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source: palm/trunk/SCRIPTS/palmrun @ 3554

Last change on this file since 3554 was 3549, checked in by raasch, 6 years ago
ssh-call for submitting batch jobs on remote systems modified to avoid output of login messages on specific systems, ssh-calls for compilations on remote systems modified to avoid output of login messages on specific systems, english translation of german comments / variable names
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.2 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 3549 2018-11-21 15:44:44Z gronemeier $
29	# ssh-call for submitting batch jobs on remote systems modified to avoid output
30	# of login messages on specific systems
31	#
32	# 3534 2018-11-19 15:35:16Z raasch
33	# batch_scp for sending back the job protocol file is called via login-node if
34	# a login-node has been set in the config-file
35	# ssh-calls rearranged to avoid output of system/user-profile messages
36	#
37	# 3505 2018-11-08 09:14:30Z raasch
38	# job folders are created in case that they do not exist
39	#
40	# 3455 2018-10-30 14:12:31Z raasch
41	# options -h and -d renamed -c and -r, respectively
42	#
43	# 3402 2018-10-23 11:49:24Z knoop
44	# job_id is set for compatibility reasons with older versions of config files
45	#
46	# 3313 2018-10-06 15:22:48Z knoop
47	# more detailed error message for outdated fileconnection file
48	#
49	# 3236 2018-09-10 09:07:06Z raasch
50	# warning issued in case of file connection file version mismatch,
51	# host_configuration renamed configuration_identifier,
52	# "host identifier" in header output renamed "config. identifier",
53	# jobname renamed run_identifier,
54	# run_id renamed run_id_number
55	# job_id renamed run_id
56	# option -r renamed -i
57	#
58	# 3151 2018-07-19 08:45:38Z raasch
59	# removed additional listing of files to be compiled, print PALM code revision
60	# in header
61	#
62	# 3132 2018-07-16 11:44:58Z raasch
63	# create consistent error messages in case of failed restarts,
64	# check existence of remote job catalog
65	#
66	# 3043 2018-05-25 10:47:54Z raasch
67	# check for setting of fast_io_catalog
68	#
69	# 3033 2018-05-23 15:26:19Z raasch
70	# -T option not required for interactive runs (tasks per node =
71	# total number of cores is assumed as default, if option is not given),
72	# reformatting of a few messages,
73	# bugfix: destination output directory is created if attribute "pe" is set in
74	# .palm.iofiles
75	#
76	# 2718 2018-01-02 08:49:38Z maronga
77	# bugfix of r2990
78	#
79	# 2718 2018-01-02 08:49:38Z maronga
80	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
81	# not in the working directory from where palmrun is called
82	#
83	# 2718 2018-01-02 08:49:38Z maronga
84	# svfout in the activation string will be replaced now by svfin in case of
85	# automatic restarts
86	#
87	# 2718 2018-01-02 08:49:38Z maronga
88	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
89	# the possible output or input of sky view factors
90	#
91	# 2718 2018-01-02 08:49:38Z maronga
92	# "fname" renamed to "jobname"
93	#
94	# 2718 2018-01-02 08:49:38Z maronga
95	# parameters are allowed in output commands (OC:)
96	#
97	# 2718 2018-01-02 08:49:38Z maronga
98	# bugfix: exit if no queue has been given neither with option -q nor in the
99	# configuration file
100	#
101	# 2718 2018-01-02 08:49:38Z maronga
102	# file connection file from trunk/SCRIPTS is taken by default
103	#
104	# 2718 2018-01-02 08:49:38Z maronga
105	# Corrected "Former revisions" section
106	#
107	# 2696 2017-12-14 17:12:51Z kanani
108	# Change in file header (GPL part)
109	#
110	# 2693 2017-12-13 12:33:49Z raasch
111	# replacement of variables given by {{<variable>}} in configuration file is now
112	# done in a more general way, variable names are written in small letters
113	#
114	# 2670 2017-12-06 16:32:19Z raasch
115	# test printouts removed
116	#
117	# 2669 2017-12-06 16:03:27Z raasch
118	# file attributes in .palm.iofiles restructured, "loc" attribute completely
119	# removed,
120	# wildcard (*) allowed in .palm.iofiles as file activation string for output
121	# files,
122	# informative messages in case of missing optional input files shortened
123	# bugfix: variable cycle explicitly interpreted with 10 as the number base
124	#
125	# 2638 2017-11-23 12:44:23Z raasch
126	# use of wildcards in file connection statements enabled
127	#
128	# 2605 2017-11-09 15:31:46Z raasch
129	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
130	# will not be sent with the job file any more, but copied into the
131	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
132	#
133	# 2600 2017-11-01 14:11:20Z raasch
134	# cycle numbers are made three digits wide
135	#
136	# 2566 2017-10-20 08:50:47Z raasch
137	# execute command for combine_plot_fields added
138	# "TEMPDIR" renamed "tempdir"
139	# temporary working directory for local batch jobs is created immediately within
140	# the user's palmrun call, due to a requirement of the "grid engine" batch
141	# system, where the working directory is given with batch directive -wd and must
142	# already exist when the job is submitted,
143	# informative messages in non-trace mode reduced and partly reformatted
144	#
145	# 2551 2017-10-18 07:25:11Z raasch
146	# TEMPDIR added as replacement string to be used in batch directives
147	#
148	# 2512 2017-10-04 08:26:59Z raasch
149	# bugfix for determining cycle numbers of NetCDF input files
150	#
151	# 2506 2017-09-29 08:30:37Z raasch
152	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
153	# host configuration added to SOURCES_FOR_RUN_... folder name
154	# host_identifier renamed host_configuration
155	# option -W added to allow for job dependencies
156	#
157	# 2501 2017-09-26 11:41:55Z raasch
158	# default value for number of cores (option -X) set to 1
159	# bugfix for mechanism which overwrites configuration file settings with values
160	# provided by palmrun options
161	#
162	# 2499 2017-09-22 16:47:58Z kanani
163	# option -h named configuration identifier
164	#
165	# 2480 2017-09-19 06:24:14Z maronga
166	# bugfix for last revision
167	#
168	# 2479 2017-09-19 06:12:16Z raasch
169	# option -A (project account number) added
170	#
171	# 2422 2017-09-08 08:25:41Z raasch
172	# initial revision
173	#
174	#--------------------------------------------------------------------------------#
175	# palmrun - script for running PALM jobs on local and remote hosts
176	#--------------------------------------------------------------------------------#
177
178
179
180	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
181
182	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
183	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
184	# (TOO MANY ARGUMENTS - PROBLEM)
185	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
186
187	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
188	typeset -i nr_of_output_files=0
189	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
190	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
191	# SCRIPT-OPTION ARGUMENTS
192	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
193	typeset -i icycle inode ival maxcycle mpi_tasks
194	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
195
196	activation_string_list=""
197	AddFilenames=""
198	combine_plot_fields=true
199	compiler_name=""
200	compiler_name_ser=""
201	compiler_options=""
202	configuration_identifier="default"
203	cores=1
204	cores_atmos=0
205	cores_ocean=0
206	coupled_dist=""
207	cpp_options=""
208	cpumax=0
209	create_batch_job=false
210	create_jobfile_only=false
211	create_remote_batch_job=false
212	dashes=" ----------------------------------------------------------------------------"
213	defaultqueue=""
214	delete_temporary_catalog=true
215	do_compile=true
216	do_trace=false
217	executable=""
218	execute_command=""
219	execution_error=false
220	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
221	global_revision=""
222	hostfile=""
223	hp=""
224	keep_data_from_previous_run=false
225	link_local_input=false
226	link_local_output=false
227	linker_options=""
228	local_jobcatalog=""
229	locat=normal
230	makefile=""
231	max_par_io_str=""
232	prc=$0
233	while [[ $(echo $prc \| grep -c "/") != 0 ]]
234	do
235	prc=`echo $prc \| cut -f2- -d"/"`
236	done
237	module_calls=""
238	palmrun_memory=""
239	palmrun_script_name=$prc
240	openmp=false
241	previous_job=""
242	project_account=""
243	queue=none
244	read_svf=""
245	restart_run=false
246	return_address=""
247	remote_jobcatalog=""
248	remote_username=""
249	running_in_batch_mode=false
250	running_in_test_mode=false
251	run_coupled_model=false
252	run_id=""
253	run_id_number=""
254	run_identifier=test
255	silent=false
256	source_list=""
257	source_path=""
258	tasks_per_node=0
259	threads_per_task=1
260	transfer_problems=false
261	user_source_path=""
262	use_existing_sources_folder=""
263	use_openmp=false
264	version="palmrun 1.0 Rev$Rev: 3549 $"
265	working_directory=`pwd`
266	write_binary=""
267	write_svf=""
268
269
270	# ERROR HANDLING IN CASE OF EXIT
271	trap 'if [[ $locat != normal && $locat != control_c ]]
272	then
273
274	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
275	(( i = 0 ))
276	while (( i < iec ))
277	do
278	(( i = i + 1 ))
279	printf "\n *** Execution of ERROR-command:\n"
280	printf " >>> ${err_command[$i]}\n"
281	eval ${err_command[$i]}
282	done
283	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
284	printf "\n\n+++ palmrun crashed \n\n"
285	exit 1
286	elif [[ $locat != normal ]]
287	then
288	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
289	printf "\n+++ palmrun killed by \"^C\" \n\n"
290	exit 2
291	else
292	printf "\n --> palmrun finished\n\n"
293	exit 0
294	fi' exit
295
296
297	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
298	trap 'locat=control_c
299	exit 1
300	' 2
301
302
303	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
304	# WHICH WILL BE USED TO START RESTART-JOBS
305	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
306	do
307	case $option in
308	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
309	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
310	(b) create_batch_job=true; prc="$prc -b";;
311	(B) delete_temporary_catalog=false; prc="$prc -B";;
312	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
313	(C) restart_run=true; prc="$prc -C";;
314	(F) create_jobfile_only=true;;
315	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
316	(i) run_id_number=$OPTARG;;
317	(j) running_in_batch_mode=true;;
318	(k) keep_data_from_previous_run=true; prc="$prc -k";;
319	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
320	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
321	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
322	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
323	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
324	(R) return_address=$OPTARG;;
325	(s) source_list=$OPTARG;;
326	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
327	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
328	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
329	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
330	(v) silent=true; prc="$prc -v";;
331	(V) use_existing_sources_folder="-V";;
332	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
333	(W) previous_job=$OPTARG;;
334	(x) do_trace=true;set -x; prc="$prc -x";;
335	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
336	(y) ocean_file_appendix=true; prc="$prc -y";;
337	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
338	(z) running_in_test_mode=true;;
339	(Z) combine_plot_fields=false; prc="$prc -Z";;
340	(\?) printf "\n +++ unknown option $OPTARG \n"
341	printf "\n --> type \"$0 ?\" for available options \n"
342	locat=parameter;exit;;
343	esac
344	done
345
346
347	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
348	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
349	(( to_shift = $OPTIND - 1 ))
350	shift $to_shift
351
352	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
353	if [[ "$1" = "?" ]]
354	then
355	(printf "\n *** Description of available palmrun options:\n"
356	printf "\n Option Description Default-Value"
357	printf "\n -a activation string list \"\" "
358	printf "\n -A project account number ---"
359	printf "\n -b batch-job on local machine ---"
360	printf "\n -B do not delete temporary directory at end ---"
361	printf "\n -c configuration identifier \"default\" "
362	printf "\n -F create batch job file only ---"
363	printf "\n -k keep data from previous run"
364	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
365	printf "\n -M Makefile name Makefile"
366	printf "\n -O threads per openMP task ---"
367	printf "\n -q queue \"$queue\" "
368	printf "\n -r run identifier test"
369	printf "\n -s filenames of routines to be compiled \"\" "
370	printf "\n must end with .f, .f90, .F, or .c !"
371	printf "\n use \"..\" for more than one file and wildcards"
372	printf "\n -s LM compiles all locally modified files"
373	printf "\n -t allowed cpu-time in seconds (batch) 0"
374	printf "\n -T tasks per node ---"
375	printf "\n -u username on remote machine \"\" "
376	printf "\n -v no prompt for confirmation ---"
377	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
378	printf "\n -w maximum parallel io streams as given by -X"
379	printf "\n -W name of job to wait for ---"
380	printf "\n -x tracing of palmrun for debug purposes ---"
381	printf "\n -X # of processors (on parallel machines) 1"
382	printf "\n -y add appendix \"_O\" to all local output"
383	printf "\n files (ocean precursor runs followed by"
384	printf "\n coupled atmosphere-ocean runs) ---"
385	printf "\n -Y run coupled model, \"#1 #2\" with"
386	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
387	printf "\n -Z skip combine_plot_fields at the end of "
388	printf "\n the simulation ---"
389	printf "\n "
390	printf "\n Possible values of positional parameter <modus>:"
391	printf "\n \"?\" - this outline \n\n") \| more
392	exit
393	elif [[ "$1" != "" ]]
394	then
395	printf "\n +++ positional parameter $1 unknown \n"
396	locat=parameter; exit
397	fi
398
399
400
401	# SHORT STARTING MESSAGE
402	printf "\n*** $version "
403	printf "\n will be executed. Please wait ..."
404
405
406	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
407	config_file=.palm.config.$configuration_identifier
408	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
409
410
411	# CHECK, IF CONFIGURATION FILE EXISTS
412	if [[ ! -f $config_file ]]
413	then
414	printf "\n\n +++ configuration file: "
415	printf "\n $config_file"
416	printf "\n does not exist"
417	locat=connect; exit
418	fi
419
420
421	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
422	if [[ -f .palm.iofiles ]]
423	then
424
425	# CHECK VERSION MISMATCH
426	if [[ $running_in_batch_mode != true ]]
427	then
428	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
429	then
430	printf "\n\n +++ WARNING: A file connection file has been found in your"
431	printf "\n working directory, but its revision does not match"
432	printf "\n the revision of the default (trunk) version."
433	printf "\n You may need to update your connection file"
434	printf "\n \"${working_directory}/.palm.iofiles\" !"
435	fi
436	fi
437
438	fileconnection_file=.palm.iofiles
439
440	fi
441
442
443	# CHECK, IF FILE CONNECTION FILE EXISTS
444	if [[ ! -f $fileconnection_file ]]
445	then
446	printf "\n\n +++ file connection file: "
447	printf "\n $fileconnection_file"
448	printf "\n does not exist"
449	locat=connect; exit
450	fi
451
452
453	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
454	if [[ "$activation_string_list" = "" ]]
455	then
456	printf "\n\n +++ no activation string list given: "
457	printf "\n please set palmrun option \"-a\" "
458	locat=palmrun_option; exit
459	fi
460
461
462	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
463	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
464	then
465	write_binary=true
466	else
467	write_binary=false
468	fi
469
470	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
471	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
472	then
473	write_svf=true
474	else
475	write_svf=false
476	fi
477
478	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
479	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
480	then
481	read_svf=true
482	else
483	read_svf=false
484	fi
485
486
487	# READ AND EVALUATE THE CONFIGURATION-FILE
488	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
489
490	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
491	while read line
492	do
493
494	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
495	eval line=\"$line\"
496
497
498	# INTERPRET THE LINE
499	if [[ "$(echo $line)" = "" ]]
500	then
501
502	# EMPTY LINE, NO ACTION
503	continue
504
505	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
506	then
507
508	# LINE IS A COMMENT LINE
509	continue
510
511	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
512	then
513
514	# LINE DEFINES AN ENVIRONMENT-VARIABLE
515	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
516	value=`echo $line \| cut -d" " -s -f2-`
517
518
519	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
520	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
521	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
522	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
523	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
524	# CONFIGURATION-FILE.
525	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
526	then
527	eval export $var="\$value"
528
529	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
530	if [[ $do_trace = true ]]
531	then
532	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
533	fi
534	fi
535
536	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
537	then
538
539	# LINE DEFINES BATCH-DIRECTIVE
540	(( ibd = ibd + 1 ))
541	line=$(echo $line \| cut -c4-)
542	batch_directive[$ibd]="$line"
543
544	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
545	then
546
547	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
548	# REMOTE TO A LOCAL HOST
549	(( ibdt = ibdt + 1 ))
550	line=$(echo $line \| cut -c5-)
551	batch_directive_transfer[$ibdt]="$line"
552
553	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
554	then
555
556	# LINE DEFINES ERROR-COMMAND
557	(( iec = iec + 1 ))
558	line=$(echo $line \| cut -c4-)
559	err_command[$iec]="$line"
560
561	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
562	then
563
564	# LINE DEFINES INPUT-COMMAND
565	(( iic = iic + 1 ))
566	line=$(echo $line \| cut -c4-)
567	in_command[$iic]="$line"
568
569	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
570	then
571
572	# LINE DEFINES OUTPUT-COMMAND
573	(( ioc = ioc + 1 ))
574	line=$(echo $line \| cut -c4-)
575	out_command[$ioc]="$line"
576
577	else
578
579	# SKIP ALL OTHER LINES
580	continue
581
582	fi
583
584	done < $config_file
585
586
587	# CHECK SETTING OF REQUIRED PARAMETERS
588	if [[ "$fast_io_catalog" = "" ]]
589	then
590	printf "\n +++ no fast_io_catalog found in $config_file"
591	printf "\n Please add line \"fast_io_catalog ...\" to that file."
592	locat=config_file; exit
593	fi
594	if [[ "$compiler_name" = "" ]]
595	then
596	printf "\n +++ no compiler name found in $config_file"
597	printf "\n Please add line \"compiler_name ...\" to that file."
598	locat=config_file; exit
599	fi
600	if [[ "$compiler_name_ser" = "" ]]
601	then
602	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
603	printf "\n Please add line \"compiler_name_ser ...\" to that file."
604	locat=config_file; exit
605	fi
606	if [[ "$compiler_options" = "" ]]
607	then
608	printf "\n +++ no compiler options found in $config_file"
609	printf "\n Please add line \"compiler_options ...\" to that file."
610	locat=config_file; exit
611	fi
612	if [[ "$linker_options" = "" ]]
613	then
614	printf "\n +++ no linker options found in $config_file"
615	printf "\n Please add line \"linker_options ...\" to that file."
616	locat=config_file; exit
617	fi
618	if [[ "$execute_command" = "" ]]
619	then
620	printf "\n +++ no execute command found in $config_file"
621	printf "\n Please add line \"execute_command ...\" to that file."
622	locat=config_file; exit
623	fi
624
625	if [[ "$hostfile" != "" ]]
626	then
627	if [[ $hostfile != auto && ! -f $hostfile ]]
628	then
629	printf "\n +++ no hostfile \"$hostfile\" found"
630	printf "\n Please check line \"hostfile ...\" in $config_file"
631	locat=config_file; exit
632	fi
633	fi
634
635
636	# DETERMINE THE CALL STATUS
637	if [[ "$return_address" != "" ]]
638	then
639
640	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
641	# BATCH MODE AND ...
642	running_on_remote=true
643
644	else
645
646	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
647	if [[ "$remote_ip" != "" ]]
648	then
649
650	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
651	create_remote_batch_job=true
652
653	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
654	if [[ "$remote_jobcatalog" = "" ]]
655	then
656	printf "\n +++ no remote jobcatalog found in $config_file"
657	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
658	locat=config_file; exit
659	fi
660
661
662	fi
663	running_on_remote=false
664	fi
665
666
667
668	# READ AND EVALUATE THE I/O-FILE LIST
669	[[ $silent = false ]] && printf "\n Reading the I/O files... "
670
671	# READ THE FILE CONNECTION FILE LINE BY LINE
672	while read line
673	do
674
675	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
676	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
677
678	# INTERPRET THE LINE
679	if [[ "$(echo $line)" = "" ]]
680	then
681	# EMPTY LINE, NO ACTION
682	continue
683
684	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
685	then
686
687	# LINE IS A COMMENT LINE
688	true
689
690	else
691
692	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
693	# s2a: in/out - field
694	# s2b: action - field (optional)
695	s1=`echo "$line" \| cut -d" " -f1`
696	s2=`echo "$line" \| cut -d" " -s -f2`
697	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
698	then
699	s2a=$s2
700	s2b=""
701	else
702	s2a=`echo $s2 \| cut -d":" -f1`
703	s2b=`echo $s2 \| cut -d":" -f2`
704	fi
705	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
706	s4=`echo "$line" \| cut -d" " -s -f4`
707	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
708	s5=`echo "$line" \| cut -d" " -s -f5`
709	s6=`echo "$line" \| cut -d" " -s -f6`
710
711
712	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
713	# INPUT- OR OUTPUT-LIST.
714	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
715	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
716	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
717	# IS NOT CHECKED AND STORED.
718	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
719	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
720	then
721	found=false
722	for actual in $activation_string_list
723	do
724	for formal in $s3
725	do
726	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
727	done
728	done
729	if [[ $found = true ]]
730	then
731	(( iin = iin + 1 ))
732	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
733	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
734	if [[ "$s2a" = inopt ]]
735	then
736	optin_pre[$iin]=yes
737	else
738	optin_pre[$iin]=no
739	fi
740
741	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
742	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
743	if [[ $running_on_remote = true && "$s2b" = tr ]]
744	then
745	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
746	fi
747
748	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
749	# THE WILDCARD FROM THE ENDING
750	if [[ "${s5: -1}" = "*" ]]
751	then
752	if [[ "$s2b" = "di" ]]
753	then
754	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
755	printf "\n see file \"$fileconnection_file\", line"
756	printf "\n$line"
757	locat=iofiles_file; exit
758	fi
759	multin[$iin]=true
760	string=${endin_pre[$iin]}
761	endin_pre[$iin]="${string%?}"
762	else
763	multin[$iin]=false
764	fi
765	fi
766	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
767	then
768	found=false
769	for actual in $activation_string_list
770	do
771	for formal in $s3
772	do
773	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
774	done
775	done
776	if [[ $found = true ]]
777	then
778	(( iout = iout + 1 ))
779	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
780	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
781
782	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
783	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
784	if [[ $formal = wildcard ]]
785	then
786	warnout_pre[$iout]=false
787	else
788	warnout_pre[$iout]=true
789	fi
790
791	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
792	# THE WILDCARD FROM THE LOCAL FILENAME
793	if [[ "${s1: -1}" = "*" ]]
794	then
795	if [[ "$s2b" = "di" ]]
796	then
797	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
798	printf "\n see file \"$fileconnection_file\", line"
799	printf "\n$line"
800	locat=iofiles_file; exit
801	fi
802	multout[$iout]=true
803	string=${localout_pre[$iout]}
804	localout_pre[$iout]="${string%?}"
805	else
806	multout[$iout]=false
807	fi
808	fi
809	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
810	then
811	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
812	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
813	locat=connect; exit
814	fi
815	IFS="$IFSALT"
816	fi
817
818	done < $fileconnection_file
819
820
821
822	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
823	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
824	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
825	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
826	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
827	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
828
829
830
831	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
832	if [[ $run_coupled_model = true ]]
833	then
834
835	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
836	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
837
838	if (( $cores_ocean + $cores_atmos != $cores ))
839	then
840
841	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
842	printf "\n PEs (total) : $cores"
843	printf "\n PEs (atmosphere): $cores_atmos"
844	printf "\n PEs (ocean) : $cores_ocean"
845	locat=coupling; exit
846
847	fi
848
849	fi
850
851
852	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
853	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
854	# FOLDER
855	if [[ $running_in_batch_mode = true ]]
856	then
857
858	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
859	then
860	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
861	printf "\n Please check the output of the palmrun-call"
862	printf "\n that you did on your local host."
863	locat=SOURCES_FOR_RUN; exit
864	fi
865
866	else
867
868	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
869	# AUTOMATIC RESTART RUN
870	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
871	if [[ $restart_run = false ]]
872	then
873
874	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
875	# THE LOCAL HOST
876	if [[ ! -d $source_path ]]
877	then
878	printf "\n\n +++ source path \"$source_path\" on local host"
879	printf "\n \"$(hostname)\" does not exist"
880	locat=source_path; exit
881	fi
882
883	rm -rf ${base_directory}/${sources_for_run_catalog}
884	mkdir -p ${base_directory}/${sources_for_run_catalog}
885
886	if [[ "$source_list" = LM ]]
887	then
888
889	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
890	source_list=""
891	cd $source_path
892
893
894	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
895	if [[ ! -d ../.svn ]]
896	then
897	printf "\n\n +++ source directory"
898	printf "\n \"$source_path\" "
899	printf "\n is not under control of \"subversion\"."
900	printf "\n Please do not use palmrun-option \"-s LM\"\n"
901	fi
902
903
904	# LIST ALL MODIFIED SOURCE CODE FILES
905	Filenames=""
906	svn status > tmp_svnstatus
907	while read line
908	do
909	firstc=`echo $line \| cut -c1`
910	if [[ $firstc = M \|\| $firstc = "?" ]]
911	then
912	Name=`echo "$line" \| cut -c8-`
913	extension=`echo $Name \| cut -d. -f2`
914	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
915	then
916	Filenames="$Filenames "$Name
917	fi
918	fi
919	done < tmp_svnstatus
920	rm -rf tmp_svnstatus
921
922
923	# COPY FILES TO SOURCES_FOR_RUN_...
924	for filename in $Filenames
925	do
926	cp $filename ${base_directory}/${sources_for_run_catalog}
927	source_list=$source_list"$filename "
928	done
929
930	cd - > /dev/null
931
932
933	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
934	elif [[ "$source_list" != "" ]]
935	then
936
937	cd $source_path
938
939	for filename in $source_list
940	do
941
942	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
943	if [[ $(echo $filename \| grep -c "/") != 0 ]]
944	then
945	printf "\n +++ source code file: $filename"
946	printf "\n must not contain (\"/\") "
947	locat=source; exit
948	fi
949
950	if [[ ! -f $filename ]]
951	then
952	printf "\n +++ source code file: $filename"
953	printf "\n does not exist"
954	locat=source; exit
955	else
956	cp $filename ${base_directory}/${sources_for_run_catalog}
957	fi
958
959	done
960
961	cd - > /dev/null
962
963	fi
964
965	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
966	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
967	if [[ ! -f $makefile ]]
968	then
969	printf "\n +++ file \"$makefile\" does not exist"
970	locat=make; exit
971	else
972	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
973	fi
974
975
976	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
977	if [[ "$user_source_path" != "" ]]
978	then
979
980	# DOES THE DIRECTORY EXIST?
981	if [[ ! -d $user_source_path ]]
982	then
983
984	printf "\n\n *** INFORMATIVE: additional source code directory"
985	printf "\n \"$user_source_path\" "
986	printf "\n does not exist or is not a directory."
987	printf "\n No source code will be used from this directory!\n"
988	user_source_path=""
989	if [[ $silent == false ]]
990	then
991	sleep 2
992	fi
993
994	else
995
996	cd $user_source_path
997
998	Names=$(ls -1 *.f90 2>&1)
999	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1000	Names=$(ls -1 *.F90 2>&1)
1001	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1002	Names=$(ls -1 *.F 2>&1)
1003	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1004	Names=$(ls -1 *.f 2>&1)
1005	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1006	Names=$(ls -1 *.c 2>&1)
1007	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1008
1009	cd - > /dev/null
1010	cd ${base_directory}/${sources_for_run_catalog}
1011
1012	# COPY MAKEFILE IF EXISTING
1013	if [[ -f $user_source_path/Makefile ]]
1014	then
1015	printf "\n\n *** user Makefile from directory"
1016	printf "\n \"$user_source_path\" is used \n"
1017	if [[ $silent == false ]]
1018	then
1019	sleep 1
1020	fi
1021	cp $user_source_path/Makefile .
1022	fi
1023
1024	for filename in $AddFilenames
1025	do
1026	if [[ -f $filename ]]
1027	then
1028	printf "\n +++ source code file \"$filename\" found in additional"
1029	printf "\n source code directory \"$user_source_path\" "
1030	printf "\n but was also given with option \"-s\" which means that it should be taken"
1031	printf "\n from directory \"$source_path\"."
1032	locat=source; exit
1033	fi
1034
1035	cp $user_source_path/$filename .
1036	source_list="$source_list $filename"
1037
1038	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1039	if [[ $(grep -c $filename Makefile) = 0 ]]
1040	then
1041	printf "\n\n +++ user file \"$filename\" "
1042	printf "\n is not listed in Makefile \n"
1043	locat=source; exit
1044	fi
1045	done
1046	cd - > /dev/null
1047	fi
1048	fi
1049
1050	# COPY CONFIGURATION FILES
1051	cp $config_file ${base_directory}/${sources_for_run_catalog}
1052	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1053
1054	# COPY SHELLSCRIPTS
1055	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1056	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1057
1058	fi
1059
1060	fi
1061
1062
1063	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1064	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1065	if [[ "$global_revision" = "" ]]
1066	then
1067	global_revision=`svnversion $source_path 2>/dev/null`
1068	global_revision="Rev: $global_revision"
1069	fi
1070
1071
1072	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1073	if [[ -n $cores ]]
1074	then
1075
1076	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1077	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1078	if [[ $tasks_per_node = 0 ]]
1079	then
1080	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1081	then
1082	printf "\n"
1083	printf "\n +++ option \"-T\" (tasks per node) is missing"
1084	printf "\n set -T option or define tasks_per_node in the config file"
1085	locat=tasks_per_node; (( iec = 0 )); exit
1086	else
1087	# DEFAULT FOR INTERACTIVE RUN
1088	tasks_per_node=$cores
1089	fi
1090	fi
1091
1092	if (( cores < tasks_per_node ))
1093	then
1094	printf "\n"
1095	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1096	printf "\n given values: -T $tasks_per_node -X $cores"
1097	locat=tasks_per_node; (( iec = 0 )); exit
1098	fi
1099
1100	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1101	(( mpi_tasks = cores / threads_per_task ))
1102	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1103	(( ii = cores / tasks_per_node ))
1104	(( remaining_cores = cores - ii * tasks_per_node ))
1105	if (( remaining_cores > 0 ))
1106	then
1107	printf "\n"
1108	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1109	printf "\n divisor of the total number of cores (option \"-X\")"
1110	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1111	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1112	(( nodes = nodes + 1 ))
1113	fi
1114
1115	fi
1116
1117
1118	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1119	if [[ "$maximum_parallel_io_streams" = "" ]]
1120	then
1121	maximum_parallel_io_streams=$cores
1122	fi
1123
1124
1125	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1126	if [[ "$scp_port" != "" ]]
1127	then
1128	PORTOPT="-P $scp_port"
1129	SSH_PORTOPT="-p $scp_port"
1130	fi
1131
1132
1133	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1134	# CONFIG-FILE
1135	if [[ "$ssh_key" != "" ]]
1136	then
1137	ssh_key="-i $HOME/.ssh/$ssh_key"
1138	fi
1139
1140
1141	# SET QUEUE, IF NOT GIVEN
1142	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1143	then
1144
1145	if [[ $queue = none && "$defaultqueue" = "" ]]
1146	then
1147	printf "\n"
1148	printf "\n +++ no default queue given in configuration file and no queue"
1149	printf "\n given with option -q"
1150	locat=queue; exit
1151	fi
1152	if [[ $queue = none ]]
1153	then
1154	queue=$defaultqueue
1155	fi
1156
1157	fi
1158
1159
1160	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1161	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1162	(( i = 0 ))
1163	(( nr_of_input_files = 0 ))
1164	while (( i < iin ))
1165	do
1166	(( i = i + 1 ))
1167
1168	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1169	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1170	if [[ "${actionin_pre[$i]}" = di ]]
1171	then
1172	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1173	else
1174	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1175	fi
1176
1177
1178	# CHECK IF FILE EXISTS
1179	if ! ls $filename* 1>/dev/null 2>&1
1180	then
1181
1182	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1183	if [[ "${optin_pre[$i]}" != "yes" ]]
1184	then
1185	printf "\n\n +++ INPUT-file: "
1186	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1187	then
1188	printf "\n $filename"
1189	else
1190	printf "\n $filename.${extin_pre[$i]}"
1191	fi
1192	printf "\n does not exist\n"
1193	locat=input; exit
1194	else
1195	(( nr_of_input_files = nr_of_input_files + 1 ))
1196	localin[$nr_of_input_files]="${localin_pre[$i]}"
1197	optin[$nr_of_input_files]="${optin_pre[$i]}"
1198	actionin[$nr_of_input_files]="unavailable"
1199	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1200	endin[$nr_of_input_files]="${endin_pre[$i]}"
1201	extin[$nr_of_input_files]="${extin_pre[$i]}"
1202	fi
1203
1204	else
1205
1206	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1207	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1208	# ENDINGS
1209	if [[ "${multin[$i]}" = true ]]
1210	then
1211	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1212	ls -1 -d ${filename} > filelist 2>/dev/null
1213	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1214	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1215
1216	endings=""
1217	while read line
1218	do
1219	# filename without path (i.e. after the last "/")
1220	basefilename=$(basename ${line})
1221
1222	# check if there is an extension and remove it
1223	ext=${basefilename##*.}
1224	if [[ "$ext" = "${extin_pre[$i]}" ]]
1225	then
1226	basefilename=${basefilename%.*}
1227	fi
1228
1229	# check for an existing cycle number and remove it
1230	cycle=${basefilename##*.}
1231	if [[ $cycle =~ ^-?[0-9]+$ ]]
1232	then
1233	basefilename=${basefilename%.*}
1234	fi
1235
1236	# remove the run_identifier from the beginning
1237	length_run_identifier=${#run_identifier}
1238	ending=${basefilename:${length_run_identifier}}
1239
1240	# remove the ending given in the .iofiles from the beginning
1241	endingstring="${endin_pre[$i]}"
1242	length_ending=${#endingstring}
1243	ending=${ending:${length_ending}}
1244
1245	if [[ "$ending" = "" ]]
1246	then
1247	# standard ending as given in the .iofiles
1248	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1249	then
1250	endings="$endings DEFAULT"
1251	fi
1252	else
1253	# ending must start with "_", otherwise its a different file
1254	if [[ "${ending:0:1}" = "_" ]]
1255	then
1256	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1257	then
1258	endings="$endings $ending"
1259	fi
1260	fi
1261	fi
1262
1263	done <filelist
1264
1265	rm filelist
1266
1267	else
1268
1269	# SINGLE NAME
1270	endings=DEFAULT
1271
1272	fi
1273
1274	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1275	for ending in $endings
1276	do
1277
1278	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1279	if [[ $ending = DEFAULT ]]
1280	then
1281	ending=""
1282	fi
1283
1284	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1285	(( nr_of_input_files = nr_of_input_files + 1 ))
1286	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1287	optin[$nr_of_input_files]="${optin_pre[$i]}"
1288	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1289	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1290	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1291	extin[$nr_of_input_files]="${extin_pre[$i]}"
1292
1293
1294	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1295	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1296	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1297	then
1298	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1299	else
1300	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1301	fi
1302
1303	# DETERMINE THE FILE'S CYCLE NUMBER
1304	(( maxcycle = 0 ))
1305	ls -1 -d $filename > filelist 2>/dev/null
1306	ls -1 -d $filename.* >> filelist 2>/dev/null
1307	while read line
1308	do
1309	# filename without path (i.e. after the last "/")
1310	basefilename=$(basename ${line})
1311
1312	# check if there is an extension
1313	extension=${basefilename##*.}
1314	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1315	then
1316	basefilename=${basefilename%.*}
1317	fi
1318
1319	# check for an existing cycle number
1320	cycle=${basefilename##*.}
1321	if [[ $cycle =~ ^-?[0-9]+$ ]]
1322	then
1323	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1324	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1325	(( icycle = $((10#$cycle)) ))
1326	else
1327	(( icycle = 0 ))
1328	fi
1329
1330	if (( icycle > maxcycle ))
1331	then
1332	(( maxcycle = icycle ))
1333
1334	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1335	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1336	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1337	then
1338	leading_zero=true
1339	else
1340	leading_zero=false
1341	fi
1342	fi
1343
1344	done <filelist
1345	rm filelist
1346
1347	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1348	if [[ $leading_zero = true ]]
1349	then
1350	cyclestring=`printf "%03d" $maxcycle`
1351	else
1352	cyclestring=$maxcycle
1353	fi
1354
1355	# APPEND CYCLE NUMBER TO FILENAME
1356	if (( maxcycle > 0 ))
1357	then
1358	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1359	then
1360	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1361	else
1362	filename=${filename}.$cyclestring
1363	fi
1364	else
1365	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1366	then
1367	filename=${filename}.${extin[$nr_of_input_files]}
1368	fi
1369	fi
1370
1371	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1372	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1373	absnamein[$nr_of_input_files]=$filename
1374	if (( maxcycle > 0 ))
1375	then
1376	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1377	then
1378	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1379	else
1380	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1381	fi
1382	else
1383	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1384	then
1385	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1386	else
1387	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1388	fi
1389	fi
1390
1391	done
1392
1393	fi
1394
1395	done
1396
1397
1398	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1399	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1400	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1401	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1402	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1403	# REMOTE HOST)
1404	(( i = 0 ))
1405	while (( i < iout ))
1406	do
1407	(( i = i + 1 ))
1408	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1409	then
1410	if [[ "${actionout_pre[$i]}" = tr ]]
1411	then
1412	actionout_pre[$i]=""
1413	elif [[ "${actionout_pre[$i]}" = trpe ]]
1414	then
1415	actionout_pre[$i]=pe
1416	elif [[ "${actionout_pre[$i]}" = tra ]]
1417	then
1418	actionout_pre[$i]=a
1419	fi
1420	(( maxcycle = 0 ))
1421	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1422	eval catalogname=${pathout_pre[$i]}
1423	if ! ls $filename* 1>/dev/null 2>&1
1424	then
1425
1426	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1427	if cat /dev/null > $filename
1428	then
1429	rm $filename
1430	else
1431
1432	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1433	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1434	if [[ ! -d $catalogname ]]
1435	then
1436	if mkdir -p $catalogname
1437	then
1438	printf "\n\n *** directory:"
1439	printf "\n $catalogname"
1440	printf "\n was created\n"
1441	else
1442	printf "\n\n +++ OUTPUT-file:"
1443	printf "\n $filename"
1444	printf "\n cannot be created, because directory does not exist"
1445	printf "\n and cannot be created either"
1446	printf "\n"
1447	locat=output ; exit
1448	fi 2>/dev/null
1449	else
1450	printf "\n\n +++ OUTPUT-file:"
1451	printf "\n $filename"
1452	printf "\n cannot be created, although directory exists"
1453	printf "\n"
1454	locat=output ; exit
1455	fi
1456	fi 2>/dev/null
1457
1458	fi
1459
1460	fi
1461	done
1462
1463
1464	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1465	if [[ $running_in_batch_mode = false ]]
1466	then
1467	run_id_number=$RANDOM
1468	run_id=${run_identifier}.$run_id_number
1469
1470	tempdir=$fast_io_catalog/$run_id
1471
1472	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1473	export job_id=$run_id
1474
1475	fi
1476
1477
1478	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1479	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1480	then
1481
1482	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1483	if [[ $ibd = 0 ]]
1484	then
1485	printf "\n"
1486	printf "\n +++ no batch directives found in configuration file"
1487	locat=config_file_batch_directives; (( iec = 0 )); exit
1488	fi
1489
1490	# CHECK IF CPUTIME IS GIVEN FOR JOB
1491	done=false
1492	cputime=$cpumax
1493	while [[ $done = false ]]
1494	do
1495	if (( cputime == 0 ))
1496	then
1497	printf "\n +++ cpu-time is undefined"
1498	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1499	printf "\n >>> "
1500	read cputime 1>/dev/null 2>&1
1501	else
1502	done=true
1503	fi
1504	done
1505	cpumax=$cputime
1506
1507	# CHECK THE MEMORY DEMAND
1508	done=false
1509	while [[ $done = false ]]
1510	do
1511	if (( memory == 0 ))
1512	then
1513	printf "\n +++ memory demand is undefined"
1514	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1515	printf "\n >>> "
1516	read memory 1>/dev/null 2>&1
1517	else
1518	done=true
1519	fi
1520	done
1521
1522	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1523	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1524	then
1525	while [[ -z $remote_username ]]
1526	do
1527	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1528	printf "\n >>> Please type username:"
1529	printf "\n >>> "
1530	read remote_username
1531	done
1532	fi
1533
1534	else
1535
1536	if [[ $running_in_batch_mode = false ]]
1537	then
1538	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1539	cpumax=$cputime
1540	else
1541	cputime=$cpumax
1542	fi
1543
1544	fi
1545
1546
1547	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1548	(( cpu_hours = cputime / 3600 ))
1549	(( resttime = cputime - cpu_hours * 3600 ))
1550	(( cpu_minutes = resttime / 60 ))
1551	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1552	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1553
1554
1555	# OUTPUT OF THE PALMRUN-HEADER
1556	calltime=$(date)
1557	printf "\n"
1558	printf "#------------------------------------------------------------------------# \n"
1559	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1560	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1561	printf "\| \| \n"
1562	column1="called on:"; column2=$(hostname)
1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1564	if [[ $create_remote_batch_job = true ]]
1565	then
1566	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1567	else
1568	if [[ $running_on_remote = true ]]
1569	then
1570	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1571	else
1572	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1573	fi
1574	fi
1575	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1576
1577	column1="running in:"
1578	if [[ $running_in_batch_mode = true ]]
1579	then
1580	column2="batch job mode"
1581	else
1582	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1583	then
1584	column2="job creation mode"
1585	else
1586	column2="interactive run mode"
1587	fi
1588	fi
1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1590
1591	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1592	then
1593	if [[ "$project_account" != "" ]]
1594	then
1595	column1="project account number:"
1596	column2="$project_account"
1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1598	fi
1599	fi
1600
1601	if [[ -n $cores ]]
1602	then
1603	if [[ $run_coupled_model = false ]]
1604	then
1605	column1="number of cores:"; column2=$cores
1606	else
1607	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1608	fi
1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1610	fi
1611	if [[ -n $tasks_per_node ]]
1612	then
1613	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1615	if (( remaining_cores > 0 ))
1616	then
1617	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1618	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1619	fi
1620	fi
1621	if [[ $maximum_parallel_io_streams != $cores ]]
1622	then
1623	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1625	fi
1626	if [[ $use_openmp = true ]]
1627	then
1628	column1="threads per task:"; column2="$threads_per_task"
1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1630	fi
1631	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1632	then
1633	column1="memory demand / PE":; column2="$memory MB"
1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1635	column1="job cpu time (h:m:s):"; column2="$timestring"
1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1637	fi
1638	printf "\| \| \n"
1639	if [[ "$source_list" != "" ]]
1640	then
1641	if [[ "$make_options" != "" ]]
1642	then
1643	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1644	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1645	line=$(echo "$make_options" \| cut -c46-)
1646	while [[ "$line" != "" ]]
1647	do
1648	column1=""
1649	column2=$(echo "$line" \| cut -c-45)
1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1651	line=$(echo "$line" \| cut -c46-)
1652	done
1653	fi
1654	fi
1655
1656	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1658	line=$(echo "$cpp_options" \| cut -c46-)
1659	while [[ "$line" != "" ]]
1660	do
1661	column1=""
1662	column2=$(echo "$line" \| cut -c-45)
1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1664	line=$(echo "$line" \| cut -c46-)
1665	done
1666
1667	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1669	line=$(echo "$compiler_options" \| cut -c46-)
1670	while [[ "$line" != "" ]]
1671	do
1672	column1=""
1673	column2=$(echo "$line" \| cut -c-45)
1674	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1675	line=$(echo "$line" \| cut -c46-)
1676	done
1677
1678	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1680	line=$(echo "$linker_options" \| cut -c46-)
1681	while [[ "$line" != "" ]]
1682	do
1683	column1=""
1684	column2=$(echo "$line" \| cut -c-45)
1685	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1686	line=$(echo "$line" \| cut -c46-)
1687	done
1688
1689	if [[ "$login_init_cmd" != "" ]]
1690	then
1691	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1692	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1693	line=$(echo "$login_init_cmd" \| cut -c46-)
1694	while [[ "$line" != "" ]]
1695	do
1696	column1=""
1697	column2=$(echo "$line" \| cut -c-45)
1698	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1699	line=$(echo "$line" \| cut -c46-)
1700	done
1701	fi
1702
1703	if [[ "$module_commands" != "" ]]
1704	then
1705	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1706	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1707	line=$(echo "$module_commands" \| cut -c46-)
1708	while [[ "$line" != "" ]]
1709	do
1710	column1=""
1711	column2=$(echo "$line" \| cut -c-45)
1712	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1713	line=$(echo "$line" \| cut -c46-)
1714	done
1715	fi
1716	printf "\| \| \n"
1717	column1="run identifier:"; column2=$run_identifier
1718	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1719	column1="activation string list:"; column2=$(echo $activation_string_list)
1720	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1721
1722	if [[ "$ocean_file_appendix" = true ]]
1723	then
1724	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1725	fi
1726
1727	if [[ "$source_list" != "" ]]
1728	then
1729	printf "\| \| \n"
1730	printf "\| Files to be compiled: \| \n"
1731	line=$source_list
1732	while [[ "$line" != "" ]]
1733	do
1734	linestart=$(echo $line \| cut -c-70)
1735	printf "\| %-70s \| \n" "$linestart"
1736	line=$(echo "$line" \| cut -c71-)
1737	done
1738	fi
1739	printf "#------------------------------------------------------------------------#"
1740
1741
1742
1743	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1744	if [[ $do_trace = true ]]
1745	then
1746	(( i = 0 ))
1747	while (( i < nr_of_input_files ))
1748	do
1749	(( i = i + 1 ))
1750	if (( i == 1 ))
1751	then
1752	printf "\n\n >>> INPUT-file assignments:\n"
1753	fi
1754	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1755	done
1756	(( i = 0 ))
1757	while (( i < iout ))
1758	do
1759	(( i = i + 1 ))
1760	if (( i == 1 ))
1761	then
1762	printf "\n\n >>> OUTPUT-file assignments:\n"
1763	fi
1764	printf "\n ${localout[$i]} : ${pathout[$i]}"
1765	done
1766	(( i = 0 ))
1767	while (( i < iic ))
1768	do
1769	(( i = i + 1 ))
1770	if (( i == 1 ))
1771	then
1772	printf "\n\n >>> INPUT-commands:\n"
1773	fi
1774	printf "\n ${in_command[$i]}"
1775	done
1776	(( i = 0 ))
1777	while (( i < ioc ))
1778	do
1779	(( i = i + 1 ))
1780	if (( i == 1 ))
1781	then
1782	printf "\n\n >>> OUTPUT-commands:\n"
1783	fi
1784	printf "\n ${out_command[$i]}"
1785	done
1786	fi
1787
1788	# QUERY FOR CONTINUE
1789	if [[ $silent = false && $running_in_batch_mode = false ]]
1790	then
1791	antwort=dummy
1792	printf "\n\n"
1793	printf " >>> everything o.k. (y/n) ? "
1794	while read antwort
1795	do
1796	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1797	then
1798	printf " >>> everything o.k. (y/n) ? "
1799	else
1800	break
1801	fi
1802	done
1803	if [[ $antwort = n \|\| $antwort = N ]]
1804	then
1805	locat=user_abort; (( iec = 0 )); exit
1806	fi
1807	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1808	then
1809	printf "\n *** batch-job will be created and submitted"
1810	else
1811	printf "\n *** PALMRUN will now continue to execute on this machine"
1812	fi
1813	fi
1814
1815
1816
1817	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1818	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1819	then
1820
1821	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1822	then
1823	printf "\n\n *** creating executable and other sources for the remote host\n"
1824	else
1825	printf "\n\n *** creating executable and other sources for the local host\n"
1826	fi
1827
1828	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1829	# IT SHALL BE CREATED
1830	ask_for_make_depository=false
1831	if [[ $create_remote_batch_job = true ]]
1832	then
1833
1834	line=`grep %base_directory $config_file`
1835	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1836	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1837
1838	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1839	then
1840	printf "\n\n +++ make depository \"${make_depository}\""
1841	printf "\n on remote host not found!"
1842	ask_for_make_depository=true
1843	fi
1844	rm ${configuration_identifier}_last_make_protokoll
1845
1846	else
1847
1848	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1849	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1850	if [[ ! -d ${make_depository} ]]
1851	then
1852	printf "\n\n +++ make depository \"${make_depository}\""
1853	printf "\n on local host not found!"
