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source: palm/trunk/SCRIPTS/palmrun @ 3538

Last change on this file since 3538 was 3534, checked in by raasch, 6 years ago
inifor integrated in build mechanism, some bugfixes in inifor to avoid compile time errors, batch_scp for sending back the job protocol file is called via login-node if a login-node has been set in the config-file, ssh-calls rearranged to avoid output of system/user-profile messages
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.3 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 3534 2018-11-19 15:35:16Z suehring $
29	# batch_scp for sending back the job protocol file is called via login-node if
30	# a login-node has been set in the config-file
31	# ssh-calls rearranged to avoid output of system/user-profile messages
32	#
33	# 3505 2018-11-08 09:14:30Z raasch
34	# job folders are created in case that they do not exist
35	#
36	# 3455 2018-10-30 14:12:31Z raasch
37	# options -h and -d renamed -c and -r, respectively
38	#
39	# 3402 2018-10-23 11:49:24Z knoop
40	# job_id is set for compatibility reasons with older versions of config files
41	#
42	# 3313 2018-10-06 15:22:48Z knoop
43	# more detailed error message for outdated fileconnection file
44	#
45	# 3236 2018-09-10 09:07:06Z raasch
46	# warning issued in case of file connection file version mismatch,
47	# host_configuration renamed configuration_identifier,
48	# "host identifier" in header output renamed "config. identifier",
49	# jobname renamed run_identifier,
50	# run_id renamed run_id_number
51	# job_id renamed run_id
52	# option -r renamed -i
53	#
54	# 3151 2018-07-19 08:45:38Z raasch
55	# removed additional listing of files to be compiled, print PALM code revision
56	# in header
57	#
58	# 3132 2018-07-16 11:44:58Z raasch
59	# create consistent error messages in case of failed restarts,
60	# check existence of remote job catalog
61	#
62	# 3043 2018-05-25 10:47:54Z raasch
63	# check for setting of fast_io_catalog
64	#
65	# 3033 2018-05-23 15:26:19Z raasch
66	# -T option not required for interactive runs (tasks per node =
67	# total number of cores is assumed as default, if option is not given),
68	# reformatting of a few messages,
69	# bugfix: destination output directory is created if attribute "pe" is set in
70	# .palm.iofiles
71	#
72	# 2718 2018-01-02 08:49:38Z maronga
73	# bugfix of r2990
74	#
75	# 2718 2018-01-02 08:49:38Z maronga
76	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
77	# not in the working directory from where palmrun is called
78	#
79	# 2718 2018-01-02 08:49:38Z maronga
80	# svfout in the activation string will be replaced now by svfin in case of
81	# automatic restarts
82	#
83	# 2718 2018-01-02 08:49:38Z maronga
84	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
85	# the possible output or input of sky view factors
86	#
87	# 2718 2018-01-02 08:49:38Z maronga
88	# "fname" renamed to "jobname"
89	#
90	# 2718 2018-01-02 08:49:38Z maronga
91	# parameters are allowed in output commands (OC:)
92	#
93	# 2718 2018-01-02 08:49:38Z maronga
94	# bugfix: exit if no queue has been given neither with option -q nor in the
95	# configuration file
96	#
97	# 2718 2018-01-02 08:49:38Z maronga
98	# file connection file from trunk/SCRIPTS is taken by default
99	#
100	# 2718 2018-01-02 08:49:38Z maronga
101	# Corrected "Former revisions" section
102	#
103	# 2696 2017-12-14 17:12:51Z kanani
104	# Change in file header (GPL part)
105	#
106	# 2693 2017-12-13 12:33:49Z raasch
107	# replacement of variables given by {{<variable>}} in configuration file is now
108	# done in a more general way, variable names are written in small letters
109	#
110	# 2670 2017-12-06 16:32:19Z raasch
111	# test printouts removed
112	#
113	# 2669 2017-12-06 16:03:27Z raasch
114	# file attributes in .palm.iofiles restructured, "loc" attribute completely
115	# removed,
116	# wildcard (*) allowed in .palm.iofiles as file activation string for output
117	# files,
118	# informative messages in case of missing optional input files shortened
119	# bugfix: variable cycle explicitly interpreted with 10 as the number base
120	#
121	# 2638 2017-11-23 12:44:23Z raasch
122	# use of wildcards in file connection statements enabled
123	#
124	# 2605 2017-11-09 15:31:46Z raasch
125	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
126	# will not be sent with the job file any more, but copied into the
127	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
128	#
129	# 2600 2017-11-01 14:11:20Z raasch
130	# cycle numbers are made three digits wide
131	#
132	# 2566 2017-10-20 08:50:47Z raasch
133	# execute command for combine_plot_fields added
134	# "TEMPDIR" renamed "tempdir"
135	# temporary working directory for local batch jobs is created immediately within
136	# the user's palmrun call, due to a requirement of the "grid engine" batch
137	# system, where the working directory is given with batch directive -wd and must
138	# already exist when the job is submitted,
139	# informative messages in non-trace mode reduced and partly reformatted
140	#
141	# 2551 2017-10-18 07:25:11Z raasch
142	# TEMPDIR added as replacement string to be used in batch directives
143	#
144	# 2512 2017-10-04 08:26:59Z raasch
145	# bugfix for determining cycle numbers of NetCDF input files
146	#
147	# 2506 2017-09-29 08:30:37Z raasch
148	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
149	# host configuration added to SOURCES_FOR_RUN_... folder name
150	# host_identifier renamed host_configuration
151	# option -W added to allow for job dependencies
152	#
153	# 2501 2017-09-26 11:41:55Z raasch
154	# default value for number of cores (option -X) set to 1
155	# bugfix for mechanism which overwrites configuration file settings with values
156	# provided by palmrun options
157	#
158	# 2499 2017-09-22 16:47:58Z kanani
159	# option -h named configuration identifier
160	#
161	# 2480 2017-09-19 06:24:14Z maronga
162	# bugfix for last revision
163	#
164	# 2479 2017-09-19 06:12:16Z raasch
165	# option -A (project account number) added
166	#
167	# 2422 2017-09-08 08:25:41Z raasch
168	# initial revision
169	#
170	#--------------------------------------------------------------------------------#
171	# palmrun - script for running PALM jobs on local and remote hosts
172	#--------------------------------------------------------------------------------#
173
174
175
176	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
177
178	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
179	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
180	# (TOO MANY ARGUMENTS - PROBLEM)
181	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
182
183	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
184	typeset -i nr_of_output_files=0
185	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
186	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
187	# SCRIPT-OPTION ARGUMENTS
188	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
189	typeset -i icycle inode ival maxcycle mpi_tasks
190	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
191
192	activation_string_list=""
193	AddFilenames=""
194	combine_plot_fields=true
195	compiler_name=""
196	compiler_name_ser=""
197	compiler_options=""
198	configuration_identifier="default"
199	cores=1
200	cores_atmos=0
201	cores_ocean=0
202	coupled_dist=""
203	cpp_options=""
204	cpumax=0
205	create_batch_job=false
206	create_jobfile_only=false
207	create_remote_batch_job=false
208	dashes=" ----------------------------------------------------------------------------"
209	defaultqueue=""
210	delete_temporary_catalog=true
211	do_compile=true
212	do_trace=false
213	executable=""
214	execute_command=""
215	execution_error=false
216	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
217	global_revision=""
218	hostfile=""
219	hp=""
220	keep_data_from_previous_run=false
221	link_local_input=false
222	link_local_output=false
223	linker_options=""
224	local_jobcatalog=""
225	locat=normal
226	makefile=""
227	max_par_io_str=""
228	prc=$0
229	while [[ $(echo $prc \| grep -c "/") != 0 ]]
230	do
231	prc=`echo $prc \| cut -f2- -d"/"`
232	done
233	module_calls=""
234	palmrun_memory=""
235	palmrun_script_name=$prc
236	openmp=false
237	previous_job=""
238	project_account=""
239	queue=none
240	read_svf=""
241	restart_run=false
242	return_address=""
243	remote_jobcatalog=""
244	remote_username=""
245	running_in_batch_mode=false
246	running_in_test_mode=false
247	run_coupled_model=false
248	run_id=""
249	run_id_number=""
250	run_identifier=test
251	silent=false
252	source_list=""
253	source_path=""
254	tasks_per_node=0
255	threads_per_task=1
256	transfer_problems=false
257	user_source_path=""
258	use_existing_sources_folder=""
259	use_openmp=false
260	version="palmrun 1.0 Rev$Rev: 3534 $"
261	working_directory=`pwd`
262	write_binary=""
263	write_svf=""
264
265
266	# ERROR HANDLING IN CASE OF EXIT
267	trap 'if [[ $locat != normal && $locat != control_c ]]
268	then
269
270	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
271	(( i = 0 ))
272	while (( i < iec ))
273	do
274	(( i = i + 1 ))
275	printf "\n *** Execution of ERROR-command:\n"
276	printf " >>> ${err_command[$i]}\n"
277	eval ${err_command[$i]}
278	done
279	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
280	printf "\n\n+++ palmrun crashed \n\n"
281	exit 1
282	elif [[ $locat != normal ]]
283	then
284	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
285	printf "\n+++ palmrun killed by \"^C\" \n\n"
286	exit 2
287	else
288	printf "\n --> palmrun finished\n\n"
289	exit 0
290	fi' exit
291
292
293	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
294	trap 'locat=control_c
295	exit 1
296	' 2
297
298
299	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
300	# WHICH WILL BE USED TO START RESTART-JOBS
301	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
302	do
303	case $option in
304	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
305	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
306	(b) create_batch_job=true; prc="$prc -b";;
307	(B) delete_temporary_catalog=false; prc="$prc -B";;
308	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
309	(C) restart_run=true; prc="$prc -C";;
310	(F) create_jobfile_only=true;;
311	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
312	(i) run_id_number=$OPTARG;;
313	(j) running_in_batch_mode=true;;
314	(k) keep_data_from_previous_run=true; prc="$prc -k";;
315	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
316	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
317	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
318	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
319	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
320	(R) return_address=$OPTARG;;
321	(s) source_list=$OPTARG;;
322	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
323	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
324	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
325	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
326	(v) silent=true; prc="$prc -v";;
327	(V) use_existing_sources_folder="-V";;
328	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
329	(W) previous_job=$OPTARG;;
330	(x) do_trace=true;set -x; prc="$prc -x";;
331	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
332	(y) ocean_file_appendix=true; prc="$prc -y";;
333	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
334	(z) running_in_test_mode=true;;
335	(Z) combine_plot_fields=false; prc="$prc -Z";;
336	(\?) printf "\n +++ unknown option $OPTARG \n"
337	printf "\n --> type \"$0 ?\" for available options \n"
338	locat=parameter;exit;;
339	esac
340	done
341
342
343	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
344	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
345	(( to_shift = $OPTIND - 1 ))
346	shift $to_shift
347
348	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
349	if [[ "$1" = "?" ]]
350	then
351	(printf "\n *** Description of available palmrun options:\n"
352	printf "\n Option Description Default-Value"
353	printf "\n -a activation string list \"\" "
354	printf "\n -A project account number ---"
355	printf "\n -b batch-job on local machine ---"
356	printf "\n -B do not delete temporary directory at end ---"
357	printf "\n -c configuration identifier \"default\" "
358	printf "\n -F create batch job file only ---"
359	printf "\n -k keep data from previous run"
360	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
361	printf "\n -M Makefile name Makefile"
362	printf "\n -O threads per openMP task ---"
363	printf "\n -q queue \"$queue\" "
364	printf "\n -r run identifier test"
365	printf "\n -s filenames of routines to be compiled \"\" "
366	printf "\n must end with .f, .f90, .F, or .c !"
