Home

Context Navigation

source: palm/trunk/SCRIPTS/mrun @ 1289

Last change on this file since 1289 was 1289, checked in by raasch, 10 years ago
script comments translated to English version update to 3.10
Property svn:keywords set to `Id Rev`
File size: 174.4 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 1997-2012 Leibniz University Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# comments translated to English
25	# necriam-, fimm-, ibmy-, and sgi-specific code removed
26	# export of variables for palm and interpret_config removed
27	#
28	# Former revisions:
29	# -----------------
30	# $Id: mrun 1289 2014-03-04 07:12:34Z raasch $
31	#
32	# 1281 2014-02-01 07:55:49Z raasch
33	# rsync-copy restricted to Cray machines, since command is unavailable on some
34	# other systems
35	#
36	# 1279 2014-01-28 12:10:14Z raasch
37	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
38	# in order to remove annoying restrictions concerning the number of processors which
39	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
40	# restriction, one of the nodes will be filled with less than the given number of
41	# tasks per node. A respective warning is given.
42	#
43	# 1274 2014-01-09 13:14:54Z heinze
44	# adjustments for lccrayh
45	#
46	# 1272 2014-01-08 10:19:32Z witha
47	# small adjustment for lcflow
48	#
49	# 1270 2013-12-16 11:05:01Z fricke
50	# call of combine_plot_fields adjusted for lccrayb/lccrayh
51	#
52	# 1255 2013-11-07 14:43:35Z raasch
53	# further adjustments for lccrayb remote access
54	#
55	# 1241 2013-10-30 11:36:58Z heinze
56	# Enable use of nudging input and input of large scale forcing from
57	# external files
58	#
59	# 1229 2013-09-20 06:55:19Z raasch
60	# further adjustments for lccrayb
61	#
62	# 1224 2013-09-16 07:27:23Z raasch
63	# first adjustments for lccrayb
64	#
65	# 1210 2013-08-14 10:58:20Z raasch
66	# fftw support added
67	#
68	# 1201 2013-07-10 16:17:59Z witha
69	# adjustments for Forwind cluster (lcflow)
70	#
71	# 1199 2013-07-05 14:52:22Z raasch
72	# adjustments for CSC Helsinki (lccrayf),
73	# executables for batch jobs can be created in advance, in order to avoid calling
74	# the compiler within the batch job (only works if batch jobs are submitted on
75	# local host)
76	#
77	# 1190 2013-06-25 09:39:21Z heinze
78	# enable use of automatic restarts for ibmh
79	# use of cluster/express queue enabled (ibmh)
80	#
81	# 1124 2013-04-09 15:46:52Z raasch
82	# variable "memory" is exported via typeset option -x, because otherwise an unknown
83	# side effect may lead to data loss while getopts is reading the script-option arguments
84	#
85	# 1122 2013-04-09 08:37:16Z heinze
86	# Bugfix: change type of variable last_char
87	#
88	# 1119 2013-04-05 15:11:19Z raasch
89	# Bugfix for setting -T option for subjob
90	#
91	# 1108 2013-03-05 07:03:32Z raasch
92	# bugfix for coupled runs on lckyut/lckyuh
93	#
94	# 1106 2013-03-04 05:31:38Z raasch
95	# --stdin argument for mpiexec on lckyuh
96	# -y and -Y settings output to header
97	#
98	# 1103 2013-02-20 02:15:53Z raasch
99	# default script runs again under ksh, because of unsolved problems with read
100	# from stdin: when bash script is called from a ksh, message "read error: 0:
101	# Resource temporarily unavailable" appears and script does not stop,
102	# further bash compatibility adjustments,
103	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
104	# on lckyuh, but mrun does not terminate and issues a warning instead
105	#
106	# 1101 2013-02-17 10:20:21Z raasch
107	# script now running under bash instead of ksh, which required small adjustments
108	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
109	# read from stdin),
110	# cross compilername on lckyuh compute nodes replaced by real compiler name
111	#
112	# 1099 2013-02-10 01:47:43Z raasch
113	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
114	# and for Forwind cluster (lcflow)
115	# small further adjustments for lckyut
116	#
117	# 1094 2013-02-03 01:52:12Z raasch
118	# explicit ssh/scp port can be set in config file with environment variable
119	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
120	# decalpha parts (yonsei) removed
121	#
122	# 2013-02-02 07:06:13Z raasch
123	# adjustments for Kyushu-University computing center (lckyut - tatara)
124	#
125	# 1083 2013-01-04 10:22:09Z maronga
126	# bugfix in parameter file check (read %cpp_options was missing)
127	#
128	# 1069 2012-11-28 16:18:43Z maronga
129	# bugfix: coupling mode was always set to mpi2, typos removed
130	#
131	# 1058 2012-11-21 07:00:35Z raasch
132	# Intel inspector (inspxe) is given the number of PEs instead of the number of
133	# nodes
134	#
135	# 1046 2012-11-09 14:38:45Z maronga
136	# code put under GPL (PALM 3.9)
137	#
138	# 21/03/94 - Siggi - first version finished
139	# 03/03/94 - Siggi - script development started
140	#
141	#--------------------------------------------------------------------------------#
142	# mrun - script for running PALM jobs
143	#--------------------------------------------------------------------------------#
144
145
146
147	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
148
149	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
150	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
151	# (TOO MANY ARGUMENTS - PROBLEM)
152	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
153
154	AddFilenames=""
155	additional_conditions=""
156	add_source_path=""
157	afname=""
158	archive_save=true
159	archive_system=none
160	check_namelist_files=true
161	combine_plot_fields=true
162	compiler_name=""
163	cond1=""
164	cond2=""
165	config_file=.mrun.config
166	coupled_dist=""
167	coupled_mode="mpi1"
168	cpp_opts=""
169	cpp_options=""
170	cpumax=0
171	cpurest=0
172	create_executable_for_batch=false
173	delete_temporary_catalog=true
174	do_batch=false
175	do_compile=true
176	do_remote=false
177	do_stagein=true
178	do_stageout=true
179	do_trace=false
180	email_notification="none"
181	exclude=""
182	executable=""
183	execution_error=false
184	fftw_inc=""
185	fftw_lib=""
186	fftw_support=false
187	fname=test
188	fromhost=""
189	global_revision=""
190	group_number=none
191	host=""
192	host_file=""
193	hp=""
194	ignore_archive_error=false
195	input_list=""
196	interpreted_config_file=""
197	job_catalog="~/job_queue"
198	job_on_file=""
199	keep_data_from_previous_run=false
200	link_local_input=false
201	link_local_output=false
202	localhost_realname=$(hostname)
203	local_dvrserver_running=.FALSE.
204	locat=normal
205	mainprog=""
206	makefile=""
207	max_par_io_str=""
208	mc=$0
209	while [[ $(echo $mc \| grep -c "/") != 0 ]]
210	do
211	mc=`echo $mc \| cut -f2- -d"/"`
212	done
213	module_calls=""
214	mrun_script_name=$mc
215	netcdf_inc=""
216	netcdf_lib=""
217	netcdf_support=false
218	node_usage=default
219	numprocs=""
220	numprocs_atmos=0
221	numprocs_ocean=0
222	OOPT=""
223	openmp=false
224	output_list=""
225	package_list=""
226	queue=none
227	read_from_config=""
228	restart_run=false
229	if [[ `hostname` = rte10 ]]
230	then
231	return_addres=133.5.185.60
232	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
233	elif [[ `hostname` = climate0 ]]
234	then
235	return_addres=165.132.26.68
236	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
237	elif [[ `hostname` = urban00 ]]
238	then
239	return_addres=147.46.30.151
240	echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
241	else
242	return_addres=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
243	fi
244	return_password=""
245	return_username=$LOGNAME
246	remotecall=false
247	remote_username=""
248	run_coupled_model=false
249	run_mode=""
250	store_on_archive_system=false
251	dashes=" ----------------------------------------------------------------------------"
252	silent=false
253	source_list=""
254	source_path=SOURCE
255	tasks_per_node=""
256	threads_per_task=1
257	tmpcreate=false
258	tmp_data_catalog=""
259	transfer_problems=false
260	usern=$LOGNAME
261	use_openmp=false
262	version="MRUN 2.1 Rev$Rev: 1289 $"
263	working_directory=`pwd`
264	TOPT=""
265	XOPT=""
266	zeit=$( date \| cut -c 12-19 )
267
268	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
269	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
270	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
271	# SCRIPT-OPTION ARGUMENTS
272	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
273
274
275
276	# ERROR HANDLING IN CASE OF EXIT
277	trap 'rm -rf $working_directory/tmp_mrun
278	if [[ $locat != normal && $locat != control_c ]]
279	then
280
281	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
282	(( i = 0 ))
283	while (( i < iec ))
284	do
285	(( i = i + 1 ))
286	printf "\n *** Execution of ERROR-command:\n"
287	printf " >>> ${err_command[$i]}\n"
288	eval ${err_command[$i]}
289	done
290	if [[ -n $interpreted_config_file ]]
291	then
292	rm -rf $interpreted_config_file
293	fi
294	if [[ -n .mrun_environment ]]
295	then
296	rm -rf .mrun_environment
297	fi
298	if [[ $tmpcreate = true ]]
299	then
300	printf "\n *** Contents of \"$TEMPDIR\":\n"
301	ls -al; cd
302	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
303	fi
304	if [[ "$dvrserver_id" != "" ]]
305	then
306	echo "+++ killing dvrserver_id=$dvrserver_id"
307	kill $dvrserver_id
308	fi
309	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
310	then
311	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
312	fi
313	printf "\n\n+++ MRUN killed \n\n"
314	elif [[ $locat != control_c ]]
315	then
316	printf "\n\n --> all actions finished\n\n"
317	printf " Bye, bye $usern !!\n\n"
318	fi' exit
319
320
321	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
322	trap 'rm -rf $working_directory/tmp_mrun
323	rm -rf $working_directory/tmp_check_namelist_files
324	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
325	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
326	then
327	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
328	fi
329	if [[ "$dvrserver_id" != "" ]]
330	then
331	echo "+++ killing dvrserver_id=$dvrserver_id"
332	kill $dvrserver_id
333	fi
334	printf "\n+++ MRUN killed by \"^C\" \n\n"
335	locat=control_c
336	exit
337	' 2
338
339
340	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
341	# BEEN SET
342	if [[ "$PALM_BIN" = "" ]]
343	then
344	printf "\n +++ environment variable PALM_BIN has not been set"
345	printf "\n please set it to the directory where the PALM scripts are located"
346	locat=palm_bin; exit
347	fi
348	export PATH=$PALM_BIN:$PATH
349
350
351
352	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
353	# WHICH WILL BE USED TO START RESTART-JOBS
354	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
355	do
356	case $option in
357	(a) afname=$OPTARG;;
358	(A) store_on_archive_system=true; mc="$mc -A";;
359	(b) do_batch=true; mc="$mc -b";;
360	(B) delete_temporary_catalog=false; mc="$mc -B";;
361	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
362	(C) restart_run=true; mc="$mc -C";;
363	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
364	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
365	(F) job_on_file="-D"; mc="$mc -F";;
366	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
367	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
368	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
369	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
370	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
371	(I) ignore_archive_error=true; mc="$mc -I";;
372	(k) keep_data_from_previous_run=true; mc="$mc -k";;
373	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
374	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
375	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
376	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
377	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
378	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
379	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
380	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
381	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
382	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
383	(R) remotecall=true;return_addres=$OPTARG; mc="$mc -R$OPTARG";;
384	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
385	(S) read_from_config=false; mc="$mc -S";;
386	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
387	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
388	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
389	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
390	(v) silent=true; mc="$mc -v";;
391	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
392	(x) do_trace=true;set -x; mc="$mc -x";;
393	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
394	(y) ocean_file_appendix=true; mc="$mc -y";;
395	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
396	(z) check_namelist_files=false; mc="$mc -z";;
397	(Z) combine_plot_fields=false; mc="$mc -Z";;
398	(\?) printf "\n +++ unknown option $OPTARG \n"
399	printf "\n --> type \"$0 ?\" for available options \n"
400	locat=parameter;exit;;
401	esac
402	done
403
404
405	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
406	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
407	(( to_shift = $OPTIND - 1 ))
408	shift $to_shift
409
410	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
411	if [[ "$1" = "?" ]]
412	then
413	(printf "\n *** mrun can be called as follows:\n"
414	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"
415	printf "\n Description of available options:\n"
416	printf "\n Option Description Default-Value"
417	printf "\n -a base name of input files equiv. -d"
418	printf "\n -A archiving when using file-attribute fl"
419	printf "\n -b batch-job on local machine ---"
420	printf "\n -B do not delete temporary directory at end ---"
421	printf "\n -c configuration file .mrun.config"
422	printf "\n -d base name of files attached to program test"
423	printf "\n -D preprocessor(cpp)-directives \"\" "
424	printf "\n -F create remote job file only ---"
425	printf "\n -h execution host $localhost_realname"
426	printf "\n -i INPUT control list \"\" "
427	printf "\n -I archiving errors of previous batch-jobs"
428	printf "\n will be ignored"
429	printf "\n -k keep data from previous run"
430	printf "\n -K additional conditions for controling"
431	printf "\n usage of conditional code and"
432	printf "\n env-variables in configuration file \"\" "
433	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
434	printf "\n -M Makefile name Makefile"
435	printf "\n -n node usage (shared/not_shared) depending on -h"
436	printf "\n -o OUTPUT control list \"\" "
437	printf "\n -O use OpenMP ---"
438	printf "\n -p software package list \"\" "
439	printf "\n -q queue \"$queue\" "
440	printf "\n -r run control list (combines -i -o) \"\" "
441	printf "\n -s filenames of routines to be compiled \"\" "
442	printf "\n must end with .f, .f90, .F, or .c !"
443	printf "\n use \"..\" for more than one file and wildcards"
444	printf "\n -s LM compiles all locally modified files"
445	printf "\n -S config file interpreted by shellscript ---"
446	printf "\n -t allowed cpu-time in seconds (batch) 0"
447	printf "\n -T tasks per node depending on -h"
448	printf "\n -u username on remote machine \"\" "
449	printf "\n -v no prompt for confirmation ---"
450	printf "\n -w maximum parallel io streams as given by -X"
451	printf "\n -x tracing of mrun for debug purposes ---"
452	printf "\n -X # of processors (on parallel machines) 1"
453	printf "\n -y add appendix \"_O\" to all local output"
454	printf "\n files (ocean precursor runs followed by"
455	printf "\n coupled atmosphere-ocean runs) ---"
456	printf "\n -Y run coupled model, \"#1 #2\" with"
457	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
458	printf "\n -z disable a priori parameter file check ---"
459	printf "\n -Z skip combine_plot_fields at the end of "
460	printf "\n the simulation ---"
461	printf "\n "
462	printf "\n Possible values of positional parameter <modus>:"
463	printf "\n \"?\" - this outline \n\n") \| more
464	exit
465	elif [[ "$1" != "" ]]
466	then
467	printf "\n +++ positional parameter $1 unknown \n"
468	locat=parameter; exit
469	fi
470
471
472
473	# SHORT STARTING MESSAGE
474	printf "\n*** $version "
475	printf "\n will be executed. Please wait ..."
