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source: palm/trunk/SCRIPTS/mrun @ 1788

Last change on this file since 1788 was 1779, checked in by raasch, 9 years ago
pmc array management changed from linked list to sequential loop; further small changes and cosmetics for the pmc
Property svn:keywords set to `Id Rev`
File size: 181.3 KB

Line
1	#!/bin/ksh
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	# test: implementing an execute mechanism where the execute command is given in the
25	# configuration file
26	# ROPTS removed from execution commands
27	# Warnings about missing optional files or user code changed to informative messages
28	#
29	# Former revisions:
30	# -----------------
31	# $Id: mrun 1779 2016-03-03 08:01:28Z maronga $
32	#
33	# 1755 2016-02-22 13:53:39Z maronga
34	# Minor bugfix to last commit
35	#
36	# 1753 2016-02-22 13:49:49Z maronga
37	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
38	#
39	# 1622 2015-07-20 06:21:36Z heinze
40	# bugfix for Mistral (lcbullhh)
41	#
42	# 1621 2015-07-17 11:39:33Z heinze
43	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
44	#
45	# 1609 2015-07-03 15:37:58Z maronga
46	# Modified the random number of the temporary working directory to match the
47	# queuing system number on HLRN-III (lccray*).
48	#
49	# 1604 2015-06-23 15:48:03Z suehring
50	# Enable coupled runs for lcmuk
51	#
52	# 1598 2015-05-29 06:45:40Z raasch
53	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
54	#
55	# 1549 2015-01-30 14:26:16Z suehring
56	# Enable interactive debug sessions with allinea debugger
57	#
58	# 1547 2015-01-29 15:09:12Z witha
59	# adjustments for ForWind computing cluster (lcflow)
60	#
61	# 1491 2014-11-12 08:12:57Z heinze
62	# correct setting of batch_job allowed for ibm-machines
63	#
64	# 1468 2014-09-24 14:06:57Z maronga
65	# Typo removed (addres->address)
66	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
67	# Added support for restart runs (remote) for lcxe6
68	#
69	# 1442 2014-07-28 07:09:10Z raasch
70	# default queues for HLRN-III (lccrayb/lccrayh) defined
71	#
72	# 1422 2014-07-02 10:01:25Z kanani
73	# automatic restarts enabled for lccrayb,
74	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
75	#
76	# 1420 2014-06-10 06:24:14Z raasch
77	# -j1 option added to aprung command for lccrayf (CSC)
78	#
79	# 1402 2014-05-09 14:25:13Z raasch
80	# batch_job added to envpar-NAMELIST
81	#
82	# 1357 2014-04-11 15:02:03Z witha
83	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
84	# possible)
85	#
86	# 1320 2014-03-20 08:40:49Z raasch
87	# check namelist file set false by default
88	#
89	# 1304 2014-03-12 10:29:42Z raasch
90	# ulimit option changed from -Ss to -s
91	#
92	# bugfix: missing "fi" in r1289
93	#
94	# 1289 2014-03-04 07:12:34Z raasch
95	# comments translated to English
96	# necriam-, fimm-, ibmy-, and sgi-specific code removed
97	# export of variables for palm and interpret_config removed
98	#
99	# 1281 2014-02-01 07:55:49Z raasch
100	# rsync-copy restricted to Cray machines, since command is unavailable on some
101	# other systems
102	#
103	# 1279 2014-01-28 12:10:14Z raasch
104	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
105	# in order to remove annoying restrictions concerning the number of processors which
106	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
107	# restriction, one of the nodes will be filled with less than the given number of
108	# tasks per node. A respective warning is given.
109	#
110	# 1274 2014-01-09 13:14:54Z heinze
111	# adjustments for lccrayh
112	#
113	# 1272 2014-01-08 10:19:32Z witha
114	# small adjustment for lcflow
115	#
116	# 1270 2013-12-16 11:05:01Z fricke
117	# call of combine_plot_fields adjusted for lccrayb/lccrayh
118	#
119	# 1255 2013-11-07 14:43:35Z raasch
120	# further adjustments for lccrayb remote access
121	#
122	# 1241 2013-10-30 11:36:58Z heinze
123	# Enable use of nudging input and input of large scale forcing from
124	# external files
125	#
126	# 1229 2013-09-20 06:55:19Z raasch
127	# further adjustments for lccrayb
128	#
129	# 1224 2013-09-16 07:27:23Z raasch
130	# first adjustments for lccrayb
131	#
132	# 1210 2013-08-14 10:58:20Z raasch
133	# fftw support added
134	#
135	# 1201 2013-07-10 16:17:59Z witha
136	# adjustments for Forwind cluster (lcflow)
137	#
138	# 1199 2013-07-05 14:52:22Z raasch
139	# adjustments for CSC Helsinki (lccrayf),
140	# executables for batch jobs can be created in advance, in order to avoid calling
141	# the compiler within the batch job (only works if batch jobs are submitted on
142	# local host)
143	#
144	# 1190 2013-06-25 09:39:21Z heinze
145	# enable use of automatic restarts for ibmh
146	# use of cluster/express queue enabled (ibmh)
147	#
148	# 1124 2013-04-09 15:46:52Z raasch
149	# variable "memory" is exported via typeset option -x, because otherwise an unknown
150	# side effect may lead to data loss while getopts is reading the script-option arguments
151	#
152	# 1122 2013-04-09 08:37:16Z heinze
153	# Bugfix: change type of variable last_char
154	#
155	# 1119 2013-04-05 15:11:19Z raasch
156	# Bugfix for setting -T option for subjob
157	#
158	# 1108 2013-03-05 07:03:32Z raasch
159	# bugfix for coupled runs on lckyut/lckyuh
160	#
161	# 1106 2013-03-04 05:31:38Z raasch
162	# --stdin argument for mpiexec on lckyuh
163	# -y and -Y settings output to header
164	#
165	# 1103 2013-02-20 02:15:53Z raasch
166	# default script runs again under ksh, because of unsolved problems with read
167	# from stdin: when bash script is called from a ksh, message "read error: 0:
168	# Resource temporarily unavailable" appears and script does not stop,
169	# further bash compatibility adjustments,
170	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
171	# on lckyuh, but mrun does not terminate and issues a warning instead
172	#
173	# 1101 2013-02-17 10:20:21Z raasch
174	# script now running under bash instead of ksh, which required small adjustments
175	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
176	# read from stdin),
177	# cross compilername on lckyuh compute nodes replaced by real compiler name
178	#
179	# 1099 2013-02-10 01:47:43Z raasch
180	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
181	# and for Forwind cluster (lcflow)
182	# small further adjustments for lckyut
183	#
184	# 1094 2013-02-03 01:52:12Z raasch
185	# explicit ssh/scp port can be set in config file with environment variable
186	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
187	# decalpha parts (yonsei) removed
188	#
189	# 2013-02-02 07:06:13Z raasch
190	# adjustments for Kyushu-University computing center (lckyut - tatara)
191	#
192	# 1083 2013-01-04 10:22:09Z maronga
193	# bugfix in parameter file check (read %cpp_options was missing)
194	#
195	# 1069 2012-11-28 16:18:43Z maronga
196	# bugfix: coupling mode was always set to mpi2, typos removed
197	#
198	# 1058 2012-11-21 07:00:35Z raasch
199	# Intel inspector (inspxe) is given the number of PEs instead of the number of
200	# nodes
201	#
202	# 1046 2012-11-09 14:38:45Z maronga
203	# code put under GPL (PALM 3.9)
204	#
205	# 21/03/94 - Siggi - first version finished
206	# 03/03/94 - Siggi - script development started
207	#
208	#--------------------------------------------------------------------------------#
209	# mrun - script for running PALM jobs
210	#--------------------------------------------------------------------------------#
211
212
213
214	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
215
216	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
217	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
218	# (TOO MANY ARGUMENTS - PROBLEM)
219	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
220
221	AddFilenames=""
222	additional_conditions=""
223	add_source_path=""
224	afname=""
225	archive_save=true
226	archive_system=none
227	check_namelist_files=false
228	combine_plot_fields=true
229	compiler_name=""
230	cond1=""
231	cond2=""
232	config_file=.mrun.config
233	coupled_dist=""
234	coupled_mode="mpi1"
235	cpp_opts=""
236	cpp_options=""
237	cpumax=0
238	cpurest=0
239	create_executable_for_batch=false
240	delete_temporary_catalog=true
241	do_batch=false
242	do_compile=true
243	do_remote=false
244	do_stagein=true
245	do_stageout=true
246	do_trace=false
247	email_notification="none"
248	exclude=""
249	executable=""
250	execute_command="none"
251	execution_error=false
252	fftw_inc=""
253	fftw_lib=""
254	fftw_support=false
255	fname=test
256	fromhost=""
257	global_revision=""
258	group_number=none
259	host=""
260	host_file=""
261	hp=""
262	ignore_archive_error=false
263	input_list=""
264	interpreted_config_file=""
265	job_catalog="~/job_queue"
266	job_on_file=""
267	keep_data_from_previous_run=false
268	link_local_input=false
269	link_local_output=false
270	localhost_realname=$(hostname)
271	local_dvrserver_running=.FALSE.
272	locat=normal
273	mainprog=""
274	makefile=""
275	max_par_io_str=""
276	mc=$0
277	while [[ $(echo $mc \| grep -c "/") != 0 ]]
278	do
279	mc=`echo $mc \| cut -f2- -d"/"`
280	done
281	module_calls=""
282	mrun_script_name=$mc
283	netcdf_inc=""
284	netcdf_lib=""
285	netcdf_support=false
286	node_usage=default
287	numprocs=""
288	numprocs_atmos=0
289	numprocs_ocean=0
290	OOPT=""
291	openmp=false
292	output_list=""
293	package_list=""
294	queue=none
295	read_from_config=""
296	restart_run=false
297	if [[ `hostname` = rte10 ]]
298	then
299	return_address=133.5.185.60
300	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
301	elif [[ `hostname` = climate0 ]]
302	then
303	return_address=165.132.26.68
304	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
305	elif [[ `hostname` = urban00 ]]
306	then
307	return_address=147.46.30.151
308	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
309	else
310	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
311	fi
312	return_password=""
313	return_username=$LOGNAME
314	remotecall=false
315	remote_username=""
316	run_coupled_model=false
317	run_mode=""
318	store_on_archive_system=false
319	dashes=" ----------------------------------------------------------------------------"
320	silent=false
321	source_list=""
322	source_path=SOURCE
323	tasks_per_node=""
324	threads_per_task=1
325	tmpcreate=false
326	tmp_data_catalog=""
327	transfer_problems=false
328	usern=$LOGNAME
329	use_openmp=false
330	version="MRUN 2.1 Rev$Rev: 1779 $"
331	working_directory=`pwd`
332	TOPT=""
333	XOPT=""
334	zeit=$( date \| cut -c 12-19 )
335
336	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
337	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
338	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
339	# SCRIPT-OPTION ARGUMENTS
340	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes sekunden tp1
341
342	# ERROR HANDLING IN CASE OF EXIT
343	trap 'rm -rf $working_directory/tmp_mrun
344	if [[ $locat != normal && $locat != control_c ]]
345	then
346
347	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
348	(( i = 0 ))
349	while (( i < iec ))
350	do
351	(( i = i + 1 ))
352	printf "\n *** Execution of ERROR-command:\n"
353	printf " >>> ${err_command[$i]}\n"
354	eval ${err_command[$i]}
355	done
356	if [[ -n $interpreted_config_file ]]
357	then
358	rm -rf $interpreted_config_file
359	fi
360	if [[ -n .mrun_environment ]]
361	then
362	rm -rf .mrun_environment
363	fi
364	if [[ $tmpcreate = true ]]
365	then
366	printf "\n *** Contents of \"$TEMPDIR\":\n"
367	ls -al; cd
368	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
369	fi
370	if [[ "$dvrserver_id" != "" ]]
371	then
372	echo "+++ killing dvrserver_id=$dvrserver_id"
373	kill $dvrserver_id
374	fi
375	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
376	then
377	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
378	fi
379	printf "\n\n+++ MRUN killed \n\n"
380	elif [[ $locat != control_c ]]
381	then
382	printf "\n\n --> all actions finished\n\n"
383	printf " Bye, bye $usern !!\n\n"
384	fi' exit
385
386
387	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
388	trap 'rm -rf $working_directory/tmp_mrun
389	rm -rf $working_directory/tmp_check_namelist_files
390	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
391	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
392	then
393	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
394	fi
395	if [[ "$dvrserver_id" != "" ]]
396	then
397	echo "+++ killing dvrserver_id=$dvrserver_id"
398	kill $dvrserver_id
399	fi
400	printf "\n+++ MRUN killed by \"^C\" \n\n"
401	locat=control_c
402	exit
403	' 2
404
405
406	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
407	# BEEN SET
408	if [[ "$PALM_BIN" = "" ]]
409	then
410	printf "\n +++ environment variable PALM_BIN has not been set"
411	printf "\n please set it to the directory where the PALM scripts are located"
412	locat=palm_bin; exit
413	fi
414	export PATH=$PALM_BIN:$PATH
415
416
417
418	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
419	# WHICH WILL BE USED TO START RESTART-JOBS
420	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
421	do
422	case $option in
423	(a) afname=$OPTARG;;
424	(A) store_on_archive_system=true; mc="$mc -A";;
425	(b) do_batch=true; mc="$mc -b";;
426	(B) delete_temporary_catalog=false; mc="$mc -B";;
427	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
428	(C) restart_run=true; mc="$mc -C";;
429	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
430	(D) cpp_opts="$cpp_opts $OPTARG"; mc="$mc -D'$OPTARG'";;
431	(F) job_on_file="-D"; mc="$mc -F";;
432	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
433	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
434	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
435	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
436	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
437	(I) ignore_archive_error=true; mc="$mc -I";;
438	(k) keep_data_from_previous_run=true; mc="$mc -k";;
439	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
440	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
441	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
442	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
443	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
444	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
445	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
446	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
447	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
448	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
449	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
450	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
451	(S) read_from_config=false; mc="$mc -S";;
452	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
453	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
454	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
455	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
456	(v) silent=true; mc="$mc -v";;
457	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
458	(x) do_trace=true;set -x; mc="$mc -x";;
459	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
460	(y) ocean_file_appendix=true; mc="$mc -y";;
461	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
462	(z) check_namelist_files=false; mc="$mc -z";;
463	(Z) combine_plot_fields=false; mc="$mc -Z";;
464	(\?) printf "\n +++ unknown option $OPTARG \n"
465	printf "\n --> type \"$0 ?\" for available options \n"
466	locat=parameter;exit;;
467	esac
468	done
469
470
471	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
472	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
473	(( to_shift = $OPTIND - 1 ))
474	shift $to_shift
475
476	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
477	if [[ "$1" = "?" ]]
478	then
479	(printf "\n *** mrun can be called as follows:\n"
480	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 -Z <modus> \n"
481	printf "\n Description of available options:\n"
482	printf "\n Option Description Default-Value"
483	printf "\n -a base name of input files equiv. -d"
484	printf "\n -A archiving when using file-attribute fl"
485	printf "\n -b batch-job on local machine ---"
486	printf "\n -B do not delete temporary directory at end ---"
487	printf "\n -c configuration file .mrun.config"
488	printf "\n -d base name of files attached to program test"
489	printf "\n -D preprocessor(cpp)-directives \"\" "
490	printf "\n -F create remote job file only ---"
491	printf "\n -h execution host $localhost_realname"
492	printf "\n -i INPUT control list \"\" "
493	printf "\n -I archiving errors of previous batch-jobs"
494	printf "\n will be ignored"
495	printf "\n -k keep data from previous run"
496	printf "\n -K additional conditions for controling"
497	printf "\n usage of conditional code and"
498	printf "\n env-variables in configuration file \"\" "
499	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
500	printf "\n -M Makefile name Makefile"
501	printf "\n -n node usage (shared/not_shared) depending on -h"
502	printf "\n -o OUTPUT control list \"\" "
503	printf "\n -O threads per openMP task ---"
504	printf "\n -p software package list \"\" "
505	printf "\n -q queue \"$queue\" "
506	printf "\n -r run control list (combines -i -o) \"\" "
507	printf "\n -s filenames of routines to be compiled \"\" "
508	printf "\n must end with .f, .f90, .F, or .c !"
509	printf "\n use \"..\" for more than one file and wildcards"
510	printf "\n -s LM compiles all locally modified files"
511	printf "\n -S config file interpreted by shellscript ---"
512	printf "\n -t allowed cpu-time in seconds (batch) 0"
513	printf "\n -T tasks per node depending on -h"
514	printf "\n -u username on remote machine \"\" "
515	printf "\n -v no prompt for confirmation ---"
516	printf "\n -w maximum parallel io streams as given by -X"
517	printf "\n -x tracing of mrun for debug purposes ---"
518	printf "\n -X # of processors (on parallel machines) 1"
519	printf "\n -y add appendix \"_O\" to all local output"
520	printf "\n files (ocean precursor runs followed by"
521	printf "\n coupled atmosphere-ocean runs) ---"
522	printf "\n -Y run coupled model, \"#1 #2\" with"
523	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
524	printf "\n -z disable a priori parameter file check ---"
525	printf "\n -Z skip combine_plot_fields at the end of "
526	printf "\n the simulation ---"
527	printf "\n "
528	printf "\n Possible values of positional parameter <modus>:"
529	printf "\n \"?\" - this outline \n\n") \| more
530	exit
531	elif [[ "$1" != "" ]]
532	then
533	printf "\n +++ positional parameter $1 unknown \n"
534	locat=parameter; exit
535	fi
536
537
538
539	# SHORT STARTING MESSAGE
540	printf "\n*** $version "
541	printf "\n will be executed. Please wait ..."
