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source: palm/trunk/SCRIPTS/mrun @ 1755

Last change on this file since 1755 was 1755, checked in by maronga, 9 years ago
minor bugfix for last commit
Property svn:keywords set to `Id Rev`
File size: 180.6 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 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# Minor bugfix to last commit
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1755 2016-02-22 13:53:39Z maronga $
29	#
30	# 1753 2016-02-22 13:49:49Z maronga
31	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
32	#
33	# 1622 2015-07-20 06:21:36Z heinze
34	# bugfix for Mistral (lcbullhh)
35	#
36	# 1621 2015-07-17 11:39:33Z heinze
37	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
38	#
39	# 1609 2015-07-03 15:37:58Z maronga
40	# Modified the random number of the temporary working directory to match the
41	# queuing system number on HLRN-III (lccray*).
42	#
43	# 1604 2015-06-23 15:48:03Z suehring
44	# Enable coupled runs for lcmuk
45	#
46	# 1598 2015-05-29 06:45:40Z raasch
47	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
48	#
49	# 1549 2015-01-30 14:26:16Z suehring
50	# Enable interactive debug sessions with allinea debugger
51	#
52	# 1547 2015-01-29 15:09:12Z witha
53	# adjustments for ForWind computing cluster (lcflow)
54	#
55	# 1491 2014-11-12 08:12:57Z heinze
56	# correct setting of batch_job allowed for ibm-machines
57	#
58	# 1468 2014-09-24 14:06:57Z maronga
59	# Typo removed (addres->address)
60	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
61	# Added support for restart runs (remote) for lcxe6
62	#
63	# 1442 2014-07-28 07:09:10Z raasch
64	# default queues for HLRN-III (lccrayb/lccrayh) defined
65	#
66	# 1422 2014-07-02 10:01:25Z kanani
67	# automatic restarts enabled for lccrayb,
68	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
69	#
70	# 1420 2014-06-10 06:24:14Z raasch
71	# -j1 option added to aprung command for lccrayf (CSC)
72	#
73	# 1402 2014-05-09 14:25:13Z raasch
74	# batch_job added to envpar-NAMELIST
75	#
76	# 1357 2014-04-11 15:02:03Z witha
77	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
78	# possible)
79	#
80	# 1320 2014-03-20 08:40:49Z raasch
81	# check namelist file set false by default
82	#
83	# 1304 2014-03-12 10:29:42Z raasch
84	# ulimit option changed from -Ss to -s
85	#
86	# bugfix: missing "fi" in r1289
87	#
88	# 1289 2014-03-04 07:12:34Z raasch
89	# comments translated to English
90	# necriam-, fimm-, ibmy-, and sgi-specific code removed
91	# export of variables for palm and interpret_config removed
92	#
93	# 1281 2014-02-01 07:55:49Z raasch
94	# rsync-copy restricted to Cray machines, since command is unavailable on some
95	# other systems
96	#
97	# 1279 2014-01-28 12:10:14Z raasch
98	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
99	# in order to remove annoying restrictions concerning the number of processors which
100	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
101	# restriction, one of the nodes will be filled with less than the given number of
102	# tasks per node. A respective warning is given.
103	#
104	# 1274 2014-01-09 13:14:54Z heinze
105	# adjustments for lccrayh
106	#
107	# 1272 2014-01-08 10:19:32Z witha
108	# small adjustment for lcflow
109	#
110	# 1270 2013-12-16 11:05:01Z fricke
111	# call of combine_plot_fields adjusted for lccrayb/lccrayh
112	#
113	# 1255 2013-11-07 14:43:35Z raasch
114	# further adjustments for lccrayb remote access
115	#
116	# 1241 2013-10-30 11:36:58Z heinze
117	# Enable use of nudging input and input of large scale forcing from
118	# external files
119	#
120	# 1229 2013-09-20 06:55:19Z raasch
121	# further adjustments for lccrayb
122	#
123	# 1224 2013-09-16 07:27:23Z raasch
124	# first adjustments for lccrayb
125	#
126	# 1210 2013-08-14 10:58:20Z raasch
127	# fftw support added
128	#
129	# 1201 2013-07-10 16:17:59Z witha
130	# adjustments for Forwind cluster (lcflow)
131	#
132	# 1199 2013-07-05 14:52:22Z raasch
133	# adjustments for CSC Helsinki (lccrayf),
134	# executables for batch jobs can be created in advance, in order to avoid calling
135	# the compiler within the batch job (only works if batch jobs are submitted on
136	# local host)
137	#
138	# 1190 2013-06-25 09:39:21Z heinze
139	# enable use of automatic restarts for ibmh
140	# use of cluster/express queue enabled (ibmh)
141	#
142	# 1124 2013-04-09 15:46:52Z raasch
143	# variable "memory" is exported via typeset option -x, because otherwise an unknown
144	# side effect may lead to data loss while getopts is reading the script-option arguments
145	#
146	# 1122 2013-04-09 08:37:16Z heinze
147	# Bugfix: change type of variable last_char
148	#
149	# 1119 2013-04-05 15:11:19Z raasch
150	# Bugfix for setting -T option for subjob
151	#
152	# 1108 2013-03-05 07:03:32Z raasch
153	# bugfix for coupled runs on lckyut/lckyuh
154	#
155	# 1106 2013-03-04 05:31:38Z raasch
156	# --stdin argument for mpiexec on lckyuh
157	# -y and -Y settings output to header
158	#
159	# 1103 2013-02-20 02:15:53Z raasch
160	# default script runs again under ksh, because of unsolved problems with read
161	# from stdin: when bash script is called from a ksh, message "read error: 0:
162	# Resource temporarily unavailable" appears and script does not stop,
163	# further bash compatibility adjustments,
164	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
165	# on lckyuh, but mrun does not terminate and issues a warning instead
166	#
167	# 1101 2013-02-17 10:20:21Z raasch
168	# script now running under bash instead of ksh, which required small adjustments
169	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
170	# read from stdin),
171	# cross compilername on lckyuh compute nodes replaced by real compiler name
172	#
173	# 1099 2013-02-10 01:47:43Z raasch
174	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
175	# and for Forwind cluster (lcflow)
176	# small further adjustments for lckyut
177	#
178	# 1094 2013-02-03 01:52:12Z raasch
179	# explicit ssh/scp port can be set in config file with environment variable
180	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
181	# decalpha parts (yonsei) removed
182	#
183	# 2013-02-02 07:06:13Z raasch
184	# adjustments for Kyushu-University computing center (lckyut - tatara)
185	#
186	# 1083 2013-01-04 10:22:09Z maronga
187	# bugfix in parameter file check (read %cpp_options was missing)
188	#
189	# 1069 2012-11-28 16:18:43Z maronga
190	# bugfix: coupling mode was always set to mpi2, typos removed
191	#
192	# 1058 2012-11-21 07:00:35Z raasch
193	# Intel inspector (inspxe) is given the number of PEs instead of the number of
194	# nodes
195	#
196	# 1046 2012-11-09 14:38:45Z maronga
197	# code put under GPL (PALM 3.9)
198	#
199	# 21/03/94 - Siggi - first version finished
200	# 03/03/94 - Siggi - script development started
201	#
202	#--------------------------------------------------------------------------------#
203	# mrun - script for running PALM jobs
204	#--------------------------------------------------------------------------------#
205
206
207
208	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
209
210	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
211	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
212	# (TOO MANY ARGUMENTS - PROBLEM)
213	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
214
215	AddFilenames=""
216	additional_conditions=""
217	add_source_path=""
218	afname=""
219	archive_save=true
220	archive_system=none
221	check_namelist_files=false
222	combine_plot_fields=true
223	compiler_name=""
224	cond1=""
225	cond2=""
226	config_file=.mrun.config
227	coupled_dist=""
228	coupled_mode="mpi1"
229	cpp_opts=""
230	cpp_options=""
231	cpumax=0
232	cpurest=0
233	create_executable_for_batch=false
234	delete_temporary_catalog=true
235	do_batch=false
236	do_compile=true
237	do_remote=false
238	do_stagein=true
239	do_stageout=true
240	do_trace=false
241	email_notification="none"
242	exclude=""
243	executable=""
244	execution_error=false
245	fftw_inc=""
246	fftw_lib=""
247	fftw_support=false
248	fname=test
249	fromhost=""
250	global_revision=""
251	group_number=none
252	host=""
253	host_file=""
254	hp=""
255	ignore_archive_error=false
256	input_list=""
257	interpreted_config_file=""
258	job_catalog="~/job_queue"
259	job_on_file=""
260	keep_data_from_previous_run=false
261	link_local_input=false
262	link_local_output=false
263	localhost_realname=$(hostname)
264	local_dvrserver_running=.FALSE.
265	locat=normal
266	mainprog=""
267	makefile=""
268	max_par_io_str=""
269	mc=$0
270	while [[ $(echo $mc \| grep -c "/") != 0 ]]
271	do
272	mc=`echo $mc \| cut -f2- -d"/"`
273	done
274	module_calls=""
275	mrun_script_name=$mc
276	netcdf_inc=""
277	netcdf_lib=""
278	netcdf_support=false
279	node_usage=default
280	numprocs=""
281	numprocs_atmos=0
282	numprocs_ocean=0
283	OOPT=""
284	openmp=false
285	output_list=""
286	package_list=""
287	queue=none
288	read_from_config=""
289	restart_run=false
290	if [[ `hostname` = rte10 ]]
291	then
292	return_address=133.5.185.60
293	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
294	elif [[ `hostname` = climate0 ]]
295	then
296	return_address=165.132.26.68
297	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
298	elif [[ `hostname` = urban00 ]]
299	then
300	return_address=147.46.30.151
301	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
302	else
303	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
304	fi
305	return_password=""
306	return_username=$LOGNAME
307	remotecall=false
308	remote_username=""
309	run_coupled_model=false
310	run_mode=""
311	store_on_archive_system=false
312	dashes=" ----------------------------------------------------------------------------"
313	silent=false
314	source_list=""
315	source_path=SOURCE
316	tasks_per_node=""
317	threads_per_task=1
318	tmpcreate=false
319	tmp_data_catalog=""
320	transfer_problems=false
321	usern=$LOGNAME
322	use_openmp=false
323	version="MRUN 2.1 Rev$Rev: 1755 $"
324	working_directory=`pwd`
325	TOPT=""
326	XOPT=""
327	zeit=$( date \| cut -c 12-19 )
328
329	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
330	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
331	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
332	# SCRIPT-OPTION ARGUMENTS
333	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
334
335	# ERROR HANDLING IN CASE OF EXIT
336	trap 'rm -rf $working_directory/tmp_mrun
337	if [[ $locat != normal && $locat != control_c ]]
338	then
339
340	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
341	(( i = 0 ))
342	while (( i < iec ))
343	do
344	(( i = i + 1 ))
345	printf "\n *** Execution of ERROR-command:\n"
346	printf " >>> ${err_command[$i]}\n"
347	eval ${err_command[$i]}
348	done
349	if [[ -n $interpreted_config_file ]]
350	then
351	rm -rf $interpreted_config_file
352	fi
353	if [[ -n .mrun_environment ]]
354	then
355	rm -rf .mrun_environment
356	fi
357	if [[ $tmpcreate = true ]]
358	then
359	printf "\n *** Contents of \"$TEMPDIR\":\n"
360	ls -al; cd
361	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
362	fi
363	if [[ "$dvrserver_id" != "" ]]
364	then
365	echo "+++ killing dvrserver_id=$dvrserver_id"
366	kill $dvrserver_id
367	fi
368	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
369	then
370	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
371	fi
372	printf "\n\n+++ MRUN killed \n\n"
373	elif [[ $locat != control_c ]]
374	then
375	printf "\n\n --> all actions finished\n\n"
376	printf " Bye, bye $usern !!\n\n"
377	fi' exit
378
379
380	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
381	trap 'rm -rf $working_directory/tmp_mrun
382	rm -rf $working_directory/tmp_check_namelist_files
383	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
384	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
385	then
386	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
387	fi
388	if [[ "$dvrserver_id" != "" ]]
389	then
390	echo "+++ killing dvrserver_id=$dvrserver_id"
391	kill $dvrserver_id
392	fi
393	printf "\n+++ MRUN killed by \"^C\" \n\n"
394	locat=control_c
395	exit
396	' 2
397
398
399	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
400	# BEEN SET
401	if [[ "$PALM_BIN" = "" ]]
402	then
403	printf "\n +++ environment variable PALM_BIN has not been set"
404	printf "\n please set it to the directory where the PALM scripts are located"
405	locat=palm_bin; exit
406	fi
407	export PATH=$PALM_BIN:$PATH
408
409
410
411	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
412	# WHICH WILL BE USED TO START RESTART-JOBS
413	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
414	do
415	case $option in
416	(a) afname=$OPTARG;;
417	(A) store_on_archive_system=true; mc="$mc -A";;
418	(b) do_batch=true; mc="$mc -b";;
419	(B) delete_temporary_catalog=false; mc="$mc -B";;
420	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
421	(C) restart_run=true; mc="$mc -C";;
422	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
423	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
424	(F) job_on_file="-D"; mc="$mc -F";;
425	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
426	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
427	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
428	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
429	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
430	(I) ignore_archive_error=true; mc="$mc -I";;
431	(k) keep_data_from_previous_run=true; mc="$mc -k";;
432	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
433	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
434	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
435	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
436	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
437	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
438	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
439	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
440	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
441	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
442	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
443	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
444	(S) read_from_config=false; mc="$mc -S";;
445	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
446	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
447	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
448	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
449	(v) silent=true; mc="$mc -v";;
450	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
451	(x) do_trace=true;set -x; mc="$mc -x";;
452	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
453	(y) ocean_file_appendix=true; mc="$mc -y";;
454	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
455	(z) check_namelist_files=false; mc="$mc -z";;
456	(Z) combine_plot_fields=false; mc="$mc -Z";;
457	(\?) printf "\n +++ unknown option $OPTARG \n"
458	printf "\n --> type \"$0 ?\" for available options \n"
459	locat=parameter;exit;;
460	esac
461	done
462
463
464	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
465	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
466	(( to_shift = $OPTIND - 1 ))
467	shift $to_shift
468
469	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
470	if [[ "$1" = "?" ]]
471	then
472	(printf "\n *** mrun can be called as follows:\n"
473	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"
474	printf "\n Description of available options:\n"
475	printf "\n Option Description Default-Value"
476	printf "\n -a base name of input files equiv. -d"
477	printf "\n -A archiving when using file-attribute fl"
478	printf "\n -b batch-job on local machine ---"
479	printf "\n -B do not delete temporary directory at end ---"
480	printf "\n -c configuration file .mrun.config"
481	printf "\n -d base name of files attached to program test"
482	printf "\n -D preprocessor(cpp)-directives \"\" "
483	printf "\n -F create remote job file only ---"
484	printf "\n -h execution host $localhost_realname"
485	printf "\n -i INPUT control list \"\" "
486	printf "\n -I archiving errors of previous batch-jobs"
487	printf "\n will be ignored"
488	printf "\n -k keep data from previous run"
489	printf "\n -K additional conditions for controling"
490	printf "\n usage of conditional code and"
491	printf "\n env-variables in configuration file \"\" "
492	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
493	printf "\n -M Makefile name Makefile"
494	printf "\n -n node usage (shared/not_shared) depending on -h"
495	printf "\n -o OUTPUT control list \"\" "
496	printf "\n -O threads per openMP task ---"
497	printf "\n -p software package list \"\" "
498	printf "\n -q queue \"$queue\" "
499	printf "\n -r run control list (combines -i -o) \"\" "
500	printf "\n -s filenames of routines to be compiled \"\" "
501	printf "\n must end with .f, .f90, .F, or .c !"