476
477
478
479	# CHECK, IF CONFIGURATION FILE EXISTS
480	if [[ ! -f $config_file ]]
481	then
482	printf "\n\n +++ configuration file: "
483	printf "\n $config_file"
484	printf "\n does not exist"
485	locat=connect; exit
486	fi
487
488
489	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
490	line=""
491	grep "%host_identifier" $config_file > tmp_mrun
492	while read line
493	do
494	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
495	then
496	HOSTNAME=`echo $line \| cut -d" " -s -f2`
497	host_identifier=`echo $line \| cut -d" " -s -f3`
498	if [[ $localhost_realname = $HOSTNAME ]]
499	then
500	localhost=$host_identifier
501	break
502	fi
503	fi
504	done < tmp_mrun
505
506	if [[ "$localhost" = "" ]]
507	then
508	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
509	printf "\n for local host \"$localhost_realname\"."
510	printf "\n Please add line"
511	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
512	printf "\n to the configuration file."
513	locat=localhost; exit
514	fi
515
516
517	# SET HOST-SPECIFIC VARIABLES
518	case $localhost_realname in
519	(r1\|r2\|h01\|b01) archive_system=tivoli;;
520	(cs*) archive_system=ut;;
521	esac
522
523
524	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
525	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
526	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
527	[[ "$afname" = "" ]] && afname=$fname
528
529
530	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
531	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
532	# STATEMENTS IN THE CONFIGURATION FILE
533	if [[ "$run_mode" != "" ]]
534	then
535	input_list="$input_list $run_mode"
536	output_list="$output_list $run_mode"
537	fi
538
539
540	# ??? is this (and the respective option -H) really required ???
541	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
542	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
543	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
544	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
545	if [[ "$fromhost" = "" ]]
546	then
547	fromhost=$localhost
548	fi
549
550
551	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
552	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
553	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
554	# TO BE SUBMITTED (I.E. do_bacth=true)
555	if [[ -n $host && "$host" != $localhost ]]
556	then
557	do_batch=true
558	do_remote=true
559	case $host in
560	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
561	(*) printf "\n"
562	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
563	printf "\n is not available"
564	locat=nqs; (( iec = 0 )); exit;;
565	esac
566	else
567	host=$localhost
568	fi
569
570
571	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
572	if [[ -n $additional_conditions ]]
573	then
574	cond1=`echo $additional_conditions \| cut -d" " -f1`
575	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
576	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
577	if [[ -n $dummy ]]
578	then
579	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
580	locat=options; exit
581	fi
582	block=_$cond1
583	[[ -n $cond2 ]] && block=${block}_$cond2
584	fi
585
586
587	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
588	if [[ $run_coupled_model = true ]]
589	then
590
591	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
592	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
593
594	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
595	then
596
597	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
598	printf "\n PEs (total) : $numprocs"
599	printf "\n PEs (atmosphere): $numprocs_atmos"
600	printf "\n PEs (ocean) : $numprocs_ocean"
601	locat=coupling; exit
602
603	fi
604
605
606	# GET coupled_mode FROM THE CONFIG FILE
607	line=""
608	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
609	while read line
610	do
611	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
612	then
613	coupled_mode="mpi2"
614	fi
615	done < tmp_mrun
616
617	fi
618
619
620	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
621	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
622	then
623	if [[ $ignore_archive_error = false ]]
624	then
625	printf "\n +++ data archiving of previous run failed"
626	printf "\n see directory \~/job_queue on remote machine"
627	locat=archive; exit
628	else
629	printf "\n +++ warning: data archiving in a previous run failed"
630	printf "\n MRUN continues, trying to get backup copy"
631	fi
632	fi
633
634
635	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
636	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
637	mrun_memory=$memory
638	mrun_group_number=$group_number
639	mrun_cpumax=$cpumax
640	mrun_numprocs=$numprocs
641
642
643	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
644	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE interpret_config
645	if [[ "$read_from_config" = false ]]
646	then
647
648	[[ $silent = false ]] && printf "\n Reading the configuration file... "
649
650	# READ THE CONFIGURATION FILE LINE BY LINE
651	while read zeile
652	do
653	[[ $silent = false ]] && printf "."
654
655
656	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
657	eval zeile=\"$zeile\"
658
659
660	# INTERPRET THE LINE
661	if [[ "$(echo $zeile)" = "" ]]
662	then
663	# EMPTY LINE, NO ACTION
664	continue
665
666	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
667	then
668
669	# LINE IS A COMMENT LINE
670	true
671
672	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
673	then
674
675	# LINE DEFINES AN ENVIRONMENT-VARIABLE
676	zeile=$(echo $zeile \| cut -c2-)
677	var=`echo $zeile \| cut -d" " -f1`
678	value=`echo $zeile \| cut -d" " -s -f2`
679	for_host=`echo $zeile \| cut -d" " -s -f3`
680	for_cond1=`echo $zeile \| cut -d" " -s -f4`
681	for_cond2=`echo $zeile \| cut -d" " -s -f5`
682
683	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
684	then
685
686	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
687	# "::" IS REPLACED BY ":".
688	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
689
690
691	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
692	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
693	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
694	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
695	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
696	# CONFIGURATION-FILE.
697	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
698	then
699	eval $var=\$value
700
701	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
702	if [[ $do_trace = true ]]
703	then
704	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
705	fi
706	fi
707
708	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
709	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
710	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
711	# MUST HAVE TO BE STARTED
712	if [[ $var = host ]]
713	then
714	if [[ -n $host && "$host" != $localhost ]]
715	then
716	do_batch=true
717	do_remote=true
718	case $host in
719	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
720	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
721	printf "\n is not available"
722	locat=nqs; exit;;
723	esac
724	else
725	host=$localhost
726	fi
727	fi
728
729	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
730	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
731	# BY MRUN (E.G. subjob)
732	export $var
733	fi
734
735
736
737
738	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
739	then
740
741	# LINE DEFINES ERROR-COMMAND
742	(( iec = iec + 1 ))
743	zeile=$(echo $zeile \| cut -c4-)
744	err_command[$iec]="$zeile"
745
746	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
747	then
748
749	# LINE DEFINES INPUT-COMMAND
750	(( iic = iic + 1 ))
751	zeile=$(echo $zeile \| cut -c4-)
752	in_command[$iic]="$zeile"
753
754	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
755	then
756
757	# LINE DEFINES OUTPUT-COMMAND
758	(( ioc = ioc + 1 ))
759	zeile=$(echo $zeile \| cut -c4-)
760	out_command[$ioc]="$zeile"
761
762	else
763
764	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
765	# s2a: in/out - field
766	# s2b: loc - field (optional)
767	# s2c: tr/ar - field (optional)
768	s1=`echo $zeile \| cut -d" " -f1`
769	s2=`echo $zeile \| cut -d" " -s -f2`
770	s2a=$(echo $s2 \| cut -d":" -f1)
771	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
772	then
773	s2b=""
774	s2c=""
775	else
776	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
777	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
778	fi
779	s3=`echo $zeile \| cut -d" " -f3`
780	s4=`echo $zeile \| cut -d" " -s -f4`
781	s5=`echo $zeile \| cut -d" " -s -f5`
782	s6=`echo $zeile \| cut -d" " -s -f6`
783
784
785	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
786	# INPUT- OR OUTPUT-LIST.
787	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
788	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
789	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
790	# IS NOT CHECKED AND STORED.
791	IFSALT="$IFS"; IFS="$IFS:"
792	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
793	then
794	found=false
795	for actual in $input_list
796	do
797	for formal in $s3
798	do
799	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
800	done
801	done
802	if [[ $found = true ]]
803	then
804	(( iin = iin + 1 ))
805	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
806	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
807	extin[$iin]=$s6
808	fi
809	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
810	then
811	found=false
812	for actual in $output_list
813	do
814	for formal in $s3
815	do
816	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
817	done
818	done
819	if [[ $found = true ]]
820	then
821	(( iout = iout + 1 ))
822	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
823	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
824	fi
825	elif [[ "$s2a" != in && "$s2a" != out ]]
826	then
827	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
828	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
829	locat=connect; exit
830	fi
831	IFS="$IFSALT"
832	fi
833	done < $config_file
834
835	else
836
837
838	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
839	[[ $silent = false ]] && printf "..."
840	interpreted_config_file=.icf.$RANDOM
841
842
843
844	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
845	cat > .mrun_environment << %%END%%
846	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
847	config_file = '$config_file', do_remote = '$do_remote',
848	do_trace = '$do_trace', host = '$host',
849	input_list = '$input_list', icf = '$interpreted_config_file',
850	localhost = '$localhost', output_list = '$output_list' /
851
852	%%END%%
853
854	if [[ "$host" != $localhost ]]
855	then
856
857	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
858	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
859	if [[ $? != 0 ]]
860	then
861	printf "\n\n +++ no interpret_config found"
862	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
863	locat=interpret_config; exit
864	fi
865	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
866	$interpret_config_executable
867
868	else
869
870	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
871	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
872	then
873	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
874	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
875	locat=interpret_config; exit
876	else
877	interpret_config${block}.x
878	fi
879
880	fi
881	rm .mrun_environment
882
883
884	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
885	chmod u+x $interpreted_config_file
886	export PATH=$PATH:.
887	. $interpreted_config_file
888	rm $interpreted_config_file
889
890	fi
891
892
893	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
894	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
895	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
896	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
897	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
898	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
899	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
900
901
902	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
903	# FOR SOURCE-FILES TO BE COMPILED.
904	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
905	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
906	if [[ "$SOURCES_COMPLETE" = "" ]]
907	then
908
909	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
910	# HAS BEEN DEFINED
911	source_path=""
912	line=""
913	grep "%source_path" $config_file > tmp_mrun
914	while read line
915	do
916	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
917	then
918	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
919	then
920	global_source_path=`echo $line \| cut -d" " -f2`
921	fi
922	fi
923	done < tmp_mrun
924
925	line=""
926	found=false
927	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
928	while read line
929	do
930	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
931	then
932	if [[ $found = true ]]
933	then
934	printf "\n\n +++ more than one source path found in configuration file"
935	printf "\n for local host \"$localhost\" "
936	locat=source_path; exit
937	fi
938	source_path=`echo $line \| cut -d" " -f2`
939	found=true
940	fi
941	done < tmp_mrun
942	rm tmp_mrun
943
944	if [[ "$source_path" = "" ]]
945	then
946	if [[ "$global_source_path" != "" ]]
947	then
948	source_path=$global_source_path
949	else
950	printf "\n\n +++ no source path found in configuration file"
951	printf "\n for local host \"$localhost\" "
952	locat=source_path; exit
953	fi
954	fi
955	eval source_path=$source_path
956
957	if [[ ! -d $source_path ]]
958	then
959	printf "\n\n +++ source path \"$source_path\" on local host"
960	printf "\n \"$localhost\" does not exist"
961	locat=source_path; exit
962	fi
963
964	fi
965
966
967	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
968	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
969	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
970	then
971	global_revision=`svnversion $source_path 2>/dev/null`
972	global_revision="Rev: $global_revision"
973	fi
974
975
976	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
977	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
978	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
979	if [[ -n $host && "$host" != $localhost ]]
980	then
981	do_batch=true
982	do_remote=true
983	case $host in
984	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
985	(*) printf "\n"
986	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
987	printf "\n is not available"
988	locat=nqs; (( iec = 0 )); exit;;
989	esac
990	else
991	host=$localhost
992	fi
993
994
995	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
996	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
997	then
998
999	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1000	if [[ ! -n $numprocs ]]
1001	then
1002	printf "\n"
1003	printf "\n +++ option \"-K parallel\" requires additional specification"
1004	printf "\n of the number of processors to be used by"
1005	printf "\n mrun-option \"-X\" or by environment-variable"
1006	printf "\n \"numprocs\" in the configuration file"
1007	locat=numprocs; (( iec = 0 )); exit
1008	fi
1009
1010	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1011	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1012	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1013	then
1014	printf "\n"
1015	printf "\n +++ option \"-T\" (tasks per node) is missing"
1016	printf "\n set -T option or define tasks_per_node in the config file"
1017	locat=tasks_per_node; (( iec = 0 )); exit
1018	fi
1019
1020	if (( numprocs < tasks_per_node ))
1021	then
1022	printf "\n"
1023	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1024	printf "\n given values: -T $tasks_per_node -X $numprocs"
1025	locat=tasks_per_node; (( iec = 0 )); exit
1026	fi
1027
1028	if [[ $host != lcflow && $host != lcxt5m ]]
1029	then
1030	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1031	(( ival = $tasks_per_node ))
1032	(( pes = numprocs ))
1033	(( ii = pes / ival ))
1034	(( remaining_pes = pes - ii * ival ))
1035	if (( remaining_pes > 0 ))
1036	then
1037	printf "\n"
1038	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1039	printf "\n divisor of the total number of processors (option \"-X\")"
1040	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1041	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1042	(( nodes = nodes + 1 ))
1043	fi
1044	fi
1045
1046
1047	# SETTINGS FOR SUBJOB-COMMAND
1048	OOPT="-O $threads_per_task"
1049
1050	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1051	if [[ "$tasks_per_node" != "" ]]
1052	then
1053	TOPT="-T $tasks_per_node"
1054	fi
1055
1056	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1057	if [[ $node_usage = default ]]
1058	then
1059	if [[ $host = ibms ]]
1060	then
1061	node_usage=shared
1062	else
1063	node_usage=not_shared
1064	fi
1065	fi
1066
1067	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1068	then
1069	printf "\n"
1070	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1071	printf "\n \"shared\" or \"not_shared\""
1072	locat=tasks_per_node; (( iec = 0 )); exit
1073	fi
1074
1075	fi
1076
1077	# CHECK IF HOSTFILE EXISTS
1078	if [[ -n $hostfile ]]
1079	then
1080	if [[ ! -f $hostfile ]]
1081	then
1082	printf "\n"
1083	printf "\n +++ hostfile \"$hostfile\" does not exist"
1084	locat=hostfile; exit
1085	fi
1086	fi
1087
1088
1089	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1090	if [[ "$maximum_parallel_io_streams" = "" ]]
1091	then
1092	maximum_parallel_io_streams=$numprocs
1093	fi
1094
1095
1096	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1097	if [[ "$scp_port" != "" ]]
1098	then
1099	PORTOPT="-P $scp_port"
1100	SSH_PORTOPT="-p $scp_port"
1101	fi
1102
1103
1104	# SET DEFAULT-QUEUE, IF NOT GIVEN
1105	if [[ $queue = none ]]
1106	then
1107	case $host in
1108	(ibmh) queue=cluster;;
1109	(ibmkisti) queue=class.32plus;;
1110	(lckiaps) queue=normal;;
1111	(lckyoto) queue=ph;;
1112	(lckyuh) queue=fx-single;;
1113	(lckyut) queue=cx-single;;
1114	(lctit) queue=S;;
1115	(nech) queue=none;;
1116	(unics) queue=unics;;
1117	esac
1118	fi
1119
1120
1121	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1122	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1123	(( i = 0 ))
1124	while (( i < iin ))
1125	do
1126	(( i = i + 1 ))
1127	(( maxcycle = 0 ))
1128
1129	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1130	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1131	if [[ "${actionin[$i]}" = di ]]
1132	then
1133	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1134	# HOST ONLY
1135	eval filename=${pathin[$i]}/${endin[$i]}
1136	else
1137	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1138	# HOST ONLY
1139	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1140	fi
1141	eval pathname=${pathin[$i]}
1142
1143	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1144	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1145	then
1146	filename_input=$filename
1147	fi
1148
1149	# CHECK IF FILE EXISTS
1150	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1151	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1152	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1153	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1154	then
1155
1156	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1157	if [[ "${transin[$i]}" != "locopt" ]]
1158	then
1159	printf "\n\n +++ INPUT-file: "
1160	if [[ "${extin[$i]}" = "" ]]
1161	then
1162	printf "\n $filename"
1163	else
1164	printf "\n $filename.${extin[$i]}"
1165	fi
1166	printf "\n does not exist\n"
1167	locat=input; exit
1168	else
1169	transin[$i]="unavailable"
1170	fi
1171	else
1172
1173	# DETERMINE THE FILE'S CYCLE NUMBER
1174	ls -1 -d $filename > filelist 2>/dev/null
1175	ls -1 -d $filename.* >> filelist 2>/dev/null
1176	while read zeile
1177	do
1178	cycle=$(echo $zeile \| cut -f2 -d".")