542
543
544
545	# CHECK, IF CONFIGURATION FILE EXISTS
546	if [[ ! -f $config_file ]]
547	then
548	printf "\n\n +++ configuration file: "
549	printf "\n $config_file"
550	printf "\n does not exist"
551	locat=connect; exit
552	fi
553
554
555	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
556	line=""
557	grep "%host_identifier" $config_file > tmp_mrun
558	while read line
559	do
560	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
561	then
562	HOSTNAME=`echo $line \| cut -d" " -s -f2`
563	host_identifier=`echo $line \| cut -d" " -s -f3`
564	if [[ $localhost_realname = $HOSTNAME ]]
565	then
566	localhost=$host_identifier
567	break
568	fi
569	fi
570	done < tmp_mrun
571
572	if [[ "$localhost" = "" ]]
573	then
574	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
575	printf "\n for local host \"$localhost_realname\"."
576	printf "\n Please add line"
577	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
578	printf "\n to the configuration file."
579	locat=localhost; exit
580	fi
581
582
583	# SET HOST-SPECIFIC VARIABLES
584	case $localhost_realname in
585	(r1\|r2\|h01\|b01) archive_system=tivoli;;
586	(cs*) archive_system=ut;;
587	esac
588
589
590	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
591	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
592	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
593	[[ "$afname" = "" ]] && afname=$fname
594
595
596	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
597	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
598	# STATEMENTS IN THE CONFIGURATION FILE
599	if [[ "$run_mode" != "" ]]
600	then
601	input_list="$input_list $run_mode"
602	output_list="$output_list $run_mode"
603	fi
604
605
606	# ??? is this (and the respective option -H) really required ???
607	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
608	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
609	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
610	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
611	if [[ "$fromhost" = "" ]]
612	then
613	fromhost=$localhost
614	fi
615
616
617	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
618	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
619	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
620	# TO BE SUBMITTED (I.E. do_batch=true)
621	if [[ -n $host && "$host" != $localhost ]]
622	then
623	do_batch=true
624	do_remote=true
625	case $host in
626	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|nech\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
627	(*) printf "\n"
628	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
629	printf "\n is not available"
630	locat=nqs; (( iec = 0 )); exit;;
631	esac
632	else
633	host=$localhost
634	fi
635
636
637	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
638	if [[ -n $additional_conditions ]]
639	then
640	cond1=`echo $additional_conditions \| cut -d" " -f1`
641	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
642	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
643	if [[ -n $dummy ]]
644	then
645	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
646	locat=options; exit
647	fi
648	block=_$cond1
649	[[ -n $cond2 ]] && block=${block}_$cond2
650	fi
651
652
653	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
654	if [[ $run_coupled_model = true ]]
655	then
656
657	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
658	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
659
660	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
661	then
662
663	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
664	printf "\n PEs (total) : $numprocs"
665	printf "\n PEs (atmosphere): $numprocs_atmos"
666	printf "\n PEs (ocean) : $numprocs_ocean"
667	locat=coupling; exit
668
669	fi
670
671
672	# GET coupled_mode FROM THE CONFIG FILE
673	line=""
674	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
675	while read line
676	do
677	echo line=\"$line\"
678	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
679	then
680	coupled_mode="mpi2"
681	fi
682	done < tmp_mrun
683
684	fi
685
686	# CHECK, IF FILE-ARCHIVING HAS FAILED IN PREVIOUS JOB (OF A JOB-CHAIN)
687	if [[ -f ~/job_queue/ARCHIVE_ERROR_$fname ]]
688	then
689	if [[ $ignore_archive_error = false ]]
690	then
691	printf "\n +++ data archiving of previous run failed"
692	printf "\n see directory \~/job_queue on remote machine"
693	locat=archive; exit
694	else
695	printf "\n +++ warning: data archiving in a previous run failed"
696	printf "\n MRUN continues, trying to get backup copy"
697	fi
698	fi
699
700
701	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
702	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
703	mrun_memory=$memory
704	mrun_group_number=$group_number
705	mrun_cpumax=$cpumax
706	mrun_numprocs=$numprocs
707
708
709	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
710	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
711	if [[ "$read_from_config" = false ]]
712	then
713	[[ $silent = false ]] && printf "\n Reading the configuration file... "
714
715	# READ THE CONFIGURATION FILE LINE BY LINE
716	while read zeile
717	do
718	[[ $silent = false ]] && printf "."
719
720
721	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
722	eval zeile=\"$zeile\"
723
724
725	# INTERPRET THE LINE
726	if [[ "$(echo $zeile)" = "" ]]
727	then
728	# EMPTY LINE, NO ACTION
729	continue
730
731	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
732	then
733
734	# LINE IS A COMMENT LINE
735	true
736
737	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
738	then
739
740	# LINE DEFINES AN ENVIRONMENT-VARIABLE
741	zeile=$(echo $zeile \| cut -c2-)
742	var=`echo $zeile \| cut -d" " -f1`
743	value=`echo $zeile \| cut -d" " -s -f2`
744	for_host=`echo $zeile \| cut -d" " -s -f3`
745	for_cond1=`echo $zeile \| cut -d" " -s -f4`
746	for_cond2=`echo $zeile \| cut -d" " -s -f5`
747
748	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
749	then
750
751	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
752	# "::" IS REPLACED BY ":".
753	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
754
755
756	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
757	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
758	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
759	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
760	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
761	# CONFIGURATION-FILE.
762	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
763	then
764	eval $var=\$value
765
766	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
767	if [[ $do_trace = true ]]
768	then
769	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
770	fi
771	fi
772
773	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
774	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
775	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
776	# MUST HAVE TO BE STARTED
777	if [[ $var = host ]]
778	then
779	if [[ -n $host && "$host" != $localhost ]]
780	then
781	do_batch=true
782	do_remote=true
783	case $host in
784	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
785	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
786	printf "\n is not available"
787	locat=nqs; exit;;
788	esac
789	else
790	host=$localhost
791	fi
792	fi
793
794	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
795	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
796	# BY MRUN (E.G. subjob)
797	export $var
798	fi
799
800
801
802
803	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
804	then
805
806	# LINE DEFINES ERROR-COMMAND
807	(( iec = iec + 1 ))
808	zeile=$(echo $zeile \| cut -c4-)
809	err_command[$iec]="$zeile"
810
811	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
812	then
813
814	# LINE DEFINES INPUT-COMMAND
815	(( iic = iic + 1 ))
816	zeile=$(echo $zeile \| cut -c4-)
817	in_command[$iic]="$zeile"
818
819	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
820	then
821
822	# LINE DEFINES OUTPUT-COMMAND
823	(( ioc = ioc + 1 ))
824	zeile=$(echo $zeile \| cut -c4-)
825	out_command[$ioc]="$zeile"
826
827	else
828
829	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
830	# s2a: in/out - field
831	# s2b: loc - field (optional)
832	# s2c: tr/ar - field (optional)
833	s1=`echo $zeile \| cut -d" " -f1`
834	s2=`echo $zeile \| cut -d" " -s -f2`
835	s2a=$(echo $s2 \| cut -d":" -f1)
836	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
837	then
838	s2b=""
839	s2c=""
840	else
841	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
842	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
843	fi
844	s3=`echo $zeile \| cut -d" " -f3`
845	s4=`echo $zeile \| cut -d" " -s -f4`
846	s5=`echo $zeile \| cut -d" " -s -f5`
847	s6=`echo $zeile \| cut -d" " -s -f6`
848
849
850	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
851	# INPUT- OR OUTPUT-LIST.
852	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
853	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
854	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
855	# IS NOT CHECKED AND STORED.
856	IFSALT="$IFS"; IFS="$IFS:"
857	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
858	then
859	found=false
860	for actual in $input_list
861	do
862	for formal in $s3
863	do
864	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
865	done
866	done
867	if [[ $found = true ]]
868	then
869	(( iin = iin + 1 ))
870	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
871	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
872	extin[$iin]=$s6
873	fi
874	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
875	then
876	found=false
877	for actual in $output_list
878	do
879	for formal in $s3
880	do
881	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
882	done
883	done
884	if [[ $found = true ]]
885	then
886	(( iout = iout + 1 ))
887	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
888	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
889	fi
890	elif [[ "$s2a" != in && "$s2a" != out ]]
891	then
892	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
893	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
894	locat=connect; exit
895	fi
896	IFS="$IFSALT"
897	fi
898	done < $config_file
899
900	else
901
902	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
903	[[ $silent = false ]] && printf "..."
904	interpreted_config_file=.icf.$RANDOM
905
906
907
908	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
909	cat > .mrun_environment << %%END%%
910	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
911	config_file = '$config_file', do_remote = '$do_remote',
912	do_trace = '$do_trace', host = '$host',
913	input_list = '$input_list', icf = '$interpreted_config_file',
914	localhost = '$localhost', output_list = '$output_list' /
915
916	%%END%%
917
918	if [[ "$host" != $localhost ]]
919	then
920
921	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
922	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
923	if [[ $? != 0 ]]
924	then
925	printf "\n\n +++ no interpret_config found"
926	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
927	locat=interpret_config; exit
928	fi
929	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
930	$interpret_config_executable
931
932	else
933
934	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
935	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
936	then
937	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
938	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
939	locat=interpret_config; exit
940	else
941	interpret_config${block}.x
942	fi
943
944	fi
945	rm .mrun_environment
946
947
948	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
949	chmod u+x $interpreted_config_file
950	export PATH=$PATH:.
951	. $interpreted_config_file
952	rm $interpreted_config_file
953
954	fi
955
956
957	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
958	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
959	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
960	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
961	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
962	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
963	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
964
965
966	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
967	# FOR SOURCE-FILES TO BE COMPILED.
968	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
969	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
970	if [[ "$SOURCES_COMPLETE" = "" ]]
971	then
972
973	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
974	# HAS BEEN DEFINED
975	source_path=""
976	line=""
977	grep "%source_path" $config_file > tmp_mrun
978	while read line
979	do
980	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
981	then
982	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
983	then
984	global_source_path=`echo $line \| cut -d" " -f2`
985	fi
986	fi
987	done < tmp_mrun
988
989	line=""
990	found=false
991	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
992	while read line
993	do
994	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
995	then
996	if [[ $found = true ]]
997	then
998	printf "\n\n +++ more than one source path found in configuration file"
999	printf "\n for local host \"$localhost\" "
1000	locat=source_path; exit
1001	fi
1002	source_path=`echo $line \| cut -d" " -f2`
1003	found=true
1004	fi
1005	done < tmp_mrun
1006	rm tmp_mrun
1007
1008	if [[ "$source_path" = "" ]]
1009	then
1010	if [[ "$global_source_path" != "" ]]
1011	then
1012	source_path=$global_source_path
1013	else
1014	printf "\n\n +++ no source path found in configuration file"
1015	printf "\n for local host \"$localhost\" "
1016	locat=source_path; exit
1017	fi
1018	fi
1019	eval source_path=$source_path
1020
1021	if [[ ! -d $source_path ]]
1022	then
1023	printf "\n\n +++ source path \"$source_path\" on local host"
1024	printf "\n \"$localhost\" does not exist"
1025	locat=source_path; exit
1026	fi
1027
1028	fi
1029
1030
1031	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1032	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1033	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1034	then
1035	global_revision=`svnversion $source_path 2>/dev/null`
1036	global_revision="Rev: $global_revision"
1037	fi
1038
1039
1040	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1041	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1042	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1043	if [[ -n $host && "$host" != $localhost ]]
1044	then
1045	do_batch=true
1046	do_remote=true
1047	case $host in
1048	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lcflow\|lckyoto\|nech\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb) true;;
1049	(*) printf "\n"
1050	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1051	printf "\n is not available"
1052	locat=nqs; (( iec = 0 )); exit;;
1053	esac
1054	else
1055	host=$localhost
1056	fi
1057
1058
1059
1060	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1061	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1062	then
1063
1064	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1065	if [[ ! -n $numprocs ]]
1066	then
1067	printf "\n"
1068	printf "\n +++ option \"-K parallel\" requires additional specification"
1069	printf "\n of the number of processors to be used by"
1070	printf "\n mrun-option \"-X\" or by environment-variable"
1071	printf "\n \"numprocs\" in the configuration file"
1072	locat=numprocs; (( iec = 0 )); exit
1073	fi
1074
1075	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1076	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1077	if [[ "$tasks_per_node" = "" && $host != lcflow && $host != lcxt5m ]]
1078	then
1079	printf "\n"
1080	printf "\n +++ option \"-T\" (tasks per node) is missing"
1081	printf "\n set -T option or define tasks_per_node in the config file"
1082	locat=tasks_per_node; (( iec = 0 )); exit
1083	fi
1084
1085	if (( numprocs < tasks_per_node ))
1086	then
1087	printf "\n"
1088	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1089	printf "\n given values: -T $tasks_per_node -X $numprocs"
1090	locat=tasks_per_node; (( iec = 0 )); exit
1091	fi
1092
1093	if [[ $host != lcflow && $host != lcxt5m ]]
1094	then
1095	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1096	(( ival = $tasks_per_node ))
1097	(( pes = numprocs ))
1098	(( ii = pes / ival ))
1099	(( remaining_pes = pes - ii * ival ))
1100	if (( remaining_pes > 0 ))
1101	then
1102	printf "\n"
1103	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1104	printf "\n divisor of the total number of processors (option \"-X\")"
1105	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1106	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1107	(( nodes = nodes + 1 ))
1108	fi
1109	fi
1110
1111
1112	# SETTINGS FOR SUBJOB-COMMAND
1113	OOPT="-O $threads_per_task"
1114
1115	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1116	if [[ "$tasks_per_node" != "" ]]
1117	then
1118	TOPT="-T $tasks_per_node"
1119	fi
1120
1121	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1122	if [[ $node_usage = default ]]
1123	then
1124	if [[ $host = ibms ]]
1125	then
1126	node_usage=shared
1127	else
1128	node_usage=not_shared
1129	fi
1130	fi
1131
1132	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1133	then
1134	printf "\n"
1135	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1136	printf "\n \"shared\" or \"not_shared\""
1137	locat=tasks_per_node; (( iec = 0 )); exit
1138	fi
1139
1140	fi
1141
1142	# CHECK IF HOSTFILE EXISTS
1143	if [[ -n $hostfile ]]
1144	then
1145	if [[ ! -f $hostfile ]]
1146	then
1147	printf "\n"
1148	printf "\n +++ hostfile \"$hostfile\" does not exist"
1149	locat=hostfile; exit
1150	fi
1151	fi
1152
1153
1154	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1155	if [[ "$maximum_parallel_io_streams" = "" ]]
1156	then
1157	maximum_parallel_io_streams=$numprocs
1158	fi
1159
1160
1161	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1162	if [[ "$scp_port" != "" ]]
1163	then
1164	PORTOPT="-P $scp_port"
1165	SSH_PORTOPT="-p $scp_port"
1166	fi
1167
1168
1169	# SET DEFAULT-QUEUE, IF NOT GIVEN
1170	if [[ $queue = none ]]
1171	then
1172	case $host in
1173	(ibmh) queue=cluster;;
1174	(ibmkisti) queue=class.32plus;;
1175	(lcbullhh) queue=compute;;
1176	(lccrayb) queue=mpp1q;;
1177	(lccrayh) queue=mpp1q;;
1178	(lckiaps) queue=normal;;
1179	(lckyoto) queue=ph;;
1180	(lckyuh) queue=fx-single;;
1181	(lckyut) queue=cx-single;;
1182	(lctit) queue=S;;
1183	(nech) queue=none;;
1184	(unics) queue=unics;;
1185	esac
1186	fi
1187
1188
1189	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1190	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1191	(( i = 0 ))
1192	while (( i < iin ))
1193	do
1194	(( i = i + 1 ))
1195	(( maxcycle = 0 ))
1196
1197	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1198	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1199	if [[ "${actionin[$i]}" = di ]]
1200	then
1201	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1202	# HOST ONLY
1203	eval filename=${pathin[$i]}/${endin[$i]}
1204	else
1205	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1206	# HOST ONLY
1207	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1208	fi
1209	eval pathname=${pathin[$i]}
1210
1211	# SAVE INPUT FILE NAME FOR PARAMETER FILE CHECK
1212	if [[ ("${transin[$i]}" = job) && (-f $filename) ]]
1213	then
1214	filename_input=$filename
1215	fi
1216
1217	# CHECK IF FILE EXISTS
1218	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1219	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1220	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1221	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1222	then
1223
1224	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1225	if [[ "${transin[$i]}" != "locopt" ]]
1226	then
1227	printf "\n\n +++ INPUT-file: "
1228	if [[ "${extin[$i]}" = "" ]]
1229	then
1230	printf "\n $filename"
1231	else
1232	printf "\n $filename.${extin[$i]}"
1233	fi
1234	printf "\n does not exist\n"
1235	locat=input; exit
1236	else
1237	transin[$i]="unavailable"
1238	fi
1239	else
1240
1241	# DETERMINE THE FILE'S CYCLE NUMBER
1242	ls -1 -d $filename > filelist 2>/dev/null
1243	ls -1 -d $filename.* >> filelist 2>/dev/null
1244	while read zeile
1245	do
1246	cycle=$(echo $zeile \| cut -f2 -d".")
1247	if [[ "$cycle" = "$zeile" ]]
1248	then
1249	(( icycle = 0 ))
1250	elif [[ "$cycle" = "${extin[$i]}" ]]
1251	then
1252	(( icycle = 0 ))
1253	else
1254	(( icycle = $cycle ))
1255	fi
1256	if (( icycle > maxcycle ))
1257	then
1258	(( maxcycle = icycle ))
1259	file_to_be_used=$zeile
1260	fi
1261	done <filelist
1262	rm filelist
1263
1264	# APPEND CYCLE NUMBER TO FILENAME
1265	if (( maxcycle > 0 ))
1266	then
1267	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1268	then
1269	filename=${filename}.$maxcycle.${extin[$i]}
1270	else
1271	filename=${filename}.$maxcycle
1272	fi
1273	else
1274	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1275	then
1276	filename=${filename}.${extin[$i]}
1277	fi
1278	fi
1279
1280	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1281	# BECAUSE IT MIGHT BE REQUIRED LATER TO RESTORE THE FILE FROM AN ARCHIVE-SYSTEM
1282	absnamein[$i]=$filename
1283	if (( maxcycle > 0 ))
1284	then
1285	if [[ "${actionin[$i]}" = di ]]
1286	then
1287	frelin[$i]=${endin[$i]}.$maxcycle
1288	else
1289	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1290	fi
1291	else
1292	if [[ "${actionin[$i]}" = di ]]
1293	then
1294	frelin[$i]=${endin[$i]}
1295	else
1296	frelin[$i]=${afname}${endin[$i]}
1297	fi
1298	fi
1299
1300	fi
1301	done
1302
1303	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1304	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1305	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1306	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1307	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1308	# REMOTE HOST)
1309	(( i = 0 ))
1310	while (( i < iout ))
1311	do
1312	(( i = i + 1 ))
1313	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1314	then
1315	if [[ "${actionout[$i]}" = tr ]]
1316	then
1317	actionout[$i]=""
1318	elif [[ "${actionout[$i]}" = trpe ]]
1319	then
1320	actionout[$i]=pe
1321	elif [[ "${actionout[$i]}" = tra ]]
1322	then
1323	actionout[$i]=a
1324	fi
1325	(( maxcycle = 0 ))
1326	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1327	eval catalogname=${pathout[$i]}
1328	if [[ $(ls $filename* 2>&1 \| grep -c "not found") = 1 \|\| \
1329	$(ls $filename* 2>&1 \| grep -c "nicht gefunden") = 1 \|\| \
1330	$(ls $filename* 2>&1 \| grep -c "No such file") = 1 \|\| \
1331	$(ls $filename* 2>&1 \| grep -c "does not exist") = 1 ]]
1332	then
1333
1334	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1335	if cat /dev/null > $filename
1336	then
1337	rm $filename
1338	else
1339
1340	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1341	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1342	if [[ ! -d $catalogname ]]
1343	then
1344	if mkdir -p $catalogname
1345	then
1346	printf "\n\n *** directory:"
1347	printf "\n $catalogname"
1348	printf "\n was created\n"
1349	else
1350	printf "\n\n +++ OUTPUT-file:"
1351	printf "\n $filename"
1352	printf "\n cannot be created, because directory does not exist"
1353	printf "\n and cannot be created either"
1354	printf "\n"
1355	locat=output ; exit
1356	fi 2>/dev/null
1357	else
1358	printf "\n\n +++ OUTPUT-file:"
1359	printf "\n $filename"
1360	printf "\n cannot be created, although directory exists"
1361	printf "\n"
1362	locat=output ; exit
1363	fi
1364	fi 2>/dev/null
1365	else
1366
1367	# DETERMINE THE CYCLE NUMBER
1368	ls -1 -d $filename > filelist 2>/dev/null
1369	ls -1 -d $filename.* >> filelist 2>/dev/null
1370	while read zeile
1371	do
1372	cycle=$(echo $zeile \| cut -f2 -d".")
1373	if [[ "$cycle" = "$zeile" \|\| "$cycle" = ${extout[$i]} ]]
1374	then
1375	(( icycle = 1 ))
1376	else
1377	(( icycle = $cycle + 1 ))
1378	fi
1379	if (( icycle > maxcycle ))
1380	then
1381	(( maxcycle = icycle ))
1382	fi
1383	done <filelist
1384	rm filelist
1385	fi
1386
1387	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1388	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1389	if [[ "${actionout[$i]}" != a ]]
1390	then
1391	if (( maxcycle > 0 ))
1392	then
1393	filename=${filename}.$maxcycle
1394	if cat /dev/null > $filename
1395	then
1396	rm $filename
1397	else
1398	printf "\n +++ OUTPUT-file:"
1399	printf "\n $filename"
1400	printf "\n cannot be created"
1401	locat=output ; exit
1402	fi
1403	fi
1404	else
1405	(( maxcycle = maxcycle - 1 ))
1406	if (( maxcycle > 0 ))
1407	then
1408	filename=${filename}.$maxcycle
1409	fi
1410	fi
1411
1412	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1413	# BECAUSE IT MIGHT BE REQUIRED LATER TO STORE THE FILE ON AN ARCHIVE-SYSTEM
1414	# OR TO PUT THIS FILENAME ON FILE OUTPUT_FILE_CONNECTIONS
1415	pathout[$i]=$filename
1416	if (( maxcycle > 0 ))
1417	then
1418	frelout[$i]=${fname}${endout[$i]}.$maxcycle
1419	else
1420	frelout[$i]=${fname}${endout[$i]}
1421	fi
1422
1423	fi
1424	done
1425
1426
1427	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1428	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1429	then
1430	if [[ "$dvr_inc" = "" ]]
1431	then
1432	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1433	printf "\n This is required for the dvrp_graphics package.\n"
1434	locat=dvr; exit
1435	fi
1436	if [[ "$dvr_lib" = "" ]]
1437	then
1438	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1439	printf "\n This is required for the dvrp_graphics package.\n"
1440	locat=dvr; exit
1441	fi
1442	fi
1443
1444
1445	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1446	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1447	if [[ "$mainprog" = "" && "$executable" = "" ]]
1448	then
1449	printf "\n +++ neither main program nor executable defined"
1450	locat=source; exit
1451	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1452	then
1453	printf "\n +++ main program as well as executable defined"
1454	locat=source; exit
1455	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1456	then
1457	do_compile=false
1458	fi
1459
1460
1461	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1462	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1463	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1464	then
1465	rm -rf SOURCES_FOR_RUN_$fname
1466	mkdir SOURCES_FOR_RUN_$fname
1467	fi
1468
1469
1470	# COLLECT ALL ROUTINES TO BE COMPILED
1471	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1472	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1473	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1474	then
1475
1476	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1477
1478	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1479	then
1480
1481	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1482	source_list=""
1483	cd $source_path
1484
1485
1486	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1487	if [[ ! -d .svn ]]
1488	then
1489	printf "\n\n +++ source directory"
1490	printf "\n \"$source_path\" "
1491	printf "\n is not under control of \"subversion\"."
1492	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1493	fi
1494
1495
1496	# LIST ALL MODIFIED SOURCE CODE FILES
1497	Filenames=""
1498	svn status > tmp_mrun
1499	while read line
1500	do
1501	firstc=`echo $line \| cut -c1`
1502	if [[ $firstc = M \|\| $firstc = "?" ]]
1503	then
1504	Name=`echo "$line" \| cut -c8-`
1505	extension=`echo $Name \| cut -d. -f2`
1506	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1507	then
1508	Filenames="$Filenames "$Name
1509	fi
1510	fi
1511	done < tmp_mrun
1512
1513
1514	# COPY FILES TO SOURCES_FOR_RUN_...
1515	for dateiname in $Filenames
1516	do
1517	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1518	source_list=$source_list"$dateiname "
1519	done
1520
1521	cd - > /dev/null
1522
1523
1524	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1525	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1526	elif [[ "$source_list" != "" && $restart_run != true ]]
1527	then
1528
1529	cd $source_path
1530
1531	for filename in $source_list
1532	do
1533
1534	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1535	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1536	then
1537	printf "\n +++ source code file: $filename"
1538	printf "\n must not contain (\"/\") "
1539	locat=source; exit
1540	fi
1541
1542	if [[ ! -f $filename ]]
1543	then
1544	printf "\n +++ source code file: $filename"
1545	printf "\n does not exist"
1546	locat=source; exit
1547	else
1548	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1549	fi
1550
1551	done
1552
1553	cd - > /dev/null
1554
1555	fi
1556
1557
1558	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1559	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1560	if [[ $restart_run != true ]]
1561	then
1562
1563	if [[ ! -f "$source_path/$mainprog" ]]
1564	then
1565	printf "\n\n +++ main program: $mainprog"
1566	printf "\n does not exist in source directory"
1567	printf "\n \"$source_path\"\n"
1568	locat=source; exit
1569	else
1570	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1571	then
1572	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1573	source_list=${mainprog}" $source_list"
1574	fi
1575	fi
1576	fi
1577
1578
1579	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1580	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1581	if [[ "$restart_run" != true ]]
1582	then
1583	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1584	if [[ ! -f $makefile ]]
1585	then
1586	printf "\n +++ file \"$makefile\" does not exist"
1587	locat=make; exit
1588	else
1589	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1590	fi
1591	fi
1592
1593
1594	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1595	if [[ $restart_run != true && "$add_source_path" != "" ]]
1596	then
1597
1598	# DOES THE DIRECTORY EXIST?
1599	if [[ ! -d $add_source_path ]]
1600	then
1601	printf "\n\n *** INFORMATIVE: additional source code directory"
1602	printf "\n \"$add_source_path\" "
1603	printf "\n does not exist or is not a directory."
1604	printf "\n No source code will be used from this directory!\n"
1605	add_source_path=""
1606	if [[ $silent == false ]]
1607	then
1608	sleep 3
1609	fi
1610	else
1611
1612	cd $add_source_path
1613	found=false
1614
1615	Names=$(ls -1 *.f90 2>&1)
1616	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1617	Names=$(ls -1 *.F90 2>&1)
1618	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1619	Names=$(ls -1 *.F 2>&1)
1620	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1621	Names=$(ls -1 *.f 2>&1)
1622	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1623	Names=$(ls -1 *.c 2>&1)
1624	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1625
1626	cd - > /dev/null
1627	cd SOURCES_FOR_RUN_$fname
1628
1629	# COPY MAKEFILE IF EXISTING
1630	if [[ -f $add_source_path/Makefile ]]
1631	then
1632	printf "\n\n *** user Makefile from directory"
1633	printf "\n \"$add_source_path\" is used \n"
1634	if [[ $silent == false ]]
1635	then
1636	sleep 1
1637	fi
1638	cp $add_source_path/Makefile .
1639	fi
1640
1641	for dateiname in $AddFilenames
1642	do
1643	if [[ -f $dateiname ]]
1644	then
1645	printf "\n +++ source code file \"$dateiname\" found in additional"
1646	printf "\n source code directory \"$add_source_path\" "
1647	printf "\n but was also given with option \"-s\" which means that it should be taken"
1648	printf "\n from directory \"$source_path\"."
1649	locat=source; exit
1650	fi
1651
1652	cp $add_source_path/$dateiname .
1653	source_list="$source_list $dateiname"
1654
1655	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1656	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1657	then
1658	printf "\n\n +++ user file \"$dateiname\" "
1659	printf "\n is not listed in Makefile \n"
1660	locat=source; exit
1661	else
1662
1663	if [[ $found = false ]]
1664	then
1665	found=true
1666	printf "\n\n *** following user file(s) added to the"
1667	printf " files to be translated:\n "
1668	fi
1669	printf "$dateiname "
1670	if [[ $silent == false ]]
1671	then
1672	sleep 0.5
1673	fi
1674
1675	fi
1676	done
1677	[[ $found = true ]] && printf "\n"
1678	cd - > /dev/null
1679	fi
1680	fi
1681
1682
1683	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1684	# TO THE LIST OF FILES TO BE COMPILED
1685	if [[ $restart_run != true && -n $package_list ]]
1686	then
1687
1688	cd $source_path
1689
1690	for package in $package_list
1691	do
1692
1693	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1694
1695	# DETERMINE FILES BELONGING TO THE PACKAGE
1696	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1697	# THE NAME OF THE DIRECTORY
1698	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1699
1700
1701	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1702	# IF THEY ARE NOT ALREADY PART OF THE LIST
1703	for source_list_name in $package_source_list
1704	do
1705	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1706	then
1707
1708	# ONLY TAKE FILES WITH VALID SUFFIX
1709	ending=`echo $source_list_name \| cut -f2 -d.`
1710	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1711	then
1712	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1713	source_list="$source_list $source_list_name"
1714	fi
1715	fi
1716	done
1717	done
1718
1719	cd - > /dev/null
1720	fi
1721
1722	fi # do_compile=true
1723
1724
1725	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1726	# AND SET PRE-PROCESSOR DIRECTIVES
1727	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1728	then
1729
1730	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1731	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1732	then
1733	cpp_options="${cpp_options},-D__ibm=__ibm"
1734	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1735	then
1736	cpp_options="$cpp_options -D__nec"
1737	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1738	then
1739	cpp_options="$cpp_options -D__lc"
1740	else
1741	cpp_options="$cpp_options -D__$localhost"
1742	fi
1743
1744	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1745	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1746	then
1747	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1748	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1749	else
1750	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1751	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1752	fi
1753
1754	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1755	if [[ -n $package_list ]]
1756	then
1757	for package in $package_list
1758	do
1759	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1760	then
1761	if [[ $package != "dvrp_graphics+1PE" ]]
1762	then
1763	cpp_options="${cpp_options},-D__$package=__$package"
1764	else
1765	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1766	export use_seperate_pe_for_dvrp_output=true
1767	fi
1768	else
1769	if [[ $package != "dvrp_graphics+1PE" ]]
1770	then
1771	cpp_options="$cpp_options -D__$package"
1772	else
1773	cpp_options="$cpp_options -D__dvrp_graphics"
1774	export use_seperate_pe_for_dvrp_output=true
1775	fi
1776	fi
1777	done
1778	fi
1779
1780	# SET DIRECTIVES GIVEN BY OPTION -D
1781	if [[ -n $cpp_opts ]]
1782	then
1783	for popts in $cpp_opts
1784	do
1785	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1786	then
1787	cpp_options="${cpp_options},-D__$popts=__$popts"
1788	else
1789	cpp_options="$cpp_options -D__$popts"
1790	fi
1791	done
1792	fi
1793
1794	else
1795
1796
1797	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1798	if [[ $do_remote = false ]]
1799	then
1800	if [[ ! -f $executable ]]
1801	then
1802	printf "\n +++ executable file: $executable"
1803	printf "\n does not exist"
1804	locat=executable; exit
1805	fi
1806	fi
1807	fi
1808
1809
1810	# DETERMINE THE JOB MODE
1811	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1812	then
1813	if [[ "$LOADLBATCH" = yes ]]
1814	then
1815	batch_job=.TRUE.
1816	jobmo=BATCH
1817	else
1818	batch_job=.FALSE.
1819	jobmo=INTERACTIVE
1820	fi
1821	else
1822	if [[ "$ENVIRONMENT" = BATCH ]]
1823	then
1824	batch_job=.TRUE.
1825	jobmo=BATCH
1826	else
1827	batch_job=.FALSE.
1828	jobmo=INTERACTIVE
1829	fi
1830	fi
1831
1832	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1833	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1834	then
1835	printf "\n +++ no interactive runs allowed on host \"$host\" "
1836	printf "\n please submit batch job using mrun option \"-b\" \n"
1837	locat=normal; exit
1838	fi
1839
1840
1841	# CHECK, IF USER DEFINED A COMPILER
1842	if [[ "$compiler_name" = "" ]]
1843	then
1844
1845	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1846	locat=compiler_name; exit
1847
1848	fi
1849
1850
1851	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1852
1853	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1854	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1855	then
1856	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1857	if [[ "$kennung" = "" ]]
1858	then
1859	kennung=$RANDOM
1860	fi
1861	else
1862	kennung=$RANDOM
1863	fi
1864
1865	if [[ "$tmp_user_catalog" = "" ]]
1866	then
1867	if [[ $localhost = ibmh ]]
1868	then
1869	tmp_user_catalog=$SCRATCH
1870	elif [[ $localhost = nech ]]
1871	then
1872	tmp_user_catalog=$WRKSHR
1873	else
1874	tmp_user_catalog=/tmp
1875	fi
1876	fi
1877	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1878
1879
1880	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1881	if [[ "$tmp_data_catalog" = "" ]]
1882	then
1883	if [[ $localhost = nech ]]
1884	then
1885	tmp_data_catalog=$WRKSHR/mrun_restart_data
1886	else
1887	tmp_data_catalog=/tmp/mrun_restart_data
1888	fi
1889	fi
1890
1891
1892	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1893	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1894	then
1895	eval fopts=\"$fopts\"
1896	eval lopts=\"$lopts\"
1897	fi
1898
1899
1900	# DETERMINE COMPILE- AND LINK-OPTIONS
1901	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1902	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1903	XOPT="-X $numprocs"
1904
1905
1906	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1907	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1908	done=false
1909	while [[ $done = false ]]
1910	do
1911	cputime=$cpumax
1912	if (( $cputime == 0 ))
1913	then
1914	if [[ $do_batch = true ]]
1915	then
1916	printf "\n +++ cpu-time is undefined"
1917	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1918	printf "\n >>> "
1919	read cputime 1>/dev/null 2>&1
1920	else
1921	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1922	fi
1923	else
1924	done=true
1925	fi
1926	cpumax=$cputime
1927	done
1928
1929	(( minuten = cputime / 60 ))
1930	(( sekunden = cputime - minuten * 60 ))
1931
1932
1933	# CHECK THE MEMORY DEMAND
1934	if [[ $do_batch = true ]]
1935	then
1936	done=false
1937	while [[ $done = false ]]
1938	do
1939	if (( memory == 0 ))
1940	then
1941	printf "\n +++ memory demand is undefined"
1942	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1943	printf "\n >>> "
1944	read memory 1>/dev/null 2>&1
1945	else
1946	done=true
1947	fi
1948	done
1949	fi
1950
1951
1952	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1953	if [[ $do_remote = true && -z $remote_username ]]
1954	then
1955	while [[ -z $remote_username ]]
1956	do
1957	printf "\n +++ username on remote host \"$host\" is undefined"
1958	printf "\n >>> Please type username:"
1959	printf "\n >>> "
1960	read remote_username
1961	done
1962	mc="$mc -u$remote_username"
1963	fi
1964
1965	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1966	if [[ "$login_init_cmd" != "" ]]
1967	then
1968	export init_cmds="${login_init_cmd};"
1969	fi
1970
1971
1972	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1973	if [[ "$modules" != "" ]]
1974	then
1975	if [[ $host = lctit ]]
1976	then
1977	export module_calls=". $modules"
1978	else
1979	export module_calls="module load ${modules};"
1980	fi
1981	fi
1982
1983	# OUTPUT OF THE MRUN-HEADER
1984	calltime=$(date)
1985	printf "\n"
1986	printf "#------------------------------------------------------------------------# \n"
1987	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1988	printf "\| \| \n"
1989	spalte1="called on:"; spalte2=$localhost_realname
1990	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1991	if [[ $do_remote = true ]]
1992	then
1993	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
1994	else
1995	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
1996	fi
1997	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
1998	if [[ -n $numprocs ]]
1999	then
2000	if [[ $run_coupled_model = false ]]
2001	then
2002	spalte1="number of PEs:"; spalte2=$numprocs
2003	else
2004	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2005	fi
2006	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2007	fi
2008	if [[ -n $tasks_per_node ]]
2009	then
2010	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2011	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2012	if (( remaining_pes > 0 ))
2013	then
2014	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2015	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2016	fi
2017	fi
2018	if [[ $maximum_parallel_io_streams != $numprocs ]]
2019	then
2020	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2021	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2022	fi
2023	if [[ $use_openmp = true ]]
2024	then
2025	spalte1="threads per task:"; spalte2="$threads_per_task"
2026	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2027	fi
2028	printf "\| \| \n"
2029	if [[ $do_compile = true ]]
2030	then
2031	if [[ "$mopts" != "" ]]
2032	then
2033	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2035	zeile=$(echo "$mopts" \| cut -c46-)
2036	while [[ "$zeile" != "" ]]
2037	do
2038	spalte1=""
2039	spalte2=$(echo "$zeile" \| cut -c-45)
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	zeile=$(echo "$zeile" \| cut -c46-)
2042	done
2043	fi
2044
2045	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2046	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2047	zeile=$(echo "$cpp_options" \| cut -c46-)
2048	while [[ "$zeile" != "" ]]
2049	do
2050	spalte1=""
2051	spalte2=$(echo "$zeile" \| cut -c-45)
2052	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2053	zeile=$(echo "$zeile" \| cut -c46-)
2054	done
2055
2056	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2057	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2058	zeile=$(echo "$fopts" \| cut -c46-)
2059	while [[ "$zeile" != "" ]]
2060	do
2061	spalte1=""
2062	spalte2=$(echo "$zeile" \| cut -c-45)
2063	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2064	zeile=$(echo "$zeile" \| cut -c46-)
2065	done
2066
2067	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2068	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2069	zeile=$(echo "$lopts" \| cut -c46-)
2070	while [[ "$zeile" != "" ]]
2071	do
2072	spalte1=""
2073	spalte2=$(echo "$zeile" \| cut -c-45)
2074	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2075	zeile=$(echo "$zeile" \| cut -c46-)
2076	done
2077
2078	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2079	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2080	zeile=$(echo "$modules" \| cut -c46-)
2081	while [[ "$zeile" != "" ]]
2082	do
2083	spalte1=""
2084	spalte2=$(echo "$zeile" \| cut -c-45)
2085	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2086	zeile=$(echo "$zeile" \| cut -c46-)
2087	done
2088
2089	spalte1="main program:"; spalte2=$mainprog
2090	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2091	else
2092	spalte1=executable:; spalte2=$executable
2093	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2094	fi
2095	printf "\| \| \n"
2096	spalte1="base name of files:"; spalte2=$fname
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098	if [[ $fname != $afname ]]
2099	then
2100	spalte1="base name of input files:"; spalte2=$afname
2101	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2102	fi
2103	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2104	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2105	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2106	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2107
2108	if [[ "$ocean_file_appendix" = true ]]
2109	then
2110	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2111	fi
2112
2113	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2114	then
2115	spalte1="memory demand / PE":; spalte2="$memory MB"
2116	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2117	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2118	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2119	fi
2120
2121	if [[ $do_compile = true ]]
2122	then
2123	printf "\| \| \n"
2124	printf "\| Files to be compiled: \| \n"
2125	zeile=$source_list
2126	while [[ "$zeile" != "" ]]
2127	do
2128	linestart=$(echo $zeile \| cut -c-70)
2129	printf "\| %-70s \| \n" "$linestart"
2130	zeile=$(echo "$zeile" \| cut -c71-)
2131	done
2132	fi
2133	printf "#------------------------------------------------------------------------#"
2134
2135
2136
2137	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2138	if [[ $do_trace = true ]]
2139	then
2140	(( i = 0 ))
2141	while (( i < iin ))
2142	do
2143	(( i = i + 1 ))
2144	if (( i == 1 ))
2145	then
2146	printf "\n\n >>> INPUT-file assignments:\n"
2147	fi
2148	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2149	done
2150	(( i = 0 ))
2151	while (( i < iout ))
2152	do
2153	(( i = i + 1 ))
2154	if (( i == 1 ))
2155	then
2156	printf "\n\n >>> OUTPUT-file assignments:\n"
2157	fi
2158	printf "\n ${localout[$i]} : ${pathout[$i]}"
2159	done
2160	(( i = 0 ))
2161	while (( i < iic ))
2162	do
2163	(( i = i + 1 ))
2164	if (( i == 1 ))
2165	then
2166	printf "\n\n >>> INPUT-commands:\n"
2167	fi
2168	printf "\n ${in_command[$i]}"
2169	done
2170	(( i = 0 ))
2171	while (( i < ioc ))
2172	do
2173	(( i = i + 1 ))
2174	if (( i == 1 ))
2175	then
2176	printf "\n\n >>> OUTPUT-commands:\n"
2177	fi
2178	printf "\n ${out_command[$i]}"
2179	done
2180	fi
2181
2182	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2183	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2184	then
2185	antwort=dummy
2186	printf "\n\n"
2187	printf " >>> everything o.k. (y/n) ? "
2188	while read antwort
2189	do
2190	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2191	then
2192	printf " >>> everything o.k. (y/n) ? "
2193	else
2194	break
2195	fi
2196	done
2197	if [[ $antwort = n \|\| $antwort = N ]]
2198	then
2199	locat=user_abort; (( iec = 0 )); exit
2200	fi
2201	if [[ $do_batch = true ]]
2202	then
2203	printf " >>> batch-job will be created and submitted"
2204	else
2205	printf " >>> MRUN will now continue to execute on this machine"
2206	fi
2207	fi
2208
2209
2210	# PERFORM PARAMETER FILE CHECK (COUPLED RUNS ARE NOT SUPPORTED YET)
2211	# DEFINE VARIABLES FOR FREQUENTLY USED DIRECTORIES
2212	check_depository="${working_directory}/trunk/UTIL"
2213	check_sources="${working_directory}/tmp_check_namelist_files"
2214	skip_check=false
2215
2216	# CHECK IF NAMELIST_FILE_CHECK HAS BEEN COMPILED SUCCESSFULLY
2217	if [[ ! -f $check_depository/check_namelist_files.tar ]]
2218	then
2219	skip_check=true
2220	reason="run on remote host or parameter file check has not been compiled."
2221	fi
2222	if [[ ! -f $PALM_BIN/check_namelist_files.x ]]
2223	then
2224	skip_check=true
2225	reason="parameter file check has not been compiled."
2226	fi
2227
2228	# CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
2229	if [[ "$cond1" != "parallel" && "$cond2" != "parallel" ]]
2230	then
2231	skip_check=true
2232	reason="serial run."
2233	fi
2234
2235	# ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT
2236	# AND IF THE EXECUTION HOST IS THE LOCAL HOST
2237	# ATTENTION: THIS ROUTINE DOES NOT WORK IF THE COMPILER ON THE LOCAL HOST
2238	# DIFFERS FROM THE COMPILER ON THE REMOTE HOST
2239	if [[ $check_namelist_files == false ]]
2240	then
2241	skip_check=true
2242	reason="-z option set."
2243	fi
2244
2245	if [[ $fromhost != $localhost ]]
2246	then
2247	skip_check=true
2248	reason="submitting host is local host."
2249	fi
2250
2251	if [[ $run_coupled_model == true ]]
2252	then
2253	skip_check=true
2254	reason="coupled run."
2255	fi
2256
2257	if [[ $restart_run == true ]]
2258	then
2259	skip_check=true
2260	reason="restart run."
2261	fi
2262
2263	# SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
2264	(( last_char_int = `echo $filename_input \| wc -c` - 1 ))
2265	last_char=`echo $filename_input \| cut -c $last_char_int`
2266	if [[ "$last_char" == "f" ]]
2267	then
2268	skip_check=true
2269	reason="restart run."
2270	fi
2271
2272	if [[ $skip_check == false ]]
2273	then
2274	tmp_check=${working_directory}/tmp_check
2275
2276	# GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_TOPO"). THIS FILE IS
2277	# NOT NECESSARILY REQUIRED
2278	line=""
2279	found=false
2280	grep "TOPOGRAPHY_DATA" $config_file > $tmp_check
2281	while read line1
2282	do
2283	line="$line1"
2284	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2285	then
2286	topo_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2287	found=true
2288	fi
2289	done < $tmp_check
2290
2291	if [[ $found = false ]]
2292	then
2293	printf "\n +++ no TOPOGRAPHY list entry found in the configuration file."
2294	fi
2295
2296	# GET NUDGING PARAMETER FILE SUFFIX (USUALLY "_NUDGE"). THIS FILE IS
2297	# NOT NECESSARILY REQUIRED
2298	line=""
2299	found=false
2300	grep "NUDGING_DATA" $config_file > $tmp_check
2301	while read line1
2302	do
2303	line="$line1"
2304	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2305	then
2306	nudge_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2307	found=true
2308	fi
2309	done < $tmp_check
2310
2311	if [[ $found = false ]]
2312	then
2313	printf "\n +++ no NUDGING list entry found in the configuration file."
2314	fi
2315
2316	# GET LARGE SCALE FORCING PARAMETER FILE SUFFIX (USUALLY "_LSF"). THIS FILE IS
2317	# NOT NECESSARILY REQUIRED
2318	line=""
2319	found=false
2320	grep "LSF_DATA" $config_file > $tmp_check
2321	while read line1
2322	do
2323	line="$line1"
2324	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2325	then
2326	lsf_suffix=`echo $line \| tr -s " " \| cut -d" " -s -f5`
2327	found=true
2328	fi
2329	done < $tmp_check
2330
2331	if [[ $found = false ]]
2332	then
2333	printf "\n +++ no LSF list entry found in the configuration file."
2334	fi
2335
2336	rm -rf ${working_directory}/tmp_check
2337
2338	# CHECK IF THE P3DF FILE MUST BE CHECKED
2339	for item in $input_list
2340	do
2341	if [[ "$item" == "restart" ]]
2342	then
2343	check_restart=1
2344	else
2345	check_restart=0
2346	fi
2347	done
2348
2349	# ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
2350	if [[ (! -f $filename_input) && ( "$filename_input" != "" ) ]]
2351	then
2352	printf "\n\n +++ ERROR: parameter file ($filename_input) not found."
2353	locat=check_namelist; exit
2354	fi
2355
2356	# CHECK IF THE RESTART PARAMETER FILE EXISTS (IF NECESSARY)
2357	if [[ $check_restart == 1 ]]
2358	then
2359
2360	filenamef="${filename_input}f"
2361	if [[ ! -f $filenamef ]]
2362	then
2363	printf "\n\n +++ WARNING: restart parameter file ($filenamef) is missing."
2364	check_restart=0
2365	answer=dummy
2366	printf "\n\n"
2367
2368	if [[ $silent == false ]]
2369	then
2370	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2371	do
2372	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2373	read answer
2374	done
2375	if [[ $answer = a \|\| $answer = A ]]
2376	then
2377	printf "\n +++ Aborting...."
2378	locat=normal; exit
2379	fi
2380	fi
2381	else
2382	check_restart=1
2383	fi
2384	fi
2385
2386	# CREATE TEMPORARY SOURCES_FOR_CHECK PATH
2387	mkdir $check_sources
2388	cd $check_sources
2389
2390
2391	# CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
2392	if [[ -d $add_source_path ]]
2393	then
2394	printf "\n\n *** copying files from $check_depository"
2395	cp $check_depository/check_namelist_files.tar ./
2396
2397	printf "\n\n *** untar of makefile and source files in $check_sources"
2398	tar -xf check_namelist_files.tar > /dev/null 2>&1
2399
2400	printf "\n\n *** adding user code."
2401	cp $add_source_path/* ./
2402	touch check_namelist_files.f90
2403
2404	# GET COMPILER OPTIONS AND PERFORM MAKE
2405	printf "\n\n *** compiling code if necessary...\n"
2406
2407	# workaround for batch jobs on local machine (lcxe6)
2408	if [[ $do_batch == true && $do_remote == false ]]
2409	then
2410	eval $init_cmds
2411	fi
2412
2413	# GET CHECK OPTIONS
2414	line=""
2415	found=false
2416
2417	grep "$localhost" ${base_directory}/${config_file} \| grep "%cpp_options" > $tmp_check
2418
2419	while read line1
2420	do
2421
2422	if [[ $(echo $line1 \| cut -d" " -s -f3-) = "$localhost" ]]
2423	then
2424	line="$line1"
2425	fi
2426
2427	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2428	then
2429	# REMOVE COLONS FROM OPTION-STRING, REMOVE ALL -D OPTIONS
2430	line="$line "
2431	copts_check=`echo $line \| cut -d" " -s -f2 \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g' \| sed 's/-D[^ ]* //g' \| sed 's/ -D.*//g'`
2432	found=true
2433	fi
2434
2435	done < $tmp_check
2436	copts_check="$copts_check -D__check -D__parallel"
2437
2438	make -f Makefile_check F90=$compiler_name_ser COPT="$copts_check"
2439
2440	# GET MAKE OUTPUT
2441	if [[ $? != 0 ]]
2442	then
2443	printf "\n +++ error during make."
2444	answer=dummy
2445	printf "\n\n"
2446	if [[ $silent == false ]]
2447	then
2448	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2449	do
2450	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2451	read answer
2452	done
2453	if [[ $answer = a \|\| $answer = A ]]
2454	then
2455	printf "\n +++ Aborting..."
2456	rm -rf $check_sources
2457	locat=normal; exit
2458	else
2459	skip_check=true
2460	fi
2461	else
2462	skip_check=true
2463	fi
2464	fi
2465	else
2466	cp $PALM_BIN/check_namelist_files.x ./
2467	fi
2468
2469	cp $filename_input ./PARIN
2470	if [[ $check_restart == 1 ]]
2471	then
2472	cp $filenamef ./PARINF
2473	fi
2474
2475	if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
2476	then
2477	printf "\n *** adding topography data"
2478	cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
2479
2480	# IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE
2481	# MUST BE INCREASED. THIS IS DUE TO THE ARRAY nzb_local AND topo_height,
2482	# WHICH REQUIRE SUFFICIENT MEMORY
2483	ulimit -s unlimited
2484	fi
2485
2486	if [[ -f ${pathname}/${fname}${nudge_suffix} && $skip_check == false ]]
2487	then
2488	printf "\n *** adding nudging data"
2489	cp ${pathname}/${fname}${nudge_suffix} ./NUDGING_DATA
2490	fi
2491
2492	if [[ -f ${pathname}/${fname}${lsf_suffix} && $skip_check == false ]]
2493	then
2494	printf "\n *** adding large scale forcing data"
2495	cp ${pathname}/${fname}${lsf_suffix} ./LSF_DATA
2496	fi
2497
2498	# CREATE ENVPAR FILE, WHICH IS NEEDED BY CHECK_NAMELIST_FILES.X
2499	cat > ENVPAR << %%END%%
2500	&envpar run_identifier = '$fname', host = '$host',
2501	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2502	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2503	maximum_cpu_time_allowed = ${cpumax}.,
2504	revision = '$global_revision',
2505	local_dvrserver_running = $local_dvrserver_running /
2506
2507	%%END%%
2508
2509	# SAFETY CHECK: ONLY PROCEED IF THE PARAMETER CHECK PROGRAM WAS PROPERLY COMPILED
2510	if [[ ! -f check_namelist_files.x && $skip_check == false ]]
2511	then
2512	printf "\n +++ WARNING: check_namelist_files.x not found."
2513	answer=dummy
2514	printf "\n\n"
2515
2516	if [[ $silent == false ]]
2517	then
2518	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2519	do
2520	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2521	read answer
2522	done
2523	if [[ $answer = a \|\| $answer = A ]]
2524	then
2525	printf "\n +++ Aborting..."
2526	rm -rf $check_sources
2527	locat=normal; exit
2528	else
2529	printf "\n *** skipping parameter file check."
2530	fi
2531	fi
2532
2533	elif [[ $skip_check == false ]]
2534	then
2535	# STARTING THE PARAMETER FILE CHECK
2536	printf "\n\n *** starting parameter file check..."
2537
2538	# CHECKING THE P3D FILE
2539	printf "\n\n (1) checking $filename_input"
2540	echo "$numprocs 0 0" > VARIN
2541	errors=`./check_namelist_files.x < VARIN 2>&1`
2542
2543	check_error=false
2544	if [[ "$errors" == "" ]]
2545	then
2546	printf " --> o.k."
2547	else
2548	printf " --> failed."
