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source: palm/trunk/SCRIPTS/mrun @ 2190

Last change on this file since 2190 was 2186, checked in by raasch, 8 years ago
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1	#!/bin/bash
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 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 2186 2017-03-21 05:36:31Z raasch $
29	#
30	# 2185 2017-03-21 05:09:29Z raasch
31	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
32	#
33	# 2148 2017-02-09 16:56:42Z scharf
34	# changed allocation of resources for lcbullhh in srun command
35	#
36	# 2141 2017-02-06 10:19:32Z gronemeier
37	# made check for existing files language independent
38	#
39	# 1944 2016-06-15 06:29:00Z raasch
40	# adjustments for using HLRN ssh-keys
41	#
42	# 1940 2016-06-14 05:15:20Z raasch $
43	# adjustments for lckiaps
44	#
45	# 1866 2016-04-15 06:50:59Z raasch
46	# adjusted for lcocean
47	#
48	# 1841 2016-04-07 19:14:06Z raasch
49	# script now running under bash
50	#
51	# 1804 2016-04-05 16:30:18Z maronga
52	# test: implementing an execute mechanism where the execute command is given in the
53	# configuration file
54	# ROPTS removed from execution commands
55	# Warnings about missing optional files or user code changed to informative messages
56	# Removed parameter file check
57	#
58	# 1755 2016-02-22 13:53:39Z maronga
59	# Minor bugfix to last commit
60	#
61	# 1753 2016-02-22 13:49:49Z maronga
62	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
63	#
64	# 1622 2015-07-20 06:21:36Z heinze
65	# bugfix for Mistral (lcbullhh)
66	#
67	# 1621 2015-07-17 11:39:33Z heinze
68	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
69	#
70	# 1609 2015-07-03 15:37:58Z maronga
71	# Modified the random number of the temporary working directory to match the
72	# queuing system number on HLRN-III (lccray*).
73	#
74	# 1604 2015-06-23 15:48:03Z suehring
75	# Enable coupled runs for lcmuk
76	#
77	# 1598 2015-05-29 06:45:40Z raasch
78	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
79	#
80	# 1549 2015-01-30 14:26:16Z suehring
81	# Enable interactive debug sessions with allinea debugger
82	#
83	# 1547 2015-01-29 15:09:12Z witha
84	# adjustments for ForWind computing cluster (lcflow)
85	#
86	# 1491 2014-11-12 08:12:57Z heinze
87	# correct setting of batch_job allowed for ibm-machines
88	#
89	# 1468 2014-09-24 14:06:57Z maronga
90	# Typo removed (addres->address)
91	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
92	# Added support for restart runs (remote) for lcxe6
93	#
94	# 1442 2014-07-28 07:09:10Z raasch
95	# default queues for HLRN-III (lccrayb/lccrayh) defined
96	#
97	# 1422 2014-07-02 10:01:25Z kanani
98	# automatic restarts enabled for lccrayb,
99	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
100	#
101	# 1420 2014-06-10 06:24:14Z raasch
102	# -j1 option added to aprung command for lccrayf (CSC)
103	#
104	# 1402 2014-05-09 14:25:13Z raasch
105	# batch_job added to envpar-NAMELIST
106	#
107	# 1357 2014-04-11 15:02:03Z witha
108	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
109	# possible)
110	#
111	# 1320 2014-03-20 08:40:49Z raasch
112	# check namelist file set false by default
113	#
114	# 1304 2014-03-12 10:29:42Z raasch
115	# ulimit option changed from -Ss to -s
116	#
117	# bugfix: missing "fi" in r1289
118	#
119	# 1289 2014-03-04 07:12:34Z raasch
120	# comments translated to English
121	# necriam-, fimm-, ibmy-, and sgi-specific code removed
122	# export of variables for palm and interpret_config removed
123	#
124	# 1281 2014-02-01 07:55:49Z raasch
125	# rsync-copy restricted to Cray machines, since command is unavailable on some
126	# other systems
127	#
128	# 1279 2014-01-28 12:10:14Z raasch
129	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
130	# in order to remove annoying restrictions concerning the number of processors which
131	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
132	# restriction, one of the nodes will be filled with less than the given number of
133	# tasks per node. A respective warning is given.
134	#
135	# 1274 2014-01-09 13:14:54Z heinze
136	# adjustments for lccrayh
137	#
138	# 1272 2014-01-08 10:19:32Z witha
139	# small adjustment for lcflow
140	#
141	# 1270 2013-12-16 11:05:01Z fricke
142	# call of combine_plot_fields adjusted for lccrayb/lccrayh
143	#
144	# 1255 2013-11-07 14:43:35Z raasch
145	# further adjustments for lccrayb remote access
146	#
147	# 1241 2013-10-30 11:36:58Z heinze
148	# Enable use of nudging input and input of large scale forcing from
149	# external files
150	#
151	# 1229 2013-09-20 06:55:19Z raasch
152	# further adjustments for lccrayb
153	#
154	# 1224 2013-09-16 07:27:23Z raasch
155	# first adjustments for lccrayb
156	#
157	# 1210 2013-08-14 10:58:20Z raasch
158	# fftw support added
159	#
160	# 1201 2013-07-10 16:17:59Z witha
161	# adjustments for Forwind cluster (lcflow)
162	#
163	# 1199 2013-07-05 14:52:22Z raasch
164	# adjustments for CSC Helsinki (lccrayf),
165	# executables for batch jobs can be created in advance, in order to avoid calling
166	# the compiler within the batch job (only works if batch jobs are submitted on
167	# local host)
168	#
169	# 1190 2013-06-25 09:39:21Z heinze
170	# enable use of automatic restarts for ibmh
171	# use of cluster/express queue enabled (ibmh)
172	#
173	# 1124 2013-04-09 15:46:52Z raasch
174	# variable "memory" is exported via typeset option -x, because otherwise an unknown
175	# side effect may lead to data loss while getopts is reading the script-option arguments
176	#
177	# 1122 2013-04-09 08:37:16Z heinze
178	# Bugfix: change type of variable last_char
179	#
180	# 1119 2013-04-05 15:11:19Z raasch
181	# Bugfix for setting -T option for subjob
182	#
183	# 1108 2013-03-05 07:03:32Z raasch
184	# bugfix for coupled runs on lckyut/lckyuh
185	#
186	# 1106 2013-03-04 05:31:38Z raasch
187	# --stdin argument for mpiexec on lckyuh
188	# -y and -Y settings output to header
189	#
190	# 1103 2013-02-20 02:15:53Z raasch
191	# default script runs again under ksh, because of unsolved problems with read
192	# from stdin: when bash script is called from a ksh, message "read error: 0:
193	# Resource temporarily unavailable" appears and script does not stop,
194	# further bash compatibility adjustments,
195	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
196	# on lckyuh, but mrun does not terminate and issues a warning instead
197	#
198	# 1101 2013-02-17 10:20:21Z raasch
199	# script now running under bash instead of ksh, which required small adjustments
200	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
201	# read from stdin),
202	# cross compilername on lckyuh compute nodes replaced by real compiler name
203	#
204	# 1099 2013-02-10 01:47:43Z raasch
205	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
206	# and for Forwind cluster (lcflow)
207	# small further adjustments for lckyut
208	#
209	# 1094 2013-02-03 01:52:12Z raasch
210	# explicit ssh/scp port can be set in config file with environment variable
211	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
212	# decalpha parts (yonsei) removed
213	#
214	# 2013-02-02 07:06:13Z raasch
215	# adjustments for Kyushu-University computing center (lckyut - tatara)
216	#
217	# 1083 2013-01-04 10:22:09Z maronga
218	# bugfix in parameter file check (read %cpp_options was missing)
219	#
220	# 1069 2012-11-28 16:18:43Z maronga
221	# bugfix: coupling mode was always set to mpi2, typos removed
222	#
223	# 1058 2012-11-21 07:00:35Z raasch
224	# Intel inspector (inspxe) is given the number of PEs instead of the number of
225	# nodes
226	#
227	# 1046 2012-11-09 14:38:45Z maronga
228	# code put under GPL (PALM 3.9)
229	#
230	# 21/03/94 - Siggi - first version finished
231	# 03/03/94 - Siggi - script development started
232	#
233	#--------------------------------------------------------------------------------#
234	# mrun - script for running PALM jobs
235	#--------------------------------------------------------------------------------#
236
237
238
239	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
240
241	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
242	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
243	# (TOO MANY ARGUMENTS - PROBLEM)
244	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
245
246	AddFilenames=""
247	additional_conditions=""
248	add_source_path=""
249	afname=""
250	archive_save=true
251	archive_system=none
252	check_namelist_files=false
253	combine_plot_fields=true
254	compiler_name=""
255	cond1=""
256	cond2=""
257	config_file=.mrun.config
258	coupled_dist=""
259	coupled_mode="mpi1"
260	cpp_opts=""
261	cpp_options=""
262	cpumax=0
263	cpurest=0
264	create_executable_for_batch=false
265	delete_temporary_catalog=true
266	do_batch=false
267	do_compile=true
268	do_remote=false
269	do_stagein=true
270	do_stageout=true
271	do_trace=false
272	email_notification="none"
273	exclude=""
274	executable=""
275	execute_command="none"
276	execution_error=false
277	fftw_inc=""
278	fftw_lib=""
279	fftw_support=false
280	fname=test
281	fromhost=""
282	global_revision=""
283	group_number=none
284	host=""
285	host_file=""
286	hp=""
287	ignore_archive_error=false
288	input_list=""
289	interpreted_config_file=""
290	job_catalog="~/job_queue"
291	job_on_file=""
292	keep_data_from_previous_run=false
293	link_local_input=false
294	link_local_output=false
295	localhost_realname=$(hostname)
296	local_dvrserver_running=.FALSE.
297	locat=normal
298	mainprog=""
299	makefile=""
300	max_par_io_str=""
301	mc=$0
302	while [[ $(echo $mc \| grep -c "/") != 0 ]]
303	do
304	mc=`echo $mc \| cut -f2- -d"/"`
305	done
306	module_calls=""
307	mrun_script_name=$mc
308	netcdf_inc=""
309	netcdf_lib=""
310	netcdf_support=false
311	node_usage=default
312	numprocs=""
313	numprocs_atmos=0
314	numprocs_ocean=0
315	OOPT=""
316	openmp=false
317	output_list=""
318	package_list=""
319	queue=none
320	read_from_config=""
321	restart_run=false
322	if [[ `hostname` = rte10 ]]
323	then
324	return_address=133.5.185.60
325	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
326	elif [[ `hostname` = climate0 ]]
327	then
328	return_address=165.132.26.68
329	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
330	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
331	then
332	return_address="schultzl-Latitude-E6540"
333	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
334	elif [[ `hostname` = urban00 ]]
335	then
336	return_address=147.46.30.151
337	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
338	else
339	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
340	fi
341	return_password=""
342	return_username=$LOGNAME
343	remotecall=false
344	remote_username=""
345	run_coupled_model=false
346	run_mode=""
347	store_on_archive_system=false
348	dashes=" ----------------------------------------------------------------------------"
349	silent=false
350	source_list=""
351	source_path=SOURCE
352	tasks_per_node=""
353	threads_per_task=1
354	tmpcreate=false
355	tmp_data_catalog=""
356	transfer_problems=false
357	usern=$LOGNAME
358	use_openmp=false
359	version="MRUN 2.1 Rev$Rev: 2186 $"
360	working_directory=`pwd`
361	TOPT=""
362	XOPT=""
363	zeit=$( date \| cut -c 12-19 )
364
365	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
366	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
367	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
368	# SCRIPT-OPTION ARGUMENTS
369	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
370
371	# ERROR HANDLING IN CASE OF EXIT
372	trap 'rm -rf $working_directory/tmp_mrun
373	if [[ $locat != normal && $locat != control_c ]]
374	then
375
376	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
377	(( i = 0 ))
378	while (( i < iec ))
379	do
380	(( i = i + 1 ))
381	printf "\n *** Execution of ERROR-command:\n"
382	printf " >>> ${err_command[$i]}\n"
383	eval ${err_command[$i]}
384	done
385	if [[ -n $interpreted_config_file ]]
386	then
387	rm -rf $interpreted_config_file
388	fi
389	if [[ -n .mrun_environment ]]
390	then
391	rm -rf .mrun_environment
392	fi
393	if [[ $tmpcreate = true ]]
394	then
395	# printf "\n *** Contents of \"$TEMPDIR\":\n"
396	# ls -al; cd
397	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
398	fi
399	if [[ "$dvrserver_id" != "" ]]
400	then
401	echo "+++ killing dvrserver_id=$dvrserver_id"
402	kill $dvrserver_id
403	fi
404	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
405	then
406	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
407	fi
408	printf "\n\n+++ MRUN killed \n\n"
409	elif [[ $locat != control_c ]]
410	then
411	printf "\n\n --> all actions finished\n\n"
412	printf " Bye, bye $usern !!\n\n"
413	fi' exit
414
415
416	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
417	trap 'rm -rf $working_directory/tmp_mrun
418	rm -rf $working_directory/tmp_check_namelist_files
419	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
420	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
421	then
422	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
423	fi
424	if [[ "$dvrserver_id" != "" ]]
425	then
426	echo "+++ killing dvrserver_id=$dvrserver_id"
427	kill $dvrserver_id
428	fi
429	printf "\n+++ MRUN killed by \"^C\" \n\n"
430	locat=control_c
431	exit
432	' 2
433
434
435	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
436	# BEEN SET
437	if [[ "$PALM_BIN" = "" ]]
438	then
439	printf "\n +++ environment variable PALM_BIN has not been set"
440	printf "\n please set it to the directory where the PALM scripts are located"
441	locat=palm_bin; exit
442	fi
443	export PATH=$PALM_BIN:$PATH
444
445
446
447	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
448	# WHICH WILL BE USED TO START RESTART-JOBS
449	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
450	do
451	case $option in
452	(a) afname=$OPTARG;;
453	(A) store_on_archive_system=true; mc="$mc -A";;
454	(b) do_batch=true; mc="$mc -b";;
455	(B) delete_temporary_catalog=false; mc="$mc -B";;
456	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
457	(C) restart_run=true; mc="$mc -C";;
458	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
459	# (D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
460	(F) job_on_file="-D"; mc="$mc -F";;
461	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
462	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
463	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
464	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
465	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
466	(I) ignore_archive_error=true; mc="$mc -I";;
467	(k) keep_data_from_previous_run=true; mc="$mc -k";;
468	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
469	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
470	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
471	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
472	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
473	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
474	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
475	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
476	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
477	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
478	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
479	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
480	(S) read_from_config=false; mc="$mc -S";;
481	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
482	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
483	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
484	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
485	(v) silent=true; mc="$mc -v";;
486	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
487	(x) do_trace=true;set -x; mc="$mc -x";;
488	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
489	(y) ocean_file_appendix=true; mc="$mc -y";;
490	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
491	(z) check_namelist_files=false; mc="$mc -z";;
492	(Z) combine_plot_fields=false; mc="$mc -Z";;
493	(\?) printf "\n +++ unknown option $OPTARG \n"
494	printf "\n --> type \"$0 ?\" for available options \n"
495	locat=parameter;exit;;
496	esac
497	done
498
499
500	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
501	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
502	(( to_shift = $OPTIND - 1 ))
503	shift $to_shift
504
505	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
506	if [[ "$1" = "?" ]]
507	then
508	(printf "\n *** mrun can be called as follows:\n"
509	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 <modus> \n"
510	printf "\n Description of available options:\n"
511	printf "\n Option Description Default-Value"
512	printf "\n -a base name of input files equiv. -d"
513	printf "\n -A archiving when using file-attribute fl"
514	printf "\n -b batch-job on local machine ---"
515	printf "\n -B do not delete temporary directory at end ---"
516	printf "\n -c configuration file .mrun.config"
517	printf "\n -d base name of files attached to program test"
518	printf "\n -D preprocessor(cpp)-directives \"\" "
519	printf "\n -F create remote job file only ---"
520	printf "\n -h execution host $localhost_realname"
521	printf "\n -i INPUT control list \"\" "
522	printf "\n -I archiving errors of previous batch-jobs"
523	printf "\n will be ignored"
524	printf "\n -k keep data from previous run"
525	printf "\n -K additional conditions for controling"
526	printf "\n usage of conditional code and"
527	printf "\n env-variables in configuration file \"\" "
528	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
529	printf "\n -M Makefile name Makefile"
530	printf "\n -n node usage (shared/not_shared) depending on -h"
531	printf "\n -o OUTPUT control list \"\" "
532	printf "\n -O threads per openMP task ---"
533	printf "\n -p software package list \"\" "
534	printf "\n -q queue \"$queue\" "
535	printf "\n -r run control list (combines -i -o) \"\" "
536	printf "\n -s filenames of routines to be compiled \"\" "
537	printf "\n must end with .f, .f90, .F, or .c !"
538	printf "\n use \"..\" for more than one file and wildcards"
539	printf "\n -s LM compiles all locally modified files"
540	printf "\n -S config file interpreted by shellscript ---"
541	printf "\n -t allowed cpu-time in seconds (batch) 0"
542	printf "\n -T tasks per node depending on -h"
543	printf "\n -u username on remote machine \"\" "
544	printf "\n -v no prompt for confirmation ---"
545	printf "\n -w maximum parallel io streams as given by -X"
546	printf "\n -x tracing of mrun for debug purposes ---"
547	printf "\n -X # of processors (on parallel machines) 1"
548	printf "\n -y add appendix \"_O\" to all local output"
549	printf "\n files (ocean precursor runs followed by"
550	printf "\n coupled atmosphere-ocean runs) ---"
551	printf "\n -Y run coupled model, \"#1 #2\" with"
552	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
553	printf "\n -Z skip combine_plot_fields at the end of "
554	printf "\n the simulation ---"
555	printf "\n "
556	printf "\n Possible values of positional parameter <modus>:"
557	printf "\n \"?\" - this outline \n\n") \| more
558	exit
559	elif [[ "$1" != "" ]]
560	then
561	printf "\n +++ positional parameter $1 unknown \n"
562	locat=parameter; exit
563	fi
564
565
566
567	# SHORT STARTING MESSAGE
568	printf "\n*** $version "
569	printf "\n will be executed. Please wait ..."
570
571
572
573	# CHECK, IF CONFIGURATION FILE EXISTS
574	if [[ ! -f $config_file ]]
575	then
576	printf "\n\n +++ configuration file: "
577	printf "\n $config_file"
578	printf "\n does not exist"
579	locat=connect; exit
580	fi
581
582
583	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
584	line=""
585	grep "%host_identifier" $config_file > tmp_mrun
586	while read line
587	do
588	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
589	then
590	HOSTNAME=`echo $line \| cut -d" " -s -f2`
591	host_identifier=`echo $line \| cut -d" " -s -f3`
592	if [[ $localhost_realname = $HOSTNAME ]]
593	then
594	localhost=$host_identifier
595	break
596	fi
597	fi
598	done < tmp_mrun
599
600	if [[ "$localhost" = "" ]]
601	then
602	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
603	printf "\n for local host \"$localhost_realname\"."
604	printf "\n Please add line"
605	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
606	printf "\n to the configuration file."
607	locat=localhost; exit
608	fi
609
610
611	# SET HOST-SPECIFIC VARIABLES
612	case $localhost_realname in
613	(r1\|r2\|h01\|b01) archive_system=tivoli;;
614	(cs*) archive_system=ut;;
615	esac
616
617
618	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
619	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
620	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
621	[[ "$afname" = "" ]] && afname=$fname
622
623
624	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
625	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
626	# STATEMENTS IN THE CONFIGURATION FILE
627	if [[ "$run_mode" != "" ]]
628	then
629	input_list="$input_list $run_mode"
630	output_list="$output_list $run_mode"
631	fi
632
633
634	# ??? is this (and the respective option -H) really required ???
635	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
636	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
637	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
638	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
639	if [[ "$fromhost" = "" ]]
640	then
641	fromhost=$localhost
642	fi
643
644
645	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
646	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
647	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
648	# TO BE SUBMITTED (I.E. do_batch=true)
649	if [[ -n $host && "$host" != $localhost ]]
650	then
651	do_batch=true
652	do_remote=true
653	case $host in
654	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
655	(*) printf "\n"
656	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
657	printf "\n is not available"
658	locat=nqs; (( iec = 0 )); exit;;
659	esac
660	else
661	host=$localhost
662	fi
663
664
665	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
666	if [[ -n $additional_conditions ]]
667	then
668	cond1=`echo $additional_conditions \| cut -d" " -f1`
669	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
670	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
671	if [[ -n $dummy ]]
672	then
673	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
674	locat=options; exit
675	fi
676	block=_$cond1
677	[[ -n $cond2 ]] && block=${block}_$cond2
678	fi
679
680
681	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
682	if [[ $run_coupled_model = true ]]
683	then
684
685	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
686	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
687
688	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
689	then
690
691	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
692	printf "\n PEs (total) : $numprocs"
693	printf "\n PEs (atmosphere): $numprocs_atmos"
694	printf "\n PEs (ocean) : $numprocs_ocean"
695	locat=coupling; exit
696
697	fi
698
699
700	# GET coupled_mode FROM THE CONFIG FILE
701	line=""
702	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
703	while read line
704	do
705	echo line=\"$line\"
706	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
707	then
708	coupled_mode="mpi2"
709	fi
710	done < tmp_mrun
711
712	fi
713
714	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
715	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
716	then
717	if [[ $ignore_archive_error = false ]]
718	then
719	printf "\n +++ data archiving of previous run failed"
720	printf "\n see directory \~/job_queue on remote machine"
721	locat=archive; exit
722	else
723	printf "\n +++ warning: data archiving in a previous run failed"
724	printf "\n MRUN continues, trying to get backup copy"
725	fi
726	fi
727
728
729	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
730	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
731	mrun_memory=$memory
732	mrun_group_number=$group_number
733	mrun_cpumax=$cpumax
734	mrun_numprocs=$numprocs
735
736
737	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
738	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
739	if [[ "$read_from_config" = false ]]
740	then
741	[[ $silent = false ]] && printf "\n Reading the configuration file... "
742
743	# READ THE CONFIGURATION FILE LINE BY LINE
744	while read zeile
745	do
746	[[ $silent = false ]] && printf "."
747
748
749	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
750	eval zeile=\"$zeile\"
751
752
753	# INTERPRET THE LINE
754	if [[ "$(echo $zeile)" = "" ]]
755	then
756	# EMPTY LINE, NO ACTION
757	continue
758
759	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
760	then
761
762	# LINE IS A COMMENT LINE
763	true
764
765	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
766	then
767
768	# LINE DEFINES AN ENVIRONMENT-VARIABLE
769	zeile=$(echo $zeile \| cut -c2-)
770	var=`echo $zeile \| cut -d" " -f1`
771	value=`echo $zeile \| cut -d" " -s -f2`
772	for_host=`echo $zeile \| cut -d" " -s -f3`
773	for_cond1=`echo $zeile \| cut -d" " -s -f4`
774	for_cond2=`echo $zeile \| cut -d" " -s -f5`
775
776	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
777	then
778
779	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
780	# "::" IS REPLACED BY ":".
781	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
782
783
784	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
785	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
786	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
787	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
788	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
789	# CONFIGURATION-FILE.
790	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
791	then
792	eval $var=\$value
793
794	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
795	if [[ $do_trace = true ]]
796	then
797	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
798	fi
799	fi
800
801	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
802	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
803	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
804	# MUST HAVE TO BE STARTED
805	if [[ $var = host ]]
806	then
807	if [[ -n $host && "$host" != $localhost ]]
808	then
809	do_batch=true
810	do_remote=true
811	case $host in
812	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
813	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
814	printf "\n is not available"
815	locat=nqs; exit;;
816	esac
817	else
818	host=$localhost
819	fi
820	fi
821
822	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
823	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
824	# BY MRUN (E.G. subjob)
825	export $var
826	fi
827
828
829
830
831	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
832	then
833
834	# LINE DEFINES ERROR-COMMAND
835	(( iec = iec + 1 ))
836	zeile=$(echo $zeile \| cut -c4-)
837	err_command[$iec]="$zeile"
838
839	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
840	then
841
842	# LINE DEFINES INPUT-COMMAND
843	(( iic = iic + 1 ))
844	zeile=$(echo $zeile \| cut -c4-)
845	in_command[$iic]="$zeile"
846
847	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
848	then
849
850	# LINE DEFINES OUTPUT-COMMAND
851	(( ioc = ioc + 1 ))
852	zeile=$(echo $zeile \| cut -c4-)
853	out_command[$ioc]="$zeile"
854
855	else
856
857	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
858	# s2a: in/out - field
859	# s2b: loc - field (optional)
860	# s2c: tr/ar - field (optional)
861	s1=`echo $zeile \| cut -d" " -f1`
862	s2=`echo $zeile \| cut -d" " -s -f2`
863	s2a=$(echo $s2 \| cut -d":" -f1)
864	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
865	then
866	s2b=""
867	s2c=""
868	else
869	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
870	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
871	fi
872	s3=`echo $zeile \| cut -d" " -f3`
873	s4=`echo $zeile \| cut -d" " -s -f4`
874	s5=`echo $zeile \| cut -d" " -s -f5`
875	s6=`echo $zeile \| cut -d" " -s -f6`
876
877
878	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
879	# INPUT- OR OUTPUT-LIST.
880	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
881	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
882	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
883	# IS NOT CHECKED AND STORED.
884	IFSALT="$IFS"; IFS="$IFS:"
885	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
886	then
887	found=false
888	for actual in $input_list
889	do
890	for formal in $s3
891	do
892	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
893	done
894	done
895	if [[ $found = true ]]
896	then
897	(( iin = iin + 1 ))
898	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
899	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
900	extin[$iin]=$s6
901	fi
902	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
903	then
904	found=false
905	for actual in $output_list
906	do
907	for formal in $s3
908	do
909	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
910	done
911	done
912	if [[ $found = true ]]
913	then
914	(( iout = iout + 1 ))
915	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
916	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
917	fi
918	elif [[ "$s2a" != in && "$s2a" != out ]]
919	then
920	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
921	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
922	locat=connect; exit
923	fi
924	IFS="$IFSALT"
925	fi
926	done < $config_file
927
928	else
929
930	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
931	[[ $silent = false ]] && printf "..."
932	interpreted_config_file=.icf.$RANDOM
933
934
935
936	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
937	cat > .mrun_environment << %%END%%
938	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
939	config_file = '$config_file', do_remote = '$do_remote',
940	do_trace = '$do_trace', host = '$host',
941	input_list = '$input_list', icf = '$interpreted_config_file',
942	localhost = '$localhost', output_list = '$output_list' /
943
944	%%END%%
945
946	if [[ "$host" != $localhost ]]
947	then
948
949	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
950	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
951	if [[ $? != 0 ]]
952	then
953	printf "\n\n +++ no interpret_config found"
954	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
955	locat=interpret_config; exit
956	fi
957	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
958	$interpret_config_executable
959
960	else
961
962	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
963	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
964	then
965	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
966	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
967	locat=interpret_config; exit
968	else
969	interpret_config${block}.x
970	fi
971
972	fi
973	rm .mrun_environment
974
975
976	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
977	chmod u+x $interpreted_config_file
978	export PATH=$PATH:.
979	. $interpreted_config_file
980	rm $interpreted_config_file
981
982	fi
983
984
985	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
986	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
987	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
988	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
989	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
990	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
991	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
992
993
994	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
995	# FOR SOURCE-FILES TO BE COMPILED.
