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source: palm/trunk/SCRIPTS/palmrun @ 3783

Last change on this file since 3783 was 3725, checked in by raasch, 6 years ago
modifications to avoid compiler warnings about unused variables, temperton-fft: GOTO statements replaced, file re-formatted corresponding to coding standards, ssh-calls for compilations on remote systems modified to avoid output of login messages on specific systems changed again (palmbuild, reverted as before r3549), error messages for failed restarts extended (palmrun)
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.1 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 3725 2019-02-07 10:11:02Z forkel $
29	# error messages for failed restarts extended
30	#
31	# 3682 2019-01-18 17:01:54Z knoop
32	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
33	# of login messages on specific systems
34	#
35	# 3574 2018-11-28 13:14:39Z raasch
36	# syntax-error in last commit fixed
37	#
38	# 3573 2018-11-28 13:03:44Z raasch
39	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
40	# removed,
41	# r3570 reverted
42	#
43	# 3570 2018-11-27 17:44:21Z kanani
44	# Rename job-id by run_id
45	#
46	# 3555 2018-11-22 13:50:37Z raasch
47	# sed-command to remove repeated space-characters replaced by tr-command, to
48	# guarantee mac compatible
49	#
50	# 3549 2018-11-21 15:44:44Z raasch
51	# ssh-call for submitting batch jobs on remote systems modified to avoid output
52	# of login messages on specific systems
53	#
54	# 3534 2018-11-19 15:35:16Z raasch
55	# batch_scp for sending back the job protocol file is called via login-node if
56	# a login-node has been set in the config-file
57	# ssh-calls rearranged to avoid output of system/user-profile messages
58	#
59	# 3505 2018-11-08 09:14:30Z raasch
60	# job folders are created in case that they do not exist
61	#
62	# 3455 2018-10-30 14:12:31Z raasch
63	# options -h and -d renamed -c and -r, respectively
64	#
65	# 3402 2018-10-23 11:49:24Z knoop
66	# job_id is set for compatibility reasons with older versions of config files
67	#
68	# 3313 2018-10-06 15:22:48Z knoop
69	# more detailed error message for outdated fileconnection file
70	#
71	# 3236 2018-09-10 09:07:06Z raasch
72	# warning issued in case of file connection file version mismatch,
73	# host_configuration renamed configuration_identifier,
74	# "host identifier" in header output renamed "config. identifier",
75	# jobname renamed run_identifier,
76	# run_id renamed run_id_number
77	# job_id renamed run_id
78	# option -r renamed -i
79	#
80	# 3151 2018-07-19 08:45:38Z raasch
81	# removed additional listing of files to be compiled, print PALM code revision
82	# in header
83	#
84	# 3132 2018-07-16 11:44:58Z raasch
85	# create consistent error messages in case of failed restarts,
86	# check existence of remote job catalog
87	#
88	# 3043 2018-05-25 10:47:54Z raasch
89	# check for setting of fast_io_catalog
90	#
91	# 3033 2018-05-23 15:26:19Z raasch
92	# -T option not required for interactive runs (tasks per node =
93	# total number of cores is assumed as default, if option is not given),
94	# reformatting of a few messages,
95	# bugfix: destination output directory is created if attribute "pe" is set in
96	# .palm.iofiles
97	#
98	# 2718 2018-01-02 08:49:38Z maronga
99	# bugfix of r2990
100	#
101	# 2718 2018-01-02 08:49:38Z maronga
102	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
103	# not in the working directory from where palmrun is called
104	#
105	# 2718 2018-01-02 08:49:38Z maronga
106	# svfout in the activation string will be replaced now by svfin in case of
107	# automatic restarts
108	#
109	# 2718 2018-01-02 08:49:38Z maronga
110	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
111	# the possible output or input of sky view factors
112	#
113	# 2718 2018-01-02 08:49:38Z maronga
114	# "fname" renamed to "jobname"
115	#
116	# 2718 2018-01-02 08:49:38Z maronga
117	# parameters are allowed in output commands (OC:)
118	#
119	# 2718 2018-01-02 08:49:38Z maronga
120	# bugfix: exit if no queue has been given neither with option -q nor in the
121	# configuration file
122	#
123	# 2718 2018-01-02 08:49:38Z maronga
124	# file connection file from trunk/SCRIPTS is taken by default
125	#
126	# 2718 2018-01-02 08:49:38Z maronga
127	# Corrected "Former revisions" section
128	#
129	# 2696 2017-12-14 17:12:51Z kanani
130	# Change in file header (GPL part)
131	#
132	# 2693 2017-12-13 12:33:49Z raasch
133	# replacement of variables given by {{<variable>}} in configuration file is now
134	# done in a more general way, variable names are written in small letters
135	#
136	# 2670 2017-12-06 16:32:19Z raasch
137	# test printouts removed
138	#
139	# 2669 2017-12-06 16:03:27Z raasch
140	# file attributes in .palm.iofiles restructured, "loc" attribute completely
141	# removed,
142	# wildcard (*) allowed in .palm.iofiles as file activation string for output
143	# files,
144	# informative messages in case of missing optional input files shortened
145	# bugfix: variable cycle explicitly interpreted with 10 as the number base
146	#
147	# 2638 2017-11-23 12:44:23Z raasch
148	# use of wildcards in file connection statements enabled
149	#
150	# 2605 2017-11-09 15:31:46Z raasch
151	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
152	# will not be sent with the job file any more, but copied into the
153	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
154	#
155	# 2600 2017-11-01 14:11:20Z raasch
156	# cycle numbers are made three digits wide
157	#
158	# 2566 2017-10-20 08:50:47Z raasch
159	# execute command for combine_plot_fields added
160	# "TEMPDIR" renamed "tempdir"
161	# temporary working directory for local batch jobs is created immediately within
162	# the user's palmrun call, due to a requirement of the "grid engine" batch
163	# system, where the working directory is given with batch directive -wd and must
164	# already exist when the job is submitted,
165	# informative messages in non-trace mode reduced and partly reformatted
166	#
167	# 2551 2017-10-18 07:25:11Z raasch
168	# TEMPDIR added as replacement string to be used in batch directives
169	#
170	# 2512 2017-10-04 08:26:59Z raasch
171	# bugfix for determining cycle numbers of NetCDF input files
172	#
173	# 2506 2017-09-29 08:30:37Z raasch
174	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
175	# host configuration added to SOURCES_FOR_RUN_... folder name
176	# host_identifier renamed host_configuration
177	# option -W added to allow for job dependencies
178	#
179	# 2501 2017-09-26 11:41:55Z raasch
180	# default value for number of cores (option -X) set to 1
181	# bugfix for mechanism which overwrites configuration file settings with values
182	# provided by palmrun options
183	#
184	# 2499 2017-09-22 16:47:58Z kanani
185	# option -h named configuration identifier
186	#
187	# 2480 2017-09-19 06:24:14Z maronga
188	# bugfix for last revision
189	#
190	# 2479 2017-09-19 06:12:16Z raasch
191	# option -A (project account number) added
192	#
193	# 2422 2017-09-08 08:25:41Z raasch
194	# initial revision
195	#
196	#--------------------------------------------------------------------------------#
197	# palmrun - script for running PALM jobs on local and remote hosts
198	#--------------------------------------------------------------------------------#
199
200
201
202	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
203
204	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
205	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
206	# (TOO MANY ARGUMENTS - PROBLEM)
207	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
208
209	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
210	typeset -i nr_of_output_files=0
211	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
212	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
213	# SCRIPT-OPTION ARGUMENTS
214	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
215	typeset -i icycle inode ival maxcycle mpi_tasks
216	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
217
218	activation_string_list=""
219	AddFilenames=""
220	combine_plot_fields=true
221	compiler_name=""
222	compiler_name_ser=""
223	compiler_options=""
224	configuration_identifier="default"
225	cores=1
226	cores_atmos=0
227	cores_ocean=0
228	coupled_dist=""
229	cpp_options=""
230	cpumax=0
231	create_batch_job=false
232	create_jobfile_only=false
233	create_remote_batch_job=false
234	dashes=" ----------------------------------------------------------------------------"
235	defaultqueue=""
236	delete_temporary_catalog=true
237	do_compile=true
238	do_trace=false
239	executable=""
240	execute_command=""
241	execution_error=false
242	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
243	global_revision=""
244	hostfile=""
245	hp=""
246	keep_data_from_previous_run=false
247	link_local_input=false
248	link_local_output=false
249	linker_options=""
250	local_jobcatalog=""
251	locat=normal
252	makefile=""
253	max_par_io_str=""
254	prc=$0
255	while [[ $(echo $prc \| grep -c "/") != 0 ]]
256	do
257	prc=`echo $prc \| cut -f2- -d"/"`
258	done
259	module_calls=""
260	palmrun_memory=""
261	palmrun_script_name=$prc
262	openmp=false
263	previous_job=""
264	project_account=""
265	queue=none
266	read_svf=""
267	restart_run=false
268	return_address=""
269	remote_jobcatalog=""
270	remote_username=""
271	running_in_batch_mode=false
272	running_in_test_mode=false
273	run_coupled_model=false
274	run_id=""
275	run_id_number=""
276	run_identifier=test
277	silent=false
278	source_list=""
279	source_path=""
280	tasks_per_node=0
281	threads_per_task=1
282	transfer_problems=false
283	user_source_path=""
284	use_existing_sources_folder=""
285	use_openmp=false
286	version="palmrun 1.0 Rev$Rev: 3725 $"
287	working_directory=`pwd`
288	write_binary=""
289	write_svf=""
290
291
292	# ERROR HANDLING IN CASE OF EXIT
293	trap 'if [[ $locat != normal && $locat != control_c ]]
294	then
295
296	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
297	(( i = 0 ))
298	while (( i < iec ))
299	do
300	(( i = i + 1 ))
301	printf "\n *** Execution of ERROR-command:\n"
302	printf " >>> ${err_command[$i]}\n"
303	eval ${err_command[$i]}
304	done
305	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
306	printf "\n\n+++ palmrun crashed \n\n"
307	exit 1
308	elif [[ $locat != normal ]]
309	then
310	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
311	printf "\n+++ palmrun killed by \"^C\" \n\n"
312	exit 2
313	else
314	printf "\n --> palmrun finished\n\n"
315	exit 0
316	fi' exit
317
318
319	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
320	trap 'locat=control_c
321	exit 1
322	' 2
323
324
325	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
326	# WHICH WILL BE USED TO START RESTART-JOBS
327	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
328	do
329	case $option in
330	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
331	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
332	(b) create_batch_job=true; prc="$prc -b";;
333	(B) delete_temporary_catalog=false; prc="$prc -B";;
334	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
335	(C) restart_run=true; prc="$prc -C";;
336	(F) create_jobfile_only=true;;
337	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
338	(i) run_id_number=$OPTARG;;
339	(j) running_in_batch_mode=true;;
340	(k) keep_data_from_previous_run=true; prc="$prc -k";;
341	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
342	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
343	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
344	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
345	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
346	(R) return_address=$OPTARG;;
347	(s) source_list=$OPTARG;;
348	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
349	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
350	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
351	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
352	(v) silent=true; prc="$prc -v";;
353	(V) use_existing_sources_folder="-V";;
354	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
355	(W) previous_job=$OPTARG;;
356	(x) do_trace=true;set -x; prc="$prc -x";;
357	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
358	(y) ocean_file_appendix=true; prc="$prc -y";;
359	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
360	(z) running_in_test_mode=true;;
361	(Z) combine_plot_fields=false; prc="$prc -Z";;
362	(\?) printf "\n +++ unknown option $OPTARG \n"
363	printf "\n --> type \"$0 ?\" for available options \n"
364	locat=parameter;exit;;
365	esac
366	done
367
368
369	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
370	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
371	(( to_shift = $OPTIND - 1 ))
372	shift $to_shift
373
374	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
375	if [[ "$1" = "?" ]]
376	then
377	(printf "\n *** Description of available palmrun options:\n"
378	printf "\n Option Description Default-Value"
379	printf "\n -a activation string list \"\" "
380	printf "\n -A project account number ---"
381	printf "\n -b batch-job on local machine ---"
382	printf "\n -B do not delete temporary directory at end ---"
383	printf "\n -c configuration identifier \"default\" "
384	printf "\n -F create batch job file only ---"
385	printf "\n -k keep data from previous run"
386	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
387	printf "\n -M Makefile name Makefile"
388	printf "\n -O threads per openMP task ---"
389	printf "\n -q queue \"$queue\" "
390	printf "\n -r run identifier test"
391	printf "\n -s filenames of routines to be compiled \"\" "
392	printf "\n must end with .f, .f90, .F, or .c !"
