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source: palm/trunk/SCRIPTS/mrun @ 2053

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

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