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source: palm/trunk/SCRIPTS/mrun @ 1936

Last change on this file since 1936 was 1917, checked in by witha, 8 years ago
Corrected documented changes in the file headers
Property svn:keywords set to `Id Rev`
File size: 169.6 KB

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1	#!/bin/bash
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1917 2016-05-27 14:28:12Z suehring $
29	#
30	# 1866 2016-04-15 06:50:59Z raasch
31	# adjusted for lcocean
32	#
33	# 1841 2016-04-07 19:14:06Z raasch
34	# script now running under bash
35	#
36	# 1804 2016-04-05 16:30:18Z maronga
37	# test: implementing an execute mechanism where the execute command is given in the
38	# configuration file
39	# ROPTS removed from execution commands
40	# Warnings about missing optional files or user code changed to informative messages
41	# Removed parameter file check
42	#
43	# 1755 2016-02-22 13:53:39Z maronga
44	# Minor bugfix to last commit
45	#
46	# 1753 2016-02-22 13:49:49Z maronga
47	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
48	#
49	# 1622 2015-07-20 06:21:36Z heinze
50	# bugfix for Mistral (lcbullhh)
51	#
52	# 1621 2015-07-17 11:39:33Z heinze
53	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
54	#
55	# 1609 2015-07-03 15:37:58Z maronga
56	# Modified the random number of the temporary working directory to match the
57	# queuing system number on HLRN-III (lccray*).
58	#
59	# 1604 2015-06-23 15:48:03Z suehring
60	# Enable coupled runs for lcmuk
61	#
62	# 1598 2015-05-29 06:45:40Z raasch
63	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
64	#
65	# 1549 2015-01-30 14:26:16Z suehring
66	# Enable interactive debug sessions with allinea debugger
67	#
68	# 1547 2015-01-29 15:09:12Z witha
69	# adjustments for ForWind computing cluster (lcflow)
70	#
71	# 1491 2014-11-12 08:12:57Z heinze
72	# correct setting of batch_job allowed for ibm-machines
73	#
74	# 1468 2014-09-24 14:06:57Z maronga
75	# Typo removed (addres->address)
76	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
77	# Added support for restart runs (remote) for lcxe6
78	#
79	# 1442 2014-07-28 07:09:10Z raasch
80	# default queues for HLRN-III (lccrayb/lccrayh) defined
81	#
82	# 1422 2014-07-02 10:01:25Z kanani
83	# automatic restarts enabled for lccrayb,
84	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
85	#
86	# 1420 2014-06-10 06:24:14Z raasch
87	# -j1 option added to aprung command for lccrayf (CSC)
88	#
89	# 1402 2014-05-09 14:25:13Z raasch
90	# batch_job added to envpar-NAMELIST
91	#
92	# 1357 2014-04-11 15:02:03Z witha
93	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
94	# possible)
95	#
96	# 1320 2014-03-20 08:40:49Z raasch
97	# check namelist file set false by default
98	#
99	# 1304 2014-03-12 10:29:42Z raasch
100	# ulimit option changed from -Ss to -s
101	#
102	# bugfix: missing "fi" in r1289
103	#
104	# 1289 2014-03-04 07:12:34Z raasch
105	# comments translated to English
106	# necriam-, fimm-, ibmy-, and sgi-specific code removed
107	# export of variables for palm and interpret_config removed
108	#
109	# 1281 2014-02-01 07:55:49Z raasch
110	# rsync-copy restricted to Cray machines, since command is unavailable on some
111	# other systems
112	#
113	# 1279 2014-01-28 12:10:14Z raasch
114	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
115	# in order to remove annoying restrictions concerning the number of processors which
116	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
117	# restriction, one of the nodes will be filled with less than the given number of
118	# tasks per node. A respective warning is given.
119	#
120	# 1274 2014-01-09 13:14:54Z heinze
121	# adjustments for lccrayh
122	#
123	# 1272 2014-01-08 10:19:32Z witha
124	# small adjustment for lcflow
125	#
126	# 1270 2013-12-16 11:05:01Z fricke
127	# call of combine_plot_fields adjusted for lccrayb/lccrayh
128	#
129	# 1255 2013-11-07 14:43:35Z raasch
130	# further adjustments for lccrayb remote access
131	#
132	# 1241 2013-10-30 11:36:58Z heinze
133	# Enable use of nudging input and input of large scale forcing from
134	# external files
135	#
136	# 1229 2013-09-20 06:55:19Z raasch
137	# further adjustments for lccrayb
138	#
139	# 1224 2013-09-16 07:27:23Z raasch
140	# first adjustments for lccrayb
141	#
142	# 1210 2013-08-14 10:58:20Z raasch
143	# fftw support added
144	#
145	# 1201 2013-07-10 16:17:59Z witha
146	# adjustments for Forwind cluster (lcflow)
147	#
148	# 1199 2013-07-05 14:52:22Z raasch
149	# adjustments for CSC Helsinki (lccrayf),
150	# executables for batch jobs can be created in advance, in order to avoid calling
151	# the compiler within the batch job (only works if batch jobs are submitted on
152	# local host)
153	#
154	# 1190 2013-06-25 09:39:21Z heinze
155	# enable use of automatic restarts for ibmh
156	# use of cluster/express queue enabled (ibmh)
157	#
158	# 1124 2013-04-09 15:46:52Z raasch
159	# variable "memory" is exported via typeset option -x, because otherwise an unknown
160	# side effect may lead to data loss while getopts is reading the script-option arguments
161	#
162	# 1122 2013-04-09 08:37:16Z heinze
163	# Bugfix: change type of variable last_char
164	#
165	# 1119 2013-04-05 15:11:19Z raasch
166	# Bugfix for setting -T option for subjob
167	#
168	# 1108 2013-03-05 07:03:32Z raasch
169	# bugfix for coupled runs on lckyut/lckyuh
170	#
171	# 1106 2013-03-04 05:31:38Z raasch
172	# --stdin argument for mpiexec on lckyuh
173	# -y and -Y settings output to header
174	#
175	# 1103 2013-02-20 02:15:53Z raasch
176	# default script runs again under ksh, because of unsolved problems with read
177	# from stdin: when bash script is called from a ksh, message "read error: 0:
178	# Resource temporarily unavailable" appears and script does not stop,
179	# further bash compatibility adjustments,
180	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
181	# on lckyuh, but mrun does not terminate and issues a warning instead
182	#
183	# 1101 2013-02-17 10:20:21Z raasch
184	# script now running under bash instead of ksh, which required small adjustments
185	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
186	# read from stdin),
187	# cross compilername on lckyuh compute nodes replaced by real compiler name
188	#
189	# 1099 2013-02-10 01:47:43Z raasch
190	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
191	# and for Forwind cluster (lcflow)
192	# small further adjustments for lckyut
193	#
194	# 1094 2013-02-03 01:52:12Z raasch
195	# explicit ssh/scp port can be set in config file with environment variable
196	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
197	# decalpha parts (yonsei) removed
198	#
199	# 2013-02-02 07:06:13Z raasch
200	# adjustments for Kyushu-University computing center (lckyut - tatara)
201	#
202	# 1083 2013-01-04 10:22:09Z maronga
203	# bugfix in parameter file check (read %cpp_options was missing)
204	#
205	# 1069 2012-11-28 16:18:43Z maronga
206	# bugfix: coupling mode was always set to mpi2, typos removed
207	#
208	# 1058 2012-11-21 07:00:35Z raasch
209	# Intel inspector (inspxe) is given the number of PEs instead of the number of
210	# nodes
211	#
212	# 1046 2012-11-09 14:38:45Z maronga
213	# code put under GPL (PALM 3.9)
214	#
215	# 21/03/94 - Siggi - first version finished
216	# 03/03/94 - Siggi - script development started
217	#
218	#--------------------------------------------------------------------------------#
219	# mrun - script for running PALM jobs
220	#--------------------------------------------------------------------------------#
221
222
223
224	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
225
226	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
227	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
228	# (TOO MANY ARGUMENTS - PROBLEM)
229	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
230
231	AddFilenames=""
232	additional_conditions=""
233	add_source_path=""
234	afname=""
235	archive_save=true
236	archive_system=none
237	check_namelist_files=false
238	combine_plot_fields=true
239	compiler_name=""
240	cond1=""
241	cond2=""
242	config_file=.mrun.config
243	coupled_dist=""
244	coupled_mode="mpi1"
245	cpp_opts=""
246	cpp_options=""
247	cpumax=0
248	cpurest=0
249	create_executable_for_batch=false
250	delete_temporary_catalog=true
251	do_batch=false
252	do_compile=true
253	do_remote=false
254	do_stagein=true
255	do_stageout=true
256	do_trace=false
257	email_notification="none"
258	exclude=""
259	executable=""
260	execute_command="none"
261	execution_error=false
262	fftw_inc=""
263	fftw_lib=""
264	fftw_support=false
265	fname=test
266	fromhost=""
267	global_revision=""
268	group_number=none
269	host=""
270	host_file=""
271	hp=""
272	ignore_archive_error=false
273	input_list=""
274	interpreted_config_file=""
275	job_catalog="~/job_queue"
276	job_on_file=""
277	keep_data_from_previous_run=false
278	link_local_input=false
279	link_local_output=false
280	localhost_realname=$(hostname)
281	local_dvrserver_running=.FALSE.
282	locat=normal
283	mainprog=""
284	makefile=""
285	max_par_io_str=""
286	mc=$0
287	while [[ $(echo $mc \| grep -c "/") != 0 ]]
288	do
289	mc=`echo $mc \| cut -f2- -d"/"`
290	done
291	module_calls=""
292	mrun_script_name=$mc
293	netcdf_inc=""
294	netcdf_lib=""
295	netcdf_support=false
296	node_usage=default
297	numprocs=""
298	numprocs_atmos=0
299	numprocs_ocean=0
300	OOPT=""
301	openmp=false
302	output_list=""
303	package_list=""
304	queue=none
305	read_from_config=""
306	restart_run=false
307	if [[ `hostname` = rte10 ]]
308	then
309	return_address=133.5.185.60
310	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
311	elif [[ `hostname` = climate0 ]]
312	then
313	return_address=165.132.26.68
314	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
315	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
316	then
317	return_address="schultzl-Latitude-E6540"
318	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
319	elif [[ `hostname` = urban00 ]]
320	then
321	return_address=147.46.30.151
322	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
323	else
324	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
325	fi
326	return_password=""
327	return_username=$LOGNAME
328	remotecall=false
329	remote_username=""
330	run_coupled_model=false
331	run_mode=""
332	store_on_archive_system=false
333	dashes=" ----------------------------------------------------------------------------"
334	silent=false
335	source_list=""
336	source_path=SOURCE
337	tasks_per_node=""
338	threads_per_task=1
339	tmpcreate=false
340	tmp_data_catalog=""
341	transfer_problems=false
342	usern=$LOGNAME
343	use_openmp=false
344	version="MRUN 2.1 Rev$Rev: 1917 $"
345	working_directory=`pwd`
346	TOPT=""
347	XOPT=""
348	zeit=$( date \| cut -c 12-19 )
349
350	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
351	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
352	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
353	# SCRIPT-OPTION ARGUMENTS
354	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
355
356	# ERROR HANDLING IN CASE OF EXIT
357	trap 'rm -rf $working_directory/tmp_mrun
358	if [[ $locat != normal && $locat != control_c ]]
359	then
360
361	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
362	(( i = 0 ))
363	while (( i < iec ))
364	do
365	(( i = i + 1 ))
366	printf "\n *** Execution of ERROR-command:\n"
367	printf " >>> ${err_command[$i]}\n"
368	eval ${err_command[$i]}
369	done
370	if [[ -n $interpreted_config_file ]]
371	then
372	rm -rf $interpreted_config_file
373	fi
374	if [[ -n .mrun_environment ]]
375	then
376	rm -rf .mrun_environment
377	fi
378	if [[ $tmpcreate = true ]]
379	then
380	printf "\n *** Contents of \"$TEMPDIR\":\n"
381	ls -al; cd
382	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
383	fi
384	if [[ "$dvrserver_id" != "" ]]
385	then
386	echo "+++ killing dvrserver_id=$dvrserver_id"
387	kill $dvrserver_id
388	fi
389	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
390	then
391	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
392	fi
393	printf "\n\n+++ MRUN killed \n\n"
394	elif [[ $locat != control_c ]]
395	then
396	printf "\n\n --> all actions finished\n\n"
397	printf " Bye, bye $usern !!\n\n"
398	fi' exit
399
400
401	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
402	trap 'rm -rf $working_directory/tmp_mrun
403	rm -rf $working_directory/tmp_check_namelist_files
404	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
405	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
406	then
407	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
408	fi
409	if [[ "$dvrserver_id" != "" ]]
410	then
411	echo "+++ killing dvrserver_id=$dvrserver_id"
412	kill $dvrserver_id
413	fi
414	printf "\n+++ MRUN killed by \"^C\" \n\n"
415	locat=control_c
416	exit
417	' 2
418
419
420	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
421	# BEEN SET
422	if [[ "$PALM_BIN" = "" ]]
423	then
424	printf "\n +++ environment variable PALM_BIN has not been set"
425	printf "\n please set it to the directory where the PALM scripts are located"
426	locat=palm_bin; exit
427	fi
428	export PATH=$PALM_BIN:$PATH
429
430
431
432	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
433	# WHICH WILL BE USED TO START RESTART-JOBS
434	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
435	do
436	case $option in
437	(a) afname=$OPTARG;;
438	(A) store_on_archive_system=true; mc="$mc -A";;
439	(b) do_batch=true; mc="$mc -b";;
440	(B) delete_temporary_catalog=false; mc="$mc -B";;
441	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
442	(C) restart_run=true; mc="$mc -C";;
443	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
444	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
445	(F) job_on_file="-D"; mc="$mc -F";;
446	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
447	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
448	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
449	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
450	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
451	(I) ignore_archive_error=true; mc="$mc -I";;
452	(k) keep_data_from_previous_run=true; mc="$mc -k";;
453	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
454	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
455	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
456	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
457	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
458	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
459	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
460	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
461	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
462	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
463	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
464	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
465	(S) read_from_config=false; mc="$mc -S";;
466	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
467	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
468	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
469	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
470	(v) silent=true; mc="$mc -v";;
471	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
472	(x) do_trace=true;set -x; mc="$mc -x";;
473	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
474	(y) ocean_file_appendix=true; mc="$mc -y";;
475	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
476	(z) check_namelist_files=false; mc="$mc -z";;
477	(Z) combine_plot_fields=false; mc="$mc -Z";;
478	(\?) printf "\n +++ unknown option $OPTARG \n"
479	printf "\n --> type \"$0 ?\" for available options \n"
480	locat=parameter;exit;;
481	esac
482	done
483
484
485	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
486	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
487	(( to_shift = $OPTIND - 1 ))
488	shift $to_shift
489
490	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
491	if [[ "$1" = "?" ]]
492	then
493	(printf "\n *** mrun can be called as follows:\n"
494	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"
495	printf "\n Description of available options:\n"
496	printf "\n Option Description Default-Value"
497	printf "\n -a base name of input files equiv. -d"
498	printf "\n -A archiving when using file-attribute fl"
499	printf "\n -b batch-job on local machine ---"
500	printf "\n -B do not delete temporary directory at end ---"
501	printf "\n -c configuration file .mrun.config"
502	printf "\n -d base name of files attached to program test"
503	printf "\n -D preprocessor(cpp)-directives \"\" "
504	printf "\n -F create remote job file only ---"
505	printf "\n -h execution host $localhost_realname"
506	printf "\n -i INPUT control list \"\" "
507	printf "\n -I archiving errors of previous batch-jobs"
508	printf "\n will be ignored"
509	printf "\n -k keep data from previous run"
510	printf "\n -K additional conditions for controling"
511	printf "\n usage of conditional code and"
512	printf "\n env-variables in configuration file \"\" "
513	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
514	printf "\n -M Makefile name Makefile"
515	printf "\n -n node usage (shared/not_shared) depending on -h"
516	printf "\n -o OUTPUT control list \"\" "
517	printf "\n -O threads per openMP task ---"
518	printf "\n -p software package list \"\" "
519	printf "\n -q queue \"$queue\" "
520	printf "\n -r run control list (combines -i -o) \"\" "
521	printf "\n -s filenames of routines to be compiled \"\" "
522	printf "\n must end with .f, .f90, .F, or .c !"
523	printf "\n use \"..\" for more than one file and wildcards"
524	printf "\n -s LM compiles all locally modified files"
525	printf "\n -S config file interpreted by shellscript ---"
526	printf "\n -t allowed cpu-time in seconds (batch) 0"
527	printf "\n -T tasks per node depending on -h"
528	printf "\n -u username on remote machine \"\" "
529	printf "\n -v no prompt for confirmation ---"
530	printf "\n -w maximum parallel io streams as given by -X"
531	printf "\n -x tracing of mrun for debug purposes ---"
532	printf "\n -X # of processors (on parallel machines) 1"
533	printf "\n -y add appendix \"_O\" to all local output"
534	printf "\n files (ocean precursor runs followed by"
535	printf "\n coupled atmosphere-ocean runs) ---"
536	printf "\n -Y run coupled model, \"#1 #2\" with"
537	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
538	printf "\n -Z skip combine_plot_fields at the end of "
539	printf "\n the simulation ---"
540	printf "\n "
541	printf "\n Possible values of positional parameter <modus>:"
542	printf "\n \"?\" - this outline \n\n") \| more
543	exit
544	elif [[ "$1" != "" ]]
545	then
546	printf "\n +++ positional parameter $1 unknown \n"
547	locat=parameter; exit
548	fi
549
550
551
552	# SHORT STARTING MESSAGE
553	printf "\n*** $version "
554	printf "\n will be executed. Please wait ..."
555
556
557
558	# CHECK, IF CONFIGURATION FILE EXISTS
559	if [[ ! -f $config_file ]]
560	then
561	printf "\n\n +++ configuration file: "
562	printf "\n $config_file"
563	printf "\n does not exist"
564	locat=connect; exit
565	fi
566
567
568	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
569	line=""
570	grep "%host_identifier" $config_file > tmp_mrun
571	while read line
572	do
573	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
574	then
575	HOSTNAME=`echo $line \| cut -d" " -s -f2`
576	host_identifier=`echo $line \| cut -d" " -s -f3`
577	if [[ $localhost_realname = $HOSTNAME ]]
578	then
579	localhost=$host_identifier
580	break
581	fi
582	fi
583	done < tmp_mrun
584
585	if [[ "$localhost" = "" ]]
586	then
587	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
588	printf "\n for local host \"$localhost_realname\"."
589	printf "\n Please add line"
590	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
591	printf "\n to the configuration file."
592	locat=localhost; exit
593	fi
594
595
596	# SET HOST-SPECIFIC VARIABLES
597	case $localhost_realname in
598	(r1\|r2\|h01\|b01) archive_system=tivoli;;
599	(cs*) archive_system=ut;;
600	esac
601
602
603	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
604	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
605	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
606	[[ "$afname" = "" ]] && afname=$fname
607
608
609	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
610	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
611	# STATEMENTS IN THE CONFIGURATION FILE
612	if [[ "$run_mode" != "" ]]
613	then
614	input_list="$input_list $run_mode"
615	output_list="$output_list $run_mode"
616	fi
617
618
619	# ??? is this (and the respective option -H) really required ???
620	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
621	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
622	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
623	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
624	if [[ "$fromhost" = "" ]]
625	then
626	fromhost=$localhost
627	fi
628
629
630	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
631	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
632	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
633	# TO BE SUBMITTED (I.E. do_batch=true)
634	if [[ -n $host && "$host" != $localhost ]]
635	then
636	do_batch=true
637	do_remote=true
638	case $host in
639	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
640	(*) printf "\n"
641	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
642	printf "\n is not available"
643	locat=nqs; (( iec = 0 )); exit;;
644	esac
645	else
646	host=$localhost
647	fi
648
649
650	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
651	if [[ -n $additional_conditions ]]
652	then
653	cond1=`echo $additional_conditions \| cut -d" " -f1`
654	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
655	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
656	if [[ -n $dummy ]]
657	then
658	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
659	locat=options; exit
660	fi
661	block=_$cond1
662	[[ -n $cond2 ]] && block=${block}_$cond2
663	fi
664
665
666	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
667	if [[ $run_coupled_model = true ]]
668	then
669
670	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
671	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
672
673	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
674	then
675
676	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
677	printf "\n PEs (total) : $numprocs"
678	printf "\n PEs (atmosphere): $numprocs_atmos"
679	printf "\n PEs (ocean) : $numprocs_ocean"
680	locat=coupling; exit
681
682	fi
683
684
685	# GET coupled_mode FROM THE CONFIG FILE
686	line=""
687	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
688	while read line
689	do
690	echo line=\"$line\"
691	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
692	then
693	coupled_mode="mpi2"
694	fi
695	done < tmp_mrun
696
697	fi
698
699	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
700	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
701	then
702	if [[ $ignore_archive_error = false ]]
703	then
704	printf "\n +++ data archiving of previous run failed"
705	printf "\n see directory \~/job_queue on remote machine"
706	locat=archive; exit
707	else
708	printf "\n +++ warning: data archiving in a previous run failed"
709	printf "\n MRUN continues, trying to get backup copy"
710	fi
711	fi
712
713
714	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
715	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
716	mrun_memory=$memory
717	mrun_group_number=$group_number
718	mrun_cpumax=$cpumax
719	mrun_numprocs=$numprocs
720
721
722	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
723	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
724	if [[ "$read_from_config" = false ]]
725	then
726	[[ $silent = false ]] && printf "\n Reading the configuration file... "
727
728	# READ THE CONFIGURATION FILE LINE BY LINE
729	while read zeile
730	do
731	[[ $silent = false ]] && printf "."
732
733
734	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
735	eval zeile=\"$zeile\"
736
737
738	# INTERPRET THE LINE
739	if [[ "$(echo $zeile)" = "" ]]
740	then
741	# EMPTY LINE, NO ACTION
742	continue
743
744	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
745	then
746
747	# LINE IS A COMMENT LINE
748	true
749
750	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
751	then
752
753	# LINE DEFINES AN ENVIRONMENT-VARIABLE
754	zeile=$(echo $zeile \| cut -c2-)
755	var=`echo $zeile \| cut -d" " -f1`
756	value=`echo $zeile \| cut -d" " -s -f2`
757	for_host=`echo $zeile \| cut -d" " -s -f3`
758	for_cond1=`echo $zeile \| cut -d" " -s -f4`
759	for_cond2=`echo $zeile \| cut -d" " -s -f5`
760
761	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
762	then
763
764	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
765	# "::" IS REPLACED BY ":".
766	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
767
768
769	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
770	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
771	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
772	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
773	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
774	# CONFIGURATION-FILE.
775	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
776	then
777	eval $var=\$value
778
779	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
780	if [[ $do_trace = true ]]
781	then
782	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
783	fi
784	fi
785
786	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
787	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
788	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
789	# MUST HAVE TO BE STARTED
790	if [[ $var = host ]]
791	then
792	if [[ -n $host && "$host" != $localhost ]]
793	then
794	do_batch=true
795	do_remote=true
796	case $host in
797	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
798	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
799	printf "\n is not available"
800	locat=nqs; exit;;
801	esac
802	else
803	host=$localhost
804	fi
805	fi
806
807	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
808	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
809	# BY MRUN (E.G. subjob)
810	export $var
811	fi
812
813
814
815
816	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
817	then
818
819	# LINE DEFINES ERROR-COMMAND
820	(( iec = iec + 1 ))
821	zeile=$(echo $zeile \| cut -c4-)
822	err_command[$iec]="$zeile"
823
824	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
825	then
826
827	# LINE DEFINES INPUT-COMMAND
828	(( iic = iic + 1 ))
829	zeile=$(echo $zeile \| cut -c4-)
830	in_command[$iic]="$zeile"
831
832	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
833	then
834
835	# LINE DEFINES OUTPUT-COMMAND
836	(( ioc = ioc + 1 ))
837	zeile=$(echo $zeile \| cut -c4-)
838	out_command[$ioc]="$zeile"
839
840	else
841
842	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
843	# s2a: in/out - field
844	# s2b: loc - field (optional)
845	# s2c: tr/ar - field (optional)
846	s1=`echo $zeile \| cut -d" " -f1`
847	s2=`echo $zeile \| cut -d" " -s -f2`
848	s2a=$(echo $s2 \| cut -d":" -f1)
849	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
850	then
851	s2b=""
852	s2c=""
853	else
854	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
855	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
856	fi
857	s3=`echo $zeile \| cut -d" " -f3`
858	s4=`echo $zeile \| cut -d" " -s -f4`
859	s5=`echo $zeile \| cut -d" " -s -f5`
860	s6=`echo $zeile \| cut -d" " -s -f6`
861
862
863	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
864	# INPUT- OR OUTPUT-LIST.
865	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
866	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
867	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
868	# IS NOT CHECKED AND STORED.
869	IFSALT="$IFS"; IFS="$IFS:"
870	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
871	then
872	found=false
873	for actual in $input_list
874	do
875	for formal in $s3
876	do
877	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
878	done
879	done
880	if [[ $found = true ]]
881	then
882	(( iin = iin + 1 ))
883	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
884	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
885	extin[$iin]=$s6
886	fi
887	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
888	then
889	found=false
890	for actual in $output_list
891	do
892	for formal in $s3
893	do
894	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
895	done
896	done
897	if [[ $found = true ]]
898	then
899	(( iout = iout + 1 ))
900	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
901	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
902	fi
903	elif [[ "$s2a" != in && "$s2a" != out ]]
904	then
905	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
906	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
907	locat=connect; exit
908	fi
909	IFS="$IFSALT"
910	fi
911	done < $config_file
912
913	else
914
915	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
916	[[ $silent = false ]] && printf "..."
917	interpreted_config_file=.icf.$RANDOM
918
919
920
921	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
922	cat > .mrun_environment << %%END%%
923	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
924	config_file = '$config_file', do_remote = '$do_remote',
925	do_trace = '$do_trace', host = '$host',
926	input_list = '$input_list', icf = '$interpreted_config_file',
927	localhost = '$localhost', output_list = '$output_list' /
928
929	%%END%%
930
931	if [[ "$host" != $localhost ]]
932	then
933
934	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
935	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
936	if [[ $? != 0 ]]
937	then
938	printf "\n\n +++ no interpret_config found"
939	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
940	locat=interpret_config; exit
941	fi
942	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
943	$interpret_config_executable
944
945	else
946
947	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
948	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
949	then
950	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
951	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
952	locat=interpret_config; exit
953	else
954	interpret_config${block}.x
955	fi
956
957	fi
958	rm .mrun_environment
959
960
961	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
962	chmod u+x $interpreted_config_file
963	export PATH=$PATH:.
964	. $interpreted_config_file
965	rm $interpreted_config_file
966
967	fi
968
969
970	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
971	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
972	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
973	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
974	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
975	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
976	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
977
978
979	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
980	# FOR SOURCE-FILES TO BE COMPILED.
