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source: palm/trunk/SCRIPTS/mrun @ 1422

Last change on this file since 1422 was 1422, checked in by kanani, 10 years ago
adjustments for automatic restarts
Property svn:keywords set to `Id Rev`
File size: 175.3 KB

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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# automatic restarts enabled for lccrayb,
25	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
26	#
27	# Former revisions:
28	# -----------------
29	# $Id: mrun 1422 2014-07-02 10:01:25Z kanani $
30	#
31	# 1420 2014-06-10 06:24:14Z raasch
32	# -j1 option added to aprung command for lccrayf (CSC)
33	#
34	# 1402 2014-05-09 14:25:13Z raasch
35	# batch_job added to envpar-NAMELIST
36	#
37	# 1357 2014-04-11 15:02:03Z witha
38	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
39	# possible)
40	#
41	# 1320 2014-03-20 08:40:49Z raasch
42	# check namelist file set false by default
43	#
44	# 1304 2014-03-12 10:29:42Z raasch
45	# ulimit option changed from -Ss to -s
46	#
47	# bugfix: missing "fi" in r1289
48	#
49	# 1289 2014-03-04 07:12:34Z raasch
50	# comments translated to English
51	# necriam-, fimm-, ibmy-, and sgi-specific code removed
52	# export of variables for palm and interpret_config removed
53	#
54	# 1281 2014-02-01 07:55:49Z raasch
55	# rsync-copy restricted to Cray machines, since command is unavailable on some
56	# other systems
57	#
58	# 1279 2014-01-28 12:10:14Z raasch
59	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
60	# in order to remove annoying restrictions concerning the number of processors which
61	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
62	# restriction, one of the nodes will be filled with less than the given number of
63	# tasks per node. A respective warning is given.
64	#
65	# 1274 2014-01-09 13:14:54Z heinze
66	# adjustments for lccrayh
67	#
68	# 1272 2014-01-08 10:19:32Z witha
69	# small adjustment for lcflow
70	#
71	# 1270 2013-12-16 11:05:01Z fricke
72	# call of combine_plot_fields adjusted for lccrayb/lccrayh
73	#
74	# 1255 2013-11-07 14:43:35Z raasch
75	# further adjustments for lccrayb remote access
76	#
77	# 1241 2013-10-30 11:36:58Z heinze
78	# Enable use of nudging input and input of large scale forcing from
79	# external files
80	#
81	# 1229 2013-09-20 06:55:19Z raasch
82	# further adjustments for lccrayb
83	#
84	# 1224 2013-09-16 07:27:23Z raasch
85	# first adjustments for lccrayb
86	#
87	# 1210 2013-08-14 10:58:20Z raasch
88	# fftw support added
89	#
90	# 1201 2013-07-10 16:17:59Z witha
91	# adjustments for Forwind cluster (lcflow)
92	#
93	# 1199 2013-07-05 14:52:22Z raasch
94	# adjustments for CSC Helsinki (lccrayf),
95	# executables for batch jobs can be created in advance, in order to avoid calling
96	# the compiler within the batch job (only works if batch jobs are submitted on
97	# local host)
98	#
99	# 1190 2013-06-25 09:39:21Z heinze
100	# enable use of automatic restarts for ibmh
101	# use of cluster/express queue enabled (ibmh)
102	#
103	# 1124 2013-04-09 15:46:52Z raasch
104	# variable "memory" is exported via typeset option -x, because otherwise an unknown
105	# side effect may lead to data loss while getopts is reading the script-option arguments
106	#
107	# 1122 2013-04-09 08:37:16Z heinze
108	# Bugfix: change type of variable last_char
109	#
110	# 1119 2013-04-05 15:11:19Z raasch
111	# Bugfix for setting -T option for subjob
112	#
113	# 1108 2013-03-05 07:03:32Z raasch
114	# bugfix for coupled runs on lckyut/lckyuh
115	#
116	# 1106 2013-03-04 05:31:38Z raasch
117	# --stdin argument for mpiexec on lckyuh
118	# -y and -Y settings output to header
119	#
120	# 1103 2013-02-20 02:15:53Z raasch
121	# default script runs again under ksh, because of unsolved problems with read
122	# from stdin: when bash script is called from a ksh, message "read error: 0:
123	# Resource temporarily unavailable" appears and script does not stop,
124	# further bash compatibility adjustments,
125	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
126	# on lckyuh, but mrun does not terminate and issues a warning instead
127	#
128	# 1101 2013-02-17 10:20:21Z raasch
129	# script now running under bash instead of ksh, which required small adjustments
130	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
131	# read from stdin),
132	# cross compilername on lckyuh compute nodes replaced by real compiler name
133	#
134	# 1099 2013-02-10 01:47:43Z raasch
135	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
136	# and for Forwind cluster (lcflow)
137	# small further adjustments for lckyut
138	#
139	# 1094 2013-02-03 01:52:12Z raasch
140	# explicit ssh/scp port can be set in config file with environment variable
141	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
142	# decalpha parts (yonsei) removed
143	#
144	# 2013-02-02 07:06:13Z raasch
145	# adjustments for Kyushu-University computing center (lckyut - tatara)
146	#
147	# 1083 2013-01-04 10:22:09Z maronga
148	# bugfix in parameter file check (read %cpp_options was missing)
149	#
150	# 1069 2012-11-28 16:18:43Z maronga
151	# bugfix: coupling mode was always set to mpi2, typos removed
152	#
153	# 1058 2012-11-21 07:00:35Z raasch
154	# Intel inspector (inspxe) is given the number of PEs instead of the number of
155	# nodes
156	#
157	# 1046 2012-11-09 14:38:45Z maronga
158	# code put under GPL (PALM 3.9)
159	#
160	# 21/03/94 - Siggi - first version finished
161	# 03/03/94 - Siggi - script development started
162	#
163	#--------------------------------------------------------------------------------#
164	# mrun - script for running PALM jobs
165	#--------------------------------------------------------------------------------#
166
167
168
169	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
170
171	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
172	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
173	# (TOO MANY ARGUMENTS - PROBLEM)
174	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
175
176	AddFilenames=""
177	additional_conditions=""
178	add_source_path=""
179	afname=""
180	archive_save=true
181	archive_system=none
182	check_namelist_files=false
183	combine_plot_fields=true
184	compiler_name=""
185	cond1=""
186	cond2=""
187	config_file=.mrun.config
188	coupled_dist=""
189	coupled_mode="mpi1"
190	cpp_opts=""
191	cpp_options=""
192	cpumax=0
193	cpurest=0
194	create_executable_for_batch=false
195	delete_temporary_catalog=true
196	do_batch=false
197	do_compile=true
198	do_remote=false
199	do_stagein=true
200	do_stageout=true
201	do_trace=false
202	email_notification="none"
203	exclude=""
204	executable=""
205	execution_error=false
206	fftw_inc=""
207	fftw_lib=""
208	fftw_support=false
209	fname=test
210	fromhost=""
211	global_revision=""
212	group_number=none
213	host=""
214	host_file=""
215	hp=""
216	ignore_archive_error=false
217	input_list=""
218	interpreted_config_file=""
219	job_catalog="~/job_queue"
220	job_on_file=""
221	keep_data_from_previous_run=false
222	link_local_input=false
223	link_local_output=false
224	localhost_realname=$(hostname)
225	local_dvrserver_running=.FALSE.
226	locat=normal
227	mainprog=""
228	makefile=""
229	max_par_io_str=""
230	mc=$0
231	while [[ $(echo $mc \| grep -c "/") != 0 ]]
232	do
233	mc=`echo $mc \| cut -f2- -d"/"`
234	done
235	module_calls=""
236	mrun_script_name=$mc
237	netcdf_inc=""
238	netcdf_lib=""
239	netcdf_support=false
240	node_usage=default
241	numprocs=""
242	numprocs_atmos=0
243	numprocs_ocean=0
244	OOPT=""
245	openmp=false
246	output_list=""
247	package_list=""
248	queue=none
249	read_from_config=""
250	restart_run=false
251	if [[ `hostname` = rte10 ]]
252	then
253	return_addres=133.5.185.60
254	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
255	elif [[ `hostname` = climate0 ]]
256	then
257	return_addres=165.132.26.68
258	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
259	elif [[ `hostname` = urban00 ]]
260	then
261	return_addres=147.46.30.151
262	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
263	else
264	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
265	fi
266	return_password=""
267	return_username=$LOGNAME
268	remotecall=false
269	remote_username=""
270	run_coupled_model=false
271	run_mode=""
272	store_on_archive_system=false
273	dashes=" ----------------------------------------------------------------------------"
274	silent=false
275	source_list=""
276	source_path=SOURCE
277	tasks_per_node=""
278	threads_per_task=1
279	tmpcreate=false
280	tmp_data_catalog=""
281	transfer_problems=false
282	usern=$LOGNAME
283	use_openmp=false
284	version="MRUN 2.1 Rev$Rev: 1422 $"
285	working_directory=`pwd`
286	TOPT=""
287	XOPT=""
288	zeit=$( date \| cut -c 12-19 )
289
290	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
291	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
292	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
293	# SCRIPT-OPTION ARGUMENTS
294	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
295
296
297
298	# ERROR HANDLING IN CASE OF EXIT
299	trap 'rm -rf $working_directory/tmp_mrun
300	if [[ $locat != normal && $locat != control_c ]]
301	then
302
303	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
304	(( i = 0 ))
305	while (( i < iec ))
306	do
307	(( i = i + 1 ))
308	printf "\n *** Execution of ERROR-command:\n"
309	printf " >>> ${err_command[$i]}\n"
310	eval ${err_command[$i]}
311	done
312	if [[ -n $interpreted_config_file ]]
313	then
314	rm -rf $interpreted_config_file
315	fi
316	if [[ -n .mrun_environment ]]
317	then
318	rm -rf .mrun_environment
319	fi
320	if [[ $tmpcreate = true ]]
321	then
322	printf "\n *** Contents of \"$TEMPDIR\":\n"
323	ls -al; cd
324	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
325	fi
326	if [[ "$dvrserver_id" != "" ]]
327	then
328	echo "+++ killing dvrserver_id=$dvrserver_id"
329	kill $dvrserver_id
330	fi
331	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
332	then
333	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
334	fi
335	printf "\n\n+++ MRUN killed \n\n"
336	elif [[ $locat != control_c ]]
337	then
338	printf "\n\n --> all actions finished\n\n"
339	printf " Bye, bye $usern !!\n\n"
340	fi' exit
341
342
343	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
344	trap 'rm -rf $working_directory/tmp_mrun
345	rm -rf $working_directory/tmp_check_namelist_files
346	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
347	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
348	then
349	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
350	fi
351	if [[ "$dvrserver_id" != "" ]]
352	then
353	echo "+++ killing dvrserver_id=$dvrserver_id"
354	kill $dvrserver_id
355	fi
356	printf "\n+++ MRUN killed by \"^C\" \n\n"
357	locat=control_c
358	exit
359	' 2
360
361
362	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
363	# BEEN SET
364	if [[ "$PALM_BIN" = "" ]]
365	then
366	printf "\n +++ environment variable PALM_BIN has not been set"
367	printf "\n please set it to the directory where the PALM scripts are located"
368	locat=palm_bin; exit
369	fi
370	export PATH=$PALM_BIN:$PATH
371
372
373
374	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
375	# WHICH WILL BE USED TO START RESTART-JOBS
376	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
377	do
378	case $option in
379	(a) afname=$OPTARG;;
380	(A) store_on_archive_system=true; mc="$mc -A";;
381	(b) do_batch=true; mc="$mc -b";;
382	(B) delete_temporary_catalog=false; mc="$mc -B";;
383	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
384	(C) restart_run=true; mc="$mc -C";;
385	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
386	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
387	(F) job_on_file="-D"; mc="$mc -F";;
388	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
389	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
390	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
391	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
392	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
393	(I) ignore_archive_error=true; mc="$mc -I";;
394	(k) keep_data_from_previous_run=true; mc="$mc -k";;
395	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
396	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
397	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
398	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
399	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
400	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
401	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
402	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
403	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
404	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
405	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
406	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
407	(S) read_from_config=false; mc="$mc -S";;
408	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
409	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
410	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
411	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
412	(v) silent=true; mc="$mc -v";;
413	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
414	(x) do_trace=true;set -x; mc="$mc -x";;
415	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
416	(y) ocean_file_appendix=true; mc="$mc -y";;
417	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
418	(z) check_namelist_files=false; mc="$mc -z";;
419	(Z) combine_plot_fields=false; mc="$mc -Z";;
420	(\?) printf "\n +++ unknown option $OPTARG \n"
421	printf "\n --> type \"$0 ?\" for available options \n"
422	locat=parameter;exit;;
423	esac
424	done
425
426
427	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
428	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
429	(( to_shift = $OPTIND - 1 ))
430	shift $to_shift
431
432	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
433	if [[ "$1" = "?" ]]
434	then
435	(printf "\n *** mrun can be called as follows:\n"
436	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"
437	printf "\n Description of available options:\n"
438	printf "\n Option Description Default-Value"
439	printf "\n -a base name of input files equiv. -d"
440	printf "\n -A archiving when using file-attribute fl"
441	printf "\n -b batch-job on local machine ---"
442	printf "\n -B do not delete temporary directory at end ---"
443	printf "\n -c configuration file .mrun.config"
444	printf "\n -d base name of files attached to program test"
445	printf "\n -D preprocessor(cpp)-directives \"\" "
446	printf "\n -F create remote job file only ---"
447	printf "\n -h execution host $localhost_realname"
448	printf "\n -i INPUT control list \"\" "
449	printf "\n -I archiving errors of previous batch-jobs"
450	printf "\n will be ignored"
451	printf "\n -k keep data from previous run"
452	printf "\n -K additional conditions for controling"
453	printf "\n usage of conditional code and"
454	printf "\n env-variables in configuration file \"\" "
455	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
456	printf "\n -M Makefile name Makefile"
457	printf "\n -n node usage (shared/not_shared) depending on -h"
458	printf "\n -o OUTPUT control list \"\" "
459	printf "\n -O threads per openMP task ---"
460	printf "\n -p software package list \"\" "
461	printf "\n -q queue \"$queue\" "
462	printf "\n -r run control list (combines -i -o) \"\" "
463	printf "\n -s filenames of routines to be compiled \"\" "
464	printf "\n must end with .f, .f90, .F, or .c !"
