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source: palm/trunk/SCRIPTS/mrun @ 2372

Last change on this file since 2372 was 2365, checked in by kanani, 7 years ago
Vertical nesting implemented (SadiqHuq?)
Property svn:keywords set to `Id Rev`
File size: 146.2 KB

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1	#!/bin/bash
2
3	# mrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 1997-2015 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: mrun 2365 2017-08-21 14:59:59Z sward $
29	# Added lckea & lckeam. KIT/IMK-IFU Garmisch cluster. LRZ (SadiqHuq)
30	# Vertical grid nesting: set vnested_mode. -N Procs for fine and coarse grid.
31	#
32	# 2303 2017-07-04 12:26:18Z raasch
33	# bugfix: setting default value for write_binary
34	#
35	# 2298 2017-06-29 09:28:18Z raasch
36	# write_binary in ENVPAR has type LOGICAL now,
37	# MPI2 coupling removed
38	#
39	# 2297 2017-06-28 14:35:57Z scharf
40	# adjustments for using lcgeohu (cirrus @ HUB)
41	# cpp_opts removed
42	#
43	# 2290 2017-06-19 11:03:06Z raasch
44	# further test output removed
45	#
46	# 2286 2017-06-15 13:31:57Z raasch
47	# test output for cycle number removed
48	#
49	# 2268 2017-06-09 10:34:09Z raasch
50	# bugfix for calculating cycle numbers for output files in r2261
51	#
52	# 2262 2017-06-08 14:52:23Z raasch
53	# bugfix for r2261
54	#
55	# 2261 2017-06-08 14:25:57Z raasch
56	# unified cycle numbers for output files are used,
57	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
58	# creation of file OUTPUT_FILE_CONNECTIONS removed,
59	# archive feature completely removed from the script,
60	# nech related parts completely removed
61	#
62	# 2257 2017-06-07 14:07:05Z witha
63	# adjustments for lceddy, removed lcflow-specific code
64	#
65	# 2186 2017-03-21 05:36:31Z raasch
66	#
67	# 2185 2017-03-21 05:09:29Z raasch
68	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
69	#
70	# 2148 2017-02-09 16:56:42Z scharf
71	# changed allocation of resources for lcbullhh in srun command
72	#
73	# 2141 2017-02-06 10:19:32Z gronemeier
74	# made check for existing files language independent
75	#
76	# 1944 2016-06-15 06:29:00Z raasch
77	# adjustments for using HLRN ssh-keys
78	#
79	# 1940 2016-06-14 05:15:20Z raasch $
80	# adjustments for lckiaps
81	#
82	# 1866 2016-04-15 06:50:59Z raasch
83	# adjusted for lcocean
84	#
85	# 1841 2016-04-07 19:14:06Z raasch
86	# script now running under bash
87	#
88	# 1804 2016-04-05 16:30:18Z maronga
89	# test: implementing an execute mechanism where the execute command is given in the
90	# configuration file
91	# ROPTS removed from execution commands
92	# Warnings about missing optional files or user code changed to informative messages
93	# Removed parameter file check
94	#
95	# 1755 2016-02-22 13:53:39Z maronga
96	# Minor bugfix to last commit
97	#
98	# 1753 2016-02-22 13:49:49Z maronga
99	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
100	#
101	# 1622 2015-07-20 06:21:36Z heinze
102	# bugfix for Mistral (lcbullhh)
103	#
104	# 1621 2015-07-17 11:39:33Z heinze
105	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
106	#
107	# 1609 2015-07-03 15:37:58Z maronga
108	# Modified the random number of the temporary working directory to match the
109	# queuing system number on HLRN-III (lccray*).
110	#
111	# 1604 2015-06-23 15:48:03Z suehring
112	# Enable coupled runs for lcmuk
113	#
114	# 1598 2015-05-29 06:45:40Z raasch
115	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
116	#
117	# 1549 2015-01-30 14:26:16Z suehring
118	# Enable interactive debug sessions with allinea debugger
119	#
120	# 1547 2015-01-29 15:09:12Z witha
121	# adjustments for ForWind computing cluster (lcflow)
122	#
123	# 1491 2014-11-12 08:12:57Z heinze
124	# correct setting of batch_job allowed for ibm-machines
125	#
126	# 1468 2014-09-24 14:06:57Z maronga
127	# Typo removed (addres->address)
128	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
129	# Added support for restart runs (remote) for lcxe6
130	#
131	# 1442 2014-07-28 07:09:10Z raasch
132	# default queues for HLRN-III (lccrayb/lccrayh) defined
133	#
134	# 1422 2014-07-02 10:01:25Z kanani
135	# automatic restarts enabled for lccrayb,
136	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
137	#
138	# 1420 2014-06-10 06:24:14Z raasch
139	# -j1 option added to aprung command for lccrayf (CSC)
140	#
141	# 1402 2014-05-09 14:25:13Z raasch
142	# batch_job added to envpar-NAMELIST
143	#
144	# 1357 2014-04-11 15:02:03Z witha
145	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
146	# possible)
147	#
148	# 1320 2014-03-20 08:40:49Z raasch
149	# check namelist file set false by default
150	#
151	# 1304 2014-03-12 10:29:42Z raasch
152	# ulimit option changed from -Ss to -s
153	#
154	# bugfix: missing "fi" in r1289
155	#
156	# 1289 2014-03-04 07:12:34Z raasch
157	# comments translated to English
158	# necriam-, fimm-, ibmy-, and sgi-specific code removed
159	# export of variables for palm and interpret_config removed
160	#
161	# 1281 2014-02-01 07:55:49Z raasch
162	# rsync-copy restricted to Cray machines, since command is unavailable on some
163	# other systems
164	#
165	# 1279 2014-01-28 12:10:14Z raasch
166	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
167	# in order to remove annoying restrictions concerning the number of processors which
168	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
169	# restriction, one of the nodes will be filled with less than the given number of
170	# tasks per node. A respective warning is given.
171	#
172	# 1274 2014-01-09 13:14:54Z heinze
173	# adjustments for lccrayh
174	#
175	# 1272 2014-01-08 10:19:32Z witha
176	# small adjustment for lcflow
177	#
178	# 1270 2013-12-16 11:05:01Z fricke
179	# call of combine_plot_fields adjusted for lccrayb/lccrayh
180	#
181	# 1255 2013-11-07 14:43:35Z raasch
182	# further adjustments for lccrayb remote access
183	#
184	# 1241 2013-10-30 11:36:58Z heinze
185	# Enable use of nudging input and input of large scale forcing from
186	# external files
187	#
188	# 1229 2013-09-20 06:55:19Z raasch
189	# further adjustments for lccrayb
190	#
191	# 1224 2013-09-16 07:27:23Z raasch
192	# first adjustments for lccrayb
193	#
194	# 1210 2013-08-14 10:58:20Z raasch
195	# fftw support added
196	#
197	# 1201 2013-07-10 16:17:59Z witha
198	# adjustments for Forwind cluster (lcflow)
199	#
200	# 1199 2013-07-05 14:52:22Z raasch
201	# adjustments for CSC Helsinki (lccrayf),
202	# executables for batch jobs can be created in advance, in order to avoid calling
203	# the compiler within the batch job (only works if batch jobs are submitted on
204	# local host)
205	#
206	# 1190 2013-06-25 09:39:21Z heinze
207	# enable use of automatic restarts for ibmh
208	# use of cluster/express queue enabled (ibmh)
209	#
210	# 1124 2013-04-09 15:46:52Z raasch
211	# variable "memory" is exported via typeset option -x, because otherwise an unknown
212	# side effect may lead to data loss while getopts is reading the script-option arguments
213	#
214	# 1122 2013-04-09 08:37:16Z heinze
215	# Bugfix: change type of variable last_char
216	#
217	# 1119 2013-04-05 15:11:19Z raasch
218	# Bugfix for setting -T option for subjob
219	#
220	# 1108 2013-03-05 07:03:32Z raasch
221	# bugfix for coupled runs on lckyut/lckyuh
222	#
223	# 1106 2013-03-04 05:31:38Z raasch
224	# --stdin argument for mpiexec on lckyuh
225	# -y and -Y settings output to header
226	#
227	# 1103 2013-02-20 02:15:53Z raasch
228	# default script runs again under ksh, because of unsolved problems with read
229	# from stdin: when bash script is called from a ksh, message "read error: 0:
230	# Resource temporarily unavailable" appears and script does not stop,
231	# further bash compatibility adjustments,
232	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
233	# on lckyuh, but mrun does not terminate and issues a warning instead
234	#
235	# 1101 2013-02-17 10:20:21Z raasch
236	# script now running under bash instead of ksh, which required small adjustments
237	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
238	# read from stdin),
239	# cross compilername on lckyuh compute nodes replaced by real compiler name
240	#
241	# 1099 2013-02-10 01:47:43Z raasch
242	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
243	# and for Forwind cluster (lcflow)
244	# small further adjustments for lckyut
245	#
246	# 1094 2013-02-03 01:52:12Z raasch
247	# explicit ssh/scp port can be set in config file with environment variable
248	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
249	# decalpha parts (yonsei) removed
250	#
251	# 2013-02-02 07:06:13Z raasch
252	# adjustments for Kyushu-University computing center (lckyut - tatara)
253	#
254	# 1083 2013-01-04 10:22:09Z maronga
255	# bugfix in parameter file check (read %cpp_options was missing)
256	#
257	# 1069 2012-11-28 16:18:43Z maronga
258	# bugfix: coupling mode was always set to mpi2, typos removed
259	#
260	# 1058 2012-11-21 07:00:35Z raasch
261	# Intel inspector (inspxe) is given the number of PEs instead of the number of
262	# nodes
263	#
264	# 1046 2012-11-09 14:38:45Z maronga
265	# code put under GPL (PALM 3.9)
266	#
267	# 21/03/94 - Siggi - first version finished
268	# 03/03/94 - Siggi - script development started
269	#
270	#--------------------------------------------------------------------------------#
271	# mrun - script for running PALM jobs
272	#--------------------------------------------------------------------------------#
273
274
275
276	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
277
278	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
279	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
280	# (TOO MANY ARGUMENTS - PROBLEM)
281	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
282
283	AddFilenames=""
284	additional_conditions=""
285	add_source_path=""
286	afname=""
287	check_namelist_files=false
288	combine_plot_fields=true
289	compiler_name=""
290	cond1=""
291	cond2=""
292	config_file=.mrun.config
293	coupled_dist=""
294	cpp_options=""
295	cpumax=0
296	cpurest=0
297	create_executable_for_batch=false
298	delete_temporary_catalog=true
299	do_batch=false
300	do_compile=true
301	do_remote=false
302	do_stagein=true
303	do_stageout=true
304	do_trace=false
305	email_notification="none"
306	exclude=""
307	executable=""
308	execute_command="none"
309	execution_error=false
310	fftw_inc=""
311	fftw_lib=""
312	fftw_support=false
313	fname=test
314	fromhost=""
315	global_revision=""
316	group_number=none
317	host=""
318	host_file=""
319	hp=""
320	input_list=""
321	interpreted_config_file=""
322	job_catalog="~/job_queue"
323	job_on_file=""
324	keep_data_from_previous_run=false
325	link_local_input=false
326	link_local_output=false
327	localhost_realname=$(hostname)
328	local_dvrserver_running=.FALSE.
