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source: palm/trunk/SCRIPTS/mrun @ 1866

Last change on this file since 1866 was 1866, checked in by raasch, 8 years ago
scripts adjusted for lcocean
Property svn:keywords set to `Id Rev`
File size: 169.6 KB

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

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