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source: palm/trunk/SCRIPTS/mrun @ 1941

Last change on this file since 1941 was 1941, checked in by raasch, 8 years ago
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1	#!/bin/bash
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1941 2016-06-14 05:17:11Z raasch $
29	#
30	# 1940 2016-06-14 05:15:20Z raasch $
31	# adjustments for lckiaps
32	#
33	# 1866 2016-04-15 06:50:59Z raasch
34	# adjusted for lcocean
35	#
36	# 1841 2016-04-07 19:14:06Z raasch
37	# script now running under bash
38	#
39	# 1804 2016-04-05 16:30:18Z maronga
40	# test: implementing an execute mechanism where the execute command is given in the
41	# configuration file
42	# ROPTS removed from execution commands
43	# Warnings about missing optional files or user code changed to informative messages
44	# Removed parameter file check
45	#
46	# 1755 2016-02-22 13:53:39Z maronga
47	# Minor bugfix to last commit
48	#
49	# 1753 2016-02-22 13:49:49Z maronga
50	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
51	#
52	# 1622 2015-07-20 06:21:36Z heinze
53	# bugfix for Mistral (lcbullhh)
54	#
55	# 1621 2015-07-17 11:39:33Z heinze
56	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
57	#
58	# 1609 2015-07-03 15:37:58Z maronga
59	# Modified the random number of the temporary working directory to match the
60	# queuing system number on HLRN-III (lccray*).
61	#
62	# 1604 2015-06-23 15:48:03Z suehring
63	# Enable coupled runs for lcmuk
64	#
65	# 1598 2015-05-29 06:45:40Z raasch
66	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
67	#
68	# 1549 2015-01-30 14:26:16Z suehring
69	# Enable interactive debug sessions with allinea debugger
70	#
71	# 1547 2015-01-29 15:09:12Z witha
72	# adjustments for ForWind computing cluster (lcflow)
73	#
74	# 1491 2014-11-12 08:12:57Z heinze
75	# correct setting of batch_job allowed for ibm-machines
76	#
77	# 1468 2014-09-24 14:06:57Z maronga
78	# Typo removed (addres->address)
79	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
80	# Added support for restart runs (remote) for lcxe6
81	#
82	# 1442 2014-07-28 07:09:10Z raasch
83	# default queues for HLRN-III (lccrayb/lccrayh) defined
84	#
85	# 1422 2014-07-02 10:01:25Z kanani
86	# automatic restarts enabled for lccrayb,
87	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
88	#
89	# 1420 2014-06-10 06:24:14Z raasch
90	# -j1 option added to aprung command for lccrayf (CSC)
91	#
92	# 1402 2014-05-09 14:25:13Z raasch
93	# batch_job added to envpar-NAMELIST
94	#
95	# 1357 2014-04-11 15:02:03Z witha
96	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
97	# possible)
98	#
99	# 1320 2014-03-20 08:40:49Z raasch
100	# check namelist file set false by default
101	#
102	# 1304 2014-03-12 10:29:42Z raasch
103	# ulimit option changed from -Ss to -s
104	#
105	# bugfix: missing "fi" in r1289
106	#
107	# 1289 2014-03-04 07:12:34Z raasch
108	# comments translated to English
109	# necriam-, fimm-, ibmy-, and sgi-specific code removed
110	# export of variables for palm and interpret_config removed
111	#
112	# 1281 2014-02-01 07:55:49Z raasch
113	# rsync-copy restricted to Cray machines, since command is unavailable on some
114	# other systems
115	#
116	# 1279 2014-01-28 12:10:14Z raasch
117	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
118	# in order to remove annoying restrictions concerning the number of processors which
119	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
120	# restriction, one of the nodes will be filled with less than the given number of
121	# tasks per node. A respective warning is given.
122	#
123	# 1274 2014-01-09 13:14:54Z heinze
124	# adjustments for lccrayh
125	#
126	# 1272 2014-01-08 10:19:32Z witha
127	# small adjustment for lcflow
128	#
129	# 1270 2013-12-16 11:05:01Z fricke
130	# call of combine_plot_fields adjusted for lccrayb/lccrayh
131	#
132	# 1255 2013-11-07 14:43:35Z raasch
133	# further adjustments for lccrayb remote access
134	#
135	# 1241 2013-10-30 11:36:58Z heinze
136	# Enable use of nudging input and input of large scale forcing from
137	# external files
138	#
139	# 1229 2013-09-20 06:55:19Z raasch
140	# further adjustments for lccrayb
141	#
142	# 1224 2013-09-16 07:27:23Z raasch
143	# first adjustments for lccrayb
144	#
145	# 1210 2013-08-14 10:58:20Z raasch
146	# fftw support added
147	#
148	# 1201 2013-07-10 16:17:59Z witha
149	# adjustments for Forwind cluster (lcflow)
150	#
151	# 1199 2013-07-05 14:52:22Z raasch
152	# adjustments for CSC Helsinki (lccrayf),
153	# executables for batch jobs can be created in advance, in order to avoid calling
154	# the compiler within the batch job (only works if batch jobs are submitted on
155	# local host)
156	#
157	# 1190 2013-06-25 09:39:21Z heinze
158	# enable use of automatic restarts for ibmh
159	# use of cluster/express queue enabled (ibmh)
160	#
161	# 1124 2013-04-09 15:46:52Z raasch
162	# variable "memory" is exported via typeset option -x, because otherwise an unknown
163	# side effect may lead to data loss while getopts is reading the script-option arguments
164	#
165	# 1122 2013-04-09 08:37:16Z heinze
166	# Bugfix: change type of variable last_char
167	#
168	# 1119 2013-04-05 15:11:19Z raasch
169	# Bugfix for setting -T option for subjob
170	#
171	# 1108 2013-03-05 07:03:32Z raasch
172	# bugfix for coupled runs on lckyut/lckyuh
173	#
174	# 1106 2013-03-04 05:31:38Z raasch
175	# --stdin argument for mpiexec on lckyuh
176	# -y and -Y settings output to header
177	#
178	# 1103 2013-02-20 02:15:53Z raasch
179	# default script runs again under ksh, because of unsolved problems with read
180	# from stdin: when bash script is called from a ksh, message "read error: 0:
181	# Resource temporarily unavailable" appears and script does not stop,
182	# further bash compatibility adjustments,
183	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
184	# on lckyuh, but mrun does not terminate and issues a warning instead
185	#
186	# 1101 2013-02-17 10:20:21Z raasch
187	# script now running under bash instead of ksh, which required small adjustments
188	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
189	# read from stdin),
190	# cross compilername on lckyuh compute nodes replaced by real compiler name
191	#
192	# 1099 2013-02-10 01:47:43Z raasch
193	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
194	# and for Forwind cluster (lcflow)
195	# small further adjustments for lckyut
196	#
197	# 1094 2013-02-03 01:52:12Z raasch
198	# explicit ssh/scp port can be set in config file with environment variable
199	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
200	# decalpha parts (yonsei) removed
201	#
202	# 2013-02-02 07:06:13Z raasch
203	# adjustments for Kyushu-University computing center (lckyut - tatara)
204	#
205	# 1083 2013-01-04 10:22:09Z maronga
206	# bugfix in parameter file check (read %cpp_options was missing)
207	#
208	# 1069 2012-11-28 16:18:43Z maronga
209	# bugfix: coupling mode was always set to mpi2, typos removed
210	#
211	# 1058 2012-11-21 07:00:35Z raasch
212	# Intel inspector (inspxe) is given the number of PEs instead of the number of
213	# nodes
214	#
215	# 1046 2012-11-09 14:38:45Z maronga
216	# code put under GPL (PALM 3.9)
217	#
218	# 21/03/94 - Siggi - first version finished
219	# 03/03/94 - Siggi - script development started
220	#
221	#--------------------------------------------------------------------------------#
222	# mrun - script for running PALM jobs
223	#--------------------------------------------------------------------------------#
224
225
226
227	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
228
229	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
230	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
231	# (TOO MANY ARGUMENTS - PROBLEM)
232	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
233
234	AddFilenames=""
235	additional_conditions=""
236	add_source_path=""
237	afname=""
238	archive_save=true
239	archive_system=none
240	check_namelist_files=false
241	combine_plot_fields=true
242	compiler_name=""
243	cond1=""
244	cond2=""
245	config_file=.mrun.config
246	coupled_dist=""
247	coupled_mode="mpi1"
248	cpp_opts=""
249	cpp_options=""
250	cpumax=0
251	cpurest=0
252	create_executable_for_batch=false
253	delete_temporary_catalog=true
254	do_batch=false
255	do_compile=true
256	do_remote=false
257	do_stagein=true
258	do_stageout=true
259	do_trace=false
260	email_notification="none"
261	exclude=""
262	executable=""
263	execute_command="none"
264	execution_error=false
265	fftw_inc=""
266	fftw_lib=""
267	fftw_support=false
268	fname=test
269	fromhost=""
270	global_revision=""
271	group_number=none
272	host=""
273	host_file=""
274	hp=""
275	ignore_archive_error=false
276	input_list=""
277	interpreted_config_file=""
278	job_catalog="~/job_queue"
279	job_on_file=""
280	keep_data_from_previous_run=false
281	link_local_input=false
282	link_local_output=false
283	localhost_realname=$(hostname)
284	local_dvrserver_running=.FALSE.
285	locat=normal
286	mainprog=""
287	makefile=""
288	max_par_io_str=""
289	mc=$0
290	while [[ $(echo $mc \| grep -c "/") != 0 ]]
291	do
292	mc=`echo $mc \| cut -f2- -d"/"`
293	done
294	module_calls=""
295	mrun_script_name=$mc
296	netcdf_inc=""
297	netcdf_lib=""
298	netcdf_support=false
299	node_usage=default
300	numprocs=""
301	numprocs_atmos=0
302	numprocs_ocean=0
303	OOPT=""
304	openmp=false
305	output_list=""
306	package_list=""
307	queue=none
308	read_from_config=""
309	restart_run=false
310	if [[ `hostname` = rte10 ]]
311	then
312	return_address=133.5.185.60
313	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
314	elif [[ `hostname` = climate0 ]]
315	then
316	return_address=165.132.26.68
317	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
318	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
319	then
320	return_address="schultzl-Latitude-E6540"
321	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
322	elif [[ `hostname` = urban00 ]]
323	then
324	return_address=147.46.30.151
325	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
326	else
327	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
328	fi
329	return_password=""
330	return_username=$LOGNAME
331	remotecall=false
332	remote_username=""
333	run_coupled_model=false
334	run_mode=""
335	store_on_archive_system=false
336	dashes=" ----------------------------------------------------------------------------"
337	silent=false
338	source_list=""
339	source_path=SOURCE
340	tasks_per_node=""
341	threads_per_task=1
342	tmpcreate=false
343	tmp_data_catalog=""
344	transfer_problems=false
345	usern=$LOGNAME
346	use_openmp=false
347	version="MRUN 2.1 Rev$Rev: 1941 $"
348	working_directory=`pwd`
349	TOPT=""
350	XOPT=""
351	zeit=$( date \| cut -c 12-19 )
352
353	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
354	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
355	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
356	# SCRIPT-OPTION ARGUMENTS
357	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
358
359	# ERROR HANDLING IN CASE OF EXIT
360	trap 'rm -rf $working_directory/tmp_mrun
361	if [[ $locat != normal && $locat != control_c ]]
362	then
363
364	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
365	(( i = 0 ))
366	while (( i < iec ))
367	do
368	(( i = i + 1 ))
369	printf "\n *** Execution of ERROR-command:\n"
370	printf " >>> ${err_command[$i]}\n"
371	eval ${err_command[$i]}
372	done
373	if [[ -n $interpreted_config_file ]]
374	then
375	rm -rf $interpreted_config_file
376	fi
377	if [[ -n .mrun_environment ]]
378	then
379	rm -rf .mrun_environment
380	fi
381	if [[ $tmpcreate = true ]]
382	then
383	printf "\n *** Contents of \"$TEMPDIR\":\n"
384	ls -al; cd
385	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
386	fi
387	if [[ "$dvrserver_id" != "" ]]
388	then
389	echo "+++ killing dvrserver_id=$dvrserver_id"
390	kill $dvrserver_id
391	fi
392	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
393	then
394	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
395	fi
396	printf "\n\n+++ MRUN killed \n\n"
397	elif [[ $locat != control_c ]]
398	then
399	printf "\n\n --> all actions finished\n\n"
400	printf " Bye, bye $usern !!\n\n"
401	fi' exit
402
403
404	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
405	trap 'rm -rf $working_directory/tmp_mrun
406	rm -rf $working_directory/tmp_check_namelist_files
407	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
408	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
409	then
410	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
411	fi
412	if [[ "$dvrserver_id" != "" ]]
413	then
414	echo "+++ killing dvrserver_id=$dvrserver_id"
415	kill $dvrserver_id
416	fi
417	printf "\n+++ MRUN killed by \"^C\" \n\n"
418	locat=control_c
419	exit
420	' 2
421
422
423	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
424	# BEEN SET
425	if [[ "$PALM_BIN" = "" ]]
426	then
427	printf "\n +++ environment variable PALM_BIN has not been set"
428	printf "\n please set it to the directory where the PALM scripts are located"
429	locat=palm_bin; exit
430	fi
431	export PATH=$PALM_BIN:$PATH
432
433
434
435	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
436	# WHICH WILL BE USED TO START RESTART-JOBS
437	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
438	do
439	case $option in
440	(a) afname=$OPTARG;;
441	(A) store_on_archive_system=true; mc="$mc -A";;
442	(b) do_batch=true; mc="$mc -b";;
443	(B) delete_temporary_catalog=false; mc="$mc -B";;
444	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
445	(C) restart_run=true; mc="$mc -C";;
446	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
447	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
448	(F) job_on_file="-D"; mc="$mc -F";;
449	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
450	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
451	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
452	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
453	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
454	(I) ignore_archive_error=true; mc="$mc -I";;
455	(k) keep_data_from_previous_run=true; mc="$mc -k";;
456	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
457	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
458	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
459	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
460	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
461	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
462	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
463	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
464	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
465	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
466	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
467	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
468	(S) read_from_config=false; mc="$mc -S";;
469	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
470	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
471	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
472	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
473	(v) silent=true; mc="$mc -v";;
474	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
475	(x) do_trace=true;set -x; mc="$mc -x";;
476	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
477	(y) ocean_file_appendix=true; mc="$mc -y";;
478	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
479	(z) check_namelist_files=false; mc="$mc -z";;
480	(Z) combine_plot_fields=false; mc="$mc -Z";;
481	(\?) printf "\n +++ unknown option $OPTARG \n"
482	printf "\n --> type \"$0 ?\" for available options \n"
483	locat=parameter;exit;;
484	esac
485	done
486
487
488	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
489	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
490	(( to_shift = $OPTIND - 1 ))
491	shift $to_shift
492
493	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
494	if [[ "$1" = "?" ]]
495	then
496	(printf "\n *** mrun can be called as follows:\n"
497	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"
498	printf "\n Description of available options:\n"
499	printf "\n Option Description Default-Value"
500	printf "\n -a base name of input files equiv. -d"
501	printf "\n -A archiving when using file-attribute fl"
502	printf "\n -b batch-job on local machine ---"
503	printf "\n -B do not delete temporary directory at end ---"
504	printf "\n -c configuration file .mrun.config"
505	printf "\n -d base name of files attached to program test"
506	printf "\n -D preprocessor(cpp)-directives \"\" "
507	printf "\n -F create remote job file only ---"
508	printf "\n -h execution host $localhost_realname"
509	printf "\n -i INPUT control list \"\" "
510	printf "\n -I archiving errors of previous batch-jobs"
511	printf "\n will be ignored"
512	printf "\n -k keep data from previous run"
513	printf "\n -K additional conditions for controling"
514	printf "\n usage of conditional code and"
515	printf "\n env-variables in configuration file \"\" "
516	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
517	printf "\n -M Makefile name Makefile"
518	printf "\n -n node usage (shared/not_shared) depending on -h"
519	printf "\n -o OUTPUT control list \"\" "
520	printf "\n -O threads per openMP task ---"
521	printf "\n -p software package list \"\" "
522	printf "\n -q queue \"$queue\" "
523	printf "\n -r run control list (combines -i -o) \"\" "
524	printf "\n -s filenames of routines to be compiled \"\" "
525	printf "\n must end with .f, .f90, .F, or .c !"
