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source: palm/trunk/SCRIPTS/palmrun @ 3917

Last change on this file since 3917 was 3917, checked in by raasch, 6 years ago
in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied into the temporary working catalog
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 104.2 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 3917 2019-04-18 11:46:37Z raasch $
29	# in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has
30	# been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied
31	# into the temporary working catalog
32	#
33	# 3860 2019-04-04 06:23:27Z raasch
34	# check added, that it is not allowed to set option -b if the configuration file has been setup
35	# for running batch jobs on remote hosts,
36	# local time added to terminal output before and after saving output files
37	#
38	# 3725 2019-02-07 10:11:02Z raasch
39	# error messages for failed restarts extended
40	#
41	# 3682 2019-01-18 17:01:54Z knoop
42	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
43	# of login messages on specific systems
44	#
45	# 3574 2018-11-28 13:14:39Z raasch
46	# syntax-error in last commit fixed
47	#
48	# 3573 2018-11-28 13:03:44Z raasch
49	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
50	# removed,
51	# r3570 reverted
52	#
53	# 3570 2018-11-27 17:44:21Z kanani
54	# Rename job-id by run_id
55	#
56	# 3555 2018-11-22 13:50:37Z raasch
57	# sed-command to remove repeated space-characters replaced by tr-command, to
58	# guarantee mac compatible
59	#
60	# 3549 2018-11-21 15:44:44Z raasch
61	# ssh-call for submitting batch jobs on remote systems modified to avoid output
62	# of login messages on specific systems
63	#
64	# 3534 2018-11-19 15:35:16Z raasch
65	# batch_scp for sending back the job protocol file is called via login-node if
66	# a login-node has been set in the config-file
67	# ssh-calls rearranged to avoid output of system/user-profile messages
68	#
69	# 3505 2018-11-08 09:14:30Z raasch
70	# job folders are created in case that they do not exist
71	#
72	# 3455 2018-10-30 14:12:31Z raasch
73	# options -h and -d renamed -c and -r, respectively
74	#
75	# 3402 2018-10-23 11:49:24Z knoop
76	# job_id is set for compatibility reasons with older versions of config files
77	#
78	# 3313 2018-10-06 15:22:48Z knoop
79	# more detailed error message for outdated fileconnection file
80	#
81	# 3236 2018-09-10 09:07:06Z raasch
82	# warning issued in case of file connection file version mismatch,
83	# host_configuration renamed configuration_identifier,
84	# "host identifier" in header output renamed "config. identifier",
85	# jobname renamed run_identifier,
86	# run_id renamed run_id_number
87	# job_id renamed run_id
88	# option -r renamed -i
89	#
90	# 3151 2018-07-19 08:45:38Z raasch
91	# removed additional listing of files to be compiled, print PALM code revision
92	# in header
93	#
94	# 3132 2018-07-16 11:44:58Z raasch
95	# create consistent error messages in case of failed restarts,
96	# check existence of remote job catalog
97	#
98	# 3043 2018-05-25 10:47:54Z raasch
99	# check for setting of fast_io_catalog
100	#
101	# 3033 2018-05-23 15:26:19Z raasch
102	# -T option not required for interactive runs (tasks per node =
103	# total number of cores is assumed as default, if option is not given),
104	# reformatting of a few messages,
105	# bugfix: destination output directory is created if attribute "pe" is set in
106	# .palm.iofiles
107	#
108	# 2718 2018-01-02 08:49:38Z maronga
109	# bugfix of r2990
110	#
111	# 2718 2018-01-02 08:49:38Z maronga
112	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
113	# not in the working directory from where palmrun is called
114	#
115	# 2718 2018-01-02 08:49:38Z maronga
116	# svfout in the activation string will be replaced now by svfin in case of
117	# automatic restarts
118	#
119	# 2718 2018-01-02 08:49:38Z maronga
120	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
121	# the possible output or input of sky view factors
122	#
123	# 2718 2018-01-02 08:49:38Z maronga
124	# "fname" renamed to "jobname"
125	#
126	# 2718 2018-01-02 08:49:38Z maronga
127	# parameters are allowed in output commands (OC:)
128	#
129	# 2718 2018-01-02 08:49:38Z maronga
130	# bugfix: exit if no queue has been given neither with option -q nor in the
131	# configuration file
132	#
133	# 2718 2018-01-02 08:49:38Z maronga
134	# file connection file from trunk/SCRIPTS is taken by default
135	#
136	# 2718 2018-01-02 08:49:38Z maronga
137	# Corrected "Former revisions" section
138	#
139	# 2696 2017-12-14 17:12:51Z kanani
140	# Change in file header (GPL part)
141	#
142	# 2693 2017-12-13 12:33:49Z raasch
143	# replacement of variables given by {{<variable>}} in configuration file is now
144	# done in a more general way, variable names are written in small letters
145	#
146	# 2670 2017-12-06 16:32:19Z raasch
147	# test printouts removed
148	#
149	# 2669 2017-12-06 16:03:27Z raasch
150	# file attributes in .palm.iofiles restructured, "loc" attribute completely
151	# removed,
152	# wildcard (*) allowed in .palm.iofiles as file activation string for output
153	# files,
154	# informative messages in case of missing optional input files shortened
155	# bugfix: variable cycle explicitly interpreted with 10 as the number base
156	#
157	# 2638 2017-11-23 12:44:23Z raasch
158	# use of wildcards in file connection statements enabled
159	#
160	# 2605 2017-11-09 15:31:46Z raasch
161	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
162	# will not be sent with the job file any more, but copied into the
163	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
164	#
165	# 2600 2017-11-01 14:11:20Z raasch
166	# cycle numbers are made three digits wide
167	#
168	# 2566 2017-10-20 08:50:47Z raasch
169	# execute command for combine_plot_fields added
170	# "TEMPDIR" renamed "tempdir"
171	# temporary working directory for local batch jobs is created immediately within
172	# the user's palmrun call, due to a requirement of the "grid engine" batch
173	# system, where the working directory is given with batch directive -wd and must
174	# already exist when the job is submitted,
175	# informative messages in non-trace mode reduced and partly reformatted
176	#
177	# 2551 2017-10-18 07:25:11Z raasch
178	# TEMPDIR added as replacement string to be used in batch directives
179	#
180	# 2512 2017-10-04 08:26:59Z raasch
181	# bugfix for determining cycle numbers of NetCDF input files
182	#
183	# 2506 2017-09-29 08:30:37Z raasch
184	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
185	# host configuration added to SOURCES_FOR_RUN_... folder name
186	# host_identifier renamed host_configuration
187	# option -W added to allow for job dependencies
188	#
189	# 2501 2017-09-26 11:41:55Z raasch
190	# default value for number of cores (option -X) set to 1
191	# bugfix for mechanism which overwrites configuration file settings with values
192	# provided by palmrun options
193	#
194	# 2499 2017-09-22 16:47:58Z kanani
195	# option -h named configuration identifier
196	#
197	# 2480 2017-09-19 06:24:14Z maronga
198	# bugfix for last revision
199	#
200	# 2479 2017-09-19 06:12:16Z raasch
201	# option -A (project account number) added
202	#
203	# 2422 2017-09-08 08:25:41Z raasch
204	# initial revision
205	#
206	#--------------------------------------------------------------------------------#
207	# palmrun - script for running PALM jobs on local and remote hosts
208	#--------------------------------------------------------------------------------#
209
210
211
212	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
213
214	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
215	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
216	# (TOO MANY ARGUMENTS - PROBLEM)
217	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
218
219	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
220	typeset -i nr_of_output_files=0
221	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
222	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
223	# SCRIPT-OPTION ARGUMENTS
224	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
225	typeset -i icycle inode ival maxcycle mpi_tasks
226	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
227
228	activation_string_list=""
229	AddFilenames=""
230	combine_plot_fields=true
231	compiler_name=""
232	compiler_name_ser=""
233	compiler_options=""
234	configuration_identifier="default"
235	cores=1
236	cores_atmos=0
237	cores_ocean=0
238	coupled_dist=""
239	cpp_options=""
240	cpumax=0
241	create_batch_job=false
242	create_jobfile_only=false
243	create_remote_batch_job=false
244	dashes=" ----------------------------------------------------------------------------"
245	defaultqueue=""
246	delete_temporary_catalog=true
247	do_compile=true
248	do_trace=false
249	executable=""
250	execute_command=""
251	execution_error=false
252	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
253	global_revision=""
254	hostfile=""
255	hp=""
256	keep_data_from_previous_run=false
257	link_local_input=false
258	link_local_output=false
259	linker_options=""
260	local_jobcatalog=""
261	locat=normal
262	makefile=""
263	max_par_io_str=""
264	prc=$0
265	while [[ $(echo $prc \| grep -c "/") != 0 ]]
266	do
267	prc=`echo $prc \| cut -f2- -d"/"`
268	done
269	module_calls=""
270	palmrun_memory=""
271	palmrun_script_name=$prc
272	openmp=false
273	previous_job=""
274	project_account=""
275	queue=none
276	read_svf=""
277	restart_run=false
278	return_address=""
279	remote_jobcatalog=""
280	remote_username=""
281	running_in_batch_mode=false
282	running_in_test_mode=false
283	run_coupled_model=false
284	run_id=""
285	run_id_number=""
286	run_identifier=test
287	silent=false
288	source_list=""
289	source_path=""
290	tasks_per_node=0
291	threads_per_task=1
292	transfer_problems=false
293	user_source_path=""
294	use_existing_sources_folder=""
295	use_openmp=false
296	version="palmrun 1.0 Rev$Rev: 3917 $"
297	working_directory=`pwd`
298	write_binary=""
299	write_svf=""
300
301
302	# ERROR HANDLING IN CASE OF EXIT
303	trap 'if [[ $locat != normal && $locat != control_c ]]
304	then