1179	if [[ "$cycle" = "$zeile" ]]
1180	then
1181	(( icycle = 0 ))
1182	elif [[ "$cycle" = "${extin[$i]}" ]]
1183	then
1184	(( icycle = 0 ))
1185	else
1186	(( icycle = $cycle ))
1187	fi
1188	if (( icycle > maxcycle ))
1189	then
1190	(( maxcycle = icycle ))
1191	file_to_be_used=$zeile
1192	fi
1193	done <filelist
1194	rm filelist
1195
1196	# APPEND CYCLE NUMBER TO FILENAME
1197	if (( maxcycle > 0 ))
1198	then
1199	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1200	then
1201	filename=${filename}.$maxcycle.${extin[$i]}
1202	else
1203	filename=${filename}.$maxcycle
1204	fi
1205	else
1206	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1207	then
1208	filename=${filename}.${extin[$i]}
1209	fi
1210	fi
1211
1212	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1213	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1214	absnamein[$i]=$filename
1215	if (( maxcycle > 0 ))
1216	then
1217	if [[ "${actionin[$i]}" = di ]]
1218	then
1219	frelin[$i]=${endin[$i]}.$maxcycle
1220	else
1221	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1222	fi
1223	else
1224	if [[ "${actionin[$i]}" = di ]]
1225	then
1226	frelin[$i]=${endin[$i]}
1227	else
1228	frelin[$i]=${afname}${endin[$i]}
1229	fi
1230	fi
1231
1232	fi
1233	done
1234
1235	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1236	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1237	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1238	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1239	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1240	# REMOTE HOST)
1241	(( i = 0 ))
1242	while (( i < iout ))
1243	do
1244	(( i = i + 1 ))
1245	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1246	then
1247	if [[ "${actionout[$i]}" = tr ]]
1248	then
1249	actionout[$i]=""
1250	elif [[ "${actionout[$i]}" = trpe ]]
1251	then
1252	actionout[$i]=pe
1253	elif [[ "${actionout[$i]}" = tra ]]
1254	then
1255	actionout[$i]=a
1256	fi
1257	(( maxcycle = 0 ))
1258	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1259	eval catalogname=${pathout[$i]}
1260	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1261	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1262	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1263	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1264	then
1265
1266	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1267	if cat /dev/null > $filename
1268	then
1269	rm $filename
1270	else
1271
1272	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1273	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1274	if [[ ! -d $catalogname ]]
1275	then
1276	if mkdir -p $catalogname
1277	then
1278	printf "\n\n *** directory:"
1279	printf "\n $catalogname"
1280	printf "\n was created\n"
1281	else
1282	printf "\n\n +++ OUTPUT-file:"
1283	printf "\n $filename"
1284	printf "\n cannot be created, because directory does not exist"
1285	printf "\n and cannot be created either"
1286	printf "\n"
1287	locat=output ; exit
1288	fi 2>/dev/null
1289	else
1290	printf "\n\n +++ OUTPUT-file:"
1291	printf "\n $filename"
1292	printf "\n cannot be created, although directory exists"
1293	printf "\n"
1294	locat=output ; exit
1295	fi
1296	fi 2>/dev/null
1297	else
1298
1299	# DETERMINE THE CYCLE NUMBER
1300	ls -1 -d $filename > filelist 2>/dev/null
1301	ls -1 -d $filename.* >> filelist 2>/dev/null
1302	while read zeile
1303	do
1304	cycle=$(echo $zeile \| cut -f2 -d".")
1305	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1306	then
1307	(( icycle = 1 ))
1308	else
1309	(( icycle = $cycle + 1 ))
1310	fi
1311	if (( icycle > maxcycle ))
1312	then
1313	(( maxcycle = icycle ))
1314	fi
1315	done <filelist
1316	rm filelist
1317	fi
1318
1319	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1320	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1321	if [[ "${actionout[$i]}" != a ]]
1322	then
1323	if (( maxcycle > 0 ))
1324	then
1325	filename=${filename}.$maxcycle
1326	if cat /dev/null > $filename
1327	then
1328	rm $filename
1329	else
1330	printf "\n +++ OUTPUT-file:"
1331	printf "\n $filename"
1332	printf "\n cannot be created"
1333	locat=output ; exit
1334	fi
1335	fi
1336	else
1337	(( maxcycle = maxcycle - 1 ))
1338	if (( maxcycle > 0 ))
1339	then
1340	filename=${filename}.$maxcycle
1341	fi
1342	fi
1343
1344	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1345	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1346	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1347	pathout[$i]=$filename
1348	if (( maxcycle > 0 ))
1349	then
1350	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1351	else
1352	frelout[$i]=${fname}${endout[$i]}
1353	fi
1354
1355	fi
1356	done
1357
1358
1359	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1360	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1361	then
1362	if [[ "$dvr_inc" = "" ]]
1363	then
1364	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1365	printf "\n This is required for the dvrp_graphics package.\n"
1366	locat=dvr; exit
1367	fi
1368	if [[ "$dvr_lib" = "" ]]
1369	then
1370	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1371	printf "\n This is required for the dvrp_graphics package.\n"
1372	locat=dvr; exit
1373	fi
1374	fi
1375
1376
1377	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1378	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1379	if [[ "$mainprog" = "" && "$executable" = "" ]]
1380	then
1381	printf "\n +++ neither main program nor executable defined"
1382	locat=source; exit
1383	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1384	then
1385	printf "\n +++ main program as well as executable defined"
1386	locat=source; exit
1387	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1388	then
1389	do_compile=false
1390	fi
1391
1392
1393	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1394	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1395	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1396	then
1397	rm -rf SOURCES_FOR_RUN_$fname
1398	mkdir SOURCES_FOR_RUN_$fname
1399	fi
1400
1401
1402	# COLLECT ALL ROUTINES TO BE COMPILED
1403	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1404	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1405	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1406	then
1407
1408	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1409
1410	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1411	then
1412
1413	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1414	source_list=""
1415	cd $source_path
1416
1417
1418	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1419	if [[ ! -d .svn ]]
1420	then
1421	printf "\n\n +++ source directory"
1422	printf "\n \"$source_path\" "
1423	printf "\n is not under control of \"subversion\"."
1424	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1425	fi
1426
1427
1428	# LIST ALL MODIFIED SOURCE CODE FILES
1429	Filenames=""
1430	svn status > tmp_mrun
1431	while read line
1432	do
1433	firstc=`echo $line \| cut -c1`
1434	if [[ $firstc = M \|\| $firstc = "?" ]]
1435	then
1436	Name=`echo "$line" \| cut -c8-`
1437	extension=`echo $Name \| cut -d. -f2`
1438	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1439	then
1440	Filenames="$Filenames "$Name
1441	fi
1442	fi
1443	done < tmp_mrun
1444
1445
1446	# COPY FILES TO SOURCES_FOR_RUN_...
1447	for dateiname in $Filenames
1448	do
1449	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1450	source_list=$source_list"$dateiname "
1451	done
1452
1453	cd - > /dev/null
1454
1455
1456	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1457	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1458	elif [[ "$source_list" != "" && $restart_run != true ]]
1459	then
1460
1461	cd $source_path
1462
1463	for filename in $source_list
1464	do
1465
1466	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1467	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1468	then
1469	printf "\n +++ source code file: $filename"
1470	printf "\n must not contain (\"/\") "
1471	locat=source; exit
1472	fi
1473
1474	if [[ ! -f $filename ]]
1475	then
1476	printf "\n +++ source code file: $filename"
1477	printf "\n does not exist"
1478	locat=source; exit
1479	else
1480	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1481	fi
1482
1483	done
1484
1485	cd - > /dev/null
1486
1487	fi
1488
1489
1490	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1491	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1492	if [[ $restart_run != true ]]
1493	then
1494
1495	if [[ ! -f "$source_path/$mainprog" ]]
1496	then
1497	printf "\n\n +++ main program: $mainprog"
1498	printf "\n does not exist in source directory"
1499	printf "\n \"$source_path\"\n"
1500	locat=source; exit
1501	else
1502	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1503	then
1504	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1505	source_list=${mainprog}" $source_list"
1506	fi
1507	fi
1508	fi
1509
1510
1511	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1512	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1513	if [[ "$restart_run" != true ]]
1514	then
1515	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1516	if [[ ! -f $makefile ]]
1517	then
1518	printf "\n +++ file \"$makefile\" does not exist"
1519	locat=make; exit
1520	else
1521	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1522	fi
1523	fi
1524
1525
1526	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1527	if [[ $restart_run != true && "$add_source_path" != "" ]]
1528	then
1529
1530	# DOES THE DIRECTORY EXIST?
1531	if [[ ! -d $add_source_path ]]
1532	then
1533	printf "\n\n +++ WARNING: additional source code directory"
1534	printf "\n \"$add_source_path\" "
1535	printf "\n does not exist or is not a directory."
1536	printf "\n No source code will be used from this directory!\n"
1537	add_source_path=""
1538	if [[ $silent == false ]]
1539	then
1540	sleep 3
1541	fi
1542	else
1543
1544	cd $add_source_path
1545	found=false
1546
1547	Names=$(ls -1 *.f90 2>&1)
1548	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1549	Names=$(ls -1 *.F90 2>&1)
1550	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1551	Names=$(ls -1 *.F 2>&1)
1552	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1553	Names=$(ls -1 *.f 2>&1)
1554	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1555	Names=$(ls -1 *.c 2>&1)
1556	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1557
1558	cd - > /dev/null
1559	cd SOURCES_FOR_RUN_$fname
1560
1561	# COPY MAKEFILE IF EXISTING
1562	if [[ -f $add_source_path/Makefile ]]
1563	then
1564	printf "\n\n *** user Makefile from directory"
1565	printf "\n \"$add_source_path\" is used \n"
1566	if [[ $silent == false ]]
1567	then
1568	sleep 1
1569	fi
1570	cp $add_source_path/Makefile .
1571	fi
1572
1573	for dateiname in $AddFilenames
1574	do
1575	if [[ -f $dateiname ]]
1576	then
1577	printf "\n +++ source code file \"$dateiname\" found in additional"
1578	printf "\n source code directory \"$add_source_path\" "
1579	printf "\n but was also given with option \"-s\" which means that it should be taken"
1580	printf "\n from directory \"$source_path\"."
1581	locat=source; exit
1582	fi
1583
1584	cp $add_source_path/$dateiname .