393	printf "\n use \"..\" for more than one file and wildcards"
394	printf "\n -s LM compiles all locally modified files"
395	printf "\n -t allowed cpu-time in seconds (batch) 0"
396	printf "\n -T tasks per node ---"
397	printf "\n -u username on remote machine \"\" "
398	printf "\n -v no prompt for confirmation ---"
399	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
400	printf "\n -w maximum parallel io streams as given by -X"
401	printf "\n -W name of job to wait for ---"
402	printf "\n -x tracing of palmrun for debug purposes ---"
403	printf "\n -X # of processors (on parallel machines) 1"
404	printf "\n -y add appendix \"_O\" to all local output"
405	printf "\n files (ocean precursor runs followed by"
406	printf "\n coupled atmosphere-ocean runs) ---"
407	printf "\n -Y run coupled model, \"#1 #2\" with"
408	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
409	printf "\n -Z skip combine_plot_fields at the end of "
410	printf "\n the simulation ---"
411	printf "\n "
412	printf "\n Possible values of positional parameter <modus>:"
413	printf "\n \"?\" - this outline \n\n") \| more
414	exit
415	elif [[ "$1" != "" ]]
416	then
417	printf "\n +++ positional parameter $1 unknown \n"
418	locat=parameter; exit
419	fi
420
421
422
423	# SHORT STARTING MESSAGE
424	printf "\n*** $version "
425	printf "\n will be executed. Please wait ..."
426
427
428	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
429	config_file=.palm.config.$configuration_identifier
430	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
431
432
433	# CHECK, IF CONFIGURATION FILE EXISTS
434	if [[ ! -f $config_file ]]
435	then
436	printf "\n\n +++ configuration file: "
437	printf "\n $config_file"
438	printf "\n does not exist"
439	locat=connect; exit
440	fi
441
442
443	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
444	if [[ -f .palm.iofiles ]]
445	then
446
447	# CHECK VERSION MISMATCH
448	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
449	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
450	if [[ $running_in_batch_mode != true && $restart_run != true ]]
451	then
452	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
453	then
454	printf "\n\n +++ WARNING: A file connection file has been found in your"
455	printf "\n working directory, but its revision does not match"
456	printf "\n the revision of the default (trunk) version."
457	printf "\n You may need to update your connection file"
458	printf "\n \"${working_directory}/.palm.iofiles\" !"
459	fi
460	fi
461
462	fileconnection_file=.palm.iofiles
463
464	fi
465
466
467	# CHECK, IF FILE CONNECTION FILE EXISTS
468	if [[ ! -f $fileconnection_file ]]
469	then
470	printf "\n\n +++ file connection file: "
471	printf "\n $fileconnection_file"
472	printf "\n does not exist"
473	locat=connect; exit
474	fi
475
476
477	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
478	if [[ "$activation_string_list" = "" ]]
479	then
480	printf "\n\n +++ no activation string list given: "
481	printf "\n please set palmrun option \"-a\" "
482	locat=palmrun_option; exit
483	fi
484
485
486	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
487	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
488	then
489	write_binary=true
490	else
491	write_binary=false
492	fi
493
494	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
495	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
496	then
497	write_svf=true
498	else
499	write_svf=false
500	fi
501
502	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
503	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
504	then
505	read_svf=true
506	else
507	read_svf=false
508	fi
509
510
511	# READ AND EVALUATE THE CONFIGURATION-FILE
512	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
513
514	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
515	while read line
516	do
517
518	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
519	eval line=\"$line\"
520
521
522	# INTERPRET THE LINE
523	if [[ "$(echo $line)" = "" ]]
524	then
525
526	# EMPTY LINE, NO ACTION
527	continue
528
529	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
530	then
531
532	# LINE IS A COMMENT LINE
533	continue
534
535	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
536	then
537
538	# LINE DEFINES AN ENVIRONMENT-VARIABLE
539	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
540	value=`echo $line \| cut -d" " -s -f2-`
541
542
543	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
544	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
545	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
546	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
547	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
548	# CONFIGURATION-FILE.
549	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
550	then
551	eval export $var="\$value"
552
553	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
554	if [[ $do_trace = true ]]
555	then
556	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
557	fi
558	fi
559
560	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
561	then
562
563	# LINE DEFINES BATCH-DIRECTIVE
564	(( ibd = ibd + 1 ))
565	line=$(echo $line \| cut -c4-)
566	batch_directive[$ibd]="$line"
567
568	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
569	then
570
571	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
572	# REMOTE TO A LOCAL HOST
573	(( ibdt = ibdt + 1 ))
574	line=$(echo $line \| cut -c5-)
575	batch_directive_transfer[$ibdt]="$line"
576
577	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
578	then
579
580	# LINE DEFINES ERROR-COMMAND
581	(( iec = iec + 1 ))
582	line=$(echo $line \| cut -c4-)
583	err_command[$iec]="$line"
584
585	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
586	then
587
588	# LINE DEFINES INPUT-COMMAND
589	(( iic = iic + 1 ))
590	line=$(echo $line \| cut -c4-)
591	in_command[$iic]="$line"
592
593	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
594	then
595
596	# LINE DEFINES OUTPUT-COMMAND
597	(( ioc = ioc + 1 ))
598	line=$(echo $line \| cut -c4-)
599	out_command[$ioc]="$line"
600
601	else
602
603	# SKIP ALL OTHER LINES
604	continue
605
606	fi
607
608	done < $config_file
609
610
611	# CHECK SETTING OF REQUIRED PARAMETERS
612	if [[ "$fast_io_catalog" = "" ]]
613	then
614	printf "\n +++ no fast_io_catalog found in $config_file"
615	printf "\n Please add line \"fast_io_catalog ...\" to that file."
616	locat=config_file; exit
617	fi
618	if [[ "$compiler_name" = "" ]]
619	then
620	printf "\n +++ no compiler name found in $config_file"
621	printf "\n Please add line \"compiler_name ...\" to that file."
622	locat=config_file; exit
623	fi
624	if [[ "$compiler_name_ser" = "" ]]
625	then
626	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
627	printf "\n Please add line \"compiler_name_ser ...\" to that file."
628	locat=config_file; exit
629	fi
630	if [[ "$compiler_options" = "" ]]
631	then
632	printf "\n +++ no compiler options found in $config_file"
633	printf "\n Please add line \"compiler_options ...\" to that file."
634	locat=config_file; exit
635	fi
636	if [[ "$execute_command" = "" ]]
637	then
638	printf "\n +++ no execute command found in $config_file"
639	printf "\n Please add line \"execute_command ...\" to that file."
640	locat=config_file; exit
641	fi
642
643	if [[ "$hostfile" != "" ]]
644	then
645	if [[ $hostfile != auto && ! -f $hostfile ]]
646	then
647	printf "\n +++ no hostfile \"$hostfile\" found"
648	printf "\n Please check line \"hostfile ...\" in $config_file"
649	locat=config_file; exit
650	fi
651	fi
652
653
654	# DETERMINE THE CALL STATUS
655	if [[ "$return_address" != "" ]]
656	then
657
658	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
659	# BATCH MODE AND ...