367	printf "\n use \"..\" for more than one file and wildcards"
368	printf "\n -s LM compiles all locally modified files"
369	printf "\n -t allowed cpu-time in seconds (batch) 0"
370	printf "\n -T tasks per node ---"
371	printf "\n -u username on remote machine \"\" "
372	printf "\n -v no prompt for confirmation ---"
373	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
374	printf "\n -w maximum parallel io streams as given by -X"
375	printf "\n -W name of job to wait for ---"
376	printf "\n -x tracing of palmrun for debug purposes ---"
377	printf "\n -X # of processors (on parallel machines) 1"
378	printf "\n -y add appendix \"_O\" to all local output"
379	printf "\n files (ocean precursor runs followed by"
380	printf "\n coupled atmosphere-ocean runs) ---"
381	printf "\n -Y run coupled model, \"#1 #2\" with"
382	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
383	printf "\n -Z skip combine_plot_fields at the end of "
384	printf "\n the simulation ---"
385	printf "\n "
386	printf "\n Possible values of positional parameter <modus>:"
387	printf "\n \"?\" - this outline \n\n") \| more
388	exit
389	elif [[ "$1" != "" ]]
390	then
391	printf "\n +++ positional parameter $1 unknown \n"
392	locat=parameter; exit
393	fi
394
395
396
397	# SHORT STARTING MESSAGE
398	printf "\n*** $version "
399	printf "\n will be executed. Please wait ..."
400
401
402	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
403	config_file=.palm.config.$configuration_identifier
404	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
405
406
407	# CHECK, IF CONFIGURATION FILE EXISTS
408	if [[ ! -f $config_file ]]
409	then
410	printf "\n\n +++ configuration file: "
411	printf "\n $config_file"
412	printf "\n does not exist"
413	locat=connect; exit
414	fi
415
416
417	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
418	if [[ -f .palm.iofiles ]]
419	then
420
421	# CHECK VERSION MISMATCH
422	if [[ $running_in_batch_mode != true ]]
423	then
424	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
425	then
426	printf "\n\n +++ WARNING: A file connection file has been found in your"
427	printf "\n working directory, but its revision does not match"
428	printf "\n the revision of the default (trunk) version."
429	printf "\n You may need to update your connection file"
430	printf "\n \"${working_directory}/.palm.iofiles\" !"
431	fi
432	fi
433
434	fileconnection_file=.palm.iofiles
435
436	fi
437
438
439	# CHECK, IF FILE CONNECTION FILE EXISTS
440	if [[ ! -f $fileconnection_file ]]
441	then
442	printf "\n\n +++ file connection file: "
443	printf "\n $fileconnection_file"
444	printf "\n does not exist"
445	locat=connect; exit
446	fi
447
448
449	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
450	if [[ "$activation_string_list" = "" ]]
451	then
452	printf "\n\n +++ no activation string list given: "
453	printf "\n please set palmrun option \"-a\" "
454	locat=palmrun_option; exit
455	fi
456
457
458	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
459	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
460	then
461	write_binary=true
462	else
463	write_binary=false
464	fi
465
466	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
467	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
468	then
469	write_svf=true
470	else
471	write_svf=false
472	fi
473
474	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
475	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
476	then
477	read_svf=true
478	else
479	read_svf=false
480	fi
481
482
483	# READ AND EVALUATE THE CONFIGURATION-FILE
484	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
485
486	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
487	while read line
488	do
489
490	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
491	eval line=\"$line\"
492
493
494	# INTERPRET THE LINE
495	if [[ "$(echo $line)" = "" ]]
496	then
497
498	# EMPTY LINE, NO ACTION
499	continue
500
501	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
502	then
503
504	# LINE IS A COMMENT LINE
505	continue
506
507	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
508	then
509
510	# LINE DEFINES AN ENVIRONMENT-VARIABLE
511	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
512	value=`echo $line \| cut -d" " -s -f2-`
513
514
515	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
516	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
517	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
518	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
519	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
520	# CONFIGURATION-FILE.
521	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
522	then
523	eval export $var="\$value"
524
525	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
526	if [[ $do_trace = true ]]
527	then
528	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
529	fi
530	fi
531
532	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
533	then
534
535	# LINE DEFINES BATCH-DIRECTIVE
536	(( ibd = ibd + 1 ))
537	line=$(echo $line \| cut -c4-)
538	batch_directive[$ibd]="$line"
539
540	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
541	then
542
543	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
544	# REMOTE TO A LOCAL HOST
545	(( ibdt = ibdt + 1 ))
546	line=$(echo $line \| cut -c5-)
547	batch_directive_transfer[$ibdt]="$line"
548
549	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
550	then
551
552	# LINE DEFINES ERROR-COMMAND
553	(( iec = iec + 1 ))
554	line=$(echo $line \| cut -c4-)
555	err_command[$iec]="$line"
556
557	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
558	then
559
560	# LINE DEFINES INPUT-COMMAND
561	(( iic = iic + 1 ))
562	line=$(echo $line \| cut -c4-)
563	in_command[$iic]="$line"
564
565	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
566	then
567
568	# LINE DEFINES OUTPUT-COMMAND
569	(( ioc = ioc + 1 ))
570	line=$(echo $line \| cut -c4-)
571	out_command[$ioc]="$line"
572
573	else
574
575	# SKIP ALL OTHER LINES
576	continue
577
578	fi
579
580	done < $config_file
581
582
583	# CHECK SETTING OF REQUIRED PARAMETERS
584	if [[ "$fast_io_catalog" = "" ]]
585	then
586	printf "\n +++ no fast_io_catalog found in $config_file"
587	printf "\n Please add line \"fast_io_catalog ...\" to that file."
588	locat=config_file; exit
589	fi
590	if [[ "$compiler_name" = "" ]]
591	then
592	printf "\n +++ no compiler name found in $config_file"
593	printf "\n Please add line \"compiler_name ...\" to that file."
594	locat=config_file; exit
595	fi
596	if [[ "$compiler_name_ser" = "" ]]
597	then
598	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
599	printf "\n Please add line \"compiler_name_ser ...\" to that file."
600	locat=config_file; exit
601	fi
602	if [[ "$compiler_options" = "" ]]
603	then
604	printf "\n +++ no compiler options found in $config_file"
605	printf "\n Please add line \"compiler_options ...\" to that file."
606	locat=config_file; exit
607	fi
608	if [[ "$linker_options" = "" ]]
609	then
610	printf "\n +++ no linker options found in $config_file"
611	printf "\n Please add line \"linker_options ...\" to that file."
612	locat=config_file; exit
613	fi
614	if [[ "$execute_command" = "" ]]
615	then
616	printf "\n +++ no execute command found in $config_file"
617	printf "\n Please add line \"execute_command ...\" to that file."
618	locat=config_file; exit
619	fi
620
621	if [[ "$hostfile" != "" ]]
622	then
623	if [[ $hostfile != auto && ! -f $hostfile ]]
624	then
625	printf "\n +++ no hostfile \"$hostfile\" found"
626	printf "\n Please check line \"hostfile ...\" in $config_file"
627	locat=config_file; exit
628	fi
629	fi
630
631
632	# DETERMINE THE CALL STATUS
633	if [[ "$return_address" != "" ]]
634	then
635
636	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
637	# BATCH MODE AND ...
