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source: palm/trunk/SCRIPTS/palmrun @ 3487

Last change on this file since 3487 was 3455, checked in by raasch, 6 years ago
options -h and -d renamed -c and -r, respectively, job_queue renamed job_logfiles in sveral configuration files
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 100.8 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
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 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 3455 2018-10-30 14:12:31Z maronga $
29	# options -h and -d renamed -c and -r, respectively
30	#
31	# 3402 2018-10-23 11:49:24Z knoop
32	# job_id is set for compatibility reasons with older versions of config files
33	#
34	# 3313 2018-10-06 15:22:48Z knoop
35	# more detailed error message for outdated fileconnection file
36	#
37	# 3236 2018-09-10 09:07:06Z raasch
38	# warning issued in case of file connection file version mismatch,
39	# host_configuration renamed configuration_identifier,
40	# "host identifier" in header output renamed "config. identifier",
41	# jobname renamed run_identifier,
42	# run_id renamed run_id_number
43	# job_id renamed run_id
44	# option -r renamed -i
45	#
46	# 3151 2018-07-19 08:45:38Z raasch
47	# removed additional listing of files to be compiled, print PALM code revision
48	# in header
49	#
50	# 3132 2018-07-16 11:44:58Z raasch
51	# create consistent error messages in case of failed restarts,
52	# check existence of remote job catalog
53	#
54	# 3043 2018-05-25 10:47:54Z raasch
55	# check for setting of fast_io_catalog
56	#
57	# 3033 2018-05-23 15:26:19Z raasch
58	# -T option not required for interactive runs (tasks per node =
59	# total number of cores is assumed as default, if option is not given),
60	# reformatting of a few messages,
61	# bugfix: destination output directory is created if attribute "pe" is set in
62	# .palm.iofiles
63	#
64	# 2718 2018-01-02 08:49:38Z maronga
65	# bugfix of r2990
66	#
67	# 2718 2018-01-02 08:49:38Z maronga
68	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
69	# not in the working directory from where palmrun is called
70	#
71	# 2718 2018-01-02 08:49:38Z maronga
72	# svfout in the activation string will be replaced now by svfin in case of
73	# automatic restarts
74	#
75	# 2718 2018-01-02 08:49:38Z maronga
76	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
77	# the possible output or input of sky view factors
78	#
79	# 2718 2018-01-02 08:49:38Z maronga
80	# "fname" renamed to "jobname"
81	#
82	# 2718 2018-01-02 08:49:38Z maronga
83	# parameters are allowed in output commands (OC:)
84	#
85	# 2718 2018-01-02 08:49:38Z maronga
86	# bugfix: exit if no queue has been given neither with option -q nor in the
87	# configuration file
88	#
89	# 2718 2018-01-02 08:49:38Z maronga
90	# file connection file from trunk/SCRIPTS is taken by default
91	#
92	# 2718 2018-01-02 08:49:38Z maronga
93	# Corrected "Former revisions" section
94	#
95	# 2696 2017-12-14 17:12:51Z kanani
96	# Change in file header (GPL part)
97	#
98	# 2693 2017-12-13 12:33:49Z raasch
99	# replacement of variables given by {{<variable>}} in configuration file is now
100	# done in a more general way, variable names are written in small letters
101	#
102	# 2670 2017-12-06 16:32:19Z raasch
103	# test printouts removed
104	#
105	# 2669 2017-12-06 16:03:27Z raasch
106	# file attributes in .palm.iofiles restructured, "loc" attribute completely
107	# removed,
108	# wildcard (*) allowed in .palm.iofiles as file activation string for output
109	# files,
110	# informative messages in case of missing optional input files shortened
111	# bugfix: variable cycle explicitly interpreted with 10 as the number base
112	#
113	# 2638 2017-11-23 12:44:23Z raasch
114	# use of wildcards in file connection statements enabled
115	#
116	# 2605 2017-11-09 15:31:46Z raasch
117	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
118	# will not be sent with the job file any more, but copied into the
119	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
120	#
121	# 2600 2017-11-01 14:11:20Z raasch
122	# cycle numbers are made three digits wide
123	#
124	# 2566 2017-10-20 08:50:47Z raasch
125	# execute command for combine_plot_fields added
126	# "TEMPDIR" renamed "tempdir"
127	# temporary working directory for local batch jobs is created immediately within
128	# the user's palmrun call, due to a requirement of the "grid engine" batch
129	# system, where the working directory is given with batch directive -wd and must
130	# already exist when the job is submitted,
131	# informative messages in non-trace mode reduced and partly reformatted
132	#
133	# 2551 2017-10-18 07:25:11Z raasch
134	# TEMPDIR added as replacement string to be used in batch directives
135	#
136	# 2512 2017-10-04 08:26:59Z raasch
137	# bugfix for determining cycle numbers of NetCDF input files
138	#
139	# 2506 2017-09-29 08:30:37Z raasch
140	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
141	# host configuration added to SOURCES_FOR_RUN_... folder name
142	# host_identifier renamed host_configuration
143	# option -W added to allow for job dependencies
144	#
145	# 2501 2017-09-26 11:41:55Z raasch
146	# default value for number of cores (option -X) set to 1
147	# bugfix for mechanism which overwrites configuration file settings with values
148	# provided by palmrun options
149	#
150	# 2499 2017-09-22 16:47:58Z kanani
151	# option -h named configuration identifier
152	#
153	# 2480 2017-09-19 06:24:14Z maronga
154	# bugfix for last revision
155	#
156	# 2479 2017-09-19 06:12:16Z raasch
157	# option -A (project account number) added
158	#
159	# 2422 2017-09-08 08:25:41Z raasch
160	# initial revision
161	#
162	#--------------------------------------------------------------------------------#
163	# palmrun - script for running PALM jobs on local and remote hosts
164	#--------------------------------------------------------------------------------#
165
166
167
168	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
169
170	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
171	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
172	# (TOO MANY ARGUMENTS - PROBLEM)
173	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
174
175	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
176	typeset -i nr_of_output_files=0
177	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
178	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
179	# SCRIPT-OPTION ARGUMENTS
180	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
181	typeset -i icycle inode ival maxcycle mpi_tasks
182	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
183
184	activation_string_list=""
185	AddFilenames=""
186	combine_plot_fields=true
187	compiler_name=""
188	compiler_name_ser=""
189	compiler_options=""
190	configuration_identifier="default"
191	cores=1
192	cores_atmos=0
193	cores_ocean=0
194	coupled_dist=""
195	cpp_options=""
196	cpumax=0
197	create_batch_job=false
198	create_jobfile_only=false
199	create_remote_batch_job=false
200	dashes=" ----------------------------------------------------------------------------"
201	defaultqueue=""
202	delete_temporary_catalog=true
203	do_compile=true
204	do_trace=false
205	executable=""
206	execute_command=""
207	execution_error=false
208	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
209	global_revision=""
210	hostfile=""
211	hp=""
212	keep_data_from_previous_run=false
213	link_local_input=false
214	link_local_output=false
215	linker_options=""
216	local_jobcatalog=""
217	locat=normal
218	makefile=""
219	max_par_io_str=""
220	prc=$0
221	while [[ $(echo $prc \| grep -c "/") != 0 ]]
222	do
223	prc=`echo $prc \| cut -f2- -d"/"`
224	done
225	module_calls=""
226	palmrun_memory=""
227	palmrun_script_name=$prc
228	openmp=false
229	previous_job=""
230	project_account=""
231	queue=none
232	read_svf=""
233	restart_run=false
234	return_address=""
235	remote_jobcatalog=""
236	remote_username=""
237	running_in_batch_mode=false
238	running_in_test_mode=false
239	run_coupled_model=false
240	run_id=""
241	run_id_number=""
242	run_identifier=test
243	silent=false
244	source_list=""
245	source_path=""
246	tasks_per_node=0
247	threads_per_task=1
248	transfer_problems=false
249	user_source_path=""
250	use_existing_sources_folder=""
251	use_openmp=false
252	version="palmrun 1.0 Rev$Rev: 3455 $"
253	working_directory=`pwd`
254	write_binary=""
255	write_svf=""
256
257
258	# ERROR HANDLING IN CASE OF EXIT
259	trap 'if [[ $locat != normal && $locat != control_c ]]
260	then
261
262	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
263	(( i = 0 ))
264	while (( i < iec ))
265	do
266	(( i = i + 1 ))
267	printf "\n *** Execution of ERROR-command:\n"
268	printf " >>> ${err_command[$i]}\n"
269	eval ${err_command[$i]}
270	done
271	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
272	printf "\n\n+++ palmrun crashed \n\n"
273	exit 1
274	elif [[ $locat != normal ]]
275	then
276	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
277	printf "\n+++ palmrun killed by \"^C\" \n\n"
278	exit 2
279	else
280	printf "\n --> palmrun finished\n\n"
281	exit 0
282	fi' exit
283
284
285	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
286	trap 'locat=control_c
287	exit 1
288	' 2
289
290
291	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
292	# WHICH WILL BE USED TO START RESTART-JOBS
293	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
294	do
295	case $option in
296	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
297	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
298	(b) create_batch_job=true; prc="$prc -b";;
299	(B) delete_temporary_catalog=false; prc="$prc -B";;
300	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
301	(C) restart_run=true; prc="$prc -C";;
302	(F) create_jobfile_only=true;;
303	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
304	(i) run_id_number=$OPTARG;;
305	(j) running_in_batch_mode=true;;
306	(k) keep_data_from_previous_run=true; prc="$prc -k";;
307	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
308	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
309	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
310	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
311	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
312	(R) return_address=$OPTARG;;
313	(s) source_list=$OPTARG;;
314	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
315	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
316	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
317	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
318	(v) silent=true; prc="$prc -v";;
319	(V) use_existing_sources_folder="-V";;
320	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
321	(W) previous_job=$OPTARG;;
322	(x) do_trace=true;set -x; prc="$prc -x";;
323	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
324	(y) ocean_file_appendix=true; prc="$prc -y";;
325	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
326	(z) running_in_test_mode=true;;
327	(Z) combine_plot_fields=false; prc="$prc -Z";;
328	(\?) printf "\n +++ unknown option $OPTARG \n"
329	printf "\n --> type \"$0 ?\" for available options \n"
330	locat=parameter;exit;;
331	esac
332	done
333
334
335	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
336	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
337	(( to_shift = $OPTIND - 1 ))
338	shift $to_shift
339
340	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
341	if [[ "$1" = "?" ]]
342	then
343	(printf "\n *** Description of available palmrun options:\n"
344	printf "\n Option Description Default-Value"
345	printf "\n -a activation string list \"\" "
346	printf "\n -A project account number ---"
347	printf "\n -b batch-job on local machine ---"
348	printf "\n -B do not delete temporary directory at end ---"
349	printf "\n -c configuration identifier \"default\" "
350	printf "\n -F create batch job file only ---"
351	printf "\n -k keep data from previous run"
352	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
353	printf "\n -M Makefile name Makefile"
354	printf "\n -O threads per openMP task ---"
355	printf "\n -q queue \"$queue\" "
356	printf "\n -r run identifier test"
357	printf "\n -s filenames of routines to be compiled \"\" "
358	printf "\n must end with .f, .f90, .F, or .c !"