329	locat=normal
330	mainprog=""
331	makefile=""
332	max_par_io_str=""
333	mc=$0
334	while [[ $(echo $mc \| grep -c "/") != 0 ]]
335	do
336	mc=`echo $mc \| cut -f2- -d"/"`
337	done
338	module_calls=""
339	mrun_script_name=$mc
340	vnested_dist=""
341	vnested_mode="vnested_twi"
342	netcdf_inc=""
343	netcdf_lib=""
344	netcdf_support=false
345	node_usage=default
346	numprocs=""
347	numprocs_atmos=0
348	numprocs_ocean=0
349	numprocs_crse=0
350	numprocs_fine=0
351	OOPT=""
352	openmp=false
353	output_list=""
354	package_list=""
355	queue=none
356	read_from_config=""
357	restart_run=false
358	if [[ `hostname` = rte10 ]]
359	then
360	return_address=133.5.185.60
361	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
362	elif [[ `hostname` = climate0 ]]
363	then
364	return_address=165.132.26.68
365	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
366	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
367	then
368	return_address="schultzl-Latitude-E6540"
369	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
370	elif [[ `hostname` = urban00 ]]
371	then
372	return_address=147.46.30.151
373	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
374	else
375	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
376	fi
377	return_password=""
378	return_username=$LOGNAME
379	remotecall=false
380	remote_username=""
381	run_coupled_model=false
382	run_mode=""
383	run_vnested_model=false
384	dashes=" ----------------------------------------------------------------------------"
385	silent=false
386	source_list=""
387	source_path=SOURCE
388	tasks_per_node=""
389	threads_per_task=1
390	tmpcreate=false
391	tmp_data_catalog=""
392	transfer_problems=false
393	usern=$LOGNAME
394	use_openmp=false
395	version="MRUN 2.1 Rev$Rev: 2365 $"
396	working_directory=`pwd`
397	write_binary=false
398	TOPT=""
399	XOPT=""
400	zeit=$( date \| cut -c 12-19 )
401
402	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
403	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
404	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
405	# SCRIPT-OPTION ARGUMENTS
406	typeset -i cputime i ii iia iii iio icycle inode ival jobges jobsek last_char_int maxcycle minuten nodes pes remaining_pes run_number sekunden tp1
407
408	# ERROR HANDLING IN CASE OF EXIT
409	trap 'rm -rf $working_directory/tmp_mrun
410	if [[ $locat != normal && $locat != control_c ]]
411	then
412
413	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
414	(( i = 0 ))
415	while (( i < iec ))
416	do
417	(( i = i + 1 ))
418	printf "\n *** Execution of ERROR-command:\n"
419	printf " >>> ${err_command[$i]}\n"
420	eval ${err_command[$i]}
421	done
422	if [[ -n $interpreted_config_file ]]
423	then
424	rm -rf $interpreted_config_file
425	fi
426	if [[ -n .mrun_environment ]]
427	then
428	rm -rf .mrun_environment
429	fi
430	if [[ $tmpcreate = true ]]
431	then
432	# printf "\n *** Contents of \"$TEMPDIR\":\n"
433	# ls -al; cd
434	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
435	fi
436	if [[ "$dvrserver_id" != "" ]]
437	then
438	echo "+++ killing dvrserver_id=$dvrserver_id"
439	kill $dvrserver_id
440	fi
441	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
442	then
443	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
444	fi
445	printf "\n\n+++ MRUN killed \n\n"
446	elif [[ $locat != control_c ]]
447	then
448	printf "\n\n --> all actions finished\n\n"
449	printf " Bye, bye $usern !!\n\n"
450	fi' exit
451
452
453	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
454	trap 'rm -rf $working_directory/tmp_mrun
455	rm -rf $working_directory/tmp_check_namelist_files
456	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
457	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
458	then
459	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
460	fi
461	if [[ "$dvrserver_id" != "" ]]
462	then
463	echo "+++ killing dvrserver_id=$dvrserver_id"
464	kill $dvrserver_id
465	fi
466	printf "\n+++ MRUN killed by \"^C\" \n\n"
467	locat=control_c
468	exit
469	' 2
470
471
472	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
473	# BEEN SET
474	if [[ "$PALM_BIN" = "" ]]
475	then
476	printf "\n +++ environment variable PALM_BIN has not been set"
477	printf "\n please set it to the directory where the PALM scripts are located"
478	locat=palm_bin; exit
479	fi
480	export PATH=$PALM_BIN:$PATH
481
482
483
484	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
485	# WHICH WILL BE USED TO START RESTART-JOBS
486	while getopts :a:bBc:Cd:Fg:G:h:H:i:kK:m:M:n:N:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
487	do
488	case $option in
489	(a) afname=$OPTARG;;
490	(b) do_batch=true; mc="$mc -b";;
491	(B) delete_temporary_catalog=false; mc="$mc -B";;
492	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
493	(C) restart_run=true; mc="$mc -C";;
494	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
495	(F) job_on_file="-D"; mc="$mc -F";;
496	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
497	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
498	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
499	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
500	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
501	(k) keep_data_from_previous_run=true; mc="$mc -k";;
502	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
503	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
504	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
505	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
506	(N) run_vnested_model=true; vnested_dist=$OPTARG; mc="$mc -N'$OPTARG'";;
507	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
508	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
509	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
510	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
511	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
512	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
513	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
514	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
515	(S) read_from_config=false; mc="$mc -S";;
516	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
517	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
518	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
519	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
520	(v) silent=true; mc="$mc -v";;
521	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
522	(x) do_trace=true;set -x; mc="$mc -x";;
523	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
524	(y) ocean_file_appendix=true; mc="$mc -y";;
525	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
526	(z) check_namelist_files=false; mc="$mc -z";;
527	(Z) combine_plot_fields=false; mc="$mc -Z";;
528	(\?) printf "\n +++ unknown option $OPTARG \n"
529	printf "\n --> type \"$0 ?\" for available options \n"
530	locat=parameter;exit;;
531	esac
532	done
533
534
535	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
536	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
537	(( to_shift = $OPTIND - 1 ))
538	shift $to_shift
539
540	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
541	if [[ "$1" = "?" ]]
542	then
543	(printf "\n *** mrun can be called as follows:\n"
544	printf "\n $mrun_script_name -b -c.. -d.. -f.. -F -h.. -i.. -I -K.. -m.. -o.. -p.. -r.. -R -s.. -t.. -T.. -v -x -X.. -y -Y.. -Z <modus> \n"
545	printf "\n Description of available options:\n"
546	printf "\n Option Description Default-Value"
547	printf "\n -a base name of input files equiv. -d"
548	printf "\n -b batch-job on local machine ---"
549	printf "\n -B do not delete temporary directory at end ---"
550	printf "\n -c configuration file .mrun.config"
551	printf "\n -d base name of files attached to program test"
552	printf "\n -F create remote job file only ---"
553	printf "\n -h execution host $localhost_realname"
554	printf "\n -i INPUT control list \"\" "
555	printf "\n -k keep data from previous run"
556	printf "\n -K additional conditions for controling"
557	printf "\n usage of conditional code and"
558	printf "\n env-variables in configuration file \"\" "
559	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
560	printf "\n -M Makefile name Makefile"
561	printf "\n -n node usage (shared/not_shared) depending on -h"
562	printf "\n -N Vertical grid nesting. Number of"
563	printf "\n PE for Coarse and Fine grid"
564	printf "\n -o OUTPUT control list \"\" "
565	printf "\n -O threads per openMP task ---"
566	printf "\n -p software package list \"\" "
567	printf "\n -q queue \"$queue\" "
568	printf "\n -r run control list (combines -i -o) \"\" "
569	printf "\n -s filenames of routines to be compiled \"\" "
570	printf "\n must end with .f, .f90, .F, or .c !"
571	printf "\n use \"..\" for more than one file and wildcards"
572	printf "\n -s LM compiles all locally modified files"
573	printf "\n -S config file interpreted by shellscript ---"
574	printf "\n -t allowed cpu-time in seconds (batch) 0"
575	printf "\n -T tasks per node depending on -h"
576	printf "\n -u username on remote machine \"\" "
577	printf "\n -v no prompt for confirmation ---"
578	printf "\n -w maximum parallel io streams as given by -X"
579	printf "\n -x tracing of mrun for debug purposes ---"
580	printf "\n -X # of processors (on parallel machines) 1"
581	printf "\n -y add appendix \"_O\" to all local output"
582	printf "\n files (ocean precursor runs followed by"
583	printf "\n coupled atmosphere-ocean runs) ---"
584	printf "\n -Y run coupled model, \"#1 #2\" with"
585	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
586	printf "\n -Z skip combine_plot_fields at the end of "
587	printf "\n the simulation ---"
588	printf "\n "
589	printf "\n Possible values of positional parameter <modus>:"
590	printf "\n \"?\" - this outline \n\n") \| more
591	exit
592	elif [[ "$1" != "" ]]
593	then
594	printf "\n +++ positional parameter $1 unknown \n"
595	locat=parameter; exit
596	fi
597
598
599
600	# SHORT STARTING MESSAGE
601	printf "\n*** $version "
602	printf "\n will be executed. Please wait ..."
603
604
605
606	# CHECK, IF CONFIGURATION FILE EXISTS
607	if [[ ! -f $config_file ]]
608	then
609	printf "\n\n +++ configuration file: "
610	printf "\n $config_file"
611	printf "\n does not exist"
612	locat=connect; exit
613	fi
614
615
616	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
617	line=""
618	grep "%host_identifier" $config_file > tmp_mrun
619	while read line
620	do
621	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
622	then
623	HOSTNAME=`echo $line \| cut -d" " -s -f2`
624	host_identifier=`echo $line \| cut -d" " -s -f3`
625	if [[ $localhost_realname = $HOSTNAME ]]
626	then
627	localhost=$host_identifier
628	break
629	fi
630	fi
631	done < tmp_mrun
632
633	if [[ "$localhost" = "" ]]
634	then
635	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
636	printf "\n for local host \"$localhost_realname\"."
637	printf "\n Please add line"
638	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
639	printf "\n to the configuration file."
640	locat=localhost; exit
641	fi
642
643
644	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
645	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
646	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
647	[[ "$afname" = "" ]] && afname=$fname
648
649
650	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
651	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
652	# STATEMENTS IN THE CONFIGURATION FILE
653	if [[ "$run_mode" != "" ]]
654	then
655	input_list="$input_list $run_mode"
656	output_list="$output_list $run_mode"
657	fi
658
659
660	# ??? is this (and the respective option -H) really required ???
661	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
662	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
663	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
664	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
665	if [[ "$fromhost" = "" ]]
666	then
667	fromhost=$localhost
668	fi
669
670
671	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
672	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
673	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
674	# TO BE SUBMITTED (I.E. do_batch=true)
675	if [[ -n $host && "$host" != $localhost ]]
676	then
677	do_batch=true
678	do_remote=true
679	case $host in
680	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
681	(*) printf "\n"
682	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
683	printf "\n is not available"
684	locat=nqs; (( iec = 0 )); exit;;
685	esac
686	else
687	host=$localhost
688	fi
689
690
691	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
692	if [[ -n $additional_conditions ]]
693	then
694	cond1=`echo $additional_conditions \| cut -d" " -f1`
695	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
696	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
697	if [[ -n $dummy ]]
698	then
699	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
700	locat=options; exit
701	fi
702	block=_$cond1
703	[[ -n $cond2 ]] && block=${block}_$cond2
704	fi
705
706
707	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
708	if [[ $run_coupled_model = true ]]
709	then
710
711	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
712	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
713
714	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
715	then
716
717	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
718	printf "\n PEs (total) : $numprocs"
719	printf "\n PEs (atmosphere): $numprocs_atmos"
720	printf "\n PEs (ocean) : $numprocs_ocean"
721	locat=coupling; exit
722
723	fi
724
725	fi
726
727	# NESTING (-N) selected and vnesting_mode specified
728	if [[ $run_vnested_model = true ]]
729	then
730
731	if [[ -n $vnested_dist ]]
732	then
733
734	numprocs_crse=`echo $vnested_dist \| cut -d" " -s -f1`
735	numprocs_fine=`echo $vnested_dist \| cut -d" " -s -f2`
736
737	if (( $numprocs_crse + $numprocs_fine != $numprocs ))
738	then
739
740	printf "\n +++ number of processors does not fit to specification by \"-N\"."
741	printf "\n PEs (total) : $numprocs"
742	printf "\n PEs (Coarse) : $numprocs_crse"
743	printf "\n PEs (Fine) : $numprocs_fine"
744	locat=vnesting; exit
745
746	fi
747
748	else
749
750	printf "\n +++ "Specify PE for fine and coarse grid: -N "nCGPE nFGPE \"-N\"."
751	locat=vnesting; exit
752
753	fi
754	vnested_dist=`echo "$numprocs_crse $numprocs_fine"`
755	fi
756
757	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
758	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
759	mrun_memory=$memory
760	mrun_group_number=$group_number
761	mrun_cpumax=$cpumax
762	mrun_numprocs=$numprocs
763
764
765	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
766	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
767	if [[ "$read_from_config" = false ]]
768	then
769	[[ $silent = false ]] && printf "\n Reading the configuration file... "
770
771	# READ THE CONFIGURATION FILE LINE BY LINE
772	while read zeile
773	do
774	[[ $silent = false ]] && printf "."
775
776
777	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
778	eval zeile=\"$zeile\"
779
780
781	# INTERPRET THE LINE
782	if [[ "$(echo $zeile)" = "" ]]
783	then
784	# EMPTY LINE, NO ACTION
785	continue
786
787	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
788	then
789
790	# LINE IS A COMMENT LINE
791	true
792
793	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
794	then
795
796	# LINE DEFINES AN ENVIRONMENT-VARIABLE
797	zeile=$(echo $zeile \| cut -c2-)
798	var=`echo $zeile \| cut -d" " -f1`
799	value=`echo $zeile \| cut -d" " -s -f2`
800	for_host=`echo $zeile \| cut -d" " -s -f3`
801	for_cond1=`echo $zeile \| cut -d" " -s -f4`
802	for_cond2=`echo $zeile \| cut -d" " -s -f5`
803
804	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
805	then
806
807	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
808	# "::" IS REPLACED BY ":".
809	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
810
811
812	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
813	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
814	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
815	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
816	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
817	# CONFIGURATION-FILE.
818	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
819	then
820	eval $var=\$value
821
822	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
823	if [[ $do_trace = true ]]
824	then
825	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
826	fi
827	fi
828
829	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
830	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
831	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
832	# MUST HAVE TO BE STARTED
833	if [[ $var = host ]]
834	then
835	if [[ -n $host && "$host" != $localhost ]]
836	then
837	do_batch=true
838	do_remote=true
839	case $host in
840	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
841	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
842	printf "\n is not available"
843	locat=nqs; exit;;
844	esac
845	else
846	host=$localhost
847	fi
848	fi
849
850	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
851	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
852	# BY MRUN (E.G. subjob)
853	export $var
854	fi
855
856
857
858
859	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
860	then
861
862	# LINE DEFINES ERROR-COMMAND
863	(( iec = iec + 1 ))
864	zeile=$(echo $zeile \| cut -c4-)
865	err_command[$iec]="$zeile"
866
867	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
868	then
869
870	# LINE DEFINES INPUT-COMMAND
871	(( iic = iic + 1 ))
872	zeile=$(echo $zeile \| cut -c4-)
873	in_command[$iic]="$zeile"
874
875	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
876	then
877
878	# LINE DEFINES OUTPUT-COMMAND
879	(( ioc = ioc + 1 ))
880	zeile=$(echo $zeile \| cut -c4-)
881	out_command[$ioc]="$zeile"
882
883	else
884
885	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
886	# s2a: in/out - field
887	# s2b: loc - field (optional)
888	# s2c: tr/ar - field (optional)
889	s1=`echo $zeile \| cut -d" " -f1`
890	s2=`echo $zeile \| cut -d" " -s -f2`
891	s2a=$(echo $s2 \| cut -d":" -f1)
892	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
893	then
894	s2b=""
895	s2c=""
896	else
897	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
898	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
899	fi
900	s3=`echo $zeile \| cut -d" " -f3`
901	s4=`echo $zeile \| cut -d" " -s -f4`
902	s5=`echo $zeile \| cut -d" " -s -f5`
903	s6=`echo $zeile \| cut -d" " -s -f6`
904
905
906	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
907	# INPUT- OR OUTPUT-LIST.