660	running_on_remote=true
661
662	else
663
664	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
665	if [[ "$remote_ip" != "" ]]
666	then
667
668	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
669	create_remote_batch_job=true
670
671	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
672	if [[ "$remote_jobcatalog" = "" ]]
673	then
674	printf "\n +++ no remote jobcatalog found in $config_file"
675	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
676	locat=config_file; exit
677	fi
678
679
680	fi
681	running_on_remote=false
682	fi
683
684
685
686	# READ AND EVALUATE THE I/O-FILE LIST
687	[[ $silent = false ]] && printf "\n Reading the I/O files... "
688
689	# READ THE FILE CONNECTION FILE LINE BY LINE
690	while read line
691	do
692
693	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
694	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
695	line=`echo "$line" \| tr -s " "`
696
697	# INTERPRET THE LINE
698	if [[ "$(echo $line)" = "" ]]
699	then
700	# EMPTY LINE, NO ACTION
701	continue
702
703	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
704	then
705
706	# LINE IS A COMMENT LINE
707	true
708
709	else
710
711	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
712	# s2a: in/out - field
713	# s2b: action - field (optional)
714	s1=`echo "$line" \| cut -d" " -f1`
715	s2=`echo "$line" \| cut -d" " -s -f2`
716	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
717	then
718	s2a=$s2
719	s2b=""
720	else
721	s2a=`echo $s2 \| cut -d":" -f1`
722	s2b=`echo $s2 \| cut -d":" -f2`
723	fi
724	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
725	s4=`echo "$line" \| cut -d" " -s -f4`
726	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
727	s5=`echo "$line" \| cut -d" " -s -f5`
728	s6=`echo "$line" \| cut -d" " -s -f6`
729
730
731	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
732	# INPUT- OR OUTPUT-LIST.
733	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
734	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
735	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
736	# IS NOT CHECKED AND STORED.
737	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
738	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
739	then
740	found=false
741	for actual in $activation_string_list
742	do
743	for formal in $s3
744	do
745	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
746	done
747	done
748	if [[ $found = true ]]
749	then
750	(( iin = iin + 1 ))
751	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
752	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
753	if [[ "$s2a" = inopt ]]
754	then
755	optin_pre[$iin]=yes
756	else
757	optin_pre[$iin]=no
758	fi
759
760	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
761	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
762	if [[ $running_on_remote = true && "$s2b" = tr ]]
763	then
764	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
765	fi
766
767	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
768	# THE WILDCARD FROM THE ENDING
769	if [[ "${s5: -1}" = "*" ]]
770	then
771	if [[ "$s2b" = "di" ]]
772	then
773	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
774	printf "\n see file \"$fileconnection_file\", line"
775	printf "\n$line"
776	locat=iofiles_file; exit
777	fi
778	multin[$iin]=true
779	string=${endin_pre[$iin]}
780	endin_pre[$iin]="${string%?}"
781	else
782	multin[$iin]=false
783	fi
784	fi
785	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
786	then
787	found=false
788	for actual in $activation_string_list
789	do
790	for formal in $s3
791	do
792	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
793	done
794	done
795	if [[ $found = true ]]
796	then
797	(( iout = iout + 1 ))
798	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
799	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
800
801	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
802	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
803	if [[ $formal = wildcard ]]
804	then
805	warnout_pre[$iout]=false
806	else
807	warnout_pre[$iout]=true
808	fi
809
810	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
811	# THE WILDCARD FROM THE LOCAL FILENAME
812	if [[ "${s1: -1}" = "*" ]]
813	then
814	if [[ "$s2b" = "di" ]]
815	then
816	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
817	printf "\n see file \"$fileconnection_file\", line"
818	printf "\n$line"
819	locat=iofiles_file; exit
820	fi
821	multout[$iout]=true
822	string=${localout_pre[$iout]}
823	localout_pre[$iout]="${string%?}"
824	else
825	multout[$iout]=false
826	fi
827	fi
828	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
829	then
830	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
831	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
832	locat=connect; exit
833	fi
834	IFS="$IFSALT"
835	fi
836
837	done < $fileconnection_file
838
839
840
841	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
842	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
843	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
844	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
845	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
846	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
847
848
849
850	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
851	if [[ $run_coupled_model = true ]]
852	then
853
854	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
855	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
856
857	if (( $cores_ocean + $cores_atmos != $cores ))
858	then
859
860	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
861	printf "\n PEs (total) : $cores"
862	printf "\n PEs (atmosphere): $cores_atmos"
863	printf "\n PEs (ocean) : $cores_ocean"
864	locat=coupling; exit
865
866	fi
867
868	fi
869
870
871	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
872	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
873	# FOLDER
874	if [[ $running_in_batch_mode = true ]]
875	then
876
877	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
878	then
879	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
880	printf "\n Please check the output of the palmrun-call"
881	printf "\n that you did on your local host."
882	locat=SOURCES_FOR_RUN; exit
883	fi
884
885	else
886
887	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
888	# AUTOMATIC RESTART RUN
889	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
890	if [[ $restart_run = false ]]
891	then
892
893	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
894	# THE LOCAL HOST
895	if [[ ! -d $source_path ]]
896	then
897	printf "\n\n +++ source path \"$source_path\" on local host"
898	printf "\n \"$(hostname)\" does not exist"
899	locat=source_path; exit
900	fi
901
902	rm -rf ${base_directory}/${sources_for_run_catalog}
903	mkdir -p ${base_directory}/${sources_for_run_catalog}
904
905	if [[ "$source_list" = LM ]]
906	then
907
908	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
909	source_list=""
910	cd $source_path
911
912
913	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
914	if [[ ! -d ../.svn ]]
915	then
916	printf "\n\n +++ source directory"
917	printf "\n \"$source_path\" "
918	printf "\n is not under control of \"subversion\"."
919	printf "\n Please do not use palmrun-option \"-s LM\"\n"
920	fi
921
922
923	# LIST ALL MODIFIED SOURCE CODE FILES
924	Filenames=""
925	svn status > tmp_svnstatus
926	while read line
927	do
928	firstc=`echo $line \| cut -c1`
929	if [[ $firstc = M \|\| $firstc = "?" ]]
930	then
931	Name=`echo "$line" \| cut -c8-`
932	extension=`echo $Name \| cut -d. -f2`
933	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
934	then
935	Filenames="$Filenames "$Name
936	fi
937	fi
938	done < tmp_svnstatus
939	rm -rf tmp_svnstatus
940
941
942	# COPY FILES TO SOURCES_FOR_RUN_...
943	for filename in $Filenames
944	do
945	cp $filename ${base_directory}/${sources_for_run_catalog}
946	source_list=$source_list"$filename "
947	done
948
949	cd - > /dev/null
950
951
952	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
953	elif [[ "$source_list" != "" ]]
954	then
955
956	cd $source_path
957
958	for filename in $source_list
959	do
960
961	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
962	if [[ $(echo $filename \| grep -c "/") != 0 ]]
963	then
964	printf "\n +++ source code file: $filename"
965	printf "\n must not contain (\"/\") "
966	locat=source; exit
967	fi
968
969	if [[ ! -f $filename ]]
970	then
971	printf "\n +++ source code file: $filename"
972	printf "\n does not exist"
973	locat=source; exit
974	else
975	cp $filename ${base_directory}/${sources_for_run_catalog}
976	fi
977
978	done
979
980	cd - > /dev/null
981
982	fi
983
984	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
985	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
986	if [[ ! -f $makefile ]]
987	then
988	printf "\n +++ file \"$makefile\" does not exist"
989	locat=make; exit
990	else
991	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
992	fi
993
994
995	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
996	if [[ "$user_source_path" != "" ]]
997	then
998
999	# DOES THE DIRECTORY EXIST?
1000	if [[ ! -d $user_source_path ]]
1001	then
1002
1003	printf "\n\n *** INFORMATIVE: additional source code directory"
1004	printf "\n \"$user_source_path\" "
1005	printf "\n does not exist or is not a directory."
1006	printf "\n No source code will be used from this directory!\n"
1007	user_source_path=""
1008	if [[ $silent == false ]]
1009	then
1010	sleep 2
1011	fi
1012
1013	else
1014
1015	cd $user_source_path
1016
1017	Names=$(ls -1 *.f90 2>&1)
1018	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1019	Names=$(ls -1 *.F90 2>&1)
1020	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1021	Names=$(ls -1 *.F 2>&1)
1022	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1023	Names=$(ls -1 *.f 2>&1)
1024	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1025	Names=$(ls -1 *.c 2>&1)
1026	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1027
1028	cd - > /dev/null
1029	cd ${base_directory}/${sources_for_run_catalog}
1030
1031	# COPY MAKEFILE IF EXISTING
1032	if [[ -f $user_source_path/Makefile ]]
1033	then
1034	printf "\n\n *** user Makefile from directory"
1035	printf "\n \"$user_source_path\" is used \n"
1036	if [[ $silent == false ]]
1037	then
1038	sleep 1
1039	fi
1040	cp $user_source_path/Makefile .
1041	fi
1042
1043	for filename in $AddFilenames
1044	do
1045	if [[ -f $filename ]]
1046	then
1047	printf "\n +++ source code file \"$filename\" found in additional"
1048	printf "\n source code directory \"$user_source_path\" "
1049	printf "\n but was also given with option \"-s\" which means that it should be taken"
1050	printf "\n from directory \"$source_path\"."
1051	locat=source; exit
1052	fi
1053
1054	cp $user_source_path/$filename .
