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source: palm/trunk/SCRIPTS/mrun @ 1944

Last change on this file since 1944 was 1944, checked in by raasch, 8 years ago
adjustments for using HLRN ssh-keys
Property svn:keywords set to `Id Rev`
File size: 169.9 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	# adjustments for using HLRN ssh-keys
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 1944 2016-06-15 06:29:00Z raasch $
29	#
30	# 1940 2016-06-14 05:15:20Z raasch $
31	# adjustments for lckiaps
32	#
33	# 1866 2016-04-15 06:50:59Z raasch
34	# adjusted for lcocean
35	#
36	# 1841 2016-04-07 19:14:06Z raasch
37	# script now running under bash
38	#
39	# 1804 2016-04-05 16:30:18Z maronga
40	# test: implementing an execute mechanism where the execute command is given in the
41	# configuration file
42	# ROPTS removed from execution commands
43	# Warnings about missing optional files or user code changed to informative messages
44	# Removed parameter file check
45	#
46	# 1755 2016-02-22 13:53:39Z maronga
47	# Minor bugfix to last commit
48	#
49	# 1753 2016-02-22 13:49:49Z maronga
50	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
51	#
52	# 1622 2015-07-20 06:21:36Z heinze
53	# bugfix for Mistral (lcbullhh)
54	#
55	# 1621 2015-07-17 11:39:33Z heinze
56	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
57	#
58	# 1609 2015-07-03 15:37:58Z maronga
59	# Modified the random number of the temporary working directory to match the
60	# queuing system number on HLRN-III (lccray*).
61	#
62	# 1604 2015-06-23 15:48:03Z suehring
63	# Enable coupled runs for lcmuk
64	#
65	# 1598 2015-05-29 06:45:40Z raasch
66	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
67	#
68	# 1549 2015-01-30 14:26:16Z suehring
69	# Enable interactive debug sessions with allinea debugger
70	#
71	# 1547 2015-01-29 15:09:12Z witha
72	# adjustments for ForWind computing cluster (lcflow)
73	#
74	# 1491 2014-11-12 08:12:57Z heinze
75	# correct setting of batch_job allowed for ibm-machines
76	#
77	# 1468 2014-09-24 14:06:57Z maronga
78	# Typo removed (addres->address)
79	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
80	# Added support for restart runs (remote) for lcxe6
81	#
82	# 1442 2014-07-28 07:09:10Z raasch
83	# default queues for HLRN-III (lccrayb/lccrayh) defined
84	#
85	# 1422 2014-07-02 10:01:25Z kanani
86	# automatic restarts enabled for lccrayb,
87	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
88	#
89	# 1420 2014-06-10 06:24:14Z raasch
90	# -j1 option added to aprung command for lccrayf (CSC)
91	#
92	# 1402 2014-05-09 14:25:13Z raasch
93	# batch_job added to envpar-NAMELIST
94	#
95	# 1357 2014-04-11 15:02:03Z witha
96	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
97	# possible)
98	#
99	# 1320 2014-03-20 08:40:49Z raasch
100	# check namelist file set false by default
101	#
102	# 1304 2014-03-12 10:29:42Z raasch
103	# ulimit option changed from -Ss to -s
104	#
105	# bugfix: missing "fi" in r1289
106	#
107	# 1289 2014-03-04 07:12:34Z raasch
108	# comments translated to English
109	# necriam-, fimm-, ibmy-, and sgi-specific code removed
110	# export of variables for palm and interpret_config removed
111	#
112	# 1281 2014-02-01 07:55:49Z raasch
113	# rsync-copy restricted to Cray machines, since command is unavailable on some
114	# other systems
115	#
116	# 1279 2014-01-28 12:10:14Z raasch
117	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
118	# in order to remove annoying restrictions concerning the number of processors which
119	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
120	# restriction, one of the nodes will be filled with less than the given number of
121	# tasks per node. A respective warning is given.
122	#
123	# 1274 2014-01-09 13:14:54Z heinze
124	# adjustments for lccrayh
125	#
126	# 1272 2014-01-08 10:19:32Z witha
127	# small adjustment for lcflow
128	#
129	# 1270 2013-12-16 11:05:01Z fricke
130	# call of combine_plot_fields adjusted for lccrayb/lccrayh
131	#
132	# 1255 2013-11-07 14:43:35Z raasch
133	# further adjustments for lccrayb remote access
134	#
135	# 1241 2013-10-30 11:36:58Z heinze
136	# Enable use of nudging input and input of large scale forcing from
137	# external files
138	#
139	# 1229 2013-09-20 06:55:19Z raasch
140	# further adjustments for lccrayb
141	#
142	# 1224 2013-09-16 07:27:23Z raasch
143	# first adjustments for lccrayb
144	#
145	# 1210 2013-08-14 10:58:20Z raasch
146	# fftw support added
147	#
148	# 1201 2013-07-10 16:17:59Z witha
149	# adjustments for Forwind cluster (lcflow)
150	#
151	# 1199 2013-07-05 14:52:22Z raasch
152	# adjustments for CSC Helsinki (lccrayf),
153	# executables for batch jobs can be created in advance, in order to avoid calling
154	# the compiler within the batch job (only works if batch jobs are submitted on
155	# local host)
156	#
157	# 1190 2013-06-25 09:39:21Z heinze
158	# enable use of automatic restarts for ibmh
159	# use of cluster/express queue enabled (ibmh)
160	#
161	# 1124 2013-04-09 15:46:52Z raasch
162	# variable "memory" is exported via typeset option -x, because otherwise an unknown
163	# side effect may lead to data loss while getopts is reading the script-option arguments
164	#
165	# 1122 2013-04-09 08:37:16Z heinze
166	# Bugfix: change type of variable last_char
167	#
168	# 1119 2013-04-05 15:11:19Z raasch
169	# Bugfix for setting -T option for subjob
170	#
171	# 1108 2013-03-05 07:03:32Z raasch
172	# bugfix for coupled runs on lckyut/lckyuh
173	#
174	# 1106 2013-03-04 05:31:38Z raasch
175	# --stdin argument for mpiexec on lckyuh
176	# -y and -Y settings output to header
177	#
178	# 1103 2013-02-20 02:15:53Z raasch
179	# default script runs again under ksh, because of unsolved problems with read
180	# from stdin: when bash script is called from a ksh, message "read error: 0:
181	# Resource temporarily unavailable" appears and script does not stop,
182	# further bash compatibility adjustments,
183	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
184	# on lckyuh, but mrun does not terminate and issues a warning instead
185	#
186	# 1101 2013-02-17 10:20:21Z raasch
187	# script now running under bash instead of ksh, which required small adjustments
188	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
189	# read from stdin),
190	# cross compilername on lckyuh compute nodes replaced by real compiler name
191	#
192	# 1099 2013-02-10 01:47:43Z raasch
193	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
194	# and for Forwind cluster (lcflow)
195	# small further adjustments for lckyut
196	#
197	# 1094 2013-02-03 01:52:12Z raasch
198	# explicit ssh/scp port can be set in config file with environment variable
199	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
200	# decalpha parts (yonsei) removed
201	#
202	# 2013-02-02 07:06:13Z raasch
203	# adjustments for Kyushu-University computing center (lckyut - tatara)
204	#
205	# 1083 2013-01-04 10:22:09Z maronga
206	# bugfix in parameter file check (read %cpp_options was missing)
207	#
208	# 1069 2012-11-28 16:18:43Z maronga
209	# bugfix: coupling mode was always set to mpi2, typos removed
210	#
211	# 1058 2012-11-21 07:00:35Z raasch
212	# Intel inspector (inspxe) is given the number of PEs instead of the number of
213	# nodes
214	#
215	# 1046 2012-11-09 14:38:45Z maronga
216	# code put under GPL (PALM 3.9)
217	#
218	# 21/03/94 - Siggi - first version finished
219	# 03/03/94 - Siggi - script development started
220	#
221	#--------------------------------------------------------------------------------#
222	# mrun - script for running PALM jobs
223	#--------------------------------------------------------------------------------#
224
225
226
227	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
228
229	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
230	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
231	# (TOO MANY ARGUMENTS - PROBLEM)
232	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
233
234	AddFilenames=""
235	additional_conditions=""
236	add_source_path=""
237	afname=""
238	archive_save=true
239	archive_system=none
240	check_namelist_files=false
241	combine_plot_fields=true
242	compiler_name=""
243	cond1=""
244	cond2=""
245	config_file=.mrun.config
246	coupled_dist=""
247	coupled_mode="mpi1"
248	cpp_opts=""
249	cpp_options=""
250	cpumax=0
251	cpurest=0
252	create_executable_for_batch=false
253	delete_temporary_catalog=true
254	do_batch=false
255	do_compile=true
256	do_remote=false
257	do_stagein=true
258	do_stageout=true
259	do_trace=false
260	email_notification="none"
261	exclude=""
262	executable=""
263	execute_command="none"
264	execution_error=false
265	fftw_inc=""
266	fftw_lib=""
267	fftw_support=false
268	fname=test
269	fromhost=""
270	global_revision=""
271	group_number=none
272	host=""
273	host_file=""
274	hp=""
275	ignore_archive_error=false
276	input_list=""
277	interpreted_config_file=""
278	job_catalog="~/job_queue"
279	job_on_file=""
280	keep_data_from_previous_run=false
281	link_local_input=false
282	link_local_output=false
283	localhost_realname=$(hostname)
284	local_dvrserver_running=.FALSE.
285	locat=normal
286	mainprog=""
287	makefile=""
288	max_par_io_str=""
289	mc=$0
290	while [[ $(echo $mc \| grep -c "/") != 0 ]]
291	do
292	mc=`echo $mc \| cut -f2- -d"/"`
293	done
294	module_calls=""
295	mrun_script_name=$mc
296	netcdf_inc=""
297	netcdf_lib=""
298	netcdf_support=false
299	node_usage=default
300	numprocs=""
301	numprocs_atmos=0
302	numprocs_ocean=0
303	OOPT=""
304	openmp=false
305	output_list=""
306	package_list=""
307	queue=none
308	read_from_config=""
309	restart_run=false
310	if [[ `hostname` = rte10 ]]
311	then
312	return_address=133.5.185.60
313	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
314	elif [[ `hostname` = climate0 ]]
315	then
316	return_address=165.132.26.68
317	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
318	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
319	then
320	return_address="schultzl-Latitude-E6540"
321	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
322	elif [[ `hostname` = urban00 ]]
323	then
324	return_address=147.46.30.151
325	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
326	else
327	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
328	fi
329	return_password=""
330	return_username=$LOGNAME
331	remotecall=false
332	remote_username=""
333	run_coupled_model=false
334	run_mode=""
335	store_on_archive_system=false
336	dashes=" ----------------------------------------------------------------------------"
337	silent=false
338	source_list=""
339	source_path=SOURCE
340	tasks_per_node=""
341	threads_per_task=1
342	tmpcreate=false
343	tmp_data_catalog=""
344	transfer_problems=false
345	usern=$LOGNAME
346	use_openmp=false
347	version="MRUN 2.1 Rev$Rev: 1944 $"
348	working_directory=`pwd`
349	TOPT=""
350	XOPT=""
351	zeit=$( date \| cut -c 12-19 )
352
353	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
354	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
355	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
356	# SCRIPT-OPTION ARGUMENTS
357	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
358
359	# ERROR HANDLING IN CASE OF EXIT
360	trap 'rm -rf $working_directory/tmp_mrun
361	if [[ $locat != normal && $locat != control_c ]]
362	then
363
364	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
365	(( i = 0 ))
366	while (( i < iec ))
367	do
368	(( i = i + 1 ))
369	printf "\n *** Execution of ERROR-command:\n"
370	printf " >>> ${err_command[$i]}\n"
371	eval ${err_command[$i]}
372	done
373	if [[ -n $interpreted_config_file ]]
374	then
375	rm -rf $interpreted_config_file
376	fi
377	if [[ -n .mrun_environment ]]
378	then
379	rm -rf .mrun_environment
380	fi
381	if [[ $tmpcreate = true ]]
382	then
383	printf "\n *** Contents of \"$TEMPDIR\":\n"
384	ls -al; cd
385	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
386	fi
387	if [[ "$dvrserver_id" != "" ]]
388	then
389	echo "+++ killing dvrserver_id=$dvrserver_id"
390	kill $dvrserver_id
391	fi
392	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
393	then
394	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
395	fi
396	printf "\n\n+++ MRUN killed \n\n"
397	elif [[ $locat != control_c ]]
398	then
399	printf "\n\n --> all actions finished\n\n"
400	printf " Bye, bye $usern !!\n\n"
401	fi' exit
402
403
404	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
405	trap 'rm -rf $working_directory/tmp_mrun
406	rm -rf $working_directory/tmp_check_namelist_files
407	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
408	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
409	then
410	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
411	fi
412	if [[ "$dvrserver_id" != "" ]]
413	then
414	echo "+++ killing dvrserver_id=$dvrserver_id"
415	kill $dvrserver_id
416	fi
417	printf "\n+++ MRUN killed by \"^C\" \n\n"
418	locat=control_c
419	exit
420	' 2
421
422
423	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
424	# BEEN SET
425	if [[ "$PALM_BIN" = "" ]]
426	then
427	printf "\n +++ environment variable PALM_BIN has not been set"
428	printf "\n please set it to the directory where the PALM scripts are located"
429	locat=palm_bin; exit
430	fi
431	export PATH=$PALM_BIN:$PATH
432
433
434
435	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
436	# WHICH WILL BE USED TO START RESTART-JOBS
437	while getopts :a:AbBc:Cd:D:Fg:G:h:H:i:IkK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
438	do
439	case $option in
440	(a) afname=$OPTARG;;
441	(A) store_on_archive_system=true; mc="$mc -A";;
442	(b) do_batch=true; mc="$mc -b";;
443	(B) delete_temporary_catalog=false; mc="$mc -B";;
444	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
445	(C) restart_run=true; mc="$mc -C";;
446	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
447	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
448	(F) job_on_file="-D"; mc="$mc -F";;
449	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
450	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
451	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
452	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
453	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
454	(I) ignore_archive_error=true; mc="$mc -I";;
455	(k) keep_data_from_previous_run=true; mc="$mc -k";;
456	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
457	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
458	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
459	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
460	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
461	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
462	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
463	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
464	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
465	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
466	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
467	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
468	(S) read_from_config=false; mc="$mc -S";;
469	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
470	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
471	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
472	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
473	(v) silent=true; mc="$mc -v";;
474	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
475	(x) do_trace=true;set -x; mc="$mc -x";;
476	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
477	(y) ocean_file_appendix=true; mc="$mc -y";;
478	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
479	(z) check_namelist_files=false; mc="$mc -z";;
480	(Z) combine_plot_fields=false; mc="$mc -Z";;
481	(\?) printf "\n +++ unknown option $OPTARG \n"
482	printf "\n --> type \"$0 ?\" for available options \n"
483	locat=parameter;exit;;
484	esac
485	done
486
487
488	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
489	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
490	(( to_shift = $OPTIND - 1 ))
491	shift $to_shift
492
493	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
494	if [[ "$1" = "?" ]]
495	then
496	(printf "\n *** mrun can be called as follows:\n"
497	printf "\n $mrun_script_name -b -c.. -d.. -D.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -Z <modus> \n"
498	printf "\n Description of available options:\n"
499	printf "\n Option Description Default-Value"
500	printf "\n -a base name of input files equiv. -d"
501	printf "\n -A archiving when using file-attribute fl"
502	printf "\n -b batch-job on local machine ---"
503	printf "\n -B do not delete temporary directory at end ---"
504	printf "\n -c configuration file .mrun.config"
505	printf "\n -d base name of files attached to program test"
506	printf "\n -D preprocessor(cpp)-directives \"\" "
507	printf "\n -F create remote job file only ---"
508	printf "\n -h execution host $localhost_realname"
509	printf "\n -i INPUT control list \"\" "
510	printf "\n -I archiving errors of previous batch-jobs"
511	printf "\n will be ignored"
512	printf "\n -k keep data from previous run"
513	printf "\n -K additional conditions for controling"
514	printf "\n usage of conditional code and"
515	printf "\n env-variables in configuration file \"\" "
516	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
517	printf "\n -M Makefile name Makefile"
518	printf "\n -n node usage (shared/not_shared) depending on -h"
519	printf "\n -o OUTPUT control list \"\" "
520	printf "\n -O threads per openMP task ---"
521	printf "\n -p software package list \"\" "
522	printf "\n -q queue \"$queue\" "
523	printf "\n -r run control list (combines -i -o) \"\" "
524	printf "\n -s filenames of routines to be compiled \"\" "
525	printf "\n must end with .f, .f90, .F, or .c !"