465	printf "\n use \"..\" for more than one file and wildcards"
466	printf "\n -s LM compiles all locally modified files"
467	printf "\n -S config file interpreted by shellscript ---"
468	printf "\n -t allowed cpu-time in seconds (batch) 0"
469	printf "\n -T tasks per node depending on -h"
470	printf "\n -u username on remote machine \"\" "
471	printf "\n -v no prompt for confirmation ---"
472	printf "\n -w maximum parallel io streams as given by -X"
473	printf "\n -x tracing of mrun for debug purposes ---"
474	printf "\n -X # of processors (on parallel machines) 1"
475	printf "\n -y add appendix \"_O\" to all local output"
476	printf "\n files (ocean precursor runs followed by"
477	printf "\n coupled atmosphere-ocean runs) ---"
478	printf "\n -Y run coupled model, \"#1 #2\" with"
479	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
480	printf "\n -z disable a priori parameter file check ---"
481	printf "\n -Z skip combine_plot_fields at the end of "
482	printf "\n the simulation ---"
483	printf "\n "
484	printf "\n Possible values of positional parameter <modus>:"
485	printf "\n \"?\" - this outline \n\n") \| more
486	exit
487	elif [[ "$1" != "" ]]
488	then
489	printf "\n +++ positional parameter $1 unknown \n"
490	locat=parameter; exit
491	fi
492
493
494
495	# SHORT STARTING MESSAGE
496	printf "\n*** $version "
497	printf "\n will be executed. Please wait ..."
498
499
500
501	# CHECK, IF CONFIGURATION FILE EXISTS
502	if [[ ! -f $config_file ]]
503	then
504	printf "\n\n +++ configuration file: "
505	printf "\n $config_file"
506	printf "\n does not exist"
507	locat=connect; exit
508	fi
509
510
511	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
512	line=""
513	grep "%host_identifier" $config_file > tmp_mrun
514	while read line
515	do
516	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
517	then
518	HOSTNAME=`echo $line \| cut -d" " -s -f2`
519	host_identifier=`echo $line \| cut -d" " -s -f3`
520	if [[ $localhost_realname = $HOSTNAME ]]
521	then
522	localhost=$host_identifier
523	break
524	fi
525	fi
526	done < tmp_mrun
527
528	if [[ "$localhost" = "" ]]
529	then
530	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
531	printf "\n for local host \"$localhost_realname\"."
532	printf "\n Please add line"
533	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
534	printf "\n to the configuration file."
535	locat=localhost; exit
536	fi
537
538
539	# SET HOST-SPECIFIC VARIABLES
540	case $localhost_realname in
541	(r1\|r2\|h01\|b01) archive_system=tivoli;;
542	(cs*) archive_system=ut;;
543	esac
544
545
546	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
547	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
548	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
549	[[ "$afname" = "" ]] && afname=$fname
550
551
552	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
553	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
554	# STATEMENTS IN THE CONFIGURATION FILE
555	if [[ "$run_mode" != "" ]]
556	then
557	input_list="$input_list $run_mode"
558	output_list="$output_list $run_mode"
559	fi
560
561
562	# ??? is this (and the respective option -H) really required ???
563	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
564	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
565	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
566	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
567	if [[ "$fromhost" = "" ]]
568	then
569	fromhost=$localhost
570	fi
571
572
573	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
574	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
575	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
576	# TO BE SUBMITTED (I.E. do_bacth=true)
577	if [[ -n $host && "$host" != $localhost ]]
578	then
579	do_batch=true
580	do_remote=true
581	case $host in
582	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
583	(*) printf "\n"
584	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
585	printf "\n is not available"
586	locat=nqs; (( iec = 0 )); exit;;
587	esac
588	else
589	host=$localhost
590	fi
591
592
593	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
594	if [[ -n $additional_conditions ]]
595	then
596	cond1=`echo $additional_conditions \| cut -d" " -f1`
597	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
598	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
599	if [[ -n $dummy ]]
600	then
601	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
602	locat=options; exit
603	fi
604	block=_$cond1
605	[[ -n $cond2 ]] && block=${block}_$cond2
606	fi
607
608
609	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
610	if [[ $run_coupled_model = true ]]
611	then
612
613	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
614	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
615
616	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
617	then
618
619	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
620	printf "\n PEs (total) : $numprocs"
621	printf "\n PEs (atmosphere): $numprocs_atmos"
622	printf "\n PEs (ocean) : $numprocs_ocean"
623	locat=coupling; exit
624
625	fi
626
627
628	# GET coupled_mode FROM THE CONFIG FILE
629	line=""
630	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
631	while read line
632	do
633	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
634	then
635	coupled_mode="mpi2"
636	fi
637	done < tmp_mrun
638
639	fi
640
641
642	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
643	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
644	then
645	if [[ $ignore_archive_error = false ]]
646	then
647	printf "\n +++ data archiving of previous run failed"
648	printf "\n see directory \~/job_queue on remote machine"
649	locat=archive; exit
650	else
651	printf "\n +++ warning: data archiving in a previous run failed"
652	printf "\n MRUN continues, trying to get backup copy"
653	fi
654	fi
655
656
657	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
658	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
659	mrun_memory=$memory
660	mrun_group_number=$group_number
661	mrun_cpumax=$cpumax
662	mrun_numprocs=$numprocs
663
664
665	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
666	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
667	if [[ "$read_from_config" = false ]]
668	then
669
670	[[ $silent = false ]] && printf "\n Reading the configuration file... "
671
672	# READ THE CONFIGURATION FILE LINE BY LINE
673	while read zeile
674	do
675	[[ $silent = false ]] && printf "."
676
677
678	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
679	eval zeile=\"$zeile\"
680
681
682	# INTERPRET THE LINE
683	if [[ "$(echo $zeile)" = "" ]]
684	then
685	# EMPTY LINE, NO ACTION
686	continue
687
688	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
689	then
690
691	# LINE IS A COMMENT LINE
692	true
693
694	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
695	then
696
697	# LINE DEFINES AN ENVIRONMENT-VARIABLE
698	zeile=$(echo $zeile \| cut -c2-)
699	var=`echo $zeile \| cut -d" " -f1`
700	value=`echo $zeile \| cut -d" " -s -f2`
701	for_host=`echo $zeile \| cut -d" " -s -f3`
702	for_cond1=`echo $zeile \| cut -d" " -s -f4`
703	for_cond2=`echo $zeile \| cut -d" " -s -f5`
704
705	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
706	then
707
708	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
709	# "::" IS REPLACED BY ":".
710	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
711
712
713	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
714	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
715	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
716	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
717	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
718	# CONFIGURATION-FILE.
719	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
720	then
721	eval $var=\$value
722
723	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
724	if [[ $do_trace = true ]]
725	then
726	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
727	fi
728	fi
729
730	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
731	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
732	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
733	# MUST HAVE TO BE STARTED
734	if [[ $var = host ]]
735	then
736	if [[ -n $host && "$host" != $localhost ]]
737	then
738	do_batch=true
739	do_remote=true
740	case $host in
741	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
742	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
743	printf "\n is not available"
744	locat=nqs; exit;;
745	esac
746	else
747	host=$localhost
748	fi
749	fi
750
751	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
752	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
753	# BY MRUN (E.G. subjob)
754	export $var
755	fi
756
757
758
759
760	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
761	then
762
763	# LINE DEFINES ERROR-COMMAND
764	(( iec = iec + 1 ))
765	zeile=$(echo $zeile \| cut -c4-)
766	err_command[$iec]="$zeile"
767
768	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
769	then
770
771	# LINE DEFINES INPUT-COMMAND
772	(( iic = iic + 1 ))
773	zeile=$(echo $zeile \| cut -c4-)
774	in_command[$iic]="$zeile"
775
776	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
777	then
778
779	# LINE DEFINES OUTPUT-COMMAND
780	(( ioc = ioc + 1 ))
781	zeile=$(echo $zeile \| cut -c4-)
782	out_command[$ioc]="$zeile"
783
784	else
785
786	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
787	# s2a: in/out - field
788	# s2b: loc - field (optional)
789	# s2c: tr/ar - field (optional)
790	s1=`echo $zeile \| cut -d" " -f1`
791	s2=`echo $zeile \| cut -d" " -s -f2`
792	s2a=$(echo $s2 \| cut -d":" -f1)
793	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
794	then
795	s2b=""
796	s2c=""
797	else
798	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
799	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
800	fi
801	s3=`echo $zeile \| cut -d" " -f3`
802	s4=`echo $zeile \| cut -d" " -s -f4`
803	s5=`echo $zeile \| cut -d" " -s -f5`
804	s6=`echo $zeile \| cut -d" " -s -f6`
805
806
807	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
808	# INPUT- OR OUTPUT-LIST.
809	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
810	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
811	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
812	# IS NOT CHECKED AND STORED.
813	IFSALT="$IFS"; IFS="$IFS:"
814	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
815	then
816	found=false
817	for actual in $input_list
818	do
819	for formal in $s3
820	do
821	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
822	done
823	done
824	if [[ $found = true ]]
825	then
826	(( iin = iin + 1 ))
827	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
828	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
829	extin[$iin]=$s6
830	fi
831	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
832	then
833	found=false
834	for actual in $output_list
835	do
836	for formal in $s3
837	do
838	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
839	done
840	done
841	if [[ $found = true ]]
842	then
843	(( iout = iout + 1 ))
844	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
845	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
846	fi
847	elif [[ "$s2a" != in && "$s2a" != out ]]
848	then
849	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
850	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
851	locat=connect; exit
852	fi
853	IFS="$IFSALT"
854	fi
855	done < $config_file
856
857	else
858
859
860	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
861	[[ $silent = false ]] && printf "..."
862	interpreted_config_file=.icf.$RANDOM
863
864
865
866	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
867	cat > .mrun_environment << %%END%%
868	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
869	config_file = '$config_file', do_remote = '$do_remote',
870	do_trace = '$do_trace', host = '$host',
871	input_list = '$input_list', icf = '$interpreted_config_file',
872	localhost = '$localhost', output_list = '$output_list' /
873
874	%%END%%
875
876	if [[ "$host" != $localhost ]]
877	then
878
879	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
880	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
881	if [[ $? != 0 ]]
882	then
883	printf "\n\n +++ no interpret_config found"
884	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
885	locat=interpret_config; exit
886	fi
887	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
888	$interpret_config_executable
889
890	else
891
892	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
893	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
894	then
895	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
896	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
897	locat=interpret_config; exit
898	else
899	interpret_config${block}.x
900	fi
901
902	fi
903	rm .mrun_environment
904
905
906	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
907	chmod u+x $interpreted_config_file
908	export PATH=$PATH:.
909	. $interpreted_config_file
910	rm $interpreted_config_file
911
912	fi
913
914
915	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
916	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
917	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
918	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
919	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
920	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
921	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
922
923
924	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
925	# FOR SOURCE-FILES TO BE COMPILED.
926	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
927	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
928	if [[ "$SOURCES_COMPLETE" = "" ]]
929	then
930
931	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
932	# HAS BEEN DEFINED
933	source_path=""
934	line=""
935	grep "%source_path" $config_file > tmp_mrun
936	while read line
937	do
938	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
939	then
940	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
941	then
942	global_source_path=`echo $line \| cut -d" " -f2`
943	fi
944	fi
945	done < tmp_mrun
946
947	line=""
948	found=false
949	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
950	while read line
951	do
952	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
953	then
954	if [[ $found = true ]]
955	then
956	printf "\n\n +++ more than one source path found in configuration file"
957	printf "\n for local host \"$localhost\" "
958	locat=source_path; exit
959	fi
960	source_path=`echo $line \| cut -d" " -f2`
961	found=true
962	fi
963	done < tmp_mrun
964	rm tmp_mrun
965
966	if [[ "$source_path" = "" ]]
967	then
968	if [[ "$global_source_path" != "" ]]
969	then
970	source_path=$global_source_path
971	else
972	printf "\n\n +++ no source path found in configuration file"
973	printf "\n for local host \"$localhost\" "
974	locat=source_path; exit
975	fi
976	fi
977	eval source_path=$source_path
978
979	if [[ ! -d $source_path ]]
980	then
981	printf "\n\n +++ source path \"$source_path\" on local host"
982	printf "\n \"$localhost\" does not exist"
983	locat=source_path; exit
984	fi
985
986	fi
987
988
989	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
990	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
991	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
992	then
993	global_revision=`svnversion $source_path 2>/dev/null`
994	global_revision="Rev: $global_revision"
995	fi
996
997
998	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
999	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1000	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1001	if [[ -n $host && "$host" != $localhost ]]
1002	then
1003	do_batch=true
1004	do_remote=true
1005	case $host in
1006	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1007	(*) printf "\n"
1008	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1009	printf "\n is not available"
1010	locat=nqs; (( iec = 0 )); exit;;
1011	esac
1012	else
1013	host=$localhost
1014	fi
1015
1016
1017	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1018	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1019	then
1020
1021	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1022	if [[ ! -n $numprocs ]]
1023	then
1024	printf "\n"
1025	printf "\n +++ option \"-K parallel\" requires additional specification"
1026	printf "\n of the number of processors to be used by"
1027	printf "\n mrun-option \"-X\" or by environment-variable"
1028	printf "\n \"numprocs\" in the configuration file"
1029	locat=numprocs; (( iec = 0 )); exit
1030	fi
1031
1032	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1033	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1034	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1035	then
1036	printf "\n"
1037	printf "\n +++ option \"-T\" (tasks per node) is missing"
1038	printf "\n set -T option or define tasks_per_node in the config file"
1039	locat=tasks_per_node; (( iec = 0 )); exit
1040	fi
1041
1042	if (( numprocs < tasks_per_node ))
1043	then
1044	printf "\n"
1045	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1046	printf "\n given values: -T $tasks_per_node -X $numprocs"
1047	locat=tasks_per_node; (( iec = 0 )); exit
1048	fi
1049
1050	if [[ $host != lcflow && $host != lcxt5m ]]
1051	then
1052	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1053	(( ival = $tasks_per_node ))
1054	(( pes = numprocs ))
1055	(( ii = pes / ival ))
1056	(( remaining_pes = pes - ii * ival ))
1057	if (( remaining_pes > 0 ))
1058	then
1059	printf "\n"
1060	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1061	printf "\n divisor of the total number of processors (option \"-X\")"
1062	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1063	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1064	(( nodes = nodes + 1 ))
1065	fi
1066	fi
1067
1068
1069	# SETTINGS FOR SUBJOB-COMMAND
1070	OOPT="-O $threads_per_task"
1071
1072	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1073	if [[ "$tasks_per_node" != "" ]]
1074	then
1075	TOPT="-T $tasks_per_node"
1076	fi
1077
1078	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1079	if [[ $node_usage = default ]]
1080	then
1081	if [[ $host = ibms ]]
1082	then
1083	node_usage=shared
1084	else
1085	node_usage=not_shared
1086	fi
1087	fi
1088
1089	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1090	then
1091	printf "\n"
1092	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1093	printf "\n \"shared\" or \"not_shared\""
1094	locat=tasks_per_node; (( iec = 0 )); exit
1095	fi
1096
1097	fi
1098
1099	# CHECK IF HOSTFILE EXISTS
1100	if [[ -n $hostfile ]]
1101	then
1102	if [[ ! -f $hostfile ]]
1103	then
1104	printf "\n"
1105	printf "\n +++ hostfile \"$hostfile\" does not exist"
1106	locat=hostfile; exit
1107	fi
1108	fi
1109
1110
1111	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1112	if [[ "$maximum_parallel_io_streams" = "" ]]
1113	then
1114	maximum_parallel_io_streams=$numprocs
1115	fi
1116
1117
1118	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1119	if [[ "$scp_port" != "" ]]
1120	then
1121	PORTOPT="-P $scp_port"
1122	SSH_PORTOPT="-p $scp_port"
1123	fi
1124
1125
1126	# SET DEFAULT-QUEUE, IF NOT GIVEN
1127	if [[ $queue = none ]]
1128	then
1129	case $host in
1130	(ibmh) queue=cluster;;
1131	(ibmkisti) queue=class.32plus;;
1132	(lckiaps) queue=normal;;
1133	(lckyoto) queue=ph;;
1134	(lckyuh) queue=fx-single;;
1135	(lckyut) queue=cx-single;;
1136	(lctit) queue=S;;
1137	(nech) queue=none;;
1138	(unics) queue=unics;;
1139	esac
1140	fi
1141
1142
1143	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1144	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1145	(( i = 0 ))
1146	while (( i < iin ))
1147	do
1148	(( i = i + 1 ))
1149	(( maxcycle = 0 ))
1150
1151	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1152	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1153	if [[ "${actionin[$i]}" = di ]]
1154	then
1155	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1156	# HOST ONLY
1157	eval filename=${pathin[$i]}/${endin[$i]}
1158	else
1159	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1160	# HOST ONLY
1161	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1162	fi
1163	eval pathname=${pathin[$i]}
1164
1165	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1166	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1167	then
1168	filename_input=$filename
1169	fi
1170
1171	# CHECK IF FILE EXISTS
1172	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1173	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1174	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1175	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1176	then
1177
1178	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1179	if [[ "${transin[$i]}" != "locopt" ]]
1180	then
1181	printf "\n\n +++ INPUT-file: "
1182	if [[ "${extin[$i]}" = "" ]]
1183	then
1184	printf "\n $filename"
1185	else
1186	printf "\n $filename.${extin[$i]}"
1187	fi
1188	printf "\n does not exist\n"
1189	locat=input; exit
1190	else
1191	transin[$i]="unavailable"
1192	fi
1193	else
1194
1195	# DETERMINE THE FILE'S CYCLE NUMBER
1196	ls -1 -d $filename > filelist 2>/dev/null
1197	ls -1 -d $filename.* >> filelist 2>/dev/null
1198	while read zeile
1199	do
1200	cycle=$(echo $zeile \| cut -f2 -d".")
