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source: palm/trunk/SCRIPTS/mrun @ 2295

Last change on this file since 2295 was 2295, checked in by raasch, 7 years ago
script adjustments for using lcgeohu, cpp_opts removed
Property svn:keywords set to `Id Rev`
File size: 143.1 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 2295 2017-06-27 14:25:52Z raasch $
29	# adjustments for using lcgeohu (cirrus @ HUB)
30	# cpp_opts removed
31	#
32	# 2290 2017-06-19 11:03:06Z raasch
33	# further test output removed
34	#
35	# 2286 2017-06-15 13:31:57Z raasch
36	# test output for cycle number removed
37	#
38	# 2268 2017-06-09 10:34:09Z raasch
39	# bugfix for calculating cycle numbers for output files in r2261
40	#
41	# 2262 2017-06-08 14:52:23Z raasch
42	# bugfix for r2261
43	#
44	# 2261 2017-06-08 14:25:57Z raasch
45	# unified cycle numbers for output files are used,
46	# paths and filenames are allowed to contain arbitrary numbers of dots ".",
47	# creation of file OUTPUT_FILE_CONNECTIONS removed,
48	# archive feature completely removed from the script,
49	# nech related parts completely removed
50	#
51	# 2257 2017-06-07 14:07:05Z witha
52	# adjustments for lceddy, removed lcflow-specific code
53	#
54	# 2186 2017-03-21 05:36:31Z raasch
55	#
56	# 2185 2017-03-21 05:09:29Z raasch
57	# adjustment for lykyo*-hosts (PJM_ENVIRONMENT defines BATCH)
58	#
59	# 2148 2017-02-09 16:56:42Z scharf
60	# changed allocation of resources for lcbullhh in srun command
61	#
62	# 2141 2017-02-06 10:19:32Z gronemeier
63	# made check for existing files language independent
64	#
65	# 1944 2016-06-15 06:29:00Z raasch
66	# adjustments for using HLRN ssh-keys
67	#
68	# 1940 2016-06-14 05:15:20Z raasch $
69	# adjustments for lckiaps
70	#
71	# 1866 2016-04-15 06:50:59Z raasch
72	# adjusted for lcocean
73	#
74	# 1841 2016-04-07 19:14:06Z raasch
75	# script now running under bash
76	#
77	# 1804 2016-04-05 16:30:18Z maronga
78	# test: implementing an execute mechanism where the execute command is given in the
79	# configuration file
80	# ROPTS removed from execution commands
81	# Warnings about missing optional files or user code changed to informative messages
82	# Removed parameter file check
83	#
84	# 1755 2016-02-22 13:53:39Z maronga
85	# Minor bugfix to last commit
86	#
87	# 1753 2016-02-22 13:49:49Z maronga
88	# Bugfix: use random job number when PBS job nummer retrieval fails on lccray*
89	#
90	# 1622 2015-07-20 06:21:36Z heinze
91	# bugfix for Mistral (lcbullhh)
92	#
93	# 1621 2015-07-17 11:39:33Z heinze
94	# adjustments for Mistral at DKRZ Hamburg (lcbullhh)
95	#
96	# 1609 2015-07-03 15:37:58Z maronga
97	# Modified the random number of the temporary working directory to match the
98	# queuing system number on HLRN-III (lccray*).
99	#
100	# 1604 2015-06-23 15:48:03Z suehring
101	# Enable coupled runs for lcmuk
102	#
103	# 1598 2015-05-29 06:45:40Z raasch
104	# bugfix for creating hostfile and total number of MPI tasks if run in openmp-mode on one node
105	#
106	# 1549 2015-01-30 14:26:16Z suehring
107	# Enable interactive debug sessions with allinea debugger
108	#
109	# 1547 2015-01-29 15:09:12Z witha
110	# adjustments for ForWind computing cluster (lcflow)
111	#
112	# 1491 2014-11-12 08:12:57Z heinze
113	# correct setting of batch_job allowed for ibm-machines
114	#
115	# 1468 2014-09-24 14:06:57Z maronga
116	# Typo removed (addres->address)
117	# Bugfix: returning files to IMUK via ssh did not work for lccrayh and lcycrayb
118	# Added support for restart runs (remote) for lcxe6
119	#
120	# 1442 2014-07-28 07:09:10Z raasch
121	# default queues for HLRN-III (lccrayb/lccrayh) defined
122	#
123	# 1422 2014-07-02 10:01:25Z kanani
124	# automatic restarts enabled for lccrayb,
125	# adjustment of path to compilervars.sh at IMUK (see automatic restarts)
126	#
127	# 1420 2014-06-10 06:24:14Z raasch
128	# -j1 option added to aprung command for lccrayf (CSC)
129	#
130	# 1402 2014-05-09 14:25:13Z raasch
131	# batch_job added to envpar-NAMELIST
132	#
133	# 1357 2014-04-11 15:02:03Z witha
134	# adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now
135	# possible)
136	#
137	# 1320 2014-03-20 08:40:49Z raasch
138	# check namelist file set false by default
139	#
140	# 1304 2014-03-12 10:29:42Z raasch
141	# ulimit option changed from -Ss to -s
142	#
143	# bugfix: missing "fi" in r1289
144	#
145	# 1289 2014-03-04 07:12:34Z raasch
146	# comments translated to English
147	# necriam-, fimm-, ibmy-, and sgi-specific code removed
148	# export of variables for palm and interpret_config removed
149	#
150	# 1281 2014-02-01 07:55:49Z raasch
151	# rsync-copy restricted to Cray machines, since command is unavailable on some
152	# other systems
153	#
154	# 1279 2014-01-28 12:10:14Z raasch
155	# tasks_per_node must not be an integral divisor of numprocs any more. This was done
156	# in order to remove annoying restrictions concerning the number of processors which
157	# appear on machines with larger nodes (e.g. containing 24 cores). Now without this
158	# restriction, one of the nodes will be filled with less than the given number of
159	# tasks per node. A respective warning is given.
160	#
161	# 1274 2014-01-09 13:14:54Z heinze
162	# adjustments for lccrayh
163	#
164	# 1272 2014-01-08 10:19:32Z witha
165	# small adjustment for lcflow
166	#
167	# 1270 2013-12-16 11:05:01Z fricke
168	# call of combine_plot_fields adjusted for lccrayb/lccrayh
169	#
170	# 1255 2013-11-07 14:43:35Z raasch
171	# further adjustments for lccrayb remote access
172	#
173	# 1241 2013-10-30 11:36:58Z heinze
174	# Enable use of nudging input and input of large scale forcing from
175	# external files
176	#
177	# 1229 2013-09-20 06:55:19Z raasch
178	# further adjustments for lccrayb
179	#
180	# 1224 2013-09-16 07:27:23Z raasch
181	# first adjustments for lccrayb
182	#
183	# 1210 2013-08-14 10:58:20Z raasch
184	# fftw support added
185	#
186	# 1201 2013-07-10 16:17:59Z witha
187	# adjustments for Forwind cluster (lcflow)
188	#
189	# 1199 2013-07-05 14:52:22Z raasch
190	# adjustments for CSC Helsinki (lccrayf),
191	# executables for batch jobs can be created in advance, in order to avoid calling
192	# the compiler within the batch job (only works if batch jobs are submitted on
193	# local host)
194	#
195	# 1190 2013-06-25 09:39:21Z heinze
196	# enable use of automatic restarts for ibmh
197	# use of cluster/express queue enabled (ibmh)
198	#
199	# 1124 2013-04-09 15:46:52Z raasch
200	# variable "memory" is exported via typeset option -x, because otherwise an unknown
201	# side effect may lead to data loss while getopts is reading the script-option arguments
202	#
203	# 1122 2013-04-09 08:37:16Z heinze
204	# Bugfix: change type of variable last_char
205	#
206	# 1119 2013-04-05 15:11:19Z raasch
207	# Bugfix for setting -T option for subjob
208	#
209	# 1108 2013-03-05 07:03:32Z raasch
210	# bugfix for coupled runs on lckyut/lckyuh
211	#
212	# 1106 2013-03-04 05:31:38Z raasch
213	# --stdin argument for mpiexec on lckyuh
214	# -y and -Y settings output to header
215	#
216	# 1103 2013-02-20 02:15:53Z raasch
217	# default script runs again under ksh, because of unsolved problems with read
218	# from stdin: when bash script is called from a ksh, message "read error: 0:
219	# Resource temporarily unavailable" appears and script does not stop,
220	# further bash compatibility adjustments,
221	# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
222	# on lckyuh, but mrun does not terminate and issues a warning instead
223	#
224	# 1101 2013-02-17 10:20:21Z raasch
225	# script now running under bash instead of ksh, which required small adjustments
226	# (output formatting with printf instead "typeset -L/-R", print replaced by echo,
227	# read from stdin),
228	# cross compilername on lckyuh compute nodes replaced by real compiler name
229	#
230	# 1099 2013-02-10 01:47:43Z raasch
231	# adjustments for Kyushu-University computing center (lckyuh - hayaka)
232	# and for Forwind cluster (lcflow)
233	# small further adjustments for lckyut
234	#
235	# 1094 2013-02-03 01:52:12Z raasch
236	# explicit ssh/scp port can be set in config file with environment variable
237	# scp_port. This port is handled to all ssh/scp/batch_scp calls.
238	# decalpha parts (yonsei) removed
239	#
240	# 2013-02-02 07:06:13Z raasch
241	# adjustments for Kyushu-University computing center (lckyut - tatara)
242	#
243	# 1083 2013-01-04 10:22:09Z maronga
244	# bugfix in parameter file check (read %cpp_options was missing)
245	#
246	# 1069 2012-11-28 16:18:43Z maronga
247	# bugfix: coupling mode was always set to mpi2, typos removed
248	#
249	# 1058 2012-11-21 07:00:35Z raasch
250	# Intel inspector (inspxe) is given the number of PEs instead of the number of
251	# nodes
252	#
253	# 1046 2012-11-09 14:38:45Z maronga
254	# code put under GPL (PALM 3.9)
255	#
256	# 21/03/94 - Siggi - first version finished
257	# 03/03/94 - Siggi - script development started
258	#
259	#--------------------------------------------------------------------------------#
260	# mrun - script for running PALM jobs
261	#--------------------------------------------------------------------------------#
262
263
264
265	# DECLARATION OF VARIABLES AND THEIR DEFUALT VALUES
266
267	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
268	# LES TO PROBLEMS IN ROUTINES CALLED BY MRUN
269	# (TOO MANY ARGUMENTS - PROBLEM)
270	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
271
272	AddFilenames=""
273	additional_conditions=""
274	add_source_path=""
275	afname=""
276	check_namelist_files=false
277	combine_plot_fields=true
278	compiler_name=""
279	cond1=""
280	cond2=""
281	config_file=.mrun.config
282	coupled_dist=""
283	coupled_mode="mpi1"
284	cpp_options=""
285	cpumax=0
286	cpurest=0
287	create_executable_for_batch=false
288	delete_temporary_catalog=true
289	do_batch=false
290	do_compile=true
291	do_remote=false
292	do_stagein=true
293	do_stageout=true
294	do_trace=false
295	email_notification="none"
296	exclude=""
297	executable=""
298	execute_command="none"
299	execution_error=false
300	fftw_inc=""
301	fftw_lib=""
302	fftw_support=false
303	fname=test
304	fromhost=""
305	global_revision=""
306	group_number=none
307	host=""
308	host_file=""
309	hp=""
310	input_list=""
311	interpreted_config_file=""
312	job_catalog="~/job_queue"
313	job_on_file=""
314	keep_data_from_previous_run=false
315	link_local_input=false
316	link_local_output=false
317	localhost_realname=$(hostname)
318	local_dvrserver_running=.FALSE.
319	locat=normal
320	mainprog=""
321	makefile=""
322	max_par_io_str=""
323	mc=$0
324	while [[ $(echo $mc \| grep -c "/") != 0 ]]
325	do
326	mc=`echo $mc \| cut -f2- -d"/"`
327	done
328	module_calls=""
329	mrun_script_name=$mc
330	netcdf_inc=""
331	netcdf_lib=""
332	netcdf_support=false
333	node_usage=default
334	numprocs=""
335	numprocs_atmos=0
336	numprocs_ocean=0
337	OOPT=""
338	openmp=false
339	output_list=""
340	package_list=""
341	queue=none
342	read_from_config=""
343	restart_run=false
344	if [[ `hostname` = rte10 ]]
345	then
346	return_address=133.5.185.60
347	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
348	elif [[ `hostname` = climate0 ]]
349	then
350	return_address=165.132.26.68
351	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
352	elif [[ `hostname` = "schultzl-Latitude-E6540" ]]
353	then
354	return_address="schultzl-Latitude-E6540"
355	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
356	elif [[ `hostname` = urban00 ]]
357	then
358	return_address=147.46.30.151
359	echo "+++ WARNING: fixed return_address = $return_address is used !!!!!"
360	else
361	return_address=$(nslookup `hostname` 2>&1 \| grep "Address:" \| tail -1 \| awk '{print $2}')
362	fi
363	return_password=""
364	return_username=$LOGNAME
365	remotecall=false
366	remote_username=""
367	run_coupled_model=false
368	run_mode=""
369	dashes=" ----------------------------------------------------------------------------"
370	silent=false
371	source_list=""
372	source_path=SOURCE
373	tasks_per_node=""
374	threads_per_task=1
375	tmpcreate=false
376	tmp_data_catalog=""
377	transfer_problems=false
378	usern=$LOGNAME
379	use_openmp=false
380	version="MRUN 2.1 Rev$Rev: 2295 $"
381	working_directory=`pwd`
382	TOPT=""
383	XOPT=""
384	zeit=$( date \| cut -c 12-19 )
385
386	typeset -i iec=0 iic=0 iin=0 ioc=0 iout=0 stagein_anz=0 stageout_anz=0
387	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
388	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
389	# SCRIPT-OPTION ARGUMENTS
390	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
391
392	# ERROR HANDLING IN CASE OF EXIT
393	trap 'rm -rf $working_directory/tmp_mrun
394	if [[ $locat != normal && $locat != control_c ]]
395	then
396
397	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
398	(( i = 0 ))
399	while (( i < iec ))
400	do
401	(( i = i + 1 ))
402	printf "\n *** Execution of ERROR-command:\n"
403	printf " >>> ${err_command[$i]}\n"
404	eval ${err_command[$i]}
405	done
406	if [[ -n $interpreted_config_file ]]
407	then
408	rm -rf $interpreted_config_file
409	fi
410	if [[ -n .mrun_environment ]]
411	then
412	rm -rf .mrun_environment
413	fi
414	if [[ $tmpcreate = true ]]
415	then
416	# printf "\n *** Contents of \"$TEMPDIR\":\n"
417	# ls -al; cd
418	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
419	fi
420	if [[ "$dvrserver_id" != "" ]]
421	then
422	echo "+++ killing dvrserver_id=$dvrserver_id"
423	kill $dvrserver_id
424	fi
425	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
426	then
427	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
428	fi
429	printf "\n\n+++ MRUN killed \n\n"
430	elif [[ $locat != control_c ]]
431	then
432	printf "\n\n --> all actions finished\n\n"
433	printf " Bye, bye $usern !!\n\n"
434	fi' exit
435
436
437	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
438	trap 'rm -rf $working_directory/tmp_mrun
439	rm -rf $working_directory/tmp_check_namelist_files
440	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
441	if [[ -f ~/job_queue/JOBINFO.$QSUB_REQID ]]
442	then
443	rm -rf ~/job_queue/JOBINFO.$QSUB_REQID
444	fi
445	if [[ "$dvrserver_id" != "" ]]
446	then
447	echo "+++ killing dvrserver_id=$dvrserver_id"
448	kill $dvrserver_id
449	fi
450	printf "\n+++ MRUN killed by \"^C\" \n\n"
451	locat=control_c
452	exit
453	' 2
454
455
456	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
457	# BEEN SET
458	if [[ "$PALM_BIN" = "" ]]
459	then
460	printf "\n +++ environment variable PALM_BIN has not been set"
461	printf "\n please set it to the directory where the PALM scripts are located"
462	locat=palm_bin; exit
463	fi
464	export PATH=$PALM_BIN:$PATH
465
466
467
468	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE MRUN-COMMAND STRING (MC),
469	# WHICH WILL BE USED TO START RESTART-JOBS
470	while getopts :a:bBc:Cd:Fg:G:h:H:i:kK:m:M:n:o:O:p:P:q:r:R:s:St:T:u:U:vw:xX:yY:zZ option
471	do
472	case $option in
473	(a) afname=$OPTARG;;
474	(b) do_batch=true; mc="$mc -b";;
475	(B) delete_temporary_catalog=false; mc="$mc -B";;
476	(c) config_file=$OPTARG; mc="$mc -c$OPTARG";;
477	(C) restart_run=true; mc="$mc -C";;
478	(d) fname=$OPTARG; mc="$mc -d$OPTARG";;
479	(F) job_on_file="-D"; mc="$mc -F";;
480	(g) group_number=$OPTARG; mc="$mc -g$OPTARG";;
481	(G) global_revision=$OPTARG; mc="$mc -G'$OPTARG'";;
482	(h) host=$OPTARG; mc="$mc -h$OPTARG";;
483	(H) fromhost=$OPTARG; mc="$mc -H$OPTARG";;
484	(i) input_list=$OPTARG; mc="$mc -i'$OPTARG'";;
485	(k) keep_data_from_previous_run=true; mc="$mc -k";;
486	(K) additional_conditions="$OPTARG"; mc="$mc -K'$OPTARG'";;
487	(m) memory=$OPTARG; mc="$mc -m$OPTARG";;
488	(M) makefile=$OPTARG; mc="$mc -M$OPTARG";;
489	(n) node_usage=$OPTARG; mc="$mc -n$OPTARG";;
490	(o) output_list=$OPTARG; mc="$mc -o'$OPTARG'";;
491	(O) use_openmp=true; threads_per_task=$OPTARG; mc="$mc -O$OPTARG";;
492	(p) package_list=$OPTARG; mc="$mc -p'$OPTARG'";;
493	(P) return_password=$OPTARG; mc="$mc -P$OPTARG";;
494	(q) queue=$OPTARG; mc="$mc -q$OPTARG";;
495	(r) run_mode=$OPTARG; mc="$mc -r'$OPTARG'";;
496	(R) remotecall=true;return_address=$OPTARG; mc="$mc -R$OPTARG";;
497	(s) source_list=$OPTARG; mc="$mc -s'$OPTARG'";;
498	(S) read_from_config=false; mc="$mc -S";;
499	(t) cpumax=$OPTARG; mc="$mc -t$OPTARG";;
500	(T) mrun_tasks_per_node=$OPTARG; mc="$mc -T$OPTARG";;
501	(u) remote_username=$OPTARG; mc="$mc -u$OPTARG";;
502	(U) return_username=$OPTARG; mc="$mc -U$OPTARG";;
503	(v) silent=true; mc="$mc -v";;
504	(w) max_par_io_str=$OPTARG; mc="$mc -w$OPTARG";;
505	(x) do_trace=true;set -x; mc="$mc -x";;
506	(X) numprocs=$OPTARG; mc="$mc -X$OPTARG";;
507	(y) ocean_file_appendix=true; mc="$mc -y";;
508	(Y) run_coupled_model=true; coupled_dist=$OPTARG; mc="$mc -Y'$OPTARG'";;
509	(z) check_namelist_files=false; mc="$mc -z";;
510	(Z) combine_plot_fields=false; mc="$mc -Z";;
511	(\?) printf "\n +++ unknown option $OPTARG \n"
512	printf "\n --> type \"$0 ?\" for available options \n"
513	locat=parameter;exit;;
514	esac
515	done
516
517
518	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
519	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
520	(( to_shift = $OPTIND - 1 ))
521	shift $to_shift
522
523	# PRINT SHORT DESCRIPTION OF MRUN OPTIONS
524	if [[ "$1" = "?" ]]
525	then
526	(printf "\n *** mrun can be called as follows:\n"
527	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"
528	printf "\n Description of available options:\n"
529	printf "\n Option Description Default-Value"
530	printf "\n -a base name of input files equiv. -d"
531	printf "\n -b batch-job on local machine ---"
532	printf "\n -B do not delete temporary directory at end ---"
533	printf "\n -c configuration file .mrun.config"
534	printf "\n -d base name of files attached to program test"
535	printf "\n -F create remote job file only ---"
536	printf "\n -h execution host $localhost_realname"
537	printf "\n -i INPUT control list \"\" "
538	printf "\n -k keep data from previous run"
539	printf "\n -K additional conditions for controling"
540	printf "\n usage of conditional code and"
541	printf "\n env-variables in configuration file \"\" "
542	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
543	printf "\n -M Makefile name Makefile"
544	printf "\n -n node usage (shared/not_shared) depending on -h"
545	printf "\n -o OUTPUT control list \"\" "
546	printf "\n -O threads per openMP task ---"
547	printf "\n -p software package list \"\" "
548	printf "\n -q queue \"$queue\" "
549	printf "\n -r run control list (combines -i -o) \"\" "
550	printf "\n -s filenames of routines to be compiled \"\" "
551	printf "\n must end with .f, .f90, .F, or .c !"