526	printf "\n use \"..\" for more than one file and wildcards"
527	printf "\n -s LM compiles all locally modified files"
528	printf "\n -S config file interpreted by shellscript ---"
529	printf "\n -t allowed cpu-time in seconds (batch) 0"
530	printf "\n -T tasks per node depending on -h"
531	printf "\n -u username on remote machine \"\" "
532	printf "\n -v no prompt for confirmation ---"
533	printf "\n -w maximum parallel io streams as given by -X"
534	printf "\n -x tracing of mrun for debug purposes ---"
535	printf "\n -X # of processors (on parallel machines) 1"
536	printf "\n -y add appendix \"_O\" to all local output"
537	printf "\n files (ocean precursor runs followed by"
538	printf "\n coupled atmosphere-ocean runs) ---"
539	printf "\n -Y run coupled model, \"#1 #2\" with"
540	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
541	printf "\n -Z skip combine_plot_fields at the end of "
542	printf "\n the simulation ---"
543	printf "\n "
544	printf "\n Possible values of positional parameter <modus>:"
545	printf "\n \"?\" - this outline \n\n") \| more
546	exit
547	elif [[ "$1" != "" ]]
548	then
549	printf "\n +++ positional parameter $1 unknown \n"
550	locat=parameter; exit
551	fi
552
553
554
555	# SHORT STARTING MESSAGE
556	printf "\n*** $version "
557	printf "\n will be executed. Please wait ..."
558
559
560
561	# CHECK, IF CONFIGURATION FILE EXISTS
562	if [[ ! -f $config_file ]]
563	then
564	printf "\n\n +++ configuration file: "
565	printf "\n $config_file"
566	printf "\n does not exist"
567	locat=connect; exit
568	fi
569
570
571	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
572	line=""
573	grep "%host_identifier" $config_file > tmp_mrun
574	while read line
575	do
576	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
577	then
578	HOSTNAME=`echo $line \| cut -d" " -s -f2`
579	host_identifier=`echo $line \| cut -d" " -s -f3`
580	if [[ $localhost_realname = $HOSTNAME ]]
581	then
582	localhost=$host_identifier
583	break
584	fi
585	fi
586	done < tmp_mrun
587
588	if [[ "$localhost" = "" ]]
589	then
590	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
591	printf "\n for local host \"$localhost_realname\"."
592	printf "\n Please add line"
593	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
594	printf "\n to the configuration file."
595	locat=localhost; exit
596	fi
597
598
599	# SET HOST-SPECIFIC VARIABLES
600	case $localhost_realname in
601	(r1\|r2\|h01\|b01) archive_system=tivoli;;
602	(cs*) archive_system=ut;;
603	esac
604
605
606	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
607	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
608	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
609	[[ "$afname" = "" ]] && afname=$fname
610
611
612	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
613	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
614	# STATEMENTS IN THE CONFIGURATION FILE
615	if [[ "$run_mode" != "" ]]
616	then
617	input_list="$input_list $run_mode"
618	output_list="$output_list $run_mode"
619	fi
620
621
622	# ??? is this (and the respective option -H) really required ???
623	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
624	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
625	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
626	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
627	if [[ "$fromhost" = "" ]]
628	then
629	fromhost=$localhost
630	fi
631
632
633	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
634	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
635	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
636	# TO BE SUBMITTED (I.E. do_batch=true)
637	if [[ -n $host && "$host" != $localhost ]]
638	then
639	do_batch=true
640	do_remote=true
641	case $host in
642	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
643	(*) printf "\n"
644	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
645	printf "\n is not available"
646	locat=nqs; (( iec = 0 )); exit;;
647	esac
648	else
649	host=$localhost
650	fi
651
652
653	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
654	if [[ -n $additional_conditions ]]
655	then
656	cond1=`echo $additional_conditions \| cut -d" " -f1`
657	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
658	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
659	if [[ -n $dummy ]]
660	then
661	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
662	locat=options; exit
663	fi
664	block=_$cond1
665	[[ -n $cond2 ]] && block=${block}_$cond2
666	fi
667
668
669	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
670	if [[ $run_coupled_model = true ]]
671	then
672
673	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
674	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
675
676	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
677	then
678
679	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
680	printf "\n PEs (total) : $numprocs"
681	printf "\n PEs (atmosphere): $numprocs_atmos"
682	printf "\n PEs (ocean) : $numprocs_ocean"
683	locat=coupling; exit
684
685	fi
686
687
688	# GET coupled_mode FROM THE CONFIG FILE
689	line=""
690	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
691	while read line
692	do
693	echo line=\"$line\"
694	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
695	then
696	coupled_mode="mpi2"
697	fi
698	done < tmp_mrun
699
700	fi
701
702	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
703	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
704	then
705	if [[ $ignore_archive_error = false ]]
706	then
707	printf "\n +++ data archiving of previous run failed"
708	printf "\n see directory \~/job_queue on remote machine"
709	locat=archive; exit
710	else
711	printf "\n +++ warning: data archiving in a previous run failed"
712	printf "\n MRUN continues, trying to get backup copy"
713	fi
714	fi
715
716
717	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
718	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
719	mrun_memory=$memory
720	mrun_group_number=$group_number
721	mrun_cpumax=$cpumax
722	mrun_numprocs=$numprocs
723
724
725	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
726	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
727	if [[ "$read_from_config" = false ]]
728	then
729	[[ $silent = false ]] && printf "\n Reading the configuration file... "
730
731	# READ THE CONFIGURATION FILE LINE BY LINE
732	while read zeile
733	do
734	[[ $silent = false ]] && printf "."
735
736
737	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
738	eval zeile=\"$zeile\"
739
740
741	# INTERPRET THE LINE
742	if [[ "$(echo $zeile)" = "" ]]
743	then
744	# EMPTY LINE, NO ACTION
745	continue
746
747	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
748	then
749
750	# LINE IS A COMMENT LINE
751	true
752
753	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
754	then
755
756	# LINE DEFINES AN ENVIRONMENT-VARIABLE
757	zeile=$(echo $zeile \| cut -c2-)
758	var=`echo $zeile \| cut -d" " -f1`
759	value=`echo $zeile \| cut -d" " -s -f2`
760	for_host=`echo $zeile \| cut -d" " -s -f3`
761	for_cond1=`echo $zeile \| cut -d" " -s -f4`
762	for_cond2=`echo $zeile \| cut -d" " -s -f5`
763
764	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
765	then
766
767	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
768	# "::" IS REPLACED BY ":".
769	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
770
771
772	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
773	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
774	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
775	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
776	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
777	# CONFIGURATION-FILE.
778	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
779	then
780	eval $var=\$value
781
782	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
783	if [[ $do_trace = true ]]
784	then
785	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
786	fi
787	fi
788
789	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
790	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
791	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
792	# MUST HAVE TO BE STARTED
793	if [[ $var = host ]]
794	then
795	if [[ -n $host && "$host" != $localhost ]]
796	then
797	do_batch=true
798	do_remote=true
799	case $host in
800	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
801	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
802	printf "\n is not available"
803	locat=nqs; exit;;
804	esac
805	else
806	host=$localhost
807	fi
808	fi
809
810	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
811	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
812	# BY MRUN (E.G. subjob)
813	export $var
814	fi
815
816
817
818
819	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
820	then
821
822	# LINE DEFINES ERROR-COMMAND
823	(( iec = iec + 1 ))
824	zeile=$(echo $zeile \| cut -c4-)
825	err_command[$iec]="$zeile"
826
827	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
828	then
829
830	# LINE DEFINES INPUT-COMMAND
831	(( iic = iic + 1 ))
832	zeile=$(echo $zeile \| cut -c4-)
833	in_command[$iic]="$zeile"
834
835	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
836	then
837
838	# LINE DEFINES OUTPUT-COMMAND
839	(( ioc = ioc + 1 ))
840	zeile=$(echo $zeile \| cut -c4-)
841	out_command[$ioc]="$zeile"
842
843	else
844
845	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
846	# s2a: in/out - field
847	# s2b: loc - field (optional)
848	# s2c: tr/ar - field (optional)
849	s1=`echo $zeile \| cut -d" " -f1`
850	s2=`echo $zeile \| cut -d" " -s -f2`
851	s2a=$(echo $s2 \| cut -d":" -f1)
852	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
853	then
854	s2b=""
855	s2c=""
856	else
857	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
858	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
859	fi
860	s3=`echo $zeile \| cut -d" " -f3`
861	s4=`echo $zeile \| cut -d" " -s -f4`
862	s5=`echo $zeile \| cut -d" " -s -f5`
863	s6=`echo $zeile \| cut -d" " -s -f6`
864
865
866	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
867	# INPUT- OR OUTPUT-LIST.
868	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
869	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
870	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
871	# IS NOT CHECKED AND STORED.
872	IFSALT="$IFS"; IFS="$IFS:"
873	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
874	then
875	found=false
876	for actual in $input_list
877	do
878	for formal in $s3
879	do
880	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
881	done
882	done
883	if [[ $found = true ]]
884	then
885	(( iin = iin + 1 ))
886	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
887	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
888	extin[$iin]=$s6
889	fi
890	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
891	then
892	found=false
893	for actual in $output_list
894	do
895	for formal in $s3
896	do
897	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
898	done
899	done
900	if [[ $found = true ]]
901	then
902	(( iout = iout + 1 ))
903	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
904	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
905	fi
906	elif [[ "$s2a" != in && "$s2a" != out ]]
907	then
908	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
909	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
910	locat=connect; exit
911	fi
912	IFS="$IFSALT"
913	fi
914	done < $config_file
915
916	else
917
918	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
919	[[ $silent = false ]] && printf "..."
920	interpreted_config_file=.icf.$RANDOM
921
922
923
924	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
925	cat > .mrun_environment << %%END%%
926	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
927	config_file = '$config_file', do_remote = '$do_remote',
928	do_trace = '$do_trace', host = '$host',
929	input_list = '$input_list', icf = '$interpreted_config_file',
930	localhost = '$localhost', output_list = '$output_list' /
931
932	%%END%%
933
934	if [[ "$host" != $localhost ]]
935	then
936
937	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
938	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
939	if [[ $? != 0 ]]
940	then
941	printf "\n\n +++ no interpret_config found"
942	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
943	locat=interpret_config; exit
944	fi
945	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
946	$interpret_config_executable
947
948	else
949
950	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
951	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
952	then
953	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
954	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
955	locat=interpret_config; exit
956	else
957	interpret_config${block}.x
958	fi
959
960	fi
961	rm .mrun_environment
962
963
964	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
965	chmod u+x $interpreted_config_file
966	export PATH=$PATH:.
967	. $interpreted_config_file
968	rm $interpreted_config_file
969
970	fi
971
972
973	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
974	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
975	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
976	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
977	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
978	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
979	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
980
981
982	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
983	# FOR SOURCE-FILES TO BE COMPILED.