1055	source_list="$source_list $filename"
1056
1057	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1058	if [[ $(grep -c $filename Makefile) = 0 ]]
1059	then
1060	printf "\n\n +++ user file \"$filename\" "
1061	printf "\n is not listed in Makefile \n"
1062	locat=source; exit
1063	fi
1064	done
1065	cd - > /dev/null
1066	fi
1067	fi
1068
1069	# COPY CONFIGURATION FILES
1070	cp $config_file ${base_directory}/${sources_for_run_catalog}
1071	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1072
1073	# COPY SHELLSCRIPTS
1074	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1075	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1076
1077	fi
1078
1079	fi
1080
1081
1082	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1083	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1084	if [[ "$global_revision" = "" ]]
1085	then
1086	global_revision=`svnversion $source_path 2>/dev/null`
1087	global_revision="Rev: $global_revision"
1088	fi
1089
1090
1091	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1092	if [[ -n $cores ]]
1093	then
1094
1095	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1096	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1097	if [[ $tasks_per_node = 0 ]]
1098	then
1099	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1100	then
1101	printf "\n"
1102	printf "\n +++ option \"-T\" (tasks per node) is missing"
1103	printf "\n set -T option or define tasks_per_node in the config file"
1104	locat=tasks_per_node; (( iec = 0 )); exit
1105	else
1106	# DEFAULT FOR INTERACTIVE RUN
1107	tasks_per_node=$cores
1108	fi
1109	fi
1110
1111	if (( cores < tasks_per_node ))
1112	then
1113	printf "\n"
1114	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1115	printf "\n given values: -T $tasks_per_node -X $cores"
1116	locat=tasks_per_node; (( iec = 0 )); exit
1117	fi
1118
1119	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1120	(( mpi_tasks = cores / threads_per_task ))
1121	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1122	(( ii = cores / tasks_per_node ))
1123	(( remaining_cores = cores - ii * tasks_per_node ))
1124	if (( remaining_cores > 0 ))
1125	then
1126	printf "\n"
1127	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1128	printf "\n divisor of the total number of cores (option \"-X\")"
1129	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1130	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1131	(( nodes = nodes + 1 ))
1132	fi
1133
1134	fi
1135
1136
1137	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1138	if [[ "$maximum_parallel_io_streams" = "" ]]
1139	then
1140	maximum_parallel_io_streams=$cores
1141	fi
1142
1143
1144	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1145	if [[ "$scp_port" != "" ]]
1146	then
1147	PORTOPT="-P $scp_port"
1148	SSH_PORTOPT="-p $scp_port"
1149	fi
1150
1151
1152	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1153	# CONFIG-FILE
1154	if [[ "$ssh_key" != "" ]]
1155	then
1156	ssh_key="-i $HOME/.ssh/$ssh_key"
1157	fi
1158
1159
1160	# SET QUEUE, IF NOT GIVEN
1161	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1162	then
1163
1164	if [[ $queue = none && "$defaultqueue" = "" ]]
1165	then
1166	printf "\n"
1167	printf "\n +++ no default queue given in configuration file and no queue"
1168	printf "\n given with option -q"
1169	locat=queue; exit
1170	fi
1171	if [[ $queue = none ]]
1172	then
1173	queue=$defaultqueue
1174	fi
1175
1176	fi
1177
1178
1179	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1180	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1181	(( i = 0 ))
1182	(( nr_of_input_files = 0 ))
1183	while (( i < iin ))
1184	do
1185	(( i = i + 1 ))
1186
1187	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1188	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1189	if [[ "${actionin_pre[$i]}" = di ]]
1190	then
1191	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1192	else
1193	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1194	fi
1195
1196
1197	# CHECK IF FILE EXISTS
1198	if ! ls $filename* 1>/dev/null 2>&1
1199	then
1200
1201	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1202	if [[ "${optin_pre[$i]}" != "yes" ]]
1203	then
1204	printf "\n\n +++ INPUT-file: "
1205	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1206	then
1207	printf "\n $filename"
1208	else
1209	printf "\n $filename.${extin_pre[$i]}"
1210	fi
1211	printf "\n does not exist\n"
1212	locat=input; exit
1213	else
1214	(( nr_of_input_files = nr_of_input_files + 1 ))
1215	localin[$nr_of_input_files]="${localin_pre[$i]}"
1216	optin[$nr_of_input_files]="${optin_pre[$i]}"
1217	actionin[$nr_of_input_files]="unavailable"
1218	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1219	endin[$nr_of_input_files]="${endin_pre[$i]}"
1220	extin[$nr_of_input_files]="${extin_pre[$i]}"
1221	fi
1222
1223	else
1224
1225	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1226	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1227	# ENDINGS
1228	if [[ "${multin[$i]}" = true ]]
1229	then
1230	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1231	ls -1 -d ${filename} > filelist 2>/dev/null
1232	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1233	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1234
1235	endings=""
1236	while read line
1237	do
1238	# filename without path (i.e. after the last "/")
1239	basefilename=$(basename ${line})
1240
1241	# check if there is an extension and remove it
1242	ext=${basefilename##*.}
1243	if [[ "$ext" = "${extin_pre[$i]}" ]]
1244	then
1245	basefilename=${basefilename%.*}
1246	fi
1247
1248	# check for an existing cycle number and remove it
1249	cycle=${basefilename##*.}
1250	if [[ $cycle =~ ^-?[0-9]+$ ]]
1251	then
1252	basefilename=${basefilename%.*}
1253	fi
1254
1255	# remove the run_identifier from the beginning
1256	length_run_identifier=${#run_identifier}
1257	ending=${basefilename:${length_run_identifier}}
1258
1259	# remove the ending given in the .iofiles from the beginning
1260	endingstring="${endin_pre[$i]}"
1261	length_ending=${#endingstring}
1262	ending=${ending:${length_ending}}
1263
1264	if [[ "$ending" = "" ]]
1265	then
1266	# standard ending as given in the .iofiles
1267	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1268	then
1269	endings="$endings DEFAULT"
1270	fi
1271	else
1272	# ending must start with "_", otherwise its a different file
1273	if [[ "${ending:0:1}" = "_" ]]
1274	then
1275	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1276	then
1277	endings="$endings $ending"
1278	fi
1279	fi
1280	fi
1281
1282	done <filelist
1283
1284	rm filelist
1285
1286	else
1287
1288	# SINGLE NAME
1289	endings=DEFAULT
1290
1291	fi
1292
1293	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1294	for ending in $endings
1295	do
1296
1297	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1298	if [[ $ending = DEFAULT ]]
1299	then
1300	ending=""
1301	fi
1302
1303	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1304	(( nr_of_input_files = nr_of_input_files + 1 ))
1305	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1306	optin[$nr_of_input_files]="${optin_pre[$i]}"
1307	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1308	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1309	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1310	extin[$nr_of_input_files]="${extin_pre[$i]}"
1311
1312
1313	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1314	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1315	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1316	then
1317	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1318	else
1319	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1320	fi
1321
1322	# DETERMINE THE FILE'S CYCLE NUMBER
1323	(( maxcycle = 0 ))
1324	ls -1 -d $filename > filelist 2>/dev/null
1325	ls -1 -d $filename.* >> filelist 2>/dev/null
1326	while read line
1327	do
1328	# filename without path (i.e. after the last "/")
1329	basefilename=$(basename ${line})
1330
1331	# check if there is an extension
1332	extension=${basefilename##*.}
1333	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1334	then
1335	basefilename=${basefilename%.*}
1336	fi
1337
1338	# check for an existing cycle number
1339	cycle=${basefilename##*.}
1340	if [[ $cycle =~ ^-?[0-9]+$ ]]
1341	then
1342	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1343	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1344	(( icycle = $((10#$cycle)) ))
1345	else
1346	(( icycle = 0 ))
1347	fi
1348
1349	if (( icycle > maxcycle ))
1350	then
1351	(( maxcycle = icycle ))
1352
1353	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1354	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1355	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1356	then
1357	leading_zero=true
1358	else
1359	leading_zero=false
1360	fi
1361	fi
1362
1363	done <filelist
1364	rm filelist
1365
1366	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1367	if [[ $leading_zero = true ]]
1368	then
1369	cyclestring=`printf "%03d" $maxcycle`
1370	else
1371	cyclestring=$maxcycle
1372	fi
1373
1374	# APPEND CYCLE NUMBER TO FILENAME
1375	if (( maxcycle > 0 ))
1376	then
1377	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1378	then
1379	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1380	else
1381	filename=${filename}.$cyclestring
1382	fi
1383	else
1384	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1385	then
1386	filename=${filename}.${extin[$nr_of_input_files]}
1387	fi
1388	fi
1389
1390	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1391	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1392	absnamein[$nr_of_input_files]=$filename
1393	if (( maxcycle > 0 ))
1394	then
1395	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1396	then
1397	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1398	else
1399	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1400	fi
1401	else
1402	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1403	then
1404	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1405	else
1406	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1407	fi
1408	fi
1409
1410	done
1411
1412	fi
1413
1414	done
1415
1416
1417	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1418	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1419	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1420	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1421	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1422	# REMOTE HOST)
1423	(( i = 0 ))
1424	while (( i < iout ))
1425	do
1426	(( i = i + 1 ))
1427	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1428	then
1429	if [[ "${actionout_pre[$i]}" = tr ]]
1430	then
1431	actionout_pre[$i]=""
1432	elif [[ "${actionout_pre[$i]}" = trpe ]]
1433	then
1434	actionout_pre[$i]=pe
1435	elif [[ "${actionout_pre[$i]}" = tra ]]
1436	then
1437	actionout_pre[$i]=a
1438	fi
1439	(( maxcycle = 0 ))
1440	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1441	eval catalogname=${pathout_pre[$i]}
1442	if ! ls $filename* 1>/dev/null 2>&1
1443	then
1444
1445	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1446	if cat /dev/null > $filename
1447	then
1448	rm $filename
1449	else
1450
1451	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1452	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1453	if [[ ! -d $catalogname ]]