552	printf "\n use \"..\" for more than one file and wildcards"
553	printf "\n -s LM compiles all locally modified files"
554	printf "\n -S config file interpreted by shellscript ---"
555	printf "\n -t allowed cpu-time in seconds (batch) 0"
556	printf "\n -T tasks per node depending on -h"
557	printf "\n -u username on remote machine \"\" "
558	printf "\n -v no prompt for confirmation ---"
559	printf "\n -w maximum parallel io streams as given by -X"
560	printf "\n -x tracing of mrun for debug purposes ---"
561	printf "\n -X # of processors (on parallel machines) 1"
562	printf "\n -y add appendix \"_O\" to all local output"
563	printf "\n files (ocean precursor runs followed by"
564	printf "\n coupled atmosphere-ocean runs) ---"
565	printf "\n -Y run coupled model, \"#1 #2\" with"
566	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
567	printf "\n -Z skip combine_plot_fields at the end of "
568	printf "\n the simulation ---"
569	printf "\n "
570	printf "\n Possible values of positional parameter <modus>:"
571	printf "\n \"?\" - this outline \n\n") \| more
572	exit
573	elif [[ "$1" != "" ]]
574	then
575	printf "\n +++ positional parameter $1 unknown \n"
576	locat=parameter; exit
577	fi
578
579
580
581	# SHORT STARTING MESSAGE
582	printf "\n*** $version "
583	printf "\n will be executed. Please wait ..."
584
585
586
587	# CHECK, IF CONFIGURATION FILE EXISTS
588	if [[ ! -f $config_file ]]
589	then
590	printf "\n\n +++ configuration file: "
591	printf "\n $config_file"
592	printf "\n does not exist"
593	locat=connect; exit
594	fi
595
596
597	# DETERMINE THE HOST-IDENTIFIER (localhost) FROM THE CONFIGURATION FILE
598	line=""
599	grep "%host_identifier" $config_file > tmp_mrun
600	while read line
601	do
602	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
603	then
604	HOSTNAME=`echo $line \| cut -d" " -s -f2`
605	host_identifier=`echo $line \| cut -d" " -s -f3`
606	if [[ $localhost_realname = $HOSTNAME ]]
607	then
608	localhost=$host_identifier
609	break
610	fi
611	fi
612	done < tmp_mrun
613
614	if [[ "$localhost" = "" ]]
615	then
616	printf "\n\n +++ no host identifier found in configuration file \"$config_file\""
617	printf "\n for local host \"$localhost_realname\"."
618	printf "\n Please add line"
619	printf "\n \"\%host_identifier $localhost_realname <identifier>\""
620	printf "\n to the configuration file."
621	locat=localhost; exit
622	fi
623
624
625	# ??? THIS SHOULD BE DECRIBED IN THE MRUN DOCUMENTATION ???
626	# SET BASENAME OF THE INPUT-FILES TO THE GENERAL BASENAME (GIVEN BY OPTION -d),
627	# IF IT HAS NOT BEEN SET BY THE USER DIFFERENTLY (USING OPTION -a)
628	[[ "$afname" = "" ]] && afname=$fname
629
630
631	# ADD RUN-FILE ACTIVATION STRINGS (GIVEN BY OPTION -r) TO THE
632	# RESPECTIVE LISTS FOR ACTIVATING THE INPUT/OUTPUT FILE CONNECTION
633	# STATEMENTS IN THE CONFIGURATION FILE
634	if [[ "$run_mode" != "" ]]
635	then
636	input_list="$input_list $run_mode"
637	output_list="$output_list $run_mode"
638	fi
639
640
641	# ??? is this (and the respective option -H) really required ???
642	# STORE HOSTNAME, FROM WHICH THE JOB IS STARTED,
643	# BUT ONLY IF IT HASN'T BEEN ALREADY SET BY OPTION -H
644	# (MRUN IS AUTOMATICALLY SETTING THIS OPTION IN THE MRUN-CALLS WITHIN
645	# THOSE BATCH-JOBS, WHICH ARE CREATED BY MRUN ITSELF)
646	if [[ "$fromhost" = "" ]]
647	then
648	fromhost=$localhost
649	fi
650
651
652	# CHECK, IF EXECUTION SHALL TO BE DONE ON THE REMOTE-MACHINE.
653	# VALUE OF do_remote IS IMPORTANT FOR THE FILE CONNECTIONS.
654	# IN CASE OF EXECUTION ON A REMOTE-MACHINE, A BATCH-JOB HAS
655	# TO BE SUBMITTED (I.E. do_batch=true)
656	if [[ -n $host && "$host" != $localhost ]]
657	then
658	do_batch=true
659	do_remote=true
660	case $host in
661	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
662	(*) printf "\n"
663	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
664	printf "\n is not available"
665	locat=nqs; (( iec = 0 )); exit;;
666	esac
667	else
668	host=$localhost
669	fi
670
671
672	# EVALUATE ADDITIONAL CONDITIONS GIVEN BY OPTION -K
673	if [[ -n $additional_conditions ]]
674	then
675	cond1=`echo $additional_conditions \| cut -d" " -f1`
676	cond2=`echo $additional_conditions \| cut -d" " -s -f2`
677	dummy=`echo $additional_conditions \| cut -d" " -s -f3`
678	if [[ -n $dummy ]]
679	then
680	printf "\n +++ more than 2 additional conditions given for Option \"-K\""
681	locat=options; exit
682	fi
683	block=_$cond1
684	[[ -n $cond2 ]] && block=${block}_$cond2
685	fi
686
687
688	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y) AND DETERMINE coupled_mode
689	if [[ $run_coupled_model = true ]]
690	then
691
692	numprocs_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
693	numprocs_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
694
695	if (( $numprocs_ocean + $numprocs_atmos != $numprocs ))
696	then
697
698	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
699	printf "\n PEs (total) : $numprocs"
700	printf "\n PEs (atmosphere): $numprocs_atmos"
701	printf "\n PEs (ocean) : $numprocs_ocean"
702	locat=coupling; exit
703
704	fi
705
706
707	# GET coupled_mode FROM THE CONFIG FILE
708	line=""
709	grep "%cpp_options.-D__mpi2.$host" $config_file > tmp_mrun
710	while read line
711	do
712	echo line=\"$line\"
713	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" && $(echo $line \| cut -d" " -s -f4) = $cond1 && $(echo $line \| cut -d" " -s -f5) = $cond2 ]]
714	then
715	coupled_mode="mpi2"
716	fi
717	done < tmp_mrun
718
719	fi
720
721	# SAVE VALUES OF MRUN-OPTIONS SICHERN IN ORDER TO OVERWRITE
722	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
723	mrun_memory=$memory
724	mrun_group_number=$group_number
725	mrun_cpumax=$cpumax
726	mrun_numprocs=$numprocs
727
728
729	# READ AND EVALUATE THE CONFIGURATION-FILE FROM WITHIN THIS SHELLSCRIPT
730	# (OPTION -S). THE DEFAULT IS USING THE ROUTINE <<<<
731	if [[ "$read_from_config" = false ]]
732	then
733	[[ $silent = false ]] && printf "\n Reading the configuration file... "
734
735	# READ THE CONFIGURATION FILE LINE BY LINE
736	while read zeile
737	do
738	[[ $silent = false ]] && printf "."
739
740
741	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
742	eval zeile=\"$zeile\"
743
744
745	# INTERPRET THE LINE
746	if [[ "$(echo $zeile)" = "" ]]
747	then
748	# EMPTY LINE, NO ACTION
749	continue
750
751	elif [[ "$(echo $zeile \| cut -c1)" = "#" ]]
752	then
753
754	# LINE IS A COMMENT LINE
755	true
756
757	elif [[ "$(echo $zeile \| cut -c1)" = "%" ]]
758	then
759
760	# LINE DEFINES AN ENVIRONMENT-VARIABLE
761	zeile=$(echo $zeile \| cut -c2-)
762	var=`echo $zeile \| cut -d" " -f1`
763	value=`echo $zeile \| cut -d" " -s -f2`
764	for_host=`echo $zeile \| cut -d" " -s -f3`
765	for_cond1=`echo $zeile \| cut -d" " -s -f4`
766	for_cond2=`echo $zeile \| cut -d" " -s -f5`
767
768	if [[ "$for_host" = "" \|\| ( "$for_host" = $host && "$for_cond1" = "$cond1" && "$for_cond2" = "$cond2" ) \|\| $(echo "$input_list$output_list"\|grep -c "$for_host") != 0 ]]
769	then
770
771	# REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
772	# "::" IS REPLACED BY ":".
773	value=`echo $value \| sed 's/::/%DUM%/g' \| sed 's/:/ /g' \| sed 's/%DUM%/:/g'`
774
775
776	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
777	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
778	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
779	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
780	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
781	# CONFIGURATION-FILE.
782	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
783	then
784	eval $var=\$value
785
786	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
787	if [[ $do_trace = true ]]
788	then
789	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
790	fi
791	fi
792
793	# IF AN ENVIRONMENT-VARIABLE DETERMINES THE HOST, THEN EVALUATE IT IMMEDIATELY:
794	# VALUE OF do-remote IS REQUIRED FOR THE FILE CONNECTIONS (COPY OF I/O FILES).
795	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MASCHINE, A BATCH-JOB
796	# MUST HAVE TO BE STARTED
797	if [[ $var = host ]]
798	then
799	if [[ -n $host && "$host" != $localhost ]]
800	then
801	do_batch=true
802	do_remote=true
803	case $host in
804	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
805	(*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
806	printf "\n is not available"
807	locat=nqs; exit;;
808	esac
809	else
810	host=$localhost
811	fi
812	fi
813
814	# USER-DEFINED ENVIRONMENT VARIABLES MUST BE EXPORTED,
815	# BECAUSE THEY MAY BE REQUIRED IN OTHER SCRIPTS CALLED
816	# BY MRUN (E.G. subjob)
817	export $var
818	fi
819
820
821
822
823	elif [[ "$(echo $zeile \| cut -c1-3)" = "EC:" ]]
824	then
825
826	# LINE DEFINES ERROR-COMMAND
827	(( iec = iec + 1 ))
828	zeile=$(echo $zeile \| cut -c4-)
829	err_command[$iec]="$zeile"
830
831	elif [[ "$(echo $zeile \| cut -c1-3)" = "IC:" ]]
832	then
833
834	# LINE DEFINES INPUT-COMMAND
835	(( iic = iic + 1 ))
836	zeile=$(echo $zeile \| cut -c4-)
837	in_command[$iic]="$zeile"
838
839	elif [[ "$(echo $zeile \| cut -c1-3)" = "OC:" ]]
840	then
841
842	# LINE DEFINES OUTPUT-COMMAND
843	(( ioc = ioc + 1 ))
844	zeile=$(echo $zeile \| cut -c4-)
845	out_command[$ioc]="$zeile"
846
847	else
848
849	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
850	# s2a: in/out - field
851	# s2b: loc - field (optional)
852	# s2c: tr/ar - field (optional)
853	s1=`echo $zeile \| cut -d" " -f1`
854	s2=`echo $zeile \| cut -d" " -s -f2`
855	s2a=$(echo $s2 \| cut -d":" -f1)
856	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
857	then
858	s2b=""
859	s2c=""
860	else
861	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
862	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
863	fi
864	s3=`echo $zeile \| cut -d" " -f3`
865	s4=`echo $zeile \| cut -d" " -s -f4`
866	s5=`echo $zeile \| cut -d" " -s -f5`
867	s6=`echo $zeile \| cut -d" " -s -f6`
868
869
870	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
871	# INPUT- OR OUTPUT-LIST.
872	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
873	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
874	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
875	# IS NOT CHECKED AND STORED.
876	IFSALT="$IFS"; IFS="$IFS:"
877	if [[ "$s2a" = in && ! ( $do_remote = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
878	then
879	found=false
880	for actual in $input_list
881	do
882	for formal in $s3
883	do
884	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
885	done
886	done
887	if [[ $found = true ]]
888	then
889	(( iin = iin + 1 ))
890	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
891	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
892	extin[$iin]=$s6
893	fi
894	elif [[ "$s2a" = out && ! ( $do_remote = true && "$s2b" = loc ) ]]
895	then
896	found=false
897	for actual in $output_list
898	do
899	for formal in $s3
900	do
901	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
902	done
903	done
904	if [[ $found = true ]]
905	then
906	(( iout = iout + 1 ))
907	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
908	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
909	fi
910	elif [[ "$s2a" != in && "$s2a" != out ]]
911	then
912	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
913	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
914	locat=connect; exit
915	fi
916	IFS="$IFSALT"
917	fi
918	done < $config_file
919
920	else
921
922	# EVALUATE THE CONFIGURATION-FILE BY FORTRAN-PROGRAM
923	[[ $silent = false ]] && printf "..."
924	interpreted_config_file=.icf.$RANDOM
925
926
927
928	# PROVIDE VALUES OF ENVIRONMENT-VARIABLE FOR interpret_config VIA NAMELIST-FILE
929	cat > .mrun_environment << EOF
930	&mrun_environment cond1 = '$cond1', cond2 = '$cond2',
931	config_file = '$config_file', do_remote = '$do_remote',
932	do_trace = '$do_trace', host = '$host',
933	input_list = '$input_list', icf = '$interpreted_config_file',
934	localhost = '$localhost', output_list = '$output_list' /
935
936	EOF
937
938	if [[ "$host" != $localhost ]]
939	then
940
941	# REMOTE JOB FROM LOCAL HOST: JUST TAKE THE FIRST EXECUTABLE FOUND
942	interpret_config_executable=`ls -1 ${PALM_BIN}/interpret_config*.x 2>/dev/null`
943	if [[ $? != 0 ]]
944	then
945	printf "\n\n +++ no interpret_config found"
946	printf "\n run \"mbuild -u -h ...\" to generate utilities for this host"
947	locat=interpret_config; exit
948	fi
949	interpret_config_executable=`echo $interpret_config_executable \| cut -d" " -f1`
950	$interpret_config_executable
951
952	else
953
954	# CHECK, IF THERE IS AN EXECUTABLE FOR THE BLOCK
955	if [[ ! -f ${PALM_BIN}/interpret_config${block}.x ]]
956	then
957	printf "\n\n +++ no interpret_config found for given block \"$cond1 $cond2\""
958	printf "\n run \"mbuild -u -h ...\" to generate utilities for this block"
959	locat=interpret_config; exit
960	else
961	interpret_config${block}.x
962	fi
963
964	fi
965	rm .mrun_environment
966
967
968	# EXECUTE SHELL-COMMANDS GENERATED BY interpret_config WITHIN THIS SHELL
969	chmod u+x $interpreted_config_file
970	export PATH=$PATH:.