2549	check_error=true
2550	printf "\n\n $errors"
2551	fi
2552
2553	# CHECKING THE PD3F FILE IF NECESSARY
2554	if [[ $check_restart == 1 && $check_error == false ]]
2555	then
2556	printf "\n\n (2) checking $filenamef"
2557
2558	# FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET
2559	# IN &INIPAR LIST
2560	found=false
2561	cat PARINF \| while read line
2562	do
2563	line=$(echo $line\|sed 's/ //g')
2564	if [[ $line == "&inipar" ]]
2565	then
2566	start_search=true
2567	fi
2568
2569	if [[ $start_search == true ]]
2570	then
2571	if [[ $line == "initializing_actions='read_restart_data'" ]]
2572	then
2573	found=true
2574	break
2575	fi
2576	fi
2577
2578	if [[ $line == "/" ]]
2579	then
2580	start_search=false
2581	fi
2582
2583	done
2584
2585	if [[ $found = false ]]
2586	then
2587	printf "\n\n +++ ERROR: initializing_actions = 'read_restart_data' not found"
2588	printf "\n in &inipar list in $fname$p3df_suffix."
2589	rm -rf $check_sources
2590	locat=check_namelist; exit
2591	fi
2592
2593	# READ max_user_pr FROM FILES
2594	if [[ -f parin_for_check ]]
2595	then
2596	read max_pr_user < parin_for_check
2597	else
2598	max_user_pr=0
2599	fi
2600
2601	echo "$numprocs 1 $max_pr_user" > VARIN
2602	errors=`./check_namelist_files.x < VARIN 2>&1`
2603
2604	if [[ "$errors" == "" ]]
2605	then
2606	printf " --> o.k."
2607	else
2608	printf " --> failed."
2609	check_error=true
2610	printf "\n\n $errors"
2611	fi
2612	fi
2613
2614	# REPORT ERRORS AND CONTINUE/EXIT
2615	if [[ $check_error == true ]]
2616	then
2617	printf "\n +++ errors found in the parameter file!\n"
2618	answer=dummy
2619	printf "\n\n"
2620
2621	while [[ "$answer" != c && "$answer" != C && "$answer" != a && "$answer" != A ]]
2622	do
2623	printf " >>> continue anyway (c(ontinue)/a(bort)) ? "
2624	read answer
2625	done
2626
2627	if [[ $answer = a \|\| $answer = A ]]
2628	then
2629	printf "\n +++ Aborting..."
2630	rm -rf $check_sources
2631	locat=normal; exit
2632	fi
2633	else
2634	printf "\n\n *** parameter file(s) seem(s) to be o.k.\n"
2635	fi
2636	rm -rf $check_sources
2637	fi
2638	else
2639	printf "\n\n +++ skipping parameter file check due to following reason: $reason \n"
2640	fi
2641
2642	# DELETE TEMPORARY DIRECTORY AND FINISH NAMELIST FILE CHECK
2643	rm -rf $check_sources
2644	cd $working_directory
2645
2646	# DETERMINE PATH FOR MAKE DEPOSITORY
2647	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2648	then
2649
2650	line=""
2651	grep "%depository_path" $config_file > tmp_mrun
2652	while read line
2653	do
2654	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2655	then
2656	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2657	then
2658	global_depository_path=`echo $line \| cut -d" " -s -f2`
2659	fi
2660	fi
2661	done < tmp_mrun
2662
2663	line=""
2664	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2665	while read line
2666	do
2667	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2668	then
2669	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2670	then
2671	local_depository_path=`echo $line \| cut -d" " -s -f2`
2672	fi
2673	fi
2674	done < tmp_mrun
2675
2676	if [[ "$local_depository_path" = "" ]]
2677	then
2678	if [[ "$global_depository_path" != "" ]]
2679	then
2680	local_depository_path=$global_depository_path
2681	else
2682	printf "\n\n +++ no depository path found in configuration file"
2683	printf "\n for local host \"$localhost\" "
2684	printf "\n please set \"\%depository_path\" in configuration file\n"
2685	locat=config_file; exit
2686	fi
2687	fi
2688	eval local_depository_path=$local_depository_path
2689	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2690	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2691
2692
2693	basename=`echo $mainprog \| cut -f1 -d"."`
2694	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2695	if [[ ! -f $make_depository ]]
2696	then
2697	printf "\n"
2698	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2699	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2700	fi
2701
2702	fi
2703
2704
2705	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2706	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2707	if [[ $do_batch = false ]]
2708	then
2709
2710
2711	# CREATE THE TEMPORARY WORKING DIRECTORY
2712	mkdir -p $TEMPDIR
2713	chmod go+rx $TEMPDIR
2714	tmpcreate=true
2715
2716
2717	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2718	# INTO THE TEMPORARY WORKING DIRECTORY
2719	if [[ $do_compile = true ]]
2720	then
2721
2722	# ON NEC, COMPILATION IS DONE ON HOST CROSS VIA CROSS COMPILING
2723	# CREATE A TEMPORARY DIRECTORY ON THAT MACHINE (HOME MOUNTED VIA NFS)
2724	if [[ $localhost = nech ]]
2725	then
2726	TEMPDIR_COMPILE=$HOME/work/${usern}.$kennung
2727	if mkdir -p $TEMPDIR_COMPILE
2728	then
2729	printf "\n *** \"$TEMPDIR_COMPILE\" "
2730	printf "\n is generated as temporary directory for cross compiling\n"
2731	else
2732	printf "\n +++ creating directory \"$TEMPDIR_COMPILE\" "
2733	printf "\n needed for cross compilation failed"
2734	locat=compile
2735	exit
2736	fi
2737	else
2738	TEMPDIR_COMPILE=$TEMPDIR
2739	fi
2740
2741	cp $make_depository $TEMPDIR_COMPILE
2742	cd $TEMPDIR_COMPILE
2743	tar -xf $make_depository > /dev/null 2>&1
2744	cd - > /dev/null
2745
2746	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2747	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2748	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2749	then
2750	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2751	else
2752	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2753	fi
2754
2755	else
2756
2757	cp $executable ${TEMPDIR}/a.out
2758
2759	fi
2760
2761
2762	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2763	cd $TEMPDIR
2764	printf "\n *** changed to temporary directory: $TEMPDIR"
2765
2766
2767	# THE FOLLOWING IS REQUIRED FPR AVS-OUTPUT WITH PALM ??? REMOVE ???
2768	# WRITE INFORMATIONS ABOUT THE OUTPUT-FILE CONNECTIONS TO A TEMPORARY FILE
2769	# THIS FILE CAN LATER BE READ FROM USER-DEFINED CODE TO DETERMINE THE
2770	# RELATION BETWEEN THE LOCAL TEMPORARY AND PERMANENT FILE NAMES
2771	(( i = 0 ))
2772	while (( i < iout ))
2773	do
2774	(( i = i + 1 ))
2775	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ]]
2776	then
2777	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${localhost}_${fname}${endout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2778	else
2779	printf "${localout[$i]} ${actionout[$i]}\n${pathout[$i]}\n${frelout[$i]}\n" >> OUTPUT_FILE_CONNECTIONS
2780	fi
2781	done
2782
2783
2784	# IF REQUIRED, START WITH COMPILING
2785	if [[ $do_compile = true ]]
2786	then
2787
2788
2789	if [[ -f a.out ]]
2790	then
2791
2792	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2793	printf "\n\n\n *** executable a.out found"
2794	printf "\n no compilation required \n"
2795
2796	else
2797
2798	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2799	printf "\n\n\n *** compilation starts \n$dashes\n"
2800	printf " *** compilation with make using following options:\n"
2801	printf " make depository: $make_depository"
2802	if [[ "$mopts" != "" ]]
2803	then
2804	printf " make options: $mopts\n"
2805	fi
2806	printf " compilername: $compiler_name\n"
2807	printf " compiler options: $fopts\n"
2808	printf " preprocessor directives: $cpp_options \n"
2809	printf " linker options: $lopts \n"
2810	if [[ "$modules" != "" ]]
2811	then
2812	printf " modules to be load: $modules \n"
2813	fi
2814	printf " source code files: $source_list \n"
2815
2816	if [[ $localhost = nech ]]
2817	then
2818	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\" "
2819	cp $TEMPDIR_COMPILE/a.out .
2820	[[ $? != 0 ]] && compile_error=true
2821	rm -rf $TEMPDIR_COMPILE
2822	elif [[ $localhost = ibmh ]]
2823	then
2824	printf " compiler is called via ssh on \"plogin1\" \n"
2825	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\" "
2826	[[ ! -f a.out ]] && compile_error=true
2827	continue # STATUS=1, IF a.out EXISTS
2828	elif [[ $localhost = lcflow ]]
2829	then
2830	printf " compiler is called via ssh on \"flow\" \n"
2831	/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\" "
2832	check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`
2833	[[ "$check_for_file" = "" ]] && compile_error=true
2834	continue # STATUS=1, IF a.out EXISTS
2835	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2836	then
2837	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2838	else
2839	[[ "$init_cmds" != "" ]] && eval $init_cmds
2840	[[ "$module_calls" != "" ]] && eval $module_calls
2841	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2842	fi
2843
2844	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2845	then
2846	printf "\n +++ error occured while compiling or linking"
2847	locat=compile
2848
2849	exit
2850	else
2851	printf "$dashes\n *** compilation finished \n"
2852	fi
2853
2854	fi
2855
2856	fi
2857
2858
2859	# PROVIDE THE INPUT FILES
2860	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2861	(( i = 0 ))
2862	while (( i < iin ))
2863	do
2864	(( i = i + 1 ))
2865	if (( i == 1 ))
2866	then
2867	printf "\n\n *** providing INPUT-files:\n$dashes"
2868	fi
2869
2870
2871	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2872	if [[ "${transin[$i]}" = unavailable ]]
2873	then
2874	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2875	then
2876	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2877	printf "\n is not available!"
2878	else
2879	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2880	printf "\n is not available!"
2881	fi
2882	continue
2883	fi
2884
2885	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2886	files_for_pes=false; datentyp=file
2887	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2888	then
2889	files_for_pes=true; datentyp=directory
2890	actionin[$i]=""
2891	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2892	then
2893	actionin[$i]=""
2894	elif [[ "${actionin[$i]}" = arpe && -n $numprocs ]]
2895	then
2896	files_for_pes=true; datentyp=directory
2897	actionin[$i]="ar"
2898	elif [[ "${actionin[$i]}" = arpe && ! -n $numprocs ]]
2899	then
2900	actionin[$i]="ar"
2901	elif [[ "${actionin[$i]}" = flpe && -n $numprocs ]]
2902	then
2903	files_for_pes=true; datentyp=directory
2904	actionin[$i]="fl"
2905	elif [[ "${actionin[$i]}" = flpe && ! -n $numprocs ]]
2906	then
2907	actionin[$i]="fl"
2908	fi
2909
2910	if [[ $files_for_pes = true ]]
2911	then
2912	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2913	else
2914	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2915	fi
2916
2917	# INPUT-FILE FOR A RESTART RUN.
2918	# CHECK, IF THIS FILE STILL EXISTS ON THE TEMPORARY DATA DIRECTORY.
2919	# IF NOT, TRY TO GET IT FROM THE ARCHIVE SYSTEM
2920	if [[ "${actionin[$i]}" = fl ]]
2921	then
2922	printf "\n $datentyp will be fetched from temporary directory \"${tmp_data_catalog}\" !"
2923	if [[ $files_for_pes = false ]]
2924	then
2925	if [[ -f "$tmp_data_catalog/${frelin[$i]}" ]]
2926	then
2927	ln $tmp_data_catalog/${frelin[$i]} ${localin[$i]}
2928	got_tmp[$i]=true
2929	elif [[ -f "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2930	then
2931	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2932	printf "\n *** trying to use backup copy in \"$WORK\" "
2933	cp $WORK/${frelin[$i]} ${localin[$i]}
2934	else
2935	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2936	printf "\n or \"$tmp_data_catalog\" does not exist!"
2937	printf "\n *** trying to get copy from archive"
2938	actionin[$i]=ar
2939	fi
2940	else
2941	if [[ -d "$tmp_data_catalog/${frelin[$i]}" ]]
2942	then
2943	mkdir ${localin[$i]}
2944	cd $tmp_data_catalog/${frelin[$i]}
2945	for file in $(ls *)
2946	do
2947	ln $file $TEMPDIR/${localin[$i]}
2948	done
2949	cd $TEMPDIR
2950	got_tmp[$i]=true
2951	elif [[ -d "$WORK/${frelin[$i]}" && $ignore_archive_error = true ]]
2952	then
2953	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" !"
2954	printf "\n *** trying to use backup copy in \"$WORK\" "
2955	cp -r $WORK/${frelin[$i]} ${localin[$i]}
2956	else
2957	printf "\n +++ $datentyp not found in \"$tmp_data_catalog\" "
2958	printf "\n or \"$tmp_data_catalog\" does not exist!"
2959	printf "\n *** trying to get copy from archive"
2960	actionin[$i]=ar
2961	fi
2962	fi
2963	fi
2964
2965
2966	# FILE IS STORED ON THE ARCHIVE SYSTEM
2967	if [[ "${actionin[$i]}" = ar ]]
2968	then
2969
2970	if [[ $files_for_pes = false ]]
2971	then
2972	printf "\n file will be restored from archive-system ($archive_system)!"
2973	else
2974	printf "\n directory will be restored from archive-system ($archive_system)!"
2975	fi
2976
2977	file_restored=false
2978
2979	if [[ $archive_system = asterix ]]
2980	then
2981	do_stagein=true
2982	(( stagein_anz = 0 ))
2983	while [[ $do_stagein = true ]]
2984	do
2985	if [[ $files_for_pes = false ]]
2986	then
2987	stagein -O ${frelin[$i]} > STAGEIN_OUTPUT
2988	else
2989	stagein -t -O ${frelin[$i]} > STAGEIN_OUTPUT
2990	fi
2991	cat STAGEIN_OUTPUT
2992	if [[ $(grep -c "st.msg:i24" STAGEIN_OUTPUT) != 0 ]]
2993	then
2994	file_restored=true
2995	do_stagein=false
2996	else
2997	(( stagein_anz = stagein_anz + 1 ))
2998	if (( stagein_anz == 10 ))
2999	then
3000	printf "\n +++ stagein stoped after 10 tries"
3001	locat=stage
3002	exit
3003	fi
3004	printf "\n +++ restoring from archive failed, trying again:"
3005	sleep 900
3006	fi
3007	done
3008	elif [[ $archive_system = DMF ]]
3009	then
3010	if [[ $files_for_pes = false ]]
3011	then
3012	printf "\n +++ restoring of single files impossible with $archive_system !\n"
3013	locat=DMF
3014	exit
3015	else
3016	find $ARCHIVE/${frelin[$i]} -type m -print \| dmget
3017	cp -r $ARCHIVE/${frelin[$i]} $PWD
3018	file_restored=true
3019	fi
3020	elif [[ $archive_system = tivoli ]]
3021	then
3022	if [[ $files_for_pes = false ]]
3023	then
3024	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cp $PERM/${frelin[$i]} $PWD"
3025	else
3026	(( inode = 0 ))
3027	while (( inode < nodes ))
3028	do
3029	ssh $SSH_PORTOPT $usern@bicedata.hlrn.de "cd $PWD; tar xf $PERM/${frelin[$i]}/${frelin[$i]}.node_$inode.tar"
3030	(( inode = inode + 1 ))
3031	done
3032	fi
3033	file_restored=true
3034	elif [[ $archive_system = ut ]]
3035	then
3036	if [[ $files_for_pes = false ]]
3037	then
3038	cp $UT/${frelin[$i]} .
3039	else
3040	(( inode = 0 ))
3041	while (( inode < nodes ))
3042	do
3043	tar xf $UT/${frelin[$i]}/${frelin[$i]}.node_$inode.tar
3044	(( inode = inode + 1 ))
3045	done
3046	fi
3047	file_restored=true
3048	else
3049	printf "\n +++ archive_system=\"$archive_system\" restore impossible!"
3050	locat=rearchive
3051	exit
3052	fi
3053
3054	if [[ $file_restored = true ]]
3055	then
3056
3057	# PUT FILE ON THE TEMPORARY DATA DIRECTORY TOO.
3058	# THIS WILL MAKE FILE ACCESS EASIER FOR LATER RUNS
3059	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog; chmod g+rx $tmp_data_catalog
3060	if [[ $files_for_pes = false ]]
3061	then
3062	ln -f ${frelin[$i]} $tmp_data_catalog/${frelin[$i]}
3063	else
3064	mkdir $tmp_data_catalog/${frelin[$i]}
3065	ln -f ${frelin[$i]}/* $tmp_data_catalog/${frelin[$i]}
3066	fi
3067	got_tmp[$i]=true
3068
3069	# PROVIDE THE FILE UNDER ITS LOCAL NAME
3070	mv ${frelin[$i]} ${localin[$i]}
3071
3072	fi
3073	fi
3074
3075
3076	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
3077	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
3078	then
3079
3080	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
3081	then
3082
3083	# FILE COPIES ARE PROVIDED FOR ALL CORES
3084	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
3085	printf "\n file will be provided for $numprocs processors"
3086	mkdir ${localin[$i]}
3087	ival=$numprocs
3088	(( ii = 0 ))
3089	while (( ii <= ival-1 ))
3090	do
3091	if (( ii < 10 ))
3092	then
3093	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
3094	elif (( ii < 100 ))
3095	then
3096	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
3097	elif (( ii < 1000 ))
3098	then
3099	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
3100	else
3101	cp ${absnamein[$i]} ${localin[$i]}/_$ii
3102	fi
3103	(( ii = ii + 1 ))
3104	done
3105
3106	else
3107
3108	if [[ $files_for_pes = true ]]
3109	then
3110
3111	# PROVIDE FILES FOR EACH CORE
3112	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
3113	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
3114	printf "\n providing $numprocs files for the respective processors"
3115	mkdir ${localin[$i]}
3116	if [[ $link_local_input = true ]]
3117	then
3118	printf " using ln -f\n"
3119	cd ${absnamein[$i]}
3120	for file in $(ls *)
3121	do
3122	ln -f $file ${localin[$i]}
3123	done
3124	cd $TEMPDIR
3125	fi
3126
3127	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
3128	if [[ ! -f "${localin[$i]}/_0000" ]]
3129	then
3130	if [[ $link_local_input = true ]]
3131	then
3132	printf " ln failed for .../_0000, using cp...\n"
3133	fi
3134	cp -r ${absnamein[$i]}/* ${localin[$i]}
3135	fi
3136
3137	else
3138
3139	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
3140	if [[ $link_local_input = true ]]
3141	then
3142	printf " using ln -f\n"
3143	ln -f ${absnamein[$i]} ${localin[$i]}
3144	fi
3145	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
3146	if [[ ! -f "${localin[$i]}" ]]
3147	then
3148	if [[ $link_local_input = true ]]
3149	then
3150	printf " ln failed, using cp...\n"
3151	fi
3152	cp ${absnamein[$i]} ${localin[$i]}
3153	fi
3154	fi
3155	fi
3156	fi
3157
3158	done
3159	if (( i != 0 ))
3160	then
3161	printf "\n$dashes\n *** all INPUT-files provided \n"
3162	fi
3163
3164
3165	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3166	(( i = 0 ))
3167	while (( i < iic ))
3168	do
3169	(( i = i + 1 ))
3170	if (( i == 1 ))
3171	then
3172	printf "\n\n *** execution of INPUT-commands:\n$dashes"
3173	fi
3174	printf "\n >>> ${in_command[$i]}"
3175	eval ${in_command[$i]}
3176	if (( i == iic ))
3177	then
3178	printf "\n$dashes\n"
3179	fi
3180	done
3181
3182
3183	# SET THE REMAINING CPU-TIME
3184	cpurest=${cpumax}.