526	printf "\n use \"..\" for more than one file and wildcards"
527	printf "\n -s LM compiles all locally modified files"
528	printf "\n -S config file interpreted by shellscript ---"
529	printf "\n -t allowed cpu-time in seconds (batch) 0"
530	printf "\n -T tasks per node depending on -h"
531	printf "\n -u username on remote machine \"\" "
532	printf "\n -v no prompt for confirmation ---"
533	printf "\n -w maximum parallel io streams as given by -X"
534	printf "\n -x tracing of mrun for debug purposes ---"
535	printf "\n -X # of processors (on parallel machines) 1"
536	printf "\n -y add appendix \"_O\" to all local output"
537	printf "\n files (ocean precursor runs followed by"
538	printf "\n coupled atmosphere-ocean runs) ---"
539	printf "\n -Y run coupled model, \"#1 #2\" with"
540	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
541	printf "\n -Z skip combine_plot_fields at the end of "
542	printf "\n the simulation ---"
543	printf "\n "
544	printf "\n Possible values of positional parameter <modus>:"
545	printf "\n \"?\" - this outline \n\n") \| more
546	exit
547	elif [[ "$1" != "" ]]
548	then
549	printf "\n +++ positional parameter $1 unknown \n"
550	locat=parameter; exit
551	fi
552
553
554
555	# SHORT STARTING MESSAGE
556	printf "\n*** $version "
557	printf "\n will be executed. Please wait ..."
558
559
560
561	# CHECK, IF CONFIGURATION FILE EXISTS
562	if [[ ! -f $config_file ]]
563	then
564	printf "\n\n +++ configuration file: "
565	printf "\n $config_file"
566	printf "\n does not exist"
567	locat=connect; exit
568	fi
569
570
571	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
572	line=""
573	grep "%host_identifier" $config_file > tmp_mrun
574	while read line
575	do
576	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
577	then
578	HOSTNAME=`echo $line \| cut -d" " -s -f2`
579	host_identifier=`echo $line \| cut -d" " -s -f3`
580	if [[ $localhost_realname = $HOSTNAME ]]
581	then
582	localhost=$host_identifier
583	break
584	fi
585	fi
586	done < tmp_mrun
587
588	if [[ "$localhost" = "" ]]
589	then
590	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
591	printf "\n for local host \"$localhost_realname\"."
592	printf "\n Please add line"
593	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
594	printf "\n to the configuration file."
595	locat=localhost; exit
596	fi
597
598
599	# SET HOST-SPECIFIC VARIABLES
600	case $localhost_realname in
601	(r1\|r2\|h01\|b01) archive_system=tivoli;;
602	(cs*) archive_system=ut;;
603	esac
604
605
606	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
607	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
608	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
609	[[ "$afname" = "" ]] && afname=$fname
610
611
612	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
613	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
614	# STATEMENTS IN THE CONFIGURATION FILE
615	if [[ "$run_mode" != "" ]]
616	then
617	input_list="$input_list $run_mode"
618	output_list="$output_list $run_mode"
619	fi
620
621
622	# ??? is this (and the respective option -H) really required ???
623	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
624	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
625	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
626	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
627	if [[ "$fromhost" = "" ]]
628	then
629	fromhost=$localhost
630	fi
631
632
633	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
634	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
635	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
636	# TO BE SUBMITTED (I.E. do_batch=true)
637	if [[ -n $host && "$host" != $localhost ]]
638	then
639	do_batch=true
640	do_remote=true
641	case $host in
642	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
643	(*) printf "\n"
644	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
645	printf "\n is not available"
646	locat=nqs; (( iec = 0 )); exit;;
647	esac
648	else
649	host=$localhost
650	fi
651
652
653	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
654	if [[ -n $additional_conditions ]]
655	then
656	cond1=`echo $additional_conditions \| cut -d" " -f1`
657	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
658	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
659	if [[ -n $dummy ]]
660	then
661	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
662	locat=options; exit
663	fi
664	block=_$cond1
665	[[ -n $cond2 ]] && block=${block}_$cond2
666	fi
667
668
669	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
670	if [[ $run_coupled_model = true ]]
671	then
672
673	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
674	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
675
676	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
677	then
678
679	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
680	printf "\n PEs (total) : $numprocs"
681	printf "\n PEs (atmosphere): $numprocs_atmos"
682	printf "\n PEs (ocean) : $numprocs_ocean"
683	locat=coupling; exit
684
685	fi
686
687
688	# GET coupled_mode FROM THE CONFIG FILE
689	line=""
690	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
691	while read line
692	do
693	echo line=\"$line\"
694	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
695	then
696	coupled_mode="mpi2"
697	fi
698	done < tmp_mrun
699
700	fi
701
702	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
703	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
704	then
705	if [[ $ignore_archive_error = false ]]
706	then
707	printf "\n +++ data archiving of previous run failed"
708	printf "\n see directory \~/job_queue on remote machine"
709	locat=archive; exit
710	else
711	printf "\n +++ warning: data archiving in a previous run failed"
712	printf "\n MRUN continues, trying to get backup copy"
713	fi
714	fi
715
716
717	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
718	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
719	mrun_memory=$memory
720	mrun_group_number=$group_number
721	mrun_cpumax=$cpumax
722	mrun_numprocs=$numprocs
723
724
725	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
726	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
727	if [[ "$read_from_config" = false ]]
728	then
729	[[ $silent = false ]] && printf "\n Reading the configuration file... "
730
731	# READ THE CONFIGURATION FILE LINE BY LINE
732	while read zeile
733	do
734	[[ $silent = false ]] && printf "."
735
736
737	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
738	eval zeile=\"$zeile\"
739
740
741	# INTERPRET THE LINE
742	if [[ "$(echo $zeile)" = "" ]]
743	then
744	# EMPTY LINE, NO ACTION
745	continue
746
747	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
748	then
749
750	# LINE IS A COMMENT LINE
751	true
752
753	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
754	then
755
756	# LINE DEFINES AN ENVIRONMENT-VARIABLE
757	zeile=$(echo $zeile \| cut -c2-)
758	var=`echo $zeile \| cut -d" " -f1`
759	value=`echo $zeile \| cut -d" " -s -f2`
760	for_host=`echo $zeile \| cut -d" " -s -f3`
761	for_cond1=`echo $zeile \| cut -d" " -s -f4`
762	for_cond2=`echo $zeile \| cut -d" " -s -f5`
763
764	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
765	then
766
767	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
768	# "::" IS REPLACED BY ":".
769	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
770
771
772	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
773	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
774	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
775	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
776	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
777	# CONFIGURATION-FILE.
778	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
779	then
780	eval $var=\$value
781
782	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
783	if [[ $do_trace = true ]]
784	then
785	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
786	fi
787	fi
788
789	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
790	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
791	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
792	# MUST HAVE TO BE STARTED
793	if [[ $var = host ]]
794	then
795	if [[ -n $host && "$host" != $localhost ]]
796	then
797	do_batch=true
798	do_remote=true
799	case $host in
800	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
801	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
802	printf "\n is not available"
803	locat=nqs; exit;;
804	esac
805	else
806	host=$localhost
807	fi
808	fi
809
810	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
811	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
812	# BY MRUN (E.G. subjob)
813	export $var
814	fi
815
816
817
818
819	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
820	then
821
822	# LINE DEFINES ERROR-COMMAND
823	(( iec = iec + 1 ))
824	zeile=$(echo $zeile \| cut -c4-)
825	err_command[$iec]="$zeile"
826
827	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
828	then
829
830	# LINE DEFINES INPUT-COMMAND
831	(( iic = iic + 1 ))
832	zeile=$(echo $zeile \| cut -c4-)
833	in_command[$iic]="$zeile"
834
835	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
836	then
837
838	# LINE DEFINES OUTPUT-COMMAND
839	(( ioc = ioc + 1 ))
840	zeile=$(echo $zeile \| cut -c4-)
841	out_command[$ioc]="$zeile"
842
843	else
844
845	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
846	# s2a: in/out - field
847	# s2b: loc - field (optional)
848	# s2c: tr/ar - field (optional)
849	s1=`echo $zeile \| cut -d" " -f1`
850	s2=`echo $zeile \| cut -d" " -s -f2`
851	s2a=$(echo $s2 \| cut -d":" -f1)
852	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
853	then
854	s2b=""
855	s2c=""
856	else
857	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
858	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
859	fi
860	s3=`echo $zeile \| cut -d" " -f3`
861	s4=`echo $zeile \| cut -d" " -s -f4`
862	s5=`echo $zeile \| cut -d" " -s -f5`
863	s6=`echo $zeile \| cut -d" " -s -f6`
864
865
866	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
867	# INPUT- OR OUTPUT-LIST.
868	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
869	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
870	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
871	# IS NOT CHECKED AND STORED.
872	IFSALT="$IFS"; IFS="$IFS:"
873	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
874	then
875	found=false
876	for actual in $input_list
877	do
878	for formal in $s3
879	do
880	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
881	done
882	done
883	if [[ $found = true ]]
884	then
885	(( iin = iin + 1 ))
886	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
887	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
888	extin[$iin]=$s6
889	fi
890	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
891	then
892	found=false
893	for actual in $output_list
894	do
895	for formal in $s3
896	do
897	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
898	done
899	done
900	if [[ $found = true ]]
901	then
902	(( iout = iout + 1 ))
903	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
904	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
905	fi
906	elif [[ "$s2a" != in && "$s2a" != out ]]
907	then
908	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
909	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
910	locat=connect; exit
911	fi
912	IFS="$IFSALT"
913	fi
914	done < $config_file
915
916	else
917
918	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
919	[[ $silent = false ]] && printf "..."
920	interpreted_config_file=.icf.$RANDOM
921
922
923
924	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
925	cat > .mrun_environment << %%END%%
926	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
927	config_file = '$config_file', do_remote = '$do_remote',
928	do_trace = '$do_trace', host = '$host',
929	input_list = '$input_list', icf = '$interpreted_config_file',
930	localhost = '$localhost', output_list = '$output_list' /
931
932	%%END%%
933
934	if [[ "$host" != $localhost ]]
935	then
936
937	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
938	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
939	if [[ $? != 0 ]]
940	then
941	printf "\n\n +++ no interpret_config found"
942	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
943	locat=interpret_config; exit
944	fi
945	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
946	$interpret_config_executable
947
948	else
949
950	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
951	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
952	then
953	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
954	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
955	locat=interpret_config; exit
956	else
957	interpret_config${block}.x
958	fi
959
960	fi
961	rm .mrun_environment
962
963
964	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
965	chmod u+x $interpreted_config_file
966	export PATH=$PATH:.
967	. $interpreted_config_file
968	rm $interpreted_config_file
969
970	fi
971
972
973	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
974	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
975	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
976	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
977	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
978	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
979	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
980
981
982	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
983	# FOR SOURCE-FILES TO BE COMPILED.
