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source: palm/trunk/SCRIPTS/mrun @ 1851

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

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