996	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
997	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
998	if [[ "$SOURCES_COMPLETE" = "" ]]
999	then
1000
1001	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
1002	# HAS BEEN DEFINED
1003	source_path=""
1004	line=""
1005	grep "%source_path" $config_file > tmp_mrun
1006	while read line
1007	do
1008	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1009	then
1010	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
1011	then
1012	global_source_path=`echo $line \| cut -d" " -f2`
1013	fi
1014	fi
1015	done < tmp_mrun
1016
1017	line=""
1018	found=false
1019	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1020	while read line
1021	do
1022	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1023	then
1024	if [[ $found = true ]]
1025	then
1026	printf "\n\n +++ more than one source path found in configuration file"
1027	printf "\n for local host \"$localhost\" "
1028	locat=source_path; exit
1029	fi
1030	source_path=`echo $line \| cut -d" " -f2`
1031	found=true
1032	fi
1033	done < tmp_mrun
1034	rm tmp_mrun
1035
1036	if [[ "$source_path" = "" ]]
1037	then
1038	if [[ "$global_source_path" != "" ]]
1039	then
1040	source_path=$global_source_path
1041	else
1042	printf "\n\n +++ no source path found in configuration file"
1043	printf "\n for local host \"$localhost\" "
1044	locat=source_path; exit
1045	fi
1046	fi
1047	eval source_path=$source_path
1048
1049	if [[ ! -d $source_path ]]
1050	then
1051	printf "\n\n +++ source path \"$source_path\" on local host"
1052	printf "\n \"$localhost\" does not exist"
1053	locat=source_path; exit
1054	fi
1055
1056	fi
1057
1058
1059	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1060	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1061	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1062	then
1063	global_revision=`svnversion $source_path 2>/dev/null`
1064	global_revision="Rev: $global_revision"
1065	fi
1066
1067
1068	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1069	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1070	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1071	if [[ -n $host && "$host" != $localhost ]]
1072	then
1073	do_batch=true
1074	do_remote=true
1075	case $host in
1076	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1077	(*) printf "\n"
1078	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1079	printf "\n is not available"
1080	locat=nqs; (( iec = 0 )); exit;;
1081	esac
1082	else
1083	host=$localhost
1084	fi
1085
1086
1087
1088	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1089	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1090	then
1091
1092	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1093	if [[ ! -n $numprocs ]]
1094	then
1095	printf "\n"
1096	printf "\n +++ option \"-K parallel\" requires additional specification"
1097	printf "\n of the number of processors to be used by"
1098	printf "\n mrun-option \"-X\" or by environment-variable"
1099	printf "\n \"numprocs\" in the configuration file"
1100	locat=numprocs; (( iec = 0 )); exit
1101	fi
1102
1103	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1104	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1105	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1106	then
1107	printf "\n"
1108	printf "\n +++ option \"-T\" (tasks per node) is missing"
1109	printf "\n set -T option or define tasks_per_node in the config file"
1110	locat=tasks_per_node; (( iec = 0 )); exit
1111	fi
1112
1113	if (( numprocs < tasks_per_node ))
1114	then
1115	printf "\n"
1116	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1117	printf "\n given values: -T $tasks_per_node -X $numprocs"
1118	locat=tasks_per_node; (( iec = 0 )); exit
1119	fi
1120
1121	if [[ $host != lcflow && $host != lcxt5m ]]
1122	then
1123	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1124	(( ival = $tasks_per_node ))
1125	(( pes = numprocs ))
1126	(( ii = pes / ival ))
1127	(( remaining_pes = pes - ii * ival ))
1128	if (( remaining_pes > 0 ))
1129	then
1130	printf "\n"
1131	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1132	printf "\n divisor of the total number of processors (option \"-X\")"
1133	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1134	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1135	(( nodes = nodes + 1 ))
1136	fi
1137	fi
1138
1139
1140	# SETTINGS FOR SUBJOB-COMMAND
1141	OOPT="-O $threads_per_task"
1142
1143	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1144	if [[ "$tasks_per_node" != "" ]]
1145	then
1146	TOPT="-T $tasks_per_node"
1147	fi
1148
1149	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1150	if [[ $node_usage = default ]]
1151	then
1152	if [[ $host = ibms ]]
1153	then
1154	node_usage=shared
1155	else
1156	node_usage=not_shared
1157	fi
1158	fi
1159
1160	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1161	then
1162	printf "\n"
1163	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1164	printf "\n \"shared\" or \"not_shared\""
1165	locat=tasks_per_node; (( iec = 0 )); exit
1166	fi
1167
1168	fi
1169
1170	# CHECK IF HOSTFILE EXISTS
1171	if [[ -n $hostfile ]]
1172	then
1173	if [[ ! -f $hostfile ]]
1174	then
1175	printf "\n"
1176	printf "\n +++ hostfile \"$hostfile\" does not exist"
1177	locat=hostfile; exit
1178	fi
1179	fi
1180
1181
1182	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1183	if [[ "$maximum_parallel_io_streams" = "" ]]
1184	then
1185	maximum_parallel_io_streams=$numprocs
1186	fi
1187
1188
1189	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1190	if [[ "$scp_port" != "" ]]
1191	then
1192	PORTOPT="-P $scp_port"
1193	SSH_PORTOPT="-p $scp_port"
1194	fi
1195
1196
1197	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1198	# CONFIG-FILE
1199	if [[ "$ssh_key" != "" ]]
1200	then
1201	ssh_key="-i $HOME/.ssh/$ssh_key"
1202	fi
1203
1204
1205	# SET DEFAULT-QUEUE, IF NOT GIVEN
1206	if [[ $queue = none ]]
1207	then
1208	case $host in
1209	(ibmh) queue=cluster;;
1210	(ibmkisti) queue=class.32plus;;
1211	(lcbullhh) queue=compute;;
1212	(lccrayb) queue=mpp1q;;
1213	(lccrayh) queue=mpp1q;;
1214	(lckiaps) queue=normal;;
1215	(lckyoto) queue=ph;;
1216	(lckyuh) queue=fx-single;;
1217	(lckyut) queue=cx-single;;
1218	(lctit) queue=S;;
1219	(nech) queue=none;;
1220	(unics) queue=unics;;
1221	esac
1222	fi
1223
1224
1225	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1226	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1227	(( i = 0 ))
1228	while (( i < iin ))
1229	do
1230	(( i = i + 1 ))
1231	(( maxcycle = 0 ))
1232
1233	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1234	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1235	if [[ "${actionin[$i]}" = di ]]
1236	then
1237	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1238	# HOST ONLY
1239	eval filename=${pathin[$i]}/${endin[$i]}
1240	else
1241	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1242	# HOST ONLY
1243	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1244	fi
1245	eval pathname=${pathin[$i]}
1246
1247	# CHECK IF FILE EXISTS
1248	if ! ls $filename* 1>/dev/null 2>&1
1249	then
1250
1251	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1252	if [[ "${transin[$i]}" != "locopt" ]]
1253	then
1254	printf "\n\n +++ INPUT-file: "
1255	if [[ "${extin[$i]}" = "" ]]
1256	then
1257	printf "\n $filename"
1258	else
1259	printf "\n $filename.${extin[$i]}"
1260	fi
1261	printf "\n does not exist\n"
1262	locat=input; exit
1263	else
1264	transin[$i]="unavailable"
1265	fi
1266	else
1267
1268	# DETERMINE THE FILE'S CYCLE NUMBER
1269	ls -1 -d $filename > filelist 2>/dev/null
1270	ls -1 -d $filename.* >> filelist 2>/dev/null
1271	while read zeile
1272	do
1273	cycle=$(echo $zeile \| cut -f2 -d".")
1274	if [[ "$cycle" = "$zeile" ]]
1275	then
1276	(( icycle = 0 ))
1277	elif [[ "$cycle" = "${extin[$i]}" ]]
1278	then
1279	(( icycle = 0 ))
1280	else
1281	(( icycle = $cycle ))
1282	fi
1283	if (( icycle > maxcycle ))
1284	then
1285	(( maxcycle = icycle ))
1286	file_to_be_used=$zeile
1287	fi
1288	done <filelist
1289	rm filelist
1290
1291	# APPEND CYCLE NUMBER TO FILENAME
1292	if (( maxcycle > 0 ))
1293	then
1294	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1295	then
1296	filename=${filename}.$maxcycle.${extin[$i]}
1297	else
1298	filename=${filename}.$maxcycle
1299	fi
1300	else
1301	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1302	then
1303	filename=${filename}.${extin[$i]}
1304	fi
1305	fi
1306
1307	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1308	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1309	absnamein[$i]=$filename
1310	if (( maxcycle > 0 ))
1311	then
1312	if [[ "${actionin[$i]}" = di ]]
1313	then
1314	frelin[$i]=${endin[$i]}.$maxcycle
1315	else
1316	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1317	fi
1318	else
1319	if [[ "${actionin[$i]}" = di ]]
1320	then
1321	frelin[$i]=${endin[$i]}
1322	else
1323	frelin[$i]=${afname}${endin[$i]}
1324	fi
1325	fi
1326
1327	fi
1328	done
1329
1330	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1331	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1332	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1333	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1334	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1335	# REMOTE HOST)
1336	(( i = 0 ))
1337	while (( i < iout ))
1338	do
1339	(( i = i + 1 ))
1340	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1341	then
1342	if [[ "${actionout[$i]}" = tr ]]
1343	then
1344	actionout[$i]=""
1345	elif [[ "${actionout[$i]}" = trpe ]]
1346	then
1347	actionout[$i]=pe
1348	elif [[ "${actionout[$i]}" = tra ]]
1349	then
1350	actionout[$i]=a
1351	fi
1352	(( maxcycle = 0 ))
1353	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1354	eval catalogname=${pathout[$i]}
1355	if ! ls $filename* 1>/dev/null 2>&1
1356	then
1357
1358	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1359	if cat /dev/null > $filename
1360	then
1361	rm $filename
1362	else
1363
1364	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1365	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1366	if [[ ! -d $catalogname ]]
1367	then
1368	if mkdir -p $catalogname
1369	then
1370	printf "\n\n *** directory:"
1371	printf "\n $catalogname"
1372	printf "\n was created\n"
1373	else
1374	printf "\n\n +++ OUTPUT-file:"
1375	printf "\n $filename"
1376	printf "\n cannot be created, because directory does not exist"
1377	printf "\n and cannot be created either"
1378	printf "\n"
1379	locat=output ; exit
1380	fi 2>/dev/null
1381	else
1382	printf "\n\n +++ OUTPUT-file:"
1383	printf "\n $filename"
1384	printf "\n cannot be created, although directory exists"
1385	printf "\n"
1386	locat=output ; exit
1387	fi
1388	fi 2>/dev/null
1389	else
1390
1391	# DETERMINE THE CYCLE NUMBER
1392	ls -1 -d $filename > filelist 2>/dev/null
1393	ls -1 -d $filename.* >> filelist 2>/dev/null
1394	while read zeile
1395	do
1396	cycle=$(echo $zeile \| cut -f2 -d".")
1397	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1398	then
1399	(( icycle = 1 ))
1400	else
1401	(( icycle = $cycle + 1 ))
1402	fi
1403	if (( icycle > maxcycle ))
1404	then
1405	(( maxcycle = icycle ))
1406	fi
1407	done <filelist
1408	rm filelist
1409	fi
1410
1411	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1412	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1413	if [[ "${actionout[$i]}" != a ]]
1414	then
1415	if (( maxcycle > 0 ))
1416	then
1417	filename=${filename}.$maxcycle
1418	if cat /dev/null > $filename
1419	then
1420	rm $filename
1421	else
1422	printf "\n +++ OUTPUT-file:"
1423	printf "\n $filename"
1424	printf "\n cannot be created"
1425	locat=output ; exit
1426	fi
1427	fi
1428	else
1429	(( maxcycle = maxcycle - 1 ))
1430	if (( maxcycle > 0 ))
1431	then
1432	filename=${filename}.$maxcycle
1433	fi
1434	fi
1435
1436	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1437	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1438	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1439	pathout[$i]=$filename
1440	if (( maxcycle > 0 ))
1441	then
1442	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1443	else
1444	frelout[$i]=${fname}${endout[$i]}
1445	fi
1446
1447	fi
1448	done
1449
1450
1451	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1452	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1453	then
1454	if [[ "$dvr_inc" = "" ]]
1455	then
1456	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1457	printf "\n This is required for the dvrp_graphics package.\n"
1458	locat=dvr; exit
1459	fi
1460	if [[ "$dvr_lib" = "" ]]
1461	then
1462	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1463	printf "\n This is required for the dvrp_graphics package.\n"
1464	locat=dvr; exit
1465	fi
1466	fi
1467
1468
1469	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1470	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1471	if [[ "$mainprog" = "" && "$executable" = "" ]]
1472	then
1473	printf "\n +++ neither main program nor executable defined"
1474	locat=source; exit
1475	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1476	then
1477	printf "\n +++ main program as well as executable defined"
1478	locat=source; exit
1479	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1480	then
1481	do_compile=false
1482	fi
1483
1484
1485	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1486	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1487	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1488	then
1489	rm -rf SOURCES_FOR_RUN_$fname
1490	mkdir SOURCES_FOR_RUN_$fname
1491	fi
1492
1493
1494	# COLLECT ALL ROUTINES TO BE COMPILED
1495	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1496	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1497	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1498	then
1499
1500	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1501
1502	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1503	then
1504
1505	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1506	source_list=""
1507	cd $source_path
1508
1509
1510	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1511	if [[ ! -d .svn ]]
1512	then
1513	printf "\n\n +++ source directory"
1514	printf "\n \"$source_path\" "
1515	printf "\n is not under control of \"subversion\"."
1516	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1517	fi
1518
1519
1520	# LIST ALL MODIFIED SOURCE CODE FILES
1521	Filenames=""
1522	svn status > tmp_mrun
1523	while read line
1524	do
1525	firstc=`echo $line \| cut -c1`
1526	if [[ $firstc = M \|\| $firstc = "?" ]]
1527	then
1528	Name=`echo "$line" \| cut -c8-`
1529	extension=`echo $Name \| cut -d. -f2`
1530	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1531	then
1532	Filenames="$Filenames "$Name
1533	fi
1534	fi
1535	done < tmp_mrun
1536
1537
1538	# COPY FILES TO SOURCES_FOR_RUN_...
1539	for dateiname in $Filenames
1540	do
1541	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1542	source_list=$source_list"$dateiname "
1543	done
1544
1545	cd - > /dev/null
1546
1547
1548	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1549	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1550	elif [[ "$source_list" != "" && $restart_run != true ]]
1551	then
1552
1553	cd $source_path
1554
1555	for filename in $source_list
1556	do
1557
1558	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1559	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1560	then
1561	printf "\n +++ source code file: $filename"
1562	printf "\n must not contain (\"/\") "
1563	locat=source; exit
1564	fi
1565
1566	if [[ ! -f $filename ]]
1567	then
1568	printf "\n +++ source code file: $filename"
1569	printf "\n does not exist"
1570	locat=source; exit
1571	else
1572	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1573	fi
1574
1575	done
1576
1577	cd - > /dev/null
1578
1579	fi
1580
1581
1582	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1583	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1584	if [[ $restart_run != true ]]
1585	then
1586
1587	if [[ ! -f "$source_path/$mainprog" ]]
1588	then
1589	printf "\n\n +++ main program: $mainprog"
1590	printf "\n does not exist in source directory"
1591	printf "\n \"$source_path\"\n"
1592	locat=source; exit
1593	else
1594	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1595	then
1596	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1597	source_list=${mainprog}" $source_list"
1598	fi
1599	fi
1600	fi
1601
1602
1603	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1604	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1605	if [[ "$restart_run" != true ]]
1606	then
1607	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1608	if [[ ! -f $makefile ]]
1609	then
1610	printf "\n +++ file \"$makefile\" does not exist"
1611	locat=make; exit
1612	else
1613	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1614	fi
1615	fi
1616
1617
1618	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1619	if [[ $restart_run != true && "$add_source_path" != "" ]]
1620	then
1621
1622	# DOES THE DIRECTORY EXIST?