984	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
985	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
986	if [[ "$SOURCES_COMPLETE" = "" ]]
987	then
988
989	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
990	# HAS BEEN DEFINED
991	source_path=""
992	line=""
993	grep "%source_path" $config_file > tmp_mrun
994	while read line
995	do
996	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
997	then
998	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
999	then
1000	global_source_path=`echo $line \| cut -d" " -f2`
1001	fi
1002	fi
1003	done < tmp_mrun
1004
1005	line=""
1006	found=false
1007	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1008	while read line
1009	do
1010	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1011	then
1012	if [[ $found = true ]]
1013	then
1014	printf "\n\n +++ more than one source path found in configuration file"
1015	printf "\n for local host \"$localhost\" "
1016	locat=source_path; exit
1017	fi
1018	source_path=`echo $line \| cut -d" " -f2`
1019	found=true
1020	fi
1021	done < tmp_mrun
1022	rm tmp_mrun
1023
1024	if [[ "$source_path" = "" ]]
1025	then
1026	if [[ "$global_source_path" != "" ]]
1027	then
1028	source_path=$global_source_path
1029	else
1030	printf "\n\n +++ no source path found in configuration file"
1031	printf "\n for local host \"$localhost\" "
1032	locat=source_path; exit
1033	fi
1034	fi
1035	eval source_path=$source_path
1036
1037	if [[ ! -d $source_path ]]
1038	then
1039	printf "\n\n +++ source path \"$source_path\" on local host"
1040	printf "\n \"$localhost\" does not exist"
1041	locat=source_path; exit
1042	fi
1043
1044	fi
1045
1046
1047	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1048	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1049	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1050	then
1051	global_revision=`svnversion $source_path 2>/dev/null`
1052	global_revision="Rev: $global_revision"
1053	fi
1054
1055
1056	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1057	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1058	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1059	if [[ -n $host && "$host" != $localhost ]]
1060	then
1061	do_batch=true
1062	do_remote=true
1063	case $host in
1064	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|lcocean\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1065	(*) printf "\n"
1066	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1067	printf "\n is not available"
1068	locat=nqs; (( iec = 0 )); exit;;
1069	esac
1070	else
1071	host=$localhost
1072	fi
1073
1074
1075
1076	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1077	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1078	then
1079
1080	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1081	if [[ ! -n $numprocs ]]
1082	then
1083	printf "\n"
1084	printf "\n +++ option \"-K parallel\" requires additional specification"
1085	printf "\n of the number of processors to be used by"
1086	printf "\n mrun-option \"-X\" or by environment-variable"
1087	printf "\n \"numprocs\" in the configuration file"
1088	locat=numprocs; (( iec = 0 )); exit
1089	fi
1090
1091	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1092	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1093	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1094	then
1095	printf "\n"
1096	printf "\n +++ option \"-T\" (tasks per node) is missing"
1097	printf "\n set -T option or define tasks_per_node in the config file"
1098	locat=tasks_per_node; (( iec = 0 )); exit
1099	fi
1100
1101	if (( numprocs < tasks_per_node ))
1102	then
1103	printf "\n"
1104	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1105	printf "\n given values: -T $tasks_per_node -X $numprocs"
1106	locat=tasks_per_node; (( iec = 0 )); exit
1107	fi
1108
1109	if [[ $host != lcflow && $host != lcxt5m ]]
1110	then
1111	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1112	(( ival = $tasks_per_node ))
1113	(( pes = numprocs ))
1114	(( ii = pes / ival ))
1115	(( remaining_pes = pes - ii * ival ))
1116	if (( remaining_pes > 0 ))
1117	then
1118	printf "\n"
1119	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1120	printf "\n divisor of the total number of processors (option \"-X\")"
1121	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1122	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1123	(( nodes = nodes + 1 ))
1124	fi
1125	fi
1126
1127
1128	# SETTINGS FOR SUBJOB-COMMAND
1129	OOPT="-O $threads_per_task"
1130
1131	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1132	if [[ "$tasks_per_node" != "" ]]
1133	then
1134	TOPT="-T $tasks_per_node"
1135	fi
1136
1137	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1138	if [[ $node_usage = default ]]
1139	then
1140	if [[ $host = ibms ]]
1141	then
1142	node_usage=shared
1143	else
1144	node_usage=not_shared
1145	fi
1146	fi
1147
1148	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1149	then
1150	printf "\n"
1151	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1152	printf "\n \"shared\" or \"not_shared\""
1153	locat=tasks_per_node; (( iec = 0 )); exit
1154	fi
1155
1156	fi
1157
1158	# CHECK IF HOSTFILE EXISTS
1159	if [[ -n $hostfile ]]
1160	then
1161	if [[ ! -f $hostfile ]]
1162	then
1163	printf "\n"
1164	printf "\n +++ hostfile \"$hostfile\" does not exist"
1165	locat=hostfile; exit
1166	fi
1167	fi
1168
1169
1170	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1171	if [[ "$maximum_parallel_io_streams" = "" ]]
1172	then
1173	maximum_parallel_io_streams=$numprocs
1174	fi
1175
1176
1177	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1178	if [[ "$scp_port" != "" ]]
1179	then
1180	PORTOPT="-P $scp_port"
1181	SSH_PORTOPT="-p $scp_port"
1182	fi
1183
1184
1185	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1186	# CONFIG-FILE
1187	if [[ "$ssh_key" != "" ]]
1188	then
1189	ssh_key="-i $HOME/.ssh/$ssh_key"
1190	fi
1191
1192
1193	# SET DEFAULT-QUEUE, IF NOT GIVEN
1194	if [[ $queue = none ]]
1195	then
1196	case $host in
1197	(ibmh) queue=cluster;;
1198	(ibmkisti) queue=class.32plus;;
1199	(lcbullhh) queue=compute;;
1200	(lccrayb) queue=mpp1q;;
1201	(lccrayh) queue=mpp1q;;
1202	(lckiaps) queue=normal;;
1203	(lckyoto) queue=ph;;
1204	(lckyuh) queue=fx-single;;
1205	(lckyut) queue=cx-single;;
1206	(lctit) queue=S;;
1207	(nech) queue=none;;
1208	(unics) queue=unics;;
1209	esac
1210	fi
1211
1212
1213	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1214	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1215	(( i = 0 ))
1216	while (( i < iin ))
1217	do
1218	(( i = i + 1 ))
1219	(( maxcycle = 0 ))
1220
1221	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1222	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1223	if [[ "${actionin[$i]}" = di ]]
1224	then
1225	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1226	# HOST ONLY
1227	eval filename=${pathin[$i]}/${endin[$i]}
1228	else
1229	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1230	# HOST ONLY
1231	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1232	fi
1233	eval pathname=${pathin[$i]}
1234
1235	# CHECK IF FILE EXISTS
1236	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1237	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1238	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1239	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1240	then
1241
1242	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1243	if [[ "${transin[$i]}" != "locopt" ]]
1244	then
1245	printf "\n\n +++ INPUT-file: "
1246	if [[ "${extin[$i]}" = "" ]]
1247	then
1248	printf "\n $filename"
1249	else
1250	printf "\n $filename.${extin[$i]}"
1251	fi
1252	printf "\n does not exist\n"
1253	locat=input; exit
1254	else
1255	transin[$i]="unavailable"
1256	fi
1257	else
1258
1259	# DETERMINE THE FILE'S CYCLE NUMBER
1260	ls -1 -d $filename > filelist 2>/dev/null
1261	ls -1 -d $filename.* >> filelist 2>/dev/null
1262	while read zeile
1263	do
1264	cycle=$(echo $zeile \| cut -f2 -d".")
1265	if [[ "$cycle" = "$zeile" ]]
1266	then
1267	(( icycle = 0 ))
1268	elif [[ "$cycle" = "${extin[$i]}" ]]
1269	then
1270	(( icycle = 0 ))
1271	else
1272	(( icycle = $cycle ))
1273	fi
1274	if (( icycle > maxcycle ))
1275	then
1276	(( maxcycle = icycle ))
1277	file_to_be_used=$zeile
1278	fi
1279	done <filelist
1280	rm filelist
1281
1282	# APPEND CYCLE NUMBER TO FILENAME
1283	if (( maxcycle > 0 ))
1284	then
1285	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1286	then
1287	filename=${filename}.$maxcycle.${extin[$i]}
1288	else
1289	filename=${filename}.$maxcycle
1290	fi
1291	else
1292	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1293	then
1294	filename=${filename}.${extin[$i]}
1295	fi
1296	fi
1297
1298	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1299	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1300	absnamein[$i]=$filename
1301	if (( maxcycle > 0 ))
1302	then
1303	if [[ "${actionin[$i]}" = di ]]
1304	then
1305	frelin[$i]=${endin[$i]}.$maxcycle
1306	else
1307	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1308	fi
1309	else
1310	if [[ "${actionin[$i]}" = di ]]
1311	then
1312	frelin[$i]=${endin[$i]}
1313	else
1314	frelin[$i]=${afname}${endin[$i]}
1315	fi
1316	fi
1317
1318	fi
1319	done
1320
1321	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1322	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1323	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1324	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1325	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1326	# REMOTE HOST)
1327	(( i = 0 ))
1328	while (( i < iout ))
1329	do
1330	(( i = i + 1 ))
1331	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1332	then
1333	if [[ "${actionout[$i]}" = tr ]]
1334	then
1335	actionout[$i]=""
1336	elif [[ "${actionout[$i]}" = trpe ]]
1337	then
1338	actionout[$i]=pe
1339	elif [[ "${actionout[$i]}" = tra ]]
1340	then
1341	actionout[$i]=a
1342	fi
1343	(( maxcycle = 0 ))
1344	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1345	eval catalogname=${pathout[$i]}
1346	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1347	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1348	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1349	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1350	then
1351
1352	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1353	if cat /dev/null > $filename
1354	then
1355	rm $filename
1356	else
1357
1358	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1359	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1360	if [[ ! -d $catalogname ]]
1361	then
1362	if mkdir -p $catalogname
1363	then
1364	printf "\n\n *** directory:"
1365	printf "\n $catalogname"
1366	printf "\n was created\n"
1367	else
1368	printf "\n\n +++ OUTPUT-file:"
1369	printf "\n $filename"
1370	printf "\n cannot be created, because directory does not exist"
1371	printf "\n and cannot be created either"
1372	printf "\n"
1373	locat=output ; exit
1374	fi 2>/dev/null
1375	else
1376	printf "\n\n +++ OUTPUT-file:"
1377	printf "\n $filename"
1378	printf "\n cannot be created, although directory exists"
1379	printf "\n"
1380	locat=output ; exit
1381	fi
1382	fi 2>/dev/null
1383	else
1384
1385	# DETERMINE THE CYCLE NUMBER
1386	ls -1 -d $filename > filelist 2>/dev/null
1387	ls -1 -d $filename.* >> filelist 2>/dev/null
1388	while read zeile
1389	do
1390	cycle=$(echo $zeile \| cut -f2 -d".")
1391	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1392	then
1393	(( icycle = 1 ))
1394	else
1395	(( icycle = $cycle + 1 ))
1396	fi
1397	if (( icycle > maxcycle ))
1398	then
1399	(( maxcycle = icycle ))
1400	fi
1401	done <filelist
1402	rm filelist
1403	fi
1404
1405	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1406	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1407	if [[ "${actionout[$i]}" != a ]]
1408	then
1409	if (( maxcycle > 0 ))
1410	then
1411	filename=${filename}.$maxcycle
1412	if cat /dev/null > $filename
1413	then
1414	rm $filename
1415	else
1416	printf "\n +++ OUTPUT-file:"
1417	printf "\n $filename"
1418	printf "\n cannot be created"
1419	locat=output ; exit
1420	fi
1421	fi
1422	else
1423	(( maxcycle = maxcycle - 1 ))
1424	if (( maxcycle > 0 ))
1425	then
1426	filename=${filename}.$maxcycle
1427	fi
1428	fi
1429
1430	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1431	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1432	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1433	pathout[$i]=$filename
1434	if (( maxcycle > 0 ))
1435	then
1436	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1437	else
1438	frelout[$i]=${fname}${endout[$i]}
1439	fi
1440
1441	fi
1442	done
1443
1444
1445	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1446	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1447	then
1448	if [[ "$dvr_inc" = "" ]]
1449	then
1450	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1451	printf "\n This is required for the dvrp_graphics package.\n"
1452	locat=dvr; exit
1453	fi
1454	if [[ "$dvr_lib" = "" ]]
1455	then
1456	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1457	printf "\n This is required for the dvrp_graphics package.\n"
1458	locat=dvr; exit
1459	fi
1460	fi
1461
1462
1463	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1464	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1465	if [[ "$mainprog" = "" && "$executable" = "" ]]
1466	then
1467	printf "\n +++ neither main program nor executable defined"
1468	locat=source; exit
1469	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1470	then
1471	printf "\n +++ main program as well as executable defined"
1472	locat=source; exit
1473	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1474	then
1475	do_compile=false
1476	fi
1477
1478
1479	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1480	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1481	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1482	then
1483	rm -rf SOURCES_FOR_RUN_$fname
1484	mkdir SOURCES_FOR_RUN_$fname
1485	fi
1486
1487
1488	# COLLECT ALL ROUTINES TO BE COMPILED
1489	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1490	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1491	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1492	then
1493
1494	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1495
1496	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1497	then
1498
1499	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1500	source_list=""
1501	cd $source_path
1502
1503
1504	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1505	if [[ ! -d .svn ]]
1506	then
1507	printf "\n\n +++ source directory"
1508	printf "\n \"$source_path\" "
1509	printf "\n is not under control of \"subversion\"."
1510	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1511	fi
1512
1513
1514	# LIST ALL MODIFIED SOURCE CODE FILES
1515	Filenames=""
1516	svn status > tmp_mrun
1517	while read line
1518	do
1519	firstc=`echo $line \| cut -c1`
1520	if [[ $firstc = M \|\| $firstc = "?" ]]
1521	then
1522	Name=`echo "$line" \| cut -c8-`
1523	extension=`echo $Name \| cut -d. -f2`
1524	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1525	then
1526	Filenames="$Filenames "$Name
1527	fi
1528	fi
1529	done < tmp_mrun
1530
1531
1532	# COPY FILES TO SOURCES_FOR_RUN_...
1533	for dateiname in $Filenames
1534	do
1535	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1536	source_list=$source_list"$dateiname "
1537	done
1538
1539	cd - > /dev/null
1540
1541
1542	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1543	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1544	elif [[ "$source_list" != "" && $restart_run != true ]]
1545	then
1546
1547	cd $source_path
1548
1549	for filename in $source_list
1550	do
1551
1552	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1553	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1554	then
1555	printf "\n +++ source code file: $filename"
1556	printf "\n must not contain (\"/\") "
1557	locat=source; exit
1558	fi
1559
1560	if [[ ! -f $filename ]]
1561	then
1562	printf "\n +++ source code file: $filename"
1563	printf "\n does not exist"
1564	locat=source; exit
1565	else
1566	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1567	fi
1568
1569	done
1570
1571	cd - > /dev/null
1572
1573	fi
1574
1575
1576	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1577	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1578	if [[ $restart_run != true ]]
1579	then
1580
1581	if [[ ! -f "$source_path/$mainprog" ]]
1582	then
1583	printf "\n\n +++ main program: $mainprog"
1584	printf "\n does not exist in source directory"
1585	printf "\n \"$source_path\"\n"
1586	locat=source; exit
1587	else
1588	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1589	then
1590	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1591	source_list=${mainprog}" $source_list"
1592	fi
1593	fi
1594	fi
1595
1596
1597	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1598	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1599	if [[ "$restart_run" != true ]]
1600	then
1601	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1602	if [[ ! -f $makefile ]]
1603	then
1604	printf "\n +++ file \"$makefile\" does not exist"
1605	locat=make; exit
1606	else
1607	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1608	fi
1609	fi
1610
1611
1612	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1613	if [[ $restart_run != true && "$add_source_path" != "" ]]
1614	then
1615
1616	# DOES THE DIRECTORY EXIST?
1617	if [[ ! -d $add_source_path ]]
1618	then
1619	printf "\n\n *** INFORMATIVE: additional source code directory"
1620	printf "\n \"$add_source_path\" "
1621	printf "\n does not exist or is not a directory."
1622	printf "\n No source code will be used from this directory!\n"
1623	add_source_path=""
1624	if [[ $silent == false ]]
1625	then
1626	sleep 3
1627	fi
1628	else
1629
1630	cd $add_source_path
1631	found=false
1632
1633	Names=$(ls -1 *.f90 2>&1)
1634	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1635	Names=$(ls -1 *.F90 2>&1)
1636	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1637	Names=$(ls -1 *.F 2>&1)
1638	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1639	Names=$(ls -1 *.f 2>&1)
1640	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1641	Names=$(ls -1 *.c 2>&1)
1642	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1643
1644	cd - > /dev/null
1645	cd SOURCES_FOR_RUN_$fname
1646
1647	# COPY MAKEFILE IF EXISTING
1648	if [[ -f $add_source_path/Makefile ]]
1649	then
1650	printf "\n\n *** user Makefile from directory"
1651	printf "\n \"$add_source_path\" is used \n"
1652	if [[ $silent == false ]]
1653	then
1654	sleep 1
1655	fi
1656	cp $add_source_path/Makefile .
1657	fi
1658
1659	for dateiname in $AddFilenames
1660	do
1661	if [[ -f $dateiname ]]
1662	then
1663	printf "\n +++ source code file \"$dateiname\" found in additional"
1664	printf "\n source code directory \"$add_source_path\" "
1665	printf "\n but was also given with option \"-s\" which means that it should be taken"
1666	printf "\n from directory \"$source_path\"."
1667	locat=source; exit
1668	fi
1669
1670	cp $add_source_path/$dateiname .
1671	source_list="$source_list $dateiname"
1672
1673	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1674	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1675	then
1676	printf "\n\n +++ user file \"$dateiname\" "
1677	printf "\n is not listed in Makefile \n"
1678	locat=source; exit
1679	else
1680
1681	if [[ $found = false ]]
1682	then
1683	found=true
1684	printf "\n\n *** following user file(s) added to the"
1685	printf " files to be translated:\n "
1686	fi
1687	printf "$dateiname "
1688	if [[ $silent == false ]]
1689	then
1690	sleep 0.5
1691	fi
1692
1693	fi
1694	done
1695	[[ $found = true ]] && printf "\n"
1696	cd - > /dev/null
1697	fi
1698	fi
1699
1700
1701	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1702	# TO THE LIST OF FILES TO BE COMPILED
1703	if [[ $restart_run != true && -n $package_list ]]
1704	then
1705
1706	cd $source_path
1707
1708	for package in $package_list
1709	do
1710
1711	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1712
1713	# DETERMINE FILES BELONGING TO THE PACKAGE
1714	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1715	# THE NAME OF THE DIRECTORY
1716	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1717
1718
1719	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1720	# IF THEY ARE NOT ALREADY PART OF THE LIST
1721	for source_list_name in $package_source_list
1722	do
1723	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1724	then
1725
1726	# ONLY TAKE FILES WITH VALID SUFFIX
1727	ending=`echo $source_list_name \| cut -f2 -d.`
1728	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1729	then
1730	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1731	source_list="$source_list $source_list_name"
1732	fi
1733	fi
1734	done
1735	done
1736
1737	cd - > /dev/null
1738	fi
1739
1740	fi # do_compile=true
1741
1742
1743	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1744	# AND SET PRE-PROCESSOR DIRECTIVES
1745	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1746	then
1747
1748	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1749	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1750	then
1751	cpp_options="${cpp_options},-D__ibm=__ibm"
1752	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1753	then
1754	cpp_options="$cpp_options -D__nec"
1755	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1756	then
1757	cpp_options="$cpp_options -D__lc"
1758	else
1759	cpp_options="$cpp_options -D__$localhost"
1760	fi
1761
1762	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1763	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1764	then
1765	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1766	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1767	else
1768	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1769	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1770	fi
1771
1772	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1773	if [[ -n $package_list ]]
1774	then
1775	for package in $package_list
1776	do
1777	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1778	then
1779	if [[ $package != "dvrp_graphics+1PE" ]]
1780	then
1781	cpp_options="${cpp_options},-D__$package=__$package"
1782	else
1783	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1784	export use_seperate_pe_for_dvrp_output=true
1785	fi
1786	else
1787	if [[ $package != "dvrp_graphics+1PE" ]]
1788	then
1789	cpp_options="$cpp_options -D__$package"
1790	else
1791	cpp_options="$cpp_options -D__dvrp_graphics"
1792	export use_seperate_pe_for_dvrp_output=true
1793	fi
1794	fi
1795	done
1796	fi
1797
1798	# SET DIRECTIVES GIVEN BY OPTION -D
1799	if [[ -n $cpp_opts ]]
1800	then
1801	for popts in $cpp_opts
1802	do
1803	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1804	then
1805	cpp_options="${cpp_options},-D__$popts=__$popts"
1806	else
1807	cpp_options="$cpp_options -D__$popts"
1808	fi
1809	done
1810	fi
1811
1812	else
1813
1814
1815	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1816	if [[ $do_remote = false ]]
1817	then
1818	if [[ ! -f $executable ]]
1819	then
1820	printf "\n +++ executable file: $executable"
1821	printf "\n does not exist"
1822	locat=executable; exit
1823	fi
1824	fi
1825	fi
1826
1827
1828	# DETERMINE THE JOB MODE
1829	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1830	then
1831	if [[ "$LOADLBATCH" = yes ]]
1832	then
1833	batch_job=.TRUE.
1834	jobmo=BATCH
1835	else
1836	batch_job=.FALSE.
1837	jobmo=INTERACTIVE
1838	fi
1839	else
1840	if [[ "$ENVIRONMENT" = BATCH ]]
1841	then
1842	batch_job=.TRUE.
1843	jobmo=BATCH
1844	else
1845	batch_job=.FALSE.
1846	jobmo=INTERACTIVE
1847	fi
1848	fi
1849
1850	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1851	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1852	then
1853	printf "\n +++ no interactive runs allowed on host \"$host\" "
1854	printf "\n please submit batch job using mrun option \"-b\" \n"
1855	locat=normal; exit
1856	fi
1857
1858
1859	# CHECK, IF USER DEFINED A COMPILER
1860	if [[ "$compiler_name" = "" ]]
1861	then
1862
1863	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1864	locat=compiler_name; exit
1865
1866	fi
1867
1868
1869	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1870
1871	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1872	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1873	then
1874	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1875	if [[ "$kennung" = "" ]]
1876	then
1877	kennung=$RANDOM
1878	fi
1879	else
1880	kennung=$RANDOM
1881	fi
1882
1883	if [[ "$tmp_user_catalog" = "" ]]
1884	then
1885	if [[ $localhost = ibmh ]]
1886	then
1887	tmp_user_catalog=$SCRATCH
1888	elif [[ $localhost = nech ]]
1889	then
1890	tmp_user_catalog=$WRKSHR
1891	else
1892	tmp_user_catalog=/tmp
1893	fi
1894	fi
1895	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1896
1897
1898	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1899	if [[ "$tmp_data_catalog" = "" ]]
1900	then
1901	if [[ $localhost = nech ]]
1902	then
1903	tmp_data_catalog=$WRKSHR/mrun_restart_data
1904	else
1905	tmp_data_catalog=/tmp/mrun_restart_data
1906	fi
1907	fi
1908
1909
1910	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1911	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1912	then
1913	eval fopts=\"$fopts\"
1914	eval lopts=\"$lopts\"
1915	fi
1916
1917
1918	# DETERMINE COMPILE- AND LINK-OPTIONS
1919	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1920	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1921	XOPT="-X $numprocs"
1922
1923
1924	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1925	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1926	done=false
1927	while [[ $done = false ]]
1928	do
1929	cputime=$cpumax
1930	if (( $cputime == 0 ))
1931	then
1932	if [[ $do_batch = true ]]
1933	then
1934	printf "\n +++ cpu-time is undefined"
1935	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1936	printf "\n >>> "
1937	read cputime 1>/dev/null 2>&1
1938	else
1939	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1940	fi
1941	else
1942	done=true
1943	fi
1944	cpumax=$cputime
1945	done
1946
1947	(( minuten = cputime / 60 ))
1948	(( sekunden = cputime - minuten * 60 ))
1949
1950
1951	# CHECK THE MEMORY DEMAND
1952	if [[ $do_batch = true ]]
1953	then
1954	done=false
1955	while [[ $done = false ]]
1956	do
1957	if (( memory == 0 ))
1958	then
1959	printf "\n +++ memory demand is undefined"
1960	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1961	printf "\n >>> "
1962	read memory 1>/dev/null 2>&1
1963	else
1964	done=true
1965	fi
1966	done
1967	fi
1968
1969
1970	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1971	if [[ $do_remote = true && -z $remote_username ]]
1972	then
1973	while [[ -z $remote_username ]]
1974	do
1975	printf "\n +++ username on remote host \"$host\" is undefined"
1976	printf "\n >>> Please type username:"
1977	printf "\n >>> "
1978	read remote_username
1979	done
1980	mc="$mc -u$remote_username"
1981	fi
1982
1983	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1984	if [[ "$login_init_cmd" != "" ]]
1985	then
1986	export init_cmds="${login_init_cmd};"
1987	fi
1988
1989
1990	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1991	if [[ "$modules" != "" ]]
1992	then
1993	if [[ $host = lctit ]]
1994	then
1995	export module_calls=". $modules"
1996	else
1997	export module_calls="module load ${modules};"
1998	fi
1999	fi
2000
2001	# OUTPUT OF THE MRUN-HEADER
2002	calltime=$(date)
2003	printf "\n"
2004	printf "#------------------------------------------------------------------------# \n"
2005	printf "\| %-35s%35s \| \n" "$version" "$calltime"
2006	printf "\| \| \n"
2007	spalte1="called on:"; spalte2=$localhost_realname
2008	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2009	if [[ $do_remote = true ]]
2010	then
2011	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2012	else
2013	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2014	fi
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	if [[ -n $numprocs ]]
2017	then
2018	if [[ $run_coupled_model = false ]]
2019	then
2020	spalte1="number of PEs:"; spalte2=$numprocs
2021	else
2022	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2023	fi
2024	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2025	fi
2026	if [[ -n $tasks_per_node ]]
2027	then
2028	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2029	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2030	if (( remaining_pes > 0 ))
2031	then
2032	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2033	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2034	fi
2035	fi
2036	if [[ $maximum_parallel_io_streams != $numprocs ]]
2037	then
2038	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2039	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2040	fi
2041	if [[ $use_openmp = true ]]
2042	then
2043	spalte1="threads per task:"; spalte2="$threads_per_task"
2044	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2045	fi
2046	printf "\| \| \n"
2047	if [[ $do_compile = true ]]
2048	then
2049	if [[ "$mopts" != "" ]]
2050	then
2051	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2052	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2053	zeile=$(echo "$mopts" \| cut -c46-)
2054	while [[ "$zeile" != "" ]]
2055	do
2056	spalte1=""
2057	spalte2=$(echo "$zeile" \| cut -c-45)
2058	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2059	zeile=$(echo "$zeile" \| cut -c46-)
2060	done
2061	fi
2062
2063	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2064	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2065	zeile=$(echo "$cpp_options" \| cut -c46-)
2066	while [[ "$zeile" != "" ]]
2067	do
2068	spalte1=""
2069	spalte2=$(echo "$zeile" \| cut -c-45)
2070	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2071	zeile=$(echo "$zeile" \| cut -c46-)
2072	done
2073
2074	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2075	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2076	zeile=$(echo "$fopts" \| cut -c46-)
2077	while [[ "$zeile" != "" ]]
2078	do
2079	spalte1=""
2080	spalte2=$(echo "$zeile" \| cut -c-45)
2081	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2082	zeile=$(echo "$zeile" \| cut -c46-)
2083	done
2084
2085	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2086	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2087	zeile=$(echo "$lopts" \| cut -c46-)
2088	while [[ "$zeile" != "" ]]
2089	do
2090	spalte1=""
2091	spalte2=$(echo "$zeile" \| cut -c-45)
2092	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2093	zeile=$(echo "$zeile" \| cut -c46-)
2094	done
2095
2096	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098	zeile=$(echo "$modules" \| cut -c46-)
2099	while [[ "$zeile" != "" ]]
2100	do
2101	spalte1=""
2102	spalte2=$(echo "$zeile" \| cut -c-45)
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	zeile=$(echo "$zeile" \| cut -c46-)
2105	done
2106
2107	spalte1="main program:"; spalte2=$mainprog
2108	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2109	else
2110	spalte1=executable:; spalte2=$executable
2111	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2112	fi
2113	printf "\| \| \n"
2114	spalte1="base name of files:"; spalte2=$fname
2115	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2116	if [[ $fname != $afname ]]
2117	then
2118	spalte1="base name of input files:"; spalte2=$afname
2119	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2120	fi
2121	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2122	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2123	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2124	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2125
2126	if [[ "$ocean_file_appendix" = true ]]
2127	then
2128	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2129	fi
2130
2131	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2132	then
2133	spalte1="memory demand / PE":; spalte2="$memory MB"
2134	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2135	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2136	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2137	fi
2138
2139	if [[ $do_compile = true ]]
2140	then
2141	printf "\| \| \n"
2142	printf "\| Files to be compiled: \| \n"
2143	zeile=$source_list
2144	while [[ "$zeile" != "" ]]
2145	do
2146	linestart=$(echo $zeile \| cut -c-70)
2147	printf "\| %-70s \| \n" "$linestart"
2148	zeile=$(echo "$zeile" \| cut -c71-)
2149	done
2150	fi
2151	printf "#------------------------------------------------------------------------#"
2152
2153
2154
2155	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2156	if [[ $do_trace = true ]]
2157	then
2158	(( i = 0 ))
2159	while (( i < iin ))
2160	do
2161	(( i = i + 1 ))
2162	if (( i == 1 ))
2163	then
2164	printf "\n\n >>> INPUT-file assignments:\n"
2165	fi
2166	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2167	done
2168	(( i = 0 ))
2169	while (( i < iout ))
2170	do
2171	(( i = i + 1 ))
2172	if (( i == 1 ))
2173	then
2174	printf "\n\n >>> OUTPUT-file assignments:\n"
2175	fi
2176	printf "\n ${localout[$i]} : ${pathout[$i]}"
2177	done
2178	(( i = 0 ))
2179	while (( i < iic ))
2180	do
2181	(( i = i + 1 ))
2182	if (( i == 1 ))
2183	then
2184	printf "\n\n >>> INPUT-commands:\n"
2185	fi
2186	printf "\n ${in_command[$i]}"
2187	done
2188	(( i = 0 ))
2189	while (( i < ioc ))
2190	do
2191	(( i = i + 1 ))
2192	if (( i == 1 ))
2193	then
2194	printf "\n\n >>> OUTPUT-commands:\n"
2195	fi
2196	printf "\n ${out_command[$i]}"
2197	done
2198	fi
2199
