Home

Context Navigation

source: palm/trunk/SCRIPTS/mrun @ 2301

Last change on this file since 2301 was 2298, checked in by raasch, 7 years ago
write_binary is of type LOGICAL now, MPI2-related code removed, obsolete variables removed, sendrecv_in_background related parts removed, missing variable descriptions added
Property svn:keywords set to `Id Rev`
File size: 141.3 KB

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

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |