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source: palm/trunk/SCRIPTS/palmrun @ 3567

Last change on this file since 3567 was 3555, checked in by raasch, 6 years ago
sed-command to remove repeated space-characters replaced by tr-command, to guarantee mac compatible
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.4 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 3555 2018-11-22 13:50:37Z maronga $
29	# sed-command to remove repeated space-characters replaced by tr-command, to
30	# guarantee mac compatible
31	#
32	# 3549 2018-11-21 15:44:44Z raasch
33	# ssh-call for submitting batch jobs on remote systems modified to avoid output
34	# of login messages on specific systems
35	#
36	# 3534 2018-11-19 15:35:16Z raasch
37	# batch_scp for sending back the job protocol file is called via login-node if
38	# a login-node has been set in the config-file
39	# ssh-calls rearranged to avoid output of system/user-profile messages
40	#
41	# 3505 2018-11-08 09:14:30Z raasch
42	# job folders are created in case that they do not exist
43	#
44	# 3455 2018-10-30 14:12:31Z raasch
45	# options -h and -d renamed -c and -r, respectively
46	#
47	# 3402 2018-10-23 11:49:24Z knoop
48	# job_id is set for compatibility reasons with older versions of config files
49	#
50	# 3313 2018-10-06 15:22:48Z knoop
51	# more detailed error message for outdated fileconnection file
52	#
53	# 3236 2018-09-10 09:07:06Z raasch
54	# warning issued in case of file connection file version mismatch,
55	# host_configuration renamed configuration_identifier,
56	# "host identifier" in header output renamed "config. identifier",
57	# jobname renamed run_identifier,
58	# run_id renamed run_id_number
59	# job_id renamed run_id
60	# option -r renamed -i
61	#
62	# 3151 2018-07-19 08:45:38Z raasch
63	# removed additional listing of files to be compiled, print PALM code revision
64	# in header
65	#
66	# 3132 2018-07-16 11:44:58Z raasch
67	# create consistent error messages in case of failed restarts,
68	# check existence of remote job catalog
69	#
70	# 3043 2018-05-25 10:47:54Z raasch
71	# check for setting of fast_io_catalog
72	#
73	# 3033 2018-05-23 15:26:19Z raasch
74	# -T option not required for interactive runs (tasks per node =
75	# total number of cores is assumed as default, if option is not given),
76	# reformatting of a few messages,
77	# bugfix: destination output directory is created if attribute "pe" is set in
78	# .palm.iofiles
79	#
80	# 2718 2018-01-02 08:49:38Z maronga
81	# bugfix of r2990
82	#
83	# 2718 2018-01-02 08:49:38Z maronga
84	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
85	# not in the working directory from where palmrun is called
86	#
87	# 2718 2018-01-02 08:49:38Z maronga
88	# svfout in the activation string will be replaced now by svfin in case of
89	# automatic restarts
90	#
91	# 2718 2018-01-02 08:49:38Z maronga
92	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
93	# the possible output or input of sky view factors
94	#
95	# 2718 2018-01-02 08:49:38Z maronga
96	# "fname" renamed to "jobname"
97	#
98	# 2718 2018-01-02 08:49:38Z maronga
99	# parameters are allowed in output commands (OC:)
100	#
101	# 2718 2018-01-02 08:49:38Z maronga
102	# bugfix: exit if no queue has been given neither with option -q nor in the
103	# configuration file
104	#
105	# 2718 2018-01-02 08:49:38Z maronga
106	# file connection file from trunk/SCRIPTS is taken by default
107	#
108	# 2718 2018-01-02 08:49:38Z maronga
109	# Corrected "Former revisions" section
110	#
111	# 2696 2017-12-14 17:12:51Z kanani
112	# Change in file header (GPL part)
113	#
114	# 2693 2017-12-13 12:33:49Z raasch
115	# replacement of variables given by {{<variable>}} in configuration file is now
116	# done in a more general way, variable names are written in small letters
117	#
118	# 2670 2017-12-06 16:32:19Z raasch
119	# test printouts removed
120	#
121	# 2669 2017-12-06 16:03:27Z raasch
122	# file attributes in .palm.iofiles restructured, "loc" attribute completely
123	# removed,
124	# wildcard (*) allowed in .palm.iofiles as file activation string for output
125	# files,
126	# informative messages in case of missing optional input files shortened
127	# bugfix: variable cycle explicitly interpreted with 10 as the number base
128	#
129	# 2638 2017-11-23 12:44:23Z raasch
130	# use of wildcards in file connection statements enabled
131	#
132	# 2605 2017-11-09 15:31:46Z raasch
133	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
134	# will not be sent with the job file any more, but copied into the
135	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
136	#
137	# 2600 2017-11-01 14:11:20Z raasch
138	# cycle numbers are made three digits wide
139	#
140	# 2566 2017-10-20 08:50:47Z raasch
141	# execute command for combine_plot_fields added
142	# "TEMPDIR" renamed "tempdir"
143	# temporary working directory for local batch jobs is created immediately within
144	# the user's palmrun call, due to a requirement of the "grid engine" batch
145	# system, where the working directory is given with batch directive -wd and must
146	# already exist when the job is submitted,
147	# informative messages in non-trace mode reduced and partly reformatted
148	#
149	# 2551 2017-10-18 07:25:11Z raasch
150	# TEMPDIR added as replacement string to be used in batch directives
151	#
152	# 2512 2017-10-04 08:26:59Z raasch
153	# bugfix for determining cycle numbers of NetCDF input files
154	#
155	# 2506 2017-09-29 08:30:37Z raasch
156	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
157	# host configuration added to SOURCES_FOR_RUN_... folder name
158	# host_identifier renamed host_configuration
159	# option -W added to allow for job dependencies
160	#
161	# 2501 2017-09-26 11:41:55Z raasch
162	# default value for number of cores (option -X) set to 1
163	# bugfix for mechanism which overwrites configuration file settings with values
164	# provided by palmrun options
165	#
166	# 2499 2017-09-22 16:47:58Z kanani
167	# option -h named configuration identifier
168	#
169	# 2480 2017-09-19 06:24:14Z maronga
170	# bugfix for last revision
171	#
172	# 2479 2017-09-19 06:12:16Z raasch
173	# option -A (project account number) added
174	#
175	# 2422 2017-09-08 08:25:41Z raasch
176	# initial revision
177	#
178	#--------------------------------------------------------------------------------#
179	# palmrun - script for running PALM jobs on local and remote hosts
180	#--------------------------------------------------------------------------------#
181
182
183
184	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
185
186	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
187	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
188	# (TOO MANY ARGUMENTS - PROBLEM)
189	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
190
191	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
192	typeset -i nr_of_output_files=0
193	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
194	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
195	# SCRIPT-OPTION ARGUMENTS
196	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
197	typeset -i icycle inode ival maxcycle mpi_tasks
198	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
199
200	activation_string_list=""
201	AddFilenames=""
202	combine_plot_fields=true
203	compiler_name=""
204	compiler_name_ser=""
205	compiler_options=""
206	configuration_identifier="default"
207	cores=1
208	cores_atmos=0
209	cores_ocean=0
210	coupled_dist=""
211	cpp_options=""
212	cpumax=0
213	create_batch_job=false
214	create_jobfile_only=false
215	create_remote_batch_job=false
216	dashes=" ----------------------------------------------------------------------------"
217	defaultqueue=""
218	delete_temporary_catalog=true
219	do_compile=true
220	do_trace=false
221	executable=""
222	execute_command=""
223	execution_error=false
224	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
225	global_revision=""
226	hostfile=""
227	hp=""
228	keep_data_from_previous_run=false
229	link_local_input=false
230	link_local_output=false
231	linker_options=""
232	local_jobcatalog=""
233	locat=normal
234	makefile=""
235	max_par_io_str=""
236	prc=$0
237	while [[ $(echo $prc \| grep -c "/") != 0 ]]
238	do
239	prc=`echo $prc \| cut -f2- -d"/"`
240	done
241	module_calls=""
242	palmrun_memory=""
243	palmrun_script_name=$prc
244	openmp=false
245	previous_job=""
246	project_account=""
247	queue=none
248	read_svf=""
249	restart_run=false
250	return_address=""
251	remote_jobcatalog=""
252	remote_username=""
253	running_in_batch_mode=false
254	running_in_test_mode=false
255	run_coupled_model=false
256	run_id=""
257	run_id_number=""
258	run_identifier=test
259	silent=false
260	source_list=""
261	source_path=""
262	tasks_per_node=0
263	threads_per_task=1
264	transfer_problems=false
265	user_source_path=""
266	use_existing_sources_folder=""
267	use_openmp=false
268	version="palmrun 1.0 Rev$Rev: 3555 $"
269	working_directory=`pwd`
270	write_binary=""
271	write_svf=""
272
273
274	# ERROR HANDLING IN CASE OF EXIT
275	trap 'if [[ $locat != normal && $locat != control_c ]]
276	then
277
278	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
279	(( i = 0 ))
280	while (( i < iec ))
281	do
282	(( i = i + 1 ))
283	printf "\n *** Execution of ERROR-command:\n"
284	printf " >>> ${err_command[$i]}\n"
285	eval ${err_command[$i]}
286	done
287	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
288	printf "\n\n+++ palmrun crashed \n\n"
289	exit 1
290	elif [[ $locat != normal ]]
291	then
292	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
293	printf "\n+++ palmrun killed by \"^C\" \n\n"
294	exit 2
295	else
296	printf "\n --> palmrun finished\n\n"
297	exit 0
298	fi' exit
299
300
301	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
302	trap 'locat=control_c
303	exit 1
304	' 2
305
306
307	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
308	# WHICH WILL BE USED TO START RESTART-JOBS
309	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
310	do
311	case $option in
312	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
313	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
314	(b) create_batch_job=true; prc="$prc -b";;
315	(B) delete_temporary_catalog=false; prc="$prc -B";;
316	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
317	(C) restart_run=true; prc="$prc -C";;
318	(F) create_jobfile_only=true;;
319	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
320	(i) run_id_number=$OPTARG;;
321	(j) running_in_batch_mode=true;;
322	(k) keep_data_from_previous_run=true; prc="$prc -k";;
323	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
324	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
325	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
326	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
327	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
328	(R) return_address=$OPTARG;;
329	(s) source_list=$OPTARG;;
330	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
331	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
332	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
333	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
334	(v) silent=true; prc="$prc -v";;
335	(V) use_existing_sources_folder="-V";;
336	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
337	(W) previous_job=$OPTARG;;
338	(x) do_trace=true;set -x; prc="$prc -x";;
339	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
340	(y) ocean_file_appendix=true; prc="$prc -y";;
341	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
342	(z) running_in_test_mode=true;;
343	(Z) combine_plot_fields=false; prc="$prc -Z";;
344	(\?) printf "\n +++ unknown option $OPTARG \n"
345	printf "\n --> type \"$0 ?\" for available options \n"
346	locat=parameter;exit;;
347	esac
348	done
349
350
351	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
352	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
353	(( to_shift = $OPTIND - 1 ))
354	shift $to_shift
355
356	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
357	if [[ "$1" = "?" ]]
358	then
359	(printf "\n *** Description of available palmrun options:\n"
360	printf "\n Option Description Default-Value"
361	printf "\n -a activation string list \"\" "
362	printf "\n -A project account number ---"
363	printf "\n -b batch-job on local machine ---"
364	printf "\n -B do not delete temporary directory at end ---"
365	printf "\n -c configuration identifier \"default\" "
366	printf "\n -F create batch job file only ---"
367	printf "\n -k keep data from previous run"
368	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
369	printf "\n -M Makefile name Makefile"
370	printf "\n -O threads per openMP task ---"
371	printf "\n -q queue \"$queue\" "
372	printf "\n -r run identifier test"
373	printf "\n -s filenames of routines to be compiled \"\" "
374	printf "\n must end with .f, .f90, .F, or .c !"
375	printf "\n use \"..\" for more than one file and wildcards"
376	printf "\n -s LM compiles all locally modified files"
377	printf "\n -t allowed cpu-time in seconds (batch) 0"
378	printf "\n -T tasks per node ---"
379	printf "\n -u username on remote machine \"\" "
380	printf "\n -v no prompt for confirmation ---"
381	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
382	printf "\n -w maximum parallel io streams as given by -X"
383	printf "\n -W name of job to wait for ---"
384	printf "\n -x tracing of palmrun for debug purposes ---"
385	printf "\n -X # of processors (on parallel machines) 1"
386	printf "\n -y add appendix \"_O\" to all local output"
387	printf "\n files (ocean precursor runs followed by"
388	printf "\n coupled atmosphere-ocean runs) ---"
389	printf "\n -Y run coupled model, \"#1 #2\" with"
390	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
391	printf "\n -Z skip combine_plot_fields at the end of "
392	printf "\n the simulation ---"
393	printf "\n "
394	printf "\n Possible values of positional parameter <modus>:"
395	printf "\n \"?\" - this outline \n\n") \| more
396	exit
397	elif [[ "$1" != "" ]]
398	then
399	printf "\n +++ positional parameter $1 unknown \n"
400	locat=parameter; exit
401	fi
402
403
404
405	# SHORT STARTING MESSAGE
406	printf "\n*** $version "
407	printf "\n will be executed. Please wait ..."
408
409
410	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
411	config_file=.palm.config.$configuration_identifier
412	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
413
414
415	# CHECK, IF CONFIGURATION FILE EXISTS
416	if [[ ! -f $config_file ]]
417	then
418	printf "\n\n +++ configuration file: "
419	printf "\n $config_file"
420	printf "\n does not exist"
421	locat=connect; exit
422	fi
423
424
425	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
426	if [[ -f .palm.iofiles ]]
427	then
428
429	# CHECK VERSION MISMATCH
430	if [[ $running_in_batch_mode != true ]]
431	then
432	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
433	then
434	printf "\n\n +++ WARNING: A file connection file has been found in your"
435	printf "\n working directory, but its revision does not match"
436	printf "\n the revision of the default (trunk) version."
437	printf "\n You may need to update your connection file"
438	printf "\n \"${working_directory}/.palm.iofiles\" !"
439	fi
440	fi
441
442	fileconnection_file=.palm.iofiles
443
444	fi
445
446
447	# CHECK, IF FILE CONNECTION FILE EXISTS
448	if [[ ! -f $fileconnection_file ]]
449	then
450	printf "\n\n +++ file connection file: "
451	printf "\n $fileconnection_file"
452	printf "\n does not exist"
453	locat=connect; exit
454	fi
455
456
457	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
458	if [[ "$activation_string_list" = "" ]]
459	then
460	printf "\n\n +++ no activation string list given: "
461	printf "\n please set palmrun option \"-a\" "
462	locat=palmrun_option; exit
463	fi
464
465
466	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
467	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
468	then
469	write_binary=true
470	else
471	write_binary=false
472	fi
473
474	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
475	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
476	then
477	write_svf=true
478	else
479	write_svf=false
480	fi
481
482	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
483	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
484	then
485	read_svf=true
486	else
487	read_svf=false
488	fi
489
490
491	# READ AND EVALUATE THE CONFIGURATION-FILE
492	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
493
494	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
495	while read line
496	do
497
498	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
499	eval line=\"$line\"
500
501
502	# INTERPRET THE LINE
503	if [[ "$(echo $line)" = "" ]]
504	then
505
506	# EMPTY LINE, NO ACTION
507	continue
508
509	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
510	then
511
512	# LINE IS A COMMENT LINE
513	continue
514
515	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
516	then
517
518	# LINE DEFINES AN ENVIRONMENT-VARIABLE
519	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
520	value=`echo $line \| cut -d" " -s -f2-`
521
522
523	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
524	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
525	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
526	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
527	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
528	# CONFIGURATION-FILE.
529	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
530	then
531	eval export $var="\$value"
532
533	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
534	if [[ $do_trace = true ]]
535	then
536	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
537	fi
538	fi
539
540	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
541	then
542
543	# LINE DEFINES BATCH-DIRECTIVE
544	(( ibd = ibd + 1 ))
545	line=$(echo $line \| cut -c4-)
546	batch_directive[$ibd]="$line"
547
548	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
549	then
550
551	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
552	# REMOTE TO A LOCAL HOST
553	(( ibdt = ibdt + 1 ))
554	line=$(echo $line \| cut -c5-)
555	batch_directive_transfer[$ibdt]="$line"
556
557	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
558	then
559
560	# LINE DEFINES ERROR-COMMAND
561	(( iec = iec + 1 ))
562	line=$(echo $line \| cut -c4-)
563	err_command[$iec]="$line"
564
565	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
566	then
567
568	# LINE DEFINES INPUT-COMMAND
569	(( iic = iic + 1 ))
570	line=$(echo $line \| cut -c4-)
571	in_command[$iic]="$line"
572
573	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
574	then
575
576	# LINE DEFINES OUTPUT-COMMAND
577	(( ioc = ioc + 1 ))
578	line=$(echo $line \| cut -c4-)
579	out_command[$ioc]="$line"
580
581	else
582
583	# SKIP ALL OTHER LINES
584	continue
585
586	fi
587
588	done < $config_file
589
590
591	# CHECK SETTING OF REQUIRED PARAMETERS
592	if [[ "$fast_io_catalog" = "" ]]
593	then
594	printf "\n +++ no fast_io_catalog found in $config_file"
595	printf "\n Please add line \"fast_io_catalog ...\" to that file."
596	locat=config_file; exit
597	fi
598	if [[ "$compiler_name" = "" ]]
599	then
600	printf "\n +++ no compiler name found in $config_file"
601	printf "\n Please add line \"compiler_name ...\" to that file."
602	locat=config_file; exit
603	fi
604	if [[ "$compiler_name_ser" = "" ]]
605	then
606	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
607	printf "\n Please add line \"compiler_name_ser ...\" to that file."
608	locat=config_file; exit
609	fi
610	if [[ "$compiler_options" = "" ]]
611	then
612	printf "\n +++ no compiler options found in $config_file"
613	printf "\n Please add line \"compiler_options ...\" to that file."
614	locat=config_file; exit
615	fi
616	if [[ "$linker_options" = "" ]]
617	then
618	printf "\n +++ no linker options found in $config_file"
619	printf "\n Please add line \"linker_options ...\" to that file."
620	locat=config_file; exit
621	fi
622	if [[ "$execute_command" = "" ]]
623	then
624	printf "\n +++ no execute command found in $config_file"
625	printf "\n Please add line \"execute_command ...\" to that file."
626	locat=config_file; exit
627	fi
628
629	if [[ "$hostfile" != "" ]]
630	then
631	if [[ $hostfile != auto && ! -f $hostfile ]]
632	then
633	printf "\n +++ no hostfile \"$hostfile\" found"
634	printf "\n Please check line \"hostfile ...\" in $config_file"
635	locat=config_file; exit
636	fi
637	fi
638
639
640	# DETERMINE THE CALL STATUS
641	if [[ "$return_address" != "" ]]
642	then
643
644	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
645	# BATCH MODE AND ...