1454	then
1455	if mkdir -p $catalogname
1456	then
1457	printf "\n\n *** directory:"
1458	printf "\n $catalogname"
1459	printf "\n was created\n"
1460	else
1461	printf "\n\n +++ OUTPUT-file:"
1462	printf "\n $filename"
1463	printf "\n cannot be created, because directory does not exist"
1464	printf "\n and cannot be created either"
1465	printf "\n"
1466	locat=output ; exit
1467	fi 2>/dev/null
1468	else
1469	printf "\n\n +++ OUTPUT-file:"
1470	printf "\n $filename"
1471	printf "\n cannot be created, although directory exists"
1472	printf "\n"
1473	locat=output ; exit
1474	fi
1475	fi 2>/dev/null
1476
1477	fi
1478
1479	fi
1480	done
1481
1482
1483	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1484	if [[ $running_in_batch_mode = false ]]
1485	then
1486	run_id_number=$RANDOM
1487	run_id=${run_identifier}.$run_id_number
1488
1489	tempdir=$fast_io_catalog/$run_id
1490
1491	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1492	export job_id=$run_id
1493
1494	fi
1495
1496
1497	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1498	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1499	then
1500
1501	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1502	if [[ $ibd = 0 ]]
1503	then
1504	printf "\n"
1505	printf "\n +++ no batch directives found in configuration file"
1506	locat=config_file_batch_directives; (( iec = 0 )); exit
1507	fi
1508
1509	# CHECK IF CPUTIME IS GIVEN FOR JOB
1510	done=false
1511	cputime=$cpumax
1512	while [[ $done = false ]]
1513	do
1514	if (( cputime == 0 ))
1515	then
1516	printf "\n +++ cpu-time is undefined"
1517	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1518	printf "\n >>> "
1519	read cputime 1>/dev/null 2>&1
1520	else
1521	done=true
1522	fi
1523	done
1524	cpumax=$cputime
1525
1526	# CHECK THE MEMORY DEMAND
1527	done=false
1528	while [[ $done = false ]]
1529	do
1530	if (( memory == 0 ))
1531	then
1532	printf "\n +++ memory demand is undefined"
1533	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1534	printf "\n >>> "
1535	read memory 1>/dev/null 2>&1
1536	else
1537	done=true
1538	fi
1539	done
1540
1541	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1542	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1543	then
1544	while [[ -z $remote_username ]]
1545	do
1546	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1547	printf "\n >>> Please type username:"
1548	printf "\n >>> "
1549	read remote_username
1550	done
1551	fi
1552
1553	else
1554
1555	if [[ $running_in_batch_mode = false ]]
1556	then
1557	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1558	cpumax=$cputime
1559	else
1560	cputime=$cpumax
1561	fi
1562
1563	fi
1564
1565
1566	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1567	(( cpu_hours = cputime / 3600 ))
1568	(( resttime = cputime - cpu_hours * 3600 ))
1569	(( cpu_minutes = resttime / 60 ))
1570	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1571	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1572
1573
1574	# OUTPUT OF THE PALMRUN-HEADER
1575	calltime=$(date)
1576	printf "\n"
1577	printf "#------------------------------------------------------------------------# \n"
1578	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1579	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1580	printf "\| \| \n"
1581	column1="called on:"; column2=$(hostname)
1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1583	if [[ $create_remote_batch_job = true ]]
1584	then
1585	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1586	else
1587	if [[ $running_on_remote = true ]]
1588	then
1589	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1590	else
1591	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1592	fi
1593	fi
1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1595
1596	column1="running in:"
1597	if [[ $running_in_batch_mode = true ]]
1598	then
1599	column2="batch job mode"
1600	else
1601	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1602	then
1603	column2="job creation mode"
1604	else
1605	column2="interactive run mode"
1606	fi
1607	fi
1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1609
1610	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1611	then
1612	if [[ "$project_account" != "" ]]
1613	then
1614	column1="project account number:"
1615	column2="$project_account"
1616	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1617	fi
1618	fi
1619
1620	if [[ -n $cores ]]
1621	then
1622	if [[ $run_coupled_model = false ]]
1623	then
1624	column1="number of cores:"; column2=$cores
1625	else
1626	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1627	fi
1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1629	fi
1630	if [[ -n $tasks_per_node ]]
1631	then
1632	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1634	if (( remaining_cores > 0 ))
1635	then
1636	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1638	fi
1639	fi
1640	if [[ $maximum_parallel_io_streams != $cores ]]
1641	then
1642	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1644	fi
1645	if [[ $use_openmp = true ]]
1646	then
1647	column1="threads per task:"; column2="$threads_per_task"
1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1649	fi
1650	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1651	then
1652	column1="memory demand / PE":; column2="$memory MB"
1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1654	column1="job cpu time (h:m:s):"; column2="$timestring"
1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1656	fi
1657	printf "\| \| \n"
1658	if [[ "$source_list" != "" ]]
1659	then
1660	if [[ "$make_options" != "" ]]
1661	then
1662	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1664	line=$(echo "$make_options" \| cut -c46-)
1665	while [[ "$line" != "" ]]
1666	do
1667	column1=""
1668	column2=$(echo "$line" \| cut -c-45)
1669	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1670	line=$(echo "$line" \| cut -c46-)
1671	done
1672	fi
1673	fi
1674
1675	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1677	line=$(echo "$cpp_options" \| cut -c46-)
1678	while [[ "$line" != "" ]]
1679	do
1680	column1=""
1681	column2=$(echo "$line" \| cut -c-45)
1682	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1683	line=$(echo "$line" \| cut -c46-)
1684	done
1685
1686	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1687	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1688	line=$(echo "$compiler_options" \| cut -c46-)
1689	while [[ "$line" != "" ]]
1690	do
1691	column1=""
1692	column2=$(echo "$line" \| cut -c-45)
1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1694	line=$(echo "$line" \| cut -c46-)
1695	done
1696
1697	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1698	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1699	line=$(echo "$linker_options" \| cut -c46-)
1700	while [[ "$line" != "" ]]
1701	do
1702	column1=""
1703	column2=$(echo "$line" \| cut -c-45)
1704	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1705	line=$(echo "$line" \| cut -c46-)
1706	done
1707
1708	if [[ "$login_init_cmd" != "" ]]
1709	then
1710	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1712	line=$(echo "$login_init_cmd" \| cut -c46-)
1713	while [[ "$line" != "" ]]
1714	do
1715	column1=""
1716	column2=$(echo "$line" \| cut -c-45)
1717	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1718	line=$(echo "$line" \| cut -c46-)
1719	done
1720	fi
1721
1722	if [[ "$module_commands" != "" ]]
1723	then
1724	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1725	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1726	line=$(echo "$module_commands" \| cut -c46-)
1727	while [[ "$line" != "" ]]
1728	do
1729	column1=""
1730	column2=$(echo "$line" \| cut -c-45)
1731	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1732	line=$(echo "$line" \| cut -c46-)
1733	done
1734	fi
1735	printf "\| \| \n"
1736	column1="run identifier:"; column2=$run_identifier
1737	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1738	column1="activation string list:"; column2=$(echo $activation_string_list)
1739	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1740
1741	if [[ "$ocean_file_appendix" = true ]]
1742	then
1743	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1744	fi
1745
1746	if [[ "$source_list" != "" ]]
1747	then
1748	printf "\| \| \n"
1749	printf "\| Files to be compiled: \| \n"
1750	line=$source_list
1751	while [[ "$line" != "" ]]
1752	do
1753	linestart=$(echo $line \| cut -c-70)
1754	printf "\| %-70s \| \n" "$linestart"
1755	line=$(echo "$line" \| cut -c71-)
1756	done
1757	fi
1758	printf "#------------------------------------------------------------------------#"
1759
1760
1761
1762	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1763	if [[ $do_trace = true ]]
1764	then
1765	(( i = 0 ))
1766	while (( i < nr_of_input_files ))
1767	do
1768	(( i = i + 1 ))
1769	if (( i == 1 ))
1770	then
1771	printf "\n\n >>> INPUT-file assignments:\n"
1772	fi
1773	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1774	done
1775	(( i = 0 ))
1776	while (( i < iout ))
1777	do
1778	(( i = i + 1 ))
1779	if (( i == 1 ))
1780	then
1781	printf "\n\n >>> OUTPUT-file assignments:\n"
1782	fi
1783	printf "\n ${localout[$i]} : ${pathout[$i]}"
1784	done
1785	(( i = 0 ))
1786	while (( i < iic ))
1787	do
1788	(( i = i + 1 ))
1789	if (( i == 1 ))
1790	then
1791	printf "\n\n >>> INPUT-commands:\n"
1792	fi
1793	printf "\n ${in_command[$i]}"
1794	done
1795	(( i = 0 ))
1796	while (( i < ioc ))
1797	do
1798	(( i = i + 1 ))
1799	if (( i == 1 ))
1800	then
1801	printf "\n\n >>> OUTPUT-commands:\n"
1802	fi
1803	printf "\n ${out_command[$i]}"
1804	done
1805	fi
1806
1807	# QUERY FOR CONTINUE
1808	if [[ $silent = false && $running_in_batch_mode = false ]]
1809	then
1810	antwort=dummy
1811	printf "\n\n"
1812	printf " >>> everything o.k. (y/n) ? "
1813	while read antwort
1814	do
1815	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1816	then
1817	printf " >>> everything o.k. (y/n) ? "
1818	else
1819	break
1820	fi
1821	done
1822	if [[ $antwort = n \|\| $antwort = N ]]
1823	then
1824	locat=user_abort; (( iec = 0 )); exit
1825	fi
1826	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1827	then
1828	printf "\n *** batch-job will be created and submitted"
1829	else
1830	printf "\n *** PALMRUN will now continue to execute on this machine"
1831	fi
1832	fi
1833
1834
1835
1836	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1837	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1838	then
1839
1840	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1841	then
1842	printf "\n\n *** creating executable and other sources for the remote host\n"
1843	else
1844	printf "\n\n *** creating executable and other sources for the local host\n"
1845	fi
1846
1847	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1848	# IT SHALL BE CREATED
1849	ask_for_make_depository=false
1850	if [[ $create_remote_batch_job = true ]]
1851	then
1852
1853	line=`grep %base_directory $config_file`
1854	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1855	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1856
1857	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1858	then
1859	printf "\n\n +++ make depository \"${make_depository}\""
1860	printf "\n on remote host not found!"