1585	source_list="$source_list $dateiname"
1586
1587	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1588	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1589	then
1590	printf "\n\n +++ user file \"$dateiname\" "
1591	printf "\n is not listed in Makefile \n"
1592	locat=source; exit
1593	else
1594
1595	if [[ $found = false ]]
1596	then
1597	found=true
1598	printf "\n\n *** following user file(s) added to the"
1599	printf " files to be translated:\n "
1600	fi
1601	printf "$dateiname "
1602	if [[ $silent == false ]]
1603	then
1604	sleep 0.5
1605	fi
1606
1607	fi
1608	done
1609	[[ $found = true ]] && printf "\n"
1610	cd - > /dev/null
1611	fi
1612	fi
1613
1614
1615	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1616	# TO THE LIST OF FILES TO BE COMPILED
1617	if [[ $restart_run != true && -n $package_list ]]
1618	then
1619
1620	cd $source_path
1621
1622	for package in $package_list
1623	do
1624
1625	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1626
1627	# DETERMINE FILES BELONGING TO THE PACKAGE
1628	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1629	# THE NAME OF THE DIRECTORY
1630	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1631
1632
1633	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1634	# IF THEY ARE NOT ALREADY PART OF THE LIST
1635	for source_list_name in $package_source_list
1636	do
1637	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1638	then
1639
1640	# ONLY TAKE FILES WITH VALID SUFFIX
1641	ending=`echo $source_list_name \| cut -f2 -d.`
1642	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1643	then
1644	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1645	source_list="$source_list $source_list_name"
1646	fi
1647	fi
1648	done
1649	done
1650
1651	cd - > /dev/null
1652	fi
1653
1654	fi # do_compile=true
1655
1656
1657	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1658	# AND SET PRE-PROCESSOR DIRECTIVES
1659	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1660	then
1661
1662	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1663	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1664	then
1665	cpp_options="${cpp_options},-D__ibm=__ibm"
1666	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1667	then
1668	cpp_options="$cpp_options -D__nec"
1669	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1670	then
1671	cpp_options="$cpp_options -D__lc"
1672	else
1673	cpp_options="$cpp_options -D__$localhost"
1674	fi
1675
1676	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1677	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1678	then
1679	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1680	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1681	else
1682	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1683	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1684	fi
1685
1686	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1687	if [[ -n $package_list ]]
1688	then
1689	for package in $package_list
1690	do
1691	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1692	then
1693	if [[ $package != "dvrp_graphics+1PE" ]]
1694	then
1695	cpp_options="${cpp_options},-D__$package=__$package"
1696	else
1697	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1698	export use_seperate_pe_for_dvrp_output=true
1699	fi
1700	else
1701	if [[ $package != "dvrp_graphics+1PE" ]]
1702	then
1703	cpp_options="$cpp_options -D__$package"
1704	else
1705	cpp_options="$cpp_options -D__dvrp_graphics"
1706	export use_seperate_pe_for_dvrp_output=true
1707	fi
1708	fi
1709	done
1710	fi
1711
1712	# SET DIRECTIVES GIVEN BY OPTION -D
1713	if [[ -n $cpp_opts ]]
1714	then
1715	for popts in $cpp_opts
1716	do
1717	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1718	then
1719	cpp_options="${cpp_options},-D__$popts=__$popts"
1720	else
1721	cpp_options="$cpp_options -D__$popts"
1722	fi
1723	done
1724	fi
1725
1726	else
1727
1728
1729	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1730	if [[ $do_remote = false ]]
1731	then
1732	if [[ ! -f $executable ]]
1733	then
1734	printf "\n +++ executable file: $executable"
1735	printf "\n does not exist"
1736	locat=executable; exit
1737	fi
1738	fi
1739	fi
1740
1741
1742	# DETERMINE THE JOB MODE
1743	if [[ "$ENVIRONMENT" = BATCH ]]
1744	then
1745	jobmo=BATCH
1746	else
1747	jobmo=INTERACTIVE
1748	fi
1749
1750
1751	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1752	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1753	then
1754	printf "\n +++ no interactive runs allowed on host \"$host\" "
1755	printf "\n please submit batch job using mrun option \"-b\" \n"
1756	locat=normal; exit
1757	fi
1758
1759
1760	# CHECK, IF USER DEFINED A COMPILER
1761	if [[ "$compiler_name" = "" ]]
1762	then
1763
1764	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1765	locat=compiler_name; exit
1766
1767	fi
1768
1769
1770	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1771	kennung=$RANDOM
1772	if [[ "$tmp_user_catalog" = "" ]]
1773	then
1774	if [[ $localhost = ibmh ]]
1775	then
1776	tmp_user_catalog=$SCRATCH
1777	elif [[ $localhost = nech ]]
1778	then
1779	tmp_user_catalog=$WRKSHR
1780	else
1781	tmp_user_catalog=/tmp
1782	fi
1783	fi
1784	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1785
1786
1787	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1788	if [[ "$tmp_data_catalog" = "" ]]
1789	then
1790	if [[ $localhost = nech ]]
1791	then
1792	tmp_data_catalog=$WRKSHR/mrun_restart_data
1793	else
1794	tmp_data_catalog=/tmp/mrun_restart_data
1795	fi
1796	fi
1797
1798
1799	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1800	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1801	then
1802	eval fopts=\"$fopts\"
1803	eval lopts=\"$lopts\"
1804	fi
1805
1806
1807
1808	# DETERMINE COMPILE- AND LINK-OPTIONS
1809	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1810	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1811	ROPTS="$ropts"
1812	# 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 ]]
1813	# then
1814	XOPT="-X $numprocs"
1815	# fi
1816
1817
1818
1819	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1820	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1821	done=false
1822	while [[ $done = false ]]
1823	do
1824	cputime=$cpumax
1825	if (( $cputime == 0 ))
1826	then
1827	if [[ $do_batch = true ]]
1828	then
1829	printf "\n +++ cpu-time is undefined"
1830	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1831	printf "\n >>> "
1832	read cputime 1>/dev/null 2>&1
1833	else
1834	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1835	fi
1836	else
1837	done=true
1838	fi
1839	cpumax=$cputime
1840	done
1841
1842	(( minuten = cputime / 60 ))
1843	(( sekunden = cputime - minuten * 60 ))
1844
1845
1846	# CHECK THE MEMORY DEMAND
1847	if [[ $do_batch = true ]]
1848	then
1849	done=false
1850	while [[ $done = false ]]
1851	do
1852	if (( memory == 0 ))
1853	then
1854	printf "\n +++ memory demand is undefined"
1855	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1856	printf "\n >>> "
1857	read memory 1>/dev/null 2>&1
1858	else
1859	done=true
1860	fi
1861	done
1862	fi
1863
1864
1865	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1866	if [[ $do_remote = true && -z $remote_username ]]
1867	then
1868	while [[ -z $remote_username ]]
1869	do
1870	printf "\n +++ username on remote host \"$host\" is undefined"
1871	printf "\n >>> Please type username:"
1872	printf "\n >>> "
1873	read remote_username
1874	done
1875	mc="$mc -u$remote_username"
1876	fi
1877
1878	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1879	if [[ "$login_init_cmd" != "" ]]
1880	then
1881	export init_cmds="${login_init_cmd};"
1882	fi
1883
1884
1885	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1886	if [[ "$modules" != "" ]]
1887	then
1888	if [[ $host = lctit ]]
1889	then
1890	export module_calls=". $modules"
1891	else
1892	export module_calls="module load ${modules};"
1893	fi
1894	fi
1895
1896
1897
1898	# OUTPUT OF THE MRUN-HEADER
1899	calltime=$(date)
1900	printf "\n"
1901	printf "#------------------------------------------------------------------------# \n"
1902	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1903	printf "\| \| \n"
1904	spalte1="called on:"; spalte2=$localhost_realname
1905	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1906	if [[ $do_remote = true ]]
1907	then
1908	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1909	else
1910	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1911	fi
1912	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1913	if [[ -n $numprocs ]]
1914	then
1915	if [[ $run_coupled_model = false ]]
1916	then
1917	spalte1="number of PEs:"; spalte2=$numprocs
1918	else
1919	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1920	fi
1921	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1922	fi
1923	if [[ -n $tasks_per_node ]]
1924	then
1925	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1926	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1927	if (( remaining_pes > 0 ))
1928	then
1929	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
1930	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1931	fi
1932	fi
1933	if [[ $maximum_parallel_io_streams != $numprocs ]]
1934	then
1935	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
1936	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1937	fi
1938	if [[ $use_openmp = true ]]
1939	then
1940	spalte1="threads per task:"; spalte2="$threads_per_task"
1941	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1942	fi
1943	printf "\| \| \n"
1944	if [[ $do_compile = true ]]
1945	then
1946	if [[ "$mopts" != "" ]]
1947	then
1948	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
1949	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1950	zeile=$(echo "$mopts" \| cut -c46-)
1951	while [[ "$zeile" != "" ]]
1952	do
1953	spalte1=""
1954	spalte2=$(echo "$zeile" \| cut -c-45)
1955	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1956	zeile=$(echo "$zeile" \| cut -c46-)
1957	done
1958	fi
1959
1960	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
1961	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1962	zeile=$(echo "$cpp_options" \| cut -c46-)
1963	while [[ "$zeile" != "" ]]
1964	do
1965	spalte1=""
1966	spalte2=$(echo "$zeile" \| cut -c-45)
1967	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1968	zeile=$(echo "$zeile" \| cut -c46-)
1969	done
1970
1971	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
1972	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1973	zeile=$(echo "$fopts" \| cut -c46-)
1974	while [[ "$zeile" != "" ]]
1975	do
1976	spalte1=""
1977	spalte2=$(echo "$zeile" \| cut -c-45)
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	zeile=$(echo "$zeile" \| cut -c46-)
1980	done
1981
1982	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
1983	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1984	zeile=$(echo "$lopts" \| cut -c46-)
1985	while [[ "$zeile" != "" ]]
1986	do
1987	spalte1=""
1988	spalte2=$(echo "$zeile" \| cut -c-45)
1989	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1990	zeile=$(echo "$zeile" \| cut -c46-)
1991	done
1992
1993	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1995	zeile=$(echo "$modules" \| cut -c46-)
1996	while [[ "$zeile" != "" ]]
1997	do
1998	spalte1=""
1999	spalte2=$(echo "$zeile" \| cut -c-45)
2000	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2001	zeile=$(echo "$zeile" \| cut -c46-)
2002	done
2003
2004	spalte1="main program:"; spalte2=$mainprog
2005	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2006	else
2007	spalte1=executable:; spalte2=$executable
2008	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2009	fi
2010	printf "\| \| \n"
2011	spalte1="base name of files:"; spalte2=$fname
2012	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2013	if [[ $fname != $afname ]]
2014	then
2015	spalte1="base name of input files:"; spalte2=$afname
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	fi
2018	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2019	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2020	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022
2023	if [[ "$ocean_file_appendix" = true ]]
2024	then
2025	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2026	fi
2027
2028	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2029	then
2030	spalte1="memory demand / PE":; spalte2="$memory MB"
2031	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2032	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	fi
2035
2036	if [[ $do_compile = true ]]
2037	then
2038	printf "\| \| \n"
2039	printf "\| Files to be compiled: \| \n"
2040	zeile=$source_list
2041	while [[ "$zeile" != "" ]]
2042	do
2043	linestart=$(echo $zeile \| cut -c-70)
2044	printf "\| %-70s \| \n" "$linestart"
2045	zeile=$(echo "$zeile" \| cut -c71-)
2046	done
2047	fi
2048	printf "#------------------------------------------------------------------------#"
2049
2050
2051
2052	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2053	if [[ $do_trace = true ]]
2054	then
2055	(( i = 0 ))
2056	while (( i < iin ))
2057	do
2058	(( i = i + 1 ))
2059	if (( i == 1 ))
2060	then
2061	printf "\n\n >>> INPUT-file assignments:\n"
2062	fi
2063	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2064	done
2065	(( i = 0 ))
2066	while (( i < iout ))
2067	do
2068	(( i = i + 1 ))
2069	if (( i == 1 ))
2070	then
2071	printf "\n\n >>> OUTPUT-file assignments:\n"
2072	fi
2073	printf "\n ${localout[$i]} : ${pathout[$i]}"
2074	done
2075	(( i = 0 ))
2076	while (( i < iic ))
2077	do
2078	(( i = i + 1 ))
2079	if (( i == 1 ))
2080	then
2081	printf "\n\n >>> INPUT-commands:\n"
2082	fi
2083	printf "\n ${in_command[$i]}"
2084	done
2085	(( i = 0 ))
2086	while (( i < ioc ))
2087	do
2088	(( i = i + 1 ))
2089	if (( i == 1 ))
2090	then
2091	printf "\n\n >>> OUTPUT-commands:\n"
2092	fi
2093	printf "\n ${out_command[$i]}"
2094	done
2095	fi
2096
2097
2098	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2099	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2100	then
2101	antwort=dummy
2102	printf "\n\n"
2103	printf " >>> everything o.k. (y/n) ? "
2104	while read antwort
2105	do
2106	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2107	then
2108	printf " >>> everything o.k. (y/n) ? "
2109	else
2110	break
2111	fi
2112	done
2113	if [[ $antwort = n \|\| $antwort = N ]]
2114	then
2115	locat=user_abort; (( iec = 0 )); exit
2116	fi
2117	if [[ $do_batch = true ]]
2118	then
2119	printf " >>> batch-job will be created and submitted"
2120	else
2121	printf " >>> MRUN will now continue to execute on this machine"
2122	fi
2123	fi
2124
2125
2126	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2127	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2128	check_depository="${working_directory}/trunk/UTIL"
2129	check_sources="${working_directory}/tmp_check_namelist_files"
2130	skip_check=false
2131
2132	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2133	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2134	then
2135	skip_check=true
2136	reason="run on remote host or parameter file check has not been compiled."
2137	fi
2138	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2139	then
2140	skip_check=true
2141	reason="parameter file check has not been compiled."
2142	fi
2143
2144	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2145	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2146	then
2147	skip_check=true
2148	reason="serial run."
2149	fi
2150
2151	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2152	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2153	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2154	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2155	if [[ $check_namelist_files == false ]]
2156	then
2157	skip_check=true
2158	reason="-z option set."
2159	fi
2160
2161	if [[ $fromhost != $localhost ]]
2162	then
2163	skip_check=true
2164	reason="submitting host is local host."
2165	fi
2166
2167	if [[ $run_coupled_model == true ]]
2168	then
2169	skip_check=true
2170	reason="coupled run."
2171	fi
2172
2173	if [[ $restart_run == true ]]
2174	then
2175	skip_check=true
2176	reason="restart run."
2177	fi
2178
2179	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2180	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2181	last_char=`echo $filename_input \| cut -c $last_char_int`
2182	if [[ "$last_char" == "f" ]]
2183	then
2184	skip_check=true
2185	reason="restart run."
2186	fi
2187
2188	if [[ $skip_check == false ]]
2189	then
2190	tmp_check=${working_directory}/tmp_check
2191
2192	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2193	# NOT NECESSARILY REQUIRED
2194	line=""
2195	found=false
2196	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2197	while read line1
2198	do
2199	line="$line1"
2200	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2201	then
2202	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2203	found=true
2204	fi
2205	done < $tmp_check
2206
2207	if [[ $found = false ]]
2208	then
2209	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2210	fi
2211
2212	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2213	# NOT NECESSARILY REQUIRED
2214	line=""
2215	found=false
2216	grep "NUDGING_DATA" $config_file > $tmp_check
2217	while read line1
2218	do
2219	line="$line1"
2220	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2221	then
2222	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2223	found=true
2224	fi
2225	done < $tmp_check
2226
2227	if [[ $found = false ]]
2228	then
2229	printf "\n +++ no NUDGING list entry found in the configuration file."
2230	fi
2231
2232	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2233	# NOT NECESSARILY REQUIRED
2234	line=""
2235	found=false
2236	grep "LSF_DATA" $config_file > $tmp_check
2237	while read line1
2238	do
2239	line="$line1"
2240	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2241	then
2242	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2243	found=true
2244	fi
2245	done < $tmp_check
2246
2247	if [[ $found = false ]]
2248	then
2249	printf "\n +++ no LSF list entry found in the configuration file."
2250	fi
2251
2252	rm -rf ${working_directory}/tmp_check
2253
2254	# CHECK IF THE P3DF FILE MUST BE CHECKED
2255	for item in $input_list
2256	do
2257	if [[ "$item" == "restart" ]]
2258	then
2259	check_restart=1
2260	else
2261	check_restart=0
2262	fi
2263	done
2264
2265	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2266	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2267	then
2268	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2269	locat=check_namelist; exit
2270	fi
2271
2272	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2273	if [[ $check_restart == 1 ]]
2274	then
2275
2276	filenamef="${filename_input}f"
2277	if [[ ! -f $filenamef ]]
2278	then
2279	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2280	check_restart=0
2281	answer=dummy
2282	printf "\n\n"
2283
2284	if [[ $silent == false ]]
2285	then
2286	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2287	do
2288	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2289	read answer
2290	done
2291	if [[ $answer = a \|\| $answer = A ]]
2292	then
2293	printf "\n +++ Aborting...."
2294	locat=normal; exit
2295	fi
2296	fi
2297	else
2298	check_restart=1
2299	fi
2300	fi
2301
2302	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2303	mkdir $check_sources
2304	cd $check_sources
2305
2306
2307	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2308	if [[ -d $add_source_path ]]
2309	then
2310	printf "\n\n *** copying files from $check_depository"
2311	cp $check_depository/check_namelist_files.tar ./
2312
2313	printf "\n\n *** untar of makefile and source files in $check_sources"
2314	tar -xf check_namelist_files.tar > /dev/null 2>&1
2315
2316	printf "\n\n *** adding user code."
