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source: palm/trunk/SCRIPTS/mrun @ 1758

Last change on this file since 1758 was 1758, checked in by maronga, 8 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1758 2016-02-22 15:53:28Z maronga $
29	#
30	# 1757 2016-02-22 15:49:32Z maronga
31	# Bugfix: use random number when PBS system is not working properly at lccray*
32	#
33	# 1755 2016-02-22 13:53:39Z maronga
34	# Minor bugfix to last commit
35	#
36	# 1753 2016-02-22 13:49:49Z maronga
37	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
38	#
39	# 1622 2015-07-20 06:21:36Z heinze
40	# bugfix for Mistral (lcbullhh)
41	#
42	# 1621 2015-07-17 11:39:33Z heinze
43	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
44	#
45	# 1609 2015-07-03 15:37:58Z maronga
46	# Modified the random number of the temporary working directory to match the
47	# queuing system number on HLRN-III (lccray*).
48	#
49	# 1604 2015-06-23 15:48:03Z suehring
50	# Enable coupled runs for lcmuk
51	#
52	# 1598 2015-05-29 06:45:40Z raasch
53	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
54	#
55	# 1549 2015-01-30 14:26:16Z suehring
56	# Enable interactive debug sessions with allinea debugger
57	#
58	# 1547 2015-01-29 15:09:12Z witha
59	# adjustments for ForWind computing cluster (lcflow)
60	#
61	# 1491 2014-11-12 08:12:57Z heinze
62	# correct setting of batch_job allowed for ibm-machines
63	#
64	# 1468 2014-09-24 14:06:57Z maronga
65	# Typo removed (addres->address)
66	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
67	# Added support for restart runs (remote) for lcxe6
68	#
69	# 1442 2014-07-28 07:09:10Z raasch
70	# default queues for HLRN-III (lccrayb/lccrayh) defined
71	#
72	# 1422 2014-07-02 10:01:25Z kanani
73	# automatic restarts enabled for lccrayb,
74	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
75	#
76	# 1420 2014-06-10 06:24:14Z raasch
77	# -j1 option added to aprung command for lccrayf (CSC)
78	#
79	# 1402 2014-05-09 14:25:13Z raasch
80	# batch_job added to envpar-NAMELIST
81	#
82	# 1357 2014-04-11 15:02:03Z witha
83	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
84	# possible)
85	#
86	# 1320 2014-03-20 08:40:49Z raasch
87	# check namelist file set false by default
88	#
89	# 1304 2014-03-12 10:29:42Z raasch
90	# ulimit option changed from -Ss to -s
91	#
92	# bugfix: missing "fi" in r1289
93	#
94	# 1289 2014-03-04 07:12:34Z raasch
95	# comments translated to English
96	# necriam-, fimm-, ibmy-, and sgi-specific code removed
97	# export of variables for palm and interpret_config removed
98	#
99	# 1281 2014-02-01 07:55:49Z raasch
100	# rsync-copy restricted to Cray machines, since command is unavailable on some
101	# other systems
102	#
103	# 1279 2014-01-28 12:10:14Z raasch
104	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
105	# in order to remove annoying restrictions concerning the number of processors which
106	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
107	# restriction, one of the nodes will be filled with less than the given number of
108	# tasks per node. A respective warning is given.
109	#
110	# 1274 2014-01-09 13:14:54Z heinze
111	# adjustments for lccrayh
112	#
113	# 1272 2014-01-08 10:19:32Z witha
114	# small adjustment for lcflow
115	#
116	# 1270 2013-12-16 11:05:01Z fricke
117	# call of combine_plot_fields adjusted for lccrayb/lccrayh
118	#
119	# 1255 2013-11-07 14:43:35Z raasch
120	# further adjustments for lccrayb remote access
121	#
122	# 1241 2013-10-30 11:36:58Z heinze
123	# Enable use of nudging input and input of large scale forcing from
124	# external files
125	#
126	# 1229 2013-09-20 06:55:19Z raasch
127	# further adjustments for lccrayb
128	#
129	# 1224 2013-09-16 07:27:23Z raasch
130	# first adjustments for lccrayb
131	#
132	# 1210 2013-08-14 10:58:20Z raasch
133	# fftw support added
134	#
135	# 1201 2013-07-10 16:17:59Z witha
136	# adjustments for Forwind cluster (lcflow)
137	#
138	# 1199 2013-07-05 14:52:22Z raasch
139	# adjustments for CSC Helsinki (lccrayf),
140	# executables for batch jobs can be created in advance, in order to avoid calling
141	# the compiler within the batch job (only works if batch jobs are submitted on
142	# local host)
143	#
144	# 1190 2013-06-25 09:39:21Z heinze
145	# enable use of automatic restarts for ibmh
146	# use of cluster/express queue enabled (ibmh)
147	#
148	# 1124 2013-04-09 15:46:52Z raasch
149	# variable "memory" is exported via typeset option -x, because otherwise an unknown
150	# side effect may lead to data loss while getopts is reading the script-option arguments
151	#
152	# 1122 2013-04-09 08:37:16Z heinze
153	# Bugfix: change type of variable last_char
154	#
155	# 1119 2013-04-05 15:11:19Z raasch
156	# Bugfix for setting -T option for subjob
157	#
158	# 1108 2013-03-05 07:03:32Z raasch
159	# bugfix for coupled runs on lckyut/lckyuh
160	#
161	# 1106 2013-03-04 05:31:38Z raasch
162	# --stdin argument for mpiexec on lckyuh
163	# -y and -Y settings output to header
164	#
165	# 1103 2013-02-20 02:15:53Z raasch
166	# default script runs again under ksh, because of unsolved problems with read
167	# from stdin: when bash script is called from a ksh, message "read error: 0:
168	# Resource temporarily unavailable" appears and script does not stop,
169	# further bash compatibility adjustments,
170	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
171	# on lckyuh, but mrun does not terminate and issues a warning instead
172	#
173	# 1101 2013-02-17 10:20:21Z raasch
174	# script now running under bash instead of ksh, which required small adjustments
175	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
176	# read from stdin),
177	# cross compilername on lckyuh compute nodes replaced by real compiler name
178	#
179	# 1099 2013-02-10 01:47:43Z raasch
180	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
181	# and for Forwind cluster (lcflow)
182	# small further adjustments for lckyut
183	#
184	# 1094 2013-02-03 01:52:12Z raasch
185	# explicit ssh/scp port can be set in config file with environment variable
186	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
187	# decalpha parts (yonsei) removed
188	#
189	# 2013-02-02 07:06:13Z raasch
190	# adjustments for Kyushu-University computing center (lckyut - tatara)
191	#
192	# 1083 2013-01-04 10:22:09Z maronga
193	# bugfix in parameter file check (read %cpp_options was missing)
194	#
195	# 1069 2012-11-28 16:18:43Z maronga
196	# bugfix: coupling mode was always set to mpi2, typos removed
197	#
198	# 1058 2012-11-21 07:00:35Z raasch
199	# Intel inspector (inspxe) is given the number of PEs instead of the number of
200	# nodes
201	#
202	# 1046 2012-11-09 14:38:45Z maronga
203	# code put under GPL (PALM 3.9)
204	#
205	# 21/03/94 - Siggi - first version finished
206	# 03/03/94 - Siggi - script development started
207	#
208	#--------------------------------------------------------------------------------#
209	# mrun - script for running PALM jobs
210	#--------------------------------------------------------------------------------#
211
212
213
214	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
215
216	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
217	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
218	# (TOO MANY ARGUMENTS - PROBLEM)
219	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
220
221	AddFilenames=""
222	additional_conditions=""
223	add_source_path=""
224	afname=""
225	archive_save=true
226	archive_system=none
227	check_namelist_files=false
228	combine_plot_fields=true
229	compiler_name=""
230	cond1=""
231	cond2=""
232	config_file=.mrun.config
233	coupled_dist=""
234	coupled_mode="mpi1"
235	cpp_opts=""
236	cpp_options=""
237	cpumax=0
238	cpurest=0
239	create_executable_for_batch=false
240	delete_temporary_catalog=true
241	do_batch=false
242	do_compile=true
243	do_remote=false
244	do_stagein=true
245	do_stageout=true
246	do_trace=false
247	email_notification="none"
248	exclude=""
249	executable=""
250	execution_error=false
251	fftw_inc=""
252	fftw_lib=""
253	fftw_support=false
254	fname=test
255	fromhost=""
256	global_revision=""
257	group_number=none
258	host=""
259	host_file=""
260	hp=""
261	ignore_archive_error=false
262	input_list=""
263	interpreted_config_file=""
264	job_catalog="~/job_queue"
265	job_on_file=""
266	keep_data_from_previous_run=false
267	link_local_input=false
268	link_local_output=false
269	localhost_realname=$(hostname)
270	local_dvrserver_running=.FALSE.
271	locat=normal
272	mainprog=""
273	makefile=""
274	max_par_io_str=""
275	mc=$0
276	while [[ $(echo $mc \| grep -c "/") != 0 ]]
277	do
278	mc=`echo $mc \| cut -f2- -d"/"`
279	done
280	module_calls=""
281	mrun_script_name=$mc
282	netcdf_inc=""
283	netcdf_lib=""
284	netcdf_support=false
285	node_usage=default
286	numprocs=""
287	numprocs_atmos=0
288	numprocs_ocean=0
289	OOPT=""
290	openmp=false
291	output_list=""
292	package_list=""
293	queue=none
294	read_from_config=""
295	restart_run=false
296	if [[ `hostname` = rte10 ]]
297	then
298	return_address=133.5.185.60
299	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
300	elif [[ `hostname` = climate0 ]]
301	then
302	return_address=165.132.26.68
303	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
304	elif [[ `hostname` = urban00 ]]
305	then
306	return_address=147.46.30.151
307	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
308	else
309	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
310	fi
311	return_password=""
312	return_username=$LOGNAME
313	remotecall=false
314	remote_username=""
315	run_coupled_model=false
316	run_mode=""
317	store_on_archive_system=false
318	dashes=" ----------------------------------------------------------------------------"
319	silent=false
320	source_list=""
321	source_path=SOURCE
322	tasks_per_node=""
323	threads_per_task=1
324	tmpcreate=false
325	tmp_data_catalog=""
326	transfer_problems=false
327	usern=$LOGNAME
328	use_openmp=false
329	version="MRUN 2.1 Rev$Rev: 1758 $"
330	working_directory=`pwd`
331	TOPT=""
332	XOPT=""
333	zeit=$( date \| cut -c 12-19 )
334
335	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
336	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
337	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
338	# SCRIPT-OPTION ARGUMENTS
339	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
340
341	# ERROR HANDLING IN CASE OF EXIT
342	trap 'rm -rf $working_directory/tmp_mrun
343	if [[ $locat != normal && $locat != control_c ]]
344	then
345
346	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
347	(( i = 0 ))
348	while (( i < iec ))
349	do
350	(( i = i + 1 ))
351	printf "\n *** Execution of ERROR-command:\n"
352	printf " >>> ${err_command[$i]}\n"
353	eval ${err_command[$i]}
354	done
355	if [[ -n $interpreted_config_file ]]
356	then
357	rm -rf $interpreted_config_file
358	fi
359	if [[ -n .mrun_environment ]]
360	then
361	rm -rf .mrun_environment
362	fi
363	if [[ $tmpcreate = true ]]
364	then
365	printf "\n *** Contents of \"$TEMPDIR\":\n"
366	ls -al; cd
367	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
368	fi
369	if [[ "$dvrserver_id" != "" ]]
370	then
371	echo "+++ killing dvrserver_id=$dvrserver_id"
372	kill $dvrserver_id
373	fi
374	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
375	then
376	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
377	fi
378	printf "\n\n+++ MRUN killed \n\n"
379	elif [[ $locat != control_c ]]
380	then
381	printf "\n\n --> all actions finished\n\n"
382	printf " Bye, bye $usern !!\n\n"
383	fi' exit
384
385
386	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
387	trap 'rm -rf $working_directory/tmp_mrun
388	rm -rf $working_directory/tmp_check_namelist_files
389	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
390	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
391	then
392	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
393	fi
394	if [[ "$dvrserver_id" != "" ]]
395	then
396	echo "+++ killing dvrserver_id=$dvrserver_id"
397	kill $dvrserver_id
398	fi
399	printf "\n+++ MRUN killed by \"^C\" \n\n"
400	locat=control_c
401	exit
402	' 2
403
404
405	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
406	# BEEN SET
407	if [[ "$PALM_BIN" = "" ]]
408	then
409	printf "\n +++ environment variable PALM_BIN has not been set"
410	printf "\n please set it to the directory where the PALM scripts are located"
411	locat=palm_bin; exit
412	fi
413	export PATH=$PALM_BIN:$PATH
414
415
416
417	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
418	# WHICH WILL BE USED TO START RESTART-JOBS
419	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
420	do
421	case $option in
422	(a) afname=$OPTARG;;
423	(A) store_on_archive_system=true; mc="$mc -A";;
424	(b) do_batch=true; mc="$mc -b";;
425	(B) delete_temporary_catalog=false; mc="$mc -B";;
426	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
427	(C) restart_run=true; mc="$mc -C";;
428	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
429	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
430	(F) job_on_file="-D"; mc="$mc -F";;
431	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
432	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
433	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
434	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
435	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
436	(I) ignore_archive_error=true; mc="$mc -I";;
437	(k) keep_data_from_previous_run=true; mc="$mc -k";;
438	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
439	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
440	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
441	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
442	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
443	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
444	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
445	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
446	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
447	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
448	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
449	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
450	(S) read_from_config=false; mc="$mc -S";;
451	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
452	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
453	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
454	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
455	(v) silent=true; mc="$mc -v";;
456	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
457	(x) do_trace=true;set -x; mc="$mc -x";;
458	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
459	(y) ocean_file_appendix=true; mc="$mc -y";;
460	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
461	(z) check_namelist_files=false; mc="$mc -z";;
462	(Z) combine_plot_fields=false; mc="$mc -Z";;
463	(\?) printf "\n +++ unknown option $OPTARG \n"
464	printf "\n --> type \"$0 ?\" for available options \n"
465	locat=parameter;exit;;
466	esac
467	done
468
469
470	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
471	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
472	(( to_shift = $OPTIND - 1 ))
473	shift $to_shift
474
475	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
476	if [[ "$1" = "?" ]]
477	then
478	(printf "\n *** mrun can be called as follows:\n"
479	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"
480	printf "\n Description of available options:\n"
481	printf "\n Option Description Default-Value"
482	printf "\n -a base name of input files equiv. -d"
483	printf "\n -A archiving when using file-attribute fl"
484	printf "\n -b batch-job on local machine ---"
485	printf "\n -B do not delete temporary directory at end ---"
486	printf "\n -c configuration file .mrun.config"
487	printf "\n -d base name of files attached to program test"
488	printf "\n -D preprocessor(cpp)-directives \"\" "
489	printf "\n -F create remote job file only ---"
490	printf "\n -h execution host $localhost_realname"
491	printf "\n -i INPUT control list \"\" "
492	printf "\n -I archiving errors of previous batch-jobs"
493	printf "\n will be ignored"
494	printf "\n -k keep data from previous run"
495	printf "\n -K additional conditions for controling"
496	printf "\n usage of conditional code and"
497	printf "\n env-variables in configuration file \"\" "
498	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
499	printf "\n -M Makefile name Makefile"
500	printf "\n -n node usage (shared/not_shared) depending on -h"
501	printf "\n -o OUTPUT control list \"\" "
502	printf "\n -O threads per openMP task ---"
503	printf "\n -p software package list \"\" "
504	printf "\n -q queue \"$queue\" "
505	printf "\n -r run control list (combines -i -o) \"\" "
506	printf "\n -s filenames of routines to be compiled \"\" "
507	printf "\n must end with .f, .f90, .F, or .c !"