646	running_on_remote=true
647
648	else
649
650	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
651	if [[ "$remote_ip" != "" ]]
652	then
653
654	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
655	create_remote_batch_job=true
656
657	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
658	if [[ "$remote_jobcatalog" = "" ]]
659	then
660	printf "\n +++ no remote jobcatalog found in $config_file"
661	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
662	locat=config_file; exit
663	fi
664
665
666	fi
667	running_on_remote=false
668	fi
669
670
671
672	# READ AND EVALUATE THE I/O-FILE LIST
673	[[ $silent = false ]] && printf "\n Reading the I/O files... "
674
675	# READ THE FILE CONNECTION FILE LINE BY LINE
676	while read line
677	do
678
679	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
680	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
681	line=`echo "$line" \| tr -s " "`
682
683	# INTERPRET THE LINE
684	if [[ "$(echo $line)" = "" ]]
685	then
686	# EMPTY LINE, NO ACTION
687	continue
688
689	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
690	then
691
692	# LINE IS A COMMENT LINE
693	true
694
695	else
696
697	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
698	# s2a: in/out - field
699	# s2b: action - field (optional)
700	s1=`echo "$line" \| cut -d" " -f1`
701	s2=`echo "$line" \| cut -d" " -s -f2`
702	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
703	then
704	s2a=$s2
705	s2b=""
706	else
707	s2a=`echo $s2 \| cut -d":" -f1`
708	s2b=`echo $s2 \| cut -d":" -f2`
709	fi
710	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
711	s4=`echo "$line" \| cut -d" " -s -f4`
712	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
713	s5=`echo "$line" \| cut -d" " -s -f5`
714	s6=`echo "$line" \| cut -d" " -s -f6`
715
716
717	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
718	# INPUT- OR OUTPUT-LIST.
719	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
720	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
721	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
722	# IS NOT CHECKED AND STORED.
723	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
724	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
725	then
726	found=false
727	for actual in $activation_string_list
728	do
729	for formal in $s3
730	do
731	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
732	done
733	done
734	if [[ $found = true ]]
735	then
736	(( iin = iin + 1 ))
737	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
738	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
739	if [[ "$s2a" = inopt ]]
740	then
741	optin_pre[$iin]=yes
742	else
743	optin_pre[$iin]=no
744	fi
745
746	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
747	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
748	if [[ $running_on_remote = true && "$s2b" = tr ]]
749	then
750	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
751	fi
752
753	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
754	# THE WILDCARD FROM THE ENDING
755	if [[ "${s5: -1}" = "*" ]]
756	then
757	if [[ "$s2b" = "di" ]]
758	then
759	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
760	printf "\n see file \"$fileconnection_file\", line"
761	printf "\n$line"
762	locat=iofiles_file; exit
763	fi
764	multin[$iin]=true
765	string=${endin_pre[$iin]}
766	endin_pre[$iin]="${string%?}"
767	else
768	multin[$iin]=false
769	fi
770	fi
771	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
772	then
773	found=false
774	for actual in $activation_string_list
775	do
776	for formal in $s3
777	do
778	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
779	done
780	done
781	if [[ $found = true ]]
782	then
783	(( iout = iout + 1 ))
784	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
785	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
786
787	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
788	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
789	if [[ $formal = wildcard ]]
790	then
791	warnout_pre[$iout]=false
792	else
793	warnout_pre[$iout]=true
794	fi
795
796	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
797	# THE WILDCARD FROM THE LOCAL FILENAME
798	if [[ "${s1: -1}" = "*" ]]
799	then
800	if [[ "$s2b" = "di" ]]
801	then
802	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
803	printf "\n see file \"$fileconnection_file\", line"
804	printf "\n$line"
805	locat=iofiles_file; exit
806	fi
807	multout[$iout]=true
808	string=${localout_pre[$iout]}
809	localout_pre[$iout]="${string%?}"
810	else
811	multout[$iout]=false
812	fi
813	fi
814	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
815	then
816	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
817	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
818	locat=connect; exit
819	fi
820	IFS="$IFSALT"
821	fi
822
823	done < $fileconnection_file
824
825
826
827	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
828	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
829	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
830	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
831	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
832	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
833
834
835
836	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
837	if [[ $run_coupled_model = true ]]
838	then
839
840	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
841	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
842
843	if (( $cores_ocean + $cores_atmos != $cores ))
844	then
845
846	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
847	printf "\n PEs (total) : $cores"
848	printf "\n PEs (atmosphere): $cores_atmos"
849	printf "\n PEs (ocean) : $cores_ocean"
850	locat=coupling; exit
851
852	fi
853
854	fi
855
856
857	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
858	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
859	# FOLDER
860	if [[ $running_in_batch_mode = true ]]
861	then
862
863	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
864	then
865	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
866	printf "\n Please check the output of the palmrun-call"
867	printf "\n that you did on your local host."
868	locat=SOURCES_FOR_RUN; exit
869	fi
870
871	else
872
873	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
874	# AUTOMATIC RESTART RUN
875	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
876	if [[ $restart_run = false ]]
877	then
878
879	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
880	# THE LOCAL HOST
881	if [[ ! -d $source_path ]]
882	then
883	printf "\n\n +++ source path \"$source_path\" on local host"
884	printf "\n \"$(hostname)\" does not exist"
885	locat=source_path; exit
886	fi
887
888	rm -rf ${base_directory}/${sources_for_run_catalog}
889	mkdir -p ${base_directory}/${sources_for_run_catalog}
890
891	if [[ "$source_list" = LM ]]
892	then
893
894	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
895	source_list=""
896	cd $source_path
897
898
899	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
900	if [[ ! -d ../.svn ]]
901	then
902	printf "\n\n +++ source directory"
903	printf "\n \"$source_path\" "
904	printf "\n is not under control of \"subversion\"."
905	printf "\n Please do not use palmrun-option \"-s LM\"\n"
906	fi
907
908
909	# LIST ALL MODIFIED SOURCE CODE FILES
910	Filenames=""
911	svn status > tmp_svnstatus
912	while read line
913	do
914	firstc=`echo $line \| cut -c1`
915	if [[ $firstc = M \|\| $firstc = "?" ]]
916	then
917	Name=`echo "$line" \| cut -c8-`
918	extension=`echo $Name \| cut -d. -f2`
919	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
920	then
921	Filenames="$Filenames "$Name
922	fi
923	fi
924	done < tmp_svnstatus
925	rm -rf tmp_svnstatus
926
927
928	# COPY FILES TO SOURCES_FOR_RUN_...
929	for filename in $Filenames
930	do
931	cp $filename ${base_directory}/${sources_for_run_catalog}
932	source_list=$source_list"$filename "
933	done
934
935	cd - > /dev/null
936
937
938	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
939	elif [[ "$source_list" != "" ]]
940	then
941
942	cd $source_path
943
944	for filename in $source_list
945	do
946
947	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
948	if [[ $(echo $filename \| grep -c "/") != 0 ]]
949	then
950	printf "\n +++ source code file: $filename"
951	printf "\n must not contain (\"/\") "
952	locat=source; exit
953	fi
954
955	if [[ ! -f $filename ]]
956	then
957	printf "\n +++ source code file: $filename"
958	printf "\n does not exist"
959	locat=source; exit
960	else
961	cp $filename ${base_directory}/${sources_for_run_catalog}
962	fi
963
964	done
965
966	cd - > /dev/null
967
968	fi
969
970	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
971	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
972	if [[ ! -f $makefile ]]
973	then
974	printf "\n +++ file \"$makefile\" does not exist"
975	locat=make; exit
976	else
977	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
978	fi
979
980
981	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
982	if [[ "$user_source_path" != "" ]]
983	then
984
985	# DOES THE DIRECTORY EXIST?
986	if [[ ! -d $user_source_path ]]
987	then
988
989	printf "\n\n *** INFORMATIVE: additional source code directory"
990	printf "\n \"$user_source_path\" "
991	printf "\n does not exist or is not a directory."
992	printf "\n No source code will be used from this directory!\n"
993	user_source_path=""
994	if [[ $silent == false ]]
995	then
996	sleep 2
997	fi
998
999	else
1000
1001	cd $user_source_path
1002
1003	Names=$(ls -1 *.f90 2>&1)
1004	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1005	Names=$(ls -1 *.F90 2>&1)
1006	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1007	Names=$(ls -1 *.F 2>&1)
1008	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1009	Names=$(ls -1 *.f 2>&1)
1010	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1011	Names=$(ls -1 *.c 2>&1)
1012	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1013
1014	cd - > /dev/null
1015	cd ${base_directory}/${sources_for_run_catalog}
1016
1017	# COPY MAKEFILE IF EXISTING
1018	if [[ -f $user_source_path/Makefile ]]
1019	then
1020	printf "\n\n *** user Makefile from directory"
1021	printf "\n \"$user_source_path\" is used \n"
1022	if [[ $silent == false ]]
1023	then
1024	sleep 1
1025	fi
1026	cp $user_source_path/Makefile .
1027	fi
1028
1029	for filename in $AddFilenames
1030	do
1031	if [[ -f $filename ]]
1032	then
1033	printf "\n +++ source code file \"$filename\" found in additional"
1034	printf "\n source code directory \"$user_source_path\" "
1035	printf "\n but was also given with option \"-s\" which means that it should be taken"
1036	printf "\n from directory \"$source_path\"."
1037	locat=source; exit
1038	fi
1039
1040	cp $user_source_path/$filename .