359	printf "\n use \"..\" for more than one file and wildcards"
360	printf "\n -s LM compiles all locally modified files"
361	printf "\n -t allowed cpu-time in seconds (batch) 0"
362	printf "\n -T tasks per node ---"
363	printf "\n -u username on remote machine \"\" "
364	printf "\n -v no prompt for confirmation ---"
365	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
366	printf "\n -w maximum parallel io streams as given by -X"
367	printf "\n -W name of job to wait for ---"
368	printf "\n -x tracing of palmrun for debug purposes ---"
369	printf "\n -X # of processors (on parallel machines) 1"
370	printf "\n -y add appendix \"_O\" to all local output"
371	printf "\n files (ocean precursor runs followed by"
372	printf "\n coupled atmosphere-ocean runs) ---"
373	printf "\n -Y run coupled model, \"#1 #2\" with"
374	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
375	printf "\n -Z skip combine_plot_fields at the end of "
376	printf "\n the simulation ---"
377	printf "\n "
378	printf "\n Possible values of positional parameter <modus>:"
379	printf "\n \"?\" - this outline \n\n") \| more
380	exit
381	elif [[ "$1" != "" ]]
382	then
383	printf "\n +++ positional parameter $1 unknown \n"
384	locat=parameter; exit
385	fi
386
387
388
389	# SHORT STARTING MESSAGE
390	printf "\n*** $version "
391	printf "\n will be executed. Please wait ..."
392
393
394	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
395	config_file=.palm.config.$configuration_identifier
396	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
397
398
399	# CHECK, IF CONFIGURATION FILE EXISTS
400	if [[ ! -f $config_file ]]
401	then
402	printf "\n\n +++ configuration file: "
403	printf "\n $config_file"
404	printf "\n does not exist"
405	locat=connect; exit
406	fi
407
408
409	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
410	if [[ -f .palm.iofiles ]]
411	then
412
413	# CHECK VERSION MISMATCH
414	if [[ $running_in_batch_mode != true ]]
415	then
416	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
417	then
418	printf "\n\n +++ WARNING: A file connection file has been found in your"
419	printf "\n working directory, but its revision does not match"
420	printf "\n the revision of the default (trunk) version."
421	printf "\n You may need to update your connection file"
422	printf "\n \"${working_directory}/.palm.iofiles\" !"
423	fi
424	fi
425
426	fileconnection_file=.palm.iofiles
427
428	fi
429
430
431	# CHECK, IF FILE CONNECTION FILE EXISTS
432	if [[ ! -f $fileconnection_file ]]
433	then
434	printf "\n\n +++ file connection file: "
435	printf "\n $fileconnection_file"
436	printf "\n does not exist"
437	locat=connect; exit
438	fi
439
440
441	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
442	if [[ "$activation_string_list" = "" ]]
443	then
444	printf "\n\n +++ no activation string list given: "
445	printf "\n please set palmrun option \"-a\" "
446	locat=palmrun_option; exit
447	fi
448
449
450	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
451	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
452	then
453	write_binary=true
454	else
455	write_binary=false
456	fi
457
458	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
459	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
460	then
461	write_svf=true
462	else
463	write_svf=false
464	fi
465
466	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
467	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
468	then
469	read_svf=true
470	else
471	read_svf=false
472	fi
473
474
475	# READ AND EVALUATE THE CONFIGURATION-FILE
476	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
477
478	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
479	while read line
480	do
481
482	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
483	eval line=\"$line\"
484
485
486	# INTERPRET THE LINE
487	if [[ "$(echo $line)" = "" ]]
488	then
489
490	# EMPTY LINE, NO ACTION
491	continue
492
493	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
494	then
495
496	# LINE IS A COMMENT LINE
497	continue
498
499	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
500	then
501
502	# LINE DEFINES AN ENVIRONMENT-VARIABLE
503	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
504	value=`echo $line \| cut -d" " -s -f2-`
505
506
507	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
508	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
509	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
510	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
511	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
512	# CONFIGURATION-FILE.
513	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
514	then
515	eval export $var="\$value"
516
517	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
518	if [[ $do_trace = true ]]
519	then
520	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
521	fi
522	fi
523
524	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
525	then
526
527	# LINE DEFINES BATCH-DIRECTIVE
528	(( ibd = ibd + 1 ))
529	line=$(echo $line \| cut -c4-)
530	batch_directive[$ibd]="$line"
531
532	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
533	then
534
535	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
536	# REMOTE TO A LOCAL HOST
537	(( ibdt = ibdt + 1 ))
538	line=$(echo $line \| cut -c5-)
539	batch_directive_transfer[$ibdt]="$line"
540
541	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
542	then
543
544	# LINE DEFINES ERROR-COMMAND
545	(( iec = iec + 1 ))
546	line=$(echo $line \| cut -c4-)
547	err_command[$iec]="$line"
548
549	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
550	then
551
552	# LINE DEFINES INPUT-COMMAND
553	(( iic = iic + 1 ))
554	line=$(echo $line \| cut -c4-)
555	in_command[$iic]="$line"
556
557	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
558	then
559
560	# LINE DEFINES OUTPUT-COMMAND
561	(( ioc = ioc + 1 ))
562	line=$(echo $line \| cut -c4-)
563	out_command[$ioc]="$line"
564
565	else
566
567	# SKIP ALL OTHER LINES
568	continue
569
570	fi
571
572	done < $config_file
573
574
575	# CHECK SETTING OF REQUIRED PARAMETERS
576	if [[ "$fast_io_catalog" = "" ]]
577	then
578	printf "\n +++ no fast_io_catalog found in $config_file"
579	printf "\n Please add line \"fast_io_catalog ...\" to that file."
580	locat=config_file; exit
581	fi
582	if [[ "$compiler_name" = "" ]]
583	then
584	printf "\n +++ no compiler name found in $config_file"
585	printf "\n Please add line \"compiler_name ...\" to that file."
586	locat=config_file; exit
587	fi
588	if [[ "$compiler_name_ser" = "" ]]
589	then
590	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
591	printf "\n Please add line \"compiler_name_ser ...\" to that file."
592	locat=config_file; exit
593	fi
594	if [[ "$compiler_options" = "" ]]
595	then
596	printf "\n +++ no compiler options found in $config_file"
597	printf "\n Please add line \"compiler_options ...\" to that file."
598	locat=config_file; exit
599	fi
600	if [[ "$linker_options" = "" ]]
601	then
602	printf "\n +++ no linker options found in $config_file"
603	printf "\n Please add line \"linker_options ...\" to that file."
604	locat=config_file; exit
605	fi
606	if [[ "$execute_command" = "" ]]
607	then
608	printf "\n +++ no execute command found in $config_file"
609	printf "\n Please add line \"execute_command ...\" to that file."
610	locat=config_file; exit
611	fi
612
613	if [[ "$hostfile" != "" ]]
614	then
615	if [[ $hostfile != auto && ! -f $hostfile ]]
616	then
617	printf "\n +++ no hostfile \"$hostfile\" found"
618	printf "\n Please check line \"hostfile ...\" in $config_file"
619	locat=config_file; exit
620	fi
621	fi
622
623
624	# DETERMINE THE CALL STATUS
625	if [[ "$return_address" != "" ]]
626	then
627
628	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
629	# BATCH MODE AND ...