1854	ask_for_make_depository=true
1855	fi
1856
1857	fi
1858
1859	if [[ $ask_for_make_depository = true ]]
1860	then
1861
1862	antwort=dummy
1863	printf "\n\n"
1864	printf " >>> Create a new one (y/n) ? "
1865	while read antwort
1866	do
1867	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1868	then
1869	printf " >>> Create a new one (y/n) ? "
1870	else
1871	break
1872	fi
1873	done
1874	if [[ $antwort = n \|\| $antwort = N ]]
1875	then
1876	locat=user_abort; (( iec = 0 )); exit
1877	fi
1878
1879	if [[ $do_trace = true ]]
1880	then
1881	palmbuild -c $configuration_identifier
1882	else
1883	palmbuild -v -c $configuration_identifier
1884	fi
1885
1886	if [[ ${PIPESTATUS[0]} != 0 ]]
1887	then
1888
1889	# ABORT IN CASE OF COMPILATION PROBLEMS
1890	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1891	locat=make_depository
1892	exit
1893	else
1894	echo " *** now continue with creating executable and other sources"
1895	fi
1896
1897	fi
1898
1899	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1900	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1901
1902	if [[ ${PIPESTATUS[0]} != 0 ]]
1903	then
1904
1905	# ABORT IN CASE OF COMPILATION PROBLEMS
1906	printf "\n +++ error while creating executable and/or other sources"
1907	locat=execution
1908	rm -rf ${base_directory}/${sources_for_run_catalog}
1909	exit
1910
1911	else
1912
1913	printf " *** executable and other sources created\n"
1914	rm -rf ${base_directory}/${sources_for_run_catalog}
1915
1916	fi
1917
1918	fi
1919
1920
1921	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1922	# WILL BE COPIED TO THE REMOTE HOST
1923	if [[ $create_remote_batch_job = true ]]
1924	then
1925	(( i = 0 ))
1926	while (( i < nr_of_input_files ))
1927	do
1928	(( i = i + 1 ))
1929	if [[ "${actionin[$i]}" = tr ]]
1930	then
1931	eval inputfile=${pathin[$i]}/${frelin[$i]}
1932	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1933	fi
1934	done
1935	if (( i > 0 ))
1936	then
1937	printf "\n\n *** input files have been copied to the remote host\n"
1938	fi
1939	fi
1940
1941
1942	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1943	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1944	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1945	then
1946
1947	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1948	if [[ $running_in_batch_mode = false ]]
1949	then
1950	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1951	# FOLDER
1952	mkdir -p $tempdir
1953	chmod go+rx $tempdir
1954	cd $tempdir
1955	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1956	printf "\n *** changed to temporary directory: $tempdir"
1957
1958	else
1959
1960	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1961	printf "\n *** running in temporary directory: $tempdir"
1962
1963	fi
1964
1965
1966	# PROVIDE THE INPUT FILES
1967	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1968	optional_files_missing=false
1969	(( i = 0 ))
1970	while (( i < nr_of_input_files ))
1971	do
1972	(( i = i + 1 ))
1973	if (( i == 1 ))
1974	then
1975	printf "\n\n *** providing INPUT-files:\n$dashes"
1976	fi
1977
1978
1979	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1980	if [[ "${actionin[$i]}" = unavailable ]]
1981	then
1982	optional_files_missing=true
1983	continue
1984	fi
1985
1986	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1987	files_for_cores=false; filetype=file
1988	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1989	then
1990	files_for_cores=true; filetype=files
1991	actionin[$i]=""
1992	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1993	then
1994	actionin[$i]=""
1995	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1996	then
1997	files_for_cores=true; filetype=files
1998	actionin[$i]="ln"
1999	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
2000	then
2001	actionin[$i]="ln"
2002	fi
2003
2004	if [[ $files_for_cores = true ]]
2005	then
2006	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2007	else
2008	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2009	fi
2010
2011	# INPUT-FILES TO BE LINKED
2012	if [[ "${actionin[$i]}" = ln ]]
2013	then
2014
2015	printf "\n $filetype will be linked"
2016	if [[ $files_for_cores = false ]]
2017	then
2018	if [[ -f "${absnamein[$i]}" ]]
2019	then
2020	ln ${absnamein[$i]} ${localin[$i]}
2021	got_tmp[$i]=true
2022	fi
2023	else
2024	if [[ -d "${absnamein[$i]}" ]]
2025	then
2026	mkdir -p ${localin[$i]}
2027	cd ${absnamein[$i]}
2028	for file in $(ls *)
2029	do
2030	ln $file $tempdir/${localin[$i]}
2031	done >\|/dev/null 2>&1
2032	cd $tempdir
2033	fi
2034
2035	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2036	if [[ ! -f "${localin[$i]}/_000000" ]]
2037	then
2038	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2039	cp -r ${absnamein[$i]}/* ${localin[$i]}
2040	fi
2041
2042	got_tmp[$i]=true
2043	fi
2044	fi
2045
2046	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2047	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2048	then
2049
2050	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2051	then
2052
2053	# FILE COPIES ARE PROVIDED FOR ALL CORES
2054	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2055	printf "\n file will be provided for $cores processors"
2056	mkdir -p ${localin[$i]}
2057	ival=$cores
2058	(( ii = 0 ))
2059	while (( ii <= ival-1 ))
2060	do
2061	if (( ii < 10 ))
2062	then
2063	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2064	elif (( ii < 100 ))
2065	then
2066	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2067	elif (( ii < 1000 ))
2068	then
2069	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2070	else
2071	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2072	fi
2073	(( ii = ii + 1 ))
2074	done
2075
2076	else
2077
2078	if [[ $files_for_cores = true ]]
2079	then
2080
2081	# PROVIDE FILES FOR EACH CORE
2082	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2083	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2084	printf "\n providing $cores files for the respective cores"
2085	mkdir -p ${localin[$i]}
2086	if [[ $link_local_input = true ]]
2087	then
2088	printf " files will be linked\n"
2089	cd ${absnamein[$i]}
2090	for file in $(ls *)
2091	do
2092	ln -f $file ${localin[$i]}
2093	done
2094	cd $tempdir
2095	fi
2096
2097	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2098	if [[ ! -f "${localin[$i]}/_000000" ]]
2099	then
2100	if [[ $link_local_input = true ]]
2101	then
2102	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2103	fi
2104	cp -r ${absnamein[$i]}/* ${localin[$i]}
2105	fi
2106
2107	else
2108
2109	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2110	if [[ $link_local_input = true ]]
2111	then
2112	printf " file will be linked\n"
2113	ln -f ${absnamein[$i]} ${localin[$i]}
2114	fi
2115	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2116	if [[ ! -f "${localin[$i]}" ]]
2117	then
2118	if [[ $link_local_input = true ]]
2119	then
2120	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2121	fi
2122	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2123	then
2124	mv ${absnamein[$i]} ${localin[$i]}
2125	else
2126	cp ${absnamein[$i]} ${localin[$i]}
2127	fi
2128	fi
2129	fi
2130	fi
2131	fi
2132
2133	done
2134	if (( i != 0 ))
2135	then
2136	if [[ $optional_files_missing = true ]]
2137	then
2138	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2139	fi
2140	printf "\n$dashes\n *** all INPUT-files provided \n"
2141	fi
2142
2143
2144	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2145	(( i = 0 ))
2146	while (( i < iic ))
2147	do
2148	(( i = i + 1 ))
2149	if (( i == 1 ))
2150	then
2151	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2152	fi
2153	printf "\n >>> ${in_command[$i]}"
2154	eval ${in_command[$i]}
2155	if (( i == iic ))
2156	then
2157	printf "\n$dashes\n"
2158	fi
2159	done
2160
2161
2162	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2163	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2164	then
2165	progress_bar_disabled=true
2166	else
2167	progress_bar_disabled=false
2168	fi
2169
2170
2171	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2172	# (FILE ENVPAR WILL BE READ BY PALM)
2173	cat > ENVPAR << EOF
2174	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2175	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2176	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2177	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2178	maximum_cpu_time_allowed = ${cpumax}.,
2179	revision = '$global_revision',
2180	progress_bar_disabled = .${progress_bar_disabled}. /
2181
2182	EOF
2183
2184
2185	# STARTING THE EXECUTABLE
2186	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2187	PATH=$PATH:$tempdir
2188
2189
2190	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2191	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2192	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2193	eval line=\"$line\"
2194	execute_command="$line"
2195
2196
2197	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2198	if [[ "$execute_command_for_combine" = "" ]]
2199	then
2200	eval line2=\"$line2\"
2201	execute_command_for_combine="$line2"
2202	fi
2203
2204
2205
2206	# PROVIDE A HOSTFILE, IF REQUIRED
2207	if [[ "$hostfile" != "" ]]
2208	then
2209
2210	if [[ $hostfile = auto ]]
2211	then
2212	# CREATE A NEW HOSTFILE
2213	(( ii = 1 ))
2214	while (( ii <= cores / threads_per_task ))
2215	do
2216	echo $(hostname) >> hostfile
2217	(( ii = ii + 1 ))
2218	done
2219	if (( cores / threads_per_task == 0 ))
2220	then
2221	echo $(hostname) >> hostfile
2222	fi
2223
2224	else
2225	cp $hostfile hostfile
2226	fi
2227	eval line=\"`head -n $ii hostfile`\"
2228	printf "\n *** running on: $line"
2229	fi
2230
2231
2232
2233	# SET THE NUMBER OF OPENMP-THREADS
2234	if [[ $use_openmp = true ]]
2235	then
2236	export OMP_NUM_THREADS=$threads_per_task
2237	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2238	else
2239	export OMP_NUM_THREADS=1
2240	fi
2241
2242
2243	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2244	if [[ $run_coupled_model = false ]]
2245	then
2246	if [[ "$ocean_file_appendix" = true ]]
2247	then
2248	echo "precursor_ocean" > coupling_steering
2249	else
2250	echo "precursor_atmos" > coupling_steering
2251	fi
2252	else
2253	(( iia = $cores_atmos / $threads_per_task ))
2254	(( iio = $cores_ocean / $threads_per_task ))
2255	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2256	printf "\n\n"
2257	echo "coupled_run $iia $iio" > coupling_steering
2258	fi
2259
2260	printf "\n *** execute command:"
2261	printf "\n \"$execute_command\" \n\n"
2262
2263
2264	if [[ $progress_bar_disabled = true ]]
2265	then
2266	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2267	exit_code=${PIPESTATUS[0]}
2268	else
2269	$execute_command < coupling_steering &> >(tee STDOUT)
2270	exit_code=${PIPESTATUS[0]}
2271	fi
2272
2273	if [[ ${exit_code} != 0 ]]
2274	then
2275
2276	# ABORT IN CASE OF RUNTIME ERRORS
2277	printf "\n +++ runtime error occured"
2278	locat=execution
2279	exit
2280
2281	else
2282
2283	printf "\n$dashes\n *** execution finished \n"
2284
2285	fi
2286
2287
2288	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2289	# BY EACH CORE INTO ONE FILE
2290	if [[ ! -f combine_plot_fields.x ]]
2291	then
2292
2293	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2294	printf "\n 2d- and/or 3d-data may be incomplete!"