2200	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2201	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2202	then
2203	antwort=dummy
2204	printf "\n\n"
2205	printf " >>> everything o.k. (y/n) ? "
2206	while read antwort
2207	do
2208	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2209	then
2210	printf " >>> everything o.k. (y/n) ? "
2211	else
2212	break
2213	fi
2214	done
2215	if [[ $antwort = n \|\| $antwort = N ]]
2216	then
2217	locat=user_abort; (( iec = 0 )); exit
2218	fi
2219	if [[ $do_batch = true ]]
2220	then
2221	printf " >>> batch-job will be created and submitted"
2222	else
2223	printf " >>> MRUN will now continue to execute on this machine"
2224	fi
2225	fi
2226
2227
2228	# DETERMINE PATH FOR MAKE DEPOSITORY
2229	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2230	then
2231
2232	line=""
2233	grep "%depository_path" $config_file > tmp_mrun
2234	while read line
2235	do
2236	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2237	then
2238	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2239	then
2240	global_depository_path=`echo $line \| cut -d" " -s -f2`
2241	fi
2242	fi
2243	done < tmp_mrun
2244
2245	line=""
2246	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2247	while read line
2248	do
2249	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2250	then
2251	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2252	then
2253	local_depository_path=`echo $line \| cut -d" " -s -f2`
2254	fi
2255	fi
2256	done < tmp_mrun
2257
2258	if [[ "$local_depository_path" = "" ]]
2259	then
2260	if [[ "$global_depository_path" != "" ]]
2261	then
2262	local_depository_path=$global_depository_path
2263	else
2264	printf "\n\n +++ no depository path found in configuration file"
2265	printf "\n for local host \"$localhost\" "
2266	printf "\n please set \"\%depository_path\" in configuration file\n"
2267	locat=config_file; exit
2268	fi
2269	fi
2270	eval local_depository_path=$local_depository_path
2271	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2272	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2273
2274
2275	basename=`echo $mainprog \| cut -f1 -d"."`
2276	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2277	if [[ ! -f $make_depository ]]
2278	then
2279	printf "\n"
2280	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2281	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2282	fi
2283
2284	fi
2285
2286
2287	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2288	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2289	if [[ $do_batch = false ]]
2290	then
2291
2292
2293	# CREATE THE TEMPORARY WORKING DIRECTORY
2294	mkdir -p $TEMPDIR
2295	chmod go+rx $TEMPDIR
2296	tmpcreate=true
2297
2298
2299	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2300	# INTO THE TEMPORARY WORKING DIRECTORY
2301	if [[ $do_compile = true ]]
2302	then
2303
2304	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2305	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2306	if [[ $localhost = nech ]]
2307	then
2308	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2309	if mkdir -p $TEMPDIR_COMPILE
2310	then
2311	printf "\n *** \"$TEMPDIR_COMPILE\" "
2312	printf "\n is generated as temporary directory for cross compiling\n"
2313	else
2314	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2315	printf "\n needed for cross compilation failed"
2316	locat=compile
2317	exit
2318	fi
2319	else
2320	TEMPDIR_COMPILE=$TEMPDIR
2321	fi
2322
2323	cp $make_depository $TEMPDIR_COMPILE
2324	cd $TEMPDIR_COMPILE
2325	tar -xf $make_depository > /dev/null 2>&1
2326	cd - > /dev/null
2327
2328	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2329	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2330	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2331	then
2332	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2333	else
2334	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2335	fi
2336
2337	else
2338
2339	cp $executable ${TEMPDIR}/a.out
2340
2341	fi
2342
2343
2344	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2345	cd $TEMPDIR
2346	printf "\n *** changed to temporary directory: $TEMPDIR"
2347
2348
2349	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2350	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2351	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2352	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2353	(( i = 0 ))
2354	while (( i < iout ))
2355	do
2356	(( i = i + 1 ))
2357	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2358	then
2359	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2360	else
2361	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2362	fi
2363	done
2364
2365
2366	# IF REQUIRED, START WITH COMPILING
2367	if [[ $do_compile = true ]]
2368	then
2369
2370
2371	if [[ -f a.out ]]
2372	then
2373
2374	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2375	printf "\n\n\n *** executable a.out found"
2376	printf "\n no compilation required \n"
2377
2378	else
2379
2380	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2381	printf "\n\n\n *** compilation starts \n$dashes\n"
2382	printf " *** compilation with make using following options:\n"
2383	printf " make depository: $make_depository"
2384	if [[ "$mopts" != "" ]]
2385	then
2386	printf " make options: $mopts\n"
2387	fi
2388	printf " compilername: $compiler_name\n"
2389	printf " compiler options: $fopts\n"
2390	printf " preprocessor directives: $cpp_options \n"
2391	printf " linker options: $lopts \n"
2392	if [[ "$modules" != "" ]]
2393	then
2394	printf " modules to be load: $modules \n"
2395	fi
2396	printf " source code files: $source_list \n"
2397
2398	if [[ $localhost = nech ]]
2399	then
2400	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\" "
2401	cp $TEMPDIR_COMPILE/a.out .
2402	[[ $? != 0 ]] && compile_error=true
2403	rm -rf $TEMPDIR_COMPILE
2404	elif [[ $localhost = ibmh ]]
2405	then
2406	printf " compiler is called via ssh on \"plogin1\" \n"
2407	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\" "
2408	[[ ! -f a.out ]] && compile_error=true
2409	continue # STATUS=1, IF a.out EXISTS
2410	elif [[ $localhost = lcocean ]]
2411	then
2412	printf " compiler is called via ssh on \"ocean\" \n"
2413	echo $PWD
2414	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\" "
2415	[[ ! -f a.out ]] && compile_error=true
2416	continue # STATUS=1, IF a.out EXISTS
2417	elif [[ $localhost = lcflow ]]
2418	then
2419	printf " compiler is called via ssh on \"flow\" \n"
2420	/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\" "
2421	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2422	[[ "$check_for_file" = "" ]] && compile_error=true
2423	continue # STATUS=1, IF a.out EXISTS
2424	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2425	then
2426	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2427	else
2428	[[ "$init_cmds" != "" ]] && eval $init_cmds
2429	[[ "$module_calls" != "" ]] && eval $module_calls
2430	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2431	fi
2432
2433	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2434	then
2435	printf "\n +++ error occured while compiling or linking"
2436	locat=compile
2437
2438	exit
2439	else
2440	printf "$dashes\n *** compilation finished \n"
2441	fi
2442
2443	fi
2444
2445	fi
2446
2447
2448	# PROVIDE THE INPUT FILES
2449	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2450	(( i = 0 ))
2451	while (( i < iin ))
2452	do
2453	(( i = i + 1 ))
2454	if (( i == 1 ))
2455	then
2456	printf "\n\n *** providing INPUT-files:\n$dashes"
2457	fi
2458
2459
2460	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2461	if [[ "${transin[$i]}" = unavailable ]]
2462	then
2463	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2464	then
2465	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2466	printf "\n is not available!"
2467	else
2468	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2469	printf "\n is not available!"
2470	fi
2471	continue
2472	fi
2473
2474	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2475	files_for_pes=false; datentyp=file
2476	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2477	then
2478	files_for_pes=true; datentyp=directory
2479	actionin[$i]=""
2480	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2481	then
2482	actionin[$i]=""
2483	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2484	then
2485	files_for_pes=true; datentyp=directory
2486	actionin[$i]="ar"
2487	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2488	then
2489	actionin[$i]="ar"
2490	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2491	then
2492	files_for_pes=true; datentyp=directory
2493	actionin[$i]="fl"
2494	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2495	then
2496	actionin[$i]="fl"
2497	fi
2498
2499	if [[ $files_for_pes = true ]]
2500	then
2501	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2502	else
2503	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2504	fi
2505
2506	# INPUT-FILE FOR A RESTART RUN.
2507	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2508	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2509	if [[ "${actionin[$i]}" = fl ]]
2510	then
2511	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2512	if [[ $files_for_pes = false ]]
2513	then
2514	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2515	then
2516	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2517	got_tmp[$i]=true
2518	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2519	then
2520	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2521	printf "\n *** trying to use backup copy in \"$WORK\" "
2522	cp $WORK/${frelin[$i]} ${localin[$i]}
2523	else
2524	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2525	printf "\n or \"$tmp_data_catalog\" does not exist!"
2526	printf "\n *** trying to get copy from archive"
2527	actionin[$i]=ar
2528	fi
2529	else
2530	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2531	then
2532	mkdir ${localin[$i]}
2533	cd $tmp_data_catalog/${frelin[$i]}
2534	for file in $(ls *)
2535	do
2536	ln $file $TEMPDIR/${localin[$i]}
2537	done
2538	cd $TEMPDIR
2539	got_tmp[$i]=true
2540	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2541	then
2542	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2543	printf "\n *** trying to use backup copy in \"$WORK\" "
2544	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2545	else
2546	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2547	printf "\n or \"$tmp_data_catalog\" does not exist!"
2548	printf "\n *** trying to get copy from archive"
2549	actionin[$i]=ar
2550	fi
2551	fi
2552	fi
2553
2554
2555	# FILE IS STORED ON THE ARCHIVE SYSTEM
2556	if [[ "${actionin[$i]}" = ar ]]
2557	then
2558
2559	if [[ $files_for_pes = false ]]
2560	then
2561	printf "\n file will be restored from archive-system ($archive_system)!"
2562	else
2563	printf "\n directory will be restored from archive-system ($archive_system)!"
2564	fi
2565
2566	file_restored=false
2567
2568	if [[ $archive_system = asterix ]]
2569	then
2570	do_stagein=true
2571	(( stagein_anz = 0 ))
2572	while [[ $do_stagein = true ]]
2573	do
2574	if [[ $files_for_pes = false ]]
2575	then
2576	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2577	else
2578	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2579	fi
2580	cat STAGEIN_OUTPUT
2581	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2582	then
2583	file_restored=true
2584	do_stagein=false
2585	else
2586	(( stagein_anz = stagein_anz + 1 ))
2587	if (( stagein_anz == 10 ))
2588	then
2589	printf "\n +++ stagein stoped after 10 tries"
2590	locat=stage
2591	exit
2592	fi
2593	printf "\n +++ restoring from archive failed, trying again:"
2594	sleep 900
2595	fi
2596	done
2597	elif [[ $archive_system = DMF ]]
2598	then
2599	if [[ $files_for_pes = false ]]
2600	then
2601	printf "\n +++ restoring of single files impossible with $archive_system !\n"
2602	locat=DMF
2603	exit
2604	else
2605	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
2606	cp -r $ARCHIVE/${frelin[$i]} $PWD
2607	file_restored=true
2608	fi
2609	elif [[ $archive_system = tivoli ]]
2610	then
2611	if [[ $files_for_pes = false ]]
2612	then
2613	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
2614	else
2615	(( inode = 0 ))
2616	while (( inode < nodes ))
2617	do
2618	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
2619	(( inode = inode + 1 ))
2620	done
2621	fi
2622	file_restored=true
2623	elif [[ $archive_system = ut ]]
2624	then
2625	if [[ $files_for_pes = false ]]
2626	then
2627	cp $UT/${frelin[$i]} .
2628	else
2629	(( inode = 0 ))
2630	while (( inode < nodes ))
2631	do
2632	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
2633	(( inode = inode + 1 ))
2634	done
2635	fi
2636	file_restored=true
2637	else
2638	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
2639	locat=rearchive
2640	exit
2641	fi
2642
2643	if [[ $file_restored = true ]]
2644	then
2645
2646	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
2647	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
2648	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
2649	if [[ $files_for_pes = false ]]
2650	then
2651	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
2652	else
2653	mkdir $tmp_data_catalog/${frelin[$i]}
2654	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
2655	fi
2656	got_tmp[$i]=true
2657
2658	# PROVIDE THE FILE UNDER ITS LOCAL NAME
2659	mv ${frelin[$i]} ${localin[$i]}
2660
2661	fi
2662	fi
2663
2664
2665	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2666	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2667	then
2668
2669	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2670	then
2671
2672	# FILE COPIES ARE PROVIDED FOR ALL CORES
2673	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2674	printf "\n file will be provided for $numprocs processors"
2675	mkdir ${localin[$i]}
2676	ival=$numprocs
2677	(( ii = 0 ))
2678	while (( ii <= ival-1 ))
2679	do
2680	if (( ii < 10 ))
2681	then
2682	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2683	elif (( ii < 100 ))
2684	then
2685	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2686	elif (( ii < 1000 ))
2687	then
2688	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2689	else
2690	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2691	fi
2692	(( ii = ii + 1 ))
2693	done
2694
2695	else
2696
2697	if [[ $files_for_pes = true ]]
2698	then
2699
2700	# PROVIDE FILES FOR EACH CORE
2701	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2702	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2703	printf "\n providing $numprocs files for the respective processors"
2704	mkdir ${localin[$i]}
2705	if [[ $link_local_input = true ]]
2706	then
2707	printf " using ln -f\n"
2708	cd ${absnamein[$i]}
2709	for file in $(ls *)
2710	do
2711	ln -f $file ${localin[$i]}
2712	done
2713	cd $TEMPDIR
2714	fi
2715
2716	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2717	if [[ ! -f "${localin[$i]}/_0000" ]]
2718	then
2719	if [[ $link_local_input = true ]]
2720	then
2721	printf " ln failed for .../_0000, using cp...\n"
2722	fi
2723	cp -r ${absnamein[$i]}/* ${localin[$i]}
2724	fi
2725
2726	else
2727
2728	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2729	if [[ $link_local_input = true ]]
2730	then
2731	printf " using ln -f\n"
2732	ln -f ${absnamein[$i]} ${localin[$i]}
2733	fi
2734	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2735	if [[ ! -f "${localin[$i]}" ]]
2736	then
2737	if [[ $link_local_input = true ]]
2738	then
2739	printf " ln failed, using cp...\n"
2740	fi
2741	cp ${absnamein[$i]} ${localin[$i]}
2742	fi
2743	fi
2744	fi
2745	fi
2746
2747	done
2748	if (( i != 0 ))
2749	then
2750	printf "\n$dashes\n *** all INPUT-files provided \n"
2751	fi
2752
2753
2754	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2755	(( i = 0 ))
2756	while (( i < iic ))
2757	do
2758	(( i = i + 1 ))
2759	if (( i == 1 ))
2760	then
2761	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2762	fi
2763	printf "\n >>> ${in_command[$i]}"
2764	eval ${in_command[$i]}
2765	if (( i == iic ))
2766	then
2767	printf "\n$dashes\n"
2768	fi
2769	done
2770
2771
2772	# SET THE REMAINING CPU-TIME
2773	cpurest=${cpumax}.
2774
2775
2776	# START DVR STREAMING SERVER
2777	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2778	then
2779	if [[ "$dvr_server" != "" ]]
2780	then
2781
2782	printf "\n\n *** preparing the dvr streaming server configuration file"
2783
2784	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2785	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2786	if [[ "$running_dvrserver_id" != "" ]]
2787	then
2788
2789	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2790	printf "\n This server is used instead starting a new one!"
2791	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2792
2793	else
2794
2795	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2796	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2797	then
2798	cp ${PALM_BIN}/.dvrserver.config .
2799
2800	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2801	user_id=`id -u`
2802	group_id=`id -g`
2803
2804	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2805	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2806	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2807	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2808	mv .dvrserver.3 .dvrserver.config
2809	rm .dvrserver.1 .dvrserver.2
2810
2811	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2812	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2813	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2814	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2815	local_dvrserver_running=.TRUE.
2816	else
2817	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2818	printf "\n \"$PALM_BIN\" "
2819	locat=dvr
2820	exit
2821	fi
2822
2823	fi
2824
2825	else
2826	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2827	fi
2828	fi
2829
2830
2831	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2832	# (FILE ENVPAR WILL BE READ BY PALM)
2833	cat > ENVPAR << %%END%%
2834	&envpar run_identifier = '$fname', host = '$localhost',
2835	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2836	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2837	maximum_cpu_time_allowed = ${cpumax}.,
2838	revision = '$global_revision',
2839	local_dvrserver_running = $local_dvrserver_running,
2840	batch_job = $batch_job /
2841
2842	%%END%%
2843
2844
2845	# STARTING THE EXECUTABLE
2846	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2847	PATH=$PATH:$TEMPDIR
2848
2849
2850	if [[ $execute_command != "none" ]]
2851	then
2852
2853	printf "\n +++ branch still not realized"
2854	locat=execution
2855	exit
2856
2857	else
2858
2859	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2860	if [[ "$mpi_debug" = true ]]
2861	then
2862	export MPI_CHECK_ARGS=1
2863	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2864	fi
2865
2866	if [[ "$totalview" = true ]]
2867	then
2868	printf "\n *** totalview debugger will be used"
2869	tv_opt="-tv"
2870	else
2871	tv_opt=""
2872	fi
2873
2874	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2875	then
2876
2877	#Interactive ALLINEA DEBUG seesion
2878	if [[ "$ENVIRONMENT" != BATCH ]]
2879	then
2880	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2881	then
2882	if [[ "$allinea" = true ]]
2883	then
2884	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2885
2886	ddt aprun -n $ii -N $tasks_per_node a.out
2887	wait
2888	fi
2889	fi
2890	fi
2891
2892	if [[ $localhost = ibmh ]]
2893	then
2894
2895	# SETUP THE IBM MPI ENVIRONMENT
2896	export MP_SHARED_MEMORY=yes
2897	export AIXTHREADS_SCOPE=S
2898	export OMP_NUM_THREADS=$threads_per_task
2899	export AUTHSTATE=files
2900	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2901
2902	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2903	export MP_ADAPTER_USE=shared
2904	export MP_CPU_USE=multiple
2905	export MP_TIMEOUT=1200
2906
2907	unset MP_TASK_AFFINITY
2908
2909	if [[ "$LOADLBATCH" = yes ]]
2910	then
2911	totalview poe a.out
2912	else
2913	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2914	export TVDSVRLAUNCHCMD=ssh
2915	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2916	fi
2917
2918	fi # END DEBUG MODE
2919
2920	else
2921
2922	# NORMAL EXECUTION
2923	if [[ -n $numprocs ]]
2924	then
2925
2926	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2927	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2928	then
2929
2930	# SETUP THE IBM MPI ENVIRONMENT
2931	if [[ $host != ibmh && $host != ibmkisti ]]
2932	then
2933	export MP_SHARED_MEMORY=yes
2934	export AIXTHREAD_SCOPE=S
2935	export OMP_NUM_THREADS=$threads_per_task
2936	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2937	export AUTHSTATE=files
2938	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2939	# export MP_PRINTENV=yes
2940
2941	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2942	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2943	export MP_WAIT_MODE=poll
2944	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2945	fi
2946
2947	if [[ $host = ibmkisti ]]
2948	then
2949	export LANG=en_US
2950	export MP_SHARED_MEMORY=yes
2951	if [[ $threads_per_task = 1 ]]
2952	then
2953	export MP_SINGLE_THREAD=yes
2954	export MEMORY_AFFINITY=MCM
2955	else
2956	export OMP_NUM_THREADS=$threads_per_task
2957	fi
2958	fi
2959
2960	if [[ "$LOADLBATCH" = yes ]]
2961	then
2962	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2963	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2964	then
2965	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2966	else
2967	if [[ $run_coupled_model = false ]]
2968	then
2969	if [[ "$ocean_file_appendix" = true ]]
2970	then
2971	echo "precursor_ocean" > runfile_atmos
2972	else
2973	echo "precursor_atmos" > runfile_atmos
2974	fi
2975	else
2976	(( iia = $numprocs_atmos / $threads_per_task ))
2977	(( iio = $numprocs_ocean / $threads_per_task ))
2978	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2979	printf "\n using $coupled_mode coupling"
2980	printf "\n\n"
2981	echo "coupled_run $iia $iio" > runfile_atmos
2982	fi
2983	poe ./a.out < runfile_atmos
2984	fi
2985	else
2986	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2987	then
2988	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2989	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2990	then
2991	if [[ -f $hostfile ]]
2992	then
2993	cp $hostfile hostfile
2994	else
2995	(( ii = 1 ))
2996	while (( ii <= $numprocs ))
2997	do
2998	echo $localhost_realname >> hostfile
2999	(( ii = ii + 1 ))
3000	done
3001	fi
3002	export MP_HOSTFILE=hostfile
3003	if [[ $run_coupled_model = false ]]
3004	then
3005	if [[ "$ocean_file_appendix" = true ]]
3006	then
3007	echo "precursor_ocean" > runfile_atmos
3008	else
3009	echo "precursor_atmos" > runfile_atmos
3010	fi
3011	else
3012	(( iia = $numprocs_atmos / $threads_per_task ))
3013	(( iio = $numprocs_ocean / $threads_per_task ))
3014	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3015	printf "\n using $coupled_mode coupling"
3016	printf "\n\n"
3017	echo "coupled_run $iia $iio" > runfile_atmos
3018	fi
3019
3020	poe ./a.out -procs $numprocs < runfile_atmos
3021
3022	else
3023	if [[ "$host_file" = "" ]]
3024	then
3025	printf "\n +++ no hostfile given in configuration file"
3026	locat=config_file
3027	exit
3028	else
3029	eval host_file=$host_file
3030	fi
3031	export MP_HOSTFILE=$host_file
3032	poe a.out -procs $numprocs -tasks_per_node $numprocs
3033	fi
3034	fi
3035
3036	elif [[ $host = nech ]] # running on NEC machines
3037	then
3038
3039	(( ii = nodes ))
3040	if [[ $ii = 1 ]]
3041	then
3042	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3043	export MPIPROGINF=YES
3044	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3045	echo "*** execution on single node with mpirun"
3046	mpirun -np $numprocs ./a.out
3047	else
3048	(( i = 0 ))
3049	while (( i < ii ))
3050	do
3051	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3052	(( i = i + 1 ))
3053	done
3054
3055	echo "#!/bin/sh" > mpi_exec_shell
3056	echo " " >> mpi_exec_shell
3057	echo "set -u" >> mpi_exec_shell
3058	echo "F_ERRCNT=0" >> mpi_exec_shell
3059	echo "MPIPROGINV=YES" >> mpi_exec_shell
3060	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3061	echo "cpurest=$cpurest" >> mpi_exec_shell
3062	echo "fname=$fname" >> mpi_exec_shell
3063	echo "localhost=$localhost" >> mpi_exec_shell
3064	echo "return_address=$return_address" >> mpi_exec_shell
3065	echo "return_username=$return_username" >> mpi_exec_shell
3066	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3067	echo "write_binary=$write_binary" >> mpi_exec_shell
3068	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3069	echo " " >> mpi_exec_shell
3070	echo "export F_ERRCNT" >> mpi_exec_shell
3071	echo "export MPIPROGINV" >> mpi_exec_shell
3072	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3073	echo "export cpurest" >> mpi_exec_shell
3074	echo "export fname" >> mpi_exec_shell
3075	echo "export localhost" >> mpi_exec_shell
3076	echo "export return_address" >> mpi_exec_shell
3077	echo "export return_username" >> mpi_exec_shell
3078	echo "export tasks_per_node" >> mpi_exec_shell
3079	echo "export write_binary" >> mpi_exec_shell
3080	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3081	echo " " >> mpi_exec_shell
3082	echo "exec ./a.out" >> mpi_exec_shell
3083
3084	chmod u+x mpi_exec_shell
3085	export MPIPROGINF=YES
3086	mpirun -f multinode_config &
3087	wait
3088
3089	fi
3090
3091	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3092	then
3093
3094	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3095	# DOES NOT EXIST
3096	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]
3097	then
3098	if [[ -f $hostfile ]]
3099	then
3100	cp $hostfile hostfile
3101	(( ii = $numprocs / $threads_per_task ))
3102	[[ $ii = 0 ]] && (( ii = 1 ))
3103	else
3104	(( ii = 1 ))
3105	while (( ii <= $numprocs / $threads_per_task ))
3106	do
3107	echo $localhost_realname >> hostfile
3108	(( ii = ii + 1 ))
3109	done
3110	if (( $numprocs / $threads_per_task == 0 ))
3111	then
3112	echo $localhost_realname >> hostfile
3113	fi
3114	fi
3115	eval zeile=\"`head -n $ii hostfile`\"
3116	printf "\n *** running on: $zeile"
3117	fi
3118
3119	(( ii = $numprocs / $threads_per_task ))
3120	[[ $ii = 0 ]] && (( ii = 1 ))
3121	export OMP_NUM_THREADS=$threads_per_task
3122
3123	if [[ $threads_per_task != 1 ]]
3124	then
3125	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3126	# MAY ABORT
3127	ulimit -s unlimited
3128	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3129	fi
3130	if [[ $run_coupled_model = false ]]
3131	then
3132	if [[ "$ocean_file_appendix" = true ]]
3133	then
3134	echo "precursor_ocean" > runfile_atmos
3135	else
3136	echo "precursor_atmos" > runfile_atmos
3137	fi
3138	printf "\n\n"
3139
3140	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3141	then
3142	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3143	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3144	elif [[ $host = lcbullhh ]]
3145	then
3146	export OMPI_MCA_pml=cm
3147	export OMPI_MCA_mtl=mxm
3148	export OMPI_MCA_coll=^ghc
3149	export OMPI_MCA_mtl_mxm_np=0
3150	export MXM_RDMA_PORTS=mlx5_0:1
3151	export MXM_LOG_LEVEL=ERROR
3152	export OMP_NUM_THREADS=$threads_per_task
3153	export KMP_AFFINITY=verbose,granularity=core,compact,1
3154	export KMP_STACKSIZE=64m
3155
3156	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3157
3158	elif [[ $host = lccrayf ]]
3159	then
3160	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3161	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3162	then
3163	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3164	elif [[ $host = lcflow ]]
3165	then
3166	mpirun -np $ii a.out < runfile_atmos
3167	elif [[ $host = lcocean ]]
3168	then
3169	mpirun a.out $ROPTS < runfile_atmos
3170	elif [[ $host = lcsb ]]
3171	then
3172	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3173	elif [[ $host = lckiaps ]]
3174	then
3175	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
3176	elif [[ $host = lckyu* ]]
3177	then
3178	mpiexec -n $ii --stdin runfile_atmos ./a.out
3179	else
3180	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3181	fi
3182
3183	else
3184
3185	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3186	(( iia = $numprocs_atmos / $threads_per_task ))
3187	(( iio = $numprocs_ocean / $threads_per_task ))
3188	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3189	printf "\n using $coupled_mode coupling"
3190	printf "\n\n"
3191
3192	if [[ $coupled_mode = "mpi2" ]]
3193	then
3194	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3195	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3196
3197	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3198	then
3199
3200	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
3201	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
3202
3203	else
3204	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3205	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
3206	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
3207	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
3208	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
3209	fi
3210	wait
3211
3212	else
3213
3214	echo "coupled_run $iia $iio" > runfile_atmos
3215
3216	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3217	then
3218
3219	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3220
3221	elif [[ $host = lck \|\| $host = lckordi ]]
3222	then
3223
3224	mpiexec -n $ii ./a.out < runfile_atmos &
3225
3226	elif [[ $host = lckyu* ]]
3227	then
3228
3229	mpiexec -n $ii --stdin runfile_atmos ./a.out
3230
3231	elif [[ $host = lcmuk ]]
3232	then
3233
3234	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3235
3236	fi
3237	wait
3238	fi
3239
3240	fi
3241
3242	elif [[ $host = lckyoto ]]
3243	then
3244	set -xv
3245	export P4_RSHCOMMAND=plesh
3246	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3247	if [[ "$ENVIRONMENT" = BATCH ]]
3248	then
3249	if [[ "$cond2" = fujitsu ]]
3250	then
3251	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3252	elif [[ "cond2" = pgi ]]
3253	then
3254	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3255	else
3256	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3257	fi
3258	else
3259	if [[ "$cond2" = "" ]]
3260	then
3261	mpiruni_rsh -np $numprocs ./a.out # for intel
3262	else
3263	mpirun -np $numprocs ./a.out
3264	fi
3265	fi
3266	set +xv
3267
3268	elif [[ $host = lctit ]]
3269	then
3270	export OMP_NUM_THREADS=$threads_per_task
3271	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3272	if [[ "$threads_per_task" != 1 ]]
3273	then
3274	export MV2_ENABLE_AFFINITY=0
3275	fi
3276	echo "----- PBS_NODEFILE content:"
3277	cat $PBS_NODEFILE
3278	echo "-----"
3279	(( ii = $numprocs / $threads_per_task ))
3280	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3281	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3282
3283	else
3284	mpprun -n $numprocs a.out
3285	fi
3286	else
3287	a.out
3288	fi
3289
3290	fi # end normal (non-debug) execution
3291
3292	fi # end explicit execute_command or host-specific execute actions
3293
3294	if [[ $? != 0 ]]
3295	then
3296
3297	# ABORT IN CASE OF RUNTIME ERRORS
3298	printf "\n +++ runtime error occured"
3299	locat=execution
3300	exit
3301
3302	else
3303
3304	printf "\n$dashes\n *** execution finished \n"
3305
3306	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3307	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3308	if [[ "$dvrserver_id" != "" ]]
3309	then
3310	kill $dvrserver_id
3311	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3312
3313	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3314	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3315	if [[ -d DATA_DVR ]]
3316	then
3317
3318	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3319	# DIRECTORY
3320	cp .dvrserver.config DATA_DVR
3321
3322	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3323	# SEQUENCE MODE DATA TOO)
3324	process_dvr_output -d DATA_DVR -f $fname -s
3325
3326	else
3327
3328	# PROCESS THE LOCAL OUTPUT
3329	process_dvr_output -l -d DATA_DVR -f $fname
3330
3331	fi
3332
3333	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3334	then
3335
3336	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3337	process_dvr_output -l -d DATA_DVR -f $fname
3338
3339	fi
3340	fi
3341
3342
3343
3344	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3345	# BY EACH CORE INTO ONE FILE
3346	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3347	then
3348	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3349	printf "\n 2d- and/or 3d-data may be incomplete!"
3350	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3351	elif [[ "$combine_plot_fields" == true ]]
3352	then
3353	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3354	then
3355	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3356	aprun -n 1 -N 1 combine_plot_fields${block}.x
3357	else
3358	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3359	combine_plot_fields${block}.x
3360	fi
3361	else
3362
3363	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3364	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3365	# ??? koennen wir das streichen ???
3366	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3367	fi
3368
3369
3370
3371	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3372	(( i = 0 ))
3373	while (( i < ioc ))
3374	do
3375	(( i = i + 1 ))
3376	if (( i == 1 ))
3377	then
3378	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3379	fi
3380	printf "\n >>> ${out_command[$i]}"
3381	eval ${out_command[$i]}
3382	if (( i == ioc ))
3383	then
3384	printf "\n$dashes\n"
3385	fi
3386	done
3387
3388
3389	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3390	if [[ $do_trace = true ]]
3391	then
3392	printf "\n\n"
3393	ls -al
3394	fi
3395
3396
3397
3398	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3399	(( i = 0 ))
3400	while (( i < iout ))
3401	do
3402	(( i = i + 1 ))
3403	if (( i == 1 ))
3404	then
3405	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3406	fi
3407
3408	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3409	files_for_pes=false; filetyp=file
3410	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3411	then
3412	files_for_pes=true; filetyp=directory
3413	actionout[$i]=""
3414	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3415	then
3416	actionout[$i]=""
3417	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3418	then
3419	files_for_pes=true; filetyp=directory
3420	actionout[$i]="ar"
3421	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3422	then
3423	actionout[$i]="ar"
3424	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3425	then
3426	files_for_pes=true; filetyp=directory
3427	actionout[$i]="fl"
3428	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3429	then
3430	actionout[$i]="fl"
3431	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3432	then
3433	files_for_pes=true; filetyp=directory
3434	actionout[$i]="tr"
3435	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3436	then
3437	actionout[$i]="tr"
3438	fi
3439
3440	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3441	then
3442	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3443	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3444	then
3445	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3446	else
3447
3448
3449	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3450	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3451	if [[ "${actionout[$i]}" = tr ]]
3452	then
3453	if [[ $localhost != $fromhost ]]
3454	then
3455	if [[ $files_for_pes = false ]]
3456	then
3457	cps=""
3458	cst=""
3459	else
3460	cps=-c
3461	cst="/"
3462	fi
3463	if [[ $localhost = nech ]]
3464	then
3465
3466	# TRANSFER IN SEPERATE JOB
3467	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3468	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3469	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3470	if [[ $files_for_pes = false ]]
3471	then
3472	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3473	else
3474	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3475	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3476	fi
3477
3478	echo "set -x" > transfer_${localout[$i]}
3479	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3480
3481	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3482	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3483	printf "\n or higher cycle\n"
3484	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]}
3485
3486	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3487
3488	if [[ $localhost = nech ]]
3489	then
3490	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3491	else
3492	if [[ "$LOGNAME" = b323013 ]]
3493	then
3494	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3495	else
3496	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3497	fi
3498	fi
3499
3500	else
3501
3502	# TRANSFER WITHIN THIS JOB
3503	transfer_failed=false
3504	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3505	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3506	if [[ $localhost = lccrayb ]]
3507	then
3508	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]}"
3509	elif [[ $localhost = lccrayh ]]
3510	then
3511	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]}"
3512	elif [[ $localhost = lcbullhh ]]
3513	then
3514	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]}"
3515	elif [[ $localhost = lcxe6 ]]
3516	then
3517	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]}"
3518	else
3519	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3520	fi
3521	[[ $? != 0 ]] && transfer_failed=true
3522
3523	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3524	if [[ $transfer_failed = true ]]
3525	then
3526	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3527	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3528
3529	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3530	eval local_catalog=${pathout[$i]}
3531	if [[ ! -d $local_catalog ]]
3532	then
3533	printf " *** local directory does not exist. Trying to create:\n"
3534	printf " $local_catalog \n"
3535	mkdir -p $local_catalog
3536	fi
3537	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3538	transfer_problems=true
3539	fi
3540	fi
3541	else
3542
3543	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3544	actionout[$i]=""
3545	fi
3546	fi
3547
3548
3549	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3550	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3551	if [[ "${actionout[$i]}" = tra ]]
3552	then
3553	if [[ $localhost != $fromhost ]]
3554	then
3555	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3556	then
3557
3558	# TRANSFER IN SEPERATE JOB
3559	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3560	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3561	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3562	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3563
3564	echo "set -x" > transfer_${localout[$i]}
3565	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3566
3567	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3568	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3569	printf "\n or higher cycle\n"
3570	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]}
3571
3572	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3573
3574	if [[ $localhost = nech ]]
3575	then
3576	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3577	else
3578	if [[ $LOGNAME = b323013 ]]
3579	then
3580	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3581	else
3582	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3583	fi
3584	fi
3585
3586	else
3587
3588	# TRANSFER WITHIN THIS JOB
3589	transfer_failed=false
3590	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3591	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3592	if [[ $localhost = lccrayb ]]
3593	then
3594	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]}"
3595	elif [[ $localhost = lccrayh ]]
3596	then
3597	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]}"
3598	elif [[ $localhost = lcxe6 ]]
3599	then
3600	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]}"
3601	else
3602	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3603	fi
3604	[[ $? != 0 ]] && transfer_failed=true
3605
3606	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3607	if [[ $transfer_failed = true ]]
3608	then
3609	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3610	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3611
3612	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3613	eval local_catalog=${pathout[$i]}
3614	if [[ ! -d $local_catalog ]]
3615	then
3616	printf " *** local directory does not exist. Trying to create:\n"
3617	printf " $local_catalog \n"
3618	mkdir -p $local_catalog
3619	fi
3620
3621	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3622	transfer_problems=true
3623	fi
3624	fi
3625	else
3626
3627	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3628	actionout[$i]=a
3629	fi
3630	fi
3631
3632
3633	# OUTPUT-FILE FOR A RESTART-RUN.
3634	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
3635	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
3636	# AS LAST ACTION, ARCHIVING IS INITIATED.
3637	if [[ "${actionout[$i]}" = fl ]]
3638	then
3639	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3640	chmod g+rx $tmp_data_catalog
3641	if [[ $files_for_pes = false ]]
3642	then
3643	printf "\n >>> OUTPUT: ${localout[$i]} to"
3644	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3645	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
3646	else
3647	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
3648	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
3649	mkdir $tmp_data_catalog/${frelout[$i]}
3650	cd ${localout[$i]}
3651	for file in $(ls *)
3652	do
3653	ln -f $file $tmp_data_catalog/${frelout[$i]}
3654	done
3655	cd $TEMPDIR
3656	fi
3657
3658
3659	# CREATE AND SUBMIT ARCHIVING-JOB
3660	if [[ $store_on_archive_system = true ]]
3661	then
3662
3663	if [[ $archive_system = asterix ]]
3664	then
3665	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3666	if [[ $files_for_pes = false ]]
3667	then
3668	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3669	else
3670	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3671	fi
3672	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3673	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
3674	echo "then" >> archive_${frelout[$i]}
3675	echo " do_stageout=false" >> archive_${frelout[$i]}
3676	echo "else" >> archive_${frelout[$i]}
3677	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
3678	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
3679	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
3680	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
3681	if [[ $files_for_pes = false ]]
3682	then
3683	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
3684	else
3685	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
3686	fi
3687	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
3688	echo "fi" >> archive_${frelout[$i]}
3689	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
3690	elif [[ $archive_system = DMF ]]
3691	then
3692	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3693	if [[ $files_for_pes = false ]]
3694	then
3695	printf "\n +++ archiving of single files impossible with $archive_system !\n"
3696	locat=DMF
3697	exit
3698	else
3699	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
3700	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
3701	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
3702	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
3703	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
3704	fi
3705	elif [[ $archive_system = tivoli ]]
3706	then
3707	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3708	if [[ $files_for_pes = false ]]
3709	then
3710	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3711	echo "set -x" >> archive_${frelout[$i]}
3712	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3713	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3714	else
3715
3716	echo "set -x" >> archive_${frelout[$i]}
3717	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
3718	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3719	cd $tmp_data_catalog
3720	all_files=`ls -1 ${frelout[$i]}/*`
3721	cd - > /dev/null
3722	(( inode = 0 ))
3723	(( tp1 = tasks_per_node + 1 ))
3724	while (( inode < nodes ))
3725	do
3726	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3727	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3728	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3729	(( inode = inode + 1 ))
3730	done
3731	fi
3732	elif [[ $archive_system = ut ]]
3733	then
3734	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
3735	if [[ $files_for_pes = false ]]
3736	then
3737	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
3738	echo "set -x" >> archive_${frelout[$i]}
3739	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3740	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3741	else
3742
3743	echo "set -x" >> archive_${frelout[$i]}
3744	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
3745	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
3746	cd $tmp_data_catalog
3747	all_files=`ls -1 ${frelout[$i]}/*`
3748	cd - > /dev/null
3749	(( inode = 0 ))
3750	(( tp1 = tasks_per_node + 1 ))
3751	while (( inode < nodes ))
3752	do
3753	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
3754	all_files=`echo $all_files \| cut -d" " -f$tp1-`
3755	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
3756	(( inode = inode + 1 ))
3757	done
3758	fi
3759	elif [[ $archive_system = none ]]
3760	then
3761	printf " +++ archiving on $localhost not available!\n"
3762	fi
3763
3764	if [[ $archive_system != none ]]
3765	then
3766	if [[ $localhost = nech ]]
3767	then
3768	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3769	fi
3770	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3771	fi
3772	else
3773	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
3774	fi
3775
3776
3777	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
3778	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3779	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3780	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3781	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3782	if [[ $files_for_pes = false ]]
3783	then
3784	cat /dev/null > ${pathout[$i]}
3785	else
3786	mkdir -p ${pathout[$i]}
3787	fi
3788
3789	fi
3790
3791
3792	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
3793	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
3794	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
3795	if [[ "${actionout[$i]}" = ar ]]
3796	then
3797	if [[ $files_for_pes = false ]]
3798	then
3799	printf "\n >>> OUTPUT: ${localout[$i]} to"
3800	printf "\n ${pathout[$i]}"
3801	printf "\n File will be copied to archive-system ($archive_system) !\n"
3802	else
3803	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
3804	printf "\n ${pathout[$i]}"
3805	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
3806	fi
3807	mv ${localout[$i]} ${frelout[$i]}
3808
3809	file_saved=false
3810
3811	if [[ $archive_system = asterix ]]
3812	then
3813	do_stageout=true
3814	(( stageout_anz = 0 ))
3815	while [[ $do_stageout = true ]]
3816	do
3817	if [[ $files_for_pes = false ]]
3818	then
3819	stageout ${frelout[$i]} > STAGE_OUTPUT
3820	else
3821	stageout -t ${frelout[$i]} > STAGE_OUTPUT
3822	fi
3823	cat STAGE_OUTPUT
3824	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
3825	then
3826	file_saved=true
3827	do_stageout=false
3828	else
3829	if [[ $files_for_pes = false ]]
3830	then
3831	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
3832	else
3833	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
3834	fi
3835	(( stageout_anz = stageout_anz + 1 ))
3836	if (( stageout_anz == 10 ))
3837	then
3838	printf "\n +++ stoped after 10 unsuccessful tries!"