630	running_on_remote=true
631
632	else
633
634	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
635	if [[ "$remote_ip" != "" ]]
636	then
637
638	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
639	create_remote_batch_job=true
640
641	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
642	if [[ "$remote_jobcatalog" = "" ]]
643	then
644	printf "\n +++ no remote jobcatalog found in $config_file"
645	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
646	locat=config_file; exit
647	fi
648
649
650	fi
651	running_on_remote=false
652	fi
653
654
655
656	# READ AND EVALUATE THE I/O-FILE LIST
657	[[ $silent = false ]] && printf "\n Reading the I/O files... "
658
659	# READ THE FILE CONNECTION FILE LINE BY LINE
660	while read line
661	do
662
663	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
664	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
665
666	# INTERPRET THE LINE
667	if [[ "$(echo $line)" = "" ]]
668	then
669	# EMPTY LINE, NO ACTION
670	continue
671
672	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
673	then
674
675	# LINE IS A COMMENT LINE
676	true
677
678	else
679
680	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
681	# s2a: in/out - field
682	# s2b: action - field (optional)
683	s1=`echo "$line" \| cut -d" " -f1`
684	s2=`echo "$line" \| cut -d" " -s -f2`
685	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
686	then
687	s2a=$s2
688	s2b=""
689	else
690	s2a=`echo $s2 \| cut -d":" -f1`
691	s2b=`echo $s2 \| cut -d":" -f2`
692	fi
693	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
694	s4=`echo "$line" \| cut -d" " -s -f4`
695	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
696	s5=`echo "$line" \| cut -d" " -s -f5`
697	s6=`echo "$line" \| cut -d" " -s -f6`
698
699
700	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
701	# INPUT- OR OUTPUT-LIST.
702	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
703	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
704	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
705	# IS NOT CHECKED AND STORED.
706	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
707	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
708	then
709	found=false
710	for actual in $activation_string_list
711	do
712	for formal in $s3
713	do
714	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
715	done
716	done
717	if [[ $found = true ]]
718	then
719	(( iin = iin + 1 ))
720	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
721	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
722	if [[ "$s2a" = inopt ]]
723	then
724	optin_pre[$iin]=yes
725	else
726	optin_pre[$iin]=no
727	fi
728
729	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
730	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
731	if [[ $running_on_remote = true && "$s2b" = tr ]]
732	then
733	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
734	fi
735
736	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
737	# THE WILDCARD FROM THE ENDING
738	if [[ "${s5: -1}" = "*" ]]
739	then
740	if [[ "$s2b" = "di" ]]
741	then
742	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
743	printf "\n see file \"$fileconnection_file\", line"
744	printf "\n$line"
745	locat=iofiles_file; exit
746	fi
747	multin[$iin]=true
748	string=${endin_pre[$iin]}
749	endin_pre[$iin]="${string%?}"
750	else
751	multin[$iin]=false
752	fi
753	fi
754	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
755	then
756	found=false
757	for actual in $activation_string_list
758	do
759	for formal in $s3
760	do
761	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
762	done
763	done
764	if [[ $found = true ]]
765	then
766	(( iout = iout + 1 ))
767	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
768	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
769
770	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
771	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
772	if [[ $formal = wildcard ]]
773	then
774	warnout_pre[$iout]=false
775	else
776	warnout_pre[$iout]=true
777	fi
778
779	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
780	# THE WILDCARD FROM THE LOCAL FILENAME
781	if [[ "${s1: -1}" = "*" ]]
782	then
783	if [[ "$s2b" = "di" ]]
784	then
785	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
786	printf "\n see file \"$fileconnection_file\", line"
787	printf "\n$line"
788	locat=iofiles_file; exit
789	fi
790	multout[$iout]=true
791	string=${localout_pre[$iout]}
792	localout_pre[$iout]="${string%?}"
793	else
794	multout[$iout]=false
795	fi
796	fi
797	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
798	then
799	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
800	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
801	locat=connect; exit
802	fi
803	IFS="$IFSALT"
804	fi
805
806	done < $fileconnection_file
807
808
809
810	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
811	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
812	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
813	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
814	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
815	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
816
817
818
819	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
820	if [[ $run_coupled_model = true ]]
821	then
822
823	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
824	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
825
826	if (( $cores_ocean + $cores_atmos != $cores ))
827	then
828
829	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
830	printf "\n PEs (total) : $cores"
831	printf "\n PEs (atmosphere): $cores_atmos"
832	printf "\n PEs (ocean) : $cores_ocean"
833	locat=coupling; exit
834
835	fi
836
837	fi
838
839
840	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
841	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
842	# FOLDER
843	if [[ $running_in_batch_mode = true ]]
844	then
845
846	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
847	then
848	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
849	printf "\n Please check the output of the palmrun-call"
850	printf "\n that you did on your local host."
851	locat=SOURCES_FOR_RUN; exit
852	fi
853
854	else
855
856	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
857	# AUTOMATIC RESTART RUN
858	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
859	if [[ $restart_run = false ]]
860	then
861
862	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
863	# THE LOCAL HOST
864	if [[ ! -d $source_path ]]
865	then
866	printf "\n\n +++ source path \"$source_path\" on local host"
867	printf "\n \"$(hostname)\" does not exist"
868	locat=source_path; exit
869	fi
870
871	rm -rf ${base_directory}/${sources_for_run_catalog}
872	mkdir -p ${base_directory}/${sources_for_run_catalog}
873
874	if [[ "$source_list" = LM ]]
875	then
876
877	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
878	source_list=""
879	cd $source_path
880
881
882	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
883	if [[ ! -d ../.svn ]]
884	then
885	printf "\n\n +++ source directory"
886	printf "\n \"$source_path\" "
887	printf "\n is not under control of \"subversion\"."
888	printf "\n Please do not use palmrun-option \"-s LM\"\n"
889	fi
890
891
892	# LIST ALL MODIFIED SOURCE CODE FILES
893	Filenames=""
894	svn status > tmp_svnstatus
895	while read line
896	do
897	firstc=`echo $line \| cut -c1`
898	if [[ $firstc = M \|\| $firstc = "?" ]]
899	then
900	Name=`echo "$line" \| cut -c8-`
901	extension=`echo $Name \| cut -d. -f2`
902	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
903	then
904	Filenames="$Filenames "$Name
905	fi
906	fi
907	done < tmp_svnstatus
908	rm -rf tmp_svnstatus
909
910
911	# COPY FILES TO SOURCES_FOR_RUN_...
912	for filename in $Filenames
913	do
914	cp $filename ${base_directory}/${sources_for_run_catalog}
915	source_list=$source_list"$filename "
916	done
917
918	cd - > /dev/null
919
920
921	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
922	elif [[ "$source_list" != "" ]]
923	then
924
925	cd $source_path
926
927	for filename in $source_list
928	do
929
930	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
931	if [[ $(echo $filename \| grep -c "/") != 0 ]]
932	then
933	printf "\n +++ source code file: $filename"
934	printf "\n must not contain (\"/\") "
935	locat=source; exit
936	fi
937
938	if [[ ! -f $filename ]]
939	then
940	printf "\n +++ source code file: $filename"
941	printf "\n does not exist"
942	locat=source; exit
943	else
944	cp $filename ${base_directory}/${sources_for_run_catalog}
945	fi
946
947	done
948
949	cd - > /dev/null
950
951	fi
952
953	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
954	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
955	if [[ ! -f $makefile ]]
956	then
957	printf "\n +++ file \"$makefile\" does not exist"
958	locat=make; exit
959	else
960	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
961	fi
962
963
964	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
965	if [[ "$user_source_path" != "" ]]
966	then
967
968	# DOES THE DIRECTORY EXIST?
969	if [[ ! -d $user_source_path ]]
970	then
971
972	printf "\n\n *** INFORMATIVE: additional source code directory"
973	printf "\n \"$user_source_path\" "
974	printf "\n does not exist or is not a directory."
975	printf "\n No source code will be used from this directory!\n"
976	user_source_path=""
977	if [[ $silent == false ]]
978	then
979	sleep 2
980	fi
981
982	else
983
984	cd $user_source_path
985
986	Names=$(ls -1 *.f90 2>&1)
987	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
988	Names=$(ls -1 *.F90 2>&1)
989	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
990	Names=$(ls -1 *.F 2>&1)
991	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
992	Names=$(ls -1 *.f 2>&1)
993	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
994	Names=$(ls -1 *.c 2>&1)
995	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
996
997	cd - > /dev/null
998	cd ${base_directory}/${sources_for_run_catalog}
999
1000	# COPY MAKEFILE IF EXISTING
1001	if [[ -f $user_source_path/Makefile ]]
1002	then
1003	printf "\n\n *** user Makefile from directory"
1004	printf "\n \"$user_source_path\" is used \n"
1005	if [[ $silent == false ]]
1006	then
1007	sleep 1
1008	fi
1009	cp $user_source_path/Makefile .
1010	fi
1011
1012	for filename in $AddFilenames
1013	do
1014	if [[ -f $filename ]]
1015	then
1016	printf "\n +++ source code file \"$filename\" found in additional"
1017	printf "\n source code directory \"$user_source_path\" "
1018	printf "\n but was also given with option \"-s\" which means that it should be taken"
1019	printf "\n from directory \"$source_path\"."
1020	locat=source; exit
1021	fi
1022
1023	cp $user_source_path/$filename .