305
306	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
307	(( i = 0 ))
308	while (( i < iec ))
309	do
310	(( i = i + 1 ))
311	printf "\n *** Execution of ERROR-command:\n"
312	printf " >>> ${err_command[$i]}\n"
313	eval ${err_command[$i]}
314	done
315	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
316	printf "\n\n+++ palmrun crashed \n\n"
317	exit 1
318	elif [[ $locat != normal ]]
319	then
320	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
321	printf "\n+++ palmrun killed by \"^C\" \n\n"
322	exit 2
323	else
324	printf "\n --> palmrun finished\n\n"
325	exit 0
326	fi' exit
327
328
329	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
330	trap 'locat=control_c
331	exit 1
332	' 2
333
334
335	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
336	# WHICH WILL BE USED TO START RESTART-JOBS
337	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
338	do
339	case $option in
340	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
341	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
342	(b) create_batch_job=true; prc="$prc -b";;
343	(B) delete_temporary_catalog=false; prc="$prc -B";;
344	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
345	(C) restart_run=true; prc="$prc -C";;
346	(F) create_jobfile_only=true;;
347	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
348	(i) run_id_number=$OPTARG;;
349	(j) running_in_batch_mode=true;;
350	(k) keep_data_from_previous_run=true; prc="$prc -k";;
351	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
352	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
353	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
354	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
355	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
356	(R) return_address=$OPTARG;;
357	(s) source_list=$OPTARG;;
358	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
359	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
360	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
361	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
362	(v) silent=true; prc="$prc -v";;
363	(V) use_existing_sources_folder="-V";;
364	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
365	(W) previous_job=$OPTARG;;
366	(x) do_trace=true;set -x; prc="$prc -x";;
367	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
368	(y) ocean_file_appendix=true; prc="$prc -y";;
369	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
370	(z) running_in_test_mode=true;;
371	(Z) combine_plot_fields=false; prc="$prc -Z";;
372	(\?) printf "\n +++ unknown option $OPTARG \n"
373	printf "\n --> type \"$0 ?\" for available options \n"
374	locat=parameter;exit;;
375	esac
376	done
377
378
379	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
380	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
381	(( to_shift = $OPTIND - 1 ))
382	shift $to_shift
383
384	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
385	if [[ "$1" = "?" ]]
386	then
387	(printf "\n *** Description of available palmrun options:\n"
388	printf "\n Option Description Default-Value"
389	printf "\n -a activation string list \"\" "
390	printf "\n -A project account number ---"
391	printf "\n -b batch-job on local machine ---"
392	printf "\n -B do not delete temporary directory at end ---"
393	printf "\n -c configuration identifier \"default\" "
394	printf "\n -F create batch job file only ---"
395	printf "\n -k keep data from previous run"
396	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
397	printf "\n -M Makefile name Makefile"
398	printf "\n -O threads per openMP task ---"
399	printf "\n -q queue \"$queue\" "
400	printf "\n -r run identifier test"
401	printf "\n -s filenames of routines to be compiled \"\" "
402	printf "\n must end with .f, .f90, .F, or .c !"
403	printf "\n use \"..\" for more than one file and wildcards"
404	printf "\n -s LM compiles all locally modified files"
405	printf "\n -t allowed cpu-time in seconds (batch) 0"
406	printf "\n -T tasks per node ---"
407	printf "\n -u username on remote machine \"\" "
408	printf "\n -v no prompt for confirmation ---"
409	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
410	printf "\n -w maximum parallel io streams as given by -X"
411	printf "\n -W name of job to wait for ---"
412	printf "\n -x tracing of palmrun for debug purposes ---"
413	printf "\n -X # of processors (on parallel machines) 1"
414	printf "\n -y add appendix \"_O\" to all local output"
415	printf "\n files (ocean precursor runs followed by"
416	printf "\n coupled atmosphere-ocean runs) ---"
417	printf "\n -Y run coupled model, \"#1 #2\" with"
418	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
419	printf "\n -Z skip combine_plot_fields at the end of "
420	printf "\n the simulation ---"
421	printf "\n "
422	printf "\n Possible values of positional parameter <modus>:"
423	printf "\n \"?\" - this outline \n\n") \| more
424	exit
425	elif [[ "$1" != "" ]]
426	then
427	printf "\n +++ positional parameter $1 unknown \n"
428	locat=parameter; exit
429	fi
430
431
432
433	# SHORT STARTING MESSAGE
434	printf "\n*** $version "
435	printf "\n will be executed. Please wait ..."
436
437
438	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
439	config_file=.palm.config.$configuration_identifier
440	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
441
442
443	# CHECK, IF CONFIGURATION FILE EXISTS
444	if [[ ! -f $config_file ]]
445	then
446	printf "\n\n +++ configuration file: "
447	printf "\n $config_file"
448	printf "\n does not exist"
449	locat=connect; exit
450	fi
451
452
453	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
454	if [[ -f .palm.iofiles ]]
455	then
456
457	# CHECK VERSION MISMATCH
458	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
459	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
460	if [[ $running_in_batch_mode != true && $restart_run != true ]]
461	then
462	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
463	then
464	printf "\n\n +++ WARNING: A file connection file has been found in your"
465	printf "\n working directory, but its revision does not match"
466	printf "\n the revision of the default (trunk) version."
467	printf "\n You may need to update your connection file"
468	printf "\n \"${working_directory}/.palm.iofiles\" !"
469	fi
470	fi
471
472	fileconnection_file=.palm.iofiles
473
474	fi
475
476
477	# CHECK, IF FILE CONNECTION FILE EXISTS
478	if [[ ! -f $fileconnection_file ]]
479	then
480	printf "\n\n +++ file connection file: "
481	printf "\n $fileconnection_file"
482	printf "\n does not exist"
483	locat=connect; exit
484	fi
485
486
487	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
488	if [[ "$activation_string_list" = "" ]]
489	then
490	printf "\n\n +++ no activation string list given: "
491	printf "\n please set palmrun option \"-a\" "
492	locat=palmrun_option; exit
493	fi
494
495
496	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
497	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
498	then
499	write_binary=true
500	else
501	write_binary=false
502	fi
503
504	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
505	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
506	then
507	write_svf=true
508	else
509	write_svf=false
510	fi
511
512	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
513	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
514	then
515	read_svf=true
516	else
517	read_svf=false
518	fi
519
520
521	# READ AND EVALUATE THE CONFIGURATION-FILE
522	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
523
524	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
525	while read line
526	do
527
528	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
529	eval line=\"$line\"
530
531
532	# INTERPRET THE LINE
533	if [[ "$(echo $line)" = "" ]]
534	then
535
536	# EMPTY LINE, NO ACTION
537	continue
538
539	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
540	then
541
542	# LINE IS A COMMENT LINE
543	continue
544
545	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
546	then
547
548	# LINE DEFINES AN ENVIRONMENT-VARIABLE
549	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
550	value=`echo $line \| cut -d" " -s -f2-`
551
552
553	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
554	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
555	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
556	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
557	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
558	# CONFIGURATION-FILE.
559	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
560	then
561	eval export $var="\$value"
562
563	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
564	if [[ $do_trace = true ]]
565	then
566	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
567	fi
568	fi
569
570	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
571	then
572
573	# LINE DEFINES BATCH-DIRECTIVE
574	(( ibd = ibd + 1 ))
575	line=$(echo $line \| cut -c4-)
576	batch_directive[$ibd]="$line"
577
578	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
579	then
580
581	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
582	# REMOTE TO A LOCAL HOST
583	(( ibdt = ibdt + 1 ))
584	line=$(echo $line \| cut -c5-)
585	batch_directive_transfer[$ibdt]="$line"
586
587	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
588	then
589
590	# LINE DEFINES ERROR-COMMAND
591	(( iec = iec + 1 ))
592	line=$(echo $line \| cut -c4-)
593	err_command[$iec]="$line"
594
595	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
596	then
597
598	# LINE DEFINES INPUT-COMMAND
599	(( iic = iic + 1 ))
600	line=$(echo $line \| cut -c4-)
601	in_command[$iic]="$line"
602
603	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
604	then
605
606	# LINE DEFINES OUTPUT-COMMAND
607	(( ioc = ioc + 1 ))
608	line=$(echo $line \| cut -c4-)
609	out_command[$ioc]="$line"
610
611	else
612
613	# SKIP ALL OTHER LINES
614	continue
615
616	fi
617
618	done < $config_file
619
620
621	# CHECK SETTING OF REQUIRED PARAMETERS
622	if [[ "$fast_io_catalog" = "" ]]
623	then
624	printf "\n\n +++ no fast_io_catalog found in $config_file"
625	printf "\n Please add line \"fast_io_catalog ...\" to that file."