984	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
985	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
986	if [[ "$SOURCES_COMPLETE" = "" ]]
987	then
988
989	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
990	# HAS BEEN DEFINED
991	source_path=""
992	line=""
993	grep "%source_path" $config_file > tmp_mrun
994	while read line
995	do
996	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
997	then
998	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
999	then
1000	global_source_path=`echo $line \| cut -d" " -f2`
1001	fi
1002	fi
1003	done < tmp_mrun
1004
1005	line=""
1006	found=false
1007	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1008	while read line
1009	do
1010	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1011	then
1012	if [[ $found = true ]]
1013	then
1014	printf "\n\n +++ more than one source path found in configuration file"
1015	printf "\n for local host \"$localhost\" "
1016	locat=source_path; exit
1017	fi
1018	source_path=`echo $line \| cut -d" " -f2`
1019	found=true
1020	fi
1021	done < tmp_mrun
1022	rm tmp_mrun
1023
1024	if [[ "$source_path" = "" ]]
1025	then
1026	if [[ "$global_source_path" != "" ]]
1027	then
1028	source_path=$global_source_path
1029	else
1030	printf "\n\n +++ no source path found in configuration file"
1031	printf "\n for local host \"$localhost\" "
1032	locat=source_path; exit
1033	fi
1034	fi
1035	eval source_path=$source_path
1036
1037	if [[ ! -d $source_path ]]
1038	then
1039	printf "\n\n +++ source path \"$source_path\" on local host"
1040	printf "\n \"$localhost\" does not exist"
1041	locat=source_path; exit
1042	fi
1043
1044	fi
1045
1046
1047	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1048	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1049	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1050	then
1051	global_revision=`svnversion $source_path 2>/dev/null`
1052	global_revision="Rev: $global_revision"
1053	fi
1054
1055
1056	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1057	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1058	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1059	if [[ -n $host && "$host" != $localhost ]]
1060	then
1061	do_batch=true
1062	do_remote=true
1063	case $host in
1064	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1065	(*) printf "\n"
1066	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1067	printf "\n is not available"
1068	locat=nqs; (( iec = 0 )); exit;;
1069	esac
1070	else
1071	host=$localhost
1072	fi
1073
1074
1075
1076	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1077	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1078	then
1079
1080	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1081	if [[ ! -n $numprocs ]]
1082	then
1083	printf "\n"
1084	printf "\n +++ option \"-K parallel\" requires additional specification"
1085	printf "\n of the number of processors to be used by"
1086	printf "\n mrun-option \"-X\" or by environment-variable"
1087	printf "\n \"numprocs\" in the configuration file"
1088	locat=numprocs; (( iec = 0 )); exit
1089	fi
1090
1091	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1092	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1093	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1094	then
1095	printf "\n"
1096	printf "\n +++ option \"-T\" (tasks per node) is missing"
1097	printf "\n set -T option or define tasks_per_node in the config file"
1098	locat=tasks_per_node; (( iec = 0 )); exit
1099	fi
1100
1101	if (( numprocs < tasks_per_node ))
1102	then
1103	printf "\n"
1104	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1105	printf "\n given values: -T $tasks_per_node -X $numprocs"
1106	locat=tasks_per_node; (( iec = 0 )); exit
1107	fi
1108
1109	if [[ $host != lcflow && $host != lcxt5m ]]
1110	then
1111	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1112	(( ival = $tasks_per_node ))
1113	(( pes = numprocs ))
1114	(( ii = pes / ival ))
1115	(( remaining_pes = pes - ii * ival ))
1116	if (( remaining_pes > 0 ))
1117	then
1118	printf "\n"
1119	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1120	printf "\n divisor of the total number of processors (option \"-X\")"
1121	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1122	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1123	(( nodes = nodes + 1 ))
1124	fi
1125	fi
1126
1127
1128	# SETTINGS FOR SUBJOB-COMMAND
1129	OOPT="-O $threads_per_task"
1130
1131	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1132	if [[ "$tasks_per_node" != "" ]]
1133	then
1134	TOPT="-T $tasks_per_node"
1135	fi
1136
1137	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1138	if [[ $node_usage = default ]]
1139	then
1140	if [[ $host = ibms ]]
1141	then
1142	node_usage=shared
1143	else
1144	node_usage=not_shared
1145	fi
1146	fi
1147
1148	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1149	then
1150	printf "\n"
1151	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1152	printf "\n \"shared\" or \"not_shared\""
1153	locat=tasks_per_node; (( iec = 0 )); exit
1154	fi
1155
1156	fi
1157
1158	# CHECK IF HOSTFILE EXISTS
1159	if [[ -n $hostfile ]]
1160	then
1161	if [[ ! -f $hostfile ]]
1162	then
1163	printf "\n"
1164	printf "\n +++ hostfile \"$hostfile\" does not exist"
1165	locat=hostfile; exit
1166	fi
1167	fi
1168
1169
1170	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1171	if [[ "$maximum_parallel_io_streams" = "" ]]
1172	then
1173	maximum_parallel_io_streams=$numprocs
1174	fi
1175
1176
1177	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1178	if [[ "$scp_port" != "" ]]
1179	then
1180	PORTOPT="-P $scp_port"
1181	SSH_PORTOPT="-p $scp_port"
1182	fi
1183
1184
1185	# SET DEFAULT-QUEUE, IF NOT GIVEN
1186	if [[ $queue = none ]]
1187	then
1188	case $host in
1189	(ibmh) queue=cluster;;
1190	(ibmkisti) queue=class.32plus;;
1191	(lcbullhh) queue=compute;;
1192	(lccrayb) queue=mpp1q;;
1193	(lccrayh) queue=mpp1q;;
1194	(lckiaps) queue=normal;;
1195	(lckyoto) queue=ph;;
1196	(lckyuh) queue=fx-single;;
1197	(lckyut) queue=cx-single;;
1198	(lctit) queue=S;;
1199	(nech) queue=none;;
1200	(unics) queue=unics;;
1201	esac
1202	fi
1203
1204
1205	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1206	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1207	(( i = 0 ))
1208	while (( i < iin ))
1209	do
1210	(( i = i + 1 ))
1211	(( maxcycle = 0 ))
1212
1213	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1214	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1215	if [[ "${actionin[$i]}" = di ]]
1216	then
1217	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1218	# HOST ONLY
1219	eval filename=${pathin[$i]}/${endin[$i]}
1220	else
1221	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1222	# HOST ONLY
1223	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1224	fi
1225	eval pathname=${pathin[$i]}
1226
1227	# CHECK IF FILE EXISTS
1228	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1229	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1230	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1231	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1232	then
1233
1234	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1235	if [[ "${transin[$i]}" != "locopt" ]]
1236	then
1237	printf "\n\n +++ INPUT-file: "
1238	if [[ "${extin[$i]}" = "" ]]
1239	then
1240	printf "\n $filename"
1241	else
1242	printf "\n $filename.${extin[$i]}"
1243	fi
1244	printf "\n does not exist\n"
1245	locat=input; exit
1246	else
1247	transin[$i]="unavailable"
1248	fi
1249	else
1250
1251	# DETERMINE THE FILE'S CYCLE NUMBER
1252	ls -1 -d $filename > filelist 2>/dev/null
1253	ls -1 -d $filename.* >> filelist 2>/dev/null
1254	while read zeile
1255	do
1256	cycle=$(echo $zeile \| cut -f2 -d".")
1257	if [[ "$cycle" = "$zeile" ]]
1258	then
1259	(( icycle = 0 ))
1260	elif [[ "$cycle" = "${extin[$i]}" ]]
1261	then
1262	(( icycle = 0 ))
1263	else
1264	(( icycle = $cycle ))
1265	fi
1266	if (( icycle > maxcycle ))
1267	then
1268	(( maxcycle = icycle ))
1269	file_to_be_used=$zeile
1270	fi
1271	done <filelist
1272	rm filelist
1273
1274	# APPEND CYCLE NUMBER TO FILENAME
1275	if (( maxcycle > 0 ))
1276	then
1277	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1278	then
1279	filename=${filename}.$maxcycle.${extin[$i]}
1280	else
1281	filename=${filename}.$maxcycle
1282	fi
1283	else
1284	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1285	then
1286	filename=${filename}.${extin[$i]}
1287	fi
1288	fi
1289
1290	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1291	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1292	absnamein[$i]=$filename
1293	if (( maxcycle > 0 ))
1294	then
1295	if [[ "${actionin[$i]}" = di ]]
1296	then
1297	frelin[$i]=${endin[$i]}.$maxcycle
1298	else
1299	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1300	fi
1301	else
1302	if [[ "${actionin[$i]}" = di ]]
1303	then
1304	frelin[$i]=${endin[$i]}
1305	else
1306	frelin[$i]=${afname}${endin[$i]}
1307	fi
1308	fi
1309
1310	fi
1311	done
1312
1313	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1314	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1315	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1316	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1317	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1318	# REMOTE HOST)
1319	(( i = 0 ))
1320	while (( i < iout ))
1321	do
1322	(( i = i + 1 ))
1323	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1324	then
1325	if [[ "${actionout[$i]}" = tr ]]
1326	then
1327	actionout[$i]=""
1328	elif [[ "${actionout[$i]}" = trpe ]]
1329	then
1330	actionout[$i]=pe
1331	elif [[ "${actionout[$i]}" = tra ]]
1332	then
1333	actionout[$i]=a
1334	fi
1335	(( maxcycle = 0 ))
1336	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1337	eval catalogname=${pathout[$i]}
1338	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1339	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1340	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1341	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1342	then
1343
1344	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1345	if cat /dev/null > $filename
1346	then
1347	rm $filename
1348	else
1349
1350	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1351	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1352	if [[ ! -d $catalogname ]]
1353	then
1354	if mkdir -p $catalogname
1355	then
1356	printf "\n\n *** directory:"
1357	printf "\n $catalogname"
1358	printf "\n was created\n"
1359	else
1360	printf "\n\n +++ OUTPUT-file:"
1361	printf "\n $filename"
1362	printf "\n cannot be created, because directory does not exist"
1363	printf "\n and cannot be created either"
1364	printf "\n"
1365	locat=output ; exit
1366	fi 2>/dev/null
1367	else
1368	printf "\n\n +++ OUTPUT-file:"
1369	printf "\n $filename"
1370	printf "\n cannot be created, although directory exists"
1371	printf "\n"
1372	locat=output ; exit
1373	fi
1374	fi 2>/dev/null
1375	else
1376
1377	# DETERMINE THE CYCLE NUMBER
1378	ls -1 -d $filename > filelist 2>/dev/null
1379	ls -1 -d $filename.* >> filelist 2>/dev/null
1380	while read zeile
1381	do
1382	cycle=$(echo $zeile \| cut -f2 -d".")
1383	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1384	then
1385	(( icycle = 1 ))
1386	else
1387	(( icycle = $cycle + 1 ))
1388	fi
1389	if (( icycle > maxcycle ))
1390	then
1391	(( maxcycle = icycle ))
1392	fi
1393	done <filelist
1394	rm filelist
1395	fi
1396
1397	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1398	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1399	if [[ "${actionout[$i]}" != a ]]
1400	then
1401	if (( maxcycle > 0 ))
1402	then
1403	filename=${filename}.$maxcycle
1404	if cat /dev/null > $filename
1405	then
1406	rm $filename
1407	else
1408	printf "\n +++ OUTPUT-file:"
1409	printf "\n $filename"
1410	printf "\n cannot be created"
1411	locat=output ; exit
1412	fi
1413	fi
1414	else
1415	(( maxcycle = maxcycle - 1 ))
1416	if (( maxcycle > 0 ))
1417	then
1418	filename=${filename}.$maxcycle
1419	fi
1420	fi
1421
1422	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1423	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1424	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1425	pathout[$i]=$filename
1426	if (( maxcycle > 0 ))
1427	then
1428	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1429	else
1430	frelout[$i]=${fname}${endout[$i]}
1431	fi
1432
1433	fi
1434	done
1435
1436
1437	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1438	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1439	then
1440	if [[ "$dvr_inc" = "" ]]
1441	then
1442	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1443	printf "\n This is required for the dvrp_graphics package.\n"
1444	locat=dvr; exit
1445	fi
1446	if [[ "$dvr_lib" = "" ]]
1447	then
1448	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1449	printf "\n This is required for the dvrp_graphics package.\n"
1450	locat=dvr; exit
1451	fi
1452	fi
1453
1454
1455	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1456	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1457	if [[ "$mainprog" = "" && "$executable" = "" ]]
1458	then
1459	printf "\n +++ neither main program nor executable defined"
1460	locat=source; exit
1461	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1462	then
1463	printf "\n +++ main program as well as executable defined"
1464	locat=source; exit
1465	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1466	then
1467	do_compile=false
1468	fi
1469
1470
1471	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1472	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1473	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1474	then
1475	rm -rf SOURCES_FOR_RUN_$fname
1476	mkdir SOURCES_FOR_RUN_$fname
1477	fi
1478
1479
1480	# COLLECT ALL ROUTINES TO BE COMPILED
1481	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1482	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1483	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1484	then
1485
1486	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1487
1488	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1489	then
1490
1491	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1492	source_list=""
1493	cd $source_path
1494
1495
1496	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1497	if [[ ! -d .svn ]]
1498	then
1499	printf "\n\n +++ source directory"
1500	printf "\n \"$source_path\" "
1501	printf "\n is not under control of \"subversion\"."
1502	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1503	fi
1504
1505
1506	# LIST ALL MODIFIED SOURCE CODE FILES
1507	Filenames=""
1508	svn status > tmp_mrun
1509	while read line
1510	do
1511	firstc=`echo $line \| cut -c1`
1512	if [[ $firstc = M \|\| $firstc = "?" ]]
1513	then
1514	Name=`echo "$line" \| cut -c8-`
1515	extension=`echo $Name \| cut -d. -f2`
1516	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1517	then
1518	Filenames="$Filenames "$Name
1519	fi
1520	fi
1521	done < tmp_mrun
1522
1523
1524	# COPY FILES TO SOURCES_FOR_RUN_...
1525	for dateiname in $Filenames
1526	do
1527	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1528	source_list=$source_list"$dateiname "
1529	done
1530
1531	cd - > /dev/null
1532
1533
1534	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1535	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1536	elif [[ "$source_list" != "" && $restart_run != true ]]
1537	then
1538
1539	cd $source_path
1540
1541	for filename in $source_list
1542	do
1543
1544	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1545	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1546	then
1547	printf "\n +++ source code file: $filename"
1548	printf "\n must not contain (\"/\") "
1549	locat=source; exit
1550	fi
1551
1552	if [[ ! -f $filename ]]
1553	then
1554	printf "\n +++ source code file: $filename"
1555	printf "\n does not exist"
1556	locat=source; exit
1557	else
1558	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1559	fi
1560
1561	done
1562
1563	cd - > /dev/null
1564
1565	fi
1566
1567
1568	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1569	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1570	if [[ $restart_run != true ]]
1571	then
1572
1573	if [[ ! -f "$source_path/$mainprog" ]]
1574	then
1575	printf "\n\n +++ main program: $mainprog"
1576	printf "\n does not exist in source directory"
1577	printf "\n \"$source_path\"\n"
1578	locat=source; exit
1579	else
1580	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1581	then
1582	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1583	source_list=${mainprog}" $source_list"
1584	fi
1585	fi
1586	fi
1587
1588
1589	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1590	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1591	if [[ "$restart_run" != true ]]
1592	then
1593	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1594	if [[ ! -f $makefile ]]
1595	then
1596	printf "\n +++ file \"$makefile\" does not exist"
1597	locat=make; exit
1598	else
1599	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1600	fi
1601	fi
1602
1603
1604	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1605	if [[ $restart_run != true && "$add_source_path" != "" ]]
1606	then
1607
1608	# DOES THE DIRECTORY EXIST?
1609	if [[ ! -d $add_source_path ]]
1610	then
1611	printf "\n\n *** INFORMATIVE: additional source code directory"
1612	printf "\n \"$add_source_path\" "
1613	printf "\n does not exist or is not a directory."