638	running_on_remote=true
639
640	else
641
642	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
643	if [[ "$remote_ip" != "" ]]
644	then
645
646	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
647	create_remote_batch_job=true
648
649	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
650	if [[ "$remote_jobcatalog" = "" ]]
651	then
652	printf "\n +++ no remote jobcatalog found in $config_file"
653	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
654	locat=config_file; exit
655	fi
656
657
658	fi
659	running_on_remote=false
660	fi
661
662
663
664	# READ AND EVALUATE THE I/O-FILE LIST
665	[[ $silent = false ]] && printf "\n Reading the I/O files... "
666
667	# READ THE FILE CONNECTION FILE LINE BY LINE
668	while read line
669	do
670
671	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
672	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
673
674	# INTERPRET THE LINE
675	if [[ "$(echo $line)" = "" ]]
676	then
677	# EMPTY LINE, NO ACTION
678	continue
679
680	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
681	then
682
683	# LINE IS A COMMENT LINE
684	true
685
686	else
687
688	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
689	# s2a: in/out - field
690	# s2b: action - field (optional)
691	s1=`echo "$line" \| cut -d" " -f1`
692	s2=`echo "$line" \| cut -d" " -s -f2`
693	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
694	then
695	s2a=$s2
696	s2b=""
697	else
698	s2a=`echo $s2 \| cut -d":" -f1`
699	s2b=`echo $s2 \| cut -d":" -f2`
700	fi
701	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
702	s4=`echo "$line" \| cut -d" " -s -f4`
703	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
704	s5=`echo "$line" \| cut -d" " -s -f5`
705	s6=`echo "$line" \| cut -d" " -s -f6`
706
707
708	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
709	# INPUT- OR OUTPUT-LIST.
710	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
711	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
712	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
713	# IS NOT CHECKED AND STORED.
714	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
715	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
716	then
717	found=false
718	for actual in $activation_string_list
719	do
720	for formal in $s3
721	do
722	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
723	done
724	done
725	if [[ $found = true ]]
726	then
727	(( iin = iin + 1 ))
728	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
729	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
730	if [[ "$s2a" = inopt ]]
731	then
732	optin_pre[$iin]=yes
733	else
734	optin_pre[$iin]=no
735	fi
736
737	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
738	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
739	if [[ $running_on_remote = true && "$s2b" = tr ]]
740	then
741	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
742	fi
743
744	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
745	# THE WILDCARD FROM THE ENDING
746	if [[ "${s5: -1}" = "*" ]]
747	then
748	if [[ "$s2b" = "di" ]]
749	then
750	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
751	printf "\n see file \"$fileconnection_file\", line"
752	printf "\n$line"
753	locat=iofiles_file; exit
754	fi
755	multin[$iin]=true
756	string=${endin_pre[$iin]}
757	endin_pre[$iin]="${string%?}"
758	else
759	multin[$iin]=false
760	fi
761	fi
762	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
763	then
764	found=false
765	for actual in $activation_string_list
766	do
767	for formal in $s3
768	do
769	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
770	done
771	done
772	if [[ $found = true ]]
773	then
774	(( iout = iout + 1 ))
775	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
776	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
777
778	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
779	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
780	if [[ $formal = wildcard ]]
781	then
782	warnout_pre[$iout]=false
783	else
784	warnout_pre[$iout]=true
785	fi
786
787	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
788	# THE WILDCARD FROM THE LOCAL FILENAME
789	if [[ "${s1: -1}" = "*" ]]
790	then
791	if [[ "$s2b" = "di" ]]
792	then
793	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
794	printf "\n see file \"$fileconnection_file\", line"
795	printf "\n$line"
796	locat=iofiles_file; exit
797	fi
798	multout[$iout]=true
799	string=${localout_pre[$iout]}
800	localout_pre[$iout]="${string%?}"
801	else
802	multout[$iout]=false
803	fi
804	fi
805	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
806	then
807	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
808	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
809	locat=connect; exit
810	fi
811	IFS="$IFSALT"
812	fi
813
814	done < $fileconnection_file
815
816
817
818	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
819	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
820	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
821	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
822	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
823	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
824
825
826
827	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
828	if [[ $run_coupled_model = true ]]
829	then
830
831	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
832	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
833
834	if (( $cores_ocean + $cores_atmos != $cores ))
835	then
836
837	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
838	printf "\n PEs (total) : $cores"
839	printf "\n PEs (atmosphere): $cores_atmos"
840	printf "\n PEs (ocean) : $cores_ocean"
841	locat=coupling; exit
842
843	fi
844
845	fi
846
847
848	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
849	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
850	# FOLDER
851	if [[ $running_in_batch_mode = true ]]
852	then
853
854	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
855	then
856	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
857	printf "\n Please check the output of the palmrun-call"
858	printf "\n that you did on your local host."
859	locat=SOURCES_FOR_RUN; exit
860	fi
861
862	else
863
864	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
865	# AUTOMATIC RESTART RUN
866	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
867	if [[ $restart_run = false ]]
868	then
869
870	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
871	# THE LOCAL HOST
872	if [[ ! -d $source_path ]]
873	then
874	printf "\n\n +++ source path \"$source_path\" on local host"
875	printf "\n \"$(hostname)\" does not exist"
876	locat=source_path; exit
877	fi
878
879	rm -rf ${base_directory}/${sources_for_run_catalog}
880	mkdir -p ${base_directory}/${sources_for_run_catalog}
881
882	if [[ "$source_list" = LM ]]
883	then
884
885	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
886	source_list=""
887	cd $source_path
888
889
890	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
891	if [[ ! -d ../.svn ]]
892	then
893	printf "\n\n +++ source directory"
894	printf "\n \"$source_path\" "
895	printf "\n is not under control of \"subversion\"."
896	printf "\n Please do not use palmrun-option \"-s LM\"\n"
897	fi
898
899
900	# LIST ALL MODIFIED SOURCE CODE FILES
901	Filenames=""
902	svn status > tmp_svnstatus
903	while read line
904	do
905	firstc=`echo $line \| cut -c1`
906	if [[ $firstc = M \|\| $firstc = "?" ]]
907	then
908	Name=`echo "$line" \| cut -c8-`
909	extension=`echo $Name \| cut -d. -f2`
910	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
911	then
912	Filenames="$Filenames "$Name
913	fi
914	fi
915	done < tmp_svnstatus
916	rm -rf tmp_svnstatus
917
918
919	# COPY FILES TO SOURCES_FOR_RUN_...
920	for filename in $Filenames
921	do
922	cp $filename ${base_directory}/${sources_for_run_catalog}
923	source_list=$source_list"$filename "
924	done
925
926	cd - > /dev/null
927
928
929	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
930	elif [[ "$source_list" != "" ]]
931	then
932
933	cd $source_path
934
935	for filename in $source_list
936	do
937
938	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
939	if [[ $(echo $filename \| grep -c "/") != 0 ]]
940	then
941	printf "\n +++ source code file: $filename"
942	printf "\n must not contain (\"/\") "
943	locat=source; exit
944	fi
945
946	if [[ ! -f $filename ]]
947	then
948	printf "\n +++ source code file: $filename"
949	printf "\n does not exist"
950	locat=source; exit
951	else
952	cp $filename ${base_directory}/${sources_for_run_catalog}
953	fi
954
955	done
956
957	cd - > /dev/null
958
959	fi
960
961	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
962	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
963	if [[ ! -f $makefile ]]
964	then
965	printf "\n +++ file \"$makefile\" does not exist"
966	locat=make; exit
967	else
968	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
969	fi
970
971
972	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
973	if [[ "$user_source_path" != "" ]]
974	then
975
976	# DOES THE DIRECTORY EXIST?
977	if [[ ! -d $user_source_path ]]
978	then
979
980	printf "\n\n *** INFORMATIVE: additional source code directory"
981	printf "\n \"$user_source_path\" "
982	printf "\n does not exist or is not a directory."
983	printf "\n No source code will be used from this directory!\n"
984	user_source_path=""
985	if [[ $silent == false ]]
986	then
987	sleep 2
988	fi
989
990	else
991
992	cd $user_source_path
993
994	Names=$(ls -1 *.f90 2>&1)
995	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
996	Names=$(ls -1 *.F90 2>&1)
997	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
998	Names=$(ls -1 *.F 2>&1)
999	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1000	Names=$(ls -1 *.f 2>&1)
1001	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1002	Names=$(ls -1 *.c 2>&1)
1003	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1004
1005	cd - > /dev/null
1006	cd ${base_directory}/${sources_for_run_catalog}
1007
1008	# COPY MAKEFILE IF EXISTING
1009	if [[ -f $user_source_path/Makefile ]]
1010	then
1011	printf "\n\n *** user Makefile from directory"
1012	printf "\n \"$user_source_path\" is used \n"
1013	if [[ $silent == false ]]
1014	then
1015	sleep 1
1016	fi
1017	cp $user_source_path/Makefile .
1018	fi
1019
1020	for filename in $AddFilenames
1021	do
1022	if [[ -f $filename ]]
1023	then
1024	printf "\n +++ source code file \"$filename\" found in additional"
1025	printf "\n source code directory \"$user_source_path\" "
1026	printf "\n but was also given with option \"-s\" which means that it should be taken"
1027	printf "\n from directory \"$source_path\"."
1028	locat=source; exit
1029	fi
1030
1031	cp $user_source_path/$filename .