1623	if [[ ! -d $add_source_path ]]
1624	then
1625	printf "\n\n *** INFORMATIVE: additional source code directory"
1626	printf "\n \"$add_source_path\" "
1627	printf "\n does not exist or is not a directory."
1628	printf "\n No source code will be used from this directory!\n"
1629	add_source_path=""
1630	if [[ $silent == false ]]
1631	then
1632	sleep 3
1633	fi
1634	else
1635
1636	cd $add_source_path
1637	found=false
1638
1639	Names=$(ls -1 *.f90 2>&1)
1640	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1641	Names=$(ls -1 *.F90 2>&1)
1642	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1643	Names=$(ls -1 *.F 2>&1)
1644	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1645	Names=$(ls -1 *.f 2>&1)
1646	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1647	Names=$(ls -1 *.c 2>&1)
1648	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1649
1650	cd - > /dev/null
1651	cd SOURCES_FOR_RUN_$fname
1652
1653	# COPY MAKEFILE IF EXISTING
1654	if [[ -f $add_source_path/Makefile ]]
1655	then
1656	printf "\n\n *** user Makefile from directory"
1657	printf "\n \"$add_source_path\" is used \n"
1658	if [[ $silent == false ]]
1659	then
1660	sleep 1
1661	fi
1662	cp $add_source_path/Makefile .
1663	fi
1664
1665	for dateiname in $AddFilenames
1666	do
1667	if [[ -f $dateiname ]]
1668	then
1669	printf "\n +++ source code file \"$dateiname\" found in additional"
1670	printf "\n source code directory \"$add_source_path\" "
1671	printf "\n but was also given with option \"-s\" which means that it should be taken"
1672	printf "\n from directory \"$source_path\"."
1673	locat=source; exit
1674	fi
1675
1676	cp $add_source_path/$dateiname .
1677	source_list="$source_list $dateiname"
1678
1679	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1680	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1681	then
1682	printf "\n\n +++ user file \"$dateiname\" "
1683	printf "\n is not listed in Makefile \n"
1684	locat=source; exit
1685	else
1686
1687	if [[ $found = false ]]
1688	then
1689	found=true
1690	printf "\n\n *** following user file(s) added to the"
1691	printf " files to be translated:\n "
1692	fi
1693	printf "$dateiname "
1694	if [[ $silent == false ]]
1695	then
1696	sleep 0.5
1697	fi
1698
1699	fi
1700	done
1701	[[ $found = true ]] && printf "\n"
1702	cd - > /dev/null
1703	fi
1704	fi
1705
1706
1707	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1708	# TO THE LIST OF FILES TO BE COMPILED
1709	if [[ $restart_run != true && -n $package_list ]]
1710	then
1711
1712	cd $source_path
1713
1714	for package in $package_list
1715	do
1716
1717	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1718
1719	# DETERMINE FILES BELONGING TO THE PACKAGE
1720	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1721	# THE NAME OF THE DIRECTORY
1722	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1723
1724
1725	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1726	# IF THEY ARE NOT ALREADY PART OF THE LIST
1727	for source_list_name in $package_source_list
1728	do
1729	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1730	then
1731
1732	# ONLY TAKE FILES WITH VALID SUFFIX
1733	ending=`echo $source_list_name \| cut -f2 -d.`
1734	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1735	then
1736	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1737	source_list="$source_list $source_list_name"
1738	fi
1739	fi
1740	done
1741	done
1742
1743	cd - > /dev/null
1744	fi
1745
1746	fi # do_compile=true
1747
1748
1749	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1750	# AND SET PRE-PROCESSOR DIRECTIVES
1751	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1752	then
1753
1754	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1755	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1756	then
1757	cpp_options="${cpp_options},-D__ibm=__ibm"
1758	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1759	then
1760	cpp_options="$cpp_options -D__nec"
1761	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1762	then
1763	cpp_options="$cpp_options -D__lc"
1764	else
1765	cpp_options="$cpp_options -D__$localhost"
1766	fi
1767
1768	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1769	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1770	then
1771	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1772	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1773	else
1774	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1775	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1776	fi
1777
1778	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1779	if [[ -n $package_list ]]
1780	then
1781	for package in $package_list
1782	do
1783	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1784	then
1785	if [[ $package != "dvrp_graphics+1PE" ]]
1786	then
1787	cpp_options="${cpp_options},-D__$package=__$package"
1788	else
1789	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1790	export use_seperate_pe_for_dvrp_output=true
1791	fi
1792	else
1793	if [[ $package != "dvrp_graphics+1PE" ]]
1794	then
1795	cpp_options="$cpp_options -D__$package"
1796	else
1797	cpp_options="$cpp_options -D__dvrp_graphics"
1798	export use_seperate_pe_for_dvrp_output=true
1799	fi
1800	fi
1801	done
1802	fi
1803
1804	# SET DIRECTIVES GIVEN BY OPTION -D
1805	if [[ -n $cpp_opts ]]
1806	then
1807	for popts in $cpp_opts
1808	do
1809	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1810	then
1811	cpp_options="${cpp_options},-D__$popts=__$popts"
1812	else
1813	cpp_options="$cpp_options -D__$popts"
1814	fi
1815	done
1816	fi
1817
1818	else
1819
1820
1821	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1822	if [[ $do_remote = false ]]
1823	then
1824	if [[ ! -f $executable ]]
1825	then
1826	printf "\n +++ executable file: $executable"
1827	printf "\n does not exist"
1828	locat=executable; exit
1829	fi
1830	fi
1831	fi
1832
1833
1834	# DETERMINE THE JOB MODE
1835	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1836	then
1837	if [[ "$LOADLBATCH" = yes ]]
1838	then
1839	batch_job=.TRUE.
1840	jobmo=BATCH
1841	else
1842	batch_job=.FALSE.
1843	jobmo=INTERACTIVE
1844	fi
1845	else
1846	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
1847	then
1848	batch_job=.TRUE.
1849	jobmo=BATCH
1850	else
1851	batch_job=.FALSE.
1852	jobmo=INTERACTIVE
1853	fi
1854	fi
1855
1856	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1857	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1858	then
1859	printf "\n +++ no interactive runs allowed on host \"$host\" "
1860	printf "\n please submit batch job using mrun option \"-b\" \n"
1861	locat=normal; exit
1862	fi
1863
1864
1865	# CHECK, IF USER DEFINED A COMPILER
1866	if [[ "$compiler_name" = "" ]]
1867	then
1868
1869	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1870	locat=compiler_name; exit
1871
1872	fi
1873
1874
1875	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1876
1877	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1878	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1879	then
1880	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1881	if [[ "$kennung" = "" ]]
1882	then
1883	kennung=$RANDOM
1884	fi
1885	else
1886	kennung=$RANDOM
1887	fi
1888
1889	if [[ "$tmp_user_catalog" = "" ]]
1890	then
1891	if [[ $localhost = ibmh ]]
1892	then
1893	tmp_user_catalog=$SCRATCH
1894	elif [[ $localhost = nech ]]
1895	then
1896	tmp_user_catalog=$WRKSHR
1897	else
1898	tmp_user_catalog=/tmp
1899	fi
1900	fi
1901	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1902
1903
1904	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1905	if [[ "$tmp_data_catalog" = "" ]]
1906	then
1907	if [[ $localhost = nech ]]
1908	then
1909	tmp_data_catalog=$WRKSHR/mrun_restart_data
1910	else
1911	tmp_data_catalog=/tmp/mrun_restart_data
1912	fi
1913	fi
1914
1915
1916	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1917	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1918	then
1919	eval fopts=\"$fopts\"
1920	eval lopts=\"$lopts\"
1921	fi
1922
1923
1924	# DETERMINE COMPILE- AND LINK-OPTIONS
1925	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1926	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1927	XOPT="-X $numprocs"
1928
1929
1930	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1931	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1932	done=false
1933	while [[ $done = false ]]
1934	do
1935	cputime=$cpumax
1936	if (( $cputime == 0 ))
1937	then
1938	if [[ $do_batch = true ]]
1939	then
1940	printf "\n +++ cpu-time is undefined"
1941	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1942	printf "\n >>> "
1943	read cputime 1>/dev/null 2>&1
1944	else
1945	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1946	fi
1947	else
1948	done=true
1949	fi
1950	cpumax=$cputime
1951	done
1952
1953	(( minuten = cputime / 60 ))
1954	(( sekunden = cputime - minuten * 60 ))
1955
1956
1957	# CHECK THE MEMORY DEMAND
1958	if [[ $do_batch = true ]]
1959	then
1960	done=false
1961	while [[ $done = false ]]
1962	do
1963	if (( memory == 0 ))
1964	then
1965	printf "\n +++ memory demand is undefined"
1966	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1967	printf "\n >>> "
1968	read memory 1>/dev/null 2>&1
1969	else
1970	done=true
1971	fi
1972	done
1973	fi
1974
1975
1976	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1977	if [[ $do_remote = true && -z $remote_username ]]
1978	then
1979	while [[ -z $remote_username ]]
1980	do
1981	printf "\n +++ username on remote host \"$host\" is undefined"
1982	printf "\n >>> Please type username:"
1983	printf "\n >>> "
1984	read remote_username
1985	done
1986	mc="$mc -u$remote_username"
1987	fi
1988
1989	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1990	if [[ "$login_init_cmd" != "" ]]
1991	then
1992	export init_cmds="${login_init_cmd};"
1993	fi
1994
1995
1996	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1997	if [[ "$modules" != "" ]]
1998	then
1999	if [[ $host = lctit ]]
2000	then
2001	export module_calls=". $modules"
2002	else
2003	export module_calls="module load ${modules};"
2004	fi
2005	fi
2006
2007	# OUTPUT OF THE MRUN-HEADER
2008	calltime=$(date)
2009	printf "\n"
2010	printf "#------------------------------------------------------------------------# \n"
2011	printf "\| %-35s%35s \| \n" "$version" "$calltime"
2012	printf "\| \| \n"
2013	spalte1="called on:"; spalte2=$localhost_realname
2014	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2015	if [[ $do_remote = true ]]
2016	then
2017	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2018	else
2019	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2020	fi
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	if [[ -n $numprocs ]]
2023	then
2024	if [[ $run_coupled_model = false ]]
2025	then
2026	spalte1="number of PEs:"; spalte2=$numprocs
2027	else
2028	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2029	fi
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	fi
2032	if [[ -n $tasks_per_node ]]
2033	then
2034	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2035	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2036	if (( remaining_pes > 0 ))
2037	then
2038	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	fi
2041	fi
2042	if [[ $maximum_parallel_io_streams != $numprocs ]]
2043	then
2044	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046	fi
2047	if [[ $use_openmp = true ]]
2048	then
2049	spalte1="threads per task:"; spalte2="$threads_per_task"
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	fi
2052	printf "\| \| \n"
2053	if [[ $do_compile = true ]]
2054	then
2055	if [[ "$mopts" != "" ]]
2056	then
2057	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2058	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2059	zeile=$(echo "$mopts" \| cut -c46-)
2060	while [[ "$zeile" != "" ]]
2061	do
2062	spalte1=""
2063	spalte2=$(echo "$zeile" \| cut -c-45)
2064	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2065	zeile=$(echo "$zeile" \| cut -c46-)
2066	done
2067	fi
2068
2069	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	zeile=$(echo "$cpp_options" \| cut -c46-)
2072	while [[ "$zeile" != "" ]]
2073	do
2074	spalte1=""
2075	spalte2=$(echo "$zeile" \| cut -c-45)
2076	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2077	zeile=$(echo "$zeile" \| cut -c46-)
2078	done
2079
2080	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2082	zeile=$(echo "$fopts" \| cut -c46-)
2083	while [[ "$zeile" != "" ]]
2084	do
2085	spalte1=""
2086	spalte2=$(echo "$zeile" \| cut -c-45)
2087	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2088	zeile=$(echo "$zeile" \| cut -c46-)
2089	done
2090
2091	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2093	zeile=$(echo "$lopts" \| cut -c46-)
2094	while [[ "$zeile" != "" ]]
2095	do
2096	spalte1=""
2097	spalte2=$(echo "$zeile" \| cut -c-45)
2098	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2099	zeile=$(echo "$zeile" \| cut -c46-)
2100	done
2101
2102	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	zeile=$(echo "$modules" \| cut -c46-)
2105	while [[ "$zeile" != "" ]]
2106	do
2107	spalte1=""
2108	spalte2=$(echo "$zeile" \| cut -c-45)
2109	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2110	zeile=$(echo "$zeile" \| cut -c46-)
2111	done
2112
2113	spalte1="main program:"; spalte2=$mainprog
2114	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2115	else
2116	spalte1=executable:; spalte2=$executable
2117	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2118	fi
2119	printf "\| \| \n"
2120	spalte1="base name of files:"; spalte2=$fname
2121	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2122	if [[ $fname != $afname ]]
2123	then
2124	spalte1="base name of input files:"; spalte2=$afname
2125	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2126	fi
2127	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2128	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2129	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2130	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2131
2132	if [[ "$ocean_file_appendix" = true ]]
2133	then
2134	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2135	fi
2136
2137	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2138	then
2139	spalte1="memory demand / PE":; spalte2="$memory MB"
2140	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2141	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2142	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2143	fi
2144
2145	if [[ $do_compile = true ]]
2146	then
2147	printf "\| \| \n"
2148	printf "\| Files to be compiled: \| \n"
2149	zeile=$source_list
2150	while [[ "$zeile" != "" ]]
2151	do
2152	linestart=$(echo $zeile \| cut -c-70)
2153	printf "\| %-70s \| \n" "$linestart"
2154	zeile=$(echo "$zeile" \| cut -c71-)
2155	done
2156	fi
2157	printf "#------------------------------------------------------------------------#"
2158
2159
2160
2161	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2162	if [[ $do_trace = true ]]
2163	then
2164	(( i = 0 ))
2165	while (( i < iin ))
2166	do
2167	(( i = i + 1 ))
2168	if (( i == 1 ))
2169	then
2170	printf "\n\n >>> INPUT-file assignments:\n"
2171	fi
2172	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2173	done
2174	(( i = 0 ))
2175	while (( i < iout ))
2176	do
2177	(( i = i + 1 ))
2178	if (( i == 1 ))
2179	then
2180	printf "\n\n >>> OUTPUT-file assignments:\n"
2181	fi
2182	printf "\n ${localout[$i]} : ${pathout[$i]}"
2183	done
2184	(( i = 0 ))
2185	while (( i < iic ))
2186	do
2187	(( i = i + 1 ))
2188	if (( i == 1 ))
2189	then
2190	printf "\n\n >>> INPUT-commands:\n"
2191	fi
2192	printf "\n ${in_command[$i]}"
2193	done
2194	(( i = 0 ))
2195	while (( i < ioc ))
2196	do
2197	(( i = i + 1 ))
2198	if (( i == 1 ))
2199	then
2200	printf "\n\n >>> OUTPUT-commands:\n"
2201	fi
2202	printf "\n ${out_command[$i]}"
2203	done
2204	fi
2205
2206	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2207	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2208	then
2209	antwort=dummy
2210	printf "\n\n"