908	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
909	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
910	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
911	# IS NOT CHECKED AND STORED.
912	IFSALT="$IFS"; IFS="$IFS:"
913	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
914	then
915	found=false
916	for actual in $input_list
917	do
918	for formal in $s3
919	do
920	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
921	done
922	done
923	if [[ $found = true ]]
924	then
925	(( iin = iin + 1 ))
926	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
927	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
928	extin[$iin]=$s6
929	fi
930	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
931	then
932	found=false
933	for actual in $output_list
934	do
935	for formal in $s3
936	do
937	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
938	done
939	done
940	if [[ $found = true ]]
941	then
942	(( iout = iout + 1 ))
943	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
944	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
945	fi
946	elif [[ "$s2a" != in && "$s2a" != out ]]
947	then
948	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
949	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
950	locat=connect; exit
951	fi
952	IFS="$IFSALT"
953	fi
954	done < $config_file
955
956	else
957
958	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
959	[[ $silent = false ]] && printf "..."
960	interpreted_config_file=.icf.$RANDOM
961
962
963
964	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
965	cat > .mrun_environment << EOF
966	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
967	config_file = '$config_file', do_remote = '$do_remote',
968	do_trace = '$do_trace', host = '$host',
969	input_list = '$input_list', icf = '$interpreted_config_file',
970	localhost = '$localhost', output_list = '$output_list' /
971
972	EOF
973
974	if [[ "$host" != $localhost ]]
975	then
976
977	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
978	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
979	if [[ $? != 0 ]]
980	then
981	printf "\n\n +++ no interpret_config found"
982	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
983	locat=interpret_config; exit
984	fi
985	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
986	$interpret_config_executable
987
988	else
989
990	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
991	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
992	then
993	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
994	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
995	locat=interpret_config; exit
996	else
997	interpret_config${block}.x
998	fi
999
1000	fi
1001	rm .mrun_environment
1002
1003
1004	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
1005	chmod u+x $interpreted_config_file
1006	export PATH=$PATH:.
1007	. $interpreted_config_file
1008	rm $interpreted_config_file
1009
1010	fi
1011
1012
1013	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
1014	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
1015	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
1016	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
1017	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
1018	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
1019	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
1020
1021
1022	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
1023	# FOR SOURCE-FILES TO BE COMPILED.
1024	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
1025	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
1026	if [[ "$SOURCES_COMPLETE" = "" ]]
1027	then
1028
1029	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
1030	# HAS BEEN DEFINED
1031	source_path=""
1032	line=""
1033	grep "%source_path" $config_file > tmp_mrun
1034	while read line
1035	do
1036	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1037	then
1038	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
1039	then
1040	global_source_path=`echo $line \| cut -d" " -f2`
1041	fi
1042	fi
1043	done < tmp_mrun
1044
1045	line=""
1046	found=false
1047	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1048	while read line
1049	do
1050	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1051	then
1052	if [[ $found = true ]]
1053	then
1054	printf "\n\n +++ more than one source path found in configuration file"
1055	printf "\n for local host \"$localhost\" "
1056	locat=source_path; exit
1057	fi
1058	source_path=`echo $line \| cut -d" " -f2`
1059	found=true
1060	fi
1061	done < tmp_mrun
1062	rm tmp_mrun
1063
1064	if [[ "$source_path" = "" ]]
1065	then
1066	if [[ "$global_source_path" != "" ]]
1067	then
1068	source_path=$global_source_path
1069	else
1070	printf "\n\n +++ no source path found in configuration file"
1071	printf "\n for local host \"$localhost\" "
1072	locat=source_path; exit
1073	fi
1074	fi
1075	eval source_path=$source_path
1076
1077	if [[ ! -d $source_path ]]
1078	then
1079	printf "\n\n +++ source path \"$source_path\" on local host"
1080	printf "\n \"$localhost\" does not exist"
1081	locat=source_path; exit
1082	fi
1083
1084	fi
1085
1086
1087	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1088	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1089	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1090	then
1091	global_revision=`svnversion $source_path 2>/dev/null`
1092	global_revision="Rev: $global_revision"
1093	fi
1094
1095
1096	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1097	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1098	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1099	if [[ -n $host && "$host" != $localhost ]]
1100	then
1101	do_batch=true
1102	do_remote=true
1103	case $host in
1104	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
1105	(*) printf "\n"
1106	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1107	printf "\n is not available"
1108	locat=nqs; (( iec = 0 )); exit;;
1109	esac
1110	else
1111	host=$localhost
1112	fi
1113
1114
1115
1116	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1117	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1118	then
1119
1120	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1121	if [[ ! -n $numprocs ]]
1122	then
1123	printf "\n"
1124	printf "\n +++ option \"-K parallel\" requires additional specification"
1125	printf "\n of the number of processors to be used by"
1126	printf "\n mrun-option \"-X\" or by environment-variable"
1127	printf "\n \"numprocs\" in the configuration file"
1128	locat=numprocs; (( iec = 0 )); exit
1129	fi
1130
1131	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1132	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1133	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
1134	then
1135	printf "\n"
1136	printf "\n +++ option \"-T\" (tasks per node) is missing"
1137	printf "\n set -T option or define tasks_per_node in the config file"
1138	locat=tasks_per_node; (( iec = 0 )); exit
1139	fi
1140
1141	if (( numprocs < tasks_per_node ))
1142	then
1143	printf "\n"
1144	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1145	printf "\n given values: -T $tasks_per_node -X $numprocs"
1146	locat=tasks_per_node; (( iec = 0 )); exit
1147	fi
1148
1149	if [[ $host != lcxt5m ]]
1150	then
1151	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1152	(( ival = $tasks_per_node ))
1153	(( pes = numprocs ))
1154	(( ii = pes / ival ))
1155	(( remaining_pes = pes - ii * ival ))
1156	if (( remaining_pes > 0 ))
1157	then
1158	printf "\n"
1159	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1160	printf "\n divisor of the total number of processors (option \"-X\")"
1161	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1162	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1163	(( nodes = nodes + 1 ))
1164	fi
1165	fi
1166
1167
1168	# SETTINGS FOR SUBJOB-COMMAND
1169	OOPT="-O $threads_per_task"
1170
1171	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1172	if [[ "$tasks_per_node" != "" ]]
1173	then
1174	TOPT="-T $tasks_per_node"
1175	fi
1176
1177	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1178	if [[ $node_usage = default ]]
1179	then
1180	if [[ $host = ibms ]]
1181	then
1182	node_usage=shared
1183	else
1184	node_usage=not_shared
1185	fi
1186	fi
1187
1188	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1189	then
1190	printf "\n"
1191	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1192	printf "\n \"shared\" or \"not_shared\""
1193	locat=tasks_per_node; (( iec = 0 )); exit
1194	fi
1195
1196	fi
1197
1198	# CHECK IF HOSTFILE EXISTS
1199	if [[ -n $hostfile ]]
1200	then
1201	if [[ ! -f $hostfile ]]
1202	then
1203	printf "\n"
1204	printf "\n +++ hostfile \"$hostfile\" does not exist"
1205	locat=hostfile; exit
1206	fi
1207	fi
1208
1209
1210	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1211	if [[ "$maximum_parallel_io_streams" = "" ]]
1212	then
1213	maximum_parallel_io_streams=$numprocs
1214	fi
1215
1216
1217	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1218	if [[ "$scp_port" != "" ]]
1219	then
1220	PORTOPT="-P $scp_port"
1221	SSH_PORTOPT="-p $scp_port"
1222	fi
1223
1224
1225	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1226	# CONFIG-FILE
1227	if [[ "$ssh_key" != "" ]]
1228	then
1229	ssh_key="-i $HOME/.ssh/$ssh_key"
1230	fi
1231
1232
1233	# SET DEFAULT-QUEUE, IF NOT GIVEN
1234	if [[ $queue = none ]]
1235	then
1236	case $host in
1237	(ibmh) queue=cluster;;
1238	(ibmkisti) queue=class.32plus;;
1239	(ibmmuc*) queue=test;;
1240	(lcbwuni) queue=develop;;
1241	(lcbullhh) queue=compute;;
1242	(lccrayb) queue=mpp1q;;
1243	(lccrayh) queue=mpp1q;;
1244	(lcgeohu) queue=short;;
1245	(lckiaps) queue=normal;;
1246	(lckyoto) queue=ph;;
1247	(lckyuh) queue=fx-single;;
1248	(lckyut) queue=cx-single;;
1249	(lclrz) queue=mpp2;;
1250	(lctit) queue=S;;
1251	(unics) queue=unics;;
1252	esac
1253	fi
1254
1255
1256	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1257	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1258	(( i = 0 ))
1259	while (( i < iin ))
1260	do
1261	(( i = i + 1 ))
1262	(( maxcycle = 0 ))
1263
1264	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1265	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1266	if [[ "${actionin[$i]}" = di ]]
1267	then
1268	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1269	# HOST ONLY
1270	eval filename=${pathin[$i]}/${endin[$i]}
1271	else
1272	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1273	# HOST ONLY
1274	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1275	fi
1276	eval pathname=${pathin[$i]}
1277
1278	# CHECK IF FILE EXISTS
1279	if ! ls $filename* 1>/dev/null 2>&1
1280	then
1281
1282	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1283	if [[ "${transin[$i]}" != "locopt" ]]
1284	then
1285	printf "\n\n +++ INPUT-file: "
1286	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1287	then
1288	printf "\n $filename"
1289	else
1290	printf "\n $filename.${extin[$i]}"
1291	fi
1292	printf "\n does not exist\n"
1293	locat=input; exit
1294	else
1295	transin[$i]="unavailable"
1296	fi
1297	else
1298
1299	# DETERMINE THE FILE'S CYCLE NUMBER
1300	ls -1 -d $filename > filelist 2>/dev/null
1301	ls -1 -d $filename.* >> filelist 2>/dev/null
1302	while read zeile
1303	do
1304	# filename without path (i.e. after the last "/")
1305	basefilename=$(basename ${zeile})
1306
1307	# check if there is an extension
1308	extension=${basefilename##*.}
1309	if [[ "$extension" = "$extin[$i]" ]]
1310	then
1311	basefilename=${basefilename&.*}
1312	fi
1313
1314	# check for an existing cycle number
1315	cycle=${basefilename##*.}
1316	if [[ $cycle =~ ^-?[0-9]+$ ]]
1317	then
1318	(( icycle = $cycle ))
1319	else
1320	(( icycle = 0 ))
1321	fi
1322
1323	if (( icycle > maxcycle ))
1324	then
1325	(( maxcycle = icycle ))
1326	fi
1327
1328	# cycle=$(echo $zeile \| cut -f2 -d".")
1329	# if [[ "$cycle" = "$zeile" ]]
1330	# then
1331	# (( icycle = 0 ))
1332	# elif [[ "$cycle" = "${extin[$i]}" ]]
1333	# then
1334	# (( icycle = 0 ))
1335	# else
1336	# (( icycle = $cycle ))
1337	# fi
1338	# if (( icycle > maxcycle ))
1339	# then
1340	# (( maxcycle = icycle ))
1341	# fi
1342	done <filelist
1343	rm filelist
1344
1345	# APPEND CYCLE NUMBER TO FILENAME
1346	if (( maxcycle > 0 ))
1347	then
1348	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1349	then
1350	filename=${filename}.$maxcycle.${extin[$i]}
1351	else
1352	filename=${filename}.$maxcycle
1353	fi
1354	else
1355	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1356	then
1357	filename=${filename}.${extin[$i]}
1358	fi
1359	fi
1360
1361	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1362	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1363	absnamein[$i]=$filename
1364	if (( maxcycle > 0 ))
1365	then
1366	if [[ "${actionin[$i]}" = di ]]
1367	then
1368	frelin[$i]=${endin[$i]}.$maxcycle
1369	else
1370	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1371	fi
1372	else
1373	if [[ "${actionin[$i]}" = di ]]
1374	then
1375	frelin[$i]=${endin[$i]}
1376	else
1377	frelin[$i]=${afname}${endin[$i]}
1378	fi
1379	fi
1380
1381	fi
1382	done
1383
1384	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1385	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1386	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1387	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1388	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1389	# REMOTE HOST)
1390	(( i = 0 ))
1391	while (( i < iout ))
1392	do
1393	(( i = i + 1 ))
1394	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1395	then
1396	if [[ "${actionout[$i]}" = tr ]]
1397	then
1398	actionout[$i]=""
1399	elif [[ "${actionout[$i]}" = trpe ]]
1400	then
1401	actionout[$i]=pe
1402	elif [[ "${actionout[$i]}" = tra ]]
1403	then
1404	actionout[$i]=a
1405	fi
1406	(( maxcycle = 0 ))
1407	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1408	eval catalogname=${pathout[$i]}
1409	if ! ls $filename* 1>/dev/null 2>&1
1410	then
1411
1412	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1413	if cat /dev/null > $filename
1414	then
1415	rm $filename
1416	else
1417
1418	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1419	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1420	if [[ ! -d $catalogname ]]
1421	then
1422	if mkdir -p $catalogname
1423	then
1424	printf "\n\n *** directory:"
1425	printf "\n $catalogname"
1426	printf "\n was created\n"
1427	else
1428	printf "\n\n +++ OUTPUT-file:"
1429	printf "\n $filename"
1430	printf "\n cannot be created, because directory does not exist"
1431	printf "\n and cannot be created either"
1432	printf "\n"
1433	locat=output ; exit
1434	fi 2>/dev/null
1435	else
1436	printf "\n\n +++ OUTPUT-file:"
1437	printf "\n $filename"
1438	printf "\n cannot be created, although directory exists"
1439	printf "\n"
1440	locat=output ; exit
1441	fi
1442	fi 2>/dev/null
1443	else
1444
1445	# DETERMINE THE CYCLE NUMBER
1446	ls -1 -d $filename > filelist 2>/dev/null
1447	ls -1 -d $filename.* >> filelist 2>/dev/null
1448	while read zeile
1449	do
1450
1451	# filename without path (i.e. after the last "/")
1452	basefilename=$(basename ${zeile})
1453
1454	# check if there is an extension
1455	extension=${basefilename##*.}
1456	if [[ "$extension" = "${extout[$i]}" ]]
1457	then
1458	basefilename=${basefilename%.*}
1459	fi
1460
1461	# check for an existing cycle number
1462	cycle=${basefilename##*.}
1463	if [[ $cycle =~ ^-?[0-9]+$ ]]
1464	then
1465	(( icycle = $cycle + 1 ))
1466	else
1467	(( icycle = 1 ))
1468	fi
1469
1470	if (( icycle > maxcycle ))
1471	then
1472	(( maxcycle = icycle ))
1473	fi
1474
1475	done <filelist
1476	rm filelist
1477	fi
1478
1479	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1480	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1481	if [[ "${actionout[$i]}" != a ]]
1482	then
1483	if (( maxcycle > 0 ))
1484	then
1485	filename_tmp=${filename}.$maxcycle
1486	if cat /dev/null > $filename_tmp
1487	then
1488	rm $filename_tmp
1489	else
1490	printf "\n +++ OUTPUT-file:"
1491	printf "\n $filename_tmp"
1492	printf "\n cannot be created"
1493	locat=output ; exit
1494	fi
1495	fi
1496	else
1497	(( maxcycle = maxcycle - 1 ))
1498	fi
1499
1500	(( cycnum[$i] = maxcycle ))
1501	pathout[$i]=$filename
1502
1503	fi
1504	done
1505
1506
1507	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1508	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1509	then
1510	if [[ "$dvr_inc" = "" ]]
1511	then
1512	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1513	printf "\n This is required for the dvrp_graphics package.\n"
1514	locat=dvr; exit
1515	fi
1516	if [[ "$dvr_lib" = "" ]]
1517	then
1518	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1519	printf "\n This is required for the dvrp_graphics package.\n"
1520	locat=dvr; exit
1521	fi
1522	fi
1523
1524
1525	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1526	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1527	if [[ "$mainprog" = "" && "$executable" = "" ]]
1528	then
1529	printf "\n +++ neither main program nor executable defined"
1530	locat=source; exit
1531	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1532	then
1533	printf "\n +++ main program as well as executable defined"
1534	locat=source; exit
1535	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1536	then
1537	do_compile=false
1538	fi
1539
1540
1541	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1542	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1543	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1544	then
1545	rm -rf SOURCES_FOR_RUN_$fname
1546	mkdir SOURCES_FOR_RUN_$fname
1547	fi
1548
1549
1550	# COLLECT ALL ROUTINES TO BE COMPILED
1551	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1552	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1553	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1554	then
1555
1556	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1557
1558	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1559	then
1560
1561	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1562	source_list=""
1563	cd $source_path
1564
1565
1566	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1567	if [[ ! -d .svn ]]
1568	then
1569	printf "\n\n +++ source directory"
1570	printf "\n \"$source_path\" "
1571	printf "\n is not under control of \"subversion\"."
1572	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1573	fi
1574
1575
1576	# LIST ALL MODIFIED SOURCE CODE FILES
1577	Filenames=""
1578	svn status > tmp_mrun
1579	while read line
1580	do
1581	firstc=`echo $line \| cut -c1`
1582	if [[ $firstc = M \|\| $firstc = "?" ]]
1583	then
1584	Name=`echo "$line" \| cut -c8-`
1585	extension=`echo $Name \| cut -d. -f2`
1586	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1587	then
1588	Filenames="$Filenames "$Name
1589	fi
1590	fi
1591	done < tmp_mrun
1592
1593
1594	# COPY FILES TO SOURCES_FOR_RUN_...
1595	for dateiname in $Filenames
1596	do
1597	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1598	source_list=$source_list"$dateiname "
1599	done
1600
1601	cd - > /dev/null
1602
1603
1604	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1605	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1606	elif [[ "$source_list" != "" && $restart_run != true ]]
1607	then
1608
1609	cd $source_path
1610
1611	for filename in $source_list
1612	do
1613
1614	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1615	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1616	then
1617	printf "\n +++ source code file: $filename"
1618	printf "\n must not contain (\"/\") "
1619	locat=source; exit
1620	fi
1621
1622	if [[ ! -f $filename ]]
1623	then
1624	printf "\n +++ source code file: $filename"
1625	printf "\n does not exist"
1626	locat=source; exit
1627	else
1628	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1629	fi
1630
1631	done
1632
1633	cd - > /dev/null
1634
1635	fi
1636
1637
1638	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1639	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1640	if [[ $restart_run != true ]]
1641	then
1642
1643	if [[ ! -f "$source_path/$mainprog" ]]
1644	then
1645	printf "\n\n +++ main program: $mainprog"
1646	printf "\n does not exist in source directory"
1647	printf "\n \"$source_path\"\n"
1648	locat=source; exit
1649	else
1650	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1651	then
1652	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1653	source_list=${mainprog}" $source_list"
1654	fi
1655	fi
1656	fi
1657
1658
1659	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1660	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1661	if [[ "$restart_run" != true ]]
1662	then
1663	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1664	if [[ ! -f $makefile ]]
1665	then
1666	printf "\n +++ file \"$makefile\" does not exist"
1667	locat=make; exit
1668	else
1669	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1670	fi
1671	fi
1672
1673
1674	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1675	if [[ $restart_run != true && "$add_source_path" != "" ]]
1676	then
1677
1678	# DOES THE DIRECTORY EXIST?
1679	if [[ ! -d $add_source_path ]]
1680	then
1681	printf "\n\n *** INFORMATIVE: additional source code directory"
1682	printf "\n \"$add_source_path\" "
1683	printf "\n does not exist or is not a directory."
1684	printf "\n No source code will be used from this directory!\n"
1685	add_source_path=""
1686	if [[ $silent == false ]]
1687	then
1688	sleep 3
1689	fi
1690	else
1691
1692	cd $add_source_path
1693	found=false
1694
1695	Names=$(ls -1 *.f90 2>&1)
1696	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1697	Names=$(ls -1 *.F90 2>&1)
1698	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1699	Names=$(ls -1 *.F 2>&1)
1700	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1701	Names=$(ls -1 *.f 2>&1)
1702	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1703	Names=$(ls -1 *.c 2>&1)
1704	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1705
1706	cd - > /dev/null
1707	cd SOURCES_FOR_RUN_$fname
1708
1709	# COPY MAKEFILE IF EXISTING
1710	if [[ -f $add_source_path/Makefile ]]
1711	then
1712	printf "\n\n *** user Makefile from directory"
1713	printf "\n \"$add_source_path\" is used \n"
1714	if [[ $silent == false ]]
1715	then
1716	sleep 1
1717	fi
1718	cp $add_source_path/Makefile .
1719	fi
1720
1721	for dateiname in $AddFilenames
1722	do
1723	if [[ -f $dateiname ]]
1724	then
1725	printf "\n +++ source code file \"$dateiname\" found in additional"
1726	printf "\n source code directory \"$add_source_path\" "
1727	printf "\n but was also given with option \"-s\" which means that it should be taken"
1728	printf "\n from directory \"$source_path\"."
1729	locat=source; exit
1730	fi
1731
1732	cp $add_source_path/$dateiname .
1733	source_list="$source_list $dateiname"
1734
1735	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1736	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1737	then
1738	printf "\n\n +++ user file \"$dateiname\" "
1739	printf "\n is not listed in Makefile \n"
1740	locat=source; exit
1741	else
1742
1743	if [[ $found = false ]]
1744	then
1745	found=true
1746	printf "\n\n *** following user file(s) added to the"
1747	printf " files to be translated:\n "
1748	fi
1749	printf "$dateiname "
1750	if [[ $silent == false ]]
1751	then
1752	sleep 0.5
1753	fi
1754
1755	fi
1756	done
1757	[[ $found = true ]] && printf "\n"
1758	cd - > /dev/null
1759	fi
1760	fi
1761
1762
1763	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1764	# TO THE LIST OF FILES TO BE COMPILED
1765	if [[ $restart_run != true && -n $package_list ]]
1766	then
1767
1768	cd $source_path
1769
1770	for package in $package_list
1771	do
1772
1773	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1774
1775	# DETERMINE FILES BELONGING TO THE PACKAGE
1776	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1777	# THE NAME OF THE DIRECTORY
1778	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1779
1780
1781	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1782	# IF THEY ARE NOT ALREADY PART OF THE LIST
1783	for source_list_name in $package_source_list
1784	do
1785	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1786	then
1787
1788	# ONLY TAKE FILES WITH VALID SUFFIX
1789	ending=`echo $source_list_name \| cut -f2 -d.`
1790	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1791	then
1792	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1793	source_list="$source_list $source_list_name"
1794	fi
1795	fi
1796	done
1797	done
1798
1799	cd - > /dev/null
1800	fi
1801
1802	fi # do_compile=true
1803
1804
1805	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1806	# AND SET PRE-PROCESSOR DIRECTIVES
1807	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1808	then
1809
1810	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1811	if [[ $(echo $localhost \| cut -c1-3) = ibm && $localhost != ibmmuc* ]]
1812	then
1813	cpp_options="${cpp_options},-D__ibm=__ibm"
1814	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1815	then
1816	cpp_options="$cpp_options -D__nec"
1817	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1818	then
1819	cpp_options="$cpp_options -D__lc"
1820	else
1821	cpp_options="$cpp_options -D__$localhost"
1822	fi
1823
1824	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1825	if [[ $(echo $localhost \| cut -c1-3) = ibm && $localhost != ibmmuc ]]
1826	then
1827	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1828	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1829	else
1830	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1831	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1832	fi
1833
1834	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1835	if [[ -n $package_list ]]
1836	then
1837	for package in $package_list
1838	do
1839	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1840	then
1841	if [[ $package != "dvrp_graphics+1PE" ]]
1842	then
1843	cpp_options="${cpp_options},-D__$package=__$package"
1844	else
1845	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1846	export use_seperate_pe_for_dvrp_output=true
1847	fi
1848	else
1849	if [[ $package != "dvrp_graphics+1PE" ]]
1850	then
1851	cpp_options="$cpp_options -D__$package"
1852	else
1853	cpp_options="$cpp_options -D__dvrp_graphics"
1854	export use_seperate_pe_for_dvrp_output=true
1855	fi
1856	fi
1857	done
1858	fi
1859
1860	else
1861
1862
1863	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1864	if [[ $do_remote = false ]]
1865	then
1866	if [[ ! -f $executable ]]
1867	then
1868	printf "\n +++ executable file: $executable"
1869	printf "\n does not exist"
1870	locat=executable; exit
1871	fi
1872	fi
1873	fi
1874
1875
1876	# DETERMINE THE JOB MODE
1877	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1878	then
1879	if [[ "$LOADLBATCH" = yes ]]
1880	then
1881	batch_job=.TRUE.
1882	jobmo=BATCH
1883	else
1884	batch_job=.FALSE.
1885	jobmo=INTERACTIVE
1886	fi
1887	else
1888	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
1889	then
1890	batch_job=.TRUE.
1891	jobmo=BATCH
1892	else
1893	batch_job=.FALSE.
1894	jobmo=INTERACTIVE
1895	fi
1896	fi
1897
1898	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1899	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1900	then
1901	printf "\n +++ no interactive runs allowed on host \"$host\" "
1902	printf "\n please submit batch job using mrun option \"-b\" \n"
1903	locat=normal; exit
1904	fi
1905
1906
1907	# CHECK, IF USER DEFINED A COMPILER
1908	if [[ "$compiler_name" = "" ]]
1909	then
1910
1911	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1912	locat=compiler_name; exit
1913
1914	fi
1915
1916
1917	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1918
1919	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1920	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1921	then
1922	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1923	if [[ "$kennung" = "" ]]
1924	then
1925	kennung=$RANDOM
1926	fi
1927	else
1928	kennung=$RANDOM
1929	fi
1930
1931	if [[ "$tmp_user_catalog" = "" ]]
1932	then
1933	if [[ $localhost = ibmh ]]
1934	then
1935	tmp_user_catalog=$SCRATCH
1936	else
1937	tmp_user_catalog=/tmp
1938	fi
1939	fi
1940
1941	if [[ $localhost = ibmmuc* ]]
1942	then
1943	TEMPDIR=$tmp_user_catalog/${USER}.$kennung
1944	else
1945	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1946	fi
1947
1948	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1949	if [[ "$tmp_data_catalog" = "" ]]
1950	then
1951	tmp_data_catalog=/tmp/mrun_restart_data
1952	fi
1953
1954
1955	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1956	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1957	then
1958	eval fopts=\"$fopts\"
1959	eval lopts=\"$lopts\"
1960	fi
1961
1962
1963	# DETERMINE COMPILE- AND LINK-OPTIONS
1964	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1965	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1966	XOPT="-X $numprocs"
1967
1968
1969	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1970	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1971	done=false
1972	while [[ $done = false ]]
1973	do
1974	cputime=$cpumax
1975	if (( $cputime == 0 ))
1976	then
1977	if [[ $do_batch = true ]]
1978	then
1979	printf "\n +++ cpu-time is undefined"
1980	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1981	printf "\n >>> "
1982	read cputime 1>/dev/null 2>&1
1983	else
1984	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1985	fi
1986	else
1987	done=true
1988	fi
1989	cpumax=$cputime
1990	done
1991
1992	(( minuten = cputime / 60 ))
1993	(( sekunden = cputime - minuten * 60 ))
1994
1995
1996	# CHECK THE MEMORY DEMAND
1997	if [[ $do_batch = true ]]
1998	then
1999	done=false
2000	while [[ $done = false ]]
2001	do
2002	if (( memory == 0 ))
2003	then
2004	printf "\n +++ memory demand is undefined"
2005	printf "\n >>> Please type memory in MByte per process as INTEGER:"
2006	printf "\n >>> "
2007	read memory 1>/dev/null 2>&1
2008	else
2009	done=true
2010	fi
2011	done
2012	fi
2013
2014
2015	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
2016	if [[ $do_remote = true && -z $remote_username ]]
2017	then
2018	while [[ -z $remote_username ]]
2019	do
2020	printf "\n +++ username on remote host \"$host\" is undefined"
2021	printf "\n >>> Please type username:"
2022	printf "\n >>> "
2023	read remote_username
2024	done
2025	mc="$mc -u$remote_username"
2026	fi
2027
2028	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
2029	if [[ "$login_init_cmd" != "" ]]
2030	then
2031	export init_cmds="${login_init_cmd};"
2032	fi
2033
2034
2035	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
2036	if [[ "$modules" != "" ]]
2037	then
2038	if [[ $host = lctit ]]
2039	then
2040	export module_calls=". $modules"
2041	else
2042	export module_calls="module load ${modules};"
2043	fi
2044	fi
2045
2046	# OUTPUT OF THE MRUN-HEADER
2047	calltime=$(date)
2048	printf "\n"
2049	printf "#------------------------------------------------------------------------# \n"
2050	printf "\| %-35s%35s \| \n" "$version" "$calltime"
2051	printf "\| \| \n"
2052	spalte1="called on:"; spalte2=$localhost_realname
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054	if [[ $do_remote = true ]]
2055	then
2056	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2057	else
2058	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2059	fi
2060	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2061	if [[ -n $numprocs ]]
2062	then
2063	if [[ $run_coupled_model = false ]]
2064	then
2065	spalte1="number of PEs:"; spalte2=$numprocs
2066	else
2067	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2068	fi
2069	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2070	fi
2071	if [[ -n $tasks_per_node ]]
2072	then
2073	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2074	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2075	if (( remaining_pes > 0 ))
2076	then
2077	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2078	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2079	fi
2080	fi
2081	if [[ $maximum_parallel_io_streams != $numprocs ]]
2082	then
2083	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2084	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2085	fi
2086	if [[ $use_openmp = true ]]
2087	then
2088	spalte1="threads per task:"; spalte2="$threads_per_task"
2089	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2090	fi
2091	printf "\| \| \n"
2092	if [[ $do_compile = true ]]
2093	then
2094	if [[ "$mopts" != "" ]]
2095	then
2096	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2097	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2098	zeile=$(echo "$mopts" \| cut -c46-)
2099	while [[ "$zeile" != "" ]]
2100	do
2101	spalte1=""
2102	spalte2=$(echo "$zeile" \| cut -c-45)
2103	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2104	zeile=$(echo "$zeile" \| cut -c46-)
2105	done
2106	fi
2107
2108	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2109	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2110	zeile=$(echo "$cpp_options" \| cut -c46-)
2111	while [[ "$zeile" != "" ]]
2112	do
2113	spalte1=""
2114	spalte2=$(echo "$zeile" \| cut -c-45)
2115	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2116	zeile=$(echo "$zeile" \| cut -c46-)
2117	done
2118
2119	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2120	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2121	zeile=$(echo "$fopts" \| cut -c46-)
2122	while [[ "$zeile" != "" ]]
2123	do
2124	spalte1=""
2125	spalte2=$(echo "$zeile" \| cut -c-45)
2126	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2127	zeile=$(echo "$zeile" \| cut -c46-)
2128	done
2129
2130	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2131	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2132	zeile=$(echo "$lopts" \| cut -c46-)
2133	while [[ "$zeile" != "" ]]
2134	do
2135	spalte1=""
2136	spalte2=$(echo "$zeile" \| cut -c-45)
2137	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2138	zeile=$(echo "$zeile" \| cut -c46-)
2139	done
2140
2141	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2142	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2143	zeile=$(echo "$modules" \| cut -c46-)
2144	while [[ "$zeile" != "" ]]
2145	do
2146	spalte1=""
2147	spalte2=$(echo "$zeile" \| cut -c-45)
2148	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2149	zeile=$(echo "$zeile" \| cut -c46-)
2150	done
2151
2152	spalte1="main program:"; spalte2=$mainprog
2153	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2154	else
2155	spalte1=executable:; spalte2=$executable
2156	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2157	fi
2158	printf "\| \| \n"
2159	spalte1="base name of files:"; spalte2=$fname
2160	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2161	if [[ $fname != $afname ]]
2162	then
2163	spalte1="base name of input files:"; spalte2=$afname
2164	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2165	fi
2166	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2167	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2168	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2169	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2170
2171	if [[ "$ocean_file_appendix" = true ]]
2172	then
2173	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2174	fi
2175
2176	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2177	then
2178	spalte1="memory demand / PE":; spalte2="$memory MB"
2179	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2180	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2181	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2182	fi
2183
2184	if [[ $do_compile = true ]]
2185	then
2186	printf "\| \| \n"
2187	printf "\| Files to be compiled: \| \n"
2188	zeile=$source_list
2189	while [[ "$zeile" != "" ]]
2190	do
2191	linestart=$(echo $zeile \| cut -c-70)
2192	printf "\| %-70s \| \n" "$linestart"
2193	zeile=$(echo "$zeile" \| cut -c71-)
2194	done
2195	fi
2196	printf "#------------------------------------------------------------------------#"
2197
2198
2199
2200	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2201	if [[ $do_trace = true ]]
2202	then
2203	(( i = 0 ))
2204	while (( i < iin ))
2205	do
2206	(( i = i + 1 ))
2207	if (( i == 1 ))
2208	then
2209	printf "\n\n >>> INPUT-file assignments:\n"
2210	fi
2211	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2212	done
2213	(( i = 0 ))
2214	while (( i < iout ))
2215	do
2216	(( i = i + 1 ))
2217	if (( i == 1 ))
2218	then
2219	printf "\n\n >>> OUTPUT-file assignments:\n"
2220	fi
2221	printf "\n ${localout[$i]} : ${pathout[$i]}"
2222	done
2223	(( i = 0 ))
2224	while (( i < iic ))
2225	do
2226	(( i = i + 1 ))
2227	if (( i == 1 ))
2228	then
2229	printf "\n\n >>> INPUT-commands:\n"
2230	fi
2231	printf "\n ${in_command[$i]}"
2232	done
2233	(( i = 0 ))
2234	while (( i < ioc ))
2235	do
2236	(( i = i + 1 ))
2237	if (( i == 1 ))
2238	then
2239	printf "\n\n >>> OUTPUT-commands:\n"
2240	fi
2241	printf "\n ${out_command[$i]}"
2242	done
2243	fi
2244
2245	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2246	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2247	then
2248	antwort=dummy
2249	printf "\n\n"
2250	printf " >>> everything o.k. (y/n) ? "
2251	while read antwort
2252	do
2253	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2254	then
2255	printf " >>> everything o.k. (y/n) ? "
2256	else
2257	break
2258	fi
2259	done
2260	if [[ $antwort = n \|\| $antwort = N ]]
2261	then
2262	locat=user_abort; (( iec = 0 )); exit
2263	fi
2264	if [[ $do_batch = true ]]
2265	then
2266	printf " >>> batch-job will be created and submitted"
2267	else
2268	printf " >>> MRUN will now continue to execute on this machine"
2269	fi
2270	fi
2271
2272
2273	# DETERMINE PATH FOR MAKE DEPOSITORY
2274	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2275	then
2276
2277	line=""
2278	grep "%depository_path" $config_file > tmp_mrun
2279	while read line
2280	do
2281	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2282	then
2283	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2284	then
2285	global_depository_path=`echo $line \| cut -d" " -s -f2`
2286	fi
2287	fi
2288	done < tmp_mrun
2289
2290	line=""
2291	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2292	while read line
2293	do
2294	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2295	then
2296	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2297	then
2298	local_depository_path=`echo $line \| cut -d" " -s -f2`
2299	fi
2300	fi
2301	done < tmp_mrun
2302
2303	if [[ "$local_depository_path" = "" ]]
2304	then
2305	if [[ "$global_depository_path" != "" ]]
2306	then
2307	local_depository_path=$global_depository_path
2308	else
2309	printf "\n\n +++ no depository path found in configuration file"
2310	printf "\n for local host \"$localhost\" "
2311	printf "\n please set \"\%depository_path\" in configuration file\n"
2312	locat=config_file; exit
2313	fi
2314	fi
2315	eval local_depository_path=$local_depository_path
2316	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2317	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2318
2319
2320	basename=`echo $mainprog \| cut -f1 -d"."`
2321	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2322	if [[ ! -f $make_depository ]]
2323	then
2324	printf "\n"
2325	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2326	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2327	fi
2328
2329	fi
2330
2331
2332	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2333	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2334	if [[ $do_batch = false ]]
2335	then
2336
2337
2338	# CREATE THE TEMPORARY WORKING DIRECTORY
2339	mkdir -p $TEMPDIR
2340	chmod go+rx $TEMPDIR
2341	tmpcreate=true
2342
2343
2344	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2345	# INTO THE TEMPORARY WORKING DIRECTORY
2346	if [[ $do_compile = true ]]
2347	then
2348
2349	TEMPDIR_COMPILE=$TEMPDIR
2350
2351	cp $make_depository $TEMPDIR_COMPILE
2352	cd $TEMPDIR_COMPILE
2353	tar -xf $make_depository > /dev/null 2>&1
2354	cd - > /dev/null
2355
2356	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2357	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2358	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2359	then
2360	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2361	else
2362	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2363	fi
2364
2365	else
2366
2367	cp $executable ${TEMPDIR}/a.out
2368
2369	fi
2370
2371
2372	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2373	cd $TEMPDIR
2374	printf "\n *** changed to temporary directory: $TEMPDIR"
2375
2376
2377	# IF REQUIRED, START WITH COMPILING
2378	if [[ $do_compile = true ]]
2379	then
2380
2381
2382	if [[ -f a.out ]]
2383	then
2384
2385	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2386	printf "\n\n\n *** executable a.out found"
2387	printf "\n no compilation required \n"
2388
2389	else
2390
2391	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2392	printf "\n\n\n *** compilation starts \n$dashes\n"
2393	printf " *** compilation with make using following options:\n"
2394	printf " make depository: $make_depository"
2395	if [[ "$mopts" != "" ]]
2396	then
2397	printf " make options: $mopts\n"
2398	fi
2399	printf " compilername: $compiler_name\n"
2400	printf " compiler options: $fopts\n"
2401	printf " preprocessor directives: $cpp_options \n"
2402	printf " linker options: $lopts \n"
2403	if [[ "$modules" != "" ]]
2404	then
2405	printf " modules to be load: $modules \n"
2406	fi
2407	printf " source code files: $source_list \n"
2408
2409	if [[ $localhost = ibmh ]]
2410	then
2411	printf " compiler is called via ssh on \"plogin1\" \n"
2412	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\" "
2413	[[ ! -f a.out ]] && compile_error=true
2414	continue # STATUS=1, IF a.out EXISTS
2415	elif [[ $localhost = lcocean ]]
2416	then
2417	printf " compiler is called via ssh on \"ocean\" \n"
2418	echo $PWD
2419	ssh $SSH_PORTOPT ocean -l $usern "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
2420	[[ ! -f a.out ]] && compile_error=true
2421	continue # STATUS=1, IF a.out EXISTS
2422	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2423	then
2424	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2425	elif [[ $localhost = lceddy ]]
2426	then
2427	which mpifc
2428	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2429	elif [[ $localhost = lcgeohu ]]
2430	then
2431	printf " compiler is called via ssh on \"cirrus\" \n"
2432	ssh $SSH_PORTOPT cirrus.geo.hu-berlin.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=\"$lopts\" "
2433	# this check did not work. Although a.out exists, it sets compile_error to true!
2434	# [[ ! -f a.out ]] && compile_error=true
2435	continue # STATUS=1, IF a.out EXISTS
2436	else
2437	[[ "$init_cmds" != "" ]] && eval $init_cmds
2438	[[ "$module_calls" != "" ]] && eval $module_calls
2439	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2440	fi
2441
2442	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2443	then
2444	printf "\n +++ error occured while compiling or linking"
2445	locat=compile
2446
2447	exit
2448	else
2449	printf "$dashes\n *** compilation finished \n"
2450	fi
2451
2452	fi
2453
2454	fi
2455
2456
2457	# PROVIDE THE INPUT FILES
2458	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2459	(( i = 0 ))
2460	while (( i < iin ))
2461	do
2462	(( i = i + 1 ))
2463	if (( i == 1 ))
2464	then
2465	printf "\n\n *** providing INPUT-files:\n$dashes"
2466	fi
2467
2468
2469	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2470	if [[ "${transin[$i]}" = unavailable ]]
2471	then
2472	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2473	then
2474	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2475	printf "\n is not available!"
2476	else
2477	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2478	printf "\n is not available!"