1041	source_list="$source_list $filename"
1042
1043	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1044	if [[ $(grep -c $filename Makefile) = 0 ]]
1045	then
1046	printf "\n\n +++ user file \"$filename\" "
1047	printf "\n is not listed in Makefile \n"
1048	locat=source; exit
1049	fi
1050	done
1051	cd - > /dev/null
1052	fi
1053	fi
1054
1055	# COPY CONFIGURATION FILES
1056	cp $config_file ${base_directory}/${sources_for_run_catalog}
1057	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1058
1059	# COPY SHELLSCRIPTS
1060	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1061	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1062
1063	fi
1064
1065	fi
1066
1067
1068	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1069	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1070	if [[ "$global_revision" = "" ]]
1071	then
1072	global_revision=`svnversion $source_path 2>/dev/null`
1073	global_revision="Rev: $global_revision"
1074	fi
1075
1076
1077	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1078	if [[ -n $cores ]]
1079	then
1080
1081	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1082	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1083	if [[ $tasks_per_node = 0 ]]
1084	then
1085	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1086	then
1087	printf "\n"
1088	printf "\n +++ option \"-T\" (tasks per node) is missing"
1089	printf "\n set -T option or define tasks_per_node in the config file"
1090	locat=tasks_per_node; (( iec = 0 )); exit
1091	else
1092	# DEFAULT FOR INTERACTIVE RUN
1093	tasks_per_node=$cores
1094	fi
1095	fi
1096
1097	if (( cores < tasks_per_node ))
1098	then
1099	printf "\n"
1100	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1101	printf "\n given values: -T $tasks_per_node -X $cores"
1102	locat=tasks_per_node; (( iec = 0 )); exit
1103	fi
1104
1105	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1106	(( mpi_tasks = cores / threads_per_task ))
1107	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1108	(( ii = cores / tasks_per_node ))
1109	(( remaining_cores = cores - ii * tasks_per_node ))
1110	if (( remaining_cores > 0 ))
1111	then
1112	printf "\n"
1113	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1114	printf "\n divisor of the total number of cores (option \"-X\")"
1115	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1116	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1117	(( nodes = nodes + 1 ))
1118	fi
1119
1120	fi
1121
1122
1123	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1124	if [[ "$maximum_parallel_io_streams" = "" ]]
1125	then
1126	maximum_parallel_io_streams=$cores
1127	fi
1128
1129
1130	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1131	if [[ "$scp_port" != "" ]]
1132	then
1133	PORTOPT="-P $scp_port"
1134	SSH_PORTOPT="-p $scp_port"
1135	fi
1136
1137
1138	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1139	# CONFIG-FILE
1140	if [[ "$ssh_key" != "" ]]
1141	then
1142	ssh_key="-i $HOME/.ssh/$ssh_key"
1143	fi
1144
1145
1146	# SET QUEUE, IF NOT GIVEN
1147	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1148	then
1149
1150	if [[ $queue = none && "$defaultqueue" = "" ]]
1151	then
1152	printf "\n"
1153	printf "\n +++ no default queue given in configuration file and no queue"
1154	printf "\n given with option -q"
1155	locat=queue; exit
1156	fi
1157	if [[ $queue = none ]]
1158	then
1159	queue=$defaultqueue
1160	fi
1161
1162	fi
1163
1164
1165	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1166	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1167	(( i = 0 ))
1168	(( nr_of_input_files = 0 ))
1169	while (( i < iin ))
1170	do
1171	(( i = i + 1 ))
1172
1173	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1174	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1175	if [[ "${actionin_pre[$i]}" = di ]]
1176	then
1177	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1178	else
1179	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1180	fi
1181
1182
1183	# CHECK IF FILE EXISTS
1184	if ! ls $filename* 1>/dev/null 2>&1
1185	then
1186
1187	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1188	if [[ "${optin_pre[$i]}" != "yes" ]]
1189	then
1190	printf "\n\n +++ INPUT-file: "
1191	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1192	then
1193	printf "\n $filename"
1194	else
1195	printf "\n $filename.${extin_pre[$i]}"
1196	fi
1197	printf "\n does not exist\n"
1198	locat=input; exit
1199	else
1200	(( nr_of_input_files = nr_of_input_files + 1 ))
1201	localin[$nr_of_input_files]="${localin_pre[$i]}"
1202	optin[$nr_of_input_files]="${optin_pre[$i]}"
1203	actionin[$nr_of_input_files]="unavailable"
1204	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1205	endin[$nr_of_input_files]="${endin_pre[$i]}"
1206	extin[$nr_of_input_files]="${extin_pre[$i]}"
1207	fi
1208
1209	else
1210
1211	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1212	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1213	# ENDINGS
1214	if [[ "${multin[$i]}" = true ]]
1215	then
1216	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1217	ls -1 -d ${filename} > filelist 2>/dev/null
1218	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1219	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1220
1221	endings=""
1222	while read line
1223	do
1224	# filename without path (i.e. after the last "/")
1225	basefilename=$(basename ${line})
1226
1227	# check if there is an extension and remove it
1228	ext=${basefilename##*.}
1229	if [[ "$ext" = "${extin_pre[$i]}" ]]
1230	then
1231	basefilename=${basefilename%.*}
1232	fi
1233
1234	# check for an existing cycle number and remove it
1235	cycle=${basefilename##*.}
1236	if [[ $cycle =~ ^-?[0-9]+$ ]]
1237	then
1238	basefilename=${basefilename%.*}
1239	fi
1240
1241	# remove the run_identifier from the beginning
1242	length_run_identifier=${#run_identifier}
1243	ending=${basefilename:${length_run_identifier}}
1244
1245	# remove the ending given in the .iofiles from the beginning
1246	endingstring="${endin_pre[$i]}"
1247	length_ending=${#endingstring}
1248	ending=${ending:${length_ending}}
1249
1250	if [[ "$ending" = "" ]]
1251	then
1252	# standard ending as given in the .iofiles
1253	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1254	then
1255	endings="$endings DEFAULT"
1256	fi
1257	else
1258	# ending must start with "_", otherwise its a different file
1259	if [[ "${ending:0:1}" = "_" ]]
1260	then
1261	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1262	then
1263	endings="$endings $ending"
1264	fi
1265	fi
1266	fi
1267
1268	done <filelist
1269
1270	rm filelist
1271
1272	else
1273
1274	# SINGLE NAME
1275	endings=DEFAULT
1276
1277	fi
1278
1279	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1280	for ending in $endings
1281	do
1282
1283	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1284	if [[ $ending = DEFAULT ]]
1285	then
1286	ending=""
1287	fi
1288
1289	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1290	(( nr_of_input_files = nr_of_input_files + 1 ))
1291	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1292	optin[$nr_of_input_files]="${optin_pre[$i]}"
1293	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1294	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1295	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1296	extin[$nr_of_input_files]="${extin_pre[$i]}"
1297
1298
1299	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1300	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1301	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1302	then
1303	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1304	else
1305	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1306	fi
1307
1308	# DETERMINE THE FILE'S CYCLE NUMBER
1309	(( maxcycle = 0 ))
1310	ls -1 -d $filename > filelist 2>/dev/null
1311	ls -1 -d $filename.* >> filelist 2>/dev/null
1312	while read line
1313	do
1314	# filename without path (i.e. after the last "/")
1315	basefilename=$(basename ${line})
1316
1317	# check if there is an extension
1318	extension=${basefilename##*.}
1319	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1320	then
1321	basefilename=${basefilename%.*}
1322	fi
1323
1324	# check for an existing cycle number
1325	cycle=${basefilename##*.}
1326	if [[ $cycle =~ ^-?[0-9]+$ ]]
1327	then
1328	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1329	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1330	(( icycle = $((10#$cycle)) ))
1331	else
1332	(( icycle = 0 ))
1333	fi
1334
1335	if (( icycle > maxcycle ))
1336	then
1337	(( maxcycle = icycle ))
1338
1339	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1340	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1341	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1342	then
1343	leading_zero=true
1344	else
1345	leading_zero=false
1346	fi
1347	fi
1348
1349	done <filelist
1350	rm filelist
1351
1352	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1353	if [[ $leading_zero = true ]]
1354	then
1355	cyclestring=`printf "%03d" $maxcycle`
1356	else
1357	cyclestring=$maxcycle
1358	fi
1359
1360	# APPEND CYCLE NUMBER TO FILENAME
1361	if (( maxcycle > 0 ))
1362	then
1363	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1364	then
1365	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1366	else
1367	filename=${filename}.$cyclestring
1368	fi
1369	else
1370	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1371	then
1372	filename=${filename}.${extin[$nr_of_input_files]}
1373	fi
1374	fi
1375
1376	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1377	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1378	absnamein[$nr_of_input_files]=$filename
1379	if (( maxcycle > 0 ))
1380	then
1381	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1382	then
1383	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1384	else
1385	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1386	fi
1387	else
1388	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1389	then
1390	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1391	else
1392	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1393	fi
1394	fi
1395
1396	done
1397
1398	fi
1399
1400	done
1401
1402
1403	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1404	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1405	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1406	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1407	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1408	# REMOTE HOST)
1409	(( i = 0 ))
1410	while (( i < iout ))
1411	do
1412	(( i = i + 1 ))
1413	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1414	then
1415	if [[ "${actionout_pre[$i]}" = tr ]]
1416	then
1417	actionout_pre[$i]=""
1418	elif [[ "${actionout_pre[$i]}" = trpe ]]
1419	then
1420	actionout_pre[$i]=pe
1421	elif [[ "${actionout_pre[$i]}" = tra ]]
1422	then
1423	actionout_pre[$i]=a
1424	fi
1425	(( maxcycle = 0 ))
1426	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1427	eval catalogname=${pathout_pre[$i]}
1428	if ! ls $filename* 1>/dev/null 2>&1
1429	then
1430
1431	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1432	if cat /dev/null > $filename
1433	then
1434	rm $filename
1435	else
1436
1437	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1438	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1439	if [[ ! -d $catalogname ]]
1440	then
1441	if mkdir -p $catalogname
1442	then
1443	printf "\n\n *** directory:"
1444	printf "\n $catalogname"
1445	printf "\n was created\n"