1032	source_list="$source_list $filename"
1033
1034	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1035	if [[ $(grep -c $filename Makefile) = 0 ]]
1036	then
1037	printf "\n\n +++ user file \"$filename\" "
1038	printf "\n is not listed in Makefile \n"
1039	locat=source; exit
1040	fi
1041	done
1042	cd - > /dev/null
1043	fi
1044	fi
1045
1046	# COPY CONFIGURATION FILES
1047	cp $config_file ${base_directory}/${sources_for_run_catalog}
1048	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1049
1050	# COPY SHELLSCRIPTS
1051	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1052	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1053
1054	fi
1055
1056	fi
1057
1058
1059	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1060	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1061	if [[ "$global_revision" = "" ]]
1062	then
1063	global_revision=`svnversion $source_path 2>/dev/null`
1064	global_revision="Rev: $global_revision"
1065	fi
1066
1067
1068	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1069	if [[ -n $cores ]]
1070	then
1071
1072	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1073	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1074	if [[ $tasks_per_node = 0 ]]
1075	then
1076	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1077	then
1078	printf "\n"
1079	printf "\n +++ option \"-T\" (tasks per node) is missing"
1080	printf "\n set -T option or define tasks_per_node in the config file"
1081	locat=tasks_per_node; (( iec = 0 )); exit
1082	else
1083	# DEFAULT FOR INTERACTIVE RUN
1084	tasks_per_node=$cores
1085	fi
1086	fi
1087
1088	if (( cores < tasks_per_node ))
1089	then
1090	printf "\n"
1091	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1092	printf "\n given values: -T $tasks_per_node -X $cores"
1093	locat=tasks_per_node; (( iec = 0 )); exit
1094	fi
1095
1096	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1097	(( mpi_tasks = cores / threads_per_task ))
1098	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1099	(( ii = cores / tasks_per_node ))
1100	(( remaining_cores = cores - ii * tasks_per_node ))
1101	if (( remaining_cores > 0 ))
1102	then
1103	printf "\n"
1104	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1105	printf "\n divisor of the total number of cores (option \"-X\")"
1106	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1107	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1108	(( nodes = nodes + 1 ))
1109	fi
1110
1111	fi
1112
1113
1114	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1115	if [[ "$maximum_parallel_io_streams" = "" ]]
1116	then
1117	maximum_parallel_io_streams=$cores
1118	fi
1119
1120
1121	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1122	if [[ "$scp_port" != "" ]]
1123	then
1124	PORTOPT="-P $scp_port"
1125	SSH_PORTOPT="-p $scp_port"
1126	fi
1127
1128
1129	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1130	# CONFIG-FILE
1131	if [[ "$ssh_key" != "" ]]
1132	then
1133	ssh_key="-i $HOME/.ssh/$ssh_key"
1134	fi
1135
1136
1137	# SET QUEUE, IF NOT GIVEN
1138	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1139	then
1140
1141	if [[ $queue = none && "$defaultqueue" = "" ]]
1142	then
1143	printf "\n"
1144	printf "\n +++ no default queue given in configuration file and no queue"
1145	printf "\n given with option -q"
1146	locat=queue; exit
1147	fi
1148	if [[ $queue = none ]]
1149	then
1150	queue=$defaultqueue
1151	fi
1152
1153	fi
1154
1155
1156	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1157	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1158	(( i = 0 ))
1159	(( nr_of_input_files = 0 ))
1160	while (( i < iin ))
1161	do
1162	(( i = i + 1 ))
1163
1164	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1165	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1166	if [[ "${actionin_pre[$i]}" = di ]]
1167	then
1168	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1169	else
1170	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1171	fi
1172
1173
1174	# CHECK IF FILE EXISTS
1175	if ! ls $filename* 1>/dev/null 2>&1
1176	then
1177
1178	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1179	if [[ "${optin_pre[$i]}" != "yes" ]]
1180	then
1181	printf "\n\n +++ INPUT-file: "
1182	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1183	then
1184	printf "\n $filename"
1185	else
1186	printf "\n $filename.${extin_pre[$i]}"
1187	fi
1188	printf "\n does not exist\n"
1189	locat=input; exit
1190	else
1191	(( nr_of_input_files = nr_of_input_files + 1 ))
1192	localin[$nr_of_input_files]="${localin_pre[$i]}"
1193	optin[$nr_of_input_files]="${optin_pre[$i]}"
1194	actionin[$nr_of_input_files]="unavailable"
1195	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1196	endin[$nr_of_input_files]="${endin_pre[$i]}"
1197	extin[$nr_of_input_files]="${extin_pre[$i]}"
1198	fi
1199
1200	else
1201
1202	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1203	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1204	# ENDINGS
1205	if [[ "${multin[$i]}" = true ]]
1206	then
1207	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1208	ls -1 -d ${filename} > filelist 2>/dev/null
1209	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1210	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1211
1212	endings=""
1213	while read line
1214	do
1215	# filename without path (i.e. after the last "/")
1216	basefilename=$(basename ${line})
1217
1218	# check if there is an extension and remove it
1219	ext=${basefilename##*.}
1220	if [[ "$ext" = "${extin_pre[$i]}" ]]
1221	then
1222	basefilename=${basefilename%.*}
1223	fi
1224
1225	# check for an existing cycle number and remove it
1226	cycle=${basefilename##*.}
1227	if [[ $cycle =~ ^-?[0-9]+$ ]]
1228	then
1229	basefilename=${basefilename%.*}
1230	fi
1231
1232	# remove the run_identifier from the beginning
1233	length_run_identifier=${#run_identifier}
1234	ending=${basefilename:${length_run_identifier}}
1235
1236	# remove the ending given in the .iofiles from the beginning
1237	endingstring="${endin_pre[$i]}"
1238	length_ending=${#endingstring}
1239	ending=${ending:${length_ending}}
1240
1241	if [[ "$ending" = "" ]]
1242	then
1243	# standard ending as given in the .iofiles
1244	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1245	then
1246	endings="$endings DEFAULT"
1247	fi
1248	else
1249	# ending must start with "_", otherwise its a different file
1250	if [[ "${ending:0:1}" = "_" ]]
1251	then
1252	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1253	then
1254	endings="$endings $ending"
1255	fi
1256	fi
1257	fi
1258
1259	done <filelist
1260
1261	rm filelist
1262
1263	else
1264
1265	# SINGLE NAME
1266	endings=DEFAULT
1267
1268	fi
1269
1270	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1271	for ending in $endings
1272	do
1273
1274	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1275	if [[ $ending = DEFAULT ]]
1276	then
1277	ending=""
1278	fi
1279
1280	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1281	(( nr_of_input_files = nr_of_input_files + 1 ))
1282	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1283	optin[$nr_of_input_files]="${optin_pre[$i]}"
1284	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1285	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1286	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1287	extin[$nr_of_input_files]="${extin_pre[$i]}"
1288
1289
1290	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1291	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1292	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1293	then
1294	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1295	else
1296	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1297	fi
1298
1299	# DETERMINE THE FILE'S CYCLE NUMBER
1300	(( maxcycle = 0 ))
1301	ls -1 -d $filename > filelist 2>/dev/null
1302	ls -1 -d $filename.* >> filelist 2>/dev/null
1303	while read line
1304	do
1305	# filename without path (i.e. after the last "/")
1306	basefilename=$(basename ${line})
1307
1308	# check if there is an extension
1309	extension=${basefilename##*.}
1310	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1311	then
1312	basefilename=${basefilename%.*}
1313	fi
1314
1315	# check for an existing cycle number
1316	cycle=${basefilename##*.}
1317	if [[ $cycle =~ ^-?[0-9]+$ ]]
1318	then
1319	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1320	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1321	(( icycle = $((10#$cycle)) ))
1322	else
1323	(( icycle = 0 ))
1324	fi
1325
1326	if (( icycle > maxcycle ))
1327	then
1328	(( maxcycle = icycle ))
1329
1330	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1331	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1332	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1333	then
1334	leading_zero=true
1335	else
1336	leading_zero=false
1337	fi
1338	fi
1339
1340	done <filelist
1341	rm filelist
1342
1343	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1344	if [[ $leading_zero = true ]]
1345	then
1346	cyclestring=`printf "%03d" $maxcycle`
1347	else
1348	cyclestring=$maxcycle
1349	fi
1350
1351	# APPEND CYCLE NUMBER TO FILENAME
1352	if (( maxcycle > 0 ))
1353	then
1354	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1355	then
1356	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1357	else
1358	filename=${filename}.$cyclestring
1359	fi
1360	else
1361	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1362	then
1363	filename=${filename}.${extin[$nr_of_input_files]}
1364	fi
1365	fi
1366
1367	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1368	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1369	absnamein[$nr_of_input_files]=$filename
1370	if (( maxcycle > 0 ))
1371	then
1372	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1373	then
1374	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1375	else
1376	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1377	fi
1378	else
1379	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1380	then
1381	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1382	else
1383	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1384	fi
1385	fi
1386
1387	done
1388
1389	fi
1390
1391	done
1392
1393
1394	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1395	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1396	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1397	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1398	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1399	# REMOTE HOST)
1400	(( i = 0 ))
1401	while (( i < iout ))
1402	do
1403	(( i = i + 1 ))
1404	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1405	then
1406	if [[ "${actionout_pre[$i]}" = tr ]]
1407	then
1408	actionout_pre[$i]=""
1409	elif [[ "${actionout_pre[$i]}" = trpe ]]
1410	then
1411	actionout_pre[$i]=pe
1412	elif [[ "${actionout_pre[$i]}" = tra ]]
1413	then
1414	actionout_pre[$i]=a
1415	fi
1416	(( maxcycle = 0 ))
1417	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1418	eval catalogname=${pathout_pre[$i]}
1419	if ! ls $filename* 1>/dev/null 2>&1
1420	then
1421
1422	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1423	if cat /dev/null > $filename
1424	then
1425	rm $filename
1426	else
1427
1428	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1429	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1430	if [[ ! -d $catalogname ]]
1431	then