2295	printf "\n Your previous palmbuild may have failed. Please check.\n"
2296
2297	elif [[ "$combine_plot_fields" == true ]]
2298	then
2299
2300	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2301	$execute_command_for_combine
2302
2303	else
2304
2305	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2306	# DATA OUTPUT
2307	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2308	fi
2309
2310
2311
2312	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2313	(( i = 0 ))
2314	while (( i < ioc ))
2315	do
2316	(( i = i + 1 ))
2317	if (( i == 1 ))
2318	then
2319	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2320	fi
2321
2322	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2323	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2324
2325	printf "\n >>> ${out_command[$i]}"
2326	eval ${out_command[$i]}
2327	if (( i == ioc ))
2328	then
2329	printf "\n$dashes\n"
2330	fi
2331	done
2332
2333
2334	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2335	# WILDCARDS
2336	(( i = 0 ))
2337	(( nr_of_output_files = 0 ))
2338
2339	while (( i < iout ))
2340	do
2341
2342	(( i = i + 1 ))
2343
2344	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2345	# CREATE A LIST FOR THE DETECTED ENDINGS
2346	if [[ "${multout[$i]}" = true ]]
2347	then
2348	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2349	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2350	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2351
2352	endings="DEFAULT"
2353	while read line
2354	do
2355	# remove the local name from the beginning
2356	localnamestring="${localout_pre[$i]}"
2357	length_localname=${#localnamestring}
2358	ending=${line:${length_localname}}
2359
2360	if [[ "$ending" != "" ]]
2361	then
2362	endings="$endings $ending"
2363	fi
2364
2365	done <filelist
2366
2367	rm filelist
2368
2369	else
2370
2371	# SINGLE NAME
2372	endings=DEFAULT
2373
2374	fi
2375
2376	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2377	for ending in $endings
2378	do
2379
2380	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2381	if [[ $ending = DEFAULT ]]
2382	then
2383	ending=""
2384	fi
2385
2386	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2387	(( nr_of_output_files = nr_of_output_files + 1 ))
2388	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2389	transout[$nr_of_output_files]="${transout_pre[$i]}"
2390	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2391	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2392	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2393	extout[$nr_of_output_files]="${extout_pre[$i]}"
2394	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2395
2396	done
2397
2398	done
2399
2400
2401
2402
2403	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2404	(( i = 0 ))
2405	while (( i < nr_of_output_files ))
2406	do
2407	(( i = i + 1 ))
2408	if (( i == 1 ))
2409	then
2410	printf "\n\n *** saving OUTPUT-files:"
2411
2412	# GET RUN NUMBER ASSIGNED BY PALM
2413	if [[ -f RUN_NUMBER ]]
2414	then
2415	read run_number < RUN_NUMBER
2416	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2417	usecycle_option="-U $run_number"
2418	else
2419	run_number=0
2420	usecycle_option=""
2421	fi
2422	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2423	then
2424	printf "\n *** in case of SCP transfers to local host"
2425	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2426	fi
2427	printf "\n$dashes"
2428	fi
2429
2430	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2431	then
2432
2433	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2434
2435	# DETERMINE THE CYCLE NUMBER
2436	ls -1 -d $filename > filelist 2>/dev/null
2437	ls -1 -d $filename.* >> filelist 2>/dev/null
2438	while read line
2439	do
2440
2441	# filename without path (i.e. after the last "/")
2442	basefilename=$(basename ${line})
2443
2444	# check if there is an extension
2445	extension=${basefilename##*.}
2446	if [[ "$extension" = "${extout[$i]}" ]]
2447	then
2448	basefilename=${basefilename%.*}
2449	fi
2450
2451	# check for an existing cycle number
2452	cycle=${basefilename##*.}
2453	if [[ $cycle =~ ^-?[0-9]+$ ]]
2454	then
2455	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2456	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2457	(( icycle = $((10#$cycle)) + 1 ))
2458	else
2459	(( icycle = 1 ))
2460	fi
2461
2462	if (( icycle > maxcycle ))
2463	then
2464	(( maxcycle = icycle ))
2465	fi
2466
2467	done <filelist
2468	rm filelist
2469
2470
2471	# SET THE CYCLE NUMBER
2472	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2473	if [[ "${actionout[$i]}" = a ]]
2474	then
2475	(( maxcycle = maxcycle - 1 ))
2476	fi
2477
2478	(( cycnum[$i] = maxcycle ))
2479	pathout[$i]=$filename
2480
2481
2482	# ADD CYCLE NUMBER TO FILENAME
2483	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2484	if [[ "${actionout[$i]}" != "a" ]]
2485	then
2486	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2487	# WITH AN EXISTING CYCLE NUMBER
2488	if (( run_number >= cycnum[$i] ))
2489	then
2490	(( cycnum[$i] = run_number ))
2491	else
2492	if (( run_number > 0 ))
2493	then
2494	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2495	fi
2496	fi
2497	fi
2498	if (( cycnum[$i] > 0 ))
2499	then
2500	cyclestring=`printf "%03d" ${cycnum[$i]}`
2501	pathout[$i]=${pathout[$i]}.$cyclestring
2502	fi
2503	fi
2504
2505	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2506	files_for_cores=false; filetype=file
2507	link_local_output=false
2508	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2509	then
2510	files_for_cores=true; filetype=directory
2511	actionout[$i]=""
2512	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2513	then
2514	actionout[$i]=""
2515	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2516	then
2517	files_for_cores=true; filetype=directory
2518	link_local_output=true
2519	actionout[$i]=""
2520	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2521	then
2522	link_local_output
2523	actionout[$i]=""
2524	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2525	then
2526	files_for_cores=true; filetype=directory
2527	actionout[$i]="tr"
2528	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2529	then
2530	actionout[$i]="tr"
2531	fi
2532
2533	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2534	then
2535	if [[ ${warnout[$i]} = true ]]
2536	then
2537	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2538	fi
2539	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2540	then
2541	if [[ ${warnout[$i]} = true ]]
2542	then
2543	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2544	fi
2545	else
2546
2547
2548	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2549	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2550	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2551	then
2552	if [[ $running_on_remote = true ]]
2553	then
2554
2555	# SET OPTIONS FOR TRANSFER
2556	if [[ "${actionout[$i]}" = tr ]]
2557	then
2558	if [[ $files_for_cores = false ]]
2559	then
2560	catalog_option=""
2561	catalog_string=""
2562	else
2563	catalog_option="-c"
2564	catalog_string="/"
2565	fi
2566	append_option=""
2567	append_string=""
2568	else
2569	append_option="-A"
2570	append_string="append"
2571	fi
2572
2573	transfer_failed=false
2574	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2575	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2576
2577	# TRANSFER VIA SCP
2578	if [[ "$remote_loginnode" != "" ]]
2579	then
2580	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]}"
2581	else
2582	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]}
2583	fi
2584	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2585
2586
2587	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2588	if [[ $transfer_failed = true ]]
2589	then
2590	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2591	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2592
2593	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2594	eval local_catalog=${pathout[$i]}
2595	if [[ ! -d $local_catalog ]]
2596	then
2597	printf " *** local directory does not exist. Trying to create:\n"
2598	printf " $local_catalog \n"
2599	mkdir -p $local_catalog
2600	fi
2601	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2602	transfer_problems=true
2603	fi
2604
2605	else
2606
2607	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2608	# BE COPIED OR APPENDED ON THIS MACHINE
2609	if [[ "${actionout[$i]}" = tr ]]
2610	then
2611	actionout[$i]=""
2612	else
2613	actionout[$i]="a"
2614	fi
2615	fi
2616	fi
2617
2618
2619	# APPEND ON THIS MACHINE
2620	if [[ "${actionout[$i]}" = "a" ]]
2621	then
2622	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2623	then
2624	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2625	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2626	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2627	else
2628	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2629	printf "\n ${pathout[$i]}\n"
2630	cat ${localout[$i]} >> ${pathout[$i]}
2631	fi
2632	fi
2633
2634	# COPY ON THIS MACHINE
2635	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2636	# ON DIFFERENT FILE-SYSTEMS
2637	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2638	then
2639
2640	# COPY IN CASE OF RUNS ON SINGLE CORES
2641	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2642	then
2643	printf "\n >>> OUTPUT: ${localout[$i]} to"
2644	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2645	if [[ $link_local_output = true ]]
2646	then
2647	printf " file will be linked\n"
2648	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2649	fi
2650	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2651	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2652	then
2653	if [[ $link_local_output = true ]]
2654	then
2655	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2656	fi
2657	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2658	else
2659	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2660	fi
2661	else
2662	printf "\n >>> OUTPUT: ${localout[$i]} to"
2663	printf "\n ${pathout[$i]}\n"
2664	if [[ $link_local_output = true ]]
2665	then
2666	printf " file will be linked\n"
2667	ln -f ${localout[$i]} ${pathout[$i]}
2668	fi
2669	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2670	if [[ ! -f "${pathout[$i]}" ]]
2671	then
2672	if [[ $link_local_output = true ]]
2673	then
2674	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2675	fi
2676	cp ${localout[$i]} ${pathout[$i]}
2677	else
2678	printf "+++ no copy because file ${pathout[$i]} exists\n"
2679	fi
2680	fi
2681
2682	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2683	then
2684
2685	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2686	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2687	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2688	printf "\n ${pathout[$i]}\n"
2689	if [[ $link_local_output = true ]]
2690	then
2691	printf " files will be linked\n"
2692	mkdir -p ${pathout[$i]}
2693	cd ${localout[$i]}
2694	for file in $(ls *)
2695	do
2696	ln -f $file ${pathout[$i]}
2697	done >\|/dev/null 2>&1
2698	cd $tempdir
2699	fi
2700
2701	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2702	if [[ ! -f "${pathout[$i]}/_000000" ]]
2703	then
2704	if [[ $link_local_output = true ]]
2705	then
2706	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2707	fi
2708	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2709	cp -r ${localout[$i]}/* ${pathout[$i]}
2710	fi
2711
2712	fi
2713	fi
2714	done
2715
2716	if (( i != 0 ))
2717	then
2718	if [[ $transfer_problems = true ]]
2719	then
2720	printf "\n$dashes\n *** OUTPUT-files saved"
2721	printf "\n +++ WARNING: some data transfers failed! \n"
2722	else
2723	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2724	fi
2725	fi
2726
2727
2728	# IF REQUIRED, START A RESTART-JOB
2729	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2730	if [[ -f CONTINUE_RUN ]]
2731	then
2732
2733	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2734	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2735	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2736	# -b START A BATCH JOB
2737	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2738	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2739	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2740
2741	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2742	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2743	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2744	then
2745	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2746	fi
2747
2748	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2749	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2750	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2751	then
2752	prc=`echo $prc \| sed 's/#/r/g'`
2753	fi
2754
2755
2756	# START THE RESTART-JOB
2757	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2758	echo " $prc"
2759	printf "\n$dashes\n"
2760	if [[ $running_on_remote = true ]]
2761	then
2762
2763	echo "*** ssh will be used to initiate restart-runs!"