971	. $interpreted_config_file
972	rm $interpreted_config_file
973
974	fi
975
976
977	# VALUES OF MRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
978	[[ $mrun_memory != 0 ]] && memory=$mrun_memory
979	[[ "$mrun_group_number" != "none" ]] && group_number=$mrun_group_number
980	[[ $mrun_cpumax != 0 ]] && cpumax=$mrun_cpumax
981	[[ "$mrun_numprocs" != "" ]] && numprocs=$mrun_numprocs
982	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
983	[[ "$mrun_tasks_per_node" != "" ]] && tasks_per_node=$mrun_tasks_per_node
984
985
986	# ON THE LOCAL MACHINE, DETERMINE (FROM THE CONFIGURATION-FILE) THE PATH
987	# FOR SOURCE-FILES TO BE COMPILED.
988	# IN A BATCH-JOB, SOURCES (ROUTINES TO BE COMPILED) ARE COMPLETE ALREADY.
989	# BEFORE MRUN IS CALLED IN THE JOB, SOURCES_COMPLETE = true IS ASSIGNED (SEE FURTHER BELOW).
990	if [[ "$SOURCES_COMPLETE" = "" ]]
991	then
992
993	# FIRST CHECK, IF A GLOBAL SOURCE PATH (TO BE USED FOR ALL HOSTS)
994	# HAS BEEN DEFINED
995	source_path=""
996	line=""
997	grep "%source_path" $config_file > tmp_mrun
998	while read line
999	do
1000	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1001	then
1002	if [[ "$(echo $line \| cut -d" " -f3)" = "" ]]
1003	then
1004	global_source_path=`echo $line \| cut -d" " -f2`
1005	fi
1006	fi
1007	done < tmp_mrun
1008
1009	line=""
1010	found=false
1011	grep " $localhost" $config_file \| grep "%source_path" > tmp_mrun
1012	while read line
1013	do
1014	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
1015	then
1016	if [[ $found = true ]]
1017	then
1018	printf "\n\n +++ more than one source path found in configuration file"
1019	printf "\n for local host \"$localhost\" "
1020	locat=source_path; exit
1021	fi
1022	source_path=`echo $line \| cut -d" " -f2`
1023	found=true
1024	fi
1025	done < tmp_mrun
1026	rm tmp_mrun
1027
1028	if [[ "$source_path" = "" ]]
1029	then
1030	if [[ "$global_source_path" != "" ]]
1031	then
1032	source_path=$global_source_path
1033	else
1034	printf "\n\n +++ no source path found in configuration file"
1035	printf "\n for local host \"$localhost\" "
1036	locat=source_path; exit
1037	fi
1038	fi
1039	eval source_path=$source_path
1040
1041	if [[ ! -d $source_path ]]
1042	then
1043	printf "\n\n +++ source path \"$source_path\" on local host"
1044	printf "\n \"$localhost\" does not exist"
1045	locat=source_path; exit
1046	fi
1047
1048	fi
1049
1050
1051	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1052	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1053	if [[ "$global_revision" = "" && $host != "ibmkisti" ]]
1054	then
1055	global_revision=`svnversion $source_path 2>/dev/null`
1056	global_revision="Rev: $global_revision"
1057	fi
1058
1059
1060	# ??? das darf doch eigentlich garnicht passieren, weil optionen config-datei uebersteuern ???
1061	# CHECK AGAIN, IF EXECUTION SHALL BE DONE ON A REMOTE-HOST (BATCH-JOB).
1062	# (HOST MAY HAVE CHANGED DUE TO SETTINGS IN THE CONFIGURATION-FILE)
1063	if [[ -n $host && "$host" != $localhost ]]
1064	then
1065	do_batch=true
1066	do_remote=true
1067	case $host in
1068	(ibm\|ibmh\|ibmkisti\|ibmku\|ibms\|lcbullhh\|lccrayb\|lccrayh\|lccrayf\|lceddy\|lckyoto\|lcocean\|unics\|lcxe6\|lcxt5m\|lck\|lckiaps\|lckordi\|lckyuh\|lckyut\|lcsb\|lcgeohu) true;;
1069	(*) printf "\n"
1070	printf "\n +++ sorry: execution of batch jobs on remote host \"$host\""
1071	printf "\n is not available"
1072	locat=nqs; (( iec = 0 )); exit;;
1073	esac
1074	else
1075	host=$localhost
1076	fi
1077
1078
1079
1080	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1081	if [[ "$cond1" = parallel \|\| "$cond2" = parallel ]]
1082	then
1083
1084	# CHECK, IF NUMBER OF CORES TO BE USED HAS BEEN GIVEN
1085	if [[ ! -n $numprocs ]]
1086	then
1087	printf "\n"
1088	printf "\n +++ option \"-K parallel\" requires additional specification"
1089	printf "\n of the number of processors to be used by"
1090	printf "\n mrun-option \"-X\" or by environment-variable"
1091	printf "\n \"numprocs\" in the configuration file"
1092	locat=numprocs; (( iec = 0 )); exit
1093	fi
1094
1095	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1096	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1097	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
1098	then
1099	printf "\n"
1100	printf "\n +++ option \"-T\" (tasks per node) is missing"
1101	printf "\n set -T option or define tasks_per_node in the config file"
1102	locat=tasks_per_node; (( iec = 0 )); exit
1103	fi
1104
1105	if (( numprocs < tasks_per_node ))
1106	then
1107	printf "\n"
1108	printf "\n +++ tasks per node (-T) cannot exceed total number of processors (-X)"
1109	printf "\n given values: -T $tasks_per_node -X $numprocs"
1110	locat=tasks_per_node; (( iec = 0 )); exit
1111	fi
1112
1113	if [[ $host != lcxt5m ]]
1114	then
1115	(( nodes = numprocs / ( tasks_per_node * threads_per_task ) ))
1116	(( ival = $tasks_per_node ))
1117	(( pes = numprocs ))
1118	(( ii = pes / ival ))
1119	(( remaining_pes = pes - ii * ival ))
1120	if (( remaining_pes > 0 ))
1121	then
1122	printf "\n"
1123	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1124	printf "\n divisor of the total number of processors (option \"-X\")"
1125	printf "\n values of this mrun-call: \"-T $tasks_per_node\" \"-X $numprocs\""
1126	printf "\n One of the nodes is filled with $remaining_pes instead of $tasks_per_node tasks"
1127	(( nodes = nodes + 1 ))
1128	fi
1129	fi
1130
1131
1132	# SETTINGS FOR SUBJOB-COMMAND
1133	OOPT="-O $threads_per_task"
1134
1135	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1136	if [[ "$tasks_per_node" != "" ]]
1137	then
1138	TOPT="-T $tasks_per_node"
1139	fi
1140
1141	# CHECK node_usage FOR ALLOWED VALUES AND SET DEFAULT VALUE, IF NECESSARY
1142	if [[ $node_usage = default ]]
1143	then
1144	if [[ $host = ibms ]]
1145	then
1146	node_usage=shared
1147	else
1148	node_usage=not_shared
1149	fi
1150	fi
1151
1152	if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage \| cut -c1-3)" != "sla" ]]
1153	then
1154	printf "\n"
1155	printf "\n +++ node usage (option \"-n\") is only allowed to be set"
1156	printf "\n \"shared\" or \"not_shared\""
1157	locat=tasks_per_node; (( iec = 0 )); exit
1158	fi
1159
1160	fi
1161
1162	# CHECK IF HOSTFILE EXISTS
1163	if [[ -n $hostfile ]]
1164	then
1165	if [[ ! -f $hostfile ]]
1166	then
1167	printf "\n"
1168	printf "\n +++ hostfile \"$hostfile\" does not exist"
1169	locat=hostfile; exit
1170	fi
1171	fi
1172
1173
1174	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1175	if [[ "$maximum_parallel_io_streams" = "" ]]
1176	then
1177	maximum_parallel_io_streams=$numprocs
1178	fi
1179
1180
1181	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP, subjob AND batch_scp SCRIPTS
1182	if [[ "$scp_port" != "" ]]
1183	then
1184	PORTOPT="-P $scp_port"
1185	SSH_PORTOPT="-p $scp_port"
1186	fi
1187
1188
1189	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1190	# CONFIG-FILE
1191	if [[ "$ssh_key" != "" ]]
1192	then
1193	ssh_key="-i $HOME/.ssh/$ssh_key"
1194	fi
1195
1196
1197	# SET DEFAULT-QUEUE, IF NOT GIVEN
1198	if [[ $queue = none ]]
1199	then
1200	case $host in
1201	(ibmh) queue=cluster;;
1202	(ibmkisti) queue=class.32plus;;
1203	(lcbullhh) queue=compute;;
1204	(lccrayb) queue=mpp1q;;
1205	(lccrayh) queue=mpp1q;;
1206	(lcgeohu) queue=short;;
1207	(lckiaps) queue=normal;;
1208	(lckyoto) queue=ph;;
1209	(lckyuh) queue=fx-single;;
1210	(lckyut) queue=cx-single;;
1211	(lctit) queue=S;;
1212	(unics) queue=unics;;
1213	esac
1214	fi
1215
1216
1217	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1218	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1219	(( i = 0 ))
1220	while (( i < iin ))
1221	do
1222	(( i = i + 1 ))
1223	(( maxcycle = 0 ))
1224
1225	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1226	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1227	if [[ "${actionin[$i]}" = di ]]
1228	then
1229	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1230	# HOST ONLY
1231	eval filename=${pathin[$i]}/${endin[$i]}
1232	else
1233	remotepathin[$i]=${pathin[$i]}/${afname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
1234	# HOST ONLY
1235	eval filename=${pathin[$i]}/${afname}${endin[$i]}
1236	fi
1237	eval pathname=${pathin[$i]}
1238
1239	# CHECK IF FILE EXISTS
1240	if ! ls $filename* 1>/dev/null 2>&1
1241	then
1242
1243	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1244	if [[ "${transin[$i]}" != "locopt" ]]
1245	then
1246	printf "\n\n +++ INPUT-file: "
1247	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1248	then
1249	printf "\n $filename"
1250	else
1251	printf "\n $filename.${extin[$i]}"
1252	fi
1253	printf "\n does not exist\n"
1254	locat=input; exit
1255	else
1256	transin[$i]="unavailable"
1257	fi
1258	else
1259
1260	# DETERMINE THE FILE'S CYCLE NUMBER
1261	ls -1 -d $filename > filelist 2>/dev/null
1262	ls -1 -d $filename.* >> filelist 2>/dev/null
1263	while read zeile
1264	do
1265	# filename without path (i.e. after the last "/")
1266	basefilename=$(basename ${zeile})
1267
1268	# check if there is an extension
1269	extension=${basefilename##*.}
1270	if [[ "$extension" = "$extin[$i]" ]]
1271	then
1272	basefilename=${basefilename&.*}
1273	fi
1274
1275	# check for an existing cycle number
1276	cycle=${basefilename##*.}
1277	if [[ $cycle =~ ^-?[0-9]+$ ]]
1278	then
1279	(( icycle = $cycle ))
1280	else
1281	(( icycle = 0 ))
1282	fi
1283
1284	if (( icycle > maxcycle ))
1285	then
1286	(( maxcycle = icycle ))
1287	fi
1288
1289	# cycle=$(echo $zeile \| cut -f2 -d".")
1290	# if [[ "$cycle" = "$zeile" ]]
1291	# then
1292	# (( icycle = 0 ))
1293	# elif [[ "$cycle" = "${extin[$i]}" ]]
1294	# then
1295	# (( icycle = 0 ))
1296	# else
1297	# (( icycle = $cycle ))
1298	# fi
1299	# if (( icycle > maxcycle ))
1300	# then
1301	# (( maxcycle = icycle ))
1302	# fi
1303	done <filelist
1304	rm filelist
1305
1306	# APPEND CYCLE NUMBER TO FILENAME
1307	if (( maxcycle > 0 ))
1308	then
1309	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1310	then
1311	filename=${filename}.$maxcycle.${extin[$i]}
1312	else
1313	filename=${filename}.$maxcycle
1314	fi
1315	else
1316	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1317	then
1318	filename=${filename}.${extin[$i]}
1319	fi
1320	fi
1321
1322	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1323	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1324	absnamein[$i]=$filename
1325	if (( maxcycle > 0 ))
1326	then
1327	if [[ "${actionin[$i]}" = di ]]
1328	then
1329	frelin[$i]=${endin[$i]}.$maxcycle
1330	else
1331	frelin[$i]=${afname}${endin[$i]}.$maxcycle
1332	fi
1333	else
1334	if [[ "${actionin[$i]}" = di ]]
1335	then
1336	frelin[$i]=${endin[$i]}
1337	else
1338	frelin[$i]=${afname}${endin[$i]}
1339	fi
1340	fi
1341
1342	fi
1343	done
1344
1345	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1346	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1347	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1348	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1349	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1350	# REMOTE HOST)
1351	(( i = 0 ))
1352	while (( i < iout ))
1353	do
1354	(( i = i + 1 ))
1355	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1356	then
1357	if [[ "${actionout[$i]}" = tr ]]
1358	then
1359	actionout[$i]=""
1360	elif [[ "${actionout[$i]}" = trpe ]]
1361	then
1362	actionout[$i]=pe
1363	elif [[ "${actionout[$i]}" = tra ]]
1364	then
1365	actionout[$i]=a
1366	fi
1367	(( maxcycle = 0 ))
1368	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1369	eval catalogname=${pathout[$i]}
1370	if ! ls $filename* 1>/dev/null 2>&1
1371	then
1372
1373	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1374	if cat /dev/null > $filename
1375	then
1376	rm $filename
1377	else
1378
1379	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1380	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1381	if [[ ! -d $catalogname ]]
1382	then
1383	if mkdir -p $catalogname
1384	then
1385	printf "\n\n *** directory:"
1386	printf "\n $catalogname"
1387	printf "\n was created\n"
1388	else
1389	printf "\n\n +++ OUTPUT-file:"
1390	printf "\n $filename"
1391	printf "\n cannot be created, because directory does not exist"
1392	printf "\n and cannot be created either"
1393	printf "\n"
1394	locat=output ; exit
1395	fi 2>/dev/null
1396	else
1397	printf "\n\n +++ OUTPUT-file:"
1398	printf "\n $filename"
1399	printf "\n cannot be created, although directory exists"
1400	printf "\n"
1401	locat=output ; exit
1402	fi
1403	fi 2>/dev/null
1404	else
1405
1406	# DETERMINE THE CYCLE NUMBER
1407	ls -1 -d $filename > filelist 2>/dev/null
1408	ls -1 -d $filename.* >> filelist 2>/dev/null
1409	while read zeile
1410	do
1411
1412	# filename without path (i.e. after the last "/")
1413	basefilename=$(basename ${zeile})
1414
1415	# check if there is an extension
1416	extension=${basefilename##*.}
1417	if [[ "$extension" = "${extout[$i]}" ]]
1418	then
1419	basefilename=${basefilename%.*}
1420	fi
1421
1422	# check for an existing cycle number
1423	cycle=${basefilename##*.}
1424	if [[ $cycle =~ ^-?[0-9]+$ ]]
1425	then
1426	(( icycle = $cycle + 1 ))
1427	else
1428	(( icycle = 1 ))
1429	fi
1430
1431	if (( icycle > maxcycle ))
1432	then
1433	(( maxcycle = icycle ))
1434	fi
1435
1436	done <filelist
1437	rm filelist
1438	fi
1439
1440	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1441	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1442	if [[ "${actionout[$i]}" != a ]]
1443	then
1444	if (( maxcycle > 0 ))
1445	then
1446	filename_tmp=${filename}.$maxcycle
1447	if cat /dev/null > $filename_tmp
1448	then
1449	rm $filename_tmp
1450	else
1451	printf "\n +++ OUTPUT-file:"
1452	printf "\n $filename_tmp"
1453	printf "\n cannot be created"
1454	locat=output ; exit
1455	fi
1456	fi
1457	else
1458	(( maxcycle = maxcycle - 1 ))
1459	fi
1460
1461	(( cycnum[$i] = maxcycle ))
1462	pathout[$i]=$filename
1463
1464	fi
1465	done
1466
1467
1468	# THE DVR-PACKAGE REQUIRES ITS OWN LIBRARY
1469	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
1470	then
1471	if [[ "$dvr_inc" = "" ]]
1472	then
1473	printf "\n\n +++ no value for \"dvr_inc\" given in configuration file"
1474	printf "\n This is required for the dvrp_graphics package.\n"
1475	locat=dvr; exit
1476	fi
1477	if [[ "$dvr_lib" = "" ]]
1478	then
1479	printf "\n\n +++ no value for \"dvr_lib\" given in configuration file"
1480	printf "\n This is required for the dvrp_graphics package.\n"
1481	locat=dvr; exit
1482	fi
1483	fi
1484
1485
1486	# CHECK, WETHER A MAIN PROGRAM OR AN EXECUTABLE HAVE BEEN DECLARED.
1487	# EXECUTABLES DO NOT NEED TO BE COMPILED.
1488	if [[ "$mainprog" = "" && "$executable" = "" ]]
1489	then
1490	printf "\n +++ neither main program nor executable defined"
1491	locat=source; exit
1492	elif [[ "$mainprog" != "" && "$executable" != "" ]]
1493	then
1494	printf "\n +++ main program as well as executable defined"
1495	locat=source; exit
1496	elif [[ "$mainprog" = "" && "$executable" != "" ]]
1497	then
1498	do_compile=false
1499	fi
1500
1501
1502	# CREATE SOURCE-DIRECTORY TO COLLECT ROUTINES TO BE COMPILED.
