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mrun @ 1402

Last change on this file since 1402 was 1402, checked in by raasch, 10 years ago

output of location messages complemented, output of location bar added
(Makefile, check_parameters, cpulog, init_pegrid, init_3d_model, message, palm, parin, time_integration, new: progress_bar)
preprocessor switch intel_compiler added, -r8 compiler options removed
(.mrun.config.default, .mrun.config.imuk, .mrun.config.kiaps)

batch_job added to envpar-NAMELIST
(mrun, parin)

Property svn:keywords set to Id Rev

File size: 174.9 KB

Line
1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# batch_job added to envpar-NAMELIST
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1402 2014-05-09 14:25:13Z raasch $
29	#
30	# 1357 2014-04-11 15:02:03Z witha
31	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
32	# possible)
33	#
34	# 1320 2014-03-20 08:40:49Z raasch
35	# check namelist file set false by default
36	#
37	# 1304 2014-03-12 10:29:42Z raasch
38	# ulimit option changed from -Ss to -s
39	#
40	# bugfix: missing "fi" in r1289
41	#
42	# 1289 2014-03-04 07:12:34Z raasch
43	# comments translated to English
44	# necriam-, fimm-, ibmy-, and sgi-specific code removed
45	# export of variables for palm and interpret_config removed
46	#
47	# 1281 2014-02-01 07:55:49Z raasch
48	# rsync-copy restricted to Cray machines, since command is unavailable on some
49	# other systems
50	#
51	# 1279 2014-01-28 12:10:14Z raasch
52	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
53	# in order to remove annoying restrictions concerning the number of processors which
54	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
55	# restriction, one of the nodes will be filled with less than the given number of
56	# tasks per node. A respective warning is given.
57	#
58	# 1274 2014-01-09 13:14:54Z heinze
59	# adjustments for lccrayh
60	#
61	# 1272 2014-01-08 10:19:32Z witha
62	# small adjustment for lcflow
63	#
64	# 1270 2013-12-16 11:05:01Z fricke
65	# call of combine_plot_fields adjusted for lccrayb/lccrayh
66	#
67	# 1255 2013-11-07 14:43:35Z raasch
68	# further adjustments for lccrayb remote access
69	#
70	# 1241 2013-10-30 11:36:58Z heinze
71	# Enable use of nudging input and input of large scale forcing from
72	# external files
73	#
74	# 1229 2013-09-20 06:55:19Z raasch
75	# further adjustments for lccrayb
76	#
77	# 1224 2013-09-16 07:27:23Z raasch
78	# first adjustments for lccrayb
79	#
80	# 1210 2013-08-14 10:58:20Z raasch
81	# fftw support added
82	#
83	# 1201 2013-07-10 16:17:59Z witha
84	# adjustments for Forwind cluster (lcflow)
85	#
86	# 1199 2013-07-05 14:52:22Z raasch
87	# adjustments for CSC Helsinki (lccrayf),
88	# executables for batch jobs can be created in advance, in order to avoid calling
89	# the compiler within the batch job (only works if batch jobs are submitted on
90	# local host)
91	#
92	# 1190 2013-06-25 09:39:21Z heinze
93	# enable use of automatic restarts for ibmh
94	# use of cluster/express queue enabled (ibmh)
95	#
96	# 1124 2013-04-09 15:46:52Z raasch
97	# variable "memory" is exported via typeset option -x, because otherwise an unknown
98	# side effect may lead to data loss while getopts is reading the script-option arguments
99	#
100	# 1122 2013-04-09 08:37:16Z heinze
101	# Bugfix: change type of variable last_char
102	#
103	# 1119 2013-04-05 15:11:19Z raasch
104	# Bugfix for setting -T option for subjob
105	#
106	# 1108 2013-03-05 07:03:32Z raasch
107	# bugfix for coupled runs on lckyut/lckyuh
108	#
109	# 1106 2013-03-04 05:31:38Z raasch
110	# --stdin argument for mpiexec on lckyuh
111	# -y and -Y settings output to header
112	#
113	# 1103 2013-02-20 02:15:53Z raasch
114	# default script runs again under ksh, because of unsolved problems with read
115	# from stdin: when bash script is called from a ksh, message "read error: 0:
116	# Resource temporarily unavailable" appears and script does not stop,
117	# further bash compatibility adjustments,
118	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
119	# on lckyuh, but mrun does not terminate and issues a warning instead
120	#
121	# 1101 2013-02-17 10:20:21Z raasch
122	# script now running under bash instead of ksh, which required small adjustments
123	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
124	# read from stdin),
125	# cross compilername on lckyuh compute nodes replaced by real compiler name
126	#
127	# 1099 2013-02-10 01:47:43Z raasch
128	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
129	# and for Forwind cluster (lcflow)
130	# small further adjustments for lckyut
131	#
132	# 1094 2013-02-03 01:52:12Z raasch
133	# explicit ssh/scp port can be set in config file with environment variable
134	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
135	# decalpha parts (yonsei) removed
136	#
137	# 2013-02-02 07:06:13Z raasch
138	# adjustments for Kyushu-University computing center (lckyut - tatara)
139	#
140	# 1083 2013-01-04 10:22:09Z maronga
141	# bugfix in parameter file check (read %cpp_options was missing)
142	#
143	# 1069 2012-11-28 16:18:43Z maronga
144	# bugfix: coupling mode was always set to mpi2, typos removed
145	#
146	# 1058 2012-11-21 07:00:35Z raasch
147	# Intel inspector (inspxe) is given the number of PEs instead of the number of
148	# nodes
149	#
150	# 1046 2012-11-09 14:38:45Z maronga
151	# code put under GPL (PALM 3.9)
152	#
153	# 21/03/94 - Siggi - first version finished
154	# 03/03/94 - Siggi - script development started
155	#
156	#--------------------------------------------------------------------------------#
157	# mrun - script for running PALM jobs
158	#--------------------------------------------------------------------------------#
159
160
161
162	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
163
164	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
165	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
166	# (TOO MANY ARGUMENTS - PROBLEM)
167	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
168
169	AddFilenames=""
170	additional_conditions=""
171	add_source_path=""
172	afname=""
173	archive_save=true
174	archive_system=none
175	check_namelist_files=false
176	combine_plot_fields=true
177	compiler_name=""
178	cond1=""
179	cond2=""
180	config_file=.mrun.config
181	coupled_dist=""
182	coupled_mode="mpi1"
183	cpp_opts=""
184	cpp_options=""
185	cpumax=0
186	cpurest=0
187	create_executable_for_batch=false
188	delete_temporary_catalog=true
189	do_batch=false
190	do_compile=true
191	do_remote=false
192	do_stagein=true
193	do_stageout=true
194	do_trace=false
195	email_notification="none"
196	exclude=""
197	executable=""
198	execution_error=false
199	fftw_inc=""
200	fftw_lib=""
201	fftw_support=false
202	fname=test
203	fromhost=""
204	global_revision=""
205	group_number=none
206	host=""
207	host_file=""
208	hp=""
209	ignore_archive_error=false
210	input_list=""
211	interpreted_config_file=""
212	job_catalog="~/job_queue"
213	job_on_file=""
214	keep_data_from_previous_run=false
215	link_local_input=false
216	link_local_output=false
217	localhost_realname=$(hostname)
218	local_dvrserver_running=.FALSE.
219	locat=normal
220	mainprog=""
221	makefile=""
222	max_par_io_str=""
223	mc=$0
224	while [[ $(echo $mc \| grep -c "/") != 0 ]]
225	do
226	mc=`echo $mc \| cut -f2- -d"/"`
227	done
228	module_calls=""
229	mrun_script_name=$mc
230	netcdf_inc=""
231	netcdf_lib=""
232	netcdf_support=false
233	node_usage=default
234	numprocs=""
235	numprocs_atmos=0
236	numprocs_ocean=0
237	OOPT=""
238	openmp=false
239	output_list=""
240	package_list=""
241	queue=none
242	read_from_config=""
243	restart_run=false
244	if [[ `hostname` = rte10 ]]
245	then
246	return_addres=133.5.185.60
247	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
248	elif [[ `hostname` = climate0 ]]
249	then
250	return_addres=165.132.26.68
251	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
252	elif [[ `hostname` = urban00 ]]
253	then
254	return_addres=147.46.30.151
255	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
256	else
257	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
258	fi
259	return_password=""
260	return_username=$LOGNAME
261	remotecall=false
262	remote_username=""
263	run_coupled_model=false
264	run_mode=""
265	store_on_archive_system=false
266	dashes=" ----------------------------------------------------------------------------"
267	silent=false
268	source_list=""
269	source_path=SOURCE
270	tasks_per_node=""
271	threads_per_task=1
272	tmpcreate=false
273	tmp_data_catalog=""
274	transfer_problems=false
275	usern=$LOGNAME
276	use_openmp=false
277	version="MRUN 2.1 Rev$Rev: 1402 $"
278	working_directory=`pwd`
279	TOPT=""
280	XOPT=""
281	zeit=$( date \| cut -c 12-19 )
282
283	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
284	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
285	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
286	# SCRIPT-OPTION ARGUMENTS
287	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
288
289
290
291	# ERROR HANDLING IN CASE OF EXIT
292	trap 'rm -rf $working_directory/tmp_mrun
293	if [[ $locat != normal && $locat != control_c ]]
294	then
295
296	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
297	(( i = 0 ))
298	while (( i < iec ))
299	do
300	(( i = i + 1 ))
301	printf "\n *** Execution of ERROR-command:\n"
302	printf " >>> ${err_command[$i]}\n"
303	eval ${err_command[$i]}
304	done
305	if [[ -n $interpreted_config_file ]]
306	then
307	rm -rf $interpreted_config_file
308	fi
309	if [[ -n .mrun_environment ]]
310	then
311	rm -rf .mrun_environment
312	fi
313	if [[ $tmpcreate = true ]]
314	then
315	printf "\n *** Contents of \"$TEMPDIR\":\n"
316	ls -al; cd
317	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
318	fi
319	if [[ "$dvrserver_id" != "" ]]
320	then
321	echo "+++ killing dvrserver_id=$dvrserver_id"
322	kill $dvrserver_id
323	fi
324	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
325	then
326	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
327	fi
328	printf "\n\n+++ MRUN killed \n\n"
329	elif [[ $locat != control_c ]]
330	then
331	printf "\n\n --> all actions finished\n\n"
332	printf " Bye, bye $usern !!\n\n"
333	fi' exit
334
335
336	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
337	trap 'rm -rf $working_directory/tmp_mrun
338	rm -rf $working_directory/tmp_check_namelist_files
339	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
340	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
341	then
342	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
343	fi
344	if [[ "$dvrserver_id" != "" ]]
345	then
346	echo "+++ killing dvrserver_id=$dvrserver_id"
347	kill $dvrserver_id
348	fi
349	printf "\n+++ MRUN killed by \"^C\" \n\n"
350	locat=control_c
351	exit
352	' 2
353
354
355	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
356	# BEEN SET
357	if [[ "$PALM_BIN" = "" ]]
358	then
359	printf "\n +++ environment variable PALM_BIN has not been set"
360	printf "\n please set it to the directory where the PALM scripts are located"
361	locat=palm_bin; exit
362	fi
363	export PATH=$PALM_BIN:$PATH
364
365
366
367	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
368	# WHICH WILL BE USED TO START RESTART-JOBS
369	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
370	do
371	case $option in
372	(a) afname=$OPTARG;;
373	(A) store_on_archive_system=true; mc="$mc -A";;
374	(b) do_batch=true; mc="$mc -b";;
375	(B) delete_temporary_catalog=false; mc="$mc -B";;
376	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
377	(C) restart_run=true; mc="$mc -C";;
378	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
379	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
380	(F) job_on_file="-D"; mc="$mc -F";;
381	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
382	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
383	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
384	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
385	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
386	(I) ignore_archive_error=true; mc="$mc -I";;
387	(k) keep_data_from_previous_run=true; mc="$mc -k";;
388	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
389	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
390	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
391	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
392	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
393	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
394	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
395	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
396	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
397	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
398	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
399	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
400	(S) read_from_config=false; mc="$mc -S";;
401	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
402	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
403	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
404	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
405	(v) silent=true; mc="$mc -v";;
406	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
407	(x) do_trace=true;set -x; mc="$mc -x";;
408	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
409	(y) ocean_file_appendix=true; mc="$mc -y";;
410	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
411	(z) check_namelist_files=false; mc="$mc -z";;
412	(Z) combine_plot_fields=false; mc="$mc -Z";;
413	(\?) printf "\n +++ unknown option $OPTARG \n"
414	printf "\n --> type \"$0 ?\" for available options \n"
415	locat=parameter;exit;;
416	esac
417	done
418
419
420	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
421	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
422	(( to_shift = $OPTIND - 1 ))
423	shift $to_shift
424
425	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
426	if [[ "$1" = "?" ]]
427	then
428	(printf "\n *** mrun can be called as follows:\n"
429	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"
430	printf "\n Description of available options:\n"
431	printf "\n Option Description Default-Value"
432	printf "\n -a base name of input files equiv. -d"
433	printf "\n -A archiving when using file-attribute fl"
434	printf "\n -b batch-job on local machine ---"
435	printf "\n -B do not delete temporary directory at end ---"
436	printf "\n -c configuration file .mrun.config"
437	printf "\n -d base name of files attached to program test"
438	printf "\n -D preprocessor(cpp)-directives \"\" "
439	printf "\n -F create remote job file only ---"
440	printf "\n -h execution host $localhost_realname"
441	printf "\n -i INPUT control list \"\" "
442	printf "\n -I archiving errors of previous batch-jobs"
443	printf "\n will be ignored"
444	printf "\n -k keep data from previous run"
445	printf "\n -K additional conditions for controling"
446	printf "\n usage of conditional code and"
447	printf "\n env-variables in configuration file \"\" "
448	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
449	printf "\n -M Makefile name Makefile"
450	printf "\n -n node usage (shared/not_shared) depending on -h"
451	printf "\n -o OUTPUT control list \"\" "
452	printf "\n -O threads per openMP task ---"
453	printf "\n -p software package list \"\" "
454	printf "\n -q queue \"$queue\" "
455	printf "\n -r run control list (combines -i -o) \"\" "
456	printf "\n -s filenames of routines to be compiled \"\" "
457	printf "\n must end with .f, .f90, .F, or .c !"
458	printf "\n use \"..\" for more than one file and wildcards"
459	printf "\n -s LM compiles all locally modified files"
460	printf "\n -S config file interpreted by shellscript ---"
461	printf "\n -t allowed cpu-time in seconds (batch) 0"
462	printf "\n -T tasks per node depending on -h"
463	printf "\n -u username on remote machine \"\" "
464	printf "\n -v no prompt for confirmation ---"
465	printf "\n -w maximum parallel io streams as given by -X"
466	printf "\n -x tracing of mrun for debug purposes ---"
467	printf "\n -X # of processors (on parallel machines) 1"
468	printf "\n -y add appendix \"_O\" to all local output"
469	printf "\n files (ocean precursor runs followed by"
470	printf "\n coupled atmosphere-ocean runs) ---"
471	printf "\n -Y run coupled model, \"#1 #2\" with"
472	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
473	printf "\n -z disable a priori parameter file check ---"
474	printf "\n -Z skip combine_plot_fields at the end of "
475	printf "\n the simulation ---"
476	printf "\n "
477	printf "\n Possible values of positional parameter <modus>:"
478	printf "\n \"?\" - this outline \n\n") \| more
479	exit
480	elif [[ "$1" != "" ]]
481	then
482	printf "\n +++ positional parameter $1 unknown \n"
483	locat=parameter; exit
484	fi
485
486
487
488	# SHORT STARTING MESSAGE
489	printf "\n*** $version "
490	printf "\n will be executed. Please wait ..."
491
492
493
494	# CHECK, IF CONFIGURATION FILE EXISTS
495	if [[ ! -f $config_file ]]
496	then
497	printf "\n\n +++ configuration file: "
498	printf "\n $config_file"
499	printf "\n does not exist"
500	locat=connect; exit
501	fi
502
503
504	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
505	line=""
506	grep "%host_identifier" $config_file > tmp_mrun
507	while read line
508	do
509	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
510	then
511	HOSTNAME=`echo $line \| cut -d" " -s -f2`
512	host_identifier=`echo $line \| cut -d" " -s -f3`
513	if [[ $localhost_realname = $HOSTNAME ]]
514	then
515	localhost=$host_identifier
516	break
517	fi
518	fi
519	done < tmp_mrun
520
521	if [[ "$localhost" = "" ]]
522	then
523	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
524	printf "\n for local host \"$localhost_realname\"."
525	printf "\n Please add line"
526	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
527	printf "\n to the configuration file."
528	locat=localhost; exit
529	fi
530
531
532	# SET HOST-SPECIFIC VARIABLES
533	case $localhost_realname in
534	(r1\|r2\|h01\|b01) archive_system=tivoli;;
535	(cs*) archive_system=ut;;
536	esac
537
538
539	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
540	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
541	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
542	[[ "$afname" = "" ]] && afname=$fname
543
544
545	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
546	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
547	# STATEMENTS IN THE CONFIGURATION FILE
548	if [[ "$run_mode" != "" ]]
549	then
550	input_list="$input_list $run_mode"
551	output_list="$output_list $run_mode"
552	fi
553
554
555	# ??? is this (and the respective option -H) really required ???
556	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
557	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
558	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
559	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
560	if [[ "$fromhost" = "" ]]
561	then
562	fromhost=$localhost
563	fi
564
565
566	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
567	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
568	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
569	# TO BE SUBMITTED (I.E. do_bacth=true)
570	if [[ -n $host && "$host" != $localhost ]]
571	then
572	do_batch=true
573	do_remote=true
574	case $host in
575	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
576	(*) printf "\n"
577	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
578	printf "\n is not available"
579	locat=nqs; (( iec = 0 )); exit;;
580	esac
581	else
582	host=$localhost
583	fi
584
585
586	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
587	if [[ -n $additional_conditions ]]
588	then
589	cond1=`echo $additional_conditions \| cut -d" " -f1`
590	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
591	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
592	if [[ -n $dummy ]]
593	then
594	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
595	locat=options; exit
596	fi
597	block=_$cond1
598	[[ -n $cond2 ]] && block=${block}_$cond2
599	fi
600
601
602	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
603	if [[ $run_coupled_model = true ]]
604	then
605
606	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
607	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
608
609	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
610	then
611
612	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
613	printf "\n PEs (total) : $numprocs"
614	printf "\n PEs (atmosphere): $numprocs_atmos"
615	printf "\n PEs (ocean) : $numprocs_ocean"
616	locat=coupling; exit
617
618	fi
619
620
621	# GET coupled_mode FROM THE CONFIG FILE
622	line=""
623	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
624	while read line
625	do
626	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
627	then
628	coupled_mode="mpi2"
629	fi
630	done < tmp_mrun
631
632	fi
633
634
635	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
636	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
637	then
638	if [[ $ignore_archive_error = false ]]
639	then
640	printf "\n +++ data archiving of previous run failed"
641	printf "\n see directory \~/job_queue on remote machine"
642	locat=archive; exit
643	else
644	printf "\n +++ warning: data archiving in a previous run failed"
645	printf "\n MRUN continues, trying to get backup copy"
646	fi
647	fi
648
649
650	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
651	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
652	mrun_memory=$memory
653	mrun_group_number=$group_number
654	mrun_cpumax=$cpumax
655	mrun_numprocs=$numprocs
656
657
658	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
659	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
660	if [[ "$read_from_config" = false ]]
661	then
662
663	[[ $silent = false ]] && printf "\n Reading the configuration file... "
664
665	# READ THE CONFIGURATION FILE LINE BY LINE
666	while read zeile
667	do
668	[[ $silent = false ]] && printf "."
669
670
671	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
672	eval zeile=\"$zeile\"
673
674
675	# INTERPRET THE LINE
676	if [[ "$(echo $zeile)" = "" ]]
677	then
678	# EMPTY LINE, NO ACTION
679	continue
680
681	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
682	then
683
684	# LINE IS A COMMENT LINE
685	true
686
687	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
688	then
689
690	# LINE DEFINES AN ENVIRONMENT-VARIABLE
691	zeile=$(echo $zeile \| cut -c2-)
692	var=`echo $zeile \| cut -d" " -f1`
693	value=`echo $zeile \| cut -d" " -s -f2`
694	for_host=`echo $zeile \| cut -d" " -s -f3`
695	for_cond1=`echo $zeile \| cut -d" " -s -f4`
696	for_cond2=`echo $zeile \| cut -d" " -s -f5`
697
698	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
699	then
700
701	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
702	# "::" IS REPLACED BY ":".
703	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
704
705
706	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
707	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
708	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
709	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
710	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
711	# CONFIGURATION-FILE.
712	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
713	then
714	eval $var=\$value
715
716	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
717	if [[ $do_trace = true ]]
718	then
719	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
720	fi
721	fi
722
723	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
724	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
725	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
726	# MUST HAVE TO BE STARTED
727	if [[ $var = host ]]
728	then
729	if [[ -n $host && "$host" != $localhost ]]
730	then
731	do_batch=true
732	do_remote=true
733	case $host in
734	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
735	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
736	printf "\n is not available"
737	locat=nqs; exit;;
738	esac
739	else
740	host=$localhost
741	fi
742	fi
743
744	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
745	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
746	# BY MRUN (E.G. subjob)
747	export $var
748	fi
749
750
751
752
753	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
754	then
755
756	# LINE DEFINES ERROR-COMMAND
757	(( iec = iec + 1 ))
758	zeile=$(echo $zeile \| cut -c4-)
759	err_command[$iec]="$zeile"
760
761	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
762	then
763
764	# LINE DEFINES INPUT-COMMAND
765	(( iic = iic + 1 ))
766	zeile=$(echo $zeile \| cut -c4-)
767	in_command[$iic]="$zeile"
768
769	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
770	then
771
772	# LINE DEFINES OUTPUT-COMMAND
773	(( ioc = ioc + 1 ))
774	zeile=$(echo $zeile \| cut -c4-)
775	out_command[$ioc]="$zeile"
776
777	else
778
779	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
780	# s2a: in/out - field
781	# s2b: loc - field (optional)
782	# s2c: tr/ar - field (optional)
783	s1=`echo $zeile \| cut -d" " -f1`
784	s2=`echo $zeile \| cut -d" " -s -f2`
785	s2a=$(echo $s2 \| cut -d":" -f1)
786	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
787	then
788	s2b=""
789	s2c=""
790	else
791	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
792	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
793	fi
794	s3=`echo $zeile \| cut -d" " -f3`
795	s4=`echo $zeile \| cut -d" " -s -f4`
796	s5=`echo $zeile \| cut -d" " -s -f5`
797	s6=`echo $zeile \| cut -d" " -s -f6`
798
799
800	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
801	# INPUT- OR OUTPUT-LIST.
802	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
803	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
804	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
805	# IS NOT CHECKED AND STORED.
806	IFSALT="$IFS"; IFS="$IFS:"
807	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
808	then
809	found=false
810	for actual in $input_list
811	do
812	for formal in $s3
813	do
814	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
815	done
816	done
817	if [[ $found = true ]]
818	then
819	(( iin = iin + 1 ))
820	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
821	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
822	extin[$iin]=$s6
823	fi
824	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
825	then
826	found=false
827	for actual in $output_list
828	do
829	for formal in $s3
830	do
831	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
832	done
833	done
834	if [[ $found = true ]]
835	then
836	(( iout = iout + 1 ))
837	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
838	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
839	fi
840	elif [[ "$s2a" != in && "$s2a" != out ]]
841	then
842	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
843	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
844	locat=connect; exit
845	fi
846	IFS="$IFSALT"
847	fi
848	done < $config_file
849
850	else
851
852
853	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
854	[[ $silent = false ]] && printf "..."
855	interpreted_config_file=.icf.$RANDOM
856
857
858
859	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
860	cat > .mrun_environment << %%END%%
861	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
862	config_file = '$config_file', do_remote = '$do_remote',
863	do_trace = '$do_trace', host = '$host',
864	input_list = '$input_list', icf = '$interpreted_config_file',
865	localhost = '$localhost', output_list = '$output_list' /
866
867	%%END%%
868
869	if [[ "$host" != $localhost ]]
870	then
871
872	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
873	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
874	if [[ $? != 0 ]]
875	then
876	printf "\n\n +++ no interpret_config found"
877	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
878	locat=interpret_config; exit
879	fi
880	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
881	$interpret_config_executable
882
883	else
884
885	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
886	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
887	then
888	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
889	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
890	locat=interpret_config; exit
891	else
892	interpret_config${block}.x
893	fi
894
895	fi
896	rm .mrun_environment
897
898
899	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
900	chmod u+x $interpreted_config_file
901	export PATH=$PATH:.
902	. $interpreted_config_file
903	rm $interpreted_config_file
904
905	fi
906
907
908	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
909	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
910	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
911	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
912	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
913	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
914	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
915
916
917	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
918	# FOR SOURCE-FILES TO BE COMPILED.
919	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
920	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
921	if [[ "$SOURCES_COMPLETE" = "" ]]
922	then
923
924	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
925	# HAS BEEN DEFINED
926	source_path=""
927	line=""
928	grep "%source_path" $config_file > tmp_mrun
929	while read line
930	do
931	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
932	then
933	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
934	then
935	global_source_path=`echo $line \| cut -d" " -f2`
936	fi
937	fi
938	done < tmp_mrun
939
940	line=""
941	found=false
942	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
943	while read line
944	do
945	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
946	then
947	if [[ $found = true ]]
948	then
949	printf "\n\n +++ more than one source path found in configuration file"
950	printf "\n for local host \"$localhost\" "
951	locat=source_path; exit
952	fi
953	source_path=`echo $line \| cut -d" " -f2`
954	found=true
955	fi
956	done < tmp_mrun
957	rm tmp_mrun
958
959	if [[ "$source_path" = "" ]]
960	then
961	if [[ "$global_source_path" != "" ]]
962	then
963	source_path=$global_source_path
964	else
965	printf "\n\n +++ no source path found in configuration file"
966	printf "\n for local host \"$localhost\" "
967	locat=source_path; exit
968	fi
969	fi
970	eval source_path=$source_path
971
972	if [[ ! -d $source_path ]]
973	then
974	printf "\n\n +++ source path \"$source_path\" on local host"
975	printf "\n \"$localhost\" does not exist"
976	locat=source_path; exit
977	fi
978
979	fi
980
981
982	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
983	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
984	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
985	then
986	global_revision=`svnversion $source_path 2>/dev/null`
987	global_revision="Rev: $global_revision"
988	fi
989
990
991	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
992	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
993	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
994	if [[ -n $host && "$host" != $localhost ]]
995	then
996	do_batch=true
997	do_remote=true
998	case $host in
999	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1000	(*) printf "\n"
1001	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1002	printf "\n is not available"
1003	locat=nqs; (( iec = 0 )); exit;;
1004	esac
1005	else
1006	host=$localhost
1007	fi
1008
1009
1010	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1011	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1012	then
1013
1014	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1015	if [[ ! -n $numprocs ]]
1016	then
1017	printf "\n"
1018	printf "\n +++ option \"-K parallel\" requires additional specification"
1019	printf "\n of the number of processors to be used by"
1020	printf "\n mrun-option \"-X\" or by environment-variable"
1021	printf "\n \"numprocs\" in the configuration file"
1022	locat=numprocs; (( iec = 0 )); exit
1023	fi
1024
1025	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1026	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1027	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1028	then
1029	printf "\n"
1030	printf "\n +++ option \"-T\" (tasks per node) is missing"
1031	printf "\n set -T option or define tasks_per_node in the config file"
1032	locat=tasks_per_node; (( iec = 0 )); exit
1033	fi
1034
1035	if (( numprocs < tasks_per_node ))
1036	then
1037	printf "\n"
1038	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1039	printf "\n given values: -T $tasks_per_node -X $numprocs"
1040	locat=tasks_per_node; (( iec = 0 )); exit
1041	fi
1042
1043	if [[ $host != lcflow && $host != lcxt5m ]]
1044	then
1045	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1046	(( ival = $tasks_per_node ))
1047	(( pes = numprocs ))
1048	(( ii = pes / ival ))
1049	(( remaining_pes = pes - ii * ival ))
1050	if (( remaining_pes > 0 ))
1051	then
1052	printf "\n"
1053	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1054	printf "\n divisor of the total number of processors (option \"-X\")"
1055	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1056	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1057	(( nodes = nodes + 1 ))
1058	fi
1059	fi
1060
1061
1062	# SETTINGS FOR SUBJOB-COMMAND
1063	OOPT="-O $threads_per_task"
1064
1065	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1066	if [[ "$tasks_per_node" != "" ]]
1067	then
1068	TOPT="-T $tasks_per_node"
1069	fi
1070
1071	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1072	if [[ $node_usage = default ]]
1073	then
1074	if [[ $host = ibms ]]
1075	then
1076	node_usage=shared
1077	else
1078	node_usage=not_shared
1079	fi
1080	fi
1081
1082	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1083	then
1084	printf "\n"
1085	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1086	printf "\n \"shared\" or \"not_shared\""
1087	locat=tasks_per_node; (( iec = 0 )); exit
1088	fi
1089
1090	fi
1091
1092	# CHECK IF HOSTFILE EXISTS
1093	if [[ -n $hostfile ]]
1094	then
1095	if [[ ! -f $hostfile ]]
1096	then
1097	printf "\n"
1098	printf "\n +++ hostfile \"$hostfile\" does not exist"
1099	locat=hostfile; exit
1100	fi
1101	fi
1102
1103
1104	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1105	if [[ "$maximum_parallel_io_streams" = "" ]]
1106	then
1107	maximum_parallel_io_streams=$numprocs
1108	fi
1109
1110
1111	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1112	if [[ "$scp_port" != "" ]]
1113	then
1114	PORTOPT="-P $scp_port"
1115	SSH_PORTOPT="-p $scp_port"
1116	fi
1117
1118
1119	# SET DEFAULT-QUEUE, IF NOT GIVEN
1120	if [[ $queue = none ]]
1121	then
1122	case $host in
1123	(ibmh) queue=cluster;;
1124	(ibmkisti) queue=class.32plus;;
1125	(lckiaps) queue=normal;;
1126	(lckyoto) queue=ph;;
1127	(lckyuh) queue=fx-single;;
1128	(lckyut) queue=cx-single;;
1129	(lctit) queue=S;;
1130	(nech) queue=none;;
1131	(unics) queue=unics;;
1132	esac
1133	fi
1134
1135
1136	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1137	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1138	(( i = 0 ))
1139	while (( i < iin ))
1140	do
1141	(( i = i + 1 ))
1142	(( maxcycle = 0 ))
1143
1144	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1145	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1146	if [[ "${actionin[$i]}" = di ]]
1147	then
1148	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1149	# HOST ONLY
1150	eval filename=${pathin[$i]}/${endin[$i]}
1151	else
1152	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1153	# HOST ONLY
1154	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1155	fi
1156	eval pathname=${pathin[$i]}
1157
1158	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1159	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1160	then
1161	filename_input=$filename
1162	fi
1163
1164	# CHECK IF FILE EXISTS
1165	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1166	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1167	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1168	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1169	then
1170
1171	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1172	if [[ "${transin[$i]}" != "locopt" ]]
1173	then
1174	printf "\n\n +++ INPUT-file: "
1175	if [[ "${extin[$i]}" = "" ]]
1176	then
1177	printf "\n $filename"
1178	else
1179	printf "\n $filename.${extin[$i]}"
1180	fi
1181	printf "\n does not exist\n"
1182	locat=input; exit
1183	else
1184	transin[$i]="unavailable"
1185	fi
1186	else
1187
1188	# DETERMINE THE FILE'S CYCLE NUMBER
1189	ls -1 -d $filename > filelist 2>/dev/null
1190	ls -1 -d $filename.* >> filelist 2>/dev/null
1191	while read zeile
1192	do
1193	cycle=$(echo $zeile \| cut -f2 -d".")