1861	ask_for_make_depository=true
1862	fi
1863	rm ${configuration_identifier}_last_make_protokoll
1864
1865	else
1866
1867	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1868	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1869	if [[ ! -d ${make_depository} ]]
1870	then
1871	printf "\n\n +++ make depository \"${make_depository}\""
1872	printf "\n on local host not found!"
1873	ask_for_make_depository=true
1874	fi
1875
1876	fi
1877
1878	if [[ $ask_for_make_depository = true ]]
1879	then
1880
1881	antwort=dummy
1882	printf "\n\n"
1883	printf " >>> Create a new one (y/n) ? "
1884	while read antwort
1885	do
1886	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1887	then
1888	printf " >>> Create a new one (y/n) ? "
1889	else
1890	break
1891	fi
1892	done
1893	if [[ $antwort = n \|\| $antwort = N ]]
1894	then
1895	locat=user_abort; (( iec = 0 )); exit
1896	fi
1897
1898	if [[ $do_trace = true ]]
1899	then
1900	palmbuild -c $configuration_identifier
1901	else
1902	palmbuild -v -c $configuration_identifier
1903	fi
1904
1905	if [[ ${PIPESTATUS[0]} != 0 ]]
1906	then
1907
1908	# ABORT IN CASE OF COMPILATION PROBLEMS
1909	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1910	locat=make_depository
1911	exit
1912	else
1913	echo " *** now continue with creating executable and other sources"
1914	fi
1915
1916	fi
1917
1918	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1919	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1920
1921	if [[ ${PIPESTATUS[0]} != 0 ]]
1922	then
1923
1924	# ABORT IN CASE OF COMPILATION PROBLEMS
1925	printf "\n +++ error while creating executable and/or other sources"
1926	locat=execution
1927	rm -rf ${base_directory}/${sources_for_run_catalog}
1928	exit
1929
1930	else
1931
1932	printf " *** executable and other sources created\n"
1933	rm -rf ${base_directory}/${sources_for_run_catalog}
1934
1935	fi
1936
1937	fi
1938
1939
1940	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1941	# WILL BE COPIED TO THE REMOTE HOST
1942	if [[ $create_remote_batch_job = true ]]
1943	then
1944	(( i = 0 ))
1945	while (( i < nr_of_input_files ))
1946	do
1947	(( i = i + 1 ))
1948	if [[ "${actionin[$i]}" = tr ]]
1949	then
1950	eval inputfile=${pathin[$i]}/${frelin[$i]}
1951	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1952	fi
1953	done
1954	if (( i > 0 ))
1955	then
1956	printf "\n\n *** input files have been copied to the remote host\n"
1957	fi
1958	fi
1959
1960
1961	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1962	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1963	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1964	then
1965
1966	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1967	if [[ $running_in_batch_mode = false ]]
1968	then
1969	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1970	# FOLDER
1971	mkdir -p $tempdir
1972	chmod go+rx $tempdir
1973	cd $tempdir
1974	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1975	printf "\n *** changed to temporary directory: $tempdir"
1976
1977	else
1978
1979	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1980	printf "\n *** running in temporary directory: $tempdir"
1981
1982	fi
1983
1984
1985	# PROVIDE THE INPUT FILES
1986	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1987	optional_files_missing=false
1988	(( i = 0 ))
1989	while (( i < nr_of_input_files ))
1990	do
1991	(( i = i + 1 ))
1992	if (( i == 1 ))
1993	then
1994	printf "\n\n *** providing INPUT-files:\n$dashes"
1995	fi
1996
1997
1998	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1999	if [[ "${actionin[$i]}" = unavailable ]]
2000	then
2001	optional_files_missing=true
2002	continue
2003	fi
2004
2005	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2006	files_for_cores=false; filetype=file
2007	if [[ "${actionin[$i]}" = pe && -n $cores ]]
2008	then
2009	files_for_cores=true; filetype=files
2010	actionin[$i]=""
2011	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
2012	then
2013	actionin[$i]=""
2014	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
2015	then
2016	files_for_cores=true; filetype=files
2017	actionin[$i]="ln"
2018	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
2019	then
2020	actionin[$i]="ln"
2021	fi
2022
2023	if [[ $files_for_cores = true ]]
2024	then
2025	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2026	else
2027	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2028	fi
2029
2030	# INPUT-FILES TO BE LINKED
2031	if [[ "${actionin[$i]}" = ln ]]
2032	then
2033
2034	printf "\n $filetype will be linked"
2035	if [[ $files_for_cores = false ]]
2036	then
2037	if [[ -f "${absnamein[$i]}" ]]
2038	then
2039	ln ${absnamein[$i]} ${localin[$i]}
2040	got_tmp[$i]=true
2041	fi
2042	else
2043	if [[ -d "${absnamein[$i]}" ]]
2044	then
2045	mkdir -p ${localin[$i]}
2046	cd ${absnamein[$i]}
2047	for file in $(ls *)
2048	do
2049	ln $file $tempdir/${localin[$i]}
2050	done >\|/dev/null 2>&1
2051	cd $tempdir
2052	fi
2053
2054	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2055	if [[ ! -f "${localin[$i]}/_000000" ]]
2056	then
2057	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2058	cp -r ${absnamein[$i]}/* ${localin[$i]}
2059	fi
2060
2061	got_tmp[$i]=true
2062	fi
2063	fi
2064
2065	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2066	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2067	then
2068
2069	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2070	then
2071
2072	# FILE COPIES ARE PROVIDED FOR ALL CORES
2073	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2074	printf "\n file will be provided for $cores processors"
2075	mkdir -p ${localin[$i]}
2076	ival=$cores
2077	(( ii = 0 ))
2078	while (( ii <= ival-1 ))
2079	do
2080	if (( ii < 10 ))
2081	then
2082	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2083	elif (( ii < 100 ))
2084	then
2085	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2086	elif (( ii < 1000 ))
2087	then
2088	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2089	else
2090	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2091	fi
2092	(( ii = ii + 1 ))
2093	done
2094
2095	else
2096
2097	if [[ $files_for_cores = true ]]
2098	then
2099
2100	# PROVIDE FILES FOR EACH CORE
2101	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2102	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2103	printf "\n providing $cores files for the respective cores"
2104	mkdir -p ${localin[$i]}
2105	if [[ $link_local_input = true ]]
2106	then
2107	printf " files will be linked\n"
2108	cd ${absnamein[$i]}
2109	for file in $(ls *)
2110	do
2111	ln -f $file ${localin[$i]}
2112	done
2113	cd $tempdir
2114	fi
2115
2116	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2117	if [[ ! -f "${localin[$i]}/_000000" ]]
2118	then
2119	if [[ $link_local_input = true ]]
2120	then
2121	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2122	fi
2123	cp -r ${absnamein[$i]}/* ${localin[$i]}
2124	fi
2125
2126	else
2127
2128	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2129	if [[ $link_local_input = true ]]
2130	then
2131	printf " file will be linked\n"
2132	ln -f ${absnamein[$i]} ${localin[$i]}
2133	fi
2134	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2135	if [[ ! -f "${localin[$i]}" ]]
2136	then
2137	if [[ $link_local_input = true ]]
2138	then
2139	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2140	fi
2141	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2142	then
2143	mv ${absnamein[$i]} ${localin[$i]}
2144	else
2145	cp ${absnamein[$i]} ${localin[$i]}
2146	fi
2147	fi
2148	fi
2149	fi
2150	fi
2151
2152	done
2153	if (( i != 0 ))
2154	then
2155	if [[ $optional_files_missing = true ]]
2156	then
2157	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2158	fi
2159	printf "\n$dashes\n *** all INPUT-files provided \n"
2160	fi
2161
2162
2163	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2164	(( i = 0 ))
2165	while (( i < iic ))
2166	do
2167	(( i = i + 1 ))
2168	if (( i == 1 ))
2169	then
2170	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2171	fi
2172	printf "\n >>> ${in_command[$i]}"
2173	eval ${in_command[$i]}
2174	if (( i == iic ))
2175	then
2176	printf "\n$dashes\n"
2177	fi
2178	done
2179
2180
2181	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2182	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2183	then
2184	progress_bar_disabled=true
2185	else
2186	progress_bar_disabled=false
2187	fi
2188
2189
2190	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2191	# (FILE ENVPAR WILL BE READ BY PALM)
2192	cat > ENVPAR << EOF
2193	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2194	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2195	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2196	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2197	maximum_cpu_time_allowed = ${cpumax}.,
2198	revision = '$global_revision',
2199	progress_bar_disabled = .${progress_bar_disabled}. /
2200
2201	EOF
2202
2203
2204	# STARTING THE EXECUTABLE
2205	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2206	PATH=$PATH:$tempdir
2207
2208
2209	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2210	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2211	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2212	eval line=\"$line\"
2213	execute_command="$line"
2214
2215
2216	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2217	if [[ "$execute_command_for_combine" = "" ]]
2218	then
2219	eval line2=\"$line2\"
2220	execute_command_for_combine="$line2"
2221	fi
2222
2223
2224
2225	# PROVIDE A HOSTFILE, IF REQUIRED
2226	if [[ "$hostfile" != "" ]]
2227	then
2228
2229	if [[ $hostfile = auto ]]
2230	then
2231	# CREATE A NEW HOSTFILE
2232	(( ii = 1 ))
2233	while (( ii <= cores / threads_per_task ))
2234	do
2235	echo $(hostname) >> hostfile
2236	(( ii = ii + 1 ))
2237	done
2238	if (( cores / threads_per_task == 0 ))
2239	then
2240	echo $(hostname) >> hostfile
2241	fi
2242
2243	else
2244	cp $hostfile hostfile
2245	fi
2246	eval line=\"`head -n $ii hostfile`\"
2247	printf "\n *** running on: $line"
2248	fi
2249
2250
2251
2252	# SET THE NUMBER OF OPENMP-THREADS
2253	if [[ $use_openmp = true ]]
2254	then
2255	export OMP_NUM_THREADS=$threads_per_task
2256	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2257	else
2258	export OMP_NUM_THREADS=1
2259	fi
2260
2261
2262	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2263	if [[ $run_coupled_model = false ]]
2264	then
2265	if [[ "$ocean_file_appendix" = true ]]
2266	then
2267	echo "precursor_ocean" > coupling_steering
2268	else
2269	echo "precursor_atmos" > coupling_steering
2270	fi
2271	else
2272	(( iia = $cores_atmos / $threads_per_task ))
2273	(( iio = $cores_ocean / $threads_per_task ))
2274	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2275	printf "\n\n"
2276	echo "coupled_run $iia $iio" > coupling_steering
2277	fi
2278
2279	printf "\n *** execute command:"
2280	printf "\n \"$execute_command\" \n\n"
2281
2282
2283	if [[ $progress_bar_disabled = true ]]
2284	then
2285	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2286	exit_code=${PIPESTATUS[0]}
2287	else
2288	$execute_command < coupling_steering &> >(tee STDOUT)
2289	exit_code=${PIPESTATUS[0]}
2290	fi
2291
2292	if [[ ${exit_code} != 0 ]]
2293	then
2294
2295	# ABORT IN CASE OF RUNTIME ERRORS
2296	printf "\n +++ runtime error occured"
2297	locat=execution
2298	exit
2299
2300	else
2301
2302	printf "\n$dashes\n *** execution finished \n"
2303
2304	fi
2305
2306
2307	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2308	# BY EACH CORE INTO ONE FILE
2309	if [[ ! -f combine_plot_fields.x ]]
2310	then
2311
2312	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2313	printf "\n 2d- and/or 3d-data may be incomplete!"
