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source: palm/trunk/SCRIPTS/mrun @ 1807

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

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