1503	# LATER THE MRUN-SCRIPT AND CONFIGURATION-FILE WILL ALSO BE COPIED TO THIS DIRECTORY.
1504	if [[ $restart_run != true && "$SOURCES_COMPLETE" = "" ]]
1505	then
1506	rm -rf SOURCES_FOR_RUN_$fname
1507	mkdir SOURCES_FOR_RUN_$fname
1508	fi
1509
1510
1511	# COLLECT ALL ROUTINES TO BE COMPILED
1512	# THIS IS NOT REQUIRED WITHIN BATCH-JOBS, BECAUSE ROUTINES HAVE ALREADY BEEN COLLECTED
1513	# BY THE MRUN-CALL WHICH CREATED THE BATCH-JOB.
1514	if [[ $do_compile = true && "$SOURCES_COMPLETE" = "" ]]
1515	then
1516
1517	[[ "$source_list" = LM ]] && source_list=LOCALLY_MODIFIED
1518
1519	if [[ "$source_list" = LOCALLY_MODIFIED ]]
1520	then
1521
1522	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
1523	source_list=""
1524	cd $source_path
1525
1526
1527	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
1528	if [[ ! -d .svn ]]
1529	then
1530	printf "\n\n +++ source directory"
1531	printf "\n \"$source_path\" "
1532	printf "\n is not under control of \"subversion\"."
1533	printf "\n Please do not use mrun-option \"-s LOCALLY_MODIFIED\"\n"
1534	fi
1535
1536
1537	# LIST ALL MODIFIED SOURCE CODE FILES
1538	Filenames=""
1539	svn status > tmp_mrun
1540	while read line
1541	do
1542	firstc=`echo $line \| cut -c1`
1543	if [[ $firstc = M \|\| $firstc = "?" ]]
1544	then
1545	Name=`echo "$line" \| cut -c8-`
1546	extension=`echo $Name \| cut -d. -f2`
1547	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
1548	then
1549	Filenames="$Filenames "$Name
1550	fi
1551	fi
1552	done < tmp_mrun
1553
1554
1555	# COPY FILES TO SOURCES_FOR_RUN_...
1556	for dateiname in $Filenames
1557	do
1558	cp $dateiname $working_directory/SOURCES_FOR_RUN_$fname
1559	source_list=$source_list"$dateiname "
1560	done
1561
1562	cd - > /dev/null
1563
1564
1565	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
1566	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
1567	elif [[ "$source_list" != "" && $restart_run != true ]]
1568	then
1569
1570	cd $source_path
1571
1572	for filename in $source_list
1573	do
1574
1575	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
1576	if [[ $(echo $filename \| grep -c "/") != 0 ]]
1577	then
1578	printf "\n +++ source code file: $filename"
1579	printf "\n must not contain (\"/\") "
1580	locat=source; exit
1581	fi
1582
1583	if [[ ! -f $filename ]]
1584	then
1585	printf "\n +++ source code file: $filename"
1586	printf "\n does not exist"
1587	locat=source; exit
1588	else
1589	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
1590	fi
1591
1592	done
1593
1594	cd - > /dev/null
1595
1596	fi
1597
1598
1599	# CHECK, IF A MAIN PROGRAM EXISTS AND IF IT IS PART OF THE LIST OF FILES
1600	# TO BE COMPILED. IF NOT, ADD IT TO THE LIST.
1601	if [[ $restart_run != true ]]
1602	then
1603
1604	if [[ ! -f "$source_path/$mainprog" ]]
1605	then
1606	printf "\n\n +++ main program: $mainprog"
1607	printf "\n does not exist in source directory"
1608	printf "\n \"$source_path\"\n"
1609	locat=source; exit
1610	else
1611	if [[ $(echo $source_list \| grep -c $mainprog) = 0 ]]
1612	then
1613	cp $source_path/$mainprog SOURCES_FOR_RUN_$fname
1614	source_list=${mainprog}" $source_list"
1615	fi
1616	fi
1617	fi
1618
1619
1620	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1621	# NOT REQUIRED FOR RESTART RUNS, SOURCES_FOR_RUN... HAS BEEN CREATED BY THE INITIAL RUN
1622	if [[ "$restart_run" != true ]]
1623	then
1624	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1625	if [[ ! -f $makefile ]]
1626	then
1627	printf "\n +++ file \"$makefile\" does not exist"
1628	locat=make; exit
1629	else
1630	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
1631	fi
1632	fi
1633
1634
1635	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1636	if [[ $restart_run != true && "$add_source_path" != "" ]]
1637	then
1638
1639	# DOES THE DIRECTORY EXIST?
1640	if [[ ! -d $add_source_path ]]
1641	then
1642	printf "\n\n *** INFORMATIVE: additional source code directory"
1643	printf "\n \"$add_source_path\" "
1644	printf "\n does not exist or is not a directory."
1645	printf "\n No source code will be used from this directory!\n"
1646	add_source_path=""
1647	if [[ $silent == false ]]
1648	then
1649	sleep 3
1650	fi
1651	else
1652
1653	cd $add_source_path
1654	found=false
1655
1656	Names=$(ls -1 *.f90 2>&1)
1657	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1658	Names=$(ls -1 *.F90 2>&1)
1659	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1660	Names=$(ls -1 *.F 2>&1)
1661	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1662	Names=$(ls -1 *.f 2>&1)
1663	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1664	Names=$(ls -1 *.c 2>&1)
1665	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1666
1667	cd - > /dev/null
1668	cd SOURCES_FOR_RUN_$fname
1669
1670	# COPY MAKEFILE IF EXISTING
1671	if [[ -f $add_source_path/Makefile ]]
1672	then
1673	printf "\n\n *** user Makefile from directory"
1674	printf "\n \"$add_source_path\" is used \n"
1675	if [[ $silent == false ]]
1676	then
1677	sleep 1
1678	fi
1679	cp $add_source_path/Makefile .
1680	fi
1681
1682	for dateiname in $AddFilenames
1683	do
1684	if [[ -f $dateiname ]]
1685	then
1686	printf "\n +++ source code file \"$dateiname\" found in additional"
1687	printf "\n source code directory \"$add_source_path\" "
1688	printf "\n but was also given with option \"-s\" which means that it should be taken"
1689	printf "\n from directory \"$source_path\"."
1690	locat=source; exit
1691	fi
1692
1693	cp $add_source_path/$dateiname .
1694	source_list="$source_list $dateiname"
1695
1696	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1697	if [[ $(grep -c $dateiname Makefile) = 0 ]]
1698	then
1699	printf "\n\n +++ user file \"$dateiname\" "
1700	printf "\n is not listed in Makefile \n"
1701	locat=source; exit
1702	else
1703
1704	if [[ $found = false ]]
1705	then
1706	found=true
1707	printf "\n\n *** following user file(s) added to the"
1708	printf " files to be translated:\n "
1709	fi
1710	printf "$dateiname "
1711	if [[ $silent == false ]]
1712	then
1713	sleep 0.5
1714	fi
1715
1716	fi
1717	done
1718	[[ $found = true ]] && printf "\n"
1719	cd - > /dev/null
1720	fi
1721	fi
1722
1723
1724	# ADD ALL ROUTINES BELONGING TO SOFTWARE PACKAGES (GIVEN BY OPTION -p)
1725	# TO THE LIST OF FILES TO BE COMPILED
1726	if [[ $restart_run != true && -n $package_list ]]
1727	then
1728
1729	cd $source_path
1730
1731	for package in $package_list
1732	do
1733
1734	[[ $package = "dvrp_graphics+1PE" ]] && package=dvrp_graphics
1735
1736	# DETERMINE FILES BELONGING TO THE PACKAGE
1737	# ERROR MESSAGE ARE REDIRECTED TO /dev/null, BECAUSE WILDCARD (*) ALSO GIVES
1738	# THE NAME OF THE DIRECTORY
1739	package_source_list=`grep "defined( __$package " * 2>/dev/null \| cut -f1 -d:`
1740
1741
1742	# ADD THESE FILES TO THE LIST OF FILES TO BE COMPILED,
1743	# IF THEY ARE NOT ALREADY PART OF THE LIST
1744	for source_list_name in $package_source_list
1745	do
1746	if [[ $(echo $source_list \| grep -c $source_list_name) = 0 ]]
1747	then
1748
1749	# ONLY TAKE FILES WITH VALID SUFFIX
1750	ending=`echo $source_list_name \| cut -f2 -d.`
1751	if [[ "$ending" = f90 \|\| "$ending" = F90 \|\| "$ending" = f \|\| "$ending" = F \|\| "$ending" = c ]]
1752	then
1753	cp $source_list_name $working_directory/SOURCES_FOR_RUN_$fname
1754	source_list="$source_list $source_list_name"
1755	fi
1756	fi
1757	done
1758	done
1759
1760	cd - > /dev/null
1761	fi
1762
1763	fi # do_compile=true
1764
1765
1766	# IF SOURCE CODE IS TO BE COMPILED, DO SOME MORE CHECKS
1767	# AND SET PRE-PROCESSOR DIRECTIVES
1768	if [[ $do_compile = true \|\| $create_executable_for_batch = true ]]
1769	then
1770
1771	# SET PREPROCESSOR-DIRECTIVES TO SELECT OPERATING SYSTEM SPECIFIC CODE
1772	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1773	then
1774	cpp_options="${cpp_options},-D__ibm=__ibm"
1775	elif [[ $(echo $localhost \| cut -c1-3) = nec ]]
1776	then
1777	cpp_options="$cpp_options -D__nec"
1778	elif [[ $(echo $localhost \| cut -c1-2) = lc ]]
1779	then
1780	cpp_options="$cpp_options -D__lc"
1781	else
1782	cpp_options="$cpp_options -D__$localhost"
1783	fi
1784
1785	# SET DIRECTIVES GIVEN BY OPTION -K (E.G. parallel)
1786	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1787	then
1788	[[ -n $cond1 ]] && cpp_options="${cpp_options},-D__$cond1=__$cond1"
1789	[[ -n $cond2 ]] && cpp_options="${cpp_options},-D__$cond2=__$cond2"
1790	else
1791	[[ -n $cond1 ]] && cpp_options="$cpp_options -D__$cond1"
1792	[[ -n $cond2 ]] && cpp_options="$cpp_options -D__$cond2"
1793	fi
1794
1795	# SET DIRECTIVES FOR ACTIVATING SOFTWARE-PACKAGES (OPTION -p)
1796	if [[ -n $package_list ]]
1797	then
1798	for package in $package_list
1799	do
1800	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1801	then
1802	if [[ $package != "dvrp_graphics+1PE" ]]
1803	then
1804	cpp_options="${cpp_options},-D__$package=__$package"
1805	else
1806	cpp_options="${cpp_options},-D__dvrp_graphics=__dvrp_graphics"
1807	export use_seperate_pe_for_dvrp_output=true
1808	fi
1809	else
1810	if [[ $package != "dvrp_graphics+1PE" ]]
1811	then
1812	cpp_options="$cpp_options -D__$package"
1813	else
1814	cpp_options="$cpp_options -D__dvrp_graphics"
1815	export use_seperate_pe_for_dvrp_output=true
1816	fi
1817	fi
1818	done
1819	fi
1820
1821	else
1822
1823
1824	# FOR LOCAL RUNS CHECK AGAIN, IF EXECUTABLE EXISTS
1825	if [[ $do_remote = false ]]
1826	then
1827	if [[ ! -f $executable ]]
1828	then
1829	printf "\n +++ executable file: $executable"
1830	printf "\n does not exist"
1831	locat=executable; exit
1832	fi
1833	fi
1834	fi
1835
1836
1837	# DETERMINE THE JOB MODE
1838	if [[ $(echo $localhost \| cut -c1-3) = ibm ]]
1839	then
1840	if [[ "$LOADLBATCH" = yes ]]
1841	then
1842	batch_job=.TRUE.
1843	jobmo=BATCH
1844	else
1845	batch_job=.FALSE.
1846	jobmo=INTERACTIVE
1847	fi
1848	else
1849	if [[ "$ENVIRONMENT" = BATCH \|\| "$PJM_ENVIRONMENT" = BATCH ]]
1850	then
1851	batch_job=.TRUE.
1852	jobmo=BATCH
1853	else
1854	batch_job=.FALSE.
1855	jobmo=INTERACTIVE
1856	fi
1857	fi
1858
1859	# NO INTERACTIVE RUNS ALLOWED ON LCTIT
1860	if [[ $host = lctit && $jobmo = INTERACTIVE && $do_batch = false ]]
1861	then
1862	printf "\n +++ no interactive runs allowed on host \"$host\" "
1863	printf "\n please submit batch job using mrun option \"-b\" \n"
1864	locat=normal; exit
1865	fi
1866
1867
1868	# CHECK, IF USER DEFINED A COMPILER
1869	if [[ "$compiler_name" = "" ]]
1870	then
1871
1872	printf "\n +++ no compiler specified for \"$host $cond1 $cond2\""
1873	locat=compiler_name; exit
1874
1875	fi
1876
1877
1878	# DETERMINE THE NAME OF MRUN'S TEMPORARY WORKING DIRECTORY
1879
1880	# ON HLRN-III, USE THE QUEUING NAME. OTHERWISE USE USERNAME AND RANDOM NUMBER
1881	if [[ $do_batch = false && $(echo $host \| cut -c1-6) = lccray ]]
1882	then
1883	kennung=$(checkjob $PBS_JOBID \| grep Reservation \| cut -d" " -s -f2 \| cut -d"." -s -f2 \| sed "s/['\"]//g")
1884	if [[ "$kennung" = "" ]]
1885	then
1886	kennung=$RANDOM
1887	fi
1888	else
1889	kennung=$RANDOM
1890	fi
1891
1892	if [[ "$tmp_user_catalog" = "" ]]
1893	then
1894	if [[ $localhost = ibmh ]]
1895	then
1896	tmp_user_catalog=$SCRATCH
1897	else
1898	tmp_user_catalog=/tmp
1899	fi
1900	fi
1901	TEMPDIR=$tmp_user_catalog/${usern}.$kennung
1902
1903
1904	# DETERMINE THE NAME OF THE DIRECTORY WHICH IS USED TO TEMPORARILY STORE DATA FOR RESTART RUNS
1905	if [[ "$tmp_data_catalog" = "" ]]
1906	then
1907	tmp_data_catalog=/tmp/mrun_restart_data
1908	fi
1909
1910
1911	# IN CASE OF LOCAL RUNS REPLACE ENVIRONMENT VARIABLES BY THEIR VALUES
1912	if [[ $do_remote = false && $do_compile = true \|\| $create_executable_for_batch = true ]]
1913	then
1914	eval fopts=\"$fopts\"
1915	eval lopts=\"$lopts\"
1916	fi
1917
1918
1919	# DETERMINE COMPILE- AND LINK-OPTIONS
1920	fopts="$fopts $netcdf_inc $fftw_inc $dvr_inc"
1921	lopts="$lopts $netcdf_lib $fftw_lib $dvr_lib"
1922	XOPT="-X $numprocs"
1923
1924
1925	# CHECK THE CPU-LIMIT. IT MUST BE GIVEN FOR BATCH-JOBS AND IS COMMUNICATED TO THE
1926	# EXECUTABLE VIA NAMELIST-PARAMETER cputime
1927	done=false
1928	while [[ $done = false ]]
1929	do
1930	cputime=$cpumax
1931	if (( $cputime == 0 ))
1932	then
1933	if [[ $do_batch = true ]]
1934	then
1935	printf "\n +++ cpu-time is undefined"
1936	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1937	printf "\n >>> "
1938	read cputime 1>/dev/null 2>&1
1939	else
1940	cputime=10000000 # NO CPU LIMIT FOR INTERACTIVE RUNS
1941	fi
1942	else
1943	done=true
1944	fi
1945	cpumax=$cputime
1946	done
1947
1948	(( minuten = cputime / 60 ))
1949	(( sekunden = cputime - minuten * 60 ))
1950
1951
1952	# CHECK THE MEMORY DEMAND
1953	if [[ $do_batch = true ]]
1954	then
1955	done=false
1956	while [[ $done = false ]]
1957	do
1958	if (( memory == 0 ))
1959	then
1960	printf "\n +++ memory demand is undefined"
1961	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1962	printf "\n >>> "
1963	read memory 1>/dev/null 2>&1
1964	else
1965	done=true
1966	fi
1967	done
1968	fi
1969
1970
1971	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1972	if [[ $do_remote = true && -z $remote_username ]]
1973	then
1974	while [[ -z $remote_username ]]
1975	do
1976	printf "\n +++ username on remote host \"$host\" is undefined"
1977	printf "\n >>> Please type username:"
1978	printf "\n >>> "
1979	read remote_username
1980	done
1981	mc="$mc -u$remote_username"
1982	fi
1983
1984	# CHECK FOR INITIAL COMMANDS AFTER LOGIN
1985	if [[ "$login_init_cmd" != "" ]]
1986	then
1987	export init_cmds="${login_init_cmd};"
1988	fi
1989
1990
1991	# SET THE MODULE-LOAD COMMAD AND EXPORT IT FOR subjob
1992	if [[ "$modules" != "" ]]
1993	then
1994	if [[ $host = lctit ]]
1995	then
1996	export module_calls=". $modules"
1997	else
1998	export module_calls="module load ${modules};"
1999	fi
2000	fi
2001
2002	# OUTPUT OF THE MRUN-HEADER
2003	calltime=$(date)
2004	printf "\n"
2005	printf "#------------------------------------------------------------------------# \n"
2006	printf "\| %-35s%35s \| \n" "$version" "$calltime"
2007	printf "\| \| \n"
2008	spalte1="called on:"; spalte2=$localhost_realname
2009	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2010	if [[ $do_remote = true ]]
2011	then
2012	spalte1="execution on:"; spalte2="$host (username: $remote_username)"
2013	else
2014	spalte1="execution on:"; spalte2="$host ($localhost_realname)"
2015	fi
2016	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2017	if [[ -n $numprocs ]]
2018	then
2019	if [[ $run_coupled_model = false ]]
2020	then
2021	spalte1="number of PEs:"; spalte2=$numprocs
2022	else
2023	spalte1="number of PEs:"; spalte2="$numprocs (atmosphere: $numprocs_atmos, ocean: $numprocs_ocean)"
2024	fi
2025	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2026	fi
2027	if [[ -n $tasks_per_node ]]
2028	then
2029	spalte1="tasks per node:"; spalte2="$tasks_per_node (number of nodes: $nodes)"
2030	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2031	if (( remaining_pes > 0 ))
2032	then
2033	spalte1=" "; spalte2="one of the nodes only filled with $remaining_pes tasks"
2034	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2035	fi
2036	fi
2037	if [[ $maximum_parallel_io_streams != $numprocs ]]
2038	then
2039	spalte1="max par io streams:"; spalte2="$maximum_parallel_io_streams"
2040	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2041	fi
2042	if [[ $use_openmp = true ]]
2043	then
2044	spalte1="threads per task:"; spalte2="$threads_per_task"
2045	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2046	fi
2047	printf "\| \| \n"
2048	if [[ $do_compile = true ]]
2049	then
2050	if [[ "$mopts" != "" ]]
2051	then
2052	spalte1="make options:"; spalte2=$(echo "$mopts" \| cut -c-45)
2053	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2054	zeile=$(echo "$mopts" \| cut -c46-)
2055	while [[ "$zeile" != "" ]]
2056	do
2057	spalte1=""