2211	printf " >>> everything o.k. (y/n) ? "
2212	while read antwort
2213	do
2214	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2215	then
2216	printf " >>> everything o.k. (y/n) ? "
2217	else
2218	break
2219	fi
2220	done
2221	if [[ $antwort = n \|\| $antwort = N ]]
2222	then
2223	locat=user_abort; (( iec = 0 )); exit
2224	fi
2225	if [[ $do_batch = true ]]
2226	then
2227	printf " >>> batch-job will be created and submitted"
2228	else
2229	printf " >>> MRUN will now continue to execute on this machine"
2230	fi
2231	fi
2232
2233
2234	# DETERMINE PATH FOR MAKE DEPOSITORY
2235	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2236	then
2237
2238	line=""
2239	grep "%depository_path" $config_file > tmp_mrun
2240	while read line
2241	do
2242	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2243	then
2244	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2245	then
2246	global_depository_path=`echo $line \| cut -d" " -s -f2`
2247	fi
2248	fi
2249	done < tmp_mrun
2250
2251	line=""
2252	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2253	while read line
2254	do
2255	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2256	then
2257	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2258	then
2259	local_depository_path=`echo $line \| cut -d" " -s -f2`
2260	fi
2261	fi
2262	done < tmp_mrun
2263
2264	if [[ "$local_depository_path" = "" ]]
2265	then
2266	if [[ "$global_depository_path" != "" ]]
2267	then
2268	local_depository_path=$global_depository_path
2269	else
2270	printf "\n\n +++ no depository path found in configuration file"
2271	printf "\n for local host \"$localhost\" "
2272	printf "\n please set \"\%depository_path\" in configuration file\n"
2273	locat=config_file; exit
2274	fi
2275	fi
2276	eval local_depository_path=$local_depository_path
2277	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2278	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2279
2280
2281	basename=`echo $mainprog \| cut -f1 -d"."`
2282	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2283	if [[ ! -f $make_depository ]]
2284	then
2285	printf "\n"
2286	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2287	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2288	fi
2289
2290	fi
2291
2292
2293	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2294	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2295	if [[ $do_batch = false ]]
2296	then
2297
2298
2299	# CREATE THE TEMPORARY WORKING DIRECTORY
2300	mkdir -p $TEMPDIR
2301	chmod go+rx $TEMPDIR
2302	tmpcreate=true
2303
2304
2305	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2306	# INTO THE TEMPORARY WORKING DIRECTORY
2307	if [[ $do_compile = true ]]
2308	then
2309
2310	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2311	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2312	if [[ $localhost = nech ]]
2313	then
2314	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2315	if mkdir -p $TEMPDIR_COMPILE
2316	then
2317	printf "\n *** \"$TEMPDIR_COMPILE\" "
2318	printf "\n is generated as temporary directory for cross compiling\n"
2319	else
2320	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2321	printf "\n needed for cross compilation failed"
2322	locat=compile
2323	exit
2324	fi
2325	else
2326	TEMPDIR_COMPILE=$TEMPDIR
2327	fi
2328
2329	cp $make_depository $TEMPDIR_COMPILE
2330	cd $TEMPDIR_COMPILE
2331	tar -xf $make_depository > /dev/null 2>&1
2332	cd - > /dev/null
2333
2334	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2335	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2336	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2337	then
2338	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2339	else
2340	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2341	fi
2342
2343	else
2344
2345	cp $executable ${TEMPDIR}/a.out
2346
2347	fi
2348
2349
2350	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2351	cd $TEMPDIR
2352	printf "\n *** changed to temporary directory: $TEMPDIR"
2353
2354
2355	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2356	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2357	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2358	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2359	(( i = 0 ))
2360	while (( i < iout ))
2361	do
2362	(( i = i + 1 ))
2363	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2364	then
2365	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2366	else
2367	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2368	fi
2369	done
2370
2371
2372	# IF REQUIRED, START WITH COMPILING
2373	if [[ $do_compile = true ]]
2374	then
2375
2376
2377	if [[ -f a.out ]]
2378	then
2379
2380	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2381	printf "\n\n\n *** executable a.out found"
2382	printf "\n no compilation required \n"
2383
2384	else
2385
2386	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2387	printf "\n\n\n *** compilation starts \n$dashes\n"
2388	printf " *** compilation with make using following options:\n"
2389	printf " make depository: $make_depository"
2390	if [[ "$mopts" != "" ]]
2391	then
2392	printf " make options: $mopts\n"
2393	fi
2394	printf " compilername: $compiler_name\n"
2395	printf " compiler options: $fopts\n"
2396	printf " preprocessor directives: $cpp_options \n"
2397	printf " linker options: $lopts \n"
2398	if [[ "$modules" != "" ]]
2399	then
2400	printf " modules to be load: $modules \n"
2401	fi
2402	printf " source code files: $source_list \n"
2403
2404	if [[ $localhost = nech ]]
2405	then
2406	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\" "
2407	cp $TEMPDIR_COMPILE/a.out .
2408	[[ $? != 0 ]] && compile_error=true
2409	rm -rf $TEMPDIR_COMPILE
2410	elif [[ $localhost = ibmh ]]
2411	then
2412	printf " compiler is called via ssh on \"plogin1\" \n"
2413	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\" "
2414	[[ ! -f a.out ]] && compile_error=true
2415	continue # STATUS=1, IF a.out EXISTS
2416	elif [[ $localhost = lcocean ]]
2417	then
2418	printf " compiler is called via ssh on \"ocean\" \n"
2419	echo $PWD
2420	ssh $SSH_PORTOPT ocean -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\" "
2421	[[ ! -f a.out ]] && compile_error=true
2422	continue # STATUS=1, IF a.out EXISTS
2423	elif [[ $localhost = lcflow ]]
2424	then
2425	printf " compiler is called via ssh on \"flow\" \n"
2426	/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\" "
2427	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2428	[[ "$check_for_file" = "" ]] && compile_error=true
2429	continue # STATUS=1, IF a.out EXISTS
2430	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2431	then
2432	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2433	else
2434	[[ "$init_cmds" != "" ]] && eval $init_cmds
2435	[[ "$module_calls" != "" ]] && eval $module_calls
2436	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2437	fi
2438
2439	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2440	then
2441	printf "\n +++ error occured while compiling or linking"
2442	locat=compile
2443
2444	exit
2445	else
2446	printf "$dashes\n *** compilation finished \n"
2447	fi
2448
2449	fi
2450
2451	fi
2452
2453
2454	# PROVIDE THE INPUT FILES
2455	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2456	(( i = 0 ))
2457	while (( i < iin ))
2458	do
2459	(( i = i + 1 ))
2460	if (( i == 1 ))
2461	then
2462	printf "\n\n *** providing INPUT-files:\n$dashes"
2463	fi
2464
2465
2466	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2467	if [[ "${transin[$i]}" = unavailable ]]
2468	then
2469	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2470	then
2471	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2472	printf "\n is not available!"
2473	else
2474	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2475	printf "\n is not available!"
2476	fi
2477	continue
2478	fi
2479
2480	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2481	files_for_pes=false; datentyp=file
2482	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2483	then
2484	files_for_pes=true; datentyp=directory
2485	actionin[$i]=""
2486	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2487	then
2488	actionin[$i]=""
2489	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2490	then
2491	files_for_pes=true; datentyp=directory
2492	actionin[$i]="ar"
2493	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2494	then
2495	actionin[$i]="ar"
2496	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2497	then
2498	files_for_pes=true; datentyp=directory
2499	actionin[$i]="fl"
2500	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2501	then
2502	actionin[$i]="fl"
2503	fi
2504
2505	if [[ $files_for_pes = true ]]
2506	then
2507	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2508	else
2509	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2510	fi
2511
2512	# INPUT-FILE FOR A RESTART RUN.
2513	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2514	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2515	if [[ "${actionin[$i]}" = fl ]]
2516	then
2517	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2518	if [[ $files_for_pes = false ]]
2519	then
2520	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2521	then
2522	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2523	got_tmp[$i]=true
2524	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2525	then
2526	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2527	printf "\n *** trying to use backup copy in \"$WORK\" "
2528	cp $WORK/${frelin[$i]} ${localin[$i]}
2529	else
2530	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2531	printf "\n or \"$tmp_data_catalog\" does not exist!"
2532	printf "\n *** trying to get copy from archive"
2533	actionin[$i]=ar
2534	fi
2535	else
2536	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2537	then
2538	mkdir ${localin[$i]}
2539	cd $tmp_data_catalog/${frelin[$i]}
2540	for file in $(ls *)
2541	do
2542	ln $file $TEMPDIR/${localin[$i]}
2543	done
2544	cd $TEMPDIR
2545	got_tmp[$i]=true
2546	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2547	then
2548	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2549	printf "\n *** trying to use backup copy in \"$WORK\" "
2550	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2551	else
2552	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2553	printf "\n or \"$tmp_data_catalog\" does not exist!"
2554	printf "\n *** trying to get copy from archive"
2555	actionin[$i]=ar
2556	fi
2557	fi
2558	fi
2559
2560
2561	# FILE IS STORED ON THE ARCHIVE SYSTEM
2562	if [[ "${actionin[$i]}" = ar ]]
2563	then
2564
2565	if [[ $files_for_pes = false ]]
2566	then
2567	printf "\n file will be restored from archive-system ($archive_system)!"
2568	else
2569	printf "\n directory will be restored from archive-system ($archive_system)!"
2570	fi
2571
2572	file_restored=false
2573
2574	if [[ $archive_system = asterix ]]
2575	then
2576	do_stagein=true
2577	(( stagein_anz = 0 ))
2578	while [[ $do_stagein = true ]]
2579	do
2580	if [[ $files_for_pes = false ]]
2581	then
2582	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2583	else
2584	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2585	fi
2586	cat STAGEIN_OUTPUT
2587	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2588	then
2589	file_restored=true
2590	do_stagein=false
2591	else
2592	(( stagein_anz = stagein_anz + 1 ))
2593	if (( stagein_anz == 10 ))
2594	then
2595	printf "\n +++ stagein stoped after 10 tries"
2596	locat=stage
2597	exit
2598	fi
2599	printf "\n +++ restoring from archive failed, trying again:"
2600	sleep 900
2601	fi
2602	done
2603	elif [[ $archive_system = DMF ]]
2604	then
2605	if [[ $files_for_pes = false ]]
2606	then
2607	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2608	locat=DMF
2609	exit
2610	else
2611	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2612	cp -r $ARCHIVE/${frelin[$i]} $PWD
2613	file_restored=true
2614	fi
2615	elif [[ $archive_system = tivoli ]]
2616	then
2617	if [[ $files_for_pes = false ]]
2618	then
2619	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2620	else
2621	(( inode = 0 ))
2622	while (( inode < nodes ))
2623	do
2624	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2625	(( inode = inode + 1 ))
2626	done
2627	fi
2628	file_restored=true
2629	elif [[ $archive_system = ut ]]
2630	then
2631	if [[ $files_for_pes = false ]]
2632	then
2633	cp $UT/${frelin[$i]} .
2634	else
2635	(( inode = 0 ))
2636	while (( inode < nodes ))
2637	do
2638	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2639	(( inode = inode + 1 ))
2640	done
2641	fi
2642	file_restored=true
2643	else
2644	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2645	locat=rearchive
2646	exit
2647	fi
2648
2649	if [[ $file_restored = true ]]
2650	then
2651
2652	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2653	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2654	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2655	if [[ $files_for_pes = false ]]
2656	then
2657	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2658	else
2659	mkdir $tmp_data_catalog/${frelin[$i]}
2660	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2661	fi
2662	got_tmp[$i]=true
2663
2664	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2665	mv ${frelin[$i]} ${localin[$i]}
2666
2667	fi
2668	fi
2669
2670
2671	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2672	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2673	then
2674
2675	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2676	then
2677
2678	# FILE COPIES ARE PROVIDED FOR ALL CORES
2679	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2680	printf "\n file will be provided for $numprocs processors"
2681	mkdir ${localin[$i]}
2682	ival=$numprocs
2683	(( ii = 0 ))
2684	while (( ii <= ival-1 ))
2685	do
2686	if (( ii < 10 ))
2687	then
2688	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2689	elif (( ii < 100 ))
2690	then
2691	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2692	elif (( ii < 1000 ))
2693	then
2694	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2695	else
2696	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2697	fi
2698	(( ii = ii + 1 ))
2699	done
2700
2701	else
2702
2703	if [[ $files_for_pes = true ]]
2704	then
2705
2706	# PROVIDE FILES FOR EACH CORE
2707	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2708	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2709	printf "\n providing $numprocs files for the respective processors"
2710	mkdir ${localin[$i]}
2711	if [[ $link_local_input = true ]]
2712	then
2713	printf " using ln -f\n"
2714	cd ${absnamein[$i]}
2715	for file in $(ls *)
2716	do
2717	ln -f $file ${localin[$i]}
2718	done
2719	cd $TEMPDIR
2720	fi
2721
2722	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2723	if [[ ! -f "${localin[$i]}/_0000" ]]
2724	then
2725	if [[ $link_local_input = true ]]
2726	then
2727	printf " ln failed for .../_0000, using cp...\n"
2728	fi
2729	cp -r ${absnamein[$i]}/* ${localin[$i]}
2730	fi
2731
2732	else
2733
2734	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2735	if [[ $link_local_input = true ]]
2736	then
2737	printf " using ln -f\n"
2738	ln -f ${absnamein[$i]} ${localin[$i]}
2739	fi
2740	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2741	if [[ ! -f "${localin[$i]}" ]]
2742	then
2743	if [[ $link_local_input = true ]]
2744	then
2745	printf " ln failed, using cp...\n"
2746	fi
2747	cp ${absnamein[$i]} ${localin[$i]}
2748	fi
2749	fi
2750	fi
2751	fi
2752
2753	done
2754	if (( i != 0 ))
2755	then
2756	printf "\n$dashes\n *** all INPUT-files provided \n"
2757	fi
2758
2759
2760	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2761	(( i = 0 ))
2762	while (( i < iic ))
2763	do
2764	(( i = i + 1 ))
2765	if (( i == 1 ))
2766	then
2767	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2768	fi
2769	printf "\n >>> ${in_command[$i]}"
2770	eval ${in_command[$i]}
2771	if (( i == iic ))
2772	then
2773	printf "\n$dashes\n"
2774	fi
2775	done
2776
2777
2778	# SET THE REMAINING CPU-TIME
2779	cpurest=${cpumax}.
2780
2781
2782	# START DVR STREAMING SERVER
2783	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2784	then
2785	if [[ "$dvr_server" != "" ]]
2786	then
2787
2788	printf "\n\n *** preparing the dvr streaming server configuration file"
2789
2790	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2791	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2792	if [[ "$running_dvrserver_id" != "" ]]
2793	then
2794
2795	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2796	printf "\n This server is used instead starting a new one!"
2797	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2798
2799	else
2800
2801	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2802	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2803	then
2804	cp ${PALM_BIN}/.dvrserver.config .
2805
2806	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2807	user_id=`id -u`
2808	group_id=`id -g`
2809
2810	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2811	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2812	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2813	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2814	mv .dvrserver.3 .dvrserver.config
2815	rm .dvrserver.1 .dvrserver.2
2816
2817	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2818	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2819	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2820	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2821	local_dvrserver_running=.TRUE.
2822	else
2823	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2824	printf "\n \"$PALM_BIN\" "
2825	locat=dvr
2826	exit
2827	fi
2828
2829	fi
2830
2831	else
2832	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2833	fi
2834	fi
2835
2836
2837	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2838	# (FILE ENVPAR WILL BE READ BY PALM)
2839	cat > ENVPAR << %%END%%
2840	&envpar run_identifier = '$fname', host = '$localhost',
2841	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2842	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2843	maximum_cpu_time_allowed = ${cpumax}.,
2844	revision = '$global_revision',
2845	local_dvrserver_running = $local_dvrserver_running,
2846	batch_job = $batch_job /
2847
2848	%%END%%
2849
2850
2851	# STARTING THE EXECUTABLE
2852	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2853	PATH=$PATH:$TEMPDIR
2854
2855
2856	if [[ $execute_command != "none" ]]
2857	then
2858
2859	printf "\n +++ branch still not realized"
2860	locat=execution
2861	exit
2862
2863	else
2864
2865	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2866	if [[ "$mpi_debug" = true ]]
2867	then
2868	export MPI_CHECK_ARGS=1
2869	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2870	fi
2871
2872	if [[ "$totalview" = true ]]
2873	then
2874	printf "\n *** totalview debugger will be used"
2875	tv_opt="-tv"
2876	else
2877	tv_opt=""
2878	fi
2879
2880	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2881	then
2882
2883	#Interactive ALLINEA DEBUG seesion
2884	if [[ "$ENVIRONMENT" != BATCH ]]
2885	then
2886	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2887	then
2888	if [[ "$allinea" = true ]]
2889	then
2890	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2891
2892	ddt aprun -n $ii -N $tasks_per_node a.out
2893	wait
2894	fi
2895	fi
2896	fi
2897
2898	if [[ $localhost = ibmh ]]
2899	then
2900
2901	# SETUP THE IBM MPI ENVIRONMENT
2902	export MP_SHARED_MEMORY=yes
2903	export AIXTHREADS_SCOPE=S
2904	export OMP_NUM_THREADS=$threads_per_task
2905	export AUTHSTATE=files
2906	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2907
2908	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2909	export MP_ADAPTER_USE=shared
2910	export MP_CPU_USE=multiple
2911	export MP_TIMEOUT=1200
2912
2913	unset MP_TASK_AFFINITY
2914
2915	if [[ "$LOADLBATCH" = yes ]]
2916	then
2917	totalview poe a.out
2918	else
2919	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2920	export TVDSVRLAUNCHCMD=ssh
2921	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2922	fi
2923
2924	fi # END DEBUG MODE
2925
2926	else
2927
2928	# NORMAL EXECUTION
2929	if [[ -n $numprocs ]]
2930	then
2931
2932	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2933	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2934	then
2935
2936	# SETUP THE IBM MPI ENVIRONMENT
2937	if [[ $host != ibmh && $host != ibmkisti ]]
2938	then
2939	export MP_SHARED_MEMORY=yes
2940	export AIXTHREAD_SCOPE=S
2941	export OMP_NUM_THREADS=$threads_per_task
2942	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2943	export AUTHSTATE=files
2944	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2945	# export MP_PRINTENV=yes
2946
2947	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2948	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2949	export MP_WAIT_MODE=poll
2950	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2951	fi
2952
2953	if [[ $host = ibmkisti ]]
2954	then
2955	export LANG=en_US
2956	export MP_SHARED_MEMORY=yes
2957	if [[ $threads_per_task = 1 ]]
2958	then
2959	export MP_SINGLE_THREAD=yes
2960	export MEMORY_AFFINITY=MCM
2961	else
2962	export OMP_NUM_THREADS=$threads_per_task
2963	fi
2964	fi
2965
2966	if [[ "$LOADLBATCH" = yes ]]
2967	then
2968	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2969	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2970	then
2971	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2972	else
2973	if [[ $run_coupled_model = false ]]
2974	then
2975	if [[ "$ocean_file_appendix" = true ]]
2976	then
2977	echo "precursor_ocean" > runfile_atmos
2978	else
2979	echo "precursor_atmos" > runfile_atmos
2980	fi
2981	else
2982	(( iia = $numprocs_atmos / $threads_per_task ))
2983	(( iio = $numprocs_ocean / $threads_per_task ))
2984	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2985	printf "\n using $coupled_mode coupling"
2986	printf "\n\n"
2987	echo "coupled_run $iia $iio" > runfile_atmos
2988	fi
2989	poe ./a.out < runfile_atmos
2990	fi
2991	else
2992	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2993	then
2994	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2995	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2996	then
2997	if [[ -f $hostfile ]]
2998	then
2999	cp $hostfile hostfile
3000	else
3001	(( ii = 1 ))
3002	while (( ii <= $numprocs ))
3003	do
3004	echo $localhost_realname >> hostfile
3005	(( ii = ii + 1 ))
3006	done
3007	fi
3008	export MP_HOSTFILE=hostfile
3009	if [[ $run_coupled_model = false ]]
3010	then
3011	if [[ "$ocean_file_appendix" = true ]]
3012	then
3013	echo "precursor_ocean" > runfile_atmos
3014	else
3015	echo "precursor_atmos" > runfile_atmos
3016	fi
3017	else
3018	(( iia = $numprocs_atmos / $threads_per_task ))
3019	(( iio = $numprocs_ocean / $threads_per_task ))
3020	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3021	printf "\n using $coupled_mode coupling"
3022	printf "\n\n"
3023	echo "coupled_run $iia $iio" > runfile_atmos
3024	fi
3025
3026	poe ./a.out -procs $numprocs < runfile_atmos
3027
3028	else
3029	if [[ "$host_file" = "" ]]
3030	then
3031	printf "\n +++ no hostfile given in configuration file"
3032	locat=config_file
3033	exit
3034	else
3035	eval host_file=$host_file
3036	fi
3037	export MP_HOSTFILE=$host_file
3038	poe a.out -procs $numprocs -tasks_per_node $numprocs
3039	fi
3040	fi
3041
3042	elif [[ $host = nech ]] # running on NEC machines
3043	then
3044
3045	(( ii = nodes ))
3046	if [[ $ii = 1 ]]
3047	then
3048	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3049	export MPIPROGINF=YES
3050	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3051	echo "*** execution on single node with mpirun"
3052	mpirun -np $numprocs ./a.out
3053	else
3054	(( i = 0 ))
3055	while (( i < ii ))
3056	do
3057	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3058	(( i = i + 1 ))
3059	done
3060
3061	echo "#!/bin/sh" > mpi_exec_shell
3062	echo " " >> mpi_exec_shell
3063	echo "set -u" >> mpi_exec_shell
3064	echo "F_ERRCNT=0" >> mpi_exec_shell
3065	echo "MPIPROGINV=YES" >> mpi_exec_shell
3066	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3067	echo "cpurest=$cpurest" >> mpi_exec_shell
3068	echo "fname=$fname" >> mpi_exec_shell
3069	echo "localhost=$localhost" >> mpi_exec_shell
3070	echo "return_address=$return_address" >> mpi_exec_shell
3071	echo "return_username=$return_username" >> mpi_exec_shell
3072	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3073	echo "write_binary=$write_binary" >> mpi_exec_shell
3074	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3075	echo " " >> mpi_exec_shell
3076	echo "export F_ERRCNT" >> mpi_exec_shell
3077	echo "export MPIPROGINV" >> mpi_exec_shell
3078	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3079	echo "export cpurest" >> mpi_exec_shell
3080	echo "export fname" >> mpi_exec_shell
3081	echo "export localhost" >> mpi_exec_shell
3082	echo "export return_address" >> mpi_exec_shell
3083	echo "export return_username" >> mpi_exec_shell
3084	echo "export tasks_per_node" >> mpi_exec_shell
3085	echo "export write_binary" >> mpi_exec_shell
3086	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3087	echo " " >> mpi_exec_shell
3088	echo "exec ./a.out" >> mpi_exec_shell
3089
3090	chmod u+x mpi_exec_shell
3091	export MPIPROGINF=YES
3092	mpirun -f multinode_config &
3093	wait
3094
3095	fi
3096
3097	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3098	then
3099
3100	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3101	# DOES NOT EXIST
3102	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]
3103	then
3104	if [[ -f $hostfile ]]
3105	then
3106	cp $hostfile hostfile
3107	(( ii = $numprocs / $threads_per_task ))
3108	[[ $ii = 0 ]] && (( ii = 1 ))
3109	else
3110	(( ii = 1 ))
3111	while (( ii <= $numprocs / $threads_per_task ))
3112	do
3113	echo $localhost_realname >> hostfile
3114	(( ii = ii + 1 ))
3115	done
3116	if (( $numprocs / $threads_per_task == 0 ))
3117	then
3118	echo $localhost_realname >> hostfile
3119	fi
3120	fi
3121	eval zeile=\"`head -n $ii hostfile`\"
3122	printf "\n *** running on: $zeile"
3123	fi
3124
3125	(( ii = $numprocs / $threads_per_task ))
3126	[[ $ii = 0 ]] && (( ii = 1 ))
3127	export OMP_NUM_THREADS=$threads_per_task
3128
3129	if [[ $threads_per_task != 1 ]]
3130	then
3131	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3132	# MAY ABORT
3133	ulimit -s unlimited
3134	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3135	fi
3136	if [[ $run_coupled_model = false ]]
3137	then
3138	if [[ "$ocean_file_appendix" = true ]]
3139	then
3140	echo "precursor_ocean" > runfile_atmos
3141	else
3142	echo "precursor_atmos" > runfile_atmos
3143	fi
3144	printf "\n\n"
3145
3146	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3147	then
3148	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3149	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3150	elif [[ $host = lcbullhh ]]
3151	then
3152	export OMPI_MCA_pml=cm
3153	export OMPI_MCA_mtl=mxm
3154	export OMPI_MCA_coll=^ghc
3155	export OMPI_MCA_mtl_mxm_np=0
3156	export MXM_RDMA_PORTS=mlx5_0:1
3157	export MXM_LOG_LEVEL=ERROR
3158	export OMP_NUM_THREADS=$threads_per_task
3159	export KMP_AFFINITY=verbose,granularity=core,compact,1
3160	export KMP_STACKSIZE=64m
3161
3162	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3163
3164	elif [[ $host = lccrayf ]]
3165	then
3166	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3167	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3168	then
3169	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3170	elif [[ $host = lcflow ]]
3171	then
3172	mpirun -np $ii a.out < runfile_atmos
3173	elif [[ $host = lcocean ]]
3174	then
3175	mpirun a.out $ROPTS < runfile_atmos
3176	elif [[ $host = lcsb ]]
3177	then
3178	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3179	elif [[ $host = lckiaps ]]
3180	then
3181	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
3182	elif [[ $host = lckyu* ]]
3183	then
3184	mpiexec -n $ii --stdin runfile_atmos ./a.out
3185	else
3186	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3187	fi
3188
3189	else
3190
3191	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3192	(( iia = $numprocs_atmos / $threads_per_task ))
3193	(( iio = $numprocs_ocean / $threads_per_task ))
3194	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3195	printf "\n using $coupled_mode coupling"
3196	printf "\n\n"
3197
3198	if [[ $coupled_mode = "mpi2" ]]
3199	then
3200	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3201	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3202
3203	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3204	then
3205
3206	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
3207	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
3208
3209	else
3210	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3211	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
3212	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
3213	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
3214	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
3215	fi
3216	wait
3217
3218	else
3219
3220	echo "coupled_run $iia $iio" > runfile_atmos
3221
3222	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3223	then
3224
3225	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3226
3227	elif [[ $host = lck \|\| $host = lckordi ]]
3228	then
3229
3230	mpiexec -n $ii ./a.out < runfile_atmos &
3231
3232	elif [[ $host = lckyu* ]]
3233	then
3234
3235	mpiexec -n $ii --stdin runfile_atmos ./a.out
3236
3237	elif [[ $host = lcmuk ]]
3238	then
3239
3240	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3241
3242	fi
3243	wait
3244	fi
3245
3246	fi
3247
3248	elif [[ $host = lckyoto ]]
3249	then
3250	set -xv
3251	export P4_RSHCOMMAND=plesh
3252	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3253	if [[ "$ENVIRONMENT" = BATCH ]]
3254	then
3255	if [[ "$cond2" = fujitsu ]]
3256	then
3257	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3258	elif [[ "cond2" = pgi ]]
3259	then
3260	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3261	else
3262	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3263	fi
3264	else
3265	if [[ "$cond2" = "" ]]
3266	then
3267	mpiruni_rsh -np $numprocs ./a.out # for intel
3268	else
3269	mpirun -np $numprocs ./a.out
3270	fi
3271	fi
3272	set +xv
3273
3274	elif [[ $host = lctit ]]
3275	then
3276	export OMP_NUM_THREADS=$threads_per_task
3277	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3278	if [[ "$threads_per_task" != 1 ]]
3279	then
3280	export MV2_ENABLE_AFFINITY=0
3281	fi
3282	echo "----- PBS_NODEFILE content:"
3283	cat $PBS_NODEFILE
3284	echo "-----"
3285	(( ii = $numprocs / $threads_per_task ))
3286	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3287	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3288
3289	else
3290	mpprun -n $numprocs a.out
3291	fi
3292	else
3293	a.out
3294	fi
3295
3296	fi # end normal (non-debug) execution
3297
3298	fi # end explicit execute_command or host-specific execute actions
3299
3300	if [[ $? != 0 ]]
3301	then
3302
3303	# ABORT IN CASE OF RUNTIME ERRORS
3304	printf "\n +++ runtime error occured"
3305	locat=execution
3306	exit
3307
3308	else
3309
3310	printf "\n$dashes\n *** execution finished \n"
3311
3312	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3313	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3314	if [[ "$dvrserver_id" != "" ]]
3315	then
3316	kill $dvrserver_id
3317	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3318
3319	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3320	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3321	if [[ -d DATA_DVR ]]
3322	then
3323
3324	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3325	# DIRECTORY
3326	cp .dvrserver.config DATA_DVR
3327
3328	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3329	# SEQUENCE MODE DATA TOO)
3330	process_dvr_output -d DATA_DVR -f $fname -s
3331
3332	else
3333
3334	# PROCESS THE LOCAL OUTPUT
3335	process_dvr_output -l -d DATA_DVR -f $fname
3336
3337	fi
3338
3339	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3340	then
3341
3342	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3343	process_dvr_output -l -d DATA_DVR -f $fname
3344
3345	fi
3346	fi
3347
3348
3349
3350	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3351	# BY EACH CORE INTO ONE FILE
3352	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3353	then
3354	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3355	printf "\n 2d- and/or 3d-data may be incomplete!"