1446	else
1447	printf "\n\n +++ OUTPUT-file:"
1448	printf "\n $filename"
1449	printf "\n cannot be created, because directory does not exist"
1450	printf "\n and cannot be created either"
1451	printf "\n"
1452	locat=output ; exit
1453	fi 2>/dev/null
1454	else
1455	printf "\n\n +++ OUTPUT-file:"
1456	printf "\n $filename"
1457	printf "\n cannot be created, although directory exists"
1458	printf "\n"
1459	locat=output ; exit
1460	fi
1461	fi 2>/dev/null
1462
1463	fi
1464
1465	fi
1466	done
1467
1468
1469	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1470	if [[ $running_in_batch_mode = false ]]
1471	then
1472	run_id_number=$RANDOM
1473	run_id=${run_identifier}.$run_id_number
1474
1475	tempdir=$fast_io_catalog/$run_id
1476
1477	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1478	export job_id=$run_id
1479
1480	fi
1481
1482
1483	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1484	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1485	then
1486
1487	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1488	if [[ $ibd = 0 ]]
1489	then
1490	printf "\n"
1491	printf "\n +++ no batch directives found in configuration file"
1492	locat=config_file_batch_directives; (( iec = 0 )); exit
1493	fi
1494
1495	# CHECK IF CPUTIME IS GIVEN FOR JOB
1496	done=false
1497	cputime=$cpumax
1498	while [[ $done = false ]]
1499	do
1500	if (( cputime == 0 ))
1501	then
1502	printf "\n +++ cpu-time is undefined"
1503	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1504	printf "\n >>> "
1505	read cputime 1>/dev/null 2>&1
1506	else
1507	done=true
1508	fi
1509	done
1510	cpumax=$cputime
1511
1512	# CHECK THE MEMORY DEMAND
1513	done=false
1514	while [[ $done = false ]]
1515	do
1516	if (( memory == 0 ))
1517	then
1518	printf "\n +++ memory demand is undefined"
1519	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1520	printf "\n >>> "
1521	read memory 1>/dev/null 2>&1
1522	else
1523	done=true
1524	fi
1525	done
1526
1527	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1528	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1529	then
1530	while [[ -z $remote_username ]]
1531	do
1532	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1533	printf "\n >>> Please type username:"
1534	printf "\n >>> "
1535	read remote_username
1536	done
1537	fi
1538
1539	else
1540
1541	if [[ $running_in_batch_mode = false ]]
1542	then
1543	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1544	cpumax=$cputime
1545	else
1546	cputime=$cpumax
1547	fi
1548
1549	fi
1550
1551
1552	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1553	(( cpu_hours = cputime / 3600 ))
1554	(( resttime = cputime - cpu_hours * 3600 ))
1555	(( cpu_minutes = resttime / 60 ))
1556	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1557	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1558
1559
1560	# OUTPUT OF THE PALMRUN-HEADER
1561	calltime=$(date)
1562	printf "\n"
1563	printf "#------------------------------------------------------------------------# \n"
1564	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1565	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1566	printf "\| \| \n"
1567	column1="called on:"; column2=$(hostname)
1568	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1569	if [[ $create_remote_batch_job = true ]]
1570	then
1571	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1572	else
1573	if [[ $running_on_remote = true ]]
1574	then
1575	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1576	else
1577	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1578	fi
1579	fi
1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1581
1582	column1="running in:"
1583	if [[ $running_in_batch_mode = true ]]
1584	then
1585	column2="batch job mode"
1586	else
1587	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1588	then
1589	column2="job creation mode"
1590	else
1591	column2="interactive run mode"
1592	fi
1593	fi
1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1595
1596	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1597	then
1598	if [[ "$project_account" != "" ]]
1599	then
1600	column1="project account number:"
1601	column2="$project_account"
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	fi
1604	fi
1605
1606	if [[ -n $cores ]]
1607	then
1608	if [[ $run_coupled_model = false ]]
1609	then
1610	column1="number of cores:"; column2=$cores
1611	else
1612	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1613	fi
1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1615	fi
1616	if [[ -n $tasks_per_node ]]
1617	then
1618	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1620	if (( remaining_cores > 0 ))
1621	then
1622	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1623	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1624	fi
1625	fi
1626	if [[ $maximum_parallel_io_streams != $cores ]]
1627	then
1628	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1630	fi
1631	if [[ $use_openmp = true ]]
1632	then
1633	column1="threads per task:"; column2="$threads_per_task"
1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1635	fi
1636	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1637	then
1638	column1="memory demand / PE":; column2="$memory MB"
1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1640	column1="job cpu time (h:m:s):"; column2="$timestring"
1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1642	fi
1643	printf "\| \| \n"
1644	if [[ "$source_list" != "" ]]
1645	then
1646	if [[ "$make_options" != "" ]]
1647	then
1648	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1649	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1650	line=$(echo "$make_options" \| cut -c46-)
1651	while [[ "$line" != "" ]]
1652	do
1653	column1=""
1654	column2=$(echo "$line" \| cut -c-45)
1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1656	line=$(echo "$line" \| cut -c46-)
1657	done
1658	fi
1659	fi
1660
1661	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1663	line=$(echo "$cpp_options" \| cut -c46-)
1664	while [[ "$line" != "" ]]
1665	do
1666	column1=""
1667	column2=$(echo "$line" \| cut -c-45)
1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1669	line=$(echo "$line" \| cut -c46-)
1670	done
1671
1672	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1674	line=$(echo "$compiler_options" \| cut -c46-)
1675	while [[ "$line" != "" ]]
1676	do
1677	column1=""
1678	column2=$(echo "$line" \| cut -c-45)
1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1680	line=$(echo "$line" \| cut -c46-)
1681	done
1682
1683	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1684	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1685	line=$(echo "$linker_options" \| cut -c46-)
1686	while [[ "$line" != "" ]]
1687	do
1688	column1=""
1689	column2=$(echo "$line" \| cut -c-45)
1690	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1691	line=$(echo "$line" \| cut -c46-)
1692	done
1693
1694	if [[ "$login_init_cmd" != "" ]]
1695	then
1696	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1698	line=$(echo "$login_init_cmd" \| cut -c46-)
1699	while [[ "$line" != "" ]]
1700	do
1701	column1=""
1702	column2=$(echo "$line" \| cut -c-45)
1703	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1704	line=$(echo "$line" \| cut -c46-)
1705	done
1706	fi
1707
1708	if [[ "$module_commands" != "" ]]
1709	then
1710	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1712	line=$(echo "$module_commands" \| cut -c46-)
1713	while [[ "$line" != "" ]]
1714	do
1715	column1=""
1716	column2=$(echo "$line" \| cut -c-45)
1717	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1718	line=$(echo "$line" \| cut -c46-)
1719	done
1720	fi
1721	printf "\| \| \n"
1722	column1="run identifier:"; column2=$run_identifier
1723	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1724	column1="activation string list:"; column2=$(echo $activation_string_list)
1725	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1726
1727	if [[ "$ocean_file_appendix" = true ]]
1728	then
1729	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1730	fi
1731
1732	if [[ "$source_list" != "" ]]
1733	then
1734	printf "\| \| \n"
1735	printf "\| Files to be compiled: \| \n"
1736	line=$source_list
1737	while [[ "$line" != "" ]]
1738	do
1739	linestart=$(echo $line \| cut -c-70)
1740	printf "\| %-70s \| \n" "$linestart"
1741	line=$(echo "$line" \| cut -c71-)
1742	done
1743	fi
1744	printf "#------------------------------------------------------------------------#"
1745
1746
1747
1748	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1749	if [[ $do_trace = true ]]
1750	then
1751	(( i = 0 ))
1752	while (( i < nr_of_input_files ))
1753	do
1754	(( i = i + 1 ))
1755	if (( i == 1 ))
1756	then
1757	printf "\n\n >>> INPUT-file assignments:\n"
1758	fi
1759	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1760	done
1761	(( i = 0 ))
1762	while (( i < iout ))
1763	do
1764	(( i = i + 1 ))
1765	if (( i == 1 ))
1766	then
1767	printf "\n\n >>> OUTPUT-file assignments:\n"
1768	fi
1769	printf "\n ${localout[$i]} : ${pathout[$i]}"
1770	done
1771	(( i = 0 ))
1772	while (( i < iic ))
1773	do
1774	(( i = i + 1 ))
1775	if (( i == 1 ))
1776	then
1777	printf "\n\n >>> INPUT-commands:\n"
1778	fi
1779	printf "\n ${in_command[$i]}"
1780	done
1781	(( i = 0 ))
1782	while (( i < ioc ))
1783	do
1784	(( i = i + 1 ))
1785	if (( i == 1 ))
1786	then
1787	printf "\n\n >>> OUTPUT-commands:\n"
1788	fi
1789	printf "\n ${out_command[$i]}"
1790	done
1791	fi
1792
1793	# QUERY FOR CONTINUE
1794	if [[ $silent = false && $running_in_batch_mode = false ]]
1795	then
1796	antwort=dummy
1797	printf "\n\n"
1798	printf " >>> everything o.k. (y/n) ? "
1799	while read antwort
1800	do
1801	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1802	then
1803	printf " >>> everything o.k. (y/n) ? "
1804	else
1805	break
1806	fi
1807	done
1808	if [[ $antwort = n \|\| $antwort = N ]]
1809	then
1810	locat=user_abort; (( iec = 0 )); exit
1811	fi
1812	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1813	then
1814	printf "\n *** batch-job will be created and submitted"
1815	else
1816	printf "\n *** PALMRUN will now continue to execute on this machine"
1817	fi
1818	fi
1819
1820
1821
1822	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1823	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1824	then
1825
1826	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1827	then
1828	printf "\n\n *** creating executable and other sources for the remote host\n"
1829	else
1830	printf "\n\n *** creating executable and other sources for the local host\n"
1831	fi
1832
1833	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1834	# IT SHALL BE CREATED
1835	ask_for_make_depository=false
1836	if [[ $create_remote_batch_job = true ]]
1837	then
1838
1839	line=`grep %base_directory $config_file`
1840	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1841	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1842
1843	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1844	then
1845	printf "\n\n +++ make depository \"${make_depository}\""
1846	printf "\n on remote host not found!"
1847	ask_for_make_depository=true
1848	fi
1849	rm ${configuration_identifier}_last_make_protokoll
1850
1851	else
1852
1853	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1854	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1855	if [[ ! -d ${make_depository} ]]
1856	then
1857	printf "\n\n +++ make depository \"${make_depository}\""
1858	printf "\n on local host not found!"