508	printf "\n use \"..\" for more than one file and wildcards"
509	printf "\n -s LM compiles all locally modified files"
510	printf "\n -S config file interpreted by shellscript ---"
511	printf "\n -t allowed cpu-time in seconds (batch) 0"
512	printf "\n -T tasks per node depending on -h"
513	printf "\n -u username on remote machine \"\" "
514	printf "\n -v no prompt for confirmation ---"
515	printf "\n -w maximum parallel io streams as given by -X"
516	printf "\n -x tracing of mrun for debug purposes ---"
517	printf "\n -X # of processors (on parallel machines) 1"
518	printf "\n -y add appendix \"_O\" to all local output"
519	printf "\n files (ocean precursor runs followed by"
520	printf "\n coupled atmosphere-ocean runs) ---"
521	printf "\n -Y run coupled model, \"#1 #2\" with"
522	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
523	printf "\n -z disable a priori parameter file check ---"
524	printf "\n -Z skip combine_plot_fields at the end of "
525	printf "\n the simulation ---"
526	printf "\n "
527	printf "\n Possible values of positional parameter <modus>:"
528	printf "\n \"?\" - this outline \n\n") \| more
529	exit
530	elif [[ "$1" != "" ]]
531	then
532	printf "\n +++ positional parameter $1 unknown \n"
533	locat=parameter; exit
534	fi
535
536
537
538	# SHORT STARTING MESSAGE
539	printf "\n*** $version "
540	printf "\n will be executed. Please wait ..."
541
542
543
544	# CHECK, IF CONFIGURATION FILE EXISTS
545	if [[ ! -f $config_file ]]
546	then
547	printf "\n\n +++ configuration file: "
548	printf "\n $config_file"
549	printf "\n does not exist"
550	locat=connect; exit
551	fi
552
553
554	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
555	line=""
556	grep "%host_identifier" $config_file > tmp_mrun
557	while read line
558	do
559	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
560	then
561	HOSTNAME=`echo $line \| cut -d" " -s -f2`
562	host_identifier=`echo $line \| cut -d" " -s -f3`
563	if [[ $localhost_realname = $HOSTNAME ]]
564	then
565	localhost=$host_identifier
566	break
567	fi
568	fi
569	done < tmp_mrun
570
571	if [[ "$localhost" = "" ]]
572	then
573	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
574	printf "\n for local host \"$localhost_realname\"."
575	printf "\n Please add line"
576	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
577	printf "\n to the configuration file."
578	locat=localhost; exit
579	fi
580
581
582	# SET HOST-SPECIFIC VARIABLES
583	case $localhost_realname in
584	(r1\|r2\|h01\|b01) archive_system=tivoli;;
585	(cs*) archive_system=ut;;
586	esac
587
588
589	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
590	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
591	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
592	[[ "$afname" = "" ]] && afname=$fname
593
594
595	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
596	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
597	# STATEMENTS IN THE CONFIGURATION FILE
598	if [[ "$run_mode" != "" ]]
599	then
600	input_list="$input_list $run_mode"
601	output_list="$output_list $run_mode"
602	fi
603
604
605	# ??? is this (and the respective option -H) really required ???
606	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
607	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
608	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
609	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
610	if [[ "$fromhost" = "" ]]
611	then
612	fromhost=$localhost
613	fi
614
615
616	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
617	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
618	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
619	# TO BE SUBMITTED (I.E. do_batch=true)
620	if [[ -n $host && "$host" != $localhost ]]
621	then
622	do_batch=true
623	do_remote=true
624	case $host in
625	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
626	(*) printf "\n"
627	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
628	printf "\n is not available"
629	locat=nqs; (( iec = 0 )); exit;;
630	esac
631	else
632	host=$localhost
633	fi
634
635
636	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
637	if [[ -n $additional_conditions ]]
638	then
639	cond1=`echo $additional_conditions \| cut -d" " -f1`
640	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
641	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
642	if [[ -n $dummy ]]
643	then
644	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
645	locat=options; exit
646	fi
647	block=_$cond1
648	[[ -n $cond2 ]] && block=${block}_$cond2
649	fi
650
651
652	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
653	if [[ $run_coupled_model = true ]]
654	then
655
656	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
657	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
658
659	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
660	then
661
662	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
663	printf "\n PEs (total) : $numprocs"
664	printf "\n PEs (atmosphere): $numprocs_atmos"
665	printf "\n PEs (ocean) : $numprocs_ocean"
666	locat=coupling; exit
667
668	fi
669
670
671	# GET coupled_mode FROM THE CONFIG FILE
672	line=""
673	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
674	while read line
675	do
676	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
677	then
678	coupled_mode="mpi2"
679	fi
680	done < tmp_mrun
681
682	fi
683
684	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
685	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
686	then
687	if [[ $ignore_archive_error = false ]]
688	then
689	printf "\n +++ data archiving of previous run failed"
690	printf "\n see directory \~/job_queue on remote machine"
691	locat=archive; exit
692	else
693	printf "\n +++ warning: data archiving in a previous run failed"
694	printf "\n MRUN continues, trying to get backup copy"
695	fi
696	fi
697
698
699	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
700	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
701	mrun_memory=$memory
702	mrun_group_number=$group_number
703	mrun_cpumax=$cpumax
704	mrun_numprocs=$numprocs
705
706
707	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
708	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
709	if [[ "$read_from_config" = false ]]
710	then
711	[[ $silent = false ]] && printf "\n Reading the configuration file... "
712
713	# READ THE CONFIGURATION FILE LINE BY LINE
714	while read zeile
715	do
716	[[ $silent = false ]] && printf "."
717
718
719	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
720	eval zeile=\"$zeile\"
721
722
723	# INTERPRET THE LINE
724	if [[ "$(echo $zeile)" = "" ]]
725	then
726	# EMPTY LINE, NO ACTION
727	continue
728
729	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
730	then
731
732	# LINE IS A COMMENT LINE
733	true
734
735	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
736	then
737
738	# LINE DEFINES AN ENVIRONMENT-VARIABLE
739	zeile=$(echo $zeile \| cut -c2-)
740	var=`echo $zeile \| cut -d" " -f1`
741	value=`echo $zeile \| cut -d" " -s -f2`
742	for_host=`echo $zeile \| cut -d" " -s -f3`
743	for_cond1=`echo $zeile \| cut -d" " -s -f4`
744	for_cond2=`echo $zeile \| cut -d" " -s -f5`
745
746	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
747	then
748
749	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
750	# "::" IS REPLACED BY ":".
751	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
752
753
754	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
755	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
756	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
757	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
758	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
759	# CONFIGURATION-FILE.
760	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
761	then
762	eval $var=\$value
763
764	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
765	if [[ $do_trace = true ]]
766	then
767	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
768	fi
769	fi
770
771	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
772	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
773	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
774	# MUST HAVE TO BE STARTED
775	if [[ $var = host ]]
776	then
777	if [[ -n $host && "$host" != $localhost ]]
778	then
779	do_batch=true
780	do_remote=true
781	case $host in
782	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
783	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
784	printf "\n is not available"
785	locat=nqs; exit;;
786	esac
787	else
788	host=$localhost
789	fi
790	fi
791
792	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
793	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
794	# BY MRUN (E.G. subjob)
795	export $var
796	fi
797
798
799
800
801	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
802	then
803
804	# LINE DEFINES ERROR-COMMAND
805	(( iec = iec + 1 ))
806	zeile=$(echo $zeile \| cut -c4-)
807	err_command[$iec]="$zeile"
808
809	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
810	then
811
812	# LINE DEFINES INPUT-COMMAND
813	(( iic = iic + 1 ))
814	zeile=$(echo $zeile \| cut -c4-)
815	in_command[$iic]="$zeile"
816
817	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
818	then
819
820	# LINE DEFINES OUTPUT-COMMAND
821	(( ioc = ioc + 1 ))
822	zeile=$(echo $zeile \| cut -c4-)
823	out_command[$ioc]="$zeile"
824
825	else
826
827	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
828	# s2a: in/out - field
829	# s2b: loc - field (optional)
830	# s2c: tr/ar - field (optional)
831	s1=`echo $zeile \| cut -d" " -f1`
832	s2=`echo $zeile \| cut -d" " -s -f2`
833	s2a=$(echo $s2 \| cut -d":" -f1)
834	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
835	then
836	s2b=""
837	s2c=""
838	else
839	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
840	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
841	fi
842	s3=`echo $zeile \| cut -d" " -f3`
843	s4=`echo $zeile \| cut -d" " -s -f4`
844	s5=`echo $zeile \| cut -d" " -s -f5`
845	s6=`echo $zeile \| cut -d" " -s -f6`
846
847
848	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
849	# INPUT- OR OUTPUT-LIST.
850	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
851	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
852	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
853	# IS NOT CHECKED AND STORED.
854	IFSALT="$IFS"; IFS="$IFS:"
855	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
856	then
857	found=false
858	for actual in $input_list
859	do
860	for formal in $s3
861	do
862	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
863	done
864	done
865	if [[ $found = true ]]
866	then
867	(( iin = iin + 1 ))
868	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
869	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
870	extin[$iin]=$s6
871	fi
872	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
873	then
874	found=false
875	for actual in $output_list
876	do
877	for formal in $s3
878	do
879	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
880	done
881	done
882	if [[ $found = true ]]
883	then
884	(( iout = iout + 1 ))
885	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
886	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
887	fi
888	elif [[ "$s2a" != in && "$s2a" != out ]]
889	then
890	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
891	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
892	locat=connect; exit
893	fi
894	IFS="$IFSALT"
895	fi
896	done < $config_file
897
898	else
899
900	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
901	[[ $silent = false ]] && printf "..."
902	interpreted_config_file=.icf.$RANDOM
903
904
905
906	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
907	cat > .mrun_environment << %%END%%
908	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
909	config_file = '$config_file', do_remote = '$do_remote',
910	do_trace = '$do_trace', host = '$host',
911	input_list = '$input_list', icf = '$interpreted_config_file',
912	localhost = '$localhost', output_list = '$output_list' /
913
914	%%END%%
915
916	if [[ "$host" != $localhost ]]
917	then
918
919	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
920	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
921	if [[ $? != 0 ]]
922	then
923	printf "\n\n +++ no interpret_config found"
924	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
925	locat=interpret_config; exit
926	fi
927	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
928	$interpret_config_executable
929
930	else
931
932	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
933	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
934	then
935	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
936	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
937	locat=interpret_config; exit
938	else
939	interpret_config${block}.x
940	fi
941
942	fi
943	rm .mrun_environment
944
945
946	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
947	chmod u+x $interpreted_config_file
948	export PATH=$PATH:.
949	. $interpreted_config_file
950	rm $interpreted_config_file
951
952	fi
953
954
955	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
956	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
957	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
958	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
959	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
960	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
961	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
962
963
964	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
965	# FOR SOURCE-FILES TO BE COMPILED.
966	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
967	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
968	if [[ "$SOURCES_COMPLETE" = "" ]]
969	then
970
971	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
972	# HAS BEEN DEFINED
973	source_path=""
974	line=""
975	grep "%source_path" $config_file > tmp_mrun
976	while read line
977	do
978	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
979	then
980	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
981	then
982	global_source_path=`echo $line \| cut -d" " -f2`
983	fi
984	fi
985	done < tmp_mrun
986
987	line=""
988	found=false
989	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
990	while read line
991	do
992	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
993	then
994	if [[ $found = true ]]
995	then
996	printf "\n\n +++ more than one source path found in configuration file"
997	printf "\n for local host \"$localhost\" "
998	locat=source_path; exit
999	fi
1000	source_path=`echo $line \| cut -d" " -f2`
1001	found=true
1002	fi
1003	done < tmp_mrun
1004	rm tmp_mrun
1005
1006	if [[ "$source_path" = "" ]]
1007	then
1008	if [[ "$global_source_path" != "" ]]
1009	then
1010	source_path=$global_source_path
1011	else
1012	printf "\n\n +++ no source path found in configuration file"
1013	printf "\n for local host \"$localhost\" "
1014	locat=source_path; exit
1015	fi
1016	fi
1017	eval source_path=$source_path
1018
1019	if [[ ! -d $source_path ]]
1020	then
1021	printf "\n\n +++ source path \"$source_path\" on local host"
1022	printf "\n \"$localhost\" does not exist"
1023	locat=source_path; exit
1024	fi
1025
1026	fi
1027
1028
1029	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1030	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1031	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1032	then
1033	global_revision=`svnversion $source_path 2>/dev/null`
1034	global_revision="Rev: $global_revision"
1035	fi
1036
1037
1038	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1039	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1040	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1041	if [[ -n $host && "$host" != $localhost ]]
1042	then
1043	do_batch=true
1044	do_remote=true
1045	case $host in
1046	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1047	(*) printf "\n"
1048	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1049	printf "\n is not available"
1050	locat=nqs; (( iec = 0 )); exit;;
1051	esac
1052	else
1053	host=$localhost
1054	fi
1055
1056
1057
1058	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1059	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1060	then
1061
1062	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1063	if [[ ! -n $numprocs ]]
1064	then
1065	printf "\n"
1066	printf "\n +++ option \"-K parallel\" requires additional specification"
1067	printf "\n of the number of processors to be used by"
1068	printf "\n mrun-option \"-X\" or by environment-variable"
1069	printf "\n \"numprocs\" in the configuration file"
1070	locat=numprocs; (( iec = 0 )); exit
1071	fi
1072
1073	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1074	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1075	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1076	then
1077	printf "\n"
1078	printf "\n +++ option \"-T\" (tasks per node) is missing"
1079	printf "\n set -T option or define tasks_per_node in the config file"
1080	locat=tasks_per_node; (( iec = 0 )); exit
1081	fi
1082
1083	if (( numprocs < tasks_per_node ))
1084	then
1085	printf "\n"
1086	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1087	printf "\n given values: -T $tasks_per_node -X $numprocs"
1088	locat=tasks_per_node; (( iec = 0 )); exit
1089	fi
1090
1091	if [[ $host != lcflow && $host != lcxt5m ]]
1092	then
1093	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1094	(( ival = $tasks_per_node ))
1095	(( pes = numprocs ))
1096	(( ii = pes / ival ))
1097	(( remaining_pes = pes - ii * ival ))
1098	if (( remaining_pes > 0 ))
1099	then
1100	printf "\n"
1101	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1102	printf "\n divisor of the total number of processors (option \"-X\")"
1103	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1104	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1105	(( nodes = nodes + 1 ))
1106	fi
1107	fi
1108
1109
1110	# SETTINGS FOR SUBJOB-COMMAND
1111	OOPT="-O $threads_per_task"
1112
1113	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1114	if [[ "$tasks_per_node" != "" ]]
1115	then
1116	TOPT="-T $tasks_per_node"
1117	fi
1118
1119	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1120	if [[ $node_usage = default ]]
1121	then
1122	if [[ $host = ibms ]]
1123	then
1124	node_usage=shared
1125	else
1126	node_usage=not_shared
1127	fi
1128	fi
1129
1130	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1131	then
1132	printf "\n"
1133	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1134	printf "\n \"shared\" or \"not_shared\""
1135	locat=tasks_per_node; (( iec = 0 )); exit
1136	fi
1137
1138	fi
1139
1140	# CHECK IF HOSTFILE EXISTS
1141	if [[ -n $hostfile ]]
1142	then
1143	if [[ ! -f $hostfile ]]
1144	then
1145	printf "\n"
1146	printf "\n +++ hostfile \"$hostfile\" does not exist"
1147	locat=hostfile; exit
1148	fi
1149	fi
1150
1151
1152	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1153	if [[ "$maximum_parallel_io_streams" = "" ]]
1154	then
1155	maximum_parallel_io_streams=$numprocs
1156	fi
1157
1158
1159	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1160	if [[ "$scp_port" != "" ]]
1161	then
1162	PORTOPT="-P $scp_port"
1163	SSH_PORTOPT="-p $scp_port"
1164	fi
1165
1166
1167	# SET DEFAULT-QUEUE, IF NOT GIVEN
1168	if [[ $queue = none ]]
1169	then
1170	case $host in
1171	(ibmh) queue=cluster;;
1172	(ibmkisti) queue=class.32plus;;
1173	(lcbullhh) queue=compute;;
1174	(lccrayb) queue=mpp1q;;
1175	(lccrayh) queue=mpp1q;;
1176	(lckiaps) queue=normal;;
1177	(lckyoto) queue=ph;;
1178	(lckyuh) queue=fx-single;;
1179	(lckyut) queue=cx-single;;
1180	(lctit) queue=S;;
1181	(nech) queue=none;;
1182	(unics) queue=unics;;
1183	esac
1184	fi
1185
1186
1187	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1188	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1189	(( i = 0 ))
1190	while (( i < iin ))
1191	do
1192	(( i = i + 1 ))
1193	(( maxcycle = 0 ))
1194
1195	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1196	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1197	if [[ "${actionin[$i]}" = di ]]
1198	then
1199	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1200	# HOST ONLY
1201	eval filename=${pathin[$i]}/${endin[$i]}
1202	else
1203	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1204	# HOST ONLY
1205	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1206	fi
1207	eval pathname=${pathin[$i]}
1208
1209	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1210	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1211	then
1212	filename_input=$filename
1213	fi
1214
1215	# CHECK IF FILE EXISTS
1216	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1217	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1218	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1219	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1220	then
1221
1222	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1223	if [[ "${transin[$i]}" != "locopt" ]]
1224	then
1225	printf "\n\n +++ INPUT-file: "
1226	if [[ "${extin[$i]}" = "" ]]
1227	then
1228	printf "\n $filename"
1229	else
1230	printf "\n $filename.${extin[$i]}"
1231	fi
1232	printf "\n does not exist\n"
1233	locat=input; exit
1234	else
1235	transin[$i]="unavailable"
1236	fi
1237	else
1238
1239	# DETERMINE THE FILE'S CYCLE NUMBER
1240	ls -1 -d $filename > filelist 2>/dev/null
1241	ls -1 -d $filename.* >> filelist 2>/dev/null
1242	while read zeile
1243	do
1244	cycle=$(echo $zeile \| cut -f2 -d".")