1024	source_list="$source_list $filename"
1025
1026	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1027	if [[ $(grep -c $filename Makefile) = 0 ]]
1028	then
1029	printf "\n\n +++ user file \"$filename\" "
1030	printf "\n is not listed in Makefile \n"
1031	locat=source; exit
1032	fi
1033	done
1034	cd - > /dev/null
1035	fi
1036	fi
1037
1038	# COPY CONFIGURATION FILES
1039	cp $config_file ${base_directory}/${sources_for_run_catalog}
1040	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1041
1042	# COPY SHELLSCRIPTS
1043	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1044	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1045
1046	fi
1047
1048	fi
1049
1050
1051	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1052	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1053	if [[ "$global_revision" = "" ]]
1054	then
1055	global_revision=`svnversion $source_path 2>/dev/null`
1056	global_revision="Rev: $global_revision"
1057	fi
1058
1059
1060	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1061	if [[ -n $cores ]]
1062	then
1063
1064	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1065	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1066	if [[ $tasks_per_node = 0 ]]
1067	then
1068	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1069	then
1070	printf "\n"
1071	printf "\n +++ option \"-T\" (tasks per node) is missing"
1072	printf "\n set -T option or define tasks_per_node in the config file"
1073	locat=tasks_per_node; (( iec = 0 )); exit
1074	else
1075	# DEFAULT FOR INTERACTIVE RUN
1076	tasks_per_node=$cores
1077	fi
1078	fi
1079
1080	if (( cores < tasks_per_node ))
1081	then
1082	printf "\n"
1083	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1084	printf "\n given values: -T $tasks_per_node -X $cores"
1085	locat=tasks_per_node; (( iec = 0 )); exit
1086	fi
1087
1088	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1089	(( mpi_tasks = cores / threads_per_task ))
1090	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1091	(( ii = cores / tasks_per_node ))
1092	(( remaining_cores = cores - ii * tasks_per_node ))
1093	if (( remaining_cores > 0 ))
1094	then
1095	printf "\n"
1096	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1097	printf "\n divisor of the total number of cores (option \"-X\")"
1098	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1099	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1100	(( nodes = nodes + 1 ))
1101	fi
1102
1103	fi
1104
1105
1106	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1107	if [[ "$maximum_parallel_io_streams" = "" ]]
1108	then
1109	maximum_parallel_io_streams=$cores
1110	fi
1111
1112
1113	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1114	if [[ "$scp_port" != "" ]]
1115	then
1116	PORTOPT="-P $scp_port"
1117	SSH_PORTOPT="-p $scp_port"
1118	fi
1119
1120
1121	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1122	# CONFIG-FILE
1123	if [[ "$ssh_key" != "" ]]
1124	then
1125	ssh_key="-i $HOME/.ssh/$ssh_key"
1126	fi
1127
1128
1129	# SET QUEUE, IF NOT GIVEN
1130	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1131	then
1132
1133	if [[ $queue = none && "$defaultqueue" = "" ]]
1134	then
1135	printf "\n"
1136	printf "\n +++ no default queue given in configuration file and no queue"
1137	printf "\n given with option -q"
1138	locat=queue; exit
1139	fi
1140	if [[ $queue = none ]]
1141	then
1142	queue=$defaultqueue
1143	fi
1144
1145	fi
1146
1147
1148	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1149	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1150	(( i = 0 ))
1151	(( nr_of_input_files = 0 ))
1152	while (( i < iin ))
1153	do
1154	(( i = i + 1 ))
1155
1156	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1157	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1158	if [[ "${actionin_pre[$i]}" = di ]]
1159	then
1160	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1161	else
1162	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1163	fi
1164
1165
1166	# CHECK IF FILE EXISTS
1167	if ! ls $filename* 1>/dev/null 2>&1
1168	then
1169
1170	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1171	if [[ "${optin_pre[$i]}" != "yes" ]]
1172	then
1173	printf "\n\n +++ INPUT-file: "
1174	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1175	then
1176	printf "\n $filename"
1177	else
1178	printf "\n $filename.${extin_pre[$i]}"
1179	fi
1180	printf "\n does not exist\n"
1181	locat=input; exit
1182	else
1183	(( nr_of_input_files = nr_of_input_files + 1 ))
1184	localin[$nr_of_input_files]="${localin_pre[$i]}"
1185	optin[$nr_of_input_files]="${optin_pre[$i]}"
1186	actionin[$nr_of_input_files]="unavailable"
1187	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1188	endin[$nr_of_input_files]="${endin_pre[$i]}"
1189	extin[$nr_of_input_files]="${extin_pre[$i]}"
1190	fi
1191
1192	else
1193
1194	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1195	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1196	# ENDINGS
1197	if [[ "${multin[$i]}" = true ]]
1198	then
1199	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1200	ls -1 -d ${filename} > filelist 2>/dev/null
1201	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1202	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1203
1204	endings=""
1205	while read line
1206	do
1207	# filename without path (i.e. after the last "/")
1208	basefilename=$(basename ${line})
1209
1210	# check if there is an extension and remove it
1211	ext=${basefilename##*.}
1212	if [[ "$ext" = "${extin_pre[$i]}" ]]
1213	then
1214	basefilename=${basefilename%.*}
1215	fi
1216
1217	# check for an existing cycle number and remove it
1218	cycle=${basefilename##*.}
1219	if [[ $cycle =~ ^-?[0-9]+$ ]]
1220	then
1221	basefilename=${basefilename%.*}
1222	fi
1223
1224	# remove the run_identifier from the beginning
1225	length_run_identifier=${#run_identifier}
1226	ending=${basefilename:${length_run_identifier}}
1227
1228	# remove the ending given in the .iofiles from the beginning
1229	endingstring="${endin_pre[$i]}"
1230	length_ending=${#endingstring}
1231	ending=${ending:${length_ending}}
1232
1233	if [[ "$ending" = "" ]]
1234	then
1235	# standard ending as given in the .iofiles
1236	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1237	then
1238	endings="$endings DEFAULT"
1239	fi
1240	else
1241	# ending must start with "_", otherwise its a different file
1242	if [[ "${ending:0:1}" = "_" ]]
1243	then
1244	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1245	then
1246	endings="$endings $ending"
1247	fi
1248	fi
1249	fi
1250
1251	done <filelist
1252
1253	rm filelist
1254
1255	else
1256
1257	# SINGLE NAME
1258	endings=DEFAULT
1259
1260	fi
1261
1262	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1263	for ending in $endings
1264	do
1265
1266	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1267	if [[ $ending = DEFAULT ]]
1268	then
1269	ending=""
1270	fi
1271
1272	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1273	(( nr_of_input_files = nr_of_input_files + 1 ))
1274	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1275	optin[$nr_of_input_files]="${optin_pre[$i]}"
1276	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1277	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1278	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1279	extin[$nr_of_input_files]="${extin_pre[$i]}"
1280
1281
1282	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1283	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1284	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1285	then
1286	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1287	else
1288	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1289	fi
1290
1291	# DETERMINE THE FILE'S CYCLE NUMBER
1292	(( maxcycle = 0 ))
1293	ls -1 -d $filename > filelist 2>/dev/null
1294	ls -1 -d $filename.* >> filelist 2>/dev/null
1295	while read line
1296	do
1297	# filename without path (i.e. after the last "/")
1298	basefilename=$(basename ${line})
1299
1300	# check if there is an extension
1301	extension=${basefilename##*.}
1302	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1303	then
1304	basefilename=${basefilename%.*}
1305	fi
1306
1307	# check for an existing cycle number
1308	cycle=${basefilename##*.}
1309	if [[ $cycle =~ ^-?[0-9]+$ ]]
1310	then
1311	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1312	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1313	(( icycle = $((10#$cycle)) ))
1314	else
1315	(( icycle = 0 ))
1316	fi
1317
1318	if (( icycle > maxcycle ))
1319	then
1320	(( maxcycle = icycle ))
1321
1322	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1323	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1324	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1325	then
1326	leading_zero=true
1327	else
1328	leading_zero=false
1329	fi
1330	fi
1331
1332	done <filelist
1333	rm filelist
1334
1335	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1336	if [[ $leading_zero = true ]]
1337	then
1338	cyclestring=`printf "%03d" $maxcycle`
1339	else
1340	cyclestring=$maxcycle
1341	fi
1342
1343	# APPEND CYCLE NUMBER TO FILENAME
1344	if (( maxcycle > 0 ))
1345	then
1346	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1347	then
1348	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1349	else
1350	filename=${filename}.$cyclestring
1351	fi
1352	else
1353	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1354	then
1355	filename=${filename}.${extin[$nr_of_input_files]}
1356	fi
1357	fi
1358
1359	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1360	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1361	absnamein[$nr_of_input_files]=$filename
1362	if (( maxcycle > 0 ))
1363	then
1364	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1365	then
1366	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1367	else
1368	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1369	fi
1370	else
1371	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1372	then
1373	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1374	else
1375	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1376	fi
1377	fi
1378
1379	done
1380
1381	fi
1382
1383	done
1384
1385
1386	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1387	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1388	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1389	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1390	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1391	# REMOTE HOST)
1392	(( i = 0 ))
1393	while (( i < iout ))
1394	do
1395	(( i = i + 1 ))
1396	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1397	then
1398	if [[ "${actionout_pre[$i]}" = tr ]]
1399	then
1400	actionout_pre[$i]=""
1401	elif [[ "${actionout_pre[$i]}" = trpe ]]
1402	then
1403	actionout_pre[$i]=pe
1404	elif [[ "${actionout_pre[$i]}" = tra ]]
1405	then
1406	actionout_pre[$i]=a
1407	fi
1408	(( maxcycle = 0 ))
1409	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1410	eval catalogname=${pathout_pre[$i]}
1411	if ! ls $filename* 1>/dev/null 2>&1
1412	then
1413
1414	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1415	if cat /dev/null > $filename
1416	then
1417	rm $filename
1418	else
1419
1420	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1421	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1422	if [[ ! -d $catalogname ]]