1859	ask_for_make_depository=true
1860	fi
1861
1862	fi
1863
1864	if [[ $ask_for_make_depository = true ]]
1865	then
1866
1867	antwort=dummy
1868	printf "\n\n"
1869	printf " >>> Create a new one (y/n) ? "
1870	while read antwort
1871	do
1872	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1873	then
1874	printf " >>> Create a new one (y/n) ? "
1875	else
1876	break
1877	fi
1878	done
1879	if [[ $antwort = n \|\| $antwort = N ]]
1880	then
1881	locat=user_abort; (( iec = 0 )); exit
1882	fi
1883
1884	if [[ $do_trace = true ]]
1885	then
1886	palmbuild -c $configuration_identifier
1887	else
1888	palmbuild -v -c $configuration_identifier
1889	fi
1890
1891	if [[ ${PIPESTATUS[0]} != 0 ]]
1892	then
1893
1894	# ABORT IN CASE OF COMPILATION PROBLEMS
1895	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1896	locat=make_depository
1897	exit
1898	else
1899	echo " *** now continue with creating executable and other sources"
1900	fi
1901
1902	fi
1903
1904	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1905	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1906
1907	if [[ ${PIPESTATUS[0]} != 0 ]]
1908	then
1909
1910	# ABORT IN CASE OF COMPILATION PROBLEMS
1911	printf "\n +++ error while creating executable and/or other sources"
1912	locat=execution
1913	rm -rf ${base_directory}/${sources_for_run_catalog}
1914	exit
1915
1916	else
1917
1918	printf " *** executable and other sources created\n"
1919	rm -rf ${base_directory}/${sources_for_run_catalog}
1920
1921	fi
1922
1923	fi
1924
1925
1926	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1927	# WILL BE COPIED TO THE REMOTE HOST
1928	if [[ $create_remote_batch_job = true ]]
1929	then
1930	(( i = 0 ))
1931	while (( i < nr_of_input_files ))
1932	do
1933	(( i = i + 1 ))
1934	if [[ "${actionin[$i]}" = tr ]]
1935	then
1936	eval inputfile=${pathin[$i]}/${frelin[$i]}
1937	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1938	fi
1939	done
1940	if (( i > 0 ))
1941	then
1942	printf "\n\n *** input files have been copied to the remote host\n"
1943	fi
1944	fi
1945
1946
1947	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1948	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1949	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1950	then
1951
1952	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1953	if [[ $running_in_batch_mode = false ]]
1954	then
1955	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1956	# FOLDER
1957	mkdir -p $tempdir
1958	chmod go+rx $tempdir
1959	cd $tempdir
1960	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1961	printf "\n *** changed to temporary directory: $tempdir"
1962
1963	else
1964
1965	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1966	printf "\n *** running in temporary directory: $tempdir"
1967
1968	fi
1969
1970
1971	# PROVIDE THE INPUT FILES
1972	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1973	optional_files_missing=false
1974	(( i = 0 ))
1975	while (( i < nr_of_input_files ))
1976	do
1977	(( i = i + 1 ))
1978	if (( i == 1 ))
1979	then
1980	printf "\n\n *** providing INPUT-files:\n$dashes"
1981	fi
1982
1983
1984	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1985	if [[ "${actionin[$i]}" = unavailable ]]
1986	then
1987	optional_files_missing=true
1988	continue
1989	fi
1990
1991	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1992	files_for_cores=false; filetype=file
1993	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1994	then
1995	files_for_cores=true; filetype=files
1996	actionin[$i]=""
1997	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1998	then
1999	actionin[$i]=""
2000	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
2001	then
2002	files_for_cores=true; filetype=files
2003	actionin[$i]="ln"
2004	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
2005	then
2006	actionin[$i]="ln"
2007	fi
2008
2009	if [[ $files_for_cores = true ]]
2010	then
2011	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2012	else
2013	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2014	fi
2015
2016	# INPUT-FILES TO BE LINKED
2017	if [[ "${actionin[$i]}" = ln ]]
2018	then
2019
2020	printf "\n $filetype will be linked"
2021	if [[ $files_for_cores = false ]]
2022	then
2023	if [[ -f "${absnamein[$i]}" ]]
2024	then
2025	ln ${absnamein[$i]} ${localin[$i]}
2026	got_tmp[$i]=true
2027	fi
2028	else
2029	if [[ -d "${absnamein[$i]}" ]]
2030	then
2031	mkdir -p ${localin[$i]}
2032	cd ${absnamein[$i]}
2033	for file in $(ls *)
2034	do
2035	ln $file $tempdir/${localin[$i]}
2036	done >\|/dev/null 2>&1
2037	cd $tempdir
2038	fi
2039
2040	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2041	if [[ ! -f "${localin[$i]}/_000000" ]]
2042	then
2043	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2044	cp -r ${absnamein[$i]}/* ${localin[$i]}
2045	fi
2046
2047	got_tmp[$i]=true
2048	fi
2049	fi
2050
2051	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2052	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2053	then
2054
2055	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2056	then
2057
2058	# FILE COPIES ARE PROVIDED FOR ALL CORES
2059	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2060	printf "\n file will be provided for $cores processors"
2061	mkdir -p ${localin[$i]}
2062	ival=$cores
2063	(( ii = 0 ))
2064	while (( ii <= ival-1 ))
2065	do
2066	if (( ii < 10 ))
2067	then
2068	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2069	elif (( ii < 100 ))
2070	then
2071	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2072	elif (( ii < 1000 ))
2073	then
2074	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2075	else
2076	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2077	fi
2078	(( ii = ii + 1 ))
2079	done
2080
2081	else
2082
2083	if [[ $files_for_cores = true ]]
2084	then
2085
2086	# PROVIDE FILES FOR EACH CORE
2087	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2088	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2089	printf "\n providing $cores files for the respective cores"
2090	mkdir -p ${localin[$i]}
2091	if [[ $link_local_input = true ]]
2092	then
2093	printf " files will be linked\n"
2094	cd ${absnamein[$i]}
2095	for file in $(ls *)
2096	do
2097	ln -f $file ${localin[$i]}
2098	done
2099	cd $tempdir
2100	fi
2101
2102	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2103	if [[ ! -f "${localin[$i]}/_000000" ]]
2104	then
2105	if [[ $link_local_input = true ]]
2106	then
2107	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2108	fi
2109	cp -r ${absnamein[$i]}/* ${localin[$i]}
2110	fi
2111
2112	else
2113
2114	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2115	if [[ $link_local_input = true ]]
2116	then
2117	printf " file will be linked\n"
2118	ln -f ${absnamein[$i]} ${localin[$i]}
2119	fi
2120	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2121	if [[ ! -f "${localin[$i]}" ]]
2122	then
2123	if [[ $link_local_input = true ]]
2124	then
2125	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2126	fi
2127	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2128	then
2129	mv ${absnamein[$i]} ${localin[$i]}
2130	else
2131	cp ${absnamein[$i]} ${localin[$i]}
2132	fi
2133	fi
2134	fi
2135	fi
2136	fi
2137
2138	done
2139	if (( i != 0 ))
2140	then
2141	if [[ $optional_files_missing = true ]]
2142	then
2143	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2144	fi
2145	printf "\n$dashes\n *** all INPUT-files provided \n"
2146	fi
2147
2148
2149	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2150	(( i = 0 ))
2151	while (( i < iic ))
2152	do
2153	(( i = i + 1 ))
2154	if (( i == 1 ))
2155	then
2156	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2157	fi
2158	printf "\n >>> ${in_command[$i]}"
2159	eval ${in_command[$i]}
2160	if (( i == iic ))
2161	then
2162	printf "\n$dashes\n"
2163	fi
2164	done
2165
2166
2167	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2168	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2169	then
2170	progress_bar_disabled=true
2171	else
2172	progress_bar_disabled=false
2173	fi
2174
2175
2176	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2177	# (FILE ENVPAR WILL BE READ BY PALM)
2178	cat > ENVPAR << EOF
2179	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2180	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2181	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2182	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2183	maximum_cpu_time_allowed = ${cpumax}.,
2184	revision = '$global_revision',
2185	progress_bar_disabled = .${progress_bar_disabled}. /
2186
2187	EOF
2188
2189
2190	# STARTING THE EXECUTABLE
2191	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2192	PATH=$PATH:$tempdir
2193
2194
2195	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2196	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2197	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2198	eval line=\"$line\"
2199	execute_command="$line"
2200
2201
2202	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2203	if [[ "$execute_command_for_combine" = "" ]]
2204	then
2205	eval line2=\"$line2\"
2206	execute_command_for_combine="$line2"
2207	fi
2208
2209
2210
2211	# PROVIDE A HOSTFILE, IF REQUIRED
2212	if [[ "$hostfile" != "" ]]
2213	then
2214
2215	if [[ $hostfile = auto ]]
2216	then
2217	# CREATE A NEW HOSTFILE
2218	(( ii = 1 ))
2219	while (( ii <= cores / threads_per_task ))
2220	do
2221	echo $(hostname) >> hostfile
2222	(( ii = ii + 1 ))
2223	done
2224	if (( cores / threads_per_task == 0 ))
2225	then
2226	echo $(hostname) >> hostfile
2227	fi
2228
2229	else
2230	cp $hostfile hostfile
2231	fi
2232	eval line=\"`head -n $ii hostfile`\"
2233	printf "\n *** running on: $line"
2234	fi
2235
2236
2237
2238	# SET THE NUMBER OF OPENMP-THREADS
2239	if [[ $use_openmp = true ]]
2240	then
2241	export OMP_NUM_THREADS=$threads_per_task
2242	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2243	else
2244	export OMP_NUM_THREADS=1
2245	fi
2246
2247
2248	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2249	if [[ $run_coupled_model = false ]]
2250	then
2251	if [[ "$ocean_file_appendix" = true ]]
2252	then
2253	echo "precursor_ocean" > coupling_steering
2254	else
2255	echo "precursor_atmos" > coupling_steering
2256	fi
2257	else
2258	(( iia = $cores_atmos / $threads_per_task ))
2259	(( iio = $cores_ocean / $threads_per_task ))
2260	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2261	printf "\n\n"
2262	echo "coupled_run $iia $iio" > coupling_steering
2263	fi
2264
2265	printf "\n *** execute command:"
2266	printf "\n \"$execute_command\" \n\n"
2267
2268
2269	if [[ $progress_bar_disabled = true ]]
2270	then
2271	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2272	exit_code=${PIPESTATUS[0]}
2273	else
2274	$execute_command < coupling_steering &> >(tee STDOUT)
2275	exit_code=${PIPESTATUS[0]}
2276	fi
2277
2278	if [[ ${exit_code} != 0 ]]
2279	then
2280
2281	# ABORT IN CASE OF RUNTIME ERRORS
2282	printf "\n +++ runtime error occured"
2283	locat=execution
2284	exit
2285
2286	else
2287
2288	printf "\n$dashes\n *** execution finished \n"
2289
2290	fi
2291
2292
2293	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2294	# BY EACH CORE INTO ONE FILE
2295	if [[ ! -f combine_plot_fields.x ]]
2296	then
2297
2298	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2299	printf "\n 2d- and/or 3d-data may be incomplete!"
2300	printf "\n Your previous palmbuild may have failed. Please check.\n"
2301
2302	elif [[ "$combine_plot_fields" == true ]]
2303	then
2304
2305	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2306	$execute_command_for_combine
2307
2308	else
2309
2310	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2311	# DATA OUTPUT
2312	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2313	fi
2314
2315
2316
2317	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2318	(( i = 0 ))
2319	while (( i < ioc ))
2320	do
2321	(( i = i + 1 ))
2322	if (( i == 1 ))
2323	then
2324	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2325	fi
2326
2327	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2328	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2329
2330	printf "\n >>> ${out_command[$i]}"
2331	eval ${out_command[$i]}
2332	if (( i == ioc ))
2333	then
2334	printf "\n$dashes\n"
2335	fi
2336	done
2337
2338
2339	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2340	# WILDCARDS
2341	(( i = 0 ))
2342	(( nr_of_output_files = 0 ))
2343
2344	while (( i < iout ))
2345	do
2346
2347	(( i = i + 1 ))
2348
2349	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2350	# CREATE A LIST FOR THE DETECTED ENDINGS
2351	if [[ "${multout[$i]}" = true ]]
2352	then
2353	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2354	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2355	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2356
2357	endings="DEFAULT"
2358	while read line
2359	do
2360	# remove the local name from the beginning
2361	localnamestring="${localout_pre[$i]}"
2362	length_localname=${#localnamestring}
2363	ending=${line:${length_localname}}
2364
2365	if [[ "$ending" != "" ]]
2366	then
2367	endings="$endings $ending"
2368	fi
2369
2370	done <filelist
2371
2372	rm filelist
2373
2374	else
2375
2376	# SINGLE NAME
2377	endings=DEFAULT
2378
2379	fi
2380
2381	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2382	for ending in $endings
2383	do
2384
2385	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2386	if [[ $ending = DEFAULT ]]
2387	then
2388	ending=""
2389	fi
2390
2391	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2392	(( nr_of_output_files = nr_of_output_files + 1 ))
2393	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2394	transout[$nr_of_output_files]="${transout_pre[$i]}"
2395	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2396	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2397	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2398	extout[$nr_of_output_files]="${extout_pre[$i]}"
2399	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2400
2401	done
2402
2403	done
2404
2405
2406
2407
2408	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2409	(( i = 0 ))
2410	while (( i < nr_of_output_files ))
2411	do
2412	(( i = i + 1 ))
2413	if (( i == 1 ))
2414	then
2415	printf "\n\n *** saving OUTPUT-files:"
2416
2417	# GET RUN NUMBER ASSIGNED BY PALM
2418	if [[ -f RUN_NUMBER ]]
2419	then
2420	read run_number < RUN_NUMBER
2421	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2422	usecycle_option="-U $run_number"
2423	else
2424	run_number=0
2425	usecycle_option=""
2426	fi
2427	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2428	then
2429	printf "\n *** in case of SCP transfers to local host"
2430	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2431	fi
2432	printf "\n$dashes"
2433	fi
2434
2435	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2436	then
2437
2438	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2439
2440	# DETERMINE THE CYCLE NUMBER
2441	ls -1 -d $filename > filelist 2>/dev/null
2442	ls -1 -d $filename.* >> filelist 2>/dev/null
2443	while read line
2444	do
2445
2446	# filename without path (i.e. after the last "/")
2447	basefilename=$(basename ${line})
2448
2449	# check if there is an extension
2450	extension=${basefilename##*.}
2451	if [[ "$extension" = "${extout[$i]}" ]]
2452	then
2453	basefilename=${basefilename%.*}
2454	fi
2455
2456	# check for an existing cycle number
2457	cycle=${basefilename##*.}
2458	if [[ $cycle =~ ^-?[0-9]+$ ]]
2459	then
2460	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2461	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2462	(( icycle = $((10#$cycle)) + 1 ))
2463	else
2464	(( icycle = 1 ))
2465	fi
2466
2467	if (( icycle > maxcycle ))
2468	then
2469	(( maxcycle = icycle ))
2470	fi
2471
2472	done <filelist
2473	rm filelist
2474
2475
2476	# SET THE CYCLE NUMBER
2477	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2478	if [[ "${actionout[$i]}" = a ]]
2479	then
2480	(( maxcycle = maxcycle - 1 ))
2481	fi
2482
2483	(( cycnum[$i] = maxcycle ))
2484	pathout[$i]=$filename
2485
2486
2487	# ADD CYCLE NUMBER TO FILENAME
2488	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2489	if [[ "${actionout[$i]}" != "a" ]]
2490	then
2491	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2492	# WITH AN EXISTING CYCLE NUMBER
2493	if (( run_number >= cycnum[$i] ))
2494	then
2495	(( cycnum[$i] = run_number ))
2496	else
2497	if (( run_number > 0 ))
2498	then
2499	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2500	fi
2501	fi
2502	fi
2503	if (( cycnum[$i] > 0 ))
2504	then
2505	cyclestring=`printf "%03d" ${cycnum[$i]}`
2506	pathout[$i]=${pathout[$i]}.$cyclestring
2507	fi
2508	fi
2509
2510	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2511	files_for_cores=false; filetype=file
2512	link_local_output=false
2513	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2514	then
2515	files_for_cores=true; filetype=directory
2516	actionout[$i]=""
2517	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2518	then
2519	actionout[$i]=""
2520	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2521	then
2522	files_for_cores=true; filetype=directory
2523	link_local_output=true
2524	actionout[$i]=""
2525	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2526	then
2527	link_local_output
2528	actionout[$i]=""
2529	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2530	then
2531	files_for_cores=true; filetype=directory
2532	actionout[$i]="tr"
2533	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2534	then
2535	actionout[$i]="tr"
2536	fi
2537
2538	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2539	then
2540	if [[ ${warnout[$i]} = true ]]
2541	then
2542	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2543	fi
2544	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2545	then
2546	if [[ ${warnout[$i]} = true ]]
2547	then
2548	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2549	fi
2550	else
2551
2552
2553	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2554	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2555	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2556	then
2557	if [[ $running_on_remote = true ]]
2558	then
2559
2560	# SET OPTIONS FOR TRANSFER
2561	if [[ "${actionout[$i]}" = tr ]]
2562	then
2563	if [[ $files_for_cores = false ]]
2564	then
2565	catalog_option=""
2566	catalog_string=""
2567	else
2568	catalog_option="-c"
2569	catalog_string="/"
2570	fi
2571	append_option=""
2572	append_string=""
2573	else
2574	append_option="-A"
2575	append_string="append"
2576	fi
2577
2578	transfer_failed=false
2579	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2580	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2581
2582	# TRANSFER VIA SCP
2583	if [[ "$remote_loginnode" != "" ]]
2584	then
2585	ssh -q $remote_username@$remote_loginnode "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]}"
2586	else
2587	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]}
2588	fi
2589	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2590
2591
2592	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2593	if [[ $transfer_failed = true ]]
2594	then
2595	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2596	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2597
2598	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2599	eval local_catalog=${pathout[$i]}
2600	if [[ ! -d $local_catalog ]]
2601	then
2602	printf " *** local directory does not exist. Trying to create:\n"
2603	printf " $local_catalog \n"
2604	mkdir -p $local_catalog
2605	fi
2606	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2607	transfer_problems=true
2608	fi
2609
2610	else
2611
2612	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2613	# BE COPIED OR APPENDED ON THIS MACHINE
2614	if [[ "${actionout[$i]}" = tr ]]
2615	then
2616	actionout[$i]=""
2617	else
2618	actionout[$i]="a"
2619	fi
2620	fi
2621	fi
2622
2623
2624	# APPEND ON THIS MACHINE
2625	if [[ "${actionout[$i]}" = "a" ]]
2626	then
2627	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2628	then
2629	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2630	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2631	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2632	else
2633	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2634	printf "\n ${pathout[$i]}\n"
2635	cat ${localout[$i]} >> ${pathout[$i]}
2636	fi
2637	fi
2638
2639	# COPY ON THIS MACHINE
2640	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2641	# ON DIFFERENT FILE-SYSTEMS
2642	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2643	then
2644
2645	# COPY IN CASE OF RUNS ON SINGLE CORES
2646	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2647	then
2648	printf "\n >>> OUTPUT: ${localout[$i]} to"
2649	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2650	if [[ $link_local_output = true ]]
2651	then
2652	printf " file will be linked\n"
2653	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2654	fi
2655	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2656	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2657	then
2658	if [[ $link_local_output = true ]]
2659	then
2660	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2661	fi
2662	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2663	else
2664	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2665	fi
2666	else
2667	printf "\n >>> OUTPUT: ${localout[$i]} to"
2668	printf "\n ${pathout[$i]}\n"
2669	if [[ $link_local_output = true ]]
2670	then
2671	printf " file will be linked\n"
2672	ln -f ${localout[$i]} ${pathout[$i]}
2673	fi
2674	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2675	if [[ ! -f "${pathout[$i]}" ]]
2676	then
2677	if [[ $link_local_output = true ]]
2678	then
2679	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2680	fi
2681	cp ${localout[$i]} ${pathout[$i]}
2682	else
2683	printf "+++ no copy because file ${pathout[$i]} exists\n"
2684	fi
2685	fi
2686
2687	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2688	then
2689
2690	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2691	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2692	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2693	printf "\n ${pathout[$i]}\n"
2694	if [[ $link_local_output = true ]]
2695	then
2696	printf " files will be linked\n"
2697	mkdir -p ${pathout[$i]}
2698	cd ${localout[$i]}
2699	for file in $(ls *)
2700	do
2701	ln -f $file ${pathout[$i]}
2702	done >\|/dev/null 2>&1
2703	cd $tempdir
2704	fi
2705
2706	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2707	if [[ ! -f "${pathout[$i]}/_000000" ]]
2708	then
2709	if [[ $link_local_output = true ]]
2710	then
2711	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2712	fi
2713	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2714	cp -r ${localout[$i]}/* ${pathout[$i]}
2715	fi
2716
2717	fi
2718	fi
2719	done
2720
2721	if (( i != 0 ))
2722	then
2723	if [[ $transfer_problems = true ]]
2724	then
2725	printf "\n$dashes\n *** OUTPUT-files saved"
2726	printf "\n +++ WARNING: some data transfers failed! \n"
2727	else
2728	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2729	fi
2730	fi
2731
2732
2733	# IF REQUIRED, START A RESTART-JOB
2734	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2735	if [[ -f CONTINUE_RUN ]]
2736	then
2737
2738	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2739	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2740	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2741	# -b START A BATCH JOB
2742	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2743	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2744	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2745
2746	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2747	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2748	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2749	then
2750	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2751	fi
2752
2753	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2754	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2755	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2756	then
2757	prc=`echo $prc \| sed 's/#/r/g'`
2758	fi
2759
2760
2761	# START THE RESTART-JOB
2762	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2763	echo " $prc"
2764	printf "\n$dashes\n"
2765	if [[ $running_on_remote = true ]]
2766	then
2767
2768	echo "*** ssh will be used to initiate restart-runs!"