1245	if [[ "$cycle" = "$zeile" ]]
1246	then
1247	(( icycle = 0 ))
1248	elif [[ "$cycle" = "${extin[$i]}" ]]
1249	then
1250	(( icycle = 0 ))
1251	else
1252	(( icycle = $cycle ))
1253	fi
1254	if (( icycle > maxcycle ))
1255	then
1256	(( maxcycle = icycle ))
1257	file_to_be_used=$zeile
1258	fi
1259	done <filelist
1260	rm filelist
1261
1262	# APPEND CYCLE NUMBER TO FILENAME
1263	if (( maxcycle > 0 ))
1264	then
1265	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1266	then
1267	filename=${filename}.$maxcycle.${extin[$i]}
1268	else
1269	filename=${filename}.$maxcycle
1270	fi
1271	else
1272	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1273	then
1274	filename=${filename}.${extin[$i]}
1275	fi
1276	fi
1277
1278	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1279	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1280	absnamein[$i]=$filename
1281	if (( maxcycle > 0 ))
1282	then
1283	if [[ "${actionin[$i]}" = di ]]
1284	then
1285	frelin[$i]=${endin[$i]}.$maxcycle
1286	else
1287	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1288	fi
1289	else
1290	if [[ "${actionin[$i]}" = di ]]
1291	then
1292	frelin[$i]=${endin[$i]}
1293	else
1294	frelin[$i]=${afname}${endin[$i]}
1295	fi
1296	fi
1297
1298	fi
1299	done
1300
1301	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1302	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1303	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1304	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1305	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1306	# REMOTE HOST)
1307	(( i = 0 ))
1308	while (( i < iout ))
1309	do
1310	(( i = i + 1 ))
1311	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1312	then
1313	if [[ "${actionout[$i]}" = tr ]]
1314	then
1315	actionout[$i]=""
1316	elif [[ "${actionout[$i]}" = trpe ]]
1317	then
1318	actionout[$i]=pe
1319	elif [[ "${actionout[$i]}" = tra ]]
1320	then
1321	actionout[$i]=a
1322	fi
1323	(( maxcycle = 0 ))
1324	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1325	eval catalogname=${pathout[$i]}
1326	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1327	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1328	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1329	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1330	then
1331
1332	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1333	if cat /dev/null > $filename
1334	then
1335	rm $filename
1336	else
1337
1338	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1339	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1340	if [[ ! -d $catalogname ]]
1341	then
1342	if mkdir -p $catalogname
1343	then
1344	printf "\n\n *** directory:"
1345	printf "\n $catalogname"
1346	printf "\n was created\n"
1347	else
1348	printf "\n\n +++ OUTPUT-file:"
1349	printf "\n $filename"
1350	printf "\n cannot be created, because directory does not exist"
1351	printf "\n and cannot be created either"
1352	printf "\n"
1353	locat=output ; exit
1354	fi 2>/dev/null
1355	else
1356	printf "\n\n +++ OUTPUT-file:"
1357	printf "\n $filename"
1358	printf "\n cannot be created, although directory exists"
1359	printf "\n"
1360	locat=output ; exit
1361	fi
1362	fi 2>/dev/null
1363	else
1364
1365	# DETERMINE THE CYCLE NUMBER
1366	ls -1 -d $filename > filelist 2>/dev/null
1367	ls -1 -d $filename.* >> filelist 2>/dev/null
1368	while read zeile
1369	do
1370	cycle=$(echo $zeile \| cut -f2 -d".")
1371	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1372	then
1373	(( icycle = 1 ))
1374	else
1375	(( icycle = $cycle + 1 ))
1376	fi
1377	if (( icycle > maxcycle ))
1378	then
1379	(( maxcycle = icycle ))
1380	fi
1381	done <filelist
1382	rm filelist
1383	fi
1384
1385	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1386	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1387	if [[ "${actionout[$i]}" != a ]]
1388	then
1389	if (( maxcycle > 0 ))
1390	then
1391	filename=${filename}.$maxcycle
1392	if cat /dev/null > $filename
1393	then
1394	rm $filename
1395	else
1396	printf "\n +++ OUTPUT-file:"
1397	printf "\n $filename"
1398	printf "\n cannot be created"
1399	locat=output ; exit
1400	fi
1401	fi
1402	else
1403	(( maxcycle = maxcycle - 1 ))
1404	if (( maxcycle > 0 ))
1405	then
1406	filename=${filename}.$maxcycle
1407	fi
1408	fi
1409
1410	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1411	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1412	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1413	pathout[$i]=$filename
1414	if (( maxcycle > 0 ))
1415	then
1416	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1417	else
1418	frelout[$i]=${fname}${endout[$i]}
1419	fi
1420
1421	fi
1422	done
1423
1424
1425	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1426	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1427	then
1428	if [[ "$dvr_inc" = "" ]]
1429	then
1430	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1431	printf "\n This is required for the dvrp_graphics package.\n"
1432	locat=dvr; exit
1433	fi
1434	if [[ "$dvr_lib" = "" ]]
1435	then
1436	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1437	printf "\n This is required for the dvrp_graphics package.\n"
1438	locat=dvr; exit
1439	fi
1440	fi
1441
1442
1443	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1444	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1445	if [[ "$mainprog" = "" && "$executable" = "" ]]
1446	then
1447	printf "\n +++ neither main program nor executable defined"
1448	locat=source; exit
1449	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1450	then
1451	printf "\n +++ main program as well as executable defined"
1452	locat=source; exit
1453	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1454	then
1455	do_compile=false
1456	fi
1457
1458
1459	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1460	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1461	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1462	then
1463	rm -rf SOURCES_FOR_RUN_$fname
1464	mkdir SOURCES_FOR_RUN_$fname
1465	fi
1466
1467
1468	# COLLECT ALL ROUTINES TO BE COMPILED
1469	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1470	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1471	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1472	then
1473
1474	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1475
1476	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1477	then
1478
1479	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1480	source_list=""
1481	cd $source_path
1482
1483
1484	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1485	if [[ ! -d .svn ]]
1486	then
1487	printf "\n\n +++ source directory"
1488	printf "\n \"$source_path\" "
1489	printf "\n is not under control of \"subversion\"."
1490	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1491	fi
1492
1493
1494	# LIST ALL MODIFIED SOURCE CODE FILES
1495	Filenames=""
1496	svn status > tmp_mrun
1497	while read line
1498	do
1499	firstc=`echo $line \| cut -c1`
1500	if [[ $firstc = M \|\| $firstc = "?" ]]
1501	then
1502	Name=`echo "$line" \| cut -c8-`
1503	extension=`echo $Name \| cut -d. -f2`
1504	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1505	then
1506	Filenames="$Filenames "$Name
1507	fi
1508	fi
1509	done < tmp_mrun
1510
1511
1512	# COPY FILES TO SOURCES_FOR_RUN_...
1513	for dateiname in $Filenames
1514	do
1515	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1516	source_list=$source_list"$dateiname "
1517	done
1518
1519	cd - > /dev/null
1520
1521
1522	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1523	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1524	elif [[ "$source_list" != "" && $restart_run != true ]]
1525	then
1526
1527	cd $source_path
1528
1529	for filename in $source_list
1530	do
1531
1532	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1533	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1534	then
1535	printf "\n +++ source code file: $filename"
1536	printf "\n must not contain (\"/\") "
1537	locat=source; exit
1538	fi
1539
1540	if [[ ! -f $filename ]]
1541	then
1542	printf "\n +++ source code file: $filename"
1543	printf "\n does not exist"
1544	locat=source; exit
1545	else
1546	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1547	fi
1548
1549	done
1550
1551	cd - > /dev/null
1552
1553	fi
1554
1555
1556	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1557	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1558	if [[ $restart_run != true ]]
1559	then
1560
1561	if [[ ! -f "$source_path/$mainprog" ]]
1562	then
1563	printf "\n\n +++ main program: $mainprog"
1564	printf "\n does not exist in source directory"
1565	printf "\n \"$source_path\"\n"
1566	locat=source; exit
1567	else
1568	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1569	then
1570	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1571	source_list=${mainprog}" $source_list"
1572	fi
1573	fi
1574	fi
1575
1576
1577	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1578	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1579	if [[ "$restart_run" != true ]]
1580	then
1581	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1582	if [[ ! -f $makefile ]]
1583	then
1584	printf "\n +++ file \"$makefile\" does not exist"
1585	locat=make; exit
1586	else
1587	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1588	fi
1589	fi
1590
1591
1592	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1593	if [[ $restart_run != true && "$add_source_path" != "" ]]
1594	then
1595
1596	# DOES THE DIRECTORY EXIST?
1597	if [[ ! -d $add_source_path ]]
1598	then
1599	printf "\n\n +++ WARNING: additional source code directory"
1600	printf "\n \"$add_source_path\" "
1601	printf "\n does not exist or is not a directory."
1602	printf "\n No source code will be used from this directory!\n"
1603	add_source_path=""
1604	if [[ $silent == false ]]
1605	then
1606	sleep 3
1607	fi
1608	else
1609
1610	cd $add_source_path
1611	found=false
1612
1613	Names=$(ls -1 *.f90 2>&1)
1614	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1615	Names=$(ls -1 *.F90 2>&1)
1616	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1617	Names=$(ls -1 *.F 2>&1)
1618	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1619	Names=$(ls -1 *.f 2>&1)
1620	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1621	Names=$(ls -1 *.c 2>&1)
1622	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1623
1624	cd - > /dev/null
1625	cd SOURCES_FOR_RUN_$fname
1626
1627	# COPY MAKEFILE IF EXISTING
1628	if [[ -f $add_source_path/Makefile ]]
1629	then
1630	printf "\n\n *** user Makefile from directory"
1631	printf "\n \"$add_source_path\" is used \n"
1632	if [[ $silent == false ]]
1633	then
1634	sleep 1
1635	fi
1636	cp $add_source_path/Makefile .
1637	fi
1638
1639	for dateiname in $AddFilenames
1640	do
1641	if [[ -f $dateiname ]]
1642	then
1643	printf "\n +++ source code file \"$dateiname\" found in additional"
1644	printf "\n source code directory \"$add_source_path\" "
1645	printf "\n but was also given with option \"-s\" which means that it should be taken"
1646	printf "\n from directory \"$source_path\"."
1647	locat=source; exit
1648	fi
1649
1650	cp $add_source_path/$dateiname .
1651	source_list="$source_list $dateiname"
1652
1653	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1654	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1655	then
1656	printf "\n\n +++ user file \"$dateiname\" "
1657	printf "\n is not listed in Makefile \n"
1658	locat=source; exit
1659	else
1660
1661	if [[ $found = false ]]
1662	then
1663	found=true
1664	printf "\n\n *** following user file(s) added to the"
1665	printf " files to be translated:\n "
1666	fi
1667	printf "$dateiname "
1668	if [[ $silent == false ]]
1669	then
1670	sleep 0.5
1671	fi
1672
1673	fi
1674	done
1675	[[ $found = true ]] && printf "\n"
1676	cd - > /dev/null
1677	fi
1678	fi
1679
1680
1681	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1682	# TO THE LIST OF FILES TO BE COMPILED
1683	if [[ $restart_run != true && -n $package_list ]]
1684	then
1685
1686	cd $source_path
1687
1688	for package in $package_list
1689	do
1690
1691	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1692
1693	# DETERMINE FILES BELONGING TO THE PACKAGE
1694	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1695	# THE NAME OF THE DIRECTORY
1696	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1697
1698
1699	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1700	# IF THEY ARE NOT ALREADY PART OF THE LIST
1701	for source_list_name in $package_source_list
1702	do
1703	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1704	then
1705
1706	# ONLY TAKE FILES WITH VALID SUFFIX
1707	ending=`echo $source_list_name \| cut -f2 -d.`
1708	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1709	then
1710	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1711	source_list="$source_list $source_list_name"
1712	fi
1713	fi
1714	done
1715	done
1716
1717	cd - > /dev/null
1718	fi
1719
1720	fi # do_compile=true
1721
1722
1723	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1724	# AND SET PRE-PROCESSOR DIRECTIVES
1725	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1726	then
1727
1728	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1729	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1730	then
1731	cpp_options="${cpp_options},-D__ibm=__ibm"
1732	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1733	then
1734	cpp_options="$cpp_options -D__nec"
1735	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1736	then
1737	cpp_options="$cpp_options -D__lc"
1738	else
1739	cpp_options="$cpp_options -D__$localhost"
1740	fi
1741
1742	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1743	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1744	then
1745	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1746	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1747	else
1748	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1749	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1750	fi
1751
1752	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1753	if [[ -n $package_list ]]
1754	then
1755	for package in $package_list
1756	do
1757	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1758	then
1759	if [[ $package != "dvrp_graphics+1PE" ]]
1760	then
1761	cpp_options="${cpp_options},-D__$package=__$package"
1762	else
1763	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1764	export use_seperate_pe_for_dvrp_output=true
1765	fi
1766	else
1767	if [[ $package != "dvrp_graphics+1PE" ]]
1768	then
1769	cpp_options="$cpp_options -D__$package"
1770	else
1771	cpp_options="$cpp_options -D__dvrp_graphics"
1772	export use_seperate_pe_for_dvrp_output=true
1773	fi
1774	fi
1775	done
1776	fi
1777
1778	# SET DIRECTIVES GIVEN BY OPTION -D
1779	if [[ -n $cpp_opts ]]
1780	then
1781	for popts in $cpp_opts
1782	do
1783	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1784	then
1785	cpp_options="${cpp_options},-D__$popts=__$popts"
1786	else
1787	cpp_options="$cpp_options -D__$popts"
1788	fi
1789	done
1790	fi
1791
1792	else
1793
1794
1795	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1796	if [[ $do_remote = false ]]
1797	then
1798	if [[ ! -f $executable ]]
1799	then
1800	printf "\n +++ executable file: $executable"
1801	printf "\n does not exist"
1802	locat=executable; exit
1803	fi
1804	fi
1805	fi
1806
1807
1808	# DETERMINE THE JOB MODE
1809	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1810	then
1811	if [[ "$LOADLBATCH" = yes ]]
1812	then
1813	batch_job=.TRUE.