3839	archive_save=false
3840	do_stageout=false
3841	else
3842	printf "\n *** new try to store on archive after 15 min:"
3843	sleep 900
3844	fi
3845	fi
3846	done
3847	elif [[ $archive_system = DMF ]]
3848	then
3849	if [[ $files_for_pes = false ]]
3850	then
3851	printf "\n +++ archiving of single files impossible on $archive_system!\n"
3852	locat=DMF
3853	exit
3854	else
3855	rm -rf $ARCHIVE/${frelout[$i]}
3856	cp -r ${frelout[$i]} $ARCHIVE
3857	fi
3858	file_saved=true
3859	elif [[ $archive_system = tivoli ]]
3860	then
3861	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3862	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3863	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3864	# WHEN THE ARCHIVE-JOB IS EXECUTED
3865	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3866	chmod g+rx $tmp_data_catalog
3867	if [[ $files_for_pes = false ]]
3868	then
3869	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3870	else
3871	mkdir $tmp_data_catalog/${frelout[$i]}
3872	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3873	fi
3874
3875	# GENERATE AND SUBMIT BATCH-JOB
3876	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3877	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3878	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3879	if [[ $files_for_pes = false ]]
3880	then
3881	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3882	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
3883	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3884	else
3885	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3886	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3887	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3888	fi
3889
3890	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
3891	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3892	file_saved=true
3893
3894	elif [[ $archive_system = ut ]]
3895	then
3896	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
3897	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
3898	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
3899	# WHEN THE ARCHIVE-JOB IS EXECUTED
3900	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
3901	chmod g+rx $tmp_data_catalog
3902	if [[ $files_for_pes = false ]]
3903	then
3904	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
3905	else
3906	mkdir $tmp_data_catalog/${frelout[$i]}
3907	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
3908	fi
3909
3910	# GENERATE AND SUBMIT BATCH-JOB
3911	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
3912	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
3913	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
3914	if [[ $files_for_pes = false ]]
3915	then
3916	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3917	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
3918	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3919	else
3920	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
3921	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
3922	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
3923	fi
3924
3925	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
3926	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
3927	file_saved=true
3928
3929	else
3930	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
3931	archive_save=false
3932	fi
3933
3934	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
3935	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
3936	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
3937	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
3938	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
3939	if [[ $file_saved = true ]]
3940	then
3941	if [[ $files_for_pes = false ]]
3942	then
3943	cat /dev/null > ${pathout[$i]}
3944	else
3945	mkdir -p ${pathout[$i]}
3946	fi
3947	fi
3948
3949	fi
3950
3951	# APPEND ON THIS MACHINE
3952	if [[ "${actionout[$i]}" = "a" ]]
3953	then
3954	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3955	then
3956	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3957	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3958	else
3959	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3960	cat ${localout[$i]} >> ${pathout[$i]}
3961	fi
3962	fi
3963
3964	# COPY ON THIS MACHINE
3965	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3966	# ON DIFFERENT FILE-SYSTEMS
3967	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3968	then
3969
3970	# COPY IN CASE OF RUNS ON SINGLE CORES
3971	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3972	then
3973	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3974	if [[ $link_local_output = true ]]
3975	then
3976	printf " using ln -f\n"
3977	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3978	fi
3979	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3980	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3981	then
3982	if [[ $link_local_output = true ]]
3983	then
3984	printf " ln failed, using cp...\n"
3985	fi
3986	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3987	fi
3988	else
3989	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3990	if [[ $link_local_output = true ]]
3991	then
3992	printf " using ln -f\n"
3993	ln -f ${localout[$i]} ${pathout[$i]}
3994	fi
3995	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3996	if [[ ! -f "${pathout[$i]}" ]]
3997	then
3998	if [[ $link_local_output = true ]]
3999	then
4000	printf " ln failed, using cp...\n"
4001	fi
4002	cp ${localout[$i]} ${pathout[$i]}
4003	fi
4004	fi
4005
4006	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4007	then
4008
4009	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4010	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4011	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4012	if [[ $link_local_output = true ]]
4013	then
4014	printf " using ln -f\n"
4015	mkdir ${pathout[$i]}
4016	cd ${localout[$i]}
4017	for file in $(ls *)
4018	do
4019	ln -f $file ${pathout[$i]}
4020	done
4021	cd $TEMPDIR
4022	fi
4023
4024	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4025	if [[ ! -f "${pathout[$i]}/_0000" ]]
4026	then
4027	if [[ $link_local_output = true ]]
4028	then
4029	printf " ln failed for .../_0000, using cp...\n"
4030	fi
4031	cp -r ${localout[$i]} ${pathout[$i]}
4032	fi
4033
4034	fi
4035	fi
4036	done
4037	if (( i != 0 ))
4038	then
4039	if [[ $transfer_problems = true ]]
4040	then
4041	printf "\n$dashes\n *** OUTPUT-files saved"
4042	printf "\n +++ WARNING: some data transfers failed! \n"
4043	else
4044	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4045	fi
4046	fi
4047
4048
4049	# IF REQUIRED, START A RESTART-JOB
4050	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4051	if [[ -f CONTINUE_RUN ]]
4052	then
4053
4054	if [[ $archive_save = true ]]
4055	then
4056
4057	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4058	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4059	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4060	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4061	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4062	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4063	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4064	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4065	then
4066	mc=`echo $mc \| sed 's/#/f/g'`
4067	fi
4068
4069
4070	# START THE RESTART-JOB
4071	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4072	echo " $mc"
4073	printf "\n$dashes\n"
4074	if [[ $localhost != $fromhost ]]
4075	then
4076
4077	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4078	then
4079	echo "*** ssh will be used to initiate restart-runs!"
4080	echo " return_address=\"$return_address\" "
4081	echo " return_username=\"$return_username\" "
4082	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4083	then
4084	if [[ $localhost = ibmh ]]
4085	then
4086	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\" "
4087	elif [[ $localhost = lcbullhh ]]
4088	then
4089	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\" "
4090	elif [[ $localhost = lccrayb ]]
4091	then
4092	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\" "
4093	elif [[ $localhost = lccrayh ]]
4094	then
4095	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\" "
4096	elif [[ $localhost = lcxe6 ]]
4097	then
4098	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\" "
4099	else
4100	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 "
4101	fi
4102	else
4103	if [[ $localhost = ibmkisti ]]
4104	then
4105	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\" "
4106	elif [[ $localhost = lcflow ]]
4107	then
4108	/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 "
4109	elif [[ $localhost = lcocean ]]
4110	then
4111	/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 "
4112	elif [[ $localhost = lccrayb ]]
4113	then
4114	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\" "
4115	elif [[ $localhost = lccrayh ]]
4116	then
4117	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\" "
4118	else
4119	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4120	fi
4121	fi
4122	else
4123	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4124	locat=restart; exit
4125	fi
4126
4127	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4128	if [[ $queue = special1q ]]
4129	then
4130	sleep 120
4131	else
4132	sleep 30
4133	fi
4134
4135	else
4136
4137	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4138	# USING SSH)
4139	cd $LOCAL_PWD
4140	if [[ $localhost = lckyuh ]]
4141	then
4142	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4143	printf "\n please restart job manually using command:\n"
4144	printf "\n \"$mc\" "
4145	else
4146	eval $mc # THE ' MUST BE EVALUATED
4147	fi
4148	cd - > /dev/null
4149	fi
4150	if [[ $localhost = lckyuh ]]
4151	then
4152	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4153	else
4154	printf "\n$dashes\n *** restart-run initiated \n"
4155	fi
4156
4157
4158	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4159	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4160	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4161	# MAY BE VERY HUGE)
4162	(( i = 0 ))
4163	while (( i < iin ))
4164	do
4165	(( i = i + 1 ))
4166	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4167	then
4168	rm -r $tmp_data_catalog/${frelin[$i]}
4169	fi
4170	done
4171
4172	else
4173
4174	printf "\n +++ no restart-run possible, since errors occured"
4175	printf "\n during the archive process"
4176	fi
4177
4178	fi
4179
4180
4181
4182	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4183	if [[ "$email_notification" != "none" ]]
4184	then
4185
4186	if [[ $localhost != $fromhost ]]
4187	then
4188	if [[ -f CONTINUE_RUN ]]
4189	then
4190	echo "PALM restart run necessary" > email_text
4191	echo "description header of actual run:" >> email_text
4192	cat CONTINUE_RUN >> email_text
4193	echo "mrun-command to restart:" >> email_text
4194	echo "$mc" >> email_text
4195	else
4196	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4197	fi
4198	mail $email_notification < email_text
4199	printf "\n *** email notification sent to \"$email_notification\" "
4200	fi
4201	fi
4202
4203
4204
4205	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4206	cd $HOME
4207	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4208
4209	else
4210
4211	# PREPARING ACTIONS,
4212	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4213
4214	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4215	mrun_com="$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 $remote_username"
4216	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4217	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4218	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4219	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4220	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4221	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4222	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4223	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4224	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4225	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4226	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4227	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4228	if [[ $use_openmp = true ]]
4229	then
4230	mrun_com=${mrun_com}" -O $threads_per_task"
4231	fi
4232	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4233	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4234	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4235	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4236	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4237	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4238	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4239	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4240	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4241	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4242	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4243	if [[ $do_remote = true ]]
4244	then
4245	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4246	fi
4247
4248
4249	# CREATE EXECUTABLE FOR BATCH JOB
4250	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4251	then
4252
4253	printf "\n *** creating the executable for batch job\n"
4254
4255	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4256	if [[ $host != $localhost ]]
4257	then
4258	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4259	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4260	locat=create_executable; exit
4261	fi
4262
4263	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4264	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4265
4266	cp $make_depository .
4267	tar -xf $make_depository > /dev/null 2>&1
4268	cp ../* . > /dev/null 2>&1
4269
4270	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4271
4272	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4273	then
4274	printf "\n +++ error occured while compiling or linking"
4275	locat=compile
4276	exit
4277	fi
4278
4279	mv a.out ..
4280	cd - > /dev/null 2>&1
4281	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4282
4283	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4284
4285	fi
4286
4287
4288	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4289	jobfile=jobfile.$RANDOM
4290
4291
4292	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4293	echo "mkdir $TEMPDIR" >> $jobfile
4294	echo "cd $TEMPDIR" >> $jobfile
4295
4296
4297	# ACTIVATE ERROR-TRACEBACK
4298	if [[ $do_trace = true ]]
4299	then
4300	echo "set -x" >> $jobfile
4301	else
4302	echo "set +vx" >> $jobfile
4303	fi
4304
4305
4306	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4307	if [[ "$init_cmds" != "" ]]
4308	then
4309	echo "$init_cmds" >> $jobfile
4310	fi
4311	if [[ "$module_calls" != "" ]]
4312	then
4313	echo "$module_calls" >> $jobfile
4314	fi
4315
4316
4317	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4318	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4319	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4320	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4321	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4322	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4323	# QUEUEING-SYSTEMS
4324	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean ]]
4325	then
4326
4327	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4328	if [[ $restart_run != true ]]
4329	then
4330	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4331	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4332	fi
4333
4334	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4335	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4336	echo "set -x" >> $jobfile
4337	if [[ $host = $localhost ]]
4338	then
4339	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4340	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4341	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4342	then
4343	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4344	else
4345	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4346	fi
4347
4348	else
4349	if [[ $host = ibmkisti ]]
4350	then
4351	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4352	echo "localdir=\`pwd\`" >> $jobfile
4353	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4354	elif [[ $host = lcbullhh ]]
4355	then
4356	echo "localdir=\`pwd\`" >> $jobfile
4357	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4358
4359	elif [[ $host = lccrayb ]]
4360	then
4361	echo "localdir=\`pwd\`" >> $jobfile
4362	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4363	elif [[ $host = lccrayh ]]
4364	then
4365	echo "localdir=\`pwd\`" >> $jobfile
4366	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4367
4368	else
4369	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4370	fi
4371	fi
4372	echo "export SOURCES_COMPLETE=true" >> $jobfile
4373
4374	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4375	# WORKING DIRECTORY OF THE JOB
4376	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4377	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4378	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4379	echo "execute_mrun=true" >> $jobfile
4380	echo " " >> $jobfile
4381
4382	else
4383
4384	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4385	if [[ $do_compile = true ]]
4386	then
4387
4388	source_catalog=SOURCES_FOR_RUN_$fname
4389
4390	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4391	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4392	echo "export SOURCES_COMPLETE=true" >> $jobfile
4393	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4394
4395	for filename in $source_list
4396	do
4397	# BACKSLASH IS USED FOR MASKING
4398	echo "cat > $filename << \"%END%\"" >> $jobfile
4399	cat $source_catalog/$filename >> $jobfile
4400	echo " " >> $jobfile
4401	echo "%END%" >> $jobfile
4402	echo " " >> $jobfile
4403	done
4404
4405	# BACKSLASH IS USED FOR MASKING
4406	echo "cat > Makefile << \"%END%\"" >> $jobfile
4407	cat $source_catalog/Makefile >> $jobfile
4408	echo " " >> $jobfile
4409	echo "%END%" >> $jobfile
4410	echo " " >> $jobfile
4411
4412	echo "cd - > /dev/null" >> $jobfile
4413
4414	fi
4415
4416
4417	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4418	# BACKSLASH IS USED FOR MASKING
4419	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4420	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4421	echo "cat > $config_file << \"%END%\"" >> $jobfile
4422	if [[ $host = lckyuh ]]
4423	then
4424	# NO CROSS-COMPILER ON COMPUTE NODE
4425	sed 's/frtpx/frt/g' $config_file >> $jobfile
4426	else
4427	sed 's/#$.*//g' $config_file >> $jobfile
4428	fi
4429	echo "%END%" >> $jobfile
4430	echo " " >> $jobfile
4431
4432
4433	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4434	# BACKSLASH IS USED FOR MASKING
4435	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4436	if [[ $host = lckyuh ]]
4437	then
4438	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4439	else
4440	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4441	fi
4442	echo "%END%" >> $jobfile
4443	echo "chmod u+x $mrun_script_name" >> $jobfile
4444	echo "execute_mrun=true" >> $jobfile
4445	echo " " >> $jobfile
4446
4447	fi
4448
4449
4450	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4451	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4452	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4453	if [[ $do_remote = true ]]
4454	then
4455	(( i = 0 ))
4456	while (( i < iin ))
4457	do
4458	(( i = i + 1 ))
4459	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4460	if [[ "${transin[$i]}" = job ]]
4461	then
4462	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4463	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4464	echo " " >> $jobfile
4465	echo "%END%" >> $jobfile
4466	else
4467	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4468	fi
4469
4470	# CHECK, IF FILE COULD BE CREATED
4471	echo "if [[ \$? = 1 ]]" >> $jobfile
4472	echo "then" >> $jobfile
4473	echo " echo \" \" " >> $jobfile
4474	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4475	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4476	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4477	echo " execute_mrun=false" >> $jobfile
4478	echo "fi" >> $jobfile
4479	done
4480	fi
4481
4482	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4483	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4484	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4485	echo "LOCAL_PWD=$working_directory" >> $jobfile
4486	echo "export LOCAL_PWD" >> $jobfile
4487
4488	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4489	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4490	echo "export LOCAL_MRUN_PATH" >> $jobfile
4491
4492	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4493	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4494	# then
4495	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4496	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4497	# fi
4498
4499	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4500	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4501	echo "set -x" >> $jobfile
4502	echo "queue=$queue" >> $jobfile
4503	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4504	echo 'ls -al; echo `pwd`' >> $jobfile
4505	echo "cd \$HOME" >> $jobfile
4506	echo "rm -rf $TEMPDIR" >> $jobfile
4507
4508
4509
4510
4511	# START THE JOB USING SUBJOB-COMMAND
4512	if [[ $silent = false ]]
4513	then
4514	printf "\n "
4515	else
4516	printf "\n\n"
4517	fi
4518
4519	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
4520	rm -rf $jobfile
4521
4522
4523	fi # END OF REMOTE-PART

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