1614	printf "\n No source code will be used from this directory!\n"
1615	add_source_path=""
1616	if [[ $silent == false ]]
1617	then
1618	sleep 3
1619	fi
1620	else
1621
1622	cd $add_source_path
1623	found=false
1624
1625	Names=$(ls -1 *.f90 2>&1)
1626	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1627	Names=$(ls -1 *.F90 2>&1)
1628	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1629	Names=$(ls -1 *.F 2>&1)
1630	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1631	Names=$(ls -1 *.f 2>&1)
1632	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1633	Names=$(ls -1 *.c 2>&1)
1634	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1635
1636	cd - > /dev/null
1637	cd SOURCES_FOR_RUN_$fname
1638
1639	# COPY MAKEFILE IF EXISTING
1640	if [[ -f $add_source_path/Makefile ]]
1641	then
1642	printf "\n\n *** user Makefile from directory"
1643	printf "\n \"$add_source_path\" is used \n"
1644	if [[ $silent == false ]]
1645	then
1646	sleep 1
1647	fi
1648	cp $add_source_path/Makefile .
1649	fi
1650
1651	for dateiname in $AddFilenames
1652	do
1653	if [[ -f $dateiname ]]
1654	then
1655	printf "\n +++ source code file \"$dateiname\" found in additional"
1656	printf "\n source code directory \"$add_source_path\" "
1657	printf "\n but was also given with option \"-s\" which means that it should be taken"
1658	printf "\n from directory \"$source_path\"."
1659	locat=source; exit
1660	fi
1661
1662	cp $add_source_path/$dateiname .
1663	source_list="$source_list $dateiname"
1664
1665	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1666	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1667	then
1668	printf "\n\n +++ user file \"$dateiname\" "
1669	printf "\n is not listed in Makefile \n"
1670	locat=source; exit
1671	else
1672
1673	if [[ $found = false ]]
1674	then
1675	found=true
1676	printf "\n\n *** following user file(s) added to the"
1677	printf " files to be translated:\n "
1678	fi
1679	printf "$dateiname "
1680	if [[ $silent == false ]]
1681	then
1682	sleep 0.5
1683	fi
1684
1685	fi
1686	done
1687	[[ $found = true ]] && printf "\n"
1688	cd - > /dev/null
1689	fi
1690	fi
1691
1692
1693	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1694	# TO THE LIST OF FILES TO BE COMPILED
1695	if [[ $restart_run != true && -n $package_list ]]
1696	then
1697
1698	cd $source_path
1699
1700	for package in $package_list
1701	do
1702
1703	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1704
1705	# DETERMINE FILES BELONGING TO THE PACKAGE
1706	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1707	# THE NAME OF THE DIRECTORY
1708	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1709
1710
1711	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1712	# IF THEY ARE NOT ALREADY PART OF THE LIST
1713	for source_list_name in $package_source_list
1714	do
1715	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1716	then
1717
1718	# ONLY TAKE FILES WITH VALID SUFFIX
1719	ending=`echo $source_list_name \| cut -f2 -d.`
1720	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1721	then
1722	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1723	source_list="$source_list $source_list_name"
1724	fi
1725	fi
1726	done
1727	done
1728
1729	cd - > /dev/null
1730	fi
1731
1732	fi # do_compile=true
1733
1734
1735	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1736	# AND SET PRE-PROCESSOR DIRECTIVES
1737	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1738	then
1739
1740	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1741	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1742	then
1743	cpp_options="${cpp_options},-D__ibm=__ibm"
1744	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1745	then
1746	cpp_options="$cpp_options -D__nec"
1747	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1748	then
1749	cpp_options="$cpp_options -D__lc"
1750	else
1751	cpp_options="$cpp_options -D__$localhost"
1752	fi
1753
1754	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1755	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1756	then
1757	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1758	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1759	else
1760	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1761	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1762	fi
1763
1764	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1765	if [[ -n $package_list ]]
1766	then
1767	for package in $package_list
1768	do
1769	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1770	then
1771	if [[ $package != "dvrp_graphics+1PE" ]]
1772	then
1773	cpp_options="${cpp_options},-D__$package=__$package"
1774	else
1775	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1776	export use_seperate_pe_for_dvrp_output=true
1777	fi
1778	else
1779	if [[ $package != "dvrp_graphics+1PE" ]]
1780	then
1781	cpp_options="$cpp_options -D__$package"
1782	else
1783	cpp_options="$cpp_options -D__dvrp_graphics"
1784	export use_seperate_pe_for_dvrp_output=true
1785	fi
1786	fi
1787	done
1788	fi
1789
1790	# SET DIRECTIVES GIVEN BY OPTION -D
1791	if [[ -n $cpp_opts ]]
1792	then
1793	for popts in $cpp_opts
1794	do
1795	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1796	then
1797	cpp_options="${cpp_options},-D__$popts=__$popts"
1798	else
1799	cpp_options="$cpp_options -D__$popts"
1800	fi
1801	done
1802	fi
1803
1804	else
1805
1806
1807	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1808	if [[ $do_remote = false ]]
1809	then
1810	if [[ ! -f $executable ]]
1811	then
1812	printf "\n +++ executable file: $executable"
1813	printf "\n does not exist"
1814	locat=executable; exit
1815	fi
1816	fi
1817	fi
1818
1819
1820	# DETERMINE THE JOB MODE
1821	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1822	then
1823	if [[ "$LOADLBATCH" = yes ]]
1824	then
1825	batch_job=.TRUE.
1826	jobmo=BATCH
1827	else
1828	batch_job=.FALSE.
1829	jobmo=INTERACTIVE
1830	fi
1831	else
1832	if [[ "$ENVIRONMENT" = BATCH ]]
1833	then
1834	batch_job=.TRUE.
1835	jobmo=BATCH
1836	else
1837	batch_job=.FALSE.
1838	jobmo=INTERACTIVE
1839	fi
1840	fi
1841
1842	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1843	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1844	then
1845	printf "\n +++ no interactive runs allowed on host \"$host\" "
1846	printf "\n please submit batch job using mrun option \"-b\" \n"
1847	locat=normal; exit
1848	fi
1849
1850
1851	# CHECK, IF USER DEFINED A COMPILER
1852	if [[ "$compiler_name" = "" ]]
1853	then
1854
1855	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1856	locat=compiler_name; exit
1857
1858	fi
1859
1860
1861	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1862
1863	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1864	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1865	then
1866	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1867	if [[ "$kennung" = "" ]]
1868	then
1869	kennung=$RANDOM
1870	fi
1871	else
1872	kennung=$RANDOM
1873	fi
1874
1875	if [[ "$tmp_user_catalog" = "" ]]
1876	then
1877	if [[ $localhost = ibmh ]]
1878	then
1879	tmp_user_catalog=$SCRATCH
1880	elif [[ $localhost = nech ]]
1881	then
1882	tmp_user_catalog=$WRKSHR
1883	else
1884	tmp_user_catalog=/tmp
1885	fi
1886	fi
1887	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1888
1889
1890	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1891	if [[ "$tmp_data_catalog" = "" ]]
1892	then
1893	if [[ $localhost = nech ]]
1894	then
1895	tmp_data_catalog=$WRKSHR/mrun_restart_data
1896	else
1897	tmp_data_catalog=/tmp/mrun_restart_data
1898	fi
1899	fi
1900
1901
1902	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1903	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1904	then
1905	eval fopts=\"$fopts\"
1906	eval lopts=\"$lopts\"
1907	fi
1908
1909
1910	# DETERMINE COMPILE- AND LINK-OPTIONS
1911	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1912	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1913	XOPT="-X $numprocs"
1914
1915
1916	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1917	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1918	done=false
1919	while [[ $done = false ]]
1920	do
1921	cputime=$cpumax
1922	if (( $cputime == 0 ))
1923	then
1924	if [[ $do_batch = true ]]
1925	then
1926	printf "\n +++ cpu-time is undefined"
1927	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1928	printf "\n >>> "
1929	read cputime 1>/dev/null 2>&1
1930	else
1931	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1932	fi
1933	else
1934	done=true
1935	fi
1936	cpumax=$cputime
1937	done
1938
1939	(( minuten = cputime / 60 ))
1940	(( sekunden = cputime - minuten * 60 ))
1941
1942
1943	# CHECK THE MEMORY DEMAND
1944	if [[ $do_batch = true ]]
1945	then
1946	done=false
1947	while [[ $done = false ]]
1948	do
1949	if (( memory == 0 ))
1950	then
1951	printf "\n +++ memory demand is undefined"
1952	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1953	printf "\n >>> "
1954	read memory 1>/dev/null 2>&1
1955	else
1956	done=true
1957	fi
1958	done
1959	fi
1960
1961
1962	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1963	if [[ $do_remote = true && -z $remote_username ]]
1964	then
1965	while [[ -z $remote_username ]]
1966	do
1967	printf "\n +++ username on remote host \"$host\" is undefined"
1968	printf "\n >>> Please type username:"
1969	printf "\n >>> "
1970	read remote_username
1971	done
1972	mc="$mc -u$remote_username"
1973	fi
1974
1975	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1976	if [[ "$login_init_cmd" != "" ]]
1977	then
1978	export init_cmds="${login_init_cmd};"
1979	fi
1980
1981
1982	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1983	if [[ "$modules" != "" ]]
1984	then
1985	if [[ $host = lctit ]]
1986	then
1987	export module_calls=". $modules"
1988	else
1989	export module_calls="module load ${modules};"
1990	fi
1991	fi
1992
1993	# OUTPUT OF THE MRUN-HEADER
1994	calltime=$(date)
1995	printf "\n"
1996	printf "#------------------------------------------------------------------------# \n"
1997	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1998	printf "\| \| \n"
1999	spalte1="called on:"; spalte2=$localhost_realname
2000	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2001	if [[ $do_remote = true ]]
2002	then
2003	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2004	else
2005	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2006	fi
2007	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2008	if [[ -n $numprocs ]]
2009	then
2010	if [[ $run_coupled_model = false ]]
2011	then
2012	spalte1="number of PEs:"; spalte2=$numprocs
2013	else
2014	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2015	fi
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	fi
2018	if [[ -n $tasks_per_node ]]
2019	then
2020	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	if (( remaining_pes > 0 ))
2023	then
2024	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2026	fi
2027	fi
2028	if [[ $maximum_parallel_io_streams != $numprocs ]]
2029	then
2030	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2031	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2032	fi
2033	if [[ $use_openmp = true ]]
2034	then
2035	spalte1="threads per task:"; spalte2="$threads_per_task"
2036	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2037	fi
2038	printf "\| \| \n"
2039	if [[ $do_compile = true ]]
2040	then
2041	if [[ "$mopts" != "" ]]
2042	then
2043	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	zeile=$(echo "$mopts" \| cut -c46-)
2046	while [[ "$zeile" != "" ]]
2047	do
2048	spalte1=""
2049	spalte2=$(echo "$zeile" \| cut -c-45)
2050	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2051	zeile=$(echo "$zeile" \| cut -c46-)
2052	done
2053	fi
2054
2055	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2056	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2057	zeile=$(echo "$cpp_options" \| cut -c46-)
2058	while [[ "$zeile" != "" ]]
2059	do
2060	spalte1=""
2061	spalte2=$(echo "$zeile" \| cut -c-45)
2062	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2063	zeile=$(echo "$zeile" \| cut -c46-)
2064	done
2065
2066	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2067	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2068	zeile=$(echo "$fopts" \| cut -c46-)
2069	while [[ "$zeile" != "" ]]
2070	do
2071	spalte1=""
2072	spalte2=$(echo "$zeile" \| cut -c-45)
2073	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2074	zeile=$(echo "$zeile" \| cut -c46-)
2075	done
2076
2077	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2079	zeile=$(echo "$lopts" \| cut -c46-)
2080	while [[ "$zeile" != "" ]]
2081	do
2082	spalte1=""
2083	spalte2=$(echo "$zeile" \| cut -c-45)
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085	zeile=$(echo "$zeile" \| cut -c46-)
2086	done
2087
2088	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2090	zeile=$(echo "$modules" \| cut -c46-)
2091	while [[ "$zeile" != "" ]]
2092	do
2093	spalte1=""
2094	spalte2=$(echo "$zeile" \| cut -c-45)
2095	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2096	zeile=$(echo "$zeile" \| cut -c46-)
2097	done
2098
2099	spalte1="main program:"; spalte2=$mainprog
2100	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2101	else
2102	spalte1=executable:; spalte2=$executable
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	fi
2105	printf "\| \| \n"
2106	spalte1="base name of files:"; spalte2=$fname
2107	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2108	if [[ $fname != $afname ]]
2109	then
2110	spalte1="base name of input files:"; spalte2=$afname
2111	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2112	fi
2113	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2114	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2115	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2116	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2117
2118	if [[ "$ocean_file_appendix" = true ]]
2119	then
2120	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2121	fi
2122
2123	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2124	then
2125	spalte1="memory demand / PE":; spalte2="$memory MB"
2126	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2127	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2128	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2129	fi
2130
2131	if [[ $do_compile = true ]]
2132	then
2133	printf "\| \| \n"
2134	printf "\| Files to be compiled: \| \n"
2135	zeile=$source_list
2136	while [[ "$zeile" != "" ]]
2137	do
2138	linestart=$(echo $zeile \| cut -c-70)
2139	printf "\| %-70s \| \n" "$linestart"
2140	zeile=$(echo "$zeile" \| cut -c71-)
2141	done
2142	fi
2143	printf "#------------------------------------------------------------------------#"
2144
2145
2146
2147	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2148	if [[ $do_trace = true ]]
2149	then
2150	(( i = 0 ))
2151	while (( i < iin ))
2152	do
2153	(( i = i + 1 ))
2154	if (( i == 1 ))
2155	then
2156	printf "\n\n >>> INPUT-file assignments:\n"
2157	fi
2158	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2159	done
2160	(( i = 0 ))
2161	while (( i < iout ))
2162	do
2163	(( i = i + 1 ))
2164	if (( i == 1 ))
2165	then
2166	printf "\n\n >>> OUTPUT-file assignments:\n"
2167	fi
2168	printf "\n ${localout[$i]} : ${pathout[$i]}"
2169	done
2170	(( i = 0 ))
2171	while (( i < iic ))
2172	do
2173	(( i = i + 1 ))
2174	if (( i == 1 ))
2175	then
2176	printf "\n\n >>> INPUT-commands:\n"
2177	fi
2178	printf "\n ${in_command[$i]}"
2179	done
2180	(( i = 0 ))
2181	while (( i < ioc ))
2182	do
2183	(( i = i + 1 ))
2184	if (( i == 1 ))
2185	then
2186	printf "\n\n >>> OUTPUT-commands:\n"
2187	fi
2188	printf "\n ${out_command[$i]}"
2189	done
2190	fi
2191
2192	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2193	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2194	then
2195	antwort=dummy
2196	printf "\n\n"
2197	printf " >>> everything o.k. (y/n) ? "
2198	while read antwort
2199	do
2200	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2201	then
2202	printf " >>> everything o.k. (y/n) ? "
2203	else
2204	break
2205	fi
2206	done
2207	if [[ $antwort = n \|\| $antwort = N ]]
2208	then
2209	locat=user_abort; (( iec = 0 )); exit
2210	fi
2211	if [[ $do_batch = true ]]
2212	then
2213	printf " >>> batch-job will be created and submitted"
2214	else
2215	printf " >>> MRUN will now continue to execute on this machine"
2216	fi
2217	fi
2218
2219
2220	# DETERMINE PATH FOR MAKE DEPOSITORY
2221	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2222	then
2223
2224	line=""
2225	grep "%depository_path" $config_file > tmp_mrun
2226	while read line
2227	do
2228	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2229	then
2230	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2231	then
2232	global_depository_path=`echo $line \| cut -d" " -s -f2`
2233	fi
2234	fi
2235	done < tmp_mrun
2236
2237	line=""
2238	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2239	while read line
2240	do
2241	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2242	then
2243	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2244	then
2245	local_depository_path=`echo $line \| cut -d" " -s -f2`
2246	fi
2247	fi
2248	done < tmp_mrun
2249
2250	if [[ "$local_depository_path" = "" ]]
2251	then
2252	if [[ "$global_depository_path" != "" ]]
2253	then
2254	local_depository_path=$global_depository_path
2255	else
2256	printf "\n\n +++ no depository path found in configuration file"
2257	printf "\n for local host \"$localhost\" "
2258	printf "\n please set \"\%depository_path\" in configuration file\n"
2259	locat=config_file; exit
2260	fi
2261	fi
2262	eval local_depository_path=$local_depository_path
2263	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2264	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2265
2266
2267	basename=`echo $mainprog \| cut -f1 -d"."`
2268	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2269	if [[ ! -f $make_depository ]]
2270	then
2271	printf "\n"
2272	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2273	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2274	fi
2275
2276	fi
2277
2278
2279	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2280	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2281	if [[ $do_batch = false ]]
2282	then
2283
2284
2285	# CREATE THE TEMPORARY WORKING DIRECTORY
2286	mkdir -p $TEMPDIR
2287	chmod go+rx $TEMPDIR
2288	tmpcreate=true
2289
2290
2291	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2292	# INTO THE TEMPORARY WORKING DIRECTORY
2293	if [[ $do_compile = true ]]
2294	then
2295
2296	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2297	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2298	if [[ $localhost = nech ]]
2299	then
2300	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2301	if mkdir -p $TEMPDIR_COMPILE
2302	then
2303	printf "\n *** \"$TEMPDIR_COMPILE\" "
2304	printf "\n is generated as temporary directory for cross compiling\n"
2305	else
2306	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2307	printf "\n needed for cross compilation failed"
2308	locat=compile
2309	exit
2310	fi
2311	else
2312	TEMPDIR_COMPILE=$TEMPDIR
2313	fi
2314
2315	cp $make_depository $TEMPDIR_COMPILE
2316	cd $TEMPDIR_COMPILE
2317	tar -xf $make_depository > /dev/null 2>&1
2318	cd - > /dev/null
2319
2320	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2321	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2322	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2323	then
2324	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2325	else
2326	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2327	fi
2328
2329	else
2330
2331	cp $executable ${TEMPDIR}/a.out
2332
2333	fi
2334
2335
2336	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2337	cd $TEMPDIR
2338	printf "\n *** changed to temporary directory: $TEMPDIR"
2339
2340
2341	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2342	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2343	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2344	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2345	(( i = 0 ))
2346	while (( i < iout ))
2347	do
2348	(( i = i + 1 ))
2349	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2350	then
2351	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2352	else
2353	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2354	fi
2355	done
2356
2357
2358	# IF REQUIRED, START WITH COMPILING
2359	if [[ $do_compile = true ]]
2360	then
2361
2362
2363	if [[ -f a.out ]]
2364	then
2365
2366	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2367	printf "\n\n\n *** executable a.out found"
2368	printf "\n no compilation required \n"
2369
2370	else
2371
2372	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2373	printf "\n\n\n *** compilation starts \n$dashes\n"
2374	printf " *** compilation with make using following options:\n"
2375	printf " make depository: $make_depository"
2376	if [[ "$mopts" != "" ]]
2377	then
2378	printf " make options: $mopts\n"
2379	fi
2380	printf " compilername: $compiler_name\n"
2381	printf " compiler options: $fopts\n"
2382	printf " preprocessor directives: $cpp_options \n"
2383	printf " linker options: $lopts \n"
2384	if [[ "$modules" != "" ]]
2385	then
2386	printf " modules to be load: $modules \n"
2387	fi
2388	printf " source code files: $source_list \n"
2389
2390	if [[ $localhost = nech ]]
2391	then
2392	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\" "
2393	cp $TEMPDIR_COMPILE/a.out .
2394	[[ $? != 0 ]] && compile_error=true
2395	rm -rf $TEMPDIR_COMPILE
2396	elif [[ $localhost = ibmh ]]
2397	then
2398	printf " compiler is called via ssh on \"plogin1\" \n"
2399	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\" "
2400	[[ ! -f a.out ]] && compile_error=true
2401	continue # STATUS=1, IF a.out EXISTS
2402	elif [[ $localhost = lcocean ]]
2403	then
2404	printf " compiler is called via ssh on \"ocean\" \n"
2405	echo $PWD
2406	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\" "
2407	[[ ! -f a.out ]] && compile_error=true
2408	continue # STATUS=1, IF a.out EXISTS
2409	elif [[ $localhost = lcflow ]]
2410	then
2411	printf " compiler is called via ssh on \"flow\" \n"
2412	/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\" "
2413	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2414	[[ "$check_for_file" = "" ]] && compile_error=true
2415	continue # STATUS=1, IF a.out EXISTS
2416	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2417	then
2418	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2419	else
2420	[[ "$init_cmds" != "" ]] && eval $init_cmds
2421	[[ "$module_calls" != "" ]] && eval $module_calls
2422	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2423	fi
2424
2425	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2426	then
2427	printf "\n +++ error occured while compiling or linking"
2428	locat=compile
2429
2430	exit
2431	else
2432	printf "$dashes\n *** compilation finished \n"
2433	fi
2434
2435	fi
2436
2437	fi
2438
2439
2440	# PROVIDE THE INPUT FILES
2441	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2442	(( i = 0 ))
2443	while (( i < iin ))
2444	do
2445	(( i = i + 1 ))
2446	if (( i == 1 ))
2447	then
2448	printf "\n\n *** providing INPUT-files:\n$dashes"
2449	fi
2450
2451
2452	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2453	if [[ "${transin[$i]}" = unavailable ]]
2454	then
2455	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2456	then
2457	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2458	printf "\n is not available!"
2459	else
2460	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2461	printf "\n is not available!"
2462	fi
2463	continue
2464	fi
2465
2466	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2467	files_for_pes=false; datentyp=file
2468	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2469	then
2470	files_for_pes=true; datentyp=directory
2471	actionin[$i]=""
2472	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2473	then
2474	actionin[$i]=""
2475	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2476	then
2477	files_for_pes=true; datentyp=directory
2478	actionin[$i]="ar"
2479	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2480	then
2481	actionin[$i]="ar"
2482	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2483	then
2484	files_for_pes=true; datentyp=directory
2485	actionin[$i]="fl"
2486	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2487	then
2488	actionin[$i]="fl"
2489	fi
2490
2491	if [[ $files_for_pes = true ]]
2492	then
2493	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2494	else
2495	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2496	fi
2497
2498	# INPUT-FILE FOR A RESTART RUN.
2499	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2500	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2501	if [[ "${actionin[$i]}" = fl ]]
2502	then
2503	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2504	if [[ $files_for_pes = false ]]
2505	then
2506	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2507	then
2508	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2509	got_tmp[$i]=true
2510	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2511	then
2512	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2513	printf "\n *** trying to use backup copy in \"$WORK\" "
2514	cp $WORK/${frelin[$i]} ${localin[$i]}
2515	else
2516	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2517	printf "\n or \"$tmp_data_catalog\" does not exist!"
2518	printf "\n *** trying to get copy from archive"
2519	actionin[$i]=ar
2520	fi
2521	else
2522	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2523	then
2524	mkdir ${localin[$i]}
2525	cd $tmp_data_catalog/${frelin[$i]}
2526	for file in $(ls *)
2527	do
2528	ln $file $TEMPDIR/${localin[$i]}
2529	done
2530	cd $TEMPDIR
2531	got_tmp[$i]=true
2532	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2533	then
2534	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2535	printf "\n *** trying to use backup copy in \"$WORK\" "
2536	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2537	else
2538	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2539	printf "\n or \"$tmp_data_catalog\" does not exist!"
2540	printf "\n *** trying to get copy from archive"
2541	actionin[$i]=ar
2542	fi
2543	fi
2544	fi
2545
2546
2547	# FILE IS STORED ON THE ARCHIVE SYSTEM
2548	if [[ "${actionin[$i]}" = ar ]]
2549	then
2550
2551	if [[ $files_for_pes = false ]]
2552	then
2553	printf "\n file will be restored from archive-system ($archive_system)!"
2554	else
2555	printf "\n directory will be restored from archive-system ($archive_system)!"
2556	fi
2557
2558	file_restored=false
2559
2560	if [[ $archive_system = asterix ]]
2561	then
2562	do_stagein=true
2563	(( stagein_anz = 0 ))
2564	while [[ $do_stagein = true ]]
2565	do
2566	if [[ $files_for_pes = false ]]
2567	then
2568	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2569	else
2570	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2571	fi
2572	cat STAGEIN_OUTPUT
2573	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2574	then
2575	file_restored=true
2576	do_stagein=false
2577	else
2578	(( stagein_anz = stagein_anz + 1 ))
2579	if (( stagein_anz == 10 ))
2580	then
2581	printf "\n +++ stagein stoped after 10 tries"
2582	locat=stage
2583	exit
2584	fi
2585	printf "\n +++ restoring from archive failed, trying again:"
2586	sleep 900
2587	fi
2588	done
2589	elif [[ $archive_system = DMF ]]
2590	then
2591	if [[ $files_for_pes = false ]]
2592	then
2593	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2594	locat=DMF
2595	exit
2596	else
2597	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2598	cp -r $ARCHIVE/${frelin[$i]} $PWD
2599	file_restored=true
2600	fi
2601	elif [[ $archive_system = tivoli ]]
2602	then
2603	if [[ $files_for_pes = false ]]
2604	then
2605	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2606	else
2607	(( inode = 0 ))
2608	while (( inode < nodes ))
2609	do
2610	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2611	(( inode = inode + 1 ))
2612	done
2613	fi
2614	file_restored=true
2615	elif [[ $archive_system = ut ]]
2616	then
2617	if [[ $files_for_pes = false ]]
2618	then
2619	cp $UT/${frelin[$i]} .
2620	else
2621	(( inode = 0 ))
2622	while (( inode < nodes ))
2623	do
2624	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2625	(( inode = inode + 1 ))
2626	done
2627	fi
2628	file_restored=true
2629	else
2630	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2631	locat=rearchive
2632	exit
2633	fi
2634
2635	if [[ $file_restored = true ]]
2636	then
2637
2638	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2639	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2640	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2641	if [[ $files_for_pes = false ]]
2642	then
2643	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2644	else
2645	mkdir $tmp_data_catalog/${frelin[$i]}
2646	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2647	fi
2648	got_tmp[$i]=true
2649
2650	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2651	mv ${frelin[$i]} ${localin[$i]}
2652
2653	fi
2654	fi
2655
2656
2657	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2658	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2659	then
2660
2661	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2662	then
2663
2664	# FILE COPIES ARE PROVIDED FOR ALL CORES
2665	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2666	printf "\n file will be provided for $numprocs processors"
2667	mkdir ${localin[$i]}
2668	ival=$numprocs
2669	(( ii = 0 ))
2670	while (( ii <= ival-1 ))
2671	do
2672	if (( ii < 10 ))
2673	then
2674	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2675	elif (( ii < 100 ))
2676	then
2677	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2678	elif (( ii < 1000 ))
2679	then
2680	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2681	else
2682	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2683	fi
2684	(( ii = ii + 1 ))
2685	done
2686
2687	else
2688
2689	if [[ $files_for_pes = true ]]
2690	then
2691
2692	# PROVIDE FILES FOR EACH CORE
2693	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2694	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2695	printf "\n providing $numprocs files for the respective processors"
2696	mkdir ${localin[$i]}
2697	if [[ $link_local_input = true ]]
2698	then
2699	printf " using ln -f\n"
2700	cd ${absnamein[$i]}
2701	for file in $(ls *)
2702	do
2703	ln -f $file ${localin[$i]}
2704	done
2705	cd $TEMPDIR
2706	fi
2707
2708	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2709	if [[ ! -f "${localin[$i]}/_0000" ]]
2710	then
2711	if [[ $link_local_input = true ]]
2712	then
2713	printf " ln failed for .../_0000, using cp...\n"
2714	fi
2715	cp -r ${absnamein[$i]}/* ${localin[$i]}
2716	fi
2717
2718	else
2719
2720	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2721	if [[ $link_local_input = true ]]
2722	then
2723	printf " using ln -f\n"
2724	ln -f ${absnamein[$i]} ${localin[$i]}
2725	fi
2726	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2727	if [[ ! -f "${localin[$i]}" ]]
2728	then
2729	if [[ $link_local_input = true ]]
2730	then
2731	printf " ln failed, using cp...\n"
2732	fi
2733	cp ${absnamein[$i]} ${localin[$i]}
2734	fi
2735	fi
2736	fi
2737	fi
2738
2739	done
2740	if (( i != 0 ))
2741	then
2742	printf "\n$dashes\n *** all INPUT-files provided \n"
2743	fi
2744
2745
2746	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2747	(( i = 0 ))
2748	while (( i < iic ))
2749	do
2750	(( i = i + 1 ))
2751	if (( i == 1 ))
2752	then
2753	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2754	fi
2755	printf "\n >>> ${in_command[$i]}"
2756	eval ${in_command[$i]}
2757	if (( i == iic ))
2758	then
2759	printf "\n$dashes\n"
2760	fi
2761	done
2762
2763
2764	# SET THE REMAINING CPU-TIME
2765	cpurest=${cpumax}.
2766
2767
2768	# START DVR STREAMING SERVER
2769	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2770	then
2771	if [[ "$dvr_server" != "" ]]
2772	then
2773
2774	printf "\n\n *** preparing the dvr streaming server configuration file"
2775
2776	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2777	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2778	if [[ "$running_dvrserver_id" != "" ]]
2779	then
2780
2781	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2782	printf "\n This server is used instead starting a new one!"
2783	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2784
2785	else
2786
2787	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2788	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2789	then
2790	cp ${PALM_BIN}/.dvrserver.config .
2791
2792	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2793	user_id=`id -u`
2794	group_id=`id -g`
2795
2796	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2797	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2798	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2799	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2800	mv .dvrserver.3 .dvrserver.config
2801	rm .dvrserver.1 .dvrserver.2
2802
2803	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2804	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2805	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2806	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2807	local_dvrserver_running=.TRUE.
2808	else
2809	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2810	printf "\n \"$PALM_BIN\" "
2811	locat=dvr
2812	exit
2813	fi
2814
2815	fi
2816
2817	else
2818	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2819	fi
2820	fi
2821
2822
2823	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2824	# (FILE ENVPAR WILL BE READ BY PALM)
2825	cat > ENVPAR << %%END%%
2826	&envpar run_identifier = '$fname', host = '$localhost',
2827	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2828	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2829	maximum_cpu_time_allowed = ${cpumax}.,
2830	revision = '$global_revision',
2831	local_dvrserver_running = $local_dvrserver_running,
2832	batch_job = $batch_job /
2833
2834	%%END%%
2835
2836
2837	# STARTING THE EXECUTABLE
2838	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2839	PATH=$PATH:$TEMPDIR
2840
2841
2842	if [[ $execute_command != "none" ]]
2843	then
2844
2845	printf "\n +++ branch still not realized"
2846	locat=execution
2847	exit
2848
2849	else
2850
2851	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2852	if [[ "$mpi_debug" = true ]]
2853	then
2854	export MPI_CHECK_ARGS=1
2855	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2856	fi
2857
2858	if [[ "$totalview" = true ]]
2859	then
2860	printf "\n *** totalview debugger will be used"
2861	tv_opt="-tv"
2862	else
2863	tv_opt=""
2864	fi
2865
2866	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2867	then
2868
2869	#Interactive ALLINEA DEBUG seesion
2870	if [[ "$ENVIRONMENT" != BATCH ]]
2871	then
2872	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2873	then
2874	if [[ "$allinea" = true ]]
2875	then
2876	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2877
2878	ddt aprun -n $ii -N $tasks_per_node a.out
2879	wait
2880	fi
2881	fi
2882	fi
2883
2884	if [[ $localhost = ibmh ]]
2885	then
2886
2887	# SETUP THE IBM MPI ENVIRONMENT
2888	export MP_SHARED_MEMORY=yes
2889	export AIXTHREADS_SCOPE=S
2890	export OMP_NUM_THREADS=$threads_per_task
2891	export AUTHSTATE=files
2892	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2893
2894	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2895	export MP_ADAPTER_USE=shared
2896	export MP_CPU_USE=multiple
2897	export MP_TIMEOUT=1200
2898
2899	unset MP_TASK_AFFINITY
2900
2901	if [[ "$LOADLBATCH" = yes ]]
2902	then
2903	totalview poe a.out
2904	else
2905	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2906	export TVDSVRLAUNCHCMD=ssh
2907	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2908	fi
2909
2910	fi # END DEBUG MODE
2911
2912	else
2913
2914	# NORMAL EXECUTION
2915	if [[ -n $numprocs ]]
2916	then
2917
2918	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2919	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2920	then
2921
2922	# SETUP THE IBM MPI ENVIRONMENT
2923	if [[ $host != ibmh && $host != ibmkisti ]]
2924	then
2925	export MP_SHARED_MEMORY=yes
2926	export AIXTHREAD_SCOPE=S
2927	export OMP_NUM_THREADS=$threads_per_task
2928	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2929	export AUTHSTATE=files
2930	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2931	# export MP_PRINTENV=yes
2932
2933	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2934	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2935	export MP_WAIT_MODE=poll
2936	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2937	fi
2938
2939	if [[ $host = ibmkisti ]]
2940	then
2941	export LANG=en_US
2942	export MP_SHARED_MEMORY=yes
2943	if [[ $threads_per_task = 1 ]]
2944	then
2945	export MP_SINGLE_THREAD=yes
2946	export MEMORY_AFFINITY=MCM
2947	else
2948	export OMP_NUM_THREADS=$threads_per_task
2949	fi
2950	fi
2951
2952	if [[ "$LOADLBATCH" = yes ]]
2953	then
2954	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2955	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2956	then
2957	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2958	else
2959	if [[ $run_coupled_model = false ]]
2960	then
2961	if [[ "$ocean_file_appendix" = true ]]
2962	then
2963	echo "precursor_ocean" > runfile_atmos
2964	else
2965	echo "precursor_atmos" > runfile_atmos
2966	fi
2967	else
2968	(( iia = $numprocs_atmos / $threads_per_task ))
2969	(( iio = $numprocs_ocean / $threads_per_task ))
2970	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2971	printf "\n using $coupled_mode coupling"
2972	printf "\n\n"
2973	echo "coupled_run $iia $iio" > runfile_atmos
2974	fi
2975	poe ./a.out < runfile_atmos
2976	fi
2977	else
2978	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2979	then
2980	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2981	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2982	then
2983	if [[ -f $hostfile ]]
2984	then
2985	cp $hostfile hostfile
2986	else
2987	(( ii = 1 ))
2988	while (( ii <= $numprocs ))
2989	do
2990	echo $localhost_realname >> hostfile
2991	(( ii = ii + 1 ))
2992	done
2993	fi
2994	export MP_HOSTFILE=hostfile
2995	if [[ $run_coupled_model = false ]]
2996	then
2997	if [[ "$ocean_file_appendix" = true ]]
2998	then
2999	echo "precursor_ocean" > runfile_atmos
3000	else
3001	echo "precursor_atmos" > runfile_atmos
3002	fi
3003	else
3004	(( iia = $numprocs_atmos / $threads_per_task ))
3005	(( iio = $numprocs_ocean / $threads_per_task ))
3006	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3007	printf "\n using $coupled_mode coupling"
3008	printf "\n\n"
3009	echo "coupled_run $iia $iio" > runfile_atmos
3010	fi
3011
3012	poe ./a.out -procs $numprocs < runfile_atmos
3013
3014	else
3015	if [[ "$host_file" = "" ]]
3016	then
3017	printf "\n +++ no hostfile given in configuration file"
3018	locat=config_file
3019	exit
3020	else
3021	eval host_file=$host_file
3022	fi
3023	export MP_HOSTFILE=$host_file
3024	poe a.out -procs $numprocs -tasks_per_node $numprocs
3025	fi
3026	fi
3027
3028	elif [[ $host = nech ]] # running on NEC machines
3029	then
3030
3031	(( ii = nodes ))
3032	if [[ $ii = 1 ]]
3033	then
3034	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3035	export MPIPROGINF=YES
3036	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3037	echo "*** execution on single node with mpirun"
3038	mpirun -np $numprocs ./a.out
3039	else
3040	(( i = 0 ))
3041	while (( i < ii ))
3042	do
3043	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3044	(( i = i + 1 ))
3045	done
3046
3047	echo "#!/bin/sh" > mpi_exec_shell
3048	echo " " >> mpi_exec_shell
3049	echo "set -u" >> mpi_exec_shell
3050	echo "F_ERRCNT=0" >> mpi_exec_shell
3051	echo "MPIPROGINV=YES" >> mpi_exec_shell
3052	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3053	echo "cpurest=$cpurest" >> mpi_exec_shell
3054	echo "fname=$fname" >> mpi_exec_shell
3055	echo "localhost=$localhost" >> mpi_exec_shell
3056	echo "return_address=$return_address" >> mpi_exec_shell
3057	echo "return_username=$return_username" >> mpi_exec_shell
3058	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3059	echo "write_binary=$write_binary" >> mpi_exec_shell
3060	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3061	echo " " >> mpi_exec_shell
3062	echo "export F_ERRCNT" >> mpi_exec_shell
3063	echo "export MPIPROGINV" >> mpi_exec_shell
3064	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3065	echo "export cpurest" >> mpi_exec_shell
3066	echo "export fname" >> mpi_exec_shell
3067	echo "export localhost" >> mpi_exec_shell
3068	echo "export return_address" >> mpi_exec_shell
3069	echo "export return_username" >> mpi_exec_shell
3070	echo "export tasks_per_node" >> mpi_exec_shell
3071	echo "export write_binary" >> mpi_exec_shell
3072	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3073	echo " " >> mpi_exec_shell
3074	echo "exec ./a.out" >> mpi_exec_shell
3075
3076	chmod u+x mpi_exec_shell
3077	export MPIPROGINF=YES
3078	mpirun -f multinode_config &
3079	wait
3080
3081	fi
3082
3083	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3084	then
3085
3086	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3087	# DOES NOT EXIST
3088	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]
3089	then
3090	if [[ -f $hostfile ]]
3091	then
3092	cp $hostfile hostfile
3093	(( ii = $numprocs / $threads_per_task ))
3094	[[ $ii = 0 ]] && (( ii = 1 ))
3095	else
3096	(( ii = 1 ))
3097	while (( ii <= $numprocs / $threads_per_task ))
3098	do
3099	echo $localhost_realname >> hostfile
3100	(( ii = ii + 1 ))
3101	done
3102	if (( $numprocs / $threads_per_task == 0 ))
3103	then
3104	echo $localhost_realname >> hostfile
3105	fi
3106	fi
3107	eval zeile=\"`head -n $ii hostfile`\"
3108	printf "\n *** running on: $zeile"
3109	fi
3110
3111	(( ii = $numprocs / $threads_per_task ))
3112	[[ $ii = 0 ]] && (( ii = 1 ))
3113	export OMP_NUM_THREADS=$threads_per_task
3114
3115	if [[ $threads_per_task != 1 ]]
3116	then
3117	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3118	# MAY ABORT
3119	ulimit -s unlimited
3120	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3121	fi
3122	if [[ $run_coupled_model = false ]]
3123	then
3124	if [[ "$ocean_file_appendix" = true ]]
3125	then
3126	echo "precursor_ocean" > runfile_atmos
3127	else
3128	echo "precursor_atmos" > runfile_atmos
3129	fi
3130	printf "\n\n"
3131
3132	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3133	then
3134	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3135	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3136	elif [[ $host = lcbullhh ]]
3137	then
3138	export OMPI_MCA_pml=cm
3139	export OMPI_MCA_mtl=mxm
3140	export OMPI_MCA_coll=^ghc
3141	export OMPI_MCA_mtl_mxm_np=0
3142	export MXM_RDMA_PORTS=mlx5_0:1
3143	export MXM_LOG_LEVEL=ERROR
3144	export OMP_NUM_THREADS=$threads_per_task
3145	export KMP_AFFINITY=verbose,granularity=core,compact,1
3146	export KMP_STACKSIZE=64m
3147
3148	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3149
3150	elif [[ $host = lccrayf ]]
3151	then
3152	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3153	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3154	then
3155	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3156	elif [[ $host = lcflow ]]
3157	then
3158	mpirun -np $ii a.out < runfile_atmos
3159	elif [[ $host = lcocean ]]
3160	then
3161	mpirun a.out $ROPTS < runfile_atmos
3162	elif [[ $host = lcsb ]]
3163	then
3164	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3165	elif [[ $host = lckiaps ]]
3166	then
3167	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
3168	elif [[ $host = lckyu* ]]
3169	then
3170	mpiexec -n $ii --stdin runfile_atmos ./a.out
3171	else
3172	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3173	fi
3174
3175	else
3176
3177	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3178	(( iia = $numprocs_atmos / $threads_per_task ))
3179	(( iio = $numprocs_ocean / $threads_per_task ))
3180	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3181	printf "\n using $coupled_mode coupling"
3182	printf "\n\n"
3183
3184	if [[ $coupled_mode = "mpi2" ]]
3185	then
3186	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3187	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3188
3189	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3190	then
3191
3192	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
3193	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
3194
3195	else
3196	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3197	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
3198	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
3199	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
3200	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
3201	fi
3202	wait
3203
3204	else
3205
3206	echo "coupled_run $iia $iio" > runfile_atmos
3207
3208	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3209	then
3210
3211	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3212
3213	elif [[ $host = lck \|\| $host = lckordi ]]
3214	then
3215
3216	mpiexec -n $ii ./a.out < runfile_atmos &
3217
3218	elif [[ $host = lckyu* ]]
3219	then
3220
3221	mpiexec -n $ii --stdin runfile_atmos ./a.out
3222
3223	elif [[ $host = lcmuk ]]
3224	then
3225
3226	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3227
3228	fi
3229	wait
3230	fi
3231
3232	fi
3233
3234	elif [[ $host = lckyoto ]]
3235	then
3236	set -xv
3237	export P4_RSHCOMMAND=plesh
3238	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3239	if [[ "$ENVIRONMENT" = BATCH ]]
3240	then
3241	if [[ "$cond2" = fujitsu ]]
3242	then
3243	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3244	elif [[ "cond2" = pgi ]]
3245	then
3246	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3247	else
3248	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3249	fi
3250	else
3251	if [[ "$cond2" = "" ]]
3252	then
3253	mpiruni_rsh -np $numprocs ./a.out # for intel
3254	else
3255	mpirun -np $numprocs ./a.out
3256	fi
3257	fi
3258	set +xv
3259
3260	elif [[ $host = lctit ]]
3261	then
3262	export OMP_NUM_THREADS=$threads_per_task
3263	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3264	if [[ "$threads_per_task" != 1 ]]
3265	then
3266	export MV2_ENABLE_AFFINITY=0
3267	fi
3268	echo "----- PBS_NODEFILE content:"
3269	cat $PBS_NODEFILE
3270	echo "-----"
3271	(( ii = $numprocs / $threads_per_task ))
3272	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3273	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3274
3275	else
3276	mpprun -n $numprocs a.out
3277	fi
3278	else
3279	a.out
3280	fi
3281
3282	fi # end normal (non-debug) execution
3283
3284	fi # end explicit execute_command or host-specific execute actions
3285
3286	if [[ $? != 0 ]]
3287	then
3288
3289	# ABORT IN CASE OF RUNTIME ERRORS
3290	printf "\n +++ runtime error occured"
3291	locat=execution
3292	exit
3293
3294	else
3295
3296	printf "\n$dashes\n *** execution finished \n"
3297
3298	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3299	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3300	if [[ "$dvrserver_id" != "" ]]
3301	then
3302	kill $dvrserver_id
3303	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3304
3305	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3306	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3307	if [[ -d DATA_DVR ]]
3308	then
3309
3310	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3311	# DIRECTORY
3312	cp .dvrserver.config DATA_DVR
3313
3314	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3315	# SEQUENCE MODE DATA TOO)
3316	process_dvr_output -d DATA_DVR -f $fname -s
3317
3318	else
3319
3320	# PROCESS THE LOCAL OUTPUT
3321	process_dvr_output -l -d DATA_DVR -f $fname
3322
3323	fi
3324
3325	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3326	then
3327
3328	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3329	process_dvr_output -l -d DATA_DVR -f $fname
3330
3331	fi
3332	fi
3333
3334
3335
3336	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3337	# BY EACH CORE INTO ONE FILE
3338	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3339	then
3340	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3341	printf "\n 2d- and/or 3d-data may be incomplete!"
3342	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3343	elif [[ "$combine_plot_fields" == true ]]
3344	then
3345	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3346	then
3347	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3348	aprun -n 1 -N 1 combine_plot_fields${block}.x
3349	else
3350	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3351	combine_plot_fields${block}.x
3352	fi
3353	else
3354
3355	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3356	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3357	# ??? koennen wir das streichen ???
3358	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3359	fi
3360
3361
3362
3363	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3364	(( i = 0 ))
3365	while (( i < ioc ))
3366	do
3367	(( i = i + 1 ))
3368	if (( i == 1 ))
3369	then
3370	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3371	fi
3372	printf "\n >>> ${out_command[$i]}"
3373	eval ${out_command[$i]}
3374	if (( i == ioc ))
3375	then
3376	printf "\n$dashes\n"
3377	fi
3378	done
3379
3380
3381	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3382	if [[ $do_trace = true ]]
3383	then
3384	printf "\n\n"
3385	ls -al
3386	fi
3387
3388
3389
3390	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3391	(( i = 0 ))
3392	while (( i < iout ))
3393	do
3394	(( i = i + 1 ))
3395	if (( i == 1 ))
3396	then
3397	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3398	fi
3399
3400	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3401	files_for_pes=false; filetyp=file
3402	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3403	then
3404	files_for_pes=true; filetyp=directory
3405	actionout[$i]=""
3406	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3407	then
3408	actionout[$i]=""
3409	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3410	then
3411	files_for_pes=true; filetyp=directory
3412	actionout[$i]="ar"
3413	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3414	then
3415	actionout[$i]="ar"
3416	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3417	then
3418	files_for_pes=true; filetyp=directory
3419	actionout[$i]="fl"
3420	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3421	then
3422	actionout[$i]="fl"
3423	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3424	then
3425	files_for_pes=true; filetyp=directory
3426	actionout[$i]="tr"
3427	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3428	then
3429	actionout[$i]="tr"
3430	fi
3431
3432	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3433	then
3434	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3435	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3436	then
3437	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3438	else
3439
3440
3441	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3442	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3443	if [[ "${actionout[$i]}" = tr ]]
3444	then
3445	if [[ $localhost != $fromhost ]]
3446	then
3447	if [[ $files_for_pes = false ]]
3448	then
3449	cps=""
3450	cst=""
3451	else
3452	cps=-c
3453	cst="/"
3454	fi
3455	if [[ $localhost = nech ]]
3456	then
3457
3458	# TRANSFER IN SEPERATE JOB
3459	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3460	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3461	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3462	if [[ $files_for_pes = false ]]
3463	then
3464	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3465	else
3466	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3467	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3468	fi
3469
3470	echo "set -x" > transfer_${localout[$i]}
3471	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3472
3473	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3474	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3475	printf "\n or higher cycle\n"
3476	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]}
3477
3478	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3479
3480	if [[ $localhost = nech ]]
3481	then
3482	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3483	else
3484	if [[ "$LOGNAME" = b323013 ]]
3485	then
3486	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3487	else
3488	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3489	fi
3490	fi
3491
3492	else
3493
3494	# TRANSFER WITHIN THIS JOB
3495	transfer_failed=false
3496	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3497	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3498	if [[ $localhost = lccrayb ]]
3499	then
3500	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]}"
3501	elif [[ $localhost = lccrayh ]]
3502	then
3503	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]}"
3504	elif [[ $localhost = lcbullhh ]]
3505	then
3506	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]}"
3507	elif [[ $localhost = lcxe6 ]]
3508	then
3509	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]}"
3510	else
3511	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3512	fi
3513	[[ $? != 0 ]] && transfer_failed=true
3514
3515	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3516	if [[ $transfer_failed = true ]]
3517	then
3518	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3519	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3520
3521	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3522	eval local_catalog=${pathout[$i]}
3523	if [[ ! -d $local_catalog ]]
3524	then
3525	printf " *** local directory does not exist. Trying to create:\n"
3526	printf " $local_catalog \n"
3527	mkdir -p $local_catalog
3528	fi
3529	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3530	transfer_problems=true
3531	fi
3532	fi
3533	else
3534
3535	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3536	actionout[$i]=""
3537	fi
3538	fi
3539
3540
3541	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3542	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3543	if [[ "${actionout[$i]}" = tra ]]
3544	then
3545	if [[ $localhost != $fromhost ]]
3546	then
3547	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3548	then
3549
3550	# TRANSFER IN SEPERATE JOB
3551	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3552	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3553	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3554	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3555
3556	echo "set -x" > transfer_${localout[$i]}
3557	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3558
3559	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3560	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3561	printf "\n or higher cycle\n"
3562	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]}
3563
3564	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3565
3566	if [[ $localhost = nech ]]
3567	then
3568	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3569	else
3570	if [[ $LOGNAME = b323013 ]]
3571	then
3572	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3573	else
3574	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3575	fi
3576	fi
3577
3578	else
3579
3580	# TRANSFER WITHIN THIS JOB
3581	transfer_failed=false
3582	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3583	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3584	if [[ $localhost = lccrayb ]]
3585	then
3586	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]}"
3587	elif [[ $localhost = lccrayh ]]
3588	then
3589	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]}"
3590	elif [[ $localhost = lcxe6 ]]
3591	then
3592	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]}"
3593	else
3594	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3595	fi
3596	[[ $? != 0 ]] && transfer_failed=true
3597
3598	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3599	if [[ $transfer_failed = true ]]
3600	then
3601	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3602	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3603
3604	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3605	eval local_catalog=${pathout[$i]}
3606	if [[ ! -d $local_catalog ]]
3607	then
3608	printf " *** local directory does not exist. Trying to create:\n"
3609	printf " $local_catalog \n"
3610	mkdir -p $local_catalog
3611	fi
3612
3613	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3614	transfer_problems=true
3615	fi
3616	fi
3617	else
3618
3619	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3620	actionout[$i]=a
3621	fi
3622	fi
3623
3624
3625	# OUTPUT-FILE FOR A RESTART-RUN.
3626	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3627	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3628	# AS LAST ACTION, ARCHIVING IS INITIATED.
3629	if [[ "${actionout[$i]}" = fl ]]
3630	then
3631	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3632	chmod g+rx $tmp_data_catalog
3633	if [[ $files_for_pes = false ]]
3634	then
3635	printf "\n >>> OUTPUT: ${localout[$i]} to"
3636	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3637	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3638	else
3639	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3640	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3641	mkdir $tmp_data_catalog/${frelout[$i]}
3642	cd ${localout[$i]}
3643	for file in $(ls *)
3644	do
3645	ln -f $file $tmp_data_catalog/${frelout[$i]}
3646	done
3647	cd $TEMPDIR
3648	fi
3649
3650
3651	# CREATE AND SUBMIT ARCHIVING-JOB
3652	if [[ $store_on_archive_system = true ]]
3653	then
3654
3655	if [[ $archive_system = asterix ]]
3656	then
3657	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3658	if [[ $files_for_pes = false ]]
3659	then
3660	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3661	else
3662	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3663	fi
3664	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3665	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3666	echo "then" >> archive_${frelout[$i]}
3667	echo " do_stageout=false" >> archive_${frelout[$i]}
3668	echo "else" >> archive_${frelout[$i]}
3669	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3670	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3671	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3672	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3673	if [[ $files_for_pes = false ]]
3674	then
3675	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3676	else
3677	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3678	fi
3679	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3680	echo "fi" >> archive_${frelout[$i]}
3681	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3682	elif [[ $archive_system = DMF ]]
3683	then
3684	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3685	if [[ $files_for_pes = false ]]
3686	then
3687	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3688	locat=DMF
3689	exit
3690	else
3691	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3692	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3693	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3694	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3695	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3696	fi
3697	elif [[ $archive_system = tivoli ]]
3698	then
3699	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3700	if [[ $files_for_pes = false ]]
3701	then
3702	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3703	echo "set -x" >> archive_${frelout[$i]}
3704	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3705	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3706	else
3707
3708	echo "set -x" >> archive_${frelout[$i]}
3709	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3710	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3711	cd $tmp_data_catalog
3712	all_files=`ls -1 ${frelout[$i]}/*`
3713	cd - > /dev/null
3714	(( inode = 0 ))
3715	(( tp1 = tasks_per_node + 1 ))
3716	while (( inode < nodes ))
3717	do
3718	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3719	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3720	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3721	(( inode = inode + 1 ))
3722	done
3723	fi
3724	elif [[ $archive_system = ut ]]
3725	then
3726	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3727	if [[ $files_for_pes = false ]]
3728	then
3729	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3730	echo "set -x" >> archive_${frelout[$i]}
3731	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3732	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3733	else
3734
3735	echo "set -x" >> archive_${frelout[$i]}
3736	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
3737	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
3738	cd $tmp_data_catalog
3739	all_files=`ls -1 ${frelout[$i]}/*`
3740	cd - > /dev/null
3741	(( inode = 0 ))
3742	(( tp1 = tasks_per_node + 1 ))
3743	while (( inode < nodes ))
3744	do
3745	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3746	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3747	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3748	(( inode = inode + 1 ))
3749	done
3750	fi
3751	elif [[ $archive_system = none ]]
3752	then
3753	printf " +++ archiving on $localhost not available!\n"
3754	fi
3755
3756	if [[ $archive_system != none ]]
3757	then
3758	if [[ $localhost = nech ]]
3759	then
3760	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3761	fi
3762	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3763	fi
3764	else
3765	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
3766	fi
3767
3768
3769	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
3770	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3771	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3772	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3773	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3774	if [[ $files_for_pes = false ]]
3775	then
3776	cat /dev/null > ${pathout[$i]}
3777	else
3778	mkdir -p ${pathout[$i]}
3779	fi
3780
3781	fi
3782
3783
3784	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
3785	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
3786	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
3787	if [[ "${actionout[$i]}" = ar ]]
3788	then
3789	if [[ $files_for_pes = false ]]
3790	then
3791	printf "\n >>> OUTPUT: ${localout[$i]} to"
3792	printf "\n ${pathout[$i]}"
3793	printf "\n File will be copied to archive-system ($archive_system) !\n"
3794	else
3795	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
3796	printf "\n ${pathout[$i]}"
3797	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
3798	fi
3799	mv ${localout[$i]} ${frelout[$i]}
3800
3801	file_saved=false
3802
3803	if [[ $archive_system = asterix ]]
3804	then
3805	do_stageout=true
3806	(( stageout_anz = 0 ))
3807	while [[ $do_stageout = true ]]
3808	do
3809	if [[ $files_for_pes = false ]]
3810	then
3811	stageout ${frelout[$i]} > STAGE_OUTPUT
3812	else
3813	stageout -t ${frelout[$i]} > STAGE_OUTPUT
3814	fi
3815	cat STAGE_OUTPUT
3816	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
3817	then
3818	file_saved=true
3819	do_stageout=false
3820	else
3821	if [[ $files_for_pes = false ]]
3822	then
3823	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
3824	else
3825	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
3826	fi
3827	(( stageout_anz = stageout_anz + 1 ))
3828	if (( stageout_anz == 10 ))
3829	then
3830	printf "\n +++ stoped after 10 unsuccessful tries!"