1814	jobmo=BATCH
1815	else
1816	batch_job=.FALSE.
1817	jobmo=INTERACTIVE
1818	fi
1819	else
1820	if [[ "$ENVIRONMENT" = BATCH ]]
1821	then
1822	batch_job=.TRUE.
1823	jobmo=BATCH
1824	else
1825	batch_job=.FALSE.
1826	jobmo=INTERACTIVE
1827	fi
1828	fi
1829
1830	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1831	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1832	then
1833	printf "\n +++ no interactive runs allowed on host \"$host\" "
1834	printf "\n please submit batch job using mrun option \"-b\" \n"
1835	locat=normal; exit
1836	fi
1837
1838
1839	# CHECK, IF USER DEFINED A COMPILER
1840	if [[ "$compiler_name" = "" ]]
1841	then
1842
1843	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1844	locat=compiler_name; exit
1845
1846	fi
1847
1848
1849	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1850
1851	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1852	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1853	then
1854	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1855	if [[ "$kennung" = "" ]]
1856	then
1857	kennung=$RANDOM
1858	fi
1859	else
1860	kennung=$RANDOM
1861	fi
1862
1863	if [[ "$tmp_user_catalog" = "" ]]
1864	then
1865	if [[ $localhost = ibmh ]]
1866	then
1867	tmp_user_catalog=$SCRATCH
1868	elif [[ $localhost = nech ]]
1869	then
1870	tmp_user_catalog=$WRKSHR
1871	else
1872	tmp_user_catalog=/tmp
1873	fi
1874	fi
1875	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1876
1877
1878	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1879	if [[ "$tmp_data_catalog" = "" ]]
1880	then
1881	if [[ $localhost = nech ]]
1882	then
1883	tmp_data_catalog=$WRKSHR/mrun_restart_data
1884	else
1885	tmp_data_catalog=/tmp/mrun_restart_data
1886	fi
1887	fi
1888
1889
1890	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1891	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1892	then
1893	eval fopts=\"$fopts\"
1894	eval lopts=\"$lopts\"
1895	fi
1896
1897
1898
1899	# DETERMINE COMPILE- AND LINK-OPTIONS
1900	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1901	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1902	ROPTS="$ropts"
1903	# 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 ]]
1904	# then
1905	XOPT="-X $numprocs"
1906	# fi
1907
1908
1909
1910	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1911	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1912	done=false
1913	while [[ $done = false ]]
1914	do
1915	cputime=$cpumax
1916	if (( $cputime == 0 ))
1917	then
1918	if [[ $do_batch = true ]]
1919	then
1920	printf "\n +++ cpu-time is undefined"
1921	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1922	printf "\n >>> "
1923	read cputime 1>/dev/null 2>&1
1924	else
1925	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1926	fi
1927	else
1928	done=true
1929	fi
1930	cpumax=$cputime
1931	done
1932
1933	(( minuten = cputime / 60 ))
1934	(( sekunden = cputime - minuten * 60 ))
1935
1936
1937	# CHECK THE MEMORY DEMAND
1938	if [[ $do_batch = true ]]
1939	then
1940	done=false
1941	while [[ $done = false ]]
1942	do
1943	if (( memory == 0 ))
1944	then
1945	printf "\n +++ memory demand is undefined"
1946	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1947	printf "\n >>> "
1948	read memory 1>/dev/null 2>&1
1949	else
1950	done=true
1951	fi
1952	done
1953	fi
1954
1955
1956	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1957	if [[ $do_remote = true && -z $remote_username ]]
1958	then
1959	while [[ -z $remote_username ]]
1960	do
1961	printf "\n +++ username on remote host \"$host\" is undefined"
1962	printf "\n >>> Please type username:"
1963	printf "\n >>> "
1964	read remote_username
1965	done
1966	mc="$mc -u$remote_username"
1967	fi
1968
1969	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1970	if [[ "$login_init_cmd" != "" ]]
1971	then
1972	export init_cmds="${login_init_cmd};"
1973	fi
1974
1975
1976	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1977	if [[ "$modules" != "" ]]
1978	then
1979	if [[ $host = lctit ]]
1980	then
1981	export module_calls=". $modules"
1982	else
1983	export module_calls="module load ${modules};"
1984	fi
1985	fi
1986
1987	# OUTPUT OF THE MRUN-HEADER
1988	calltime=$(date)
1989	printf "\n"
1990	printf "#------------------------------------------------------------------------# \n"
1991	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1992	printf "\| \| \n"
1993	spalte1="called on:"; spalte2=$localhost_realname
1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1995	if [[ $do_remote = true ]]
1996	then
1997	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1998	else
1999	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2000	fi
2001	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2002	if [[ -n $numprocs ]]
2003	then
2004	if [[ $run_coupled_model = false ]]
2005	then
2006	spalte1="number of PEs:"; spalte2=$numprocs
2007	else
2008	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2009	fi
2010	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2011	fi
2012	if [[ -n $tasks_per_node ]]
2013	then
2014	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	if (( remaining_pes > 0 ))
2017	then
2018	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2020	fi
2021	fi
2022	if [[ $maximum_parallel_io_streams != $numprocs ]]
2023	then
2024	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2026	fi
2027	if [[ $use_openmp = true ]]
2028	then
2029	spalte1="threads per task:"; spalte2="$threads_per_task"
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	fi
2032	printf "\| \| \n"
2033	if [[ $do_compile = true ]]
2034	then
2035	if [[ "$mopts" != "" ]]
2036	then
2037	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2038	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2039	zeile=$(echo "$mopts" \| cut -c46-)
2040	while [[ "$zeile" != "" ]]
2041	do
2042	spalte1=""
2043	spalte2=$(echo "$zeile" \| cut -c-45)
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	zeile=$(echo "$zeile" \| cut -c46-)
2046	done
2047	fi
2048
2049	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	zeile=$(echo "$cpp_options" \| cut -c46-)
2052	while [[ "$zeile" != "" ]]
2053	do
2054	spalte1=""
2055	spalte2=$(echo "$zeile" \| cut -c-45)
2056	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2057	zeile=$(echo "$zeile" \| cut -c46-)
2058	done
2059
2060	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2061	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2062	zeile=$(echo "$fopts" \| cut -c46-)
2063	while [[ "$zeile" != "" ]]
2064	do
2065	spalte1=""
2066	spalte2=$(echo "$zeile" \| cut -c-45)
2067	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2068	zeile=$(echo "$zeile" \| cut -c46-)
2069	done
2070
2071	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2072	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2073	zeile=$(echo "$lopts" \| cut -c46-)
2074	while [[ "$zeile" != "" ]]
2075	do
2076	spalte1=""
2077	spalte2=$(echo "$zeile" \| cut -c-45)
2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2079	zeile=$(echo "$zeile" \| cut -c46-)
2080	done
2081
2082	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2083	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2084	zeile=$(echo "$modules" \| cut -c46-)
2085	while [[ "$zeile" != "" ]]
2086	do
2087	spalte1=""
2088	spalte2=$(echo "$zeile" \| cut -c-45)
2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2090	zeile=$(echo "$zeile" \| cut -c46-)
2091	done
2092
2093	spalte1="main program:"; spalte2=$mainprog
2094	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2095	else
2096	spalte1=executable:; spalte2=$executable
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098	fi
2099	printf "\| \| \n"
2100	spalte1="base name of files:"; spalte2=$fname
2101	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2102	if [[ $fname != $afname ]]
2103	then
2104	spalte1="base name of input files:"; spalte2=$afname
2105	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2106	fi
2107	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2108	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2109	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2110	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2111
2112	if [[ "$ocean_file_appendix" = true ]]
2113	then
2114	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2115	fi
2116
2117	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2118	then
2119	spalte1="memory demand / PE":; spalte2="$memory MB"
2120	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2121	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2122	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2123	fi
2124
2125	if [[ $do_compile = true ]]
2126	then
2127	printf "\| \| \n"
2128	printf "\| Files to be compiled: \| \n"
2129	zeile=$source_list
2130	while [[ "$zeile" != "" ]]
2131	do
2132	linestart=$(echo $zeile \| cut -c-70)
2133	printf "\| %-70s \| \n" "$linestart"
2134	zeile=$(echo "$zeile" \| cut -c71-)
2135	done
2136	fi
2137	printf "#------------------------------------------------------------------------#"
2138
2139
2140
2141	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2142	if [[ $do_trace = true ]]
2143	then
2144	(( i = 0 ))
2145	while (( i < iin ))
2146	do
2147	(( i = i + 1 ))
2148	if (( i == 1 ))
2149	then
2150	printf "\n\n >>> INPUT-file assignments:\n"
2151	fi
2152	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2153	done
2154	(( i = 0 ))
2155	while (( i < iout ))
2156	do
2157	(( i = i + 1 ))
2158	if (( i == 1 ))
2159	then
2160	printf "\n\n >>> OUTPUT-file assignments:\n"
2161	fi
2162	printf "\n ${localout[$i]} : ${pathout[$i]}"
2163	done
2164	(( i = 0 ))
2165	while (( i < iic ))
2166	do
2167	(( i = i + 1 ))
2168	if (( i == 1 ))
2169	then
2170	printf "\n\n >>> INPUT-commands:\n"
2171	fi
2172	printf "\n ${in_command[$i]}"
2173	done
2174	(( i = 0 ))
2175	while (( i < ioc ))
2176	do
2177	(( i = i + 1 ))
2178	if (( i == 1 ))
2179	then
2180	printf "\n\n >>> OUTPUT-commands:\n"
2181	fi
2182	printf "\n ${out_command[$i]}"
2183	done
2184	fi
2185
2186	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2187	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2188	then
2189	antwort=dummy
2190	printf "\n\n"
2191	printf " >>> everything o.k. (y/n) ? "
2192	while read antwort
2193	do
2194	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2195	then
2196	printf " >>> everything o.k. (y/n) ? "
2197	else
2198	break
2199	fi
2200	done
2201	if [[ $antwort = n \|\| $antwort = N ]]
2202	then
2203	locat=user_abort; (( iec = 0 )); exit
2204	fi
2205	if [[ $do_batch = true ]]
2206	then
2207	printf " >>> batch-job will be created and submitted"
2208	else
2209	printf " >>> MRUN will now continue to execute on this machine"
2210	fi
2211	fi
2212
2213
2214	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2215	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2216	check_depository="${working_directory}/trunk/UTIL"
2217	check_sources="${working_directory}/tmp_check_namelist_files"
2218	skip_check=false
2219
2220	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2221	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2222	then
2223	skip_check=true
2224	reason="run on remote host or parameter file check has not been compiled."
2225	fi
2226	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2227	then
2228	skip_check=true
2229	reason="parameter file check has not been compiled."
2230	fi
2231
2232	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2233	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2234	then
2235	skip_check=true
2236	reason="serial run."
2237	fi
2238
2239	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2240	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2241	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2242	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2243	if [[ $check_namelist_files == false ]]
2244	then
2245	skip_check=true
2246	reason="-z option set."
2247	fi
2248
2249	if [[ $fromhost != $localhost ]]
2250	then
2251	skip_check=true
2252	reason="submitting host is local host."
2253	fi
2254
2255	if [[ $run_coupled_model == true ]]
2256	then
2257	skip_check=true
2258	reason="coupled run."
2259	fi
2260
2261	if [[ $restart_run == true ]]
2262	then
2263	skip_check=true
2264	reason="restart run."
2265	fi
2266
2267	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2268	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2269	last_char=`echo $filename_input \| cut -c $last_char_int`
2270	if [[ "$last_char" == "f" ]]
2271	then
2272	skip_check=true
2273	reason="restart run."
2274	fi
2275
2276	if [[ $skip_check == false ]]
2277	then
2278	tmp_check=${working_directory}/tmp_check
2279
2280	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2281	# NOT NECESSARILY REQUIRED
2282	line=""
2283	found=false
2284	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2285	while read line1
2286	do
2287	line="$line1"
2288	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2289	then
2290	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2291	found=true
2292	fi
2293	done < $tmp_check
2294
2295	if [[ $found = false ]]
2296	then
2297	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2298	fi
2299
2300	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2301	# NOT NECESSARILY REQUIRED
2302	line=""
2303	found=false
2304	grep "NUDGING_DATA" $config_file > $tmp_check
2305	while read line1
2306	do
2307	line="$line1"
2308	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2309	then
2310	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2311	found=true
2312	fi
2313	done < $tmp_check
2314
2315	if [[ $found = false ]]
2316	then
2317	printf "\n +++ no NUDGING list entry found in the configuration file."
2318	fi
2319
2320	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2321	# NOT NECESSARILY REQUIRED
2322	line=""
2323	found=false
2324	grep "LSF_DATA" $config_file > $tmp_check
2325	while read line1
2326	do
2327	line="$line1"
2328	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2329	then
2330	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2331	found=true
2332	fi
2333	done < $tmp_check
2334
2335	if [[ $found = false ]]
2336	then
2337	printf "\n +++ no LSF list entry found in the configuration file."
2338	fi
2339
2340	rm -rf ${working_directory}/tmp_check
2341
2342	# CHECK IF THE P3DF FILE MUST BE CHECKED
2343	for item in $input_list
2344	do
2345	if [[ "$item" == "restart" ]]
2346	then
2347	check_restart=1
2348	else
2349	check_restart=0
2350	fi
2351	done
2352
2353	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2354	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2355	then
2356	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2357	locat=check_namelist; exit
2358	fi
2359
2360	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2361	if [[ $check_restart == 1 ]]
2362	then
2363
2364	filenamef="${filename_input}f"
2365	if [[ ! -f $filenamef ]]
2366	then
2367	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2368	check_restart=0
2369	answer=dummy
2370	printf "\n\n"
2371
2372	if [[ $silent == false ]]
2373	then
2374	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2375	do
2376	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2377	read answer
2378	done
2379	if [[ $answer = a \|\| $answer = A ]]
2380	then
2381	printf "\n +++ Aborting...."
2382	locat=normal; exit
2383	fi
2384	fi
2385	else
2386	check_restart=1
2387	fi
2388	fi
2389
2390	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2391	mkdir $check_sources
2392	cd $check_sources
2393
2394
2395	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2396	if [[ -d $add_source_path ]]
2397	then
2398	printf "\n\n *** copying files from $check_depository"
2399	cp $check_depository/check_namelist_files.tar ./
2400
2401	printf "\n\n *** untar of makefile and source files in $check_sources"
2402	tar -xf check_namelist_files.tar > /dev/null 2>&1
2403
2404	printf "\n\n *** adding user code."
2405	cp $add_source_path/* ./
2406	touch check_namelist_files.f90
2407
2408	# GET COMPILER OPTIONS AND PERFORM MAKE
2409	printf "\n\n *** compiling code if necessary...\n"
2410
2411	# workaround for batch jobs on local machine (lcxe6)
2412	if [[ $do_batch == true && $do_remote == false ]]
2413	then
2414	eval $init_cmds
2415	fi
2416
2417	# GET CHECK OPTIONS
2418	line=""
2419	found=false
2420
2421	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2422
2423	while read line1
2424	do
2425
2426	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2427	then
2428	line="$line1"
2429	fi
2430
2431	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2432	then
2433	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2434	line="$line "
2435	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'`
2436	found=true
2437	fi
2438
2439	done < $tmp_check
2440	copts_check="$copts_check -D__check -D__parallel"
2441
2442	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2443
2444	# GET MAKE OUTPUT
2445	if [[ $? != 0 ]]
2446	then
2447	printf "\n +++ error during make."
2448	answer=dummy
2449	printf "\n\n"
2450	if [[ $silent == false ]]
2451	then
2452	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2453	do
2454	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2455	read answer
2456	done
2457	if [[ $answer = a \|\| $answer = A ]]
2458	then
2459	printf "\n +++ Aborting..."
2460	rm -rf $check_sources
2461	locat=normal; exit
2462	else
2463	skip_check=true
2464	fi
2465	else
2466	skip_check=true
2467	fi
2468	fi
2469	else
2470	cp $PALM_BIN/check_namelist_files.x ./
2471	fi
2472
2473	cp $filename_input ./PARIN
2474	if [[ $check_restart == 1 ]]
2475	then
2476	cp $filenamef ./PARINF
2477	fi
2478
2479	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2480	then
2481	printf "\n *** adding topography data"
2482	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2483
2484	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2485	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2486	# WHICH REQUIRE SUFFICIENT MEMORY
2487	ulimit -s unlimited
2488	fi
2489
2490	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2491	then
2492	printf "\n *** adding nudging data"
2493	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2494	fi
2495
2496	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2497	then
2498	printf "\n *** adding large scale forcing data"
2499	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2500	fi
2501
2502	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2503	cat > ENVPAR << %%END%%
2504	&envpar run_identifier = '$fname', host = '$host',
2505	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2506	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2507	maximum_cpu_time_allowed = ${cpumax}.,
2508	revision = '$global_revision',
2509	local_dvrserver_running = $local_dvrserver_running /
2510
2511	%%END%%
2512
2513	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2514	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2515	then
2516	printf "\n +++ WARNING: check_namelist_files.x not found."
2517	answer=dummy
2518	printf "\n\n"
2519
2520	if [[ $silent == false ]]
2521	then
2522	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2523	do
2524	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2525	read answer
2526	done
2527	if [[ $answer = a \|\| $answer = A ]]
2528	then
2529	printf "\n +++ Aborting..."
2530	rm -rf $check_sources
2531	locat=normal; exit
2532	else
2533	printf "\n *** skipping parameter file check."
2534	fi
2535	fi
2536
2537	elif [[ $skip_check == false ]]
2538	then
2539	# STARTING THE PARAMETER FILE CHECK
2540	printf "\n\n *** starting parameter file check..."
2541
2542	# CHECKING THE P3D FILE
2543	printf "\n\n (1) checking $filename_input"
2544	echo "$numprocs 0 0" > VARIN
2545	errors=`./check_namelist_files.x < VARIN 2>&1`
2546
2547	check_error=false
2548	if [[ "$errors" == "" ]]
2549	then
2550	printf " --> o.k."
2551	else
2552	printf " --> failed."
2553	check_error=true
2554	printf "\n\n $errors"
2555	fi
2556
2557	# CHECKING THE PD3F FILE IF NECESSARY
2558	if [[ $check_restart == 1 && $check_error == false ]]
2559	then
2560	printf "\n\n (2) checking $filenamef"
2561
2562	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2563	# IN &INIPAR LIST
2564	found=false
2565	cat PARINF \| while read line
2566	do
2567	line=$(echo $line\|sed 's/ //g')
2568	if [[ $line == "&inipar" ]]
2569	then
2570	start_search=true
2571	fi
2572
2573	if [[ $start_search == true ]]
2574	then
2575	if [[ $line == "initializing_actions='read_restart_data'" ]]
2576	then
2577	found=true
2578	break
2579	fi
2580	fi
2581
2582	if [[ $line == "/" ]]
2583	then
2584	start_search=false
2585	fi
2586
2587	done
2588
2589	if [[ $found = false ]]
2590	then
2591	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2592	printf "\n in &inipar list in $fname$p3df_suffix."
2593	rm -rf $check_sources
2594	locat=check_namelist; exit
2595	fi
2596
2597	# READ max_user_pr FROM FILES
2598	if [[ -f parin_for_check ]]
2599	then
2600	read max_pr_user < parin_for_check
2601	else
2602	max_user_pr=0
2603	fi
2604
2605	echo "$numprocs 1 $max_pr_user" > VARIN
2606	errors=`./check_namelist_files.x < VARIN 2>&1`
2607
2608	if [[ "$errors" == "" ]]
2609	then
2610	printf " --> o.k."
2611	else
2612	printf " --> failed."
2613	check_error=true
2614	printf "\n\n $errors"
2615	fi
2616	fi
2617
2618	# REPORT ERRORS AND CONTINUE/EXIT
2619	if [[ $check_error == true ]]
2620	then
2621	printf "\n +++ errors found in the parameter file!\n"
2622	answer=dummy
2623	printf "\n\n"
2624
2625	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2626	do
2627	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2628	read answer
2629	done
2630
2631	if [[ $answer = a \|\| $answer = A ]]
2632	then
2633	printf "\n +++ Aborting..."
2634	rm -rf $check_sources
2635	locat=normal; exit
2636	fi
2637	else
2638	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2639	fi
2640	rm -rf $check_sources
2641	fi
2642	else
2643	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2644	fi
2645
2646	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2647	rm -rf $check_sources
2648	cd $working_directory
2649
2650	# DETERMINE PATH FOR MAKE DEPOSITORY
2651	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2652	then
2653
2654	line=""
2655	grep "%depository_path" $config_file > tmp_mrun
2656	while read line
2657	do
2658	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2659	then
2660	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2661	then
2662	global_depository_path=`echo $line \| cut -d" " -s -f2`
2663	fi
2664	fi
2665	done < tmp_mrun
2666
2667	line=""
2668	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2669	while read line
2670	do
2671	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2672	then
2673	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2674	then
2675	local_depository_path=`echo $line \| cut -d" " -s -f2`
2676	fi
2677	fi
2678	done < tmp_mrun
2679
2680	if [[ "$local_depository_path" = "" ]]
2681	then
2682	if [[ "$global_depository_path" != "" ]]
2683	then
2684	local_depository_path=$global_depository_path
2685	else
2686	printf "\n\n +++ no depository path found in configuration file"
2687	printf "\n for local host \"$localhost\" "
2688	printf "\n please set \"\%depository_path\" in configuration file\n"
2689	locat=config_file; exit
2690	fi
2691	fi
2692	eval local_depository_path=$local_depository_path
2693	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2694	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2695
2696
2697	basename=`echo $mainprog \| cut -f1 -d"."`
2698	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2699	if [[ ! -f $make_depository ]]
2700	then
2701	printf "\n"
2702	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2703	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2704	fi
2705
2706	fi
2707
2708
2709	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2710	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2711	if [[ $do_batch = false ]]
2712	then
2713
2714
2715	# CREATE THE TEMPORARY WORKING DIRECTORY
2716	mkdir -p $TEMPDIR
2717	chmod go+rx $TEMPDIR
2718	tmpcreate=true
2719
2720
2721	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2722	# INTO THE TEMPORARY WORKING DIRECTORY
2723	if [[ $do_compile = true ]]
2724	then
2725
2726	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2727	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2728	if [[ $localhost = nech ]]
2729	then
2730	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2731	if mkdir -p $TEMPDIR_COMPILE
2732	then
2733	printf "\n *** \"$TEMPDIR_COMPILE\" "
2734	printf "\n is generated as temporary directory for cross compiling\n"
2735	else
2736	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2737	printf "\n needed for cross compilation failed"
2738	locat=compile
2739	exit
2740	fi
2741	else
2742	TEMPDIR_COMPILE=$TEMPDIR
2743	fi
2744
2745	cp $make_depository $TEMPDIR_COMPILE
2746	cd $TEMPDIR_COMPILE
2747	tar -xf $make_depository > /dev/null 2>&1
2748	cd - > /dev/null
2749
2750	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2751	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2752	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2753	then
2754	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2755	else
2756	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2757	fi
2758
2759	else
2760
2761	cp $executable ${TEMPDIR}/a.out
2762
2763	fi
2764
2765
2766	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2767	cd $TEMPDIR
2768	printf "\n *** changed to temporary directory: $TEMPDIR"
2769
2770
2771	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2772	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2773	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2774	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2775	(( i = 0 ))
2776	while (( i < iout ))
2777	do
2778	(( i = i + 1 ))
2779	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2780	then
2781	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2782	else
2783	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2784	fi
2785	done
2786
2787
2788	# IF REQUIRED, START WITH COMPILING
2789	if [[ $do_compile = true ]]
2790	then
2791
2792
2793	if [[ -f a.out ]]
2794	then
2795
2796	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2797	printf "\n\n\n *** executable a.out found"
2798	printf "\n no compilation required \n"
2799
2800	else
2801
2802	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2803	printf "\n\n\n *** compilation starts \n$dashes\n"
2804	printf " *** compilation with make using following options:\n"
2805	printf " make depository: $make_depository"
2806	if [[ "$mopts" != "" ]]
2807	then
2808	printf " make options: $mopts\n"
2809	fi
2810	printf " compilername: $compiler_name\n"
2811	printf " compiler options: $fopts\n"
2812	printf " preprocessor directives: $cpp_options \n"
2813	printf " linker options: $lopts \n"
2814	if [[ "$modules" != "" ]]
2815	then
2816	printf " modules to be load: $modules \n"
2817	fi
2818	printf " source code files: $source_list \n"
2819
2820	if [[ $localhost = nech ]]
2821	then
2822	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\" "
2823	cp $TEMPDIR_COMPILE/a.out .
2824	[[ $? != 0 ]] && compile_error=true
2825	rm -rf $TEMPDIR_COMPILE
2826	elif [[ $localhost = ibmh ]]
2827	then
2828	printf " compiler is called via ssh on \"plogin1\" \n"
2829	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\" "
2830	[[ ! -f a.out ]] && compile_error=true
2831	continue # STATUS=1, IF a.out EXISTS
2832	elif [[ $localhost = lcflow ]]
2833	then
2834	printf " compiler is called via ssh on \"flow\" \n"
2835	/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\" "
2836	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2837	[[ "$check_for_file" = "" ]] && compile_error=true
2838	continue # STATUS=1, IF a.out EXISTS
2839	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2840	then
2841	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2842	else
2843	[[ "$init_cmds" != "" ]] && eval $init_cmds
2844	[[ "$module_calls" != "" ]] && eval $module_calls
2845	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2846	fi
2847
2848	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2849	then
2850	printf "\n +++ error occured while compiling or linking"
2851	locat=compile
2852
2853	exit
2854	else
2855	printf "$dashes\n *** compilation finished \n"
2856	fi
2857
2858	fi
2859
2860	fi
2861
2862
2863	# PROVIDE THE INPUT FILES
2864	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2865	(( i = 0 ))
2866	while (( i < iin ))
2867	do
2868	(( i = i + 1 ))
2869	if (( i == 1 ))
2870	then
2871	printf "\n\n *** providing INPUT-files:\n$dashes"
2872	fi
2873
2874
2875	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2876	if [[ "${transin[$i]}" = unavailable ]]
2877	then
2878	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2879	then
2880	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2881	printf "\n is not available!"
2882	else
2883	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2884	printf "\n is not available!"
2885	fi
2886	continue
2887	fi
2888
2889	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2890	files_for_pes=false; datentyp=file
2891	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2892	then
2893	files_for_pes=true; datentyp=directory
2894	actionin[$i]=""
2895	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2896	then
2897	actionin[$i]=""
2898	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2899	then
2900	files_for_pes=true; datentyp=directory
2901	actionin[$i]="ar"
2902	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2903	then
2904	actionin[$i]="ar"
2905	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2906	then
2907	files_for_pes=true; datentyp=directory
2908	actionin[$i]="fl"
2909	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2910	then
2911	actionin[$i]="fl"
2912	fi
2913
2914	if [[ $files_for_pes = true ]]
2915	then
2916	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2917	else
2918	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2919	fi
2920
2921	# INPUT-FILE FOR A RESTART RUN.
2922	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2923	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2924	if [[ "${actionin[$i]}" = fl ]]
2925	then
2926	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2927	if [[ $files_for_pes = false ]]
2928	then
2929	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2930	then
2931	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2932	got_tmp[$i]=true
2933	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2934	then
2935	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2936	printf "\n *** trying to use backup copy in \"$WORK\" "
2937	cp $WORK/${frelin[$i]} ${localin[$i]}
2938	else
2939	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2940	printf "\n or \"$tmp_data_catalog\" does not exist!"
2941	printf "\n *** trying to get copy from archive"
2942	actionin[$i]=ar
2943	fi
2944	else
2945	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2946	then
2947	mkdir ${localin[$i]}
2948	cd $tmp_data_catalog/${frelin[$i]}
2949	for file in $(ls *)
2950	do
2951	ln $file $TEMPDIR/${localin[$i]}
2952	done
2953	cd $TEMPDIR
2954	got_tmp[$i]=true
2955	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2956	then
2957	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2958	printf "\n *** trying to use backup copy in \"$WORK\" "
2959	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2960	else
2961	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2962	printf "\n or \"$tmp_data_catalog\" does not exist!"
2963	printf "\n *** trying to get copy from archive"
2964	actionin[$i]=ar
2965	fi
2966	fi
2967	fi
2968
2969
2970	# FILE IS STORED ON THE ARCHIVE SYSTEM
2971	if [[ "${actionin[$i]}" = ar ]]
2972	then
2973
2974	if [[ $files_for_pes = false ]]
2975	then
2976	printf "\n file will be restored from archive-system ($archive_system)!"
2977	else
2978	printf "\n directory will be restored from archive-system ($archive_system)!"