2479	fi
2480	continue
2481	fi
2482
2483	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2484	files_for_pes=false; datentyp=file
2485	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2486	then
2487	files_for_pes=true; datentyp=files
2488	actionin[$i]=""
2489	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2490	then
2491	actionin[$i]=""
2492	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
2493	then
2494	files_for_pes=true; datentyp=files
2495	actionin[$i]="ln"
2496	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
2497	then
2498	actionin[$i]="ln"
2499	fi
2500
2501	if [[ $files_for_pes = true ]]
2502	then
2503	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2504	else
2505	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2506	fi
2507
2508	# INPUT-FILES TO BE LINKED
2509	if [[ "${actionin[$i]}" = ln ]]
2510	then
2511
2512	printf "\n $datentyp will be linked"
2513	if [[ $files_for_pes = false ]]
2514	then
2515	if [[ -f "${absnamein[$i]}" ]]
2516	then
2517	ln ${absnamein[$i]} ${localin[$i]}
2518	got_tmp[$i]=true
2519	fi
2520	else
2521	if [[ -d "${absnamein[$i]}" ]]
2522	then
2523	mkdir ${localin[$i]}
2524	cd ${absnamein[$i]}
2525	for file in $(ls *)
2526	do
2527	ln $file $TEMPDIR/${localin[$i]}
2528	done >\|/dev/null 2>&1
2529	cd $TEMPDIR
2530	fi
2531
2532	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2533	if [[ ! -f "${localin[$i]}/_000000" ]]
2534	then
2535	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2536	cp -r ${absnamein[$i]}/* ${localin[$i]}
2537	fi
2538
2539	got_tmp[$i]=true
2540	fi
2541	fi
2542
2543	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2544	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2545	then
2546
2547	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2548	then
2549
2550	# FILE COPIES ARE PROVIDED FOR ALL CORES
2551	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2552	printf "\n file will be provided for $numprocs processors"
2553	mkdir ${localin[$i]}
2554	ival=$numprocs
2555	(( ii = 0 ))
2556	while (( ii <= ival-1 ))
2557	do
2558	if (( ii < 10 ))
2559	then
2560	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2561	elif (( ii < 100 ))
2562	then
2563	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2564	elif (( ii < 1000 ))
2565	then
2566	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2567	else
2568	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2569	fi
2570	(( ii = ii + 1 ))
2571	done
2572
2573	else
2574
2575	if [[ $files_for_pes = true ]]
2576	then
2577
2578	# PROVIDE FILES FOR EACH CORE
2579	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2580	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2581	printf "\n providing $numprocs files for the respective processors"
2582	mkdir ${localin[$i]}
2583	if [[ $link_local_input = true ]]
2584	then
2585	printf " files will be linked\n"
2586	cd ${absnamein[$i]}
2587	for file in $(ls *)
2588	do
2589	ln -f $file ${localin[$i]}
2590	done
2591	cd $TEMPDIR
2592	fi
2593
2594	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2595	if [[ ! -f "${localin[$i]}/_000000" ]]
2596	then
2597	if [[ $link_local_input = true ]]
2598	then
2599	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2600	fi
2601	cp -r ${absnamein[$i]}/* ${localin[$i]}
2602	fi
2603
2604	else
2605
2606	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2607	if [[ $link_local_input = true ]]
2608	then
2609	printf " file will be linked\n"
2610	ln -f ${absnamein[$i]} ${localin[$i]}
2611	fi
2612	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2613	if [[ ! -f "${localin[$i]}" ]]
2614	then
2615	if [[ $link_local_input = true ]]
2616	then
2617	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2618	fi
2619	cp ${absnamein[$i]} ${localin[$i]}
2620	fi
2621	fi
2622	fi
2623	fi
2624
2625	done
2626	if (( i != 0 ))
2627	then
2628	printf "\n$dashes\n *** all INPUT-files provided \n"
2629	fi
2630
2631
2632	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2633	(( i = 0 ))
2634	while (( i < iic ))
2635	do
2636	(( i = i + 1 ))
2637	if (( i == 1 ))
2638	then
2639	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2640	fi
2641	printf "\n >>> ${in_command[$i]}"
2642	eval ${in_command[$i]}
2643	if (( i == iic ))
2644	then
2645	printf "\n$dashes\n"
2646	fi
2647	done
2648
2649
2650	# SET THE REMAINING CPU-TIME
2651	cpurest=${cpumax}.
2652
2653
2654	# START DVR STREAMING SERVER
2655	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2656	then
2657	if [[ "$dvr_server" != "" ]]
2658	then
2659
2660	printf "\n\n *** preparing the dvr streaming server configuration file"
2661
2662	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2663	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2664	if [[ "$running_dvrserver_id" != "" ]]
2665	then
2666
2667	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2668	printf "\n This server is used instead starting a new one!"
2669	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2670
2671	else
2672
2673	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2674	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2675	then
2676	cp ${PALM_BIN}/.dvrserver.config .
2677
2678	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2679	user_id=`id -u`
2680	group_id=`id -g`
2681
2682	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2683	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2684	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2685	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2686	mv .dvrserver.3 .dvrserver.config
2687	rm .dvrserver.1 .dvrserver.2
2688
2689	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2690	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2691	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2692	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2693	local_dvrserver_running=.TRUE.
2694	else
2695	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2696	printf "\n \"$PALM_BIN\" "
2697	locat=dvr
2698	exit
2699	fi
2700
2701	fi
2702
2703	else
2704	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2705	fi
2706	fi
2707
2708
2709	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2710	# (FILE ENVPAR WILL BE READ BY PALM)
2711	cat > ENVPAR << EOF
2712	&envpar run_identifier = '$fname', host = '$localhost',
2713	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2714	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2715	maximum_cpu_time_allowed = ${cpumax}.,
2716	revision = '$global_revision',
2717	local_dvrserver_running = $local_dvrserver_running,
2718	batch_job = $batch_job /
2719
2720	EOF
2721
2722
2723	# STARTING THE EXECUTABLE
2724	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2725	PATH=$PATH:$TEMPDIR
2726
2727
2728	if [[ $execute_command != "none" ]]
2729	then
2730
2731	printf "\n +++ branch still not realized"
2732	locat=execution
2733	exit
2734
2735	else
2736
2737	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2738	if [[ "$mpi_debug" = true ]]
2739	then
2740	export MPI_CHECK_ARGS=1
2741	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2742	fi
2743
2744	if [[ "$totalview" = true ]]
2745	then
2746	printf "\n *** totalview debugger will be used"
2747	tv_opt="-tv"
2748	else
2749	tv_opt=""
2750	fi
2751
2752	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2753	then
2754
2755	#Interactive ALLINEA DEBUG seesion
2756	if [[ "$ENVIRONMENT" != BATCH ]]
2757	then
2758	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2759	then
2760	if [[ "$allinea" = true ]]
2761	then
2762	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2763
2764	ddt aprun -n $ii -N $tasks_per_node a.out
2765	wait
2766	fi
2767	fi
2768	fi
2769
2770	if [[ $localhost = ibmh ]]
2771	then
2772
2773	# SETUP THE IBM MPI ENVIRONMENT
2774	export MP_SHARED_MEMORY=yes
2775	export AIXTHREADS_SCOPE=S
2776	export OMP_NUM_THREADS=$threads_per_task
2777	export AUTHSTATE=files
2778	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2779
2780	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2781	export MP_ADAPTER_USE=shared
2782	export MP_CPU_USE=multiple
2783	export MP_TIMEOUT=1200
2784
2785	unset MP_TASK_AFFINITY
2786
2787	if [[ "$LOADLBATCH" = yes ]]
2788	then
2789	totalview poe a.out
2790	else
2791	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2792	export TVDSVRLAUNCHCMD=ssh
2793	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2794	fi
2795
2796	fi # END DEBUG MODE
2797
2798	else
2799
2800	# NORMAL EXECUTION
2801	if [[ -n $numprocs ]]
2802	then
2803
2804	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2805	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2806	then
2807
2808	# SETUP THE IBM MPI ENVIRONMENT
2809	if [[ $host != ibmh && $host != ibmkisti ]]
2810	then
2811	export MP_SHARED_MEMORY=yes
2812	export AIXTHREAD_SCOPE=S
2813	export OMP_NUM_THREADS=$threads_per_task
2814	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2815	export AUTHSTATE=files
2816	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2817	# export MP_PRINTENV=yes
2818
2819	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2820	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2821	export MP_WAIT_MODE=poll
2822	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2823	fi
2824
2825	if [[ $host = ibmkisti ]]
2826	then
2827	export LANG=en_US
2828	export MP_SHARED_MEMORY=yes
2829	if [[ $threads_per_task = 1 ]]
2830	then
2831	export MP_SINGLE_THREAD=yes
2832	export MEMORY_AFFINITY=MCM
2833	else
2834	export OMP_NUM_THREADS=$threads_per_task
2835	fi
2836	fi
2837
2838	if [[ "$LOADLBATCH" = yes ]]
2839	then
2840	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2841	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2842	then
2843	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2844	elif [[ $localhost = ibmmuc* ]]
2845	then
2846	ulimit -c unlimited # only for debgingg
2847	echo $MP_NODES > ~/job_queue/hostfile.$kennung
2848	echo $MP_PROCS >> ~/job_queue/hostfile.$kennung
2849	cat $LOADL_HOSTFILE >> ~/job_queue/hostfile.$kennung
2850	export MP_NODES=$nodes
2851	export MP_PROCS=$numprocs
2852	# export MPI_SINGLE_THREAD=no # LRZ NetCDF
2853	# export MP_TASKS_PER_NODE=$tasks_per_node
2854	echo "Resource Info: "
2855	echo "numprocs: " $numprocs " MP_PROCS " $MP_PROCS
2856	echo "nodes: " $nodes " MP_NODES " $MP_NODES
2857	echo "tasks_per_node: " $tasks_per_node
2858	echo "threads_per_task: " $threads_per_task
2859	export OMP_NUM_THREADS=1
2860	source /lrz/sys/share/modules/init/bash
2861	module li
2862	echo "runfile_atmos"
2863
2864	if [[ $run_vnested_model = true ]]
2865	then
2866
2867	printf "\n Nested run ($numprocs_crse Coarse, $numprocs_fine Fine)"
2868	printf "\n using $nested_mode nesting"
2869	printf "\n\n"
2870
2871	echo "$vnested_mode $numprocs_crse $numprocs_fine" > runfile_atmos
2872
2873	poe ./a.out < runfile_atmos
2874	# mpiexec -n $numprocs ./a.out < runfile_atmos
2875	else
2876	echo "precursor_atmos" > runfile_atmos
2877	poe ./a.out -proc $numprocs -nodes $nodes < runfile_atmos
2878	# mpiexec -n $numprocs ./a.out < runfile_atmos
2879
2880	fi
2881	else
2882	if [[ $run_coupled_model = false ]]
2883	then
2884	if [[ "$ocean_file_appendix" = true ]]
2885	then
2886	echo "precursor_ocean" > runfile_atmos
2887	else
2888	echo "precursor_atmos" > runfile_atmos
2889	fi
2890	else
2891	(( iia = $numprocs_atmos / $threads_per_task ))
2892	(( iio = $numprocs_ocean / $threads_per_task ))
2893	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2894	printf "\n\n"
2895	echo "coupled_run $iia $iio" > runfile_atmos
2896	fi
2897	poe ./a.out < runfile_atmos
2898	fi
2899	else
2900	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2901	then
2902	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2903	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2904	then
2905	if [[ -f $hostfile ]]
2906	then
2907	cp $hostfile hostfile
2908	else
2909	(( ii = 1 ))
2910	while (( ii <= $numprocs ))
2911	do
2912	echo $localhost_realname >> hostfile
2913	(( ii = ii + 1 ))
2914	done
2915	fi
2916	export MP_HOSTFILE=hostfile
2917	if [[ $run_coupled_model = false ]]
2918	then
2919	if [[ "$ocean_file_appendix" = true ]]
2920	then
2921	echo "precursor_ocean" > runfile_atmos
2922	else
2923	echo "precursor_atmos" > runfile_atmos
2924	fi
2925	else
2926	(( iia = $numprocs_atmos / $threads_per_task ))
2927	(( iio = $numprocs_ocean / $threads_per_task ))
2928	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2929	printf "\n\n"
2930	echo "coupled_run $iia $iio" > runfile_atmos
2931	fi
2932
2933	poe ./a.out -procs $numprocs < runfile_atmos
2934
2935	else
2936	if [[ "$host_file" = "" ]]
2937	then
2938	printf "\n +++ no hostfile given in configuration file"
2939	locat=config_file
2940	exit
2941	else
2942	eval host_file=$host_file
2943	fi
2944	export MP_HOSTFILE=$host_file
2945	poe a.out -procs $numprocs -tasks_per_node $numprocs
2946	fi
2947	fi
2948
2949	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
2950	then
2951
2952	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
2953	# DOES NOT EXIST
2954	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
2955	then
2956	if [[ -f $hostfile ]]
2957	then
2958	cp $hostfile hostfile
2959	(( ii = $numprocs / $threads_per_task ))
2960	[[ $ii = 0 ]] && (( ii = 1 ))
2961	else
2962	(( ii = 1 ))
2963	while (( ii <= $numprocs / $threads_per_task ))
2964	do
2965	echo $localhost_realname >> hostfile
2966	(( ii = ii + 1 ))
2967	done
2968	if (( $numprocs / $threads_per_task == 0 ))
2969	then
2970	echo $localhost_realname >> hostfile
2971	fi
2972	fi
2973	eval zeile=\"`head -n $ii hostfile`\"
2974	printf "\n *** running on: $zeile"
2975	fi
2976
2977	(( ii = $numprocs / $threads_per_task ))
2978	[[ $ii = 0 ]] && (( ii = 1 ))
2979	export OMP_NUM_THREADS=$threads_per_task
2980
2981	if [[ $threads_per_task != 1 ]]
2982	then
2983	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
2984	# MAY ABORT
2985	ulimit -s unlimited
2986	printf "\n threads per task: $threads_per_task stacksize: unlimited"
2987	fi
2988	if [[ $run_coupled_model = false && $run_vnested_model = false ]]
2989	then
2990	if [[ "$ocean_file_appendix" = true ]]
2991	then
2992	echo "precursor_ocean" > runfile_atmos
2993	else
2994	echo "precursor_atmos" > runfile_atmos
2995	fi
2996	printf "\n\n"
2997
2998	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2999	then
3000	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
3001	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3002	elif [[ $host = lcbullhh ]]
3003	then
3004	export OMPI_MCA_pml=cm
3005	export OMPI_MCA_mtl=mxm
3006	export OMPI_MCA_coll=^ghc
3007	export OMPI_MCA_mtl_mxm_np=0
3008	export MXM_RDMA_PORTS=mlx5_0:1
3009	export MXM_LOG_LEVEL=ERROR
3010	export OMP_NUM_THREADS=$threads_per_task
3011	export KMP_AFFINITY=verbose,granularity=core,compact,1
3012	export KMP_STACKSIZE=64m
3013
3014	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
3015
3016	elif [[ $host = lccrayf ]]
3017	then
3018	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
3019	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
3020	then
3021	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3022	elif [[ $host = lceddy ]]
3023	then
3024	echo $ii
3025	echo $tasks_per_node
3026	echo $nodes
3027	mpirun -n $ii a.out < runfile_atmos
3028	elif [[ $host = lcgeohu ]]
3029	then
3030	srun -n $ii a.out < runfile_atmos
3031	elif [[ $host = lcocean ]]
3032	then
3033	mpirun a.out $ROPTS < runfile_atmos
3034	elif [[ $host = lcsb ]]
3035	then
3036	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
3037	elif [[ $host = lclrz \|\| $host = lcbwuni ]]
3038	then
3039	mpiexec -n $ii a.out < runfile_atmos $ROPTeS
3040	elif [[ $host = lckea* ]]
3041	then
3042	srun -n $ii a.out < runfile_atmos $ROPTeS
3043	elif [[ $host = lckiaps ]]
3044	then
3045	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
3046	elif [[ $host = lckyu* ]]
3047	then
3048	mpiexec -n $ii --stdin runfile_atmos ./a.out
3049	else
3050	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3051	fi
3052
3053	elif [[ $run_coupled_model = true ]]
3054	then
3055	# COUPLED RUN
3056	(( iia = $numprocs_atmos / $threads_per_task ))
3057	(( iio = $numprocs_ocean / $threads_per_task ))
3058	printf "\n coupled run ($iia atmosphere, $iio ocean)"
3059	printf "\n\n"
3060
3061	echo "coupled_run $iia $iio" > runfile_atmos
3062
3063	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3064	then
3065
3066	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3067
3068	elif [[ $host = lck \|\| $host = lckordi ]]
3069	then
3070
3071	mpiexec -n $ii ./a.out < runfile_atmos &
3072
3073	elif [[ $host = lckyu* ]]
3074	then
3075
3076	mpiexec -n $ii --stdin runfile_atmos ./a.out
3077
3078	elif [[ $host = lcmuk ]]
3079	then
3080
3081	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3082
3083	fi
3084	wait
3085
3086
3087	elif [[ $run_vnested_model = true ]]
3088	then
3089	printf "\n Vertical Nested run ($numprocs_crse Coarse, $numprocs_fine Fine)"
3090	printf "\n using $vnested_mode vnesting"
3091	printf "\n\n"
3092
3093	echo "$vnested_mode $numprocs_crse $numprocs_fine" > runfile_atmos
3094
3095	if [[ $host = lcbwuni \|\| $host = lclrz* ]]
3096	then
3097	mpiexec -n $ii a.out < runfile_atmos $ROPTeS
3098	elif [[ $host = lckea* ]]
3099	then
3100	srun -n $ii a.out < runfile_atmos $ROPTeS
3101	else
3102	mpirun -np $numprocs ./a.out $ROPTS < runfile_atmos
3103	fi
3104	wait
3105	fi
3106
3107	elif [[ $host = lckyoto ]]
3108	then
3109	set -xv
3110	export P4_RSHCOMMAND=plesh
3111	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3112	if [[ "$ENVIRONMENT" = BATCH ]]
3113	then
3114	if [[ "$cond2" = fujitsu ]]
3115	then
3116	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3117	elif [[ "cond2" = pgi ]]
3118	then
3119	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3120	else
3121	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3122	fi
3123	else
3124	if [[ "$cond2" = "" ]]
3125	then
3126	mpiruni_rsh -np $numprocs ./a.out # for intel
3127	else
3128	mpirun -np $numprocs ./a.out
3129	fi
3130	fi
3131	set +xv
3132
3133	elif [[ $host = lctit ]]
3134	then
3135	export OMP_NUM_THREADS=$threads_per_task
3136	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3137	if [[ "$threads_per_task" != 1 ]]
3138	then
3139	export MV2_ENABLE_AFFINITY=0
3140	fi
3141	echo "----- PBS_NODEFILE content:"
3142	cat $PBS_NODEFILE
3143	echo "-----"
3144	(( ii = $numprocs / $threads_per_task ))
3145	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3146	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3147
3148	else
3149	mpprun -n $numprocs a.out
3150	fi
3151	else
3152	a.out
3153	fi
3154
3155	fi # end normal (non-debug) execution
3156
3157	fi # end explicit execute_command or host-specific execute actions
3158
3159	if [[ $? != 0 ]]
3160	then
3161
3162	# ABORT IN CASE OF RUNTIME ERRORS
3163	printf "\n +++ runtime error occured"
3164	locat=execution
3165	exit
3166
3167	else
3168
3169	printf "\n$dashes\n *** execution finished \n"
3170
3171	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3172	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3173	if [[ "$dvrserver_id" != "" ]]
3174	then
3175	kill $dvrserver_id
3176	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3177
3178	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3179	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3180	if [[ -d DATA_DVR ]]
3181	then
3182
3183	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3184	# DIRECTORY
3185	cp .dvrserver.config DATA_DVR
3186
3187	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3188	# SEQUENCE MODE DATA TOO)
3189	process_dvr_output -d DATA_DVR -f $fname -s
3190
3191	else
3192
3193	# PROCESS THE LOCAL OUTPUT
3194	process_dvr_output -l -d DATA_DVR -f $fname
3195
3196	fi
3197
3198	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3199	then
3200
3201	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3202	process_dvr_output -l -d DATA_DVR -f $fname
3203
3204	fi
3205	fi
3206
3207
3208
3209	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3210	# BY EACH CORE INTO ONE FILE
3211	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3212	then
3213	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3214	printf "\n 2d- and/or 3d-data may be incomplete!"
3215	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3216	elif [[ "$combine_plot_fields" == true ]]
3217	then
3218	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3219	then
3220	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3221	aprun -n 1 -N 1 combine_plot_fields${block}.x
3222	else
3223	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3224	combine_plot_fields${block}.x
3225	fi
3226	else
3227
3228	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3229	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3230	# ??? koennen wir das streichen ???
3231	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3232	fi
3233
3234
3235
3236	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3237	(( i = 0 ))
3238	while (( i < ioc ))
3239	do
3240	(( i = i + 1 ))
3241	if (( i == 1 ))
3242	then
3243	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3244	fi
3245	printf "\n >>> ${out_command[$i]}"
3246	eval ${out_command[$i]}
3247	if (( i == ioc ))
3248	then
3249	printf "\n$dashes\n"
3250	fi
3251	done
3252
3253
3254	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3255	if [[ $do_trace = true ]]
3256	then
3257	printf "\n\n"
3258	ls -al
3259	fi
3260
3261
3262	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3263	(( i = 0 ))
3264	while (( i < iout ))
3265	do
3266	(( i = i + 1 ))
3267	if (( i == 1 ))
3268	then
3269	printf "\n\n *** saving OUTPUT-files:"
3270
3271	# GET RUN NUMBER ASSIGNED BY PALM
3272	if [[ -f RUN_NUMBER ]]
3273	then
3274	read run_number < RUN_NUMBER
3275	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
3276	usecycle_option="-U $run_number"
3277	else
3278	run_number=0
3279	usecycle_option=""
3280	fi
3281	printf "\n$dashes"
3282	fi
3283
3284	# ADD CYCLE NUMBER TO FILENAME
3285	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
3286	then
3287
3288	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
3289	if [[ "${actionout[$i]}" != "a" ]]
3290	then
3291	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
3292	# WITH AN EXISTING CYCLE NUMBER
3293	if (( run_number >= cycnum[$i] ))
3294	then
3295	(( cycnum[$i] = run_number ))
3296	else
3297	if (( run_number > 0 ))
3298	then
3299	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
3300	fi
3301	fi
3302	fi
3303	if (( cycnum[$i] > 0 ))
3304	then
3305	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
3306	fi
3307	fi
3308
3309	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3310	files_for_pes=false; filetyp=file
3311	link_local_output=false
3312	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3313	then
3314	files_for_pes=true; filetyp=directory
3315	actionout[$i]=""
3316	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3317	then
3318	actionout[$i]=""
3319	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
3320	then
3321	files_for_pes=true; filetyp=directory
3322	link_local_output=true
3323	actionout[$i]=""
3324	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
3325	then
3326	link_local_output
3327	actionout[$i]=""
3328	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3329	then
3330	files_for_pes=true; filetyp=directory
3331	actionout[$i]="tr"
3332	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3333	then
3334	actionout[$i]="tr"
3335	fi
3336
3337	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3338	then
3339	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3340	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3341	then
3342	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3343	else
3344
3345
3346	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3347	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3348	if [[ "${actionout[$i]}" = tr ]]
3349	then
3350	if [[ $localhost != $fromhost ]]
3351	then
3352	if [[ $files_for_pes = false ]]
3353	then
3354	cps=""
3355	cst=""
3356	else
3357	cps=-c
3358	cst="/"
3359	fi
3360
3361	transfer_failed=false
3362	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3363	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3364	if [[ $localhost = lccrayb ]]
3365	then
3366	ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3367	elif [[ $localhost = lccrayh ]]
3368	then
3369	ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3370	elif [[ $localhost = lcbullhh ]]
3371	then
3372	ssh $usern@mlogin101 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3373	elif [[ $localhost = lcxe6 ]]
3374	then
3375	ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3376	else
3377	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3378	fi
3379	[[ $? != 0 ]] && transfer_failed=true
3380
3381	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3382	if [[ $transfer_failed = true ]]
3383	then
3384	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3385	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3386
3387	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3388	eval local_catalog=${pathout[$i]}
3389	if [[ ! -d $local_catalog ]]
3390	then
3391	printf " *** local directory does not exist. Trying to create:\n"
3392	printf " $local_catalog \n"
3393	mkdir -p $local_catalog
3394	fi
3395	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3396	transfer_problems=true
3397	fi
3398
3399	else
3400
3401	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3402	actionout[$i]=""
3403	fi
3404	fi
3405
3406
3407	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3408	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3409	if [[ "${actionout[$i]}" = tra ]]
3410	then
3411	if [[ $localhost != $fromhost ]]
3412	then
3413	if [[ $localhost = ibmh ]]
3414	then
3415
3416	# TRANSFER IN SEPERATE JOB
3417	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3418	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3419	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3420	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3421
3422	echo "set -x" > transfer_${localout[$i]}
3423	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3424
3425	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3426	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3427	printf "\n or higher cycle\n"
3428	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]}
3429
3430	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3431
3432	if [[ $LOGNAME = b323013 ]]
3433	then
3434	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3435	else
3436	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3437	fi
3438
3439	else
3440
3441	# TRANSFER WITHIN THIS JOB
3442	transfer_failed=false
3443	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3444	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3445	if [[ $localhost = lccrayb ]]
3446	then
3447	ssh $usern@blogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3448	elif [[ $localhost = lccrayh ]]
3449	then
3450	ssh $usern@hlogin1 ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3451	elif [[ $localhost = lcxe6 ]]
3452	then
3453	ssh $usern@hexagon ". \\$HOME/.bashrc; cd $TEMPDIR; batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${localhost}_${fname}${endout[$i]} ${extout[$i]}"
3454	else
3455	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3456	fi
3457	[[ $? != 0 ]] && transfer_failed=true
3458
3459	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3460	if [[ $transfer_failed = true ]]
3461	then
3462	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3463	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3464
3465	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3466	eval local_catalog=${pathout[$i]}
3467	if [[ ! -d $local_catalog ]]
3468	then
3469	printf " *** local directory does not exist. Trying to create:\n"
3470	printf " $local_catalog \n"
3471	mkdir -p $local_catalog
3472	fi
3473
3474	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3475	transfer_problems=true
3476	fi
3477	fi
3478	else
3479
3480	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3481	actionout[$i]=a
3482	fi
3483	fi
3484
3485
3486	# APPEND ON THIS MACHINE
3487	if [[ "${actionout[$i]}" = "a" ]]
3488	then
3489	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3490	then
3491	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3492	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3493	else
3494	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3495	cat ${localout[$i]} >> ${pathout[$i]}
3496	fi
3497	fi
3498
3499	# COPY ON THIS MACHINE
3500	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3501	# ON DIFFERENT FILE-SYSTEMS
3502	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3503	then
3504
3505	# COPY IN CASE OF RUNS ON SINGLE CORES
3506	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3507	then
3508	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3509	if [[ $link_local_output = true ]]
3510	then
3511	printf " file will be linked\n"
3512	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3513	fi
3514	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3515	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3516	then
3517	if [[ $link_local_output = true ]]
3518	then
3519	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3520	fi
3521	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3522	else
3523	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
3524	fi
3525	else
3526	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3527	if [[ $link_local_output = true ]]
3528	then
3529	printf " file will be linked\n"
3530	ln -f ${localout[$i]} ${pathout[$i]}
3531	fi
3532	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3533	if [[ ! -f "${pathout[$i]}" ]]
3534	then
3535	if [[ $link_local_output = true ]]
3536	then
3537	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3538	fi
3539	cp ${localout[$i]} ${pathout[$i]}
3540	else
3541	printf "+++ no copy because file ${pathout[$i]} exists\n"
3542	fi
3543	fi
3544
3545	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
3546	then
3547
3548	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
3549	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
3550	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
3551	if [[ $link_local_output = true ]]
3552	then
3553	printf " files will be linked\n"
3554	mkdir ${pathout[$i]}
3555	cd ${localout[$i]}
3556	for file in $(ls *)
3557	do
3558	ln -f $file ${pathout[$i]}
3559	done >\|/dev/null 2>&1
3560	cd $TEMPDIR
3561	fi
3562
3563	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
3564	if [[ ! -f "${pathout[$i]}/_000000" ]]
3565	then
3566	if [[ $link_local_output = true ]]
3567	then
3568	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3569	fi
3570	cp -r ${localout[$i]}/* ${pathout[$i]}
3571	fi
3572
3573	fi
3574	fi
3575	done
3576	if (( i != 0 ))
3577	then
3578	if [[ $transfer_problems = true ]]
3579	then
3580	printf "\n$dashes\n *** OUTPUT-files saved"
3581	printf "\n +++ WARNING: some data transfers failed! \n"
3582	else
3583	printf "\n$dashes\n *** all OUTPUT-files saved \n"
3584	fi
3585	fi
3586
3587
3588	# IF REQUIRED, START A RESTART-JOB
3589	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
3590	if [[ -f CONTINUE_RUN ]]
3591	then
3592
3593	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
3594	# -C TELLS MRUN THAT IT IS A RESTART-RUN
3595	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
3596	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
3597	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
3598	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
3599	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
3600	if [[ $(echo $mc \| grep -c "#") != 0 ]]
3601	then
3602	mc=`echo $mc \| sed 's/#/f/g'`
3603	fi
3604
3605
3606	# START THE RESTART-JOB
3607	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
3608	echo " $mc"
3609	printf "\n$dashes\n"
3610	if [[ $localhost != $fromhost ]]
3611	then
3612
3613	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 \|\| $localhost = lcgeohu ]]
3614	then
3615	echo "*** ssh will be used to initiate restart-runs!"
3616	echo " return_address=\"$return_address\" "
3617	echo " return_username=\"$return_username\" "
3618	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
3619	then
3620	if [[ $localhost = ibmh ]]
3621	then
3622	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\" "
3623	elif [[ $localhost = lcbullhh ]]
3624	then
3625	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\" "
3626	elif [[ $localhost = lccrayb ]]
3627	then
3628	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\" "
3629	elif [[ $localhost = lccrayh ]]
3630	then
3631	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\" "
3632	elif [[ $localhost = lcxe6 ]]
3633	then
3634	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\" "
3635	else
3636	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 "
3637	fi
3638	else
3639	if [[ $localhost = ibmkisti ]]
3640	then
3641	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\" "
3642	elif [[ $localhost = lceddy ]]
3643	then
3644	/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 "
3645	elif [[ $localhost = lcocean ]]
3646	then
3647	/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 "
3648	elif [[ $localhost = lccrayb ]]
3649	then
3650	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\" "
3651	elif [[ $localhost = lccrayh ]]
3652	then
3653	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\" "
3654	elif [[ $localhost = lccgeohu ]]
3655	then
3656	ssh $usern@cirrus.geo.hu-berlin.de "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" "
3657	else
3658	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
3659	fi
3660	fi
3661	else
3662	printf "\n +++ no restart mechanism available for host \"$localhost\" "
3663	locat=restart; exit
3664	fi
3665
3666	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
3667	if [[ $queue = special1q ]]
3668	then
3669	sleep 120
3670	else
3671	sleep 30
3672	fi
3673
3674	else
3675
3676	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
3677	# USING SSH)
3678	cd $LOCAL_PWD
3679	if [[ $localhost = lckyuh ]]
3680	then
3681	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
3682	printf "\n please restart job manually using command:\n"
3683	printf "\n \"$mc\" "
3684	else
3685	eval $mc # THE ' MUST BE EVALUATED
3686	fi
3687	cd - > /dev/null
3688	fi
3689	if [[ $localhost = lckyuh ]]
3690	then
3691	printf "\n$dashes\n *** restart-run to be initiated manually\n"
3692	else
3693	printf "\n$dashes\n *** restart-run initiated \n"
3694	fi
3695
3696
3697	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
3698	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
3699	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
3700	# MAY BE VERY HUGE)
3701	(( i = 0 ))
3702	while (( i < iin ))
3703	do
3704	(( i = i + 1 ))
3705	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
3706	then
3707	rm -r ${absnamein[$i]}
3708	fi
3709	done
3710
3711	fi
3712
3713
3714
3715	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
3716	if [[ "$email_notification" != "none" ]]
3717	then
3718
3719	if [[ $localhost != $fromhost ]]
3720	then
3721	if [[ -f CONTINUE_RUN ]]
3722	then
3723	echo "PALM restart run necessary" > email_text
3724	echo "description header of actual run:" >> email_text
3725	cat CONTINUE_RUN >> email_text
3726	echo "mrun-command to restart:" >> email_text
3727	echo "$mc" >> email_text
3728	else
3729	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
3730	fi
3731	mail $email_notification < email_text
3732	printf "\n *** email notification sent to \"$email_notification\" "
3733	fi
3734	fi
3735
3736
3737
3738	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
3739	cd $HOME
3740	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
3741
3742	else
3743
3744	# PREPARING ACTIONS,
3745	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
3746
3747	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
3748	mrun_com="$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 $remote_username"
3749	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
3750	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
3751	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
3752	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
3753	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
3754	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
3755	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
3756	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
3757	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
3758	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
3759	if [[ $use_openmp = true ]]
3760	then
3761	mrun_com=${mrun_com}" -O $threads_per_task"
3762	fi
3763	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
3764	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
3765	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
3766	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
3767	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
3768	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
3769	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
3770	[[ $run_vnested_model = true ]] && mrun_com=${mrun_com}" -N \"$vnested_dist\""
3771	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
3772	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
3773	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
3774	if [[ $do_remote = true ]]
3775	then
3776	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
3777	fi
3778
3779
3780	# CREATE EXECUTABLE FOR BATCH JOB
3781	if [[ $create_executable_for_batch = true && $restart_run != true ]]
3782	then
3783
3784	printf "\n *** creating the executable for batch job\n"
3785
3786	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
3787	if [[ $host != $localhost ]]
3788	then
3789	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
3790	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
3791	locat=create_executable; exit
3792	fi
3793
3794	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3795	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3796
3797	cp $make_depository .
3798	tar -xf $make_depository > /dev/null 2>&1
3799	cp ../* . > /dev/null 2>&1
3800
3801	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
3802
3803	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
3804	then
3805	printf "\n +++ error occured while compiling or linking"
3806	locat=compile
3807	exit
3808	fi
3809
3810	mv a.out ..
3811	cd - > /dev/null 2>&1
3812	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3813
3814	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
3815
3816	fi
3817
3818
3819	# BUILD THE JOB-SCRIPTS ON FILE jobfile
3820	jobfile=jobfile.$RANDOM
3821
3822
3823	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
3824	echo "mkdir $TEMPDIR" >> $jobfile
3825	echo "cd $TEMPDIR" >> $jobfile
3826
3827
3828	# ACTIVATE ERROR-TRACEBACK
3829	if [[ $do_trace = true ]]
3830	then
3831	echo "set -x" >> $jobfile
3832	else
3833	echo "set +vx" >> $jobfile
3834	fi
3835
3836
3837	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
3838	if [[ "$init_cmds" != "" ]]
3839	then
3840	echo "$init_cmds" >> $jobfile
3841	fi
3842	if [[ "$module_calls" != "" ]]
3843	then
3844	echo "$module_calls" >> $jobfile
3845	fi
3846
3847
3848	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
3849	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
3850	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
3851	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
3852	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
3853	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
3854	# QUEUEING-SYSTEMS
3855	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean \|\| $host = lcgeohu ]]
3856	then
3857
3858	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
3859	if [[ $restart_run != true ]]
3860	then
3861	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
3862	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
3863	fi
3864
3865	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
3866	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
3867	echo "set -x" >> $jobfile
3868	if [[ $host = $localhost ]]
3869	then
3870	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
3871	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
3872	if [[ $(echo $host \| cut -c1-6) = lccray ]]
3873	then
3874	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3875	else
3876	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3877	fi
3878
3879	else
3880	if [[ $host = ibmkisti ]]
3881	then
3882	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
3883	echo "localdir=\`pwd\`" >> $jobfile
3884	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3885	elif [[ $host = lcbullhh ]]
3886	then
3887	echo "localdir=\`pwd\`" >> $jobfile
3888	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3889
3890	elif [[ $host = lccrayb ]]
3891	then
3892	echo "localdir=\`pwd\`" >> $jobfile
3893	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3894	elif [[ $host = lccrayh ]]
3895	then
3896	echo "localdir=\`pwd\`" >> $jobfile
3897	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3898
3899	else
3900	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3901	fi
3902	fi
3903	echo "export SOURCES_COMPLETE=true" >> $jobfile
3904
3905	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
3906	# WORKING DIRECTORY OF THE JOB
3907	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
3908	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
3909	echo "chmod u+rwx $mrun_script_name" >> $jobfile
3910	echo "execute_mrun=true" >> $jobfile
3911	echo " " >> $jobfile
3912
3913	else
3914
3915	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
3916	if [[ $do_compile = true ]]
3917	then
3918
3919	source_catalog=SOURCES_FOR_RUN_$fname
3920
3921	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
3922	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
3923	echo "export SOURCES_COMPLETE=true" >> $jobfile
3924	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
3925
3926	for filename in $source_list
3927	do
3928	# BACKSLASH IS USED FOR MASKING
3929	echo "cat > $filename << \"%END%\"" >> $jobfile
3930	cat $source_catalog/$filename >> $jobfile
3931	echo " " >> $jobfile
3932	echo "%END%" >> $jobfile
3933	echo " " >> $jobfile
3934	done
3935
3936	# BACKSLASH IS USED FOR MASKING
3937	echo "cat > Makefile << \"%END%\"" >> $jobfile
3938	cat $source_catalog/Makefile >> $jobfile
3939	echo " " >> $jobfile
3940	echo "%END%" >> $jobfile
3941	echo " " >> $jobfile
3942
3943	echo "cd - > /dev/null" >> $jobfile
3944
3945	fi
3946
3947
3948	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
3949	# BACKSLASH IS USED FOR MASKING
3950	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
3951	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
3952	echo "cat > $config_file << \"%END%\"" >> $jobfile
3953	if [[ $host = lckyuh ]]
3954	then
3955	# NO CROSS-COMPILER ON COMPUTE NODE
3956	sed 's/frtpx/frt/g' $config_file >> $jobfile
3957	else
3958	sed 's/#$.*//g' $config_file >> $jobfile
3959	fi
3960	echo "%END%" >> $jobfile
3961	echo " " >> $jobfile
3962
3963
3964	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
3965	# BACKSLASH IS USED FOR MASKING
3966	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
3967	if [[ $host = lckyuh ]]
3968	then
3969	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
3970	else
3971	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
3972	fi
3973	echo "%END%" >> $jobfile
3974	echo "chmod u+x $mrun_script_name" >> $jobfile
3975	echo "execute_mrun=true" >> $jobfile
3976	echo " " >> $jobfile
3977
3978	fi
3979
3980
3981	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
3982	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
3983	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
3984	if [[ $do_remote = true ]]
3985	then
3986	(( i = 0 ))
3987	while (( i < iin ))
3988	do
3989	(( i = i + 1 ))
3990	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
3991	if [[ "${transin[$i]}" = job ]]
3992	then
3993	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
3994	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
3995	echo " " >> $jobfile
3996	echo "%END%" >> $jobfile
3997	else
3998	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
3999	fi
4000
4001	# CHECK, IF FILE COULD BE CREATED
4002	echo "if [[ \$? = 1 ]]" >> $jobfile
4003	echo "then" >> $jobfile
4004	echo " echo \" \" " >> $jobfile
4005	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
4006	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
4007	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
4008	echo " execute_mrun=false" >> $jobfile
4009	echo "fi" >> $jobfile
4010	done
4011	fi
4012
4013	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
4014	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
4015	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
4016	echo "LOCAL_PWD=$working_directory" >> $jobfile
4017	echo "export LOCAL_PWD" >> $jobfile
4018
4019	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
4020	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
4021	echo "export LOCAL_MRUN_PATH" >> $jobfile
4022
4023	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
4024	if [[ $host = lceddy \|\| $localhost = lceddy ]]
4025	then
4026	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
4027	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
4028	fi
4029
4030	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
4031	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
4032	echo "set -x" >> $jobfile
4033	echo "queue=$queue" >> $jobfile
4034	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
4035	echo 'ls -al; echo `pwd`' >> $jobfile
4036	echo "cd \$HOME" >> $jobfile
4037	echo "rm -rf $TEMPDIR" >> $jobfile
4038
4039
4040
4041
4042	# START THE JOB USING SUBJOB-COMMAND
4043	if [[ $silent = false ]]
4044	then
4045	printf "\n "
4046	else
4047	printf "\n\n"
4048	fi
4049
4050	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
4051	rm -rf $jobfile
4052
4053
4054	fi # END OF REMOTE-PART

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