1432	if mkdir -p $catalogname
1433	then
1434	printf "\n\n *** directory:"
1435	printf "\n $catalogname"
1436	printf "\n was created\n"
1437	else
1438	printf "\n\n +++ OUTPUT-file:"
1439	printf "\n $filename"
1440	printf "\n cannot be created, because directory does not exist"
1441	printf "\n and cannot be created either"
1442	printf "\n"
1443	locat=output ; exit
1444	fi 2>/dev/null
1445	else
1446	printf "\n\n +++ OUTPUT-file:"
1447	printf "\n $filename"
1448	printf "\n cannot be created, although directory exists"
1449	printf "\n"
1450	locat=output ; exit
1451	fi
1452	fi 2>/dev/null
1453
1454	fi
1455
1456	fi
1457	done
1458
1459
1460	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1461	if [[ $running_in_batch_mode = false ]]
1462	then
1463	run_id_number=$RANDOM
1464	run_id=${run_identifier}.$run_id_number
1465
1466	tempdir=$fast_io_catalog/$run_id
1467
1468	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1469	export job_id=$run_id
1470
1471	fi
1472
1473
1474	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1475	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1476	then
1477
1478	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1479	if [[ $ibd = 0 ]]
1480	then
1481	printf "\n"
1482	printf "\n +++ no batch directives found in configuration file"
1483	locat=config_file_batch_directives; (( iec = 0 )); exit
1484	fi
1485
1486	# CHECK IF CPUTIME IS GIVEN FOR JOB
1487	done=false
1488	cputime=$cpumax
1489	while [[ $done = false ]]
1490	do
1491	if (( cputime == 0 ))
1492	then
1493	printf "\n +++ cpu-time is undefined"
1494	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1495	printf "\n >>> "
1496	read cputime 1>/dev/null 2>&1
1497	else
1498	done=true
1499	fi
1500	done
1501	cpumax=$cputime
1502
1503	# CHECK THE MEMORY DEMAND
1504	done=false
1505	while [[ $done = false ]]
1506	do
1507	if (( memory == 0 ))
1508	then
1509	printf "\n +++ memory demand is undefined"
1510	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1511	printf "\n >>> "
1512	read memory 1>/dev/null 2>&1
1513	else
1514	done=true
1515	fi
1516	done
1517
1518	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1519	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1520	then
1521	while [[ -z $remote_username ]]
1522	do
1523	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1524	printf "\n >>> Please type username:"
1525	printf "\n >>> "
1526	read remote_username
1527	done
1528	fi
1529
1530	else
1531
1532	if [[ $running_in_batch_mode = false ]]
1533	then
1534	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1535	cpumax=$cputime
1536	else
1537	cputime=$cpumax
1538	fi
1539
1540	fi
1541
1542
1543	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1544	(( cpu_hours = cputime / 3600 ))
1545	(( resttime = cputime - cpu_hours * 3600 ))
1546	(( cpu_minutes = resttime / 60 ))
1547	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1548	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1549
1550
1551	# OUTPUT OF THE PALMRUN-HEADER
1552	calltime=$(date)
1553	printf "\n"
1554	printf "#------------------------------------------------------------------------# \n"
1555	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1556	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1557	printf "\| \| \n"
1558	column1="called on:"; column2=$(hostname)
1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1560	if [[ $create_remote_batch_job = true ]]
1561	then
1562	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1563	else
1564	if [[ $running_on_remote = true ]]
1565	then
1566	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1567	else
1568	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1569	fi
1570	fi
1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1572
1573	column1="running in:"
1574	if [[ $running_in_batch_mode = true ]]
1575	then
1576	column2="batch job mode"
1577	else
1578	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1579	then
1580	column2="job creation mode"
1581	else
1582	column2="interactive run mode"
1583	fi
1584	fi
1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1586
1587	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1588	then
1589	if [[ "$project_account" != "" ]]
1590	then
1591	column1="project account number:"
1592	column2="$project_account"
1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1594	fi
1595	fi
1596
1597	if [[ -n $cores ]]
1598	then
1599	if [[ $run_coupled_model = false ]]
1600	then
1601	column1="number of cores:"; column2=$cores
1602	else
1603	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1604	fi
1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1606	fi
1607	if [[ -n $tasks_per_node ]]
1608	then
1609	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1611	if (( remaining_cores > 0 ))
1612	then
1613	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1615	fi
1616	fi
1617	if [[ $maximum_parallel_io_streams != $cores ]]
1618	then
1619	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1620	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1621	fi
1622	if [[ $use_openmp = true ]]
1623	then
1624	column1="threads per task:"; column2="$threads_per_task"
1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1626	fi
1627	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1628	then
1629	column1="memory demand / PE":; column2="$memory MB"
1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1631	column1="job cpu time (h:m:s):"; column2="$timestring"
1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1633	fi
1634	printf "\| \| \n"
1635	if [[ "$source_list" != "" ]]
1636	then
1637	if [[ "$make_options" != "" ]]
1638	then
1639	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1641	line=$(echo "$make_options" \| cut -c46-)
1642	while [[ "$line" != "" ]]
1643	do
1644	column1=""
1645	column2=$(echo "$line" \| cut -c-45)
1646	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1647	line=$(echo "$line" \| cut -c46-)
1648	done
1649	fi
1650	fi
1651
1652	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1654	line=$(echo "$cpp_options" \| cut -c46-)
1655	while [[ "$line" != "" ]]
1656	do
1657	column1=""
1658	column2=$(echo "$line" \| cut -c-45)
1659	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1660	line=$(echo "$line" \| cut -c46-)
1661	done
1662
1663	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1664	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1665	line=$(echo "$compiler_options" \| cut -c46-)
1666	while [[ "$line" != "" ]]
1667	do
1668	column1=""
1669	column2=$(echo "$line" \| cut -c-45)
1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1671	line=$(echo "$line" \| cut -c46-)
1672	done
1673
1674	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1676	line=$(echo "$linker_options" \| cut -c46-)
1677	while [[ "$line" != "" ]]
1678	do
1679	column1=""
1680	column2=$(echo "$line" \| cut -c-45)
1681	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1682	line=$(echo "$line" \| cut -c46-)
1683	done
1684
1685	if [[ "$login_init_cmd" != "" ]]
1686	then
1687	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1688	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1689	line=$(echo "$login_init_cmd" \| cut -c46-)
1690	while [[ "$line" != "" ]]
1691	do
1692	column1=""
1693	column2=$(echo "$line" \| cut -c-45)
1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1695	line=$(echo "$line" \| cut -c46-)
1696	done
1697	fi
1698
1699	if [[ "$module_commands" != "" ]]
1700	then
1701	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1702	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1703	line=$(echo "$module_commands" \| cut -c46-)
1704	while [[ "$line" != "" ]]
1705	do
1706	column1=""
1707	column2=$(echo "$line" \| cut -c-45)
1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1709	line=$(echo "$line" \| cut -c46-)
1710	done
1711	fi
1712	printf "\| \| \n"
1713	column1="run identifier:"; column2=$run_identifier
1714	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1715	column1="activation string list:"; column2=$(echo $activation_string_list)
1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1717
1718	if [[ "$ocean_file_appendix" = true ]]
1719	then
1720	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1721	fi
1722
1723	if [[ "$source_list" != "" ]]
1724	then
1725	printf "\| \| \n"
1726	printf "\| Files to be compiled: \| \n"
1727	line=$source_list
1728	while [[ "$line" != "" ]]
1729	do
1730	linestart=$(echo $line \| cut -c-70)
1731	printf "\| %-70s \| \n" "$linestart"
1732	line=$(echo "$line" \| cut -c71-)
1733	done
1734	fi
1735	printf "#------------------------------------------------------------------------#"
1736
1737
1738
1739	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1740	if [[ $do_trace = true ]]
1741	then
1742	(( i = 0 ))
1743	while (( i < nr_of_input_files ))
1744	do
1745	(( i = i + 1 ))
1746	if (( i == 1 ))
1747	then
1748	printf "\n\n >>> INPUT-file assignments:\n"
1749	fi
1750	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1751	done
1752	(( i = 0 ))
1753	while (( i < iout ))
1754	do
1755	(( i = i + 1 ))
1756	if (( i == 1 ))
1757	then
1758	printf "\n\n >>> OUTPUT-file assignments:\n"
1759	fi
1760	printf "\n ${localout[$i]} : ${pathout[$i]}"
1761	done
1762	(( i = 0 ))
1763	while (( i < iic ))
1764	do
1765	(( i = i + 1 ))
1766	if (( i == 1 ))
1767	then
1768	printf "\n\n >>> INPUT-commands:\n"
1769	fi
1770	printf "\n ${in_command[$i]}"
1771	done
1772	(( i = 0 ))
1773	while (( i < ioc ))
1774	do
1775	(( i = i + 1 ))
1776	if (( i == 1 ))
1777	then
1778	printf "\n\n >>> OUTPUT-commands:\n"
1779	fi
1780	printf "\n ${out_command[$i]}"
1781	done
1782	fi
1783
1784	# QUERY FOR CONTINUE
1785	if [[ $silent = false && $running_in_batch_mode = false ]]
1786	then
1787	antwort=dummy
1788	printf "\n\n"
1789	printf " >>> everything o.k. (y/n) ? "
1790	while read antwort
1791	do
1792	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1793	then
1794	printf " >>> everything o.k. (y/n) ? "
1795	else
1796	break
1797	fi
1798	done
1799	if [[ $antwort = n \|\| $antwort = N ]]
1800	then
1801	locat=user_abort; (( iec = 0 )); exit
1802	fi
1803	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1804	then
1805	printf "\n *** batch-job will be created and submitted"
1806	else
1807	printf "\n *** PALMRUN will now continue to execute on this machine"
1808	fi
1809	fi
1810
1811
1812
1813	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1814	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1815	then
1816
1817	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1818	then
1819	printf "\n\n *** creating executable and other sources for the remote host\n"
1820	else
1821	printf "\n\n *** creating executable and other sources for the local host\n"
1822	fi
1823
1824	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1825	# IT SHALL BE CREATED
1826	ask_for_make_depository=false
1827	if [[ $create_remote_batch_job = true ]]
1828	then
1829
1830	line=`grep %base_directory $config_file`
1831	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1832	### echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1833	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1834
1835	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1836	then
1837	printf "\n\n +++ make depository \"${make_depository}\""
1838	printf "\n on remote host not found!"