1423	then
1424	if mkdir -p $catalogname
1425	then
1426	printf "\n\n *** directory:"
1427	printf "\n $catalogname"
1428	printf "\n was created\n"
1429	else
1430	printf "\n\n +++ OUTPUT-file:"
1431	printf "\n $filename"
1432	printf "\n cannot be created, because directory does not exist"
1433	printf "\n and cannot be created either"
1434	printf "\n"
1435	locat=output ; exit
1436	fi 2>/dev/null
1437	else
1438	printf "\n\n +++ OUTPUT-file:"
1439	printf "\n $filename"
1440	printf "\n cannot be created, although directory exists"
1441	printf "\n"
1442	locat=output ; exit
1443	fi
1444	fi 2>/dev/null
1445
1446	fi
1447
1448	fi
1449	done
1450
1451
1452	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1453	if [[ $running_in_batch_mode = false ]]
1454	then
1455	run_id_number=$RANDOM
1456	run_id=${run_identifier}.$run_id_number
1457
1458	tempdir=$fast_io_catalog/$run_id
1459
1460	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1461	export job_id=$run_id
1462
1463	fi
1464
1465
1466	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1467	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1468	then
1469
1470	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1471	if [[ $ibd = 0 ]]
1472	then
1473	printf "\n"
1474	printf "\n +++ no batch directives found in configuration file"
1475	locat=config_file_batch_directives; (( iec = 0 )); exit
1476	fi
1477
1478	# CHECK IF CPUTIME IS GIVEN FOR JOB
1479	done=false
1480	cputime=$cpumax
1481	while [[ $done = false ]]
1482	do
1483	if (( cputime == 0 ))
1484	then
1485	printf "\n +++ cpu-time is undefined"
1486	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1487	printf "\n >>> "
1488	read cputime 1>/dev/null 2>&1
1489	else
1490	done=true
1491	fi
1492	done
1493	cpumax=$cputime
1494
1495	# CHECK THE MEMORY DEMAND
1496	done=false
1497	while [[ $done = false ]]
1498	do
1499	if (( memory == 0 ))
1500	then
1501	printf "\n +++ memory demand is undefined"
1502	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1503	printf "\n >>> "
1504	read memory 1>/dev/null 2>&1
1505	else
1506	done=true
1507	fi
1508	done
1509
1510	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1511	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1512	then
1513	while [[ -z $remote_username ]]
1514	do
1515	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1516	printf "\n >>> Please type username:"
1517	printf "\n >>> "
1518	read remote_username
1519	done
1520	fi
1521
1522	else
1523
1524	if [[ $running_in_batch_mode = false ]]
1525	then
1526	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1527	cpumax=$cputime
1528	else
1529	cputime=$cpumax
1530	fi
1531
1532	fi
1533
1534
1535	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1536	(( cpu_hours = cputime / 3600 ))
1537	(( resttime = cputime - cpu_hours * 3600 ))
1538	(( cpu_minutes = resttime / 60 ))
1539	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1540	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1541
1542
1543	# OUTPUT OF THE PALMRUN-HEADER
1544	calltime=$(date)
1545	printf "\n"
1546	printf "#------------------------------------------------------------------------# \n"
1547	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1548	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1549	printf "\| \| \n"
1550	column1="called on:"; column2=$(hostname)
1551	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1552	if [[ $create_remote_batch_job = true ]]
1553	then
1554	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1555	else
1556	if [[ $running_on_remote = true ]]
1557	then
1558	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1559	else
1560	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1561	fi
1562	fi
1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1564
1565	column1="running in:"
1566	if [[ $running_in_batch_mode = true ]]
1567	then
1568	column2="batch job mode"
1569	else
1570	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1571	then
1572	column2="job creation mode"
1573	else
1574	column2="interactive run mode"
1575	fi
1576	fi
1577	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1578
1579	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1580	then
1581	if [[ "$project_account" != "" ]]
1582	then
1583	column1="project account number:"
1584	column2="$project_account"
1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1586	fi
1587	fi
1588
1589	if [[ -n $cores ]]
1590	then
1591	if [[ $run_coupled_model = false ]]
1592	then
1593	column1="number of cores:"; column2=$cores
1594	else
1595	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1596	fi
1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1598	fi
1599	if [[ -n $tasks_per_node ]]
1600	then
1601	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	if (( remaining_cores > 0 ))
1604	then
1605	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1606	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1607	fi
1608	fi
1609	if [[ $maximum_parallel_io_streams != $cores ]]
1610	then
1611	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1612	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1613	fi
1614	if [[ $use_openmp = true ]]
1615	then
1616	column1="threads per task:"; column2="$threads_per_task"
1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1618	fi
1619	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1620	then
1621	column1="memory demand / PE":; column2="$memory MB"
1622	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1623	column1="job cpu time (h:m:s):"; column2="$timestring"
1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1625	fi
1626	printf "\| \| \n"
1627	if [[ "$source_list" != "" ]]
1628	then
1629	if [[ "$make_options" != "" ]]
1630	then
1631	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1633	line=$(echo "$make_options" \| cut -c46-)
1634	while [[ "$line" != "" ]]
1635	do
1636	column1=""
1637	column2=$(echo "$line" \| cut -c-45)
1638	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1639	line=$(echo "$line" \| cut -c46-)
1640	done
1641	fi
1642	fi
1643
1644	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1646	line=$(echo "$cpp_options" \| cut -c46-)
1647	while [[ "$line" != "" ]]
1648	do
1649	column1=""
1650	column2=$(echo "$line" \| cut -c-45)
1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1652	line=$(echo "$line" \| cut -c46-)
1653	done
1654
1655	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1657	line=$(echo "$compiler_options" \| cut -c46-)
1658	while [[ "$line" != "" ]]
1659	do
1660	column1=""
1661	column2=$(echo "$line" \| cut -c-45)
1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1663	line=$(echo "$line" \| cut -c46-)
1664	done
1665
1666	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1667	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1668	line=$(echo "$linker_options" \| cut -c46-)
1669	while [[ "$line" != "" ]]
1670	do
1671	column1=""
1672	column2=$(echo "$line" \| cut -c-45)
1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1674	line=$(echo "$line" \| cut -c46-)
1675	done
1676
1677	if [[ "$login_init_cmd" != "" ]]
1678	then
1679	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1680	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1681	line=$(echo "$login_init_cmd" \| cut -c46-)
1682	while [[ "$line" != "" ]]
1683	do
1684	column1=""
1685	column2=$(echo "$line" \| cut -c-45)
1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1687	line=$(echo "$line" \| cut -c46-)
1688	done
1689	fi
1690
1691	if [[ "$module_commands" != "" ]]
1692	then
1693	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1695	line=$(echo "$module_commands" \| cut -c46-)
1696	while [[ "$line" != "" ]]
1697	do
1698	column1=""
1699	column2=$(echo "$line" \| cut -c-45)
1700	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1701	line=$(echo "$line" \| cut -c46-)
1702	done
1703	fi
1704	printf "\| \| \n"
1705	column1="run identifier:"; column2=$run_identifier
1706	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1707	column1="activation string list:"; column2=$(echo $activation_string_list)
1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1709
1710	if [[ "$ocean_file_appendix" = true ]]
1711	then
1712	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1713	fi
1714
1715	if [[ "$source_list" != "" ]]
1716	then
1717	printf "\| \| \n"
1718	printf "\| Files to be compiled: \| \n"
1719	line=$source_list
1720	while [[ "$line" != "" ]]
1721	do
1722	linestart=$(echo $line \| cut -c-70)
1723	printf "\| %-70s \| \n" "$linestart"
1724	line=$(echo "$line" \| cut -c71-)
1725	done
1726	fi
1727	printf "#------------------------------------------------------------------------#"
1728
1729
1730
1731	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1732	if [[ $do_trace = true ]]
1733	then
1734	(( i = 0 ))
1735	while (( i < nr_of_input_files ))
1736	do
1737	(( i = i + 1 ))
1738	if (( i == 1 ))
1739	then
1740	printf "\n\n >>> INPUT-file assignments:\n"
1741	fi
1742	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1743	done
1744	(( i = 0 ))
1745	while (( i < iout ))
1746	do
1747	(( i = i + 1 ))
1748	if (( i == 1 ))
1749	then
1750	printf "\n\n >>> OUTPUT-file assignments:\n"
1751	fi
1752	printf "\n ${localout[$i]} : ${pathout[$i]}"
1753	done
1754	(( i = 0 ))
1755	while (( i < iic ))
1756	do
1757	(( i = i + 1 ))
1758	if (( i == 1 ))
1759	then
1760	printf "\n\n >>> INPUT-commands:\n"
1761	fi
1762	printf "\n ${in_command[$i]}"
1763	done
1764	(( i = 0 ))
1765	while (( i < ioc ))
1766	do
1767	(( i = i + 1 ))
1768	if (( i == 1 ))
1769	then
1770	printf "\n\n >>> OUTPUT-commands:\n"
1771	fi
1772	printf "\n ${out_command[$i]}"
1773	done
1774	fi
1775
1776	# QUERY FOR CONTINUE
1777	if [[ $silent = false && $running_in_batch_mode = false ]]
1778	then
1779	antwort=dummy
1780	printf "\n\n"
1781	printf " >>> everything o.k. (y/n) ? "
1782	while read antwort
1783	do
1784	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1785	then
1786	printf " >>> everything o.k. (y/n) ? "
1787	else
1788	break
1789	fi
1790	done
1791	if [[ $antwort = n \|\| $antwort = N ]]
1792	then
1793	locat=user_abort; (( iec = 0 )); exit
1794	fi
1795	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1796	then
1797	printf "\n *** batch-job will be created and submitted"
1798	else
1799	printf "\n *** PALMRUN will now continue to execute on this machine"
1800	fi
1801	fi
1802
1803
1804
1805	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1806	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1807	then
1808
1809	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1810	then
1811	printf "\n\n *** creating executable and other sources for the remote host\n"
1812	else
1813	printf "\n\n *** creating executable and other sources for the local host\n"
1814	fi
1815
1816	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1817	# IT SHALL BE CREATED
1818	ask_for_make_depository=false
1819	if [[ $create_remote_batch_job = true ]]
1820	then
1821
1822	line=`grep %base_directory $config_file`
1823	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1824	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1825
1826	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1827	then
1828	printf "\n\n +++ make depository \"${make_depository}\""
1829	printf "\n on remote host not found!"
1830	ask_for_make_depository=true
1831	fi
1832	rm ${configuration_identifier}_last_make_protokoll
1833
1834	else
1835
1836	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1837	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1838	if [[ ! -d ${make_depository} ]]
1839	then
1840	printf "\n\n +++ make depository \"${make_depository}\""
1841	printf "\n on local host not found!"
1842	ask_for_make_depository=true
1843	fi
1844
1845	fi
1846
1847	if [[ $ask_for_make_depository = true ]]
1848	then
1849
1850	antwort=dummy
1851	printf "\n\n"
1852	printf " >>> Create a new one (y/n) ? "
1853	while read antwort
1854	do
1855	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1856	then
1857	printf " >>> Create a new one (y/n) ? "
1858	else
1859	break
1860	fi
1861	done
1862	if [[ $antwort = n \|\| $antwort = N ]]
1863	then
1864	locat=user_abort; (( iec = 0 )); exit
1865	fi
1866
1867	if [[ $do_trace = true ]]
1868	then
1869	palmbuild -c $configuration_identifier
1870	else
1871	palmbuild -v -c $configuration_identifier
1872	fi
1873
1874	if [[ ${PIPESTATUS[0]} != 0 ]]
1875	then
1876
1877	# ABORT IN CASE OF COMPILATION PROBLEMS
1878	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1879	locat=make_depository
1880	exit
1881	else
1882	echo " *** now continue with creating executable and other sources"
1883	fi
1884
1885	fi
1886
1887	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1888	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1889
1890	if [[ ${PIPESTATUS[0]} != 0 ]]
1891	then
1892
1893	# ABORT IN CASE OF COMPILATION PROBLEMS
1894	printf "\n +++ error while creating executable and/or other sources"
1895	locat=execution
1896	rm -rf ${base_directory}/${sources_for_run_catalog}
1897	exit
1898
1899	else
1900
1901	printf " *** executable and other sources created\n"
1902	rm -rf ${base_directory}/${sources_for_run_catalog}
1903
1904	fi
1905
1906	fi
1907
1908
1909	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1910	# WILL BE COPIED TO THE REMOTE HOST
1911	if [[ $create_remote_batch_job = true ]]
1912	then
1913	(( i = 0 ))
1914	while (( i < nr_of_input_files ))
1915	do
1916	(( i = i + 1 ))
1917	if [[ "${actionin[$i]}" = tr ]]
1918	then
1919	eval inputfile=${pathin[$i]}/${frelin[$i]}
1920	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1921	fi
1922	done
1923	if (( i > 0 ))
1924	then
1925	printf "\n\n *** input files have been copied to the remote host\n"
1926	fi
1927	fi
1928
1929
1930	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1931	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1932	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1933	then
1934
1935	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1936	if [[ $running_in_batch_mode = false ]]
1937	then
1938	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1939	# FOLDER
1940	mkdir -p $tempdir
1941	chmod go+rx $tempdir
1942	cd $tempdir
1943	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1944	printf "\n *** changed to temporary directory: $tempdir"
1945
1946	else
1947
1948	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1949	printf "\n *** running in temporary directory: $tempdir"
1950
1951	fi
1952
1953
1954	# PROVIDE THE INPUT FILES
1955	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1956	optional_files_missing=false
1957	(( i = 0 ))
1958	while (( i < nr_of_input_files ))
1959	do
1960	(( i = i + 1 ))
1961	if (( i == 1 ))
1962	then
1963	printf "\n\n *** providing INPUT-files:\n$dashes"
1964	fi
1965
1966
1967	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1968	if [[ "${actionin[$i]}" = unavailable ]]
1969	then
1970	optional_files_missing=true
1971	continue
1972	fi
1973
1974	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1975	files_for_cores=false; filetype=file
1976	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1977	then
1978	files_for_cores=true; filetype=files
1979	actionin[$i]=""
1980	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1981	then
1982	actionin[$i]=""
1983	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1984	then
1985	files_for_cores=true; filetype=files
1986	actionin[$i]="ln"
1987	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1988	then
1989	actionin[$i]="ln"
1990	fi
1991
1992	if [[ $files_for_cores = true ]]
1993	then
1994	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1995	else
1996	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1997	fi
1998
1999	# INPUT-FILES TO BE LINKED
2000	if [[ "${actionin[$i]}" = ln ]]
2001	then
2002
2003	printf "\n $filetype will be linked"
2004	if [[ $files_for_cores = false ]]
2005	then
2006	if [[ -f "${absnamein[$i]}" ]]
2007	then
2008	ln ${absnamein[$i]} ${localin[$i]}
2009	got_tmp[$i]=true
2010	fi
2011	else
2012	if [[ -d "${absnamein[$i]}" ]]
2013	then
2014	mkdir -p ${localin[$i]}
2015	cd ${absnamein[$i]}
2016	for file in $(ls *)
2017	do
2018	ln $file $tempdir/${localin[$i]}
2019	done >\|/dev/null 2>&1
2020	cd $tempdir
2021	fi
2022
2023	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2024	if [[ ! -f "${localin[$i]}/_000000" ]]
2025	then
2026	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2027	cp -r ${absnamein[$i]}/* ${localin[$i]}
2028	fi
2029
2030	got_tmp[$i]=true
2031	fi
2032	fi
2033
2034	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2035	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2036	then
2037
2038	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2039	then
2040
2041	# FILE COPIES ARE PROVIDED FOR ALL CORES
2042	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2043	printf "\n file will be provided for $cores processors"
2044	mkdir -p ${localin[$i]}
2045	ival=$cores
2046	(( ii = 0 ))
2047	while (( ii <= ival-1 ))
2048	do
2049	if (( ii < 10 ))
2050	then
2051	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2052	elif (( ii < 100 ))
2053	then
2054	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2055	elif (( ii < 1000 ))
2056	then
2057	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2058	else
2059	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2060	fi
2061	(( ii = ii + 1 ))
2062	done
2063
2064	else
2065
2066	if [[ $files_for_cores = true ]]
2067	then
2068
2069	# PROVIDE FILES FOR EACH CORE
2070	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2071	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2072	printf "\n providing $cores files for the respective cores"
2073	mkdir -p ${localin[$i]}
2074	if [[ $link_local_input = true ]]
2075	then
2076	printf " files will be linked\n"
2077	cd ${absnamein[$i]}
2078	for file in $(ls *)
2079	do
2080	ln -f $file ${localin[$i]}
2081	done
2082	cd $tempdir
2083	fi
2084
2085	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2086	if [[ ! -f "${localin[$i]}/_000000" ]]
2087	then
2088	if [[ $link_local_input = true ]]
2089	then
2090	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2091	fi
2092	cp -r ${absnamein[$i]}/* ${localin[$i]}
2093	fi
2094
2095	else
2096
2097	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2098	if [[ $link_local_input = true ]]
2099	then
2100	printf " file will be linked\n"
2101	ln -f ${absnamein[$i]} ${localin[$i]}
2102	fi
2103	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2104	if [[ ! -f "${localin[$i]}" ]]
2105	then
2106	if [[ $link_local_input = true ]]
2107	then
2108	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2109	fi
2110	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2111	then
2112	mv ${absnamein[$i]} ${localin[$i]}
2113	else
2114	cp ${absnamein[$i]} ${localin[$i]}
2115	fi
2116	fi
2117	fi
2118	fi
2119	fi
2120
2121	done
2122	if (( i != 0 ))
2123	then
2124	if [[ $optional_files_missing = true ]]
2125	then
2126	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2127	fi
2128	printf "\n$dashes\n *** all INPUT-files provided \n"
2129	fi
2130
2131
2132	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2133	(( i = 0 ))
2134	while (( i < iic ))
2135	do
2136	(( i = i + 1 ))
2137	if (( i == 1 ))
2138	then
2139	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2140	fi
2141	printf "\n >>> ${in_command[$i]}"
2142	eval ${in_command[$i]}
2143	if (( i == iic ))
2144	then
2145	printf "\n$dashes\n"
2146	fi
2147	done
2148
2149
2150	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2151	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2152	then
2153	progress_bar_disabled=true
2154	else
2155	progress_bar_disabled=false
2156	fi
2157
2158
2159	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2160	# (FILE ENVPAR WILL BE READ BY PALM)
2161	cat > ENVPAR << EOF
2162	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2163	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2164	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2165	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2166	maximum_cpu_time_allowed = ${cpumax}.,
2167	revision = '$global_revision',
2168	progress_bar_disabled = .${progress_bar_disabled}. /
2169
2170	EOF
2171
2172
2173	# STARTING THE EXECUTABLE
2174	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2175	PATH=$PATH:$tempdir
2176
2177
2178	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2179	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2180	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2181	eval line=\"$line\"
2182	execute_command="$line"
2183
2184
2185	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2186	if [[ "$execute_command_for_combine" = "" ]]
2187	then
2188	eval line2=\"$line2\"
2189	execute_command_for_combine="$line2"
2190	fi
2191
2192
2193
2194	# PROVIDE A HOSTFILE, IF REQUIRED
2195	if [[ "$hostfile" != "" ]]
2196	then
2197
2198	if [[ $hostfile = auto ]]
2199	then
2200	# CREATE A NEW HOSTFILE
2201	(( ii = 1 ))
2202	while (( ii <= cores / threads_per_task ))
2203	do
2204	echo $(hostname) >> hostfile
2205	(( ii = ii + 1 ))
2206	done
2207	if (( cores / threads_per_task == 0 ))
2208	then
2209	echo $(hostname) >> hostfile
2210	fi
2211
2212	else
2213	cp $hostfile hostfile
2214	fi
2215	eval line=\"`head -n $ii hostfile`\"
2216	printf "\n *** running on: $line"
2217	fi
2218
2219
2220
2221	# SET THE NUMBER OF OPENMP-THREADS
2222	if [[ $use_openmp = true ]]
2223	then
2224	export OMP_NUM_THREADS=$threads_per_task
2225	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2226	else
2227	export OMP_NUM_THREADS=1
2228	fi
2229
2230
2231	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2232	if [[ $run_coupled_model = false ]]
2233	then
2234	if [[ "$ocean_file_appendix" = true ]]
2235	then
2236	echo "precursor_ocean" > coupling_steering
2237	else
2238	echo "precursor_atmos" > coupling_steering
2239	fi
2240	else
2241	(( iia = $cores_atmos / $threads_per_task ))
2242	(( iio = $cores_ocean / $threads_per_task ))
2243	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2244	printf "\n\n"
2245	echo "coupled_run $iia $iio" > coupling_steering
2246	fi
2247
2248	printf "\n *** execute command:"
2249	printf "\n \"$execute_command\" \n\n"
2250
2251
2252	if [[ $progress_bar_disabled = true ]]
2253	then
2254	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2255	exit_code=${PIPESTATUS[0]}
2256	else
2257	$execute_command < coupling_steering &> >(tee STDOUT)
2258	exit_code=${PIPESTATUS[0]}
2259	fi
2260
2261	if [[ ${exit_code} != 0 ]]
2262	then
2263
2264	# ABORT IN CASE OF RUNTIME ERRORS
2265	printf "\n +++ runtime error occured"
2266	locat=execution
2267	exit
2268
2269	else
2270
2271	printf "\n$dashes\n *** execution finished \n"
2272
2273	fi
2274
2275
2276	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2277	# BY EACH CORE INTO ONE FILE
2278	if [[ ! -f combine_plot_fields.x ]]
2279	then
2280
2281	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2282	printf "\n 2d- and/or 3d-data may be incomplete!"