2058	spalte2=$(echo "$zeile" \| cut -c-45)
2059	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2060	zeile=$(echo "$zeile" \| cut -c46-)
2061	done
2062	fi
2063
2064	spalte1="cpp directives:"; spalte2=$(echo "$cpp_options" \| cut -c-45)
2065	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2066	zeile=$(echo "$cpp_options" \| cut -c46-)
2067	while [[ "$zeile" != "" ]]
2068	do
2069	spalte1=""
2070	spalte2=$(echo "$zeile" \| cut -c-45)
2071	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2072	zeile=$(echo "$zeile" \| cut -c46-)
2073	done
2074
2075	spalte1="compiler options:"; spalte2=$(echo "$fopts" \| cut -c-45)
2076	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2077	zeile=$(echo "$fopts" \| cut -c46-)
2078	while [[ "$zeile" != "" ]]
2079	do
2080	spalte1=""
2081	spalte2=$(echo "$zeile" \| cut -c-45)
2082	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2083	zeile=$(echo "$zeile" \| cut -c46-)
2084	done
2085
2086	spalte1="linker options:"; spalte2=$(echo "$lopts" \| cut -c-45)
2087	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2088	zeile=$(echo "$lopts" \| cut -c46-)
2089	while [[ "$zeile" != "" ]]
2090	do
2091	spalte1=""
2092	spalte2=$(echo "$zeile" \| cut -c-45)
2093	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2094	zeile=$(echo "$zeile" \| cut -c46-)
2095	done
2096
2097	spalte1="modules to be load:"; spalte2=$(echo "$modules" \| cut -c-45)
2098	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2099	zeile=$(echo "$modules" \| cut -c46-)
2100	while [[ "$zeile" != "" ]]
2101	do
2102	spalte1=""
2103	spalte2=$(echo "$zeile" \| cut -c-45)
2104	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2105	zeile=$(echo "$zeile" \| cut -c46-)
2106	done
2107
2108	spalte1="main program:"; spalte2=$mainprog
2109	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2110	else
2111	spalte1=executable:; spalte2=$executable
2112	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2113	fi
2114	printf "\| \| \n"
2115	spalte1="base name of files:"; spalte2=$fname
2116	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2117	if [[ $fname != $afname ]]
2118	then
2119	spalte1="base name of input files:"; spalte2=$afname
2120	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2121	fi
2122	spalte1="INPUT control list:"; spalte2=$(echo $input_list)
2123	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2124	spalte1="OUTPUT control list:"; spalte2=$(echo $output_list)
2125	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2126
2127	if [[ "$ocean_file_appendix" = true ]]
2128	then
2129	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
2130	fi
2131
2132	if [[ $do_batch = true \|\| "$LOADLBATCH" = yes ]]
2133	then
2134	spalte1="memory demand / PE":; spalte2="$memory MB"
2135	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2136	spalte1=CPU-time:; spalte2="$minuten:$sekunden"
2137	printf "\| %-25s%-45s \| \n" "$spalte1" "$spalte2"
2138	fi
2139
2140	if [[ $do_compile = true ]]
2141	then
2142	printf "\| \| \n"
2143	printf "\| Files to be compiled: \| \n"
2144	zeile=$source_list
2145	while [[ "$zeile" != "" ]]
2146	do
2147	linestart=$(echo $zeile \| cut -c-70)
2148	printf "\| %-70s \| \n" "$linestart"
2149	zeile=$(echo "$zeile" \| cut -c71-)
2150	done
2151	fi
2152	printf "#------------------------------------------------------------------------#"
2153
2154
2155
2156	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
2157	if [[ $do_trace = true ]]
2158	then
2159	(( i = 0 ))
2160	while (( i < iin ))
2161	do
2162	(( i = i + 1 ))
2163	if (( i == 1 ))
2164	then
2165	printf "\n\n >>> INPUT-file assignments:\n"
2166	fi
2167	printf "\n ${localin[$i]} : ${absnamein[$i]}"
2168	done
2169	(( i = 0 ))
2170	while (( i < iout ))
2171	do
2172	(( i = i + 1 ))
2173	if (( i == 1 ))
2174	then
2175	printf "\n\n >>> OUTPUT-file assignments:\n"
2176	fi
2177	printf "\n ${localout[$i]} : ${pathout[$i]}"
2178	done
2179	(( i = 0 ))
2180	while (( i < iic ))
2181	do
2182	(( i = i + 1 ))
2183	if (( i == 1 ))
2184	then
2185	printf "\n\n >>> INPUT-commands:\n"
2186	fi
2187	printf "\n ${in_command[$i]}"
2188	done
2189	(( i = 0 ))
2190	while (( i < ioc ))
2191	do
2192	(( i = i + 1 ))
2193	if (( i == 1 ))
2194	then
2195	printf "\n\n >>> OUTPUT-commands:\n"
2196	fi
2197	printf "\n ${out_command[$i]}"
2198	done
2199	fi
2200
2201	# QUERY FOR CONTINUE (ON LOCAL MACHINES ONLY)
2202	if [[ $remotecall = false && $silent = false && $jobmo != BATCH ]]
2203	then
2204	antwort=dummy
2205	printf "\n\n"
2206	printf " >>> everything o.k. (y/n) ? "
2207	while read antwort
2208	do
2209	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
2210	then
2211	printf " >>> everything o.k. (y/n) ? "
2212	else
2213	break
2214	fi
2215	done
2216	if [[ $antwort = n \|\| $antwort = N ]]
2217	then
2218	locat=user_abort; (( iec = 0 )); exit
2219	fi
2220	if [[ $do_batch = true ]]
2221	then
2222	printf " >>> batch-job will be created and submitted"
2223	else
2224	printf " >>> MRUN will now continue to execute on this machine"
2225	fi
2226	fi
2227
2228
2229	# DETERMINE PATH FOR MAKE DEPOSITORY
2230	if [[ $do_batch = false \|\| $create_executable_for_batch = true ]]
2231	then
2232
2233	line=""
2234	grep "%depository_path" $config_file > tmp_mrun
2235	while read line
2236	do
2237	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2238	then
2239	if [[ "$(echo $line \| cut -d" " -s -f3)" = "" ]]
2240	then
2241	global_depository_path=`echo $line \| cut -d" " -s -f2`
2242	fi
2243	fi
2244	done < tmp_mrun
2245
2246	line=""
2247	grep " $localhost" $config_file \| grep "%depository_path" > tmp_mrun
2248	while read line
2249	do
2250	if [[ "$line" != "" && $(echo $line \| cut -c1) != "#" ]]
2251	then
2252	if [[ "$(echo $line \| cut -d" " -s -f4)" = "$cond1" && "$(echo $line \| cut -d" " -s -f5)" = "$cond2" ]]
2253	then
2254	local_depository_path=`echo $line \| cut -d" " -s -f2`
2255	fi
2256	fi
2257	done < tmp_mrun
2258
2259	if [[ "$local_depository_path" = "" ]]
2260	then
2261	if [[ "$global_depository_path" != "" ]]
2262	then
2263	local_depository_path=$global_depository_path
2264	else
2265	printf "\n\n +++ no depository path found in configuration file"
2266	printf "\n for local host \"$localhost\" "
2267	printf "\n please set \"\%depository_path\" in configuration file\n"
2268	locat=config_file; exit
2269	fi
2270	fi
2271	eval local_depository_path=$local_depository_path
2272	[[ "$cond1" != "" ]] && local_depository_path=${local_depository_path}_$cond1
2273	[[ "$cond2" != "" ]] && local_depository_path=${local_depository_path}_$cond2
2274
2275
2276	basename=`echo $mainprog \| cut -f1 -d"."`
2277	eval make_depository=${local_depository_path}/${basename}_current_version.tar
2278	if [[ ! -f $make_depository ]]
2279	then
2280	printf "\n"
2281	printf "\n *** WARNING: make depository \"$make_depository\" not found"
2282	printf "\n \"make\" will fail, if the Makefile or other source files are missing\n"
2283	fi
2284
2285	fi
2286
2287
2288	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
2289	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
2290	if [[ $do_batch = false ]]
2291	then
2292
2293
2294	# CREATE THE TEMPORARY WORKING DIRECTORY
2295	mkdir -p $TEMPDIR
2296	chmod go+rx $TEMPDIR
2297	tmpcreate=true
2298
2299
2300	# COPY EITHER THE COMPLETE SOURCE CODE FILES TO BE COMPILED OR THE EXECUTABLE
2301	# INTO THE TEMPORARY WORKING DIRECTORY
2302	if [[ $do_compile = true ]]
2303	then
2304
2305	TEMPDIR_COMPILE=$TEMPDIR
2306
2307	cp $make_depository $TEMPDIR_COMPILE
2308	cd $TEMPDIR_COMPILE
2309	tar -xf $make_depository > /dev/null 2>&1
2310	cd - > /dev/null
2311
2312	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
2313	# FILES ON CRAY XC30 SYSTEMS (HLRN III), rsync IS USED INSTEAD
2314	if [[ $(echo $host \| cut -c1-6) = lccray ]]
2315	then
2316	rsync -av -t SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2317	else
2318	cp SOURCES_FOR_RUN_$fname/* $TEMPDIR_COMPILE > /dev/null
2319	fi
2320
2321	else
2322
2323	cp $executable ${TEMPDIR}/a.out
2324
2325	fi
2326
2327
2328	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
2329	cd $TEMPDIR
2330	printf "\n *** changed to temporary directory: $TEMPDIR"
2331
2332
2333	# IF REQUIRED, START WITH COMPILING
2334	if [[ $do_compile = true ]]
2335	then
2336
2337
2338	if [[ -f a.out ]]
2339	then
2340
2341	# EXECUTABLE WAS CREATED DURING INTERACTIVE CALL OF MRUN
2342	printf "\n\n\n *** executable a.out found"
2343	printf "\n no compilation required \n"
2344
2345	else
2346
2347	# COMPILING WITH MAKE (ON NEC COMPILER IS CALLED ON HOST CROSS)
2348	printf "\n\n\n *** compilation starts \n$dashes\n"
2349	printf " *** compilation with make using following options:\n"
2350	printf " make depository: $make_depository"
2351	if [[ "$mopts" != "" ]]
2352	then
2353	printf " make options: $mopts\n"
2354	fi
2355	printf " compilername: $compiler_name\n"
2356	printf " compiler options: $fopts\n"
2357	printf " preprocessor directives: $cpp_options \n"
2358	printf " linker options: $lopts \n"
2359	if [[ "$modules" != "" ]]
2360	then
2361	printf " modules to be load: $modules \n"
2362	fi
2363	printf " source code files: $source_list \n"
2364
2365	if [[ $localhost = ibmh ]]
2366	then
2367	printf " compiler is called via ssh on \"plogin1\" \n"
2368	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\" "
2369	[[ ! -f a.out ]] && compile_error=true
2370	continue # STATUS=1, IF a.out EXISTS
2371	elif [[ $localhost = lcocean ]]
2372	then
2373	printf " compiler is called via ssh on \"ocean\" \n"
2374	echo $PWD
2375	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\" "
2376	[[ ! -f a.out ]] && compile_error=true
2377	continue # STATUS=1, IF a.out EXISTS
2378	elif [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayf \|\| $localhost = lccrayh ]]
2379	then
2380	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2381	elif [[ $localhost = lceddy ]]
2382	then
2383	which mpifc
2384	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2385	elif [[ $localhost = lcgeohu ]]
2386	then
2387	printf " compiler is called via ssh on \"cirrus\" \n"
2388	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=\"$lopts\" "
2389	# this check did not work. Although a.out exists, it sets compile_error to true!
2390	# [[ ! -f a.out ]] && compile_error=true
2391	continue # STATUS=1, IF a.out EXISTS
2392	else
2393	[[ "$init_cmds" != "" ]] && eval $init_cmds
2394	[[ "$module_calls" != "" ]] && eval $module_calls
2395	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
2396	fi
2397
2398	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
2399	then
2400	printf "\n +++ error occured while compiling or linking"
2401	locat=compile
2402
2403	exit
2404	else
2405	printf "$dashes\n *** compilation finished \n"
2406	fi
2407
2408	fi
2409
2410	fi
2411
2412
2413	# PROVIDE THE INPUT FILES
2414	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2415	(( i = 0 ))
2416	while (( i < iin ))
2417	do
2418	(( i = i + 1 ))
2419	if (( i == 1 ))
2420	then
2421	printf "\n\n *** providing INPUT-files:\n$dashes"
2422	fi
2423
2424
2425	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2426	if [[ "${transin[$i]}" = unavailable ]]
2427	then
2428	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
2429	then
2430	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}\" "
2431	printf "\n is not available!"
2432	else
2433	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${afname}${endin[$i]}.${extin[$i]}\" "
2434	printf "\n is not available!"
2435	fi
2436	continue
2437	fi
2438
2439	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2440	files_for_pes=false; datentyp=file
2441	if [[ "${actionin[$i]}" = pe && -n $numprocs ]]
2442	then
2443	files_for_pes=true; datentyp=files
2444	actionin[$i]=""
2445	elif [[ "${actionin[$i]}" = pe && ! -n $numprocs ]]
2446	then
2447	actionin[$i]=""
2448	elif [[ "${actionin[$i]}" = lnpe && -n $numprocs ]]
2449	then
2450	files_for_pes=true; datentyp=files
2451	actionin[$i]="ln"
2452	elif [[ "${actionin[$i]}" = lnpe && ! -n $numprocs ]]
2453	then
2454	actionin[$i]="ln"
2455	fi
2456
2457	if [[ $files_for_pes = true ]]
2458	then
2459	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2460	else
2461	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2462	fi
2463
2464	# INPUT-FILES TO BE LINKED
2465	if [[ "${actionin[$i]}" = ln ]]
2466	then
2467
2468	printf "\n $datentyp will be linked"
2469	if [[ $files_for_pes = false ]]
2470	then
2471	if [[ -f "${absnamein[$i]}" ]]
2472	then
2473	ln ${absnamein[$i]} ${localin[$i]}
2474	got_tmp[$i]=true
2475	fi
2476	else
2477	if [[ -d "${absnamein[$i]}" ]]
2478	then
2479	mkdir ${localin[$i]}
2480	cd ${absnamein[$i]}
2481	for file in $(ls *)
2482	do
2483	ln $file $TEMPDIR/${localin[$i]}
2484	done >\|/dev/null 2>&1
2485	cd $TEMPDIR
2486	fi
2487
2488	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2489	if [[ ! -f "${localin[$i]}/_000000" ]]
2490	then
2491	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2492	cp -r ${absnamein[$i]}/* ${localin[$i]}
2493	fi
2494
2495	got_tmp[$i]=true
2496	fi
2497	fi
2498
2499	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2500	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
2501	then
2502
2503	if [[ "${actionin[$i]}" = "npe" && -n $numprocs ]]
2504	then
2505
2506	# FILE COPIES ARE PROVIDED FOR ALL CORES
2507	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2508	printf "\n file will be provided for $numprocs processors"
2509	mkdir ${localin[$i]}
2510	ival=$numprocs
2511	(( ii = 0 ))
2512	while (( ii <= ival-1 ))
2513	do
2514	if (( ii < 10 ))
2515	then
2516	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2517	elif (( ii < 100 ))
2518	then
2519	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2520	elif (( ii < 1000 ))
2521	then
2522	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2523	else
2524	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2525	fi
2526	(( ii = ii + 1 ))
2527	done
2528
2529	else
2530
2531	if [[ $files_for_pes = true ]]
2532	then
2533
2534	# PROVIDE FILES FOR EACH CORE
2535	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2536	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2537	printf "\n providing $numprocs files for the respective processors"
2538	mkdir ${localin[$i]}
2539	if [[ $link_local_input = true ]]
2540	then
2541	printf " files will be linked\n"
2542	cd ${absnamein[$i]}
2543	for file in $(ls *)
2544	do
2545	ln -f $file ${localin[$i]}
2546	done
2547	cd $TEMPDIR
2548	fi
2549
2550	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2551	if [[ ! -f "${localin[$i]}/_000000" ]]
2552	then
2553	if [[ $link_local_input = true ]]
2554	then
2555	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2556	fi
2557	cp -r ${absnamein[$i]}/* ${localin[$i]}
2558	fi
2559
2560	else
2561
2562	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2563	if [[ $link_local_input = true ]]
2564	then
2565	printf " file will be linked\n"
2566	ln -f ${absnamein[$i]} ${localin[$i]}
2567	fi
2568	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
2569	if [[ ! -f "${localin[$i]}" ]]
2570	then
2571	if [[ $link_local_input = true ]]
2572	then
2573	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2574	fi
2575	cp ${absnamein[$i]} ${localin[$i]}
2576	fi
2577	fi
2578	fi
2579	fi
2580
2581	done
2582	if (( i != 0 ))
2583	then
2584	printf "\n$dashes\n *** all INPUT-files provided \n"
2585	fi
2586
2587
2588	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2589	(( i = 0 ))
2590	while (( i < iic ))
2591	do
2592	(( i = i + 1 ))
2593	if (( i == 1 ))
2594	then
2595	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2596	fi
2597	printf "\n >>> ${in_command[$i]}"
2598	eval ${in_command[$i]}
2599	if (( i == iic ))
2600	then
2601	printf "\n$dashes\n"
2602	fi
2603	done
2604
2605
2606	# SET THE REMAINING CPU-TIME
2607	cpurest=${cpumax}.