3831	archive_save=false
3832	do_stageout=false
3833	else
3834	printf "\n *** new try to store on archive after 15 min:"
3835	sleep 900
3836	fi
3837	fi
3838	done
3839	elif [[ $archive_system = DMF ]]
3840	then
3841	if [[ $files_for_pes = false ]]
3842	then
3843	printf "\n +++ archiving of single files impossible on $archive_system!\n"
3844	locat=DMF
3845	exit
3846	else
3847	rm -rf $ARCHIVE/${frelout[$i]}
3848	cp -r ${frelout[$i]} $ARCHIVE
3849	fi
3850	file_saved=true
3851	elif [[ $archive_system = tivoli ]]
3852	then
3853	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3854	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3855	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3856	# WHEN THE ARCHIVE-JOB IS EXECUTED
3857	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3858	chmod g+rx $tmp_data_catalog
3859	if [[ $files_for_pes = false ]]
3860	then
3861	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3862	else
3863	mkdir $tmp_data_catalog/${frelout[$i]}
3864	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3865	fi
3866
3867	# GENERATE AND SUBMIT BATCH-JOB
3868	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3869	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3870	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3871	if [[ $files_for_pes = false ]]
3872	then
3873	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3874	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3875	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3876	else
3877	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3878	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3879	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3880	fi
3881
3882	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
3883	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3884	file_saved=true
3885
3886	elif [[ $archive_system = ut ]]
3887	then
3888	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3889	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3890	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3891	# WHEN THE ARCHIVE-JOB IS EXECUTED
3892	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3893	chmod g+rx $tmp_data_catalog
3894	if [[ $files_for_pes = false ]]
3895	then
3896	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3897	else
3898	mkdir $tmp_data_catalog/${frelout[$i]}
3899	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3900	fi
3901
3902	# GENERATE AND SUBMIT BATCH-JOB
3903	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3904	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3905	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3906	if [[ $files_for_pes = false ]]
3907	then
3908	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3909	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3910	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3911	else
3912	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3913	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3914	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3915	fi
3916
3917	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3918	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3919	file_saved=true
3920
3921	else
3922	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
3923	archive_save=false
3924	fi
3925
3926	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
3927	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3928	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3929	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3930	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3931	if [[ $file_saved = true ]]
3932	then
3933	if [[ $files_for_pes = false ]]
3934	then
3935	cat /dev/null > ${pathout[$i]}
3936	else
3937	mkdir -p ${pathout[$i]}
3938	fi
3939	fi
3940
3941	fi
3942
3943	# APPEND ON THIS MACHINE
3944	if [[ "${actionout[$i]}" = "a" ]]
3945	then
3946	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3947	then
3948	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3949	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3950	else
3951	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3952	cat ${localout[$i]} >> ${pathout[$i]}
3953	fi
3954	fi
3955
3956	# COPY ON THIS MACHINE
3957	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3958	# ON DIFFERENT FILE-SYSTEMS
3959	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3960	then
3961
3962	# COPY IN CASE OF RUNS ON SINGLE CORES
3963	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3964	then
3965	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3966	if [[ $link_local_output = true ]]
3967	then
3968	printf " using ln -f\n"
3969	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3970	fi
3971	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3972	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3973	then
3974	if [[ $link_local_output = true ]]
3975	then
3976	printf " ln failed, using cp...\n"
3977	fi
3978	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3979	fi
3980	else
3981	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3982	if [[ $link_local_output = true ]]
3983	then
3984	printf " using ln -f\n"
3985	ln -f ${localout[$i]} ${pathout[$i]}
3986	fi
3987	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3988	if [[ ! -f "${pathout[$i]}" ]]
3989	then
3990	if [[ $link_local_output = true ]]
3991	then
3992	printf " ln failed, using cp...\n"
3993	fi
3994	cp ${localout[$i]} ${pathout[$i]}
3995	fi
3996	fi
3997
3998	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
3999	then
4000
4001	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4002	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4003	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4004	if [[ $link_local_output = true ]]
4005	then
4006	printf " using ln -f\n"
4007	mkdir ${pathout[$i]}
4008	cd ${localout[$i]}
4009	for file in $(ls *)
4010	do
4011	ln -f $file ${pathout[$i]}
4012	done
4013	cd $TEMPDIR
4014	fi
4015
4016	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4017	if [[ ! -f "${pathout[$i]}/_0000" ]]
4018	then
4019	if [[ $link_local_output = true ]]
4020	then
4021	printf " ln failed for .../_0000, using cp...\n"
4022	fi
4023	cp -r ${localout[$i]} ${pathout[$i]}
4024	fi
4025
4026	fi
4027	fi
4028	done
4029	if (( i != 0 ))
4030	then
4031	if [[ $transfer_problems = true ]]
4032	then
4033	printf "\n$dashes\n *** OUTPUT-files saved"
4034	printf "\n +++ WARNING: some data transfers failed! \n"
4035	else
4036	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4037	fi
4038	fi
4039
4040
4041	# IF REQUIRED, START A RESTART-JOB
4042	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4043	if [[ -f CONTINUE_RUN ]]
4044	then
4045
4046	if [[ $archive_save = true ]]
4047	then
4048
4049	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4050	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4051	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4052	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4053	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4054	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4055	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4056	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4057	then
4058	mc=`echo $mc \| sed 's/#/f/g'`
4059	fi
4060
4061
4062	# START THE RESTART-JOB
4063	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4064	echo " $mc"
4065	printf "\n$dashes\n"
4066	if [[ $localhost != $fromhost ]]
4067	then
4068
4069	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4070	then
4071	echo "*** ssh will be used to initiate restart-runs!"
4072	echo " return_address=\"$return_address\" "
4073	echo " return_username=\"$return_username\" "
4074	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4075	then
4076	if [[ $localhost = ibmh ]]
4077	then
4078	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\" "
4079	elif [[ $localhost = lcbullhh ]]
4080	then
4081	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\" "
4082	elif [[ $localhost = lccrayb ]]
4083	then
4084	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\" "
4085	elif [[ $localhost = lccrayh ]]
4086	then
4087	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\" "
4088	elif [[ $localhost = lcxe6 ]]
4089	then
4090	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\" "
4091	else
4092	ssh $SSH_PORTOPT $return_address -l $return_username ". \\\$HOME/.profile; module load intel-compiler hdf5 netcdf; PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4093	fi
4094	else
4095	if [[ $localhost = ibmkisti ]]
4096	then
4097	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\" "
4098	elif [[ $localhost = lcflow ]]
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 = lcocean ]]
4102	then
4103	/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 "
4104	elif [[ $localhost = lccrayb ]]
4105	then
4106	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\" "
4107	elif [[ $localhost = lccrayh ]]
4108	then
4109	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\" "
4110	else
4111	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4112	fi
4113	fi
4114	else
4115	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4116	locat=restart; exit
4117	fi
4118
4119	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4120	if [[ $queue = special1q ]]
4121	then
4122	sleep 120
4123	else
4124	sleep 30
4125	fi
4126
4127	else
4128
4129	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4130	# USING SSH)
4131	cd $LOCAL_PWD
4132	if [[ $localhost = lckyuh ]]
4133	then
4134	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4135	printf "\n please restart job manually using command:\n"
4136	printf "\n \"$mc\" "
4137	else
4138	eval $mc # THE ' MUST BE EVALUATED
4139	fi
4140	cd - > /dev/null
4141	fi
4142	if [[ $localhost = lckyuh ]]
4143	then
4144	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4145	else
4146	printf "\n$dashes\n *** restart-run initiated \n"
4147	fi
4148
4149
4150	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4151	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4152	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4153	# MAY BE VERY HUGE)
4154	(( i = 0 ))
4155	while (( i < iin ))
4156	do
4157	(( i = i + 1 ))
4158	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4159	then
4160	rm -r $tmp_data_catalog/${frelin[$i]}
4161	fi
4162	done
4163
4164	else
4165
4166	printf "\n +++ no restart-run possible, since errors occured"
4167	printf "\n during the archive process"
4168	fi
4169
4170	fi
4171
4172
4173
4174	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4175	if [[ "$email_notification" != "none" ]]
4176	then
4177
4178	if [[ $localhost != $fromhost ]]
4179	then
4180	if [[ -f CONTINUE_RUN ]]
4181	then
4182	echo "PALM restart run necessary" > email_text
4183	echo "description header of actual run:" >> email_text
4184	cat CONTINUE_RUN >> email_text
4185	echo "mrun-command to restart:" >> email_text
4186	echo "$mc" >> email_text
4187	else
4188	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4189	fi
4190	mail $email_notification < email_text
4191	printf "\n *** email notification sent to \"$email_notification\" "
4192	fi
4193	fi
4194
4195
4196
4197	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4198	cd $HOME
4199	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4200
4201	else
4202
4203	# PREPARING ACTIONS,
4204	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4205
4206	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4207	mrun_com="$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 $remote_username"
4208	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4209	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4210	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4211	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4212	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4213	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4214	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4215	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4216	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4217	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4218	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4219	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4220	if [[ $use_openmp = true ]]
4221	then
4222	mrun_com=${mrun_com}" -O $threads_per_task"
4223	fi
4224	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4225	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4226	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4227	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4228	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4229	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4230	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4231	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4232	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4233	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4234	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4235	if [[ $do_remote = true ]]
4236	then
4237	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4238	fi
4239
4240
4241	# CREATE EXECUTABLE FOR BATCH JOB
4242	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4243	then
4244
4245	printf "\n *** creating the executable for batch job\n"
4246
4247	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4248	if [[ $host != $localhost ]]
4249	then
4250	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4251	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4252	locat=create_executable; exit
4253	fi
4254
4255	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4256	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4257
4258	cp $make_depository .
4259	tar -xf $make_depository > /dev/null 2>&1
4260	cp ../* . > /dev/null 2>&1
4261
4262	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4263
4264	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4265	then
4266	printf "\n +++ error occured while compiling or linking"
4267	locat=compile
4268	exit
4269	fi
4270
4271	mv a.out ..
4272	cd - > /dev/null 2>&1
4273	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4274
4275	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4276
4277	fi
4278
4279
4280	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4281	jobfile=jobfile.$RANDOM
4282
4283
4284	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4285	echo "mkdir $TEMPDIR" >> $jobfile
4286	echo "cd $TEMPDIR" >> $jobfile
4287
4288
4289	# ACTIVATE ERROR-TRACEBACK
4290	if [[ $do_trace = true ]]
4291	then
4292	echo "set -x" >> $jobfile
4293	else
4294	echo "set +vx" >> $jobfile
4295	fi
4296
4297
4298	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4299	if [[ "$init_cmds" != "" ]]
4300	then
4301	echo "$init_cmds" >> $jobfile
4302	fi
4303	if [[ "$module_calls" != "" ]]
4304	then
4305	echo "$module_calls" >> $jobfile
4306	fi
4307
4308
4309	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4310	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4311	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4312	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4313	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4314	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4315	# QUEUEING-SYSTEMS
4316	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
4317	then
4318
4319	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4320	if [[ $restart_run != true ]]
4321	then
4322	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4323	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4324	fi
4325
4326	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4327	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4328	echo "set -x" >> $jobfile
4329	if [[ $host = $localhost ]]
4330	then
4331	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4332	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4333	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4334	then
4335	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4336	else
4337	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4338	fi
4339
4340	else
4341	if [[ $host = ibmkisti ]]
4342	then
4343	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4344	echo "localdir=\`pwd\`" >> $jobfile
4345	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4346	elif [[ $host = lcbullhh ]]
4347	then
4348	echo "localdir=\`pwd\`" >> $jobfile
4349	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4350
4351	elif [[ $host = lccrayb ]]
4352	then
4353	echo "localdir=\`pwd\`" >> $jobfile
4354	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4355	elif [[ $host = lccrayh ]]
4356	then
4357	echo "localdir=\`pwd\`" >> $jobfile
4358	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4359
4360	else
4361	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4362	fi
4363	fi
4364	echo "export SOURCES_COMPLETE=true" >> $jobfile
4365
4366	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4367	# WORKING DIRECTORY OF THE JOB
4368	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4369	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4370	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4371	echo "execute_mrun=true" >> $jobfile
4372	echo " " >> $jobfile
4373
4374	else
4375
4376	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4377	if [[ $do_compile = true ]]
4378	then
4379
4380	source_catalog=SOURCES_FOR_RUN_$fname
4381
4382	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4383	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4384	echo "export SOURCES_COMPLETE=true" >> $jobfile
4385	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4386
4387	for filename in $source_list
4388	do
4389	# BACKSLASH IS USED FOR MASKING
4390	echo "cat > $filename << \"%END%\"" >> $jobfile
4391	cat $source_catalog/$filename >> $jobfile
4392	echo " " >> $jobfile
4393	echo "%END%" >> $jobfile
4394	echo " " >> $jobfile
4395	done
4396
4397	# BACKSLASH IS USED FOR MASKING
4398	echo "cat > Makefile << \"%END%\"" >> $jobfile
4399	cat $source_catalog/Makefile >> $jobfile
4400	echo " " >> $jobfile
4401	echo "%END%" >> $jobfile
4402	echo " " >> $jobfile
4403
4404	echo "cd - > /dev/null" >> $jobfile
4405
4406	fi
4407
4408
4409	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4410	# BACKSLASH IS USED FOR MASKING
4411	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4412	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4413	echo "cat > $config_file << \"%END%\"" >> $jobfile
4414	if [[ $host = lckyuh ]]
4415	then
4416	# NO CROSS-COMPILER ON COMPUTE NODE
4417	sed 's/frtpx/frt/g' $config_file >> $jobfile
4418	else
4419	sed 's/#$.*//g' $config_file >> $jobfile
4420	fi
4421	echo "%END%" >> $jobfile
4422	echo " " >> $jobfile
4423
4424
4425	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4426	# BACKSLASH IS USED FOR MASKING
4427	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4428	if [[ $host = lckyuh ]]
4429	then
4430	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4431	else
4432	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4433	fi
4434	echo "%END%" >> $jobfile
4435	echo "chmod u+x $mrun_script_name" >> $jobfile
4436	echo "execute_mrun=true" >> $jobfile
4437	echo " " >> $jobfile
4438
4439	fi
4440
4441
4442	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4443	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4444	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4445	if [[ $do_remote = true ]]
4446	then
4447	(( i = 0 ))
4448	while (( i < iin ))
4449	do
4450	(( i = i + 1 ))
4451	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4452	if [[ "${transin[$i]}" = job ]]
4453	then
4454	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4455	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4456	echo " " >> $jobfile
4457	echo "%END%" >> $jobfile
4458	else
4459	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4460	fi
4461
4462	# CHECK, IF FILE COULD BE CREATED
4463	echo "if [[ \$? = 1 ]]" >> $jobfile
4464	echo "then" >> $jobfile
4465	echo " echo \" \" " >> $jobfile
4466	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4467	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4468	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4469	echo " execute_mrun=false" >> $jobfile
4470	echo "fi" >> $jobfile
4471	done
4472	fi
4473
4474	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4475	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4476	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4477	echo "LOCAL_PWD=$working_directory" >> $jobfile
4478	echo "export LOCAL_PWD" >> $jobfile
4479
4480	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4481	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4482	echo "export LOCAL_MRUN_PATH" >> $jobfile
4483
4484	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4485	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4486	# then
4487	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4488	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4489	# fi
4490
4491	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4492	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4493	echo "set -x" >> $jobfile
4494	echo "queue=$queue" >> $jobfile
4495	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4496	echo 'ls -al; echo `pwd`' >> $jobfile
4497	echo "cd \$HOME" >> $jobfile
4498	echo "rm -rf $TEMPDIR" >> $jobfile
4499
4500
4501
4502
4503	# START THE JOB USING SUBJOB-COMMAND
4504	if [[ $silent = false ]]
4505	then
4506	printf "\n "
4507	else
4508	printf "\n\n"
4509	fi
4510
4511	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
4512	rm -rf $jobfile
4513
4514
4515	fi # END OF REMOTE-PART

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