1839	ask_for_make_depository=true
1840	fi
1841	rm ${configuration_identifier}_last_make_protokoll
1842
1843	else
1844
1845	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1846	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1847	if [[ ! -d ${make_depository} ]]
1848	then
1849	printf "\n\n +++ make depository \"${make_depository}\""
1850	printf "\n on local host not found!"
1851	ask_for_make_depository=true
1852	fi
1853
1854	fi
1855
1856	if [[ $ask_for_make_depository = true ]]
1857	then
1858
1859	antwort=dummy
1860	printf "\n\n"
1861	printf " >>> Create a new one (y/n) ? "
1862	while read antwort
1863	do
1864	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1865	then
1866	printf " >>> Create a new one (y/n) ? "
1867	else
1868	break
1869	fi
1870	done
1871	if [[ $antwort = n \|\| $antwort = N ]]
1872	then
1873	locat=user_abort; (( iec = 0 )); exit
1874	fi
1875
1876	if [[ $do_trace = true ]]
1877	then
1878	palmbuild -c $configuration_identifier
1879	else
1880	palmbuild -v -c $configuration_identifier
1881	fi
1882
1883	if [[ ${PIPESTATUS[0]} != 0 ]]
1884	then
1885
1886	# ABORT IN CASE OF COMPILATION PROBLEMS
1887	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1888	locat=make_depository
1889	exit
1890	else
1891	echo " *** now continue with creating executable and other sources"
1892	fi
1893
1894	fi
1895
1896	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1897	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1898
1899	if [[ ${PIPESTATUS[0]} != 0 ]]
1900	then
1901
1902	# ABORT IN CASE OF COMPILATION PROBLEMS
1903	printf "\n +++ error while creating executable and/or other sources"
1904	locat=execution
1905	rm -rf ${base_directory}/${sources_for_run_catalog}
1906	exit
1907
1908	else
1909
1910	printf " *** executable and other sources created\n"
1911	rm -rf ${base_directory}/${sources_for_run_catalog}
1912
1913	fi
1914
1915	fi
1916
1917
1918	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1919	# WILL BE COPIED TO THE REMOTE HOST
1920	if [[ $create_remote_batch_job = true ]]
1921	then
1922	(( i = 0 ))
1923	while (( i < nr_of_input_files ))
1924	do
1925	(( i = i + 1 ))
1926	if [[ "${actionin[$i]}" = tr ]]
1927	then
1928	eval inputfile=${pathin[$i]}/${frelin[$i]}
1929	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1930	fi
1931	done
1932	if (( i > 0 ))
1933	then
1934	printf "\n\n *** input files have been copied to the remote host\n"
1935	fi
1936	fi
1937
1938
1939	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1940	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1941	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1942	then
1943
1944	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1945	if [[ $running_in_batch_mode = false ]]
1946	then
1947	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1948	# FOLDER
1949	mkdir -p $tempdir
1950	chmod go+rx $tempdir
1951	cd $tempdir
1952	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1953	printf "\n *** changed to temporary directory: $tempdir"
1954
1955	else
1956
1957	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1958	printf "\n *** running in temporary directory: $tempdir"
1959
1960	fi
1961
1962
1963	# PROVIDE THE INPUT FILES
1964	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1965	optional_files_missing=false
1966	(( i = 0 ))
1967	while (( i < nr_of_input_files ))
1968	do
1969	(( i = i + 1 ))
1970	if (( i == 1 ))
1971	then
1972	printf "\n\n *** providing INPUT-files:\n$dashes"
1973	fi
1974
1975
1976	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1977	if [[ "${actionin[$i]}" = unavailable ]]
1978	then
1979	optional_files_missing=true
1980	continue
1981	fi
1982
1983	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1984	files_for_cores=false; filetype=file
1985	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1986	then
1987	files_for_cores=true; filetype=files
1988	actionin[$i]=""
1989	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1990	then
1991	actionin[$i]=""
1992	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1993	then
1994	files_for_cores=true; filetype=files
1995	actionin[$i]="ln"
1996	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1997	then
1998	actionin[$i]="ln"
1999	fi
2000
2001	if [[ $files_for_cores = true ]]
2002	then
2003	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2004	else
2005	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2006	fi
2007
2008	# INPUT-FILES TO BE LINKED
2009	if [[ "${actionin[$i]}" = ln ]]
2010	then
2011
2012	printf "\n $filetype will be linked"
2013	if [[ $files_for_cores = false ]]
2014	then
2015	if [[ -f "${absnamein[$i]}" ]]
2016	then
2017	ln ${absnamein[$i]} ${localin[$i]}
2018	got_tmp[$i]=true
2019	fi
2020	else
2021	if [[ -d "${absnamein[$i]}" ]]
2022	then
2023	mkdir -p ${localin[$i]}
2024	cd ${absnamein[$i]}
2025	for file in $(ls *)
2026	do
2027	ln $file $tempdir/${localin[$i]}
2028	done >\|/dev/null 2>&1
2029	cd $tempdir
2030	fi
2031
2032	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2033	if [[ ! -f "${localin[$i]}/_000000" ]]
2034	then
2035	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2036	cp -r ${absnamein[$i]}/* ${localin[$i]}
2037	fi
2038
2039	got_tmp[$i]=true
2040	fi
2041	fi
2042
2043	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2044	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2045	then
2046
2047	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2048	then
2049
2050	# FILE COPIES ARE PROVIDED FOR ALL CORES
2051	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2052	printf "\n file will be provided for $cores processors"
2053	mkdir -p ${localin[$i]}
2054	ival=$cores
2055	(( ii = 0 ))
2056	while (( ii <= ival-1 ))
2057	do
2058	if (( ii < 10 ))
2059	then
2060	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2061	elif (( ii < 100 ))
2062	then
2063	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2064	elif (( ii < 1000 ))
2065	then
2066	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2067	else
2068	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2069	fi
2070	(( ii = ii + 1 ))
2071	done
2072
2073	else
2074
2075	if [[ $files_for_cores = true ]]
2076	then
2077
2078	# PROVIDE FILES FOR EACH CORE
2079	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2080	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2081	printf "\n providing $cores files for the respective cores"
2082	mkdir -p ${localin[$i]}
2083	if [[ $link_local_input = true ]]
2084	then
2085	printf " files will be linked\n"
2086	cd ${absnamein[$i]}
2087	for file in $(ls *)
2088	do
2089	ln -f $file ${localin[$i]}
2090	done
2091	cd $tempdir
2092	fi
2093
2094	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2095	if [[ ! -f "${localin[$i]}/_000000" ]]
2096	then
2097	if [[ $link_local_input = true ]]
2098	then
2099	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2100	fi
2101	cp -r ${absnamein[$i]}/* ${localin[$i]}
2102	fi
2103
2104	else
2105
2106	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2107	if [[ $link_local_input = true ]]
2108	then
2109	printf " file will be linked\n"
2110	ln -f ${absnamein[$i]} ${localin[$i]}
2111	fi
2112	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2113	if [[ ! -f "${localin[$i]}" ]]
2114	then
2115	if [[ $link_local_input = true ]]
2116	then
2117	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2118	fi
2119	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2120	then
2121	mv ${absnamein[$i]} ${localin[$i]}
2122	else
2123	cp ${absnamein[$i]} ${localin[$i]}
2124	fi
2125	fi
2126	fi
2127	fi
2128	fi
2129
2130	done
2131	if (( i != 0 ))
2132	then
2133	if [[ $optional_files_missing = true ]]
2134	then
2135	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2136	fi
2137	printf "\n$dashes\n *** all INPUT-files provided \n"
2138	fi
2139
2140
2141	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2142	(( i = 0 ))
2143	while (( i < iic ))
2144	do
2145	(( i = i + 1 ))
2146	if (( i == 1 ))
2147	then
2148	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2149	fi
2150	printf "\n >>> ${in_command[$i]}"
2151	eval ${in_command[$i]}
2152	if (( i == iic ))
2153	then
2154	printf "\n$dashes\n"
2155	fi
2156	done
2157
2158
2159	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2160	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2161	then
2162	progress_bar_disabled=true
2163	else
2164	progress_bar_disabled=false
2165	fi
2166
2167
2168	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2169	# (FILE ENVPAR WILL BE READ BY PALM)
2170	cat > ENVPAR << EOF
2171	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2172	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2173	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2174	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2175	maximum_cpu_time_allowed = ${cpumax}.,
2176	revision = '$global_revision',
2177	progress_bar_disabled = .${progress_bar_disabled}. /
2178
2179	EOF
2180
2181
2182	# STARTING THE EXECUTABLE
2183	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2184	PATH=$PATH:$tempdir
2185
2186
2187	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2188	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2189	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2190	eval line=\"$line\"
2191	execute_command="$line"
2192
2193
2194	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2195	if [[ "$execute_command_for_combine" = "" ]]
2196	then
2197	eval line2=\"$line2\"
2198	execute_command_for_combine="$line2"
2199	fi
2200
2201
2202
2203	# PROVIDE A HOSTFILE, IF REQUIRED
2204	if [[ "$hostfile" != "" ]]
2205	then
2206
2207	if [[ $hostfile = auto ]]
2208	then
2209	# CREATE A NEW HOSTFILE
2210	(( ii = 1 ))
2211	while (( ii <= cores / threads_per_task ))
2212	do
2213	echo $(hostname) >> hostfile
2214	(( ii = ii + 1 ))
2215	done
2216	if (( cores / threads_per_task == 0 ))
2217	then
2218	echo $(hostname) >> hostfile
2219	fi
2220
2221	else
2222	cp $hostfile hostfile
2223	fi
2224	eval line=\"`head -n $ii hostfile`\"
2225	printf "\n *** running on: $line"
2226	fi
2227
2228
2229
2230	# SET THE NUMBER OF OPENMP-THREADS
2231	if [[ $use_openmp = true ]]
2232	then
2233	export OMP_NUM_THREADS=$threads_per_task
2234	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2235	else
2236	export OMP_NUM_THREADS=1
2237	fi
2238
2239
2240	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2241	if [[ $run_coupled_model = false ]]
2242	then
2243	if [[ "$ocean_file_appendix" = true ]]
2244	then
2245	echo "precursor_ocean" > coupling_steering
2246	else
2247	echo "precursor_atmos" > coupling_steering
2248	fi
2249	else
2250	(( iia = $cores_atmos / $threads_per_task ))
2251	(( iio = $cores_ocean / $threads_per_task ))
2252	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2253	printf "\n\n"
2254	echo "coupled_run $iia $iio" > coupling_steering
2255	fi
2256
2257	printf "\n *** execute command:"
2258	printf "\n \"$execute_command\" \n\n"
2259
2260
2261	if [[ $progress_bar_disabled = true ]]
2262	then
2263	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2264	exit_code=${PIPESTATUS[0]}
2265	else
2266	$execute_command < coupling_steering &> >(tee STDOUT)
2267	exit_code=${PIPESTATUS[0]}
2268	fi
2269
2270	if [[ ${exit_code} != 0 ]]
2271	then
2272
2273	# ABORT IN CASE OF RUNTIME ERRORS
2274	printf "\n +++ runtime error occured"
2275	locat=execution
2276	exit
2277
2278	else
2279
2280	printf "\n$dashes\n *** execution finished \n"
2281
2282	fi
2283
2284
2285	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2286	# BY EACH CORE INTO ONE FILE
2287	if [[ ! -f combine_plot_fields.x ]]
2288	then
2289
2290	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2291	printf "\n 2d- and/or 3d-data may be incomplete!"
2292	printf "\n Your previous palmbuild may have failed. Please check.\n"
2293
2294	elif [[ "$combine_plot_fields" == true ]]
2295	then
2296
2297	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2298	$execute_command_for_combine
2299
2300	else
2301
2302	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2303	# DATA OUTPUT
2304	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2305	fi
2306
2307
2308
2309	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2310	(( i = 0 ))
2311	while (( i < ioc ))
2312	do
2313	(( i = i + 1 ))
2314	if (( i == 1 ))
2315	then
2316	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2317	fi
2318
2319	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2320	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2321
2322	printf "\n >>> ${out_command[$i]}"
2323	eval ${out_command[$i]}
2324	if (( i == ioc ))
2325	then
2326	printf "\n$dashes\n"
2327	fi
2328	done
2329
2330
2331	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2332	# WILDCARDS
2333	(( i = 0 ))
2334	(( nr_of_output_files = 0 ))
2335
2336	while (( i < iout ))
2337	do
2338
2339	(( i = i + 1 ))
2340
2341	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2342	# CREATE A LIST FOR THE DETECTED ENDINGS
2343	if [[ "${multout[$i]}" = true ]]
2344	then
2345	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2346	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2347	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2348
2349	endings="DEFAULT"
2350	while read line
2351	do
2352	# remove the local name from the beginning
2353	localnamestring="${localout_pre[$i]}"
2354	length_localname=${#localnamestring}
2355	ending=${line:${length_localname}}
2356
2357	if [[ "$ending" != "" ]]
2358	then
2359	endings="$endings $ending"
2360	fi
2361
2362	done <filelist
2363
2364	rm filelist
2365
2366	else
2367
2368	# SINGLE NAME
2369	endings=DEFAULT
2370
2371	fi
2372
2373	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2374	for ending in $endings
2375	do
2376
2377	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2378	if [[ $ending = DEFAULT ]]
2379	then
2380	ending=""
2381	fi
2382
2383	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2384	(( nr_of_output_files = nr_of_output_files + 1 ))
2385	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2386	transout[$nr_of_output_files]="${transout_pre[$i]}"
2387	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2388	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2389	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2390	extout[$nr_of_output_files]="${extout_pre[$i]}"
2391	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2392
2393	done
2394
2395	done
2396
2397
2398
2399
2400	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2401	(( i = 0 ))
2402	while (( i < nr_of_output_files ))
2403	do
2404	(( i = i + 1 ))
2405	if (( i == 1 ))
2406	then
2407	printf "\n\n *** saving OUTPUT-files:"
2408
2409	# GET RUN NUMBER ASSIGNED BY PALM
2410	if [[ -f RUN_NUMBER ]]
2411	then
2412	read run_number < RUN_NUMBER
2413	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2414	usecycle_option="-U $run_number"
2415	else
2416	run_number=0
2417	usecycle_option=""
2418	fi
2419	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2420	then
2421	printf "\n *** in case of SCP transfers to local host"
2422	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2423	fi
2424	printf "\n$dashes"
2425	fi
2426
2427	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2428	then
2429
2430	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2431
2432	# DETERMINE THE CYCLE NUMBER
2433	ls -1 -d $filename > filelist 2>/dev/null
2434	ls -1 -d $filename.* >> filelist 2>/dev/null
2435	while read line
2436	do
2437
2438	# filename without path (i.e. after the last "/")
2439	basefilename=$(basename ${line})
2440
2441	# check if there is an extension
2442	extension=${basefilename##*.}
2443	if [[ "$extension" = "${extout[$i]}" ]]
2444	then
2445	basefilename=${basefilename%.*}
2446	fi
2447
2448	# check for an existing cycle number
2449	cycle=${basefilename##*.}
2450	if [[ $cycle =~ ^-?[0-9]+$ ]]
2451	then
2452	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2453	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2454	(( icycle = $((10#$cycle)) + 1 ))
2455	else
2456	(( icycle = 1 ))
2457	fi
2458
2459	if (( icycle > maxcycle ))
2460	then
2461	(( maxcycle = icycle ))
2462	fi
2463
2464	done <filelist
2465	rm filelist
2466
2467
2468	# SET THE CYCLE NUMBER
2469	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2470	if [[ "${actionout[$i]}" = a ]]
2471	then
2472	(( maxcycle = maxcycle - 1 ))
2473	fi
2474
2475	(( cycnum[$i] = maxcycle ))
2476	pathout[$i]=$filename
2477
2478
2479	# ADD CYCLE NUMBER TO FILENAME
2480	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2481	if [[ "${actionout[$i]}" != "a" ]]
2482	then
2483	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2484	# WITH AN EXISTING CYCLE NUMBER
2485	if (( run_number >= cycnum[$i] ))
2486	then
2487	(( cycnum[$i] = run_number ))
2488	else
2489	if (( run_number > 0 ))
2490	then
2491	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2492	fi
2493	fi
2494	fi
2495	if (( cycnum[$i] > 0 ))
2496	then
2497	cyclestring=`printf "%03d" ${cycnum[$i]}`
2498	pathout[$i]=${pathout[$i]}.$cyclestring
2499	fi
2500	fi
2501
2502	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2503	files_for_cores=false; filetype=file
2504	link_local_output=false
2505	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2506	then
2507	files_for_cores=true; filetype=directory
2508	actionout[$i]=""
2509	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2510	then
2511	actionout[$i]=""
2512	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2513	then
2514	files_for_cores=true; filetype=directory
2515	link_local_output=true
2516	actionout[$i]=""
2517	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2518	then
2519	link_local_output
2520	actionout[$i]=""
2521	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2522	then
2523	files_for_cores=true; filetype=directory
2524	actionout[$i]="tr"
2525	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2526	then
2527	actionout[$i]="tr"
2528	fi
2529
2530	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2531	then
2532	if [[ ${warnout[$i]} = true ]]
2533	then
2534	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2535	fi
2536	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2537	then
2538	if [[ ${warnout[$i]} = true ]]
2539	then
2540	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2541	fi
2542	else
2543
2544
2545	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2546	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2547	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2548	then
2549	if [[ $running_on_remote = true ]]
2550	then
2551
2552	# SET OPTIONS FOR TRANSFER
2553	if [[ "${actionout[$i]}" = tr ]]
2554	then
2555	if [[ $files_for_cores = false ]]
2556	then
2557	catalog_option=""
2558	catalog_string=""
2559	else
2560	catalog_option="-c"
2561	catalog_string="/"
2562	fi
2563	append_option=""
2564	append_string=""
2565	else
2566	append_option="-A"
2567	append_string="append"
2568	fi
2569
2570	transfer_failed=false
2571	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2572	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2573
2574	# TRANSFER VIA SCP
2575	if [[ "$remote_loginnode" != "" ]]
2576	then
2577	### echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2578	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]}"
2579	else
2580	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	fi
2582	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2583
2584
2585	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2586	if [[ $transfer_failed = true ]]
2587	then
2588	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2589	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2590
2591	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2592	eval local_catalog=${pathout[$i]}
2593	if [[ ! -d $local_catalog ]]
2594	then
2595	printf " *** local directory does not exist. Trying to create:\n"
2596	printf " $local_catalog \n"
2597	mkdir -p $local_catalog
2598	fi
2599	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2600	transfer_problems=true
2601	fi
2602
2603	else
2604
2605	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2606	# BE COPIED OR APPENDED ON THIS MACHINE
2607	if [[ "${actionout[$i]}" = tr ]]
2608	then
2609	actionout[$i]=""
2610	else
2611	actionout[$i]="a"
2612	fi
2613	fi
2614	fi
2615
2616
2617	# APPEND ON THIS MACHINE
2618	if [[ "${actionout[$i]}" = "a" ]]
2619	then
2620	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2621	then
2622	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2623	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2624	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2625	else
2626	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2627	printf "\n ${pathout[$i]}\n"
2628	cat ${localout[$i]} >> ${pathout[$i]}
2629	fi
2630	fi
2631
2632	# COPY ON THIS MACHINE
2633	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2634	# ON DIFFERENT FILE-SYSTEMS
2635	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2636	then
2637
2638	# COPY IN CASE OF RUNS ON SINGLE CORES
2639	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2640	then
2641	printf "\n >>> OUTPUT: ${localout[$i]} to"
2642	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2643	if [[ $link_local_output = true ]]
2644	then
2645	printf " file will be linked\n"
2646	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2647	fi
2648	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2649	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2650	then
2651	if [[ $link_local_output = true ]]
2652	then
2653	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2654	fi
2655	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2656	else
2657	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2658	fi
2659	else
2660	printf "\n >>> OUTPUT: ${localout[$i]} to"
2661	printf "\n ${pathout[$i]}\n"
2662	if [[ $link_local_output = true ]]
2663	then
2664	printf " file will be linked\n"
2665	ln -f ${localout[$i]} ${pathout[$i]}
2666	fi
2667	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2668	if [[ ! -f "${pathout[$i]}" ]]
2669	then
2670	if [[ $link_local_output = true ]]
2671	then
2672	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2673	fi
2674	cp ${localout[$i]} ${pathout[$i]}
2675	else
2676	printf "+++ no copy because file ${pathout[$i]} exists\n"
2677	fi
2678	fi
2679
2680	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2681	then
2682
2683	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2684	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2685	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2686	printf "\n ${pathout[$i]}\n"
2687	if [[ $link_local_output = true ]]
2688	then
2689	printf " files will be linked\n"
2690	mkdir -p ${pathout[$i]}
2691	cd ${localout[$i]}
2692	for file in $(ls *)
2693	do
2694	ln -f $file ${pathout[$i]}
2695	done >\|/dev/null 2>&1
2696	cd $tempdir
2697	fi
2698
2699	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2700	if [[ ! -f "${pathout[$i]}/_000000" ]]
2701	then
2702	if [[ $link_local_output = true ]]
2703	then
2704	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2705	fi
2706	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2707	cp -r ${localout[$i]}/* ${pathout[$i]}
2708	fi
2709
2710	fi
2711	fi
2712	done
2713
2714	if (( i != 0 ))
2715	then
2716	if [[ $transfer_problems = true ]]
2717	then
2718	printf "\n$dashes\n *** OUTPUT-files saved"
2719	printf "\n +++ WARNING: some data transfers failed! \n"
2720	else
2721	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2722	fi
2723	fi
2724
2725
2726	# IF REQUIRED, START A RESTART-JOB
2727	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2728	if [[ -f CONTINUE_RUN ]]
2729	then
2730
2731	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2732	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2733	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2734	# -b START A BATCH JOB
2735	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2736	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2737	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2738
2739	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2740	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2741	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2742	then
2743	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2744	fi
2745
2746	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2747	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2748	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2749	then
2750	prc=`echo $prc \| sed 's/#/r/g'`
2751	fi
2752
2753
2754	# START THE RESTART-JOB
2755	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2756	echo " $prc"
2757	printf "\n$dashes\n"
2758	if [[ $running_on_remote = true ]]
2759	then
2760
2761	echo "*** ssh will be used to initiate restart-runs!"