2608
2609
2610	# START DVR STREAMING SERVER
2611	if [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
2612	then
2613	if [[ "$dvr_server" != "" ]]
2614	then
2615
2616	printf "\n\n *** preparing the dvr streaming server configuration file"
2617
2618	# CHECK, IF A DVR SERVER IS ALREADY RUNNING
2619	running_dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config \| grep -v grep) \| cut -d" " -f2`
2620	if [[ "$running_dvrserver_id" != "" ]]
2621	then
2622
2623	printf "\n\n +++ WARNING: A dvr server with id=$running_dvrserver_id is already running!"
2624	printf "\n This server is used instead starting a new one!"
2625	printf "\n If required, script \"process_dvr_output\" has to be run manually."
2626
2627	else
2628
2629	# COPY CONFIGURATION FILE FOR STREAMING SERVER FROM REPOSITORY TO HERE
2630	if [[ -f ${PALM_BIN}/.dvrserver.config ]]
2631	then
2632	cp ${PALM_BIN}/.dvrserver.config .
2633
2634	# ENTERING THE BASEDIR, UID AND GID INTO THIS FILE
2635	user_id=`id -u`
2636	group_id=`id -g`
2637
2638	# "&" IS REQUIRED AS A SEPERATOR, BECAUSE TEMPDIR CONTAINS "/"
2639	sed "s&<replace by dvr data directory>&${TEMPDIR}&g" .dvrserver.config > .dvrserver.1
2640	sed "s/<replace by user id>/$user_id/g" .dvrserver.1 > .dvrserver.2
2641	sed "s/<replace by group id>/$group_id/g" .dvrserver.2 > .dvrserver.3
2642	mv .dvrserver.3 .dvrserver.config
2643	rm .dvrserver.1 .dvrserver.2
2644
2645	# START DVR SERVER IN BACKGROUND, GET HIS ID AND PRINT ON TERMINAL
2646	$dvr_server .dvrserver.config >> DVR_LOGFILE 2>&1 &
2647	dvrserver_id=`echo $(ps -edaf \| grep .dvrserver.config) \| cut -d" " -f2`
2648	printf "\n *** streaming server with id=$dvrserver_id is started in background"
2649	local_dvrserver_running=.TRUE.
2650	else
2651	printf "\n +++ missing file \".dvrserver.config\" in directory:"
2652	printf "\n \"$PALM_BIN\" "
2653	locat=dvr
2654	exit
2655	fi
2656
2657	fi
2658
2659	else
2660	printf "\n\n --- INFORMATIVE: no dvr streaming server will be started"
2661	fi
2662	fi
2663
2664
2665	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2666	# (FILE ENVPAR WILL BE READ BY PALM)
2667	cat > ENVPAR << EOF
2668	&envpar run_identifier = '$fname', host = '$localhost',
2669	write_binary = '$write_binary', tasks_per_node = $tasks_per_node,
2670	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2671	maximum_cpu_time_allowed = ${cpumax}.,
2672	revision = '$global_revision',
2673	local_dvrserver_running = $local_dvrserver_running,
2674	batch_job = $batch_job /
2675
2676	EOF
2677
2678
2679	# STARTING THE EXECUTABLE
2680	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2681	PATH=$PATH:$TEMPDIR
2682
2683
2684	if [[ $execute_command != "none" ]]
2685	then
2686
2687	printf "\n +++ branch still not realized"
2688	locat=execution
2689	exit
2690
2691	else
2692
2693	# MPI DEBUG OPTION (ARGUMENT CHECKING, SLOWS DOWN EXECUTION DUE TO INCREASED LATENCY)
2694	if [[ "$mpi_debug" = true ]]
2695	then
2696	export MPI_CHECK_ARGS=1
2697	printf "\n +++ MPI_CHECK_ARGS=$MPI_CHECK_ARGS"
2698	fi
2699
2700	if [[ "$totalview" = true ]]
2701	then
2702	printf "\n *** totalview debugger will be used"
2703	tv_opt="-tv"
2704	else
2705	tv_opt=""
2706	fi
2707
2708	if [[ "$cond1" = debug \|\| "$cond2" = debug ]]
2709	then
2710
2711	#Interactive ALLINEA DEBUG seesion
2712	if [[ "$ENVIRONMENT" != BATCH ]]
2713	then
2714	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2715	then
2716	if [[ "$allinea" = true ]]
2717	then
2718	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2719
2720	ddt aprun -n $ii -N $tasks_per_node a.out
2721	wait
2722	fi
2723	fi
2724	fi
2725
2726	if [[ $localhost = ibmh ]]
2727	then
2728
2729	# SETUP THE IBM MPI ENVIRONMENT
2730	export MP_SHARED_MEMORY=yes
2731	export AIXTHREADS_SCOPE=S
2732	export OMP_NUM_THREADS=$threads_per_task
2733	export AUTHSTATE=files
2734	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2735
2736	# FOLLOWING OPTIONS ARE MANDATORY FOR TOTALVIEW
2737	export MP_ADAPTER_USE=shared
2738	export MP_CPU_USE=multiple
2739	export MP_TIMEOUT=1200
2740
2741	unset MP_TASK_AFFINITY
2742
2743	if [[ "$LOADLBATCH" = yes ]]
2744	then
2745	totalview poe a.out
2746	else
2747	echo totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2748	export TVDSVRLAUNCHCMD=ssh
2749	totalview poe -a a.out -procs $numprocs -rmpool 0 -nodes 1
2750	fi
2751
2752	fi # END DEBUG MODE
2753
2754	else
2755
2756	# NORMAL EXECUTION
2757	if [[ -n $numprocs ]]
2758	then
2759
2760	# RUNNING THE PROGRAM ON PARALLEL MACHINES
2761	if [[ $(echo $host \| cut -c1-3) = ibm ]]
2762	then
2763
2764	# SETUP THE IBM MPI ENVIRONMENT
2765	if [[ $host != ibmh && $host != ibmkisti ]]
2766	then
2767	export MP_SHARED_MEMORY=yes
2768	export AIXTHREAD_SCOPE=S
2769	export OMP_NUM_THREADS=$threads_per_task
2770	export XLSMPOPTS="spins=0:yields=0:stack=20000000"
2771	export AUTHSTATE=files
2772	export XLFRTEOPTS="nlwidth=132:err_recovery=no" # RECORD-LENGTH OF NAMELIST-OUTPUT
2773	# export MP_PRINTENV=yes
2774
2775	# TUNING-VARIABLES TO IMPROVE COMMUNICATION SPEED
2776	# DO NOT SHOW SIGNIFICANT EFFECTS (SEP 04, FEDERATION-SWITCH)
2777	export MP_WAIT_MODE=poll
2778	[[ $node_usage = not_shared ]] && export MP_SINGLE_THREAD=yes
2779	fi
2780
2781	if [[ $host = ibmkisti ]]
2782	then
2783	export LANG=en_US
2784	export MP_SHARED_MEMORY=yes
2785	if [[ $threads_per_task = 1 ]]
2786	then
2787	export MP_SINGLE_THREAD=yes
2788	export MEMORY_AFFINITY=MCM
2789	else
2790	export OMP_NUM_THREADS=$threads_per_task
2791	fi
2792	fi
2793
2794	if [[ "$LOADLBATCH" = yes ]]
2795	then
2796	printf "\n--- Control: OMP_NUM_THREADS = \"$OMP_NUM_THREADS\" \n"
2797	if [[ "$cond1" = hpmcount \|\| "$cond2" = hpmcount ]]
2798	then
2799	/opt/optibm/HPM_2_4_1/bin/hpmcount a.out
2800	else
2801	if [[ $run_coupled_model = false ]]
2802	then
2803	if [[ "$ocean_file_appendix" = true ]]
2804	then
2805	echo "precursor_ocean" > runfile_atmos
2806	else
2807	echo "precursor_atmos" > runfile_atmos
2808	fi
2809	else
2810	(( iia = $numprocs_atmos / $threads_per_task ))
2811	(( iio = $numprocs_ocean / $threads_per_task ))
2812	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2813	printf "\n using $coupled_mode coupling"
2814	printf "\n\n"
2815	echo "coupled_run $iia $iio" > runfile_atmos
2816	fi
2817	poe ./a.out < runfile_atmos
2818	fi
2819	else
2820	if [[ $localhost = ibmh \|\| $localhost = ibms ]]
2821	then
2822	poe a.out -procs $numprocs -nodes 1 -rmpool 0
2823	elif [[ $localhost = ibmkisti \|\| $localhost = ibmku ]]
2824	then
2825	if [[ -f $hostfile ]]
2826	then
2827	cp $hostfile hostfile
2828	else
2829	(( ii = 1 ))
2830	while (( ii <= $numprocs ))
2831	do
2832	echo $localhost_realname >> hostfile
2833	(( ii = ii + 1 ))
2834	done
2835	fi
2836	export MP_HOSTFILE=hostfile
2837	if [[ $run_coupled_model = false ]]
2838	then
2839	if [[ "$ocean_file_appendix" = true ]]
2840	then
2841	echo "precursor_ocean" > runfile_atmos
2842	else
2843	echo "precursor_atmos" > runfile_atmos
2844	fi
2845	else
2846	(( iia = $numprocs_atmos / $threads_per_task ))
2847	(( iio = $numprocs_ocean / $threads_per_task ))
2848	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2849	printf "\n using $coupled_mode coupling"
2850	printf "\n\n"
2851	echo "coupled_run $iia $iio" > runfile_atmos
2852	fi
2853
2854	poe ./a.out -procs $numprocs < runfile_atmos
2855
2856	else
2857	if [[ "$host_file" = "" ]]
2858	then
2859	printf "\n +++ no hostfile given in configuration file"
2860	locat=config_file
2861	exit
2862	else
2863	eval host_file=$host_file
2864	fi
2865	export MP_HOSTFILE=$host_file
2866	poe a.out -procs $numprocs -tasks_per_node $numprocs
2867	fi
2868	fi
2869
2870	elif [[ $(echo $host \| cut -c1-2) = lc && $host != lckyoto && $host != lctit ]]
2871	then
2872
2873	# COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT
2874	# DOES NOT EXIST
2875	if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]]
2876	then
2877	if [[ -f $hostfile ]]
2878	then
2879	cp $hostfile hostfile
2880	(( ii = $numprocs / $threads_per_task ))
2881	[[ $ii = 0 ]] && (( ii = 1 ))
2882	else
2883	(( ii = 1 ))
2884	while (( ii <= $numprocs / $threads_per_task ))
2885	do
2886	echo $localhost_realname >> hostfile
2887	(( ii = ii + 1 ))
2888	done
2889	if (( $numprocs / $threads_per_task == 0 ))
2890	then
2891	echo $localhost_realname >> hostfile
2892	fi
2893	fi
2894	eval zeile=\"`head -n $ii hostfile`\"
2895	printf "\n *** running on: $zeile"
2896	fi
2897
2898	(( ii = $numprocs / $threads_per_task ))
2899	[[ $ii = 0 ]] && (( ii = 1 ))
2900	export OMP_NUM_THREADS=$threads_per_task
2901
2902	if [[ $threads_per_task != 1 ]]
2903	then
2904	# INCREASE STACK SIZE TO UNLIMITED, BECAUSE OTHERWISE LARGE RUNS
2905	# MAY ABORT
2906	ulimit -s unlimited
2907	printf "\n threads per task: $threads_per_task stacksize: unlimited"
2908	fi
2909	if [[ $run_coupled_model = false ]]
2910	then
2911	if [[ "$ocean_file_appendix" = true ]]
2912	then
2913	echo "precursor_ocean" > runfile_atmos
2914	else
2915	echo "precursor_atmos" > runfile_atmos
2916	fi
2917	printf "\n\n"
2918
2919	if [[ $host = lccrayb \|\| $host = lccrayh ]]
2920	then
2921	echo "--- aprun -n $ii -N $tasks_per_node a.out < runfile_atmos"
2922	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
2923	elif [[ $host = lcbullhh ]]
2924	then
2925	export OMPI_MCA_pml=cm
2926	export OMPI_MCA_mtl=mxm
2927	export OMPI_MCA_coll=^ghc
2928	export OMPI_MCA_mtl_mxm_np=0
2929	export MXM_RDMA_PORTS=mlx5_0:1
2930	export MXM_LOG_LEVEL=ERROR
2931	export OMP_NUM_THREADS=$threads_per_task
2932	export KMP_AFFINITY=verbose,granularity=core,compact,1
2933	export KMP_STACKSIZE=64m
2934
2935	srun -n $ii --ntasks-per-node=$tasks_per_node ./a.out < runfile_atmos
2936
2937	elif [[ $host = lccrayf ]]
2938	then
2939	aprun -j1 -n $ii -N $tasks_per_node -m ${memory}M a.out < runfile_atmos
2940	elif [[ $host = lcxe6 \|\| $host = lcxt5m ]]
2941	then
2942	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
2943	elif [[ $host = lceddy ]]
2944	then
2945	echo $ii
2946	echo $tasks_per_node
2947	echo $nodes
2948	mpirun -n $ii a.out < runfile_atmos
2949	elif [[ $host = lcgeohu ]]
2950	then
2951	srun -n $ii a.out < runfile_atmos
2952	elif [[ $host = lcocean ]]
2953	then
2954	mpirun a.out $ROPTS < runfile_atmos
2955	elif [[ $host = lcsb ]]
2956	then
2957	mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE \| wc -l` a.out < runfile_atmos
2958
2959	elif [[ $host = lckiaps ]]
2960	then
2961	mpirun -np $ii -machinefile $PBS_NODEFILE ./a.out < runfile_atmos
2962	elif [[ $host = lckyu* ]]
2963	then
2964	mpiexec -n $ii --stdin runfile_atmos ./a.out
2965	else
2966	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
2967	fi
2968
2969	else
2970
2971	# CURRENTLY THERE IS NO FULL MPI-2 SUPPORT ON ICE AND XT4
2972	(( iia = $numprocs_atmos / $threads_per_task ))
2973	(( iio = $numprocs_ocean / $threads_per_task ))
2974	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2975	printf "\n using $coupled_mode coupling"
2976	printf "\n\n"
2977
2978	if [[ $coupled_mode = "mpi2" ]]
2979	then
2980	echo "atmosphere_to_ocean $iia $iio" > runfile_atmos
2981	echo "ocean_to_atmosphere $iia $iio" > runfile_ocean
2982
2983	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
2984	then
2985
2986	aprun -n $iia -N $tasks_per_node a.out < runfile_atmos &
2987	aprun -n $iio -N $tasks_per_node a.out < runfile_ocean &
2988
2989	else
2990	# WORKAROUND BECAUSE mpiexec WITH -env option IS NOT AVAILABLE ON SOME SYSTEMS
2991	mpiexec -machinefile hostfile -n $iia a.out < runfile_atmos &
2992	mpiexec -machinefile hostfile -n $iio a.out < runfile_ocean &
2993	# mpiexec -machinefile hostfile -n $iia -env coupling_mode atmosphere_to_ocean a.out &
2994	# mpiexec -machinefile hostfile -n $iio -env coupling_mode ocean_to_atmosphere a.out &
2995	fi
2996	wait
2997
2998	else
2999
3000	echo "coupled_run $iia $iio" > runfile_atmos
3001
3002	if [[ $host = lccrayf \|\| $host = lcxe6 \|\| $host = lcxt5m ]]
3003	then
3004
3005	aprun -n $ii -N $tasks_per_node a.out < runfile_atmos
3006
3007	elif [[ $host = lck \|\| $host = lckordi ]]
3008	then
3009
3010	mpiexec -n $ii ./a.out < runfile_atmos &
3011
3012	elif [[ $host = lckyu* ]]
3013	then
3014
3015	mpiexec -n $ii --stdin runfile_atmos ./a.out
3016
3017	elif [[ $host = lcmuk ]]
3018	then
3019
3020	mpiexec -machinefile hostfile -n $ii a.out < runfile_atmos
3021
3022	fi
3023	wait
3024	fi
3025
3026	fi
3027
3028	elif [[ $host = lckyoto ]]
3029	then
3030	set -xv
3031	export P4_RSHCOMMAND=plesh
3032	echo " P4_RSHCOMMAND = $P4_RSHCOMMAND"
3033	if [[ "$ENVIRONMENT" = BATCH ]]
3034	then
3035	if [[ "$cond2" = fujitsu ]]
3036	then
3037	mpiexec -n $numprocs ./a.out # for fujitsu-compiler
3038	elif [[ "cond2" = pgi ]]
3039	then
3040	mpirun -np $numprocs -machinefile ${QSUB_NODEINF} ./a.out
3041	else
3042	mpirun_rsh -np $numprocs -hostfile ${QSUB_NODEINF} MV2_USE_SRQ=0 ./a.out \|\| /bin/true
3043	fi
3044	else
3045	if [[ "$cond2" = "" ]]
3046	then
3047	mpiruni_rsh -np $numprocs ./a.out # for intel
3048	else
3049	mpirun -np $numprocs ./a.out
3050	fi
3051	fi
3052	set +xv
3053
3054	elif [[ $host = lctit ]]
3055	then
3056	export OMP_NUM_THREADS=$threads_per_task
3057	echo "OMP_NUM_THREADS=$OMP_NUM_THREADS"
3058	if [[ "$threads_per_task" != 1 ]]
3059	then
3060	export MV2_ENABLE_AFFINITY=0
3061	fi
3062	echo "----- PBS_NODEFILE content:"
3063	cat $PBS_NODEFILE
3064	echo "-----"
3065	(( ii = $numprocs / $threads_per_task ))
3066	echo "mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out"
3067	mpirun -np $ii -hostfile $PBS_NODEFILE ./a.out
3068
3069	else
3070	mpprun -n $numprocs a.out
3071	fi
3072	else
3073	a.out
3074	fi
3075
3076	fi # end normal (non-debug) execution
3077
3078	fi # end explicit execute_command or host-specific execute actions
3079
3080	if [[ $? != 0 ]]
3081	then
3082
3083	# ABORT IN CASE OF RUNTIME ERRORS
3084	printf "\n +++ runtime error occured"
3085	locat=execution
3086	exit
3087
3088	else
3089
3090	printf "\n$dashes\n *** execution finished \n"
3091
3092	# STOP THE DVR STREAMING SERVER AND PROCESS THE DVR OUTPUT IN ORDER
3093	# TO CREAT DVRS- AND HTML-FILES CONTAINING ALL STREAMS
3094	if [[ "$dvrserver_id" != "" ]]
3095	then
3096	kill $dvrserver_id
3097	printf "\n *** dvr server with id=$dvrserver_id has been stopped"
3098
3099	# IF THERE IS A DIRECTORY, DATA HAVE BEEN OUTPUT BY THE
3100	# STREAMING SERVER. OTHERWISE, USER HAS CHOSEN dvrp_output=local
3101	if [[ -d DATA_DVR ]]
3102	then
3103
3104	# ADD THE CURRENT DVR CONFIGURATION FILE TO THE DVR OUTPUT
3105	# DIRECTORY
3106	cp .dvrserver.config DATA_DVR
3107
3108	# PROCESS THE DVR OUTPUT (OPTION -s FOR GENERATING
3109	# SEQUENCE MODE DATA TOO)
3110	process_dvr_output -d DATA_DVR -f $fname -s
3111
3112	else
3113
3114	# PROCESS THE LOCAL OUTPUT
3115	process_dvr_output -l -d DATA_DVR -f $fname
3116
3117	fi
3118
3119	elif [[ $(echo $package_list \| grep -c dvrp_graphics) != 0 ]]
3120	then
3121
3122	# PROCESS DVR OUTPUT GENERATD IN LOCAL MODE (dvrp_output=local)
3123	process_dvr_output -l -d DATA_DVR -f $fname
3124
3125	fi
3126	fi
3127
3128
3129
3130	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
3131	# BY EACH CORE INTO ONE FILE
3132	if [[ ! -f ${PALM_BIN}/combine_plot_fields${block}.x ]]
3133	then
3134	printf "\n\n\n +++ WARNING: no combine_plot_fields found for given block \"$cond1 $cond2\""
3135	printf "\n 2d- and/or 3d-data may be incomplete!"