2283	printf "\n Your previous palmbuild may have failed. Please check.\n"
2284
2285	elif [[ "$combine_plot_fields" == true ]]
2286	then
2287
2288	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2289	$execute_command_for_combine
2290
2291	else
2292
2293	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2294	# DATA OUTPUT
2295	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2296	fi
2297
2298
2299
2300	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2301	(( i = 0 ))
2302	while (( i < ioc ))
2303	do
2304	(( i = i + 1 ))
2305	if (( i == 1 ))
2306	then
2307	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2308	fi
2309
2310	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2311	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2312
2313	printf "\n >>> ${out_command[$i]}"
2314	eval ${out_command[$i]}
2315	if (( i == ioc ))
2316	then
2317	printf "\n$dashes\n"
2318	fi
2319	done
2320
2321
2322	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2323	# WILDCARDS
2324	(( i = 0 ))
2325	(( nr_of_output_files = 0 ))
2326
2327	while (( i < iout ))
2328	do
2329
2330	(( i = i + 1 ))
2331
2332	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2333	# CREATE A LIST FOR THE DETECTED ENDINGS
2334	if [[ "${multout[$i]}" = true ]]
2335	then
2336	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2337	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2338	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2339
2340	endings="DEFAULT"
2341	while read line
2342	do
2343	# remove the local name from the beginning
2344	localnamestring="${localout_pre[$i]}"
2345	length_localname=${#localnamestring}
2346	ending=${line:${length_localname}}
2347
2348	if [[ "$ending" != "" ]]
2349	then
2350	endings="$endings $ending"
2351	fi
2352
2353	done <filelist
2354
2355	rm filelist
2356
2357	else
2358
2359	# SINGLE NAME
2360	endings=DEFAULT
2361
2362	fi
2363
2364	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2365	for ending in $endings
2366	do
2367
2368	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2369	if [[ $ending = DEFAULT ]]
2370	then
2371	ending=""
2372	fi
2373
2374	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2375	(( nr_of_output_files = nr_of_output_files + 1 ))
2376	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2377	transout[$nr_of_output_files]="${transout_pre[$i]}"
2378	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2379	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2380	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2381	extout[$nr_of_output_files]="${extout_pre[$i]}"
2382	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2383
2384	done
2385
2386	done
2387
2388
2389
2390
2391	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2392	(( i = 0 ))
2393	while (( i < nr_of_output_files ))
2394	do
2395	(( i = i + 1 ))
2396	if (( i == 1 ))
2397	then
2398	printf "\n\n *** saving OUTPUT-files:"
2399
2400	# GET RUN NUMBER ASSIGNED BY PALM
2401	if [[ -f RUN_NUMBER ]]
2402	then
2403	read run_number < RUN_NUMBER
2404	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2405	usecycle_option="-U $run_number"
2406	else
2407	run_number=0
2408	usecycle_option=""
2409	fi
2410	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2411	then
2412	printf "\n *** in case of SCP transfers to local host"
2413	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2414	fi
2415	printf "\n$dashes"
2416	fi
2417
2418	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2419	then
2420
2421	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2422
2423	# DETERMINE THE CYCLE NUMBER
2424	ls -1 -d $filename > filelist 2>/dev/null
2425	ls -1 -d $filename.* >> filelist 2>/dev/null
2426	while read line
2427	do
2428
2429	# filename without path (i.e. after the last "/")
2430	basefilename=$(basename ${line})
2431
2432	# check if there is an extension
2433	extension=${basefilename##*.}
2434	if [[ "$extension" = "${extout[$i]}" ]]
2435	then
2436	basefilename=${basefilename%.*}
2437	fi
2438
2439	# check for an existing cycle number
2440	cycle=${basefilename##*.}
2441	if [[ $cycle =~ ^-?[0-9]+$ ]]
2442	then
2443	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2444	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2445	(( icycle = $((10#$cycle)) + 1 ))
2446	else
2447	(( icycle = 1 ))
2448	fi
2449
2450	if (( icycle > maxcycle ))
2451	then
2452	(( maxcycle = icycle ))
2453	fi
2454
2455	done <filelist
2456	rm filelist
2457
2458
2459	# SET THE CYCLE NUMBER
2460	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2461	if [[ "${actionout[$i]}" = a ]]
2462	then
2463	(( maxcycle = maxcycle - 1 ))
2464	fi
2465
2466	(( cycnum[$i] = maxcycle ))
2467	pathout[$i]=$filename
2468
2469
2470	# ADD CYCLE NUMBER TO FILENAME
2471	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2472	if [[ "${actionout[$i]}" != "a" ]]
2473	then
2474	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2475	# WITH AN EXISTING CYCLE NUMBER
2476	if (( run_number >= cycnum[$i] ))
2477	then
2478	(( cycnum[$i] = run_number ))
2479	else
2480	if (( run_number > 0 ))
2481	then
2482	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2483	fi
2484	fi
2485	fi
2486	if (( cycnum[$i] > 0 ))
2487	then
2488	cyclestring=`printf "%03d" ${cycnum[$i]}`
2489	pathout[$i]=${pathout[$i]}.$cyclestring
2490	fi
2491	fi
2492
2493	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2494	files_for_cores=false; filetype=file
2495	link_local_output=false
2496	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2497	then
2498	files_for_cores=true; filetype=directory
2499	actionout[$i]=""
2500	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2501	then
2502	actionout[$i]=""
2503	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2504	then
2505	files_for_cores=true; filetype=directory
2506	link_local_output=true
2507	actionout[$i]=""
2508	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2509	then
2510	link_local_output
2511	actionout[$i]=""
2512	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2513	then
2514	files_for_cores=true; filetype=directory
2515	actionout[$i]="tr"
2516	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2517	then
2518	actionout[$i]="tr"
2519	fi
2520
2521	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2522	then
2523	if [[ ${warnout[$i]} = true ]]
2524	then
2525	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2526	fi
2527	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2528	then
2529	if [[ ${warnout[$i]} = true ]]
2530	then
2531	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2532	fi
2533	else
2534
2535
2536	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2537	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2538	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2539	then
2540	if [[ $running_on_remote = true ]]
2541	then
2542
2543	# SET OPTIONS FOR TRANSFER
2544	if [[ "${actionout[$i]}" = tr ]]
2545	then
2546	if [[ $files_for_cores = false ]]
2547	then
2548	catalog_option=""
2549	catalog_string=""
2550	else
2551	catalog_option="-c"
2552	catalog_string="/"
2553	fi
2554	append_option=""
2555	append_string=""
2556	else
2557	append_option="-A"
2558	append_string="append"
2559	fi
2560
2561	transfer_failed=false
2562	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2563	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2564
2565	# TRANSFER VIA SCP
2566	if [[ "$remote_loginnode" != "" ]]
2567	then
2568	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2569	else
2570	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
2571	fi
2572	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2573
2574
2575	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2576	if [[ $transfer_failed = true ]]
2577	then
2578	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2579	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2580
2581	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2582	eval local_catalog=${pathout[$i]}
2583	if [[ ! -d $local_catalog ]]
2584	then
2585	printf " *** local directory does not exist. Trying to create:\n"
2586	printf " $local_catalog \n"
2587	mkdir -p $local_catalog
2588	fi
2589	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2590	transfer_problems=true
2591	fi
2592
2593	else
2594
2595	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2596	# BE COPIED OR APPENDED ON THIS MACHINE
2597	if [[ "${actionout[$i]}" = tr ]]
2598	then
2599	actionout[$i]=""
2600	else
2601	actionout[$i]="a"
2602	fi
2603	fi
2604	fi
2605
2606
2607	# APPEND ON THIS MACHINE
2608	if [[ "${actionout[$i]}" = "a" ]]
2609	then
2610	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2611	then
2612	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2613	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2614	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2615	else
2616	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2617	printf "\n ${pathout[$i]}\n"
2618	cat ${localout[$i]} >> ${pathout[$i]}
2619	fi
2620	fi
2621
2622	# COPY ON THIS MACHINE
2623	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2624	# ON DIFFERENT FILE-SYSTEMS
2625	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2626	then
2627
2628	# COPY IN CASE OF RUNS ON SINGLE CORES
2629	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2630	then
2631	printf "\n >>> OUTPUT: ${localout[$i]} to"
2632	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2633	if [[ $link_local_output = true ]]
2634	then
2635	printf " file will be linked\n"
2636	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2637	fi
2638	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2639	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2640	then
2641	if [[ $link_local_output = true ]]
2642	then
2643	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2644	fi
2645	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2646	else
2647	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2648	fi
2649	else
2650	printf "\n >>> OUTPUT: ${localout[$i]} to"
2651	printf "\n ${pathout[$i]}\n"
2652	if [[ $link_local_output = true ]]
2653	then
2654	printf " file will be linked\n"
2655	ln -f ${localout[$i]} ${pathout[$i]}
2656	fi
2657	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2658	if [[ ! -f "${pathout[$i]}" ]]
2659	then
2660	if [[ $link_local_output = true ]]
2661	then
2662	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2663	fi
2664	cp ${localout[$i]} ${pathout[$i]}
2665	else
2666	printf "+++ no copy because file ${pathout[$i]} exists\n"
2667	fi
2668	fi
2669
2670	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2671	then
2672
2673	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2674	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2675	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2676	printf "\n ${pathout[$i]}\n"
2677	if [[ $link_local_output = true ]]
2678	then
2679	printf " files will be linked\n"
2680	mkdir -p ${pathout[$i]}
2681	cd ${localout[$i]}
2682	for file in $(ls *)
2683	do
2684	ln -f $file ${pathout[$i]}
2685	done >\|/dev/null 2>&1
2686	cd $tempdir
2687	fi
2688
2689	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2690	if [[ ! -f "${pathout[$i]}/_000000" ]]
2691	then
2692	if [[ $link_local_output = true ]]
2693	then
2694	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2695	fi
2696	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2697	cp -r ${localout[$i]}/* ${pathout[$i]}
2698	fi
2699
2700	fi
2701	fi
2702	done
2703
2704	if (( i != 0 ))
2705	then
2706	if [[ $transfer_problems = true ]]
2707	then
2708	printf "\n$dashes\n *** OUTPUT-files saved"
2709	printf "\n +++ WARNING: some data transfers failed! \n"
2710	else
2711	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2712	fi
2713	fi
2714
2715
2716	# IF REQUIRED, START A RESTART-JOB
2717	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2718	if [[ -f CONTINUE_RUN ]]
2719	then
2720
2721	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2722	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2723	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2724	# -b START A BATCH JOB
2725	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2726	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2727	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2728
2729	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2730	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2731	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2732	then
2733	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2734	fi
2735
2736	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2737	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2738	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2739	then
2740	prc=`echo $prc \| sed 's/#/r/g'`
2741	fi
2742
2743
2744	# START THE RESTART-JOB
2745	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2746	echo " $prc"
2747	printf "\n$dashes\n"
2748	if [[ $running_on_remote = true ]]
2749	then
2750
2751	echo "*** ssh will be used to initiate restart-runs!"
2752	echo " return_address=\"$return_address\" "
2753	echo " return_username=\"$local_username\" "
2754
2755	if [[ "$remote_loginnode" != "" ]]
2756	then
2757	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode \| tee palmrun_restart.log
2758	else
2759	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2760	fi
2761
2762	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2763	sleep 30
2764
2765	else
2766
2767	# START THE RESTART JOB ON THE LOCAL HOST
2768	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2769	cd - > /dev/null
2770
2771	fi
2772
2773	# CHECK, IF RESTART JOB HAS BEEN STARTED
2774	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2775	then
2776	printf "\n$dashes\n +++ creating restart run failed \n"
2777	locat=create_restart
2778	rm palmrun_restart.log
2779	exit
2780	else
2781	printf "\n$dashes\n *** restart run initiated \n"
2782	rm palmrun_restart.log
2783	fi
2784
2785
2786	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2787	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2788	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2789	# MAY BE VERY HUGE)
2790	(( i = 0 ))
2791	while (( i < nr_of_input_files ))
2792	do
2793	(( i = i + 1 ))
2794	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2795	then
2796	rm -r ${absnamein[$i]}
2797	fi
2798	done
2799
2800	fi
2801
2802
2803	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2804	cd $HOME
2805	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2806
2807
2808	else
2809
2810
2811	# PREPARING ACTIONS,
2812	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2813
2814	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2815	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2816	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2817	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2818	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2819	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2820	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2821	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2822	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2823	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2824	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2825	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2826	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2827	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2828	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2829	if [[ $create_remote_batch_job = true ]]
2830	then
2831	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2832	if [[ $do_trace = true ]]
2833	then
2834	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2835	fi
2836	elif [[ $create_batch_job = true ]]
2837	then
2838	palmrun_com=${palmrun_com}" -j"
2839	if [[ $do_trace = true ]]
2840	then
2841	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2842	fi
2843	fi
2844
2845
2846	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2847	# REMOTE HOST
2848	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2849	job_protocol_file=$job_protocol_file_local
2850	if [[ $create_remote_batch_job = true ]]
2851	then
2852	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2853	job_protocol_file=$job_protocol_file_remote
2854	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2855	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2856	fi
2857
2858
2859	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2860	jobfile=jobfile.$run_id_number
2861
2862
2863	# FIRST CREATE THE BATCH DIRECTIVES
2864	(( i = 0 ))
2865	while (( i < ibd ))
2866	do
2867	(( i = i + 1 ))
2868	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2869	eval line=\"$line\"
2870	echo "$line" >> $jobfile
2871	done
2872	echo " " >> $jobfile
2873
2874
2875	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2876	# PROTOCOL
2877	if [[ $create_remote_batch_job = true ]]
2878	then
2879	echo "set +vx" >> $jobfile
2880	echo "trap '" >> $jobfile
2881	echo "set +vx" >> $jobfile
2882	echo "cd ${remote_jobcatalog}" >> $jobfile
2883	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2884
2885	# ADD THE BATCH DIRECTIVES
2886	(( i = 0 ))
2887	while (( i < ibdt ))
2888	do
2889	(( i = i + 1 ))
2890	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2891	eval line=\"$line\"
2892	echo "$line" >> $jobfile
2893	done
2894	echo " " >> $jobfile
2895
2896	echo "set -x" >> $jobfile
2897	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
2898	echo "%%END%%" >> $jobfile
2899	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2900	echo "$submit_command $scpjob_file" >> $jobfile
2901	echo "rm $scpjob_file" >> $jobfile
2902	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2903	echo "set -x" >> $jobfile
2904	echo " ' exit" >> $jobfile
2905	fi
2906
2907
2908	# ACTIVATE ERROR-TRACEBACK
2909	if [[ $do_trace = true ]]
2910	then
2911	echo "set -x" >> $jobfile
2912	else
2913	echo "set +vx" >> $jobfile
2914	fi
2915
2916
2917	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2918	if [[ "$login_init_cmd" != "" ]]
2919	then
2920	echo "$login_init_cmd" >> $jobfile
2921	fi
2922	if [[ "$module_commands" != "" ]]
2923	then
2924	echo "$module_commands" >> $jobfile
2925	fi
2926
2927
2928	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2929	if [[ $create_remote_batch_job = true ]]
2930	then
2931	echo "mkdir $tempdir" >> $jobfile
2932	echo "chmod go+rx $tempdir" >> $jobfile
2933	else
2934	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2935	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2936	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2937	mkdir $tempdir
2938	chmod go+rx $tempdir
2939	fi
2940	echo "cd $tempdir" >> $jobfile
2941	echo "export tempdir=$tempdir" >> $jobfile
2942	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2943	echo "export PATH=.:\$PATH" >> $jobfile
2944	echo "export execute_palmrun=true" >> $jobfile
2945
2946
2947	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2948	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2949	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2950	echo "LOCAL_PWD=$working_directory" >> $jobfile
2951	echo "export LOCAL_PWD" >> $jobfile
2952
2953
2954	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2955	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2956	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2957
2958
2959	# CALL PALMRUN WITHIN THE JOB
2960	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2961	echo "set -x" >> $jobfile
2962	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2963
2964
2965	# TRANSFER JOBFILE TO THE TARGET HOST
2966	if [[ $create_jobfile_only = false ]]
2967	then
2968
2969	if [[ $create_remote_batch_job = true ]]
2970	then
2971
2972	echo " "
2973	echo " *** transfer of job to remote host via scp"
2974	if [[ $do_trace = true ]]
2975	then
2976	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
2977	fi
2978	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
2979
2980	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2981	if [[ $do_trace = true ]]
2982	then
2983	echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2984	fi
2985	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2986
2987	elif [[ $create_batch_job = true ]]
2988	then
2989
2990	eval local_jobcatalog=$local_jobcatalog
2991	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
2992	cd $local_jobcatalog
2993	echo " "
2994	echo " *** submit the job"
2995	if [[ $do_trace = true ]]
2996	then
2997	echo "$submit_command ${configuration_identifier}_${run_id}"
2998	fi
2999	$submit_command ${configuration_identifier}_${run_id}
3000	rm ${configuration_identifier}_${run_id}
3001	cd - > /dev/null
3002
3003	fi
3004
3005	rm -rf $jobfile
3006
3007	else
3008
3009	printf "\n *** jobfile created under name \"$jobfile\" "
3010	printf "\n no batch-job has been sent!"
3011
3012	fi
3013
3014	fi # END OF REMOTE-PART

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