981	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
982	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
983	if [[ "$SOURCES_COMPLETE" = "" ]]
984	then
985
986	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
987	# HAS BEEN DEFINED
988	source_path=""
989	line=""
990	grep "%source_path" $config_file > tmp_mrun
991	while read line
992	do
993	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
994	then
995	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
996	then
997	global_source_path=`echo $line \| cut -d" " -f2`
998	fi
999	fi
1000	done < tmp_mrun
1001
1002	line=""
1003	found=false
1004	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1005	while read line
1006	do
1007	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1008	then
1009	if [[ $found = true ]]
1010	then
1011	printf "\n\n +++ more than one source path found in configuration file"
1012	printf "\n for local host \"$localhost\" "
1013	locat=source_path; exit
1014	fi
1015	source_path=`echo $line \| cut -d" " -f2`
1016	found=true
1017	fi
1018	done < tmp_mrun
1019	rm tmp_mrun
1020
1021	if [[ "$source_path" = "" ]]
1022	then
1023	if [[ "$global_source_path" != "" ]]
1024	then
1025	source_path=$global_source_path
1026	else
1027	printf "\n\n +++ no source path found in configuration file"
1028	printf "\n for local host \"$localhost\" "
1029	locat=source_path; exit
1030	fi
1031	fi
1032	eval source_path=$source_path
1033
1034	if [[ ! -d $source_path ]]
1035	then
1036	printf "\n\n +++ source path \"$source_path\" on local host"
1037	printf "\n \"$localhost\" does not exist"
1038	locat=source_path; exit
1039	fi
1040
1041	fi
1042
1043
1044	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1045	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1046	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1047	then
1048	global_revision=`svnversion $source_path 2>/dev/null`
1049	global_revision="Rev: $global_revision"
1050	fi
1051
1052
1053	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1054	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1055	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1056	if [[ -n $host && "$host" != $localhost ]]
1057	then
1058	do_batch=true
1059	do_remote=true
1060	case $host in
1061	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1062	(*) printf "\n"
1063	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1064	printf "\n is not available"
1065	locat=nqs; (( iec = 0 )); exit;;
1066	esac
1067	else
1068	host=$localhost
1069	fi
1070
1071
1072
1073	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1074	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1075	then
1076
1077	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1078	if [[ ! -n $numprocs ]]
1079	then
1080	printf "\n"
1081	printf "\n +++ option \"-K parallel\" requires additional specification"
1082	printf "\n of the number of processors to be used by"
1083	printf "\n mrun-option \"-X\" or by environment-variable"
1084	printf "\n \"numprocs\" in the configuration file"
1085	locat=numprocs; (( iec = 0 )); exit
1086	fi
1087
1088	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1089	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1090	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1091	then
1092	printf "\n"
1093	printf "\n +++ option \"-T\" (tasks per node) is missing"
1094	printf "\n set -T option or define tasks_per_node in the config file"
1095	locat=tasks_per_node; (( iec = 0 )); exit
1096	fi
1097
1098	if (( numprocs < tasks_per_node ))
1099	then
1100	printf "\n"
1101	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1102	printf "\n given values: -T $tasks_per_node -X $numprocs"
1103	locat=tasks_per_node; (( iec = 0 )); exit
1104	fi
1105
1106	if [[ $host != lcflow && $host != lcxt5m ]]
1107	then
1108	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1109	(( ival = $tasks_per_node ))
1110	(( pes = numprocs ))
1111	(( ii = pes / ival ))
1112	(( remaining_pes = pes - ii * ival ))
1113	if (( remaining_pes > 0 ))
1114	then
1115	printf "\n"
1116	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1117	printf "\n divisor of the total number of processors (option \"-X\")"
1118	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1119	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1120	(( nodes = nodes + 1 ))
1121	fi
1122	fi
1123
1124
1125	# SETTINGS FOR SUBJOB-COMMAND
1126	OOPT="-O $threads_per_task"
1127
1128	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1129	if [[ "$tasks_per_node" != "" ]]
1130	then
1131	TOPT="-T $tasks_per_node"
1132	fi
1133
1134	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1135	if [[ $node_usage = default ]]
1136	then
1137	if [[ $host = ibms ]]
1138	then
1139	node_usage=shared
1140	else
1141	node_usage=not_shared
1142	fi
1143	fi
1144
1145	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1146	then
1147	printf "\n"
1148	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1149	printf "\n \"shared\" or \"not_shared\""
1150	locat=tasks_per_node; (( iec = 0 )); exit
1151	fi
1152
1153	fi
1154
1155	# CHECK IF HOSTFILE EXISTS
1156	if [[ -n $hostfile ]]
1157	then
1158	if [[ ! -f $hostfile ]]
1159	then
1160	printf "\n"
1161	printf "\n +++ hostfile \"$hostfile\" does not exist"
1162	locat=hostfile; exit
1163	fi
1164	fi
1165
1166
1167	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1168	if [[ "$maximum_parallel_io_streams" = "" ]]
1169	then
1170	maximum_parallel_io_streams=$numprocs
1171	fi
1172
1173
1174	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1175	if [[ "$scp_port" != "" ]]
1176	then
1177	PORTOPT="-P $scp_port"
1178	SSH_PORTOPT="-p $scp_port"
1179	fi
1180
1181
1182	# SET DEFAULT-QUEUE, IF NOT GIVEN
1183	if [[ $queue = none ]]
1184	then
1185	case $host in
1186	(ibmh) queue=cluster;;
1187	(ibmkisti) queue=class.32plus;;
1188	(lcbullhh) queue=compute;;
1189	(lccrayb) queue=mpp1q;;
1190	(lccrayh) queue=mpp1q;;
1191	(lckiaps) queue=normal;;
1192	(lckyoto) queue=ph;;
1193	(lckyuh) queue=fx-single;;
1194	(lckyut) queue=cx-single;;
1195	(lctit) queue=S;;
1196	(nech) queue=none;;
1197	(unics) queue=unics;;
1198	esac
1199	fi
1200
1201
1202	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1203	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1204	(( i = 0 ))
1205	while (( i < iin ))
1206	do
1207	(( i = i + 1 ))
1208	(( maxcycle = 0 ))
1209
1210	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1211	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1212	if [[ "${actionin[$i]}" = di ]]
1213	then
1214	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1215	# HOST ONLY
1216	eval filename=${pathin[$i]}/${endin[$i]}
1217	else
1218	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1219	# HOST ONLY
1220	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1221	fi
1222	eval pathname=${pathin[$i]}
1223
1224	# CHECK IF FILE EXISTS
1225	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1226	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1227	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1228	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1229	then
1230
1231	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1232	if [[ "${transin[$i]}" != "locopt" ]]
1233	then
1234	printf "\n\n +++ INPUT-file: "
1235	if [[ "${extin[$i]}" = "" ]]
1236	then
1237	printf "\n $filename"
1238	else
1239	printf "\n $filename.${extin[$i]}"
1240	fi
1241	printf "\n does not exist\n"
1242	locat=input; exit
1243	else
1244	transin[$i]="unavailable"
1245	fi
1246	else
1247
1248	# DETERMINE THE FILE'S CYCLE NUMBER
1249	ls -1 -d $filename > filelist 2>/dev/null
1250	ls -1 -d $filename.* >> filelist 2>/dev/null
1251	while read zeile
1252	do
1253	cycle=$(echo $zeile \| cut -f2 -d".")
1254	if [[ "$cycle" = "$zeile" ]]
1255	then
1256	(( icycle = 0 ))
1257	elif [[ "$cycle" = "${extin[$i]}" ]]
1258	then
1259	(( icycle = 0 ))
1260	else
1261	(( icycle = $cycle ))
1262	fi
1263	if (( icycle > maxcycle ))
1264	then
1265	(( maxcycle = icycle ))
1266	file_to_be_used=$zeile
1267	fi
1268	done <filelist
1269	rm filelist
1270
1271	# APPEND CYCLE NUMBER TO FILENAME
1272	if (( maxcycle > 0 ))
1273	then
1274	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1275	then
1276	filename=${filename}.$maxcycle.${extin[$i]}
1277	else
1278	filename=${filename}.$maxcycle
1279	fi
1280	else
1281	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1282	then
1283	filename=${filename}.${extin[$i]}
1284	fi
1285	fi
1286
1287	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1288	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1289	absnamein[$i]=$filename
1290	if (( maxcycle > 0 ))
1291	then
1292	if [[ "${actionin[$i]}" = di ]]
1293	then
1294	frelin[$i]=${endin[$i]}.$maxcycle
1295	else
1296	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1297	fi
1298	else
1299	if [[ "${actionin[$i]}" = di ]]
1300	then
1301	frelin[$i]=${endin[$i]}
1302	else
1303	frelin[$i]=${afname}${endin[$i]}
1304	fi
1305	fi
1306
1307	fi
1308	done
1309
1310	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1311	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1312	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1313	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1314	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1315	# REMOTE HOST)
1316	(( i = 0 ))
1317	while (( i < iout ))
1318	do
1319	(( i = i + 1 ))
1320	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1321	then
1322	if [[ "${actionout[$i]}" = tr ]]
1323	then
1324	actionout[$i]=""
1325	elif [[ "${actionout[$i]}" = trpe ]]
1326	then
1327	actionout[$i]=pe
1328	elif [[ "${actionout[$i]}" = tra ]]
1329	then
1330	actionout[$i]=a
1331	fi
1332	(( maxcycle = 0 ))
1333	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1334	eval catalogname=${pathout[$i]}
1335	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1336	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1337	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1338	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1339	then
1340
1341	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1342	if cat /dev/null > $filename
1343	then
1344	rm $filename
1345	else
1346
1347	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1348	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1349	if [[ ! -d $catalogname ]]
1350	then
1351	if mkdir -p $catalogname
1352	then
1353	printf "\n\n *** directory:"
1354	printf "\n $catalogname"
1355	printf "\n was created\n"
1356	else
1357	printf "\n\n +++ OUTPUT-file:"
1358	printf "\n $filename"
1359	printf "\n cannot be created, because directory does not exist"
1360	printf "\n and cannot be created either"
1361	printf "\n"
1362	locat=output ; exit
1363	fi 2>/dev/null
1364	else
1365	printf "\n\n +++ OUTPUT-file:"
1366	printf "\n $filename"
1367	printf "\n cannot be created, although directory exists"
1368	printf "\n"
1369	locat=output ; exit
1370	fi
1371	fi 2>/dev/null
1372	else
1373
1374	# DETERMINE THE CYCLE NUMBER
1375	ls -1 -d $filename > filelist 2>/dev/null
1376	ls -1 -d $filename.* >> filelist 2>/dev/null
1377	while read zeile
1378	do
1379	cycle=$(echo $zeile \| cut -f2 -d".")
1380	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1381	then
1382	(( icycle = 1 ))
1383	else
1384	(( icycle = $cycle + 1 ))
1385	fi
1386	if (( icycle > maxcycle ))
1387	then
1388	(( maxcycle = icycle ))
1389	fi
1390	done <filelist
1391	rm filelist
1392	fi
1393
1394	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1395	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1396	if [[ "${actionout[$i]}" != a ]]
1397	then
1398	if (( maxcycle > 0 ))
1399	then
1400	filename=${filename}.$maxcycle
1401	if cat /dev/null > $filename
1402	then
1403	rm $filename
1404	else
1405	printf "\n +++ OUTPUT-file:"
1406	printf "\n $filename"
1407	printf "\n cannot be created"
1408	locat=output ; exit
1409	fi
1410	fi
1411	else
1412	(( maxcycle = maxcycle - 1 ))
1413	if (( maxcycle > 0 ))
1414	then
1415	filename=${filename}.$maxcycle
1416	fi
1417	fi
1418
1419	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1420	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1421	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1422	pathout[$i]=$filename
1423	if (( maxcycle > 0 ))
1424	then
1425	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1426	else
1427	frelout[$i]=${fname}${endout[$i]}
1428	fi
1429
1430	fi
1431	done
1432
1433
1434	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1435	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1436	then
1437	if [[ "$dvr_inc" = "" ]]
1438	then
1439	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1440	printf "\n This is required for the dvrp_graphics package.\n"
1441	locat=dvr; exit
1442	fi
1443	if [[ "$dvr_lib" = "" ]]
1444	then
1445	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1446	printf "\n This is required for the dvrp_graphics package.\n"
1447	locat=dvr; exit
1448	fi
1449	fi
1450
1451
1452	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1453	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1454	if [[ "$mainprog" = "" && "$executable" = "" ]]
1455	then
1456	printf "\n +++ neither main program nor executable defined"
1457	locat=source; exit
1458	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1459	then
1460	printf "\n +++ main program as well as executable defined"
1461	locat=source; exit
1462	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1463	then
1464	do_compile=false
1465	fi
1466
1467
1468	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1469	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1470	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1471	then
1472	rm -rf SOURCES_FOR_RUN_$fname
1473	mkdir SOURCES_FOR_RUN_$fname
1474	fi
1475
1476
1477	# COLLECT ALL ROUTINES TO BE COMPILED
1478	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1479	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1480	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1481	then
1482
1483	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1484
1485	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1486	then
1487
1488	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1489	source_list=""
1490	cd $source_path
1491
1492
1493	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1494	if [[ ! -d .svn ]]
1495	then
1496	printf "\n\n +++ source directory"
1497	printf "\n \"$source_path\" "
1498	printf "\n is not under control of \"subversion\"."
1499	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1500	fi
1501
1502
1503	# LIST ALL MODIFIED SOURCE CODE FILES
1504	Filenames=""
1505	svn status > tmp_mrun
1506	while read line
1507	do
1508	firstc=`echo $line \| cut -c1`
1509	if [[ $firstc = M \|\| $firstc = "?" ]]
1510	then
1511	Name=`echo "$line" \| cut -c8-`
1512	extension=`echo $Name \| cut -d. -f2`
1513	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1514	then
1515	Filenames="$Filenames "$Name
1516	fi
1517	fi
1518	done < tmp_mrun
1519
1520
1521	# COPY FILES TO SOURCES_FOR_RUN_...
1522	for dateiname in $Filenames
1523	do
1524	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1525	source_list=$source_list"$dateiname "
1526	done
1527
1528	cd - > /dev/null
1529
1530
1531	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1532	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1533	elif [[ "$source_list" != "" && $restart_run != true ]]
1534	then
1535
1536	cd $source_path
1537
1538	for filename in $source_list
1539	do
1540
1541	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1542	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1543	then
1544	printf "\n +++ source code file: $filename"
1545	printf "\n must not contain (\"/\") "
1546	locat=source; exit
1547	fi
1548
1549	if [[ ! -f $filename ]]
1550	then
1551	printf "\n +++ source code file: $filename"
1552	printf "\n does not exist"
1553	locat=source; exit
1554	else
1555	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1556	fi
1557
1558	done
1559
1560	cd - > /dev/null
1561
1562	fi
1563
1564
1565	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1566	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1567	if [[ $restart_run != true ]]
1568	then
1569
1570	if [[ ! -f "$source_path/$mainprog" ]]
1571	then
1572	printf "\n\n +++ main program: $mainprog"
1573	printf "\n does not exist in source directory"
1574	printf "\n \"$source_path\"\n"
1575	locat=source; exit
1576	else
1577	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1578	then
1579	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1580	source_list=${mainprog}" $source_list"
1581	fi
1582	fi
1583	fi
1584
1585
1586	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1587	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1588	if [[ "$restart_run" != true ]]
1589	then
1590	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1591	if [[ ! -f $makefile ]]
1592	then
1593	printf "\n +++ file \"$makefile\" does not exist"
1594	locat=make; exit
1595	else
1596	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1597	fi
1598	fi
1599
1600
1601	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1602	if [[ $restart_run != true && "$add_source_path" != "" ]]
1603	then
1604
1605	# DOES THE DIRECTORY EXIST?
1606	if [[ ! -d $add_source_path ]]
1607	then
1608	printf "\n\n *** INFORMATIVE: additional source code directory"
1609	printf "\n \"$add_source_path\" "
1610	printf "\n does not exist or is not a directory."
1611	printf "\n No source code will be used from this directory!\n"
1612	add_source_path=""
1613	if [[ $silent == false ]]
1614	then
1615	sleep 3
1616	fi
1617	else
1618
1619	cd $add_source_path
1620	found=false
1621
1622	Names=$(ls -1 *.f90 2>&1)
1623	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1624	Names=$(ls -1 *.F90 2>&1)
1625	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1626	Names=$(ls -1 *.F 2>&1)
1627	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1628	Names=$(ls -1 *.f 2>&1)
1629	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1630	Names=$(ls -1 *.c 2>&1)
1631	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1632
1633	cd - > /dev/null
1634	cd SOURCES_FOR_RUN_$fname
1635
1636	# COPY MAKEFILE IF EXISTING
1637	if [[ -f $add_source_path/Makefile ]]
1638	then
1639	printf "\n\n *** user Makefile from directory"
1640	printf "\n \"$add_source_path\" is used \n"
1641	if [[ $silent == false ]]
1642	then
1643	sleep 1
1644	fi
1645	cp $add_source_path/Makefile .
1646	fi
1647
1648	for dateiname in $AddFilenames
1649	do
1650	if [[ -f $dateiname ]]
1651	then
1652	printf "\n +++ source code file \"$dateiname\" found in additional"
1653	printf "\n source code directory \"$add_source_path\" "
1654	printf "\n but was also given with option \"-s\" which means that it should be taken"
1655	printf "\n from directory \"$source_path\"."
1656	locat=source; exit
1657	fi
1658
1659	cp $add_source_path/$dateiname .
1660	source_list="$source_list $dateiname"
1661
1662	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1663	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1664	then
1665	printf "\n\n +++ user file \"$dateiname\" "
1666	printf "\n is not listed in Makefile \n"
1667	locat=source; exit
1668	else
1669
1670	if [[ $found = false ]]
1671	then
1672	found=true
1673	printf "\n\n *** following user file(s) added to the"
1674	printf " files to be translated:\n "
1675	fi
1676	printf "$dateiname "
1677	if [[ $silent == false ]]
1678	then
1679	sleep 0.5
1680	fi
1681
1682	fi
1683	done
1684	[[ $found = true ]] && printf "\n"
1685	cd - > /dev/null
1686	fi
1687	fi
1688
1689
1690	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1691	# TO THE LIST OF FILES TO BE COMPILED
1692	if [[ $restart_run != true && -n $package_list ]]
1693	then
1694
1695	cd $source_path
1696
1697	for package in $package_list
1698	do
1699
1700	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1701
1702	# DETERMINE FILES BELONGING TO THE PACKAGE
1703	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1704	# THE NAME OF THE DIRECTORY
1705	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1706
1707
1708	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1709	# IF THEY ARE NOT ALREADY PART OF THE LIST
1710	for source_list_name in $package_source_list
1711	do
1712	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1713	then
1714
1715	# ONLY TAKE FILES WITH VALID SUFFIX
1716	ending=`echo $source_list_name \| cut -f2 -d.`
1717	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1718	then
1719	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1720	source_list="$source_list $source_list_name"
1721	fi
1722	fi
1723	done
1724	done
1725
1726	cd - > /dev/null
1727	fi
1728
1729	fi # do_compile=true
1730
1731
1732	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1733	# AND SET PRE-PROCESSOR DIRECTIVES
1734	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1735	then
1736
1737	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1738	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1739	then
1740	cpp_options="${cpp_options},-D__ibm=__ibm"
1741	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1742	then
1743	cpp_options="$cpp_options -D__nec"
1744	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1745	then
1746	cpp_options="$cpp_options -D__lc"
1747	else
1748	cpp_options="$cpp_options -D__$localhost"
1749	fi
1750
1751	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1752	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1753	then
1754	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1755	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1756	else
1757	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1758	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1759	fi
1760
1761	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1762	if [[ -n $package_list ]]
1763	then
1764	for package in $package_list
1765	do
1766	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1767	then
1768	if [[ $package != "dvrp_graphics+1PE" ]]
1769	then
1770	cpp_options="${cpp_options},-D__$package=__$package"
1771	else
1772	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1773	export use_seperate_pe_for_dvrp_output=true
1774	fi
1775	else
1776	if [[ $package != "dvrp_graphics+1PE" ]]
1777	then
1778	cpp_options="$cpp_options -D__$package"
1779	else
1780	cpp_options="$cpp_options -D__dvrp_graphics"
1781	export use_seperate_pe_for_dvrp_output=true
1782	fi
1783	fi
1784	done
1785	fi
1786
1787	# SET DIRECTIVES GIVEN BY OPTION -D
1788	if [[ -n $cpp_opts ]]
1789	then
1790	for popts in $cpp_opts
1791	do
1792	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1793	then
1794	cpp_options="${cpp_options},-D__$popts=__$popts"
1795	else
1796	cpp_options="$cpp_options -D__$popts"
1797	fi
1798	done
1799	fi
1800
1801	else
1802
1803
1804	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1805	if [[ $do_remote = false ]]
1806	then
1807	if [[ ! -f $executable ]]
1808	then
1809	printf "\n +++ executable file: $executable"
1810	printf "\n does not exist"
1811	locat=executable; exit
1812	fi
1813	fi
1814	fi
1815
1816
1817	# DETERMINE THE JOB MODE
1818	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1819	then
1820	if [[ "$LOADLBATCH" = yes ]]
1821	then
1822	batch_job=.TRUE.
1823	jobmo=BATCH
1824	else
1825	batch_job=.FALSE.
1826	jobmo=INTERACTIVE
1827	fi
1828	else
1829	if [[ "$ENVIRONMENT" = BATCH ]]
1830	then
1831	batch_job=.TRUE.
1832	jobmo=BATCH
1833	else
1834	batch_job=.FALSE.
1835	jobmo=INTERACTIVE
1836	fi
1837	fi
1838
1839	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1840	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1841	then
1842	printf "\n +++ no interactive runs allowed on host \"$host\" "
1843	printf "\n please submit batch job using mrun option \"-b\" \n"
1844	locat=normal; exit
1845	fi
1846
1847
1848	# CHECK, IF USER DEFINED A COMPILER
1849	if [[ "$compiler_name" = "" ]]
1850	then
1851
1852	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1853	locat=compiler_name; exit
1854
1855	fi
1856
1857
1858	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1859
1860	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1861	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1862	then
1863	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1864	if [[ "$kennung" = "" ]]
1865	then
1866	kennung=$RANDOM
1867	fi
1868	else
1869	kennung=$RANDOM
1870	fi
1871
1872	if [[ "$tmp_user_catalog" = "" ]]
1873	then
1874	if [[ $localhost = ibmh ]]
1875	then
1876	tmp_user_catalog=$SCRATCH
1877	elif [[ $localhost = nech ]]
1878	then
1879	tmp_user_catalog=$WRKSHR
1880	else
1881	tmp_user_catalog=/tmp
1882	fi
1883	fi
1884	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1885
1886
1887	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1888	if [[ "$tmp_data_catalog" = "" ]]
1889	then
1890	if [[ $localhost = nech ]]
1891	then
1892	tmp_data_catalog=$WRKSHR/mrun_restart_data
1893	else
1894	tmp_data_catalog=/tmp/mrun_restart_data
1895	fi
1896	fi
1897
1898
1899	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1900	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1901	then
1902	eval fopts=\"$fopts\"
1903	eval lopts=\"$lopts\"
1904	fi
1905
1906
1907	# DETERMINE COMPILE- AND LINK-OPTIONS
1908	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1909	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1910	XOPT="-X $numprocs"
1911
1912
1913	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1914	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1915	done=false
1916	while [[ $done = false ]]
1917	do
1918	cputime=$cpumax
1919	if (( $cputime == 0 ))
1920	then
1921	if [[ $do_batch = true ]]
1922	then
1923	printf "\n +++ cpu-time is undefined"
1924	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1925	printf "\n >>> "
1926	read cputime 1>/dev/null 2>&1
1927	else
1928	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1929	fi
1930	else
1931	done=true
1932	fi
1933	cpumax=$cputime
1934	done
1935
1936	(( minuten = cputime / 60 ))
1937	(( sekunden = cputime - minuten * 60 ))
1938
1939
1940	# CHECK THE MEMORY DEMAND
1941	if [[ $do_batch = true ]]
1942	then
1943	done=false
1944	while [[ $done = false ]]
1945	do
1946	if (( memory == 0 ))
1947	then
1948	printf "\n +++ memory demand is undefined"
1949	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1950	printf "\n >>> "
1951	read memory 1>/dev/null 2>&1
1952	else
1953	done=true
1954	fi
1955	done
1956	fi
1957
1958
1959	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1960	if [[ $do_remote = true && -z $remote_username ]]
1961	then
1962	while [[ -z $remote_username ]]
1963	do
1964	printf "\n +++ username on remote host \"$host\" is undefined"
1965	printf "\n >>> Please type username:"
1966	printf "\n >>> "
1967	read remote_username
1968	done
1969	mc="$mc -u$remote_username"
1970	fi
1971
1972	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1973	if [[ "$login_init_cmd" != "" ]]
1974	then
1975	export init_cmds="${login_init_cmd};"
1976	fi
1977
1978
1979	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1980	if [[ "$modules" != "" ]]
1981	then
1982	if [[ $host = lctit ]]
1983	then
1984	export module_calls=". $modules"
1985	else
1986	export module_calls="module load ${modules};"
1987	fi
1988	fi
1989
1990	# OUTPUT OF THE MRUN-HEADER
1991	calltime=$(date)
1992	printf "\n"
1993	printf "#------------------------------------------------------------------------# \n"
1994	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1995	printf "\| \| \n"
1996	spalte1="called on:"; spalte2=$localhost_realname
1997	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1998	if [[ $do_remote = true ]]
1999	then
2000	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2001	else
2002	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2003	fi
2004	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2005	if [[ -n $numprocs ]]
2006	then
2007	if [[ $run_coupled_model = false ]]
2008	then
2009	spalte1="number of PEs:"; spalte2=$numprocs
2010	else
2011	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2012	fi
2013	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2014	fi
2015	if [[ -n $tasks_per_node ]]
2016	then
2017	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2018	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2019	if (( remaining_pes > 0 ))
2020	then
2021	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2022	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2023	fi
2024	fi
2025	if [[ $maximum_parallel_io_streams != $numprocs ]]
2026	then
2027	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2028	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2029	fi
2030	if [[ $use_openmp = true ]]
2031	then
2032	spalte1="threads per task:"; spalte2="$threads_per_task"
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	fi
2035	printf "\| \| \n"
2036	if [[ $do_compile = true ]]
2037	then
2038	if [[ "$mopts" != "" ]]
2039	then
2040	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2041	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2042	zeile=$(echo "$mopts" \| cut -c46-)
2043	while [[ "$zeile" != "" ]]
2044	do
2045	spalte1=""
2046	spalte2=$(echo "$zeile" \| cut -c-45)
2047	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2048	zeile=$(echo "$zeile" \| cut -c46-)
2049	done
2050	fi
2051
2052	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054	zeile=$(echo "$cpp_options" \| cut -c46-)
2055	while [[ "$zeile" != "" ]]
2056	do
2057	spalte1=""
2058	spalte2=$(echo "$zeile" \| cut -c-45)
2059	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2060	zeile=$(echo "$zeile" \| cut -c46-)
2061	done
2062
2063	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2064	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2065	zeile=$(echo "$fopts" \| cut -c46-)
2066	while [[ "$zeile" != "" ]]
2067	do
2068	spalte1=""
2069	spalte2=$(echo "$zeile" \| cut -c-45)
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	zeile=$(echo "$zeile" \| cut -c46-)
2072	done
2073
2074	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2075	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2076	zeile=$(echo "$lopts" \| cut -c46-)
2077	while [[ "$zeile" != "" ]]
2078	do
2079	spalte1=""
2080	spalte2=$(echo "$zeile" \| cut -c-45)
2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2082	zeile=$(echo "$zeile" \| cut -c46-)
2083	done
2084
2085	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2086	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2087	zeile=$(echo "$modules" \| cut -c46-)
2088	while [[ "$zeile" != "" ]]
2089	do
2090	spalte1=""
2091	spalte2=$(echo "$zeile" \| cut -c-45)
2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2093	zeile=$(echo "$zeile" \| cut -c46-)
2094	done
2095
2096	spalte1="main program:"; spalte2=$mainprog
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098	else
2099	spalte1=executable:; spalte2=$executable
2100	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2101	fi
2102	printf "\| \| \n"
2103	spalte1="base name of files:"; spalte2=$fname
2104	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2105	if [[ $fname != $afname ]]
2106	then
2107	spalte1="base name of input files:"; spalte2=$afname
2108	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2109	fi
2110	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2111	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2112	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2113	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2114
2115	if [[ "$ocean_file_appendix" = true ]]
2116	then
2117	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2118	fi
2119
2120	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2121	then
2122	spalte1="memory demand / PE":; spalte2="$memory MB"
2123	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2124	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2125	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2126	fi
2127
2128	if [[ $do_compile = true ]]
2129	then
2130	printf "\| \| \n"
2131	printf "\| Files to be compiled: \| \n"
2132	zeile=$source_list
2133	while [[ "$zeile" != "" ]]
2134	do
2135	linestart=$(echo $zeile \| cut -c-70)
2136	printf "\| %-70s \| \n" "$linestart"
2137	zeile=$(echo "$zeile" \| cut -c71-)
2138	done
2139	fi
2140	printf "#------------------------------------------------------------------------#"
2141
2142
2143
2144	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2145	if [[ $do_trace = true ]]
2146	then
2147	(( i = 0 ))
2148	while (( i < iin ))
2149	do
2150	(( i = i + 1 ))
2151	if (( i == 1 ))
2152	then
2153	printf "\n\n >>> INPUT-file assignments:\n"
2154	fi
2155	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2156	done
2157	(( i = 0 ))
2158	while (( i < iout ))
2159	do
2160	(( i = i + 1 ))
2161	if (( i == 1 ))
2162	then
2163	printf "\n\n >>> OUTPUT-file assignments:\n"
2164	fi
2165	printf "\n ${localout[$i]} : ${pathout[$i]}"
2166	done
2167	(( i = 0 ))
2168	while (( i < iic ))
2169	do
2170	(( i = i + 1 ))
2171	if (( i == 1 ))
2172	then
2173	printf "\n\n >>> INPUT-commands:\n"
2174	fi
2175	printf "\n ${in_command[$i]}"
2176	done
2177	(( i = 0 ))
2178	while (( i < ioc ))
2179	do
2180	(( i = i + 1 ))
2181	if (( i == 1 ))
2182	then
2183	printf "\n\n >>> OUTPUT-commands:\n"
2184	fi
2185	printf "\n ${out_command[$i]}"
2186	done
2187	fi
2188
2189	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2190	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2191	then
2192	antwort=dummy
2193	printf "\n\n"
2194	printf " >>> everything o.k. (y/n) ? "
2195	while read antwort
2196	do
2197	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2198	then
2199	printf " >>> everything o.k. (y/n) ? "
2200	else
2201	break
2202	fi
2203	done
2204	if [[ $antwort = n \|\| $antwort = N ]]
2205	then
2206	locat=user_abort; (( iec = 0 )); exit
2207	fi
2208	if [[ $do_batch = true ]]
2209	then
2210	printf " >>> batch-job will be created and submitted"
2211	else
2212	printf " >>> MRUN will now continue to execute on this machine"
2213	fi
2214	fi
2215
2216
2217	# DETERMINE PATH FOR MAKE DEPOSITORY
2218	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2219	then
2220
2221	line=""
2222	grep "%depository_path" $config_file > tmp_mrun
2223	while read line
2224	do
2225	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2226	then
2227	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2228	then
2229	global_depository_path=`echo $line \| cut -d" " -s -f2`
2230	fi
2231	fi
2232	done < tmp_mrun
2233
2234	line=""
2235	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2236	while read line
2237	do
2238	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2239	then
2240	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2241	then
2242	local_depository_path=`echo $line \| cut -d" " -s -f2`
2243	fi
2244	fi
2245	done < tmp_mrun
2246
2247	if [[ "$local_depository_path" = "" ]]
2248	then
2249	if [[ "$global_depository_path" != "" ]]
2250	then
2251	local_depository_path=$global_depository_path
2252	else
2253	printf "\n\n +++ no depository path found in configuration file"
2254	printf "\n for local host \"$localhost\" "
2255	printf "\n please set \"\%depository_path\" in configuration file\n"
2256	locat=config_file; exit
2257	fi
2258	fi
2259	eval local_depository_path=$local_depository_path
2260	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2261	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2262
2263
2264	basename=`echo $mainprog \| cut -f1 -d"."`
2265	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2266	if [[ ! -f $make_depository ]]
2267	then
2268	printf "\n"
2269	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2270	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2271	fi
2272
2273	fi
2274
2275
2276	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2277	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2278	if [[ $do_batch = false ]]
2279	then
2280
2281
2282	# CREATE THE TEMPORARY WORKING DIRECTORY
2283	mkdir -p $TEMPDIR
2284	chmod go+rx $TEMPDIR
2285	tmpcreate=true
2286
2287
2288	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2289	# INTO THE TEMPORARY WORKING DIRECTORY
2290	if [[ $do_compile = true ]]
2291	then
2292
2293	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2294	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2295	if [[ $localhost = nech ]]
2296	then
2297	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2298	if mkdir -p $TEMPDIR_COMPILE
2299	then
2300	printf "\n *** \"$TEMPDIR_COMPILE\" "
2301	printf "\n is generated as temporary directory for cross compiling\n"
2302	else
2303	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2304	printf "\n needed for cross compilation failed"
2305	locat=compile
2306	exit
2307	fi
2308	else
2309	TEMPDIR_COMPILE=$TEMPDIR
2310	fi
2311
2312	cp $make_depository $TEMPDIR_COMPILE
2313	cd $TEMPDIR_COMPILE
2314	tar -xf $make_depository > /dev/null 2>&1
2315	cd - > /dev/null
2316
2317	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2318	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2319	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2320	then
2321	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2322	else
2323	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2324	fi
2325
2326	else
2327
2328	cp $executable ${TEMPDIR}/a.out
2329
2330	fi
2331
2332
2333	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2334	cd $TEMPDIR
2335	printf "\n *** changed to temporary directory: $TEMPDIR"
2336
2337
2338	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2339	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2340	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2341	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2342	(( i = 0 ))
2343	while (( i < iout ))
2344	do
2345	(( i = i + 1 ))
2346	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2347	then
2348	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2349	else
2350	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2351	fi
2352	done
2353
2354
2355	# IF REQUIRED, START WITH COMPILING
2356	if [[ $do_compile = true ]]
2357	then
2358
2359
2360	if [[ -f a.out ]]
2361	then
2362
2363	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2364	printf "\n\n\n *** executable a.out found"
2365	printf "\n no compilation required \n"
2366
2367	else
2368
2369	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2370	printf "\n\n\n *** compilation starts \n$dashes\n"
2371	printf " *** compilation with make using following options:\n"
2372	printf " make depository: $make_depository"
2373	if [[ "$mopts" != "" ]]
2374	then
2375	printf " make options: $mopts\n"
2376	fi
2377	printf " compilername: $compiler_name\n"
2378	printf " compiler options: $fopts\n"
2379	printf " preprocessor directives: $cpp_options \n"
2380	printf " linker options: $lopts \n"
2381	if [[ "$modules" != "" ]]
2382	then
2383	printf " modules to be load: $modules \n"
2384	fi
2385	printf " source code files: $source_list \n"
2386
2387	if [[ $localhost = nech ]]
2388	then
2389	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\" "
2390	cp $TEMPDIR_COMPILE/a.out .
2391	[[ $? != 0 ]] && compile_error=true
2392	rm -rf $TEMPDIR_COMPILE
2393	elif [[ $localhost = ibmh ]]
2394	then
2395	printf " compiler is called via ssh on \"plogin1\" \n"
2396	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\" "
2397	[[ ! -f a.out ]] && compile_error=true
2398	continue # STATUS=1, IF a.out EXISTS
2399	elif [[ $localhost = lcocean ]]
2400	then
2401	printf " compiler is called via ssh on \"ocean\" \n"
2402	echo $PWD
2403	ssh $SSH_PORTOPT ocean -l $usern "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
2404	[[ ! -f a.out ]] && compile_error=true
2405	continue # STATUS=1, IF a.out EXISTS
2406	elif [[ $localhost = lcflow ]]
2407	then
2408	printf " compiler is called via ssh on \"flow\" \n"
2409	/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\" "
2410	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2411	[[ "$check_for_file" = "" ]] && compile_error=true
2412	continue # STATUS=1, IF a.out EXISTS
2413	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2414	then
2415	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2416	else
2417	[[ "$init_cmds" != "" ]] && eval $init_cmds
2418	[[ "$module_calls" != "" ]] && eval $module_calls
2419	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2420	fi
2421
2422	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2423	then
2424	printf "\n +++ error occured while compiling or linking"
2425	locat=compile
2426
2427	exit
2428	else
2429	printf "$dashes\n *** compilation finished \n"
2430	fi
2431
2432	fi
2433
2434	fi
2435
2436
2437	# PROVIDE THE INPUT FILES
2438	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2439	(( i = 0 ))
2440	while (( i < iin ))
2441	do
2442	(( i = i + 1 ))
2443	if (( i == 1 ))
2444	then
2445	printf "\n\n *** providing INPUT-files:\n$dashes"
2446	fi
2447
2448
2449	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2450	if [[ "${transin[$i]}" = unavailable ]]
2451	then
2452	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2453	then
2454	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2455	printf "\n is not available!"
2456	else
2457	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2458	printf "\n is not available!"
2459	fi
2460	continue
2461	fi
2462
2463	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2464	files_for_pes=false; datentyp=file
2465	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2466	then
2467	files_for_pes=true; datentyp=directory
2468	actionin[$i]=""
2469	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2470	then
2471	actionin[$i]=""
2472	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2473	then
2474	files_for_pes=true; datentyp=directory
2475	actionin[$i]="ar"
2476	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2477	then
2478	actionin[$i]="ar"
2479	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2480	then
2481	files_for_pes=true; datentyp=directory
2482	actionin[$i]="fl"
2483	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2484	then
2485	actionin[$i]="fl"
2486	fi
2487
2488	if [[ $files_for_pes = true ]]
2489	then
2490	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2491	else
2492	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2493	fi
2494
2495	# INPUT-FILE FOR A RESTART RUN.
2496	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2497	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2498	if [[ "${actionin[$i]}" = fl ]]
2499	then
2500	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2501	if [[ $files_for_pes = false ]]
2502	then
2503	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2504	then
2505	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2506	got_tmp[$i]=true
2507	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2508	then
2509	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2510	printf "\n *** trying to use backup copy in \"$WORK\" "
2511	cp $WORK/${frelin[$i]} ${localin[$i]}
2512	else
2513	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2514	printf "\n or \"$tmp_data_catalog\" does not exist!"
2515	printf "\n *** trying to get copy from archive"
2516	actionin[$i]=ar
2517	fi
2518	else
2519	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2520	then
2521	mkdir ${localin[$i]}
2522	cd $tmp_data_catalog/${frelin[$i]}
2523	for file in $(ls *)
2524	do
2525	ln $file $TEMPDIR/${localin[$i]}
2526	done
2527	cd $TEMPDIR
2528	got_tmp[$i]=true
2529	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2530	then
2531	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2532	printf "\n *** trying to use backup copy in \"$WORK\" "
2533	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2534	else
2535	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2536	printf "\n or \"$tmp_data_catalog\" does not exist!"
2537	printf "\n *** trying to get copy from archive"
2538	actionin[$i]=ar
2539	fi
2540	fi
2541	fi
2542
2543
2544	# FILE IS STORED ON THE ARCHIVE SYSTEM
2545	if [[ "${actionin[$i]}" = ar ]]
2546	then
2547
2548	if [[ $files_for_pes = false ]]
2549	then
2550	printf "\n file will be restored from archive-system ($archive_system)!"
2551	else
2552	printf "\n directory will be restored from archive-system ($archive_system)!"
2553	fi
2554
2555	file_restored=false
2556
2557	if [[ $archive_system = asterix ]]
2558	then
2559	do_stagein=true
2560	(( stagein_anz = 0 ))
2561	while [[ $do_stagein = true ]]
2562	do
2563	if [[ $files_for_pes = false ]]
2564	then
2565	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2566	else
2567	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2568	fi
2569	cat STAGEIN_OUTPUT
2570	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2571	then
2572	file_restored=true
2573	do_stagein=false
2574	else
2575	(( stagein_anz = stagein_anz + 1 ))
2576	if (( stagein_anz == 10 ))
2577	then
2578	printf "\n +++ stagein stoped after 10 tries"
2579	locat=stage
2580	exit
2581	fi
2582	printf "\n +++ restoring from archive failed, trying again:"
2583	sleep 900
2584	fi
2585	done
2586	elif [[ $archive_system = DMF ]]
2587	then
2588	if [[ $files_for_pes = false ]]
2589	then
2590	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2591	locat=DMF
2592	exit
2593	else
2594	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2595	cp -r $ARCHIVE/${frelin[$i]} $PWD
2596	file_restored=true
2597	fi
2598	elif [[ $archive_system = tivoli ]]
2599	then
2600	if [[ $files_for_pes = false ]]
2601	then
2602	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2603	else
2604	(( inode = 0 ))
2605	while (( inode < nodes ))
2606	do
2607	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2608	(( inode = inode + 1 ))
2609	done
2610	fi
2611	file_restored=true
2612	elif [[ $archive_system = ut ]]
2613	then
2614	if [[ $files_for_pes = false ]]
2615	then
2616	cp $UT/${frelin[$i]} .
2617	else
2618	(( inode = 0 ))
2619	while (( inode < nodes ))
2620	do
2621	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2622	(( inode = inode + 1 ))
2623	done
2624	fi
2625	file_restored=true
2626	else
2627	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2628	locat=rearchive
2629	exit
2630	fi
2631
2632	if [[ $file_restored = true ]]
2633	then
2634
2635	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2636	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2637	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2638	if [[ $files_for_pes = false ]]
2639	then
2640	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2641	else
2642	mkdir $tmp_data_catalog/${frelin[$i]}
2643	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2644	fi
2645	got_tmp[$i]=true
2646
2647	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2648	mv ${frelin[$i]} ${localin[$i]}
2649
2650	fi
2651	fi
2652
2653
2654	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2655	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2656	then
2657
2658	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2659	then
2660
2661	# FILE COPIES ARE PROVIDED FOR ALL CORES
2662	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2663	printf "\n file will be provided for $numprocs processors"
2664	mkdir ${localin[$i]}
2665	ival=$numprocs
2666	(( ii = 0 ))
2667	while (( ii <= ival-1 ))
2668	do
2669	if (( ii < 10 ))
2670	then
2671	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2672	elif (( ii < 100 ))
2673	then
2674	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2675	elif (( ii < 1000 ))
2676	then
2677	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2678	else
2679	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2680	fi
2681	(( ii = ii + 1 ))
2682	done
2683
2684	else
2685
2686	if [[ $files_for_pes = true ]]
2687	then
2688
2689	# PROVIDE FILES FOR EACH CORE
2690	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2691	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2692	printf "\n providing $numprocs files for the respective processors"
2693	mkdir ${localin[$i]}
2694	if [[ $link_local_input = true ]]
2695	then
2696	printf " using ln -f\n"
2697	cd ${absnamein[$i]}
2698	for file in $(ls *)
2699	do
2700	ln -f $file ${localin[$i]}
2701	done
2702	cd $TEMPDIR
2703	fi
2704
2705	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2706	if [[ ! -f "${localin[$i]}/_0000" ]]
2707	then
2708	if [[ $link_local_input = true ]]
2709	then
2710	printf " ln failed for .../_0000, using cp...\n"
2711	fi
2712	cp -r ${absnamein[$i]}/* ${localin[$i]}
2713	fi
2714
2715	else
2716
2717	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2718	if [[ $link_local_input = true ]]
2719	then
2720	printf " using ln -f\n"
2721	ln -f ${absnamein[$i]} ${localin[$i]}
2722	fi
2723	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2724	if [[ ! -f "${localin[$i]}" ]]
2725	then
2726	if [[ $link_local_input = true ]]
2727	then
2728	printf " ln failed, using cp...\n"
2729	fi
2730	cp ${absnamein[$i]} ${localin[$i]}
2731	fi
2732	fi
2733	fi
2734	fi
2735
2736	done
2737	if (( i != 0 ))
2738	then
2739	printf "\n$dashes\n *** all INPUT-files provided \n"
2740	fi
2741
2742
2743	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2744	(( i = 0 ))
2745	while (( i < iic ))
2746	do
2747	(( i = i + 1 ))
2748	if (( i == 1 ))
2749	then
2750	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2751	fi
2752	printf "\n >>> ${in_command[$i]}"
2753	eval ${in_command[$i]}
2754	if (( i == iic ))
2755	then
2756	printf "\n$dashes\n"
2757	fi
2758	done
2759
2760
2761	# SET THE REMAINING CPU-TIME
2762	cpurest=${cpumax}.
2763
2764
2765	# START DVR STREAMING SERVER
2766	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2767	then
2768	if [[ "$dvr_server" != "" ]]
2769	then
2770
2771	printf "\n\n *** preparing the dvr streaming server configuration file"
2772
2773	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2774	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2775	if [[ "$running_dvrserver_id" != "" ]]
2776	then
2777
2778	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2779	printf "\n This server is used instead starting a new one!"
2780	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2781
2782	else
2783
2784	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2785	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2786	then
2787	cp ${PALM_BIN}/.dvrserver.config .
2788
2789	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2790	user_id=`id -u`
2791	group_id=`id -g`
2792
2793	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2794	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2795	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2796	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2797	mv .dvrserver.3 .dvrserver.config
2798	rm .dvrserver.1 .dvrserver.2
2799
2800	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2801	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2802	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2803	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2804	local_dvrserver_running=.TRUE.
2805	else
2806	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2807	printf "\n \"$PALM_BIN\" "
2808	locat=dvr
2809	exit
2810	fi
2811
2812	fi
2813
2814	else
2815	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2816	fi
2817	fi
2818
2819
2820	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2821	# (FILE ENVPAR WILL BE READ BY PALM)
2822	cat > ENVPAR << %%END%%
2823	&envpar run_identifier = '$fname', host = '$localhost',
2824	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2825	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2826	maximum_cpu_time_allowed = ${cpumax}.,
2827	revision = '$global_revision',
2828	local_dvrserver_running = $local_dvrserver_running,
2829	batch_job = $batch_job /
2830
2831	%%END%%
2832
2833
2834	# STARTING THE EXECUTABLE
2835	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2836	PATH=$PATH:$TEMPDIR
2837
2838
2839	if [[ $execute_command != "none" ]]
2840	then
2841
2842	printf "\n +++ branch still not realized"
2843	locat=execution
2844	exit
2845
2846	else
2847
2848	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2849	if [[ "$mpi_debug" = true ]]
2850	then
2851	export MPI_CHECK_ARGS=1
2852	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2853	fi
2854
2855	if [[ "$totalview" = true ]]
2856	then
2857	printf "\n *** totalview debugger will be used"
2858	tv_opt="-tv"
2859	else
2860	tv_opt=""
2861	fi
2862
2863	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2864	then
2865
2866	#Interactive ALLINEA DEBUG seesion
2867	if [[ "$ENVIRONMENT" != BATCH ]]
2868	then
2869	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2870	then
2871	if [[ "$allinea" = true ]]
2872	then
2873	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2874
2875	ddt aprun -n $ii -N $tasks_per_node a.out
2876	wait
2877	fi
2878	fi
2879	fi
2880
2881	if [[ $localhost = ibmh ]]
2882	then
2883
2884	# SETUP THE IBM MPI ENVIRONMENT
2885	export MP_SHARED_MEMORY=yes
2886	export AIXTHREADS_SCOPE=S
2887	export OMP_NUM_THREADS=$threads_per_task
2888	export AUTHSTATE=files
2889	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2890
2891	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2892	export MP_ADAPTER_USE=shared
2893	export MP_CPU_USE=multiple
2894	export MP_TIMEOUT=1200
2895
2896	unset MP_TASK_AFFINITY
2897
2898	if [[ "$LOADLBATCH" = yes ]]
2899	then
2900	totalview poe a.out
2901	else
2902	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2903	export TVDSVRLAUNCHCMD=ssh
2904	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2905	fi
2906
2907	fi # END DEBUG MODE
2908
2909	else
2910
2911	# NORMAL EXECUTION
2912	if [[ -n $numprocs ]]
2913	then
2914
2915	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2916	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2917	then
2918
2919	# SETUP THE IBM MPI ENVIRONMENT
2920	if [[ $host != ibmh && $host != ibmkisti ]]
2921	then
2922	export MP_SHARED_MEMORY=yes
2923	export AIXTHREAD_SCOPE=S
2924	export OMP_NUM_THREADS=$threads_per_task
2925	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2926	export AUTHSTATE=files
2927	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2928	# export MP_PRINTENV=yes
2929
2930	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2931	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2932	export MP_WAIT_MODE=poll
2933	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2934	fi
2935
2936	if [[ $host = ibmkisti ]]
2937	then
2938	export LANG=en_US
2939	export MP_SHARED_MEMORY=yes
2940	if [[ $threads_per_task = 1 ]]
2941	then
2942	export MP_SINGLE_THREAD=yes
2943	export MEMORY_AFFINITY=MCM
2944	else
2945	export OMP_NUM_THREADS=$threads_per_task
2946	fi
2947	fi
2948
2949	if [[ "$LOADLBATCH" = yes ]]
2950	then
2951	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2952	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2953	then
2954	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2955	else
2956	if [[ $run_coupled_model = false ]]
2957	then
2958	if [[ "$ocean_file_appendix" = true ]]
2959	then
2960	echo "precursor_ocean" > runfile_atmos
2961	else
2962	echo "precursor_atmos" > runfile_atmos
2963	fi
2964	else
2965	(( iia = $numprocs_atmos / $threads_per_task ))
2966	(( iio = $numprocs_ocean / $threads_per_task ))
2967	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2968	printf "\n using $coupled_mode coupling"
2969	printf "\n\n"
2970	echo "coupled_run $iia $iio" > runfile_atmos
2971	fi
2972	poe ./a.out < runfile_atmos
2973	fi
2974	else
2975	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2976	then
2977	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2978	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2979	then
2980	if [[ -f $hostfile ]]
2981	then
2982	cp $hostfile hostfile
2983	else
2984	(( ii = 1 ))
2985	while (( ii <= $numprocs ))
2986	do
2987	echo $localhost_realname >> hostfile
2988	(( ii = ii + 1 ))
2989	done
2990	fi
2991	export MP_HOSTFILE=hostfile
2992	if [[ $run_coupled_model = false ]]
2993	then
2994	if [[ "$ocean_file_appendix" = true ]]
2995	then
2996	echo "precursor_ocean" > runfile_atmos
2997	else
2998	echo "precursor_atmos" > runfile_atmos
2999	fi
3000	else
3001	(( iia = $numprocs_atmos / $threads_per_task ))
3002	(( iio = $numprocs_ocean / $threads_per_task ))
3003	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3004	printf "\n using $coupled_mode coupling"
3005	printf "\n\n"
3006	echo "coupled_run $iia $iio" > runfile_atmos
3007	fi
3008
3009	poe ./a.out -procs $numprocs < runfile_atmos
3010
3011	else
3012	if [[ "$host_file" = "" ]]
3013	then
3014	printf "\n +++ no hostfile given in configuration file"
3015	locat=config_file
3016	exit
3017	else
3018	eval host_file=$host_file
3019	fi
3020	export MP_HOSTFILE=$host_file
3021	poe a.out -procs $numprocs -tasks_per_node $numprocs
3022	fi
3023	fi
3024
3025	elif [[ $host = nech ]] # running on NEC machines
3026	then
3027
3028	(( ii = nodes ))
3029	if [[ $ii = 1 ]]
3030	then
3031	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3032	export MPIPROGINF=YES
3033	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3034	echo "*** execution on single node with mpirun"
3035	mpirun -np $numprocs ./a.out
3036	else
3037	(( i = 0 ))
3038	while (( i < ii ))
3039	do
3040	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3041	(( i = i + 1 ))
3042	done
3043
3044	echo "#!/bin/sh" > mpi_exec_shell
3045	echo " " >> mpi_exec_shell
3046	echo "set -u" >> mpi_exec_shell
3047	echo "F_ERRCNT=0" >> mpi_exec_shell
3048	echo "MPIPROGINV=YES" >> mpi_exec_shell
3049	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3050	echo "cpurest=$cpurest" >> mpi_exec_shell
3051	echo "fname=$fname" >> mpi_exec_shell
3052	echo "localhost=$localhost" >> mpi_exec_shell
3053	echo "return_address=$return_address" >> mpi_exec_shell
3054	echo "return_username=$return_username" >> mpi_exec_shell
3055	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3056	echo "write_binary=$write_binary" >> mpi_exec_shell
3057	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3058	echo " " >> mpi_exec_shell
3059	echo "export F_ERRCNT" >> mpi_exec_shell
3060	echo "export MPIPROGINV" >> mpi_exec_shell
3061	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3062	echo "export cpurest" >> mpi_exec_shell
3063	echo "export fname" >> mpi_exec_shell
3064	echo "export localhost" >> mpi_exec_shell
3065	echo "export return_address" >> mpi_exec_shell
3066	echo "export return_username" >> mpi_exec_shell
3067	echo "export tasks_per_node" >> mpi_exec_shell
3068	echo "export write_binary" >> mpi_exec_shell
3069	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3070	echo " " >> mpi_exec_shell
3071	echo "exec ./a.out" >> mpi_exec_shell
3072
3073	chmod u+x mpi_exec_shell
3074	export MPIPROGINF=YES
3075	mpirun -f multinode_config &
3076	wait
3077
3078	fi
3079
3080	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3081	then
3082
3083	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3084	# DOES NOT EXIST
3085	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]
3086	then
3087	if [[ -f $hostfile ]]
3088	then
3089	cp $hostfile hostfile
3090	(( ii = $numprocs / $threads_per_task ))
3091	[[ $ii = 0 ]] && (( ii = 1 ))
3092	else
3093	(( ii = 1 ))
3094	while (( ii <= $numprocs / $threads_per_task ))
3095	do
3096	echo $localhost_realname >> hostfile
3097	(( ii = ii + 1 ))
3098	done
3099	if (( $numprocs / $threads_per_task == 0 ))
3100	then
3101	echo $localhost_realname >> hostfile
3102	fi
3103	fi
3104	eval zeile=\"`head -n $ii hostfile`\"
3105	printf "\n *** running on: $zeile"
3106	fi
3107
3108	(( ii = $numprocs / $threads_per_task ))
3109	[[ $ii = 0 ]] && (( ii = 1 ))
3110	export OMP_NUM_THREADS=$threads_per_task
3111
3112	if [[ $threads_per_task != 1 ]]
3113	then
3114	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3115	# MAY ABORT
3116	ulimit -s unlimited
3117	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3118	fi
3119	if [[ $run_coupled_model = false ]]
3120	then
3121	if [[ "$ocean_file_appendix" = true ]]
3122	then
3123	echo "precursor_ocean" > runfile_atmos
3124	else
3125	echo "precursor_atmos" > runfile_atmos
3126	fi
3127	printf "\n\n"
3128
3129	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3130	then
3131	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3132	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3133	elif [[ $host = lcbullhh ]]
3134	then
3135	export OMPI_MCA_pml=cm
3136	export OMPI_MCA_mtl=mxm
3137	export OMPI_MCA_coll=^ghc
3138	export OMPI_MCA_mtl_mxm_np=0
3139	export MXM_RDMA_PORTS=mlx5_0:1
3140	export MXM_LOG_LEVEL=ERROR
3141	export OMP_NUM_THREADS=$threads_per_task
3142	export KMP_AFFINITY=verbose,granularity=core,compact,1
3143	export KMP_STACKSIZE=64m
3144
3145	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3146
3147	elif [[ $host = lccrayf ]]
3148	then
3149	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3150	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3151	then
3152	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3153	elif [[ $host = lcflow ]]
3154	then
3155	mpirun -np $ii a.out < runfile_atmos
3156	elif [[ $host = lcocean ]]
3157	then
3158	mpirun a.out $ROPTS < runfile_atmos
3159	elif [[ $host = lcsb ]]
3160	then
3161	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3162	elif [[ $host = lckiaps ]]
3163	then
3164	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos
3165	elif [[ $host = lckyu* ]]
3166	then
3167	mpiexec -n $ii --stdin runfile_atmos ./a.out
3168	else
3169	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3170	fi
3171
3172	else
3173
3174	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3175	(( iia = $numprocs_atmos / $threads_per_task ))
3176	(( iio = $numprocs_ocean / $threads_per_task ))
3177	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3178	printf "\n using $coupled_mode coupling"
3179	printf "\n\n"
3180
3181	if [[ $coupled_mode = "mpi2" ]]
3182	then
3183	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3184	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3185
3186	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3187	then
3188
3189	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
3190	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
3191
3192	else
3193	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3194	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
3195	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
3196	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
3197	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
3198	fi
3199	wait
3200
3201	else
3202
3203	echo "coupled_run $iia $iio" > runfile_atmos
3204
3205	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3206	then
3207
3208	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3209
3210	elif [[ $host = lck \|\| $host = lckordi ]]
3211	then
3212
3213	mpiexec -n $ii ./a.out < runfile_atmos &
3214
3215	elif [[ $host = lckyu* ]]
3216	then
3217
3218	mpiexec -n $ii --stdin runfile_atmos ./a.out
3219
3220	elif [[ $host = lcmuk ]]
3221	then
3222
3223	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3224
3225	fi
3226	wait
3227	fi
3228
3229	fi
3230
3231	elif [[ $host = lckyoto ]]
3232	then
3233	set -xv
3234	export P4_RSHCOMMAND=plesh
3235	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3236	if [[ "$ENVIRONMENT" = BATCH ]]
3237	then
3238	if [[ "$cond2" = fujitsu ]]
3239	then
3240	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3241	elif [[ "cond2" = pgi ]]
3242	then
3243	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3244	else
3245	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3246	fi
3247	else
3248	if [[ "$cond2" = "" ]]
3249	then
3250	mpiruni_rsh -np $numprocs ./a.out # for intel
3251	else
3252	mpirun -np $numprocs ./a.out
3253	fi
3254	fi
3255	set +xv
3256
3257	elif [[ $host = lctit ]]
3258	then
3259	export OMP_NUM_THREADS=$threads_per_task
3260	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3261	if [[ "$threads_per_task" != 1 ]]
3262	then
3263	export MV2_ENABLE_AFFINITY=0
3264	fi
3265	echo "----- PBS_NODEFILE content:"
3266	cat $PBS_NODEFILE
3267	echo "-----"
3268	(( ii = $numprocs / $threads_per_task ))
3269	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3270	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3271
3272	else
3273	mpprun -n $numprocs a.out
3274	fi
3275	else
3276	a.out
3277	fi
3278
3279	fi # end normal (non-debug) execution
3280
3281	fi # end explicit execute_command or host-specific execute actions
3282
3283	if [[ $? != 0 ]]
3284	then
3285
3286	# ABORT IN CASE OF RUNTIME ERRORS
3287	printf "\n +++ runtime error occured"
3288	locat=execution
3289	exit
3290
3291	else
3292
3293	printf "\n$dashes\n *** execution finished \n"
3294
3295	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3296	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3297	if [[ "$dvrserver_id" != "" ]]
3298	then
3299	kill $dvrserver_id
3300	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3301
3302	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3303	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3304	if [[ -d DATA_DVR ]]
3305	then
3306
3307	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3308	# DIRECTORY
3309	cp .dvrserver.config DATA_DVR
3310
3311	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3312	# SEQUENCE MODE DATA TOO)
3313	process_dvr_output -d DATA_DVR -f $fname -s
3314
3315	else
3316
3317	# PROCESS THE LOCAL OUTPUT
3318	process_dvr_output -l -d DATA_DVR -f $fname
3319
3320	fi
3321
3322	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3323	then
3324
3325	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3326	process_dvr_output -l -d DATA_DVR -f $fname
3327
3328	fi
3329	fi
3330
3331
3332
3333	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3334	# BY EACH CORE INTO ONE FILE
3335	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3336	then
3337	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3338	printf "\n 2d- and/or 3d-data may be incomplete!"
3339	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3340	elif [[ "$combine_plot_fields" == true ]]
3341	then
3342	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3343	then
3344	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3345	aprun -n 1 -N 1 combine_plot_fields${block}.x
3346	else
3347	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3348	combine_plot_fields${block}.x
3349	fi
3350	else
3351
3352	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3353	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3354	# ??? koennen wir das streichen ???
3355	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3356	fi
3357
3358
3359
3360	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3361	(( i = 0 ))
3362	while (( i < ioc ))
3363	do
3364	(( i = i + 1 ))
3365	if (( i == 1 ))
3366	then
3367	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3368	fi
3369	printf "\n >>> ${out_command[$i]}"
3370	eval ${out_command[$i]}
3371	if (( i == ioc ))
3372	then
3373	printf "\n$dashes\n"
3374	fi
3375	done
3376
3377
3378	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3379	if [[ $do_trace = true ]]
3380	then
3381	printf "\n\n"
3382	ls -al
3383	fi
3384
3385
3386
3387	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3388	(( i = 0 ))
3389	while (( i < iout ))
3390	do
3391	(( i = i + 1 ))
3392	if (( i == 1 ))
3393	then
3394	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3395	fi
3396
3397	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3398	files_for_pes=false; filetyp=file
3399	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3400	then
3401	files_for_pes=true; filetyp=directory
3402	actionout[$i]=""
3403	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3404	then
3405	actionout[$i]=""
3406	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3407	then
3408	files_for_pes=true; filetyp=directory
3409	actionout[$i]="ar"
3410	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3411	then
3412	actionout[$i]="ar"
3413	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3414	then
3415	files_for_pes=true; filetyp=directory
3416	actionout[$i]="fl"
3417	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3418	then
3419	actionout[$i]="fl"
3420	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3421	then
3422	files_for_pes=true; filetyp=directory
3423	actionout[$i]="tr"
3424	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3425	then
3426	actionout[$i]="tr"
3427	fi
3428
3429	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3430	then
3431	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3432	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3433	then
3434	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3435	else
3436
3437
3438	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3439	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3440	if [[ "${actionout[$i]}" = tr ]]
3441	then
3442	if [[ $localhost != $fromhost ]]
3443	then
3444	if [[ $files_for_pes = false ]]
3445	then
3446	cps=""
3447	cst=""
3448	else
3449	cps=-c
3450	cst="/"
3451	fi
3452	if [[ $localhost = nech ]]
3453	then
3454
3455	# TRANSFER IN SEPERATE JOB
3456	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3457	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3458	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3459	if [[ $files_for_pes = false ]]
3460	then
3461	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3462	else
3463	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3464	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3465	fi
3466
3467	echo "set -x" > transfer_${localout[$i]}
3468	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3469
3470	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3471	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3472	printf "\n or higher cycle\n"
3473	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]}
3474
3475	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3476
3477	if [[ $localhost = nech ]]
3478	then
3479	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3480	else
3481	if [[ "$LOGNAME" = b323013 ]]
3482	then
3483	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3484	else
3485	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3486	fi
3487	fi
3488
3489	else
3490
3491	# TRANSFER WITHIN THIS JOB
3492	transfer_failed=false
3493	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3494	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3495	if [[ $localhost = lccrayb ]]
3496	then
3497	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]}"
3498	elif [[ $localhost = lccrayh ]]
3499	then
3500	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]}"
3501	elif [[ $localhost = lcbullhh ]]
3502	then
3503	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]}"
3504	elif [[ $localhost = lcxe6 ]]
3505	then
3506	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]}"
3507	else
3508	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3509	fi
3510	[[ $? != 0 ]] && transfer_failed=true
3511
3512	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3513	if [[ $transfer_failed = true ]]
3514	then
3515	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3516	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3517
3518	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3519	eval local_catalog=${pathout[$i]}
3520	if [[ ! -d $local_catalog ]]
3521	then
3522	printf " *** local directory does not exist. Trying to create:\n"
3523	printf " $local_catalog \n"
3524	mkdir -p $local_catalog
3525	fi
3526	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3527	transfer_problems=true
3528	fi
3529	fi
3530	else
3531
3532	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3533	actionout[$i]=""
3534	fi
3535	fi
3536
3537
3538	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3539	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3540	if [[ "${actionout[$i]}" = tra ]]
3541	then
3542	if [[ $localhost != $fromhost ]]
3543	then
3544	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3545	then
3546
3547	# TRANSFER IN SEPERATE JOB
3548	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3549	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3550	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3551	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3552
3553	echo "set -x" > transfer_${localout[$i]}
3554	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3555
3556	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3557	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3558	printf "\n or higher cycle\n"
3559	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]}
3560
3561	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3562
3563	if [[ $localhost = nech ]]
3564	then
3565	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3566	else
3567	if [[ $LOGNAME = b323013 ]]
3568	then
3569	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3570	else
3571	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3572	fi
3573	fi
3574
3575	else
3576
3577	# TRANSFER WITHIN THIS JOB
3578	transfer_failed=false
3579	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3580	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3581	if [[ $localhost = lccrayb ]]
3582	then
3583	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]}"
3584	elif [[ $localhost = lccrayh ]]
3585	then
3586	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]}"
3587	elif [[ $localhost = lcxe6 ]]
3588	then
3589	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]}"
3590	else
3591	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3592	fi
3593	[[ $? != 0 ]] && transfer_failed=true
3594
3595	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3596	if [[ $transfer_failed = true ]]
3597	then
3598	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3599	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3600
3601	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3602	eval local_catalog=${pathout[$i]}
3603	if [[ ! -d $local_catalog ]]
3604	then
3605	printf " *** local directory does not exist. Trying to create:\n"
3606	printf " $local_catalog \n"
3607	mkdir -p $local_catalog
3608	fi
3609
3610	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3611	transfer_problems=true
3612	fi
3613	fi
3614	else
3615
3616	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3617	actionout[$i]=a
3618	fi
3619	fi
3620
3621
3622	# OUTPUT-FILE FOR A RESTART-RUN.
3623	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3624	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3625	# AS LAST ACTION, ARCHIVING IS INITIATED.
3626	if [[ "${actionout[$i]}" = fl ]]
3627	then
3628	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3629	chmod g+rx $tmp_data_catalog
3630	if [[ $files_for_pes = false ]]
3631	then
3632	printf "\n >>> OUTPUT: ${localout[$i]} to"
3633	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3634	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3635	else
3636	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3637	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3638	mkdir $tmp_data_catalog/${frelout[$i]}
3639	cd ${localout[$i]}
3640	for file in $(ls *)
3641	do
3642	ln -f $file $tmp_data_catalog/${frelout[$i]}
3643	done
3644	cd $TEMPDIR
3645	fi
3646
3647
3648	# CREATE AND SUBMIT ARCHIVING-JOB
3649	if [[ $store_on_archive_system = true ]]
3650	then
3651
3652	if [[ $archive_system = asterix ]]
3653	then
3654	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3655	if [[ $files_for_pes = false ]]
3656	then
3657	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3658	else
3659	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3660	fi
3661	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3662	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3663	echo "then" >> archive_${frelout[$i]}
3664	echo " do_stageout=false" >> archive_${frelout[$i]}
3665	echo "else" >> archive_${frelout[$i]}
3666	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3667	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3668	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3669	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3670	if [[ $files_for_pes = false ]]
3671	then
3672	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3673	else
3674	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3675	fi
3676	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3677	echo "fi" >> archive_${frelout[$i]}
3678	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3679	elif [[ $archive_system = DMF ]]
3680	then
3681	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3682	if [[ $files_for_pes = false ]]
3683	then
3684	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3685	locat=DMF
3686	exit
3687	else
3688	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3689	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3690	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3691	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3692	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3693	fi
3694	elif [[ $archive_system = tivoli ]]
3695	then
3696	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3697	if [[ $files_for_pes = false ]]
3698	then
3699	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3700	echo "set -x" >> archive_${frelout[$i]}
3701	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3702	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3703	else
3704
3705	echo "set -x" >> archive_${frelout[$i]}
3706	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3707	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3708	cd $tmp_data_catalog
3709	all_files=`ls -1 ${frelout[$i]}/*`
3710	cd - > /dev/null
3711	(( inode = 0 ))
3712	(( tp1 = tasks_per_node + 1 ))
3713	while (( inode < nodes ))
3714	do
3715	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3716	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3717	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3718	(( inode = inode + 1 ))
3719	done
3720	fi
3721	elif [[ $archive_system = ut ]]
3722	then
3723	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3724	if [[ $files_for_pes = false ]]
3725	then
3726	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3727	echo "set -x" >> archive_${frelout[$i]}
3728	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3729	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3730	else
3731
3732	echo "set -x" >> archive_${frelout[$i]}
3733	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
3734	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
3735	cd $tmp_data_catalog
3736	all_files=`ls -1 ${frelout[$i]}/*`
3737	cd - > /dev/null
3738	(( inode = 0 ))
3739	(( tp1 = tasks_per_node + 1 ))
3740	while (( inode < nodes ))
3741	do
3742	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3743	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3744	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3745	(( inode = inode + 1 ))
3746	done
3747	fi
3748	elif [[ $archive_system = none ]]
3749	then
3750	printf " +++ archiving on $localhost not available!\n"
3751	fi
3752
3753	if [[ $archive_system != none ]]
3754	then
3755	if [[ $localhost = nech ]]
3756	then
3757	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3758	fi
3759	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3760	fi
3761	else
3762	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
3763	fi
3764
3765
3766	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
3767	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3768	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3769	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3770	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3771	if [[ $files_for_pes = false ]]
3772	then
3773	cat /dev/null > ${pathout[$i]}
3774	else
3775	mkdir -p ${pathout[$i]}
3776	fi
3777
3778	fi
3779
3780
3781	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
3782	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
3783	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
3784	if [[ "${actionout[$i]}" = ar ]]
3785	then
3786	if [[ $files_for_pes = false ]]
3787	then
3788	printf "\n >>> OUTPUT: ${localout[$i]} to"
3789	printf "\n ${pathout[$i]}"
3790	printf "\n File will be copied to archive-system ($archive_system) !\n"
3791	else
3792	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
3793	printf "\n ${pathout[$i]}"
3794	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
3795	fi
3796	mv ${localout[$i]} ${frelout[$i]}
3797
3798	file_saved=false
3799
3800	if [[ $archive_system = asterix ]]
3801	then
3802	do_stageout=true
3803	(( stageout_anz = 0 ))
3804	while [[ $do_stageout = true ]]
3805	do
3806	if [[ $files_for_pes = false ]]
3807	then
3808	stageout ${frelout[$i]} > STAGE_OUTPUT
3809	else
3810	stageout -t ${frelout[$i]} > STAGE_OUTPUT
3811	fi
3812	cat STAGE_OUTPUT
3813	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
3814	then
3815	file_saved=true
3816	do_stageout=false
3817	else
3818	if [[ $files_for_pes = false ]]
3819	then
3820	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
3821	else
3822	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
3823	fi
3824	(( stageout_anz = stageout_anz + 1 ))
3825	if (( stageout_anz == 10 ))
3826	then
3827	printf "\n +++ stoped after 10 unsuccessful tries!"
3828	archive_save=false
3829	do_stageout=false
3830	else
3831	printf "\n *** new try to store on archive after 15 min:"
3832	sleep 900
3833	fi
3834	fi
3835	done
3836	elif [[ $archive_system = DMF ]]
3837	then
3838	if [[ $files_for_pes = false ]]
3839	then
3840	printf "\n +++ archiving of single files impossible on $archive_system!\n"
3841	locat=DMF
3842	exit
3843	else
3844	rm -rf $ARCHIVE/${frelout[$i]}
3845	cp -r ${frelout[$i]} $ARCHIVE
3846	fi
3847	file_saved=true
3848	elif [[ $archive_system = tivoli ]]
3849	then
3850	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3851	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3852	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3853	# WHEN THE ARCHIVE-JOB IS EXECUTED
3854	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3855	chmod g+rx $tmp_data_catalog
3856	if [[ $files_for_pes = false ]]
3857	then
3858	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3859	else
3860	mkdir $tmp_data_catalog/${frelout[$i]}
3861	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3862	fi
3863
3864	# GENERATE AND SUBMIT BATCH-JOB
3865	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3866	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3867	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3868	if [[ $files_for_pes = false ]]
3869	then
3870	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3871	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3872	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3873	else
3874	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3875	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3876	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3877	fi
3878
3879	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
3880	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3881	file_saved=true
3882
3883	elif [[ $archive_system = ut ]]
3884	then
3885	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3886	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3887	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3888	# WHEN THE ARCHIVE-JOB IS EXECUTED
3889	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3890	chmod g+rx $tmp_data_catalog
3891	if [[ $files_for_pes = false ]]
3892	then
3893	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3894	else
3895	mkdir $tmp_data_catalog/${frelout[$i]}
3896	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3897	fi
3898
3899	# GENERATE AND SUBMIT BATCH-JOB
3900	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3901	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3902	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3903	if [[ $files_for_pes = false ]]
3904	then
3905	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3906	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3907	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3908	else
3909	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3910	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3911	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3912	fi
3913
3914	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3915	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3916	file_saved=true
3917
3918	else
3919	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
3920	archive_save=false
3921	fi
3922
3923	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
3924	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3925	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3926	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3927	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3928	if [[ $file_saved = true ]]
3929	then
3930	if [[ $files_for_pes = false ]]
3931	then
3932	cat /dev/null > ${pathout[$i]}
3933	else
3934	mkdir -p ${pathout[$i]}
3935	fi
3936	fi
3937
3938	fi
3939
3940	# APPEND ON THIS MACHINE
3941	if [[ "${actionout[$i]}" = "a" ]]
3942	then
3943	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3944	then
3945	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3946	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3947	else
3948	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3949	cat ${localout[$i]} >> ${pathout[$i]}
3950	fi
3951	fi
3952
3953	# COPY ON THIS MACHINE
3954	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3955	# ON DIFFERENT FILE-SYSTEMS
3956	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3957	then
3958
3959	# COPY IN CASE OF RUNS ON SINGLE CORES
3960	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3961	then
3962	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3963	if [[ $link_local_output = true ]]
3964	then
3965	printf " using ln -f\n"
3966	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3967	fi
3968	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3969	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3970	then
3971	if [[ $link_local_output = true ]]
3972	then
3973	printf " ln failed, using cp...\n"
3974	fi
3975	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3976	fi
3977	else
3978	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3979	if [[ $link_local_output = true ]]
3980	then
3981	printf " using ln -f\n"
3982	ln -f ${localout[$i]} ${pathout[$i]}
3983	fi
3984	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3985	if [[ ! -f "${pathout[$i]}" ]]
3986	then
3987	if [[ $link_local_output = true ]]
3988	then
3989	printf " ln failed, using cp...\n"
3990	fi
3991	cp ${localout[$i]} ${pathout[$i]}
3992	fi
3993	fi
3994
3995	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
3996	then
3997
3998	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
3999	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4000	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4001	if [[ $link_local_output = true ]]
4002	then
4003	printf " using ln -f\n"
4004	mkdir ${pathout[$i]}
4005	cd ${localout[$i]}
4006	for file in $(ls *)
4007	do
4008	ln -f $file ${pathout[$i]}
4009	done
4010	cd $TEMPDIR
4011	fi
4012
4013	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4014	if [[ ! -f "${pathout[$i]}/_0000" ]]
4015	then
4016	if [[ $link_local_output = true ]]
4017	then
4018	printf " ln failed for .../_0000, using cp...\n"
4019	fi
4020	cp -r ${localout[$i]} ${pathout[$i]}
4021	fi
4022
4023	fi
4024	fi
4025	done
4026	if (( i != 0 ))
4027	then
4028	if [[ $transfer_problems = true ]]
4029	then
4030	printf "\n$dashes\n *** OUTPUT-files saved"
4031	printf "\n +++ WARNING: some data transfers failed! \n"
4032	else
4033	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4034	fi
4035	fi
4036
4037
4038	# IF REQUIRED, START A RESTART-JOB
4039	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4040	if [[ -f CONTINUE_RUN ]]
4041	then
4042
4043	if [[ $archive_save = true ]]
4044	then
4045
4046	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4047	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4048	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4049	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4050	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4051	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4052	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4053	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4054	then
4055	mc=`echo $mc \| sed 's/#/f/g'`
4056	fi
4057
4058
4059	# START THE RESTART-JOB
4060	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4061	echo " $mc"
4062	printf "\n$dashes\n"
4063	if [[ $localhost != $fromhost ]]
4064	then
4065
4066	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4067	then
4068	echo "*** ssh will be used to initiate restart-runs!"
4069	echo " return_address=\"$return_address\" "
4070	echo " return_username=\"$return_username\" "
4071	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4072	then
4073	if [[ $localhost = ibmh ]]
4074	then
4075	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\" "
4076	elif [[ $localhost = lcbullhh ]]
4077	then
4078	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\" "
4079	elif [[ $localhost = lccrayb ]]
4080	then
4081	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\" "
4082	elif [[ $localhost = lccrayh ]]
4083	then
4084	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\" "
4085	elif [[ $localhost = lcxe6 ]]
4086	then
4087	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\" "
4088	else
4089	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4090	fi
4091	else
4092	if [[ $localhost = ibmkisti ]]
4093	then
4094	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\" "
4095	elif [[ $localhost = lcflow ]]
4096	then
4097	/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 "
4098	elif [[ $localhost = lcocean ]]
4099	then
4100	/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 "
4101	elif [[ $localhost = lccrayb ]]
4102	then
4103	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\" "
4104	elif [[ $localhost = lccrayh ]]
4105	then
4106	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\" "
4107	else
4108	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4109	fi
4110	fi
4111	else
4112	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4113	locat=restart; exit
4114	fi
4115
4116	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4117	if [[ $queue = special1q ]]
4118	then
4119	sleep 120
4120	else
4121	sleep 30
4122	fi
4123
4124	else
4125
4126	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4127	# USING SSH)
4128	cd $LOCAL_PWD
4129	if [[ $localhost = lckyuh ]]
4130	then
4131	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4132	printf "\n please restart job manually using command:\n"
4133	printf "\n \"$mc\" "
4134	else
4135	eval $mc # THE ' MUST BE EVALUATED
4136	fi
4137	cd - > /dev/null
4138	fi
4139	if [[ $localhost = lckyuh ]]
4140	then
4141	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4142	else
4143	printf "\n$dashes\n *** restart-run initiated \n"
4144	fi
4145
4146
4147	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4148	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4149	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4150	# MAY BE VERY HUGE)
4151	(( i = 0 ))
4152	while (( i < iin ))
4153	do
4154	(( i = i + 1 ))
4155	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4156	then
4157	rm -r $tmp_data_catalog/${frelin[$i]}
4158	fi
4159	done
4160
4161	else
4162
4163	printf "\n +++ no restart-run possible, since errors occured"
4164	printf "\n during the archive process"
4165	fi
4166
4167	fi
4168
4169
4170
4171	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4172	if [[ "$email_notification" != "none" ]]
4173	then
4174
4175	if [[ $localhost != $fromhost ]]
4176	then
4177	if [[ -f CONTINUE_RUN ]]
4178	then
4179	echo "PALM restart run necessary" > email_text
4180	echo "description header of actual run:" >> email_text
4181	cat CONTINUE_RUN >> email_text
4182	echo "mrun-command to restart:" >> email_text
4183	echo "$mc" >> email_text
4184	else
4185	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4186	fi
4187	mail $email_notification < email_text
4188	printf "\n *** email notification sent to \"$email_notification\" "
4189	fi
4190	fi
4191
4192
4193
4194	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4195	cd $HOME
4196	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4197
4198	else
4199
4200	# PREPARING ACTIONS,
4201	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4202
4203	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4204	mrun_com="$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 $remote_username"
4205	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4206	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4207	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4208	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4209	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4210	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4211	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4212	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4213	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4214	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4215	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4216	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4217	if [[ $use_openmp = true ]]
4218	then
4219	mrun_com=${mrun_com}" -O $threads_per_task"
4220	fi
4221	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4222	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4223	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4224	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4225	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4226	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4227	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4228	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4229	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4230	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4231	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4232	if [[ $do_remote = true ]]
4233	then
4234	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4235	fi
4236
4237
4238	# CREATE EXECUTABLE FOR BATCH JOB
4239	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4240	then
4241
4242	printf "\n *** creating the executable for batch job\n"
4243
4244	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4245	if [[ $host != $localhost ]]
4246	then
4247	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4248	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4249	locat=create_executable; exit
4250	fi
4251
4252	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4253	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4254
4255	cp $make_depository .
4256	tar -xf $make_depository > /dev/null 2>&1
4257	cp ../* . > /dev/null 2>&1
4258
4259	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4260
4261	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4262	then
4263	printf "\n +++ error occured while compiling or linking"
4264	locat=compile
4265	exit
4266	fi
4267
4268	mv a.out ..
4269	cd - > /dev/null 2>&1
4270	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4271
4272	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4273
4274	fi
4275
4276
4277	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4278	jobfile=jobfile.$RANDOM
4279
4280
4281	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4282	echo "mkdir $TEMPDIR" >> $jobfile
4283	echo "cd $TEMPDIR" >> $jobfile
4284
4285
4286	# ACTIVATE ERROR-TRACEBACK
4287	if [[ $do_trace = true ]]
4288	then
4289	echo "set -x" >> $jobfile
4290	else
4291	echo "set +vx" >> $jobfile
4292	fi
4293
4294
4295	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4296	if [[ "$init_cmds" != "" ]]
4297	then
4298	echo "$init_cmds" >> $jobfile
4299	fi
4300	if [[ "$module_calls" != "" ]]
4301	then
4302	echo "$module_calls" >> $jobfile
4303	fi
4304
4305
4306	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4307	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4308	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4309	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4310	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4311	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4312	# QUEUEING-SYSTEMS
4313	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
4314	then
4315
4316	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4317	if [[ $restart_run != true ]]
4318	then
4319	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4320	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4321	fi
4322
4323	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4324	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4325	echo "set -x" >> $jobfile
4326	if [[ $host = $localhost ]]
4327	then
4328	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4329	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4330	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4331	then
4332	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4333	else
4334	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4335	fi
4336
4337	else
4338	if [[ $host = ibmkisti ]]
4339	then
4340	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4341	echo "localdir=\`pwd\`" >> $jobfile
4342	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4343	elif [[ $host = lcbullhh ]]
4344	then
4345	echo "localdir=\`pwd\`" >> $jobfile
4346	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4347
4348	elif [[ $host = lccrayb ]]
4349	then
4350	echo "localdir=\`pwd\`" >> $jobfile
4351	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4352	elif [[ $host = lccrayh ]]
4353	then
4354	echo "localdir=\`pwd\`" >> $jobfile
4355	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4356
4357	else
4358	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4359	fi
4360	fi
4361	echo "export SOURCES_COMPLETE=true" >> $jobfile
4362
4363	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4364	# WORKING DIRECTORY OF THE JOB
4365	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4366	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4367	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4368	echo "execute_mrun=true" >> $jobfile
4369	echo " " >> $jobfile
4370
4371	else
4372
4373	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4374	if [[ $do_compile = true ]]
4375	then
4376
4377	source_catalog=SOURCES_FOR_RUN_$fname
4378
4379	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4380	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4381	echo "export SOURCES_COMPLETE=true" >> $jobfile
4382	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4383
4384	for filename in $source_list
4385	do
4386	# BACKSLASH IS USED FOR MASKING
4387	echo "cat > $filename << \"%END%\"" >> $jobfile
4388	cat $source_catalog/$filename >> $jobfile
4389	echo " " >> $jobfile
4390	echo "%END%" >> $jobfile
4391	echo " " >> $jobfile
4392	done
4393
4394	# BACKSLASH IS USED FOR MASKING
4395	echo "cat > Makefile << \"%END%\"" >> $jobfile
4396	cat $source_catalog/Makefile >> $jobfile
4397	echo " " >> $jobfile
4398	echo "%END%" >> $jobfile
4399	echo " " >> $jobfile
4400
4401	echo "cd - > /dev/null" >> $jobfile
4402
4403	fi
4404
4405
4406	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4407	# BACKSLASH IS USED FOR MASKING
4408	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4409	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4410	echo "cat > $config_file << \"%END%\"" >> $jobfile
4411	if [[ $host = lckyuh ]]
4412	then
4413	# NO CROSS-COMPILER ON COMPUTE NODE
4414	sed 's/frtpx/frt/g' $config_file >> $jobfile
4415	else
4416	sed 's/#$.*//g' $config_file >> $jobfile
4417	fi
4418	echo "%END%" >> $jobfile
4419	echo " " >> $jobfile
4420
4421
4422	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4423	# BACKSLASH IS USED FOR MASKING
4424	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4425	if [[ $host = lckyuh ]]
4426	then
4427	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4428	else
4429	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4430	fi
4431	echo "%END%" >> $jobfile
4432	echo "chmod u+x $mrun_script_name" >> $jobfile
4433	echo "execute_mrun=true" >> $jobfile
4434	echo " " >> $jobfile
4435
4436	fi
4437
4438
4439	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4440	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4441	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4442	if [[ $do_remote = true ]]
4443	then
4444	(( i = 0 ))
4445	while (( i < iin ))
4446	do
4447	(( i = i + 1 ))
4448	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4449	if [[ "${transin[$i]}" = job ]]
4450	then
4451	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4452	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4453	echo " " >> $jobfile
4454	echo "%END%" >> $jobfile
4455	else
4456	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4457	fi
4458
4459	# CHECK, IF FILE COULD BE CREATED
4460	echo "if [[ \$? = 1 ]]" >> $jobfile
4461	echo "then" >> $jobfile
4462	echo " echo \" \" " >> $jobfile
4463	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4464	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4465	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4466	echo " execute_mrun=false" >> $jobfile
4467	echo "fi" >> $jobfile
4468	done
4469	fi
4470
4471	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4472	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4473	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4474	echo "LOCAL_PWD=$working_directory" >> $jobfile
4475	echo "export LOCAL_PWD" >> $jobfile
4476
4477	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4478	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4479	echo "export LOCAL_MRUN_PATH" >> $jobfile
4480
4481	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4482	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4483	# then
4484	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4485	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4486	# fi
4487
4488	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4489	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4490	echo "set -x" >> $jobfile
4491	echo "queue=$queue" >> $jobfile
4492	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4493	echo 'ls -al; echo `pwd`' >> $jobfile
4494	echo "cd \$HOME" >> $jobfile
4495	echo "rm -rf $TEMPDIR" >> $jobfile
4496
4497
4498
4499
4500	# START THE JOB USING SUBJOB-COMMAND
4501	if [[ $silent = false ]]
4502	then
4503	printf "\n "
4504	else
4505	printf "\n\n"
4506	fi
4507
4508	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
4509	rm -rf $jobfile
4510
4511
4512	fi # END OF REMOTE-PART

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