3136	printf "\n Run \"mbuild -u -h $localhost\" to generate utilities for this block.\n"
3137	elif [[ "$combine_plot_fields" == true ]]
3138	then
3139	if [[ $localhost = lccrayh \|\| $localhost = lccrayb ]]
3140	then
3141	printf "\n\n\n *** post-processing: now executing \"aprun -n 1 -N 1 combine_plot_fields${block}.x\" ..."
3142	aprun -n 1 -N 1 combine_plot_fields${block}.x
3143	else
3144	printf "\n\n\n *** post-processing: now executing \"combine_plot_fields${block}.x\" ..."
3145	combine_plot_fields${block}.x
3146	fi
3147	else
3148
3149	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
3150	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
3151	# ??? koennen wir das streichen ???
3152	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
3153	fi
3154
3155
3156
3157	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
3158	(( i = 0 ))
3159	while (( i < ioc ))
3160	do
3161	(( i = i + 1 ))
3162	if (( i == 1 ))
3163	then
3164	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
3165	fi
3166	printf "\n >>> ${out_command[$i]}"
3167	eval ${out_command[$i]}
3168	if (( i == ioc ))
3169	then
3170	printf "\n$dashes\n"
3171	fi
3172	done
3173
3174
3175	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
3176	if [[ $do_trace = true ]]
3177	then
3178	printf "\n\n"
3179	ls -al
3180	fi
3181
3182
3183	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
3184	(( i = 0 ))
3185	while (( i < iout ))
3186	do
3187	(( i = i + 1 ))
3188	if (( i == 1 ))
3189	then
3190	printf "\n\n *** saving OUTPUT-files:"
3191
3192	# GET RUN NUMBER ASSIGNED BY PALM
3193	if [[ -f RUN_NUMBER ]]
3194	then
3195	read run_number < RUN_NUMBER
3196	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
3197	usecycle_option="-U $run_number"
3198	else
3199	run_number=0
3200	usecycle_option=""
3201	fi
3202	printf "\n$dashes"
3203	fi
3204
3205	# ADD CYCLE NUMBER TO FILENAME
3206	if [[ ! ( $fromhost != $localhost && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
3207	then
3208
3209	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
3210	if [[ "${actionout[$i]}" != "a" ]]
3211	then
3212	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
3213	# WITH AN EXISTING CYCLE NUMBER
3214	if (( run_number >= cycnum[$i] ))
3215	then
3216	(( cycnum[$i] = run_number ))
3217	else
3218	if (( run_number > 0 ))
3219	then
3220	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
3221	fi
3222	fi
3223	fi
3224	if (( cycnum[$i] > 0 ))
3225	then
3226	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
3227	fi
3228	fi
3229
3230	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
3231	files_for_pes=false; filetyp=file
3232	link_local_output=false
3233	if [[ "${actionout[$i]}" = pe && -n $numprocs ]]
3234	then
3235	files_for_pes=true; filetyp=directory
3236	actionout[$i]=""
3237	elif [[ "${actionout[$i]}" = pe && ! -n $numprocs ]]
3238	then
3239	actionout[$i]=""
3240	elif [[ "${actionout[$i]}" = lnpe && -n $numprocs ]]
3241	then
3242	files_for_pes=true; filetyp=directory
3243	link_local_output=true
3244	actionout[$i]=""
3245	elif [[ "${actionout[$i]}" = lnpe && ! -n $numprocs ]]
3246	then
3247	link_local_output
3248	actionout[$i]=""
3249	elif [[ "${actionout[$i]}" = trpe && -n $numprocs ]]
3250	then
3251	files_for_pes=true; filetyp=directory
3252	actionout[$i]="tr"
3253	elif [[ "${actionout[$i]}" = trpe && ! -n $numprocs ]]
3254	then
3255	actionout[$i]="tr"
3256	fi
3257
3258	if [[ ! -f ${localout[$i]} && $files_for_pes = false ]]
3259	then
3260	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
3261	elif [[ ! -d ${localout[$i]} && $files_for_pes = true ]]
3262	then
3263	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
3264	else
3265
3266
3267	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3268	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3269	if [[ "${actionout[$i]}" = tr ]]
3270	then
3271	if [[ $localhost != $fromhost ]]
3272	then
3273	if [[ $files_for_pes = false ]]
3274	then
3275	cps=""
3276	cst=""
3277	else
3278	cps=-c
3279	cst="/"
3280	fi
3281
3282	transfer_failed=false
3283	printf "\n >>> OUTPUT: ${localout[$i]}$cst by SCP to"
3284	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}$cst\n"
3285	if [[ $localhost = lccrayb ]]
3286	then
3287	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]}"
3288	elif [[ $localhost = lccrayh ]]
3289	then
3290	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]}"
3291	elif [[ $localhost = lcbullhh ]]
3292	then
3293	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]}"
3294	elif [[ $localhost = lcxe6 ]]
3295	then
3296	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]}"
3297	else
3298	batch_scp $PORTOPT $cps -b -m $usecycle_option -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3299	fi
3300	[[ $? != 0 ]] && transfer_failed=true
3301
3302	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3303	if [[ $transfer_failed = true ]]
3304	then
3305	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3306	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3307
3308	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3309	eval local_catalog=${pathout[$i]}
3310	if [[ ! -d $local_catalog ]]
3311	then
3312	printf " *** local directory does not exist. Trying to create:\n"
3313	printf " $local_catalog \n"
3314	mkdir -p $local_catalog
3315	fi
3316	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3317	transfer_problems=true
3318	fi
3319
3320	else
3321
3322	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE COPIED ON THIS MACHINE
3323	actionout[$i]=""
3324	fi
3325	fi
3326
3327
3328	# APPEND VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
3329	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
3330	if [[ "${actionout[$i]}" = tra ]]
3331	then
3332	if [[ $localhost != $fromhost ]]
3333	then
3334	if [[ $localhost = ibmh ]]
3335	then
3336
3337	# TRANSFER IN SEPERATE JOB
3338	# FIRST COPY FILE TO TEMPORY DATA DIRECTORY
3339	[[ ! -d $tmp_data_catalog/TRANSFER ]] && mkdir -p $tmp_data_catalog/TRANSFER
3340	file_to_transfer=${fname}_${localout[$i]}_to_transfer_$kennung
3341	ln -f ${localout[$i]} $tmp_data_catalog/TRANSFER/$file_to_transfer
3342
3343	echo "set -x" > transfer_${localout[$i]}
3344	echo "cd $tmp_data_catalog/TRANSFER" >> transfer_${localout[$i]}
3345
3346	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP in seperate job to"
3347	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}"
3348	printf "\n or higher cycle\n"
3349	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]}
3350
3351	echo "[[ \$? = 0 ]] && rm $file_to_transfer" >> transfer_${localout[$i]}
3352
3353	if [[ $LOGNAME = b323013 ]]
3354	then
3355	subjob -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3356	else
3357	subjob -d -v -q c1 -X 0 -m 1000 -t 900 -c $job_catalog $PORTOPT transfer_${localout[$i]}
3358	fi
3359
3360	else
3361
3362	# TRANSFER WITHIN THIS JOB
3363	transfer_failed=false
3364	printf "\n >>> OUTPUT: ${localout[$i]} append by SCP to"
3365	printf "\n ${pathout[$i]}/${localhost}_${fname}${endout[$i]}\n"
3366	if [[ $localhost = lccrayb ]]
3367	then
3368	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]}"
3369	elif [[ $localhost = lccrayh ]]
3370	then
3371	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]}"
3372	elif [[ $localhost = lcxe6 ]]
3373	then
3374	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]}"
3375	else
3376	batch_scp $PORTOPT -A -b -m -u $return_username $return_address ${localout[$i]} "${pathout[$i]}" ${localhost}_${fname}${endout[$i]} ${extout[$i]}
3377	fi
3378	[[ $? != 0 ]] && transfer_failed=true
3379
3380	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
3381	if [[ $transfer_failed = true ]]
3382	then
3383	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
3384	printf " ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung\n"
3385
3386	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
3387	eval local_catalog=${pathout[$i]}
3388	if [[ ! -d $local_catalog ]]
3389	then
3390	printf " *** local directory does not exist. Trying to create:\n"
3391	printf " $local_catalog \n"
3392	mkdir -p $local_catalog
3393	fi
3394
3395	eval cp ${localout[$i]} ${pathout[$i]}/${localhost}_${fname}${endout[$i]}_$kennung
3396	transfer_problems=true
3397	fi
3398	fi
3399	else
3400
3401	# RESET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST BE APPENDED ON THIS MACHINE
3402	actionout[$i]=a
3403	fi
3404	fi
3405
3406
3407	# APPEND ON THIS MACHINE
3408	if [[ "${actionout[$i]}" = "a" ]]
3409	then
3410	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3411	then
3412	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}.${extout[$i]}\n"
3413	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
3414	else
3415	printf "\n >>> OUTPUT: ${localout[$i]} append to ${pathout[$i]}\n"
3416	cat ${localout[$i]} >> ${pathout[$i]}
3417	fi
3418	fi
3419
3420	# COPY ON THIS MACHINE
3421	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
3422	# ON DIFFERENT FILE-SYSTEMS
3423	if [[ "${actionout[$i]}" = "" && $files_for_pes = false ]]
3424	then
3425
3426	# COPY IN CASE OF RUNS ON SINGLE CORES
3427	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
3428	then
3429	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}.${extout[$i]}\n"
3430	if [[ $link_local_output = true ]]
3431	then
3432	printf " file will be linked\n"
3433	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3434	fi
3435	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3436	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
3437	then
3438	if [[ $link_local_output = true ]]
3439	then
3440	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3441	fi
3442	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
3443	else
3444	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
3445	fi
3446	else
3447	printf "\n >>> OUTPUT: ${localout[$i]} to ${pathout[$i]}\n"
3448	if [[ $link_local_output = true ]]
3449	then
3450	printf " file will be linked\n"
3451	ln -f ${localout[$i]} ${pathout[$i]}
3452	fi
3453	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
3454	if [[ ! -f "${pathout[$i]}" ]]
3455	then
3456	if [[ $link_local_output = true ]]
3457	then
3458	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3459	fi
3460	cp ${localout[$i]} ${pathout[$i]}
3461	else
3462	printf "+++ no copy because file ${pathout[$i]} exists\n"
3463	fi
3464	fi
3465
3466	elif [[ "${actionout[$i]}" = "" && $files_for_pes = true ]]
3467	then
3468
3469	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
3470	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
3471	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to ${pathout[$i]}\n"
3472	if [[ $link_local_output = true ]]
3473	then
3474	printf " files will be linked\n"
3475	mkdir ${pathout[$i]}
3476	cd ${localout[$i]}
3477	for file in $(ls *)
3478	do
3479	ln -f $file ${pathout[$i]}
3480	done >\|/dev/null 2>&1
3481	cd $TEMPDIR
3482	fi
3483
3484	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
3485	if [[ ! -f "${pathout[$i]}/_000000" ]]
3486	then
3487	if [[ $link_local_output = true ]]
3488	then
3489	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
3490	fi
3491	cp -r ${localout[$i]}/* ${pathout[$i]}
3492	fi
3493
3494	fi
3495	fi
3496	done
3497	if (( i != 0 ))
3498	then
3499	if [[ $transfer_problems = true ]]
3500	then
3501	printf "\n$dashes\n *** OUTPUT-files saved"
3502	printf "\n +++ WARNING: some data transfers failed! \n"
3503	else
3504	printf "\n$dashes\n *** all OUTPUT-files saved \n"
3505	fi
3506	fi
3507
3508
3509	# IF REQUIRED, START A RESTART-JOB
3510	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
3511	if [[ -f CONTINUE_RUN ]]
3512	then
3513
3514	# ADD RESTART-OPTIONS TO THE MRUN-CALL (IF THEY ARE NOT USED ALREADY):
3515	# -C TELLS MRUN THAT IT IS A RESTART-RUN
3516	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
3517	# -n BATCH-MODE (IMPORTANT ONLY IN CASE OF BATCH JOBS ON THE LOCAL MACHINE)
3518	[[ $(echo $mc \| grep -c "\-C") = 0 ]] && mc="$mc -C"
3519	[[ $(echo $mc \| grep -c "\-v") = 0 ]] && mc="$mc -v"
3520	[[ $(echo $mc \| grep -c "\-b") = 0 ]] && mc="$mc -b"
3521	if [[ $(echo $mc \| grep -c "#") != 0 ]]
3522	then
3523	mc=`echo $mc \| sed 's/#/f/g'`
3524	fi
3525
3526
3527	# START THE RESTART-JOB
3528	printf "\n\n *** initiating restart-run on \"$return_address\" using command:\n"
3529	echo " $mc"
3530	printf "\n$dashes\n"
3531	if [[ $localhost != $fromhost ]]
3532	then
3533
3534	if [[ $localhost = lcbullhh \|\| $localhost = lccrayb \|\| $localhost = lccrayh \|\| $localhost = ibmh \|\| $localhost = ibmkisti \|\| $localhost = ibmku \|\| $localhost = ibms \|\| $localhost = lceddy \|\| $localhost = lckyu* \|\| $localhost = lcxe6 \|\| $localhost = lcgeohu ]]
3535	then
3536	echo "*** ssh will be used to initiate restart-runs!"