502	printf "\n use \"..\" for more than one file and wildcards"
503	printf "\n -s LM compiles all locally modified files"
504	printf "\n -S config file interpreted by shellscript ---"
505	printf "\n -t allowed cpu-time in seconds (batch) 0"
506	printf "\n -T tasks per node depending on -h"
507	printf "\n -u username on remote machine \"\" "
508	printf "\n -v no prompt for confirmation ---"
509	printf "\n -w maximum parallel io streams as given by -X"
510	printf "\n -x tracing of mrun for debug purposes ---"
511	printf "\n -X # of processors (on parallel machines) 1"
512	printf "\n -y add appendix \"_O\" to all local output"
513	printf "\n files (ocean precursor runs followed by"
514	printf "\n coupled atmosphere-ocean runs) ---"
515	printf "\n -Y run coupled model, \"#1 #2\" with"
516	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
517	printf "\n -z disable a priori parameter file check ---"
518	printf "\n -Z skip combine_plot_fields at the end of "
519	printf "\n the simulation ---"
520	printf "\n "
521	printf "\n Possible values of positional parameter <modus>:"
522	printf "\n \"?\" - this outline \n\n") \| more
523	exit
524	elif [[ "$1" != "" ]]
525	then
526	printf "\n +++ positional parameter $1 unknown \n"
527	locat=parameter; exit
528	fi
529
530
531
532	# SHORT STARTING MESSAGE
533	printf "\n*** $version "
534	printf "\n will be executed. Please wait ..."
535
536
537
538	# CHECK, IF CONFIGURATION FILE EXISTS
539	if [[ ! -f $config_file ]]
540	then
541	printf "\n\n +++ configuration file: "
542	printf "\n $config_file"
543	printf "\n does not exist"
544	locat=connect; exit
545	fi
546
547
548	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
549	line=""
550	grep "%host_identifier" $config_file > tmp_mrun
551	while read line
552	do
553	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
554	then
555	HOSTNAME=`echo $line \| cut -d" " -s -f2`
556	host_identifier=`echo $line \| cut -d" " -s -f3`
557	if [[ $localhost_realname = $HOSTNAME ]]
558	then
559	localhost=$host_identifier
560	break
561	fi
562	fi
563	done < tmp_mrun
564
565	if [[ "$localhost" = "" ]]
566	then
567	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
568	printf "\n for local host \"$localhost_realname\"."
569	printf "\n Please add line"
570	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
571	printf "\n to the configuration file."
572	locat=localhost; exit
573	fi
574
575
576	# SET HOST-SPECIFIC VARIABLES
577	case $localhost_realname in
578	(r1\|r2\|h01\|b01) archive_system=tivoli;;
579	(cs*) archive_system=ut;;
580	esac
581
582
583	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
584	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
585	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
586	[[ "$afname" = "" ]] && afname=$fname
587
588
589	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
590	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
591	# STATEMENTS IN THE CONFIGURATION FILE
592	if [[ "$run_mode" != "" ]]
593	then
594	input_list="$input_list $run_mode"
595	output_list="$output_list $run_mode"
596	fi
597
598
599	# ??? is this (and the respective option -H) really required ???
600	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
601	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
602	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
603	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
604	if [[ "$fromhost" = "" ]]
605	then
606	fromhost=$localhost
607	fi
608
609
610	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
611	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
612	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
613	# TO BE SUBMITTED (I.E. do_batch=true)
614	if [[ -n $host && "$host" != $localhost ]]
615	then
616	do_batch=true
617	do_remote=true
618	case $host in
619	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
620	(*) printf "\n"
621	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
622	printf "\n is not available"
623	locat=nqs; (( iec = 0 )); exit;;
624	esac
625	else
626	host=$localhost
627	fi
628
629
630	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
631	if [[ -n $additional_conditions ]]
632	then
633	cond1=`echo $additional_conditions \| cut -d" " -f1`
634	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
635	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
636	if [[ -n $dummy ]]
637	then
638	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
639	locat=options; exit
640	fi
641	block=_$cond1
642	[[ -n $cond2 ]] && block=${block}_$cond2
643	fi
644
645
646	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
647	if [[ $run_coupled_model = true ]]
648	then
649
650	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
651	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
652
653	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
654	then
655
656	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
657	printf "\n PEs (total) : $numprocs"
658	printf "\n PEs (atmosphere): $numprocs_atmos"
659	printf "\n PEs (ocean) : $numprocs_ocean"
660	locat=coupling; exit
661
662	fi
663
664
665	# GET coupled_mode FROM THE CONFIG FILE
666	line=""
667	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
668	while read line
669	do
670	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
671	then
672	coupled_mode="mpi2"
673	fi
674	done < tmp_mrun
675
676	fi
677
678	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
679	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
680	then
681	if [[ $ignore_archive_error = false ]]
682	then
683	printf "\n +++ data archiving of previous run failed"
684	printf "\n see directory \~/job_queue on remote machine"
685	locat=archive; exit
686	else
687	printf "\n +++ warning: data archiving in a previous run failed"
688	printf "\n MRUN continues, trying to get backup copy"
689	fi
690	fi
691
692
693	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
694	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
695	mrun_memory=$memory
696	mrun_group_number=$group_number
697	mrun_cpumax=$cpumax
698	mrun_numprocs=$numprocs
699
700
701	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
702	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
703	if [[ "$read_from_config" = false ]]
704	then
705	[[ $silent = false ]] && printf "\n Reading the configuration file... "
706
707	# READ THE CONFIGURATION FILE LINE BY LINE
708	while read zeile
709	do
710	[[ $silent = false ]] && printf "."
711
712
713	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
714	eval zeile=\"$zeile\"
715
716
717	# INTERPRET THE LINE
718	if [[ "$(echo $zeile)" = "" ]]
719	then
720	# EMPTY LINE, NO ACTION
721	continue
722
723	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
724	then
725
726	# LINE IS A COMMENT LINE
727	true
728
729	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
730	then
731
732	# LINE DEFINES AN ENVIRONMENT-VARIABLE
733	zeile=$(echo $zeile \| cut -c2-)
734	var=`echo $zeile \| cut -d" " -f1`
735	value=`echo $zeile \| cut -d" " -s -f2`
736	for_host=`echo $zeile \| cut -d" " -s -f3`
737	for_cond1=`echo $zeile \| cut -d" " -s -f4`
738	for_cond2=`echo $zeile \| cut -d" " -s -f5`
739
740	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
741	then
742
743	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
744	# "::" IS REPLACED BY ":".
745	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
746
747
748	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
749	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
750	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
751	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
752	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
753	# CONFIGURATION-FILE.
754	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
755	then
756	eval $var=\$value
757
758	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
759	if [[ $do_trace = true ]]
760	then
761	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
762	fi
763	fi
764
765	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
766	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
767	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
768	# MUST HAVE TO BE STARTED
769	if [[ $var = host ]]
770	then
771	if [[ -n $host && "$host" != $localhost ]]
772	then
773	do_batch=true
774	do_remote=true
775	case $host in
776	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
777	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
778	printf "\n is not available"
779	locat=nqs; exit;;
780	esac
781	else
782	host=$localhost
783	fi
784	fi
785
786	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
787	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
788	# BY MRUN (E.G. subjob)
789	export $var
790	fi
791
792
793
794
795	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
796	then
797
798	# LINE DEFINES ERROR-COMMAND
799	(( iec = iec + 1 ))
800	zeile=$(echo $zeile \| cut -c4-)
801	err_command[$iec]="$zeile"
802
803	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
804	then
805
806	# LINE DEFINES INPUT-COMMAND
807	(( iic = iic + 1 ))
808	zeile=$(echo $zeile \| cut -c4-)
809	in_command[$iic]="$zeile"
810
811	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
812	then
813
814	# LINE DEFINES OUTPUT-COMMAND
815	(( ioc = ioc + 1 ))
816	zeile=$(echo $zeile \| cut -c4-)
817	out_command[$ioc]="$zeile"
818
819	else
820
821	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
822	# s2a: in/out - field
823	# s2b: loc - field (optional)
824	# s2c: tr/ar - field (optional)
825	s1=`echo $zeile \| cut -d" " -f1`
826	s2=`echo $zeile \| cut -d" " -s -f2`
827	s2a=$(echo $s2 \| cut -d":" -f1)
828	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
829	then
830	s2b=""
831	s2c=""
832	else
833	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
834	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
835	fi
836	s3=`echo $zeile \| cut -d" " -f3`
837	s4=`echo $zeile \| cut -d" " -s -f4`
838	s5=`echo $zeile \| cut -d" " -s -f5`
839	s6=`echo $zeile \| cut -d" " -s -f6`
840
841
842	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
843	# INPUT- OR OUTPUT-LIST.
844	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
845	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
846	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
847	# IS NOT CHECKED AND STORED.
848	IFSALT="$IFS"; IFS="$IFS:"
849	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
850	then
851	found=false
852	for actual in $input_list
853	do
854	for formal in $s3
855	do
856	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
857	done
858	done
859	if [[ $found = true ]]
860	then
861	(( iin = iin + 1 ))
862	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
863	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
864	extin[$iin]=$s6
865	fi
866	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
867	then
868	found=false
869	for actual in $output_list
870	do
871	for formal in $s3
872	do
873	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
874	done
875	done
876	if [[ $found = true ]]
877	then
878	(( iout = iout + 1 ))
879	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
880	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
881	fi
882	elif [[ "$s2a" != in && "$s2a" != out ]]
883	then
884	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
885	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
886	locat=connect; exit
887	fi
888	IFS="$IFSALT"
889	fi
890	done < $config_file
891
892	else
893
894	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
895	[[ $silent = false ]] && printf "..."
896	interpreted_config_file=.icf.$RANDOM
897
898
899
900	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
901	cat > .mrun_environment << %%END%%
902	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
903	config_file = '$config_file', do_remote = '$do_remote',
904	do_trace = '$do_trace', host = '$host',
905	input_list = '$input_list', icf = '$interpreted_config_file',
906	localhost = '$localhost', output_list = '$output_list' /
907
908	%%END%%
909
910	if [[ "$host" != $localhost ]]
911	then
912
913	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
914	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
915	if [[ $? != 0 ]]
916	then
917	printf "\n\n +++ no interpret_config found"
918	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
919	locat=interpret_config; exit
920	fi
921	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
922	$interpret_config_executable
923
924	else
925
926	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
927	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
928	then
929	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
930	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
931	locat=interpret_config; exit
932	else
933	interpret_config${block}.x
934	fi
935
936	fi
937	rm .mrun_environment
938
939
940	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
941	chmod u+x $interpreted_config_file
942	export PATH=$PATH:.
943	. $interpreted_config_file
944	rm $interpreted_config_file
945
946	fi
947
948
949	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
950	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
951	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
952	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
953	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
954	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
955	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
956
957
958	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
959	# FOR SOURCE-FILES TO BE COMPILED.
960	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
961	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
962	if [[ "$SOURCES_COMPLETE" = "" ]]
963	then
964
965	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
966	# HAS BEEN DEFINED
967	source_path=""
968	line=""
969	grep "%source_path" $config_file > tmp_mrun
970	while read line
971	do
972	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
973	then
974	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
975	then
976	global_source_path=`echo $line \| cut -d" " -f2`
977	fi
978	fi
979	done < tmp_mrun
980
981	line=""
982	found=false
983	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
984	while read line
985	do
986	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
987	then
988	if [[ $found = true ]]
989	then
990	printf "\n\n +++ more than one source path found in configuration file"
991	printf "\n for local host \"$localhost\" "
992	locat=source_path; exit
993	fi
994	source_path=`echo $line \| cut -d" " -f2`
995	found=true
996	fi
997	done < tmp_mrun
998	rm tmp_mrun
999
1000	if [[ "$source_path" = "" ]]
1001	then
1002	if [[ "$global_source_path" != "" ]]
1003	then
1004	source_path=$global_source_path
1005	else
1006	printf "\n\n +++ no source path found in configuration file"
1007	printf "\n for local host \"$localhost\" "
1008	locat=source_path; exit
1009	fi
1010	fi
1011	eval source_path=$source_path
1012
1013	if [[ ! -d $source_path ]]
1014	then
1015	printf "\n\n +++ source path \"$source_path\" on local host"
1016	printf "\n \"$localhost\" does not exist"
1017	locat=source_path; exit
1018	fi
1019
1020	fi
1021
1022
1023	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1024	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1025	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1026	then
1027	global_revision=`svnversion $source_path 2>/dev/null`
1028	global_revision="Rev: $global_revision"
1029	fi
1030
1031
1032	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1033	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1034	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1035	if [[ -n $host && "$host" != $localhost ]]
1036	then
1037	do_batch=true
1038	do_remote=true
1039	case $host in
1040	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1041	(*) printf "\n"
1042	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1043	printf "\n is not available"
1044	locat=nqs; (( iec = 0 )); exit;;
1045	esac
1046	else
1047	host=$localhost
1048	fi
1049
1050
1051
1052	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1053	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1054	then
1055
1056	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1057	if [[ ! -n $numprocs ]]
1058	then
1059	printf "\n"
1060	printf "\n +++ option \"-K parallel\" requires additional specification"
1061	printf "\n of the number of processors to be used by"
1062	printf "\n mrun-option \"-X\" or by environment-variable"
1063	printf "\n \"numprocs\" in the configuration file"
1064	locat=numprocs; (( iec = 0 )); exit
1065	fi
1066
1067	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1068	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1069	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1070	then
1071	printf "\n"
1072	printf "\n +++ option \"-T\" (tasks per node) is missing"
1073	printf "\n set -T option or define tasks_per_node in the config file"
1074	locat=tasks_per_node; (( iec = 0 )); exit
1075	fi
1076
1077	if (( numprocs < tasks_per_node ))
1078	then
1079	printf "\n"
1080	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1081	printf "\n given values: -T $tasks_per_node -X $numprocs"
1082	locat=tasks_per_node; (( iec = 0 )); exit
1083	fi
1084
1085	if [[ $host != lcflow && $host != lcxt5m ]]
1086	then
1087	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1088	(( ival = $tasks_per_node ))
1089	(( pes = numprocs ))
1090	(( ii = pes / ival ))
1091	(( remaining_pes = pes - ii * ival ))
1092	if (( remaining_pes > 0 ))
1093	then
1094	printf "\n"
1095	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1096	printf "\n divisor of the total number of processors (option \"-X\")"
1097	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1098	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1099	(( nodes = nodes + 1 ))
1100	fi
1101	fi
1102
1103
1104	# SETTINGS FOR SUBJOB-COMMAND
1105	OOPT="-O $threads_per_task"
1106
1107	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1108	if [[ "$tasks_per_node" != "" ]]
1109	then
1110	TOPT="-T $tasks_per_node"
1111	fi
1112
1113	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1114	if [[ $node_usage = default ]]
1115	then
1116	if [[ $host = ibms ]]
1117	then
1118	node_usage=shared
1119	else
1120	node_usage=not_shared
1121	fi
1122	fi
1123
1124	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1125	then
1126	printf "\n"
1127	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1128	printf "\n \"shared\" or \"not_shared\""
1129	locat=tasks_per_node; (( iec = 0 )); exit
1130	fi
1131
1132	fi
1133
1134	# CHECK IF HOSTFILE EXISTS
1135	if [[ -n $hostfile ]]
1136	then
1137	if [[ ! -f $hostfile ]]
1138	then
1139	printf "\n"
1140	printf "\n +++ hostfile \"$hostfile\" does not exist"
1141	locat=hostfile; exit
1142	fi
1143	fi
1144
1145
1146	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1147	if [[ "$maximum_parallel_io_streams" = "" ]]
1148	then
1149	maximum_parallel_io_streams=$numprocs
1150	fi
1151
1152
1153	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1154	if [[ "$scp_port" != "" ]]
1155	then
1156	PORTOPT="-P $scp_port"
1157	SSH_PORTOPT="-p $scp_port"
1158	fi
1159
1160
1161	# SET DEFAULT-QUEUE, IF NOT GIVEN
1162	if [[ $queue = none ]]
1163	then
1164	case $host in
1165	(ibmh) queue=cluster;;
1166	(ibmkisti) queue=class.32plus;;
1167	(lcbullhh) queue=compute;;
1168	(lccrayb) queue=mpp1q;;
1169	(lccrayh) queue=mpp1q;;
1170	(lckiaps) queue=normal;;
1171	(lckyoto) queue=ph;;
1172	(lckyuh) queue=fx-single;;
1173	(lckyut) queue=cx-single;;
1174	(lctit) queue=S;;
1175	(nech) queue=none;;
1176	(unics) queue=unics;;
1177	esac
1178	fi
1179
1180
1181	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1182	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1183	(( i = 0 ))
1184	while (( i < iin ))
1185	do
1186	(( i = i + 1 ))
1187	(( maxcycle = 0 ))
1188
1189	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1190	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1191	if [[ "${actionin[$i]}" = di ]]
1192	then
1193	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1194	# HOST ONLY
1195	eval filename=${pathin[$i]}/${endin[$i]}
1196	else
1197	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1198	# HOST ONLY
1199	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1200	fi
1201	eval pathname=${pathin[$i]}
1202
1203	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1204	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1205	then
1206	filename_input=$filename
1207	fi
1208
1209	# CHECK IF FILE EXISTS
1210	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1211	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1212	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1213	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1214	then
1215
1216	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1217	if [[ "${transin[$i]}" != "locopt" ]]
1218	then
1219	printf "\n\n +++ INPUT-file: "
1220	if [[ "${extin[$i]}" = "" ]]
1221	then
1222	printf "\n $filename"
1223	else
1224	printf "\n $filename.${extin[$i]}"
1225	fi
1226	printf "\n does not exist\n"
1227	locat=input; exit
1228	else
1229	transin[$i]="unavailable"
1230	fi
1231	else
1232
1233	# DETERMINE THE FILE'S CYCLE NUMBER
1234	ls -1 -d $filename > filelist 2>/dev/null
1235	ls -1 -d $filename.* >> filelist 2>/dev/null
1236	while read zeile
1237	do
1238	cycle=$(echo $zeile \| cut -f2 -d".")