2769	echo " return_address=\"$return_address\" "
2770	echo " return_username=\"$local_username\" "
2771
2772	if [[ "$remote_loginnode" != "" ]]
2773	then
2774	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
2775	else
2776	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2777	fi
2778
2779	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2780	sleep 30
2781
2782	else
2783
2784	# START THE RESTART JOB ON THE LOCAL HOST
2785	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2786	cd - > /dev/null
2787
2788	fi
2789
2790	# CHECK, IF RESTART JOB HAS BEEN STARTED
2791	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2792	then
2793	printf "\n$dashes\n +++ creating restart run failed \n"
2794	locat=create_restart
2795	rm palmrun_restart.log
2796	exit
2797	else
2798	printf "\n$dashes\n *** restart run initiated \n"
2799	rm palmrun_restart.log
2800	fi
2801
2802
2803	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2804	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2805	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2806	# MAY BE VERY HUGE)
2807	(( i = 0 ))
2808	while (( i < nr_of_input_files ))
2809	do
2810	(( i = i + 1 ))
2811	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2812	then
2813	rm -r ${absnamein[$i]}
2814	fi
2815	done
2816
2817	fi
2818
2819
2820	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2821	cd $HOME
2822	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2823
2824
2825	else
2826
2827
2828	# PREPARING ACTIONS,
2829	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2830
2831	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2832	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2833	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2834	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2835	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2836	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2837	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2838	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2839	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2840	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2841	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2842	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2843	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2844	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2845	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2846	if [[ $create_remote_batch_job = true ]]
2847	then
2848	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2849	if [[ $do_trace = true ]]
2850	then
2851	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2852	fi
2853	elif [[ $create_batch_job = true ]]
2854	then
2855	palmrun_com=${palmrun_com}" -j"
2856	if [[ $do_trace = true ]]
2857	then
2858	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2859	fi
2860	fi
2861
2862
2863	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2864	# REMOTE HOST
2865	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2866	job_protocol_file=$job_protocol_file_local
2867	if [[ $create_remote_batch_job = true ]]
2868	then
2869	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2870	job_protocol_file=$job_protocol_file_remote
2871	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2872	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2873	fi
2874
2875
2876	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2877	jobfile=jobfile.$run_id_number
2878
2879
2880	# FIRST CREATE THE BATCH DIRECTIVES
2881	(( i = 0 ))
2882	while (( i < ibd ))
2883	do
2884	(( i = i + 1 ))
2885	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2886	eval line=\"$line\"
2887	echo "$line" >> $jobfile
2888	done
2889	echo " " >> $jobfile
2890
2891
2892	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2893	# PROTOCOL
2894	if [[ $create_remote_batch_job = true ]]
2895	then
2896	echo "set +vx" >> $jobfile
2897	echo "trap '" >> $jobfile
2898	echo "set +vx" >> $jobfile
2899	echo "cd ${remote_jobcatalog}" >> $jobfile
2900	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2901
2902	# ADD THE BATCH DIRECTIVES
2903	(( i = 0 ))
2904	while (( i < ibdt ))
2905	do
2906	(( i = i + 1 ))
2907	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2908	eval line=\"$line\"
2909	echo "$line" >> $jobfile
2910	done
2911	echo " " >> $jobfile
2912
2913	echo "set -x" >> $jobfile
2914	if [[ "$remote_loginnode" != "" ]]
2915	then
2916	echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${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}\" " >> $jobfile
2917	else
2918	echo "${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
2919	fi
2920	echo "%%END%%" >> $jobfile
2921	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2922	echo "$submit_command $scpjob_file" >> $jobfile
2923	echo "rm $scpjob_file" >> $jobfile
2924	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2925	echo "set -x" >> $jobfile
2926	echo " ' exit" >> $jobfile
2927	fi
2928
2929
2930	# ACTIVATE ERROR-TRACEBACK
2931	if [[ $do_trace = true ]]
2932	then
2933	echo "set -x" >> $jobfile
2934	else
2935	echo "set +vx" >> $jobfile
2936	fi
2937
2938
2939	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2940	if [[ "$login_init_cmd" != "" ]]
2941	then
2942	echo "$login_init_cmd" >> $jobfile
2943	fi
2944	if [[ "$module_commands" != "" ]]
2945	then
2946	echo "$module_commands" >> $jobfile
2947	fi
2948
2949
2950	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2951	if [[ $create_remote_batch_job = true ]]
2952	then
2953	echo "mkdir $tempdir" >> $jobfile
2954	echo "chmod go+rx $tempdir" >> $jobfile
2955	else
2956	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2957	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2958	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2959	mkdir $tempdir
2960	chmod go+rx $tempdir
2961	fi
2962	echo "cd $tempdir" >> $jobfile
2963	echo "export tempdir=$tempdir" >> $jobfile
2964	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2965	echo "export PATH=.:\$PATH" >> $jobfile
2966	echo "export execute_palmrun=true" >> $jobfile
2967
2968
2969	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2970	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2971	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2972	echo "LOCAL_PWD=$working_directory" >> $jobfile
2973	echo "export LOCAL_PWD" >> $jobfile
2974
2975
2976	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2977	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2978	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2979
2980
2981	# CALL PALMRUN WITHIN THE JOB
2982	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2983	echo "set -x" >> $jobfile
2984	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2985
2986
2987	# TRANSFER JOBFILE TO THE TARGET HOST
2988	if [[ $create_jobfile_only = false ]]
2989	then
2990
2991	# CREATE LOCAL JOB FOLDER
2992	eval local_jobcatalog=$local_jobcatalog
2993	if [[ ! -d $local_jobcatalog ]]
2994	then
2995	echo " "
2996	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
2997	mkdir $local_jobcatalog
2998	fi
2999
3000	if [[ $create_remote_batch_job = true ]]
3001	then
3002
3003	echo " "
3004	echo " *** transfer of job to remote host via scp"
3005
3006	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3007	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
3008
3009	# COPY THE JOB FILE
3010	if [[ $do_trace = true ]]
3011	then
3012	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
3013	fi
3014	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
3015
3016	# SUBMIT THE JOB
3017	printf " *** submit the job (output of submit command, e.g. the job-id, may follow) \n"
3018	if [[ $do_trace = true ]]
3019	then
3020	echo " 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>/dev/null"
3021	fi
3022	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>/dev/null
3023
3024	elif [[ $create_batch_job = true ]]
3025	then
3026
3027	eval local_jobcatalog=$local_jobcatalog
3028	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3029	cd $local_jobcatalog
3030	echo " "
3031	echo " *** submit the job"
3032	if [[ $do_trace = true ]]
3033	then
3034	echo "$submit_command ${configuration_identifier}_${run_id}"
3035	fi
3036	$submit_command ${configuration_identifier}_${run_id}
3037	rm ${configuration_identifier}_${run_id}
3038	cd - > /dev/null
3039
3040	fi
3041
3042	rm -rf $jobfile
3043
3044	else
3045
3046	printf "\n *** jobfile created under name \"$jobfile\" "
3047	printf "\n no batch-job has been sent!"
3048
3049	fi
3050
3051	fi # END OF REMOTE-PART

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