2317	cp $add_source_path/* ./
2318	touch check_namelist_files.f90
2319
2320	# GET COMPILER OPTIONS AND PERFORM MAKE
2321	printf "\n\n *** compiling code if necessary...\n"
2322
2323	# workaround for batch jobs on local machine (lcxe6)
2324	if [[ $do_batch == true && $do_remote == false ]]
2325	then
2326	eval $init_cmds
2327	fi
2328
2329	# GET CHECK OPTIONS
2330	line=""
2331	found=false
2332
2333	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2334
2335	while read line1
2336	do
2337
2338	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2339	then
2340	line="$line1"
2341	fi
2342
2343	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2344	then
2345	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2346	line="$line "
2347	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'`
2348	found=true
2349	fi
2350
2351	done < $tmp_check
2352	copts_check="$copts_check -D__check -D__parallel"
2353
2354	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2355
2356	# GET MAKE OUTPUT
2357	if [[ $? != 0 ]]
2358	then
2359	printf "\n +++ error during make."
2360	answer=dummy
2361	printf "\n\n"
2362	if [[ $silent == false ]]
2363	then
2364	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2365	do
2366	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2367	read answer
2368	done
2369	if [[ $answer = a \|\| $answer = A ]]
2370	then
2371	printf "\n +++ Aborting..."
2372	rm -rf $check_sources
2373	locat=normal; exit
2374	else
2375	skip_check=true
2376	fi
2377	else
2378	skip_check=true
2379	fi
2380	fi
2381	else
2382	cp $PALM_BIN/check_namelist_files.x ./
2383	fi
2384
2385	cp $filename_input ./PARIN
2386	if [[ $check_restart == 1 ]]
2387	then
2388	cp $filenamef ./PARINF
2389	fi
2390
2391	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2392	then
2393	printf "\n *** adding topography data"
2394	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2395
2396	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2397	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2398	# WHICH REQUIRE SUFFICIENT MEMORY
2399	ulimit -s unlimited
2400	fi
2401
2402	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2403	then
2404	printf "\n *** adding nudging data"
2405	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2406	fi
2407
2408	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2409	then
2410	printf "\n *** adding large scale forcing data"
2411	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2412	fi
2413
2414	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2415	cat > ENVPAR << %%END%%
2416	&envpar run_identifier = '$fname', host = '$host',
2417	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2418	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2419	maximum_cpu_time_allowed = ${cpumax}.,
2420	revision = '$global_revision',
2421	local_dvrserver_running = $local_dvrserver_running /
2422
2423	%%END%%
2424
2425	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2426	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2427	then
2428	printf "\n +++ WARNING: check_namelist_files.x not found."
2429	answer=dummy
2430	printf "\n\n"
2431
2432	if [[ $silent == false ]]
2433	then
2434	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2435	do
2436	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2437	read answer
2438	done
2439	if [[ $answer = a \|\| $answer = A ]]
2440	then
2441	printf "\n +++ Aborting..."
2442	rm -rf $check_sources
2443	locat=normal; exit
2444	else
2445	printf "\n *** skipping parameter file check."
2446	fi
2447	fi
2448
2449	elif [[ $skip_check == false ]]
2450	then
2451	# STARTING THE PARAMETER FILE CHECK
2452	printf "\n\n *** starting parameter file check..."
2453
2454	# CHECKING THE P3D FILE
2455	printf "\n\n (1) checking $filename_input"
2456	echo "$numprocs 0 0" > VARIN
2457	errors=`./check_namelist_files.x < VARIN 2>&1`
2458
2459	check_error=false
2460	if [[ "$errors" == "" ]]
2461	then
2462	printf " --> o.k."
2463	else
2464	printf " --> failed."
2465	check_error=true
2466	printf "\n\n $errors"
2467	fi
2468
2469	# CHECKING THE PD3F FILE IF NECESSARY
2470	if [[ $check_restart == 1 && $check_error == false ]]
2471	then
2472	printf "\n\n (2) checking $filenamef"
2473
2474	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2475	# IN &INIPAR LIST
2476	found=false
2477	cat PARINF \| while read line
2478	do
2479	line=$(echo $line\|sed 's/ //g')
2480	if [[ $line == "&inipar" ]]
2481	then
2482	start_search=true
2483	fi
2484
2485	if [[ $start_search == true ]]
2486	then
2487	if [[ $line == "initializing_actions='read_restart_data'" ]]
2488	then
2489	found=true
2490	break
2491	fi
2492	fi
2493
2494	if [[ $line == "/" ]]
2495	then
2496	start_search=false
2497	fi
2498
2499	done
2500
2501	if [[ $found = false ]]
2502	then
2503	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2504	printf "\n in &inipar list in $fname$p3df_suffix."
2505	rm -rf $check_sources
2506	locat=check_namelist; exit
2507	fi
2508
2509	# READ max_user_pr FROM FILES
2510	if [[ -f parin_for_check ]]
2511	then
2512	read max_pr_user < parin_for_check
2513	else
2514	max_user_pr=0
2515	fi
2516
2517	echo "$numprocs 1 $max_pr_user" > VARIN
2518	errors=`./check_namelist_files.x < VARIN 2>&1`
2519
2520	if [[ "$errors" == "" ]]
2521	then
2522	printf " --> o.k."
2523	else
2524	printf " --> failed."
2525	check_error=true
2526	printf "\n\n $errors"
2527	fi
2528	fi
2529
2530	# REPORT ERRORS AND CONTINUE/EXIT
2531	if [[ $check_error == true ]]
2532	then
2533	printf "\n +++ errors found in the parameter file!\n"
2534	answer=dummy
2535	printf "\n\n"
2536
2537	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2538	do
2539	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2540	read answer
2541	done
2542
2543	if [[ $answer = a \|\| $answer = A ]]
2544	then
2545	printf "\n +++ Aborting..."
2546	rm -rf $check_sources
2547	locat=normal; exit
2548	fi
2549	else
2550	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2551	fi
2552	rm -rf $check_sources
2553	fi
2554	else
2555	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2556	fi
2557
2558	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2559	rm -rf $check_sources
2560	cd $working_directory
2561
2562
2563	# DETERMINE PATH FOR MAKE DEPOSITORY
2564	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2565	then
2566
2567	line=""
2568	grep "%depository_path" $config_file > tmp_mrun
2569	while read line
2570	do
2571	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2572	then
2573	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2574	then
2575	global_depository_path=`echo $line \| cut -d" " -s -f2`
2576	fi
2577	fi
2578	done < tmp_mrun
2579
2580	line=""
2581	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2582	while read line
2583	do
2584	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2585	then
2586	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2587	then
2588	local_depository_path=`echo $line \| cut -d" " -s -f2`
2589	fi
2590	fi
2591	done < tmp_mrun
2592
2593	if [[ "$local_depository_path" = "" ]]
2594	then
2595	if [[ "$global_depository_path" != "" ]]
2596	then
2597	local_depository_path=$global_depository_path
2598	else
2599	printf "\n\n +++ no depository path found in configuration file"
2600	printf "\n for local host \"$localhost\" "
2601	printf "\n please set \"\%depository_path\" in configuration file\n"
2602	locat=config_file; exit
2603	fi
2604	fi
2605	eval local_depository_path=$local_depository_path
2606	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2607	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2608
2609
2610	basename=`echo $mainprog \| cut -f1 -d"."`
2611	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2612	if [[ ! -f $make_depository ]]
2613	then
2614	printf "\n"
2615	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2616	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2617	fi
2618
2619	fi
2620
2621
2622	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2623	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2624	if [[ $do_batch = false ]]
2625	then
2626
2627
2628	# CREATE THE TEMPORARY WORKING DIRECTORY
2629	mkdir -p $TEMPDIR
2630	chmod go+rx $TEMPDIR
2631	tmpcreate=true
2632
2633
2634	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2635	# INTO THE TEMPORARY WORKING DIRECTORY
2636	if [[ $do_compile = true ]]
2637	then
2638
2639	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2640	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2641	if [[ $localhost = nech ]]
2642	then
2643	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2644	if mkdir -p $TEMPDIR_COMPILE
2645	then
2646	printf "\n *** \"$TEMPDIR_COMPILE\" "
2647	printf "\n is generated as temporary directory for cross compiling\n"
2648	else
2649	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2650	printf "\n needed for cross compilation failed"
2651	locat=compile
2652	exit
2653	fi
2654	else
2655	TEMPDIR_COMPILE=$TEMPDIR
2656	fi
2657
2658	cp $make_depository $TEMPDIR_COMPILE
2659	cd $TEMPDIR_COMPILE
2660	tar -xf $make_depository > /dev/null 2>&1
2661	cd - > /dev/null
2662
2663	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2664	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2665	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2666	then
2667	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2668	else
2669	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2670	fi
2671
2672	else
2673
2674	cp $executable ${TEMPDIR}/a.out
2675
2676	fi
2677
2678
2679	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2680	cd $TEMPDIR
2681	printf "\n *** changed to temporary directory: $TEMPDIR"
2682
2683
2684	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2685	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2686	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2687	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2688	(( i = 0 ))
2689	while (( i < iout ))
2690	do
2691	(( i = i + 1 ))
2692	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2693	then
2694	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2695	else
2696	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2697	fi
2698	done
2699
2700
2701	# IF REQUIRED, START WITH COMPILING
2702	if [[ $do_compile = true ]]
2703	then
2704
2705
2706	if [[ -f a.out ]]
2707	then
2708
2709	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2710	printf "\n\n\n *** executable a.out found"
2711	printf "\n no compilation required \n"
2712
2713	else
2714
2715	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2716	printf "\n\n\n *** compilation starts \n$dashes\n"
2717	printf " *** compilation with make using following options:\n"
2718	printf " make depository: $make_depository"
2719	if [[ "$mopts" != "" ]]
2720	then
2721	printf " make options: $mopts\n"
2722	fi
2723	printf " compilername: $compiler_name\n"
2724	printf " compiler options: $fopts\n"
2725	printf " preprocessor directives: $cpp_options \n"
2726	printf " linker options: $lopts \n"
2727	if [[ "$modules" != "" ]]
2728	then
2729	printf " modules to be load: $modules \n"
2730	fi
2731	printf " source code files: $source_list \n"
2732
2733	if [[ $localhost = nech ]]
2734	then
2735	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\" "
2736	cp $TEMPDIR_COMPILE/a.out .
2737	[[ $? != 0 ]] && compile_error=true
2738	rm -rf $TEMPDIR_COMPILE
2739	elif [[ $localhost = ibmh ]]
2740	then
2741	printf " compiler is called via ssh on \"plogin1\" \n"
2742	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\" "
2743	[[ ! -f a.out ]] && compile_error=true
2744	continue # STATUS=1, IF a.out EXISTS
2745	elif [[ $localhost = lcflow ]]
2746	then
2747	printf " compiler is called via ssh on \"flow\" \n"
2748	/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\" "
2749	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2750	[[ "$check_for_file" = "" ]] && compile_error=true
2751	continue # STATUS=1, IF a.out EXISTS
2752	elif [[ $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2753	then
2754	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2755	else
2756	[[ "$init_cmds" != "" ]] && eval $init_cmds
2757	[[ "$module_calls" != "" ]] && eval $module_calls
2758	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2759	fi
2760
2761	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2762	then
2763	printf "\n +++ error occured while compiling or linking"
2764	locat=compile
2765
2766	exit
2767	else
2768	printf "$dashes\n *** compilation finished \n"
2769	fi
2770
2771	fi
2772
2773	fi
2774
2775
2776	# PROVIDE THE INPUT FILES
2777	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2778	(( i = 0 ))
2779	while (( i < iin ))
2780	do
2781	(( i = i + 1 ))
2782	if (( i == 1 ))
2783	then
2784	printf "\n\n *** providing INPUT-files:\n$dashes"
2785	fi
2786
2787
2788	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2789	if [[ "${transin[$i]}" = unavailable ]]
2790	then
2791	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2792	then
2793	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2794	printf "\n is not available!"
2795	else
2796	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2797	printf "\n is not available!"
2798	fi
2799	continue
2800	fi
2801
2802	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2803	files_for_pes=false; datentyp=file
2804	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2805	then
2806	files_for_pes=true; datentyp=directory
2807	actionin[$i]=""
2808	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2809	then
2810	actionin[$i]=""
2811	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2812	then
2813	files_for_pes=true; datentyp=directory
2814	actionin[$i]="ar"
2815	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2816	then
2817	actionin[$i]="ar"
2818	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2819	then
2820	files_for_pes=true; datentyp=directory
2821	actionin[$i]="fl"
2822	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2823	then
2824	actionin[$i]="fl"
2825	fi
2826
2827	if [[ $files_for_pes = true ]]
2828	then
2829	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2830	else
2831	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2832	fi
2833
2834	# INPUT-FILE FOR A RESTART RUN.
2835	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2836	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2837	if [[ "${actionin[$i]}" = fl ]]
2838	then
2839	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2840	if [[ $files_for_pes = false ]]
2841	then
2842	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2843	then
2844	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2845	got_tmp[$i]=true
2846	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2847	then
2848	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2849	printf "\n *** trying to use backup copy in \"$WORK\" "
2850	cp $WORK/${frelin[$i]} ${localin[$i]}
2851	else
2852	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2853	printf "\n or \"$tmp_data_catalog\" does not exist!"
2854	printf "\n *** trying to get copy from archive"
2855	actionin[$i]=ar
2856	fi
2857	else
2858	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2859	then
2860	mkdir ${localin[$i]}
2861	cd $tmp_data_catalog/${frelin[$i]}
2862	for file in $(ls *)
2863	do
2864	ln $file $TEMPDIR/${localin[$i]}
2865	done
2866	cd $TEMPDIR
2867	got_tmp[$i]=true
2868	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2869	then
2870	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2871	printf "\n *** trying to use backup copy in \"$WORK\" "
2872	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2873	else
2874	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2875	printf "\n or \"$tmp_data_catalog\" does not exist!"
2876	printf "\n *** trying to get copy from archive"
2877	actionin[$i]=ar
2878	fi
2879	fi
2880	fi
2881
2882
2883	# FILE IS STORED ON THE ARCHIVE SYSTEM
2884	if [[ "${actionin[$i]}" = ar ]]
2885	then
2886
2887	if [[ $files_for_pes = false ]]
2888	then
2889	printf "\n file will be restored from archive-system ($archive_system)!"
2890	else
2891	printf "\n directory will be restored from archive-system ($archive_system)!"
2892	fi
2893
2894	file_restored=false
2895
2896	if [[ $archive_system = asterix ]]
2897	then
2898	do_stagein=true
2899	(( stagein_anz = 0 ))
2900	while [[ $do_stagein = true ]]
2901	do
2902	if [[ $files_for_pes = false ]]
2903	then
2904	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2905	else
2906	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2907	fi
2908	cat STAGEIN_OUTPUT
2909	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2910	then
2911	file_restored=true
2912	do_stagein=false
2913	else
2914	(( stagein_anz = stagein_anz + 1 ))
2915	if (( stagein_anz == 10 ))
2916	then
2917	printf "\n +++ stagein stoped after 10 tries"
2918	locat=stage
2919	exit
2920	fi
2921	printf "\n +++ restoring from archive failed, trying again:"
2922	sleep 900
2923	fi
2924	done
2925	elif [[ $archive_system = DMF ]]
2926	then
2927	if [[ $files_for_pes = false ]]
2928	then
2929	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2930	locat=DMF
2931	exit
2932	else
2933	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2934	cp -r $ARCHIVE/${frelin[$i]} $PWD
2935	file_restored=true
2936	fi
2937	elif [[ $archive_system = tivoli ]]
2938	then
2939	if [[ $files_for_pes = false ]]
2940	then
2941	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2942	else
2943	(( inode = 0 ))
2944	while (( inode < nodes ))
2945	do
2946	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2947	(( inode = inode + 1 ))
2948	done
2949	fi
2950	file_restored=true
2951	elif [[ $archive_system = ut ]]
2952	then
2953	if [[ $files_for_pes = false ]]
2954	then
2955	cp $UT/${frelin[$i]} .
2956	else
2957	(( inode = 0 ))
2958	while (( inode < nodes ))
2959	do
2960	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2961	(( inode = inode + 1 ))
2962	done
2963	fi
2964	file_restored=true
2965	else
2966	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2967	locat=rearchive
2968	exit
2969	fi
2970
2971	if [[ $file_restored = true ]]
2972	then
2973
2974	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2975	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2976	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2977	if [[ $files_for_pes = false ]]
2978	then
2979	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2980	else
2981	mkdir $tmp_data_catalog/${frelin[$i]}
2982	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2983	fi
2984	got_tmp[$i]=true
2985
2986	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2987	mv ${frelin[$i]} ${localin[$i]}
2988
2989	fi
2990	fi
2991
2992
2993	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2994	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2995	then
2996
2997	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2998	then
2999
3000	# FILE COPIES ARE PROVIDED FOR ALL CORES
3001	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3002	printf "\n file will be provided for $numprocs processors"
3003	mkdir ${localin[$i]}
3004	ival=$numprocs
3005	(( ii = 0 ))
3006	while (( ii <= ival-1 ))
3007	do
3008	if (( ii < 10 ))
3009	then
3010	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3011	elif (( ii < 100 ))
3012	then
3013	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3014	elif (( ii < 1000 ))
3015	then
3016	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3017	else
3018	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3019	fi
3020	(( ii = ii + 1 ))
3021	done
3022
3023	else
3024
3025	if [[ $files_for_pes = true ]]
3026	then
3027
3028	# PROVIDE FILES FOR EACH CORE
3029	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3030	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3031	printf "\n providing $numprocs files for the respective processors"
3032	mkdir ${localin[$i]}
3033	if [[ $link_local_input = true ]]
3034	then
3035	printf " using ln -f\n"
3036	cd ${absnamein[$i]}
3037	for file in $(ls *)
3038	do
3039	ln -f $file ${localin[$i]}
3040	done
3041	cd $TEMPDIR
3042	fi
3043
3044	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3045	if [[ ! -f "${localin[$i]}/_0000" ]]
3046	then
3047	if [[ $link_local_input = true ]]
3048	then
3049	printf " ln failed for .../_0000, using cp...\n"
3050	fi
3051	cp -r ${absnamein[$i]}/* ${localin[$i]}
3052	fi
3053
3054	else
3055
3056	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3057	if [[ $link_local_input = true ]]
3058	then
3059	printf " using ln -f\n"
3060	ln -f ${absnamein[$i]} ${localin[$i]}
3061	fi
3062	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3063	if [[ ! -f "${localin[$i]}" ]]
3064	then
3065	if [[ $link_local_input = true ]]
3066	then
3067	printf " ln failed, using cp...\n"
3068	fi
3069	cp ${absnamein[$i]} ${localin[$i]}
3070	fi
3071	fi
3072	fi
3073	fi
3074
3075	done
3076	if (( i != 0 ))
3077	then
3078	printf "\n$dashes\n *** all INPUT-files provided \n"
3079	fi
3080
3081
3082	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3083	(( i = 0 ))
3084	while (( i < iic ))
3085	do
3086	(( i = i + 1 ))
3087	if (( i == 1 ))
3088	then
3089	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3090	fi
3091	printf "\n >>> ${in_command[$i]}"
3092	eval ${in_command[$i]}
3093	if (( i == iic ))
3094	then
3095	printf "\n$dashes\n"
3096	fi
3097	done
3098
3099
3100	# SET THE REMAINING CPU-TIME
3101	cpurest=${cpumax}.
3102
3103
3104	# START DVR STREAMING SERVER
3105	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3106	then
3107	if [[ "$dvr_server" != "" ]]
3108	then
3109
3110	printf "\n\n *** preparing the dvr streaming server configuration file"
3111
3112	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3113	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3114	if [[ "$running_dvrserver_id" != "" ]]
3115	then
3116
3117	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3118	printf "\n This server is used instead starting a new one!"
3119	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3120
3121	else
3122
3123	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3124	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3125	then
3126	cp ${PALM_BIN}/.dvrserver.config .
3127
3128	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3129	user_id=`id -u`
3130	group_id=`id -g`
3131
3132	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3133	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3134	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3135	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3136	mv .dvrserver.3 .dvrserver.config
3137	rm .dvrserver.1 .dvrserver.2
3138
3139	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3140	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3141	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3142	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3143	local_dvrserver_running=.TRUE.
3144	else
3145	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3146	printf "\n \"$PALM_BIN\" "
3147	locat=dvr
3148	exit
3149	fi
3150
3151	fi
3152
3153	else
3154	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3155	fi
3156	fi
3157
3158
3159	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3160	# (FILE ENVPAR WILL BE READ BY PALM)
3161	cat > ENVPAR << %%END%%
3162	&envpar run_identifier = '$fname', host = '$localhost',
3163	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3164	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3165	maximum_cpu_time_allowed = ${cpumax}.,
3166	revision = '$global_revision',
3167	local_dvrserver_running = $local_dvrserver_running /
3168
3169	%%END%%
3170
3171
3172	# STARTING THE EXECUTABLE
3173	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3174	PATH=$PATH:$TEMPDIR
3175
3176	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3177	if [[ "$mpi_debug" = true ]]
3178	then
3179	export MPI_CHECK_ARGS=1
3180	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3181	fi
3182
3183	if [[ "$totalview" = true ]]
3184	then
3185	printf "\n *** totalview debugger will be used"
3186	tv_opt="-tv"
3187	else
3188	tv_opt=""
3189	fi
3190
3191	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3192	then
3193	if [[ "$ENVIRONMENT" = BATCH ]]
3194	then
3195	continue
3196	fi
3197	if [[ $localhost = ibmh ]]
3198	then
3199
3200	# SETUP THE IBM MPI ENVIRONMENT
3201	export MP_SHARED_MEMORY=yes
3202	export AIXTHREADS_SCOPE=S
3203	export OMP_NUM_THREADS=$threads_per_task
3204	export AUTHSTATE=files
3205	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3206
3207	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3208	export MP_ADAPTER_USE=shared
3209	export MP_CPU_USE=multiple
3210	export MP_TIMEOUT=1200
3211
3212	unset MP_TASK_AFFINITY
3213
3214	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3215	#(( ii = 1 ))
3216	#while (( ii <= $numprocs ))
3217	#do
3218	# echo $localhost_realname >> hostfile
3219	# (( ii = ii + 1 ))
3220	#done
3221	#export MP_HOSTFILE=hostfile
3222
3223	if [[ "$LOADLBATCH" = yes ]]
3224	then
3225	totalview poe a.out $ROPTS
3226	else
3227	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3228	export TVDSVRLAUNCHCMD=ssh
3229	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3230	fi
3231
3232	# END DEBUG MODE
3233	else
3234
3235	# NORMAL EXECUTION
3236	if [[ -n $numprocs ]]
3237	then
3238
3239	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3240	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3241	then
3242
3243	# SETUP THE IBM MPI ENVIRONMENT
3244	if [[ $host != ibmh && $host != ibmkisti ]]
3245	then
3246	export MP_SHARED_MEMORY=yes
3247	export AIXTHREAD_SCOPE=S
3248	export OMP_NUM_THREADS=$threads_per_task
3249	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3250	export AUTHSTATE=files
3251	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3252	# export MP_PRINTENV=yes
3253
3254	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3255	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3256	export MP_WAIT_MODE=poll
3257	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3258	fi
3259
3260	if [[ $host = ibmkisti ]]
3261	then
3262	export LANG=en_US
3263	export MP_SHARED_MEMORY=yes
3264	if [[ $threads_per_task = 1 ]]
3265	then
3266	export MP_SINGLE_THREAD=yes
3267	export MEMORY_AFFINITY=MCM
3268	else
3269	export OMP_NUM_THREADS=$threads_per_task
3270	fi
3271	fi
3272
3273	if [[ "$LOADLBATCH" = yes ]]
3274	then
3275	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3276	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3277	then
3278	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3279	else
3280	if [[ $run_coupled_model = false ]]
3281	then
3282	if [[ "$ocean_file_appendix" = true ]]
3283	then
3284	echo "precursor_ocean" > runfile_atmos
3285	else
3286	echo "precursor_atmos" > runfile_atmos
3287	fi
3288	else
3289	(( iia = $numprocs_atmos / $threads_per_task ))
3290	(( iio = $numprocs_ocean / $threads_per_task ))
3291	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3292	printf "\n using $coupled_mode coupling"
3293	printf "\n\n"
3294	echo "coupled_run $iia $iio" > runfile_atmos
3295	fi
3296	poe ./a.out $ROPTS < runfile_atmos
3297	fi
3298	else
3299	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3300	then
3301	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3302	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3303	then
3304	if [[ -f $hostfile ]]
3305	then
3306	cp $hostfile hostfile
3307	else
3308	(( ii = 1 ))
3309	while (( ii <= $numprocs ))
3310	do
3311	echo $localhost_realname >> hostfile
3312	(( ii = ii + 1 ))
3313	done
3314	fi
3315	export MP_HOSTFILE=hostfile
3316	if [[ $run_coupled_model = false ]]
3317	then
3318	if [[ "$ocean_file_appendix" = true ]]
3319	then
3320	echo "precursor_ocean" > runfile_atmos
3321	else
3322	echo "precursor_atmos" > runfile_atmos
3323	fi
3324	else
3325	(( iia = $numprocs_atmos / $threads_per_task ))
3326	(( iio = $numprocs_ocean / $threads_per_task ))
3327	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3328	printf "\n using $coupled_mode coupling"
3329	printf "\n\n"
3330	echo "coupled_run $iia $iio" > runfile_atmos
3331	fi
3332
3333	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3334
3335	else
3336	if [[ "$host_file" = "" ]]
3337	then
3338	printf "\n +++ no hostfile given in configuration file"
3339	locat=config_file
3340	exit
3341	else
3342	eval host_file=$host_file
3343	fi
3344	export MP_HOSTFILE=$host_file
3345	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3346	fi
3347	fi
3348	elif [[ $host = nech ]]
3349	then
3350	(( ii = nodes ))
3351	if [[ $ii = 1 ]]
3352	then
3353	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3354	export MPIPROGINF=YES
3355	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3356	echo "*** execution on single node with mpirun"
3357	mpirun -np $numprocs ./a.out $ROPTS
3358	else
3359	(( i = 0 ))
3360	while (( i < ii ))
3361	do
3362	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3363	(( i = i + 1 ))
3364	done
3365
3366	echo "#!/bin/sh" > mpi_exec_shell
3367	echo " " >> mpi_exec_shell
3368	echo "set -u" >> mpi_exec_shell
3369	echo "F_ERRCNT=0" >> mpi_exec_shell
3370	echo "MPIPROGINV=YES" >> mpi_exec_shell
3371	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3372	echo "cpurest=$cpurest" >> mpi_exec_shell
3373	echo "fname=$fname" >> mpi_exec_shell
3374	echo "localhost=$localhost" >> mpi_exec_shell
3375	echo "return_addres=$return_addres" >> mpi_exec_shell
3376	echo "return_username=$return_username" >> mpi_exec_shell
3377	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3378	echo "write_binary=$write_binary" >> mpi_exec_shell
3379	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3380	echo " " >> mpi_exec_shell
3381	echo "export F_ERRCNT" >> mpi_exec_shell
3382	echo "export MPIPROGINV" >> mpi_exec_shell
3383	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3384	echo "export cpurest" >> mpi_exec_shell
3385	echo "export fname" >> mpi_exec_shell
3386	echo "export localhost" >> mpi_exec_shell
3387	echo "export return_addres" >> mpi_exec_shell
3388	echo "export return_username" >> mpi_exec_shell
3389	echo "export tasks_per_node" >> mpi_exec_shell
3390	echo "export write_binary" >> mpi_exec_shell
3391	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3392	echo " " >> mpi_exec_shell
3393	echo "exec ./a.out" >> mpi_exec_shell
3394
3395	chmod u+x mpi_exec_shell
3396	export MPIPROGINF=YES
3397	mpirun -f multinode_config &
3398	wait
3399
3400	fi
3401	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3402	then
3403
3404	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3405	# DOES NOT EXIST
3406	if [[ $host != lccrayb &&$host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3407	then
3408	if [[ -f $hostfile ]]
3409	then
3410	cp $hostfile hostfile
3411	(( ii = $numprocs / $threads_per_task ))
3412	else
3413	(( ii = 1 ))
3414	while (( ii <= $numprocs / $threads_per_task ))
3415	do
3416	echo $localhost_realname >> hostfile
3417	(( ii = ii + 1 ))
3418	done
3419	fi
3420	eval zeile=\"`head -n $ii hostfile`\"
3421	printf "\n *** running on: $zeile"
3422	fi
3423
3424	(( ii = $numprocs / $threads_per_task ))
3425	export OMP_NUM_THREADS=$threads_per_task
3426
3427	if [[ $threads_per_task != 1 ]]
3428	then
3429	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3430	# MAY ABORT
3431	ulimit -Ss unlimited
3432	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3433	fi
3434	if [[ $run_coupled_model = false ]]
3435	then
3436	if [[ "$ocean_file_appendix" = true ]]
3437	then
3438	echo "precursor_ocean" > runfile_atmos
3439	else
3440	echo "precursor_atmos" > runfile_atmos
3441	fi
3442	printf "\n\n"
3443
3444	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3445	then
3446	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3447	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3448	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3449	elif [[ $host = lccrayf ]]
3450	then
3451	aprun -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3452	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3453	then
3454	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3455	elif [[ $host = lcflow ]]
3456	then
3457	mpirun -bootstrap sge -np $ii -env I_MPI_FABRICS shm:ofa a.out < runfile_atmos $ROPTS
3458	elif [[ $host = lcsb ]]
3459	then
3460	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3461	elif [[ $host = lckiaps ]]
3462	then
3463	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3464	elif [[ $host = lckyu* ]]
3465	then
3466	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3467	else
3468	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3469	fi
3470	else
3471
3472	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3473	(( iia = $numprocs_atmos / $threads_per_task ))
3474	(( iio = $numprocs_ocean / $threads_per_task ))
3475	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3476	printf "\n using $coupled_mode coupling"
3477	printf "\n\n"
3478
3479	if [[ $coupled_mode = "mpi2" ]]
3480	then
3481	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3482	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3483
3484	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3485	then
3486
3487	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3488	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3489
3490	else
3491	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3492	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3493	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3494	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3495	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3496	fi
3497	wait
3498
3499	else
3500
3501	echo "coupled_run $iia $iio" > runfile_atmos
3502
3503	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3504	then
3505
3506	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3507
3508	elif [[ $host = lck \|\| $host = lckordi ]]
3509	then
3510
3511	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3512
3513	elif [[ $host = lckyu* ]]
3514	then
3515
3516	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3517
3518	fi
3519	wait
3520	fi
3521
3522	fi
3523
3524	elif [[ $host = lckyoto ]]
3525	then
3526	set -xv
3527	export P4_RSHCOMMAND=plesh
3528	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3529	if [[ "$ENVIRONMENT" = BATCH ]]
3530	then
3531	if [[ "$cond2" = fujitsu ]]
3532	then
3533	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3534	elif [[ "cond2" = pgi ]]
3535	then
3536	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3537	else
3538	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3539	fi
3540	else
3541	if [[ "$cond2" = "" ]]
3542	then
3543	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3544	else
3545	mpirun -np $numprocs ./a.out $ROPTS
3546	fi
3547	fi
3548	set +xv
3549
3550	elif [[ $host = lctit ]]
3551	then
3552	export OMP_NUM_THREADS=$threads_per_task
3553	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3554	if [[ "$threads_per_task" != 1 ]]
3555	then
3556	export MV2_ENABLE_AFFINITY=0
3557	fi
3558	echo "----- PBS_NODEFILE content:"
3559	cat $PBS_NODEFILE
3560	echo "-----"
3561	(( ii = $numprocs / $threads_per_task ))
3562	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3563	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3564	else
3565	mpprun -n $numprocs a.out $ROPTS
3566	fi
3567	else
3568	a.out $ROPTS
3569	fi
3570	fi
3571
3572	if [[ $? != 0 ]]
3573	then
3574
3575	# ABORT IN CASE OF RUNTIME ERRORS
3576	printf "\n +++ runtime error occured"
3577	locat=execution
3578	exit
3579
3580	else
3581
3582	printf "\n$dashes\n *** execution finished \n"
3583
3584	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3585	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3586	if [[ "$dvrserver_id" != "" ]]
3587	then
3588	kill $dvrserver_id
3589	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3590
3591	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3592	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3593	if [[ -d DATA_DVR ]]
3594	then
3595
3596	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3597	# DIRECTORY
3598	cp .dvrserver.config DATA_DVR
3599
3600	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3601	# SEQUENCE MODE DATA TOO)
3602	process_dvr_output -d DATA_DVR -f $fname -s
3603
3604	else
3605
3606	# PROCESS THE LOCAL OUTPUT
3607	process_dvr_output -l -d DATA_DVR -f $fname
3608
3609	fi
3610
3611	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3612	then
3613
3614	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3615	process_dvr_output -l -d DATA_DVR -f $fname
3616
3617	fi
3618	fi
3619
3620
3621
3622	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3623	# BY EACH CORE INTO ONE FILE
3624	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3625	then
3626	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3627	printf "\n 2d- and/or 3d-data may be incomplete!"
