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source: palm/trunk/SCRIPTS/mrun @ 1468

Last change on this file since 1468 was 1468, checked in by maronga, 10 years ago
New flag files allow to force unscheduled termination/restarts of batch jobs, progress output is made for batch runs, small adjustments for lxce6 and lccrayh/lccrayb
Property svn:keywords set to `Id Rev`
File size: 176.6 KB

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

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