3356	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3357	elif [[ "$combine_plot_fields" == true ]]
3358	then
3359	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3360	then
3361	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3362	aprun -n 1 -N 1 combine_plot_fields${block}.x
3363	else
3364	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3365	combine_plot_fields${block}.x
3366	fi
3367	else
3368
3369	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3370	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3371	# ??? koennen wir das streichen ???
3372	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3373	fi
3374
3375
3376
3377	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3378	(( i = 0 ))
3379	while (( i < ioc ))
3380	do
3381	(( i = i + 1 ))
3382	if (( i == 1 ))
3383	then
3384	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3385	fi
3386	printf "\n >>> ${out_command[$i]}"
3387	eval ${out_command[$i]}
3388	if (( i == ioc ))
3389	then
3390	printf "\n$dashes\n"
3391	fi
3392	done
3393
3394
3395	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3396	if [[ $do_trace = true ]]
3397	then
3398	printf "\n\n"
3399	ls -al
3400	fi
3401
3402
3403
3404	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3405	(( i = 0 ))
3406	while (( i < iout ))
3407	do
3408	(( i = i + 1 ))
3409	if (( i == 1 ))
3410	then
3411	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3412	fi
3413
3414	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3415	files_for_pes=false; filetyp=file
3416	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3417	then
3418	files_for_pes=true; filetyp=directory
3419	actionout[$i]=""
3420	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3421	then
3422	actionout[$i]=""
3423	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3424	then
3425	files_for_pes=true; filetyp=directory
3426	actionout[$i]="ar"
3427	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3428	then
3429	actionout[$i]="ar"
3430	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3431	then
3432	files_for_pes=true; filetyp=directory
3433	actionout[$i]="fl"
3434	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3435	then
3436	actionout[$i]="fl"
3437	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3438	then
3439	files_for_pes=true; filetyp=directory
3440	actionout[$i]="tr"
3441	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3442	then
3443	actionout[$i]="tr"
3444	fi
3445
3446	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3447	then
3448	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3449	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3450	then
3451	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3452	else
3453
3454
3455	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3456	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3457	if [[ "${actionout[$i]}" = tr ]]
3458	then
3459	if [[ $localhost != $fromhost ]]
3460	then
3461	if [[ $files_for_pes = false ]]
3462	then
3463	cps=""
3464	cst=""
3465	else
3466	cps=-c
3467	cst="/"
3468	fi
3469	if [[ $localhost = nech ]]
3470	then
3471
3472	# TRANSFER IN SEPERATE JOB
3473	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3474	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3475	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3476	if [[ $files_for_pes = false ]]
3477	then
3478	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3479	else
3480	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3481	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3482	fi
3483
3484	echo "set -x" > transfer_${localout[$i]}
3485	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3486
3487	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3488	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3489	printf "\n or higher cycle\n"
3490	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]}
3491
3492	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3493
3494	if [[ $localhost = nech ]]
3495	then
3496	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3497	else
3498	if [[ "$LOGNAME" = b323013 ]]
3499	then
3500	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3501	else
3502	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3503	fi
3504	fi
3505
3506	else
3507
3508	# TRANSFER WITHIN THIS JOB
3509	transfer_failed=false
3510	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3511	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3512	if [[ $localhost = lccrayb ]]
3513	then
3514	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]}"
3515	elif [[ $localhost = lccrayh ]]
3516	then
3517	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]}"
3518	elif [[ $localhost = lcbullhh ]]
3519	then
3520	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]}"
3521	elif [[ $localhost = lcxe6 ]]
3522	then
3523	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]}"
3524	else
3525	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3526	fi
3527	[[ $? != 0 ]] && transfer_failed=true
3528
3529	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3530	if [[ $transfer_failed = true ]]
3531	then
3532	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3533	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3534
3535	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3536	eval local_catalog=${pathout[$i]}
3537	if [[ ! -d $local_catalog ]]
3538	then
3539	printf " *** local directory does not exist. Trying to create:\n"
3540	printf " $local_catalog \n"
3541	mkdir -p $local_catalog
3542	fi
3543	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3544	transfer_problems=true
3545	fi
3546	fi
3547	else
3548
3549	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3550	actionout[$i]=""
3551	fi
3552	fi
3553
3554
3555	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3556	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3557	if [[ "${actionout[$i]}" = tra ]]
3558	then
3559	if [[ $localhost != $fromhost ]]
3560	then
3561	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3562	then
3563
3564	# TRANSFER IN SEPERATE JOB
3565	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3566	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3567	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3568	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3569
3570	echo "set -x" > transfer_${localout[$i]}
3571	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3572
3573	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3574	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3575	printf "\n or higher cycle\n"
3576	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]}
3577
3578	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3579
3580	if [[ $localhost = nech ]]
3581	then
3582	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3583	else
3584	if [[ $LOGNAME = b323013 ]]
3585	then
3586	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3587	else
3588	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3589	fi
3590	fi
3591
3592	else
3593
3594	# TRANSFER WITHIN THIS JOB
3595	transfer_failed=false
3596	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3597	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3598	if [[ $localhost = lccrayb ]]
3599	then
3600	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]}"
3601	elif [[ $localhost = lccrayh ]]
3602	then
3603	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]}"
3604	elif [[ $localhost = lcxe6 ]]
3605	then
3606	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]}"
3607	else
3608	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3609	fi
3610	[[ $? != 0 ]] && transfer_failed=true
3611
3612	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3613	if [[ $transfer_failed = true ]]
3614	then
3615	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3616	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3617
3618	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3619	eval local_catalog=${pathout[$i]}
3620	if [[ ! -d $local_catalog ]]
3621	then
3622	printf " *** local directory does not exist. Trying to create:\n"
3623	printf " $local_catalog \n"
3624	mkdir -p $local_catalog
3625	fi
3626
3627	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3628	transfer_problems=true
3629	fi
3630	fi
3631	else
3632
3633	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3634	actionout[$i]=a
3635	fi
3636	fi
3637
3638
3639	# OUTPUT-FILE FOR A RESTART-RUN.
3640	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3641	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3642	# AS LAST ACTION, ARCHIVING IS INITIATED.
3643	if [[ "${actionout[$i]}" = fl ]]
3644	then
3645	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3646	chmod g+rx $tmp_data_catalog
3647	if [[ $files_for_pes = false ]]
3648	then
3649	printf "\n >>> OUTPUT: ${localout[$i]} to"
3650	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3651	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3652	else
3653	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3654	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3655	mkdir $tmp_data_catalog/${frelout[$i]}
3656	cd ${localout[$i]}
3657	for file in $(ls *)
3658	do
3659	ln -f $file $tmp_data_catalog/${frelout[$i]}
3660	done
3661	cd $TEMPDIR
3662	fi
3663
3664
3665	# CREATE AND SUBMIT ARCHIVING-JOB
3666	if [[ $store_on_archive_system = true ]]
3667	then
3668
3669	if [[ $archive_system = asterix ]]
3670	then
3671	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3672	if [[ $files_for_pes = false ]]
3673	then
3674	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3675	else
3676	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3677	fi
3678	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3679	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3680	echo "then" >> archive_${frelout[$i]}
3681	echo " do_stageout=false" >> archive_${frelout[$i]}
3682	echo "else" >> archive_${frelout[$i]}
3683	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3684	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3685	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3686	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3687	if [[ $files_for_pes = false ]]
3688	then
3689	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3690	else
3691	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3692	fi
3693	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3694	echo "fi" >> archive_${frelout[$i]}
3695	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3696	elif [[ $archive_system = DMF ]]
3697	then
3698	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3699	if [[ $files_for_pes = false ]]
3700	then
3701	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3702	locat=DMF
3703	exit
3704	else
3705	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3706	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3707	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3708	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3709	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3710	fi
3711	elif [[ $archive_system = tivoli ]]
3712	then
3713	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3714	if [[ $files_for_pes = false ]]
3715	then
3716	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3717	echo "set -x" >> archive_${frelout[$i]}
3718	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3719	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3720	else
3721
3722	echo "set -x" >> archive_${frelout[$i]}
3723	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3724	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3725	cd $tmp_data_catalog
3726	all_files=`ls -1 ${frelout[$i]}/*`
3727	cd - > /dev/null
3728	(( inode = 0 ))
3729	(( tp1 = tasks_per_node + 1 ))
3730	while (( inode < nodes ))
3731	do
3732	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3733	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3734	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3735	(( inode = inode + 1 ))
3736	done
3737	fi
3738	elif [[ $archive_system = ut ]]
3739	then
3740	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3741	if [[ $files_for_pes = false ]]
3742	then
3743	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3744	echo "set -x" >> archive_${frelout[$i]}
3745	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3746	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3747	else
3748
3749	echo "set -x" >> archive_${frelout[$i]}
3750	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
3751	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
3752	cd $tmp_data_catalog
3753	all_files=`ls -1 ${frelout[$i]}/*`
3754	cd - > /dev/null
3755	(( inode = 0 ))
3756	(( tp1 = tasks_per_node + 1 ))
3757	while (( inode < nodes ))
3758	do
3759	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3760	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3761	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3762	(( inode = inode + 1 ))
3763	done
3764	fi
3765	elif [[ $archive_system = none ]]
3766	then
3767	printf " +++ archiving on $localhost not available!\n"
3768	fi
3769
3770	if [[ $archive_system != none ]]
3771	then
3772	if [[ $localhost = nech ]]
3773	then
3774	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3775	fi
3776	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3777	fi
3778	else
3779	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
3780	fi
3781
3782
3783	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
3784	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3785	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3786	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3787	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3788	if [[ $files_for_pes = false ]]
3789	then
3790	cat /dev/null > ${pathout[$i]}
3791	else
3792	mkdir -p ${pathout[$i]}
3793	fi
3794
3795	fi
3796
3797
3798	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
3799	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
3800	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
3801	if [[ "${actionout[$i]}" = ar ]]
3802	then
3803	if [[ $files_for_pes = false ]]
3804	then
3805	printf "\n >>> OUTPUT: ${localout[$i]} to"
3806	printf "\n ${pathout[$i]}"
3807	printf "\n File will be copied to archive-system ($archive_system) !\n"
3808	else
3809	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
3810	printf "\n ${pathout[$i]}"
3811	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
3812	fi
3813	mv ${localout[$i]} ${frelout[$i]}
3814
3815	file_saved=false
3816
3817	if [[ $archive_system = asterix ]]
3818	then
3819	do_stageout=true
3820	(( stageout_anz = 0 ))
3821	while [[ $do_stageout = true ]]
3822	do
3823	if [[ $files_for_pes = false ]]
3824	then
3825	stageout ${frelout[$i]} > STAGE_OUTPUT
3826	else
3827	stageout -t ${frelout[$i]} > STAGE_OUTPUT
3828	fi
3829	cat STAGE_OUTPUT
3830	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
3831	then
3832	file_saved=true
3833	do_stageout=false
3834	else
3835	if [[ $files_for_pes = false ]]
3836	then
3837	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
3838	else
3839	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
3840	fi
3841	(( stageout_anz = stageout_anz + 1 ))
3842	if (( stageout_anz == 10 ))
3843	then
3844	printf "\n +++ stoped after 10 unsuccessful tries!"