626	locat=config_file; exit
627	fi
628	if [[ "$compiler_name" = "" ]]
629	then
630	printf "\n\n +++ no compiler name found in $config_file"
631	printf "\n Please add line \"compiler_name ...\" to that file."
632	locat=config_file; exit
633	fi
634	if [[ "$compiler_name_ser" = "" ]]
635	then
636	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
637	printf "\n Please add line \"compiler_name_ser ...\" to that file."
638	locat=config_file; exit
639	fi
640	if [[ "$compiler_options" = "" ]]
641	then
642	printf "\n\n +++ no compiler options found in $config_file"
643	printf "\n Please add line \"compiler_options ...\" to that file."
644	locat=config_file; exit
645	fi
646	if [[ "$execute_command" = "" ]]
647	then
648	printf "\n\n +++ no execute command found in $config_file"
649	printf "\n Please add line \"execute_command ...\" to that file."
650	locat=config_file; exit
651	fi
652
653	if [[ "$hostfile" != "" ]]
654	then
655	if [[ $hostfile != auto && ! -f $hostfile ]]
656	then
657	printf "\n\n +++ no hostfile \"$hostfile\" found"
658	printf "\n Please check line \"hostfile ...\" in $config_file"
659	locat=config_file; exit
660	fi
661	fi
662
663
664	# DETERMINE THE CALL STATUS
665	if [[ "$return_address" != "" ]]
666	then
667
668	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
669	# BATCH MODE AND ...
670	running_on_remote=true
671
672	else
673
674	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
675	if [[ "$remote_ip" != "" ]]
676	then
677
678	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
679	create_remote_batch_job=true
680
681	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
682	if [[ "$remote_jobcatalog" = "" ]]
683	then
684	printf "\n\n +++ no remote jobcatalog found in $config_file"
685	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
686	locat=config_file; exit
687	fi
688
689	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
690	if [[ $create_batch_job = true ]]
691	then
692	printf "\n\n +++ option -b must not be set because configuration file has been setup"
693	printf "\n for running jobs on a remote host"
694	locat=config_file; exit
695	fi
696
697	fi
698	running_on_remote=false
699	fi
700
701
702
703	# READ AND EVALUATE THE I/O-FILE LIST
704	[[ $silent = false ]] && printf "\n Reading the I/O files... "
705
706	# READ THE FILE CONNECTION FILE LINE BY LINE
707	while read line
708	do
709
710	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
711	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
712	line=`echo "$line" \| tr -s " "`
713
714	# INTERPRET THE LINE
715	if [[ "$(echo $line)" = "" ]]
716	then
717	# EMPTY LINE, NO ACTION
718	continue
719
720	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
721	then
722
723	# LINE IS A COMMENT LINE
724	true
725
726	else
727
728	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
729	# s2a: in/out - field
730	# s2b: action - field (optional)
731	s1=`echo "$line" \| cut -d" " -f1`
732	s2=`echo "$line" \| cut -d" " -s -f2`
733	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
734	then
735	s2a=$s2
736	s2b=""
737	else
738	s2a=`echo $s2 \| cut -d":" -f1`
739	s2b=`echo $s2 \| cut -d":" -f2`
740	fi
741	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
742	s4=`echo "$line" \| cut -d" " -s -f4`
743	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
744	s5=`echo "$line" \| cut -d" " -s -f5`
745	s6=`echo "$line" \| cut -d" " -s -f6`
746
747
748	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
749	# INPUT- OR OUTPUT-LIST.
750	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
751	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
752	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
753	# IS NOT CHECKED AND STORED.
754	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
755	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
756	then
757	found=false
758	for actual in $activation_string_list
759	do
760	for formal in $s3
761	do
762	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
763	done
764	done
765	if [[ $found = true ]]
766	then
767	(( iin = iin + 1 ))
768	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
769	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
770	if [[ "$s2a" = inopt ]]
771	then
772	optin_pre[$iin]=yes
773	else
774	optin_pre[$iin]=no
775	fi
776
777	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
778	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
779	if [[ $running_on_remote = true && "$s2b" = tr ]]
780	then
781	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
782	fi
783
784	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
785	# THE WILDCARD FROM THE ENDING
786	if [[ "${s5: -1}" = "*" ]]
787	then
788	if [[ "$s2b" = "di" ]]
789	then
790	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
791	printf "\n see file \"$fileconnection_file\", line"
792	printf "\n$line"
793	locat=iofiles_file; exit
794	fi
795	multin[$iin]=true
796	string=${endin_pre[$iin]}
797	endin_pre[$iin]="${string%?}"
798	else
799	multin[$iin]=false
800	fi
801	fi
802	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
803	then
804	found=false
805	for actual in $activation_string_list
806	do
807	for formal in $s3
808	do
809	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
810	done
811	done
812	if [[ $found = true ]]
813	then
814	(( iout = iout + 1 ))
815	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
816	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
817
818	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
819	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
820	if [[ $formal = wildcard ]]
821	then
822	warnout_pre[$iout]=false
823	else
824	warnout_pre[$iout]=true
825	fi
826
827	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
828	# THE WILDCARD FROM THE LOCAL FILENAME
829	if [[ "${s1: -1}" = "*" ]]
830	then
831	if [[ "$s2b" = "di" ]]
832	then
833	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
834	printf "\n see file \"$fileconnection_file\", line"
835	printf "\n$line"
836	locat=iofiles_file; exit
837	fi
838	multout[$iout]=true
839	string=${localout_pre[$iout]}
840	localout_pre[$iout]="${string%?}"
841	else
842	multout[$iout]=false
843	fi
844	fi
845	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
846	then
847	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
848	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
849	locat=connect; exit
850	fi
851	IFS="$IFSALT"
852	fi
853
854	done < $fileconnection_file
855
856
857
858	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
859	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
860	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
861	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
862	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
863	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
864
865
866
867	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
868	if [[ $run_coupled_model = true ]]
869	then
870
871	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
872	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
873
874	if (( $cores_ocean + $cores_atmos != $cores ))
875	then
876
877	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
878	printf "\n PEs (total) : $cores"
879	printf "\n PEs (atmosphere): $cores_atmos"
880	printf "\n PEs (ocean) : $cores_ocean"
881	locat=coupling; exit
882
883	fi
884
885	fi
886
887
888	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
889	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
890	# FOLDER
891	if [[ $running_in_batch_mode = true ]]
892	then
893
894	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
895	then
896	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
897	printf "\n Please check the output of the palmrun-call"
898	printf "\n that you did on your local host."
899	locat=SOURCES_FOR_RUN; exit
900	fi
901
902	else
903
904	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
905	# AUTOMATIC RESTART RUN
906	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
907	if [[ $restart_run = false ]]
908	then
909
910	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
911	# THE LOCAL HOST
912	if [[ ! -d $source_path ]]
913	then
914	printf "\n\n +++ source path \"$source_path\" on local host"
915	printf "\n \"$(hostname)\" does not exist"
916	locat=source_path; exit
917	fi
918
919	rm -rf ${base_directory}/${sources_for_run_catalog}
920	mkdir -p ${base_directory}/${sources_for_run_catalog}
921
922	if [[ "$source_list" = LM ]]
923	then
924
925	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
926	source_list=""
927	cd $source_path
928
929
930	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
931	if [[ ! -d ../.svn ]]
932	then
933	printf "\n\n +++ source directory"
934	printf "\n \"$source_path\" "
935	printf "\n is not under control of \"subversion\"."
936	printf "\n Please do not use palmrun-option \"-s LM\"\n"
937	fi
938
939
940	# LIST ALL MODIFIED SOURCE CODE FILES
941	Filenames=""
942	svn status > tmp_svnstatus
943	while read line
944	do
945	firstc=`echo $line \| cut -c1`
946	if [[ $firstc = M \|\| $firstc = "?" ]]
947	then
948	Name=`echo "$line" \| cut -c8-`
949	extension=`echo $Name \| cut -d. -f2`
950	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
951	then
952	Filenames="$Filenames "$Name
953	fi
954	fi
955	done < tmp_svnstatus
956	rm -rf tmp_svnstatus
957
958
959	# COPY FILES TO SOURCES_FOR_RUN_...
960	for filename in $Filenames
961	do
962	cp $filename ${base_directory}/${sources_for_run_catalog}
963	source_list=$source_list"$filename "
964	done
965
966	cd - > /dev/null
967
968
969	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
970	elif [[ "$source_list" != "" ]]
971	then
972
973	cd $source_path
974
975	for filename in $source_list
976	do
977
978	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
979	if [[ $(echo $filename \| grep -c "/") != 0 ]]
980	then
981	printf "\n +++ source code file: $filename"
982	printf "\n must not contain (\"/\") "
983	locat=source; exit
984	fi
985
986	if [[ ! -f $filename ]]
987	then
988	printf "\n +++ source code file: $filename"
989	printf "\n does not exist"
990	locat=source; exit
991	else
992	cp $filename ${base_directory}/${sources_for_run_catalog}
993	fi
994
995	done
996
997	cd - > /dev/null
998
999	fi
1000
1001	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1002	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1003	if [[ ! -f $makefile ]]
1004	then
1005	printf "\n +++ file \"$makefile\" does not exist"
1006	locat=make; exit
1007	else
1008	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
1009	fi
1010
1011
1012	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1013	if [[ "$user_source_path" != "" ]]
1014	then
1015
1016	# DOES THE DIRECTORY EXIST?