1239	if [[ "$cycle" = "$zeile" ]]
1240	then
1241	(( icycle = 0 ))
1242	elif [[ "$cycle" = "${extin[$i]}" ]]
1243	then
1244	(( icycle = 0 ))
1245	else
1246	(( icycle = $cycle ))
1247	fi
1248	if (( icycle > maxcycle ))
1249	then
1250	(( maxcycle = icycle ))
1251	file_to_be_used=$zeile
1252	fi
1253	done <filelist
1254	rm filelist
1255
1256	# APPEND CYCLE NUMBER TO FILENAME
1257	if (( maxcycle > 0 ))
1258	then
1259	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1260	then
1261	filename=${filename}.$maxcycle.${extin[$i]}
1262	else
1263	filename=${filename}.$maxcycle
1264	fi
1265	else
1266	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1267	then
1268	filename=${filename}.${extin[$i]}
1269	fi
1270	fi
1271
1272	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1273	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1274	absnamein[$i]=$filename
1275	if (( maxcycle > 0 ))
1276	then
1277	if [[ "${actionin[$i]}" = di ]]
1278	then
1279	frelin[$i]=${endin[$i]}.$maxcycle
1280	else
1281	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1282	fi
1283	else
1284	if [[ "${actionin[$i]}" = di ]]
1285	then
1286	frelin[$i]=${endin[$i]}
1287	else
1288	frelin[$i]=${afname}${endin[$i]}
1289	fi
1290	fi
1291
1292	fi
1293	done
1294
1295	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1296	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1297	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1298	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1299	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1300	# REMOTE HOST)
1301	(( i = 0 ))
1302	while (( i < iout ))
1303	do
1304	(( i = i + 1 ))
1305	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1306	then
1307	if [[ "${actionout[$i]}" = tr ]]
1308	then
1309	actionout[$i]=""
1310	elif [[ "${actionout[$i]}" = trpe ]]
1311	then
1312	actionout[$i]=pe
1313	elif [[ "${actionout[$i]}" = tra ]]
1314	then
1315	actionout[$i]=a
1316	fi
1317	(( maxcycle = 0 ))
1318	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1319	eval catalogname=${pathout[$i]}
1320	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1321	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1322	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1323	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1324	then
1325
1326	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1327	if cat /dev/null > $filename
1328	then
1329	rm $filename
1330	else
1331
1332	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1333	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1334	if [[ ! -d $catalogname ]]
1335	then
1336	if mkdir -p $catalogname
1337	then
1338	printf "\n\n *** directory:"
1339	printf "\n $catalogname"
1340	printf "\n was created\n"
1341	else
1342	printf "\n\n +++ OUTPUT-file:"
1343	printf "\n $filename"
1344	printf "\n cannot be created, because directory does not exist"
1345	printf "\n and cannot be created either"
1346	printf "\n"
1347	locat=output ; exit
1348	fi 2>/dev/null
1349	else
1350	printf "\n\n +++ OUTPUT-file:"
1351	printf "\n $filename"
1352	printf "\n cannot be created, although directory exists"
1353	printf "\n"
1354	locat=output ; exit
1355	fi
1356	fi 2>/dev/null
1357	else
1358
1359	# DETERMINE THE CYCLE NUMBER
1360	ls -1 -d $filename > filelist 2>/dev/null
1361	ls -1 -d $filename.* >> filelist 2>/dev/null
1362	while read zeile
1363	do
1364	cycle=$(echo $zeile \| cut -f2 -d".")
1365	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1366	then
1367	(( icycle = 1 ))
1368	else
1369	(( icycle = $cycle + 1 ))
1370	fi
1371	if (( icycle > maxcycle ))
1372	then
1373	(( maxcycle = icycle ))
1374	fi
1375	done <filelist
1376	rm filelist
1377	fi
1378
1379	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1380	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1381	if [[ "${actionout[$i]}" != a ]]
1382	then
1383	if (( maxcycle > 0 ))
1384	then
1385	filename=${filename}.$maxcycle
1386	if cat /dev/null > $filename
1387	then
1388	rm $filename
1389	else
1390	printf "\n +++ OUTPUT-file:"
1391	printf "\n $filename"
1392	printf "\n cannot be created"
1393	locat=output ; exit
1394	fi
1395	fi
1396	else
1397	(( maxcycle = maxcycle - 1 ))
1398	if (( maxcycle > 0 ))
1399	then
1400	filename=${filename}.$maxcycle
1401	fi
1402	fi
1403
1404	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1405	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1406	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1407	pathout[$i]=$filename
1408	if (( maxcycle > 0 ))
1409	then
1410	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1411	else
1412	frelout[$i]=${fname}${endout[$i]}
1413	fi
1414
1415	fi
1416	done
1417
1418
1419	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1420	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1421	then
1422	if [[ "$dvr_inc" = "" ]]
1423	then
1424	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1425	printf "\n This is required for the dvrp_graphics package.\n"
1426	locat=dvr; exit
1427	fi
1428	if [[ "$dvr_lib" = "" ]]
1429	then
1430	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1431	printf "\n This is required for the dvrp_graphics package.\n"
1432	locat=dvr; exit
1433	fi
1434	fi
1435
1436
1437	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1438	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1439	if [[ "$mainprog" = "" && "$executable" = "" ]]
1440	then
1441	printf "\n +++ neither main program nor executable defined"
1442	locat=source; exit
1443	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1444	then
1445	printf "\n +++ main program as well as executable defined"
1446	locat=source; exit
1447	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1448	then
1449	do_compile=false
1450	fi
1451
1452
1453	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1454	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1455	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1456	then
1457	rm -rf SOURCES_FOR_RUN_$fname
1458	mkdir SOURCES_FOR_RUN_$fname
1459	fi
1460
1461
1462	# COLLECT ALL ROUTINES TO BE COMPILED
1463	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1464	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1465	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1466	then
1467
1468	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1469
1470	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1471	then
1472
1473	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1474	source_list=""
1475	cd $source_path
1476
1477
1478	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1479	if [[ ! -d .svn ]]
1480	then
1481	printf "\n\n +++ source directory"
1482	printf "\n \"$source_path\" "
1483	printf "\n is not under control of \"subversion\"."
1484	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1485	fi
1486
1487
1488	# LIST ALL MODIFIED SOURCE CODE FILES
1489	Filenames=""
1490	svn status > tmp_mrun
1491	while read line
1492	do
1493	firstc=`echo $line \| cut -c1`
1494	if [[ $firstc = M \|\| $firstc = "?" ]]
1495	then
1496	Name=`echo "$line" \| cut -c8-`
1497	extension=`echo $Name \| cut -d. -f2`
1498	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1499	then
1500	Filenames="$Filenames "$Name
1501	fi
1502	fi
1503	done < tmp_mrun
1504
1505
1506	# COPY FILES TO SOURCES_FOR_RUN_...
1507	for dateiname in $Filenames
1508	do
1509	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1510	source_list=$source_list"$dateiname "
1511	done
1512
1513	cd - > /dev/null
1514
1515
1516	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1517	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1518	elif [[ "$source_list" != "" && $restart_run != true ]]
1519	then
1520
1521	cd $source_path
1522
1523	for filename in $source_list
1524	do
1525
1526	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1527	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1528	then
1529	printf "\n +++ source code file: $filename"
1530	printf "\n must not contain (\"/\") "
1531	locat=source; exit
1532	fi
1533
1534	if [[ ! -f $filename ]]
1535	then
1536	printf "\n +++ source code file: $filename"
1537	printf "\n does not exist"
1538	locat=source; exit
1539	else
1540	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1541	fi
1542
1543	done
1544
1545	cd - > /dev/null
1546
1547	fi
1548
1549
1550	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1551	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1552	if [[ $restart_run != true ]]
1553	then
1554
1555	if [[ ! -f "$source_path/$mainprog" ]]
1556	then
1557	printf "\n\n +++ main program: $mainprog"
1558	printf "\n does not exist in source directory"
1559	printf "\n \"$source_path\"\n"
1560	locat=source; exit
1561	else
1562	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1563	then
1564	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1565	source_list=${mainprog}" $source_list"
1566	fi
1567	fi
1568	fi
1569
1570
1571	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1572	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1573	if [[ "$restart_run" != true ]]
1574	then
1575	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1576	if [[ ! -f $makefile ]]
1577	then
1578	printf "\n +++ file \"$makefile\" does not exist"
1579	locat=make; exit
1580	else
1581	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1582	fi
1583	fi
1584
1585
1586	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1587	if [[ $restart_run != true && "$add_source_path" != "" ]]
1588	then
1589
1590	# DOES THE DIRECTORY EXIST?
1591	if [[ ! -d $add_source_path ]]
1592	then
1593	printf "\n\n +++ WARNING: additional source code directory"
1594	printf "\n \"$add_source_path\" "
1595	printf "\n does not exist or is not a directory."
1596	printf "\n No source code will be used from this directory!\n"
1597	add_source_path=""
1598	if [[ $silent == false ]]
1599	then
1600	sleep 3
1601	fi
1602	else
1603
1604	cd $add_source_path
1605	found=false
1606
1607	Names=$(ls -1 *.f90 2>&1)
1608	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1609	Names=$(ls -1 *.F90 2>&1)
1610	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1611	Names=$(ls -1 *.F 2>&1)
1612	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1613	Names=$(ls -1 *.f 2>&1)
1614	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1615	Names=$(ls -1 *.c 2>&1)
1616	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1617
1618	cd - > /dev/null
1619	cd SOURCES_FOR_RUN_$fname
1620
1621	# COPY MAKEFILE IF EXISTING
1622	if [[ -f $add_source_path/Makefile ]]
1623	then
1624	printf "\n\n *** user Makefile from directory"
1625	printf "\n \"$add_source_path\" is used \n"
1626	if [[ $silent == false ]]
1627	then
1628	sleep 1
1629	fi
1630	cp $add_source_path/Makefile .
1631	fi
1632
1633	for dateiname in $AddFilenames
1634	do
1635	if [[ -f $dateiname ]]
1636	then
1637	printf "\n +++ source code file \"$dateiname\" found in additional"
1638	printf "\n source code directory \"$add_source_path\" "
1639	printf "\n but was also given with option \"-s\" which means that it should be taken"
1640	printf "\n from directory \"$source_path\"."
1641	locat=source; exit
1642	fi
1643
1644	cp $add_source_path/$dateiname .
1645	source_list="$source_list $dateiname"
1646
1647	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1648	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1649	then
1650	printf "\n\n +++ user file \"$dateiname\" "
1651	printf "\n is not listed in Makefile \n"
1652	locat=source; exit
1653	else
1654
1655	if [[ $found = false ]]
1656	then
1657	found=true
1658	printf "\n\n *** following user file(s) added to the"
1659	printf " files to be translated:\n "
1660	fi
1661	printf "$dateiname "
1662	if [[ $silent == false ]]
1663	then
1664	sleep 0.5
1665	fi
1666
1667	fi
1668	done
1669	[[ $found = true ]] && printf "\n"
1670	cd - > /dev/null
1671	fi
1672	fi
1673
1674
1675	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1676	# TO THE LIST OF FILES TO BE COMPILED
1677	if [[ $restart_run != true && -n $package_list ]]
1678	then
1679
1680	cd $source_path
1681
1682	for package in $package_list
1683	do
1684
1685	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1686
1687	# DETERMINE FILES BELONGING TO THE PACKAGE
1688	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1689	# THE NAME OF THE DIRECTORY
1690	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1691
1692
1693	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1694	# IF THEY ARE NOT ALREADY PART OF THE LIST
1695	for source_list_name in $package_source_list
1696	do
1697	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1698	then
1699
1700	# ONLY TAKE FILES WITH VALID SUFFIX
1701	ending=`echo $source_list_name \| cut -f2 -d.`
1702	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1703	then
1704	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1705	source_list="$source_list $source_list_name"
1706	fi
1707	fi
1708	done
1709	done
1710
1711	cd - > /dev/null
1712	fi
1713
1714	fi # do_compile=true
1715
1716
1717	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1718	# AND SET PRE-PROCESSOR DIRECTIVES
1719	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1720	then
1721
1722	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1723	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1724	then
1725	cpp_options="${cpp_options},-D__ibm=__ibm"
1726	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1727	then
1728	cpp_options="$cpp_options -D__nec"
1729	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1730	then
1731	cpp_options="$cpp_options -D__lc"
1732	else
1733	cpp_options="$cpp_options -D__$localhost"
1734	fi
1735
1736	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1737	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1738	then
1739	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1740	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1741	else
1742	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1743	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1744	fi
1745
1746	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1747	if [[ -n $package_list ]]
1748	then
1749	for package in $package_list
1750	do
1751	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1752	then
1753	if [[ $package != "dvrp_graphics+1PE" ]]
1754	then
1755	cpp_options="${cpp_options},-D__$package=__$package"
1756	else
1757	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1758	export use_seperate_pe_for_dvrp_output=true
1759	fi
1760	else
1761	if [[ $package != "dvrp_graphics+1PE" ]]
1762	then
1763	cpp_options="$cpp_options -D__$package"
1764	else
1765	cpp_options="$cpp_options -D__dvrp_graphics"
1766	export use_seperate_pe_for_dvrp_output=true
1767	fi
1768	fi
1769	done
1770	fi
1771
1772	# SET DIRECTIVES GIVEN BY OPTION -D
1773	if [[ -n $cpp_opts ]]
1774	then
1775	for popts in $cpp_opts
1776	do
1777	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1778	then
1779	cpp_options="${cpp_options},-D__$popts=__$popts"
1780	else
1781	cpp_options="$cpp_options -D__$popts"
1782	fi
1783	done
1784	fi
1785
1786	else
1787
1788
1789	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1790	if [[ $do_remote = false ]]
1791	then
1792	if [[ ! -f $executable ]]
1793	then
1794	printf "\n +++ executable file: $executable"
1795	printf "\n does not exist"
1796	locat=executable; exit
1797	fi
1798	fi
1799	fi
1800
1801
1802	# DETERMINE THE JOB MODE
1803	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1804	then
1805	if [[ "$LOADLBATCH" = yes ]]
1806	then
1807	batch_job=.TRUE.
1808	jobmo=BATCH
1809	else
1810	batch_job=.FALSE.
1811	jobmo=INTERACTIVE
1812	fi
1813	else
1814	if [[ "$ENVIRONMENT" = BATCH ]]
1815	then
1816	batch_job=.TRUE.
1817	jobmo=BATCH
1818	else
1819	batch_job=.FALSE.
1820	jobmo=INTERACTIVE
1821	fi
1822	fi
1823
1824	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1825	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1826	then
1827	printf "\n +++ no interactive runs allowed on host \"$host\" "
1828	printf "\n please submit batch job using mrun option \"-b\" \n"
1829	locat=normal; exit
1830	fi
1831
1832
1833	# CHECK, IF USER DEFINED A COMPILER
1834	if [[ "$compiler_name" = "" ]]
1835	then
1836
1837	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1838	locat=compiler_name; exit
1839
1840	fi
1841
1842
1843	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1844
1845	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1846	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1847	then
1848	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1849	if [[ "$kennung" = "" ]]
1850	then
1851	kennung=$RANDOM
1852	fi
1853	else
1854	kennung=$RANDOM
1855	fi
1856
1857	if [[ "$tmp_user_catalog" = "" ]]
1858	then
1859	if [[ $localhost = ibmh ]]
1860	then
1861	tmp_user_catalog=$SCRATCH
1862	elif [[ $localhost = nech ]]
1863	then
1864	tmp_user_catalog=$WRKSHR
1865	else
1866	tmp_user_catalog=/tmp
1867	fi
1868	fi
1869	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1870
1871
1872	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1873	if [[ "$tmp_data_catalog" = "" ]]
1874	then
1875	if [[ $localhost = nech ]]
1876	then
1877	tmp_data_catalog=$WRKSHR/mrun_restart_data
1878	else
1879	tmp_data_catalog=/tmp/mrun_restart_data
1880	fi
1881	fi
1882
1883
1884	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1885	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1886	then
1887	eval fopts=\"$fopts\"
1888	eval lopts=\"$lopts\"
1889	fi
1890
1891
1892
1893	# DETERMINE COMPILE- AND LINK-OPTIONS
1894	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1895	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1896	ROPTS="$ropts"
1897	# 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 ]]
1898	# then
1899	XOPT="-X $numprocs"
1900	# fi
1901
1902
1903
1904	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1905	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1906	done=false
1907	while [[ $done = false ]]
1908	do
1909	cputime=$cpumax
1910	if (( $cputime == 0 ))
1911	then
1912	if [[ $do_batch = true ]]
1913	then
1914	printf "\n +++ cpu-time is undefined"
1915	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1916	printf "\n >>> "
1917	read cputime 1>/dev/null 2>&1
1918	else
1919	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1920	fi
1921	else
1922	done=true
1923	fi
1924	cpumax=$cputime
1925	done
1926
1927	(( minuten = cputime / 60 ))
1928	(( sekunden = cputime - minuten * 60 ))
1929
1930
1931	# CHECK THE MEMORY DEMAND
1932	if [[ $do_batch = true ]]
1933	then
1934	done=false
1935	while [[ $done = false ]]
1936	do
1937	if (( memory == 0 ))
1938	then
1939	printf "\n +++ memory demand is undefined"
1940	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1941	printf "\n >>> "
1942	read memory 1>/dev/null 2>&1
1943	else
1944	done=true
1945	fi
1946	done
1947	fi
1948
1949
1950	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1951	if [[ $do_remote = true && -z $remote_username ]]
1952	then
1953	while [[ -z $remote_username ]]
1954	do
1955	printf "\n +++ username on remote host \"$host\" is undefined"
1956	printf "\n >>> Please type username:"
1957	printf "\n >>> "
1958	read remote_username
1959	done
1960	mc="$mc -u$remote_username"
1961	fi
1962
1963	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1964	if [[ "$login_init_cmd" != "" ]]
1965	then
1966	export init_cmds="${login_init_cmd};"
1967	fi
1968
1969
1970	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1971	if [[ "$modules" != "" ]]
1972	then
1973	if [[ $host = lctit ]]
1974	then
1975	export module_calls=". $modules"
1976	else
1977	export module_calls="module load ${modules};"
1978	fi
1979	fi
1980
1981	# OUTPUT OF THE MRUN-HEADER
1982	calltime=$(date)
1983	printf "\n"
1984	printf "#------------------------------------------------------------------------# \n"
1985	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1986	printf "\| \| \n"
1987	spalte1="called on:"; spalte2=$localhost_realname
1988	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1989	if [[ $do_remote = true ]]
1990	then
1991	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1992	else
1993	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1994	fi
1995	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1996	if [[ -n $numprocs ]]
1997	then
1998	if [[ $run_coupled_model = false ]]
1999	then
2000	spalte1="number of PEs:"; spalte2=$numprocs
2001	else
2002	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2003	fi
2004	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2005	fi
2006	if [[ -n $tasks_per_node ]]
2007	then
2008	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2009	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2010	if (( remaining_pes > 0 ))
2011	then
2012	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	fi
2015	fi
2016	if [[ $maximum_parallel_io_streams != $numprocs ]]
2017	then
2018	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2020	fi
2021	if [[ $use_openmp = true ]]
2022	then
2023	spalte1="threads per task:"; spalte2="$threads_per_task"
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	fi
2026	printf "\| \| \n"
2027	if [[ $do_compile = true ]]
2028	then
2029	if [[ "$mopts" != "" ]]
2030	then
2031	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033	zeile=$(echo "$mopts" \| cut -c46-)
2034	while [[ "$zeile" != "" ]]
2035	do
2036	spalte1=""
2037	spalte2=$(echo "$zeile" \| cut -c-45)
2038	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2039	zeile=$(echo "$zeile" \| cut -c46-)
2040	done
2041	fi
2042
2043	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	zeile=$(echo "$cpp_options" \| cut -c46-)
2046	while [[ "$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="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2055	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2056	zeile=$(echo "$fopts" \| 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 "$zeile" \| cut -c46-)
2063	done
2064
2065	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2066	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2067	zeile=$(echo "$lopts" \| cut -c46-)
2068	while [[ "$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="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2077	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2078	zeile=$(echo "$modules" \| cut -c46-)
2079	while [[ "$zeile" != "" ]]
2080	do
2081	spalte1=""
2082	spalte2=$(echo "$zeile" \| cut -c-45)
2083	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2084	zeile=$(echo "$zeile" \| cut -c46-)
2085	done
2086
2087	spalte1="main program:"; spalte2=$mainprog
2088	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2089	else
2090	spalte1=executable:; spalte2=$executable
2091	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2092	fi
2093	printf "\| \| \n"
2094	spalte1="base name of files:"; spalte2=$fname
2095	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2096	if [[ $fname != $afname ]]
2097	then
2098	spalte1="base name of input files:"; spalte2=$afname
2099	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2100	fi
2101	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2102	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2103	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2104	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2105
2106	if [[ "$ocean_file_appendix" = true ]]
2107	then
2108	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2109	fi
2110
2111	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2112	then
2113	spalte1="memory demand / PE":; spalte2="$memory MB"
2114	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2115	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2116	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2117	fi
2118
2119	if [[ $do_compile = true ]]
2120	then
2121	printf "\| \| \n"
2122	printf "\| Files to be compiled: \| \n"
2123	zeile=$source_list
2124	while [[ "$zeile" != "" ]]
2125	do
2126	linestart=$(echo $zeile \| cut -c-70)
2127	printf "\| %-70s \| \n" "$linestart"
2128	zeile=$(echo "$zeile" \| cut -c71-)
2129	done
2130	fi
2131	printf "#------------------------------------------------------------------------#"
2132
2133
2134
2135	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2136	if [[ $do_trace = true ]]
2137	then
2138	(( i = 0 ))
2139	while (( i < iin ))
2140	do
2141	(( i = i + 1 ))
2142	if (( i == 1 ))
2143	then
2144	printf "\n\n >>> INPUT-file assignments:\n"
2145	fi
2146	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2147	done
2148	(( i = 0 ))
2149	while (( i < iout ))
2150	do
2151	(( i = i + 1 ))
2152	if (( i == 1 ))
2153	then
2154	printf "\n\n >>> OUTPUT-file assignments:\n"
2155	fi
2156	printf "\n ${localout[$i]} : ${pathout[$i]}"
2157	done
2158	(( i = 0 ))
2159	while (( i < iic ))
2160	do
2161	(( i = i + 1 ))
2162	if (( i == 1 ))
2163	then
2164	printf "\n\n >>> INPUT-commands:\n"
2165	fi
2166	printf "\n ${in_command[$i]}"
2167	done
2168	(( i = 0 ))
2169	while (( i < ioc ))
2170	do
2171	(( i = i + 1 ))
2172	if (( i == 1 ))
2173	then
2174	printf "\n\n >>> OUTPUT-commands:\n"
2175	fi
2176	printf "\n ${out_command[$i]}"
2177	done
2178	fi
2179
2180	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2181	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2182	then
2183	antwort=dummy
2184	printf "\n\n"
2185	printf " >>> everything o.k. (y/n) ? "
2186	while read antwort
2187	do
2188	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2189	then
2190	printf " >>> everything o.k. (y/n) ? "
2191	else
2192	break
2193	fi
2194	done
2195	if [[ $antwort = n \|\| $antwort = N ]]
2196	then
2197	locat=user_abort; (( iec = 0 )); exit
2198	fi
2199	if [[ $do_batch = true ]]
2200	then
2201	printf " >>> batch-job will be created and submitted"
2202	else
2203	printf " >>> MRUN will now continue to execute on this machine"
2204	fi
2205	fi
2206
2207
2208	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2209	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2210	check_depository="${working_directory}/trunk/UTIL"
2211	check_sources="${working_directory}/tmp_check_namelist_files"
2212	skip_check=false
2213
2214	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2215	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2216	then
2217	skip_check=true
2218	reason="run on remote host or parameter file check has not been compiled."
2219	fi
2220	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2221	then
2222	skip_check=true
2223	reason="parameter file check has not been compiled."
2224	fi
2225
2226	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2227	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2228	then
2229	skip_check=true
2230	reason="serial run."
2231	fi
2232
2233	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2234	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2235	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2236	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2237	if [[ $check_namelist_files == false ]]
2238	then
2239	skip_check=true
2240	reason="-z option set."
2241	fi
2242
2243	if [[ $fromhost != $localhost ]]
2244	then
2245	skip_check=true
2246	reason="submitting host is local host."
2247	fi
2248
2249	if [[ $run_coupled_model == true ]]
2250	then
2251	skip_check=true
2252	reason="coupled run."
2253	fi
2254
2255	if [[ $restart_run == true ]]
2256	then
2257	skip_check=true
2258	reason="restart run."
2259	fi
2260
2261	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2262	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2263	last_char=`echo $filename_input \| cut -c $last_char_int`
2264	if [[ "$last_char" == "f" ]]
2265	then
2266	skip_check=true
2267	reason="restart run."
2268	fi
2269
2270	if [[ $skip_check == false ]]
2271	then
2272	tmp_check=${working_directory}/tmp_check
2273
2274	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2275	# NOT NECESSARILY REQUIRED
2276	line=""
2277	found=false
2278	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2279	while read line1
2280	do
2281	line="$line1"
2282	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2283	then
2284	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2285	found=true
2286	fi
2287	done < $tmp_check
2288
2289	if [[ $found = false ]]
2290	then
2291	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2292	fi
2293
2294	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2295	# NOT NECESSARILY REQUIRED
2296	line=""
2297	found=false
2298	grep "NUDGING_DATA" $config_file > $tmp_check
2299	while read line1
2300	do
2301	line="$line1"
2302	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2303	then
2304	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2305	found=true
2306	fi
2307	done < $tmp_check
2308
2309	if [[ $found = false ]]
2310	then
2311	printf "\n +++ no NUDGING list entry found in the configuration file."
2312	fi
2313
2314	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2315	# NOT NECESSARILY REQUIRED
2316	line=""
2317	found=false
2318	grep "LSF_DATA" $config_file > $tmp_check
2319	while read line1
2320	do
2321	line="$line1"
2322	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2323	then
2324	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2325	found=true
2326	fi
2327	done < $tmp_check
2328
2329	if [[ $found = false ]]
2330	then
2331	printf "\n +++ no LSF list entry found in the configuration file."
2332	fi
2333
2334	rm -rf ${working_directory}/tmp_check
2335
2336	# CHECK IF THE P3DF FILE MUST BE CHECKED
2337	for item in $input_list
2338	do
2339	if [[ "$item" == "restart" ]]
2340	then
2341	check_restart=1
2342	else
2343	check_restart=0
2344	fi
2345	done
2346
2347	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2348	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2349	then
2350	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2351	locat=check_namelist; exit
2352	fi
2353
2354	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2355	if [[ $check_restart == 1 ]]
2356	then
2357
2358	filenamef="${filename_input}f"
2359	if [[ ! -f $filenamef ]]
2360	then
2361	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2362	check_restart=0
2363	answer=dummy
2364	printf "\n\n"
2365
2366	if [[ $silent == false ]]
2367	then
2368	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2369	do
2370	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2371	read answer
2372	done
2373	if [[ $answer = a \|\| $answer = A ]]
2374	then
2375	printf "\n +++ Aborting...."
2376	locat=normal; exit
2377	fi
2378	fi
2379	else
2380	check_restart=1
2381	fi
2382	fi
2383
2384	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2385	mkdir $check_sources
2386	cd $check_sources
2387
2388
2389	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2390	if [[ -d $add_source_path ]]
2391	then
2392	printf "\n\n *** copying files from $check_depository"
2393	cp $check_depository/check_namelist_files.tar ./
2394
2395	printf "\n\n *** untar of makefile and source files in $check_sources"
2396	tar -xf check_namelist_files.tar > /dev/null 2>&1
2397
2398	printf "\n\n *** adding user code."
2399	cp $add_source_path/* ./
2400	touch check_namelist_files.f90
2401
2402	# GET COMPILER OPTIONS AND PERFORM MAKE
2403	printf "\n\n *** compiling code if necessary...\n"
2404
2405	# workaround for batch jobs on local machine (lcxe6)
2406	if [[ $do_batch == true && $do_remote == false ]]
2407	then
2408	eval $init_cmds
2409	fi
2410
2411	# GET CHECK OPTIONS
2412	line=""
2413	found=false
2414
2415	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2416
2417	while read line1
2418	do
2419
2420	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2421	then
2422	line="$line1"
2423	fi
2424
2425	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2426	then
2427	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2428	line="$line "
2429	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'`
2430	found=true
2431	fi
2432
2433	done < $tmp_check
2434	copts_check="$copts_check -D__check -D__parallel"
2435
2436	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2437
2438	# GET MAKE OUTPUT
2439	if [[ $? != 0 ]]
2440	then
2441	printf "\n +++ error during make."
2442	answer=dummy
2443	printf "\n\n"
2444	if [[ $silent == false ]]
2445	then
2446	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2447	do
2448	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2449	read answer
2450	done
2451	if [[ $answer = a \|\| $answer = A ]]
2452	then
2453	printf "\n +++ Aborting..."
2454	rm -rf $check_sources
2455	locat=normal; exit
2456	else
2457	skip_check=true
2458	fi
2459	else
2460	skip_check=true
2461	fi
2462	fi
2463	else
2464	cp $PALM_BIN/check_namelist_files.x ./
2465	fi
2466
2467	cp $filename_input ./PARIN
2468	if [[ $check_restart == 1 ]]
2469	then
2470	cp $filenamef ./PARINF
2471	fi
2472
2473	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2474	then
2475	printf "\n *** adding topography data"
2476	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2477
2478	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2479	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2480	# WHICH REQUIRE SUFFICIENT MEMORY
2481	ulimit -s unlimited
2482	fi
2483
2484	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2485	then
2486	printf "\n *** adding nudging data"
2487	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2488	fi
2489
2490	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2491	then
2492	printf "\n *** adding large scale forcing data"
2493	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2494	fi
2495
2496	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2497	cat > ENVPAR << %%END%%
2498	&envpar run_identifier = '$fname', host = '$host',
2499	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2500	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2501	maximum_cpu_time_allowed = ${cpumax}.,
2502	revision = '$global_revision',
2503	local_dvrserver_running = $local_dvrserver_running /
2504
2505	%%END%%
2506
2507	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2508	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2509	then
2510	printf "\n +++ WARNING: check_namelist_files.x not found."
2511	answer=dummy
2512	printf "\n\n"
2513
2514	if [[ $silent == false ]]
2515	then
2516	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2517	do
2518	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2519	read answer
2520	done
2521	if [[ $answer = a \|\| $answer = A ]]
2522	then
2523	printf "\n +++ Aborting..."
2524	rm -rf $check_sources
2525	locat=normal; exit
2526	else
2527	printf "\n *** skipping parameter file check."
2528	fi
2529	fi
2530
2531	elif [[ $skip_check == false ]]
2532	then
2533	# STARTING THE PARAMETER FILE CHECK
2534	printf "\n\n *** starting parameter file check..."
2535
2536	# CHECKING THE P3D FILE
2537	printf "\n\n (1) checking $filename_input"
2538	echo "$numprocs 0 0" > VARIN
2539	errors=`./check_namelist_files.x < VARIN 2>&1`
2540
2541	check_error=false
2542	if [[ "$errors" == "" ]]
2543	then
2544	printf " --> o.k."
2545	else
2546	printf " --> failed."
2547	check_error=true
2548	printf "\n\n $errors"
2549	fi
2550
2551	# CHECKING THE PD3F FILE IF NECESSARY
2552	if [[ $check_restart == 1 && $check_error == false ]]
2553	then
2554	printf "\n\n (2) checking $filenamef"
2555
2556	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2557	# IN &INIPAR LIST
2558	found=false
2559	cat PARINF \| while read line
2560	do
2561	line=$(echo $line\|sed 's/ //g')
2562	if [[ $line == "&inipar" ]]
2563	then
2564	start_search=true
2565	fi
2566
2567	if [[ $start_search == true ]]
2568	then
2569	if [[ $line == "initializing_actions='read_restart_data'" ]]
2570	then
2571	found=true
2572	break
2573	fi
2574	fi
2575
2576	if [[ $line == "/" ]]
2577	then
2578	start_search=false
2579	fi
2580
2581	done
2582
2583	if [[ $found = false ]]
2584	then
2585	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2586	printf "\n in &inipar list in $fname$p3df_suffix."
2587	rm -rf $check_sources
2588	locat=check_namelist; exit
2589	fi
2590
2591	# READ max_user_pr FROM FILES
2592	if [[ -f parin_for_check ]]
2593	then
2594	read max_pr_user < parin_for_check
2595	else
2596	max_user_pr=0
2597	fi
2598
2599	echo "$numprocs 1 $max_pr_user" > VARIN
2600	errors=`./check_namelist_files.x < VARIN 2>&1`
2601
2602	if [[ "$errors" == "" ]]
2603	then
2604	printf " --> o.k."
2605	else
2606	printf " --> failed."
2607	check_error=true
2608	printf "\n\n $errors"
2609	fi
2610	fi
2611
2612	# REPORT ERRORS AND CONTINUE/EXIT
2613	if [[ $check_error == true ]]
2614	then
2615	printf "\n +++ errors found in the parameter file!\n"
2616	answer=dummy
2617	printf "\n\n"
2618
2619	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2620	do
2621	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2622	read answer
2623	done
2624
2625	if [[ $answer = a \|\| $answer = A ]]
2626	then
2627	printf "\n +++ Aborting..."
2628	rm -rf $check_sources
2629	locat=normal; exit
2630	fi
2631	else
2632	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2633	fi
2634	rm -rf $check_sources
2635	fi
2636	else
2637	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2638	fi
2639
2640	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2641	rm -rf $check_sources
2642	cd $working_directory
2643
2644	# DETERMINE PATH FOR MAKE DEPOSITORY
2645	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2646	then
2647
2648	line=""
2649	grep "%depository_path" $config_file > tmp_mrun
2650	while read line
2651	do
2652	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2653	then
2654	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2655	then
2656	global_depository_path=`echo $line \| cut -d" " -s -f2`
2657	fi
2658	fi
2659	done < tmp_mrun
2660
2661	line=""
2662	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2663	while read line
2664	do
2665	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2666	then
2667	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2668	then
2669	local_depository_path=`echo $line \| cut -d" " -s -f2`
2670	fi
2671	fi
2672	done < tmp_mrun
2673
2674	if [[ "$local_depository_path" = "" ]]
2675	then
2676	if [[ "$global_depository_path" != "" ]]
2677	then
2678	local_depository_path=$global_depository_path
2679	else
2680	printf "\n\n +++ no depository path found in configuration file"
2681	printf "\n for local host \"$localhost\" "
2682	printf "\n please set \"\%depository_path\" in configuration file\n"
2683	locat=config_file; exit
2684	fi
2685	fi
2686	eval local_depository_path=$local_depository_path
2687	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2688	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2689
2690
2691	basename=`echo $mainprog \| cut -f1 -d"."`
2692	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2693	if [[ ! -f $make_depository ]]
2694	then
2695	printf "\n"
2696	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2697	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2698	fi
2699
2700	fi
2701
2702
2703	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2704	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2705	if [[ $do_batch = false ]]
2706	then
2707
2708
2709	# CREATE THE TEMPORARY WORKING DIRECTORY
2710	mkdir -p $TEMPDIR
2711	chmod go+rx $TEMPDIR
2712	tmpcreate=true
2713
2714
2715	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2716	# INTO THE TEMPORARY WORKING DIRECTORY
2717	if [[ $do_compile = true ]]
2718	then
2719
2720	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2721	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2722	if [[ $localhost = nech ]]
2723	then
2724	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2725	if mkdir -p $TEMPDIR_COMPILE
2726	then
2727	printf "\n *** \"$TEMPDIR_COMPILE\" "
2728	printf "\n is generated as temporary directory for cross compiling\n"
2729	else
2730	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2731	printf "\n needed for cross compilation failed"
2732	locat=compile
2733	exit
2734	fi
2735	else
2736	TEMPDIR_COMPILE=$TEMPDIR
2737	fi
2738
2739	cp $make_depository $TEMPDIR_COMPILE
2740	cd $TEMPDIR_COMPILE
2741	tar -xf $make_depository > /dev/null 2>&1
2742	cd - > /dev/null
2743
2744	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2745	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2746	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2747	then
2748	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2749	else
2750	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2751	fi
2752
2753	else
2754
2755	cp $executable ${TEMPDIR}/a.out
2756
2757	fi
2758
2759
2760	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2761	cd $TEMPDIR
2762	printf "\n *** changed to temporary directory: $TEMPDIR"
2763
2764
2765	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2766	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2767	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2768	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2769	(( i = 0 ))
2770	while (( i < iout ))
2771	do
2772	(( i = i + 1 ))
2773	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2774	then
2775	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2776	else
2777	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2778	fi
2779	done
2780
2781
2782	# IF REQUIRED, START WITH COMPILING
2783	if [[ $do_compile = true ]]
2784	then
2785
2786
2787	if [[ -f a.out ]]
2788	then
2789
2790	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2791	printf "\n\n\n *** executable a.out found"
2792	printf "\n no compilation required \n"
2793
2794	else
2795
2796	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2797	printf "\n\n\n *** compilation starts \n$dashes\n"
2798	printf " *** compilation with make using following options:\n"
2799	printf " make depository: $make_depository"
2800	if [[ "$mopts" != "" ]]
2801	then
2802	printf " make options: $mopts\n"
2803	fi
2804	printf " compilername: $compiler_name\n"
2805	printf " compiler options: $fopts\n"
2806	printf " preprocessor directives: $cpp_options \n"
2807	printf " linker options: $lopts \n"
2808	if [[ "$modules" != "" ]]
2809	then
2810	printf " modules to be load: $modules \n"
2811	fi
2812	printf " source code files: $source_list \n"
2813
2814	if [[ $localhost = nech ]]
2815	then
2816	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\" "
2817	cp $TEMPDIR_COMPILE/a.out .
2818	[[ $? != 0 ]] && compile_error=true
2819	rm -rf $TEMPDIR_COMPILE
2820	elif [[ $localhost = ibmh ]]
2821	then
2822	printf " compiler is called via ssh on \"plogin1\" \n"
2823	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\" "
2824	[[ ! -f a.out ]] && compile_error=true
2825	continue # STATUS=1, IF a.out EXISTS
2826	elif [[ $localhost = lcflow ]]
2827	then
2828	printf " compiler is called via ssh on \"flow\" \n"
2829	/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\" "
2830	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2831	[[ "$check_for_file" = "" ]] && compile_error=true
2832	continue # STATUS=1, IF a.out EXISTS
2833	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2834	then
2835	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2836	else
2837	[[ "$init_cmds" != "" ]] && eval $init_cmds
2838	[[ "$module_calls" != "" ]] && eval $module_calls
2839	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2840	fi
2841
2842	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2843	then
2844	printf "\n +++ error occured while compiling or linking"
2845	locat=compile
2846
2847	exit
2848	else
2849	printf "$dashes\n *** compilation finished \n"
2850	fi
2851
2852	fi
2853
2854	fi
2855
2856
2857	# PROVIDE THE INPUT FILES
2858	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2859	(( i = 0 ))
2860	while (( i < iin ))
2861	do
2862	(( i = i + 1 ))
2863	if (( i == 1 ))
2864	then
2865	printf "\n\n *** providing INPUT-files:\n$dashes"
2866	fi
2867
2868
2869	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2870	if [[ "${transin[$i]}" = unavailable ]]
2871	then
2872	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2873	then
2874	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2875	printf "\n is not available!"
2876	else
2877	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2878	printf "\n is not available!"
2879	fi
2880	continue
2881	fi
2882
2883	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2884	files_for_pes=false; datentyp=file
2885	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2886	then
2887	files_for_pes=true; datentyp=directory
2888	actionin[$i]=""
2889	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2890	then
2891	actionin[$i]=""
2892	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2893	then
2894	files_for_pes=true; datentyp=directory
2895	actionin[$i]="ar"
2896	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2897	then
2898	actionin[$i]="ar"
2899	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2900	then
2901	files_for_pes=true; datentyp=directory
2902	actionin[$i]="fl"
2903	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2904	then
2905	actionin[$i]="fl"
2906	fi
2907
2908	if [[ $files_for_pes = true ]]
2909	then
2910	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2911	else
2912	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2913	fi
2914
2915	# INPUT-FILE FOR A RESTART RUN.
2916	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2917	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2918	if [[ "${actionin[$i]}" = fl ]]
2919	then
2920	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2921	if [[ $files_for_pes = false ]]
2922	then
2923	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2924	then
2925	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2926	got_tmp[$i]=true
2927	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2928	then
2929	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2930	printf "\n *** trying to use backup copy in \"$WORK\" "
2931	cp $WORK/${frelin[$i]} ${localin[$i]}
2932	else
2933	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2934	printf "\n or \"$tmp_data_catalog\" does not exist!"
2935	printf "\n *** trying to get copy from archive"
2936	actionin[$i]=ar
2937	fi
2938	else
2939	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2940	then
2941	mkdir ${localin[$i]}
2942	cd $tmp_data_catalog/${frelin[$i]}
2943	for file in $(ls *)
2944	do
2945	ln $file $TEMPDIR/${localin[$i]}
2946	done
2947	cd $TEMPDIR
2948	got_tmp[$i]=true
2949	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2950	then
2951	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2952	printf "\n *** trying to use backup copy in \"$WORK\" "
2953	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2954	else
2955	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2956	printf "\n or \"$tmp_data_catalog\" does not exist!"
2957	printf "\n *** trying to get copy from archive"
2958	actionin[$i]=ar
2959	fi
2960	fi
2961	fi
2962
2963
2964	# FILE IS STORED ON THE ARCHIVE SYSTEM
2965	if [[ "${actionin[$i]}" = ar ]]
2966	then
2967
2968	if [[ $files_for_pes = false ]]
2969	then
2970	printf "\n file will be restored from archive-system ($archive_system)!"
2971	else
2972	printf "\n directory will be restored from archive-system ($archive_system)!"