2764	echo " return_address=\"$return_address\" "
2765	echo " return_username=\"$local_username\" "
2766
2767	if [[ "$remote_loginnode" != "" ]]
2768	then
2769	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
2770	else
2771	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2772	fi
2773
2774	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2775	sleep 30
2776
2777	else
2778
2779	# START THE RESTART JOB ON THE LOCAL HOST
2780	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2781	cd - > /dev/null
2782
2783	fi
2784
2785	# CHECK, IF RESTART JOB HAS BEEN STARTED
2786	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2787	then
2788	printf "\n$dashes\n +++ creating restart run failed \n"
2789	locat=create_restart
2790	rm palmrun_restart.log
2791	exit
2792	else
2793	printf "\n$dashes\n *** restart run initiated \n"
2794	rm palmrun_restart.log
2795	fi
2796
2797
2798	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2799	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2800	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2801	# MAY BE VERY HUGE)
2802	(( i = 0 ))
2803	while (( i < nr_of_input_files ))
2804	do
2805	(( i = i + 1 ))
2806	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2807	then
2808	rm -r ${absnamein[$i]}
2809	fi
2810	done
2811
2812	fi
2813
2814
2815	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2816	cd $HOME
2817	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2818
2819
2820	else
2821
2822
2823	# PREPARING ACTIONS,
2824	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2825
2826	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2827	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2828	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2829	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2830	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2831	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2832	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2833	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2834	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2835	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2836	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2837	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2838	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2839	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2840	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2841	if [[ $create_remote_batch_job = true ]]
2842	then
2843	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2844	if [[ $do_trace = true ]]
2845	then
2846	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2847	fi
2848	elif [[ $create_batch_job = true ]]
2849	then
2850	palmrun_com=${palmrun_com}" -j"
2851	if [[ $do_trace = true ]]
2852	then
2853	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2854	fi
2855	fi
2856
2857
2858	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2859	# REMOTE HOST
2860	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2861	job_protocol_file=$job_protocol_file_local
2862	if [[ $create_remote_batch_job = true ]]
2863	then
2864	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2865	job_protocol_file=$job_protocol_file_remote
2866	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2867	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2868	fi
2869
2870
2871	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2872	jobfile=jobfile.$run_id_number
2873
2874
2875	# FIRST CREATE THE BATCH DIRECTIVES
2876	(( i = 0 ))
2877	while (( i < ibd ))
2878	do
2879	(( i = i + 1 ))
2880	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2881	eval line=\"$line\"
2882	echo "$line" >> $jobfile
2883	done
2884	echo " " >> $jobfile
2885
2886
2887	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2888	# PROTOCOL
2889	if [[ $create_remote_batch_job = true ]]
2890	then
2891	echo "set +vx" >> $jobfile
2892	echo "trap '" >> $jobfile
2893	echo "set +vx" >> $jobfile
2894	echo "cd ${remote_jobcatalog}" >> $jobfile
2895	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2896
2897	# ADD THE BATCH DIRECTIVES
2898	(( i = 0 ))
2899	while (( i < ibdt ))
2900	do
2901	(( i = i + 1 ))
2902	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2903	eval line=\"$line\"
2904	echo "$line" >> $jobfile
2905	done
2906	echo " " >> $jobfile
2907
2908	echo "set -x" >> $jobfile
2909	if [[ "$remote_loginnode" != "" ]]
2910	then
2911	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}\" " >> $jobfile
2912	else
2913	echo "${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
2914	fi
2915	echo "%%END%%" >> $jobfile
2916	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2917	echo "$submit_command $scpjob_file" >> $jobfile
2918	echo "rm $scpjob_file" >> $jobfile
2919	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2920	echo "set -x" >> $jobfile
2921	echo " ' exit" >> $jobfile
2922	fi
2923
2924
2925	# ACTIVATE ERROR-TRACEBACK
2926	if [[ $do_trace = true ]]
2927	then
2928	echo "set -x" >> $jobfile
2929	else
2930	echo "set +vx" >> $jobfile
2931	fi
2932
2933
2934	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2935	if [[ "$login_init_cmd" != "" ]]
2936	then
2937	echo "$login_init_cmd" >> $jobfile
2938	fi
2939	if [[ "$module_commands" != "" ]]
2940	then
2941	echo "$module_commands" >> $jobfile
2942	fi
2943
2944
2945	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2946	if [[ $create_remote_batch_job = true ]]
2947	then
2948	echo "mkdir $tempdir" >> $jobfile
2949	echo "chmod go+rx $tempdir" >> $jobfile
2950	else
2951	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2952	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2953	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2954	mkdir $tempdir
2955	chmod go+rx $tempdir
2956	fi
2957	echo "cd $tempdir" >> $jobfile
2958	echo "export tempdir=$tempdir" >> $jobfile
2959	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2960	echo "export PATH=.:\$PATH" >> $jobfile
2961	echo "export execute_palmrun=true" >> $jobfile
2962
2963
2964	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2965	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2966	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2967	echo "LOCAL_PWD=$working_directory" >> $jobfile
2968	echo "export LOCAL_PWD" >> $jobfile
2969
2970
2971	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2972	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2973	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2974
2975
2976	# CALL PALMRUN WITHIN THE JOB
2977	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2978	echo "set -x" >> $jobfile
2979	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2980
2981
2982	# TRANSFER JOBFILE TO THE TARGET HOST
2983	if [[ $create_jobfile_only = false ]]
2984	then
2985
2986	# CREATE LOCAL JOB FOLDER
2987	eval local_jobcatalog=$local_jobcatalog
2988	if [[ ! -d $local_jobcatalog ]]
2989	then
2990	echo " "
2991	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
2992	mkdir $local_jobcatalog
2993	fi
2994
2995	if [[ $create_remote_batch_job = true ]]
2996	then
2997
2998	echo " "
2999	echo " *** transfer of job to remote host via scp"
3000
3001	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3002	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
3003
3004	# COPY THE JOB FILE
3005	if [[ $do_trace = true ]]
3006	then
3007	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
3008	fi
3009	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
3010
3011	# SUBMIT THE JOB
3012	printf " *** submit the job (output of submit command, e.g. the job-id, may follow) \n"
3013	if [[ $do_trace = true ]]
3014	then
3015	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"
3016	fi
3017	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
3018
3019	elif [[ $create_batch_job = true ]]
3020	then
3021
3022	eval local_jobcatalog=$local_jobcatalog
3023	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3024	cd $local_jobcatalog
3025	echo " "
3026	echo " *** submit the job"
3027	if [[ $do_trace = true ]]
3028	then
3029	echo "$submit_command ${configuration_identifier}_${run_id}"
3030	fi
3031	$submit_command ${configuration_identifier}_${run_id}
3032	rm ${configuration_identifier}_${run_id}
3033	cd - > /dev/null
3034
3035	fi
3036
3037	rm -rf $jobfile
3038
3039	else
3040
3041	printf "\n *** jobfile created under name \"$jobfile\" "
3042	printf "\n no batch-job has been sent!"
3043
3044	fi
3045
3046	fi # END OF REMOTE-PART

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