3628	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3629	elif [[ "$combine_plot_fields" == true ]]
3630	then
3631	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3632	then
3633	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3634	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3635	else
3636	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3637	combine_plot_fields${block}.x
3638	fi
3639	else
3640
3641	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3642	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3643	# ??? koennen wir das streichen ???
3644	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3645	fi
3646
3647
3648
3649	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3650	(( i = 0 ))
3651	while (( i < ioc ))
3652	do
3653	(( i = i + 1 ))
3654	if (( i == 1 ))
3655	then
3656	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3657	fi
3658	printf "\n >>> ${out_command[$i]}"
3659	eval ${out_command[$i]}
3660	if (( i == ioc ))
3661	then
3662	printf "\n$dashes\n"
3663	fi
3664	done
3665
3666
3667	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3668	if [[ $do_trace = true ]]
3669	then
3670	printf "\n\n"
3671	ls -al
3672	fi
3673
3674
3675
3676	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3677	(( i = 0 ))
3678	while (( i < iout ))
3679	do
3680	(( i = i + 1 ))
3681	if (( i == 1 ))
3682	then
3683	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3684	fi
3685
3686	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3687	files_for_pes=false; filetyp=file
3688	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3689	then
3690	files_for_pes=true; filetyp=directory
3691	actionout[$i]=""
3692	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3693	then
3694	actionout[$i]=""
3695	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3696	then
3697	files_for_pes=true; filetyp=directory
3698	actionout[$i]="ar"
3699	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3700	then
3701	actionout[$i]="ar"
3702	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3703	then
3704	files_for_pes=true; filetyp=directory
3705	actionout[$i]="fl"
3706	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3707	then
3708	actionout[$i]="fl"
3709	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3710	then
3711	files_for_pes=true; filetyp=directory
3712	actionout[$i]="tr"
3713	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3714	then
3715	actionout[$i]="tr"
3716	fi
3717
3718	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3719	then
3720	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3721	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3722	then
3723	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3724	else
3725
3726
3727	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3728	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3729	if [[ "${actionout[$i]}" = tr ]]
3730	then
3731	if [[ $localhost != $fromhost ]]
3732	then
3733	if [[ $files_for_pes = false ]]
3734	then
3735	cps=""
3736	cst=""
3737	else
3738	cps=-c
3739	cst="/"
3740	fi
3741	if [[ $localhost = nech ]]
3742	then
3743
3744	# TRANSFER IN SEPERATE JOB
3745	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3746	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3747	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3748	if [[ $files_for_pes = false ]]
3749	then
3750	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3751	else
3752	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3753	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3754	fi
3755
3756	echo "set -x" > transfer_${localout[$i]}
3757	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3758
3759	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3760	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3761	printf "\n or higher cycle\n"
3762	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]}
3763
3764	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3765
3766	if [[ $localhost = nech ]]
3767	then
3768	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3769	else
3770	if [[ "$LOGNAME" = b323013 ]]
3771	then
3772	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3773	else
3774	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3775	fi
3776	fi
3777
3778	else
3779
3780	# TRANSFER WITHIN THIS JOB
3781	transfer_failed=false
3782	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3783	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3784	if [[ $localhost = lccrayb ]]
3785	then
3786	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]}"
3787	elif [[ $localhost = lccrayh ]]
3788	then
3789	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]}"
3790	else
3791	batch_scp $PORTOPT $cps -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3792	fi
3793	[[ $? != 0 ]] && transfer_failed=true
3794
3795	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3796	if [[ $transfer_failed = true ]]
3797	then
3798	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3799	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3800
3801	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3802	eval local_catalog=${pathout[$i]}
3803	if [[ ! -d $local_catalog ]]
3804	then
3805	printf " *** local directory does not exist. Trying to create:\n"
3806	printf " $local_catalog \n"
3807	mkdir -p $local_catalog
3808	fi
3809	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3810	transfer_problems=true
3811	fi
3812	fi
3813	else
3814
3815	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3816	actionout[$i]=""
3817	fi
3818	fi
3819
3820
3821	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3822	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3823	if [[ "${actionout[$i]}" = tra ]]
3824	then
3825	if [[ $localhost != $fromhost ]]
3826	then
3827	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3828	then
3829
3830	# TRANSFER IN SEPERATE JOB
3831	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3832	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3833	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3834	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3835
3836	echo "set -x" > transfer_${localout[$i]}
3837	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3838
3839	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3840	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3841	printf "\n or higher cycle\n"
3842	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]}
3843
3844	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3845
3846	if [[ $localhost = nech ]]
3847	then
3848	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3849	else
3850	if [[ $LOGNAME = b323013 ]]
3851	then
3852	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3853	else
3854	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3855	fi
3856	fi
3857
3858	else
3859
3860	# TRANSFER WITHIN THIS JOB
3861	transfer_failed=false
3862	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3863	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3864	if [[ $localhost = lccrayb ]]
3865	then
3866	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]}"
3867	elif [[ $localhost = lccrayh ]]
3868	then
3869	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]}"
3870	else
3871	batch_scp $PORTOPT -A -b -m -u $return_username $return_addres ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3872	fi
3873	[[ $? != 0 ]] && transfer_failed=true
3874
3875	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3876	if [[ $transfer_failed = true ]]
3877	then
3878	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3879	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3880
3881	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3882	eval local_catalog=${pathout[$i]}
3883	if [[ ! -d $local_catalog ]]
3884	then
3885	printf " *** local directory does not exist. Trying to create:\n"
3886	printf " $local_catalog \n"
3887	mkdir -p $local_catalog
3888	fi
3889
3890	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3891	transfer_problems=true
3892	fi
3893	fi
3894	else
3895
3896	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3897	actionout[$i]=a
3898	fi
3899	fi
3900
3901
3902	# OUTPUT-FILE FOR A RESTART-RUN.
3903	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3904	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3905	# AS LAST ACTION, ARCHIVING IS INITIATED.
3906	if [[ "${actionout[$i]}" = fl ]]
3907	then
3908	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3909	chmod g+rx $tmp_data_catalog
3910	if [[ $files_for_pes = false ]]
3911	then
3912	printf "\n >>> OUTPUT: ${localout[$i]} to"
3913	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3914	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3915	else
3916	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3917	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3918	mkdir $tmp_data_catalog/${frelout[$i]}
3919	cd ${localout[$i]}
3920	for file in $(ls *)
3921	do
3922	ln -f $file $tmp_data_catalog/${frelout[$i]}
3923	done
3924	cd $TEMPDIR
3925	fi
3926
3927
3928	# CREATE AND SUBMIT ARCHIVING-JOB
3929	if [[ $store_on_archive_system = true ]]
3930	then
3931
3932	if [[ $archive_system = asterix ]]
3933	then
3934	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3935	if [[ $files_for_pes = false ]]
3936	then
3937	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3938	else
3939	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3940	fi
3941	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3942	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3943	echo "then" >> archive_${frelout[$i]}
3944	echo " do_stageout=false" >> archive_${frelout[$i]}
3945	echo "else" >> archive_${frelout[$i]}
3946	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3947	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3948	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3949	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3950	if [[ $files_for_pes = false ]]
3951	then
3952	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3953	else
3954	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3955	fi
3956	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3957	echo "fi" >> archive_${frelout[$i]}
3958	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3959	elif [[ $archive_system = DMF ]]
3960	then
3961	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3962	if [[ $files_for_pes = false ]]
3963	then
3964	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3965	locat=DMF
3966	exit
3967	else
3968	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3969	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3970	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3971	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3972	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3973	fi
3974	elif [[ $archive_system = tivoli ]]
3975	then
3976	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3977	if [[ $files_for_pes = false ]]
3978	then
3979	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3980	echo "set -x" >> archive_${frelout[$i]}
3981	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3982	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3983	else
3984
3985	echo "set -x" >> archive_${frelout[$i]}
3986	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3987	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3988	cd $tmp_data_catalog
3989	all_files=`ls -1 ${frelout[$i]}/*`
3990	cd - > /dev/null
3991	(( inode = 0 ))
3992	(( tp1 = tasks_per_node + 1 ))
3993	while (( inode < nodes ))
3994	do
3995	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3996	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3997	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3998	(( inode = inode + 1 ))
3999	done
4000	fi
4001	elif [[ $archive_system = ut ]]
4002	then
4003	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4004	if [[ $files_for_pes = false ]]
4005	then
4006	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4007	echo "set -x" >> archive_${frelout[$i]}
4008	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4009	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4010	else
4011
4012	echo "set -x" >> archive_${frelout[$i]}
4013	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4014	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4015	cd $tmp_data_catalog
4016	all_files=`ls -1 ${frelout[$i]}/*`
4017	cd - > /dev/null
4018	(( inode = 0 ))
4019	(( tp1 = tasks_per_node + 1 ))
4020	while (( inode < nodes ))
4021	do
4022	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4023	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4024	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4025	(( inode = inode + 1 ))
4026	done
4027	fi
4028	elif [[ $archive_system = none ]]
4029	then
4030	printf " +++ archiving on $localhost not available!\n"
4031	fi
4032
4033	if [[ $archive_system != none ]]
4034	then
4035	if [[ $localhost = nech ]]
4036	then
4037	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4038	fi
4039	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4040	fi
4041	else
4042	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4043	fi
4044
4045
4046	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4047	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4048	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4049	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4050	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4051	if [[ $files_for_pes = false ]]
4052	then
4053	cat /dev/null > ${pathout[$i]}
4054	else
4055	mkdir -p ${pathout[$i]}
4056	fi
4057
4058	fi
4059
4060
4061	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4062	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4063	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4064	if [[ "${actionout[$i]}" = ar ]]
4065	then
4066	if [[ $files_for_pes = false ]]
4067	then
4068	printf "\n >>> OUTPUT: ${localout[$i]} to"
4069	printf "\n ${pathout[$i]}"
4070	printf "\n File will be copied to archive-system ($archive_system) !\n"
4071	else
4072	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4073	printf "\n ${pathout[$i]}"
4074	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4075	fi
4076	mv ${localout[$i]} ${frelout[$i]}
4077
4078	file_saved=false
4079
4080	if [[ $archive_system = asterix ]]
4081	then
4082	do_stageout=true
4083	(( stageout_anz = 0 ))
4084	while [[ $do_stageout = true ]]
4085	do
4086	if [[ $files_for_pes = false ]]
4087	then
4088	stageout ${frelout[$i]} > STAGE_OUTPUT
4089	else
4090	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4091	fi
4092	cat STAGE_OUTPUT
4093	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4094	then
4095	file_saved=true
4096	do_stageout=false
4097	else
4098	if [[ $files_for_pes = false ]]
4099	then
4100	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4101	else
4102	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4103	fi
4104	(( stageout_anz = stageout_anz + 1 ))
4105	if (( stageout_anz == 10 ))
4106	then
4107	printf "\n +++ stoped after 10 unsuccessful tries!"