2314	printf "\n Your previous palmbuild may have failed. Please check.\n"
2315
2316	elif [[ "$combine_plot_fields" == true ]]
2317	then
2318
2319	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2320	$execute_command_for_combine
2321
2322	else
2323
2324	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2325	# DATA OUTPUT
2326	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2327	fi
2328
2329
2330
2331	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2332	(( i = 0 ))
2333	while (( i < ioc ))
2334	do
2335	(( i = i + 1 ))
2336	if (( i == 1 ))
2337	then
2338	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2339	fi
2340
2341	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2342	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2343
2344	printf "\n >>> ${out_command[$i]}"
2345	eval ${out_command[$i]}
2346	if (( i == ioc ))
2347	then
2348	printf "\n$dashes\n"
2349	fi
2350	done
2351
2352
2353	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2354	# WILDCARDS
2355	(( i = 0 ))
2356	(( nr_of_output_files = 0 ))
2357
2358	while (( i < iout ))
2359	do
2360
2361	(( i = i + 1 ))
2362
2363	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2364	# CREATE A LIST FOR THE DETECTED ENDINGS
2365	if [[ "${multout[$i]}" = true ]]
2366	then
2367	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2368	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2369	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2370
2371	endings="DEFAULT"
2372	while read line
2373	do
2374	# remove the local name from the beginning
2375	localnamestring="${localout_pre[$i]}"
2376	length_localname=${#localnamestring}
2377	ending=${line:${length_localname}}
2378
2379	if [[ "$ending" != "" ]]
2380	then
2381	endings="$endings $ending"
2382	fi
2383
2384	done <filelist
2385
2386	rm filelist
2387
2388	else
2389
2390	# SINGLE NAME
2391	endings=DEFAULT
2392
2393	fi
2394
2395	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2396	for ending in $endings
2397	do
2398
2399	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2400	if [[ $ending = DEFAULT ]]
2401	then
2402	ending=""
2403	fi
2404
2405	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2406	(( nr_of_output_files = nr_of_output_files + 1 ))
2407	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2408	transout[$nr_of_output_files]="${transout_pre[$i]}"
2409	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2410	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2411	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2412	extout[$nr_of_output_files]="${extout_pre[$i]}"
2413	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2414
2415	done
2416
2417	done
2418
2419
2420
2421
2422	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2423	(( i = 0 ))
2424	while (( i < nr_of_output_files ))
2425	do
2426	(( i = i + 1 ))
2427	if (( i == 1 ))
2428	then
2429	printf "\n\n *** saving OUTPUT-files:"
2430
2431	# GET RUN NUMBER ASSIGNED BY PALM
2432	if [[ -f RUN_NUMBER ]]
2433	then
2434	read run_number < RUN_NUMBER
2435	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2436	usecycle_option="-U $run_number"
2437	else
2438	run_number=0
2439	usecycle_option=""
2440	fi
2441	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2442	then
2443	printf "\n *** in case of SCP transfers to local host"
2444	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2445	fi
2446	printf "\n$dashes"
2447	fi
2448
2449	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2450	then
2451
2452	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2453
2454	# DETERMINE THE CYCLE NUMBER
2455	ls -1 -d $filename > filelist 2>/dev/null
2456	ls -1 -d $filename.* >> filelist 2>/dev/null
2457	while read line
2458	do
2459
2460	# filename without path (i.e. after the last "/")
2461	basefilename=$(basename ${line})
2462
2463	# check if there is an extension
2464	extension=${basefilename##*.}
2465	if [[ "$extension" = "${extout[$i]}" ]]
2466	then
2467	basefilename=${basefilename%.*}
2468	fi
2469
2470	# check for an existing cycle number
2471	cycle=${basefilename##*.}
2472	if [[ $cycle =~ ^-?[0-9]+$ ]]
2473	then
2474	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2475	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2476	(( icycle = $((10#$cycle)) + 1 ))
2477	else
2478	(( icycle = 1 ))
2479	fi
2480
2481	if (( icycle > maxcycle ))
2482	then
2483	(( maxcycle = icycle ))
2484	fi
2485
2486	done <filelist
2487	rm filelist
2488
2489
2490	# SET THE CYCLE NUMBER
2491	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2492	if [[ "${actionout[$i]}" = a ]]
2493	then
2494	(( maxcycle = maxcycle - 1 ))
2495	fi
2496
2497	(( cycnum[$i] = maxcycle ))
2498	pathout[$i]=$filename
2499
2500
2501	# ADD CYCLE NUMBER TO FILENAME
2502	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2503	if [[ "${actionout[$i]}" != "a" ]]
2504	then
2505	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2506	# WITH AN EXISTING CYCLE NUMBER
2507	if (( run_number >= cycnum[$i] ))
2508	then
2509	(( cycnum[$i] = run_number ))
2510	else
2511	if (( run_number > 0 ))
2512	then
2513	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2514	fi
2515	fi
2516	fi
2517	if (( cycnum[$i] > 0 ))
2518	then
2519	cyclestring=`printf "%03d" ${cycnum[$i]}`
2520	pathout[$i]=${pathout[$i]}.$cyclestring
2521	fi
2522	fi
2523
2524	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2525	files_for_cores=false; filetype=file
2526	link_local_output=false
2527	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2528	then
2529	files_for_cores=true; filetype=directory
2530	actionout[$i]=""
2531	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2532	then
2533	actionout[$i]=""
2534	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2535	then
2536	files_for_cores=true; filetype=directory
2537	link_local_output=true
2538	actionout[$i]=""
2539	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2540	then
2541	link_local_output
2542	actionout[$i]=""
2543	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2544	then
2545	files_for_cores=true; filetype=directory
2546	actionout[$i]="tr"
2547	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2548	then
2549	actionout[$i]="tr"
2550	fi
2551
2552	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2553	then
2554	if [[ ${warnout[$i]} = true ]]
2555	then
2556	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2557	fi
2558	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2559	then
2560	if [[ ${warnout[$i]} = true ]]
2561	then
2562	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2563	fi
2564	else
2565
2566
2567	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2568	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2569	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2570	then
2571	if [[ $running_on_remote = true ]]
2572	then
2573
2574	# SET OPTIONS FOR TRANSFER
2575	if [[ "${actionout[$i]}" = tr ]]
2576	then
2577	if [[ $files_for_cores = false ]]
2578	then
2579	catalog_option=""
2580	catalog_string=""
2581	else
2582	catalog_option="-c"
2583	catalog_string="/"
2584	fi
2585	append_option=""
2586	append_string=""
2587	else
2588	append_option="-A"
2589	append_string="append"
2590	fi
2591
2592	transfer_failed=false
2593	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2594	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2595
2596	# TRANSFER VIA SCP
2597	if [[ "$remote_loginnode" != "" ]]
2598	then
2599	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]}"
2600	else
2601	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]}
2602	fi
2603	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2604
2605
2606	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2607	if [[ $transfer_failed = true ]]
2608	then
2609	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2610	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2611
2612	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2613	eval local_catalog=${pathout[$i]}
2614	if [[ ! -d $local_catalog ]]
2615	then
2616	printf " *** local directory does not exist. Trying to create:\n"
2617	printf " $local_catalog \n"
2618	mkdir -p $local_catalog
2619	fi
2620	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2621	transfer_problems=true
2622	fi
2623
2624	else
2625
2626	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2627	# BE COPIED OR APPENDED ON THIS MACHINE
2628	if [[ "${actionout[$i]}" = tr ]]
2629	then
2630	actionout[$i]=""
2631	else
2632	actionout[$i]="a"
2633	fi
2634	fi
2635	fi
2636
2637
2638	# APPEND ON THIS MACHINE
2639	if [[ "${actionout[$i]}" = "a" ]]
2640	then
2641	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2642	then
2643	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2644	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2645	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2646	else
2647	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2648	printf "\n ${pathout[$i]}\n"
2649	cat ${localout[$i]} >> ${pathout[$i]}
2650	fi
2651	fi
2652
2653	# COPY ON THIS MACHINE
2654	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2655	# ON DIFFERENT FILE-SYSTEMS
2656	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2657	then
2658
2659	# COPY IN CASE OF RUNS ON SINGLE CORES
2660	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2661	then
2662	printf "\n >>> OUTPUT: ${localout[$i]} to"
2663	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2664	if [[ $link_local_output = true ]]
2665	then
2666	printf " file will be linked\n"
2667	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2668	fi
2669	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2670	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2671	then
2672	if [[ $link_local_output = true ]]
2673	then
2674	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2675	fi
2676	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2677	else
2678	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2679	fi
2680	else
2681	printf "\n >>> OUTPUT: ${localout[$i]} to"
2682	printf "\n ${pathout[$i]}\n"
2683	if [[ $link_local_output = true ]]
2684	then
2685	printf " file will be linked\n"
2686	ln -f ${localout[$i]} ${pathout[$i]}
2687	fi
2688	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2689	if [[ ! -f "${pathout[$i]}" ]]
2690	then
2691	if [[ $link_local_output = true ]]
2692	then
2693	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2694	fi
2695	cp ${localout[$i]} ${pathout[$i]}
2696	else
2697	printf "+++ no copy because file ${pathout[$i]} exists\n"
2698	fi
2699	fi
2700
2701	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2702	then
2703
2704	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2705	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2706	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2707	printf "\n ${pathout[$i]}\n"
2708	if [[ $link_local_output = true ]]
2709	then
2710	printf " files will be linked\n"
2711	mkdir -p ${pathout[$i]}
2712	cd ${localout[$i]}
2713	for file in $(ls *)
2714	do
2715	ln -f $file ${pathout[$i]}
2716	done >\|/dev/null 2>&1
2717	cd $tempdir
2718	fi
2719
2720	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2721	if [[ ! -f "${pathout[$i]}/_000000" ]]
2722	then
2723	if [[ $link_local_output = true ]]
2724	then
2725	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2726	fi
2727	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2728	cp -r ${localout[$i]}/* ${pathout[$i]}
2729	fi
2730
2731	fi
2732	fi
2733	done
2734
2735	if (( i != 0 ))
2736	then
2737	if [[ $transfer_problems = true ]]
2738	then
2739	printf "\n$dashes\n *** OUTPUT-files saved"
2740	printf "\n +++ WARNING: some data transfers failed! \n"
2741	else
2742	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2743	fi
2744	fi
2745
2746
2747	# IF REQUIRED, START A RESTART-JOB
2748	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2749	if [[ -f CONTINUE_RUN ]]
2750	then
2751
2752	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2753	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2754	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2755	# -b START A BATCH JOB
2756	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2757	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2758	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2759
2760	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2761	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2762	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2763	then
2764	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2765	fi
2766
2767	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2768	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2769	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2770	then
2771	prc=`echo $prc \| sed 's/#/r/g'`
2772	fi
2773
2774
2775	# START THE RESTART-JOB
2776	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2777	echo " $prc"
2778	printf "\n$dashes\n"
2779	if [[ $running_on_remote = true ]]
2780	then
2781
2782	echo "*** ssh will be used to initiate restart-runs!"