2979	fi
2980
2981	file_restored=false
2982
2983	if [[ $archive_system = asterix ]]
2984	then
2985	do_stagein=true
2986	(( stagein_anz = 0 ))
2987	while [[ $do_stagein = true ]]
2988	do
2989	if [[ $files_for_pes = false ]]
2990	then
2991	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2992	else
2993	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2994	fi
2995	cat STAGEIN_OUTPUT
2996	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2997	then
2998	file_restored=true
2999	do_stagein=false
3000	else
3001	(( stagein_anz = stagein_anz + 1 ))
3002	if (( stagein_anz == 10 ))
3003	then
3004	printf "\n +++ stagein stoped after 10 tries"
3005	locat=stage
3006	exit
3007	fi
3008	printf "\n +++ restoring from archive failed, trying again:"
3009	sleep 900
3010	fi
3011	done
3012	elif [[ $archive_system = DMF ]]
3013	then
3014	if [[ $files_for_pes = false ]]
3015	then
3016	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3017	locat=DMF
3018	exit
3019	else
3020	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3021	cp -r $ARCHIVE/${frelin[$i]} $PWD
3022	file_restored=true
3023	fi
3024	elif [[ $archive_system = tivoli ]]
3025	then
3026	if [[ $files_for_pes = false ]]
3027	then
3028	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3029	else
3030	(( inode = 0 ))
3031	while (( inode < nodes ))
3032	do
3033	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3034	(( inode = inode + 1 ))
3035	done
3036	fi
3037	file_restored=true
3038	elif [[ $archive_system = ut ]]
3039	then
3040	if [[ $files_for_pes = false ]]
3041	then
3042	cp $UT/${frelin[$i]} .
3043	else
3044	(( inode = 0 ))
3045	while (( inode < nodes ))
3046	do
3047	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3048	(( inode = inode + 1 ))
3049	done
3050	fi
3051	file_restored=true
3052	else
3053	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3054	locat=rearchive
3055	exit
3056	fi
3057
3058	if [[ $file_restored = true ]]
3059	then
3060
3061	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3062	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3063	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3064	if [[ $files_for_pes = false ]]
3065	then
3066	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3067	else
3068	mkdir $tmp_data_catalog/${frelin[$i]}
3069	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3070	fi
3071	got_tmp[$i]=true
3072
3073	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3074	mv ${frelin[$i]} ${localin[$i]}
3075
3076	fi
3077	fi
3078
3079
3080	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3081	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3082	then
3083
3084	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3085	then
3086
3087	# FILE COPIES ARE PROVIDED FOR ALL CORES
3088	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3089	printf "\n file will be provided for $numprocs processors"
3090	mkdir ${localin[$i]}
3091	ival=$numprocs
3092	(( ii = 0 ))
3093	while (( ii <= ival-1 ))
3094	do
3095	if (( ii < 10 ))
3096	then
3097	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3098	elif (( ii < 100 ))
3099	then
3100	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3101	elif (( ii < 1000 ))
3102	then
3103	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3104	else
3105	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3106	fi
3107	(( ii = ii + 1 ))
3108	done
3109
3110	else
3111
3112	if [[ $files_for_pes = true ]]
3113	then
3114
3115	# PROVIDE FILES FOR EACH CORE
3116	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3117	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3118	printf "\n providing $numprocs files for the respective processors"
3119	mkdir ${localin[$i]}
3120	if [[ $link_local_input = true ]]
3121	then
3122	printf " using ln -f\n"
3123	cd ${absnamein[$i]}
3124	for file in $(ls *)
3125	do
3126	ln -f $file ${localin[$i]}
3127	done
3128	cd $TEMPDIR
3129	fi
3130
3131	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3132	if [[ ! -f "${localin[$i]}/_0000" ]]
3133	then
3134	if [[ $link_local_input = true ]]
3135	then
3136	printf " ln failed for .../_0000, using cp...\n"
3137	fi
3138	cp -r ${absnamein[$i]}/* ${localin[$i]}
3139	fi
3140
3141	else
3142
3143	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3144	if [[ $link_local_input = true ]]
3145	then
3146	printf " using ln -f\n"
3147	ln -f ${absnamein[$i]} ${localin[$i]}
3148	fi
3149	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3150	if [[ ! -f "${localin[$i]}" ]]
3151	then
3152	if [[ $link_local_input = true ]]
3153	then
3154	printf " ln failed, using cp...\n"
3155	fi
3156	cp ${absnamein[$i]} ${localin[$i]}
3157	fi
3158	fi
3159	fi
3160	fi
3161
3162	done
3163	if (( i != 0 ))
3164	then
3165	printf "\n$dashes\n *** all INPUT-files provided \n"
3166	fi
3167
3168
3169	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3170	(( i = 0 ))
3171	while (( i < iic ))
3172	do
3173	(( i = i + 1 ))
3174	if (( i == 1 ))
3175	then
3176	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3177	fi
3178	printf "\n >>> ${in_command[$i]}"
3179	eval ${in_command[$i]}
3180	if (( i == iic ))
3181	then
3182	printf "\n$dashes\n"
3183	fi
3184	done
3185
3186
3187	# SET THE REMAINING CPU-TIME
3188	cpurest=${cpumax}.
3189
3190
3191	# START DVR STREAMING SERVER
3192	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3193	then
3194	if [[ "$dvr_server" != "" ]]
3195	then
3196
3197	printf "\n\n *** preparing the dvr streaming server configuration file"
3198
3199	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3200	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3201	if [[ "$running_dvrserver_id" != "" ]]
3202	then
3203
3204	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3205	printf "\n This server is used instead starting a new one!"
3206	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3207
3208	else
3209
3210	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3211	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3212	then
3213	cp ${PALM_BIN}/.dvrserver.config .
3214
3215	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3216	user_id=`id -u`
3217	group_id=`id -g`
3218
3219	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3220	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3221	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3222	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3223	mv .dvrserver.3 .dvrserver.config
3224	rm .dvrserver.1 .dvrserver.2
3225
3226	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3227	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3228	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3229	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3230	local_dvrserver_running=.TRUE.
3231	else
3232	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3233	printf "\n \"$PALM_BIN\" "
3234	locat=dvr
3235	exit
3236	fi
3237
3238	fi
3239
3240	else
3241	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3242	fi
3243	fi
3244
3245
3246	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3247	# (FILE ENVPAR WILL BE READ BY PALM)
3248	cat > ENVPAR << %%END%%
3249	&envpar run_identifier = '$fname', host = '$localhost',
3250	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3251	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3252	maximum_cpu_time_allowed = ${cpumax}.,
3253	revision = '$global_revision',
3254	local_dvrserver_running = $local_dvrserver_running,
3255	batch_job = $batch_job /
3256
3257	%%END%%
3258
3259
3260	# STARTING THE EXECUTABLE
3261	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3262	PATH=$PATH:$TEMPDIR
3263
3264	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3265	if [[ "$mpi_debug" = true ]]
3266	then
3267	export MPI_CHECK_ARGS=1
3268	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3269	fi
3270
3271	if [[ "$totalview" = true ]]
3272	then
3273	printf "\n *** totalview debugger will be used"
3274	tv_opt="-tv"
3275	else
3276	tv_opt=""
3277	fi
3278
3279	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3280	then
3281
3282	#Interactive ALLINEA DEBUG seesion
3283	if [[ "$ENVIRONMENT" != BATCH ]]
3284	then
3285	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3286	then
3287	if [[ "$allinea" = true ]]
3288	then
3289	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3290
3291	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3292	wait
3293	fi
3294	fi
3295	fi
3296
3297	if [[ "$ENVIRONMENT" = BATCH ]]
3298	then
3299	continue
3300	fi
3301	if [[ $localhost = ibmh ]]
3302	then
3303
3304	# SETUP THE IBM MPI ENVIRONMENT
3305	export MP_SHARED_MEMORY=yes
3306	export AIXTHREADS_SCOPE=S
3307	export OMP_NUM_THREADS=$threads_per_task
3308	export AUTHSTATE=files
3309	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3310
3311	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3312	export MP_ADAPTER_USE=shared
3313	export MP_CPU_USE=multiple
3314	export MP_TIMEOUT=1200
3315
3316	unset MP_TASK_AFFINITY
3317
3318	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3319	#(( ii = 1 ))
3320	#while (( ii <= $numprocs ))
3321	#do
3322	# echo $localhost_realname >> hostfile
3323	# (( ii = ii + 1 ))
3324	#done
3325	#export MP_HOSTFILE=hostfile
3326
3327	if [[ "$LOADLBATCH" = yes ]]
3328	then
3329	totalview poe a.out $ROPTS
3330	else
3331	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3332	export TVDSVRLAUNCHCMD=ssh
3333	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3334	fi
3335
3336	fi # END DEBUG MODE
3337
3338	else
3339
3340	# NORMAL EXECUTION
3341	if [[ -n $numprocs ]]
3342	then
3343
3344	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3345	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3346	then
3347
3348	# SETUP THE IBM MPI ENVIRONMENT
3349	if [[ $host != ibmh && $host != ibmkisti ]]
3350	then
3351	export MP_SHARED_MEMORY=yes
3352	export AIXTHREAD_SCOPE=S
3353	export OMP_NUM_THREADS=$threads_per_task
3354	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3355	export AUTHSTATE=files
3356	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3357	# export MP_PRINTENV=yes
3358
3359	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3360	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3361	export MP_WAIT_MODE=poll
3362	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3363	fi
3364
3365	if [[ $host = ibmkisti ]]
3366	then
3367	export LANG=en_US
3368	export MP_SHARED_MEMORY=yes
3369	if [[ $threads_per_task = 1 ]]
3370	then
3371	export MP_SINGLE_THREAD=yes
3372	export MEMORY_AFFINITY=MCM
3373	else
3374	export OMP_NUM_THREADS=$threads_per_task
3375	fi
3376	fi
3377
3378	if [[ "$LOADLBATCH" = yes ]]
3379	then
3380	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3381	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3382	then
3383	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3384	else
3385	if [[ $run_coupled_model = false ]]
3386	then
3387	if [[ "$ocean_file_appendix" = true ]]
3388	then
3389	echo "precursor_ocean" > runfile_atmos
3390	else
3391	echo "precursor_atmos" > runfile_atmos
3392	fi
3393	else
3394	(( iia = $numprocs_atmos / $threads_per_task ))
3395	(( iio = $numprocs_ocean / $threads_per_task ))
3396	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3397	printf "\n using $coupled_mode coupling"
3398	printf "\n\n"
3399	echo "coupled_run $iia $iio" > runfile_atmos
3400	fi
3401	poe ./a.out $ROPTS < runfile_atmos
3402	fi
3403	else
3404	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3405	then
3406	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3407	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3408	then
3409	if [[ -f $hostfile ]]
3410	then
3411	cp $hostfile hostfile
3412	else
3413	(( ii = 1 ))
3414	while (( ii <= $numprocs ))
3415	do
3416	echo $localhost_realname >> hostfile
3417	(( ii = ii + 1 ))
3418	done
3419	fi
3420	export MP_HOSTFILE=hostfile
3421	if [[ $run_coupled_model = false ]]
3422	then
3423	if [[ "$ocean_file_appendix" = true ]]
3424	then
3425	echo "precursor_ocean" > runfile_atmos
3426	else
3427	echo "precursor_atmos" > runfile_atmos
3428	fi
3429	else
3430	(( iia = $numprocs_atmos / $threads_per_task ))
3431	(( iio = $numprocs_ocean / $threads_per_task ))
3432	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3433	printf "\n using $coupled_mode coupling"
3434	printf "\n\n"
3435	echo "coupled_run $iia $iio" > runfile_atmos
3436	fi
3437
3438	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3439
3440	else
3441	if [[ "$host_file" = "" ]]
3442	then
3443	printf "\n +++ no hostfile given in configuration file"
3444	locat=config_file
3445	exit
3446	else
3447	eval host_file=$host_file
3448	fi
3449	export MP_HOSTFILE=$host_file
3450	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3451	fi
3452	fi
3453	elif [[ $host = nech ]]
3454	then
3455	(( ii = nodes ))
3456	if [[ $ii = 1 ]]
3457	then
3458	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3459	export MPIPROGINF=YES
3460	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3461	echo "*** execution on single node with mpirun"
3462	mpirun -np $numprocs ./a.out $ROPTS
3463	else
3464	(( i = 0 ))
3465	while (( i < ii ))
3466	do
3467	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3468	(( i = i + 1 ))
3469	done
3470
3471	echo "#!/bin/sh" > mpi_exec_shell
3472	echo " " >> mpi_exec_shell
3473	echo "set -u" >> mpi_exec_shell
3474	echo "F_ERRCNT=0" >> mpi_exec_shell
3475	echo "MPIPROGINV=YES" >> mpi_exec_shell
3476	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3477	echo "cpurest=$cpurest" >> mpi_exec_shell
3478	echo "fname=$fname" >> mpi_exec_shell
3479	echo "localhost=$localhost" >> mpi_exec_shell
3480	echo "return_address=$return_address" >> mpi_exec_shell
3481	echo "return_username=$return_username" >> mpi_exec_shell
3482	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3483	echo "write_binary=$write_binary" >> mpi_exec_shell
3484	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3485	echo " " >> mpi_exec_shell
3486	echo "export F_ERRCNT" >> mpi_exec_shell
3487	echo "export MPIPROGINV" >> mpi_exec_shell
3488	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3489	echo "export cpurest" >> mpi_exec_shell
3490	echo "export fname" >> mpi_exec_shell
3491	echo "export localhost" >> mpi_exec_shell
3492	echo "export return_address" >> mpi_exec_shell
3493	echo "export return_username" >> mpi_exec_shell
3494	echo "export tasks_per_node" >> mpi_exec_shell
3495	echo "export write_binary" >> mpi_exec_shell
3496	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3497	echo " " >> mpi_exec_shell
3498	echo "exec ./a.out" >> mpi_exec_shell
3499
3500	chmod u+x mpi_exec_shell
3501	export MPIPROGINF=YES
3502	mpirun -f multinode_config &
3503	wait
3504
3505	fi
3506	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3507	then
3508
3509	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3510	# DOES NOT EXIST
3511	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3512
3513	then
3514	if [[ -f $hostfile ]]
3515	then
3516	cp $hostfile hostfile
3517	(( ii = $numprocs / $threads_per_task ))
3518	[[ $ii = 0 ]] && (( ii = 1 ))
3519	else
3520	(( ii = 1 ))
3521	while (( ii <= $numprocs / $threads_per_task ))
3522	do
3523	echo $localhost_realname >> hostfile
3524	(( ii = ii + 1 ))
3525	done
3526	if (( $numprocs / $threads_per_task == 0 ))
3527	then
3528	echo $localhost_realname >> hostfile
3529	fi
3530	fi
3531	eval zeile=\"`head -n $ii hostfile`\"
3532	printf "\n *** running on: $zeile"
3533	fi
3534
3535	(( ii = $numprocs / $threads_per_task ))
3536	[[ $ii = 0 ]] && (( ii = 1 ))
3537	export OMP_NUM_THREADS=$threads_per_task
3538
3539	if [[ $threads_per_task != 1 ]]
3540	then
3541	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3542	# MAY ABORT
3543	ulimit -s unlimited
3544	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3545	fi
3546	if [[ $run_coupled_model = false ]]
3547	then
3548	if [[ "$ocean_file_appendix" = true ]]
3549	then
3550	echo "precursor_ocean" > runfile_atmos
3551	else
3552	echo "precursor_atmos" > runfile_atmos
3553	fi
3554	printf "\n\n"
3555
3556	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3557	then
3558	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3559	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3560	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3561
3562	elif [[ $host = lcbullhh ]]
3563	then
3564	export OMPI_MCA_pml=cm
3565	export OMPI_MCA_mtl=mxm
3566	export OMPI_MCA_coll=^ghc
3567	export OMPI_MCA_mtl_mxm_np=0
3568	export MXM_RDMA_PORTS=mlx5_0:1
3569	export MXM_LOG_LEVEL=ERROR
3570	export OMP_NUM_THREADS=$threads_per_task
3571	export KMP_AFFINITY=verbose,granularity=core,compact,1
3572	export KMP_STACKSIZE=64m
3573
3574	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out
3575
3576	elif [[ $host = lccrayf ]]
3577	then
3578	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3579	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3580	then
3581	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3582	elif [[ $host = lcflow ]]
3583	then
3584	mpirun -np $ii a.out < runfile_atmos $ROPTS
3585	elif [[ $host = lcsb ]]
3586	then
3587	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3588	elif [[ $host = lckiaps ]]
3589	then
3590	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3591	elif [[ $host = lckyu* ]]
3592	then
3593	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3594	else
3595	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3596	fi
3597	else
3598
3599	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3600	(( iia = $numprocs_atmos / $threads_per_task ))
3601	(( iio = $numprocs_ocean / $threads_per_task ))
3602	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3603	printf "\n using $coupled_mode coupling"
3604	printf "\n\n"
3605
3606	if [[ $coupled_mode = "mpi2" ]]
3607	then
3608	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3609	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3610
3611	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3612	then
3613
3614	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3615	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3616
3617	else
3618	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3619	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3620	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3621	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3622	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3623	fi
3624	wait
3625
3626	else
3627
3628	echo "coupled_run $iia $iio" > runfile_atmos
3629
3630	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3631	then
3632
3633	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3634
3635	elif [[ $host = lck \|\| $host = lckordi ]]
3636	then
3637
3638	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3639
3640	elif [[ $host = lckyu* ]]
3641	then
3642
3643	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3644
3645	elif [[ $host = lcmuk ]]
3646	then
3647
3648	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3649
3650	fi
3651	wait
3652	fi
3653
3654	fi
3655
3656	elif [[ $host = lckyoto ]]
3657	then
3658	set -xv
3659	export P4_RSHCOMMAND=plesh
3660	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3661	if [[ "$ENVIRONMENT" = BATCH ]]
3662	then
3663	if [[ "$cond2" = fujitsu ]]
3664	then
3665	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3666	elif [[ "cond2" = pgi ]]
3667	then
3668	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3669	else
3670	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3671	fi
3672	else
3673	if [[ "$cond2" = "" ]]
3674	then
3675	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3676	else
3677	mpirun -np $numprocs ./a.out $ROPTS
3678	fi
3679	fi
3680	set +xv
3681
3682	elif [[ $host = lctit ]]
3683	then
3684	export OMP_NUM_THREADS=$threads_per_task
3685	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3686	if [[ "$threads_per_task" != 1 ]]
3687	then
3688	export MV2_ENABLE_AFFINITY=0
3689	fi
3690	echo "----- PBS_NODEFILE content:"
3691	cat $PBS_NODEFILE
3692	echo "-----"
3693	(( ii = $numprocs / $threads_per_task ))
3694	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3695	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3696
3697	else
3698	mpprun -n $numprocs a.out $ROPTS
3699	fi
3700	else
3701	a.out $ROPTS
3702	fi
3703	fi
3704
3705	if [[ $? != 0 ]]
3706	then
3707
3708	# ABORT IN CASE OF RUNTIME ERRORS
3709	printf "\n +++ runtime error occured"
3710	locat=execution
3711	exit
3712
3713	else
3714
3715	printf "\n$dashes\n *** execution finished \n"
3716
3717	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3718	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3719	if [[ "$dvrserver_id" != "" ]]
3720	then
3721	kill $dvrserver_id
3722	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3723
3724	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3725	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3726	if [[ -d DATA_DVR ]]
3727	then
3728
3729	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3730	# DIRECTORY
3731	cp .dvrserver.config DATA_DVR
3732
3733	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3734	# SEQUENCE MODE DATA TOO)
3735	process_dvr_output -d DATA_DVR -f $fname -s
3736
3737	else
3738
3739	# PROCESS THE LOCAL OUTPUT
3740	process_dvr_output -l -d DATA_DVR -f $fname
3741
3742	fi
3743
3744	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3745	then
3746
3747	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3748	process_dvr_output -l -d DATA_DVR -f $fname
3749
3750	fi
3751	fi
3752
3753
3754
3755	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3756	# BY EACH CORE INTO ONE FILE
3757	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3758	then
3759	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3760	printf "\n 2d- and/or 3d-data may be incomplete!"