3185
3186
3187	# START DVR STREAMING SERVER
3188	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3189	then
3190	if [[ "$dvr_server" != "" ]]
3191	then
3192
3193	printf "\n\n *** preparing the dvr streaming server configuration file"
3194
3195	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
3196	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
3197	if [[ "$running_dvrserver_id" != "" ]]
3198	then
3199
3200	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
3201	printf "\n This server is used instead starting a new one!"
3202	printf "\n If required, script \"process_dvr_output\" has to be run manually."
3203
3204	else
3205
3206	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
3207	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
3208	then
3209	cp ${PALM_BIN}/.dvrserver.config .
3210
3211	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
3212	user_id=`id -u`
3213	group_id=`id -g`
3214
3215	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
3216	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
3217	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
3218	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
3219	mv .dvrserver.3 .dvrserver.config
3220	rm .dvrserver.1 .dvrserver.2
3221
3222	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
3223	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
3224	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
3225	printf "\n *** streaming server with id=$dvrserver_id is started in background"
3226	local_dvrserver_running=.TRUE.
3227	else
3228	printf "\n +++ missing file \".dvrserver.config\" in directory:"
3229	printf "\n \"$PALM_BIN\" "
3230	locat=dvr
3231	exit
3232	fi
3233
3234	fi
3235
3236	else
3237	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
3238	fi
3239	fi
3240
3241
3242	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
3243	# (FILE ENVPAR WILL BE READ BY PALM)
3244	cat > ENVPAR << %%END%%
3245	&envpar run_identifier = '$fname', host = '$localhost',
3246	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
3247	maximum_parallel_io_streams = $maximum_parallel_io_streams,
3248	maximum_cpu_time_allowed = ${cpumax}.,
3249	revision = '$global_revision',
3250	local_dvrserver_running = $local_dvrserver_running,
3251	batch_job = $batch_job /
3252
3253	%%END%%
3254
3255
3256	# STARTING THE EXECUTABLE
3257	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
3258	PATH=$PATH:$TEMPDIR
3259
3260
3261	if [[ $execute_command != "none" ]]
3262	then
3263
3264	printf "\n +++ branch still not realized"
3265	locat=execution
3266	exit
3267
3268	else
3269
3270	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
3271	if [[ "$mpi_debug" = true ]]
3272	then
3273	export MPI_CHECK_ARGS=1
3274	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
3275	fi
3276
3277	if [[ "$totalview" = true ]]
3278	then
3279	printf "\n *** totalview debugger will be used"
3280	tv_opt="-tv"
3281	else
3282	tv_opt=""
3283	fi
3284
3285	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
3286	then
3287
3288	#Interactive ALLINEA DEBUG seesion
3289	if [[ "$ENVIRONMENT" != BATCH ]]
3290	then
3291	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3292	then
3293	if [[ "$allinea" = true ]]
3294	then
3295	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3296
3297	ddt aprun -n $ii -N $tasks_per_node a.out
3298	wait
3299	fi
3300	fi
3301	fi
3302
3303	if [[ $localhost = ibmh ]]
3304	then
3305
3306	# SETUP THE IBM MPI ENVIRONMENT
3307	export MP_SHARED_MEMORY=yes
3308	export AIXTHREADS_SCOPE=S
3309	export OMP_NUM_THREADS=$threads_per_task
3310	export AUTHSTATE=files
3311	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3312
3313	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
3314	export MP_ADAPTER_USE=shared
3315	export MP_CPU_USE=multiple
3316	export MP_TIMEOUT=1200
3317
3318	unset MP_TASK_AFFINITY
3319
3320	if [[ "$LOADLBATCH" = yes ]]
3321	then
3322	totalview poe a.out
3323	else
3324	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
3325	export TVDSVRLAUNCHCMD=ssh
3326	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
3327	fi
3328
3329	fi # END DEBUG MODE
3330
3331	else
3332
3333	# NORMAL EXECUTION
3334	if [[ -n $numprocs ]]
3335	then
3336
3337	# RUNNING THE PROGRAM ON PARALLEL MACHINES
3338	if [[ $(echo $host \| cut -c1-3) = ibm ]]
3339	then
3340
3341	# SETUP THE IBM MPI ENVIRONMENT
3342	if [[ $host != ibmh && $host != ibmkisti ]]
3343	then
3344	export MP_SHARED_MEMORY=yes
3345	export AIXTHREAD_SCOPE=S
3346	export OMP_NUM_THREADS=$threads_per_task
3347	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
3348	export AUTHSTATE=files
3349	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
3350	# export MP_PRINTENV=yes
3351
3352	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
3353	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
3354	export MP_WAIT_MODE=poll
3355	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
3356	fi
3357
3358	if [[ $host = ibmkisti ]]
3359	then
3360	export LANG=en_US
3361	export MP_SHARED_MEMORY=yes
3362	if [[ $threads_per_task = 1 ]]
3363	then
3364	export MP_SINGLE_THREAD=yes
3365	export MEMORY_AFFINITY=MCM
3366	else
3367	export OMP_NUM_THREADS=$threads_per_task
3368	fi
3369	fi
3370
3371	if [[ "$LOADLBATCH" = yes ]]
3372	then
3373	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
3374	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
3375	then
3376	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
3377	else
3378	if [[ $run_coupled_model = false ]]
3379	then
3380	if [[ "$ocean_file_appendix" = true ]]
3381	then
3382	echo "precursor_ocean" > runfile_atmos
3383	else
3384	echo "precursor_atmos" > runfile_atmos
3385	fi
3386	else
3387	(( iia = $numprocs_atmos / $threads_per_task ))
3388	(( iio = $numprocs_ocean / $threads_per_task ))
3389	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3390	printf "\n using $coupled_mode coupling"
3391	printf "\n\n"
3392	echo "coupled_run $iia $iio" > runfile_atmos
3393	fi
3394	poe ./a.out < runfile_atmos
3395	fi
3396	else
3397	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
3398	then
3399	poe a.out -procs $numprocs -nodes 1 -rmpool 0
3400	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
3401	then
3402	if [[ -f $hostfile ]]
3403	then
3404	cp $hostfile hostfile
3405	else
3406	(( ii = 1 ))
3407	while (( ii <= $numprocs ))
3408	do
3409	echo $localhost_realname >> hostfile
3410	(( ii = ii + 1 ))
3411	done
3412	fi
3413	export MP_HOSTFILE=hostfile
3414	if [[ $run_coupled_model = false ]]
3415	then
3416	if [[ "$ocean_file_appendix" = true ]]
3417	then
3418	echo "precursor_ocean" > runfile_atmos
3419	else
3420	echo "precursor_atmos" > runfile_atmos
3421	fi
3422	else
3423	(( iia = $numprocs_atmos / $threads_per_task ))
3424	(( iio = $numprocs_ocean / $threads_per_task ))
3425	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3426	printf "\n using $coupled_mode coupling"
3427	printf "\n\n"
3428	echo "coupled_run $iia $iio" > runfile_atmos
3429	fi
3430
3431	poe ./a.out -procs $numprocs < runfile_atmos
3432
3433	else
3434	if [[ "$host_file" = "" ]]
3435	then
3436	printf "\n +++ no hostfile given in configuration file"
3437	locat=config_file
3438	exit
3439	else
3440	eval host_file=$host_file
3441	fi
3442	export MP_HOSTFILE=$host_file
3443	poe a.out -procs $numprocs -tasks_per_node $numprocs
3444	fi
3445	fi
3446
3447	elif [[ $host = nech ]] # running on NEC machines
3448	then
3449
3450	(( ii = nodes ))
3451	if [[ $ii = 1 ]]
3452	then
3453	export F_ERRCNT=0 # acceptable number of errors before program is stopped
3454	export MPIPROGINF=YES
3455	# export F_TRACE=YES\|FMT1\|FMT2 # output of ftrace informations to job protocol
3456	echo "*** execution on single node with mpirun"
3457	mpirun -np $numprocs ./a.out
3458	else
3459	(( i = 0 ))
3460	while (( i < ii ))
3461	do
3462	echo "-h $i -p $tasks_per_node -e ./mpi_exec_shell" >> multinode_config
3463	(( i = i + 1 ))
3464	done
3465
3466	echo "#!/bin/sh" > mpi_exec_shell
3467	echo " " >> mpi_exec_shell
3468	echo "set -u" >> mpi_exec_shell
3469	echo "F_ERRCNT=0" >> mpi_exec_shell
3470	echo "MPIPROGINV=YES" >> mpi_exec_shell
3471	echo "OMP_NUM_THREADS=$threads_per_task" >> mpi_exec_shell
3472	echo "cpurest=$cpurest" >> mpi_exec_shell
3473	echo "fname=$fname" >> mpi_exec_shell
3474	echo "localhost=$localhost" >> mpi_exec_shell
3475	echo "return_address=$return_address" >> mpi_exec_shell
3476	echo "return_username=$return_username" >> mpi_exec_shell
3477	echo "tasks_per_node=$tasks_per_node" >> mpi_exec_shell
3478	echo "write_binary=$write_binary" >> mpi_exec_shell
3479	echo "use_seperate_pe_for_dvrp_output=$use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3480	echo " " >> mpi_exec_shell
3481	echo "export F_ERRCNT" >> mpi_exec_shell
3482	echo "export MPIPROGINV" >> mpi_exec_shell
3483	echo "export OMP_NUM_THREADS" >> mpi_exec_shell
3484	echo "export cpurest" >> mpi_exec_shell
3485	echo "export fname" >> mpi_exec_shell
3486	echo "export localhost" >> mpi_exec_shell
3487	echo "export return_address" >> mpi_exec_shell
3488	echo "export return_username" >> mpi_exec_shell
3489	echo "export tasks_per_node" >> mpi_exec_shell
3490	echo "export write_binary" >> mpi_exec_shell
3491	echo "export use_seperate_pe_for_dvrp_output" >> mpi_exec_shell
3492	echo " " >> mpi_exec_shell
3493	echo "exec ./a.out" >> mpi_exec_shell
3494
3495	chmod u+x mpi_exec_shell
3496	export MPIPROGINF=YES
3497	mpirun -f multinode_config &
3498	wait
3499
3500	fi
3501
3502	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
3503	then
3504
3505	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
3506	# DOES NOT EXIST
3507	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut ]]
3508	then
3509	if [[ -f $hostfile ]]
3510	then
3511	cp $hostfile hostfile
3512	(( ii = $numprocs / $threads_per_task ))
3513	[[ $ii = 0 ]] && (( ii = 1 ))
3514	else
3515	(( ii = 1 ))
3516	while (( ii <= $numprocs / $threads_per_task ))
3517	do
3518	echo $localhost_realname >> hostfile
3519	(( ii = ii + 1 ))
3520	done
3521	if (( $numprocs / $threads_per_task == 0 ))
3522	then
3523	echo $localhost_realname >> hostfile
3524	fi
3525	fi
3526	eval zeile=\"`head -n $ii hostfile`\"
3527	printf "\n *** running on: $zeile"
3528	fi
3529
3530	(( ii = $numprocs / $threads_per_task ))
3531	[[ $ii = 0 ]] && (( ii = 1 ))
3532	export OMP_NUM_THREADS=$threads_per_task
3533
3534	if [[ $threads_per_task != 1 ]]
3535	then
3536	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
3537	# MAY ABORT
3538	ulimit -s unlimited
3539	printf "\n threads per task: $threads_per_task stacksize: unlimited"
3540	fi
3541	if [[ $run_coupled_model = false ]]
3542	then
3543	if [[ "$ocean_file_appendix" = true ]]
3544	then
3545	echo "precursor_ocean" > runfile_atmos
3546	else
3547	echo "precursor_atmos" > runfile_atmos
3548	fi
3549	printf "\n\n"
3550
3551	if [[ $host = lccrayb \|\| $host = lccrayh ]]
3552	then
3553	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3554	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3555	elif [[ $host = lcbullhh ]]
3556	then
3557	export OMPI_MCA_pml=cm
3558	export OMPI_MCA_mtl=mxm
3559	export OMPI_MCA_coll=^ghc
3560	export OMPI_MCA_mtl_mxm_np=0
3561	export MXM_RDMA_PORTS=mlx5_0:1
3562	export MXM_LOG_LEVEL=ERROR
3563	export OMP_NUM_THREADS=$threads_per_task
3564	export KMP_AFFINITY=verbose,granularity=core,compact,1
3565	export KMP_STACKSIZE=64m
3566
3567	srun --nodes=$nodes --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3568
3569	elif [[ $host = lccrayf ]]
3570	then
3571	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3572	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3573	then
3574	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3575	elif [[ $host = lcflow ]]
3576	then
3577	mpirun -np $ii a.out < runfile_atmos
3578	elif [[ $host = lcsb ]]
3579	then
3580	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3581	elif [[ $host = lckiaps ]]
3582	then
3583	mpirun -np $ii -f $PBS_NODEFILE a.out < runfile_atmos
3584	elif [[ $host = lckyu* ]]
3585	then
3586	mpiexec -n $ii --stdin runfile_atmos ./a.out
3587	else
3588	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3589	fi
3590
3591	else
3592
3593	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
3594	(( iia = $numprocs_atmos / $threads_per_task ))
3595	(( iio = $numprocs_ocean / $threads_per_task ))
3596	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3597	printf "\n using $coupled_mode coupling"
3598	printf "\n\n"
3599
3600	if [[ $coupled_mode = "mpi2" ]]
3601	then
3602	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
3603	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
3604
3605	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3606	then
3607
3608	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
3609	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
3610
3611	else
3612	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
3613	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
3614	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
3615	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
3616	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
3617	fi
3618	wait
3619
3620	else
3621
3622	echo "coupled_run $iia $iio" > runfile_atmos
3623
3624	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3625	then
3626
3627	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3628
3629	elif [[ $host = lck \|\| $host = lckordi ]]
3630	then
3631
3632	mpiexec -n $ii ./a.out < runfile_atmos &
3633
3634	elif [[ $host = lckyu* ]]
3635	then
3636
3637	mpiexec -n $ii --stdin runfile_atmos ./a.out
3638
3639	elif [[ $host = lcmuk ]]
3640	then
3641
3642	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3643
3644	fi
3645	wait
3646	fi
3647
3648	fi
3649
3650	elif [[ $host = lckyoto ]]
3651	then
3652	set -xv
3653	export P4_RSHCOMMAND=plesh
3654	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3655	if [[ "$ENVIRONMENT" = BATCH ]]
3656	then
3657	if [[ "$cond2" = fujitsu ]]
3658	then
3659	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3660	elif [[ "cond2" = pgi ]]
3661	then
3662	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3663	else
3664	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3665	fi
3666	else
3667	if [[ "$cond2" = "" ]]
3668	then
3669	mpiruni_rsh -np $numprocs ./a.out # for intel
3670	else
3671	mpirun -np $numprocs ./a.out
3672	fi
3673	fi
3674	set +xv
3675
3676	elif [[ $host = lctit ]]
3677	then
3678	export OMP_NUM_THREADS=$threads_per_task
3679	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3680	if [[ "$threads_per_task" != 1 ]]
3681	then
3682	export MV2_ENABLE_AFFINITY=0
3683	fi
3684	echo "----- PBS_NODEFILE content:"
3685	cat $PBS_NODEFILE
3686	echo "-----"
3687	(( ii = $numprocs / $threads_per_task ))
3688	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3689	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3690
3691	else
3692	mpprun -n $numprocs a.out
3693	fi
3694	else
3695	a.out
3696	fi
3697
3698	fi # end normal (non-debug) execution
3699
3700	fi # end explicit execute_command or host-specific execute actions
3701
3702	if [[ $? != 0 ]]
3703	then
3704
3705	# ABORT IN CASE OF RUNTIME ERRORS
3706	printf "\n +++ runtime error occured"
3707	locat=execution
3708	exit
3709
3710	else
3711
3712	printf "\n$dashes\n *** execution finished \n"
3713
3714	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3715	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3716	if [[ "$dvrserver_id" != "" ]]
3717	then
3718	kill $dvrserver_id
3719	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3720
3721	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3722	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3723	if [[ -d DATA_DVR ]]
3724	then
3725
3726	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3727	# DIRECTORY
3728	cp .dvrserver.config DATA_DVR
3729
3730	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3731	# SEQUENCE MODE DATA TOO)
3732	process_dvr_output -d DATA_DVR -f $fname -s
3733
3734	else
3735
3736	# PROCESS THE LOCAL OUTPUT
3737	process_dvr_output -l -d DATA_DVR -f $fname
3738
3739	fi
3740
3741	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3742	then
3743
3744	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3745	process_dvr_output -l -d DATA_DVR -f $fname
3746
3747	fi
3748	fi
3749
3750
3751
3752	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3753	# BY EACH CORE INTO ONE FILE
3754	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3755	then
3756	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3757	printf "\n 2d- and/or 3d-data may be incomplete!"