1194	if [[ "$cycle" = "$zeile" ]]
1195	then
1196	(( icycle = 0 ))
1197	elif [[ "$cycle" = "${extin[$i]}" ]]
1198	then
1199	(( icycle = 0 ))
1200	else
1201	(( icycle = $cycle ))
1202	fi
1203	if (( icycle > maxcycle ))
1204	then
1205	(( maxcycle = icycle ))
1206	file_to_be_used=$zeile
1207	fi
1208	done <filelist
1209	rm filelist
1210
1211	# APPEND CYCLE NUMBER TO FILENAME
1212	if (( maxcycle > 0 ))
1213	then
1214	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1215	then
1216	filename=${filename}.$maxcycle.${extin[$i]}
1217	else
1218	filename=${filename}.$maxcycle
1219	fi
1220	else
1221	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1222	then
1223	filename=${filename}.${extin[$i]}
1224	fi
1225	fi
1226
1227	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1228	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1229	absnamein[$i]=$filename
1230	if (( maxcycle > 0 ))
1231	then
1232	if [[ "${actionin[$i]}" = di ]]
1233	then
1234	frelin[$i]=${endin[$i]}.$maxcycle
1235	else
1236	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1237	fi
1238	else
1239	if [[ "${actionin[$i]}" = di ]]
1240	then
1241	frelin[$i]=${endin[$i]}
1242	else
1243	frelin[$i]=${afname}${endin[$i]}
1244	fi
1245	fi
1246
1247	fi
1248	done
1249
1250	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1251	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1252	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1253	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1254	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1255	# REMOTE HOST)
1256	(( i = 0 ))
1257	while (( i < iout ))
1258	do
1259	(( i = i + 1 ))
1260	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1261	then
1262	if [[ "${actionout[$i]}" = tr ]]
1263	then
1264	actionout[$i]=""
1265	elif [[ "${actionout[$i]}" = trpe ]]
1266	then
1267	actionout[$i]=pe
1268	elif [[ "${actionout[$i]}" = tra ]]
1269	then
1270	actionout[$i]=a
1271	fi
1272	(( maxcycle = 0 ))
1273	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1274	eval catalogname=${pathout[$i]}
1275	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1276	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1277	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1278	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1279	then
1280
1281	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1282	if cat /dev/null > $filename
1283	then
1284	rm $filename
1285	else
1286
1287	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1288	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1289	if [[ ! -d $catalogname ]]
1290	then
1291	if mkdir -p $catalogname
1292	then
1293	printf "\n\n *** directory:"
1294	printf "\n $catalogname"
1295	printf "\n was created\n"
1296	else
1297	printf "\n\n +++ OUTPUT-file:"
1298	printf "\n $filename"
1299	printf "\n cannot be created, because directory does not exist"
1300	printf "\n and cannot be created either"
1301	printf "\n"
1302	locat=output ; exit
1303	fi 2>/dev/null
1304	else
1305	printf "\n\n +++ OUTPUT-file:"
1306	printf "\n $filename"
1307	printf "\n cannot be created, although directory exists"
1308	printf "\n"
1309	locat=output ; exit
1310	fi
1311	fi 2>/dev/null
1312	else
1313
1314	# DETERMINE THE CYCLE NUMBER
1315	ls -1 -d $filename > filelist 2>/dev/null
1316	ls -1 -d $filename.* >> filelist 2>/dev/null
1317	while read zeile
1318	do
1319	cycle=$(echo $zeile \| cut -f2 -d".")
1320	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1321	then
1322	(( icycle = 1 ))
1323	else
1324	(( icycle = $cycle + 1 ))
1325	fi
1326	if (( icycle > maxcycle ))
1327	then
1328	(( maxcycle = icycle ))
1329	fi
1330	done <filelist
1331	rm filelist
1332	fi
1333
1334	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1335	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1336	if [[ "${actionout[$i]}" != a ]]
1337	then
1338	if (( maxcycle > 0 ))
1339	then
1340	filename=${filename}.$maxcycle
1341	if cat /dev/null > $filename
1342	then
1343	rm $filename
1344	else
1345	printf "\n +++ OUTPUT-file:"
1346	printf "\n $filename"
1347	printf "\n cannot be created"
1348	locat=output ; exit
1349	fi
1350	fi
1351	else
1352	(( maxcycle = maxcycle - 1 ))
1353	if (( maxcycle > 0 ))
1354	then
1355	filename=${filename}.$maxcycle
1356	fi
1357	fi
1358
1359	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1360	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1361	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1362	pathout[$i]=$filename
1363	if (( maxcycle > 0 ))
1364	then
1365	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1366	else
1367	frelout[$i]=${fname}${endout[$i]}
1368	fi
1369
1370	fi
1371	done
1372
1373
1374	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1375	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1376	then
1377	if [[ "$dvr_inc" = "" ]]
1378	then
1379	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1380	printf "\n This is required for the dvrp_graphics package.\n"
1381	locat=dvr; exit
1382	fi
1383	if [[ "$dvr_lib" = "" ]]
1384	then
1385	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1386	printf "\n This is required for the dvrp_graphics package.\n"
1387	locat=dvr; exit
1388	fi
1389	fi
1390
1391
1392	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1393	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1394	if [[ "$mainprog" = "" && "$executable" = "" ]]
1395	then
1396	printf "\n +++ neither main program nor executable defined"
1397	locat=source; exit
1398	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1399	then
1400	printf "\n +++ main program as well as executable defined"
1401	locat=source; exit
1402	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1403	then
1404	do_compile=false
1405	fi
1406
1407
1408	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1409	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1410	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1411	then
1412	rm -rf SOURCES_FOR_RUN_$fname
1413	mkdir SOURCES_FOR_RUN_$fname
1414	fi
1415
1416
1417	# COLLECT ALL ROUTINES TO BE COMPILED
1418	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1419	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1420	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1421	then
1422
1423	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1424
1425	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1426	then
1427
1428	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1429	source_list=""
1430	cd $source_path
1431
1432
1433	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1434	if [[ ! -d .svn ]]
1435	then
1436	printf "\n\n +++ source directory"
1437	printf "\n \"$source_path\" "
1438	printf "\n is not under control of \"subversion\"."
1439	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1440	fi
1441
1442
1443	# LIST ALL MODIFIED SOURCE CODE FILES
1444	Filenames=""
1445	svn status > tmp_mrun
1446	while read line
1447	do
1448	firstc=`echo $line \| cut -c1`
1449	if [[ $firstc = M \|\| $firstc = "?" ]]
1450	then
1451	Name=`echo "$line" \| cut -c8-`
1452	extension=`echo $Name \| cut -d. -f2`
1453	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1454	then
1455	Filenames="$Filenames "$Name
1456	fi
1457	fi
1458	done < tmp_mrun
1459
1460
1461	# COPY FILES TO SOURCES_FOR_RUN_...
1462	for dateiname in $Filenames
1463	do
1464	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1465	source_list=$source_list"$dateiname "
1466	done
1467
1468	cd - > /dev/null
1469
1470
1471	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1472	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1473	elif [[ "$source_list" != "" && $restart_run != true ]]
1474	then
1475
1476	cd $source_path
1477
1478	for filename in $source_list
1479	do
1480
1481	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1482	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1483	then
1484	printf "\n +++ source code file: $filename"
1485	printf "\n must not contain (\"/\") "
1486	locat=source; exit
1487	fi
1488
1489	if [[ ! -f $filename ]]
1490	then
1491	printf "\n +++ source code file: $filename"
1492	printf "\n does not exist"
1493	locat=source; exit
1494	else
1495	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1496	fi
1497
1498	done
1499
1500	cd - > /dev/null
1501
1502	fi
1503
1504
1505	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1506	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1507	if [[ $restart_run != true ]]
1508	then
1509
1510	if [[ ! -f "$source_path/$mainprog" ]]
1511	then
1512	printf "\n\n +++ main program: $mainprog"
1513	printf "\n does not exist in source directory"
1514	printf "\n \"$source_path\"\n"
1515	locat=source; exit
1516	else
1517	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1518	then
1519	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1520	source_list=${mainprog}" $source_list"
1521	fi
1522	fi
1523	fi
1524
1525
1526	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1527	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1528	if [[ "$restart_run" != true ]]
1529	then
1530	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1531	if [[ ! -f $makefile ]]
1532	then
1533	printf "\n +++ file \"$makefile\" does not exist"
1534	locat=make; exit
1535	else
1536	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1537	fi
1538	fi
1539
1540
1541	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1542	if [[ $restart_run != true && "$add_source_path" != "" ]]
1543	then
1544
1545	# DOES THE DIRECTORY EXIST?
1546	if [[ ! -d $add_source_path ]]
1547	then
1548	printf "\n\n +++ WARNING: additional source code directory"
1549	printf "\n \"$add_source_path\" "
1550	printf "\n does not exist or is not a directory."
1551	printf "\n No source code will be used from this directory!\n"
1552	add_source_path=""
1553	if [[ $silent == false ]]
1554	then
1555	sleep 3
1556	fi
1557	else
1558
1559	cd $add_source_path
1560	found=false
1561
1562	Names=$(ls -1 *.f90 2>&1)
1563	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1564	Names=$(ls -1 *.F90 2>&1)
1565	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1566	Names=$(ls -1 *.F 2>&1)
1567	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1568	Names=$(ls -1 *.f 2>&1)
1569	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1570	Names=$(ls -1 *.c 2>&1)
1571	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1572
1573	cd - > /dev/null
1574	cd SOURCES_FOR_RUN_$fname
1575
1576	# COPY MAKEFILE IF EXISTING
1577	if [[ -f $add_source_path/Makefile ]]
1578	then
1579	printf "\n\n *** user Makefile from directory"
1580	printf "\n \"$add_source_path\" is used \n"
1581	if [[ $silent == false ]]
1582	then
1583	sleep 1
1584	fi
1585	cp $add_source_path/Makefile .
1586	fi
1587
1588	for dateiname in $AddFilenames
1589	do
1590	if [[ -f $dateiname ]]
1591	then
1592	printf "\n +++ source code file \"$dateiname\" found in additional"
1593	printf "\n source code directory \"$add_source_path\" "
1594	printf "\n but was also given with option \"-s\" which means that it should be taken"
1595	printf "\n from directory \"$source_path\"."
1596	locat=source; exit
1597	fi
1598
1599	cp $add_source_path/$dateiname .
1600	source_list="$source_list $dateiname"
1601
1602	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1603	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1604	then
1605	printf "\n\n +++ user file \"$dateiname\" "
1606	printf "\n is not listed in Makefile \n"
1607	locat=source; exit
1608	else
1609
1610	if [[ $found = false ]]
1611	then
1612	found=true
1613	printf "\n\n *** following user file(s) added to the"
1614	printf " files to be translated:\n "
1615	fi
1616	printf "$dateiname "
1617	if [[ $silent == false ]]
1618	then
1619	sleep 0.5
1620	fi
1621
1622	fi
1623	done
1624	[[ $found = true ]] && printf "\n"
1625	cd - > /dev/null
1626	fi
1627	fi
1628
1629
1630	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1631	# TO THE LIST OF FILES TO BE COMPILED
1632	if [[ $restart_run != true && -n $package_list ]]
1633	then
1634
1635	cd $source_path
1636
1637	for package in $package_list
1638	do
1639
1640	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1641
1642	# DETERMINE FILES BELONGING TO THE PACKAGE
1643	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1644	# THE NAME OF THE DIRECTORY
1645	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1646
1647
1648	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1649	# IF THEY ARE NOT ALREADY PART OF THE LIST
1650	for source_list_name in $package_source_list
1651	do
1652	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1653	then
1654
1655	# ONLY TAKE FILES WITH VALID SUFFIX
1656	ending=`echo $source_list_name \| cut -f2 -d.`
1657	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1658	then
1659	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1660	source_list="$source_list $source_list_name"
1661	fi
1662	fi
1663	done
1664	done
1665
1666	cd - > /dev/null
1667	fi
1668
1669	fi # do_compile=true
1670
1671
1672	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1673	# AND SET PRE-PROCESSOR DIRECTIVES
1674	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1675	then
1676
1677	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1678	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1679	then
1680	cpp_options="${cpp_options},-D__ibm=__ibm"
1681	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1682	then
1683	cpp_options="$cpp_options -D__nec"
1684	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1685	then
1686	cpp_options="$cpp_options -D__lc"
1687	else
1688	cpp_options="$cpp_options -D__$localhost"
1689	fi
1690
1691	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1692	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1693	then
1694	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1695	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1696	else
1697	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1698	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1699	fi
1700
1701	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1702	if [[ -n $package_list ]]
1703	then
1704	for package in $package_list
1705	do
1706	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1707	then
1708	if [[ $package != "dvrp_graphics+1PE" ]]
1709	then
1710	cpp_options="${cpp_options},-D__$package=__$package"
1711	else
1712	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1713	export use_seperate_pe_for_dvrp_output=true
1714	fi
1715	else
1716	if [[ $package != "dvrp_graphics+1PE" ]]
1717	then
1718	cpp_options="$cpp_options -D__$package"
1719	else
1720	cpp_options="$cpp_options -D__dvrp_graphics"
1721	export use_seperate_pe_for_dvrp_output=true
1722	fi
1723	fi
1724	done
1725	fi
1726
1727	# SET DIRECTIVES GIVEN BY OPTION -D
1728	if [[ -n $cpp_opts ]]
1729	then
1730	for popts in $cpp_opts
1731	do
1732	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1733	then
1734	cpp_options="${cpp_options},-D__$popts=__$popts"
1735	else
1736	cpp_options="$cpp_options -D__$popts"
1737	fi
1738	done
1739	fi
1740
1741	else
1742
1743
1744	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1745	if [[ $do_remote = false ]]
1746	then
1747	if [[ ! -f $executable ]]
1748	then
1749	printf "\n +++ executable file: $executable"
1750	printf "\n does not exist"
1751	locat=executable; exit
1752	fi
1753	fi
1754	fi
1755
1756
1757	# DETERMINE THE JOB MODE
1758	if [[ "$ENVIRONMENT" = BATCH ]]
1759	then
1760	batch_job=.TRUE.