1201	if [[ "$cycle" = "$zeile" ]]
1202	then
1203	(( icycle = 0 ))
1204	elif [[ "$cycle" = "${extin[$i]}" ]]
1205	then
1206	(( icycle = 0 ))
1207	else
1208	(( icycle = $cycle ))
1209	fi
1210	if (( icycle > maxcycle ))
1211	then
1212	(( maxcycle = icycle ))
1213	file_to_be_used=$zeile
1214	fi
1215	done <filelist
1216	rm filelist
1217
1218	# APPEND CYCLE NUMBER TO FILENAME
1219	if (( maxcycle > 0 ))
1220	then
1221	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1222	then
1223	filename=${filename}.$maxcycle.${extin[$i]}
1224	else
1225	filename=${filename}.$maxcycle
1226	fi
1227	else
1228	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1229	then
1230	filename=${filename}.${extin[$i]}
1231	fi
1232	fi
1233
1234	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1235	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1236	absnamein[$i]=$filename
1237	if (( maxcycle > 0 ))
1238	then
1239	if [[ "${actionin[$i]}" = di ]]
1240	then
1241	frelin[$i]=${endin[$i]}.$maxcycle
1242	else
1243	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1244	fi
1245	else
1246	if [[ "${actionin[$i]}" = di ]]
1247	then
1248	frelin[$i]=${endin[$i]}
1249	else
1250	frelin[$i]=${afname}${endin[$i]}
1251	fi
1252	fi
1253
1254	fi
1255	done
1256
1257	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1258	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1259	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1260	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1261	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1262	# REMOTE HOST)
1263	(( i = 0 ))
1264	while (( i < iout ))
1265	do
1266	(( i = i + 1 ))
1267	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1268	then
1269	if [[ "${actionout[$i]}" = tr ]]
1270	then
1271	actionout[$i]=""
1272	elif [[ "${actionout[$i]}" = trpe ]]
1273	then
1274	actionout[$i]=pe
1275	elif [[ "${actionout[$i]}" = tra ]]
1276	then
1277	actionout[$i]=a
1278	fi
1279	(( maxcycle = 0 ))
1280	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1281	eval catalogname=${pathout[$i]}
1282	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1283	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1284	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1285	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1286	then
1287
1288	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1289	if cat /dev/null > $filename
1290	then
1291	rm $filename
1292	else
1293
1294	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1295	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1296	if [[ ! -d $catalogname ]]
1297	then
1298	if mkdir -p $catalogname
1299	then
1300	printf "\n\n *** directory:"
1301	printf "\n $catalogname"
1302	printf "\n was created\n"
1303	else
1304	printf "\n\n +++ OUTPUT-file:"
1305	printf "\n $filename"
1306	printf "\n cannot be created, because directory does not exist"
1307	printf "\n and cannot be created either"
1308	printf "\n"
1309	locat=output ; exit
1310	fi 2>/dev/null
1311	else
1312	printf "\n\n +++ OUTPUT-file:"
1313	printf "\n $filename"
1314	printf "\n cannot be created, although directory exists"
1315	printf "\n"
1316	locat=output ; exit
1317	fi
1318	fi 2>/dev/null
1319	else
1320
1321	# DETERMINE THE CYCLE NUMBER
1322	ls -1 -d $filename > filelist 2>/dev/null
1323	ls -1 -d $filename.* >> filelist 2>/dev/null
1324	while read zeile
1325	do
1326	cycle=$(echo $zeile \| cut -f2 -d".")
1327	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1328	then
1329	(( icycle = 1 ))
1330	else
1331	(( icycle = $cycle + 1 ))
1332	fi
1333	if (( icycle > maxcycle ))
1334	then
1335	(( maxcycle = icycle ))
1336	fi
1337	done <filelist
1338	rm filelist
1339	fi
1340
1341	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1342	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1343	if [[ "${actionout[$i]}" != a ]]
1344	then
1345	if (( maxcycle > 0 ))
1346	then
1347	filename=${filename}.$maxcycle
1348	if cat /dev/null > $filename
1349	then
1350	rm $filename
1351	else
1352	printf "\n +++ OUTPUT-file:"
1353	printf "\n $filename"
1354	printf "\n cannot be created"
1355	locat=output ; exit
1356	fi
1357	fi
1358	else
1359	(( maxcycle = maxcycle - 1 ))
1360	if (( maxcycle > 0 ))
1361	then
1362	filename=${filename}.$maxcycle
1363	fi
1364	fi
1365
1366	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1367	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1368	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1369	pathout[$i]=$filename
1370	if (( maxcycle > 0 ))
1371	then
1372	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1373	else
1374	frelout[$i]=${fname}${endout[$i]}
1375	fi
1376
1377	fi
1378	done
1379
1380
1381	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1382	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1383	then
1384	if [[ "$dvr_inc" = "" ]]
1385	then
1386	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1387	printf "\n This is required for the dvrp_graphics package.\n"
1388	locat=dvr; exit
1389	fi
1390	if [[ "$dvr_lib" = "" ]]
1391	then
1392	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1393	printf "\n This is required for the dvrp_graphics package.\n"
1394	locat=dvr; exit
1395	fi
1396	fi
1397
1398
1399	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1400	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1401	if [[ "$mainprog" = "" && "$executable" = "" ]]
1402	then
1403	printf "\n +++ neither main program nor executable defined"
1404	locat=source; exit
1405	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1406	then
1407	printf "\n +++ main program as well as executable defined"
1408	locat=source; exit
1409	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1410	then
1411	do_compile=false
1412	fi
1413
1414
1415	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1416	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1417	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1418	then
1419	rm -rf SOURCES_FOR_RUN_$fname
1420	mkdir SOURCES_FOR_RUN_$fname
1421	fi
1422
1423
1424	# COLLECT ALL ROUTINES TO BE COMPILED
1425	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1426	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1427	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1428	then
1429
1430	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1431
1432	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1433	then
1434
1435	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1436	source_list=""
1437	cd $source_path
1438
1439
1440	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1441	if [[ ! -d .svn ]]
1442	then
1443	printf "\n\n +++ source directory"
1444	printf "\n \"$source_path\" "
1445	printf "\n is not under control of \"subversion\"."
1446	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1447	fi
1448
1449
1450	# LIST ALL MODIFIED SOURCE CODE FILES
1451	Filenames=""
1452	svn status > tmp_mrun
1453	while read line
1454	do
1455	firstc=`echo $line \| cut -c1`
1456	if [[ $firstc = M \|\| $firstc = "?" ]]
1457	then
1458	Name=`echo "$line" \| cut -c8-`
1459	extension=`echo $Name \| cut -d. -f2`
1460	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1461	then
1462	Filenames="$Filenames "$Name
1463	fi
1464	fi
1465	done < tmp_mrun
1466
1467
1468	# COPY FILES TO SOURCES_FOR_RUN_...
1469	for dateiname in $Filenames
1470	do
1471	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1472	source_list=$source_list"$dateiname "
1473	done
1474
1475	cd - > /dev/null
1476
1477
1478	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1479	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1480	elif [[ "$source_list" != "" && $restart_run != true ]]
1481	then
1482
1483	cd $source_path
1484
1485	for filename in $source_list
1486	do
1487
1488	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1489	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1490	then
1491	printf "\n +++ source code file: $filename"
1492	printf "\n must not contain (\"/\") "
1493	locat=source; exit
1494	fi
1495
1496	if [[ ! -f $filename ]]
1497	then
1498	printf "\n +++ source code file: $filename"
1499	printf "\n does not exist"
1500	locat=source; exit
1501	else
1502	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1503	fi
1504
1505	done
1506
1507	cd - > /dev/null
1508
1509	fi
1510
1511
1512	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1513	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1514	if [[ $restart_run != true ]]
1515	then
1516
1517	if [[ ! -f "$source_path/$mainprog" ]]
1518	then
1519	printf "\n\n +++ main program: $mainprog"
1520	printf "\n does not exist in source directory"
1521	printf "\n \"$source_path\"\n"
1522	locat=source; exit
1523	else
1524	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1525	then
1526	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1527	source_list=${mainprog}" $source_list"
1528	fi
1529	fi
1530	fi
1531
1532
1533	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1534	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1535	if [[ "$restart_run" != true ]]
1536	then
1537	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1538	if [[ ! -f $makefile ]]
1539	then
1540	printf "\n +++ file \"$makefile\" does not exist"
1541	locat=make; exit
1542	else
1543	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1544	fi
1545	fi
1546
1547
1548	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1549	if [[ $restart_run != true && "$add_source_path" != "" ]]
1550	then
1551
1552	# DOES THE DIRECTORY EXIST?
1553	if [[ ! -d $add_source_path ]]
1554	then
1555	printf "\n\n +++ WARNING: additional source code directory"
1556	printf "\n \"$add_source_path\" "
1557	printf "\n does not exist or is not a directory."
1558	printf "\n No source code will be used from this directory!\n"
1559	add_source_path=""
1560	if [[ $silent == false ]]
1561	then
1562	sleep 3
1563	fi
1564	else
1565
1566	cd $add_source_path
1567	found=false
1568
1569	Names=$(ls -1 *.f90 2>&1)
1570	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1571	Names=$(ls -1 *.F90 2>&1)
1572	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1573	Names=$(ls -1 *.F 2>&1)
1574	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1575	Names=$(ls -1 *.f 2>&1)
1576	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1577	Names=$(ls -1 *.c 2>&1)
1578	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1579
1580	cd - > /dev/null
1581	cd SOURCES_FOR_RUN_$fname
1582
1583	# COPY MAKEFILE IF EXISTING
1584	if [[ -f $add_source_path/Makefile ]]
1585	then
1586	printf "\n\n *** user Makefile from directory"
1587	printf "\n \"$add_source_path\" is used \n"
1588	if [[ $silent == false ]]
1589	then
1590	sleep 1
1591	fi
1592	cp $add_source_path/Makefile .
1593	fi
1594
1595	for dateiname in $AddFilenames
1596	do
1597	if [[ -f $dateiname ]]
1598	then
1599	printf "\n +++ source code file \"$dateiname\" found in additional"
1600	printf "\n source code directory \"$add_source_path\" "
1601	printf "\n but was also given with option \"-s\" which means that it should be taken"
1602	printf "\n from directory \"$source_path\"."
1603	locat=source; exit
1604	fi
1605
1606	cp $add_source_path/$dateiname .
1607	source_list="$source_list $dateiname"
1608
1609	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1610	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1611	then
1612	printf "\n\n +++ user file \"$dateiname\" "
1613	printf "\n is not listed in Makefile \n"
1614	locat=source; exit
1615	else
1616
1617	if [[ $found = false ]]
1618	then
1619	found=true
1620	printf "\n\n *** following user file(s) added to the"
1621	printf " files to be translated:\n "
1622	fi
1623	printf "$dateiname "
1624	if [[ $silent == false ]]
1625	then
1626	sleep 0.5
1627	fi
1628
1629	fi
1630	done
1631	[[ $found = true ]] && printf "\n"
1632	cd - > /dev/null
1633	fi
1634	fi
1635
1636
1637	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1638	# TO THE LIST OF FILES TO BE COMPILED
1639	if [[ $restart_run != true && -n $package_list ]]
1640	then
1641
1642	cd $source_path
1643
1644	for package in $package_list
1645	do
1646
1647	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1648
1649	# DETERMINE FILES BELONGING TO THE PACKAGE
1650	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1651	# THE NAME OF THE DIRECTORY
1652	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1653
1654
1655	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1656	# IF THEY ARE NOT ALREADY PART OF THE LIST
1657	for source_list_name in $package_source_list
1658	do
1659	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1660	then
1661
1662	# ONLY TAKE FILES WITH VALID SUFFIX
1663	ending=`echo $source_list_name \| cut -f2 -d.`
1664	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1665	then
1666	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1667	source_list="$source_list $source_list_name"
1668	fi
1669	fi
1670	done
1671	done
1672
1673	cd - > /dev/null
1674	fi
1675
1676	fi # do_compile=true
1677
1678
1679	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1680	# AND SET PRE-PROCESSOR DIRECTIVES
1681	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1682	then
1683
1684	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1685	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1686	then
1687	cpp_options="${cpp_options},-D__ibm=__ibm"
1688	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1689	then
1690	cpp_options="$cpp_options -D__nec"
1691	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1692	then
1693	cpp_options="$cpp_options -D__lc"
1694	else
1695	cpp_options="$cpp_options -D__$localhost"
1696	fi
1697
1698	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1699	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1700	then
1701	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1702	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1703	else
1704	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1705	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1706	fi
1707
1708	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1709	if [[ -n $package_list ]]
1710	then
1711	for package in $package_list
1712	do
1713	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1714	then
1715	if [[ $package != "dvrp_graphics+1PE" ]]
1716	then
1717	cpp_options="${cpp_options},-D__$package=__$package"
1718	else
1719	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1720	export use_seperate_pe_for_dvrp_output=true
1721	fi
1722	else
1723	if [[ $package != "dvrp_graphics+1PE" ]]
1724	then
1725	cpp_options="$cpp_options -D__$package"
1726	else
1727	cpp_options="$cpp_options -D__dvrp_graphics"
1728	export use_seperate_pe_for_dvrp_output=true
1729	fi
1730	fi
1731	done
1732	fi
1733
1734	# SET DIRECTIVES GIVEN BY OPTION -D
1735	if [[ -n $cpp_opts ]]
1736	then
1737	for popts in $cpp_opts
1738	do
1739	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1740	then
1741	cpp_options="${cpp_options},-D__$popts=__$popts"
1742	else
1743	cpp_options="$cpp_options -D__$popts"
1744	fi
1745	done
1746	fi
1747
1748	else
1749
1750
1751	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1752	if [[ $do_remote = false ]]
1753	then
1754	if [[ ! -f $executable ]]
1755	then
1756	printf "\n +++ executable file: $executable"
1757	printf "\n does not exist"
1758	locat=executable; exit
1759	fi
1760	fi
1761	fi
1762
1763
1764	# DETERMINE THE JOB MODE
1765	if [[ "$ENVIRONMENT" = BATCH ]]
1766	then
1767	batch_job=.TRUE.
1768	jobmo=BATCH
1769	else
1770	batch_job=.FALSE.
1771	jobmo=INTERACTIVE
1772	fi
1773
1774
1775	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1776	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1777	then
1778	printf "\n +++ no interactive runs allowed on host \"$host\" "
1779	printf "\n please submit batch job using mrun option \"-b\" \n"
1780	locat=normal; exit
1781	fi
1782
1783
1784	# CHECK, IF USER DEFINED A COMPILER
1785	if [[ "$compiler_name" = "" ]]
1786	then
1787
1788	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1789	locat=compiler_name; exit
1790
1791	fi
1792
1793
1794	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1795	kennung=$RANDOM
1796	if [[ "$tmp_user_catalog" = "" ]]
1797	then
1798	if [[ $localhost = ibmh ]]
1799	then
1800	tmp_user_catalog=$SCRATCH
1801	elif [[ $localhost = nech ]]
1802	then
1803	tmp_user_catalog=$WRKSHR
1804	else
1805	tmp_user_catalog=/tmp
1806	fi
1807	fi
1808	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1809
1810
1811	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1812	if [[ "$tmp_data_catalog" = "" ]]
1813	then
1814	if [[ $localhost = nech ]]
1815	then
1816	tmp_data_catalog=$WRKSHR/mrun_restart_data
1817	else
1818	tmp_data_catalog=/tmp/mrun_restart_data
1819	fi
1820	fi
1821
1822
1823	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1824	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1825	then
1826	eval fopts=\"$fopts\"
1827	eval lopts=\"$lopts\"
1828	fi
1829
1830
1831
1832	# DETERMINE COMPILE- AND LINK-OPTIONS
1833	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1834	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1835	ROPTS="$ropts"
1836	# 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 ]]
1837	# then
1838	XOPT="-X $numprocs"
1839	# fi
1840
1841
1842
1843	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1844	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1845	done=false
1846	while [[ $done = false ]]
1847	do
1848	cputime=$cpumax
1849	if (( $cputime == 0 ))
1850	then
1851	if [[ $do_batch = true ]]
1852	then
1853	printf "\n +++ cpu-time is undefined"
1854	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1855	printf "\n >>> "
1856	read cputime 1>/dev/null 2>&1
1857	else
1858	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1859	fi
1860	else
1861	done=true
1862	fi
1863	cpumax=$cputime
1864	done
1865
1866	(( minuten = cputime / 60 ))
1867	(( sekunden = cputime - minuten * 60 ))
1868
1869
1870	# CHECK THE MEMORY DEMAND
1871	if [[ $do_batch = true ]]
1872	then
1873	done=false
1874	while [[ $done = false ]]
1875	do
1876	if (( memory == 0 ))
1877	then
1878	printf "\n +++ memory demand is undefined"
1879	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1880	printf "\n >>> "
1881	read memory 1>/dev/null 2>&1
1882	else
1883	done=true
1884	fi
1885	done
1886	fi
1887
1888
1889	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1890	if [[ $do_remote = true && -z $remote_username ]]
1891	then
1892	while [[ -z $remote_username ]]
1893	do
1894	printf "\n +++ username on remote host \"$host\" is undefined"
1895	printf "\n >>> Please type username:"
1896	printf "\n >>> "
1897	read remote_username
1898	done
1899	mc="$mc -u$remote_username"
1900	fi
1901
1902	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1903	if [[ "$login_init_cmd" != "" ]]
1904	then
1905	export init_cmds="${login_init_cmd};"
1906	fi
1907
1908
1909	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1910	if [[ "$modules" != "" ]]
1911	then
1912	if [[ $host = lctit ]]
1913	then
1914	export module_calls=". $modules"
1915	else
1916	export module_calls="module load ${modules};"
1917	fi
1918	fi
1919
1920
1921
1922	# OUTPUT OF THE MRUN-HEADER
1923	calltime=$(date)
1924	printf "\n"
1925	printf "#------------------------------------------------------------------------# \n"
1926	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1927	printf "\| \| \n"
1928	spalte1="called on:"; spalte2=$localhost_realname
1929	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1930	if [[ $do_remote = true ]]
1931	then
1932	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1933	else
1934	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1935	fi
1936	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1937	if [[ -n $numprocs ]]
1938	then
1939	if [[ $run_coupled_model = false ]]
1940	then
1941	spalte1="number of PEs:"; spalte2=$numprocs
1942	else
1943	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1944	fi
1945	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1946	fi
1947	if [[ -n $tasks_per_node ]]
1948	then
1949	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1950	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1951	if (( remaining_pes > 0 ))
1952	then
1953	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1954	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1955	fi
1956	fi
1957	if [[ $maximum_parallel_io_streams != $numprocs ]]
1958	then
1959	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1960	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1961	fi
1962	if [[ $use_openmp = true ]]
1963	then
1964	spalte1="threads per task:"; spalte2="$threads_per_task"
1965	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1966	fi
1967	printf "\| \| \n"
1968	if [[ $do_compile = true ]]
1969	then
1970	if [[ "$mopts" != "" ]]
1971	then
1972	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1973	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1974	zeile=$(echo "$mopts" \| cut -c46-)
1975	while [[ "$zeile" != "" ]]
1976	do
1977	spalte1=""
1978	spalte2=$(echo "$zeile" \| cut -c-45)
1979	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1980	zeile=$(echo "$zeile" \| cut -c46-)
1981	done
1982	fi
1983
1984	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1985	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1986	zeile=$(echo "$cpp_options" \| cut -c46-)
1987	while [[ "$zeile" != "" ]]
1988	do
1989	spalte1=""
1990	spalte2=$(echo "$zeile" \| cut -c-45)
1991	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1992	zeile=$(echo "$zeile" \| cut -c46-)
1993	done
1994
1995	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1996	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1997	zeile=$(echo "$fopts" \| cut -c46-)
1998	while [[ "$zeile" != "" ]]
1999	do
2000	spalte1=""
2001	spalte2=$(echo "$zeile" \| cut -c-45)
2002	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2003	zeile=$(echo "$zeile" \| cut -c46-)
2004	done
2005
2006	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2007	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2008	zeile=$(echo "$lopts" \| cut -c46-)
2009	while [[ "$zeile" != "" ]]
2010	do
2011	spalte1=""
2012	spalte2=$(echo "$zeile" \| cut -c-45)
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	zeile=$(echo "$zeile" \| cut -c46-)
2015	done
2016
2017	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2019	zeile=$(echo "$modules" \| cut -c46-)
2020	while [[ "$zeile" != "" ]]
2021	do
2022	spalte1=""
2023	spalte2=$(echo "$zeile" \| cut -c-45)
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	zeile=$(echo "$zeile" \| cut -c46-)
2026	done
2027
2028	spalte1="main program:"; spalte2=$mainprog
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030	else
2031	spalte1=executable:; spalte2=$executable
2032	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2033	fi
2034	printf "\| \| \n"
2035	spalte1="base name of files:"; spalte2=$fname
2036	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2037	if [[ $fname != $afname ]]
2038	then
2039	spalte1="base name of input files:"; spalte2=$afname
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	fi
2042	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2043	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2044	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046
2047	if [[ "$ocean_file_appendix" = true ]]
2048	then
2049	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2050	fi
2051
2052	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2053	then
2054	spalte1="memory demand / PE":; spalte2="$memory MB"
2055	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2056	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2057	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2058	fi
2059
2060	if [[ $do_compile = true ]]
2061	then
2062	printf "\| \| \n"
2063	printf "\| Files to be compiled: \| \n"
2064	zeile=$source_list
2065	while [[ "$zeile" != "" ]]
2066	do
2067	linestart=$(echo $zeile \| cut -c-70)
2068	printf "\| %-70s \| \n" "$linestart"
2069	zeile=$(echo "$zeile" \| cut -c71-)
2070	done
2071	fi
2072	printf "#------------------------------------------------------------------------#"
2073
2074
2075
2076	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2077	if [[ $do_trace = true ]]
2078	then
2079	(( i = 0 ))
2080	while (( i < iin ))
2081	do
2082	(( i = i + 1 ))
2083	if (( i == 1 ))
2084	then
2085	printf "\n\n >>> INPUT-file assignments:\n"
2086	fi
2087	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2088	done
2089	(( i = 0 ))
2090	while (( i < iout ))
2091	do
2092	(( i = i + 1 ))
2093	if (( i == 1 ))
2094	then
2095	printf "\n\n >>> OUTPUT-file assignments:\n"
2096	fi
2097	printf "\n ${localout[$i]} : ${pathout[$i]}"
2098	done
2099	(( i = 0 ))
2100	while (( i < iic ))
2101	do
2102	(( i = i + 1 ))
2103	if (( i == 1 ))
2104	then
2105	printf "\n\n >>> INPUT-commands:\n"
2106	fi
2107	printf "\n ${in_command[$i]}"
2108	done
2109	(( i = 0 ))
2110	while (( i < ioc ))
2111	do
2112	(( i = i + 1 ))
2113	if (( i == 1 ))
2114	then
2115	printf "\n\n >>> OUTPUT-commands:\n"
2116	fi
2117	printf "\n ${out_command[$i]}"
2118	done
2119	fi
2120
2121
2122	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2123	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2124	then
2125	antwort=dummy
2126	printf "\n\n"
2127	printf " >>> everything o.k. (y/n) ? "
2128	while read antwort
2129	do
2130	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2131	then
2132	printf " >>> everything o.k. (y/n) ? "
2133	else
2134	break
2135	fi
2136	done
2137	if [[ $antwort = n \|\| $antwort = N ]]
2138	then
2139	locat=user_abort; (( iec = 0 )); exit
2140	fi
2141	if [[ $do_batch = true ]]
2142	then
2143	printf " >>> batch-job will be created and submitted"
2144	else
2145	printf " >>> MRUN will now continue to execute on this machine"
2146	fi
2147	fi
2148
2149
2150	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2151	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2152	check_depository="${working_directory}/trunk/UTIL"
2153	check_sources="${working_directory}/tmp_check_namelist_files"
2154	skip_check=false
2155
2156	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2157	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2158	then
2159	skip_check=true
2160	reason="run on remote host or parameter file check has not been compiled."
2161	fi
2162	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2163	then
2164	skip_check=true
2165	reason="parameter file check has not been compiled."
2166	fi
2167
2168	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2169	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2170	then
2171	skip_check=true
2172	reason="serial run."
2173	fi
2174
2175	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2176	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2177	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2178	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2179	if [[ $check_namelist_files == false ]]
2180	then
2181	skip_check=true
2182	reason="-z option set."
2183	fi
2184
2185	if [[ $fromhost != $localhost ]]
2186	then
2187	skip_check=true
2188	reason="submitting host is local host."
2189	fi
2190
2191	if [[ $run_coupled_model == true ]]
2192	then
2193	skip_check=true
2194	reason="coupled run."
2195	fi
2196
2197	if [[ $restart_run == true ]]
2198	then
2199	skip_check=true
2200	reason="restart run."
2201	fi
2202
2203	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2204	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2205	last_char=`echo $filename_input \| cut -c $last_char_int`
2206	if [[ "$last_char" == "f" ]]
2207	then
2208	skip_check=true
2209	reason="restart run."
2210	fi
2211
2212	if [[ $skip_check == false ]]
2213	then
2214	tmp_check=${working_directory}/tmp_check
2215
2216	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2217	# NOT NECESSARILY REQUIRED
2218	line=""
2219	found=false
2220	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2221	while read line1
2222	do
2223	line="$line1"
2224	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2225	then
2226	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2227	found=true
2228	fi
2229	done < $tmp_check
2230
2231	if [[ $found = false ]]
2232	then
2233	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2234	fi
2235
2236	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2237	# NOT NECESSARILY REQUIRED
2238	line=""
2239	found=false
2240	grep "NUDGING_DATA" $config_file > $tmp_check
2241	while read line1
2242	do
2243	line="$line1"
2244	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2245	then
2246	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2247	found=true
2248	fi
2249	done < $tmp_check
2250
2251	if [[ $found = false ]]
2252	then
2253	printf "\n +++ no NUDGING list entry found in the configuration file."
2254	fi
2255
2256	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2257	# NOT NECESSARILY REQUIRED
2258	line=""
2259	found=false
2260	grep "LSF_DATA" $config_file > $tmp_check
2261	while read line1
2262	do
2263	line="$line1"
2264	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2265	then
2266	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2267	found=true
2268	fi
2269	done < $tmp_check
2270
2271	if [[ $found = false ]]
2272	then
2273	printf "\n +++ no LSF list entry found in the configuration file."
2274	fi
2275
2276	rm -rf ${working_directory}/tmp_check
2277
2278	# CHECK IF THE P3DF FILE MUST BE CHECKED
2279	for item in $input_list
2280	do
2281	if [[ "$item" == "restart" ]]
2282	then
2283	check_restart=1
2284	else
2285	check_restart=0
2286	fi
2287	done
2288
2289	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2290	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2291	then
2292	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2293	locat=check_namelist; exit
2294	fi
2295
2296	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2297	if [[ $check_restart == 1 ]]
2298	then
2299
2300	filenamef="${filename_input}f"
2301	if [[ ! -f $filenamef ]]
2302	then
2303	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2304	check_restart=0
2305	answer=dummy
2306	printf "\n\n"
2307
2308	if [[ $silent == false ]]
2309	then
2310	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2311	do
2312	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2313	read answer
2314	done
2315	if [[ $answer = a \|\| $answer = A ]]
2316	then
2317	printf "\n +++ Aborting...."
2318	locat=normal; exit
2319	fi
2320	fi
2321	else
2322	check_restart=1
2323	fi
2324	fi
2325
2326	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2327	mkdir $check_sources
2328	cd $check_sources
2329
2330
2331	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2332	if [[ -d $add_source_path ]]
2333	then
2334	printf "\n\n *** copying files from $check_depository"
2335	cp $check_depository/check_namelist_files.tar ./
2336
2337	printf "\n\n *** untar of makefile and source files in $check_sources"
2338	tar -xf check_namelist_files.tar > /dev/null 2>&1
2339
2340	printf "\n\n *** adding user code."
2341	cp $add_source_path/* ./
2342	touch check_namelist_files.f90
2343
2344	# GET COMPILER OPTIONS AND PERFORM MAKE
2345	printf "\n\n *** compiling code if necessary...\n"
2346
2347	# workaround for batch jobs on local machine (lcxe6)
2348	if [[ $do_batch == true && $do_remote == false ]]
2349	then
2350	eval $init_cmds
2351	fi
2352
2353	# GET CHECK OPTIONS
2354	line=""
2355	found=false
2356
2357	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2358
2359	while read line1
2360	do
2361
2362	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2363	then
2364	line="$line1"
2365	fi
2366
2367	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2368	then
2369	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2370	line="$line "
2371	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'`
2372	found=true
2373	fi
2374
2375	done < $tmp_check
2376	copts_check="$copts_check -D__check -D__parallel"
2377
2378	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2379
2380	# GET MAKE OUTPUT
2381	if [[ $? != 0 ]]
2382	then
2383	printf "\n +++ error during make."
2384	answer=dummy
2385	printf "\n\n"
2386	if [[ $silent == false ]]
2387	then
2388	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2389	do
2390	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2391	read answer
2392	done
2393	if [[ $answer = a \|\| $answer = A ]]
2394	then
2395	printf "\n +++ Aborting..."
2396	rm -rf $check_sources
2397	locat=normal; exit
2398	else
2399	skip_check=true
2400	fi
2401	else
2402	skip_check=true
2403	fi
2404	fi
2405	else
2406	cp $PALM_BIN/check_namelist_files.x ./
2407	fi
2408
2409	cp $filename_input ./PARIN
2410	if [[ $check_restart == 1 ]]
2411	then
2412	cp $filenamef ./PARINF
2413	fi
2414
2415	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2416	then
2417	printf "\n *** adding topography data"
2418	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2419
2420	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2421	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2422	# WHICH REQUIRE SUFFICIENT MEMORY
2423	ulimit -s unlimited
2424	fi
2425
2426	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2427	then
2428	printf "\n *** adding nudging data"
2429	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2430	fi
2431
2432	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2433	then
2434	printf "\n *** adding large scale forcing data"
2435	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2436	fi
2437
2438	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2439	cat > ENVPAR << %%END%%
2440	&envpar run_identifier = '$fname', host = '$host',
2441	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2442	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2443	maximum_cpu_time_allowed = ${cpumax}.,
2444	revision = '$global_revision',
2445	local_dvrserver_running = $local_dvrserver_running /
2446
2447	%%END%%
2448
2449	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2450	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2451	then
2452	printf "\n +++ WARNING: check_namelist_files.x not found."
2453	answer=dummy
2454	printf "\n\n"
2455
2456	if [[ $silent == false ]]
2457	then
2458	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2459	do
2460	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2461	read answer
2462	done
2463	if [[ $answer = a \|\| $answer = A ]]
2464	then
2465	printf "\n +++ Aborting..."
2466	rm -rf $check_sources
2467	locat=normal; exit
2468	else
2469	printf "\n *** skipping parameter file check."
2470	fi
2471	fi
2472
2473	elif [[ $skip_check == false ]]
2474	then
2475	# STARTING THE PARAMETER FILE CHECK
2476	printf "\n\n *** starting parameter file check..."
2477
2478	# CHECKING THE P3D FILE
2479	printf "\n\n (1) checking $filename_input"
2480	echo "$numprocs 0 0" > VARIN
2481	errors=`./check_namelist_files.x < VARIN 2>&1`
2482
2483	check_error=false
2484	if [[ "$errors" == "" ]]
2485	then
2486	printf " --> o.k."
2487	else
2488	printf " --> failed."
2489	check_error=true
2490	printf "\n\n $errors"
2491	fi
2492
2493	# CHECKING THE PD3F FILE IF NECESSARY
2494	if [[ $check_restart == 1 && $check_error == false ]]
2495	then
2496	printf "\n\n (2) checking $filenamef"
2497
2498	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2499	# IN &INIPAR LIST
2500	found=false
2501	cat PARINF \| while read line
2502	do
2503	line=$(echo $line\|sed 's/ //g')
2504	if [[ $line == "&inipar" ]]
2505	then
2506	start_search=true
2507	fi
2508
2509	if [[ $start_search == true ]]
2510	then
2511	if [[ $line == "initializing_actions='read_restart_data'" ]]
2512	then
2513	found=true
2514	break
2515	fi
2516	fi
2517
2518	if [[ $line == "/" ]]
2519	then
2520	start_search=false
2521	fi
2522
2523	done
2524
2525	if [[ $found = false ]]
2526	then
2527	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2528	printf "\n in &inipar list in $fname$p3df_suffix."
2529	rm -rf $check_sources
2530	locat=check_namelist; exit
2531	fi
2532
2533	# READ max_user_pr FROM FILES
2534	if [[ -f parin_for_check ]]
2535	then
2536	read max_pr_user < parin_for_check
2537	else
2538	max_user_pr=0
2539	fi
2540
2541	echo "$numprocs 1 $max_pr_user" > VARIN
2542	errors=`./check_namelist_files.x < VARIN 2>&1`
2543
2544	if [[ "$errors" == "" ]]
2545	then
2546	printf " --> o.k."
2547	else
2548	printf " --> failed."
2549	check_error=true
2550	printf "\n\n $errors"
2551	fi
2552	fi
2553
2554	# REPORT ERRORS AND CONTINUE/EXIT
2555	if [[ $check_error == true ]]
2556	then
2557	printf "\n +++ errors found in the parameter file!\n"
2558	answer=dummy
2559	printf "\n\n"
2560
2561	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2562	do
2563	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2564	read answer
2565	done
2566
2567	if [[ $answer = a \|\| $answer = A ]]
2568	then
2569	printf "\n +++ Aborting..."
2570	rm -rf $check_sources
2571	locat=normal; exit
2572	fi
2573	else
2574	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2575	fi
2576	rm -rf $check_sources
2577	fi
2578	else
2579	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2580	fi
2581
2582	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2583	rm -rf $check_sources
2584	cd $working_directory
2585
2586
2587	# DETERMINE PATH FOR MAKE DEPOSITORY
2588	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2589	then
2590
2591	line=""
2592	grep "%depository_path" $config_file > tmp_mrun
2593	while read line
2594	do
2595	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2596	then
2597	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2598	then
2599	global_depository_path=`echo $line \| cut -d" " -s -f2`
2600	fi
2601	fi
2602	done < tmp_mrun
2603
2604	line=""
2605	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2606	while read line
2607	do
2608	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2609	then
2610	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2611	then
2612	local_depository_path=`echo $line \| cut -d" " -s -f2`
2613	fi
2614	fi
2615	done < tmp_mrun
2616
2617	if [[ "$local_depository_path" = "" ]]
2618	then
2619	if [[ "$global_depository_path" != "" ]]
2620	then
2621	local_depository_path=$global_depository_path
2622	else
2623	printf "\n\n +++ no depository path found in configuration file"
2624	printf "\n for local host \"$localhost\" "
2625	printf "\n please set \"\%depository_path\" in configuration file\n"
2626	locat=config_file; exit
2627	fi
2628	fi
2629	eval local_depository_path=$local_depository_path
2630	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2631	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2632
2633
2634	basename=`echo $mainprog \| cut -f1 -d"."`
2635	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2636	if [[ ! -f $make_depository ]]
2637	then
2638	printf "\n"
2639	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2640	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2641	fi
2642
2643	fi
2644
2645
2646	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2647	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2648	if [[ $do_batch = false ]]
2649	then
2650
2651
2652	# CREATE THE TEMPORARY WORKING DIRECTORY
2653	mkdir -p $TEMPDIR
2654	chmod go+rx $TEMPDIR
2655	tmpcreate=true
2656
2657
2658	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2659	# INTO THE TEMPORARY WORKING DIRECTORY
2660	if [[ $do_compile = true ]]
2661	then
2662
2663	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2664	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2665	if [[ $localhost = nech ]]
2666	then
2667	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2668	if mkdir -p $TEMPDIR_COMPILE
2669	then
2670	printf "\n *** \"$TEMPDIR_COMPILE\" "
2671	printf "\n is generated as temporary directory for cross compiling\n"
2672	else
2673	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2674	printf "\n needed for cross compilation failed"
2675	locat=compile
2676	exit
2677	fi
2678	else
2679	TEMPDIR_COMPILE=$TEMPDIR
2680	fi
2681
2682	cp $make_depository $TEMPDIR_COMPILE
2683	cd $TEMPDIR_COMPILE
2684	tar -xf $make_depository > /dev/null 2>&1
2685	cd - > /dev/null
2686
2687	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2688	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2689	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2690	then
2691	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2692	else
2693	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2694	fi
2695
2696	else
2697
2698	cp $executable ${TEMPDIR}/a.out
2699
2700	fi
2701
2702
2703	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2704	cd $TEMPDIR
2705	printf "\n *** changed to temporary directory: $TEMPDIR"
2706
2707
2708	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2709	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2710	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2711	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2712	(( i = 0 ))
2713	while (( i < iout ))
2714	do
2715	(( i = i + 1 ))
2716	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2717	then
2718	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2719	else
2720	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2721	fi
2722	done
2723
2724
2725	# IF REQUIRED, START WITH COMPILING
2726	if [[ $do_compile = true ]]
2727	then
2728
2729
2730	if [[ -f a.out ]]
2731	then
2732
2733	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2734	printf "\n\n\n *** executable a.out found"
2735	printf "\n no compilation required \n"
2736
2737	else
2738
2739	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2740	printf "\n\n\n *** compilation starts \n$dashes\n"
2741	printf " *** compilation with make using following options:\n"
2742	printf " make depository: $make_depository"
2743	if [[ "$mopts" != "" ]]
2744	then
2745	printf " make options: $mopts\n"
2746	fi
2747	printf " compilername: $compiler_name\n"
2748	printf " compiler options: $fopts\n"
2749	printf " preprocessor directives: $cpp_options \n"
2750	printf " linker options: $lopts \n"
2751	if [[ "$modules" != "" ]]
2752	then
2753	printf " modules to be load: $modules \n"
2754	fi
2755	printf " source code files: $source_list \n"
2756
2757	if [[ $localhost = nech ]]
2758	then
2759	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\" "
2760	cp $TEMPDIR_COMPILE/a.out .
2761	[[ $? != 0 ]] && compile_error=true
2762	rm -rf $TEMPDIR_COMPILE
2763	elif [[ $localhost = ibmh ]]
2764	then
2765	printf " compiler is called via ssh on \"plogin1\" \n"
2766	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\" "
2767	[[ ! -f a.out ]] && compile_error=true
2768	continue # STATUS=1, IF a.out EXISTS
2769	elif [[ $localhost = lcflow ]]
2770	then
2771	printf " compiler is called via ssh on \"flow\" \n"
2772	/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\" "
2773	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2774	[[ "$check_for_file" = "" ]] && compile_error=true
2775	continue # STATUS=1, IF a.out EXISTS
2776	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2777	then
2778	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2779	else
2780	[[ "$init_cmds" != "" ]] && eval $init_cmds
2781	[[ "$module_calls" != "" ]] && eval $module_calls
2782	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2783	fi
2784
2785	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2786	then
2787	printf "\n +++ error occured while compiling or linking"
2788	locat=compile
2789
2790	exit
2791	else
2792	printf "$dashes\n *** compilation finished \n"
2793	fi
2794
2795	fi
2796
2797	fi
2798
2799
2800	# PROVIDE THE INPUT FILES
2801	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2802	(( i = 0 ))
2803	while (( i < iin ))
2804	do
2805	(( i = i + 1 ))
2806	if (( i == 1 ))
2807	then
2808	printf "\n\n *** providing INPUT-files:\n$dashes"
2809	fi
2810
2811
2812	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2813	if [[ "${transin[$i]}" = unavailable ]]
2814	then
2815	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2816	then
2817	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2818	printf "\n is not available!"
2819	else
2820	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2821	printf "\n is not available!"
2822	fi
2823	continue
2824	fi
2825
2826	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2827	files_for_pes=false; datentyp=file
2828	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2829	then
2830	files_for_pes=true; datentyp=directory
2831	actionin[$i]=""
2832	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2833	then
2834	actionin[$i]=""
2835	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2836	then
2837	files_for_pes=true; datentyp=directory
2838	actionin[$i]="ar"
2839	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2840	then
2841	actionin[$i]="ar"
2842	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2843	then
2844	files_for_pes=true; datentyp=directory
2845	actionin[$i]="fl"
2846	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2847	then
2848	actionin[$i]="fl"
2849	fi
2850
2851	if [[ $files_for_pes = true ]]
2852	then
2853	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2854	else
2855	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2856	fi
2857
2858	# INPUT-FILE FOR A RESTART RUN.
2859	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2860	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2861	if [[ "${actionin[$i]}" = fl ]]
2862	then
2863	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2864	if [[ $files_for_pes = false ]]
2865	then
2866	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2867	then
2868	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2869	got_tmp[$i]=true
2870	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2871	then
2872	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2873	printf "\n *** trying to use backup copy in \"$WORK\" "
2874	cp $WORK/${frelin[$i]} ${localin[$i]}
2875	else
2876	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2877	printf "\n or \"$tmp_data_catalog\" does not exist!"
2878	printf "\n *** trying to get copy from archive"
2879	actionin[$i]=ar
2880	fi
2881	else
2882	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2883	then
2884	mkdir ${localin[$i]}
2885	cd $tmp_data_catalog/${frelin[$i]}
2886	for file in $(ls *)
2887	do
2888	ln $file $TEMPDIR/${localin[$i]}
2889	done
2890	cd $TEMPDIR
2891	got_tmp[$i]=true
2892	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2893	then
2894	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2895	printf "\n *** trying to use backup copy in \"$WORK\" "
2896	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2897	else
2898	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2899	printf "\n or \"$tmp_data_catalog\" does not exist!"
2900	printf "\n *** trying to get copy from archive"
2901	actionin[$i]=ar
2902	fi
2903	fi
2904	fi
2905
2906
2907	# FILE IS STORED ON THE ARCHIVE SYSTEM
2908	if [[ "${actionin[$i]}" = ar ]]
2909	then
2910
2911	if [[ $files_for_pes = false ]]
2912	then
2913	printf "\n file will be restored from archive-system ($archive_system)!"
2914	else
2915	printf "\n directory will be restored from archive-system ($archive_system)!"
2916	fi
2917
2918	file_restored=false
2919
2920	if [[ $archive_system = asterix ]]
2921	then
2922	do_stagein=true
2923	(( stagein_anz = 0 ))
2924	while [[ $do_stagein = true ]]
2925	do
2926	if [[ $files_for_pes = false ]]
2927	then
2928	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2929	else
2930	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2931	fi
2932	cat STAGEIN_OUTPUT
2933	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2934	then
2935	file_restored=true
2936	do_stagein=false
2937	else
2938	(( stagein_anz = stagein_anz + 1 ))
2939	if (( stagein_anz == 10 ))
2940	then
2941	printf "\n +++ stagein stoped after 10 tries"
2942	locat=stage
2943	exit
2944	fi
2945	printf "\n +++ restoring from archive failed, trying again:"
2946	sleep 900
2947	fi
2948	done
2949	elif [[ $archive_system = DMF ]]
2950	then
2951	if [[ $files_for_pes = false ]]
2952	then
2953	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2954	locat=DMF
2955	exit
2956	else
2957	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2958	cp -r $ARCHIVE/${frelin[$i]} $PWD
2959	file_restored=true
2960	fi
2961	elif [[ $archive_system = tivoli ]]
2962	then
2963	if [[ $files_for_pes = false ]]
2964	then
2965	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2966	else
2967	(( inode = 0 ))
2968	while (( inode < nodes ))
2969	do
2970	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2971	(( inode = inode + 1 ))
2972	done
2973	fi
2974	file_restored=true
2975	elif [[ $archive_system = ut ]]
2976	then
2977	if [[ $files_for_pes = false ]]
2978	then
2979	cp $UT/${frelin[$i]} .
2980	else
2981	(( inode = 0 ))
2982	while (( inode < nodes ))
2983	do
2984	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2985	(( inode = inode + 1 ))
2986	done
2987	fi
2988	file_restored=true
2989	else
2990	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2991	locat=rearchive
2992	exit
2993	fi
2994
2995	if [[ $file_restored = true ]]
2996	then
2997
2998	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2999	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3000	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3001	if [[ $files_for_pes = false ]]
3002	then
3003	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3004	else
3005	mkdir $tmp_data_catalog/${frelin[$i]}
3006	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3007	fi
3008	got_tmp[$i]=true
3009
3010	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3011	mv ${frelin[$i]} ${localin[$i]}
3012
3013	fi
3014	fi
3015
3016
3017	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3018	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3019	then
3020
3021	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3022	then
3023
3024	# FILE COPIES ARE PROVIDED FOR ALL CORES
3025	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3026	printf "\n file will be provided for $numprocs processors"
3027	mkdir ${localin[$i]}
3028	ival=$numprocs
3029	(( ii = 0 ))
3030	while (( ii <= ival-1 ))
3031	do
3032	if (( ii < 10 ))
3033	then
3034	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3035	elif (( ii < 100 ))
3036	then
3037	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3038	elif (( ii < 1000 ))
3039	then
3040	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3041	else
3042	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3043	fi
3044	(( ii = ii + 1 ))
3045	done
3046
3047	else
3048
3049	if [[ $files_for_pes = true ]]
3050	then
3051
3052	# PROVIDE FILES FOR EACH CORE
3053	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3054	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3055	printf "\n providing $numprocs files for the respective processors"
3056	mkdir ${localin[$i]}
3057	if [[ $link_local_input = true ]]
3058	then
3059	printf " using ln -f\n"
3060	cd ${absnamein[$i]}
3061	for file in $(ls *)
3062	do
3063	ln -f $file ${localin[$i]}
3064	done
3065	cd $TEMPDIR
3066	fi
3067
3068	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3069	if [[ ! -f "${localin[$i]}/_0000" ]]
3070	then
3071	if [[ $link_local_input = true ]]
3072	then
3073	printf " ln failed for .../_0000, using cp...\n"
3074	fi
3075	cp -r ${absnamein[$i]}/* ${localin[$i]}
3076	fi
3077
3078	else
3079
3080	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3081	if [[ $link_local_input = true ]]
3082	then
3083	printf " using ln -f\n"
3084	ln -f ${absnamein[$i]} ${localin[$i]}
3085	fi
3086	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3087	if [[ ! -f "${localin[$i]}" ]]
3088	then
3089	if [[ $link_local_input = true ]]
3090	then
3091	printf " ln failed, using cp...\n"
3092	fi
3093	cp ${absnamein[$i]} ${localin[$i]}
3094	fi
3095	fi
3096	fi
3097	fi
3098
3099	done
3100	if (( i != 0 ))
3101	then
3102	printf "\n$dashes\n *** all INPUT-files provided \n"
3103	fi
3104
3105
3106	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3107	(( i = 0 ))
3108	while (( i < iic ))
3109	do
3110	(( i = i + 1 ))
3111	if (( i == 1 ))
3112	then
3113	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3114	fi
3115	printf "\n >>> ${in_command[$i]}"
3116	eval ${in_command[$i]}
3117	if (( i == iic ))
3118	then
3119	printf "\n$dashes\n"
3120	fi
3121	done
3122
3123
3124	# SET THE REMAINING CPU-TIME
3125	cpurest=${cpumax}.
3126
3127
3128	# START DVR STREAMING SERVER
3129	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3130	then
3131	if [[ "$dvr_server" != "" ]]
3132	then
3133
3134	printf "\n\n *** preparing the dvr streaming server configuration file"
3135
3136	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3137	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3138	if [[ "$running_dvrserver_id" != "" ]]
3139	then
3140
3141	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3142	printf "\n This server is used instead starting a new one!"
3143	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3144
3145	else
3146
3147	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3148	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3149	then
3150	cp ${PALM_BIN}/.dvrserver.config .
3151
3152	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3153	user_id=`id -u`
3154	group_id=`id -g`
3155
3156	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3157	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3158	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3159	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3160	mv .dvrserver.3 .dvrserver.config
3161	rm .dvrserver.1 .dvrserver.2
3162
3163	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3164	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3165	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3166	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3167	local_dvrserver_running=.TRUE.
3168	else
3169	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3170	printf "\n \"$PALM_BIN\" "
3171	locat=dvr
3172	exit
3173	fi
3174
3175	fi
3176
3177	else
3178	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3179	fi
3180	fi
3181
3182
3183	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3184	# (FILE ENVPAR WILL BE READ BY PALM)
3185	cat > ENVPAR << %%END%%
3186	&envpar run_identifier = '$fname', host = '$localhost',
3187	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3188	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3189	maximum_cpu_time_allowed = ${cpumax}.,
3190	revision = '$global_revision',
3191	local_dvrserver_running = $local_dvrserver_running,
3192	batch_job = $batch_job /
3193
3194	%%END%%
3195
3196
3197	# STARTING THE EXECUTABLE
3198	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3199	PATH=$PATH:$TEMPDIR
3200
3201	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3202	if [[ "$mpi_debug" = true ]]
3203	then
3204	export MPI_CHECK_ARGS=1
3205	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3206	fi
3207
3208	if [[ "$totalview" = true ]]
3209	then
3210	printf "\n *** totalview debugger will be used"
3211	tv_opt="-tv"
3212	else
3213	tv_opt=""
3214	fi
3215
3216	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3217	then
3218	if [[ "$ENVIRONMENT" = BATCH ]]
3219	then
3220	continue
3221	fi
3222	if [[ $localhost = ibmh ]]
3223	then
3224
3225	# SETUP THE IBM MPI ENVIRONMENT
3226	export MP_SHARED_MEMORY=yes
3227	export AIXTHREADS_SCOPE=S
3228	export OMP_NUM_THREADS=$threads_per_task
3229	export AUTHSTATE=files
3230	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3231
3232	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3233	export MP_ADAPTER_USE=shared
3234	export MP_CPU_USE=multiple
3235	export MP_TIMEOUT=1200
3236
3237	unset MP_TASK_AFFINITY
3238
3239	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3240	#(( ii = 1 ))
3241	#while (( ii <= $numprocs ))
3242	#do
3243	# echo $localhost_realname >> hostfile
3244	# (( ii = ii + 1 ))
3245	#done
3246	#export MP_HOSTFILE=hostfile
3247
3248	if [[ "$LOADLBATCH" = yes ]]
3249	then
3250	totalview poe a.out $ROPTS
3251	else
3252	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3253	export TVDSVRLAUNCHCMD=ssh
3254	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3255	fi
3256
3257	fi # END DEBUG MODE
3258
3259	else
3260
3261	# NORMAL EXECUTION
3262	if [[ -n $numprocs ]]
3263	then
3264
3265	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3266	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3267	then
3268
3269	# SETUP THE IBM MPI ENVIRONMENT
3270	if [[ $host != ibmh && $host != ibmkisti ]]
3271	then
3272	export MP_SHARED_MEMORY=yes
3273	export AIXTHREAD_SCOPE=S
3274	export OMP_NUM_THREADS=$threads_per_task
3275	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3276	export AUTHSTATE=files
3277	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3278	# export MP_PRINTENV=yes
3279
3280	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3281	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3282	export MP_WAIT_MODE=poll
3283	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3284	fi
3285
3286	if [[ $host = ibmkisti ]]
3287	then
3288	export LANG=en_US
3289	export MP_SHARED_MEMORY=yes
3290	if [[ $threads_per_task = 1 ]]
3291	then
3292	export MP_SINGLE_THREAD=yes
3293	export MEMORY_AFFINITY=MCM
3294	else
3295	export OMP_NUM_THREADS=$threads_per_task
3296	fi
3297	fi
3298
3299	if [[ "$LOADLBATCH" = yes ]]
3300	then
3301	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3302	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3303	then
3304	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3305	else
3306	if [[ $run_coupled_model = false ]]
3307	then
3308	if [[ "$ocean_file_appendix" = true ]]
3309	then
3310	echo "precursor_ocean" > runfile_atmos
3311	else
3312	echo "precursor_atmos" > runfile_atmos
3313	fi
3314	else
3315	(( iia = $numprocs_atmos / $threads_per_task ))
3316	(( iio = $numprocs_ocean / $threads_per_task ))
3317	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3318	printf "\n using $coupled_mode coupling"
3319	printf "\n\n"
3320	echo "coupled_run $iia $iio" > runfile_atmos
3321	fi
3322	poe ./a.out $ROPTS < runfile_atmos
3323	fi
3324	else
3325	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3326	then
3327	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3328	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3329	then
3330	if [[ -f $hostfile ]]
3331	then
3332	cp $hostfile hostfile
3333	else
3334	(( ii = 1 ))
3335	while (( ii <= $numprocs ))
3336	do
3337	echo $localhost_realname >> hostfile
3338	(( ii = ii + 1 ))
3339	done
3340	fi
3341	export MP_HOSTFILE=hostfile
3342	if [[ $run_coupled_model = false ]]
3343	then
3344	if [[ "$ocean_file_appendix" = true ]]
3345	then
3346	echo "precursor_ocean" > runfile_atmos
3347	else
3348	echo "precursor_atmos" > runfile_atmos
3349	fi
3350	else
3351	(( iia = $numprocs_atmos / $threads_per_task ))
3352	(( iio = $numprocs_ocean / $threads_per_task ))
3353	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3354	printf "\n using $coupled_mode coupling"
3355	printf "\n\n"
3356	echo "coupled_run $iia $iio" > runfile_atmos
3357	fi
3358
3359	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3360
3361	else
3362	if [[ "$host_file" = "" ]]
3363	then
3364	printf "\n +++ no hostfile given in configuration file"
3365	locat=config_file
3366	exit
3367	else
3368	eval host_file=$host_file
3369	fi
3370	export MP_HOSTFILE=$host_file
3371	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3372	fi
3373	fi
3374	elif [[ $host = nech ]]
3375	then
3376	(( ii = nodes ))
3377	if [[ $ii = 1 ]]
3378	then
3379	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3380	export MPIPROGINF=YES
3381	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3382	echo "*** execution on single node with mpirun"
3383	mpirun -np $numprocs ./a.out $ROPTS
3384	else
3385	(( i = 0 ))
3386	while (( i < ii ))
3387	do
3388	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3389	(( i = i + 1 ))
3390	done
3391
3392	echo "#!/bin/sh" > mpi_exec_shell
3393	echo " " >> mpi_exec_shell
3394	echo "set -u" >> mpi_exec_shell
3395	echo "F_ERRCNT=0" >> mpi_exec_shell
3396	echo "MPIPROGINV=YES" >> mpi_exec_shell
3397	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3398	echo "cpurest=$cpurest" >> mpi_exec_shell
3399	echo "fname=$fname" >> mpi_exec_shell
3400	echo "localhost=$localhost" >> mpi_exec_shell
3401	echo "return_addres=$return_addres" >> mpi_exec_shell
3402	echo "return_username=$return_username" >> mpi_exec_shell
3403	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3404	echo "write_binary=$write_binary" >> mpi_exec_shell
3405	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3406	echo " " >> mpi_exec_shell
3407	echo "export F_ERRCNT" >> mpi_exec_shell
3408	echo "export MPIPROGINV" >> mpi_exec_shell
3409	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3410	echo "export cpurest" >> mpi_exec_shell
3411	echo "export fname" >> mpi_exec_shell
3412	echo "export localhost" >> mpi_exec_shell
3413	echo "export return_addres" >> mpi_exec_shell
3414	echo "export return_username" >> mpi_exec_shell
3415	echo "export tasks_per_node" >> mpi_exec_shell
3416	echo "export write_binary" >> mpi_exec_shell
3417	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3418	echo " " >> mpi_exec_shell
3419	echo "exec ./a.out" >> mpi_exec_shell
3420
3421	chmod u+x mpi_exec_shell
3422	export MPIPROGINF=YES
3423	mpirun -f multinode_config &
3424	wait
3425
3426	fi
3427	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3428	then
3429
3430	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3431	# DOES NOT EXIST
3432	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3433	then
3434	if [[ -f $hostfile ]]
3435	then
3436	cp $hostfile hostfile
3437	(( ii = $numprocs / $threads_per_task ))
3438	else
3439	(( ii = 1 ))
3440	while (( ii <= $numprocs / $threads_per_task ))
3441	do
3442	echo $localhost_realname >> hostfile
3443	(( ii = ii + 1 ))
3444	done
3445	fi
3446	eval zeile=\"`head -n $ii hostfile`\"
3447	printf "\n *** running on: $zeile"
3448	fi
3449
3450	(( ii = $numprocs / $threads_per_task ))
3451	export OMP_NUM_THREADS=$threads_per_task
3452
3453	if [[ $threads_per_task != 1 ]]
3454	then
3455	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3456	# MAY ABORT
3457	ulimit -s unlimited
3458	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3459	fi
3460	if [[ $run_coupled_model = false ]]
3461	then
3462	if [[ "$ocean_file_appendix" = true ]]
3463	then
3464	echo "precursor_ocean" > runfile_atmos
3465	else
3466	echo "precursor_atmos" > runfile_atmos
3467	fi
3468	printf "\n\n"
3469
3470	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3471	then
3472	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3473	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3474	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3475	elif [[ $host = lccrayf ]]
3476	then
3477	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3478	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3479	then
3480	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3481	elif [[ $host = lcflow ]]
3482	then
3483	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3484	elif [[ $host = lcsb ]]
3485	then
3486	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3487	elif [[ $host = lckiaps ]]
3488	then
3489	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3490	elif [[ $host = lckyu* ]]
3491	then
3492	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3493	else
3494	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3495	fi
3496	else
3497
3498	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3499	(( iia = $numprocs_atmos / $threads_per_task ))
3500	(( iio = $numprocs_ocean / $threads_per_task ))
3501	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3502	printf "\n using $coupled_mode coupling"
3503	printf "\n\n"
3504
3505	if [[ $coupled_mode = "mpi2" ]]
3506	then
3507	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3508	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3509
3510	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3511	then
3512
3513	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3514	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3515
3516	else
3517	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3518	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3519	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3520	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3521	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3522	fi
3523	wait
3524
3525	else
3526
3527	echo "coupled_run $iia $iio" > runfile_atmos
3528
3529	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3530	then
3531
3532	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3533
3534	elif [[ $host = lck \|\| $host = lckordi ]]
3535	then
3536
3537	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3538
3539	elif [[ $host = lckyu* ]]
3540	then
3541
3542	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3543
3544	fi
3545	wait
3546	fi
3547
3548	fi
3549
3550	elif [[ $host = lckyoto ]]
3551	then
3552	set -xv
3553	export P4_RSHCOMMAND=plesh
3554	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3555	if [[ "$ENVIRONMENT" = BATCH ]]
3556	then
3557	if [[ "$cond2" = fujitsu ]]
3558	then
3559	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3560	elif [[ "cond2" = pgi ]]
3561	then
3562	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3563	else
3564	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3565	fi
3566	else
3567	if [[ "$cond2" = "" ]]
3568	then
3569	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3570	else
3571	mpirun -np $numprocs ./a.out $ROPTS
3572	fi
3573	fi
3574	set +xv
3575
3576	elif [[ $host = lctit ]]
3577	then
3578	export OMP_NUM_THREADS=$threads_per_task
3579	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3580	if [[ "$threads_per_task" != 1 ]]
3581	then
3582	export MV2_ENABLE_AFFINITY=0
3583	fi
3584	echo "----- PBS_NODEFILE content:"
3585	cat $PBS_NODEFILE
3586	echo "-----"
3587	(( ii = $numprocs / $threads_per_task ))
3588	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3589	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3590	else
3591	mpprun -n $numprocs a.out $ROPTS
3592	fi
3593	else
3594	a.out $ROPTS
3595	fi
3596	fi
3597
3598	if [[ $? != 0 ]]
3599	then
3600
3601	# ABORT IN CASE OF RUNTIME ERRORS
3602	printf "\n +++ runtime error occured"
3603	locat=execution
3604	exit
3605
3606	else
3607
3608	printf "\n$dashes\n *** execution finished \n"
3609
3610	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3611	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3612	if [[ "$dvrserver_id" != "" ]]
3613	then
3614	kill $dvrserver_id
3615	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3616
3617	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3618	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3619	if [[ -d DATA_DVR ]]
3620	then
3621
3622	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3623	# DIRECTORY
3624	cp .dvrserver.config DATA_DVR
3625
3626	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3627	# SEQUENCE MODE DATA TOO)
3628	process_dvr_output -d DATA_DVR -f $fname -s
3629
3630	else
3631
3632	# PROCESS THE LOCAL OUTPUT
3633	process_dvr_output -l -d DATA_DVR -f $fname
3634
3635	fi
3636
3637	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3638	then
3639
3640	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3641	process_dvr_output -l -d DATA_DVR -f $fname
3642
3643	fi
3644	fi
3645
3646
3647
3648	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3649	# BY EACH CORE INTO ONE FILE
3650	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3651	then
3652	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3653	printf "\n 2d- and/or 3d-data may be incomplete!"
3654	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3655	elif [[ "$combine_plot_fields" == true ]]
3656	then
3657	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3658	then
3659	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3660	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3661	else
3662	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3663	combine_plot_fields${block}.x
3664	fi
3665	else
3666
3667	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3668	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3669	# ??? koennen wir das streichen ???
3670	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3671	fi
3672
3673
3674
3675	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3676	(( i = 0 ))
3677	while (( i < ioc ))
3678	do
3679	(( i = i + 1 ))
3680	if (( i == 1 ))
3681	then
3682	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3683	fi
3684	printf "\n >>> ${out_command[$i]}"
3685	eval ${out_command[$i]}
3686	if (( i == ioc ))
3687	then
3688	printf "\n$dashes\n"
3689	fi
3690	done
3691
3692
3693	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3694	if [[ $do_trace = true ]]
3695	then
3696	printf "\n\n"
3697	ls -al
3698	fi
3699
3700
3701
3702	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3703	(( i = 0 ))
3704	while (( i < iout ))
3705	do
3706	(( i = i + 1 ))
3707	if (( i == 1 ))
3708	then
3709	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3710	fi
3711
3712	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3713	files_for_pes=false; filetyp=file
3714	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3715	then
3716	files_for_pes=true; filetyp=directory
3717	actionout[$i]=""
3718	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3719	then
3720	actionout[$i]=""
3721	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3722	then
3723	files_for_pes=true; filetyp=directory
3724	actionout[$i]="ar"
3725	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3726	then
3727	actionout[$i]="ar"
3728	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3729	then
3730	files_for_pes=true; filetyp=directory
3731	actionout[$i]="fl"
3732	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3733	then
3734	actionout[$i]="fl"
3735	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3736	then
3737	files_for_pes=true; filetyp=directory
3738	actionout[$i]="tr"
3739	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3740	then
3741	actionout[$i]="tr"
3742	fi
3743
3744	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3745	then
3746	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3747	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3748	then
3749	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3750	else
3751
3752
3753	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3754	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3755	if [[ "${actionout[$i]}" = tr ]]
3756	then
3757	if [[ $localhost != $fromhost ]]
3758	then
3759	if [[ $files_for_pes = false ]]
3760	then
3761	cps=""
3762	cst=""
3763	else
3764	cps=-c
3765	cst="/"
3766	fi
3767	if [[ $localhost = nech ]]
3768	then
3769
3770	# TRANSFER IN SEPERATE JOB
3771	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3772	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3773	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3774	if [[ $files_for_pes = false ]]
3775	then
3776	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3777	else
3778	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3779	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3780	fi
3781
3782	echo "set -x" > transfer_${localout[$i]}
3783	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3784
3785	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3786	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3787	printf "\n or higher cycle\n"
3788	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3789
3790	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3791
3792	if [[ $localhost = nech ]]
3793	then
3794	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3795	else
3796	if [[ "$LOGNAME" = b323013 ]]
3797	then
3798	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3799	else
3800	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3801	fi
3802	fi
3803
3804	else
3805
3806	# TRANSFER WITHIN THIS JOB
3807	transfer_failed=false
3808	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3809	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3810	if [[ $localhost = lccrayb ]]
3811	then
3812	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3813	elif [[ $localhost = lccrayh ]]
3814	then
3815	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3816	else
3817	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3818	fi
3819	[[ $? != 0 ]] && transfer_failed=true
3820
3821	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3822	if [[ $transfer_failed = true ]]
3823	then
3824	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3825	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3826
3827	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3828	eval local_catalog=${pathout[$i]}
3829	if [[ ! -d $local_catalog ]]
3830	then
3831	printf " *** local directory does not exist. Trying to create:\n"
3832	printf " $local_catalog \n"
3833	mkdir -p $local_catalog
3834	fi
3835	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3836	transfer_problems=true
3837	fi
3838	fi
3839	else
3840
3841	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3842	actionout[$i]=""
3843	fi
3844	fi
3845
3846
3847	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3848	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3849	if [[ "${actionout[$i]}" = tra ]]
3850	then
3851	if [[ $localhost != $fromhost ]]
3852	then
3853	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3854	then
3855
3856	# TRANSFER IN SEPERATE JOB
3857	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3858	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3859	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3860	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3861
3862	echo "set -x" > transfer_${localout[$i]}
3863	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3864
3865	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3866	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3867	printf "\n or higher cycle\n"
3868	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_addres $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3869
3870	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3871
3872	if [[ $localhost = nech ]]
3873	then
3874	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3875	else
3876	if [[ $LOGNAME = b323013 ]]
3877	then
3878	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3879	else
3880	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3881	fi
3882	fi
3883
3884	else
3885
3886	# TRANSFER WITHIN THIS JOB
3887	transfer_failed=false
3888	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3889	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3890	if [[ $localhost = lccrayb ]]
3891	then
3892	ssh $usern@blogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3893	elif [[ $localhost = lccrayh ]]
3894	then
3895	ssh $usern@hlogin1 "cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3896	else
3897	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3898	fi
3899	[[ $? != 0 ]] && transfer_failed=true
3900
3901	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3902	if [[ $transfer_failed = true ]]
3903	then
3904	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3905	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3906
3907	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3908	eval local_catalog=${pathout[$i]}
3909	if [[ ! -d $local_catalog ]]
3910	then
3911	printf " *** local directory does not exist. Trying to create:\n"
3912	printf " $local_catalog \n"
3913	mkdir -p $local_catalog
3914	fi
3915
3916	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3917	transfer_problems=true
3918	fi
3919	fi
3920	else
3921
3922	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3923	actionout[$i]=a
3924	fi
3925	fi
3926
3927
3928	# OUTPUT-FILE FOR A RESTART-RUN.
3929	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3930	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3931	# AS LAST ACTION, ARCHIVING IS INITIATED.
3932	if [[ "${actionout[$i]}" = fl ]]
3933	then
3934	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3935	chmod g+rx $tmp_data_catalog
3936	if [[ $files_for_pes = false ]]
3937	then
3938	printf "\n >>> OUTPUT: ${localout[$i]} to"
3939	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3940	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3941	else
3942	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3943	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3944	mkdir $tmp_data_catalog/${frelout[$i]}
3945	cd ${localout[$i]}
3946	for file in $(ls *)
3947	do
3948	ln -f $file $tmp_data_catalog/${frelout[$i]}
3949	done
3950	cd $TEMPDIR
3951	fi
3952
3953
3954	# CREATE AND SUBMIT ARCHIVING-JOB
3955	if [[ $store_on_archive_system = true ]]
3956	then
3957
3958	if [[ $archive_system = asterix ]]
3959	then
3960	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3961	if [[ $files_for_pes = false ]]
3962	then
3963	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3964	else
3965	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3966	fi
3967	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3968	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3969	echo "then" >> archive_${frelout[$i]}
3970	echo " do_stageout=false" >> archive_${frelout[$i]}
3971	echo "else" >> archive_${frelout[$i]}
3972	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3973	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3974	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3975	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3976	if [[ $files_for_pes = false ]]
3977	then
3978	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3979	else
3980	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3981	fi
3982	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3983	echo "fi" >> archive_${frelout[$i]}
3984	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3985	elif [[ $archive_system = DMF ]]
3986	then
3987	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3988	if [[ $files_for_pes = false ]]
3989	then
3990	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3991	locat=DMF
3992	exit
3993	else
3994	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3995	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3996	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3997	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3998	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3999	fi
4000	elif [[ $archive_system = tivoli ]]
4001	then
4002	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4003	if [[ $files_for_pes = false ]]
4004	then
4005	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4006	echo "set -x" >> archive_${frelout[$i]}
4007	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4008	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4009	else
4010
4011	echo "set -x" >> archive_${frelout[$i]}
4012	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4013	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4014	cd $tmp_data_catalog
4015	all_files=`ls -1 ${frelout[$i]}/*`
4016	cd - > /dev/null
4017	(( inode = 0 ))
4018	(( tp1 = tasks_per_node + 1 ))
4019	while (( inode < nodes ))
4020	do
4021	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4022	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4023	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4024	(( inode = inode + 1 ))
4025	done
4026	fi
4027	elif [[ $archive_system = ut ]]
4028	then
4029	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4030	if [[ $files_for_pes = false ]]
4031	then
4032	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4033	echo "set -x" >> archive_${frelout[$i]}
4034	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4035	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4036	else
4037
4038	echo "set -x" >> archive_${frelout[$i]}
4039	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4040	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4041	cd $tmp_data_catalog
4042	all_files=`ls -1 ${frelout[$i]}/*`
4043	cd - > /dev/null
4044	(( inode = 0 ))
4045	(( tp1 = tasks_per_node + 1 ))
4046	while (( inode < nodes ))
4047	do
4048	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4049	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4050	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4051	(( inode = inode + 1 ))
4052	done
4053	fi
4054	elif [[ $archive_system = none ]]
4055	then
4056	printf " +++ archiving on $localhost not available!\n"
4057	fi
4058
4059	if [[ $archive_system != none ]]
4060	then
4061	if [[ $localhost = nech ]]
4062	then
4063	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4064	fi
4065	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4066	fi
4067	else
4068	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4069	fi
4070
4071
4072	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4073	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4074	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4075	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4076	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4077	if [[ $files_for_pes = false ]]
4078	then
4079	cat /dev/null > ${pathout[$i]}
4080	else
4081	mkdir -p ${pathout[$i]}
4082	fi
4083
4084	fi
4085
4086
4087	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4088	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4089	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4090	if [[ "${actionout[$i]}" = ar ]]
4091	then
4092	if [[ $files_for_pes = false ]]
4093	then
4094	printf "\n >>> OUTPUT: ${localout[$i]} to"
4095	printf "\n ${pathout[$i]}"
4096	printf "\n File will be copied to archive-system ($archive_system) !\n"
4097	else
4098	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4099	printf "\n ${pathout[$i]}"
4100	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4101	fi
4102	mv ${localout[$i]} ${frelout[$i]}
4103
4104	file_saved=false
4105
4106	if [[ $archive_system = asterix ]]
4107	then
4108	do_stageout=true
4109	(( stageout_anz = 0 ))
4110	while [[ $do_stageout = true ]]
4111	do
4112	if [[ $files_for_pes = false ]]
4113	then
4114	stageout ${frelout[$i]} > STAGE_OUTPUT
4115	else
4116	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4117	fi
4118	cat STAGE_OUTPUT
4119	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4120	then
4121	file_saved=true
4122	do_stageout=false
4123	else
4124	if [[ $files_for_pes = false ]]
4125	then
4126	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4127	else
4128	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4129	fi
4130	(( stageout_anz = stageout_anz + 1 ))
4131	if (( stageout_anz == 10 ))
4132	then
4133	printf "\n +++ stoped after 10 unsuccessful tries!"
4134	archive_save=false
4135	do_stageout=false
4136	else
4137	printf "\n *** new try to store on archive after 15 min:"
4138	sleep 900
4139	fi
4140	fi
4141	done
4142	elif [[ $archive_system = DMF ]]
4143	then
4144	if [[ $files_for_pes = false ]]
4145	then
4146	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4147	locat=DMF
4148	exit
4149	else
4150	rm -rf $ARCHIVE/${frelout[$i]}
4151	cp -r ${frelout[$i]} $ARCHIVE
4152	fi
4153	file_saved=true
4154	elif [[ $archive_system = tivoli ]]
4155	then
4156	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4157	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4158	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4159	# WHEN THE ARCHIVE-JOB IS EXECUTED
4160	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4161	chmod g+rx $tmp_data_catalog
4162	if [[ $files_for_pes = false ]]
4163	then
4164	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4165	else
4166	mkdir $tmp_data_catalog/${frelout[$i]}
4167	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4168	fi
4169
4170	# GENERATE AND SUBMIT BATCH-JOB
4171	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4172	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4173	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4174	if [[ $files_for_pes = false ]]
4175	then
4176	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4177	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4178	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4179	else
4180	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4181	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4182	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4183	fi
4184
4185	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4186	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4187	file_saved=true
4188
4189	elif [[ $archive_system = ut ]]
4190	then
4191	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4192	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4193	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4194	# WHEN THE ARCHIVE-JOB IS EXECUTED
4195	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4196	chmod g+rx $tmp_data_catalog
4197	if [[ $files_for_pes = false ]]
4198	then
4199	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4200	else
4201	mkdir $tmp_data_catalog/${frelout[$i]}
4202	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4203	fi
4204
4205	# GENERATE AND SUBMIT BATCH-JOB
4206	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4207	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4208	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4209	if [[ $files_for_pes = false ]]
4210	then
4211	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4212	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4213	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4214	else
4215	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4216	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4217	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4218	fi
4219
4220	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4221	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4222	file_saved=true
4223
4224	else
4225	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4226	archive_save=false
4227	fi
4228
4229	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4230	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4231	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4232	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4233	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4234	if [[ $file_saved = true ]]
4235	then
4236	if [[ $files_for_pes = false ]]
4237	then
4238	cat /dev/null > ${pathout[$i]}
4239	else
4240	mkdir -p ${pathout[$i]}
4241	fi
4242	fi
4243
4244	fi
4245
4246	# APPEND ON THIS MACHINE
4247	if [[ "${actionout[$i]}" = "a" ]]
4248	then
4249	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4250	then
4251	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4252	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4253	else
4254	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4255	cat ${localout[$i]} >> ${pathout[$i]}
4256	fi
4257	fi
4258
4259	# COPY ON THIS MACHINE
4260	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4261	# ON DIFFERENT FILE-SYSTEMS
4262	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4263	then
4264
4265	# COPY IN CASE OF RUNS ON SINGLE CORES
4266	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4267	then
4268	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4269	if [[ $link_local_output = true ]]
4270	then
4271	printf " using ln -f\n"
4272	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4273	fi
4274	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4275	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4276	then
4277	if [[ $link_local_output = true ]]
4278	then
4279	printf " ln failed, using cp...\n"
4280	fi
4281	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4282	fi
4283	else
4284	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4285	if [[ $link_local_output = true ]]
4286	then
4287	printf " using ln -f\n"
4288	ln -f ${localout[$i]} ${pathout[$i]}
4289	fi
4290	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4291	if [[ ! -f "${pathout[$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]}
4298	fi
4299	fi
4300
4301	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4302	then
4303
4304	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4305	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4306	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4307	if [[ $link_local_output = true ]]
4308	then
4309	printf " using ln -f\n"
4310	mkdir ${pathout[$i]}
4311	cd ${localout[$i]}
4312	for file in $(ls *)
4313	do
4314	ln -f $file ${pathout[$i]}
4315	done
4316	cd $TEMPDIR
4317	fi
4318
4319	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4320	if [[ ! -f "${pathout[$i]}/_0000" ]]
4321	then
4322	if [[ $link_local_output = true ]]
4323	then
4324	printf " ln failed for .../_0000, using cp...\n"
4325	fi
4326	cp -r ${localout[$i]} ${pathout[$i]}
4327	fi
4328
4329	fi
4330	fi
4331	done
4332	if (( i != 0 ))
4333	then
4334	if [[ $transfer_problems = true ]]
4335	then
4336	printf "\n$dashes\n *** OUTPUT-files saved"
4337	printf "\n +++ WARNING: some data transfers failed! \n"
4338	else
4339	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4340	fi
4341	fi
4342
4343
4344	# IF REQUIRED, START A RESTART-JOB
4345	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4346	if [[ -f CONTINUE_RUN ]]
4347	then
4348
4349	if [[ $archive_save = true ]]
4350	then
4351
4352	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4353	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4354	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4355	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4356	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4357	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4358	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4359	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4360	then
4361	mc=`echo $mc \| sed 's/#/f/g'`
4362	fi
4363
4364
4365	# START THE RESTART-JOB
4366	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4367	echo " $mc"
4368	printf "\n$dashes\n"
4369	if [[ $localhost != $fromhost ]]
4370	then
4371
4372	if [[ $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4373	then
4374	echo "*** ssh will be used to initiate restart-runs!"
4375	echo " return_addres=\"$return_addres\" "
4376	echo " return_username=\"$return_username\" "
4377	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4378	then
4379	if [[ $localhost = ibmh ]]
4380	then
4381	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4382	elif [[ $localhost = lccrayb ]]
4383	then
4384	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4385	elif [[ $localhost = lccrayh ]]
4386	then
4387	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4388
4389	else
4390	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft_i/packages/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4391	fi
4392	else
4393	if [[ $localhost = ibmkisti ]]
4394	then
4395	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4396	elif [[ $localhost = lcflow ]]
4397	then
4398	/usr/bin/ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4399	elif [[ $localhost = lccrayb ]]
4400	then
4401	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4402	elif [[ $localhost = lccrayh ]]
4403	then
4404	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4405	else
4406	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4407	fi
4408	fi
4409	else
4410	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4411	locat=restart; exit
4412	fi
4413
4414	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4415	if [[ $queue = special1q ]]
4416	then
4417	sleep 120
4418	else
4419	sleep 30
4420	fi
4421
4422	else
4423
4424	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4425	# USING SSH)
4426	cd $LOCAL_PWD
4427	if [[ $localhost = lckyuh ]]
4428	then
4429	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4430	printf "\n please restart job manually using command:\n"
4431	printf "\n \"$mc\" "
4432	else
4433	eval $mc # THE ' MUST BE EVALUATED
4434	fi
4435	cd - > /dev/null
4436	fi
4437	if [[ $localhost = lckyuh ]]
4438	then
4439	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4440	else
4441	printf "\n$dashes\n *** restart-run initiated \n"
4442	fi
4443
4444
4445	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4446	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4447	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4448	# MAY BE VERY HUGE)
4449	(( i = 0 ))
4450	while (( i < iin ))
4451	do
4452	(( i = i + 1 ))
4453	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4454	then
4455	rm -r $tmp_data_catalog/${frelin[$i]}
4456	fi
4457	done
4458
4459	else
4460
4461	printf "\n +++ no restart-run possible, since errors occured"
4462	printf "\n during the archive process"
4463	fi
4464
4465	fi
4466
4467
4468
4469	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4470	if [[ "$email_notification" != "none" ]]
4471	then
4472
4473	if [[ $localhost != $fromhost ]]
4474	then
4475	if [[ -f CONTINUE_RUN ]]
4476	then
4477	echo "PALM restart run necessary" > email_text
4478	echo "description header of actual run:" >> email_text
4479	cat CONTINUE_RUN >> email_text
4480	echo "mrun-command to restart:" >> email_text
4481	echo "$mc" >> email_text
4482	else
4483	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4484	fi
4485	mail $email_notification < email_text
4486	printf "\n *** email notification sent to \"$email_notification\" "
4487	fi
4488	fi
4489
4490
4491
4492	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4493	cd $HOME
4494	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4495
4496	else
4497
4498
4499	# PREPARING ACTIONS,
4500	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4501
4502	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4503	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_addres -U $return_username -u $remote_username"
4504	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4505	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4506	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4507	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4508	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4509	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4510	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4511	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4512	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4513	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4514	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4515	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4516	if [[ $use_openmp = true ]]
4517	then
4518	mrun_com=${mrun_com}" -O $threads_per_task"
4519	fi
4520	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4521	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4522	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4523	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4524	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4525	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4526	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4527	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4528	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4529	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4530	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4531	if [[ $do_remote = true ]]
4532	then
4533	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4534	fi
4535
4536
4537	# CREATE EXECUTABLE FOR BATCH JOB
4538	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4539	then
4540
4541	printf "\n *** creating the executable for batch job\n"
4542
4543	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4544	if [[ $host != $localhost ]]
4545	then
4546	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4547	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4548	locat=create_executable; exit
4549	fi
4550
4551	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4552	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4553
4554	cp $make_depository .
4555	tar -xf $make_depository > /dev/null 2>&1
4556	cp ../* . > /dev/null 2>&1
4557
4558	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4559
4560	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4561	then
4562	printf "\n +++ error occured while compiling or linking"
4563	locat=compile
4564	exit
4565	fi
4566
4567	mv a.out ..
4568	cd - > /dev/null 2>&1
4569	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4570
4571	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4572
4573	fi
4574
4575
4576	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4577	jobfile=jobfile.$RANDOM
4578
4579
4580	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4581	echo "mkdir $TEMPDIR" >> $jobfile
4582	echo "cd $TEMPDIR" >> $jobfile
4583
4584
4585	# ACTIVATE ERROR-TRACEBACK
4586	if [[ $do_trace = true ]]
4587	then
4588	echo "set -x" >> $jobfile
4589	else
4590	echo "set +vx" >> $jobfile
4591	fi
4592
4593
4594	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4595	if [[ "$init_cmds" != "" ]]
4596	then
4597	echo "$init_cmds" >> $jobfile
4598	fi
4599	if [[ "$module_calls" != "" ]]
4600	then
4601	echo "$module_calls" >> $jobfile
4602	fi
4603
4604
4605	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4606	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4607	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4608	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4609	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4610	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4611	# QUEUEING-SYSTEMS
4612	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4613	then
4614
4615	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4616	if [[ $restart_run != true ]]
4617	then
4618	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4619	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4620	fi
4621
4622	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4623	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4624	echo "set -x" >> $jobfile
4625	if [[ $host = $localhost ]]
4626	then
4627
4628	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4629	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4630	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4631	then
4632	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4633	else
4634	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4635	fi
4636
4637	else
4638	if [[ $host = ibmkisti ]]
4639	then
4640	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4641	echo "localdir=\`pwd\`" >> $jobfile
4642	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4643	elif [[ $host = lccrayb ]]
4644	then
4645	echo "localdir=\`pwd\`" >> $jobfile
4646	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4647	elif [[ $host = lccrayh ]]
4648	then
4649	echo "localdir=\`pwd\`" >> $jobfile
4650	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4651
4652	else
4653	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4654	fi
4655	fi
4656	echo "export SOURCES_COMPLETE=true" >> $jobfile
4657
4658	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4659	# WORKING DIRECTORY OF THE JOB
4660	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4661	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4662	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4663	echo "execute_mrun=true" >> $jobfile
4664	echo " " >> $jobfile
4665
4666	else
4667
4668	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4669	if [[ $do_compile = true ]]
4670	then
4671
4672	source_catalog=SOURCES_FOR_RUN_$fname
4673
4674	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4675	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4676	echo "export SOURCES_COMPLETE=true" >> $jobfile
4677	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4678
4679	for filename in $source_list
4680	do
4681	# BACKSLASH IS USED FOR MASKING
4682	echo "cat > $filename << \"%END%\"" >> $jobfile
4683	cat $source_catalog/$filename >> $jobfile
4684	echo " " >> $jobfile
4685	echo "%END%" >> $jobfile
4686	echo " " >> $jobfile
4687	done
4688
4689	# BACKSLASH IS USED FOR MASKING
4690	echo "cat > Makefile << \"%END%\"" >> $jobfile
4691	cat $source_catalog/Makefile >> $jobfile
4692	echo " " >> $jobfile
4693	echo "%END%" >> $jobfile
4694	echo " " >> $jobfile
4695
4696	echo "cd - > /dev/null" >> $jobfile
4697
4698	fi
4699
4700
4701	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4702	# BACKSLASH IS USED FOR MASKING
4703	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4704	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4705	echo "cat > $config_file << \"%END%\"" >> $jobfile
4706	if [[ $host = lckyuh ]]
4707	then
4708	# NO CROSS-COMPILER ON COMPUTE NODE
4709	sed 's/frtpx/frt/g' $config_file >> $jobfile
4710	else
4711	sed 's/#$.*//g' $config_file >> $jobfile
4712	fi
4713	echo "%END%" >> $jobfile
4714	echo " " >> $jobfile
4715
4716
4717	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4718	# BACKSLASH IS USED FOR MASKING
4719	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4720	if [[ $host = lckyuh ]]
4721	then
4722	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4723	else
4724	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4725	fi
4726	echo "%END%" >> $jobfile
4727	echo "chmod u+x $mrun_script_name" >> $jobfile
4728	echo "execute_mrun=true" >> $jobfile
4729	echo " " >> $jobfile
4730
4731	fi
4732
4733
4734	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4735	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4736	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4737	if [[ $do_remote = true ]]
4738	then
4739	(( i = 0 ))
4740	while (( i < iin ))
4741	do
4742	(( i = i + 1 ))
4743	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4744	if [[ "${transin[$i]}" = job ]]
4745	then
4746	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4747	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4748	echo " " >> $jobfile
4749	echo "%END%" >> $jobfile
4750	else
4751	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4752	fi
4753
4754	# CHECK, IF FILE COULD BE CREATED
4755	echo "if [[ \$? = 1 ]]" >> $jobfile
4756	echo "then" >> $jobfile
4757	echo " echo \" \" " >> $jobfile
4758	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4759	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4760	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4761	echo " execute_mrun=false" >> $jobfile
4762	echo "fi" >> $jobfile
4763	done
4764	fi
4765
4766	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4767	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4768	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4769	echo "LOCAL_PWD=$working_directory" >> $jobfile
4770	echo "export LOCAL_PWD" >> $jobfile
4771
4772	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4773	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4774	echo "export LOCAL_MRUN_PATH" >> $jobfile
4775
4776	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4777	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4778	then
4779	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4780	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4781	fi
4782
4783	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4784	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4785	echo "set -x" >> $jobfile
4786	echo "queue=$queue" >> $jobfile
4787	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4788	echo 'ls -al; echo `pwd`' >> $jobfile
4789	echo "cd \$HOME" >> $jobfile
4790	echo "rm -rf $TEMPDIR" >> $jobfile
4791
4792
4793
4794
4795	# START THE JOB USING SUBJOB-COMMAND
4796	if [[ $silent = false ]]
4797	then
4798	printf "\n "
4799	else
4800	printf "\n\n"
4801	fi
4802
4803	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
4804	rm -rf $jobfile
4805
4806
4807	fi # END OF REMOTE-PART

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