3758	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3759	elif [[ "$combine_plot_fields" == true ]]
3760	then
3761	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3762	then
3763	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3764	aprun -n 1 -N 1 combine_plot_fields${block}.x
3765	else
3766	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3767	combine_plot_fields${block}.x
3768	fi
3769	else
3770
3771	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3772	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3773	# ??? koennen wir das streichen ???
3774	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3775	fi
3776
3777
3778
3779	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3780	(( i = 0 ))
3781	while (( i < ioc ))
3782	do
3783	(( i = i + 1 ))
3784	if (( i == 1 ))
3785	then
3786	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3787	fi
3788	printf "\n >>> ${out_command[$i]}"
3789	eval ${out_command[$i]}
3790	if (( i == ioc ))
3791	then
3792	printf "\n$dashes\n"
3793	fi
3794	done
3795
3796
3797	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3798	if [[ $do_trace = true ]]
3799	then
3800	printf "\n\n"
3801	ls -al
3802	fi
3803
3804
3805
3806	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3807	(( i = 0 ))
3808	while (( i < iout ))
3809	do
3810	(( i = i + 1 ))
3811	if (( i == 1 ))
3812	then
3813	printf "\n\n *** saving OUTPUT-files:\n$dashes"
3814	fi
3815
3816	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3817	files_for_pes=false; filetyp=file
3818	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3819	then
3820	files_for_pes=true; filetyp=directory
3821	actionout[$i]=""
3822	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3823	then
3824	actionout[$i]=""
3825	elif [[ "${actionout[$i]}" = arpe && -n $numprocs ]]
3826	then
3827	files_for_pes=true; filetyp=directory
3828	actionout[$i]="ar"
3829	elif [[ "${actionout[$i]}" = arpe && ! -n $numprocs ]]
3830	then
3831	actionout[$i]="ar"
3832	elif [[ "${actionout[$i]}" = flpe && -n $numprocs ]]
3833	then
3834	files_for_pes=true; filetyp=directory
3835	actionout[$i]="fl"
3836	elif [[ "${actionout[$i]}" = flpe && ! -n $numprocs ]]
3837	then
3838	actionout[$i]="fl"
3839	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3840	then
3841	files_for_pes=true; filetyp=directory
3842	actionout[$i]="tr"
3843	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3844	then
3845	actionout[$i]="tr"
3846	fi
3847
3848	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3849	then
3850	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3851	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3852	then
3853	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3854	else
3855
3856
3857	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3858	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3859	if [[ "${actionout[$i]}" = tr ]]
3860	then
3861	if [[ $localhost != $fromhost ]]
3862	then
3863	if [[ $files_for_pes = false ]]
3864	then
3865	cps=""
3866	cst=""
3867	else
3868	cps=-c
3869	cst="/"
3870	fi
3871	if [[ $localhost = nech ]]
3872	then
3873
3874	# TRANSFER IN SEPERATE JOB
3875	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3876	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3877	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3878	if [[ $files_for_pes = false ]]
3879	then
3880	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3881	else
3882	mkdir $tmp_data_catalog/TRANSFER/$file_to_transfer
3883	ln ${localout[$i]}/* $tmp_data_catalog/TRANSFER/$file_to_transfer
3884	fi
3885
3886	echo "set -x" > transfer_${localout[$i]}
3887	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3888
3889	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP in seperate job to"
3890	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst"
3891	printf "\n or higher cycle\n"
3892	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]}
3893
3894	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3895
3896	if [[ $localhost = nech ]]
3897	then
3898	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3899	else
3900	if [[ "$LOGNAME" = b323013 ]]
3901	then
3902	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3903	else
3904	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3905	fi
3906	fi
3907
3908	else
3909
3910	# TRANSFER WITHIN THIS JOB
3911	transfer_failed=false
3912	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3913	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3914	if [[ $localhost = lccrayb ]]
3915	then
3916	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]}"
3917	elif [[ $localhost = lccrayh ]]
3918	then
3919	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]}"
3920	elif [[ $localhost = lcbullhh ]]
3921	then
3922	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]}"
3923	elif [[ $localhost = lcxe6 ]]
3924	then
3925	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]}"
3926	else
3927	batch_scp $PORTOPT $cps -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3928	fi
3929	[[ $? != 0 ]] && transfer_failed=true
3930
3931	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3932	if [[ $transfer_failed = true ]]
3933	then
3934	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3935	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3936
3937	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3938	eval local_catalog=${pathout[$i]}
3939	if [[ ! -d $local_catalog ]]
3940	then
3941	printf " *** local directory does not exist. Trying to create:\n"
3942	printf " $local_catalog \n"
3943	mkdir -p $local_catalog
3944	fi
3945	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3946	transfer_problems=true
3947	fi
3948	fi
3949	else
3950
3951	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3952	actionout[$i]=""
3953	fi
3954	fi
3955
3956
3957	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3958	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3959	if [[ "${actionout[$i]}" = tra ]]
3960	then
3961	if [[ $localhost != $fromhost ]]
3962	then
3963	if [[ $localhost = ibmh \|\| $localhost = nech ]]
3964	then
3965
3966	# TRANSFER IN SEPERATE JOB
3967	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3968	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3969	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3970	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3971
3972	echo "set -x" > transfer_${localout[$i]}
3973	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3974
3975	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3976	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3977	printf "\n or higher cycle\n"
3978	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]}
3979
3980	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3981
3982	if [[ $localhost = nech ]]
3983	then
3984	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 900 $PORTOPT transfer_${localout[$i]}
3985	else
3986	if [[ $LOGNAME = b323013 ]]
3987	then
3988	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3989	else
3990	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3991	fi
3992	fi
3993
3994	else
3995
3996	# TRANSFER WITHIN THIS JOB
3997	transfer_failed=false
3998	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3999	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
4000	if [[ $localhost = lccrayb ]]
4001	then
4002	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]}"
4003	elif [[ $localhost = lccrayh ]]
4004	then
4005	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]}"
4006	elif [[ $localhost = lcxe6 ]]
4007	then
4008	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]}"
4009	else
4010	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
4011	fi
4012	[[ $? != 0 ]] && transfer_failed=true
4013
4014	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
4015	if [[ $transfer_failed = true ]]
4016	then
4017	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
4018	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
4019
4020	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
4021	eval local_catalog=${pathout[$i]}
4022	if [[ ! -d $local_catalog ]]
4023	then
4024	printf " *** local directory does not exist. Trying to create:\n"
4025	printf " $local_catalog \n"
4026	mkdir -p $local_catalog
4027	fi
4028
4029	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
4030	transfer_problems=true
4031	fi
4032	fi
4033	else
4034
4035	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
4036	actionout[$i]=a
4037	fi
4038	fi
4039
4040
4041	# OUTPUT-FILE FOR A RESTART-RUN.
4042	# FILE IS MOVED TO THE TEMPORARY DATA DIRECTORY USING link COMMAND.
4043	# OPTION -f IS USED TO OVERWRITE EXISTING FILES.
4044	# AS LAST ACTION, ARCHIVING IS INITIATED.
4045	if [[ "${actionout[$i]}" = fl ]]
4046	then
4047	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4048	chmod g+rx $tmp_data_catalog
4049	if [[ $files_for_pes = false ]]
4050	then
4051	printf "\n >>> OUTPUT: ${localout[$i]} to"
4052	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4053	ln -f ${localout[$i]} $tmp_data_catalog/${frelout[$i]}
4054	else
4055	printf "\n >>> OUTPUT: ${localout[$i]}/.... to"
4056	printf "\n $tmp_data_catalog/${frelout[$i]} (temporary data catalog)\n"
4057	mkdir $tmp_data_catalog/${frelout[$i]}
4058	cd ${localout[$i]}
4059	for file in $(ls *)
4060	do
4061	ln -f $file $tmp_data_catalog/${frelout[$i]}
4062	done
4063	cd $TEMPDIR
4064	fi
4065
4066
4067	# CREATE AND SUBMIT ARCHIVING-JOB
4068	if [[ $store_on_archive_system = true ]]
4069	then
4070
4071	if [[ $archive_system = asterix ]]
4072	then
4073	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4074	if [[ $files_for_pes = false ]]
4075	then
4076	echo "stageout ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4077	else
4078	echo "stageout -t ${frelout[$i]} > STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4079	fi
4080	echo "cat STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4081	echo "if [[ \$(grep -c \"st.msg:150\" STAGE_OUTPUT${i}_$kennung) != 0 ]]" >> archive_${frelout[$i]}
4082	echo "then" >> archive_${frelout[$i]}
4083	echo " do_stageout=false" >> archive_${frelout[$i]}
4084	echo "else" >> archive_${frelout[$i]}
4085	echo " echo \" +++ $filetyp ${frelout[$i]} could not be stored on archive-system\" " >> archive_${frelout[$i]}
4086	echo " cat /dev/null > ~/job_queue/ARCHIVE_ERROR_$fname" >> archive_${frelout[$i]}
4087	echo " cat STAGE_OUTPUT${i}_$kennung > ~/job_queue/archive_${frelout[$i]}_error" >> archive_${frelout[$i]}
4088	echo " echo \" *** $filetyp ${frelout[$i]} will be copied to \$WORK as backup\" " >> archive_${frelout[$i]}
4089	if [[ $files_for_pes = false ]]
4090	then
4091	echo " cp ${frelout[$i]} \$WORK" >> archive_${frelout[$i]}
4092	else
4093	echo " cp -r ${frelout[$i]} \$WORK/${frelout[$i]}" >> archive_${frelout[$i]}
4094	fi
4095	echo " echo \" *** $filetyp ${frelout[$i]} saved\" " >> archive_${frelout[$i]}
4096	echo "fi" >> archive_${frelout[$i]}
4097	echo "rm STAGE_OUTPUT${i}_$kennung" >> archive_${frelout[$i]}
4098	elif [[ $archive_system = DMF ]]
4099	then
4100	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4101	if [[ $files_for_pes = false ]]
4102	then
4103	printf "\n +++ archiving of single files impossible with $archive_system !\n"
4104	locat=DMF
4105	exit
4106	else
4107	# ??? nicht benÃ¶tigte Archiv-Systeme entfernen ???
4108	# FUER RECHNER IN JUELICH. DORT KOENNTEN AUCH
4109	# EINZELNE DATEIEN GESICHERT WERDEN (SPAETER KORR.)
4110	echo "rm -rf \$ARCHIVE/${frelout[$i]}" >> archive_${frelout[$i]}
4111	echo "cp -r ${frelout[$i]} \$ARCHIVE" >> archive_${frelout[$i]}
4112	fi
4113	elif [[ $archive_system = tivoli ]]
4114	then
4115	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4116	if [[ $files_for_pes = false ]]
4117	then
4118	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4119	echo "set -x" >> archive_${frelout[$i]}
4120	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4121	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4122	else
4123
4124	echo "set -x" >> archive_${frelout[$i]}
4125	echo "rm -rf \$PERM/${frelout[$i]}/*" >> archive_${frelout[$i]}
4126	echo "[[ ! -d \$PERM/${frelout[$i]} ]] && mkdir $PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4127	cd $tmp_data_catalog
4128	all_files=`ls -1 ${frelout[$i]}/*`
4129	cd - > /dev/null
4130	(( inode = 0 ))
4131	(( tp1 = tasks_per_node + 1 ))
4132	while (( inode < nodes ))
4133	do
4134	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4135	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4136	echo "tar cvf \$PERM/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4137	(( inode = inode + 1 ))
4138	done
4139	fi
4140	elif [[ $archive_system = ut ]]
4141	then
4142	echo "cd $tmp_data_catalog" >> archive_${frelout[$i]}
4143	if [[ $files_for_pes = false ]]
4144	then
4145	# REMOVE EXISTING OLD FILES FROM THE ARCHIVE
4146	echo "set -x" >> archive_${frelout[$i]}
4147	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4148	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4149	else
4150
4151	echo "set -x" >> archive_${frelout[$i]}
4152	echo "rm -rf \$UT/${frelout[$i]}/*" >> archive_${frelout[$i]}
4153	echo "[[ ! -d \$UT/${frelout[$i]} ]] && mkdir $UT/${frelout[$i]}" >> archive_${frelout[$i]}
4154	cd $tmp_data_catalog
4155	all_files=`ls -1 ${frelout[$i]}/*`
4156	cd - > /dev/null
4157	(( inode = 0 ))
4158	(( tp1 = tasks_per_node + 1 ))
4159	while (( inode < nodes ))
4160	do
4161	files=`echo $all_files \| cut -d" " -f1-$tasks_per_node`
4162	all_files=`echo $all_files \| cut -d" " -f$tp1-`
4163	echo "tar cvf \$UT/${frelout[$i]}/${frelout[$i]}.node_$inode.tar $files" >> archive_${frelout[$i]}
4164	(( inode = inode + 1 ))
4165	done
4166	fi
4167	elif [[ $archive_system = none ]]
4168	then
4169	printf " +++ archiving on $localhost not available!\n"
4170	fi
4171
4172	if [[ $archive_system != none ]]
4173	then
4174	if [[ $localhost = nech ]]
4175	then
4176	subjob -d -c /pf/b/$usern/job_queue -v -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4177	fi
4178	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4179	fi
4180	else
4181	printf " +++ caution: option -A is switched off. No archiving on $archive_system!\n"
4182	fi
4183
4184
4185	# CREATE AN EMPTY DIRECTORY IN THE USERS PERMANENT DIRECTORY,
4186	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4187	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4188	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4189	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4190	if [[ $files_for_pes = false ]]
4191	then
4192	cat /dev/null > ${pathout[$i]}
4193	else
4194	mkdir -p ${pathout[$i]}
4195	fi
4196
4197	fi
4198
4199
4200	# COPY FROM THIS HOST TO THE ARCHIVE-SYSTEM
4201	# IF ANY ARCHIVING FAILS, AN ERROR-FLAG-FILE IS SET
4202	# THIS FILE REMAINS TO BE SET, EVEN IF ARCHIVING OF FURTHER FILES IS SUCCESSFULL
4203	if [[ "${actionout[$i]}" = ar ]]
4204	then
4205	if [[ $files_for_pes = false ]]
4206	then
4207	printf "\n >>> OUTPUT: ${localout[$i]} to"
4208	printf "\n ${pathout[$i]}"
4209	printf "\n File will be copied to archive-system ($archive_system) !\n"
4210	else
4211	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
4212	printf "\n ${pathout[$i]}"
4213	printf "\n Directory will be copied to archive-system ($archive_system) !\n"
4214	fi
4215	mv ${localout[$i]} ${frelout[$i]}
4216
4217	file_saved=false
4218
4219	if [[ $archive_system = asterix ]]
4220	then
4221	do_stageout=true
4222	(( stageout_anz = 0 ))
4223	while [[ $do_stageout = true ]]
4224	do
4225	if [[ $files_for_pes = false ]]
4226	then
4227	stageout ${frelout[$i]} > STAGE_OUTPUT
4228	else
4229	stageout -t ${frelout[$i]} > STAGE_OUTPUT
4230	fi
4231	cat STAGE_OUTPUT
4232	if [[ $(grep -c "st.msg:150" STAGE_OUTPUT) != 0 ]]
4233	then
4234	file_saved=true
4235	do_stageout=false
4236	else
4237	if [[ $files_for_pes = false ]]
4238	then
4239	printf "\n +++ file ${frelout[$i]} could not be saved on archive-system"
4240	else
4241	printf "\n +++ directory ${frelout[$i]} could not be saved on archive-system"
4242	fi
4243	(( stageout_anz = stageout_anz + 1 ))
4244	if (( stageout_anz == 10 ))
4245	then
4246	printf "\n +++ stoped after 10 unsuccessful tries!"
4247	archive_save=false
4248	do_stageout=false
4249	else
4250	printf "\n *** new try to store on archive after 15 min:"
4251	sleep 900
4252	fi
4253	fi
4254	done
4255	elif [[ $archive_system = DMF ]]
4256	then
4257	if [[ $files_for_pes = false ]]
4258	then
4259	printf "\n +++ archiving of single files impossible on $archive_system!\n"
4260	locat=DMF
4261	exit
4262	else
4263	rm -rf $ARCHIVE/${frelout[$i]}
4264	cp -r ${frelout[$i]} $ARCHIVE
4265	fi
4266	file_saved=true
4267	elif [[ $archive_system = tivoli ]]
4268	then
4269	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4270	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4271	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4272	# WHEN THE ARCHIVE-JOB IS EXECUTED
4273	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4274	chmod g+rx $tmp_data_catalog
4275	if [[ $files_for_pes = false ]]
4276	then
4277	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4278	else
4279	mkdir $tmp_data_catalog/${frelout[$i]}
4280	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4281	fi
4282
4283	# GENERATE AND SUBMIT BATCH-JOB
4284	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4285	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4286	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4287	if [[ $files_for_pes = false ]]
4288	then
4289	echo "rm -rf \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4290	echo "cp ${frelout[$i]} \$PERM/${frelout[$i]}" >> archive_${frelout[$i]}
4291	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4292	else
4293	echo "rm -rf \$PERM/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4294	echo "tar cvf \$PERM/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4295	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4296	fi
4297
4298	subjob -v -d -q cdata -X 0 -m 1000 -t 43200 -c $job_catalog $PORTOPT archive_${frelout[$i]}
4299	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4300	file_saved=true
4301
4302	elif [[ $archive_system = ut ]]
4303	then
4304	# ARCHIVING ONLY POSSIBLE VIA BATCH-JOB
4305	# IN THE MEANTIME, FILE IS STORED IN THE TEMPORARY DATA DIRECTORY,
4306	# BECAUSE MRUN'S CURRENT TEMPORARY WORKING DIRECTORY MAY ALREADY BE DELETED
4307	# WHEN THE ARCHIVE-JOB IS EXECUTED
4308	[[ ! -d $tmp_data_catalog ]] && mkdir -p $tmp_data_catalog
4309	chmod g+rx $tmp_data_catalog
4310	if [[ $files_for_pes = false ]]
4311	then
4312	ln -f ${frelout[$i]} $tmp_data_catalog/${frelout[$i]}
4313	else
4314	mkdir $tmp_data_catalog/${frelout[$i]}
4315	ln -f ${frelout[$i]}/* $tmp_data_catalog/${frelout[$i]}
4316	fi
4317
4318	# GENERATE AND SUBMIT BATCH-JOB
4319	# FILE HAS TO BE DELETED FROM THE TEMPORARY DATA DIRECTORY
4320	# DELETE OLD EXISTING FILES FROM THE ARCHIVE
4321	echo "cd $tmp_data_catalog" > archive_${frelout[$i]}
4322	if [[ $files_for_pes = false ]]
4323	then
4324	echo "rm -rf \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4325	echo "cp ${frelout[$i]} \$UT/${frelout[$i]}" >> archive_${frelout[$i]}
4326	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4327	else
4328	echo "rm -rf \$UT/${frelout[$i]}.tar" >> archive_${frelout[$i]}
4329	echo "tar cvf \$UT/${frelout[$i]}.tar ${frelout[$i]}" >> archive_${frelout[$i]}
4330	echo "rm -rf ${frelout[$i]}" >> archive_${frelout[$i]}
4331	fi
4332
4333	subjob -v -c /pf/b/$usern/job_queue -d -q pp -X 0 -m 1000 -t 7200 $PORTOPT archive_${frelout[$i]}
4334	printf " Archiving of $tmp_data_catalog/${frelout[$i]} initiated (batch job submitted)\n"
4335	file_saved=true
4336
4337	else
4338	printf "\n +++ archive_system=\"$archive_system\" archiving impossible!"
4339	archive_save=false
4340	fi
4341
4342	# CREATE EMPTY FLAG-FILE OR -DIRECTORY
4343	# IN ORDER TO NOTE THE RESPECTIVE CYCLE NUMBER ON THE ARCHIVE SYSTEM
4344	# RESTART-JOBS ARE USING THESE EMPTY-DIRECTORIES TO GET THE CURRENT HIGHEST
4345	# CYCLE NUMBER ON THE ARCHIVE SYSTEM (IN CASE THAT INFORMATIONS ARE DIFFICULT TO
4346	# TO ACCESS FROM THE ARCHIVE-SYSTEM DIRECTLY))
4347	if [[ $file_saved = true ]]
4348	then
4349	if [[ $files_for_pes = false ]]
4350	then
4351	cat /dev/null > ${pathout[$i]}
4352	else
4353	mkdir -p ${pathout[$i]}
4354	fi
4355	fi
4356
4357	fi
4358
4359	# APPEND ON THIS MACHINE
4360	if [[ "${actionout[$i]}" = "a" ]]
4361	then
4362	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4363	then
4364	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
4365	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
4366	else
4367	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
4368	cat ${localout[$i]} >> ${pathout[$i]}
4369	fi
4370	fi
4371
4372	# COPY ON THIS MACHINE
4373	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
4374	# ON DIFFERENT FILE-SYSTEMS
4375	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
4376	then
4377
4378	# COPY IN CASE OF RUNS ON SINGLE CORES
4379	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
4380	then
4381	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
4382	if [[ $link_local_output = true ]]
4383	then
4384	printf " using ln -f\n"
4385	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4386	fi
4387	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4388	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
4389	then
4390	if [[ $link_local_output = true ]]
4391	then
4392	printf " ln failed, using cp...\n"
4393	fi
4394	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
4395	fi
4396	else
4397	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
4398	if [[ $link_local_output = true ]]
4399	then
4400	printf " using ln -f\n"
4401	ln -f ${localout[$i]} ${pathout[$i]}
4402	fi
4403	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
4404	if [[ ! -f "${pathout[$i]}" ]]
4405	then
4406	if [[ $link_local_output = true ]]
4407	then
4408	printf " ln failed, using cp...\n"
4409	fi
4410	cp ${localout[$i]} ${pathout[$i]}
4411	fi
4412	fi
4413
4414	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
4415	then
4416
4417	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
4418	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
4419	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
4420	if [[ $link_local_output = true ]]
4421	then
4422	printf " using ln -f\n"
4423	mkdir ${pathout[$i]}
4424	cd ${localout[$i]}
4425	for file in $(ls *)
4426	do
4427	ln -f $file ${pathout[$i]}
4428	done
4429	cd $TEMPDIR
4430	fi
4431
4432	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
4433	if [[ ! -f "${pathout[$i]}/_0000" ]]
4434	then
4435	if [[ $link_local_output = true ]]
4436	then
4437	printf " ln failed for .../_0000, using cp...\n"
4438	fi
4439	cp -r ${localout[$i]} ${pathout[$i]}
4440	fi
4441
4442	fi
4443	fi
4444	done
4445	if (( i != 0 ))
4446	then
4447	if [[ $transfer_problems = true ]]
4448	then
4449	printf "\n$dashes\n *** OUTPUT-files saved"
4450	printf "\n +++ WARNING: some data transfers failed! \n"
4451	else
4452	printf "\n$dashes\n *** all OUTPUT-files saved \n"
4453	fi
4454	fi
4455
4456
4457	# IF REQUIRED, START A RESTART-JOB
4458	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
4459	if [[ -f CONTINUE_RUN ]]
4460	then
4461
4462	if [[ $archive_save = true ]]
4463	then
4464
4465	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
4466	# -C TELLS MRUN THAT IT IS A RESTART-RUN
4467	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
4468	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
4469	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
4470	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
4471	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
4472	if [[ $(echo $mc \| grep -c "#") != 0 ]]
4473	then
4474	mc=`echo $mc \| sed 's/#/f/g'`
4475	fi
4476
4477
4478	# START THE RESTART-JOB
4479	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
4480	echo " $mc"
4481	printf "\n$dashes\n"
4482	if [[ $localhost != $fromhost ]]
4483	then
4484
4485	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = nech \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lcflow \|\| $localhost = lckyu* \|\| $localhost = lcxe6 ]]
4486	then
4487	echo "*** ssh will be used to initiate restart-runs!"
4488	echo " return_address=\"$return_address\" "
4489	echo " return_username=\"$return_username\" "
4490	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
4491	then
4492	if [[ $localhost = ibmh ]]
4493	then
4494	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\" "
4495	elif [[ $localhost = lcbullhh ]]
4496	then
4497	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\" "
4498	elif [[ $localhost = lccrayb ]]
4499	then
4500	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\" "
4501	elif [[ $localhost = lccrayh ]]
4502	then
4503	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\" "
4504	elif [[ $localhost = lcxe6 ]]
4505	then
4506	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\" "
4507	else
4508	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 "
4509	fi
4510	else
4511	if [[ $localhost = ibmkisti ]]
4512	then
4513	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\" "
4514	elif [[ $localhost = lcflow ]]
4515	then
4516	/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 "
4517	elif [[ $localhost = lccrayb ]]
4518	then
4519	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\" "
4520	elif [[ $localhost = lccrayh ]]
4521	then
4522	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\" "
4523	else
4524	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
4525	fi
4526	fi
4527	else
4528	printf "\n +++ no restart mechanism available for host \"$localhost\" "
4529	locat=restart; exit
4530	fi
4531
4532	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
4533	if [[ $queue = special1q ]]
4534	then
4535	sleep 120
4536	else
4537	sleep 30
4538	fi
4539
4540	else
4541
4542	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
4543	# USING SSH)
4544	cd $LOCAL_PWD
4545	if [[ $localhost = lckyuh ]]
4546	then
4547	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
4548	printf "\n please restart job manually using command:\n"
4549	printf "\n \"$mc\" "
4550	else
4551	eval $mc # THE ' MUST BE EVALUATED
4552	fi
4553	cd - > /dev/null
4554	fi
4555	if [[ $localhost = lckyuh ]]
4556	then
4557	printf "\n$dashes\n *** restart-run to be initiated manually\n"
4558	else
4559	printf "\n$dashes\n *** restart-run initiated \n"
4560	fi
4561
4562
4563	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
4564	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
4565	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
4566	# MAY BE VERY HUGE)
4567	(( i = 0 ))
4568	while (( i < iin ))
4569	do
4570	(( i = i + 1 ))
4571	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
4572	then
4573	rm -r $tmp_data_catalog/${frelin[$i]}
4574	fi
4575	done
4576
4577	else
4578
4579	printf "\n +++ no restart-run possible, since errors occured"
4580	printf "\n during the archive process"
4581	fi
4582
4583	fi
4584
4585
4586
4587	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
4588	if [[ "$email_notification" != "none" ]]
4589	then
4590
4591	if [[ $localhost != $fromhost ]]
4592	then
4593	if [[ -f CONTINUE_RUN ]]
4594	then
4595	echo "PALM restart run necessary" > email_text
4596	echo "description header of actual run:" >> email_text
4597	cat CONTINUE_RUN >> email_text
4598	echo "mrun-command to restart:" >> email_text
4599	echo "$mc" >> email_text
4600	else
4601	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
4602	fi
4603	mail $email_notification < email_text
4604	printf "\n *** email notification sent to \"$email_notification\" "
4605	fi
4606	fi
4607
4608
4609
4610	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
4611	cd $HOME
4612	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
4613
4614	else
4615
4616	# PREPARING ACTIONS,
4617	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
4618
4619	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
4620	mrun_com="$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 $remote_username"
4621	[[ "$cpp_opts" != "" ]] && mrun_com=${mrun_com}" -D \"$cpp_opts\""
4622	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
4623	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
4624	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
4625	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
4626	[[ $ignore_archive_error = true ]] && mrun_com=${mrun_com}" -I"
4627	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
4628	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
4629	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
4630	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
4631	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
4632	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
4633	if [[ $use_openmp = true ]]
4634	then
4635	mrun_com=${mrun_com}" -O $threads_per_task"
4636	fi
4637	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
4638	[[ $store_on_archive_system = true ]] && mrun_com=${mrun_com}" -A"
4639	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
4640	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
4641	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
4642	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
4643	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
4644	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
4645	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
4646	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
4647	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
4648	if [[ $do_remote = true ]]
4649	then
4650	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
4651	fi
4652
4653
4654	# CREATE EXECUTABLE FOR BATCH JOB
4655	if [[ $create_executable_for_batch = true && $restart_run != true ]]
4656	then
4657
4658	printf "\n *** creating the executable for batch job\n"
4659
4660	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
4661	if [[ $host != $localhost ]]
4662	then
4663	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
4664	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
4665	locat=create_executable; exit
4666	fi
4667
4668	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4669	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4670
4671	cp $make_depository .
4672	tar -xf $make_depository > /dev/null 2>&1
4673	cp ../* . > /dev/null 2>&1
4674
4675	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
4676
4677	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
4678	then
4679	printf "\n +++ error occured while compiling or linking"
4680	locat=compile
4681	exit
4682	fi
4683
4684	mv a.out ..
4685	cd - > /dev/null 2>&1
4686	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
4687
4688	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
4689
4690	fi
4691
4692
4693	# BUILD THE JOB-SCRIPTS ON FILE jobfile
4694	jobfile=jobfile.$RANDOM
4695
4696
4697	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
4698	echo "mkdir $TEMPDIR" >> $jobfile
4699	echo "cd $TEMPDIR" >> $jobfile
4700
4701
4702	# ACTIVATE ERROR-TRACEBACK
4703	if [[ $do_trace = true ]]
4704	then
4705	echo "set -x" >> $jobfile
4706	else
4707	echo "set +vx" >> $jobfile
4708	fi
4709
4710
4711	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
4712	if [[ "$init_cmds" != "" ]]
4713	then
4714	echo "$init_cmds" >> $jobfile
4715	fi
4716	if [[ "$module_calls" != "" ]]
4717	then
4718	echo "$module_calls" >> $jobfile
4719	fi
4720
4721
4722	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
4723	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
4724	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
4725	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
4726	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
4727	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
4728	# QUEUEING-SYSTEMS
4729	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh ]]
4730	then
4731
4732	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
4733	if [[ $restart_run != true ]]
4734	then
4735	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
4736	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
4737	fi
4738
4739	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
4740	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
4741	echo "set -x" >> $jobfile
4742	if [[ $host = $localhost ]]
4743	then
4744	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
4745	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
4746	if [[ $(echo $host \| cut -c1-6) = lccray ]]
4747	then
4748	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4749	else
4750	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4751	fi
4752
4753	else
4754	if [[ $host = ibmkisti ]]
4755	then
4756	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
4757	echo "localdir=\`pwd\`" >> $jobfile
4758	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4759	elif [[ $host = lcbullhh ]]
4760	then
4761	echo "localdir=\`pwd\`" >> $jobfile
4762	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4763
4764	elif [[ $host = lccrayb ]]
4765	then
4766	echo "localdir=\`pwd\`" >> $jobfile
4767	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4768	elif [[ $host = lccrayh ]]
4769	then
4770	echo "localdir=\`pwd\`" >> $jobfile
4771	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
4772
4773	else
4774	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
4775	fi
4776	fi
4777	echo "export SOURCES_COMPLETE=true" >> $jobfile
4778
4779	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
4780	# WORKING DIRECTORY OF THE JOB
4781	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
4782	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
4783	echo "chmod u+rwx $mrun_script_name" >> $jobfile
4784	echo "execute_mrun=true" >> $jobfile
4785	echo " " >> $jobfile
4786
4787	else
4788
4789	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
4790	if [[ $do_compile = true ]]
4791	then
4792
4793	source_catalog=SOURCES_FOR_RUN_$fname
4794
4795	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
4796	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
4797	echo "export SOURCES_COMPLETE=true" >> $jobfile
4798	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
4799
4800	for filename in $source_list
4801	do
4802	# BACKSLASH IS USED FOR MASKING
4803	echo "cat > $filename << \"%END%\"" >> $jobfile
4804	cat $source_catalog/$filename >> $jobfile
4805	echo " " >> $jobfile
4806	echo "%END%" >> $jobfile
4807	echo " " >> $jobfile
4808	done
4809
4810	# BACKSLASH IS USED FOR MASKING
4811	echo "cat > Makefile << \"%END%\"" >> $jobfile
4812	cat $source_catalog/Makefile >> $jobfile
4813	echo " " >> $jobfile
4814	echo "%END%" >> $jobfile
4815	echo " " >> $jobfile
4816
4817	echo "cd - > /dev/null" >> $jobfile
4818
4819	fi
4820
4821
4822	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
4823	# BACKSLASH IS USED FOR MASKING
4824	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
4825	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
4826	echo "cat > $config_file << \"%END%\"" >> $jobfile
4827	if [[ $host = lckyuh ]]
4828	then
4829	# NO CROSS-COMPILER ON COMPUTE NODE
4830	sed 's/frtpx/frt/g' $config_file >> $jobfile
4831	else
4832	sed 's/#$.*//g' $config_file >> $jobfile
4833	fi
4834	echo "%END%" >> $jobfile
4835	echo " " >> $jobfile
4836
4837
4838	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
4839	# BACKSLASH IS USED FOR MASKING
4840	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
4841	if [[ $host = lckyuh ]]
4842	then
4843	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
4844	else
4845	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
4846	fi
4847	echo "%END%" >> $jobfile
4848	echo "chmod u+x $mrun_script_name" >> $jobfile
4849	echo "execute_mrun=true" >> $jobfile
4850	echo " " >> $jobfile
4851
4852	fi
4853
4854
4855	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
4856	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
4857	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
4858	if [[ $do_remote = true ]]
4859	then
4860	(( i = 0 ))
4861	while (( i < iin ))
4862	do
4863	(( i = i + 1 ))
4864	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
4865	if [[ "${transin[$i]}" = job ]]
4866	then
4867	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
4868	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
4869	echo " " >> $jobfile
4870	echo "%END%" >> $jobfile
4871	else
4872	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
4873	fi
4874
4875	# CHECK, IF FILE COULD BE CREATED
4876	echo "if [[ \$? = 1 ]]" >> $jobfile
4877	echo "then" >> $jobfile
4878	echo " echo \" \" " >> $jobfile
4879	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4880	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4881	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4882	echo " execute_mrun=false" >> $jobfile
4883	echo "fi" >> $jobfile
4884	done
4885	fi
4886
4887	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4888	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4889	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4890	echo "LOCAL_PWD=$working_directory" >> $jobfile
4891	echo "export LOCAL_PWD" >> $jobfile
4892
4893	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4894	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4895	echo "export LOCAL_MRUN_PATH" >> $jobfile
4896
4897	# lcflow ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4898	# if [[ $host = lcflow \|\| $localhost = lcflow ]]
4899	# then
4900	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4901	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4902	# fi
4903
4904	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4905	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4906	echo "set -x" >> $jobfile
4907	echo "queue=$queue" >> $jobfile
4908	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4909	echo 'ls -al; echo `pwd`' >> $jobfile
4910	echo "cd \$HOME" >> $jobfile
4911	echo "rm -rf $TEMPDIR" >> $jobfile
4912
4913
4914
4915
4916	# START THE JOB USING SUBJOB-COMMAND
4917	if [[ $silent = false ]]
4918	then
4919	printf "\n "
4920	else
4921	printf "\n\n"
4922	fi
4923
4924	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
4925	rm -rf $jobfile
4926
4927
4928	fi # END OF REMOTE-PART

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