2973	fi
2974
2975	file_restored=false
2976
2977	if [[ $archive_system = asterix ]]
2978	then
2979	do_stagein=true
2980	(( stagein_anz = 0 ))
2981	while [[ $do_stagein = true ]]
2982	do
2983	if [[ $files_for_pes = false ]]
2984	then
2985	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2986	else
2987	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2988	fi
2989	cat STAGEIN_OUTPUT
2990	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2991	then
2992	file_restored=true
2993	do_stagein=false
2994	else
2995	(( stagein_anz = stagein_anz + 1 ))
2996	if (( stagein_anz == 10 ))
2997	then
2998	printf "\n +++ stagein stoped after 10 tries"
2999	locat=stage
3000	exit
3001	fi
3002	printf "\n +++ restoring from archive failed, trying again:"
3003	sleep 900
3004	fi
3005	done
3006	elif [[ $archive_system = DMF ]]
3007	then
3008	if [[ $files_for_pes = false ]]
3009	then
3010	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3011	locat=DMF
3012	exit
3013	else
3014	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3015	cp -r $ARCHIVE/${frelin[$i]} $PWD
3016	file_restored=true
3017	fi
3018	elif [[ $archive_system = tivoli ]]
3019	then
3020	if [[ $files_for_pes = false ]]
3021	then
3022	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3023	else
3024	(( inode = 0 ))
3025	while (( inode < nodes ))
3026	do
3027	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3028	(( inode = inode + 1 ))
3029	done
3030	fi
3031	file_restored=true
3032	elif [[ $archive_system = ut ]]
3033	then
3034	if [[ $files_for_pes = false ]]
3035	then
3036	cp $UT/${frelin[$i]} .
3037	else
3038	(( inode = 0 ))
3039	while (( inode < nodes ))
3040	do
3041	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3042	(( inode = inode + 1 ))
3043	done
3044	fi
3045	file_restored=true
3046	else
3047	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3048	locat=rearchive
3049	exit
3050	fi
3051
3052	if [[ $file_restored = true ]]
3053	then
3054
3055	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3056	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3057	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3058	if [[ $files_for_pes = false ]]
3059	then
3060	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3061	else
3062	mkdir $tmp_data_catalog/${frelin[$i]}
3063	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3064	fi
3065	got_tmp[$i]=true
3066
3067	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3068	mv ${frelin[$i]} ${localin[$i]}
3069
3070	fi
3071	fi
3072
3073
3074	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3075	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3076	then
3077
3078	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3079	then
3080
3081	# FILE COPIES ARE PROVIDED FOR ALL CORES
3082	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3083	printf "\n file will be provided for $numprocs processors"
3084	mkdir ${localin[$i]}
3085	ival=$numprocs
3086	(( ii = 0 ))
3087	while (( ii <= ival-1 ))
3088	do
3089	if (( ii < 10 ))
3090	then
3091	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3092	elif (( ii < 100 ))
3093	then
3094	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3095	elif (( ii < 1000 ))
3096	then
3097	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3098	else
3099	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3100	fi
3101	(( ii = ii + 1 ))
3102	done
3103
3104	else
3105
3106	if [[ $files_for_pes = true ]]
3107	then
3108
3109	# PROVIDE FILES FOR EACH CORE
3110	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3111	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3112	printf "\n providing $numprocs files for the respective processors"
3113	mkdir ${localin[$i]}
3114	if [[ $link_local_input = true ]]
3115	then
3116	printf " using ln -f\n"
3117	cd ${absnamein[$i]}
3118	for file in $(ls *)
3119	do
3120	ln -f $file ${localin[$i]}
3121	done
3122	cd $TEMPDIR
3123	fi
3124
3125	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3126	if [[ ! -f "${localin[$i]}/_0000" ]]
3127	then
3128	if [[ $link_local_input = true ]]
3129	then
3130	printf " ln failed for .../_0000, using cp...\n"
3131	fi
3132	cp -r ${absnamein[$i]}/* ${localin[$i]}
3133	fi
3134
3135	else
3136
3137	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3138	if [[ $link_local_input = true ]]
3139	then
3140	printf " using ln -f\n"
3141	ln -f ${absnamein[$i]} ${localin[$i]}
3142	fi
3143	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3144	if [[ ! -f "${localin[$i]}" ]]
3145	then
3146	if [[ $link_local_input = true ]]
3147	then
3148	printf " ln failed, using cp...\n"
3149	fi
3150	cp ${absnamein[$i]} ${localin[$i]}
3151	fi
3152	fi
3153	fi
3154	fi
3155
3156	done
3157	if (( i != 0 ))
3158	then
3159	printf "\n$dashes\n *** all INPUT-files provided \n"
3160	fi
3161
3162
3163	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3164	(( i = 0 ))
3165	while (( i < iic ))
3166	do
3167	(( i = i + 1 ))
3168	if (( i == 1 ))
3169	then
3170	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3171	fi
3172	printf "\n >>> ${in_command[$i]}"
3173	eval ${in_command[$i]}
3174	if (( i == iic ))
3175	then
3176	printf "\n$dashes\n"
3177	fi
3178	done
3179
3180
3181	# SET THE REMAINING CPU-TIME
3182	cpurest=${cpumax}.
3183
3184
3185	# START DVR STREAMING SERVER
3186	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3187	then
3188	if [[ "$dvr_server" != "" ]]
3189	then
3190
3191	printf "\n\n *** preparing the dvr streaming server configuration file"
3192
3193	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3194	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3195	if [[ "$running_dvrserver_id" != "" ]]
3196	then
3197
3198	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3199	printf "\n This server is used instead starting a new one!"
3200	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3201
3202	else
3203
3204	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3205	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3206	then
3207	cp ${PALM_BIN}/.dvrserver.config .
3208
3209	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3210	user_id=`id -u`
3211	group_id=`id -g`
3212
3213	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3214	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3215	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3216	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3217	mv .dvrserver.3 .dvrserver.config
3218	rm .dvrserver.1 .dvrserver.2
3219
3220	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3221	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3222	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3223	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3224	local_dvrserver_running=.TRUE.
3225	else
3226	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3227	printf "\n \"$PALM_BIN\" "
3228	locat=dvr
3229	exit
3230	fi
3231
3232	fi
3233
3234	else
3235	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3236	fi
3237	fi
3238
3239
3240	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3241	# (FILE ENVPAR WILL BE READ BY PALM)
3242	cat > ENVPAR << %%END%%
3243	&envpar run_identifier = '$fname', host = '$localhost',
3244	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3245	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3246	maximum_cpu_time_allowed = ${cpumax}.,
3247	revision = '$global_revision',
3248	local_dvrserver_running = $local_dvrserver_running,
3249	batch_job = $batch_job /
3250
3251	%%END%%
3252
3253
3254	# STARTING THE EXECUTABLE
3255	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3256	PATH=$PATH:$TEMPDIR
3257
3258	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3259	if [[ "$mpi_debug" = true ]]
3260	then
3261	export MPI_CHECK_ARGS=1
3262	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3263	fi
3264
3265	if [[ "$totalview" = true ]]
3266	then
3267	printf "\n *** totalview debugger will be used"
3268	tv_opt="-tv"
3269	else
3270	tv_opt=""
3271	fi
3272
3273	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3274	then
3275
3276	#Interactive ALLINEA DEBUG seesion
3277	if [[ "$ENVIRONMENT" != BATCH ]]
3278	then
3279	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3280	then
3281	if [[ "$allinea" = true ]]
3282	then
3283	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3284
3285	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3286	wait
3287	fi
3288	fi
3289	fi
3290
3291	if [[ "$ENVIRONMENT" = BATCH ]]
3292	then
3293	continue
3294	fi
3295	if [[ $localhost = ibmh ]]
3296	then
3297
3298	# SETUP THE IBM MPI ENVIRONMENT
3299	export MP_SHARED_MEMORY=yes
3300	export AIXTHREADS_SCOPE=S
3301	export OMP_NUM_THREADS=$threads_per_task
3302	export AUTHSTATE=files
3303	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3304
3305	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3306	export MP_ADAPTER_USE=shared
3307	export MP_CPU_USE=multiple
3308	export MP_TIMEOUT=1200
3309
3310	unset MP_TASK_AFFINITY
3311
3312	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3313	#(( ii = 1 ))
3314	#while (( ii <= $numprocs ))
3315	#do
3316	# echo $localhost_realname >> hostfile
3317	# (( ii = ii + 1 ))
3318	#done
3319	#export MP_HOSTFILE=hostfile
3320
3321	if [[ "$LOADLBATCH" = yes ]]
3322	then
3323	totalview poe a.out $ROPTS
3324	else
3325	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3326	export TVDSVRLAUNCHCMD=ssh
3327	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3328	fi
3329
3330	fi # END DEBUG MODE
3331
3332	else
3333
3334	# NORMAL EXECUTION
3335	if [[ -n $numprocs ]]
3336	then
3337
3338	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3339	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3340	then
3341
3342	# SETUP THE IBM MPI ENVIRONMENT
3343	if [[ $host != ibmh && $host != ibmkisti ]]
3344	then
3345	export MP_SHARED_MEMORY=yes
3346	export AIXTHREAD_SCOPE=S
3347	export OMP_NUM_THREADS=$threads_per_task
3348	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3349	export AUTHSTATE=files
3350	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3351	# export MP_PRINTENV=yes
3352
3353	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3354	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3355	export MP_WAIT_MODE=poll
3356	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3357	fi
3358
3359	if [[ $host = ibmkisti ]]
3360	then
3361	export LANG=en_US
3362	export MP_SHARED_MEMORY=yes
3363	if [[ $threads_per_task = 1 ]]
3364	then
3365	export MP_SINGLE_THREAD=yes
3366	export MEMORY_AFFINITY=MCM
3367	else
3368	export OMP_NUM_THREADS=$threads_per_task
3369	fi
3370	fi
3371
3372	if [[ "$LOADLBATCH" = yes ]]
3373	then
3374	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3375	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3376	then
3377	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3378	else
3379	if [[ $run_coupled_model = false ]]
3380	then
3381	if [[ "$ocean_file_appendix" = true ]]
3382	then
3383	echo "precursor_ocean" > runfile_atmos
3384	else
3385	echo "precursor_atmos" > runfile_atmos
3386	fi
3387	else
3388	(( iia = $numprocs_atmos / $threads_per_task ))
3389	(( iio = $numprocs_ocean / $threads_per_task ))
3390	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3391	printf "\n using $coupled_mode coupling"
3392	printf "\n\n"
3393	echo "coupled_run $iia $iio" > runfile_atmos
3394	fi
3395	poe ./a.out $ROPTS < runfile_atmos
3396	fi
3397	else
3398	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3399	then
3400	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3401	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3402	then
3403	if [[ -f $hostfile ]]
3404	then
3405	cp $hostfile hostfile
3406	else
3407	(( ii = 1 ))
3408	while (( ii <= $numprocs ))
3409	do
3410	echo $localhost_realname >> hostfile
3411	(( ii = ii + 1 ))
3412	done
3413	fi
3414	export MP_HOSTFILE=hostfile
3415	if [[ $run_coupled_model = false ]]
3416	then
3417	if [[ "$ocean_file_appendix" = true ]]
3418	then
3419	echo "precursor_ocean" > runfile_atmos
3420	else
3421	echo "precursor_atmos" > runfile_atmos
3422	fi
3423	else
3424	(( iia = $numprocs_atmos / $threads_per_task ))
3425	(( iio = $numprocs_ocean / $threads_per_task ))
3426	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3427	printf "\n using $coupled_mode coupling"
3428	printf "\n\n"
3429	echo "coupled_run $iia $iio" > runfile_atmos
3430	fi
3431
3432	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3433
3434	else
3435	if [[ "$host_file" = "" ]]
3436	then
3437	printf "\n +++ no hostfile given in configuration file"
3438	locat=config_file
3439	exit
3440	else
3441	eval host_file=$host_file
3442	fi
3443	export MP_HOSTFILE=$host_file
3444	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3445	fi
3446	fi
3447	elif [[ $host = nech ]]
3448	then
3449	(( ii = nodes ))
3450	if [[ $ii = 1 ]]
3451	then
3452	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3453	export MPIPROGINF=YES
3454	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3455	echo "*** execution on single node with mpirun"
3456	mpirun -np $numprocs ./a.out $ROPTS
3457	else
3458	(( i = 0 ))
3459	while (( i < ii ))
3460	do
3461	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3462	(( i = i + 1 ))
3463	done
3464
3465	echo "#!/bin/sh" > mpi_exec_shell
3466	echo " " >> mpi_exec_shell
3467	echo "set -u" >> mpi_exec_shell
3468	echo "F_ERRCNT=0" >> mpi_exec_shell
3469	echo "MPIPROGINV=YES" >> mpi_exec_shell
3470	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3471	echo "cpurest=$cpurest" >> mpi_exec_shell
3472	echo "fname=$fname" >> mpi_exec_shell
3473	echo "localhost=$localhost" >> mpi_exec_shell
3474	echo "return_address=$return_address" >> mpi_exec_shell
3475	echo "return_username=$return_username" >> mpi_exec_shell
3476	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3477	echo "write_binary=$write_binary" >> mpi_exec_shell
3478	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3479	echo " " >> mpi_exec_shell
3480	echo "export F_ERRCNT" >> mpi_exec_shell
3481	echo "export MPIPROGINV" >> mpi_exec_shell
3482	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3483	echo "export cpurest" >> mpi_exec_shell
3484	echo "export fname" >> mpi_exec_shell
3485	echo "export localhost" >> mpi_exec_shell
3486	echo "export return_address" >> mpi_exec_shell
3487	echo "export return_username" >> mpi_exec_shell
3488	echo "export tasks_per_node" >> mpi_exec_shell
3489	echo "export write_binary" >> mpi_exec_shell
3490	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3491	echo " " >> mpi_exec_shell
3492	echo "exec ./a.out" >> mpi_exec_shell
3493
3494	chmod u+x mpi_exec_shell
3495	export MPIPROGINF=YES
3496	mpirun -f multinode_config &
3497	wait
3498
3499	fi
3500	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3501	then
3502
3503	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3504	# DOES NOT EXIST
3505	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3506
3507	then
3508	if [[ -f $hostfile ]]
3509	then
3510	cp $hostfile hostfile
3511	(( ii = $numprocs / $threads_per_task ))
3512	[[ $ii = 0 ]] && (( ii = 1 ))
3513	else
3514	(( ii = 1 ))
3515	while (( ii <= $numprocs / $threads_per_task ))
3516	do
3517	echo $localhost_realname >> hostfile
3518	(( ii = ii + 1 ))
3519	done
3520	if (( $numprocs / $threads_per_task == 0 ))
3521	then
3522	echo $localhost_realname >> hostfile
3523	fi
3524	fi
3525	eval zeile=\"`head -n $ii hostfile`\"
3526	printf "\n *** running on: $zeile"
3527	fi
3528
3529	(( ii = $numprocs / $threads_per_task ))
3530	[[ $ii = 0 ]] && (( ii = 1 ))
3531	export OMP_NUM_THREADS=$threads_per_task
3532
3533	if [[ $threads_per_task != 1 ]]
3534	then
3535	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3536	# MAY ABORT
3537	ulimit -s unlimited
3538	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3539	fi
3540	if [[ $run_coupled_model = false ]]
3541	then
3542	if [[ "$ocean_file_appendix" = true ]]
3543	then
3544	echo "precursor_ocean" > runfile_atmos
3545	else
3546	echo "precursor_atmos" > runfile_atmos
3547	fi
3548	printf "\n\n"
3549
3550	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3551	then
3552	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3553	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3554	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3555
3556	elif [[ $host = lcbullhh ]]
3557	then
3558	export OMPI_MCA_pml=cm
3559	export OMPI_MCA_mtl=mxm
3560	export OMPI_MCA_coll=^ghc
3561	export OMPI_MCA_mtl_mxm_np=0
3562	export MXM_RDMA_PORTS=mlx5_0:1
3563	export MXM_LOG_LEVEL=ERROR
3564	export OMP_NUM_THREADS=$threads_per_task
3565	export KMP_AFFINITY=verbose,granularity=core,compact,1
3566	export KMP_STACKSIZE=64m
3567
3568	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out
3569
3570	elif [[ $host = lccrayf ]]
3571	then
3572	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3573	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3574	then
3575	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3576	elif [[ $host = lcflow ]]
3577	then
3578	mpirun -np $ii a.out < runfile_atmos $ROPTS
3579	elif [[ $host = lcsb ]]
3580	then
3581	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3582	elif [[ $host = lckiaps ]]
3583	then
3584	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3585	elif [[ $host = lckyu* ]]
3586	then
3587	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3588	else
3589	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3590	fi
3591	else
3592
3593	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3594	(( iia = $numprocs_atmos / $threads_per_task ))
3595	(( iio = $numprocs_ocean / $threads_per_task ))
3596	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3597	printf "\n using $coupled_mode coupling"
3598	printf "\n\n"
3599
3600	if [[ $coupled_mode = "mpi2" ]]
3601	then
3602	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3603	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3604
3605	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3606	then
3607
3608	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3609	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3610
3611	else
3612	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3613	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3614	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3615	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3616	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3617	fi
3618	wait
3619
3620	else
3621
3622	echo "coupled_run $iia $iio" > runfile_atmos
3623
3624	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3625	then
3626
3627	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3628
3629	elif [[ $host = lck \|\| $host = lckordi ]]
3630	then
3631
3632	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3633
3634	elif [[ $host = lckyu* ]]
3635	then
3636
3637	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3638
3639	elif [[ $host = lcmuk ]]
3640	then
3641
3642	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3643
3644	fi
3645	wait
3646	fi
3647
3648	fi
3649
3650	elif [[ $host = lckyoto ]]
3651	then
3652	set -xv
3653	export P4_RSHCOMMAND=plesh
3654	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3655	if [[ "$ENVIRONMENT" = BATCH ]]
3656	then
3657	if [[ "$cond2" = fujitsu ]]
3658	then
3659	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3660	elif [[ "cond2" = pgi ]]
3661	then
3662	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3663	else
3664	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3665	fi
3666	else
3667	if [[ "$cond2" = "" ]]
3668	then
3669	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3670	else
3671	mpirun -np $numprocs ./a.out $ROPTS
3672	fi
3673	fi
3674	set +xv
3675
3676	elif [[ $host = lctit ]]
3677	then
3678	export OMP_NUM_THREADS=$threads_per_task
3679	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3680	if [[ "$threads_per_task" != 1 ]]
3681	then
3682	export MV2_ENABLE_AFFINITY=0
3683	fi
3684	echo "----- PBS_NODEFILE content:"
3685	cat $PBS_NODEFILE
3686	echo "-----"
3687	(( ii = $numprocs / $threads_per_task ))
3688	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3689	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3690
3691	else
3692	mpprun -n $numprocs a.out $ROPTS
3693	fi
3694	else
3695	a.out $ROPTS
3696	fi
3697	fi
3698
3699	if [[ $? != 0 ]]
3700	then
3701
3702	# ABORT IN CASE OF RUNTIME ERRORS
3703	printf "\n +++ runtime error occured"
3704	locat=execution
3705	exit
3706
3707	else
3708
3709	printf "\n$dashes\n *** execution finished \n"
3710
3711	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3712	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3713	if [[ "$dvrserver_id" != "" ]]
3714	then
3715	kill $dvrserver_id
3716	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3717
3718	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3719	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3720	if [[ -d DATA_DVR ]]
3721	then
3722
3723	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3724	# DIRECTORY
3725	cp .dvrserver.config DATA_DVR
3726
3727	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3728	# SEQUENCE MODE DATA TOO)
3729	process_dvr_output -d DATA_DVR -f $fname -s
3730
3731	else
3732
3733	# PROCESS THE LOCAL OUTPUT
3734	process_dvr_output -l -d DATA_DVR -f $fname
3735
3736	fi
3737
3738	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3739	then
3740
3741	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3742	process_dvr_output -l -d DATA_DVR -f $fname
3743
3744	fi
3745	fi
3746
3747
3748
3749	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3750	# BY EACH CORE INTO ONE FILE
3751	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3752	then
3753	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3754	printf "\n 2d- and/or 3d-data may be incomplete!"
3755	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3756	elif [[ "$combine_plot_fields" == true ]]
3757	then
3758	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3759	then
3760	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3761	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3762	else
3763	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3764	combine_plot_fields${block}.x
3765	fi
3766	else
3767
3768	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3769	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3770	# ??? koennen wir das streichen ???
3771	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3772	fi
3773
3774
3775
3776	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3777	(( i = 0 ))
3778	while (( i < ioc ))
3779	do
3780	(( i = i + 1 ))
3781	if (( i == 1 ))
3782	then
3783	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3784	fi
3785	printf "\n >>> ${out_command[$i]}"
3786	eval ${out_command[$i]}
3787	if (( i == ioc ))
3788	then
3789	printf "\n$dashes\n"
3790	fi
3791	done
3792
3793
3794	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3795	if [[ $do_trace = true ]]
3796	then
3797	printf "\n\n"
3798	ls -al
3799	fi
3800
3801
3802
3803	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3804	(( i = 0 ))
3805	while (( i < iout ))
3806	do
3807	(( i = i + 1 ))
3808	if (( i == 1 ))
3809	then
3810	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3811	fi
3812
3813	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3814	files_for_pes=false; filetyp=file
3815	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3816	then
3817	files_for_pes=true; filetyp=directory
3818	actionout[$i]=""
3819	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3820	then
3821	actionout[$i]=""
3822	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3823	then
3824	files_for_pes=true; filetyp=directory
3825	actionout[$i]="ar"
3826	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3827	then
3828	actionout[$i]="ar"
3829	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3830	then
3831	files_for_pes=true; filetyp=directory
3832	actionout[$i]="fl"
3833	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3834	then
3835	actionout[$i]="fl"
3836	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3837	then
3838	files_for_pes=true; filetyp=directory
3839	actionout[$i]="tr"
3840	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3841	then
3842	actionout[$i]="tr"
3843	fi
3844
3845	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3846	then
3847	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3848	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3849	then
3850	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3851	else
3852
3853
3854	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3855	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3856	if [[ "${actionout[$i]}" = tr ]]
3857	then
3858	if [[ $localhost != $fromhost ]]
3859	then
3860	if [[ $files_for_pes = false ]]
3861	then
3862	cps=""
3863	cst=""
3864	else
3865	cps=-c
3866	cst="/"
3867	fi
3868	if [[ $localhost = nech ]]
3869	then
3870
3871	# TRANSFER IN SEPERATE JOB
3872	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3873	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3874	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3875	if [[ $files_for_pes = false ]]
3876	then
3877	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3878	else
3879	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3880	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3881	fi
3882
3883	echo "set -x" > transfer_${localout[$i]}
3884	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3885
3886	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3887	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3888	printf "\n or higher cycle\n"
3889	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]}
3890
3891	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3892
3893	if [[ $localhost = nech ]]
3894	then
3895	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3896	else
3897	if [[ "$LOGNAME" = b323013 ]]
3898	then
3899	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3900	else
3901	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3902	fi
3903	fi
3904
3905	else
3906
3907	# TRANSFER WITHIN THIS JOB
3908	transfer_failed=false
3909	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3910	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3911	if [[ $localhost = lccrayb ]]
3912	then
3913	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]}"
3914	elif [[ $localhost = lccrayh ]]
3915	then
3916	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]}"
3917	elif [[ $localhost = lcbullhh ]]
3918	then
3919	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]}"
3920	elif [[ $localhost = lcxe6 ]]
3921	then
3922	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]}"
3923	else
3924	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3925	fi
3926	[[ $? != 0 ]] && transfer_failed=true
3927
3928	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3929	if [[ $transfer_failed = true ]]
3930	then
3931	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3932	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3933
3934	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3935	eval local_catalog=${pathout[$i]}
3936	if [[ ! -d $local_catalog ]]
3937	then
3938	printf " *** local directory does not exist. Trying to create:\n"
3939	printf " $local_catalog \n"
3940	mkdir -p $local_catalog
3941	fi
3942	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3943	transfer_problems=true
3944	fi
3945	fi
3946	else
3947
3948	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3949	actionout[$i]=""
3950	fi
3951	fi
3952
3953
3954	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3955	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3956	if [[ "${actionout[$i]}" = tra ]]
3957	then
3958	if [[ $localhost != $fromhost ]]
3959	then
3960	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3961	then
3962
3963	# TRANSFER IN SEPERATE JOB
3964	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3965	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3966	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3967	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3968
3969	echo "set -x" > transfer_${localout[$i]}
3970	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3971
3972	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3973	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3974	printf "\n or higher cycle\n"
3975	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]}
3976
3977	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3978
3979	if [[ $localhost = nech ]]
3980	then
3981	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3982	else
3983	if [[ $LOGNAME = b323013 ]]
3984	then
3985	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3986	else
3987	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3988	fi
3989	fi
3990
3991	else
3992
3993	# TRANSFER WITHIN THIS JOB
3994	transfer_failed=false
3995	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3996	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3997	if [[ $localhost = lccrayb ]]
3998	then
3999	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]}"
4000	elif [[ $localhost = lccrayh ]]
4001	then
4002	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]}"
4003	elif [[ $localhost = lcxe6 ]]
4004	then
4005	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]}"
4006	else
4007	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
4008	fi
4009	[[ $? != 0 ]] && transfer_failed=true
4010
4011	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
4012	if [[ $transfer_failed = true ]]
4013	then
4014	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4015	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4016
4017	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4018	eval local_catalog=${pathout[$i]}
4019	if [[ ! -d $local_catalog ]]
4020	then
4021	printf " *** local directory does not exist. Trying to create:\n"
4022	printf " $local_catalog \n"
4023	mkdir -p $local_catalog
4024	fi
4025
4026	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4027	transfer_problems=true
4028	fi
4029	fi
4030	else
4031
4032	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4033	actionout[$i]=a
4034	fi
4035	fi
4036
4037
4038	# OUTPUT-FILE FOR A RESTART-RUN.
4039	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4040	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4041	# AS LAST ACTION, ARCHIVING IS INITIATED.
4042	if [[ "${actionout[$i]}" = fl ]]
4043	then
4044	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4045	chmod g+rx $tmp_data_catalog
4046	if [[ $files_for_pes = false ]]
4047	then
4048	printf "\n >>> OUTPUT: ${localout[$i]} to"
4049	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4050	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4051	else
4052	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4053	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4054	mkdir $tmp_data_catalog/${frelout[$i]}
4055	cd ${localout[$i]}
4056	for file in $(ls *)
4057	do
4058	ln -f $file $tmp_data_catalog/${frelout[$i]}
4059	done
4060	cd $TEMPDIR
4061	fi
4062
4063
4064	# CREATE AND SUBMIT ARCHIVING-JOB
4065	if [[ $store_on_archive_system = true ]]
4066	then
4067
4068	if [[ $archive_system = asterix ]]
4069	then
4070	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4071	if [[ $files_for_pes = false ]]
4072	then
4073	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4074	else
4075	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4076	fi
4077	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4078	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4079	echo "then" >> archive_${frelout[$i]}
4080	echo " do_stageout=false" >> archive_${frelout[$i]}
4081	echo "else" >> archive_${frelout[$i]}
4082	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4083	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4084	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4085	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4086	if [[ $files_for_pes = false ]]
4087	then
4088	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4089	else
4090	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4091	fi
4092	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4093	echo "fi" >> archive_${frelout[$i]}
4094	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4095	elif [[ $archive_system = DMF ]]
4096	then
4097	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4098	if [[ $files_for_pes = false ]]
4099	then
4100	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4101	locat=DMF
4102	exit
4103	else
4104	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4105	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4106	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4107	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4108	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4109	fi
4110	elif [[ $archive_system = tivoli ]]
4111	then
4112	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4113	if [[ $files_for_pes = false ]]
4114	then
4115	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4116	echo "set -x" >> archive_${frelout[$i]}
4117	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4118	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4119	else
4120
4121	echo "set -x" >> archive_${frelout[$i]}
4122	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4123	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4124	cd $tmp_data_catalog
4125	all_files=`ls -1 ${frelout[$i]}/*`
4126	cd - > /dev/null
4127	(( inode = 0 ))
4128	(( tp1 = tasks_per_node + 1 ))
4129	while (( inode < nodes ))
4130	do
4131	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4132	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4133	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4134	(( inode = inode + 1 ))
4135	done
4136	fi
4137	elif [[ $archive_system = ut ]]
4138	then
4139	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4140	if [[ $files_for_pes = false ]]
4141	then
4142	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4143	echo "set -x" >> archive_${frelout[$i]}
4144	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4145	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4146	else
4147
4148	echo "set -x" >> archive_${frelout[$i]}
4149	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4150	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4151	cd $tmp_data_catalog
4152	all_files=`ls -1 ${frelout[$i]}/*`
4153	cd - > /dev/null
4154	(( inode = 0 ))
4155	(( tp1 = tasks_per_node + 1 ))
4156	while (( inode < nodes ))
4157	do
4158	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4159	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4160	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4161	(( inode = inode + 1 ))
4162	done
4163	fi
4164	elif [[ $archive_system = none ]]
4165	then
4166	printf " +++ archiving on $localhost not available!\n"
4167	fi
4168
4169	if [[ $archive_system != none ]]
4170	then
4171	if [[ $localhost = nech ]]
4172	then
4173	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4174	fi
4175	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4176	fi
4177	else
4178	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4179	fi
4180
4181
4182	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4183	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4184	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4185	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4186	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4187	if [[ $files_for_pes = false ]]
4188	then
4189	cat /dev/null > ${pathout[$i]}
4190	else
4191	mkdir -p ${pathout[$i]}
4192	fi
4193
4194	fi
4195
4196
4197	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4198	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4199	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4200	if [[ "${actionout[$i]}" = ar ]]
4201	then
4202	if [[ $files_for_pes = false ]]
4203	then
4204	printf "\n >>> OUTPUT: ${localout[$i]} to"
4205	printf "\n ${pathout[$i]}"
4206	printf "\n File will be copied to archive-system ($archive_system) !\n"
4207	else
4208	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4209	printf "\n ${pathout[$i]}"
4210	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4211	fi
4212	mv ${localout[$i]} ${frelout[$i]}
4213
4214	file_saved=false
4215
4216	if [[ $archive_system = asterix ]]
4217	then
4218	do_stageout=true
4219	(( stageout_anz = 0 ))
4220	while [[ $do_stageout = true ]]
4221	do
4222	if [[ $files_for_pes = false ]]
4223	then
4224	stageout ${frelout[$i]} > STAGE_OUTPUT
4225	else
4226	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4227	fi
4228	cat STAGE_OUTPUT
4229	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4230	then
4231	file_saved=true
4232	do_stageout=false
4233	else
4234	if [[ $files_for_pes = false ]]
4235	then
4236	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4237	else
4238	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4239	fi
4240	(( stageout_anz = stageout_anz + 1 ))
4241	if (( stageout_anz == 10 ))
4242	then
4243	printf "\n +++ stoped after 10 unsuccessful tries!"
4244	archive_save=false
4245	do_stageout=false
4246	else
4247	printf "\n *** new try to store on archive after 15 min:"
4248	sleep 900
4249	fi
4250	fi
4251	done
4252	elif [[ $archive_system = DMF ]]
4253	then
4254	if [[ $files_for_pes = false ]]
4255	then
4256	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4257	locat=DMF
4258	exit
4259	else
4260	rm -rf $ARCHIVE/${frelout[$i]}
4261	cp -r ${frelout[$i]} $ARCHIVE
4262	fi
4263	file_saved=true
4264	elif [[ $archive_system = tivoli ]]
4265	then
4266	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4267	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4268	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4269	# WHEN THE ARCHIVE-JOB IS EXECUTED
4270	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4271	chmod g+rx $tmp_data_catalog
4272	if [[ $files_for_pes = false ]]
4273	then
4274	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4275	else
4276	mkdir $tmp_data_catalog/${frelout[$i]}
4277	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4278	fi
4279
4280	# GENERATE AND SUBMIT BATCH-JOB
4281	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4282	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4283	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4284	if [[ $files_for_pes = false ]]
4285	then
4286	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4287	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4288	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4289	else
4290	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4291	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4292	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4293	fi
4294
4295	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4296	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4297	file_saved=true
4298
4299	elif [[ $archive_system = ut ]]
4300	then
4301	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4302	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4303	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4304	# WHEN THE ARCHIVE-JOB IS EXECUTED
4305	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4306	chmod g+rx $tmp_data_catalog
4307	if [[ $files_for_pes = false ]]
4308	then
4309	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4310	else
4311	mkdir $tmp_data_catalog/${frelout[$i]}
4312	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4313	fi
4314
4315	# GENERATE AND SUBMIT BATCH-JOB
4316	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4317	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4318	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4319	if [[ $files_for_pes = false ]]
4320	then
4321	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4322	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4323	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4324	else
4325	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4326	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4327	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4328	fi
4329
4330	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4331	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4332	file_saved=true
4333
4334	else
4335	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4336	archive_save=false
4337	fi
4338
4339	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4340	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4341	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4342	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4343	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4344	if [[ $file_saved = true ]]
4345	then
4346	if [[ $files_for_pes = false ]]
4347	then
4348	cat /dev/null > ${pathout[$i]}
4349	else
4350	mkdir -p ${pathout[$i]}
4351	fi
4352	fi
4353
4354	fi
4355
4356	# APPEND ON THIS MACHINE
4357	if [[ "${actionout[$i]}" = "a" ]]
4358	then
4359	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4360	then
4361	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4362	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4363	else
4364	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4365	cat ${localout[$i]} >> ${pathout[$i]}
4366	fi
4367	fi
4368
4369	# COPY ON THIS MACHINE
4370	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4371	# ON DIFFERENT FILE-SYSTEMS
4372	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4373	then
4374
4375	# COPY IN CASE OF RUNS ON SINGLE CORES
4376	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4377	then
4378	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4379	if [[ $link_local_output = true ]]
4380	then
4381	printf " using ln -f\n"
4382	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4383	fi
4384	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4385	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4386	then
4387	if [[ $link_local_output = true ]]
4388	then
4389	printf " ln failed, using cp...\n"
4390	fi
4391	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4392	fi
4393	else
4394	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4395	if [[ $link_local_output = true ]]
4396	then
4397	printf " using ln -f\n"
4398	ln -f ${localout[$i]} ${pathout[$i]}
4399	fi
4400	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4401	if [[ ! -f "${pathout[$i]}" ]]
4402	then
4403	if [[ $link_local_output = true ]]
4404	then
4405	printf " ln failed, using cp...\n"
4406	fi
4407	cp ${localout[$i]} ${pathout[$i]}
4408	fi
4409	fi
4410
4411	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4412	then
4413
4414	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4415	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4416	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4417	if [[ $link_local_output = true ]]
4418	then
4419	printf " using ln -f\n"
4420	mkdir ${pathout[$i]}
4421	cd ${localout[$i]}
4422	for file in $(ls *)
4423	do
4424	ln -f $file ${pathout[$i]}
4425	done
4426	cd $TEMPDIR
4427	fi
4428
4429	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4430	if [[ ! -f "${pathout[$i]}/_0000" ]]
4431	then
4432	if [[ $link_local_output = true ]]
4433	then
4434	printf " ln failed for .../_0000, using cp...\n"
4435	fi
4436	cp -r ${localout[$i]} ${pathout[$i]}
4437	fi
4438
4439	fi
4440	fi
4441	done
4442	if (( i != 0 ))
4443	then
4444	if [[ $transfer_problems = true ]]
4445	then
4446	printf "\n$dashes\n *** OUTPUT-files saved"
4447	printf "\n +++ WARNING: some data transfers failed! \n"
4448	else
4449	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4450	fi
4451	fi
4452
4453
4454	# IF REQUIRED, START A RESTART-JOB
4455	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4456	if [[ -f CONTINUE_RUN ]]
4457	then
4458
4459	if [[ $archive_save = true ]]
4460	then
4461
4462	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4463	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4464	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4465	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4466	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4467	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4468	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4469	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4470	then
4471	mc=`echo $mc \| sed 's/#/f/g'`
4472	fi
4473
4474
4475	# START THE RESTART-JOB
4476	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4477	echo " $mc"
4478	printf "\n$dashes\n"
4479	if [[ $localhost != $fromhost ]]
4480	then
4481
4482	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4483	then
4484	echo "*** ssh will be used to initiate restart-runs!"
4485	echo " return_address=\"$return_address\" "
4486	echo " return_username=\"$return_username\" "
4487	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4488	then
4489	if [[ $localhost = ibmh ]]
4490	then
4491	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\" "
4492	elif [[ $localhost = lcbullhh ]]
4493	then
4494	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\" "
4495	elif [[ $localhost = lccrayb ]]
4496	then
4497	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\" "
4498	elif [[ $localhost = lccrayh ]]
4499	then
4500	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\" "
4501	elif [[ $localhost = lcxe6 ]]
4502	then
4503	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\" "
4504	else
4505	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 "
4506	fi
4507	else
4508	if [[ $localhost = ibmkisti ]]
4509	then
4510	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\" "
4511	elif [[ $localhost = lcflow ]]
4512	then
4513	/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 "
4514	elif [[ $localhost = lccrayb ]]
4515	then
4516	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\" "
4517	elif [[ $localhost = lccrayh ]]
4518	then
4519	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\" "
4520	else
4521	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4522	fi
4523	fi
4524	else
4525	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4526	locat=restart; exit
4527	fi
4528
4529	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4530	if [[ $queue = special1q ]]
4531	then
4532	sleep 120
4533	else
4534	sleep 30
4535	fi
4536
4537	else
4538
4539	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4540	# USING SSH)
4541	cd $LOCAL_PWD
4542	if [[ $localhost = lckyuh ]]
4543	then
4544	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4545	printf "\n please restart job manually using command:\n"
4546	printf "\n \"$mc\" "
4547	else
4548	eval $mc # THE ' MUST BE EVALUATED
4549	fi
4550	cd - > /dev/null
4551	fi
4552	if [[ $localhost = lckyuh ]]
4553	then
4554	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4555	else
4556	printf "\n$dashes\n *** restart-run initiated \n"
4557	fi
4558
4559
4560	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4561	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4562	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4563	# MAY BE VERY HUGE)
4564	(( i = 0 ))
4565	while (( i < iin ))
4566	do
4567	(( i = i + 1 ))
4568	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4569	then
4570	rm -r $tmp_data_catalog/${frelin[$i]}
4571	fi
4572	done
4573
4574	else
4575
4576	printf "\n +++ no restart-run possible, since errors occured"
4577	printf "\n during the archive process"
4578	fi
4579
4580	fi
4581
4582
4583
4584	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4585	if [[ "$email_notification" != "none" ]]
4586	then
4587
4588	if [[ $localhost != $fromhost ]]
4589	then
4590	if [[ -f CONTINUE_RUN ]]
4591	then
4592	echo "PALM restart run necessary" > email_text
4593	echo "description header of actual run:" >> email_text
4594	cat CONTINUE_RUN >> email_text
4595	echo "mrun-command to restart:" >> email_text
4596	echo "$mc" >> email_text
4597	else
4598	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4599	fi
4600	mail $email_notification < email_text
4601	printf "\n *** email notification sent to \"$email_notification\" "
4602	fi
4603	fi
4604
4605
4606
4607	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4608	cd $HOME
4609	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4610
4611	else
4612
4613	# PREPARING ACTIONS,
4614	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4615
4616	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4617	mrun_com="$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 $remote_username"
4618	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4619	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4620	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4621	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4622	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4623	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4624	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4625	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4626	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4627	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4628	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4629	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4630	if [[ $use_openmp = true ]]
4631	then
4632	mrun_com=${mrun_com}" -O $threads_per_task"
4633	fi
4634	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4635	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4636	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4637	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4638	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4639	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4640	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4641	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4642	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4643	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4644	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4645	if [[ $do_remote = true ]]
4646	then
4647	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4648	fi
4649
4650
4651	# CREATE EXECUTABLE FOR BATCH JOB
4652	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4653	then
4654
4655	printf "\n *** creating the executable for batch job\n"
4656
4657	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4658	if [[ $host != $localhost ]]
4659	then
4660	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4661	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4662	locat=create_executable; exit
4663	fi
4664
4665	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4666	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4667
4668	cp $make_depository .
4669	tar -xf $make_depository > /dev/null 2>&1
4670	cp ../* . > /dev/null 2>&1
4671
4672	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4673
4674	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4675	then
4676	printf "\n +++ error occured while compiling or linking"
4677	locat=compile
4678	exit
4679	fi
4680
4681	mv a.out ..
4682	cd - > /dev/null 2>&1
4683	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4684
4685	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4686
4687	fi
4688
4689
4690	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4691	jobfile=jobfile.$RANDOM
4692
4693
4694	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4695	echo "mkdir $TEMPDIR" >> $jobfile
4696	echo "cd $TEMPDIR" >> $jobfile
4697
4698
4699	# ACTIVATE ERROR-TRACEBACK
4700	if [[ $do_trace = true ]]
4701	then
4702	echo "set -x" >> $jobfile
4703	else
4704	echo "set +vx" >> $jobfile
4705	fi
4706
4707
4708	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4709	if [[ "$init_cmds" != "" ]]
4710	then
4711	echo "$init_cmds" >> $jobfile
4712	fi
4713	if [[ "$module_calls" != "" ]]
4714	then
4715	echo "$module_calls" >> $jobfile
4716	fi
4717
4718
4719	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4720	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4721	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4722	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4723	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4724	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4725	# QUEUEING-SYSTEMS
4726	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4727	then
4728
4729	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4730	if [[ $restart_run != true ]]
4731	then
4732	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4733	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4734	fi
4735
4736	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4737	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4738	echo "set -x" >> $jobfile
4739	if [[ $host = $localhost ]]
4740	then
4741	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4742	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4743	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4744	then
4745	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4746	else
4747	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4748	fi
4749
4750	else
4751	if [[ $host = ibmkisti ]]
4752	then
4753	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4754	echo "localdir=\`pwd\`" >> $jobfile
4755	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4756	elif [[ $host = lcbullhh ]]
4757	then
4758	echo "localdir=\`pwd\`" >> $jobfile
4759	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4760
4761	elif [[ $host = lccrayb ]]
4762	then
4763	echo "localdir=\`pwd\`" >> $jobfile
4764	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4765	elif [[ $host = lccrayh ]]
4766	then
4767	echo "localdir=\`pwd\`" >> $jobfile
4768	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4769
4770	else
4771	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4772	fi
4773	fi
4774	echo "export SOURCES_COMPLETE=true" >> $jobfile
4775
4776	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4777	# WORKING DIRECTORY OF THE JOB
4778	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4779	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4780	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4781	echo "execute_mrun=true" >> $jobfile
4782	echo " " >> $jobfile
4783
4784	else
4785
4786	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4787	if [[ $do_compile = true ]]
4788	then
4789
4790	source_catalog=SOURCES_FOR_RUN_$fname
4791
4792	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4793	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4794	echo "export SOURCES_COMPLETE=true" >> $jobfile
4795	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4796
4797	for filename in $source_list
4798	do
4799	# BACKSLASH IS USED FOR MASKING
4800	echo "cat > $filename << \"%END%\"" >> $jobfile
4801	cat $source_catalog/$filename >> $jobfile
4802	echo " " >> $jobfile
4803	echo "%END%" >> $jobfile
4804	echo " " >> $jobfile
4805	done
4806
4807	# BACKSLASH IS USED FOR MASKING
4808	echo "cat > Makefile << \"%END%\"" >> $jobfile
4809	cat $source_catalog/Makefile >> $jobfile
4810	echo " " >> $jobfile
4811	echo "%END%" >> $jobfile
4812	echo " " >> $jobfile
4813
4814	echo "cd - > /dev/null" >> $jobfile
4815
4816	fi
4817
4818
4819	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4820	# BACKSLASH IS USED FOR MASKING
4821	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4822	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4823	echo "cat > $config_file << \"%END%\"" >> $jobfile
4824	if [[ $host = lckyuh ]]
4825	then
4826	# NO CROSS-COMPILER ON COMPUTE NODE
4827	sed 's/frtpx/frt/g' $config_file >> $jobfile
4828	else
4829	sed 's/#$.*//g' $config_file >> $jobfile
4830	fi
4831	echo "%END%" >> $jobfile
4832	echo " " >> $jobfile
4833
4834
4835	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4836	# BACKSLASH IS USED FOR MASKING
4837	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4838	if [[ $host = lckyuh ]]
4839	then
4840	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4841	else
4842	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4843	fi
4844	echo "%END%" >> $jobfile
4845	echo "chmod u+x $mrun_script_name" >> $jobfile
4846	echo "execute_mrun=true" >> $jobfile
4847	echo " " >> $jobfile
4848
4849	fi
4850
4851
4852	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4853	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4854	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4855	if [[ $do_remote = true ]]
4856	then
4857	(( i = 0 ))
4858	while (( i < iin ))
4859	do
4860	(( i = i + 1 ))
4861	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4862	if [[ "${transin[$i]}" = job ]]
4863	then
4864	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4865	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4866	echo " " >> $jobfile
4867	echo "%END%" >> $jobfile
4868	else
4869	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4870	fi
4871
4872	# CHECK, IF FILE COULD BE CREATED
4873	echo "if [[ \$? = 1 ]]" >> $jobfile
4874	echo "then" >> $jobfile
4875	echo " echo \" \" " >> $jobfile
4876	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4877	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4878	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4879	echo " execute_mrun=false" >> $jobfile
4880	echo "fi" >> $jobfile
4881	done
4882	fi
4883
4884	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4885	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4886	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4887	echo "LOCAL_PWD=$working_directory" >> $jobfile
4888	echo "export LOCAL_PWD" >> $jobfile
4889
4890	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4891	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4892	echo "export LOCAL_MRUN_PATH" >> $jobfile
4893
4894	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4895	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4896	# then
4897	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4898	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4899	# fi
4900
4901	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4902	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4903	echo "set -x" >> $jobfile
4904	echo "queue=$queue" >> $jobfile
4905	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4906	echo 'ls -al; echo `pwd`' >> $jobfile
4907	echo "cd \$HOME" >> $jobfile
4908	echo "rm -rf $TEMPDIR" >> $jobfile
4909
4910
4911
4912
4913	# START THE JOB USING SUBJOB-COMMAND
4914	if [[ $silent = false ]]
4915	then
4916	printf "\n "
4917	else
4918	printf "\n\n"
4919	fi
4920
4921	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
4922	rm -rf $jobfile
4923
4924
4925	fi # END OF REMOTE-PART

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