3537	echo " return_address=\"$return_address\" "
3538	echo " return_username=\"$return_username\" "
3539	if [[ $(echo $return_address \| grep -c "130.75.105") = 1 ]]
3540	then
3541	if [[ $localhost = ibmh ]]
3542	then
3543	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\" "
3544	elif [[ $localhost = lcbullhh ]]
3545	then
3546	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\" "
3547	elif [[ $localhost = lccrayb ]]
3548	then
3549	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\" "
3550	elif [[ $localhost = lccrayh ]]
3551	then
3552	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\" "
3553	elif [[ $localhost = lcxe6 ]]
3554	then
3555	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\" "
3556	else
3557	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 "
3558	fi
3559	else
3560	if [[ $localhost = ibmkisti ]]
3561	then
3562	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\" "
3563	elif [[ $localhost = lceddy ]]
3564	then
3565	/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 "
3566	elif [[ $localhost = lcocean ]]
3567	then
3568	/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 "
3569	elif [[ $localhost = lccrayb ]]
3570	then
3571	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\" "
3572	elif [[ $localhost = lccrayh ]]
3573	then
3574	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\" "
3575	elif [[ $localhost = lccgeohu ]]
3576	then
3577	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\" "
3578	else
3579	ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc "
3580	fi
3581	fi
3582	else
3583	printf "\n +++ no restart mechanism available for host \"$localhost\" "
3584	locat=restart; exit
3585	fi
3586
3587	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
3588	if [[ $queue = special1q ]]
3589	then
3590	sleep 120
3591	else
3592	sleep 30
3593	fi
3594
3595	else
3596
3597	# JOBS RUNNING (AND STARTED) ON THE LOCAL MACHINE CAN DIRECTLY CALL MRUN (WITHOUT
3598	# USING SSH)
3599	cd $LOCAL_PWD
3600	if [[ $localhost = lckyuh ]]
3601	then
3602	printf "\n +++ WARNING: no restart mechanism available for host \"$localhost\" "
3603	printf "\n please restart job manually using command:\n"
3604	printf "\n \"$mc\" "
3605	else
3606	eval $mc # THE ' MUST BE EVALUATED
3607	fi
3608	cd - > /dev/null
3609	fi
3610	if [[ $localhost = lckyuh ]]
3611	then
3612	printf "\n$dashes\n *** restart-run to be initiated manually\n"
3613	else
3614	printf "\n$dashes\n *** restart-run initiated \n"
3615	fi
3616
3617
3618	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
3619	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
3620	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
3621	# MAY BE VERY HUGE)
3622	(( i = 0 ))
3623	while (( i < iin ))
3624	do
3625	(( i = i + 1 ))
3626	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
3627	then
3628	rm -r ${absnamein[$i]}
3629	fi
3630	done
3631
3632	fi
3633
3634
3635
3636	# SEND EMAIL NOTIFICATION ABOUT THE FINISHED RUN
3637	if [[ "$email_notification" != "none" ]]
3638	then
3639
3640	if [[ $localhost != $fromhost ]]
3641	then
3642	if [[ -f CONTINUE_RUN ]]
3643	then
3644	echo "PALM restart run necessary" > email_text
3645	echo "description header of actual run:" >> email_text
3646	cat CONTINUE_RUN >> email_text
3647	echo "mrun-command to restart:" >> email_text
3648	echo "$mc" >> email_text
3649	else
3650	echo "PALM run with base filename \"$fname\" on host \"$localhost\" finished" > email_text
3651	fi
3652	mail $email_notification < email_text
3653	printf "\n *** email notification sent to \"$email_notification\" "
3654	fi
3655	fi
3656
3657
3658
3659	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
3660	cd $HOME
3661	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
3662
3663	else
3664
3665	# PREPARING ACTIONS,
3666	# IF A BATCH-JOB IS TO BE GENERATED AND STARTED ON A REMOTE-MACHINE GERECHNET
3667
3668	# BUILD THE MRUN-COMMAND TO BE CALLED IN THE BATCH-JOB ON THE REMOTE-MACHINE
3669	mrun_com="$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 $remote_username"
3670	[[ "$global_revision" != "" ]] && mrun_com=${mrun_com}" -G \"$global_revision\""
3671	[[ $group_number != none ]] && mrun_com=${mrun_com}" -g $group_number"
3672	[[ $do_compile = true ]] && mrun_com=${mrun_com}" -s \"$source_list\""
3673	[[ "$input_list" != "" ]] && mrun_com=${mrun_com}" -i \"$input_list\""
3674	[[ $keep_data_from_previous_run = true ]] && mrun_com=${mrun_com}" -k"
3675	[[ "$additional_conditions" != "" ]] && mrun_com=${mrun_com}" -K \"$additional_conditions\""
3676	[[ "$output_list" != "" ]] && mrun_com=${mrun_com}" -o \"$output_list\""
3677	[[ "$read_from_config" = false ]] && mrun_com=${mrun_com}" -S"
3678	[[ $do_trace = true ]] && mrun_com=${mrun_com}" -x"
3679	[[ "$numprocs" != "" ]] && mrun_com=${mrun_com}" -X $numprocs"
3680	if [[ $use_openmp = true ]]
3681	then
3682	mrun_com=${mrun_com}" -O $threads_per_task"
3683	fi
3684	[[ "$tasks_per_node" != "" ]] && mrun_com=${mrun_com}" -T $tasks_per_node"
3685	[[ $package_list != "" ]] && mrun_com=${mrun_com}" -p \"$package_list\""
3686	[[ $return_password != "" ]] && mrun_com=${mrun_com}" -P $return_password"
3687	[[ $delete_temporary_catalog = false ]] && mrun_com=${mrun_com}" -B"
3688	[[ $node_usage != default && "$(echo $node_usage \| cut -c1-3)" != "sla" && $node_usage != novice ]] && mrun_com=${mrun_com}" -n $node_usage"
3689	[[ "$ocean_file_appendix" = true ]] && mrun_com=${mrun_com}" -y"
3690	[[ $run_coupled_model = true ]] && mrun_com=${mrun_com}" -Y \"$coupled_dist\""
3691	[[ "$check_namelist_files" = false ]] && mrun_com=${mrun_com}" -z"
3692	[[ "$combine_plot_fields" = false ]] && mrun_com=${mrun_com}" -Z"
3693	[[ "$max_par_io_str" != "" ]] && mrun_com=${mrun_com}" -w $max_par_io_str"
3694	if [[ $do_remote = true ]]
3695	then
3696	printf "\n>>>> MRUN-command on execution host:\n>>>> $mrun_com \n"
3697	fi
3698
3699
3700	# CREATE EXECUTABLE FOR BATCH JOB
3701	if [[ $create_executable_for_batch = true && $restart_run != true ]]
3702	then
3703
3704	printf "\n *** creating the executable for batch job\n"
3705
3706	# METHOD ONLY WORKS FOR BATCH JOBS ON LOCAL HOSTS
3707	if [[ $host != $localhost ]]
3708	then
3709	printf "\n +++ creation of executables is only allowed for batch jobs on local hosts."
3710	printf "\n Please set create_executable_for_batch = false in the config-file.\n"
3711	locat=create_executable; exit
3712	fi
3713
3714	mkdir $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3715	cd $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3716
3717	cp $make_depository .
3718	tar -xf $make_depository > /dev/null 2>&1
3719	cp ../* . > /dev/null 2>&1
3720
3721	make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts"
3722
3723	if [[ $? != 0 \|\| "$compile_error" = true \|\| "$module_compile_error" = true ]]
3724	then
3725	printf "\n +++ error occured while compiling or linking"
3726	locat=compile
3727	exit
3728	fi
3729
3730	mv a.out ..
3731	cd - > /dev/null 2>&1
3732	rm -rf $working_directory/SOURCES_FOR_RUN_${fname}/TMPDIR_FOR_CREATING_EXECUTABLE
3733
3734	printf " *** executable created in \"$working_directory/SOURCES_FOR_RUN_${fname}\"\n "
3735
3736	fi
3737
3738
3739	# BUILD THE JOB-SCRIPTS ON FILE jobfile
3740	jobfile=jobfile.$RANDOM
3741
3742
3743	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
3744	echo "mkdir $TEMPDIR" >> $jobfile
3745	echo "cd $TEMPDIR" >> $jobfile
3746
3747
3748	# ACTIVATE ERROR-TRACEBACK
3749	if [[ $do_trace = true ]]
3750	then
3751	echo "set -x" >> $jobfile
3752	else
3753	echo "set +vx" >> $jobfile
3754	fi
3755
3756
3757	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
3758	if [[ "$init_cmds" != "" ]]
3759	then
3760	echo "$init_cmds" >> $jobfile
3761	fi
3762	if [[ "$module_calls" != "" ]]
3763	then
3764	echo "$module_calls" >> $jobfile
3765	fi
3766
3767
3768	# PROVIDE SOURCE-CODE FILES, MRUN-SCRIPT AND CONFIGURATION-FILE FOR THE JOB
3769	# then-CLAUSE: FILES ARE COLLECTED IN THE SOURCES_FOR_RUN_... DIRECTORY ON THE LOCAL HOST,
3770	# WHICH IS THEN FETCHED FROM THE BATCH-JOB BY USING cp/scp
3771	# THE SOURCE-CODE FILES ALREADY EXIST IN THIS DIRECTORY
3772	# else-CLAUSE: FILE-CONTENTS ARE PUT INTO THE JOB-FILE AS HERE-DOCUMENTS
3773	# THIS MAY CREATE A QUITE LARGE JOB-FILE, WHICH CAN CAUSE PROBLEMS WITH SOME
3774	# QUEUEING-SYSTEMS
3775	if [[ $host = ibmkisti \|\| $host = lcbullhh \|\| $host = lccrayb \|\| $host = lccrayf \|\| $host = lccrayh \|\| $host = lcocean \|\| $host = lcgeohu ]]
3776	then
3777
3778	# COPY CONFIGURATION-FILE AND MRUN-SCRIPT INTO THE SOURCES_FOR_RUN... DIRECTORY
3779	if [[ $restart_run != true ]]
3780	then
3781	cp $config_file $working_directory/SOURCES_FOR_RUN_$fname
3782	cp ${PALM_BIN}/$mrun_script_name $working_directory/SOURCES_FOR_RUN_$fname
3783	fi
3784
3785	# COPY THE SOURCES_FOR_RUN... DIRECTORY FROM THE LOCAL HOST TO THE JOB VIA scp
3786	# (then-CLAUSE: JOBS ON THE LOCAL HOST CAN JUST USE cp)
3787	echo "set -x" >> $jobfile
3788	if [[ $host = $localhost ]]
3789	then
3790	# DUE TO UNKNOWN REASONS, COPY WITH cp COMMAND CREATES CORRUPT
3791	# FILES ON CRAY XC30 SYSTEMS (CSC HELSINKI), rsync IS USED INSTEAD
3792	if [[ $(echo $host \| cut -c1-6) = lccray ]]
3793	then
3794	echo "rsync -av -t $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3795	else
3796	echo "cp -r $working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3797	fi
3798
3799	else
3800	if [[ $host = ibmkisti ]]
3801	then
3802	# ON KISTI'S IBM FIREWALL IS ONLY OPENED ON INTERACTIVE NODE
3803	echo "localdir=\`pwd\`" >> $jobfile
3804	echo "ssh $SSH_PORTOPT $remote_username@gaiad \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3805	elif [[ $host = lcbullhh ]]
3806	then
3807	echo "localdir=\`pwd\`" >> $jobfile
3808	echo "ssh $SSH_PORTOPT $remote_username@mlogin101 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3809
3810	elif [[ $host = lccrayb ]]
3811	then
3812	echo "localdir=\`pwd\`" >> $jobfile
3813	echo "ssh $SSH_PORTOPT $remote_username@blogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3814	elif [[ $host = lccrayh ]]
3815	then
3816	echo "localdir=\`pwd\`" >> $jobfile
3817	echo "ssh $SSH_PORTOPT $remote_username@hlogin1 \"cd \$localdir; scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname .\" " >> $jobfile
3818
3819	else
3820	echo "scp $PORTOPT -r $return_username@$return_address:$working_directory/SOURCES_FOR_RUN_$fname ." >> $jobfile
3821	fi
3822	fi
3823	echo "export SOURCES_COMPLETE=true" >> $jobfile
3824
3825	# MOVE MRUN-SCRIPT AND CONFIGURATION-FILE FROM THE SOURCES_FOR_RUN... DIRECTORY TO THE
3826	# WORKING DIRECTORY OF THE JOB
3827	echo "mv SOURCES_FOR_RUN_$fname/$config_file . " >> $jobfile
3828	echo "mv SOURCES_FOR_RUN_$fname/$mrun_script_name . " >> $jobfile
3829	echo "chmod u+rwx $mrun_script_name" >> $jobfile
3830	echo "execute_mrun=true" >> $jobfile
3831	echo " " >> $jobfile
3832
3833	else
3834
3835	# PROVIDE SOURCE-CODE FILES AND MAKEFILE AS HERE DOCUMENT
3836	if [[ $do_compile = true ]]
3837	then
3838
3839	source_catalog=SOURCES_FOR_RUN_$fname
3840
3841	# CREATE SOURCES_FOR_RUN... DIRECTORY TO STORE THE SOURCE CODE FILES AND THE MAKEFILE
3842	echo "mkdir SOURCES_FOR_RUN_$fname" >> $jobfile
3843	echo "export SOURCES_COMPLETE=true" >> $jobfile
3844	echo "cd SOURCES_FOR_RUN_$fname" >> $jobfile
3845
3846	for filename in $source_list
3847	do
3848	# BACKSLASH IS USED FOR MASKING
3849	echo "cat > $filename << \"%END%\"" >> $jobfile
3850	cat $source_catalog/$filename >> $jobfile
3851	echo " " >> $jobfile
3852	echo "%END%" >> $jobfile
3853	echo " " >> $jobfile
3854	done
3855
3856	# BACKSLASH IS USED FOR MASKING
3857	echo "cat > Makefile << \"%END%\"" >> $jobfile
3858	cat $source_catalog/Makefile >> $jobfile
3859	echo " " >> $jobfile
3860	echo "%END%" >> $jobfile
3861	echo " " >> $jobfile
3862
3863	echo "cd - > /dev/null" >> $jobfile
3864
3865	fi
3866
3867
3868	# PROVIDE THE CONFIGURATION-FILE AS HERE-DOCUMENT
3869	# BACKSLASH IS USED FOR MASKING
3870	# LINES WITH #$ IN THE CONFIGURATION-FILE, COMING FROM THE SVN KEYWORD SUBSTITUTION,
3871	# ARE REMOVED FROM THE FILE IN ORDER TO AVOID PROBLEMS WITH THE SGE BATCH SYSTEM
3872	echo "cat > $config_file << \"%END%\"" >> $jobfile
3873	if [[ $host = lckyuh ]]
3874	then
3875	# NO CROSS-COMPILER ON COMPUTE NODE
3876	sed 's/frtpx/frt/g' $config_file >> $jobfile
3877	else
3878	sed 's/#$.*//g' $config_file >> $jobfile
3879	fi
3880	echo "%END%" >> $jobfile
3881	echo " " >> $jobfile
3882
3883
3884	# PROVIDE THE MRUN-SCRIPTS AS HERE-DOCUMENT
3885	# BACKSLASH IS USED FOR MASKING
3886	echo "cat > $mrun_script_name <<\"%END%\"" >> $jobfile
3887	if [[ $host = lckyuh ]]
3888	then
3889	sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name >> $jobfile
3890	else
3891	cat ${PALM_BIN}/$mrun_script_name >> $jobfile
3892	fi
3893	echo "%END%" >> $jobfile
3894	echo "chmod u+x $mrun_script_name" >> $jobfile
3895	echo "execute_mrun=true" >> $jobfile
3896	echo " " >> $jobfile
3897
3898	fi
3899
3900
3901	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
3902	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
3903	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
3904	if [[ $do_remote = true ]]
3905	then
3906	(( i = 0 ))
3907	while (( i < iin ))
3908	do
3909	(( i = i + 1 ))
3910	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
3911	if [[ "${transin[$i]}" = job ]]
3912	then
3913	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
3914	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
3915	echo " " >> $jobfile
3916	echo "%END%" >> $jobfile
3917	else
3918	echo "batch_scp $PORTOPT -b -o -g -s -u $return_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
3919	fi
3920
3921	# CHECK, IF FILE COULD BE CREATED
3922	echo "if [[ \$? = 1 ]]" >> $jobfile
3923	echo "then" >> $jobfile
3924	echo " echo \" \" " >> $jobfile
3925	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
3926	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
3927	echo " echo \"+++ MRUN will not be continued\" " >> $jobfile
3928	echo " execute_mrun=false" >> $jobfile
3929	echo "fi" >> $jobfile
3930	done
3931	fi
3932
3933	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
3934	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY MRUN
3935	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
3936	echo "LOCAL_PWD=$working_directory" >> $jobfile
3937	echo "export LOCAL_PWD" >> $jobfile
3938
3939	# PROVIDE THE PATH OF THE LOCAL MRUN-SCRIPT FOR THE SAME REASON
3940	echo "LOCAL_MRUN_PATH=$PALM_BIN" >> $jobfile
3941	echo "export LOCAL_MRUN_PATH" >> $jobfile
3942
3943	# lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS
3944	if [[ $host = lceddy \|\| $localhost = lceddy ]]
3945	then
3946	echo "export PALM_BIN=$PALM_BIN" \| sed -e 's:'$HOME':$HOME:' >> $jobfile
3947	echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile
3948	fi
3949
3950	# CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti)
3951	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
3952	echo "set -x" >> $jobfile
3953	echo "queue=$queue" >> $jobfile
3954	echo "[[ \$execute_mrun = true ]] && ./$mrun_com" >> $jobfile
3955	echo 'ls -al; echo `pwd`' >> $jobfile
3956	echo "cd \$HOME" >> $jobfile
3957	echo "rm -rf $TEMPDIR" >> $jobfile
3958
3959
3960
3961
3962	# START THE JOB USING SUBJOB-COMMAND
3963	if [[ $silent = false ]]
3964	then
3965	printf "\n "
3966	else
3967	printf "\n\n"
3968	fi
3969
3970	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
3971	rm -rf $jobfile
3972
3973
3974	fi # END OF REMOTE-PART

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