1017	if [[ ! -d $user_source_path ]]
1018	then
1019
1020	printf "\n\n *** INFORMATIVE: additional source code directory"
1021	printf "\n \"$user_source_path\" "
1022	printf "\n does not exist or is not a directory."
1023	printf "\n No source code will be used from this directory!\n"
1024	user_source_path=""
1025	if [[ $silent == false ]]
1026	then
1027	sleep 2
1028	fi
1029
1030	else
1031
1032	cd $user_source_path
1033
1034	Names=$(ls -1 *.f90 2>&1)
1035	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1036	Names=$(ls -1 *.F90 2>&1)
1037	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1038	Names=$(ls -1 *.F 2>&1)
1039	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1040	Names=$(ls -1 *.f 2>&1)
1041	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1042	Names=$(ls -1 *.c 2>&1)
1043	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1044
1045	cd - > /dev/null
1046	cd ${base_directory}/${sources_for_run_catalog}
1047
1048	# COPY MAKEFILE IF EXISTING
1049	if [[ -f $user_source_path/Makefile ]]
1050	then
1051	printf "\n\n *** user Makefile from directory"
1052	printf "\n \"$user_source_path\" is used \n"
1053	if [[ $silent == false ]]
1054	then
1055	sleep 1
1056	fi
1057	cp $user_source_path/Makefile .
1058	fi
1059
1060	for filename in $AddFilenames
1061	do
1062	if [[ -f $filename ]]
1063	then
1064	printf "\n +++ source code file \"$filename\" found in additional"
1065	printf "\n source code directory \"$user_source_path\" "
1066	printf "\n but was also given with option \"-s\" which means that it should be taken"
1067	printf "\n from directory \"$source_path\"."
1068	locat=source; exit
1069	fi
1070
1071	cp $user_source_path/$filename .
1072	source_list="$source_list $filename"
1073
1074	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1075	if [[ $(grep -c $filename Makefile) = 0 ]]
1076	then
1077	printf "\n\n +++ user file \"$filename\" "
1078	printf "\n is not listed in Makefile \n"
1079	locat=source; exit
1080	fi
1081	done
1082	cd - > /dev/null
1083	fi
1084	fi
1085
1086	# COPY CONFIGURATION FILES
1087	cp $config_file ${base_directory}/${sources_for_run_catalog}
1088	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1089
1090	# COPY SHELLSCRIPTS
1091	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1092	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1093
1094	fi
1095
1096	fi
1097
1098
1099	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1100	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1101	if [[ "$global_revision" = "" ]]
1102	then
1103	global_revision=`svnversion $source_path 2>/dev/null`
1104	global_revision="Rev: $global_revision"
1105	fi
1106
1107
1108	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1109	if [[ -n $cores ]]
1110	then
1111
1112	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1113	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1114	if [[ $tasks_per_node = 0 ]]
1115	then
1116	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1117	then
1118	printf "\n"
1119	printf "\n +++ option \"-T\" (tasks per node) is missing"
1120	printf "\n set -T option or define tasks_per_node in the config file"
1121	locat=tasks_per_node; (( iec = 0 )); exit
1122	else
1123	# DEFAULT FOR INTERACTIVE RUN
1124	tasks_per_node=$cores
1125	fi
1126	fi
1127
1128	if (( cores < tasks_per_node ))
1129	then
1130	printf "\n"
1131	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1132	printf "\n given values: -T $tasks_per_node -X $cores"
1133	locat=tasks_per_node; (( iec = 0 )); exit
1134	fi
1135
1136	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1137	(( mpi_tasks = cores / threads_per_task ))
1138	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1139	(( ii = cores / tasks_per_node ))
1140	(( remaining_cores = cores - ii * tasks_per_node ))
1141	if (( remaining_cores > 0 ))
1142	then
1143	printf "\n"
1144	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1145	printf "\n divisor of the total number of cores (option \"-X\")"
1146	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1147	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1148	(( nodes = nodes + 1 ))
1149	fi
1150
1151	fi
1152
1153
1154	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1155	if [[ "$maximum_parallel_io_streams" = "" ]]
1156	then
1157	maximum_parallel_io_streams=$cores
1158	fi
1159
1160
1161	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1162	if [[ "$scp_port" != "" ]]
1163	then
1164	PORTOPT="-P $scp_port"
1165	SSH_PORTOPT="-p $scp_port"
1166	fi
1167
1168
1169	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1170	# CONFIG-FILE
1171	if [[ "$ssh_key" != "" ]]
1172	then
1173	ssh_key="-i $HOME/.ssh/$ssh_key"
1174	fi
1175
1176
1177	# SET QUEUE, IF NOT GIVEN
1178	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1179	then
1180
1181	if [[ $queue = none && "$defaultqueue" = "" ]]
1182	then
1183	printf "\n"
1184	printf "\n +++ no default queue given in configuration file and no queue"
1185	printf "\n given with option -q"
1186	locat=queue; exit
1187	fi
1188	if [[ $queue = none ]]
1189	then
1190	queue=$defaultqueue
1191	fi
1192
1193	fi
1194
1195
1196	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1197	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1198	(( i = 0 ))
1199	(( nr_of_input_files = 0 ))
1200	while (( i < iin ))
1201	do
1202	(( i = i + 1 ))
1203
1204	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1205	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1206	if [[ "${actionin_pre[$i]}" = di ]]
1207	then
1208	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1209	else
1210	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1211	fi
1212
1213
1214	# CHECK IF FILE EXISTS
1215	if ! ls $filename* 1>/dev/null 2>&1
1216	then
1217
1218	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1219	if [[ "${optin_pre[$i]}" != "yes" ]]
1220	then
1221	printf "\n\n +++ INPUT-file: "
1222	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1223	then
1224	printf "\n $filename"
1225	else
1226	printf "\n $filename.${extin_pre[$i]}"
1227	fi
1228	printf "\n does not exist\n"
1229	locat=input; exit
1230	else
1231	(( nr_of_input_files = nr_of_input_files + 1 ))
1232	localin[$nr_of_input_files]="${localin_pre[$i]}"
1233	optin[$nr_of_input_files]="${optin_pre[$i]}"
1234	actionin[$nr_of_input_files]="unavailable"
1235	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1236	endin[$nr_of_input_files]="${endin_pre[$i]}"
1237	extin[$nr_of_input_files]="${extin_pre[$i]}"
1238	fi
1239
1240	else
1241
1242	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1243	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1244	# ENDINGS
1245	if [[ "${multin[$i]}" = true ]]
1246	then
1247	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1248	ls -1 -d ${filename} > filelist 2>/dev/null
1249	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1250	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1251
1252	endings=""
1253	while read line
1254	do
1255	# filename without path (i.e. after the last "/")
1256	basefilename=$(basename ${line})
1257
1258	# check if there is an extension and remove it
1259	ext=${basefilename##*.}
1260	if [[ "$ext" = "${extin_pre[$i]}" ]]
1261	then
1262	basefilename=${basefilename%.*}
1263	fi
1264
1265	# check for an existing cycle number and remove it
1266	cycle=${basefilename##*.}
1267	if [[ $cycle =~ ^-?[0-9]+$ ]]
1268	then
1269	basefilename=${basefilename%.*}
1270	fi
1271
1272	# remove the run_identifier from the beginning
1273	length_run_identifier=${#run_identifier}
1274	ending=${basefilename:${length_run_identifier}}
1275
1276	# remove the ending given in the .iofiles from the beginning
1277	endingstring="${endin_pre[$i]}"
1278	length_ending=${#endingstring}
1279	ending=${ending:${length_ending}}
1280
1281	if [[ "$ending" = "" ]]
1282	then
1283	# standard ending as given in the .iofiles
1284	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1285	then
1286	endings="$endings DEFAULT"
1287	fi
1288	else
1289	# ending must start with "_", otherwise its a different file
1290	if [[ "${ending:0:1}" = "_" ]]
1291	then
1292	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1293	then
1294	endings="$endings $ending"
1295	fi
1296	fi
1297	fi
1298
1299	done <filelist
1300
1301	rm filelist
1302
1303	else
1304
1305	# SINGLE NAME
1306	endings=DEFAULT
1307
1308	fi
1309
1310	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1311	for ending in $endings
1312	do
1313
1314	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1315	if [[ $ending = DEFAULT ]]
1316	then
1317	ending=""
1318	fi
1319
1320	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1321	(( nr_of_input_files = nr_of_input_files + 1 ))
1322	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1323	optin[$nr_of_input_files]="${optin_pre[$i]}"
1324	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1325	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1326	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1327	extin[$nr_of_input_files]="${extin_pre[$i]}"
1328
1329
1330	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1331	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1332	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1333	then
1334	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1335	else
1336	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1337	fi
1338
1339	# DETERMINE THE FILE'S CYCLE NUMBER
1340	(( maxcycle = 0 ))
1341	ls -1 -d $filename > filelist 2>/dev/null
1342	ls -1 -d $filename.* >> filelist 2>/dev/null
1343	while read line
1344	do
1345	# filename without path (i.e. after the last "/")
1346	basefilename=$(basename ${line})
1347
1348	# check if there is an extension
1349	extension=${basefilename##*.}
1350	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1351	then
1352	basefilename=${basefilename%.*}
1353	fi
1354
1355	# check for an existing cycle number
1356	cycle=${basefilename##*.}
1357	if [[ $cycle =~ ^-?[0-9]+$ ]]
1358	then
1359	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1360	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1361	(( icycle = $((10#$cycle)) ))
1362	else
1363	(( icycle = 0 ))
1364	fi
1365
1366	if (( icycle > maxcycle ))
1367	then
1368	(( maxcycle = icycle ))
1369
1370	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1371	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1372	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1373	then
1374	leading_zero=true
1375	else
1376	leading_zero=false
1377	fi
1378	fi
1379
1380	done <filelist
1381	rm filelist
1382
1383	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1384	if [[ $leading_zero = true ]]
1385	then
1386	cyclestring=`printf "%03d" $maxcycle`
1387	else
1388	cyclestring=$maxcycle
1389	fi
1390
1391	# APPEND CYCLE NUMBER TO FILENAME
1392	if (( maxcycle > 0 ))
1393	then
1394	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1395	then
1396	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1397	else
1398	filename=${filename}.$cyclestring
1399	fi
1400	else
1401	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1402	then
1403	filename=${filename}.${extin[$nr_of_input_files]}
1404	fi
1405	fi
1406
1407	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1408	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1409	absnamein[$nr_of_input_files]=$filename
1410	if (( maxcycle > 0 ))
1411	then
1412	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1413	then
1414	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1415	else
1416	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1417	fi
1418	else
1419	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1420	then
1421	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1422	else
1423	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1424	fi
1425	fi
1426
1427	done
1428
1429	fi
1430
1431	done
1432
1433
1434	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1435	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1436	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1437	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1438	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1439	# REMOTE HOST)
1440	(( i = 0 ))
1441	while (( i < iout ))
1442	do
1443	(( i = i + 1 ))
1444	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1445	then
1446	if [[ "${actionout_pre[$i]}" = tr ]]
1447	then
1448	actionout_pre[$i]=""
1449	elif [[ "${actionout_pre[$i]}" = trpe ]]
1450	then
1451	actionout_pre[$i]=pe
1452	elif [[ "${actionout_pre[$i]}" = tra ]]
1453	then
1454	actionout_pre[$i]=a
1455	fi
1456	(( maxcycle = 0 ))
1457	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1458	eval catalogname=${pathout_pre[$i]}
1459	if ! ls $filename* 1>/dev/null 2>&1
1460	then
1461
1462	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1463	if cat /dev/null > $filename
1464	then
1465	rm $filename
1466	else
1467
1468	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1469	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1470	if [[ ! -d $catalogname ]]
1471	then
1472	if mkdir -p $catalogname
1473	then
1474	printf "\n\n *** directory:"
1475	printf "\n $catalogname"
1476	printf "\n was created\n"
1477	else
1478	printf "\n\n +++ OUTPUT-file:"
1479	printf "\n $filename"
1480	printf "\n cannot be created, because directory does not exist"
1481	printf "\n and cannot be created either"
1482	printf "\n"
1483	locat=output ; exit
1484	fi 2>/dev/null
1485	else
1486	printf "\n\n +++ OUTPUT-file:"
1487	printf "\n $filename"
1488	printf "\n cannot be created, although directory exists"
1489	printf "\n"
1490	locat=output ; exit
1491	fi
1492	fi 2>/dev/null
1493
1494	fi
1495
1496	fi
1497	done
1498
1499
1500	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1501	if [[ $running_in_batch_mode = false ]]
1502	then
1503	run_id_number=$RANDOM
1504	run_id=${run_identifier}.$run_id_number
1505
1506	tempdir=$fast_io_catalog/$run_id
1507
1508	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1509	export job_id=$run_id
1510
1511	fi
1512
1513
1514	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1515	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1516	then
1517
1518	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1519	if [[ $ibd = 0 ]]
1520	then
1521	printf "\n"
1522	printf "\n +++ no batch directives found in configuration file"
1523	locat=config_file_batch_directives; (( iec = 0 )); exit
1524	fi
1525
1526	# CHECK IF CPUTIME IS GIVEN FOR JOB
1527	done=false
1528	cputime=$cpumax
1529	while [[ $done = false ]]
1530	do
1531	if (( cputime == 0 ))
1532	then
1533	printf "\n +++ cpu-time is undefined"
1534	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1535	printf "\n >>> "
1536	read cputime 1>/dev/null 2>&1
1537	else
1538	done=true
1539	fi
1540	done
1541	cpumax=$cputime
1542
1543	# CHECK THE MEMORY DEMAND
1544	done=false
1545	while [[ $done = false ]]
1546	do
1547	if (( memory == 0 ))
1548	then
1549	printf "\n +++ memory demand is undefined"
1550	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1551	printf "\n >>> "
1552	read memory 1>/dev/null 2>&1
1553	else
1554	done=true
1555	fi
1556	done
1557
1558	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1559	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1560	then
1561	while [[ -z $remote_username ]]
1562	do
1563	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1564	printf "\n >>> Please type username:"
1565	printf "\n >>> "
1566	read remote_username
1567	done
1568	fi
1569
1570	else
1571
1572	if [[ $running_in_batch_mode = false ]]
1573	then
1574	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1575	cpumax=$cputime
1576	else
1577	cputime=$cpumax
1578	fi
1579
1580	fi
1581
1582
1583	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1584	(( cpu_hours = cputime / 3600 ))
1585	(( resttime = cputime - cpu_hours * 3600 ))
1586	(( cpu_minutes = resttime / 60 ))
1587	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1588	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1589
1590
1591	# OUTPUT OF THE PALMRUN-HEADER
1592	calltime=$(date)
1593	printf "\n"
1594	printf "#------------------------------------------------------------------------# \n"
1595	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1596	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1597	printf "\| \| \n"
1598	column1="called on:"; column2=$(hostname)
1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1600	if [[ $create_remote_batch_job = true ]]
1601	then
1602	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1603	else
1604	if [[ $running_on_remote = true ]]
1605	then
1606	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1607	else
1608	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1609	fi
1610	fi
1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1612
1613	column1="running in:"
1614	if [[ $running_in_batch_mode = true ]]
1615	then
1616	column2="batch job mode"
1617	else
1618	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1619	then
1620	column2="job creation mode"
1621	else
1622	column2="interactive run mode"
1623	fi
1624	fi
1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1626
1627	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1628	then
1629	if [[ "$project_account" != "" ]]
1630	then
1631	column1="project account number:"
1632	column2="$project_account"
1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1634	fi
1635	fi
1636
1637	if [[ -n $cores ]]
1638	then
1639	if [[ $run_coupled_model = false ]]
1640	then
1641	column1="number of cores:"; column2=$cores
1642	else
1643	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1644	fi
1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1646	fi
1647	if [[ -n $tasks_per_node ]]
1648	then
1649	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1651	if (( remaining_cores > 0 ))
1652	then
1653	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1654	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1655	fi
1656	fi
1657	if [[ $maximum_parallel_io_streams != $cores ]]
1658	then
1659	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1661	fi
1662	if [[ $use_openmp = true ]]