3761	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3762	elif [[ "$combine_plot_fields" == true ]]
3763	then
3764	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3765	then
3766	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3767	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3768	else
3769	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3770	combine_plot_fields${block}.x
3771	fi
3772	else
3773
3774	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3775	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3776	# ??? koennen wir das streichen ???
3777	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3778	fi
3779
3780
3781
3782	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3783	(( i = 0 ))
3784	while (( i < ioc ))
3785	do
3786	(( i = i + 1 ))
3787	if (( i == 1 ))
3788	then
3789	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3790	fi
3791	printf "\n >>> ${out_command[$i]}"
3792	eval ${out_command[$i]}
3793	if (( i == ioc ))
3794	then
3795	printf "\n$dashes\n"
3796	fi
3797	done
3798
3799
3800	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3801	if [[ $do_trace = true ]]
3802	then
3803	printf "\n\n"
3804	ls -al
3805	fi
3806
3807
3808
3809	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3810	(( i = 0 ))
3811	while (( i < iout ))
3812	do
3813	(( i = i + 1 ))
3814	if (( i == 1 ))
3815	then
3816	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3817	fi
3818
3819	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3820	files_for_pes=false; filetyp=file
3821	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3822	then
3823	files_for_pes=true; filetyp=directory
3824	actionout[$i]=""
3825	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3826	then
3827	actionout[$i]=""
3828	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3829	then
3830	files_for_pes=true; filetyp=directory
3831	actionout[$i]="ar"
3832	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3833	then
3834	actionout[$i]="ar"
3835	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3836	then
3837	files_for_pes=true; filetyp=directory
3838	actionout[$i]="fl"
3839	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3840	then
3841	actionout[$i]="fl"
3842	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3843	then
3844	files_for_pes=true; filetyp=directory
3845	actionout[$i]="tr"
3846	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3847	then
3848	actionout[$i]="tr"
3849	fi
3850
3851	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3852	then
3853	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3854	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3855	then
3856	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3857	else
3858
3859
3860	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3861	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3862	if [[ "${actionout[$i]}" = tr ]]
3863	then
3864	if [[ $localhost != $fromhost ]]
3865	then
3866	if [[ $files_for_pes = false ]]
3867	then
3868	cps=""
3869	cst=""
3870	else
3871	cps=-c
3872	cst="/"
3873	fi
3874	if [[ $localhost = nech ]]
3875	then
3876
3877	# TRANSFER IN SEPERATE JOB
3878	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3879	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3880	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3881	if [[ $files_for_pes = false ]]
3882	then
3883	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3884	else
3885	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3886	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3887	fi
3888
3889	echo "set -x" > transfer_${localout[$i]}
3890	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3891
3892	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3893	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3894	printf "\n or higher cycle\n"
3895	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]}
3896
3897	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3898
3899	if [[ $localhost = nech ]]
3900	then
3901	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3902	else
3903	if [[ "$LOGNAME" = b323013 ]]
3904	then
3905	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3906	else
3907	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3908	fi
3909	fi
3910
3911	else
3912
3913	# TRANSFER WITHIN THIS JOB
3914	transfer_failed=false
3915	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3916	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3917	if [[ $localhost = lccrayb ]]
3918	then
3919	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]}"
3920	elif [[ $localhost = lccrayh ]]
3921	then
3922	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]}"
3923	elif [[ $localhost = lcbullhh ]]
3924	then
3925	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]}"
3926	elif [[ $localhost = lcxe6 ]]
3927	then
3928	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]}"
3929	else
3930	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3931	fi
3932	[[ $? != 0 ]] && transfer_failed=true
3933
3934	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3935	if [[ $transfer_failed = true ]]
3936	then
3937	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3938	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3939
3940	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3941	eval local_catalog=${pathout[$i]}
3942	if [[ ! -d $local_catalog ]]
3943	then
3944	printf " *** local directory does not exist. Trying to create:\n"
3945	printf " $local_catalog \n"
3946	mkdir -p $local_catalog
3947	fi
3948	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3949	transfer_problems=true
3950	fi
3951	fi
3952	else
3953
3954	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3955	actionout[$i]=""
3956	fi
3957	fi
3958
3959
3960	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3961	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3962	if [[ "${actionout[$i]}" = tra ]]
3963	then
3964	if [[ $localhost != $fromhost ]]
3965	then
3966	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3967	then
3968
3969	# TRANSFER IN SEPERATE JOB
3970	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3971	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3972	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3973	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3974
3975	echo "set -x" > transfer_${localout[$i]}
3976	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3977
3978	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3979	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3980	printf "\n or higher cycle\n"
3981	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]}
3982
3983	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3984
3985	if [[ $localhost = nech ]]
3986	then
3987	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3988	else
3989	if [[ $LOGNAME = b323013 ]]
3990	then
3991	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3992	else
3993	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3994	fi
3995	fi
3996
3997	else
3998
3999	# TRANSFER WITHIN THIS JOB
4000	transfer_failed=false
4001	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
4002	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
4003	if [[ $localhost = lccrayb ]]
4004	then
4005	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]}"
4006	elif [[ $localhost = lccrayh ]]
4007	then
4008	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]}"
4009	elif [[ $localhost = lcxe6 ]]
4010	then
4011	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]}"
4012	else
4013	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
4014	fi
4015	[[ $? != 0 ]] && transfer_failed=true
4016
4017	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
4018	if [[ $transfer_failed = true ]]
4019	then
4020	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4021	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4022
4023	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4024	eval local_catalog=${pathout[$i]}
4025	if [[ ! -d $local_catalog ]]
4026	then
4027	printf " *** local directory does not exist. Trying to create:\n"
4028	printf " $local_catalog \n"
4029	mkdir -p $local_catalog
4030	fi
4031
4032	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4033	transfer_problems=true
4034	fi
4035	fi
4036	else
4037
4038	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4039	actionout[$i]=a
4040	fi
4041	fi
4042
4043
4044	# OUTPUT-FILE FOR A RESTART-RUN.
4045	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4046	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4047	# AS LAST ACTION, ARCHIVING IS INITIATED.
4048	if [[ "${actionout[$i]}" = fl ]]
4049	then
4050	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4051	chmod g+rx $tmp_data_catalog
4052	if [[ $files_for_pes = false ]]
4053	then
4054	printf "\n >>> OUTPUT: ${localout[$i]} to"
4055	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4056	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4057	else
4058	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4059	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4060	mkdir $tmp_data_catalog/${frelout[$i]}
4061	cd ${localout[$i]}
4062	for file in $(ls *)
4063	do
4064	ln -f $file $tmp_data_catalog/${frelout[$i]}
4065	done
4066	cd $TEMPDIR
4067	fi
4068
4069
4070	# CREATE AND SUBMIT ARCHIVING-JOB
4071	if [[ $store_on_archive_system = true ]]
4072	then
4073
4074	if [[ $archive_system = asterix ]]
4075	then
4076	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4077	if [[ $files_for_pes = false ]]
4078	then
4079	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4080	else
4081	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4082	fi
4083	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4084	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4085	echo "then" >> archive_${frelout[$i]}
4086	echo " do_stageout=false" >> archive_${frelout[$i]}
4087	echo "else" >> archive_${frelout[$i]}
4088	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4089	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4090	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4091	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4092	if [[ $files_for_pes = false ]]
4093	then
4094	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4095	else
4096	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4097	fi
4098	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4099	echo "fi" >> archive_${frelout[$i]}
4100	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4101	elif [[ $archive_system = DMF ]]
4102	then
4103	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4104	if [[ $files_for_pes = false ]]
4105	then
4106	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4107	locat=DMF
4108	exit
4109	else
4110	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4111	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4112	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4113	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4114	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4115	fi
4116	elif [[ $archive_system = tivoli ]]
4117	then
4118	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4119	if [[ $files_for_pes = false ]]
4120	then
4121	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4122	echo "set -x" >> archive_${frelout[$i]}
4123	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4124	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4125	else
4126
4127	echo "set -x" >> archive_${frelout[$i]}
4128	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4129	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4130	cd $tmp_data_catalog
4131	all_files=`ls -1 ${frelout[$i]}/*`
4132	cd - > /dev/null
4133	(( inode = 0 ))
4134	(( tp1 = tasks_per_node + 1 ))
4135	while (( inode < nodes ))
4136	do
4137	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4138	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4139	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4140	(( inode = inode + 1 ))
4141	done
4142	fi
4143	elif [[ $archive_system = ut ]]
4144	then
4145	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4146	if [[ $files_for_pes = false ]]
4147	then
4148	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4149	echo "set -x" >> archive_${frelout[$i]}
4150	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4151	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4152	else
4153
4154	echo "set -x" >> archive_${frelout[$i]}
4155	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4156	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4157	cd $tmp_data_catalog
4158	all_files=`ls -1 ${frelout[$i]}/*`
4159	cd - > /dev/null
4160	(( inode = 0 ))
4161	(( tp1 = tasks_per_node + 1 ))
4162	while (( inode < nodes ))
4163	do
4164	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4165	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4166	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4167	(( inode = inode + 1 ))
4168	done
4169	fi
4170	elif [[ $archive_system = none ]]
4171	then
4172	printf " +++ archiving on $localhost not available!\n"
4173	fi
4174
4175	if [[ $archive_system != none ]]
4176	then
4177	if [[ $localhost = nech ]]
4178	then
4179	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4180	fi
4181	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4182	fi
4183	else
4184	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4185	fi
4186
4187
4188	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4189	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4190	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4191	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4192	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4193	if [[ $files_for_pes = false ]]
4194	then
4195	cat /dev/null > ${pathout[$i]}
4196	else
4197	mkdir -p ${pathout[$i]}
4198	fi
4199
4200	fi
4201
4202
4203	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4204	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4205	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4206	if [[ "${actionout[$i]}" = ar ]]
4207	then
4208	if [[ $files_for_pes = false ]]
4209	then
4210	printf "\n >>> OUTPUT: ${localout[$i]} to"
4211	printf "\n ${pathout[$i]}"
4212	printf "\n File will be copied to archive-system ($archive_system) !\n"
4213	else
4214	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4215	printf "\n ${pathout[$i]}"
4216	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4217	fi
4218	mv ${localout[$i]} ${frelout[$i]}
4219
4220	file_saved=false
4221
4222	if [[ $archive_system = asterix ]]
4223	then
4224	do_stageout=true
4225	(( stageout_anz = 0 ))
4226	while [[ $do_stageout = true ]]
4227	do
4228	if [[ $files_for_pes = false ]]
4229	then
4230	stageout ${frelout[$i]} > STAGE_OUTPUT
4231	else
4232	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4233	fi
4234	cat STAGE_OUTPUT
4235	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4236	then
4237	file_saved=true
4238	do_stageout=false
4239	else
4240	if [[ $files_for_pes = false ]]
4241	then
4242	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4243	else
4244	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4245	fi
4246	(( stageout_anz = stageout_anz + 1 ))
4247	if (( stageout_anz == 10 ))
4248	then
4249	printf "\n +++ stoped after 10 unsuccessful tries!"
