
3937	fi
3938
3939
3940	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3941	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3942	if [[ "${actionout[$i]}" = tra ]]
3943	then
3944	if [[ $localhost != $fromhost ]]
3945	then
3946	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3947	then
3948
3949	# TRANSFER IN SEPERATE JOB
3950	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3951	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3952	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3953	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3954
3955	echo "set -x" > transfer_${localout[$i]}
3956	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3957
3958	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3959	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3960	printf "\n or higher cycle\n"
3961	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]}
3962
3963	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3964
3965	if [[ $localhost = nech ]]
3966	then
3967	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3968	else
3969	if [[ $LOGNAME = b323013 ]]
3970	then
3971	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3972	else
3973	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3974	fi
3975	fi
3976
3977	else
3978
3979	# TRANSFER WITHIN THIS JOB
3980	transfer_failed=false
3981	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3982	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3983	if [[ $localhost = lccrayb ]]
3984	then
3985	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]}"
3986	elif [[ $localhost = lccrayh ]]
3987	then
3988	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]}"
3989	elif [[ $localhost = lcxe6 ]]
3990	then
3991	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]}"
3992	else
3993	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3994	fi
3995	[[ $? != 0 ]] && transfer_failed=true
3996
3997	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3998	if [[ $transfer_failed = true ]]
3999	then
4000	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4001	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4002
4003	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4004	eval local_catalog=${pathout[$i]}
4005	if [[ ! -d $local_catalog ]]
4006	then
4007	printf " *** local directory does not exist. Trying to create:\n"
4008	printf " $local_catalog \n"
4009	mkdir -p $local_catalog
4010	fi
4011
4012	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4013	transfer_problems=true
4014	fi
4015	fi
4016	else
4017
4018	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4019	actionout[$i]=a
4020	fi
4021	fi
4022
4023
4024	# OUTPUT-FILE FOR A RESTART-RUN.
4025	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4026	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4027	# AS LAST ACTION, ARCHIVING IS INITIATED.
4028	if [[ "${actionout[$i]}" = fl ]]
4029	then
4030	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4031	chmod g+rx $tmp_data_catalog
4032	if [[ $files_for_pes = false ]]
4033	then
4034	printf "\n >>> OUTPUT: ${localout[$i]} to"
4035	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4036	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4037	else
4038	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4039	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4040	mkdir $tmp_data_catalog/${frelout[$i]}
4041	cd ${localout[$i]}
4042	for file in $(ls *)
4043	do
4044	ln -f $file $tmp_data_catalog/${frelout[$i]}
4045	done
4046	cd $TEMPDIR
4047	fi
4048
4049
4050	# CREATE AND SUBMIT ARCHIVING-JOB
4051	if [[ $store_on_archive_system = true ]]
4052	then
4053
4054	if [[ $archive_system = asterix ]]
4055	then
4056	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4057	if [[ $files_for_pes = false ]]
4058	then
4059	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4060	else
4061	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4062	fi
4063	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4064	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4065	echo "then" >> archive_${frelout[$i]}
4066	echo " do_stageout=false" >> archive_${frelout[$i]}
4067	echo "else" >> archive_${frelout[$i]}
4068	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4069	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4070	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4071	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4072	if [[ $files_for_pes = false ]]
4073	then
4074	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4075	else
4076	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4077	fi
4078	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4079	echo "fi" >> archive_${frelout[$i]}
4080	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4081	elif [[ $archive_system = DMF ]]
4082	then
4083	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4084	if [[ $files_for_pes = false ]]
4085	then
4086	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4087	locat=DMF
4088	exit
4089	else
4090	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4091	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4092	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4093	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4094	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4095	fi
4096	elif [[ $archive_system = tivoli ]]
4097	then
4098	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4099	if [[ $files_for_pes = false ]]
4100	then
4101	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4102	echo "set -x" >> archive_${frelout[$i]}
4103	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4104	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4105	else
4106
4107	echo "set -x" >> archive_${frelout[$i]}
4108	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4109	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4110	cd $tmp_data_catalog
4111	all_files=`ls -1 ${frelout[$i]}/*`
4112	cd - > /dev/null
4113	(( inode = 0 ))
4114	(( tp1 = tasks_per_node + 1 ))
4115	while (( inode < nodes ))
4116	do