1761	jobmo=BATCH
1762	else
1763	batch_job=.FALSE.
1764	jobmo=INTERACTIVE
1765	fi
1766
1767
1768	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1769	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1770	then
1771	printf "\n +++ no interactive runs allowed on host \"$host\" "
1772	printf "\n please submit batch job using mrun option \"-b\" \n"
1773	locat=normal; exit
1774	fi
1775
1776
1777	# CHECK, IF USER DEFINED A COMPILER
1778	if [[ "$compiler_name" = "" ]]
1779	then
1780
1781	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1782	locat=compiler_name; exit
1783
1784	fi
1785
1786
1787	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1788	kennung=$RANDOM
1789	if [[ "$tmp_user_catalog" = "" ]]
1790	then
1791	if [[ $localhost = ibmh ]]
1792	then
1793	tmp_user_catalog=$SCRATCH
1794	elif [[ $localhost = nech ]]
1795	then
1796	tmp_user_catalog=$WRKSHR
1797	else
1798	tmp_user_catalog=/tmp
1799	fi
1800	fi
1801	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1802
1803
1804	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1805	if [[ "$tmp_data_catalog" = "" ]]
1806	then
1807	if [[ $localhost = nech ]]
1808	then
1809	tmp_data_catalog=$WRKSHR/mrun_restart_data
1810	else
1811	tmp_data_catalog=/tmp/mrun_restart_data
1812	fi
1813	fi
1814
1815
1816	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1817	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1818	then
1819	eval fopts=\"$fopts\"
1820	eval lopts=\"$lopts\"
1821	fi
1822
1823
1824
1825	# DETERMINE COMPILE- AND LINK-OPTIONS
1826	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1827	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1828	ROPTS="$ropts"
1829	# 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 ]]
1830	# then
1831	XOPT="-X $numprocs"
1832	# fi
1833
1834
1835
1836	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1837	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1838	done=false
1839	while [[ $done = false ]]
1840	do
1841	cputime=$cpumax
1842	if (( $cputime == 0 ))
1843	then
1844	if [[ $do_batch = true ]]
1845	then
1846	printf "\n +++ cpu-time is undefined"
1847	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1848	printf "\n >>> "
1849	read cputime 1>/dev/null 2>&1
1850	else
1851	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1852	fi
1853	else
1854	done=true
1855	fi
1856	cpumax=$cputime
1857	done
1858
1859	(( minuten = cputime / 60 ))
1860	(( sekunden = cputime - minuten * 60 ))
1861
1862
1863	# CHECK THE MEMORY DEMAND
1864	if [[ $do_batch = true ]]
1865	then
1866	done=false
1867	while [[ $done = false ]]
1868	do
1869	if (( memory == 0 ))
1870	then
1871	printf "\n +++ memory demand is undefined"
1872	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1873	printf "\n >>> "
1874	read memory 1>/dev/null 2>&1
1875	else
1876	done=true
1877	fi
1878	done
1879	fi
1880
1881
1882	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1883	if [[ $do_remote = true && -z $remote_username ]]
1884	then
1885	while [[ -z $remote_username ]]
1886	do
1887	printf "\n +++ username on remote host \"$host\" is undefined"
1888	printf "\n >>> Please type username:"
1889	printf "\n >>> "
1890	read remote_username
1891	done
1892	mc="$mc -u$remote_username"
1893	fi
1894
1895	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1896	if [[ "$login_init_cmd" != "" ]]
1897	then
1898	export init_cmds="${login_init_cmd};"
1899	fi
1900
1901
1902	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1903	if [[ "$modules" != "" ]]
1904	then
1905	if [[ $host = lctit ]]
1906	then
1907	export module_calls=". $modules"
1908	else
1909	export module_calls="module load ${modules};"
1910	fi
1911	fi
1912
1913
1914
1915	# OUTPUT OF THE MRUN-HEADER
1916	calltime=$(date)
1917	printf "\n"
1918	printf "#------------------------------------------------------------------------# \n"
1919	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1920	printf "\| \| \n"
1921	spalte1="called on:"; spalte2=$localhost_realname
1922	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1923	if [[ $do_remote = true ]]
1924	then
1925	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1926	else
1927	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1928	fi
1929	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1930	if [[ -n $numprocs ]]
1931	then
1932	if [[ $run_coupled_model = false ]]
1933	then
1934	spalte1="number of PEs:"; spalte2=$numprocs
1935	else
1936	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1937	fi
1938	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1939	fi
1940	if [[ -n $tasks_per_node ]]
1941	then
1942	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1943	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1944	if (( remaining_pes > 0 ))
1945	then
1946	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1947	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1948	fi
1949	fi
1950	if [[ $maximum_parallel_io_streams != $numprocs ]]
1951	then
1952	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1953	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1954	fi
1955	if [[ $use_openmp = true ]]
1956	then
1957	spalte1="threads per task:"; spalte2="$threads_per_task"
1958	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1959	fi
1960	printf "\| \| \n"
1961	if [[ $do_compile = true ]]
1962	then
1963	if [[ "$mopts" != "" ]]
1964	then
1965	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1966	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1967	zeile=$(echo "$mopts" \| cut -c46-)
1968	while [[ "$zeile" != "" ]]
1969	do
1970	spalte1=""
1971	spalte2=$(echo "$zeile" \| cut -c-45)
1972	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1973	zeile=$(echo "$zeile" \| cut -c46-)
1974	done
1975	fi
1976
1977	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	zeile=$(echo "$cpp_options" \| cut -c46-)
1980	while [[ "$zeile" != "" ]]
1981	do
1982	spalte1=""
1983	spalte2=$(echo "$zeile" \| cut -c-45)
1984	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1985	zeile=$(echo "$zeile" \| cut -c46-)
1986	done
1987
1988	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1989	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1990	zeile=$(echo "$fopts" \| cut -c46-)
1991	while [[ "$zeile" != "" ]]
1992	do
1993	spalte1=""
1994	spalte2=$(echo "$zeile" \| cut -c-45)
1995	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1996	zeile=$(echo "$zeile" \| cut -c46-)
1997	done
1998
1999	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2000	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2001	zeile=$(echo "$lopts" \| cut -c46-)
2002	while [[ "$zeile" != "" ]]
2003	do
2004	spalte1=""
2005	spalte2=$(echo "$zeile" \| cut -c-45)
2006	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2007	zeile=$(echo "$zeile" \| cut -c46-)
2008	done
2009
2010	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2012	zeile=$(echo "$modules" \| cut -c46-)
2013	while [[ "$zeile" != "" ]]
2014	do
2015	spalte1=""
2016	spalte2=$(echo "$zeile" \| cut -c-45)
2017	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2018	zeile=$(echo "$zeile" \| cut -c46-)
2019	done
2020
2021	spalte1="main program:"; spalte2=$mainprog
2022	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2023	else
2024	spalte1=executable:; spalte2=$executable
2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2026	fi
2027	printf "\| \| \n"
2028	spalte1="base name of files:"; spalte2=$fname
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030	if [[ $fname != $afname ]]
2031	then
2032	spalte1="base name of input files:"; spalte2=$afname
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	fi
2035	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2036	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2037	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2038	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2039
2040	if [[ "$ocean_file_appendix" = true ]]
2041	then
2042	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2043	fi
2044
2045	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2046	then
2047	spalte1="memory demand / PE":; spalte2="$memory MB"
2048	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2049	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	fi
2052
2053	if [[ $do_compile = true ]]
2054	then
2055	printf "\| \| \n"
2056	printf "\| Files to be compiled: \| \n"
2057	zeile=$source_list
2058	while [[ "$zeile" != "" ]]
2059	do
2060	linestart=$(echo $zeile \| cut -c-70)
2061	printf "\| %-70s \| \n" "$linestart"
2062	zeile=$(echo "$zeile" \| cut -c71-)
2063	done
2064	fi
2065	printf "#------------------------------------------------------------------------#"
2066
2067
2068
2069	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2070	if [[ $do_trace = true ]]
2071	then
2072	(( i = 0 ))
2073	while (( i < iin ))
2074	do
2075	(( i = i + 1 ))
2076	if (( i == 1 ))
2077	then
2078	printf "\n\n >>> INPUT-file assignments:\n"
2079	fi
2080	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2081	done
2082	(( i = 0 ))
2083	while (( i < iout ))
2084	do
2085	(( i = i + 1 ))
2086	if (( i == 1 ))
2087	then
2088	printf "\n\n >>> OUTPUT-file assignments:\n"
2089	fi
2090	printf "\n ${localout[$i]} : ${pathout[$i]}"
2091	done
2092	(( i = 0 ))
2093	while (( i < iic ))
2094	do
2095	(( i = i + 1 ))
2096	if (( i == 1 ))
2097	then
2098	printf "\n\n >>> INPUT-commands:\n"
2099	fi
2100	printf "\n ${in_command[$i]}"
2101	done
2102	(( i = 0 ))
2103	while (( i < ioc ))
2104	do
2105	(( i = i + 1 ))
2106	if (( i == 1 ))
2107	then
2108	printf "\n\n >>> OUTPUT-commands:\n"
2109	fi
2110	printf "\n ${out_command[$i]}"
2111	done
2112	fi
2113
2114
2115	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2116	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2117	then
2118	antwort=dummy
2119	printf "\n\n"
2120	printf " >>> everything o.k. (y/n) ? "
2121	while read antwort
2122	do
2123	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2124	then
2125	printf " >>> everything o.k. (y/n) ? "
2126	else
2127	break
2128	fi
2129	done
2130	if [[ $antwort = n \|\| $antwort = N ]]
2131	then
2132	locat=user_abort; (( iec = 0 )); exit
2133	fi
2134	if [[ $do_batch = true ]]
2135	then
2136	printf " >>> batch-job will be created and submitted"
2137	else
2138	printf " >>> MRUN will now continue to execute on this machine"
2139	fi
2140	fi
2141
2142
2143	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2144	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2145	check_depository="${working_directory}/trunk/UTIL"
2146	check_sources="${working_directory}/tmp_check_namelist_files"
2147	skip_check=false
2148
2149	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2150	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2151	then
2152	skip_check=true
2153	reason="run on remote host or parameter file check has not been compiled."
2154	fi
2155	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2156	then
2157	skip_check=true
2158	reason="parameter file check has not been compiled."
2159	fi
2160
2161	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2162	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2163	then
2164	skip_check=true
2165	reason="serial run."
2166	fi
2167
2168	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2169	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2170	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2171	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2172	if [[ $check_namelist_files == false ]]
2173	then
2174	skip_check=true
2175	reason="-z option set."
2176	fi
2177
2178	if [[ $fromhost != $localhost ]]
2179	then
2180	skip_check=true
2181	reason="submitting host is local host."
2182	fi
2183
2184	if [[ $run_coupled_model == true ]]
2185	then
2186	skip_check=true
2187	reason="coupled run."
2188	fi
2189
2190	if [[ $restart_run == true ]]
2191	then
2192	skip_check=true
2193	reason="restart run."
2194	fi
2195
2196	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2197	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2198	last_char=`echo $filename_input \| cut -c $last_char_int`
2199	if [[ "$last_char" == "f" ]]
2200	then
2201	skip_check=true
2202	reason="restart run."
2203	fi
2204
2205	if [[ $skip_check == false ]]
2206	then
2207	tmp_check=${working_directory}/tmp_check
2208
2209	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2210	# NOT NECESSARILY REQUIRED
2211	line=""
2212	found=false
2213	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2214	while read line1
2215	do
2216	line="$line1"
2217	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2218	then
2219	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2220	found=true
2221	fi
2222	done < $tmp_check
2223
2224	if [[ $found = false ]]
2225	then
2226	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2227	fi
2228
2229	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2230	# NOT NECESSARILY REQUIRED
2231	line=""
2232	found=false
2233	grep "NUDGING_DATA" $config_file > $tmp_check
2234	while read line1
2235	do
2236	line="$line1"
2237	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2238	then
2239	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2240	found=true
2241	fi
2242	done < $tmp_check
2243
2244	if [[ $found = false ]]
2245	then
2246	printf "\n +++ no NUDGING list entry found in the configuration file."
2247	fi
2248
2249	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2250	# NOT NECESSARILY REQUIRED
2251	line=""
2252	found=false
2253	grep "LSF_DATA" $config_file > $tmp_check
2254	while read line1
2255	do
2256	line="$line1"
2257	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2258	then
2259	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2260	found=true
2261	fi
2262	done < $tmp_check
2263
2264	if [[ $found = false ]]
2265	then
2266	printf "\n +++ no LSF list entry found in the configuration file."
2267	fi
2268
2269	rm -rf ${working_directory}/tmp_check
2270
2271	# CHECK IF THE P3DF FILE MUST BE CHECKED
2272	for item in $input_list
2273	do
2274	if [[ "$item" == "restart" ]]
2275	then
2276	check_restart=1
2277	else
2278	check_restart=0
2279	fi
2280	done
2281
2282	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2283	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2284	then
2285	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2286	locat=check_namelist; exit
2287	fi
2288
2289	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2290	if [[ $check_restart == 1 ]]
2291	then
2292
2293	filenamef="${filename_input}f"
2294	if [[ ! -f $filenamef ]]
2295	then
2296	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2297	check_restart=0
2298	answer=dummy
2299	printf "\n\n"
2300
2301	if [[ $silent == false ]]
2302	then
2303	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2304	do
2305	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2306	read answer
2307	done
2308	if [[ $answer = a \|\| $answer = A ]]
2309	then
2310	printf "\n +++ Aborting...."
2311	locat=normal; exit
2312	fi
2313	fi
2314	else
2315	check_restart=1
2316	fi
2317	fi
2318
2319	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2320	mkdir $check_sources
2321	cd $check_sources
2322
2323
2324	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2325	if [[ -d $add_source_path ]]
2326	then
2327	printf "\n\n *** copying files from $check_depository"
2328	cp $check_depository/check_namelist_files.tar ./
2329
2330	printf "\n\n *** untar of makefile and source files in $check_sources"
2331	tar -xf check_namelist_files.tar > /dev/null 2>&1
2332
2333	printf "\n\n *** adding user code."
2334	cp $add_source_path/* ./
2335	touch check_namelist_files.f90
2336
2337	# GET COMPILER OPTIONS AND PERFORM MAKE
2338	printf "\n\n *** compiling code if necessary...\n"
2339
2340	# workaround for batch jobs on local machine (lcxe6)
2341	if [[ $do_batch == true && $do_remote == false ]]
2342	then
2343	eval $init_cmds
2344	fi
2345
2346	# GET CHECK OPTIONS
2347	line=""
2348	found=false
2349
2350	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2351
2352	while read line1
2353	do
2354
2355	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2356	then
2357	line="$line1"
2358	fi
2359
2360	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2361	then
2362	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2363	line="$line "
2364	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'`
2365	found=true
2366	fi
2367
2368	done < $tmp_check
2369	copts_check="$copts_check -D__check -D__parallel"
2370
2371	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2372
2373	# GET MAKE OUTPUT
2374	if [[ $? != 0 ]]
2375	then
2376	printf "\n +++ error during make."
2377	answer=dummy
2378	printf "\n\n"
2379	if [[ $silent == false ]]
2380	then
2381	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2382	do
2383	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2384	read answer
2385	done
2386	if [[ $answer = a \|\| $answer = A ]]
2387	then
2388	printf "\n +++ Aborting..."
2389	rm -rf $check_sources
2390	locat=normal; exit
2391	else
2392	skip_check=true
2393	fi
2394	else
2395	skip_check=true
2396	fi
2397	fi
2398	else
2399	cp $PALM_BIN/check_namelist_files.x ./
2400	fi
2401
2402	cp $filename_input ./PARIN
2403	if [[ $check_restart == 1 ]]
2404	then
2405	cp $filenamef ./PARINF
2406	fi
2407
2408	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2409	then
2410	printf "\n *** adding topography data"
2411	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2412
2413	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2414	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2415	# WHICH REQUIRE SUFFICIENT MEMORY
2416	ulimit -s unlimited
2417	fi
2418
2419	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2420	then
2421	printf "\n *** adding nudging data"
2422	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2423	fi
2424
2425	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2426	then
2427	printf "\n *** adding large scale forcing data"
2428	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2429	fi
2430
2431	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2432	cat > ENVPAR << %%END%%
2433	&envpar run_identifier = '$fname', host = '$host',
2434	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2435	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2436	maximum_cpu_time_allowed = ${cpumax}.,
2437	revision = '$global_revision',
2438	local_dvrserver_running = $local_dvrserver_running /
2439
2440	%%END%%
2441
2442	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2443	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2444	then
2445	printf "\n +++ WARNING: check_namelist_files.x not found."
2446	answer=dummy
2447	printf "\n\n"
2448
2449	if [[ $silent == false ]]
2450	then
2451	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2452	do
2453	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2454	read answer
2455	done
2456	if [[ $answer = a \|\| $answer = A ]]
2457	then
2458	printf "\n +++ Aborting..."
2459	rm -rf $check_sources
2460	locat=normal; exit
2461	else
2462	printf "\n *** skipping parameter file check."
2463	fi
2464	fi
2465
2466	elif [[ $skip_check == false ]]
2467	then
2468	# STARTING THE PARAMETER FILE CHECK
2469	printf "\n\n *** starting parameter file check..."
2470
2471	# CHECKING THE P3D FILE
2472	printf "\n\n (1) checking $filename_input"
2473	echo "$numprocs 0 0" > VARIN
2474	errors=`./check_namelist_files.x < VARIN 2>&1`
2475
2476	check_error=false
2477	if [[ "$errors" == "" ]]
2478	then
2479	printf " --> o.k."
2480	else
2481	printf " --> failed."
2482	check_error=true
2483	printf "\n\n $errors"
2484	fi
2485
2486	# CHECKING THE PD3F FILE IF NECESSARY
2487	if [[ $check_restart == 1 && $check_error == false ]]
2488	then
2489	printf "\n\n (2) checking $filenamef"
2490
2491	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2492	# IN &INIPAR LIST
2493	found=false
2494	cat PARINF \| while read line
2495	do
2496	line=$(echo $line\|sed 's/ //g')
2497	if [[ $line == "&inipar" ]]
2498	then
2499	start_search=true
2500	fi
2501
2502	if [[ $start_search == true ]]
2503	then
2504	if [[ $line == "initializing_actions='read_restart_data'" ]]
2505	then
2506	found=true
2507	break
2508	fi
2509	fi
2510
2511	if [[ $line == "/" ]]
2512	then
2513	start_search=false
2514	fi
2515
2516	done
2517
2518	if [[ $found = false ]]
2519	then
2520	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2521	printf "\n in &inipar list in $fname$p3df_suffix."
2522	rm -rf $check_sources
2523	locat=check_namelist; exit
2524	fi
2525
2526	# READ max_user_pr FROM FILES
2527	if [[ -f parin_for_check ]]
2528	then
2529	read max_pr_user < parin_for_check
2530	else
2531	max_user_pr=0
2532	fi
2533
2534	echo "$numprocs 1 $max_pr_user" > VARIN
2535	errors=`./check_namelist_files.x < VARIN 2>&1`
2536
2537	if [[ "$errors" == "" ]]
2538	then
2539	printf " --> o.k."
2540	else
2541	printf " --> failed."
2542	check_error=true
2543	printf "\n\n $errors"
2544	fi
2545	fi
2546
2547	# REPORT ERRORS AND CONTINUE/EXIT
2548	if [[ $check_error == true ]]
2549	then
2550	printf "\n +++ errors found in the parameter file!\n"
2551	answer=dummy
2552	printf "\n\n"
2553
2554	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2555	do
2556	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2557	read answer
2558	done
2559
2560	if [[ $answer = a \|\| $answer = A ]]
2561	then
2562	printf "\n +++ Aborting..."
2563	rm -rf $check_sources
2564	locat=normal; exit
2565	fi
2566	else
2567	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2568	fi
2569	rm -rf $check_sources
2570	fi
2571	else
2572	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2573	fi
2574
2575	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2576	rm -rf $check_sources
2577	cd $working_directory
2578
2579
2580	# DETERMINE PATH FOR MAKE DEPOSITORY
2581	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2582	then
2583
2584	line=""
2585	grep "%depository_path" $config_file > tmp_mrun
2586	while read line
2587	do
2588	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2589	then
2590	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2591	then
2592	global_depository_path=`echo $line \| cut -d" " -s -f2`
2593	fi
2594	fi
2595	done < tmp_mrun
2596
2597	line=""
2598	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2599	while read line
2600	do
2601	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2602	then
2603	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2604	then
2605	local_depository_path=`echo $line \| cut -d" " -s -f2`
2606	fi
2607	fi
2608	done < tmp_mrun
2609
2610	if [[ "$local_depository_path" = "" ]]
2611	then
2612	if [[ "$global_depository_path" != "" ]]
2613	then
2614	local_depository_path=$global_depository_path
2615	else
2616	printf "\n\n +++ no depository path found in configuration file"
2617	printf "\n for local host \"$localhost\" "
2618	printf "\n please set \"\%depository_path\" in configuration file\n"
2619	locat=config_file; exit
2620	fi
2621	fi
2622	eval local_depository_path=$local_depository_path
2623	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2624	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2625
2626
2627	basename=`echo $mainprog \| cut -f1 -d"."`
2628	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2629	if [[ ! -f $make_depository ]]
2630	then
2631	printf "\n"
2632	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2633	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2634	fi
2635
2636	fi
2637
2638
2639	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2640	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2641	if [[ $do_batch = false ]]
2642	then
2643
2644
2645	# CREATE THE TEMPORARY WORKING DIRECTORY
2646	mkdir -p $TEMPDIR
2647	chmod go+rx $TEMPDIR
2648	tmpcreate=true
2649
2650
2651	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2652	# INTO THE TEMPORARY WORKING DIRECTORY
2653	if [[ $do_compile = true ]]
2654	then
2655
2656	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2657	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2658	if [[ $localhost = nech ]]
2659	then
2660	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2661	if mkdir -p $TEMPDIR_COMPILE
2662	then
2663	printf "\n *** \"$TEMPDIR_COMPILE\" "
2664	printf "\n is generated as temporary directory for cross compiling\n"
2665	else
2666	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2667	printf "\n needed for cross compilation failed"
2668	locat=compile
2669	exit
2670	fi
2671	else
2672	TEMPDIR_COMPILE=$TEMPDIR
2673	fi
2674
2675	cp $make_depository $TEMPDIR_COMPILE
2676	cd $TEMPDIR_COMPILE
2677	tar -xf $make_depository > /dev/null 2>&1
2678	cd - > /dev/null
2679
2680	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2681	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2682	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2683	then
2684	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2685	else
2686	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2687	fi
2688
2689	else
2690
2691	cp $executable ${TEMPDIR}/a.out
2692
2693	fi
2694
2695
2696	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2697	cd $TEMPDIR
2698	printf "\n *** changed to temporary directory: $TEMPDIR"
2699
2700
2701	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2702	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2703	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2704	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2705	(( i = 0 ))
2706	while (( i < iout ))
2707	do
2708	(( i = i + 1 ))
2709	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2710	then
2711	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2712	else
2713	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2714	fi
2715	done
2716
2717
2718	# IF REQUIRED, START WITH COMPILING
2719	if [[ $do_compile = true ]]
2720	then
2721
2722
2723	if [[ -f a.out ]]
2724	then
2725
2726	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2727	printf "\n\n\n *** executable a.out found"
2728	printf "\n no compilation required \n"
2729
2730	else
2731
2732	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2733	printf "\n\n\n *** compilation starts \n$dashes\n"
2734	printf " *** compilation with make using following options:\n"
2735	printf " make depository: $make_depository"
2736	if [[ "$mopts" != "" ]]
2737	then
2738	printf " make options: $mopts\n"
2739	fi
2740	printf " compilername: $compiler_name\n"
2741	printf " compiler options: $fopts\n"
2742	printf " preprocessor directives: $cpp_options \n"
2743	printf " linker options: $lopts \n"
2744	if [[ "$modules" != "" ]]
2745	then
2746	printf " modules to be load: $modules \n"
2747	fi
2748	printf " source code files: $source_list \n"
2749
2750	if [[ $localhost = nech ]]
2751	then
2752	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\" "
2753	cp $TEMPDIR_COMPILE/a.out .
2754	[[ $? != 0 ]] && compile_error=true
2755	rm -rf $TEMPDIR_COMPILE
2756	elif [[ $localhost = ibmh ]]
2757	then
2758	printf " compiler is called via ssh on \"plogin1\" \n"
2759	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\" "
2760	[[ ! -f a.out ]] && compile_error=true
2761	continue # STATUS=1, IF a.out EXISTS
2762	elif [[ $localhost = lcflow ]]
2763	then
2764	printf " compiler is called via ssh on \"flow\" \n"
2765	/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\" "
2766	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2767	[[ "$check_for_file" = "" ]] && compile_error=true
2768	continue # STATUS=1, IF a.out EXISTS
2769	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2770	then
2771	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2772	else
2773	[[ "$init_cmds" != "" ]] && eval $init_cmds
2774	[[ "$module_calls" != "" ]] && eval $module_calls
2775	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2776	fi
2777
2778	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2779	then
2780	printf "\n +++ error occured while compiling or linking"
2781	locat=compile
2782
2783	exit
2784	else
2785	printf "$dashes\n *** compilation finished \n"
2786	fi
2787
2788	fi
2789
2790	fi
2791
2792
2793	# PROVIDE THE INPUT FILES
2794	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2795	(( i = 0 ))
2796	while (( i < iin ))
2797	do
2798	(( i = i + 1 ))
2799	if (( i == 1 ))
2800	then
2801	printf "\n\n *** providing INPUT-files:\n$dashes"
2802	fi
2803
2804
2805	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2806	if [[ "${transin[$i]}" = unavailable ]]
2807	then
2808	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2809	then
2810	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2811	printf "\n is not available!"
2812	else
2813	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2814	printf "\n is not available!"
2815	fi
2816	continue
2817	fi
2818
2819	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2820	files_for_pes=false; datentyp=file
2821	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2822	then
2823	files_for_pes=true; datentyp=directory
2824	actionin[$i]=""
2825	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2826	then
2827	actionin[$i]=""
2828	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2829	then
2830	files_for_pes=true; datentyp=directory
2831	actionin[$i]="ar"
2832	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2833	then
2834	actionin[$i]="ar"
2835	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2836	then
2837	files_for_pes=true; datentyp=directory
2838	actionin[$i]="fl"
2839	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2840	then
2841	actionin[$i]="fl"
2842	fi
2843
2844	if [[ $files_for_pes = true ]]
2845	then
2846	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2847	else
2848	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2849	fi
2850
2851	# INPUT-FILE FOR A RESTART RUN.
2852	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2853	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2854	if [[ "${actionin[$i]}" = fl ]]
2855	then
2856	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2857	if [[ $files_for_pes = false ]]
2858	then
2859	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2860	then
2861	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2862	got_tmp[$i]=true
2863	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2864	then
2865	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2866	printf "\n *** trying to use backup copy in \"$WORK\" "
2867	cp $WORK/${frelin[$i]} ${localin[$i]}
2868	else
2869	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2870	printf "\n or \"$tmp_data_catalog\" does not exist!"
2871	printf "\n *** trying to get copy from archive"
2872	actionin[$i]=ar
2873	fi
2874	else
2875	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2876	then
2877	mkdir ${localin[$i]}
2878	cd $tmp_data_catalog/${frelin[$i]}
2879	for file in $(ls *)
2880	do
2881	ln $file $TEMPDIR/${localin[$i]}
2882	done
2883	cd $TEMPDIR
2884	got_tmp[$i]=true
2885	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2886	then
2887	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2888	printf "\n *** trying to use backup copy in \"$WORK\" "
2889	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2890	else
2891	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2892	printf "\n or \"$tmp_data_catalog\" does not exist!"
2893	printf "\n *** trying to get copy from archive"
2894	actionin[$i]=ar
2895	fi
2896	fi
2897	fi
2898
2899
2900	# FILE IS STORED ON THE ARCHIVE SYSTEM
2901	if [[ "${actionin[$i]}" = ar ]]
2902	then
2903
2904	if [[ $files_for_pes = false ]]
2905	then
2906	printf "\n file will be restored from archive-system ($archive_system)!"
2907	else
2908	printf "\n directory will be restored from archive-system ($archive_system)!"
2909	fi
2910
2911	file_restored=false
2912
2913	if [[ $archive_system = asterix ]]
2914	then
2915	do_stagein=true
2916	(( stagein_anz = 0 ))
2917	while [[ $do_stagein = true ]]
2918	do
2919	if [[ $files_for_pes = false ]]
2920	then
2921	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2922	else
2923	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2924	fi
2925	cat STAGEIN_OUTPUT
2926	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2927	then
2928	file_restored=true
2929	do_stagein=false
2930	else
2931	(( stagein_anz = stagein_anz + 1 ))
2932	if (( stagein_anz == 10 ))
2933	then
2934	printf "\n +++ stagein stoped after 10 tries"
2935	locat=stage
2936	exit
2937	fi
2938	printf "\n +++ restoring from archive failed, trying again:"
2939	sleep 900
2940	fi
2941	done
2942	elif [[ $archive_system = DMF ]]
2943	then
2944	if [[ $files_for_pes = false ]]
2945	then
2946	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2947	locat=DMF
2948	exit
2949	else
2950	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2951	cp -r $ARCHIVE/${frelin[$i]} $PWD
2952	file_restored=true
2953	fi
2954	elif [[ $archive_system = tivoli ]]
2955	then
2956	if [[ $files_for_pes = false ]]
2957	then
2958	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2959	else
2960	(( inode = 0 ))
2961	while (( inode < nodes ))
2962	do
2963	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2964	(( inode = inode + 1 ))
2965	done
2966	fi
2967	file_restored=true
2968	elif [[ $archive_system = ut ]]
2969	then
2970	if [[ $files_for_pes = false ]]
2971	then
2972	cp $UT/${frelin[$i]} .
2973	else
2974	(( inode = 0 ))
2975	while (( inode < nodes ))
2976	do
2977	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2978	(( inode = inode + 1 ))
2979	done
2980	fi
2981	file_restored=true
2982	else
2983	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2984	locat=rearchive
2985	exit
2986	fi
2987
2988	if [[ $file_restored = true ]]
2989	then
2990
2991	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2992	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2993	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2994	if [[ $files_for_pes = false ]]
2995	then
2996	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2997	else
2998	mkdir $tmp_data_catalog/${frelin[$i]}
2999	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3000	fi
3001	got_tmp[$i]=true
3002
3003	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3004	mv ${frelin[$i]} ${localin[$i]}
3005
3006	fi
3007	fi
3008
3009
3010	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3011	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3012	then
3013
3014	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3015	then
3016
3017	# FILE COPIES ARE PROVIDED FOR ALL CORES
3018	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3019	printf "\n file will be provided for $numprocs processors"
3020	mkdir ${localin[$i]}
3021	ival=$numprocs
3022	(( ii = 0 ))
3023	while (( ii <= ival-1 ))
3024	do
3025	if (( ii < 10 ))
3026	then
3027	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3028	elif (( ii < 100 ))
3029	then
3030	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3031	elif (( ii < 1000 ))
3032	then
3033	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3034	else
3035	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3036	fi
3037	(( ii = ii + 1 ))
3038	done
3039
3040	else
3041
3042	if [[ $files_for_pes = true ]]
3043	then
3044
3045	# PROVIDE FILES FOR EACH CORE
3046	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3047	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3048	printf "\n providing $numprocs files for the respective processors"
3049	mkdir ${localin[$i]}
3050	if [[ $link_local_input = true ]]
3051	then
3052	printf " using ln -f\n"
3053	cd ${absnamein[$i]}
3054	for file in $(ls *)
3055	do
3056	ln -f $file ${localin[$i]}
3057	done
3058	cd $TEMPDIR
3059	fi
3060
3061	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3062	if [[ ! -f "${localin[$i]}/_0000" ]]
3063	then
3064	if [[ $link_local_input = true ]]
3065	then
3066	printf " ln failed for .../_0000, using cp...\n"
3067	fi
3068	cp -r ${absnamein[$i]}/* ${localin[$i]}
3069	fi
3070
3071	else
3072
3073	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3074	if [[ $link_local_input = true ]]
3075	then
3076	printf " using ln -f\n"
3077	ln -f ${absnamein[$i]} ${localin[$i]}
3078	fi
3079	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3080	if [[ ! -f "${localin[$i]}" ]]
3081	then
3082	if [[ $link_local_input = true ]]
3083	then
3084	printf " ln failed, using cp...\n"
3085	fi
3086	cp ${absnamein[$i]} ${localin[$i]}
3087	fi
3088	fi
3089	fi
3090	fi
3091
3092	done
3093	if (( i != 0 ))
3094	then
3095	printf "\n$dashes\n *** all INPUT-files provided \n"
3096	fi
3097
3098
3099	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3100	(( i = 0 ))
3101	while (( i < iic ))
3102	do
3103	(( i = i + 1 ))
3104	if (( i == 1 ))
3105	then
3106	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3107	fi
3108	printf "\n >>> ${in_command[$i]}"
3109	eval ${in_command[$i]}
3110	if (( i == iic ))
3111	then
3112	printf "\n$dashes\n"
3113	fi
3114	done
3115
3116
3117	# SET THE REMAINING CPU-TIME
3118	cpurest=${cpumax}.
3119
3120
3121	# START DVR STREAMING SERVER
3122	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3123	then
3124	if [[ "$dvr_server" != "" ]]
3125	then
3126
3127	printf "\n\n *** preparing the dvr streaming server configuration file"
3128
3129	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3130	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3131	if [[ "$running_dvrserver_id" != "" ]]
3132	then
3133
3134	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3135	printf "\n This server is used instead starting a new one!"
3136	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3137
3138	else
3139
3140	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3141	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3142	then
3143	cp ${PALM_BIN}/.dvrserver.config .
3144
3145	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3146	user_id=`id -u`
3147	group_id=`id -g`
3148
3149	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3150	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3151	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3152	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3153	mv .dvrserver.3 .dvrserver.config
3154	rm .dvrserver.1 .dvrserver.2
3155
3156	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3157	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3158	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3159	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3160	local_dvrserver_running=.TRUE.
3161	else
3162	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3163	printf "\n \"$PALM_BIN\" "
3164	locat=dvr
3165	exit
3166	fi
3167
3168	fi
3169
3170	else
3171	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3172	fi
3173	fi
3174
3175
3176	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3177	# (FILE ENVPAR WILL BE READ BY PALM)
3178	cat > ENVPAR << %%END%%
3179	&envpar run_identifier = '$fname', host = '$localhost',
3180	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3181	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3182	maximum_cpu_time_allowed = ${cpumax}.,
3183	revision = '$global_revision',
3184	local_dvrserver_running = $local_dvrserver_running,
3185	batch_job = $batch_job /
3186
3187	%%END%%
3188
3189
3190	# STARTING THE EXECUTABLE
3191	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3192	PATH=$PATH:$TEMPDIR
3193
3194	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3195	if [[ "$mpi_debug" = true ]]
3196	then
3197	export MPI_CHECK_ARGS=1
3198	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3199	fi
3200
3201	if [[ "$totalview" = true ]]
3202	then
3203	printf "\n *** totalview debugger will be used"
3204	tv_opt="-tv"
3205	else
3206	tv_opt=""
3207	fi
3208
3209	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3210	then
3211	if [[ "$ENVIRONMENT" = BATCH ]]
3212	then
3213	continue
3214	fi
3215	if [[ $localhost = ibmh ]]
3216	then
3217
3218	# SETUP THE IBM MPI ENVIRONMENT
3219	export MP_SHARED_MEMORY=yes
3220	export AIXTHREADS_SCOPE=S
3221	export OMP_NUM_THREADS=$threads_per_task
3222	export AUTHSTATE=files
3223	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3224
3225	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3226	export MP_ADAPTER_USE=shared
3227	export MP_CPU_USE=multiple
3228	export MP_TIMEOUT=1200
3229
3230	unset MP_TASK_AFFINITY
3231
3232	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3233	#(( ii = 1 ))
3234	#while (( ii <= $numprocs ))
3235	#do
3236	# echo $localhost_realname >> hostfile
3237	# (( ii = ii + 1 ))
3238	#done
3239	#export MP_HOSTFILE=hostfile
3240
3241	if [[ "$LOADLBATCH" = yes ]]
3242	then
3243	totalview poe a.out $ROPTS
3244	else
3245	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3246	export TVDSVRLAUNCHCMD=ssh
3247	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3248	fi
3249
3250	fi # END DEBUG MODE
3251
3252	else
3253
3254	# NORMAL EXECUTION
3255	if [[ -n $numprocs ]]
3256	then
3257
3258	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3259	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3260	then
3261
3262	# SETUP THE IBM MPI ENVIRONMENT
3263	if [[ $host != ibmh && $host != ibmkisti ]]
3264	then
3265	export MP_SHARED_MEMORY=yes
3266	export AIXTHREAD_SCOPE=S
3267	export OMP_NUM_THREADS=$threads_per_task
3268	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3269	export AUTHSTATE=files
3270	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3271	# export MP_PRINTENV=yes
3272
3273	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3274	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3275	export MP_WAIT_MODE=poll
3276	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3277	fi
3278
3279	if [[ $host = ibmkisti ]]
3280	then
3281	export LANG=en_US
3282	export MP_SHARED_MEMORY=yes
3283	if [[ $threads_per_task = 1 ]]
3284	then
3285	export MP_SINGLE_THREAD=yes
3286	export MEMORY_AFFINITY=MCM
3287	else
3288	export OMP_NUM_THREADS=$threads_per_task
3289	fi
3290	fi
3291
3292	if [[ "$LOADLBATCH" = yes ]]
3293	then
3294	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3295	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3296	then
3297	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3298	else
3299	if [[ $run_coupled_model = false ]]
3300	then
3301	if [[ "$ocean_file_appendix" = true ]]
3302	then
3303	echo "precursor_ocean" > runfile_atmos
3304	else
3305	echo "precursor_atmos" > runfile_atmos
3306	fi
3307	else
3308	(( iia = $numprocs_atmos / $threads_per_task ))
3309	(( iio = $numprocs_ocean / $threads_per_task ))
3310	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3311	printf "\n using $coupled_mode coupling"
3312	printf "\n\n"
3313	echo "coupled_run $iia $iio" > runfile_atmos
3314	fi
3315	poe ./a.out $ROPTS < runfile_atmos
3316	fi
3317	else
3318	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3319	then
3320	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3321	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3322	then
3323	if [[ -f $hostfile ]]
3324	then
3325	cp $hostfile hostfile
3326	else
3327	(( ii = 1 ))
3328	while (( ii <= $numprocs ))
3329	do
3330	echo $localhost_realname >> hostfile
3331	(( ii = ii + 1 ))
3332	done
3333	fi
3334	export MP_HOSTFILE=hostfile
3335	if [[ $run_coupled_model = false ]]
3336	then
3337	if [[ "$ocean_file_appendix" = true ]]
3338	then
3339	echo "precursor_ocean" > runfile_atmos
3340	else
3341	echo "precursor_atmos" > runfile_atmos
3342	fi
3343	else
3344	(( iia = $numprocs_atmos / $threads_per_task ))
3345	(( iio = $numprocs_ocean / $threads_per_task ))
3346	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3347	printf "\n using $coupled_mode coupling"
3348	printf "\n\n"
3349	echo "coupled_run $iia $iio" > runfile_atmos
3350	fi
3351
3352	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3353
3354	else
3355	if [[ "$host_file" = "" ]]
3356	then
3357	printf "\n +++ no hostfile given in configuration file"
3358	locat=config_file
3359	exit
3360	else
3361	eval host_file=$host_file
3362	fi
3363	export MP_HOSTFILE=$host_file
3364	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3365	fi
3366	fi
3367	elif [[ $host = nech ]]
3368	then
3369	(( ii = nodes ))
3370	if [[ $ii = 1 ]]
3371	then
3372	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3373	export MPIPROGINF=YES
3374	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3375	echo "*** execution on single node with mpirun"
3376	mpirun -np $numprocs ./a.out $ROPTS
3377	else
3378	(( i = 0 ))
3379	while (( i < ii ))
3380	do
3381	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3382	(( i = i + 1 ))
3383	done
3384
3385	echo "#!/bin/sh" > mpi_exec_shell
3386	echo " " >> mpi_exec_shell
3387	echo "set -u" >> mpi_exec_shell
3388	echo "F_ERRCNT=0" >> mpi_exec_shell
3389	echo "MPIPROGINV=YES" >> mpi_exec_shell
3390	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3391	echo "cpurest=$cpurest" >> mpi_exec_shell
3392	echo "fname=$fname" >> mpi_exec_shell
3393	echo "localhost=$localhost" >> mpi_exec_shell
3394	echo "return_addres=$return_addres" >> mpi_exec_shell
3395	echo "return_username=$return_username" >> mpi_exec_shell
3396	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3397	echo "write_binary=$write_binary" >> mpi_exec_shell
3398	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3399	echo " " >> mpi_exec_shell
3400	echo "export F_ERRCNT" >> mpi_exec_shell
3401	echo "export MPIPROGINV" >> mpi_exec_shell
3402	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3403	echo "export cpurest" >> mpi_exec_shell
3404	echo "export fname" >> mpi_exec_shell
3405	echo "export localhost" >> mpi_exec_shell
3406	echo "export return_addres" >> mpi_exec_shell
3407	echo "export return_username" >> mpi_exec_shell
3408	echo "export tasks_per_node" >> mpi_exec_shell
3409	echo "export write_binary" >> mpi_exec_shell
3410	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3411	echo " " >> mpi_exec_shell
3412	echo "exec ./a.out" >> mpi_exec_shell
3413
3414	chmod u+x mpi_exec_shell
3415	export MPIPROGINF=YES
3416	mpirun -f multinode_config &
3417	wait
3418
3419	fi
3420	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3421	then
3422
3423	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3424	# DOES NOT EXIST
3425	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3426	then
3427	if [[ -f $hostfile ]]
3428	then
3429	cp $hostfile hostfile
3430	(( ii = $numprocs / $threads_per_task ))
3431	else
3432	(( ii = 1 ))
3433	while (( ii <= $numprocs / $threads_per_task ))
3434	do
3435	echo $localhost_realname >> hostfile
3436	(( ii = ii + 1 ))
3437	done
3438	fi
3439	eval zeile=\"`head -n $ii hostfile`\"
3440	printf "\n *** running on: $zeile"
3441	fi
3442
3443	(( ii = $numprocs / $threads_per_task ))
3444	export OMP_NUM_THREADS=$threads_per_task
3445
3446	if [[ $threads_per_task != 1 ]]
3447	then
3448	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3449	# MAY ABORT
3450	ulimit -s unlimited
3451	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3452	fi
3453	if [[ $run_coupled_model = false ]]
3454	then
3455	if [[ "$ocean_file_appendix" = true ]]
3456	then
3457	echo "precursor_ocean" > runfile_atmos
3458	else
3459	echo "precursor_atmos" > runfile_atmos
3460	fi
3461	printf "\n\n"
3462
3463	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3464	then
3465	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3466	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3467	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3468	elif [[ $host = lccrayf ]]
3469	then
3470	aprun -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3471	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3472	then
3473	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3474	elif [[ $host = lcflow ]]
3475	then
3476	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3477	elif [[ $host = lcsb ]]
3478	then
3479	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3480	elif [[ $host = lckiaps ]]
3481	then
3482	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3483	elif [[ $host = lckyu* ]]
3484	then
3485	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3486	else
3487	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3488	fi
3489	else
3490
3491	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3492	(( iia = $numprocs_atmos / $threads_per_task ))
3493	(( iio = $numprocs_ocean / $threads_per_task ))
3494	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3495	printf "\n using $coupled_mode coupling"
3496	printf "\n\n"
3497
3498	if [[ $coupled_mode = "mpi2" ]]
3499	then
3500	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3501	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3502
3503	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3504	then
3505
3506	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3507	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3508
3509	else
3510	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3511	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3512	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3513	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3514	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3515	fi
3516	wait
3517
3518	else
3519
3520	echo "coupled_run $iia $iio" > runfile_atmos
3521
3522	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3523	then
3524
3525	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3526
3527	elif [[ $host = lck \|\| $host = lckordi ]]
3528	then
3529
3530	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3531
3532	elif [[ $host = lckyu* ]]
3533	then
3534
3535	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3536
3537	fi
3538	wait
3539	fi
3540
3541	fi
3542
3543	elif [[ $host = lckyoto ]]
3544	then
3545	set -xv
3546	export P4_RSHCOMMAND=plesh
3547	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3548	if [[ "$ENVIRONMENT" = BATCH ]]
3549	then
3550	if [[ "$cond2" = fujitsu ]]
3551	then
3552	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3553	elif [[ "cond2" = pgi ]]
3554	then
3555	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3556	else
3557	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3558	fi
3559	else
3560	if [[ "$cond2" = "" ]]
3561	then
3562	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3563	else
3564	mpirun -np $numprocs ./a.out $ROPTS
3565	fi
3566	fi
3567	set +xv
3568
3569	elif [[ $host = lctit ]]
3570	then
3571	export OMP_NUM_THREADS=$threads_per_task
3572	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3573	if [[ "$threads_per_task" != 1 ]]
3574	then
3575	export MV2_ENABLE_AFFINITY=0
3576	fi
3577	echo "----- PBS_NODEFILE content:"
3578	cat $PBS_NODEFILE
3579	echo "-----"
3580	(( ii = $numprocs / $threads_per_task ))
3581	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3582	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3583	else
3584	mpprun -n $numprocs a.out $ROPTS
3585	fi
3586	else
3587	a.out $ROPTS
3588	fi
3589	fi
3590
3591	if [[ $? != 0 ]]
3592	then
3593
3594	# ABORT IN CASE OF RUNTIME ERRORS
3595	printf "\n +++ runtime error occured"
3596	locat=execution
3597	exit
3598
3599	else
3600
3601	printf "\n$dashes\n *** execution finished \n"
3602
3603	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3604	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3605	if [[ "$dvrserver_id" != "" ]]
3606	then
3607	kill $dvrserver_id
3608	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3609
3610	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3611	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3612	if [[ -d DATA_DVR ]]
3613	then
3614
3615	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3616	# DIRECTORY
3617	cp .dvrserver.config DATA_DVR
3618
3619	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3620	# SEQUENCE MODE DATA TOO)
3621	process_dvr_output -d DATA_DVR -f $fname -s
3622
3623	else
3624
3625	# PROCESS THE LOCAL OUTPUT
3626	process_dvr_output -l -d DATA_DVR -f $fname
3627
3628	fi
3629
3630	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3631	then
3632
3633	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3634	process_dvr_output -l -d DATA_DVR -f $fname
3635
3636	fi
3637	fi
3638
3639
3640
3641	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3642	# BY EACH CORE INTO ONE FILE
3643	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3644	then
3645	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3646	printf "\n 2d- and/or 3d-data may be incomplete!"
3647	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3648	elif [[ "$combine_plot_fields" == true ]]
3649	then
3650	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3651	then
3652	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3653	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3654	else
3655	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3656	combine_plot_fields${block}.x
3657	fi
3658	else
3659
3660	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3661	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3662	# ??? koennen wir das streichen ???
3663	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3664	fi
3665
3666
3667
3668	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3669	(( i = 0 ))
3670	while (( i < ioc ))
3671	do
3672	(( i = i + 1 ))
3673	if (( i == 1 ))
3674	then
3675	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3676	fi
3677	printf "\n >>> ${out_command[$i]}"
3678	eval ${out_command[$i]}
3679	if (( i == ioc ))
3680	then
3681	printf "\n$dashes\n"
3682	fi
3683	done
3684
3685
3686	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3687	if [[ $do_trace = true ]]
3688	then
3689	printf "\n\n"
3690	ls -al
3691	fi
3692
3693
3694
3695	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3696	(( i = 0 ))
3697	while (( i < iout ))
3698	do
3699	(( i = i + 1 ))
3700	if (( i == 1 ))
3701	then
3702	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3703	fi
3704
3705	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3706	files_for_pes=false; filetyp=file
3707	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3708	then
3709	files_for_pes=true; filetyp=directory
3710	actionout[$i]=""
3711	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3712	then
3713	actionout[$i]=""
3714	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3715	then
3716	files_for_pes=true; filetyp=directory
3717	actionout[$i]="ar"
3718	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3719	then
3720	actionout[$i]="ar"
3721	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3722	then
3723	files_for_pes=true; filetyp=directory
3724	actionout[$i]="fl"
3725	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3726	then
3727	actionout[$i]="fl"
3728	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3729	then
3730	files_for_pes=true; filetyp=directory
3731	actionout[$i]="tr"
3732	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3733	then
3734	actionout[$i]="tr"
3735	fi
3736
3737	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3738	then
3739	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3740	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3741	then
3742	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3743	else
3744
3745
3746	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3747	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3748	if [[ "${actionout[$i]}" = tr ]]
3749	then
3750	if [[ $localhost != $fromhost ]]
3751	then
3752	if [[ $files_for_pes = false ]]
3753	then
3754	cps=""
3755	cst=""
3756	else
3757	cps=-c
3758	cst="/"
3759	fi
3760	if [[ $localhost = nech ]]
3761	then
3762
3763	# TRANSFER IN SEPERATE JOB
3764	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3765	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3766	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3767	if [[ $files_for_pes = false ]]
3768	then
3769	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3770	else
3771	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3772	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3773	fi
3774
3775	echo "set -x" > transfer_${localout[$i]}
3776	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3777
3778	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3779	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3780	printf "\n or higher cycle\n"
3781	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]}
3782
3783	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3784
3785	if [[ $localhost = nech ]]
3786	then
3787	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3788	else
3789	if [[ "$LOGNAME" = b323013 ]]
3790	then
3791	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3792	else
3793	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3794	fi
3795	fi
3796
3797	else
3798
3799	# TRANSFER WITHIN THIS JOB
3800	transfer_failed=false
3801	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3802	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3803	if [[ $localhost = lccrayb ]]
3804	then
3805	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]}"
3806	elif [[ $localhost = lccrayh ]]
3807	then
3808	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]}"
3809	else
3810	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3811	fi
3812	[[ $? != 0 ]] && transfer_failed=true
3813
3814	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3815	if [[ $transfer_failed = true ]]
3816	then
3817	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3818	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3819
3820	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3821	eval local_catalog=${pathout[$i]}
3822	if [[ ! -d $local_catalog ]]
3823	then
3824	printf " *** local directory does not exist. Trying to create:\n"
3825	printf " $local_catalog \n"
3826	mkdir -p $local_catalog
3827	fi
3828	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3829	transfer_problems=true
3830	fi
3831	fi
3832	else
3833
3834	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3835	actionout[$i]=""
3836	fi
3837	fi
3838
3839
3840	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3841	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3842	if [[ "${actionout[$i]}" = tra ]]
3843	then
3844	if [[ $localhost != $fromhost ]]
3845	then
3846	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3847	then
3848
3849	# TRANSFER IN SEPERATE JOB
3850	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3851	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3852	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3853	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3854
3855	echo "set -x" > transfer_${localout[$i]}
3856	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3857
3858	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3859	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3860	printf "\n or higher cycle\n"
3861	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]}
3862
3863	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3864
3865	if [[ $localhost = nech ]]
3866	then
3867	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3868	else
3869	if [[ $LOGNAME = b323013 ]]
3870	then
3871	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3872	else
3873	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3874	fi
3875	fi
3876
3877	else
3878
3879	# TRANSFER WITHIN THIS JOB
3880	transfer_failed=false
3881	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3882	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3883	if [[ $localhost = lccrayb ]]
3884	then
3885	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]}"
3886	elif [[ $localhost = lccrayh ]]
3887	then
3888	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]}"
3889	else
3890	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3891	fi
3892	[[ $? != 0 ]] && transfer_failed=true
3893
3894	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3895	if [[ $transfer_failed = true ]]
3896	then
3897	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3898	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3899
3900	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3901	eval local_catalog=${pathout[$i]}
3902	if [[ ! -d $local_catalog ]]
3903	then
3904	printf " *** local directory does not exist. Trying to create:\n"
3905	printf " $local_catalog \n"
3906	mkdir -p $local_catalog
3907	fi
3908
3909	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3910	transfer_problems=true
3911	fi
3912	fi
3913	else
3914
3915	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3916	actionout[$i]=a
3917	fi
3918	fi
3919
3920
3921	# OUTPUT-FILE FOR A RESTART-RUN.
3922	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3923	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3924	# AS LAST ACTION, ARCHIVING IS INITIATED.
3925	if [[ "${actionout[$i]}" = fl ]]
3926	then
3927	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3928	chmod g+rx $tmp_data_catalog
3929	if [[ $files_for_pes = false ]]
3930	then
3931	printf "\n >>> OUTPUT: ${localout[$i]} to"
3932	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3933	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3934	else
3935	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3936	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3937	mkdir $tmp_data_catalog/${frelout[$i]}
3938	cd ${localout[$i]}
3939	for file in $(ls *)
3940	do
3941	ln -f $file $tmp_data_catalog/${frelout[$i]}
3942	done
3943	cd $TEMPDIR
3944	fi
3945
3946
3947	# CREATE AND SUBMIT ARCHIVING-JOB
3948	if [[ $store_on_archive_system = true ]]
3949	then
3950
3951	if [[ $archive_system = asterix ]]
3952	then
3953	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3954	if [[ $files_for_pes = false ]]
3955	then
3956	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3957	else
3958	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3959	fi
3960	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3961	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3962	echo "then" >> archive_${frelout[$i]}
3963	echo " do_stageout=false" >> archive_${frelout[$i]}
3964	echo "else" >> archive_${frelout[$i]}
3965	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3966	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3967	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3968	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3969	if [[ $files_for_pes = false ]]
3970	then
3971	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3972	else
3973	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3974	fi
3975	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3976	echo "fi" >> archive_${frelout[$i]}
3977	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3978	elif [[ $archive_system = DMF ]]
3979	then
3980	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3981	if [[ $files_for_pes = false ]]
3982	then
3983	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3984	locat=DMF
3985	exit
3986	else
3987	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3988	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3989	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3990	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3991	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3992	fi
3993	elif [[ $archive_system = tivoli ]]
3994	then
3995	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3996	if [[ $files_for_pes = false ]]
3997	then
3998	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3999	echo "set -x" >> archive_${frelout[$i]}
4000	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4001	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4002	else
4003
4004	echo "set -x" >> archive_${frelout[$i]}
4005	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4006	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4007	cd $tmp_data_catalog
4008	all_files=`ls -1 ${frelout[$i]}/*`
4009	cd - > /dev/null
4010	(( inode = 0 ))
4011	(( tp1 = tasks_per_node + 1 ))
4012	while (( inode < nodes ))
4013	do
4014	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4015	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4016	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4017	(( inode = inode + 1 ))
4018	done
4019	fi
4020	elif [[ $archive_system = ut ]]
4021	then
4022	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4023	if [[ $files_for_pes = false ]]
4024	then
4025	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4026	echo "set -x" >> archive_${frelout[$i]}
4027	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4028	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4029	else
4030
4031	echo "set -x" >> archive_${frelout[$i]}
4032	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4033	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4034	cd $tmp_data_catalog
4035	all_files=`ls -1 ${frelout[$i]}/*`
4036	cd - > /dev/null
4037	(( inode = 0 ))
4038	(( tp1 = tasks_per_node + 1 ))
4039	while (( inode < nodes ))
4040	do
4041	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4042	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4043	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4044	(( inode = inode + 1 ))
4045	done
4046	fi
4047	elif [[ $archive_system = none ]]
4048	then
4049	printf " +++ archiving on $localhost not available!\n"
4050	fi
4051
4052	if [[ $archive_system != none ]]
4053	then
4054	if [[ $localhost = nech ]]
4055	then
4056	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4057	fi
4058	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4059	fi
4060	else
4061	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4062	fi
4063
4064
4065	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4066	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4067	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4068	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4069	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4070	if [[ $files_for_pes = false ]]
4071	then
4072	cat /dev/null > ${pathout[$i]}
4073	else
4074	mkdir -p ${pathout[$i]}
4075	fi
4076
4077	fi
4078
4079
4080	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4081	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4082	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4083	if [[ "${actionout[$i]}" = ar ]]
4084	then
4085	if [[ $files_for_pes = false ]]
4086	then
4087	printf "\n >>> OUTPUT: ${localout[$i]} to"
4088	printf "\n ${pathout[$i]}"
4089	printf "\n File will be copied to archive-system ($archive_system) !\n"
4090	else
4091	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4092	printf "\n ${pathout[$i]}"
4093	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4094	fi
4095	mv ${localout[$i]} ${frelout[$i]}
4096
4097	file_saved=false
4098
4099	if [[ $archive_system = asterix ]]
4100	then
4101	do_stageout=true
4102	(( stageout_anz = 0 ))
4103	while [[ $do_stageout = true ]]
4104	do
4105	if [[ $files_for_pes = false ]]
4106	then
4107	stageout ${frelout[$i]} > STAGE_OUTPUT
4108	else
4109	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4110	fi
4111	cat STAGE_OUTPUT
4112	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4113	then
4114	file_saved=true
4115	do_stageout=false
4116	else
4117	if [[ $files_for_pes = false ]]
4118	then
4119	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4120	else
4121	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4122	fi
4123	(( stageout_anz = stageout_anz + 1 ))
4124	if (( stageout_anz == 10 ))
4125	then
4126	printf "\n +++ stoped after 10 unsuccessful tries!"
4127	archive_save=false
4128	do_stageout=false
4129	else
4130	printf "\n *** new try to store on archive after 15 min:"
4131	sleep 900
4132	fi
4133	fi
4134	done
4135	elif [[ $archive_system = DMF ]]
4136	then
4137	if [[ $files_for_pes = false ]]
4138	then
4139	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4140	locat=DMF
4141	exit
4142	else
4143	rm -rf $ARCHIVE/${frelout[$i]}
4144	cp -r ${frelout[$i]} $ARCHIVE
4145	fi
4146	file_saved=true
4147	elif [[ $archive_system = tivoli ]]
4148	then
4149	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4150	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4151	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4152	# WHEN THE ARCHIVE-JOB IS EXECUTED
4153	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4154	chmod g+rx $tmp_data_catalog
4155	if [[ $files_for_pes = false ]]
4156	then
4157	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4158	else
4159	mkdir $tmp_data_catalog/${frelout[$i]}
4160	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4161	fi
4162
4163	# GENERATE AND SUBMIT BATCH-JOB
4164	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4165	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4166	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4167	if [[ $files_for_pes = false ]]
4168	then
4169	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4170	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4171	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4172	else
4173	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4174	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4175	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4176	fi
4177
4178	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4179	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4180	file_saved=true
4181
4182	elif [[ $archive_system = ut ]]
4183	then
4184	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4185	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4186	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4187	# WHEN THE ARCHIVE-JOB IS EXECUTED
4188	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4189	chmod g+rx $tmp_data_catalog
4190	if [[ $files_for_pes = false ]]
4191	then
4192	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4193	else
4194	mkdir $tmp_data_catalog/${frelout[$i]}
4195	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4196	fi
4197
4198	# GENERATE AND SUBMIT BATCH-JOB
4199	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4200	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4201	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4202	if [[ $files_for_pes = false ]]
4203	then
4204	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4205	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4206	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4207	else
4208	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4209	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4210	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4211	fi
4212
4213	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4214	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4215	file_saved=true
4216
4217	else
4218	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4219	archive_save=false
4220	fi
4221
4222	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4223	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4224	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4225	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4226	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4227	if [[ $file_saved = true ]]
4228	then
4229	if [[ $files_for_pes = false ]]
4230	then
4231	cat /dev/null > ${pathout[$i]}
4232	else
4233	mkdir -p ${pathout[$i]}
4234	fi
4235	fi
4236
4237	fi
4238
4239	# APPEND ON THIS MACHINE
4240	if [[ "${actionout[$i]}" = "a" ]]
4241	then
4242	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4243	then
4244	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4245	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4246	else
4247	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4248	cat ${localout[$i]} >> ${pathout[$i]}
4249	fi
4250	fi
4251
4252	# COPY ON THIS MACHINE
4253	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4254	# ON DIFFERENT FILE-SYSTEMS
4255	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4256	then
4257
4258	# COPY IN CASE OF RUNS ON SINGLE CORES
4259	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4260	then
4261	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4262	if [[ $link_local_output = true ]]
4263	then
4264	printf " using ln -f\n"
4265	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4266	fi
4267	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4268	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4269	then
4270	if [[ $link_local_output = true ]]
4271	then
4272	printf " ln failed, using cp...\n"
4273	fi
4274	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4275	fi
4276	else
4277	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4278	if [[ $link_local_output = true ]]
4279	then
4280	printf " using ln -f\n"
4281	ln -f ${localout[$i]} ${pathout[$i]}
4282	fi
4283	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4284	if [[ ! -f "${pathout[$i]}" ]]
4285	then
4286	if [[ $link_local_output = true ]]
4287	then
4288	printf " ln failed, using cp...\n"
4289	fi
4290	cp ${localout[$i]} ${pathout[$i]}
4291	fi
4292	fi
4293
4294	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4295	then
4296
4297	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4298	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4299	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4300	if [[ $link_local_output = true ]]
4301	then
4302	printf " using ln -f\n"
4303	mkdir ${pathout[$i]}
4304	cd ${localout[$i]}
4305	for file in $(ls *)
4306	do
4307	ln -f $file ${pathout[$i]}
4308	done
4309	cd $TEMPDIR
4310	fi
4311
4312	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4313	if [[ ! -f "${pathout[$i]}/_0000" ]]
4314	then
4315	if [[ $link_local_output = true ]]
4316	then
4317	printf " ln failed for .../_0000, using cp...\n"
4318	fi
4319	cp -r ${localout[$i]} ${pathout[$i]}
4320	fi
4321
4322	fi
4323	fi
4324	done
4325	if (( i != 0 ))
4326	then
4327	if [[ $transfer_problems = true ]]
4328	then
4329	printf "\n$dashes\n *** OUTPUT-files saved"
4330	printf "\n +++ WARNING: some data transfers failed! \n"
4331	else
4332	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4333	fi
4334	fi
4335
4336
4337	# IF REQUIRED, START A RESTART-JOB
4338	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4339	if [[ -f CONTINUE_RUN ]]
4340	then
4341
4342	if [[ $archive_save = true ]]
4343	then
4344
4345	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4346	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4347	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4348	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4349	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4350	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4351	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4352	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4353	then
4354	mc=`echo $mc \| sed 's/#/f/g'`
4355	fi
4356
4357
4358	# START THE RESTART-JOB
4359	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4360	echo " $mc"
4361	printf "\n$dashes\n"
4362	if [[ $localhost != $fromhost ]]
4363	then
4364
4365	if [[ $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4366	then
4367	echo "*** ssh will be used to initiate restart-runs!"
4368	echo " return_addres=\"$return_addres\" "
4369	echo " return_username=\"$return_username\" "
4370	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4371	then
4372	if [[ $localhost = ibmh ]]
4373	then
4374	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4375	elif [[ $localhost = lccrayb ]]
4376	then
4377	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4378	elif [[ $localhost = lccrayh ]]
4379	then
4380	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4381
4382	else
4383	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;. /muksoft/packages/intel/bin/compilervars.sh intel64;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4384	fi
4385	else
4386	if [[ $localhost = ibmkisti ]]
4387	then
4388	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\" "
4389	elif [[ $localhost = lcflow ]]
4390	then
4391	/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 "
4392	elif [[ $localhost = lccrayb ]]
4393	then
4394	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\" "
4395	elif [[ $localhost = lccrayh ]]
4396	then
4397	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\" "
4398	else
4399	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4400	fi
4401	fi
4402	else
4403	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4404	locat=restart; exit
4405	fi
4406
4407	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4408	if [[ $queue = special1q ]]
4409	then
4410	sleep 120
4411	else
4412	sleep 30
4413	fi
4414
4415	else
4416
4417	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4418	# USING SSH)
4419	cd $LOCAL_PWD
4420	if [[ $localhost = lckyuh ]]
4421	then
4422	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4423	printf "\n please restart job manually using command:\n"
4424	printf "\n \"$mc\" "
4425	else
4426	eval $mc # THE ' MUST BE EVALUATED
4427	fi
4428	cd - > /dev/null
4429	fi
4430	if [[ $localhost = lckyuh ]]
4431	then
4432	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4433	else
4434	printf "\n$dashes\n *** restart-run initiated \n"
4435	fi
4436
4437
4438	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4439	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4440	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4441	# MAY BE VERY HUGE)
4442	(( i = 0 ))
4443	while (( i < iin ))
4444	do
4445	(( i = i + 1 ))
4446	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4447	then
4448	rm -r $tmp_data_catalog/${frelin[$i]}
4449	fi
4450	done
4451
4452	else
4453
4454	printf "\n +++ no restart-run possible, since errors occured"
4455	printf "\n during the archive process"
4456	fi
4457
4458	fi
4459
4460
4461
4462	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4463	if [[ "$email_notification" != "none" ]]
4464	then
4465
4466	if [[ $localhost != $fromhost ]]
4467	then
4468	if [[ -f CONTINUE_RUN ]]
4469	then
4470	echo "PALM restart run necessary" > email_text
4471	echo "description header of actual run:" >> email_text
4472	cat CONTINUE_RUN >> email_text
4473	echo "mrun-command to restart:" >> email_text
4474	echo "$mc" >> email_text
4475	else
4476	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4477	fi
4478	mail $email_notification < email_text
4479	printf "\n *** email notification sent to \"$email_notification\" "
4480	fi
4481	fi
4482
4483
4484
4485	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4486	cd $HOME
4487	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4488
4489	else
4490
4491
4492	# PREPARING ACTIONS,
4493	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4494
4495	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4496	mrun_com="$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 $remote_username"
4497	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4498	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4499	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4500	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4501	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4502	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4503	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4504	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4505	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4506	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4507	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4508	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4509	if [[ $use_openmp = true ]]
4510	then
4511	mrun_com=${mrun_com}" -O $threads_per_task"
4512	fi
4513	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4514	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4515	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4516	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4517	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4518	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4519	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4520	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4521	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4522	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4523	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4524	if [[ $do_remote = true ]]
4525	then
4526	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4527	fi
4528
4529
4530	# CREATE EXECUTABLE FOR BATCH JOB
4531	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4532	then
4533
4534	printf "\n *** creating the executable for batch job\n"
4535
4536	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4537	if [[ $host != $localhost ]]
4538	then
4539	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4540	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4541	locat=create_executable; exit
4542	fi
4543
4544	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4545	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4546
4547	cp $make_depository .
4548	tar -xf $make_depository > /dev/null 2>&1
4549	cp ../* . > /dev/null 2>&1
4550
4551	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4552
4553	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4554	then
4555	printf "\n +++ error occured while compiling or linking"
4556	locat=compile
4557	exit
4558	fi
4559
4560	mv a.out ..
4561	cd - > /dev/null 2>&1
4562	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4563
4564	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4565
4566	fi
4567
4568
4569	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4570	jobfile=jobfile.$RANDOM
4571
4572
4573	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4574	echo "mkdir $TEMPDIR" >> $jobfile
4575	echo "cd $TEMPDIR" >> $jobfile
4576
4577
4578	# ACTIVATE ERROR-TRACEBACK
4579	if [[ $do_trace = true ]]
4580	then
4581	echo "set -x" >> $jobfile
4582	else
4583	echo "set +vx" >> $jobfile
4584	fi
4585
4586
4587	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4588	if [[ "$init_cmds" != "" ]]
4589	then
4590	echo "$init_cmds" >> $jobfile
4591	fi
4592	if [[ "$module_calls" != "" ]]
4593	then
4594	echo "$module_calls" >> $jobfile
4595	fi
4596
4597
4598	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4599	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4600	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4601	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4602	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4603	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4604	# QUEUEING-SYSTEMS
4605	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4606	then
4607
4608	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4609	if [[ $restart_run != true ]]
4610	then
4611	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4612	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4613	fi
4614
4615	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4616	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4617	echo "set -x" >> $jobfile
4618	if [[ $host = $localhost ]]
4619	then
4620
4621	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4622	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4623	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4624	then
4625	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4626	else
4627	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4628	fi
4629
4630	else
4631	if [[ $host = ibmkisti ]]
4632	then
4633	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4634	echo "localdir=\`pwd\`" >> $jobfile
4635	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4636	elif [[ $host = lccrayb ]]
4637	then
4638	echo "localdir=\`pwd\`" >> $jobfile
4639	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4640	elif [[ $host = lccrayh ]]
4641	then
4642	echo "localdir=\`pwd\`" >> $jobfile
4643	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4644
4645	else
4646	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4647	fi
4648	fi
4649	echo "export SOURCES_COMPLETE=true" >> $jobfile
4650
4651	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4652	# WORKING DIRECTORY OF THE JOB
4653	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4654	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4655	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4656	echo "execute_mrun=true" >> $jobfile
4657	echo " " >> $jobfile
4658
4659	else
4660
4661	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4662	if [[ $do_compile = true ]]
4663	then
4664
4665	source_catalog=SOURCES_FOR_RUN_$fname
4666
4667	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4668	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4669	echo "export SOURCES_COMPLETE=true" >> $jobfile
4670	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4671
4672	for filename in $source_list
4673	do
4674	# BACKSLASH IS USED FOR MASKING
4675	echo "cat > $filename << \"%END%\"" >> $jobfile
4676	cat $source_catalog/$filename >> $jobfile
4677	echo " " >> $jobfile
4678	echo "%END%" >> $jobfile
4679	echo " " >> $jobfile
4680	done
4681
4682	# BACKSLASH IS USED FOR MASKING
4683	echo "cat > Makefile << \"%END%\"" >> $jobfile
4684	cat $source_catalog/Makefile >> $jobfile
4685	echo " " >> $jobfile
4686	echo "%END%" >> $jobfile
4687	echo " " >> $jobfile
4688
4689	echo "cd - > /dev/null" >> $jobfile
4690
4691	fi
4692
4693
4694	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4695	# BACKSLASH IS USED FOR MASKING
4696	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4697	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4698	echo "cat > $config_file << \"%END%\"" >> $jobfile
4699	if [[ $host = lckyuh ]]
4700	then
4701	# NO CROSS-COMPILER ON COMPUTE NODE
4702	sed 's/frtpx/frt/g' $config_file >> $jobfile
4703	else
4704	sed 's/#$.*//g' $config_file >> $jobfile
4705	fi
4706	echo "%END%" >> $jobfile
4707	echo " " >> $jobfile
4708
4709
4710	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4711	# BACKSLASH IS USED FOR MASKING
4712	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4713	if [[ $host = lckyuh ]]
4714	then
4715	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4716	else
4717	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4718	fi
4719	echo "%END%" >> $jobfile
4720	echo "chmod u+x $mrun_script_name" >> $jobfile
4721	echo "execute_mrun=true" >> $jobfile
4722	echo " " >> $jobfile
4723
4724	fi
4725
4726
4727	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4728	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4729	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4730	if [[ $do_remote = true ]]
4731	then
4732	(( i = 0 ))
4733	while (( i < iin ))
4734	do
4735	(( i = i + 1 ))
4736	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4737	if [[ "${transin[$i]}" = job ]]
4738	then
4739	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4740	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4741	echo " " >> $jobfile
4742	echo "%END%" >> $jobfile
4743	else
4744	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4745	fi
4746
4747	# CHECK, IF FILE COULD BE CREATED
4748	echo "if [[ \$? = 1 ]]" >> $jobfile
4749	echo "then" >> $jobfile
4750	echo " echo \" \" " >> $jobfile
4751	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4752	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4753	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4754	echo " execute_mrun=false" >> $jobfile
4755	echo "fi" >> $jobfile
4756	done
4757	fi
4758
4759	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4760	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4761	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4762	echo "LOCAL_PWD=$working_directory" >> $jobfile
4763	echo "export LOCAL_PWD" >> $jobfile
4764
4765	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4766	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4767	echo "export LOCAL_MRUN_PATH" >> $jobfile
4768
4769	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4770	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4771	then
4772	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4773	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4774	fi
4775
4776	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4777	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4778	echo "set -x" >> $jobfile
4779	echo "queue=$queue" >> $jobfile
4780	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4781	echo 'ls -al; echo `pwd`' >> $jobfile
4782	echo "cd \$HOME" >> $jobfile
4783	echo "rm -rf $TEMPDIR" >> $jobfile
4784
4785
4786
4787
4788	# START THE JOB USING SUBJOB-COMMAND
4789	if [[ $silent = false ]]
4790	then
4791	printf "\n "
4792	else
4793	printf "\n\n"
4794	fi
4795
4796	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
4797	rm -rf $jobfile
4798
4799
4800	fi # END OF REMOTE-PART

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source: palm/trunk/SCRIPTS/mrun @ 1402

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