4250	archive_save=false
4251	do_stageout=false
4252	else
4253	printf "\n *** new try to store on archive after 15 min:"
4254	sleep 900
4255	fi
4256	fi
4257	done
4258	elif [[ $archive_system = DMF ]]
4259	then
4260	if [[ $files_for_pes = false ]]
4261	then
4262	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4263	locat=DMF
4264	exit
4265	else
4266	rm -rf $ARCHIVE/${frelout[$i]}
4267	cp -r ${frelout[$i]} $ARCHIVE
4268	fi
4269	file_saved=true
4270	elif [[ $archive_system = tivoli ]]
4271	then
4272	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4273	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4274	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4275	# WHEN THE ARCHIVE-JOB IS EXECUTED
4276	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4277	chmod g+rx $tmp_data_catalog
4278	if [[ $files_for_pes = false ]]
4279	then
4280	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4281	else
4282	mkdir $tmp_data_catalog/${frelout[$i]}
4283	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4284	fi
4285
4286	# GENERATE AND SUBMIT BATCH-JOB
4287	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4288	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4289	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4290	if [[ $files_for_pes = false ]]
4291	then
4292	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4293	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4294	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4295	else
4296	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4297	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4298	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4299	fi
4300
4301	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4302	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4303	file_saved=true
4304
4305	elif [[ $archive_system = ut ]]
4306	then
4307	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4308	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4309	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4310	# WHEN THE ARCHIVE-JOB IS EXECUTED
4311	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4312	chmod g+rx $tmp_data_catalog
4313	if [[ $files_for_pes = false ]]
4314	then
4315	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4316	else
4317	mkdir $tmp_data_catalog/${frelout[$i]}
4318	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4319	fi
4320
4321	# GENERATE AND SUBMIT BATCH-JOB
4322	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4323	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4324	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4325	if [[ $files_for_pes = false ]]
4326	then
4327	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4328	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4329	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4330	else
4331	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4332	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4333	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4334	fi
4335
4336	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4337	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4338	file_saved=true
4339
4340	else
4341	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4342	archive_save=false
4343	fi
4344
4345	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4346	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4347	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4348	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4349	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4350	if [[ $file_saved = true ]]
4351	then
4352	if [[ $files_for_pes = false ]]
4353	then
4354	cat /dev/null > ${pathout[$i]}
4355	else
4356	mkdir -p ${pathout[$i]}
4357	fi
4358	fi
4359
4360	fi
4361
4362	# APPEND ON THIS MACHINE
4363	if [[ "${actionout[$i]}" = "a" ]]
4364	then
4365	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4366	then
4367	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4368	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4369	else
4370	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4371	cat ${localout[$i]} >> ${pathout[$i]}
4372	fi
4373	fi
4374
4375	# COPY ON THIS MACHINE
4376	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4377	# ON DIFFERENT FILE-SYSTEMS
4378	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4379	then
4380
4381	# COPY IN CASE OF RUNS ON SINGLE CORES
4382	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4383	then
4384	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4385	if [[ $link_local_output = true ]]
4386	then
4387	printf " using ln -f\n"
4388	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4389	fi
4390	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4391	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4392	then
4393	if [[ $link_local_output = true ]]
4394	then
4395	printf " ln failed, using cp...\n"
4396	fi
4397	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4398	fi
4399	else
4400	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4401	if [[ $link_local_output = true ]]
4402	then
4403	printf " using ln -f\n"
4404	ln -f ${localout[$i]} ${pathout[$i]}
4405	fi
4406	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4407	if [[ ! -f "${pathout[$i]}" ]]
4408	then
4409	if [[ $link_local_output = true ]]
4410	then
4411	printf " ln failed, using cp...\n"
4412	fi
4413	cp ${localout[$i]} ${pathout[$i]}
4414	fi
4415	fi
4416
4417	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4418	then
4419
4420	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4421	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4422	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4423	if [[ $link_local_output = true ]]
4424	then
4425	printf " using ln -f\n"
4426	mkdir ${pathout[$i]}
4427	cd ${localout[$i]}
4428	for file in $(ls *)
4429	do
4430	ln -f $file ${pathout[$i]}
4431	done
4432	cd $TEMPDIR
4433	fi
4434
4435	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4436	if [[ ! -f "${pathout[$i]}/_0000" ]]
4437	then
4438	if [[ $link_local_output = true ]]
4439	then
4440	printf " ln failed for .../_0000, using cp...\n"
4441	fi
4442	cp -r ${localout[$i]} ${pathout[$i]}
4443	fi
4444
4445	fi
4446	fi
4447	done
4448	if (( i != 0 ))
4449	then
4450	if [[ $transfer_problems = true ]]
4451	then
4452	printf "\n$dashes\n *** OUTPUT-files saved"
4453	printf "\n +++ WARNING: some data transfers failed! \n"
4454	else
4455	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4456	fi
4457	fi
4458
4459
4460	# IF REQUIRED, START A RESTART-JOB
4461	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4462	if [[ -f CONTINUE_RUN ]]
4463	then
4464
4465	if [[ $archive_save = true ]]
4466	then
4467
4468	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4469	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4470	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4471	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4472	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4473	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4474	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4475	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4476	then
4477	mc=`echo $mc \| sed 's/#/f/g'`
4478	fi
4479
4480
4481	# START THE RESTART-JOB
4482	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4483	echo " $mc"
4484	printf "\n$dashes\n"
4485	if [[ $localhost != $fromhost ]]
4486	then
4487
4488	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4489	then
4490	echo "*** ssh will be used to initiate restart-runs!"
4491	echo " return_address=\"$return_address\" "
4492	echo " return_username=\"$return_username\" "
4493	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4494	then
4495	if [[ $localhost = ibmh ]]
4496	then
4497	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\" "
4498	elif [[ $localhost = lcbullhh ]]
4499	then
4500	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\" "
4501	elif [[ $localhost = lccrayb ]]
4502	then
4503	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\" "
4504	elif [[ $localhost = lccrayh ]]
4505	then
4506	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\" "
4507	elif [[ $localhost = lcxe6 ]]
4508	then
4509	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\" "
4510	else
4511	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 "
4512	fi
4513	else
4514	if [[ $localhost = ibmkisti ]]
4515	then
4516	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\" "
4517	elif [[ $localhost = lcflow ]]
4518	then
4519	/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 "
4520	elif [[ $localhost = lccrayb ]]
4521	then
4522	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\" "
4523	elif [[ $localhost = lccrayh ]]
4524	then
4525	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\" "
4526	else
4527	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4528	fi
4529	fi
4530	else
4531	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4532	locat=restart; exit
4533	fi
4534
4535	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4536	if [[ $queue = special1q ]]
4537	then
4538	sleep 120
4539	else
4540	sleep 30
4541	fi
4542
4543	else
4544
4545	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4546	# USING SSH)
4547	cd $LOCAL_PWD
4548	if [[ $localhost = lckyuh ]]
4549	then
4550	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4551	printf "\n please restart job manually using command:\n"
4552	printf "\n \"$mc\" "
4553	else
4554	eval $mc # THE ' MUST BE EVALUATED
4555	fi
4556	cd - > /dev/null
4557	fi
4558	if [[ $localhost = lckyuh ]]
4559	then
4560	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4561	else
4562	printf "\n$dashes\n *** restart-run initiated \n"
4563	fi
4564
4565
4566	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4567	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4568	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4569	# MAY BE VERY HUGE)
4570	(( i = 0 ))
4571	while (( i < iin ))
4572	do
4573	(( i = i + 1 ))
4574	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4575	then
4576	rm -r $tmp_data_catalog/${frelin[$i]}
4577	fi
4578	done
4579
4580	else
4581
4582	printf "\n +++ no restart-run possible, since errors occured"
4583	printf "\n during the archive process"
4584	fi
4585
4586	fi
4587
4588
4589
4590	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4591	if [[ "$email_notification" != "none" ]]
4592	then
4593
4594	if [[ $localhost != $fromhost ]]
4595	then
4596	if [[ -f CONTINUE_RUN ]]
4597	then
4598	echo "PALM restart run necessary" > email_text
4599	echo "description header of actual run:" >> email_text
4600	cat CONTINUE_RUN >> email_text
4601	echo "mrun-command to restart:" >> email_text
4602	echo "$mc" >> email_text
4603	else
4604	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4605	fi
4606	mail $email_notification < email_text
4607	printf "\n *** email notification sent to \"$email_notification\" "
4608	fi
4609	fi
4610
4611
4612
4613	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4614	cd $HOME
4615	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4616
4617	else
4618
4619	# PREPARING ACTIONS,
4620	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4621
4622	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4623	mrun_com="$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 $remote_username"
4624	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4625	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4626	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4627	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4628	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4629	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4630	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4631	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4632	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4633	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4634	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4635	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4636	if [[ $use_openmp = true ]]
4637	then
4638	mrun_com=${mrun_com}" -O $threads_per_task"
4639	fi
4640	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4641	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4642	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4643	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4644	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4645	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4646	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4647	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4648	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4649	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4650	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4651	if [[ $do_remote = true ]]
4652	then
4653	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4654	fi
4655
4656
4657	# CREATE EXECUTABLE FOR BATCH JOB
4658	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4659	then
4660
4661	printf "\n *** creating the executable for batch job\n"
4662
4663	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4664	if [[ $host != $localhost ]]
4665	then
4666	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4667	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4668	locat=create_executable; exit
4669	fi
4670
4671	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4672	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4673
4674	cp $make_depository .
4675	tar -xf $make_depository > /dev/null 2>&1
4676	cp ../* . > /dev/null 2>&1
4677
4678	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4679
4680	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4681	then
4682	printf "\n +++ error occured while compiling or linking"
4683	locat=compile
4684	exit
4685	fi
4686
4687	mv a.out ..
4688	cd - > /dev/null 2>&1
4689	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4690
4691	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4692
4693	fi
4694
4695
4696	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4697	jobfile=jobfile.$RANDOM
4698
4699
4700	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4701	echo "mkdir $TEMPDIR" >> $jobfile
4702	echo "cd $TEMPDIR" >> $jobfile
4703
4704
4705	# ACTIVATE ERROR-TRACEBACK
4706	if [[ $do_trace = true ]]
4707	then
4708	echo "set -x" >> $jobfile
4709	else
4710	echo "set +vx" >> $jobfile
4711	fi
4712
4713
4714	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4715	if [[ "$init_cmds" != "" ]]
4716	then
4717	echo "$init_cmds" >> $jobfile
4718	fi
4719	if [[ "$module_calls" != "" ]]
4720	then
4721	echo "$module_calls" >> $jobfile
4722	fi
4723
4724
4725	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4726	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4727	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4728	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4729	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4730	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4731	# QUEUEING-SYSTEMS
4732	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4733	then
4734
4735	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4736	if [[ $restart_run != true ]]
4737	then
4738	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4739	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4740	fi
4741
4742	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4743	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4744	echo "set -x" >> $jobfile
4745	if [[ $host = $localhost ]]
4746	then
4747	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4748	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4749	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4750	then
4751	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4752	else
4753	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4754	fi
4755
4756	else
4757	if [[ $host = ibmkisti ]]
4758	then
4759	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4760	echo "localdir=\`pwd\`" >> $jobfile
4761	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4762	elif [[ $host = lcbullhh ]]
4763	then
4764	echo "localdir=\`pwd\`" >> $jobfile
4765	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4766
4767	elif [[ $host = lccrayb ]]
4768	then
4769	echo "localdir=\`pwd\`" >> $jobfile
4770	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4771	elif [[ $host = lccrayh ]]
4772	then
4773	echo "localdir=\`pwd\`" >> $jobfile
4774	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4775
4776	else
4777	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4778	fi
4779	fi
4780	echo "export SOURCES_COMPLETE=true" >> $jobfile
4781
4782	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4783	# WORKING DIRECTORY OF THE JOB
4784	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4785	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4786	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4787	echo "execute_mrun=true" >> $jobfile
4788	echo " " >> $jobfile
4789
4790	else
4791
4792	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4793	if [[ $do_compile = true ]]
4794	then
4795
4796	source_catalog=SOURCES_FOR_RUN_$fname
4797
4798	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4799	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4800	echo "export SOURCES_COMPLETE=true" >> $jobfile
4801	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4802
4803	for filename in $source_list
4804	do
4805	# BACKSLASH IS USED FOR MASKING
4806	echo "cat > $filename << \"%END%\"" >> $jobfile
4807	cat $source_catalog/$filename >> $jobfile
4808	echo " " >> $jobfile
4809	echo "%END%" >> $jobfile
4810	echo " " >> $jobfile
4811	done
4812
4813	# BACKSLASH IS USED FOR MASKING
4814	echo "cat > Makefile << \"%END%\"" >> $jobfile
4815	cat $source_catalog/Makefile >> $jobfile
4816	echo " " >> $jobfile
4817	echo "%END%" >> $jobfile
4818	echo " " >> $jobfile
4819
4820	echo "cd - > /dev/null" >> $jobfile
4821
4822	fi
4823
4824
4825	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4826	# BACKSLASH IS USED FOR MASKING
4827	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4828	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4829	echo "cat > $config_file << \"%END%\"" >> $jobfile
4830	if [[ $host = lckyuh ]]
4831	then
4832	# NO CROSS-COMPILER ON COMPUTE NODE
4833	sed 's/frtpx/frt/g' $config_file >> $jobfile
4834	else
4835	sed 's/#$.*//g' $config_file >> $jobfile
4836	fi
4837	echo "%END%" >> $jobfile
4838	echo " " >> $jobfile
4839
4840
4841	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4842	# BACKSLASH IS USED FOR MASKING
4843	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4844	if [[ $host = lckyuh ]]
4845	then
4846	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4847	else
4848	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4849	fi
4850	echo "%END%" >> $jobfile
4851	echo "chmod u+x $mrun_script_name" >> $jobfile
4852	echo "execute_mrun=true" >> $jobfile
4853	echo " " >> $jobfile
4854
4855	fi
4856
4857
4858	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4859	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4860	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4861	if [[ $do_remote = true ]]
4862	then
4863	(( i = 0 ))
4864	while (( i < iin ))
4865	do
4866	(( i = i + 1 ))
4867	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4868	if [[ "${transin[$i]}" = job ]]
4869	then
4870	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4871	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4872	echo " " >> $jobfile
4873	echo "%END%" >> $jobfile
4874	else
4875	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4876	fi
4877
4878	# CHECK, IF FILE COULD BE CREATED
4879	echo "if [[ \$? = 1 ]]" >> $jobfile
4880	echo "then" >> $jobfile
4881	echo " echo \" \" " >> $jobfile
4882	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4883	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4884	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4885	echo " execute_mrun=false" >> $jobfile
4886	echo "fi" >> $jobfile
4887	done
4888	fi
4889
4890	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4891	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4892	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4893	echo "LOCAL_PWD=$working_directory" >> $jobfile
4894	echo "export LOCAL_PWD" >> $jobfile
4895
4896	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4897	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4898	echo "export LOCAL_MRUN_PATH" >> $jobfile
4899
4900	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4901	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4902	# then
4903	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4904	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4905	# fi
4906
4907	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4908	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4909	echo "set -x" >> $jobfile
4910	echo "queue=$queue" >> $jobfile
4911	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4912	echo 'ls -al; echo `pwd`' >> $jobfile
4913	echo "cd \$HOME" >> $jobfile
4914	echo "rm -rf $TEMPDIR" >> $jobfile
4915
4916
4917
4918
4919	# START THE JOB USING SUBJOB-COMMAND
4920	if [[ $silent = false ]]
4921	then
4922	printf "\n "
4923	else
4924	printf "\n\n"
4925	fi
4926
4927	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
4928	rm -rf $jobfile
4929
4930
4931	fi # END OF REMOTE-PART

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