4108	archive_save=false
4109	do_stageout=false
4110	else
4111	printf "\n *** new try to store on archive after 15 min:"
4112	sleep 900
4113	fi
4114	fi
4115	done
4116	elif [[ $archive_system = DMF ]]
4117	then
4118	if [[ $files_for_pes = false ]]
4119	then
4120	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4121	locat=DMF
4122	exit
4123	else
4124	rm -rf $ARCHIVE/${frelout[$i]}
4125	cp -r ${frelout[$i]} $ARCHIVE
4126	fi
4127	file_saved=true
4128	elif [[ $archive_system = tivoli ]]
4129	then
4130	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4131	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4132	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4133	# WHEN THE ARCHIVE-JOB IS EXECUTED
4134	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4135	chmod g+rx $tmp_data_catalog
4136	if [[ $files_for_pes = false ]]
4137	then
4138	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4139	else
4140	mkdir $tmp_data_catalog/${frelout[$i]}
4141	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4142	fi
4143
4144	# GENERATE AND SUBMIT BATCH-JOB
4145	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4146	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4147	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4148	if [[ $files_for_pes = false ]]
4149	then
4150	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4151	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4152	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4153	else
4154	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4155	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4156	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4157	fi
4158
4159	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4160	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4161	file_saved=true
4162
4163	elif [[ $archive_system = ut ]]
4164	then
4165	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4166	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4167	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4168	# WHEN THE ARCHIVE-JOB IS EXECUTED
4169	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4170	chmod g+rx $tmp_data_catalog
4171	if [[ $files_for_pes = false ]]
4172	then
4173	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4174	else
4175	mkdir $tmp_data_catalog/${frelout[$i]}
4176	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4177	fi
4178
4179	# GENERATE AND SUBMIT BATCH-JOB
4180	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4181	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4182	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4183	if [[ $files_for_pes = false ]]
4184	then
4185	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4186	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4187	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4188	else
4189	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4190	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4191	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4192	fi
4193
4194	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4195	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4196	file_saved=true
4197
4198	else
4199	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4200	archive_save=false
4201	fi
4202
4203	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4204	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4205	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4206	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4207	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4208	if [[ $file_saved = true ]]
4209	then
4210	if [[ $files_for_pes = false ]]
4211	then
4212	cat /dev/null > ${pathout[$i]}
4213	else
4214	mkdir -p ${pathout[$i]}
4215	fi
4216	fi
4217
4218	fi
4219
4220	# APPEND ON THIS MACHINE
4221	if [[ "${actionout[$i]}" = "a" ]]
4222	then
4223	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4224	then
4225	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4226	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4227	else
4228	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4229	cat ${localout[$i]} >> ${pathout[$i]}
4230	fi
4231	fi
4232
4233	# COPY ON THIS MACHINE
4234	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4235	# ON DIFFERENT FILE-SYSTEMS
4236	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4237	then
4238
4239	# COPY IN CASE OF RUNS ON SINGLE CORES
4240	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4241	then
4242	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4243	if [[ $link_local_output = true ]]
4244	then
4245	printf " using ln -f\n"
4246	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4247	fi
4248	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4249	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4250	then
4251	if [[ $link_local_output = true ]]
4252	then
4253	printf " ln failed, using cp...\n"
4254	fi
4255	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4256	fi
4257	else
4258	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4259	if [[ $link_local_output = true ]]
4260	then
4261	printf " using ln -f\n"
4262	ln -f ${localout[$i]} ${pathout[$i]}
4263	fi
4264	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4265	if [[ ! -f "${pathout[$i]}" ]]
4266	then
4267	if [[ $link_local_output = true ]]
4268	then
4269	printf " ln failed, using cp...\n"
4270	fi
4271	cp ${localout[$i]} ${pathout[$i]}
4272	fi
4273	fi
4274
4275	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4276	then
4277
4278	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4279	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4280	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4281	if [[ $link_local_output = true ]]
4282	then
4283	printf " using ln -f\n"
4284	mkdir ${pathout[$i]}
4285	cd ${localout[$i]}
4286	for file in $(ls *)
4287	do
4288	ln -f $file ${pathout[$i]}
4289	done
4290	cd $TEMPDIR
4291	fi
4292
4293	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4294	if [[ ! -f "${pathout[$i]}/_0000" ]]
4295	then
4296	if [[ $link_local_output = true ]]
4297	then
4298	printf " ln failed for .../_0000, using cp...\n"
4299	fi
4300	cp -r ${localout[$i]} ${pathout[$i]}
4301	fi
4302
4303	fi
4304	fi
4305	done
4306	if (( i != 0 ))
4307	then
4308	if [[ $transfer_problems = true ]]
4309	then
4310	printf "\n$dashes\n *** OUTPUT-files saved"
4311	printf "\n +++ WARNING: some data transfers failed! \n"
4312	else
4313	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4314	fi
4315	fi
4316
4317
4318	# IF REQUIRED, START A RESTART-JOB
4319	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4320	if [[ -f CONTINUE_RUN ]]
4321	then
4322
4323	if [[ $archive_save = true ]]
4324	then
4325
4326	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4327	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4328	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4329	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4330	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4331	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4332	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4333	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4334	then
4335	mc=`echo $mc \| sed 's/#/f/g'`
4336	fi
4337
4338
4339	# START THE RESTART-JOB
4340	printf "\n\n *** initiating restart-run on \"$return_addres\" using command:\n"
4341	echo " $mc"
4342	printf "\n$dashes\n"
4343	if [[ $localhost != $fromhost ]]
4344	then
4345
4346	if [[ $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* ]]
4347	then
4348	echo "*** ssh will be used to initiate restart-runs!"
4349	echo " return_addres=\"$return_addres\" "
4350	echo " return_username=\"$return_username\" "
4351	if [[ $(echo $return_addres \| grep -c "130.75.105") = 1 ]]
4352	then
4353	if [[ $localhost = ibmh ]]
4354	then
4355	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\" "
4356	elif [[ $localhost = lccrayb ]]
4357	then
4358	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\" "
4359	elif [[ $localhost = lccrayh ]]
4360	then
4361	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\" "
4362
4363	else
4364	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 "
4365	fi
4366	else
4367	if [[ $localhost = ibmkisti ]]
4368	then
4369	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\" "
4370	elif [[ $localhost = lcflow ]]
4371	then
4372	/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 "
4373	elif [[ $localhost = lccrayb ]]
4374	then
4375	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\" "
4376	elif [[ $localhost = lccrayh ]]
4377	then
4378	ssh $usern@130.75.4.1 "ssh $SSH_PORTOPT $return_addres -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4379	else
4380	ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4381	fi
4382	fi
4383	else
4384	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4385	locat=restart; exit
4386	fi
4387
4388	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4389	if [[ $queue = special1q ]]
4390	then
4391	sleep 120
4392	else
4393	sleep 30
4394	fi
4395
4396	else
4397
4398	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4399	# USING SSH)
4400	cd $LOCAL_PWD
4401	if [[ $localhost = lckyuh ]]
4402	then
4403	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4404	printf "\n please restart job manually using command:\n"
4405	printf "\n \"$mc\" "
4406	else
4407	eval $mc # THE ' MUST BE EVALUATED
4408	fi
4409	cd - > /dev/null
4410	fi
4411	if [[ $localhost = lckyuh ]]
4412	then
4413	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4414	else
4415	printf "\n$dashes\n *** restart-run initiated \n"
4416	fi
4417
4418
4419	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4420	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4421	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4422	# MAY BE VERY HUGE)
4423	(( i = 0 ))
4424	while (( i < iin ))
4425	do
4426	(( i = i + 1 ))
4427	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4428	then
4429	rm -r $tmp_data_catalog/${frelin[$i]}
4430	fi
4431	done
4432
4433	else
4434
4435	printf "\n +++ no restart-run possible, since errors occured"
4436	printf "\n during the archive process"
4437	fi
4438
4439	fi
4440
4441
4442
4443	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4444	if [[ "$email_notification" != "none" ]]
4445	then
4446
4447	if [[ $localhost != $fromhost ]]
4448	then
4449	if [[ -f CONTINUE_RUN ]]
4450	then
4451	echo "PALM restart run necessary" > email_text
4452	echo "description header of actual run:" >> email_text
4453	cat CONTINUE_RUN >> email_text
4454	echo "mrun-command to restart:" >> email_text
4455	echo "$mc" >> email_text
4456	else
4457	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4458	fi
4459	mail $email_notification < email_text
4460	printf "\n *** email notification sent to \"$email_notification\" "
4461	fi
4462	fi
4463
4464
4465
4466	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4467	cd $HOME
4468	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4469
4470	else
4471
4472
4473	# PREPARING ACTIONS,
4474	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4475
4476	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4477	mrun_com="$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 $remote_username"
4478	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4479	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4480	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4481	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4482	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4483	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4484	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4485	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4486	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4487	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4488	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4489	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4490	if [[ $use_openmp = true ]]
4491	then
4492	mrun_com=${mrun_com}" -O $threads_per_task"
4493	fi
4494	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4495	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4496	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4497	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4498	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4499	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4500	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4501	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4502	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4503	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4504	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4505	if [[ $do_remote = true ]]
4506	then
4507	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4508	fi
4509
4510
4511	# CREATE EXECUTABLE FOR BATCH JOB
4512	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4513	then
4514
4515	printf "\n *** creating the executable for batch job\n"
4516
4517	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4518	if [[ $host != $localhost ]]
4519	then
4520	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4521	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4522	locat=create_executable; exit
4523	fi
4524
4525	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4526	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4527
4528	cp $make_depository .
4529	tar -xf $make_depository > /dev/null 2>&1
4530	cp ../* . > /dev/null 2>&1
4531
4532	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4533
4534	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4535	then
4536	printf "\n +++ error occured while compiling or linking"
4537	locat=compile
4538	exit
4539	fi
4540
4541	mv a.out ..
4542	cd - > /dev/null 2>&1
4543	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4544
4545	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4546
4547	fi
4548
4549
4550	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4551	jobfile=jobfile.$RANDOM
4552
4553
4554	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4555	echo "mkdir $TEMPDIR" >> $jobfile
4556	echo "cd $TEMPDIR" >> $jobfile
4557
4558
4559	# ACTIVATE ERROR-TRACEBACK
4560	if [[ $do_trace = true ]]
4561	then
4562	echo "set -x" >> $jobfile
4563	else
4564	echo "set +vx" >> $jobfile
4565	fi
4566
4567
4568	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4569	if [[ "$init_cmds" != "" ]]
4570	then
4571	echo "$init_cmds" >> $jobfile
4572	fi
4573	if [[ "$module_calls" != "" ]]
4574	then
4575	echo "$module_calls" >> $jobfile
4576	fi
4577
4578
4579	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4580	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4581	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4582	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4583	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4584	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4585	# QUEUEING-SYSTEMS
4586	if [[ $host = ibmkisti \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4587	then
4588
4589	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4590	if [[ $restart_run != true ]]
4591	then
4592	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4593	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4594	fi
4595
4596	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4597	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4598	echo "set -x" >> $jobfile
4599	if [[ $host = $localhost ]]
4600	then
4601
4602	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4603	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4604	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4605	then
4606	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4607	else
4608	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4609	fi
4610
4611	else
4612	if [[ $host = ibmkisti ]]
4613	then
4614	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4615	echo "localdir=\`pwd\`" >> $jobfile
4616	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4617	elif [[ $host = lccrayb ]]
4618	then
4619	echo "localdir=\`pwd\`" >> $jobfile
4620	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4621	elif [[ $host = lccrayh ]]
4622	then
4623	echo "localdir=\`pwd\`" >> $jobfile
4624	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4625
4626	else
4627	echo "scp $PORTOPT -r $return_username@$return_addres:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4628	fi
4629	fi
4630	echo "export SOURCES_COMPLETE=true" >> $jobfile
4631
4632	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4633	# WORKING DIRECTORY OF THE JOB
4634	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4635	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4636	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4637	echo "execute_mrun=true" >> $jobfile
4638	echo " " >> $jobfile
4639
4640	else
4641
4642	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4643	if [[ $do_compile = true ]]
4644	then
4645
4646	source_catalog=SOURCES_FOR_RUN_$fname
4647
4648	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4649	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4650	echo "export SOURCES_COMPLETE=true" >> $jobfile
4651	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4652
4653	for filename in $source_list
4654	do
4655	# BACKSLASH IS USED FOR MASKING
4656	echo "cat > $filename << \"%END%\"" >> $jobfile
4657	cat $source_catalog/$filename >> $jobfile
4658	echo " " >> $jobfile
4659	echo "%END%" >> $jobfile
4660	echo " " >> $jobfile
4661	done
4662
4663	# BACKSLASH IS USED FOR MASKING
4664	echo "cat > Makefile << \"%END%\"" >> $jobfile
4665	cat $source_catalog/Makefile >> $jobfile
4666	echo " " >> $jobfile
4667	echo "%END%" >> $jobfile
4668	echo " " >> $jobfile
4669
4670	echo "cd - > /dev/null" >> $jobfile
4671
4672	fi
4673
4674
4675	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4676	# BACKSLASH IS USED FOR MASKING
4677	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4678	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4679	echo "cat > $config_file << \"%END%\"" >> $jobfile
4680	if [[ $host = lckyuh ]]
4681	then
4682	# NO CROSS-COMPILER ON COMPUTE NODE
4683	sed 's/frtpx/frt/g' $config_file >> $jobfile
4684	else
4685	sed 's/#$.*//g' $config_file >> $jobfile
4686	fi
4687	echo "%END%" >> $jobfile
4688	echo " " >> $jobfile
4689
4690
4691	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4692	# BACKSLASH IS USED FOR MASKING
4693	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4694	if [[ $host = lckyuh ]]
4695	then
4696	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4697	else
4698	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4699	fi
4700	echo "%END%" >> $jobfile
4701	echo "chmod u+x $mrun_script_name" >> $jobfile
4702	echo "execute_mrun=true" >> $jobfile
4703	echo " " >> $jobfile
4704
4705	fi
4706
4707
4708	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4709	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4710	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4711	if [[ $do_remote = true ]]
4712	then
4713	(( i = 0 ))
4714	while (( i < iin ))
4715	do
4716	(( i = i + 1 ))
4717	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4718	if [[ "${transin[$i]}" = job ]]
4719	then
4720	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4721	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4722	echo " " >> $jobfile
4723	echo "%END%" >> $jobfile
4724	else
4725	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_addres ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4726	fi
4727
4728	# CHECK, IF FILE COULD BE CREATED
4729	echo "if [[ \$? = 1 ]]" >> $jobfile
4730	echo "then" >> $jobfile
4731	echo " echo \" \" " >> $jobfile
4732	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4733	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4734	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4735	echo " execute_mrun=false" >> $jobfile
4736	echo "fi" >> $jobfile
4737	done
4738	fi
4739
4740	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4741	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4742	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4743	echo "LOCAL_PWD=$working_directory" >> $jobfile
4744	echo "export LOCAL_PWD" >> $jobfile
4745
4746	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4747	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4748	echo "export LOCAL_MRUN_PATH" >> $jobfile
4749
4750	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4751	if [[ $host = lcflow \|\| $localhost = lcflow ]]
4752	then
4753	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4754	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4755	fi
4756
4757	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4758	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4759	echo "set -x" >> $jobfile
4760	echo "queue=$queue" >> $jobfile
4761	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4762	echo 'ls -al; echo `pwd`' >> $jobfile
4763	echo "cd \$HOME" >> $jobfile
4764	echo "rm -rf $TEMPDIR" >> $jobfile
4765
4766
4767
4768
4769	# START THE JOB USING SUBJOB-COMMAND
4770	if [[ $silent = false ]]
4771	then
4772	printf "\n "
4773	else
4774	printf "\n\n"
4775	fi
4776
4777	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
4778	rm -rf $jobfile
4779
4780
4781	fi # END OF REMOTE-PART

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |