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source: palm/trunk/SCRIPTS/mrun @ 1621

Last change on this file since 1621 was 1621, checked in by heinze, 9 years ago
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1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2014 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1621 2015-07-17 11:39:33Z heinze $
29	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
30	#
31	# 1609 2015-07-03 15:37:58Z maronga
32	# Modified the random number of the temporary working directory to match the
33	# queuing system number on HLRN-III (lccray*).
34	#
35	# 1604 2015-06-23 15:48:03Z suehring
36	# Enable coupled runs for lcmuk
37	#
38	# 1598 2015-05-29 06:45:40Z raasch
39	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
40	#
41	# 1549 2015-01-30 14:26:16Z suehring
42	# Enable interactive debug sessions with allinea debugger
43	#
44	# 1547 2015-01-29 15:09:12Z witha
45	# adjustments for ForWind computing cluster (lcflow)
46	#
47	# 1491 2014-11-12 08:12:57Z heinze
48	# correct setting of batch_job allowed for ibm-machines
49	#
50	# 1468 2014-09-24 14:06:57Z maronga
51	# Typo removed (addres->address)
52	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
53	# Added support for restart runs (remote) for lcxe6
54	#
55	# 1442 2014-07-28 07:09:10Z raasch
56	# default queues for HLRN-III (lccrayb/lccrayh) defined
57	#
58	# 1422 2014-07-02 10:01:25Z kanani
59	# automatic restarts enabled for lccrayb,
60	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
61	#
62	# 1420 2014-06-10 06:24:14Z raasch
63	# -j1 option added to aprung command for lccrayf (CSC)
64	#
65	# 1402 2014-05-09 14:25:13Z raasch
66	# batch_job added to envpar-NAMELIST
67	#
68	# 1357 2014-04-11 15:02:03Z witha
69	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
70	# possible)
71	#
72	# 1320 2014-03-20 08:40:49Z raasch
73	# check namelist file set false by default
74	#
75	# 1304 2014-03-12 10:29:42Z raasch
76	# ulimit option changed from -Ss to -s
77	#
78	# bugfix: missing "fi" in r1289
79	#
80	# 1289 2014-03-04 07:12:34Z raasch
81	# comments translated to English
82	# necriam-, fimm-, ibmy-, and sgi-specific code removed
83	# export of variables for palm and interpret_config removed
84	#
85	# 1281 2014-02-01 07:55:49Z raasch
86	# rsync-copy restricted to Cray machines, since command is unavailable on some
87	# other systems
88	#
89	# 1279 2014-01-28 12:10:14Z raasch
90	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
91	# in order to remove annoying restrictions concerning the number of processors which
92	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
93	# restriction, one of the nodes will be filled with less than the given number of
94	# tasks per node. A respective warning is given.
95	#
96	# 1274 2014-01-09 13:14:54Z heinze
97	# adjustments for lccrayh
98	#
99	# 1272 2014-01-08 10:19:32Z witha
100	# small adjustment for lcflow
101	#
102	# 1270 2013-12-16 11:05:01Z fricke
103	# call of combine_plot_fields adjusted for lccrayb/lccrayh
104	#
105	# 1255 2013-11-07 14:43:35Z raasch
106	# further adjustments for lccrayb remote access
107	#
108	# 1241 2013-10-30 11:36:58Z heinze
109	# Enable use of nudging input and input of large scale forcing from
110	# external files
111	#
112	# 1229 2013-09-20 06:55:19Z raasch
113	# further adjustments for lccrayb
114	#
115	# 1224 2013-09-16 07:27:23Z raasch
116	# first adjustments for lccrayb
117	#
118	# 1210 2013-08-14 10:58:20Z raasch
119	# fftw support added
120	#
121	# 1201 2013-07-10 16:17:59Z witha
122	# adjustments for Forwind cluster (lcflow)
123	#
124	# 1199 2013-07-05 14:52:22Z raasch
125	# adjustments for CSC Helsinki (lccrayf),
126	# executables for batch jobs can be created in advance, in order to avoid calling
127	# the compiler within the batch job (only works if batch jobs are submitted on
128	# local host)
129	#
130	# 1190 2013-06-25 09:39:21Z heinze
131	# enable use of automatic restarts for ibmh
132	# use of cluster/express queue enabled (ibmh)
133	#
134	# 1124 2013-04-09 15:46:52Z raasch
135	# variable "memory" is exported via typeset option -x, because otherwise an unknown
136	# side effect may lead to data loss while getopts is reading the script-option arguments
137	#
138	# 1122 2013-04-09 08:37:16Z heinze
139	# Bugfix: change type of variable last_char
140	#
141	# 1119 2013-04-05 15:11:19Z raasch
142	# Bugfix for setting -T option for subjob
143	#
144	# 1108 2013-03-05 07:03:32Z raasch
145	# bugfix for coupled runs on lckyut/lckyuh
146	#
147	# 1106 2013-03-04 05:31:38Z raasch
148	# --stdin argument for mpiexec on lckyuh
149	# -y and -Y settings output to header
150	#
151	# 1103 2013-02-20 02:15:53Z raasch
152	# default script runs again under ksh, because of unsolved problems with read
153	# from stdin: when bash script is called from a ksh, message "read error: 0:
154	# Resource temporarily unavailable" appears and script does not stop,
155	# further bash compatibility adjustments,
156	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
157	# on lckyuh, but mrun does not terminate and issues a warning instead
158	#
159	# 1101 2013-02-17 10:20:21Z raasch
160	# script now running under bash instead of ksh, which required small adjustments
161	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
162	# read from stdin),
163	# cross compilername on lckyuh compute nodes replaced by real compiler name
164	#
165	# 1099 2013-02-10 01:47:43Z raasch
166	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
167	# and for Forwind cluster (lcflow)
168	# small further adjustments for lckyut
169	#
170	# 1094 2013-02-03 01:52:12Z raasch
171	# explicit ssh/scp port can be set in config file with environment variable
172	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
173	# decalpha parts (yonsei) removed
174	#
175	# 2013-02-02 07:06:13Z raasch
176	# adjustments for Kyushu-University computing center (lckyut - tatara)
177	#
178	# 1083 2013-01-04 10:22:09Z maronga
179	# bugfix in parameter file check (read %cpp_options was missing)
180	#
181	# 1069 2012-11-28 16:18:43Z maronga
182	# bugfix: coupling mode was always set to mpi2, typos removed
183	#
184	# 1058 2012-11-21 07:00:35Z raasch
185	# Intel inspector (inspxe) is given the number of PEs instead of the number of
186	# nodes
187	#
188	# 1046 2012-11-09 14:38:45Z maronga
189	# code put under GPL (PALM 3.9)
190	#
191	# 21/03/94 - Siggi - first version finished
192	# 03/03/94 - Siggi - script development started
193	#
194	#--------------------------------------------------------------------------------#
195	# mrun - script for running PALM jobs
196	#--------------------------------------------------------------------------------#
197
198
199
200	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
201
202	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
203	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
204	# (TOO MANY ARGUMENTS - PROBLEM)
205	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
206
207	AddFilenames=""
208	additional_conditions=""
209	add_source_path=""
210	afname=""
211	archive_save=true
212	archive_system=none
213	check_namelist_files=false
214	combine_plot_fields=true
215	compiler_name=""
216	cond1=""
217	cond2=""
218	config_file=.mrun.config
219	coupled_dist=""
220	coupled_mode="mpi1"
221	cpp_opts=""
222	cpp_options=""
223	cpumax=0
224	cpurest=0
225	create_executable_for_batch=false
226	delete_temporary_catalog=true
227	do_batch=false
228	do_compile=true
229	do_remote=false
230	do_stagein=true
231	do_stageout=true
232	do_trace=false
233	email_notification="none"
234	exclude=""
235	executable=""
236	execution_error=false
237	fftw_inc=""
238	fftw_lib=""
239	fftw_support=false
240	fname=test
241	fromhost=""
242	global_revision=""
243	group_number=none
244	host=""
245	host_file=""
246	hp=""
247	ignore_archive_error=false
248	input_list=""
249	interpreted_config_file=""
250	job_catalog="~/job_queue"
251	job_on_file=""
252	keep_data_from_previous_run=false
253	link_local_input=false
254	link_local_output=false
255	localhost_realname=$(hostname)
256	local_dvrserver_running=.FALSE.
257	locat=normal
258	mainprog=""
259	makefile=""
260	max_par_io_str=""
261	mc=$0
262	while [[ $(echo $mc \| grep -c "/") != 0 ]]
263	do
264	mc=`echo $mc \| cut -f2- -d"/"`
265	done
266	module_calls=""
267	mrun_script_name=$mc
268	netcdf_inc=""
269	netcdf_lib=""
270	netcdf_support=false
271	node_usage=default
272	numprocs=""
273	numprocs_atmos=0
274	numprocs_ocean=0
275	OOPT=""
276	openmp=false
277	output_list=""
278	package_list=""
279	queue=none
280	read_from_config=""
281	restart_run=false
282	if [[ `hostname` = rte10 ]]
283	then
284	return_address=133.5.185.60
285	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
286	elif [[ `hostname` = climate0 ]]
287	then
288	return_address=165.132.26.68
289	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
290	elif [[ `hostname` = urban00 ]]
291	then
292	return_address=147.46.30.151
293	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
294	else
295	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
296	fi
297	return_password=""
298	return_username=$LOGNAME
299	remotecall=false
300	remote_username=""
301	run_coupled_model=false
302	run_mode=""
303	store_on_archive_system=false
304	dashes=" ----------------------------------------------------------------------------"
305	silent=false
306	source_list=""
307	source_path=SOURCE
308	tasks_per_node=""
309	threads_per_task=1
310	tmpcreate=false
311	tmp_data_catalog=""
312	transfer_problems=false
313	usern=$LOGNAME
314	use_openmp=false
315	version="MRUN 2.1 Rev$Rev: 1621 $"
316	working_directory=`pwd`
317	TOPT=""
318	XOPT=""
319	zeit=$( date \| cut -c 12-19 )
320
321	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
322	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
323	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
324	# SCRIPT-OPTION ARGUMENTS
325	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
326
327	# ERROR HANDLING IN CASE OF EXIT
328	trap 'rm -rf $working_directory/tmp_mrun
329	if [[ $locat != normal && $locat != control_c ]]
330	then
331
332	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
333	(( i = 0 ))
334	while (( i < iec ))
335	do
336	(( i = i + 1 ))
337	printf "\n *** Execution of ERROR-command:\n"
338	printf " >>> ${err_command[$i]}\n"
339	eval ${err_command[$i]}
340	done
341	if [[ -n $interpreted_config_file ]]
342	then
343	rm -rf $interpreted_config_file
344	fi
345	if [[ -n .mrun_environment ]]
346	then
347	rm -rf .mrun_environment
348	fi
349	if [[ $tmpcreate = true ]]
350	then
351	printf "\n *** Contents of \"$TEMPDIR\":\n"
352	ls -al; cd
353	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
354	fi
355	if [[ "$dvrserver_id" != "" ]]
356	then
357	echo "+++ killing dvrserver_id=$dvrserver_id"
358	kill $dvrserver_id
359	fi
360	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
361	then
362	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
363	fi
364	printf "\n\n+++ MRUN killed \n\n"
365	elif [[ $locat != control_c ]]
366	then
367	printf "\n\n --> all actions finished\n\n"
368	printf " Bye, bye $usern !!\n\n"
369	fi' exit
370
371
372	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
373	trap 'rm -rf $working_directory/tmp_mrun
374	rm -rf $working_directory/tmp_check_namelist_files
375	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
376	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
377	then
378	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
379	fi
380	if [[ "$dvrserver_id" != "" ]]
381	then
382	echo "+++ killing dvrserver_id=$dvrserver_id"
383	kill $dvrserver_id
384	fi
385	printf "\n+++ MRUN killed by \"^C\" \n\n"
386	locat=control_c
387	exit
388	' 2
389
390
391	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
392	# BEEN SET
393	if [[ "$PALM_BIN" = "" ]]
394	then
395	printf "\n +++ environment variable PALM_BIN has not been set"
396	printf "\n please set it to the directory where the PALM scripts are located"
397	locat=palm_bin; exit
398	fi
399	export PATH=$PALM_BIN:$PATH
400
401
402
403	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
404	# WHICH WILL BE USED TO START RESTART-JOBS
405	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
406	do
407	case $option in
408	(a) afname=$OPTARG;;
409	(A) store_on_archive_system=true; mc="$mc -A";;
410	(b) do_batch=true; mc="$mc -b";;
411	(B) delete_temporary_catalog=false; mc="$mc -B";;
412	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
413	(C) restart_run=true; mc="$mc -C";;
414	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
415	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
416	(F) job_on_file="-D"; mc="$mc -F";;
417	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
418	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
419	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
420	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
421	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
422	(I) ignore_archive_error=true; mc="$mc -I";;
423	(k) keep_data_from_previous_run=true; mc="$mc -k";;
424	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
425	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
426	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
427	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
428	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
429	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
430	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
431	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
432	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
433	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
434	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
435	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
436	(S) read_from_config=false; mc="$mc -S";;
437	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
438	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
439	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
440	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
441	(v) silent=true; mc="$mc -v";;
442	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
443	(x) do_trace=true;set -x; mc="$mc -x";;
444	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
445	(y) ocean_file_appendix=true; mc="$mc -y";;
446	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
447	(z) check_namelist_files=false; mc="$mc -z";;
448	(Z) combine_plot_fields=false; mc="$mc -Z";;
449	(\?) printf "\n +++ unknown option $OPTARG \n"
450	printf "\n --> type \"$0 ?\" for available options \n"
451	locat=parameter;exit;;
452	esac
453	done
454
455
456	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
457	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
458	(( to_shift = $OPTIND - 1 ))
459	shift $to_shift
460
461	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
462	if [[ "$1" = "?" ]]
463	then
464	(printf "\n *** mrun can be called as follows:\n"
465	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"
466	printf "\n Description of available options:\n"
467	printf "\n Option Description Default-Value"
468	printf "\n -a base name of input files equiv. -d"
469	printf "\n -A archiving when using file-attribute fl"
470	printf "\n -b batch-job on local machine ---"
471	printf "\n -B do not delete temporary directory at end ---"
472	printf "\n -c configuration file .mrun.config"
473	printf "\n -d base name of files attached to program test"
474	printf "\n -D preprocessor(cpp)-directives \"\" "
475	printf "\n -F create remote job file only ---"
476	printf "\n -h execution host $localhost_realname"
477	printf "\n -i INPUT control list \"\" "
478	printf "\n -I archiving errors of previous batch-jobs"
479	printf "\n will be ignored"
480	printf "\n -k keep data from previous run"
481	printf "\n -K additional conditions for controling"
482	printf "\n usage of conditional code and"
483	printf "\n env-variables in configuration file \"\" "
484	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
485	printf "\n -M Makefile name Makefile"
486	printf "\n -n node usage (shared/not_shared) depending on -h"
487	printf "\n -o OUTPUT control list \"\" "
488	printf "\n -O threads per openMP task ---"
489	printf "\n -p software package list \"\" "
490	printf "\n -q queue \"$queue\" "
491	printf "\n -r run control list (combines -i -o) \"\" "
492	printf "\n -s filenames of routines to be compiled \"\" "
493	printf "\n must end with .f, .f90, .F, or .c !"
494	printf "\n use \"..\" for more than one file and wildcards"
495	printf "\n -s LM compiles all locally modified files"
496	printf "\n -S config file interpreted by shellscript ---"
497	printf "\n -t allowed cpu-time in seconds (batch) 0"
498	printf "\n -T tasks per node depending on -h"
499	printf "\n -u username on remote machine \"\" "
500	printf "\n -v no prompt for confirmation ---"
501	printf "\n -w maximum parallel io streams as given by -X"
502	printf "\n -x tracing of mrun for debug purposes ---"
503	printf "\n -X # of processors (on parallel machines) 1"
504	printf "\n -y add appendix \"_O\" to all local output"
505	printf "\n files (ocean precursor runs followed by"
506	printf "\n coupled atmosphere-ocean runs) ---"
507	printf "\n -Y run coupled model, \"#1 #2\" with"
508	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
509	printf "\n -z disable a priori parameter file check ---"
510	printf "\n -Z skip combine_plot_fields at the end of "
511	printf "\n the simulation ---"
512	printf "\n "
513	printf "\n Possible values of positional parameter <modus>:"
514	printf "\n \"?\" - this outline \n\n") \| more
515	exit
516	elif [[ "$1" != "" ]]
517	then
518	printf "\n +++ positional parameter $1 unknown \n"
519	locat=parameter; exit
520	fi
521
522
523
524	# SHORT STARTING MESSAGE
525	printf "\n*** $version "
526	printf "\n will be executed. Please wait ..."
527
528
529
530	# CHECK, IF CONFIGURATION FILE EXISTS
531	if [[ ! -f $config_file ]]
532	then
533	printf "\n\n +++ configuration file: "
534	printf "\n $config_file"
535	printf "\n does not exist"
536	locat=connect; exit
537	fi
538
539
540	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
541	line=""
542	grep "%host_identifier" $config_file > tmp_mrun
543	while read line
544	do
545	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
546	then
547	HOSTNAME=`echo $line \| cut -d" " -s -f2`
548	host_identifier=`echo $line \| cut -d" " -s -f3`
549	if [[ $localhost_realname = $HOSTNAME ]]
550	then
551	localhost=$host_identifier
552	break
553	fi
554	fi
555	done < tmp_mrun
556
557	if [[ "$localhost" = "" ]]
558	then
559	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
560	printf "\n for local host \"$localhost_realname\"."
561	printf "\n Please add line"
562	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
563	printf "\n to the configuration file."
564	locat=localhost; exit
565	fi
566
567
568	# SET HOST-SPECIFIC VARIABLES
569	case $localhost_realname in
570	(r1\|r2\|h01\|b01) archive_system=tivoli;;
571	(cs*) archive_system=ut;;
572	esac
573
574
575	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
576	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
577	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
578	[[ "$afname" = "" ]] && afname=$fname
579
580
581	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
582	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
583	# STATEMENTS IN THE CONFIGURATION FILE
584	if [[ "$run_mode" != "" ]]
585	then
586	input_list="$input_list $run_mode"
587	output_list="$output_list $run_mode"
588	fi
589
590
591	# ??? is this (and the respective option -H) really required ???
592	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
593	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
594	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
595	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
596	if [[ "$fromhost" = "" ]]
597	then
598	fromhost=$localhost
599	fi
600
601
602	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
603	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
604	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
605	# TO BE SUBMITTED (I.E. do_batch=true)
606	if [[ -n $host && "$host" != $localhost ]]
607	then
608	do_batch=true
609	do_remote=true
610	case $host in
611	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
612	(*) printf "\n"
613	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
614	printf "\n is not available"
615	locat=nqs; (( iec = 0 )); exit;;
616	esac
617	else
618	host=$localhost
619	fi
620
621
622	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
623	if [[ -n $additional_conditions ]]
624	then
625	cond1=`echo $additional_conditions \| cut -d" " -f1`
626	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
627	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
628	if [[ -n $dummy ]]
629	then
630	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
631	locat=options; exit
632	fi
633	block=_$cond1
634	[[ -n $cond2 ]] && block=${block}_$cond2
635	fi
636
637
638	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
639	if [[ $run_coupled_model = true ]]
640	then
641
642	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
643	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
644
645	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
646	then
647
648	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
649	printf "\n PEs (total) : $numprocs"
650	printf "\n PEs (atmosphere): $numprocs_atmos"
651	printf "\n PEs (ocean) : $numprocs_ocean"
652	locat=coupling; exit
653
654	fi
655
656
657	# GET coupled_mode FROM THE CONFIG FILE
658	line=""
659	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
660	while read line
661	do
662	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f4) = $cond2 ]]
663	then
664	coupled_mode="mpi2"
665	fi
666	done < tmp_mrun
667
668	fi
669
670	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
671	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
672	then
673	if [[ $ignore_archive_error = false ]]
674	then
675	printf "\n +++ data archiving of previous run failed"
676	printf "\n see directory \~/job_queue on remote machine"
677	locat=archive; exit
678	else
679	printf "\n +++ warning: data archiving in a previous run failed"
680	printf "\n MRUN continues, trying to get backup copy"
681	fi
682	fi
683
684
685	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
686	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
687	mrun_memory=$memory
688	mrun_group_number=$group_number
689	mrun_cpumax=$cpumax
690	mrun_numprocs=$numprocs
691
692
693	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
694	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
695	if [[ "$read_from_config" = false ]]
696	then
697	[[ $silent = false ]] && printf "\n Reading the configuration file... "
698
699	# READ THE CONFIGURATION FILE LINE BY LINE
700	while read zeile
701	do
702	[[ $silent = false ]] && printf "."
703
704
705	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
706	eval zeile=\"$zeile\"
707
708
709	# INTERPRET THE LINE
710	if [[ "$(echo $zeile)" = "" ]]
711	then
712	# EMPTY LINE, NO ACTION
713	continue
714
715	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
716	then
717
718	# LINE IS A COMMENT LINE
719	true
720
721	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
722	then
723
724	# LINE DEFINES AN ENVIRONMENT-VARIABLE
725	zeile=$(echo $zeile \| cut -c2-)
726	var=`echo $zeile \| cut -d" " -f1`
727	value=`echo $zeile \| cut -d" " -s -f2`
728	for_host=`echo $zeile \| cut -d" " -s -f3`
729	for_cond1=`echo $zeile \| cut -d" " -s -f4`
730	for_cond2=`echo $zeile \| cut -d" " -s -f5`
731
732	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
733	then
734
735	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
736	# "::" IS REPLACED BY ":".
737	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
738
739
740	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
741	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
742	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
743	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
744	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
745	# CONFIGURATION-FILE.
746	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
747	then
748	eval $var=\$value
749
750	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
751	if [[ $do_trace = true ]]
752	then
753	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
754	fi
755	fi
756
757	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
758	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
759	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
760	# MUST HAVE TO BE STARTED
761	if [[ $var = host ]]
762	then
763	if [[ -n $host && "$host" != $localhost ]]
764	then
765	do_batch=true
766	do_remote=true
767	case $host in
768	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
769	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
770	printf "\n is not available"
771	locat=nqs; exit;;
772	esac
773	else
774	host=$localhost
775	fi
776	fi
777
778	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
779	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
780	# BY MRUN (E.G. subjob)
781	export $var
782	fi
783
784
785
786
787	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
788	then
789
790	# LINE DEFINES ERROR-COMMAND
791	(( iec = iec + 1 ))
792	zeile=$(echo $zeile \| cut -c4-)
793	err_command[$iec]="$zeile"
794
795	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
796	then
797
798	# LINE DEFINES INPUT-COMMAND
799	(( iic = iic + 1 ))
800	zeile=$(echo $zeile \| cut -c4-)
801	in_command[$iic]="$zeile"
802
803	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
804	then
805
806	# LINE DEFINES OUTPUT-COMMAND
807	(( ioc = ioc + 1 ))
808	zeile=$(echo $zeile \| cut -c4-)
809	out_command[$ioc]="$zeile"
810
811	else
812
813	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
814	# s2a: in/out - field
815	# s2b: loc - field (optional)
816	# s2c: tr/ar - field (optional)
817	s1=`echo $zeile \| cut -d" " -f1`
818	s2=`echo $zeile \| cut -d" " -s -f2`
819	s2a=$(echo $s2 \| cut -d":" -f1)
820	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
821	then
822	s2b=""
823	s2c=""
824	else
825	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
826	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
827	fi
828	s3=`echo $zeile \| cut -d" " -f3`
829	s4=`echo $zeile \| cut -d" " -s -f4`
830	s5=`echo $zeile \| cut -d" " -s -f5`
831	s6=`echo $zeile \| cut -d" " -s -f6`
832
833
834	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
835	# INPUT- OR OUTPUT-LIST.
836	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
837	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
838	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
839	# IS NOT CHECKED AND STORED.
840	IFSALT="$IFS"; IFS="$IFS:"
841	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
842	then
843	found=false
844	for actual in $input_list
845	do
846	for formal in $s3
847	do
848	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
849	done
850	done
851	if [[ $found = true ]]
852	then
853	(( iin = iin + 1 ))
854	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
855	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
856	extin[$iin]=$s6
857	fi
858	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
859	then
860	found=false
861	for actual in $output_list
862	do
863	for formal in $s3
864	do
865	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
866	done
867	done
868	if [[ $found = true ]]
869	then
870	(( iout = iout + 1 ))
871	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
872	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
873	fi
874	elif [[ "$s2a" != in && "$s2a" != out ]]
875	then
876	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
877	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
878	locat=connect; exit
879	fi
880	IFS="$IFSALT"
881	fi
882	done < $config_file
883
884	else
885
886	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
887	[[ $silent = false ]] && printf "..."
888	interpreted_config_file=.icf.$RANDOM
889
890
891
892	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
893	cat > .mrun_environment << %%END%%
894	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
895	config_file = '$config_file', do_remote = '$do_remote',
896	do_trace = '$do_trace', host = '$host',
897	input_list = '$input_list', icf = '$interpreted_config_file',
898	localhost = '$localhost', output_list = '$output_list' /
899
900	%%END%%
901
902	if [[ "$host" != $localhost ]]
903	then
904
905	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
906	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
907	if [[ $? != 0 ]]
908	then
909	printf "\n\n +++ no interpret_config found"
910	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
911	locat=interpret_config; exit
912	fi
913	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
914	$interpret_config_executable
915
916	else
917
918	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
919	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
920	then
921	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
922	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
923	locat=interpret_config; exit
924	else
925	interpret_config${block}.x
926	fi
927
928	fi
929	rm .mrun_environment
930
931
932	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
933	chmod u+x $interpreted_config_file
934	export PATH=$PATH:.
935	. $interpreted_config_file
936	rm $interpreted_config_file
937
938	fi
939
940
941	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
942	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
943	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
944	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
945	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
946	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
947	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
948
949
950	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
951	# FOR SOURCE-FILES TO BE COMPILED.
952	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
953	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
954	if [[ "$SOURCES_COMPLETE" = "" ]]
955	then
956
957	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
958	# HAS BEEN DEFINED
959	source_path=""
960	line=""
961	grep "%source_path" $config_file > tmp_mrun
962	while read line
963	do
964	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
965	then
966	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
967	then
968	global_source_path=`echo $line \| cut -d" " -f2`
969	fi
970	fi
971	done < tmp_mrun
972
973	line=""
974	found=false
975	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
976	while read line
977	do
978	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
979	then
980	if [[ $found = true ]]
981	then
982	printf "\n\n +++ more than one source path found in configuration file"
983	printf "\n for local host \"$localhost\" "
984	locat=source_path; exit
985	fi
986	source_path=`echo $line \| cut -d" " -f2`
987	found=true
988	fi
989	done < tmp_mrun
990	rm tmp_mrun
991
992	if [[ "$source_path" = "" ]]
993	then
994	if [[ "$global_source_path" != "" ]]
995	then
996	source_path=$global_source_path
997	else
998	printf "\n\n +++ no source path found in configuration file"
999	printf "\n for local host \"$localhost\" "
1000	locat=source_path; exit
1001	fi
1002	fi
1003	eval source_path=$source_path
1004
1005	if [[ ! -d $source_path ]]
1006	then
1007	printf "\n\n +++ source path \"$source_path\" on local host"
1008	printf "\n \"$localhost\" does not exist"
1009	locat=source_path; exit
1010	fi
1011
1012	fi
1013
1014
1015	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1016	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1017	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1018	then
1019	global_revision=`svnversion $source_path 2>/dev/null`
1020	global_revision="Rev: $global_revision"
1021	fi
1022
1023
1024	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1025	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1026	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1027	if [[ -n $host && "$host" != $localhost ]]
1028	then
1029	do_batch=true
1030	do_remote=true
1031	case $host in
1032	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1033	(*) printf "\n"
1034	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1035	printf "\n is not available"
1036	locat=nqs; (( iec = 0 )); exit;;
1037	esac
1038	else
1039	host=$localhost
1040	fi
1041
1042
1043
1044	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1045	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1046	then
1047
1048	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1049	if [[ ! -n $numprocs ]]
1050	then
1051	printf "\n"
1052	printf "\n +++ option \"-K parallel\" requires additional specification"
1053	printf "\n of the number of processors to be used by"
1054	printf "\n mrun-option \"-X\" or by environment-variable"
1055	printf "\n \"numprocs\" in the configuration file"
1056	locat=numprocs; (( iec = 0 )); exit
1057	fi
1058
1059	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1060	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1061	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1062	then
1063	printf "\n"
1064	printf "\n +++ option \"-T\" (tasks per node) is missing"
1065	printf "\n set -T option or define tasks_per_node in the config file"
1066	locat=tasks_per_node; (( iec = 0 )); exit
1067	fi
1068
1069	if (( numprocs < tasks_per_node ))
1070	then
1071	printf "\n"
1072	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1073	printf "\n given values: -T $tasks_per_node -X $numprocs"
1074	locat=tasks_per_node; (( iec = 0 )); exit
1075	fi
1076
1077	if [[ $host != lcflow && $host != lcxt5m ]]
1078	then
1079	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1080	(( ival = $tasks_per_node ))
1081	(( pes = numprocs ))
1082	(( ii = pes / ival ))
1083	(( remaining_pes = pes - ii * ival ))
1084	if (( remaining_pes > 0 ))
1085	then
1086	printf "\n"
1087	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1088	printf "\n divisor of the total number of processors (option \"-X\")"
1089	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1090	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1091	(( nodes = nodes + 1 ))
1092	fi
1093	fi
1094
1095
1096	# SETTINGS FOR SUBJOB-COMMAND
1097	OOPT="-O $threads_per_task"
1098
1099	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1100	if [[ "$tasks_per_node" != "" ]]
1101	then
1102	TOPT="-T $tasks_per_node"
1103	fi
1104
1105	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1106	if [[ $node_usage = default ]]
1107	then
1108	if [[ $host = ibms ]]
1109	then
1110	node_usage=shared
1111	else
1112	node_usage=not_shared
1113	fi
1114	fi
1115
1116	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1117	then
1118	printf "\n"
1119	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1120	printf "\n \"shared\" or \"not_shared\""
1121	locat=tasks_per_node; (( iec = 0 )); exit
1122	fi
1123
1124	fi
1125
1126	# CHECK IF HOSTFILE EXISTS
1127	if [[ -n $hostfile ]]
1128	then
1129	if [[ ! -f $hostfile ]]
1130	then
1131	printf "\n"
1132	printf "\n +++ hostfile \"$hostfile\" does not exist"
1133	locat=hostfile; exit
1134	fi
1135	fi
1136
1137
1138	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1139	if [[ "$maximum_parallel_io_streams" = "" ]]
1140	then
1141	maximum_parallel_io_streams=$numprocs
1142	fi
1143
1144
1145	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1146	if [[ "$scp_port" != "" ]]
1147	then
1148	PORTOPT="-P $scp_port"
1149	SSH_PORTOPT="-p $scp_port"
1150	fi
1151
1152
1153	# SET DEFAULT-QUEUE, IF NOT GIVEN
1154	if [[ $queue = none ]]
1155	then
1156	case $host in
1157	(ibmh) queue=cluster;;
1158	(ibmkisti) queue=class.32plus;;
1159	(lcbullhh) queue=compute;;
1160	(lccrayb) queue=mpp1q;;
1161	(lccrayh) queue=mpp1q;;
1162	(lckiaps) queue=normal;;
1163	(lckyoto) queue=ph;;
1164	(lckyuh) queue=fx-single;;
1165	(lckyut) queue=cx-single;;
1166	(lctit) queue=S;;
1167	(nech) queue=none;;
1168	(unics) queue=unics;;
1169	esac
1170	fi
1171
1172
1173	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1174	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1175	(( i = 0 ))
1176	while (( i < iin ))
1177	do
1178	(( i = i + 1 ))
1179	(( maxcycle = 0 ))
1180
1181	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1182	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1183	if [[ "${actionin[$i]}" = di ]]
1184	then
1185	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1186	# HOST ONLY
1187	eval filename=${pathin[$i]}/${endin[$i]}
1188	else
1189	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1190	# HOST ONLY
1191	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1192	fi
1193	eval pathname=${pathin[$i]}
1194
1195	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1196	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1197	then
1198	filename_input=$filename
1199	fi
1200
1201	# CHECK IF FILE EXISTS
1202	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1203	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1204	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1205	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1206	then
1207
1208	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1209	if [[ "${transin[$i]}" != "locopt" ]]
1210	then
1211	printf "\n\n +++ INPUT-file: "
1212	if [[ "${extin[$i]}" = "" ]]
1213	then
1214	printf "\n $filename"
1215	else
1216	printf "\n $filename.${extin[$i]}"
1217	fi
1218	printf "\n does not exist\n"
1219	locat=input; exit
1220	else
1221	transin[$i]="unavailable"
1222	fi
1223	else
1224
1225	# DETERMINE THE FILE'S CYCLE NUMBER
1226	ls -1 -d $filename > filelist 2>/dev/null
1227	ls -1 -d $filename.* >> filelist 2>/dev/null
1228	while read zeile
1229	do
1230	cycle=$(echo $zeile \| cut -f2 -d".")
1231	if [[ "$cycle" = "$zeile" ]]
1232	then
1233	(( icycle = 0 ))
1234	elif [[ "$cycle" = "${extin[$i]}" ]]
1235	then
1236	(( icycle = 0 ))
1237	else
1238	(( icycle = $cycle ))
1239	fi
1240	if (( icycle > maxcycle ))
1241	then
1242	(( maxcycle = icycle ))
1243	file_to_be_used=$zeile
1244	fi
1245	done <filelist
1246	rm filelist
1247
1248	# APPEND CYCLE NUMBER TO FILENAME
1249	if (( maxcycle > 0 ))
1250	then
1251	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1252	then
1253	filename=${filename}.$maxcycle.${extin[$i]}
1254	else
1255	filename=${filename}.$maxcycle
1256	fi
1257	else
1258	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1259	then
1260	filename=${filename}.${extin[$i]}
1261	fi
1262	fi
1263
1264	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1265	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1266	absnamein[$i]=$filename
1267	if (( maxcycle > 0 ))
1268	then
1269	if [[ "${actionin[$i]}" = di ]]
1270	then
1271	frelin[$i]=${endin[$i]}.$maxcycle
1272	else
1273	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1274	fi
1275	else
1276	if [[ "${actionin[$i]}" = di ]]
1277	then
1278	frelin[$i]=${endin[$i]}
1279	else
1280	frelin[$i]=${afname}${endin[$i]}
1281	fi
1282	fi
1283
1284	fi
1285	done
1286
1287	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1288	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1289	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1290	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1291	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1292	# REMOTE HOST)
1293	(( i = 0 ))
1294	while (( i < iout ))
1295	do
1296	(( i = i + 1 ))
1297	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1298	then
1299	if [[ "${actionout[$i]}" = tr ]]
1300	then
1301	actionout[$i]=""
1302	elif [[ "${actionout[$i]}" = trpe ]]
1303	then
1304	actionout[$i]=pe
1305	elif [[ "${actionout[$i]}" = tra ]]
1306	then
1307	actionout[$i]=a
1308	fi
1309	(( maxcycle = 0 ))
1310	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1311	eval catalogname=${pathout[$i]}
1312	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1313	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1314	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1315	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1316	then
1317
1318	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1319	if cat /dev/null > $filename
1320	then
1321	rm $filename
1322	else
1323
1324	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1325	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1326	if [[ ! -d $catalogname ]]
1327	then
1328	if mkdir -p $catalogname
1329	then
1330	printf "\n\n *** directory:"
1331	printf "\n $catalogname"
1332	printf "\n was created\n"
1333	else
1334	printf "\n\n +++ OUTPUT-file:"
1335	printf "\n $filename"
1336	printf "\n cannot be created, because directory does not exist"
1337	printf "\n and cannot be created either"
1338	printf "\n"
1339	locat=output ; exit
1340	fi 2>/dev/null
1341	else
1342	printf "\n\n +++ OUTPUT-file:"
1343	printf "\n $filename"
1344	printf "\n cannot be created, although directory exists"
1345	printf "\n"
1346	locat=output ; exit
1347	fi
1348	fi 2>/dev/null
1349	else
1350
1351	# DETERMINE THE CYCLE NUMBER
1352	ls -1 -d $filename > filelist 2>/dev/null
1353	ls -1 -d $filename.* >> filelist 2>/dev/null
1354	while read zeile
1355	do
1356	cycle=$(echo $zeile \| cut -f2 -d".")
1357	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1358	then
1359	(( icycle = 1 ))
1360	else
1361	(( icycle = $cycle + 1 ))
1362	fi
1363	if (( icycle > maxcycle ))
1364	then
1365	(( maxcycle = icycle ))
1366	fi
1367	done <filelist
1368	rm filelist
1369	fi
1370
1371	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1372	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1373	if [[ "${actionout[$i]}" != a ]]
1374	then
1375	if (( maxcycle > 0 ))
1376	then
1377	filename=${filename}.$maxcycle
1378	if cat /dev/null > $filename
1379	then
1380	rm $filename
1381	else
1382	printf "\n +++ OUTPUT-file:"
1383	printf "\n $filename"
1384	printf "\n cannot be created"
1385	locat=output ; exit
1386	fi
1387	fi
1388	else
1389	(( maxcycle = maxcycle - 1 ))
1390	if (( maxcycle > 0 ))
1391	then
1392	filename=${filename}.$maxcycle
1393	fi
1394	fi
1395
1396	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1397	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1398	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1399	pathout[$i]=$filename
1400	if (( maxcycle > 0 ))
1401	then
1402	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1403	else
1404	frelout[$i]=${fname}${endout[$i]}
1405	fi
1406
1407	fi
1408	done
1409
1410
1411	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1412	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1413	then
1414	if [[ "$dvr_inc" = "" ]]
1415	then
1416	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1417	printf "\n This is required for the dvrp_graphics package.\n"
1418	locat=dvr; exit
1419	fi
1420	if [[ "$dvr_lib" = "" ]]
1421	then
1422	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1423	printf "\n This is required for the dvrp_graphics package.\n"
1424	locat=dvr; exit
1425	fi
1426	fi
1427
1428
1429	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1430	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1431	if [[ "$mainprog" = "" && "$executable" = "" ]]
1432	then
1433	printf "\n +++ neither main program nor executable defined"
1434	locat=source; exit
1435	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1436	then
1437	printf "\n +++ main program as well as executable defined"
1438	locat=source; exit
1439	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1440	then
1441	do_compile=false
1442	fi
1443
1444
1445	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1446	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1447	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1448	then
1449	rm -rf SOURCES_FOR_RUN_$fname
1450	mkdir SOURCES_FOR_RUN_$fname
1451	fi
1452
1453
1454	# COLLECT ALL ROUTINES TO BE COMPILED
1455	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1456	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1457	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1458	then
1459
1460	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1461
1462	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1463	then
1464
1465	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1466	source_list=""
1467	cd $source_path
1468
1469
1470	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1471	if [[ ! -d .svn ]]
1472	then
1473	printf "\n\n +++ source directory"
1474	printf "\n \"$source_path\" "
1475	printf "\n is not under control of \"subversion\"."
1476	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1477	fi
1478
1479
1480	# LIST ALL MODIFIED SOURCE CODE FILES
1481	Filenames=""
1482	svn status > tmp_mrun
1483	while read line
1484	do
1485	firstc=`echo $line \| cut -c1`
1486	if [[ $firstc = M \|\| $firstc = "?" ]]
1487	then
1488	Name=`echo "$line" \| cut -c8-`
1489	extension=`echo $Name \| cut -d. -f2`
1490	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1491	then
1492	Filenames="$Filenames "$Name
1493	fi
1494	fi
1495	done < tmp_mrun
1496
1497
1498	# COPY FILES TO SOURCES_FOR_RUN_...
1499	for dateiname in $Filenames
1500	do
1501	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1502	source_list=$source_list"$dateiname "
1503	done
1504
1505	cd - > /dev/null
1506
1507
1508	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1509	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1510	elif [[ "$source_list" != "" && $restart_run != true ]]
1511	then
1512
1513	cd $source_path
1514
1515	for filename in $source_list
1516	do
1517
1518	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1519	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1520	then
1521	printf "\n +++ source code file: $filename"
1522	printf "\n must not contain (\"/\") "
1523	locat=source; exit
1524	fi
1525
1526	if [[ ! -f $filename ]]
1527	then
1528	printf "\n +++ source code file: $filename"
1529	printf "\n does not exist"
1530	locat=source; exit
1531	else
1532	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1533	fi
1534
1535	done
1536
1537	cd - > /dev/null
1538
1539	fi
1540
1541
1542	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1543	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1544	if [[ $restart_run != true ]]
1545	then
1546
1547	if [[ ! -f "$source_path/$mainprog" ]]
1548	then
1549	printf "\n\n +++ main program: $mainprog"
1550	printf "\n does not exist in source directory"
1551	printf "\n \"$source_path\"\n"
1552	locat=source; exit
1553	else
1554	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1555	then
1556	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1557	source_list=${mainprog}" $source_list"
1558	fi
1559	fi
1560	fi
1561
1562
1563	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1564	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1565	if [[ "$restart_run" != true ]]
1566	then
1567	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1568	if [[ ! -f $makefile ]]
1569	then
1570	printf "\n +++ file \"$makefile\" does not exist"
1571	locat=make; exit
1572	else
1573	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1574	fi
1575	fi
1576
1577
1578	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1579	if [[ $restart_run != true && "$add_source_path" != "" ]]
1580	then
1581
1582	# DOES THE DIRECTORY EXIST?
1583	if [[ ! -d $add_source_path ]]
1584	then
1585	printf "\n\n +++ WARNING: additional source code directory"
1586	printf "\n \"$add_source_path\" "
1587	printf "\n does not exist or is not a directory."
1588	printf "\n No source code will be used from this directory!\n"
1589	add_source_path=""
1590	if [[ $silent == false ]]
1591	then
1592	sleep 3
1593	fi
1594	else
1595
1596	cd $add_source_path
1597	found=false
1598
1599	Names=$(ls -1 *.f90 2>&1)
1600	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1601	Names=$(ls -1 *.F90 2>&1)
1602	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1603	Names=$(ls -1 *.F 2>&1)
1604	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1605	Names=$(ls -1 *.f 2>&1)
1606	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1607	Names=$(ls -1 *.c 2>&1)
1608	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1609
1610	cd - > /dev/null
1611	cd SOURCES_FOR_RUN_$fname
1612
1613	# COPY MAKEFILE IF EXISTING
1614	if [[ -f $add_source_path/Makefile ]]
1615	then
1616	printf "\n\n *** user Makefile from directory"
1617	printf "\n \"$add_source_path\" is used \n"
1618	if [[ $silent == false ]]
1619	then
1620	sleep 1
1621	fi
1622	cp $add_source_path/Makefile .
1623	fi
1624
1625	for dateiname in $AddFilenames
1626	do
1627	if [[ -f $dateiname ]]
1628	then
1629	printf "\n +++ source code file \"$dateiname\" found in additional"
1630	printf "\n source code directory \"$add_source_path\" "
1631	printf "\n but was also given with option \"-s\" which means that it should be taken"
1632	printf "\n from directory \"$source_path\"."
1633	locat=source; exit
1634	fi
1635
1636	cp $add_source_path/$dateiname .
1637	source_list="$source_list $dateiname"
1638
1639	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1640	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1641	then
1642	printf "\n\n +++ user file \"$dateiname\" "
1643	printf "\n is not listed in Makefile \n"
1644	locat=source; exit
1645	else
1646
1647	if [[ $found = false ]]
1648	then
1649	found=true
1650	printf "\n\n *** following user file(s) added to the"
1651	printf " files to be translated:\n "
1652	fi
1653	printf "$dateiname "
1654	if [[ $silent == false ]]
1655	then
1656	sleep 0.5
1657	fi
1658
1659	fi
1660	done
1661	[[ $found = true ]] && printf "\n"
1662	cd - > /dev/null
1663	fi
1664	fi
1665
1666
1667	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1668	# TO THE LIST OF FILES TO BE COMPILED
1669	if [[ $restart_run != true && -n $package_list ]]
1670	then
1671
1672	cd $source_path
1673
1674	for package in $package_list
1675	do
1676
1677	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1678
1679	# DETERMINE FILES BELONGING TO THE PACKAGE
1680	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1681	# THE NAME OF THE DIRECTORY
1682	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1683
1684
1685	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1686	# IF THEY ARE NOT ALREADY PART OF THE LIST
1687	for source_list_name in $package_source_list
1688	do
1689	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1690	then
1691
1692	# ONLY TAKE FILES WITH VALID SUFFIX
1693	ending=`echo $source_list_name \| cut -f2 -d.`
1694	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1695	then
1696	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1697	source_list="$source_list $source_list_name"
1698	fi
1699	fi
1700	done
1701	done
1702
1703	cd - > /dev/null
1704	fi
1705
1706	fi # do_compile=true
1707
1708
1709	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1710	# AND SET PRE-PROCESSOR DIRECTIVES
1711	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1712	then
1713
1714	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1715	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1716	then
1717	cpp_options="${cpp_options},-D__ibm=__ibm"
1718	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1719	then
1720	cpp_options="$cpp_options -D__nec"
1721	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1722	then
1723	cpp_options="$cpp_options -D__lc"
1724	else
1725	cpp_options="$cpp_options -D__$localhost"
1726	fi
1727
1728	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1729	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1730	then
1731	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1732	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1733	else
1734	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1735	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1736	fi
1737
1738	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1739	if [[ -n $package_list ]]
1740	then
1741	for package in $package_list
1742	do
1743	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1744	then
1745	if [[ $package != "dvrp_graphics+1PE" ]]
1746	then
1747	cpp_options="${cpp_options},-D__$package=__$package"
1748	else
1749	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1750	export use_seperate_pe_for_dvrp_output=true
1751	fi
1752	else
1753	if [[ $package != "dvrp_graphics+1PE" ]]
1754	then
1755	cpp_options="$cpp_options -D__$package"
1756	else
1757	cpp_options="$cpp_options -D__dvrp_graphics"
1758	export use_seperate_pe_for_dvrp_output=true
1759	fi
1760	fi
1761	done
1762	fi
1763
1764	# SET DIRECTIVES GIVEN BY OPTION -D
1765	if [[ -n $cpp_opts ]]
1766	then
1767	for popts in $cpp_opts
1768	do
1769	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1770	then
1771	cpp_options="${cpp_options},-D__$popts=__$popts"
1772	else
1773	cpp_options="$cpp_options -D__$popts"
1774	fi
1775	done
1776	fi
1777
1778	else
1779
1780
1781	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1782	if [[ $do_remote = false ]]
1783	then
1784	if [[ ! -f $executable ]]
1785	then
1786	printf "\n +++ executable file: $executable"
1787	printf "\n does not exist"
1788	locat=executable; exit
1789	fi
1790	fi
1791	fi
1792
1793
1794	# DETERMINE THE JOB MODE
1795	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1796	then
1797	if [[ "$LOADLBATCH" = yes ]]
1798	then
1799	batch_job=.TRUE.
1800	jobmo=BATCH
1801	else
1802	batch_job=.FALSE.
1803	jobmo=INTERACTIVE
1804	fi
1805	else
1806	if [[ "$ENVIRONMENT" = BATCH ]]
1807	then
1808	batch_job=.TRUE.
1809	jobmo=BATCH
1810	else
1811	batch_job=.FALSE.
1812	jobmo=INTERACTIVE
1813	fi
1814	fi
1815
1816	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1817	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1818	then
1819	printf "\n +++ no interactive runs allowed on host \"$host\" "
1820	printf "\n please submit batch job using mrun option \"-b\" \n"
1821	locat=normal; exit
1822	fi
1823
1824
1825	# CHECK, IF USER DEFINED A COMPILER
1826	if [[ "$compiler_name" = "" ]]
1827	then
1828
1829	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1830	locat=compiler_name; exit
1831
1832	fi
1833
1834
1835	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1836
1837	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1838	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1839	then
1840	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1841	else
1842	kennung=$RANDOM
1843	fi
1844
1845	if [[ "$tmp_user_catalog" = "" ]]
1846	then
1847	if [[ $localhost = ibmh ]]
1848	then
1849	tmp_user_catalog=$SCRATCH
1850	elif [[ $localhost = nech ]]
1851	then
1852	tmp_user_catalog=$WRKSHR
1853	else
1854	tmp_user_catalog=/tmp
1855	fi
1856	fi
1857	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1858
1859
1860	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1861	if [[ "$tmp_data_catalog" = "" ]]
1862	then
1863	if [[ $localhost = nech ]]
1864	then
1865	tmp_data_catalog=$WRKSHR/mrun_restart_data
1866	else
1867	tmp_data_catalog=/tmp/mrun_restart_data
1868	fi
1869	fi
1870
1871
1872	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1873	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1874	then
1875	eval fopts=\"$fopts\"
1876	eval lopts=\"$lopts\"
1877	fi
1878
1879
1880
1881	# DETERMINE COMPILE- AND LINK-OPTIONS
1882	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1883	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1884	ROPTS="$ropts"
1885	# 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 ]]
1886	# then
1887	XOPT="-X $numprocs"
1888	# fi
1889
1890
1891
1892	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1893	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1894	done=false
1895	while [[ $done = false ]]
1896	do
1897	cputime=$cpumax
1898	if (( $cputime == 0 ))
1899	then
1900	if [[ $do_batch = true ]]
1901	then
1902	printf "\n +++ cpu-time is undefined"
1903	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1904	printf "\n >>> "
1905	read cputime 1>/dev/null 2>&1
1906	else
1907	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1908	fi
1909	else
1910	done=true
1911	fi
1912	cpumax=$cputime
1913	done
1914
1915	(( minuten = cputime / 60 ))
1916	(( sekunden = cputime - minuten * 60 ))
1917
1918
1919	# CHECK THE MEMORY DEMAND
1920	if [[ $do_batch = true ]]
1921	then
1922	done=false
1923	while [[ $done = false ]]
1924	do
1925	if (( memory == 0 ))
1926	then
1927	printf "\n +++ memory demand is undefined"
1928	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1929	printf "\n >>> "
1930	read memory 1>/dev/null 2>&1
1931	else
1932	done=true
1933	fi
1934	done
1935	fi
1936
1937
1938	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1939	if [[ $do_remote = true && -z $remote_username ]]
1940	then
1941	while [[ -z $remote_username ]]
1942	do
1943	printf "\n +++ username on remote host \"$host\" is undefined"
1944	printf "\n >>> Please type username:"
1945	printf "\n >>> "
1946	read remote_username
1947	done
1948	mc="$mc -u$remote_username"
1949	fi
1950
1951	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1952	if [[ "$login_init_cmd" != "" ]]
1953	then
1954	export init_cmds="${login_init_cmd};"
1955	fi
1956
1957
1958	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1959	if [[ "$modules" != "" ]]
1960	then
1961	if [[ $host = lctit ]]
1962	then
1963	export module_calls=". $modules"
1964	else
1965	export module_calls="module load ${modules};"
1966	fi
1967	fi
1968
1969
1970
1971	# OUTPUT OF THE MRUN-HEADER
1972	calltime=$(date)
1973	printf "\n"
1974	printf "#------------------------------------------------------------------------# \n"
1975	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1976	printf "\| \| \n"
1977	spalte1="called on:"; spalte2=$localhost_realname
1978	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1979	if [[ $do_remote = true ]]
1980	then
1981	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1982	else
1983	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1984	fi
1985	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1986	if [[ -n $numprocs ]]
1987	then
1988	if [[ $run_coupled_model = false ]]
1989	then
1990	spalte1="number of PEs:"; spalte2=$numprocs
1991	else
1992	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
1993	fi
1994	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1995	fi
1996	if [[ -n $tasks_per_node ]]
1997	then
1998	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
1999	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2000	if (( remaining_pes > 0 ))
2001	then
2002	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2003	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2004	fi
2005	fi
2006	if [[ $maximum_parallel_io_streams != $numprocs ]]
2007	then
2008	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2009	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2010	fi
2011	if [[ $use_openmp = true ]]
2012	then
2013	spalte1="threads per task:"; spalte2="$threads_per_task"
2014	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2015	fi
2016	printf "\| \| \n"
2017	if [[ $do_compile = true ]]
2018	then
2019	if [[ "$mopts" != "" ]]
2020	then
2021	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2022	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2023	zeile=$(echo "$mopts" \| cut -c46-)
2024	while [[ "$zeile" != "" ]]
2025	do
2026	spalte1=""
2027	spalte2=$(echo "$zeile" \| cut -c-45)
2028	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2029	zeile=$(echo "$zeile" \| cut -c46-)
2030	done
2031	fi
2032
2033	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2035	zeile=$(echo "$cpp_options" \| cut -c46-)
2036	while [[ "$zeile" != "" ]]
2037	do
2038	spalte1=""
2039	spalte2=$(echo "$zeile" \| cut -c-45)
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	zeile=$(echo "$zeile" \| cut -c46-)
2042	done
2043
2044	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046	zeile=$(echo "$fopts" \| cut -c46-)
2047	while [[ "$zeile" != "" ]]
2048	do
2049	spalte1=""
2050	spalte2=$(echo "$zeile" \| cut -c-45)
2051	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2052	zeile=$(echo "$zeile" \| cut -c46-)
2053	done
2054
2055	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2056	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2057	zeile=$(echo "$lopts" \| cut -c46-)
2058	while [[ "$zeile" != "" ]]
2059	do
2060	spalte1=""
2061	spalte2=$(echo "$zeile" \| cut -c-45)
2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2063	zeile=$(echo "$zeile" \| cut -c46-)
2064	done
2065
2066	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2067	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2068	zeile=$(echo "$modules" \| cut -c46-)
2069	while [[ "$zeile" != "" ]]
2070	do
2071	spalte1=""
2072	spalte2=$(echo "$zeile" \| cut -c-45)
2073	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2074	zeile=$(echo "$zeile" \| cut -c46-)
2075	done
2076
2077	spalte1="main program:"; spalte2=$mainprog
2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2079	else
2080	spalte1=executable:; spalte2=$executable
2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2082	fi
2083	printf "\| \| \n"
2084	spalte1="base name of files:"; spalte2=$fname
2085	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2086	if [[ $fname != $afname ]]
2087	then
2088	spalte1="base name of input files:"; spalte2=$afname
2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2090	fi
2091	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2093	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2094	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2095
2096	if [[ "$ocean_file_appendix" = true ]]
2097	then
2098	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2099	fi
2100
2101	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2102	then
2103	spalte1="memory demand / PE":; spalte2="$memory MB"
2104	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2105	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2106	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2107	fi
2108
2109	if [[ $do_compile = true ]]
2110	then
2111	printf "\| \| \n"
2112	printf "\| Files to be compiled: \| \n"
2113	zeile=$source_list
2114	while [[ "$zeile" != "" ]]
2115	do
2116	linestart=$(echo $zeile \| cut -c-70)
2117	printf "\| %-70s \| \n" "$linestart"
2118	zeile=$(echo "$zeile" \| cut -c71-)
2119	done
2120	fi
2121	printf "#------------------------------------------------------------------------#"
2122
2123
2124
2125	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2126	if [[ $do_trace = true ]]
2127	then
2128	(( i = 0 ))
2129	while (( i < iin ))
2130	do
2131	(( i = i + 1 ))
2132	if (( i == 1 ))
2133	then
2134	printf "\n\n >>> INPUT-file assignments:\n"
2135	fi
2136	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2137	done
2138	(( i = 0 ))
2139	while (( i < iout ))
2140	do
2141	(( i = i + 1 ))
2142	if (( i == 1 ))
2143	then
2144	printf "\n\n >>> OUTPUT-file assignments:\n"
2145	fi
2146	printf "\n ${localout[$i]} : ${pathout[$i]}"
2147	done
2148	(( i = 0 ))
2149	while (( i < iic ))
2150	do
2151	(( i = i + 1 ))
2152	if (( i == 1 ))
2153	then
2154	printf "\n\n >>> INPUT-commands:\n"
2155	fi
2156	printf "\n ${in_command[$i]}"
2157	done
2158	(( i = 0 ))
2159	while (( i < ioc ))
2160	do
2161	(( i = i + 1 ))
2162	if (( i == 1 ))
2163	then
2164	printf "\n\n >>> OUTPUT-commands:\n"
2165	fi
2166	printf "\n ${out_command[$i]}"
2167	done
2168	fi
2169
2170	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2171	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2172	then
2173	antwort=dummy
2174	printf "\n\n"
2175	printf " >>> everything o.k. (y/n) ? "
2176	while read antwort
2177	do
2178	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2179	then
2180	printf " >>> everything o.k. (y/n) ? "
2181	else
2182	break
2183	fi
2184	done
2185	if [[ $antwort = n \|\| $antwort = N ]]
2186	then
2187	locat=user_abort; (( iec = 0 )); exit
2188	fi
2189	if [[ $do_batch = true ]]
2190	then
2191	printf " >>> batch-job will be created and submitted"
2192	else
2193	printf " >>> MRUN will now continue to execute on this machine"
2194	fi
2195	fi
2196
2197
2198	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2199	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2200	check_depository="${working_directory}/trunk/UTIL"
2201	check_sources="${working_directory}/tmp_check_namelist_files"
2202	skip_check=false
2203
2204	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2205	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2206	then
2207	skip_check=true
2208	reason="run on remote host or parameter file check has not been compiled."
2209	fi
2210	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2211	then
2212	skip_check=true
2213	reason="parameter file check has not been compiled."
2214	fi
2215
2216	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2217	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2218	then
2219	skip_check=true
2220	reason="serial run."
2221	fi
2222
2223	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2224	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2225	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2226	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2227	if [[ $check_namelist_files == false ]]
2228	then
2229	skip_check=true
2230	reason="-z option set."
2231	fi
2232
2233	if [[ $fromhost != $localhost ]]
2234	then
2235	skip_check=true
2236	reason="submitting host is local host."
2237	fi
2238
2239	if [[ $run_coupled_model == true ]]
2240	then
2241	skip_check=true
2242	reason="coupled run."
2243	fi
2244
2245	if [[ $restart_run == true ]]
2246	then
2247	skip_check=true
2248	reason="restart run."
2249	fi
2250
2251	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2252	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2253	last_char=`echo $filename_input \| cut -c $last_char_int`
2254	if [[ "$last_char" == "f" ]]
2255	then
2256	skip_check=true
2257	reason="restart run."
2258	fi
2259
2260	if [[ $skip_check == false ]]
2261	then
2262	tmp_check=${working_directory}/tmp_check
2263
2264	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2265	# NOT NECESSARILY REQUIRED
2266	line=""
2267	found=false
2268	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2269	while read line1
2270	do
2271	line="$line1"
2272	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2273	then
2274	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2275	found=true
2276	fi
2277	done < $tmp_check
2278
2279	if [[ $found = false ]]
2280	then
2281	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2282	fi
2283
2284	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2285	# NOT NECESSARILY REQUIRED
2286	line=""
2287	found=false
2288	grep "NUDGING_DATA" $config_file > $tmp_check
2289	while read line1
2290	do
2291	line="$line1"
2292	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2293	then
2294	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2295	found=true
2296	fi
2297	done < $tmp_check
2298
2299	if [[ $found = false ]]
2300	then
2301	printf "\n +++ no NUDGING list entry found in the configuration file."
2302	fi
2303
2304	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2305	# NOT NECESSARILY REQUIRED
2306	line=""
2307	found=false
2308	grep "LSF_DATA" $config_file > $tmp_check
2309	while read line1
2310	do
2311	line="$line1"
2312	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2313	then
2314	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2315	found=true
2316	fi
2317	done < $tmp_check
2318
2319	if [[ $found = false ]]
2320	then
2321	printf "\n +++ no LSF list entry found in the configuration file."
2322	fi
2323
2324	rm -rf ${working_directory}/tmp_check
2325
2326	# CHECK IF THE P3DF FILE MUST BE CHECKED
2327	for item in $input_list
2328	do
2329	if [[ "$item" == "restart" ]]
2330	then
2331	check_restart=1
2332	else
2333	check_restart=0
2334	fi
2335	done
2336
2337	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2338	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2339	then
2340	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2341	locat=check_namelist; exit
2342	fi
2343
2344	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2345	if [[ $check_restart == 1 ]]
2346	then
2347
2348	filenamef="${filename_input}f"
2349	if [[ ! -f $filenamef ]]
2350	then
2351	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2352	check_restart=0
2353	answer=dummy
2354	printf "\n\n"
2355
2356	if [[ $silent == false ]]
2357	then
2358	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2359	do
2360	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2361	read answer
2362	done
2363	if [[ $answer = a \|\| $answer = A ]]
2364	then
2365	printf "\n +++ Aborting...."
2366	locat=normal; exit
2367	fi
2368	fi
2369	else
2370	check_restart=1
2371	fi
2372	fi
2373
2374	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2375	mkdir $check_sources
2376	cd $check_sources
2377
2378
2379	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2380	if [[ -d $add_source_path ]]
2381	then
2382	printf "\n\n *** copying files from $check_depository"
2383	cp $check_depository/check_namelist_files.tar ./
2384
2385	printf "\n\n *** untar of makefile and source files in $check_sources"
2386	tar -xf check_namelist_files.tar > /dev/null 2>&1
2387
2388	printf "\n\n *** adding user code."
2389	cp $add_source_path/* ./
2390	touch check_namelist_files.f90
2391
2392	# GET COMPILER OPTIONS AND PERFORM MAKE
2393	printf "\n\n *** compiling code if necessary...\n"
2394
2395	# workaround for batch jobs on local machine (lcxe6)
2396	if [[ $do_batch == true && $do_remote == false ]]
2397	then
2398	eval $init_cmds
2399	fi
2400
2401	# GET CHECK OPTIONS
2402	line=""
2403	found=false
2404
2405	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2406
2407	while read line1
2408	do
2409
2410	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2411	then
2412	line="$line1"
2413	fi
2414
2415	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2416	then
2417	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2418	line="$line "
2419	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'`
2420	found=true
2421	fi
2422
2423	done < $tmp_check
2424	copts_check="$copts_check -D__check -D__parallel"
2425
2426	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2427
2428	# GET MAKE OUTPUT
2429	if [[ $? != 0 ]]
2430	then
2431	printf "\n +++ error during make."
2432	answer=dummy
2433	printf "\n\n"
2434	if [[ $silent == false ]]
2435	then
2436	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2437	do
2438	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2439	read answer
2440	done
2441	if [[ $answer = a \|\| $answer = A ]]
2442	then
2443	printf "\n +++ Aborting..."
2444	rm -rf $check_sources
2445	locat=normal; exit
2446	else
2447	skip_check=true
2448	fi
2449	else
2450	skip_check=true
2451	fi
2452	fi
2453	else
2454	cp $PALM_BIN/check_namelist_files.x ./
2455	fi
2456
2457	cp $filename_input ./PARIN
2458	if [[ $check_restart == 1 ]]
2459	then
2460	cp $filenamef ./PARINF
2461	fi
2462
2463	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2464	then
2465	printf "\n *** adding topography data"
2466	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2467
2468	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2469	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2470	# WHICH REQUIRE SUFFICIENT MEMORY
2471	ulimit -s unlimited
2472	fi
2473
2474	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2475	then
2476	printf "\n *** adding nudging data"
2477	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2478	fi
2479
2480	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2481	then
2482	printf "\n *** adding large scale forcing data"
2483	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2484	fi
2485
2486	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2487	cat > ENVPAR << %%END%%
2488	&envpar run_identifier = '$fname', host = '$host',
2489	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2490	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2491	maximum_cpu_time_allowed = ${cpumax}.,
2492	revision = '$global_revision',
2493	local_dvrserver_running = $local_dvrserver_running /
2494
2495	%%END%%
2496
2497	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2498	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2499	then
2500	printf "\n +++ WARNING: check_namelist_files.x not found."
2501	answer=dummy
2502	printf "\n\n"
2503
2504	if [[ $silent == false ]]
2505	then
2506	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2507	do
2508	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2509	read answer
2510	done
2511	if [[ $answer = a \|\| $answer = A ]]
2512	then
2513	printf "\n +++ Aborting..."
2514	rm -rf $check_sources
2515	locat=normal; exit
2516	else
2517	printf "\n *** skipping parameter file check."
2518	fi
2519	fi
2520
2521	elif [[ $skip_check == false ]]
2522	then
2523	# STARTING THE PARAMETER FILE CHECK
2524	printf "\n\n *** starting parameter file check..."
2525
2526	# CHECKING THE P3D FILE
2527	printf "\n\n (1) checking $filename_input"
2528	echo "$numprocs 0 0" > VARIN
2529	errors=`./check_namelist_files.x < VARIN 2>&1`
2530
2531	check_error=false
2532	if [[ "$errors" == "" ]]
2533	then
2534	printf " --> o.k."
2535	else
2536	printf " --> failed."
2537	check_error=true
2538	printf "\n\n $errors"
2539	fi
2540
2541	# CHECKING THE PD3F FILE IF NECESSARY
2542	if [[ $check_restart == 1 && $check_error == false ]]
2543	then
2544	printf "\n\n (2) checking $filenamef"
2545
2546	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2547	# IN &INIPAR LIST
2548	found=false
2549	cat PARINF \| while read line
2550	do
2551	line=$(echo $line\|sed 's/ //g')
2552	if [[ $line == "&inipar" ]]
2553	then
2554	start_search=true
2555	fi
2556
2557	if [[ $start_search == true ]]
2558	then
2559	if [[ $line == "initializing_actions='read_restart_data'" ]]
2560	then
2561	found=true
2562	break
2563	fi
2564	fi
2565
2566	if [[ $line == "/" ]]
2567	then
2568	start_search=false
2569	fi
2570
2571	done
2572
2573	if [[ $found = false ]]
2574	then
2575	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2576	printf "\n in &inipar list in $fname$p3df_suffix."
2577	rm -rf $check_sources
2578	locat=check_namelist; exit
2579	fi
2580
2581	# READ max_user_pr FROM FILES
2582	if [[ -f parin_for_check ]]
2583	then
2584	read max_pr_user < parin_for_check
2585	else
2586	max_user_pr=0
2587	fi
2588
2589	echo "$numprocs 1 $max_pr_user" > VARIN
2590	errors=`./check_namelist_files.x < VARIN 2>&1`
2591
2592	if [[ "$errors" == "" ]]
2593	then
2594	printf " --> o.k."
2595	else
2596	printf " --> failed."
2597	check_error=true
2598	printf "\n\n $errors"
2599	fi
2600	fi
2601
2602	# REPORT ERRORS AND CONTINUE/EXIT
2603	if [[ $check_error == true ]]
2604	then
2605	printf "\n +++ errors found in the parameter file!\n"
2606	answer=dummy
2607	printf "\n\n"
2608
2609	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2610	do
2611	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2612	read answer
2613	done
2614
2615	if [[ $answer = a \|\| $answer = A ]]
2616	then
2617	printf "\n +++ Aborting..."
2618	rm -rf $check_sources
2619	locat=normal; exit
2620	fi
2621	else
2622	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2623	fi
2624	rm -rf $check_sources
2625	fi
2626	else
2627	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2628	fi
2629
2630	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2631	rm -rf $check_sources
2632	cd $working_directory
2633
2634	# DETERMINE PATH FOR MAKE DEPOSITORY
2635	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2636	then
2637
2638	line=""
2639	grep "%depository_path" $config_file > tmp_mrun
2640	while read line
2641	do
2642	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2643	then
2644	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2645	then
2646	global_depository_path=`echo $line \| cut -d" " -s -f2`
2647	fi
2648	fi
2649	done < tmp_mrun
2650
2651	line=""
2652	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2653	while read line
2654	do
2655	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2656	then
2657	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2658	then
2659	local_depository_path=`echo $line \| cut -d" " -s -f2`
2660	fi
2661	fi
2662	done < tmp_mrun
2663
2664	if [[ "$local_depository_path" = "" ]]
2665	then
2666	if [[ "$global_depository_path" != "" ]]
2667	then
2668	local_depository_path=$global_depository_path
2669	else
2670	printf "\n\n +++ no depository path found in configuration file"
2671	printf "\n for local host \"$localhost\" "
2672	printf "\n please set \"\%depository_path\" in configuration file\n"
2673	locat=config_file; exit
2674	fi
2675	fi
2676	eval local_depository_path=$local_depository_path
2677	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2678	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2679
2680
2681	basename=`echo $mainprog \| cut -f1 -d"."`
2682	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2683	if [[ ! -f $make_depository ]]
2684	then
2685	printf "\n"
2686	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2687	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2688	fi
2689
2690	fi
2691
2692
2693	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2694	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2695	if [[ $do_batch = false ]]
2696	then
2697
2698
2699	# CREATE THE TEMPORARY WORKING DIRECTORY
2700	mkdir -p $TEMPDIR
2701	chmod go+rx $TEMPDIR
2702	tmpcreate=true
2703
2704
2705	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2706	# INTO THE TEMPORARY WORKING DIRECTORY
2707	if [[ $do_compile = true ]]
2708	then
2709
2710	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2711	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2712	if [[ $localhost = nech ]]
2713	then
2714	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2715	if mkdir -p $TEMPDIR_COMPILE
2716	then
2717	printf "\n *** \"$TEMPDIR_COMPILE\" "
2718	printf "\n is generated as temporary directory for cross compiling\n"
2719	else
2720	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2721	printf "\n needed for cross compilation failed"
2722	locat=compile
2723	exit
2724	fi
2725	else
2726	TEMPDIR_COMPILE=$TEMPDIR
2727	fi
2728
2729	cp $make_depository $TEMPDIR_COMPILE
2730	cd $TEMPDIR_COMPILE
2731	tar -xf $make_depository > /dev/null 2>&1
2732	cd - > /dev/null
2733
2734	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2735	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2736	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2737	then
2738	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2739	else
2740	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2741	fi
2742
2743	else
2744
2745	cp $executable ${TEMPDIR}/a.out
2746
2747	fi
2748
2749
2750	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2751	cd $TEMPDIR
2752	printf "\n *** changed to temporary directory: $TEMPDIR"
2753
2754
2755	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2756	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2757	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2758	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2759	(( i = 0 ))
2760	while (( i < iout ))
2761	do
2762	(( i = i + 1 ))
2763	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2764	then
2765	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2766	else
2767	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2768	fi
2769	done
2770
2771
2772	# IF REQUIRED, START WITH COMPILING
2773	if [[ $do_compile = true ]]
2774	then
2775
2776
2777	if [[ -f a.out ]]
2778	then
2779
2780	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2781	printf "\n\n\n *** executable a.out found"
2782	printf "\n no compilation required \n"
2783
2784	else
2785
2786	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2787	printf "\n\n\n *** compilation starts \n$dashes\n"
2788	printf " *** compilation with make using following options:\n"
2789	printf " make depository: $make_depository"
2790	if [[ "$mopts" != "" ]]
2791	then
2792	printf " make options: $mopts\n"
2793	fi
2794	printf " compilername: $compiler_name\n"
2795	printf " compiler options: $fopts\n"
2796	printf " preprocessor directives: $cpp_options \n"
2797	printf " linker options: $lopts \n"
2798	if [[ "$modules" != "" ]]
2799	then
2800	printf " modules to be load: $modules \n"
2801	fi
2802	printf " source code files: $source_list \n"
2803
2804	if [[ $localhost = nech ]]
2805	then
2806	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\" "
2807	cp $TEMPDIR_COMPILE/a.out .
2808	[[ $? != 0 ]] && compile_error=true
2809	rm -rf $TEMPDIR_COMPILE
2810	elif [[ $localhost = ibmh ]]
2811	then
2812	printf " compiler is called via ssh on \"plogin1\" \n"
2813	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\" "
2814	[[ ! -f a.out ]] && compile_error=true
2815	continue # STATUS=1, IF a.out EXISTS
2816	elif [[ $localhost = lcflow ]]
2817	then
2818	printf " compiler is called via ssh on \"flow\" \n"
2819	/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\" "
2820	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2821	[[ "$check_for_file" = "" ]] && compile_error=true
2822	continue # STATUS=1, IF a.out EXISTS
2823	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2824	then
2825	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2826	else
2827	[[ "$init_cmds" != "" ]] && eval $init_cmds
2828	[[ "$module_calls" != "" ]] && eval $module_calls
2829	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2830	fi
2831
2832	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2833	then
2834	printf "\n +++ error occured while compiling or linking"
2835	locat=compile
2836
2837	exit
2838	else
2839	printf "$dashes\n *** compilation finished \n"
2840	fi
2841
2842	fi
2843
2844	fi
2845
2846
2847	# PROVIDE THE INPUT FILES
2848	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2849	(( i = 0 ))
2850	while (( i < iin ))
2851	do
2852	(( i = i + 1 ))
2853	if (( i == 1 ))
2854	then
2855	printf "\n\n *** providing INPUT-files:\n$dashes"
2856	fi
2857
2858
2859	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2860	if [[ "${transin[$i]}" = unavailable ]]
2861	then
2862	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2863	then
2864	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2865	printf "\n is not available!"
2866	else
2867	printf "\n +++ WARNING: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2868	printf "\n is not available!"
2869	fi
2870	continue
2871	fi
2872
2873	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2874	files_for_pes=false; datentyp=file
2875	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2876	then
2877	files_for_pes=true; datentyp=directory
2878	actionin[$i]=""
2879	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2880	then
2881	actionin[$i]=""
2882	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2883	then
2884	files_for_pes=true; datentyp=directory
2885	actionin[$i]="ar"
2886	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2887	then
2888	actionin[$i]="ar"
2889	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2890	then
2891	files_for_pes=true; datentyp=directory
2892	actionin[$i]="fl"
2893	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2894	then
2895	actionin[$i]="fl"
2896	fi
2897
2898	if [[ $files_for_pes = true ]]
2899	then
2900	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2901	else
2902	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2903	fi
2904
2905	# INPUT-FILE FOR A RESTART RUN.
2906	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2907	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2908	if [[ "${actionin[$i]}" = fl ]]
2909	then
2910	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2911	if [[ $files_for_pes = false ]]
2912	then
2913	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2914	then
2915	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2916	got_tmp[$i]=true
2917	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2918	then
2919	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2920	printf "\n *** trying to use backup copy in \"$WORK\" "
2921	cp $WORK/${frelin[$i]} ${localin[$i]}
2922	else
2923	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2924	printf "\n or \"$tmp_data_catalog\" does not exist!"
2925	printf "\n *** trying to get copy from archive"
2926	actionin[$i]=ar
2927	fi
2928	else
2929	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2930	then
2931	mkdir ${localin[$i]}
2932	cd $tmp_data_catalog/${frelin[$i]}
2933	for file in $(ls *)
2934	do
2935	ln $file $TEMPDIR/${localin[$i]}
2936	done
2937	cd $TEMPDIR
2938	got_tmp[$i]=true
2939	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2940	then
2941	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2942	printf "\n *** trying to use backup copy in \"$WORK\" "
2943	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2944	else
2945	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2946	printf "\n or \"$tmp_data_catalog\" does not exist!"
2947	printf "\n *** trying to get copy from archive"
2948	actionin[$i]=ar
2949	fi
2950	fi
2951	fi
2952
2953
2954	# FILE IS STORED ON THE ARCHIVE SYSTEM
2955	if [[ "${actionin[$i]}" = ar ]]
2956	then
2957
2958	if [[ $files_for_pes = false ]]
2959	then
2960	printf "\n file will be restored from archive-system ($archive_system)!"
2961	else
2962	printf "\n directory will be restored from archive-system ($archive_system)!"
2963	fi
2964
2965	file_restored=false
2966
2967	if [[ $archive_system = asterix ]]
2968	then
2969	do_stagein=true
2970	(( stagein_anz = 0 ))
2971	while [[ $do_stagein = true ]]
2972	do
2973	if [[ $files_for_pes = false ]]
2974	then
2975	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2976	else
2977	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2978	fi
2979	cat STAGEIN_OUTPUT
2980	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2981	then
2982	file_restored=true
2983	do_stagein=false
2984	else
2985	(( stagein_anz = stagein_anz + 1 ))
2986	if (( stagein_anz == 10 ))
2987	then
2988	printf "\n +++ stagein stoped after 10 tries"
2989	locat=stage
2990	exit
2991	fi
2992	printf "\n +++ restoring from archive failed, trying again:"
2993	sleep 900
2994	fi
2995	done
2996	elif [[ $archive_system = DMF ]]
2997	then
2998	if [[ $files_for_pes = false ]]
2999	then
3000	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3001	locat=DMF
3002	exit
3003	else
3004	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3005	cp -r $ARCHIVE/${frelin[$i]} $PWD
3006	file_restored=true
3007	fi
3008	elif [[ $archive_system = tivoli ]]
3009	then
3010	if [[ $files_for_pes = false ]]
3011	then
3012	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3013	else
3014	(( inode = 0 ))
3015	while (( inode < nodes ))
3016	do
3017	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3018	(( inode = inode + 1 ))
3019	done
3020	fi
3021	file_restored=true
3022	elif [[ $archive_system = ut ]]
3023	then
3024	if [[ $files_for_pes = false ]]
3025	then
3026	cp $UT/${frelin[$i]} .
3027	else
3028	(( inode = 0 ))
3029	while (( inode < nodes ))
3030	do
3031	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3032	(( inode = inode + 1 ))
3033	done
3034	fi
3035	file_restored=true
3036	else
3037	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3038	locat=rearchive
3039	exit
3040	fi
3041
3042	if [[ $file_restored = true ]]
3043	then
3044
3045	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3046	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3047	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3048	if [[ $files_for_pes = false ]]
3049	then
3050	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3051	else
3052	mkdir $tmp_data_catalog/${frelin[$i]}
3053	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3054	fi
3055	got_tmp[$i]=true
3056
3057	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3058	mv ${frelin[$i]} ${localin[$i]}
3059
3060	fi
3061	fi
3062
3063
3064	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3065	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3066	then
3067
3068	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3069	then
3070
3071	# FILE COPIES ARE PROVIDED FOR ALL CORES
3072	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3073	printf "\n file will be provided for $numprocs processors"
3074	mkdir ${localin[$i]}
3075	ival=$numprocs
3076	(( ii = 0 ))
3077	while (( ii <= ival-1 ))
3078	do
3079	if (( ii < 10 ))
3080	then
3081	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3082	elif (( ii < 100 ))
3083	then
3084	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3085	elif (( ii < 1000 ))
3086	then
3087	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3088	else
3089	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3090	fi
3091	(( ii = ii + 1 ))
3092	done
3093
3094	else
3095
3096	if [[ $files_for_pes = true ]]
3097	then
3098
3099	# PROVIDE FILES FOR EACH CORE
3100	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3101	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3102	printf "\n providing $numprocs files for the respective processors"
3103	mkdir ${localin[$i]}
3104	if [[ $link_local_input = true ]]
3105	then
3106	printf " using ln -f\n"
3107	cd ${absnamein[$i]}
3108	for file in $(ls *)
3109	do
3110	ln -f $file ${localin[$i]}
3111	done
3112	cd $TEMPDIR
3113	fi
3114
3115	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3116	if [[ ! -f "${localin[$i]}/_0000" ]]
3117	then
3118	if [[ $link_local_input = true ]]
3119	then
3120	printf " ln failed for .../_0000, using cp...\n"
3121	fi
3122	cp -r ${absnamein[$i]}/* ${localin[$i]}
3123	fi
3124
3125	else
3126
3127	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3128	if [[ $link_local_input = true ]]
3129	then
3130	printf " using ln -f\n"
3131	ln -f ${absnamein[$i]} ${localin[$i]}
3132	fi
3133	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3134	if [[ ! -f "${localin[$i]}" ]]
3135	then
3136	if [[ $link_local_input = true ]]
3137	then
3138	printf " ln failed, using cp...\n"
3139	fi
3140	cp ${absnamein[$i]} ${localin[$i]}
3141	fi
3142	fi
3143	fi
3144	fi
3145
3146	done
3147	if (( i != 0 ))
3148	then
3149	printf "\n$dashes\n *** all INPUT-files provided \n"
3150	fi
3151
3152
3153	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3154	(( i = 0 ))
3155	while (( i < iic ))
3156	do
3157	(( i = i + 1 ))
3158	if (( i == 1 ))
3159	then
3160	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3161	fi
3162	printf "\n >>> ${in_command[$i]}"
3163	eval ${in_command[$i]}
3164	if (( i == iic ))
3165	then
3166	printf "\n$dashes\n"
3167	fi
3168	done
3169
3170
3171	# SET THE REMAINING CPU-TIME
3172	cpurest=${cpumax}.
3173
3174
3175	# START DVR STREAMING SERVER
3176	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3177	then
3178	if [[ "$dvr_server" != "" ]]
3179	then
3180
3181	printf "\n\n *** preparing the dvr streaming server configuration file"
3182
3183	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3184	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3185	if [[ "$running_dvrserver_id" != "" ]]
3186	then
3187
3188	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3189	printf "\n This server is used instead starting a new one!"
3190	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3191
3192	else
3193
3194	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3195	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3196	then
3197	cp ${PALM_BIN}/.dvrserver.config .
3198
3199	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3200	user_id=`id -u`
3201	group_id=`id -g`
3202
3203	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3204	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3205	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3206	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3207	mv .dvrserver.3 .dvrserver.config
3208	rm .dvrserver.1 .dvrserver.2
3209
3210	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3211	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3212	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3213	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3214	local_dvrserver_running=.TRUE.
3215	else
3216	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3217	printf "\n \"$PALM_BIN\" "
3218	locat=dvr
3219	exit
3220	fi
3221
3222	fi
3223
3224	else
3225	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3226	fi
3227	fi
3228
3229
3230	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3231	# (FILE ENVPAR WILL BE READ BY PALM)
3232	cat > ENVPAR << %%END%%
3233	&envpar run_identifier = '$fname', host = '$localhost',
3234	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3235	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3236	maximum_cpu_time_allowed = ${cpumax}.,
3237	revision = '$global_revision',
3238	local_dvrserver_running = $local_dvrserver_running,
3239	batch_job = $batch_job /
3240
3241	%%END%%
3242
3243
3244	# STARTING THE EXECUTABLE
3245	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3246	PATH=$PATH:$TEMPDIR
3247
3248	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3249	if [[ "$mpi_debug" = true ]]
3250	then
3251	export MPI_CHECK_ARGS=1
3252	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3253	fi
3254
3255	if [[ "$totalview" = true ]]
3256	then
3257	printf "\n *** totalview debugger will be used"
3258	tv_opt="-tv"
3259	else
3260	tv_opt=""
3261	fi
3262
3263	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3264	then
3265
3266	#Interactive ALLINEA DEBUG seesion
3267	if [[ "$ENVIRONMENT" != BATCH ]]
3268	then
3269	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3270	then
3271	if [[ "$allinea" = true ]]
3272	then
3273	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3274
3275	ddt aprun -n $ii -N $tasks_per_node a.out $ROPTS
3276	wait
3277	fi
3278	fi
3279	fi
3280
3281	if [[ "$ENVIRONMENT" = BATCH ]]
3282	then
3283	continue
3284	fi
3285	if [[ $localhost = ibmh ]]
3286	then
3287
3288	# SETUP THE IBM MPI ENVIRONMENT
3289	export MP_SHARED_MEMORY=yes
3290	export AIXTHREADS_SCOPE=S
3291	export OMP_NUM_THREADS=$threads_per_task
3292	export AUTHSTATE=files
3293	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3294
3295	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3296	export MP_ADAPTER_USE=shared
3297	export MP_CPU_USE=multiple
3298	export MP_TIMEOUT=1200
3299
3300	unset MP_TASK_AFFINITY
3301
3302	# SO FAR, TOTALVIEW NEEDS HOSTFILE MECHANISM FOR EXECUTION
3303	#(( ii = 1 ))
3304	#while (( ii <= $numprocs ))
3305	#do
3306	# echo $localhost_realname >> hostfile
3307	# (( ii = ii + 1 ))
3308	#done
3309	#export MP_HOSTFILE=hostfile
3310
3311	if [[ "$LOADLBATCH" = yes ]]
3312	then
3313	totalview poe a.out $ROPTS
3314	else
3315	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3316	export TVDSVRLAUNCHCMD=ssh
3317	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1 $ROPTS
3318	fi
3319
3320	fi # END DEBUG MODE
3321
3322	else
3323
3324	# NORMAL EXECUTION
3325	if [[ -n $numprocs ]]
3326	then
3327
3328	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3329	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3330	then
3331
3332	# SETUP THE IBM MPI ENVIRONMENT
3333	if [[ $host != ibmh && $host != ibmkisti ]]
3334	then
3335	export MP_SHARED_MEMORY=yes
3336	export AIXTHREAD_SCOPE=S
3337	export OMP_NUM_THREADS=$threads_per_task
3338	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3339	export AUTHSTATE=files
3340	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3341	# export MP_PRINTENV=yes
3342
3343	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3344	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3345	export MP_WAIT_MODE=poll
3346	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3347	fi
3348
3349	if [[ $host = ibmkisti ]]
3350	then
3351	export LANG=en_US
3352	export MP_SHARED_MEMORY=yes
3353	if [[ $threads_per_task = 1 ]]
3354	then
3355	export MP_SINGLE_THREAD=yes
3356	export MEMORY_AFFINITY=MCM
3357	else
3358	export OMP_NUM_THREADS=$threads_per_task
3359	fi
3360	fi
3361
3362	if [[ "$LOADLBATCH" = yes ]]
3363	then
3364	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3365	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3366	then
3367	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out $ROPTS
3368	else
3369	if [[ $run_coupled_model = false ]]
3370	then
3371	if [[ "$ocean_file_appendix" = true ]]
3372	then
3373	echo "precursor_ocean" > runfile_atmos
3374	else
3375	echo "precursor_atmos" > runfile_atmos
3376	fi
3377	else
3378	(( iia = $numprocs_atmos / $threads_per_task ))
3379	(( iio = $numprocs_ocean / $threads_per_task ))
3380	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3381	printf "\n using $coupled_mode coupling"
3382	printf "\n\n"
3383	echo "coupled_run $iia $iio" > runfile_atmos
3384	fi
3385	poe ./a.out $ROPTS < runfile_atmos
3386	fi
3387	else
3388	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3389	then
3390	poe a.out -procs $numprocs -nodes 1 -rmpool 0 $ROPTS
3391	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3392	then
3393	if [[ -f $hostfile ]]
3394	then
3395	cp $hostfile hostfile
3396	else
3397	(( ii = 1 ))
3398	while (( ii <= $numprocs ))
3399	do
3400	echo $localhost_realname >> hostfile
3401	(( ii = ii + 1 ))
3402	done
3403	fi
3404	export MP_HOSTFILE=hostfile
3405	if [[ $run_coupled_model = false ]]
3406	then
3407	if [[ "$ocean_file_appendix" = true ]]
3408	then
3409	echo "precursor_ocean" > runfile_atmos
3410	else
3411	echo "precursor_atmos" > runfile_atmos
3412	fi
3413	else
3414	(( iia = $numprocs_atmos / $threads_per_task ))
3415	(( iio = $numprocs_ocean / $threads_per_task ))
3416	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3417	printf "\n using $coupled_mode coupling"
3418	printf "\n\n"
3419	echo "coupled_run $iia $iio" > runfile_atmos
3420	fi
3421
3422	poe ./a.out -procs $numprocs $ROPTS < runfile_atmos
3423
3424	else
3425	if [[ "$host_file" = "" ]]
3426	then
3427	printf "\n +++ no hostfile given in configuration file"
3428	locat=config_file
3429	exit
3430	else
3431	eval host_file=$host_file
3432	fi
3433	export MP_HOSTFILE=$host_file
3434	poe a.out -procs $numprocs -tasks_per_node $numprocs $ROPTS
3435	fi
3436	fi
3437	elif [[ $host = nech ]]
3438	then
3439	(( ii = nodes ))
3440	if [[ $ii = 1 ]]
3441	then
3442	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3443	export MPIPROGINF=YES
3444	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3445	echo "*** execution on single node with mpirun"
3446	mpirun -np $numprocs ./a.out $ROPTS
3447	else
3448	(( i = 0 ))
3449	while (( i < ii ))
3450	do
3451	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3452	(( i = i + 1 ))
3453	done
3454
3455	echo "#!/bin/sh" > mpi_exec_shell
3456	echo " " >> mpi_exec_shell
3457	echo "set -u" >> mpi_exec_shell
3458	echo "F_ERRCNT=0" >> mpi_exec_shell
3459	echo "MPIPROGINV=YES" >> mpi_exec_shell
3460	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3461	echo "cpurest=$cpurest" >> mpi_exec_shell
3462	echo "fname=$fname" >> mpi_exec_shell
3463	echo "localhost=$localhost" >> mpi_exec_shell
3464	echo "return_address=$return_address" >> mpi_exec_shell
3465	echo "return_username=$return_username" >> mpi_exec_shell
3466	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3467	echo "write_binary=$write_binary" >> mpi_exec_shell
3468	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3469	echo " " >> mpi_exec_shell
3470	echo "export F_ERRCNT" >> mpi_exec_shell
3471	echo "export MPIPROGINV" >> mpi_exec_shell
3472	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3473	echo "export cpurest" >> mpi_exec_shell
3474	echo "export fname" >> mpi_exec_shell
3475	echo "export localhost" >> mpi_exec_shell
3476	echo "export return_address" >> mpi_exec_shell
3477	echo "export return_username" >> mpi_exec_shell
3478	echo "export tasks_per_node" >> mpi_exec_shell
3479	echo "export write_binary" >> mpi_exec_shell
3480	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3481	echo " " >> mpi_exec_shell
3482	echo "exec ./a.out" >> mpi_exec_shell
3483
3484	chmod u+x mpi_exec_shell
3485	export MPIPROGINF=YES
3486	mpirun -f multinode_config &
3487	wait
3488
3489	fi
3490	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3491	then
3492
3493	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3494	# DOES NOT EXIST
3495	if [[ $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3496	then
3497	if [[ -f $hostfile ]]
3498	then
3499	cp $hostfile hostfile
3500	(( ii = $numprocs / $threads_per_task ))
3501	[[ $ii = 0 ]] && (( ii = 1 ))
3502	else
3503	(( ii = 1 ))
3504	while (( ii <= $numprocs / $threads_per_task ))
3505	do
3506	echo $localhost_realname >> hostfile
3507	(( ii = ii + 1 ))
3508	done
3509	if (( $numprocs / $threads_per_task == 0 ))
3510	then
3511	echo $localhost_realname >> hostfile
3512	fi
3513	fi
3514	eval zeile=\"`head -n $ii hostfile`\"
3515	printf "\n *** running on: $zeile"
3516	fi
3517
3518	(( ii = $numprocs / $threads_per_task ))
3519	[[ $ii = 0 ]] && (( ii = 1 ))
3520	export OMP_NUM_THREADS=$threads_per_task
3521
3522	if [[ $threads_per_task != 1 ]]
3523	then
3524	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3525	# MAY ABORT
3526	ulimit -s unlimited
3527	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3528	fi
3529	if [[ $run_coupled_model = false ]]
3530	then
3531	if [[ "$ocean_file_appendix" = true ]]
3532	then
3533	echo "precursor_ocean" > runfile_atmos
3534	else
3535	echo "precursor_atmos" > runfile_atmos
3536	fi
3537	printf "\n\n"
3538
3539	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3540	then
3541	echo "--- aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos"
3542	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3543	# aprun -n $ii -ss -r2 -j1 a.out $ROPTS < runfile_atmos
3544	elif [[ $host = lccrayf ]]
3545	then
3546	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out $ROPTS < runfile_atmos
3547	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3548	then
3549	aprun -n $ii -N $tasks_per_node a.out $ROPTS < runfile_atmos
3550	elif [[ $host = lcflow ]]
3551	then
3552	mpirun -np $ii a.out < runfile_atmos $ROPTS
3553	elif [[ $host = lcsb ]]
3554	then
3555	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos $ROPTS
3556	elif [[ $host = lckiaps ]]
3557	then
3558	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos $ROPTS
3559	elif [[ $host = lckyu* ]]
3560	then
3561	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3562	else
3563	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3564	fi
3565	else
3566
3567	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3568	(( iia = $numprocs_atmos / $threads_per_task ))
3569	(( iio = $numprocs_ocean / $threads_per_task ))
3570	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3571	printf "\n using $coupled_mode coupling"
3572	printf "\n\n"
3573
3574	if [[ $coupled_mode = "mpi2" ]]
3575	then
3576	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3577	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3578
3579	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3580	then
3581
3582	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos $ROPTS &
3583	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean $ROPTS &
3584
3585	else
3586	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3587	mpiexec -machinefile hostfile -n $iia a.out $ROPTS < runfile_atmos &
3588	mpiexec -machinefile hostfile -n $iio a.out $ROPTS < runfile_ocean &
3589	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out $ROPTS &
3590	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out $ROPTS &
3591	fi
3592	wait
3593
3594	else
3595
3596	echo "coupled_run $iia $iio" > runfile_atmos
3597
3598	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3599	then
3600
3601	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos $ROPTS
3602
3603	elif [[ $host = lck \|\| $host = lckordi ]]
3604	then
3605
3606	mpiexec -n $ii ./a.out $ROPTS < runfile_atmos &
3607
3608	elif [[ $host = lckyu* ]]
3609	then
3610
3611	mpiexec -n $ii --stdin runfile_atmos ./a.out $ROPTS
3612
3613	elif [[ $host = lcmuk ]]
3614	then
3615
3616	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos $ROPTS
3617
3618	fi
3619	wait
3620	fi
3621
3622	fi
3623
3624	elif [[ $host = lckyoto ]]
3625	then
3626	set -xv
3627	export P4_RSHCOMMAND=plesh
3628	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3629	if [[ "$ENVIRONMENT" = BATCH ]]
3630	then
3631	if [[ "$cond2" = fujitsu ]]
3632	then
3633	mpiexec -n $numprocs ./a.out $ROPTS # for fujitsu-compiler
3634	elif [[ "cond2" = pgi ]]
3635	then
3636	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out $ROPTS
3637	else
3638	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out ${ROPTS} \|\| /bin/true
3639	fi
3640	else
3641	if [[ "$cond2" = "" ]]
3642	then
3643	mpiruni_rsh -np $numprocs ./a.out $ROPTS # for intel
3644	else
3645	mpirun -np $numprocs ./a.out $ROPTS
3646	fi
3647	fi
3648	set +xv
3649
3650	elif [[ $host = lctit ]]
3651	then
3652	export OMP_NUM_THREADS=$threads_per_task
3653	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3654	if [[ "$threads_per_task" != 1 ]]
3655	then
3656	export MV2_ENABLE_AFFINITY=0
3657	fi
3658	echo "----- PBS_NODEFILE content:"
3659	cat $PBS_NODEFILE
3660	echo "-----"
3661	(( ii = $numprocs / $threads_per_task ))
3662	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS"
3663	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out $ROPTS
3664
3665	elif [[ $host = lcbullhh ]]
3666	then
3667	export OMPI_MCA_pml=cm
3668	export OMPI_MCA_mtl=mxm
3669	export OMPI_MCA_coll=^ghc
3670	export OMPI_MCA_mtl_mxm_np=0
3671	export MXM_RDMA_PORTS=mlx5_0:1
3672	export MXM_LOG_LEVEL=ERROR
3673	export OMP_NUM_THREADS=$threads_per_task
3674	export KMP_AFFINITY=verbose,granularity=core,compact,1
3675	export KMP_STACKSIZE=64m
3676
3677	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out
3678	else
3679	mpprun -n $numprocs a.out $ROPTS
3680	fi
3681	else
3682	a.out $ROPTS
3683	fi
3684	fi
3685
3686	if [[ $? != 0 ]]
3687	then
3688
3689	# ABORT IN CASE OF RUNTIME ERRORS
3690	printf "\n +++ runtime error occured"
3691	locat=execution
3692	exit
3693
3694	else
3695
3696	printf "\n$dashes\n *** execution finished \n"
3697
3698	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3699	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3700	if [[ "$dvrserver_id" != "" ]]
3701	then
3702	kill $dvrserver_id
3703	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3704
3705	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3706	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3707	if [[ -d DATA_DVR ]]
3708	then
3709
3710	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3711	# DIRECTORY
3712	cp .dvrserver.config DATA_DVR
3713
3714	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3715	# SEQUENCE MODE DATA TOO)
3716	process_dvr_output -d DATA_DVR -f $fname -s
3717
3718	else
3719
3720	# PROCESS THE LOCAL OUTPUT
3721	process_dvr_output -l -d DATA_DVR -f $fname
3722
3723	fi
3724
3725	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3726	then
3727
3728	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3729	process_dvr_output -l -d DATA_DVR -f $fname
3730
3731	fi
3732	fi
3733
3734
3735
3736	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3737	# BY EACH CORE INTO ONE FILE
3738	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3739	then
3740	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3741	printf "\n 2d- and/or 3d-data may be incomplete!"
3742	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3743	elif [[ "$combine_plot_fields" == true ]]
3744	then
3745	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3746	then
3747	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3748	aprun -n 1 -N 1 combine_plot_fields${block}.x #$ROPTS < runfile_atmos
3749	else
3750	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3751	combine_plot_fields${block}.x
3752	fi
3753	else
3754
3755	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3756	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3757	# ??? koennen wir das streichen ???
3758	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3759	fi
3760
3761
3762
3763	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3764	(( i = 0 ))
3765	while (( i < ioc ))
3766	do
3767	(( i = i + 1 ))
3768	if (( i == 1 ))
3769	then
3770	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3771	fi
3772	printf "\n >>> ${out_command[$i]}"
3773	eval ${out_command[$i]}
3774	if (( i == ioc ))
3775	then
3776	printf "\n$dashes\n"
3777	fi
3778	done
3779
3780
3781	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3782	if [[ $do_trace = true ]]
3783	then
3784	printf "\n\n"
3785	ls -al
3786	fi
3787
3788
3789
3790	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3791	(( i = 0 ))
3792	while (( i < iout ))
3793	do
3794	(( i = i + 1 ))
3795	if (( i == 1 ))
3796	then
3797	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3798	fi
3799
3800	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3801	files_for_pes=false; filetyp=file
3802	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3803	then
3804	files_for_pes=true; filetyp=directory
3805	actionout[$i]=""
3806	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3807	then
3808	actionout[$i]=""
3809	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3810	then
3811	files_for_pes=true; filetyp=directory
3812	actionout[$i]="ar"
3813	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3814	then
3815	actionout[$i]="ar"
3816	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3817	then
3818	files_for_pes=true; filetyp=directory
3819	actionout[$i]="fl"
3820	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3821	then
3822	actionout[$i]="fl"
3823	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3824	then
3825	files_for_pes=true; filetyp=directory
3826	actionout[$i]="tr"
3827	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3828	then
3829	actionout[$i]="tr"
3830	fi
3831
3832	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3833	then
3834	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3835	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3836	then
3837	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3838	else
3839
3840
3841	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3842	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3843	if [[ "${actionout[$i]}" = tr ]]
3844	then
3845	if [[ $localhost != $fromhost ]]
3846	then
3847	if [[ $files_for_pes = false ]]
3848	then
3849	cps=""
3850	cst=""
3851	else
3852	cps=-c
3853	cst="/"
3854	fi
3855	if [[ $localhost = nech ]]
3856	then
3857
3858	# TRANSFER IN SEPERATE JOB
3859	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3860	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3861	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3862	if [[ $files_for_pes = false ]]
3863	then
3864	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3865	else
3866	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3867	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3868	fi
3869
3870	echo "set -x" > transfer_${localout[$i]}
3871	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3872
3873	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3874	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3875	printf "\n or higher cycle\n"
3876	echo "batch_scp $PORTOPT $cps -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3877
3878	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3879
3880	if [[ $localhost = nech ]]
3881	then
3882	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3883	else
3884	if [[ "$LOGNAME" = b323013 ]]
3885	then
3886	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3887	else
3888	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3889	fi
3890	fi
3891
3892	else
3893
3894	# TRANSFER WITHIN THIS JOB
3895	transfer_failed=false
3896	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3897	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3898	if [[ $localhost = lccrayb ]]
3899	then
3900	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3901	elif [[ $localhost = lccrayh ]]
3902	then
3903	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3904	elif [[ $localhost = lcbullhh ]]
3905	then
3906	ssh $usern@mlogin101 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3907	elif [[ $localhost = lcxe6 ]]
3908	then
3909	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3910	else
3911	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3912	fi
3913	[[ $? != 0 ]] && transfer_failed=true
3914
3915	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3916	if [[ $transfer_failed = true ]]
3917	then
3918	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3919	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3920
3921	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3922	eval local_catalog=${pathout[$i]}
3923	if [[ ! -d $local_catalog ]]
3924	then
3925	printf " *** local directory does not exist. Trying to create:\n"
3926	printf " $local_catalog \n"
3927	mkdir -p $local_catalog
3928	fi
3929	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3930	transfer_problems=true
3931	fi
3932	fi
3933	else
3934
3935	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3936	actionout[$i]=""
3937	fi
3938	fi
3939
3940
3941	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3942	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3943	if [[ "${actionout[$i]}" = tra ]]
3944	then
3945	if [[ $localhost != $fromhost ]]
3946	then
3947	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3948	then
3949
3950	# TRANSFER IN SEPERATE JOB
3951	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3952	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3953	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3954	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3955
3956	echo "set -x" > transfer_${localout[$i]}
3957	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3958
3959	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3960	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3961	printf "\n or higher cycle\n"
3962	echo "batch_scp $PORTOPT -A -b -m -u $return_username $return_address $file_to_transfer \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}" >> transfer_${localout[$i]}
3963
3964	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3965
3966	if [[ $localhost = nech ]]
3967	then
3968	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3969	else
3970	if [[ $LOGNAME = b323013 ]]
3971	then
3972	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3973	else
3974	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3975	fi
3976	fi
3977
3978	else
3979
3980	# TRANSFER WITHIN THIS JOB
3981	transfer_failed=false
3982	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3983	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3984	if [[ $localhost = lccrayb ]]
3985	then
3986	ssh $usern@blogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3987	elif [[ $localhost = lccrayh ]]
3988	then
3989	ssh $usern@hlogin1 ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3990	elif [[ $localhost = lcxe6 ]]
3991	then
3992	ssh $usern@hexagon ". \\$HOME/.profile; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3993	else
3994	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3995	fi
3996	[[ $? != 0 ]] && transfer_failed=true
3997
3998	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3999	if [[ $transfer_failed = true ]]
4000	then
4001	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4002	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4003
4004	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4005	eval local_catalog=${pathout[$i]}
4006	if [[ ! -d $local_catalog ]]
4007	then
4008	printf " *** local directory does not exist. Trying to create:\n"
4009	printf " $local_catalog \n"
4010	mkdir -p $local_catalog
4011	fi
4012
4013	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4014	transfer_problems=true
4015	fi
4016	fi
4017	else
4018
4019	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4020	actionout[$i]=a
4021	fi
4022	fi
4023
4024
4025	# OUTPUT-FILE FOR A RESTART-RUN.
4026	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4027	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4028	# AS LAST ACTION, ARCHIVING IS INITIATED.
4029	if [[ "${actionout[$i]}" = fl ]]
4030	then
4031	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4032	chmod g+rx $tmp_data_catalog
4033	if [[ $files_for_pes = false ]]
4034	then
4035	printf "\n >>> OUTPUT: ${localout[$i]} to"
4036	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4037	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4038	else
4039	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4040	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4041	mkdir $tmp_data_catalog/${frelout[$i]}
4042	cd ${localout[$i]}
4043	for file in $(ls *)
4044	do
4045	ln -f $file $tmp_data_catalog/${frelout[$i]}
4046	done
4047	cd $TEMPDIR
4048	fi
4049
4050
4051	# CREATE AND SUBMIT ARCHIVING-JOB
4052	if [[ $store_on_archive_system = true ]]
4053	then
4054
4055	if [[ $archive_system = asterix ]]
4056	then
4057	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4058	if [[ $files_for_pes = false ]]
4059	then
4060	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4061	else
4062	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4063	fi
4064	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4065	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4066	echo "then" >> archive_${frelout[$i]}
4067	echo " do_stageout=false" >> archive_${frelout[$i]}
4068	echo "else" >> archive_${frelout[$i]}
4069	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4070	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4071	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4072	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4073	if [[ $files_for_pes = false ]]
4074	then
4075	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4076	else
4077	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4078	fi
4079	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4080	echo "fi" >> archive_${frelout[$i]}
4081	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4082	elif [[ $archive_system = DMF ]]
4083	then
4084	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4085	if [[ $files_for_pes = false ]]
4086	then
4087	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4088	locat=DMF
4089	exit
4090	else
4091	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4092	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4093	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4094	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4095	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4096	fi
4097	elif [[ $archive_system = tivoli ]]
4098	then
4099	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4100	if [[ $files_for_pes = false ]]
4101	then
4102	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4103	echo "set -x" >> archive_${frelout[$i]}
4104	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4105	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4106	else
4107
4108	echo "set -x" >> archive_${frelout[$i]}
4109	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4110	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4111	cd $tmp_data_catalog
4112	all_files=`ls -1 ${frelout[$i]}/*`
4113	cd - > /dev/null
4114	(( inode = 0 ))
4115	(( tp1 = tasks_per_node + 1 ))
4116	while (( inode < nodes ))
4117	do
4118	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4119	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4120	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4121	(( inode = inode + 1 ))
4122	done
4123	fi
4124	elif [[ $archive_system = ut ]]
4125	then
4126	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4127	if [[ $files_for_pes = false ]]
4128	then
4129	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4130	echo "set -x" >> archive_${frelout[$i]}
4131	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4132	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4133	else
4134
4135	echo "set -x" >> archive_${frelout[$i]}
4136	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4137	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4138	cd $tmp_data_catalog
4139	all_files=`ls -1 ${frelout[$i]}/*`
4140	cd - > /dev/null
4141	(( inode = 0 ))
4142	(( tp1 = tasks_per_node + 1 ))
4143	while (( inode < nodes ))
4144	do
4145	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4146	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4147	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4148	(( inode = inode + 1 ))
4149	done
4150	fi
4151	elif [[ $archive_system = none ]]
4152	then
4153	printf " +++ archiving on $localhost not available!\n"
4154	fi
4155
4156	if [[ $archive_system != none ]]
4157	then
4158	if [[ $localhost = nech ]]
4159	then
4160	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4161	fi
4162	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4163	fi
4164	else
4165	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4166	fi
4167
4168
4169	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4170	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4171	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4172	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4173	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4174	if [[ $files_for_pes = false ]]
4175	then
4176	cat /dev/null > ${pathout[$i]}
4177	else
4178	mkdir -p ${pathout[$i]}
4179	fi
4180
4181	fi
4182
4183
4184	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4185	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4186	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4187	if [[ "${actionout[$i]}" = ar ]]
4188	then
4189	if [[ $files_for_pes = false ]]
4190	then
4191	printf "\n >>> OUTPUT: ${localout[$i]} to"
4192	printf "\n ${pathout[$i]}"
4193	printf "\n File will be copied to archive-system ($archive_system) !\n"
4194	else
4195	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4196	printf "\n ${pathout[$i]}"
4197	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4198	fi
4199	mv ${localout[$i]} ${frelout[$i]}
4200
4201	file_saved=false
4202
4203	if [[ $archive_system = asterix ]]
4204	then
4205	do_stageout=true
4206	(( stageout_anz = 0 ))
4207	while [[ $do_stageout = true ]]
4208	do
4209	if [[ $files_for_pes = false ]]
4210	then
4211	stageout ${frelout[$i]} > STAGE_OUTPUT
4212	else
4213	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4214	fi
4215	cat STAGE_OUTPUT
4216	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4217	then
4218	file_saved=true
4219	do_stageout=false
4220	else
4221	if [[ $files_for_pes = false ]]
4222	then
4223	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4224	else
4225	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4226	fi
4227	(( stageout_anz = stageout_anz + 1 ))
4228	if (( stageout_anz == 10 ))
4229	then
4230	printf "\n +++ stoped after 10 unsuccessful tries!"
4231	archive_save=false
4232	do_stageout=false
4233	else
4234	printf "\n *** new try to store on archive after 15 min:"
4235	sleep 900
4236	fi
4237	fi
4238	done
4239	elif [[ $archive_system = DMF ]]
4240	then
4241	if [[ $files_for_pes = false ]]
4242	then
4243	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4244	locat=DMF
4245	exit
4246	else
4247	rm -rf $ARCHIVE/${frelout[$i]}
4248	cp -r ${frelout[$i]} $ARCHIVE
4249	fi
4250	file_saved=true
4251	elif [[ $archive_system = tivoli ]]
4252	then
4253	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4254	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4255	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4256	# WHEN THE ARCHIVE-JOB IS EXECUTED
4257	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4258	chmod g+rx $tmp_data_catalog
4259	if [[ $files_for_pes = false ]]
4260	then
4261	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4262	else
4263	mkdir $tmp_data_catalog/${frelout[$i]}
4264	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4265	fi
4266
4267	# GENERATE AND SUBMIT BATCH-JOB
4268	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4269	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4270	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4271	if [[ $files_for_pes = false ]]
4272	then
4273	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4274	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4275	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4276	else
4277	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4278	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4279	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4280	fi
4281
4282	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4283	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4284	file_saved=true
4285
4286	elif [[ $archive_system = ut ]]
4287	then
4288	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4289	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4290	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4291	# WHEN THE ARCHIVE-JOB IS EXECUTED
4292	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4293	chmod g+rx $tmp_data_catalog
4294	if [[ $files_for_pes = false ]]
4295	then
4296	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4297	else
4298	mkdir $tmp_data_catalog/${frelout[$i]}
4299	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4300	fi
4301
4302	# GENERATE AND SUBMIT BATCH-JOB
4303	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4304	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4305	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4306	if [[ $files_for_pes = false ]]
4307	then
4308	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4309	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4310	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4311	else
4312	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4313	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4314	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4315	fi
4316
4317	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4318	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4319	file_saved=true
4320
4321	else
4322	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4323	archive_save=false
4324	fi
4325
4326	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4327	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4328	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4329	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4330	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4331	if [[ $file_saved = true ]]
4332	then
4333	if [[ $files_for_pes = false ]]
4334	then
4335	cat /dev/null > ${pathout[$i]}
4336	else
4337	mkdir -p ${pathout[$i]}
4338	fi
4339	fi
4340
4341	fi
4342
4343	# APPEND ON THIS MACHINE
4344	if [[ "${actionout[$i]}" = "a" ]]
4345	then
4346	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4347	then
4348	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4349	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4350	else
4351	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4352	cat ${localout[$i]} >> ${pathout[$i]}
4353	fi
4354	fi
4355
4356	# COPY ON THIS MACHINE
4357	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4358	# ON DIFFERENT FILE-SYSTEMS
4359	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4360	then
4361
4362	# COPY IN CASE OF RUNS ON SINGLE CORES
4363	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4364	then
4365	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4366	if [[ $link_local_output = true ]]
4367	then
4368	printf " using ln -f\n"
4369	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4370	fi
4371	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4372	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4373	then
4374	if [[ $link_local_output = true ]]
4375	then
4376	printf " ln failed, using cp...\n"
4377	fi
4378	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4379	fi
4380	else
4381	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4382	if [[ $link_local_output = true ]]
4383	then
4384	printf " using ln -f\n"
4385	ln -f ${localout[$i]} ${pathout[$i]}
4386	fi
4387	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4388	if [[ ! -f "${pathout[$i]}" ]]
4389	then
4390	if [[ $link_local_output = true ]]
4391	then
4392	printf " ln failed, using cp...\n"
4393	fi
4394	cp ${localout[$i]} ${pathout[$i]}
4395	fi
4396	fi
4397
4398	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4399	then
4400
4401	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4402	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4403	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4404	if [[ $link_local_output = true ]]
4405	then
4406	printf " using ln -f\n"
4407	mkdir ${pathout[$i]}
4408	cd ${localout[$i]}
4409	for file in $(ls *)
4410	do
4411	ln -f $file ${pathout[$i]}
4412	done
4413	cd $TEMPDIR
4414	fi
4415
4416	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4417	if [[ ! -f "${pathout[$i]}/_0000" ]]
4418	then
4419	if [[ $link_local_output = true ]]
4420	then
4421	printf " ln failed for .../_0000, using cp...\n"
4422	fi
4423	cp -r ${localout[$i]} ${pathout[$i]}
4424	fi
4425
4426	fi
4427	fi
4428	done
4429	if (( i != 0 ))
4430	then
4431	if [[ $transfer_problems = true ]]
4432	then
4433	printf "\n$dashes\n *** OUTPUT-files saved"
4434	printf "\n +++ WARNING: some data transfers failed! \n"
4435	else
4436	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4437	fi
4438	fi
4439
4440
4441	# IF REQUIRED, START A RESTART-JOB
4442	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4443	if [[ -f CONTINUE_RUN ]]
4444	then
4445
4446	if [[ $archive_save = true ]]
4447	then
4448
4449	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4450	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4451	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4452	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4453	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4454	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4455	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4456	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4457	then
4458	mc=`echo $mc \| sed 's/#/f/g'`
4459	fi
4460
4461
4462	# START THE RESTART-JOB
4463	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4464	echo " $mc"
4465	printf "\n$dashes\n"
4466	if [[ $localhost != $fromhost ]]
4467	then
4468
4469	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4470	then
4471	echo "*** ssh will be used to initiate restart-runs!"
4472	echo " return_address=\"$return_address\" "
4473	echo " return_username=\"$return_username\" "
4474	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4475	then
4476	if [[ $localhost = ibmh ]]
4477	then
4478	ssh $SSH_PORTOPT $usern@136.172.40.15 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4479	elif [[ $localhost = lcbullhh ]]
4480	then
4481	ssh $SSH_PORTOPT $usern@mlogin101 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4482	elif [[ $localhost = lccrayb ]]
4483	then
4484	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4485	elif [[ $localhost = lccrayh ]]
4486	then
4487	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4488	elif [[ $localhost = lcxe6 ]]
4489	then
4490	ssh $usern@hexagon "ssh $SSH_PORTOPT $return_address -l $return_username \". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\\\$PATH:$LOCAL_MRUN_PATH; export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4491	else
4492	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4493	fi
4494	else
4495	if [[ $localhost = ibmkisti ]]
4496	then
4497	ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4498	elif [[ $localhost = lcflow ]]
4499	then
4500	/usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4501	elif [[ $localhost = lccrayb ]]
4502	then
4503	ssh $usern@blogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4504	elif [[ $localhost = lccrayh ]]
4505	then
4506	ssh $usern@hlogin1 "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
4507	else
4508	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4509	fi
4510	fi
4511	else
4512	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4513	locat=restart; exit
4514	fi
4515
4516	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4517	if [[ $queue = special1q ]]
4518	then
4519	sleep 120
4520	else
4521	sleep 30
4522	fi
4523
4524	else
4525
4526	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4527	# USING SSH)
4528	cd $LOCAL_PWD
4529	if [[ $localhost = lckyuh ]]
4530	then
4531	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4532	printf "\n please restart job manually using command:\n"
4533	printf "\n \"$mc\" "
4534	else
4535	eval $mc # THE ' MUST BE EVALUATED
4536	fi
4537	cd - > /dev/null
4538	fi
4539	if [[ $localhost = lckyuh ]]
4540	then
4541	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4542	else
4543	printf "\n$dashes\n *** restart-run initiated \n"
4544	fi
4545
4546
4547	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4548	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4549	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4550	# MAY BE VERY HUGE)
4551	(( i = 0 ))
4552	while (( i < iin ))
4553	do
4554	(( i = i + 1 ))
4555	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4556	then
4557	rm -r $tmp_data_catalog/${frelin[$i]}
4558	fi
4559	done
4560
4561	else
4562
4563	printf "\n +++ no restart-run possible, since errors occured"
4564	printf "\n during the archive process"
4565	fi
4566
4567	fi
4568
4569
4570
4571	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4572	if [[ "$email_notification" != "none" ]]
4573	then
4574
4575	if [[ $localhost != $fromhost ]]
4576	then
4577	if [[ -f CONTINUE_RUN ]]
4578	then
4579	echo "PALM restart run necessary" > email_text
4580	echo "description header of actual run:" >> email_text
4581	cat CONTINUE_RUN >> email_text
4582	echo "mrun-command to restart:" >> email_text
4583	echo "$mc" >> email_text
4584	else
4585	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4586	fi
4587	mail $email_notification < email_text
4588	printf "\n *** email notification sent to \"$email_notification\" "
4589	fi
4590	fi
4591
4592
4593
4594	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4595	cd $HOME
4596	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4597
4598	else
4599
4600	# PREPARING ACTIONS,
4601	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4602
4603	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4604	mrun_com="$mrun_script_name -a $afname -c $config_file -d $fname -h $host -H $fromhost -m $memory -t $cpumax -q $queue -R $return_address -U $return_username -u $remote_username"
4605	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4606	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4607	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4608	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4609	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4610	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4611	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4612	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4613	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4614	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4615	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4616	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4617	if [[ $use_openmp = true ]]
4618	then
4619	mrun_com=${mrun_com}" -O $threads_per_task"
4620	fi
4621	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4622	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4623	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4624	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4625	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4626	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4627	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4628	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4629	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4630	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4631	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4632	if [[ $do_remote = true ]]
4633	then
4634	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4635	fi
4636
4637
4638	# CREATE EXECUTABLE FOR BATCH JOB
4639	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4640	then
4641
4642	printf "\n *** creating the executable for batch job\n"
4643
4644	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4645	if [[ $host != $localhost ]]
4646	then
4647	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4648	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4649	locat=create_executable; exit
4650	fi
4651
4652	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4653	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4654
4655	cp $make_depository .
4656	tar -xf $make_depository > /dev/null 2>&1
4657	cp ../* . > /dev/null 2>&1
4658
4659	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4660
4661	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4662	then
4663	printf "\n +++ error occured while compiling or linking"
4664	locat=compile
4665	exit
4666	fi
4667
4668	mv a.out ..
4669	cd - > /dev/null 2>&1
4670	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4671
4672	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4673
4674	fi
4675
4676
4677	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4678	jobfile=jobfile.$RANDOM
4679
4680
4681	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4682	echo "mkdir $TEMPDIR" >> $jobfile
4683	echo "cd $TEMPDIR" >> $jobfile
4684
4685
4686	# ACTIVATE ERROR-TRACEBACK
4687	if [[ $do_trace = true ]]
4688	then
4689	echo "set -x" >> $jobfile
4690	else
4691	echo "set +vx" >> $jobfile
4692	fi
4693
4694
4695	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4696	if [[ "$init_cmds" != "" ]]
4697	then
4698	echo "$init_cmds" >> $jobfile
4699	fi
4700	if [[ "$module_calls" != "" ]]
4701	then
4702	echo "$module_calls" >> $jobfile
4703	fi
4704
4705
4706	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4707	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4708	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4709	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4710	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4711	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4712	# QUEUEING-SYSTEMS
4713	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4714	then
4715
4716	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4717	if [[ $restart_run != true ]]
4718	then
4719	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4720	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4721	fi
4722
4723	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4724	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4725	echo "set -x" >> $jobfile
4726	if [[ $host = $localhost ]]
4727	then
4728	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4729	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4730	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4731	then
4732	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4733	else
4734	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4735	fi
4736
4737	else
4738	if [[ $host = ibmkisti ]]
4739	then
4740	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4741	echo "localdir=\`pwd\`" >> $jobfile
4742	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4743	elif [[ $host = lcbullhh ]]
4744	then
4745	echo "localdir=\`pwd\`" >> $jobfile
4746	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4747
4748	elif [[ $host = lccrayb ]]
4749	then
4750	echo "localdir=\`pwd\`" >> $jobfile
4751	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4752	elif [[ $host = lccrayh ]]
4753	then
4754	echo "localdir=\`pwd\`" >> $jobfile
4755	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4756
4757	else
4758	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4759	fi
4760	fi
4761	echo "export SOURCES_COMPLETE=true" >> $jobfile
4762
4763	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4764	# WORKING DIRECTORY OF THE JOB
4765	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4766	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4767	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4768	echo "execute_mrun=true" >> $jobfile
4769	echo " " >> $jobfile
4770
4771	else
4772
4773	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4774	if [[ $do_compile = true ]]
4775	then
4776
4777	source_catalog=SOURCES_FOR_RUN_$fname
4778
4779	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4780	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4781	echo "export SOURCES_COMPLETE=true" >> $jobfile
4782	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4783
4784	for filename in $source_list
4785	do
4786	# BACKSLASH IS USED FOR MASKING
4787	echo "cat > $filename << \"%END%\"" >> $jobfile
4788	cat $source_catalog/$filename >> $jobfile
4789	echo " " >> $jobfile
4790	echo "%END%" >> $jobfile
4791	echo " " >> $jobfile
4792	done
4793
4794	# BACKSLASH IS USED FOR MASKING
4795	echo "cat > Makefile << \"%END%\"" >> $jobfile
4796	cat $source_catalog/Makefile >> $jobfile
4797	echo " " >> $jobfile
4798	echo "%END%" >> $jobfile
4799	echo " " >> $jobfile
4800
4801	echo "cd - > /dev/null" >> $jobfile
4802
4803	fi
4804
4805
4806	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4807	# BACKSLASH IS USED FOR MASKING
4808	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4809	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4810	echo "cat > $config_file << \"%END%\"" >> $jobfile
4811	if [[ $host = lckyuh ]]
4812	then
4813	# NO CROSS-COMPILER ON COMPUTE NODE
4814	sed 's/frtpx/frt/g' $config_file >> $jobfile
4815	else
4816	sed 's/#$.*//g' $config_file >> $jobfile
4817	fi
4818	echo "%END%" >> $jobfile
4819	echo " " >> $jobfile
4820
4821
4822	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4823	# BACKSLASH IS USED FOR MASKING
4824	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4825	if [[ $host = lckyuh ]]
4826	then
4827	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4828	else
4829	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4830	fi
4831	echo "%END%" >> $jobfile
4832	echo "chmod u+x $mrun_script_name" >> $jobfile
4833	echo "execute_mrun=true" >> $jobfile
4834	echo " " >> $jobfile
4835
4836	fi
4837
4838
4839	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4840	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4841	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4842	if [[ $do_remote = true ]]
4843	then
4844	(( i = 0 ))
4845	while (( i < iin ))
4846	do
4847	(( i = i + 1 ))
4848	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4849	if [[ "${transin[$i]}" = job ]]
4850	then
4851	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4852	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4853	echo " " >> $jobfile
4854	echo "%END%" >> $jobfile
4855	else
4856	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4857	fi
4858
4859	# CHECK, IF FILE COULD BE CREATED
4860	echo "if [[ \$? = 1 ]]" >> $jobfile
4861	echo "then" >> $jobfile
4862	echo " echo \" \" " >> $jobfile
4863	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4864	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4865	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4866	echo " execute_mrun=false" >> $jobfile
4867	echo "fi" >> $jobfile
4868	done
4869	fi
4870
4871	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4872	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4873	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4874	echo "LOCAL_PWD=$working_directory" >> $jobfile
4875	echo "export LOCAL_PWD" >> $jobfile
4876
4877	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4878	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4879	echo "export LOCAL_MRUN_PATH" >> $jobfile
4880
4881	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4882	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4883	# then
4884	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4885	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4886	# fi
4887
4888	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4889	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4890	echo "set -x" >> $jobfile
4891	echo "queue=$queue" >> $jobfile
4892	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4893	echo 'ls -al; echo `pwd`' >> $jobfile
4894	echo "cd \$HOME" >> $jobfile
4895	echo "rm -rf $TEMPDIR" >> $jobfile
4896
4897
4898
4899
4900	# START THE JOB USING SUBJOB-COMMAND
4901	if [[ $silent = false ]]
4902	then
4903	printf "\n "
4904	else
4905	printf "\n\n"
4906	fi
4907
4908	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
4909	rm -rf $jobfile
4910
4911
4912	fi # END OF REMOTE-PART

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