1663	then
1664	column1="threads per task:"; column2="$threads_per_task"
1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1666	fi
1667	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1668	then
1669	column1="memory demand / PE":; column2="$memory MB"
1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1671	column1="job cpu time (h:m:s):"; column2="$timestring"
1672	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1673	fi
1674	printf "\| \| \n"
1675	if [[ "$source_list" != "" ]]
1676	then
1677	if [[ "$make_options" != "" ]]
1678	then
1679	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1680	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1681	line=$(echo "$make_options" \| cut -c46-)
1682	while [[ "$line" != "" ]]
1683	do
1684	column1=""
1685	column2=$(echo "$line" \| cut -c-45)
1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1687	line=$(echo "$line" \| cut -c46-)
1688	done
1689	fi
1690	fi
1691
1692	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1694	line=$(echo "$cpp_options" \| cut -c46-)
1695	while [[ "$line" != "" ]]
1696	do
1697	column1=""
1698	column2=$(echo "$line" \| cut -c-45)
1699	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1700	line=$(echo "$line" \| cut -c46-)
1701	done
1702
1703	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1704	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1705	line=$(echo "$compiler_options" \| cut -c46-)
1706	while [[ "$line" != "" ]]
1707	do
1708	column1=""
1709	column2=$(echo "$line" \| cut -c-45)
1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1711	line=$(echo "$line" \| cut -c46-)
1712	done
1713
1714	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1715	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1716	line=$(echo "$linker_options" \| cut -c46-)
1717	while [[ "$line" != "" ]]
1718	do
1719	column1=""
1720	column2=$(echo "$line" \| cut -c-45)
1721	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1722	line=$(echo "$line" \| cut -c46-)
1723	done
1724
1725	if [[ "$login_init_cmd" != "" ]]
1726	then
1727	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1728	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1729	line=$(echo "$login_init_cmd" \| cut -c46-)
1730	while [[ "$line" != "" ]]
1731	do
1732	column1=""
1733	column2=$(echo "$line" \| cut -c-45)
1734	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1735	line=$(echo "$line" \| cut -c46-)
1736	done
1737	fi
1738
1739	if [[ "$module_commands" != "" ]]
1740	then
1741	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1742	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1743	line=$(echo "$module_commands" \| cut -c46-)
1744	while [[ "$line" != "" ]]
1745	do
1746	column1=""
1747	column2=$(echo "$line" \| cut -c-45)
1748	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1749	line=$(echo "$line" \| cut -c46-)
1750	done
1751	fi
1752	printf "\| \| \n"
1753	column1="run identifier:"; column2=$run_identifier
1754	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1755	column1="activation string list:"; column2=$(echo $activation_string_list)
1756	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1757
1758	if [[ "$ocean_file_appendix" = true ]]
1759	then
1760	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1761	fi
1762
1763	if [[ "$source_list" != "" ]]
1764	then
1765	printf "\| \| \n"
1766	printf "\| Files to be compiled: \| \n"
1767	line=$source_list
1768	while [[ "$line" != "" ]]
1769	do
1770	linestart=$(echo $line \| cut -c-70)
1771	printf "\| %-70s \| \n" "$linestart"
1772	line=$(echo "$line" \| cut -c71-)
1773	done
1774	fi
1775	printf "#------------------------------------------------------------------------#"
1776
1777
1778
1779	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1780	if [[ $do_trace = true ]]
1781	then
1782	(( i = 0 ))
1783	while (( i < nr_of_input_files ))
1784	do
1785	(( i = i + 1 ))
1786	if (( i == 1 ))
1787	then
1788	printf "\n\n >>> INPUT-file assignments:\n"
1789	fi
1790	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1791	done
1792	(( i = 0 ))
1793	while (( i < iout ))
1794	do
1795	(( i = i + 1 ))
1796	if (( i == 1 ))
1797	then
1798	printf "\n\n >>> OUTPUT-file assignments:\n"
1799	fi
1800	printf "\n ${localout[$i]} : ${pathout[$i]}"
1801	done
1802	(( i = 0 ))
1803	while (( i < iic ))
1804	do
1805	(( i = i + 1 ))
1806	if (( i == 1 ))
1807	then
1808	printf "\n\n >>> INPUT-commands:\n"
1809	fi
1810	printf "\n ${in_command[$i]}"
1811	done
1812	(( i = 0 ))
1813	while (( i < ioc ))
1814	do
1815	(( i = i + 1 ))
1816	if (( i == 1 ))
1817	then
1818	printf "\n\n >>> OUTPUT-commands:\n"
1819	fi
1820	printf "\n ${out_command[$i]}"
1821	done
1822	fi
1823
1824	# QUERY FOR CONTINUE
1825	if [[ $silent = false && $running_in_batch_mode = false ]]
1826	then
1827	antwort=dummy
1828	printf "\n\n"
1829	printf " >>> everything o.k. (y/n) ? "
1830	while read antwort
1831	do
1832	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1833	then
1834	printf " >>> everything o.k. (y/n) ? "
1835	else
1836	break
1837	fi
1838	done
1839	if [[ $antwort = n \|\| $antwort = N ]]
1840	then
1841	locat=user_abort; (( iec = 0 )); exit
1842	fi
1843	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1844	then
1845	printf "\n *** batch-job will be created and submitted"
1846	else
1847	printf "\n *** PALMRUN will now continue to execute on this machine"
1848	fi
1849	fi
1850
1851
1852
1853	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1854	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1855	then
1856
1857	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1858	then
1859	printf "\n\n *** creating executable and other sources for the remote host\n"
1860	else
1861	printf "\n\n *** creating executable and other sources for the local host\n"
1862	fi
1863
1864	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1865	# IT SHALL BE CREATED
1866	ask_for_make_depository=false
1867	if [[ $create_remote_batch_job = true ]]
1868	then
1869
1870	line=`grep %base_directory $config_file`
1871	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1872	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1873
1874	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1875	then
1876	printf "\n\n +++ make depository \"${make_depository}\""
1877	printf "\n on remote host not found!"
1878	ask_for_make_depository=true
1879	fi
1880	rm ${configuration_identifier}_last_make_protokoll
1881
1882	else
1883
1884	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1885	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1886	if [[ ! -d ${make_depository} ]]
1887	then
1888	printf "\n\n +++ make depository \"${make_depository}\""
1889	printf "\n on local host not found!"
1890	ask_for_make_depository=true
1891	fi
1892
1893	fi
1894
1895	if [[ $ask_for_make_depository = true ]]
1896	then
1897
1898	antwort=dummy
1899	printf "\n\n"
1900	printf " >>> Create a new one (y/n) ? "
1901	while read antwort
1902	do
1903	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1904	then
1905	printf " >>> Create a new one (y/n) ? "
1906	else
1907	break
1908	fi
1909	done
1910	if [[ $antwort = n \|\| $antwort = N ]]
1911	then
1912	locat=user_abort; (( iec = 0 )); exit
1913	fi
1914
1915	if [[ $do_trace = true ]]
1916	then
1917	palmbuild -c $configuration_identifier
1918	else
1919	palmbuild -v -c $configuration_identifier
1920	fi
1921
1922	if [[ ${PIPESTATUS[0]} != 0 ]]
1923	then
1924
1925	# ABORT IN CASE OF COMPILATION PROBLEMS
1926	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1927	locat=make_depository
1928	exit
1929	else
1930	echo " *** now continue with creating executable and other sources"
1931	fi
1932
1933	fi
1934
1935	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1936	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1937
1938	if [[ ${PIPESTATUS[0]} != 0 ]]
1939	then
1940
1941	# ABORT IN CASE OF COMPILATION PROBLEMS
1942	printf "\n +++ error while creating executable and/or other sources"
1943	locat=execution
1944	rm -rf ${base_directory}/${sources_for_run_catalog}
1945	exit
1946
1947	else
1948
1949	printf " *** executable and other sources created\n"
1950	rm -rf ${base_directory}/${sources_for_run_catalog}
1951
1952	fi
1953
1954	fi
1955
1956
1957	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1958	# WILL BE COPIED TO THE REMOTE HOST
1959	if [[ $create_remote_batch_job = true ]]
1960	then
1961	(( i = 0 ))
1962	while (( i < nr_of_input_files ))
1963	do
1964	(( i = i + 1 ))
1965	if [[ "${actionin[$i]}" = tr ]]
1966	then
1967	eval inputfile=${pathin[$i]}/${frelin[$i]}
1968	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1969	fi
1970	done
1971	if (( i > 0 ))
1972	then
1973	printf "\n\n *** input files have been copied to the remote host\n"
1974	fi
1975	fi
1976
1977
1978	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1979	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1980	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1981	then
1982
1983	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1984	if [[ $running_in_batch_mode = false ]]
1985	then
1986	# CREATE THE DIRECTORY
1987	mkdir -p $tempdir
1988	chmod go+rx $tempdir
1989	cd $tempdir
1990	printf "\n *** changed to temporary directory: $tempdir"
1991
1992	else
1993
1994	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1995	printf "\n *** running in temporary directory: $tempdir"
1996
1997	fi
1998
1999
2000	# PROVIDE THE INPUT FILES
2001	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2002	optional_files_missing=false
2003	(( i = 0 ))
2004	while (( i < nr_of_input_files ))
2005	do
2006	(( i = i + 1 ))
2007	if (( i == 1 ))
2008	then
2009	printf "\n\n *** providing INPUT-files:\n$dashes"
2010	fi
2011
2012
2013	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2014	if [[ "${actionin[$i]}" = unavailable ]]
2015	then
2016	optional_files_missing=true
2017	continue
2018	fi
2019
2020	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2021	files_for_cores=false; filetype=file
2022	if [[ "${actionin[$i]}" = pe && -n $cores ]]
2023	then
2024	files_for_cores=true; filetype=files
2025	actionin[$i]=""
2026	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
2027	then
2028	actionin[$i]=""
2029	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
2030	then
2031	files_for_cores=true; filetype=files
2032	actionin[$i]="ln"
2033	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
2034	then
2035	actionin[$i]="ln"
2036	fi
2037
2038	if [[ $files_for_cores = true ]]
2039	then
2040	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2041	else
2042	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2043	fi
2044
2045	# INPUT-FILES TO BE LINKED
2046	if [[ "${actionin[$i]}" = ln ]]
2047	then
2048
2049	printf "\n $filetype will be linked"
2050	if [[ $files_for_cores = false ]]
2051	then
2052	if [[ -f "${absnamein[$i]}" ]]
2053	then
2054	ln ${absnamein[$i]} ${localin[$i]}
2055	got_tmp[$i]=true
2056	fi
2057	else
2058	if [[ -d "${absnamein[$i]}" ]]
2059	then
2060	mkdir -p ${localin[$i]}
2061	cd ${absnamein[$i]}
2062	for file in $(ls *)
2063	do
2064	ln $file $tempdir/${localin[$i]}
2065	done >\|/dev/null 2>&1
2066	cd $tempdir
2067	fi
2068
2069	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2070	if [[ ! -f "${localin[$i]}/_000000" ]]
2071	then
2072	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2073	cp -r ${absnamein[$i]}/* ${localin[$i]}
2074	fi
2075
2076	got_tmp[$i]=true
2077	fi
2078	fi
2079
2080	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2081	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2082	then
2083
2084	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2085	then
2086
2087	# FILE COPIES ARE PROVIDED FOR ALL CORES
2088	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2089	printf "\n file will be provided for $cores processors"
2090	mkdir -p ${localin[$i]}
2091	ival=$cores
2092	(( ii = 0 ))
2093	while (( ii <= ival-1 ))
2094	do
2095	if (( ii < 10 ))
2096	then
2097	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2098	elif (( ii < 100 ))
2099	then
2100	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2101	elif (( ii < 1000 ))
2102	then
2103	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2104	else
2105	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2106	fi
2107	(( ii = ii + 1 ))
2108	done
2109
2110	else
2111
2112	if [[ $files_for_cores = true ]]
2113	then
2114
2115	# PROVIDE FILES FOR EACH CORE
2116	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2117	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2118	printf "\n providing $cores files for the respective cores"
2119	mkdir -p ${localin[$i]}
2120	if [[ $link_local_input = true ]]
2121	then
2122	printf " files will be linked\n"
2123	cd ${absnamein[$i]}
2124	for file in $(ls *)
2125	do
2126	ln -f $file ${localin[$i]}
2127	done
2128	cd $tempdir
2129	fi
2130
2131	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2132	if [[ ! -f "${localin[$i]}/_000000" ]]
2133	then
2134	if [[ $link_local_input = true ]]
2135	then
2136	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2137	fi
2138	cp -r ${absnamein[$i]}/* ${localin[$i]}
2139	fi
2140
2141	else
2142
2143	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2144	if [[ $link_local_input = true ]]
2145	then
2146	printf " file will be linked\n"
2147	ln -f ${absnamein[$i]} ${localin[$i]}
2148	fi
2149	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2150	if [[ ! -f "${localin[$i]}" ]]
2151	then
2152	if [[ $link_local_input = true ]]
2153	then
2154	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2155	fi
2156	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2157	then
2158	mv ${absnamein[$i]} ${localin[$i]}
2159	else
2160	cp ${absnamein[$i]} ${localin[$i]}
2161	fi
2162	fi
2163	fi
2164	fi
2165	fi
2166
2167	done
2168	if (( i != 0 ))
2169	then
2170	if [[ $optional_files_missing = true ]]
2171	then
2172	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2173	fi
2174	printf "\n$dashes\n *** all INPUT-files provided \n"
2175	fi
2176
2177	# NOW COPY FILES (.f90, .o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY
2178	# WORKING DIRECTORY
2179	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
2180
2181
2182	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2183	(( i = 0 ))
2184	while (( i < iic ))
2185	do
2186	(( i = i + 1 ))
2187	if (( i == 1 ))
2188	then
2189	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2190	fi
2191	printf "\n >>> ${in_command[$i]}"
2192	eval ${in_command[$i]}
2193	if (( i == iic ))
2194	then
2195	printf "\n$dashes\n"
2196	fi
2197	done
2198
2199
2200	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2201	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2202	then
2203	progress_bar_disabled=true
2204	else
2205	progress_bar_disabled=false
2206	fi
2207
2208
2209	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2210	# (FILE ENVPAR WILL BE READ BY PALM)
2211	cat > ENVPAR << EOF
2212	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2213	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2214	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2215	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2216	maximum_cpu_time_allowed = ${cpumax}.,
2217	revision = '$global_revision',
2218	progress_bar_disabled = .${progress_bar_disabled}. /
2219
2220	EOF
2221
2222
2223	# STARTING THE EXECUTABLE
2224	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2225	PATH=$PATH:$tempdir
2226
2227
2228	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2229	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2230	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2231	eval line=\"$line\"
2232	execute_command="$line"
2233
2234
2235	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2236	if [[ "$execute_command_for_combine" = "" ]]
2237	then
2238	eval line2=\"$line2\"
2239	execute_command_for_combine="$line2"
2240	fi
2241
2242
2243
2244	# PROVIDE A HOSTFILE, IF REQUIRED
2245	if [[ "$hostfile" != "" ]]
2246	then
2247
2248	if [[ $hostfile = auto ]]
2249	then
2250	# CREATE A NEW HOSTFILE
2251	(( ii = 1 ))
2252	while (( ii <= cores / threads_per_task ))
2253	do
2254	echo $(hostname) >> hostfile
2255	(( ii = ii + 1 ))
2256	done
2257	if (( cores / threads_per_task == 0 ))
2258	then
2259	echo $(hostname) >> hostfile
2260	fi
2261
2262	else
2263	cp $hostfile hostfile
2264	fi
2265	eval line=\"`head -n $ii hostfile`\"
2266	printf "\n *** running on: $line"
2267	fi
2268
2269
2270
2271	# SET THE NUMBER OF OPENMP-THREADS
2272	if [[ $use_openmp = true ]]
2273	then
2274	export OMP_NUM_THREADS=$threads_per_task
2275	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2276	else
2277	export OMP_NUM_THREADS=1
2278	fi
2279
2280
2281	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2282	if [[ $run_coupled_model = false ]]
2283	then
2284	if [[ "$ocean_file_appendix" = true ]]
2285	then
2286	echo "precursor_ocean" > coupling_steering
2287	else
2288	echo "precursor_atmos" > coupling_steering
2289	fi
2290	else
2291	(( iia = $cores_atmos / $threads_per_task ))
2292	(( iio = $cores_ocean / $threads_per_task ))
2293	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2294	printf "\n\n"
2295	echo "coupled_run $iia $iio" > coupling_steering
2296	fi
2297
2298	printf "\n *** execute command:"
2299	printf "\n \"$execute_command\" \n\n"
2300
2301
2302	if [[ $progress_bar_disabled = true ]]
2303	then
2304	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2305	exit_code=${PIPESTATUS[0]}
2306	else
2307	$execute_command < coupling_steering &> >(tee STDOUT)
2308	exit_code=${PIPESTATUS[0]}
2309	fi
2310
2311	if [[ ${exit_code} != 0 ]]
2312	then
2313
2314	# ABORT IN CASE OF RUNTIME ERRORS
2315	printf "\n +++ runtime error occured"
2316	locat=execution
2317	exit
2318
2319	else
2320
2321	printf "\n$dashes\n *** execution finished \n"
2322
2323	fi
2324
2325
2326	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2327	# BY EACH CORE INTO ONE FILE
2328	if [[ ! -f combine_plot_fields.x ]]
2329	then
2330
2331	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2332	printf "\n 2d- and/or 3d-data may be incomplete!"