3845	archive_save=false
3846	do_stageout=false
3847	else
3848	printf "\n *** new try to store on archive after 15 min:"
3849	sleep 900
3850	fi
3851	fi
3852	done
3853	elif [[ $archive_system = DMF ]]
3854	then
3855	if [[ $files_for_pes = false ]]
3856	then
3857	printf "\n +++ archiving of single files impossible on $archive_system!\n"
3858	locat=DMF
3859	exit
3860	else
3861	rm -rf $ARCHIVE/${frelout[$i]}
3862	cp -r ${frelout[$i]} $ARCHIVE
3863	fi
3864	file_saved=true
3865	elif [[ $archive_system = tivoli ]]
3866	then
3867	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3868	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3869	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3870	# WHEN THE ARCHIVE-JOB IS EXECUTED
3871	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3872	chmod g+rx $tmp_data_catalog
3873	if [[ $files_for_pes = false ]]
3874	then
3875	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3876	else
3877	mkdir $tmp_data_catalog/${frelout[$i]}
3878	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3879	fi
3880
3881	# GENERATE AND SUBMIT BATCH-JOB
3882	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3883	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3884	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3885	if [[ $files_for_pes = false ]]
3886	then
3887	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3888	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3889	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3890	else
3891	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3892	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3893	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3894	fi
3895
3896	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
3897	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3898	file_saved=true
3899
3900	elif [[ $archive_system = ut ]]
3901	then
3902	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3903	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3904	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3905	# WHEN THE ARCHIVE-JOB IS EXECUTED
3906	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3907	chmod g+rx $tmp_data_catalog
3908	if [[ $files_for_pes = false ]]
3909	then
3910	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3911	else
3912	mkdir $tmp_data_catalog/${frelout[$i]}
3913	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3914	fi
3915
3916	# GENERATE AND SUBMIT BATCH-JOB
3917	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3918	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3919	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3920	if [[ $files_for_pes = false ]]
3921	then
3922	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3923	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3924	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3925	else
3926	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3927	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3928	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3929	fi
3930
3931	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3932	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3933	file_saved=true
3934
3935	else
3936	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
3937	archive_save=false
3938	fi
3939
3940	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
3941	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3942	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3943	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3944	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3945	if [[ $file_saved = true ]]
3946	then
3947	if [[ $files_for_pes = false ]]
3948	then
3949	cat /dev/null > ${pathout[$i]}
3950	else
3951	mkdir -p ${pathout[$i]}
3952	fi
3953	fi
3954
3955	fi
3956
3957	# APPEND ON THIS MACHINE
3958	if [[ "${actionout[$i]}" = "a" ]]
3959	then
3960	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3961	then
3962	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3963	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3964	else
3965	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3966	cat ${localout[$i]} >> ${pathout[$i]}
3967	fi
3968	fi
3969
3970	# COPY ON THIS MACHINE
3971	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3972	# ON DIFFERENT FILE-SYSTEMS
3973	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3974	then
3975
3976	# COPY IN CASE OF RUNS ON SINGLE CORES
3977	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3978	then
3979	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3980	if [[ $link_local_output = true ]]
3981	then
3982	printf " using ln -f\n"
3983	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3984	fi
3985	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3986	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3987	then
3988	if [[ $link_local_output = true ]]
3989	then
3990	printf " ln failed, using cp...\n"
3991	fi
3992	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3993	fi
3994	else
3995	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3996	if [[ $link_local_output = true ]]
3997	then
3998	printf " using ln -f\n"
3999	ln -f ${localout[$i]} ${pathout[$i]}
4000	fi
4001	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4002	if [[ ! -f "${pathout[$i]}" ]]
4003	then
4004	if [[ $link_local_output = true ]]
4005	then
4006	printf " ln failed, using cp...\n"
4007	fi
4008	cp ${localout[$i]} ${pathout[$i]}
4009	fi
4010	fi
4011
4012	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4013	then
4014
4015	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4016	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4017	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4018	if [[ $link_local_output = true ]]
4019	then
4020	printf " using ln -f\n"
4021	mkdir ${pathout[$i]}
4022	cd ${localout[$i]}
4023	for file in $(ls *)
4024	do
4025	ln -f $file ${pathout[$i]}
4026	done
4027	cd $TEMPDIR
4028	fi
4029
4030	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4031	if [[ ! -f "${pathout[$i]}/_0000" ]]
4032	then
4033	if [[ $link_local_output = true ]]
4034	then
4035	printf " ln failed for .../_0000, using cp...\n"
4036	fi
4037	cp -r ${localout[$i]} ${pathout[$i]}
4038	fi
4039
4040	fi
4041	fi
4042	done
4043	if (( i != 0 ))
4044	then
4045	if [[ $transfer_problems = true ]]
4046	then
4047	printf "\n$dashes\n *** OUTPUT-files saved"
4048	printf "\n +++ WARNING: some data transfers failed! \n"
4049	else
4050	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4051	fi
4052	fi
4053
4054
4055	# IF REQUIRED, START A RESTART-JOB
4056	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4057	if [[ -f CONTINUE_RUN ]]
4058	then
4059
4060	if [[ $archive_save = true ]]
4061	then
4062
4063	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4064	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4065	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4066	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4067	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4068	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4069	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4070	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4071	then
4072	mc=`echo $mc \| sed 's/#/f/g'`
4073	fi
4074
4075
4076	# START THE RESTART-JOB
4077	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4078	echo " $mc"
4079	printf "\n$dashes\n"
4080	if [[ $localhost != $fromhost ]]
4081	then
4082
4083	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4084	then
4085	echo "*** ssh will be used to initiate restart-runs!"
4086	echo " return_address=\"$return_address\" "
4087	echo " return_username=\"$return_username\" "
4088	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4089	then
4090	if [[ $localhost = ibmh ]]
4091	then
4092	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\" "
4093	elif [[ $localhost = lcbullhh ]]
4094	then
4095	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\" "
4096	elif [[ $localhost = lccrayb ]]
4097	then
4098	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\" "
4099	elif [[ $localhost = lccrayh ]]
4100	then
4101	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\" "
4102	elif [[ $localhost = lcxe6 ]]
4103	then
4104	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\" "
4105	else
4106	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 "
4107	fi
4108	else
4109	if [[ $localhost = ibmkisti ]]
4110	then
4111	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\" "
4112	elif [[ $localhost = lcflow ]]
4113	then
4114	/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 "
4115	elif [[ $localhost = lcocean ]]
4116	then
4117	/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 "
4118	elif [[ $localhost = lccrayb ]]
4119	then
4120	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\" "
4121	elif [[ $localhost = lccrayh ]]
4122	then
4123	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\" "
4124	else
4125	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4126	fi
4127	fi
4128	else
4129	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4130	locat=restart; exit
4131	fi
4132
4133	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4134	if [[ $queue = special1q ]]
4135	then
4136	sleep 120
4137	else
4138	sleep 30
4139	fi
4140
4141	else
4142
4143	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4144	# USING SSH)
4145	cd $LOCAL_PWD
4146	if [[ $localhost = lckyuh ]]
4147	then
4148	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4149	printf "\n please restart job manually using command:\n"
4150	printf "\n \"$mc\" "
4151	else
4152	eval $mc # THE ' MUST BE EVALUATED
4153	fi
4154	cd - > /dev/null
4155	fi
4156	if [[ $localhost = lckyuh ]]
4157	then
4158	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4159	else
4160	printf "\n$dashes\n *** restart-run initiated \n"
4161	fi
4162
4163
4164	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4165	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4166	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4167	# MAY BE VERY HUGE)
4168	(( i = 0 ))
4169	while (( i < iin ))
4170	do
4171	(( i = i + 1 ))
4172	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4173	then
4174	rm -r $tmp_data_catalog/${frelin[$i]}
4175	fi
4176	done
4177
4178	else
4179
4180	printf "\n +++ no restart-run possible, since errors occured"
4181	printf "\n during the archive process"
4182	fi
4183
4184	fi
4185
4186
4187
4188	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4189	if [[ "$email_notification" != "none" ]]
4190	then
4191
4192	if [[ $localhost != $fromhost ]]
4193	then
4194	if [[ -f CONTINUE_RUN ]]
4195	then
4196	echo "PALM restart run necessary" > email_text
4197	echo "description header of actual run:" >> email_text
4198	cat CONTINUE_RUN >> email_text
4199	echo "mrun-command to restart:" >> email_text
4200	echo "$mc" >> email_text
4201	else
4202	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4203	fi
4204	mail $email_notification < email_text
4205	printf "\n *** email notification sent to \"$email_notification\" "
4206	fi
4207	fi
4208
4209
4210
4211	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4212	cd $HOME
4213	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4214
4215	else
4216
4217	# PREPARING ACTIONS,
4218	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4219
4220	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4221	mrun_com="$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 $remote_username"
4222	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4223	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4224	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4225	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4226	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4227	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4228	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4229	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4230	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4231	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4232	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4233	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4234	if [[ $use_openmp = true ]]
4235	then
4236	mrun_com=${mrun_com}" -O $threads_per_task"
4237	fi
4238	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4239	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4240	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4241	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4242	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4243	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4244	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4245	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4246	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4247	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4248	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4249	if [[ $do_remote = true ]]
4250	then
4251	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4252	fi
4253
4254
4255	# CREATE EXECUTABLE FOR BATCH JOB
4256	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4257	then
4258
4259	printf "\n *** creating the executable for batch job\n"
4260
4261	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4262	if [[ $host != $localhost ]]
4263	then
4264	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4265	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4266	locat=create_executable; exit
4267	fi
4268
4269	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4270	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4271
4272	cp $make_depository .
4273	tar -xf $make_depository > /dev/null 2>&1
4274	cp ../* . > /dev/null 2>&1
4275
4276	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4277
4278	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4279	then
4280	printf "\n +++ error occured while compiling or linking"
4281	locat=compile
4282	exit
4283	fi
4284
4285	mv a.out ..
4286	cd - > /dev/null 2>&1
4287	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4288
4289	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4290
4291	fi
4292
4293
4294	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4295	jobfile=jobfile.$RANDOM
4296
4297
4298	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4299	echo "mkdir $TEMPDIR" >> $jobfile
4300	echo "cd $TEMPDIR" >> $jobfile
4301
4302
4303	# ACTIVATE ERROR-TRACEBACK
4304	if [[ $do_trace = true ]]
4305	then
4306	echo "set -x" >> $jobfile
4307	else
4308	echo "set +vx" >> $jobfile
4309	fi
4310
4311
4312	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4313	if [[ "$init_cmds" != "" ]]
4314	then
4315	echo "$init_cmds" >> $jobfile
4316	fi
4317	if [[ "$module_calls" != "" ]]
4318	then
4319	echo "$module_calls" >> $jobfile
4320	fi
4321
4322
4323	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4324	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4325	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4326	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4327	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4328	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4329	# QUEUEING-SYSTEMS
4330	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
4331	then
4332
4333	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4334	if [[ $restart_run != true ]]
4335	then
4336	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4337	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4338	fi
4339
4340	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4341	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4342	echo "set -x" >> $jobfile
4343	if [[ $host = $localhost ]]
4344	then
4345	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4346	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4347	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4348	then
4349	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4350	else
4351	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4352	fi
4353
4354	else
4355	if [[ $host = ibmkisti ]]
4356	then
4357	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4358	echo "localdir=\`pwd\`" >> $jobfile
4359	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4360	elif [[ $host = lcbullhh ]]
4361	then
4362	echo "localdir=\`pwd\`" >> $jobfile
4363	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4364
4365	elif [[ $host = lccrayb ]]
4366	then
4367	echo "localdir=\`pwd\`" >> $jobfile
4368	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4369	elif [[ $host = lccrayh ]]
4370	then
4371	echo "localdir=\`pwd\`" >> $jobfile
4372	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4373
4374	else
4375	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4376	fi
4377	fi
4378	echo "export SOURCES_COMPLETE=true" >> $jobfile
4379
4380	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4381	# WORKING DIRECTORY OF THE JOB
4382	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4383	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4384	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4385	echo "execute_mrun=true" >> $jobfile
4386	echo " " >> $jobfile
4387
4388	else
4389
4390	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4391	if [[ $do_compile = true ]]
4392	then
4393
4394	source_catalog=SOURCES_FOR_RUN_$fname
4395
4396	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4397	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4398	echo "export SOURCES_COMPLETE=true" >> $jobfile
4399	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4400
4401	for filename in $source_list
4402	do
4403	# BACKSLASH IS USED FOR MASKING
4404	echo "cat > $filename << \"%END%\"" >> $jobfile
4405	cat $source_catalog/$filename >> $jobfile
4406	echo " " >> $jobfile
4407	echo "%END%" >> $jobfile
4408	echo " " >> $jobfile
4409	done
4410
4411	# BACKSLASH IS USED FOR MASKING
4412	echo "cat > Makefile << \"%END%\"" >> $jobfile
4413	cat $source_catalog/Makefile >> $jobfile
4414	echo " " >> $jobfile
4415	echo "%END%" >> $jobfile
4416	echo " " >> $jobfile
4417
4418	echo "cd - > /dev/null" >> $jobfile
4419
4420	fi
4421
4422
4423	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4424	# BACKSLASH IS USED FOR MASKING
4425	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4426	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4427	echo "cat > $config_file << \"%END%\"" >> $jobfile
4428	if [[ $host = lckyuh ]]
4429	then
4430	# NO CROSS-COMPILER ON COMPUTE NODE
4431	sed 's/frtpx/frt/g' $config_file >> $jobfile
4432	else
4433	sed 's/#$.*//g' $config_file >> $jobfile
4434	fi
4435	echo "%END%" >> $jobfile
4436	echo " " >> $jobfile
4437
4438
4439	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4440	# BACKSLASH IS USED FOR MASKING
4441	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4442	if [[ $host = lckyuh ]]
4443	then
4444	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4445	else
4446	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4447	fi
4448	echo "%END%" >> $jobfile
4449	echo "chmod u+x $mrun_script_name" >> $jobfile
4450	echo "execute_mrun=true" >> $jobfile
4451	echo " " >> $jobfile
4452
4453	fi
4454
4455
4456	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4457	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4458	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4459	if [[ $do_remote = true ]]
4460	then
4461	(( i = 0 ))
4462	while (( i < iin ))
4463	do
4464	(( i = i + 1 ))
4465	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4466	if [[ "${transin[$i]}" = job ]]
4467	then
4468	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4469	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4470	echo " " >> $jobfile
4471	echo "%END%" >> $jobfile
4472	else
4473	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4474	fi
4475
4476	# CHECK, IF FILE COULD BE CREATED
4477	echo "if [[ \$? = 1 ]]" >> $jobfile
4478	echo "then" >> $jobfile
4479	echo " echo \" \" " >> $jobfile
4480	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4481	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4482	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4483	echo " execute_mrun=false" >> $jobfile
4484	echo "fi" >> $jobfile
4485	done
4486	fi
4487
4488	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4489	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4490	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4491	echo "LOCAL_PWD=$working_directory" >> $jobfile
4492	echo "export LOCAL_PWD" >> $jobfile
4493
4494	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4495	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4496	echo "export LOCAL_MRUN_PATH" >> $jobfile
4497
4498	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4499	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4500	# then
4501	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4502	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4503	# fi
4504
4505	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4506	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4507	echo "set -x" >> $jobfile
4508	echo "queue=$queue" >> $jobfile
4509	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4510	echo 'ls -al; echo `pwd`' >> $jobfile
4511	echo "cd \$HOME" >> $jobfile
4512	echo "rm -rf $TEMPDIR" >> $jobfile
4513
4514
4515
4516
4517	# START THE JOB USING SUBJOB-COMMAND
4518	if [[ $silent = false ]]
4519	then
4520	printf "\n "
4521	else
4522	printf "\n\n"
4523	fi
4524
4525	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
4526	rm -rf $jobfile
4527
4528
4529	fi # END OF REMOTE-PART

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