4117	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4118	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4119	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4120	(( inode = inode + 1 ))
4121	done
4122	fi
4123	elif [[ $archive_system = ut ]]
4124	then
4125	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4126	if [[ $files_for_pes = false ]]
4127	then
4128	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4129	echo "set -x" >> archive_${frelout[$i]}
4130	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4131	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4132	else
4133
4134	echo "set -x" >> archive_${frelout[$i]}
4135	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4136	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4137	cd $tmp_data_catalog
4138	all_files=`ls -1 ${frelout[$i]}/*`
4139	cd - > /dev/null
4140	(( inode = 0 ))
4141	(( tp1 = tasks_per_node + 1 ))
4142	while (( inode < nodes ))
4143	do
4144	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4145	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4146	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4147	(( inode = inode + 1 ))
4148	done
4149	fi
4150	elif [[ $archive_system = none ]]
4151	then
4152	printf " +++ archiving on $localhost not available!\n"
4153	fi
4154
4155	if [[ $archive_system != none ]]
4156	then
4157	if [[ $localhost = nech ]]
4158	then
4159	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4160	fi
4161	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4162	fi
4163	else
4164	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4165	fi
4166
4167
4168	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4169	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4170	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4171	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4172	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4173	if [[ $files_for_pes = false ]]
4174	then
4175	cat /dev/null > ${pathout[$i]}
4176	else
4177	mkdir -p ${pathout[$i]}
4178	fi
4179
4180	fi
4181
4182
4183	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4184	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4185	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4186	if [[ "${actionout[$i]}" = ar ]]
4187	then
4188	if [[ $files_for_pes = false ]]
4189	then
4190	printf "\n >>> OUTPUT: ${localout[$i]} to"
4191	printf "\n ${pathout[$i]}"
4192	printf "\n File will be copied to archive-system ($archive_system) !\n"
4193	else
4194	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4195	printf "\n ${pathout[$i]}"
4196	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4197	fi
4198	mv ${localout[$i]} ${frelout[$i]}
4199
4200	file_saved=false
4201
4202	if [[ $archive_system = asterix ]]
4203	then
4204	do_stageout=true
4205	(( stageout_anz = 0 ))
4206	while [[ $do_stageout = true ]]
4207	do
4208	if [[ $files_for_pes = false ]]
4209	then
4210	stageout ${frelout[$i]} > STAGE_OUTPUT
4211	else
4212	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4213	fi
4214	cat STAGE_OUTPUT
4215	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4216	then
4217	file_saved=true
4218	do_stageout=false
4219	else
4220	if [[ $files_for_pes = false ]]
4221	then
4222	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4223	else
4224	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4225	fi
4226	(( stageout_anz = stageout_anz + 1 ))
4227	if (( stageout_anz == 10 ))
4228	then
4229	printf "\n +++ stoped after 10 unsuccessful tries!"
4230	archive_save=false
4231	do_stageout=false
4232	else
4233	printf "\n *** new try to store on archive after 15 min:"
4234	sleep 900
4235	fi
4236	fi
4237	done
4238	elif [[ $archive_system = DMF ]]
4239	then
4240	if [[ $files_for_pes = false ]]
4241	then
4242	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4243	locat=DMF
4244	exit
4245	else
4246	rm -rf $ARCHIVE/${frelout[$i]}
4247	cp -r ${frelout[$i]} $ARCHIVE
4248	fi
4249	file_saved=true
4250	elif [[ $archive_system = tivoli ]]
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 [[ $files_for_pes = false ]]
4271	then
4272	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4273	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4274	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4275	else
4276	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4277	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4278	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4279	fi
4280
4281	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4282	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4283	file_saved=true
4284
4285	elif [[ $archive_system = ut ]]
4286	then
4287	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4288	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4289	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4290	# WHEN THE ARCHIVE-JOB IS EXECUTED
4291	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4292	chmod g+rx $tmp_data_catalog
4293	if [[ $files_for_pes = false ]]
4294	then
4295	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4296	else
4297	mkdir $tmp_data_catalog/${frelout[$i]}
4298	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4299	fi
4300
4301	# GENERATE AND SUBMIT BATCH-JOB
4302	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4303	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4304	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4305	if [[ $files_for_pes = false ]]
4306	then
4307	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4308	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4309	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4310	else
4311	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4312	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4313	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4314	fi
4315
4316	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4317	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4318	file_saved=true
4319
4320	else
4321	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4322	archive_save=false
4323	fi
4324
4325	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4326	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4327	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4328	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4329	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4330	if [[ $file_saved = true ]]
4331	then
4332	if [[ $files_for_pes = false ]]
4333	then
4334	cat /dev/null > ${pathout[$i]}
4335	else
4336	mkdir -p ${pathout[$i]}
4337	fi
4338	fi
4339
4340	fi
4341
4342	# APPEND ON THIS MACHINE
4343	if [[ "${actionout[$i]}" = "a" ]]
4344	then
4345	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4346	then
4347	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4348	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4349	else
4350	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4351	cat ${localout[$i]} >> ${pathout[$i]}
4352	fi
4353	fi
4354
4355	# COPY ON THIS MACHINE
4356	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4357	# ON DIFFERENT FILE-SYSTEMS
4358	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4359	then
4360
4361	# COPY IN CASE OF RUNS ON SINGLE CORES
4362	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4363	then
4364	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4365	if [[ $link_local_output = true ]]
4366	then
4367	printf " using ln -f\n"
4368	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4369	fi
4370	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4371	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4372	then
4373	if [[ $link_local_output = true ]]
4374	then
4375	printf " ln failed, using cp...\n"
4376	fi
4377	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4378	fi
4379	else
4380	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4381	if [[ $link_local_output = true ]]
4382	then
4383	printf " using ln -f\n"
4384	ln -f ${localout[$i]} ${pathout[$i]}
4385	fi
4386	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4387	if [[ ! -f "${pathout[$i]}" ]]
4388	then
4389	if [[ $link_local_output = true ]]
4390	then
4391	printf " ln failed, using cp...\n"
4392	fi
4393	cp ${localout[$i]} ${pathout[$i]}
4394	fi
4395	fi
4396
4397	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4398	then
4399
4400	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4401	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4402	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4403	if [[ $link_local_output = true ]]
4404	then
4405	printf " using ln -f\n"
4406	mkdir ${pathout[$i]}
4407	cd ${localout[$i]}
4408	for file in $(ls *)
4409	do
4410	ln -f $file ${pathout[$i]}
4411	done
4412	cd $TEMPDIR
4413	fi
4414
4415	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4416	if [[ ! -f "${pathout[$i]}/_0000" ]]
4417	then
4418	if [[ $link_local_output = true ]]
4419	then
4420	printf " ln failed for .../_0000, using cp...\n"
4421	fi
4422	cp -r ${localout[$i]} ${pathout[$i]}
4423	fi
4424
4425	fi
4426	fi
4427	done
4428	if (( i != 0 ))
4429	then
4430	if [[ $transfer_problems = true ]]
4431	then
4432	printf "\n$dashes\n *** OUTPUT-files saved"
4433	printf "\n +++ WARNING: some data transfers failed! \n"
4434	else
4435	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4436	fi
4437	fi
4438
4439
4440	# IF REQUIRED, START A RESTART-JOB
4441	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4442	if [[ -f CONTINUE_RUN ]]
4443	then
4444
4445	if [[ $archive_save = true ]]
4446	then
4447
4448	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4449	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4450	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4451	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4452	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4453	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4454	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4455	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4456	then
4457	mc=`echo $mc \| sed 's/#/f/g'`
4458	fi
4459
4460
4461	# START THE RESTART-JOB
4462	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4463	echo " $mc"
4464	printf "\n$dashes\n"
4465	if [[ $localhost != $fromhost ]]
4466	then
4467
4468	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4469	then
4470	echo "*** ssh will be used to initiate restart-runs!"
4471	echo " return_address=\"$return_address\" "
4472	echo " return_username=\"$return_username\" "
4473	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4474	then
4475	if [[ $localhost = ibmh ]]
4476	then
4477	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\" "
4478	elif [[ $localhost = lcbullhh ]]
4479	then
4480	ssh $SSH_PORTOPT $usern@mlogin101 "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\" "
4481	elif [[ $localhost = lccrayb ]]
4482	then
4483	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\" "
4484	elif [[ $localhost = lccrayh ]]
4485	then
4486	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\" "
4487	elif [[ $localhost = lcxe6 ]]
4488	then
4489	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\" "
4490	else
4491	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 "
4492	fi
4493	else
4494	if [[ $localhost = ibmkisti ]]
4495	then
4496	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\" "
4497	elif [[ $localhost = lcflow ]]
4498	then
4499	/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 "
4500	elif [[ $localhost = lccrayb ]]
4501	then
4502	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\" "
4503	elif [[ $localhost = lccrayh ]]
4504	then
4505	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\" "
4506	else
4507	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4508	fi
4509	fi
4510	else
4511	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4512	locat=restart; exit
4513	fi
4514
4515	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4516	if [[ $queue = special1q ]]
4517	then
4518	sleep 120
4519	else
4520	sleep 30
4521	fi
4522
4523	else
4524
4525	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4526	# USING SSH)
4527	cd $LOCAL_PWD
4528	if [[ $localhost = lckyuh ]]
4529	then
4530	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4531	printf "\n please restart job manually using command:\n"
4532	printf "\n \"$mc\" "
4533	else
4534	eval $mc # THE ' MUST BE EVALUATED
4535	fi
4536	cd - > /dev/null
4537	fi
4538	if [[ $localhost = lckyuh ]]
4539	then
4540	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4541	else
4542	printf "\n$dashes\n *** restart-run initiated \n"
4543	fi
4544
4545
4546	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4547	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4548	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4549	# MAY BE VERY HUGE)
4550	(( i = 0 ))
4551	while (( i < iin ))
4552	do
4553	(( i = i + 1 ))
4554	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4555	then
4556	rm -r $tmp_data_catalog/${frelin[$i]}
4557	fi
4558	done
4559
4560	else
4561
4562	printf "\n +++ no restart-run possible, since errors occured"
4563	printf "\n during the archive process"
4564	fi
4565
4566	fi
4567
4568
4569
4570	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4571	if [[ "$email_notification" != "none" ]]
4572	then
4573
4574	if [[ $localhost != $fromhost ]]
4575	then
4576	if [[ -f CONTINUE_RUN ]]
4577	then
4578	echo "PALM restart run necessary" > email_text
4579	echo "description header of actual run:" >> email_text
4580	cat CONTINUE_RUN >> email_text
4581	echo "mrun-command to restart:" >> email_text
4582	echo "$mc" >> email_text
4583	else
4584	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4585	fi
4586	mail $email_notification < email_text
4587	printf "\n *** email notification sent to \"$email_notification\" "
4588	fi
4589	fi
4590
4591
4592
4593	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4594	cd $HOME
4595	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4596
4597	else
4598
4599	# PREPARING ACTIONS,
4600	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4601
4602	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4603	mrun_com="$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 $remote_username"
4604	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4605	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4606	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4607	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4608	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4609	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4610	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4611	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4612	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4613	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4614	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4615	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4616	if [[ $use_openmp = true ]]
4617	then
4618	mrun_com=${mrun_com}" -O $threads_per_task"
4619	fi
4620	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4621	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4622	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4623	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4624	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4625	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4626	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4627	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4628	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4629	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4630	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4631	if [[ $do_remote = true ]]
4632	then
4633	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4634	fi
4635
4636
4637	# CREATE EXECUTABLE FOR BATCH JOB
4638	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4639	then
4640
4641	printf "\n *** creating the executable for batch job\n"
4642
4643	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4644	if [[ $host != $localhost ]]
4645	then
4646	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4647	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4648	locat=create_executable; exit
4649	fi
4650
4651	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4652	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4653
4654	cp $make_depository .
4655	tar -xf $make_depository > /dev/null 2>&1
4656	cp ../* . > /dev/null 2>&1
4657
4658	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4659
4660	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4661	then
4662	printf "\n +++ error occured while compiling or linking"
4663	locat=compile
4664	exit
4665	fi
4666
4667	mv a.out ..
4668	cd - > /dev/null 2>&1
4669	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4670
4671	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4672
4673	fi
4674
4675
4676	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4677	jobfile=jobfile.$RANDOM
4678
4679
4680	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4681	echo "mkdir $TEMPDIR" >> $jobfile
4682	echo "cd $TEMPDIR" >> $jobfile
4683
4684
4685	# ACTIVATE ERROR-TRACEBACK
4686	if [[ $do_trace = true ]]
4687	then
4688	echo "set -x" >> $jobfile
4689	else
4690	echo "set +vx" >> $jobfile
4691	fi
4692
4693
4694	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4695	if [[ "$init_cmds" != "" ]]
4696	then
4697	echo "$init_cmds" >> $jobfile
4698	fi
4699	if [[ "$module_calls" != "" ]]
4700	then
4701	echo "$module_calls" >> $jobfile
4702	fi
4703
4704
4705	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4706	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4707	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4708	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4709	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4710	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4711	# QUEUEING-SYSTEMS
4712	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4713	then
4714
4715	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4716	if [[ $restart_run != true ]]
4717	then
4718	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4719	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4720	fi
4721
4722	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4723	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4724	echo "set -x" >> $jobfile
4725	if [[ $host = $localhost ]]
4726	then
4727	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4728	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4729	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4730	then
4731	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4732	else
4733	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4734	fi
4735
4736	else
4737	if [[ $host = ibmkisti ]]
4738	then
4739	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4740	echo "localdir=\`pwd\`" >> $jobfile
4741	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4742	elif [[ $host = lcbullhh ]]
4743	then
4744	echo "localdir=\`pwd\`" >> $jobfile
4745	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4746
4747	elif [[ $host = lccrayb ]]
4748	then
4749	echo "localdir=\`pwd\`" >> $jobfile
4750	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4751	elif [[ $host = lccrayh ]]
4752	then
4753	echo "localdir=\`pwd\`" >> $jobfile
4754	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4755
4756	else
4757	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4758	fi
4759	fi
4760	echo "export SOURCES_COMPLETE=true" >> $jobfile
4761
4762	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4763	# WORKING DIRECTORY OF THE JOB
4764	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4765	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4766	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4767	echo "execute_mrun=true" >> $jobfile
4768	echo " " >> $jobfile
4769
4770	else
4771
4772	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4773	if [[ $do_compile = true ]]
4774	then
4775
4776	source_catalog=SOURCES_FOR_RUN_$fname
4777
4778	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4779	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4780	echo "export SOURCES_COMPLETE=true" >> $jobfile
4781	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4782
4783	for filename in $source_list
4784	do
4785	# BACKSLASH IS USED FOR MASKING
4786	echo "cat > $filename << \"%END%\"" >> $jobfile
4787	cat $source_catalog/$filename >> $jobfile
4788	echo " " >> $jobfile
4789	echo "%END%" >> $jobfile
4790	echo " " >> $jobfile
4791	done
4792
4793	# BACKSLASH IS USED FOR MASKING
4794	echo "cat > Makefile << \"%END%\"" >> $jobfile
4795	cat $source_catalog/Makefile >> $jobfile
4796	echo " " >> $jobfile
4797	echo "%END%" >> $jobfile
4798	echo " " >> $jobfile
4799
4800	echo "cd - > /dev/null" >> $jobfile
4801
4802	fi
4803
4804
4805	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4806	# BACKSLASH IS USED FOR MASKING
4807	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4808	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4809	echo "cat > $config_file << \"%END%\"" >> $jobfile
4810	if [[ $host = lckyuh ]]
4811	then
4812	# NO CROSS-COMPILER ON COMPUTE NODE
4813	sed 's/frtpx/frt/g' $config_file >> $jobfile
4814	else
4815	sed 's/#$.*//g' $config_file >> $jobfile
4816	fi
4817	echo "%END%" >> $jobfile
4818	echo " " >> $jobfile
4819
4820
4821	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4822	# BACKSLASH IS USED FOR MASKING
4823	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4824	if [[ $host = lckyuh ]]
4825	then
4826	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4827	else
4828	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4829	fi
4830	echo "%END%" >> $jobfile
4831	echo "chmod u+x $mrun_script_name" >> $jobfile
4832	echo "execute_mrun=true" >> $jobfile
4833	echo " " >> $jobfile
4834
4835	fi
4836
4837
4838	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4839	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4840	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4841	if [[ $do_remote = true ]]
4842	then
4843	(( i = 0 ))
4844	while (( i < iin ))
4845	do
4846	(( i = i + 1 ))
4847	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4848	if [[ "${transin[$i]}" = job ]]
4849	then
4850	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4851	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4852	echo " " >> $jobfile
4853	echo "%END%" >> $jobfile
4854	else
4855	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4856	fi
4857
4858	# CHECK, IF FILE COULD BE CREATED
4859	echo "if [[ \$? = 1 ]]" >> $jobfile
4860	echo "then" >> $jobfile
4861	echo " echo \" \" " >> $jobfile
4862	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4863	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4864	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4865	echo " execute_mrun=false" >> $jobfile
4866	echo "fi" >> $jobfile
4867	done
4868	fi
4869
4870	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4871	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4872	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4873	echo "LOCAL_PWD=$working_directory" >> $jobfile
4874	echo "export LOCAL_PWD" >> $jobfile
4875
4876	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4877	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4878	echo "export LOCAL_MRUN_PATH" >> $jobfile
4879
4880	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4881	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4882	# then
4883	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4884	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4885	# fi
4886
4887	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4888	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4889	echo "set -x" >> $jobfile
4890	echo "queue=$queue" >> $jobfile
4891	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4892	echo 'ls -al; echo `pwd`' >> $jobfile
4893	echo "cd \$HOME" >> $jobfile
4894	echo "rm -rf $TEMPDIR" >> $jobfile
4895
4896
4897
4898
4899	# START THE JOB USING SUBJOB-COMMAND
4900	if [[ $silent = false ]]
4901	then
4902	printf "\n "
4903	else
4904	printf "\n\n"
4905	fi
4906
4907	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
4908	rm -rf $jobfile
4909
4910
4911	fi # END OF REMOTE-PART

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