2783	echo " return_address=\"$return_address\" "
2784	echo " return_username=\"$local_username\" "
2785
2786	if [[ "$remote_loginnode" != "" ]]
2787	then
2788	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
2789	else
2790	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2791	fi
2792
2793	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2794	sleep 30
2795
2796	else
2797
2798	# START THE RESTART JOB ON THE LOCAL HOST
2799	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2800
2801	fi
2802
2803	# CHECK, IF RESTART JOB HAS BEEN STARTED
2804	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
2805	then
2806	printf "\n$dashes\n +++ creating restart run failed \n"
2807	locat=create_restart
2808	rm palmrun_restart.log
2809	exit
2810	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
2811	then
2812	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
2813	locat=create_restart
2814	rm palmrun_restart.log
2815	exit
2816	else
2817	printf "\n$dashes\n *** restart run initiated \n"
2818	rm palmrun_restart.log
2819	fi
2820
2821
2822	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2823	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2824	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2825	# MAY BE VERY HUGE)
2826	(( i = 0 ))
2827	while (( i < nr_of_input_files ))
2828	do
2829	(( i = i + 1 ))
2830	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2831	then
2832	rm -r ${absnamein[$i]}
2833	fi
2834	done
2835
2836	fi
2837
2838
2839	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2840	cd $HOME
2841	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2842
2843
2844	else
2845
2846
2847	# PREPARING ACTIONS,
2848	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2849
2850	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2851	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2852	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2853	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2854	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2855	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2856	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2857	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2858	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2859	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2860	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2861	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2862	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2863	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2864	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2865	if [[ $create_remote_batch_job = true ]]
2866	then
2867	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2868	if [[ $do_trace = true ]]
2869	then
2870	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2871	fi
2872	elif [[ $create_batch_job = true ]]
2873	then
2874	palmrun_com=${palmrun_com}" -j"
2875	if [[ $do_trace = true ]]
2876	then
2877	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2878	fi
2879	fi
2880
2881
2882	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2883	# REMOTE HOST
2884	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2885	job_protocol_file=$job_protocol_file_local
2886	if [[ $create_remote_batch_job = true ]]
2887	then
2888	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2889	job_protocol_file=$job_protocol_file_remote
2890	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2891	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2892	fi
2893
2894
2895	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2896	jobfile=jobfile.$run_id_number
2897
2898
2899	# FIRST CREATE THE BATCH DIRECTIVES
2900	(( i = 0 ))
2901	while (( i < ibd ))
2902	do
2903	(( i = i + 1 ))
2904	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2905	eval line=\"$line\"
2906	echo "$line" >> $jobfile
2907	done
2908	echo " " >> $jobfile
2909
2910
2911	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2912	# PROTOCOL
2913	if [[ $create_remote_batch_job = true ]]
2914	then
2915	echo "set +vx" >> $jobfile
2916	echo "trap '" >> $jobfile
2917	echo "set +vx" >> $jobfile
2918	echo "cd ${remote_jobcatalog}" >> $jobfile
2919	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2920
2921	# ADD THE BATCH DIRECTIVES
2922	(( i = 0 ))
2923	while (( i < ibdt ))
2924	do
2925	(( i = i + 1 ))
2926	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2927	eval line=\"$line\"
2928	echo "$line" >> $jobfile
2929	done
2930	echo " " >> $jobfile
2931
2932	echo "set -x" >> $jobfile
2933	if [[ "$remote_loginnode" != "" ]]
2934	then
2935	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}\" " >> $jobfile
2936	else
2937	echo "${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
2938	fi
2939	echo "%%END%%" >> $jobfile
2940	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2941	echo "$submit_command $scpjob_file" >> $jobfile
2942	echo "rm $scpjob_file" >> $jobfile
2943	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2944	echo "set -x" >> $jobfile
2945	echo " ' exit" >> $jobfile
2946	fi
2947
2948
2949	# ACTIVATE ERROR-TRACEBACK
2950	if [[ $do_trace = true ]]
2951	then
2952	echo "set -x" >> $jobfile
2953	else
2954	echo "set +vx" >> $jobfile
2955	fi
2956
2957
2958	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2959	if [[ "$login_init_cmd" != "" ]]
2960	then
2961	echo "$login_init_cmd" >> $jobfile
2962	fi
2963	if [[ "$module_commands" != "" ]]
2964	then
2965	echo "$module_commands" >> $jobfile
2966	fi
2967
2968
2969	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2970	if [[ $create_remote_batch_job = true ]]
2971	then
2972	echo "mkdir $tempdir" >> $jobfile
2973	echo "chmod go+rx $tempdir" >> $jobfile
2974	else
2975	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2976	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2977	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2978	mkdir $tempdir
2979	chmod go+rx $tempdir
2980	fi
2981	echo "cd $tempdir" >> $jobfile
2982	echo "export tempdir=$tempdir" >> $jobfile
2983	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2984	echo "export PATH=.:\$PATH" >> $jobfile
2985	echo "export execute_palmrun=true" >> $jobfile
2986
2987
2988	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2989	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2990	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2991	echo "LOCAL_PWD=$working_directory" >> $jobfile
2992	echo "export LOCAL_PWD" >> $jobfile
2993
2994
2995	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2996	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2997	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2998
2999
3000	# CALL PALMRUN WITHIN THE JOB
3001	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
3002	echo "set -x" >> $jobfile
3003	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
3004
3005
3006	# TRANSFER JOBFILE TO THE TARGET HOST
3007	if [[ $create_jobfile_only = false ]]
3008	then
3009
3010	# CREATE LOCAL JOB FOLDER
3011	eval local_jobcatalog=$local_jobcatalog
3012	if [[ ! -d $local_jobcatalog ]]
3013	then
3014	echo " "
3015	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
3016	mkdir $local_jobcatalog
3017	fi
3018
3019	if [[ $create_remote_batch_job = true ]]
3020	then
3021
3022	echo " "
3023	echo " *** transfer of job to remote host via scp"
3024
3025	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3026	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
3027
3028	# COPY THE JOB FILE
3029	if [[ $do_trace = true ]]
3030	then
3031	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
3032	fi
3033	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
3034
3035	# SUBMIT THE JOB
3036	printf " *** submit the job (output of submit command, \n"
3037	printf " e.g. the job-id given by the batch-system, may follow) \n"
3038	if [[ $do_trace = true ]]
3039	then
3040	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}\" "
3041	fi
3042	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
3043
3044	elif [[ $create_batch_job = true ]]
3045	then
3046
3047	eval local_jobcatalog=$local_jobcatalog
3048	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3049	cd $local_jobcatalog
3050	echo " "
3051	echo " *** submit the job"
3052	if [[ $do_trace = true ]]
3053	then
3054	echo "$submit_command ${configuration_identifier}_${run_id}"
3055	fi
3056	$submit_command ${configuration_identifier}_${run_id}
3057	rm ${configuration_identifier}_${run_id}
3058	cd - > /dev/null
3059
3060	fi
3061
3062	rm -rf $jobfile
3063
3064	else
3065
3066	printf "\n *** jobfile created under name \"$jobfile\" "
3067	printf "\n no batch-job has been sent!"
3068
3069	fi
3070
3071	fi # END OF REMOTE-PART

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