2762	echo " return_address=\"$return_address\" "
2763	echo " return_username=\"$local_username\" "
2764
2765	if [[ "$remote_loginnode" != "" ]]
2766	then
2767	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
2768	else
2769	### echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2770	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2771	fi
2772
2773	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2774	sleep 30
2775
2776	else
2777
2778	# START THE RESTART JOB ON THE LOCAL HOST
2779	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2780	cd - > /dev/null
2781
2782	fi
2783
2784	# CHECK, IF RESTART JOB HAS BEEN STARTED
2785	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2786	then
2787	printf "\n$dashes\n +++ creating restart run failed \n"
2788	locat=create_restart
2789	rm palmrun_restart.log
2790	exit
2791	else
2792	printf "\n$dashes\n *** restart run initiated \n"
2793	rm palmrun_restart.log
2794	fi
2795
2796
2797	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2798	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2799	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2800	# MAY BE VERY HUGE)
2801	(( i = 0 ))
2802	while (( i < nr_of_input_files ))
2803	do
2804	(( i = i + 1 ))
2805	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2806	then
2807	rm -r ${absnamein[$i]}
2808	fi
2809	done
2810
2811	fi
2812
2813
2814	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2815	cd $HOME
2816	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2817
2818
2819	else
2820
2821
2822	# PREPARING ACTIONS,
2823	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2824
2825	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2826	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2827	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2828	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2829	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2830	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2831	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2832	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2833	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2834	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2835	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2836	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2837	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2838	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2839	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2840	if [[ $create_remote_batch_job = true ]]
2841	then
2842	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2843	if [[ $do_trace = true ]]
2844	then
2845	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2846	fi
2847	elif [[ $create_batch_job = true ]]
2848	then
2849	palmrun_com=${palmrun_com}" -j"
2850	if [[ $do_trace = true ]]
2851	then
2852	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2853	fi
2854	fi
2855
2856
2857	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2858	# REMOTE HOST
2859	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2860	job_protocol_file=$job_protocol_file_local
2861	if [[ $create_remote_batch_job = true ]]
2862	then
2863	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2864	job_protocol_file=$job_protocol_file_remote
2865	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2866	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2867	fi
2868
2869
2870	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2871	jobfile=jobfile.$run_id_number
2872
2873
2874	# FIRST CREATE THE BATCH DIRECTIVES
2875	(( i = 0 ))
2876	while (( i < ibd ))
2877	do
2878	(( i = i + 1 ))
2879	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2880	eval line=\"$line\"
2881	echo "$line" >> $jobfile
2882	done
2883	echo " " >> $jobfile
2884
2885
2886	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2887	# PROTOCOL
2888	if [[ $create_remote_batch_job = true ]]
2889	then
2890	echo "set +vx" >> $jobfile
2891	echo "trap '" >> $jobfile
2892	echo "set +vx" >> $jobfile
2893	echo "cd ${remote_jobcatalog}" >> $jobfile
2894	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2895
2896	# ADD THE BATCH DIRECTIVES
2897	(( i = 0 ))
2898	while (( i < ibdt ))
2899	do
2900	(( i = i + 1 ))
2901	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2902	eval line=\"$line\"
2903	echo "$line" >> $jobfile
2904	done
2905	echo " " >> $jobfile
2906
2907	echo "set -x" >> $jobfile
2908	if [[ "$remote_loginnode" != "" ]]
2909	then
2910	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}\" " >> $jobfile
2911	else
2912	echo "${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
2913	fi
2914	echo "%%END%%" >> $jobfile
2915	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2916	echo "$submit_command $scpjob_file" >> $jobfile
2917	echo "rm $scpjob_file" >> $jobfile
2918	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2919	echo "set -x" >> $jobfile
2920	echo " ' exit" >> $jobfile
2921	fi
2922
2923
2924	# ACTIVATE ERROR-TRACEBACK
2925	if [[ $do_trace = true ]]
2926	then
2927	echo "set -x" >> $jobfile
2928	else
2929	echo "set +vx" >> $jobfile
2930	fi
2931
2932
2933	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2934	if [[ "$login_init_cmd" != "" ]]
2935	then
2936	echo "$login_init_cmd" >> $jobfile
2937	fi
2938	if [[ "$module_commands" != "" ]]
2939	then
2940	echo "$module_commands" >> $jobfile
2941	fi
2942
2943
2944	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2945	if [[ $create_remote_batch_job = true ]]
2946	then
2947	echo "mkdir $tempdir" >> $jobfile
2948	echo "chmod go+rx $tempdir" >> $jobfile
2949	else
2950	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2951	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2952	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2953	mkdir $tempdir
2954	chmod go+rx $tempdir
2955	fi
2956	echo "cd $tempdir" >> $jobfile
2957	echo "export tempdir=$tempdir" >> $jobfile
2958	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2959	echo "export PATH=.:\$PATH" >> $jobfile
2960	echo "export execute_palmrun=true" >> $jobfile
2961
2962
2963	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2964	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2965	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2966	echo "LOCAL_PWD=$working_directory" >> $jobfile
2967	echo "export LOCAL_PWD" >> $jobfile
2968
2969
2970	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2971	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2972	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2973
2974
2975	# CALL PALMRUN WITHIN THE JOB
2976	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2977	echo "set -x" >> $jobfile
2978	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2979
2980
2981	# TRANSFER JOBFILE TO THE TARGET HOST
2982	if [[ $create_jobfile_only = false ]]
2983	then
2984
2985	# CREATE LOCAL JOB FOLDER
2986	eval local_jobcatalog=$local_jobcatalog
2987	if [[ ! -d $local_jobcatalog ]]
2988	then
2989	echo " "
2990	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
2991	mkdir $local_jobcatalog
2992	fi
2993
2994	if [[ $create_remote_batch_job = true ]]
2995	then
2996
2997	echo " "
2998	echo " *** transfer of job to remote host via scp"
2999
3000	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3001	### echo "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
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)"
3013	if [[ $do_trace = true ]]
3014	then
3015	### echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
3016	echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" 2>&1"
3017	fi
3018	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
3019	### ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" 2>&1
3020
3021	elif [[ $create_batch_job = true ]]
3022	then
3023
3024	eval local_jobcatalog=$local_jobcatalog
3025	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3026	cd $local_jobcatalog
3027	echo " "
3028	echo " *** submit the job"
3029	if [[ $do_trace = true ]]
3030	then
3031	echo "$submit_command ${configuration_identifier}_${run_id}"
3032	fi
3033	$submit_command ${configuration_identifier}_${run_id}
3034	rm ${configuration_identifier}_${run_id}
3035	cd - > /dev/null
3036
3037	fi
3038
3039	rm -rf $jobfile
3040
3041	else
3042
3043	printf "\n *** jobfile created under name \"$jobfile\" "
3044	printf "\n no batch-job has been sent!"
3045
3046	fi
3047
3048	fi # END OF REMOTE-PART

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