2333	printf "\n Your previous palmbuild may have failed. Please check.\n"
2334
2335	elif [[ "$combine_plot_fields" == true ]]
2336	then
2337
2338	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2339	$execute_command_for_combine
2340
2341	else
2342
2343	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2344	# DATA OUTPUT
2345	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2346	fi
2347
2348
2349
2350	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2351	(( i = 0 ))
2352	while (( i < ioc ))
2353	do
2354	(( i = i + 1 ))
2355	if (( i == 1 ))
2356	then
2357	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2358	fi
2359
2360	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2361	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2362
2363	printf "\n >>> ${out_command[$i]}"
2364	eval ${out_command[$i]}
2365	if (( i == ioc ))
2366	then
2367	printf "\n$dashes\n"
2368	fi
2369	done
2370
2371
2372	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2373	# WILDCARDS
2374	(( i = 0 ))
2375	(( nr_of_output_files = 0 ))
2376
2377	while (( i < iout ))
2378	do
2379
2380	(( i = i + 1 ))
2381
2382	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2383	# CREATE A LIST FOR THE DETECTED ENDINGS
2384	if [[ "${multout[$i]}" = true ]]
2385	then
2386	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2387	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2388	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2389
2390	endings="DEFAULT"
2391	while read line
2392	do
2393	# remove the local name from the beginning
2394	localnamestring="${localout_pre[$i]}"
2395	length_localname=${#localnamestring}
2396	ending=${line:${length_localname}}
2397
2398	if [[ "$ending" != "" ]]
2399	then
2400	endings="$endings $ending"
2401	fi
2402
2403	done <filelist
2404
2405	rm filelist
2406
2407	else
2408
2409	# SINGLE NAME
2410	endings=DEFAULT
2411
2412	fi
2413
2414	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2415	for ending in $endings
2416	do
2417
2418	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2419	if [[ $ending = DEFAULT ]]
2420	then
2421	ending=""
2422	fi
2423
2424	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2425	(( nr_of_output_files = nr_of_output_files + 1 ))
2426	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2427	transout[$nr_of_output_files]="${transout_pre[$i]}"
2428	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2429	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2430	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2431	extout[$nr_of_output_files]="${extout_pre[$i]}"
2432	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2433
2434	done
2435
2436	done
2437
2438
2439
2440
2441	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2442	(( i = 0 ))
2443	while (( i < nr_of_output_files ))
2444	do
2445	(( i = i + 1 ))
2446	if (( i == 1 ))
2447	then
2448	timestring=`date +%H:%M:%S`
2449	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
2450
2451	# GET RUN NUMBER ASSIGNED BY PALM
2452	if [[ -f RUN_NUMBER ]]
2453	then
2454	read run_number < RUN_NUMBER
2455	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2456	usecycle_option="-U $run_number"
2457	else
2458	run_number=0
2459	usecycle_option=""
2460	fi
2461	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2462	then
2463	printf "\n *** in case of SCP transfers to local host"
2464	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2465	fi
2466	printf "\n$dashes"
2467	fi
2468
2469	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2470	then
2471
2472	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2473
2474	# DETERMINE THE CYCLE NUMBER
2475	ls -1 -d $filename > filelist 2>/dev/null
2476	ls -1 -d $filename.* >> filelist 2>/dev/null
2477	while read line
2478	do
2479
2480	# filename without path (i.e. after the last "/")
2481	basefilename=$(basename ${line})
2482
2483	# check if there is an extension
2484	extension=${basefilename##*.}
2485	if [[ "$extension" = "${extout[$i]}" ]]
2486	then
2487	basefilename=${basefilename%.*}
2488	fi
2489
2490	# check for an existing cycle number
2491	cycle=${basefilename##*.}
2492	if [[ $cycle =~ ^-?[0-9]+$ ]]
2493	then
2494	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2495	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2496	(( icycle = $((10#$cycle)) + 1 ))
2497	else
2498	(( icycle = 1 ))
2499	fi
2500
2501	if (( icycle > maxcycle ))
2502	then
2503	(( maxcycle = icycle ))
2504	fi
2505
2506	done <filelist
2507	rm filelist
2508
2509
2510	# SET THE CYCLE NUMBER
2511	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2512	if [[ "${actionout[$i]}" = a ]]
2513	then
2514	(( maxcycle = maxcycle - 1 ))
2515	fi
2516
2517	(( cycnum[$i] = maxcycle ))
2518	pathout[$i]=$filename
2519
2520
2521	# ADD CYCLE NUMBER TO FILENAME
2522	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2523	if [[ "${actionout[$i]}" != "a" ]]
2524	then
2525	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2526	# WITH AN EXISTING CYCLE NUMBER
2527	if (( run_number >= cycnum[$i] ))
2528	then
2529	(( cycnum[$i] = run_number ))
2530	else
2531	if (( run_number > 0 ))
2532	then
2533	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2534	fi
2535	fi
2536	fi
2537	if (( cycnum[$i] > 0 ))
2538	then
2539	cyclestring=`printf "%03d" ${cycnum[$i]}`
2540	pathout[$i]=${pathout[$i]}.$cyclestring
2541	fi
2542	fi
2543
2544	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2545	files_for_cores=false; filetype=file
2546	link_local_output=false
2547	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2548	then
2549	files_for_cores=true; filetype=directory
2550	actionout[$i]=""
2551	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2552	then
2553	actionout[$i]=""
2554	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2555	then
2556	files_for_cores=true; filetype=directory
2557	link_local_output=true
2558	actionout[$i]=""
2559	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2560	then
2561	link_local_output
2562	actionout[$i]=""
2563	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2564	then
2565	files_for_cores=true; filetype=directory
2566	actionout[$i]="tr"
2567	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2568	then
2569	actionout[$i]="tr"
2570	fi
2571
2572	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2573	then
2574	if [[ ${warnout[$i]} = true ]]
2575	then
2576	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2577	fi
2578	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2579	then
2580	if [[ ${warnout[$i]} = true ]]
2581	then
2582	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2583	fi
2584	else
2585
2586
2587	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2588	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2589	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2590	then
2591	if [[ $running_on_remote = true ]]
2592	then
2593
2594	# SET OPTIONS FOR TRANSFER
2595	if [[ "${actionout[$i]}" = tr ]]
2596	then
2597	if [[ $files_for_cores = false ]]
2598	then
2599	catalog_option=""
2600	catalog_string=""
2601	else
2602	catalog_option="-c"
2603	catalog_string="/"
2604	fi
2605	append_option=""
2606	append_string=""
2607	else
2608	append_option="-A"
2609	append_string="append"
2610	fi
2611
2612	transfer_failed=false
2613	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2614	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2615
2616	# TRANSFER VIA SCP
2617	if [[ "$remote_loginnode" != "" ]]
2618	then
2619	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]}"
2620	else
2621	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]}
2622	fi
2623	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2624
2625
2626	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2627	if [[ $transfer_failed = true ]]
2628	then
2629	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2630	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2631
2632	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2633	eval local_catalog=${pathout[$i]}
2634	if [[ ! -d $local_catalog ]]
2635	then
2636	printf " *** local directory does not exist. Trying to create:\n"
2637	printf " $local_catalog \n"
2638	mkdir -p $local_catalog
2639	fi
2640	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2641	transfer_problems=true
2642	fi
2643
2644	else
2645
2646	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2647	# BE COPIED OR APPENDED ON THIS MACHINE
2648	if [[ "${actionout[$i]}" = tr ]]
2649	then
2650	actionout[$i]=""
2651	else
2652	actionout[$i]="a"
2653	fi
2654	fi
2655	fi
2656
2657
2658	# APPEND ON THIS MACHINE
2659	if [[ "${actionout[$i]}" = "a" ]]
2660	then
2661	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2662	then
2663	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2664	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2665	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2666	else
2667	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2668	printf "\n ${pathout[$i]}\n"
2669	cat ${localout[$i]} >> ${pathout[$i]}
2670	fi
2671	fi
2672
2673	# COPY ON THIS MACHINE
2674	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2675	# ON DIFFERENT FILE-SYSTEMS
2676	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2677	then
2678
2679	# COPY IN CASE OF RUNS ON SINGLE CORES
2680	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2681	then
2682	printf "\n >>> OUTPUT: ${localout[$i]} to"
2683	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2684	if [[ $link_local_output = true ]]
2685	then
2686	printf " file will be linked\n"
2687	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2688	fi
2689	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2690	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2691	then
2692	if [[ $link_local_output = true ]]
2693	then
2694	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2695	fi
2696	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2697	else
2698	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2699	fi
2700	else
2701	printf "\n >>> OUTPUT: ${localout[$i]} to"
2702	printf "\n ${pathout[$i]}\n"
2703	if [[ $link_local_output = true ]]
2704	then
2705	printf " file will be linked\n"
2706	ln -f ${localout[$i]} ${pathout[$i]}
2707	fi
2708	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2709	if [[ ! -f "${pathout[$i]}" ]]
2710	then
2711	if [[ $link_local_output = true ]]
2712	then
2713	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2714	fi
2715	cp ${localout[$i]} ${pathout[$i]}
2716	else
2717	printf "+++ no copy because file ${pathout[$i]} exists\n"
2718	fi
2719	fi
2720
2721	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2722	then
2723
2724	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2725	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2726	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2727	printf "\n ${pathout[$i]}\n"
2728	if [[ $link_local_output = true ]]
2729	then
2730	printf " files will be linked\n"
2731	mkdir -p ${pathout[$i]}
2732	cd ${localout[$i]}
2733	for file in $(ls *)
2734	do
2735	ln -f $file ${pathout[$i]}
2736	done >\|/dev/null 2>&1
2737	cd $tempdir
2738	fi
2739
2740	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2741	if [[ ! -f "${pathout[$i]}/_000000" ]]
2742	then
2743	if [[ $link_local_output = true ]]
2744	then
2745	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2746	fi
2747	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2748	cp -r ${localout[$i]}/* ${pathout[$i]}
2749	fi
2750
2751	fi
2752	fi
2753	done
2754
2755	if (( i != 0 ))
2756	then
2757	timestring=`date +%H:%M:%S`
2758	if [[ $transfer_problems = true ]]
2759	then
2760	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
2761	printf "\n +++ WARNING: some data transfers failed! \n"
2762	else
2763	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
2764	fi
2765	fi
2766
2767
2768	# IF REQUIRED, START A RESTART-JOB
2769	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2770	if [[ -f CONTINUE_RUN ]]
2771	then
2772
2773	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2774	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2775	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2776	# -b START A BATCH JOB
2777	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2778	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2779	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2780
2781	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2782	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2783	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2784	then
2785	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2786	fi
2787
2788	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2789	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2790	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2791	then
2792	prc=`echo $prc \| sed 's/#/r/g'`
2793	fi
2794
2795
2796	# START THE RESTART-JOB
2797	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2798	echo " $prc"
2799	printf "\n$dashes\n"
2800	if [[ $running_on_remote = true ]]
2801	then
2802
2803	echo "*** ssh will be used to initiate restart-runs!"
2804	echo " return_address=\"$return_address\" "
2805	echo " return_username=\"$local_username\" "
2806
2807	if [[ "$remote_loginnode" != "" ]]
2808	then
2809	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
2810	else
2811	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2812	fi
2813
2814	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2815	sleep 30
2816
2817	else
2818
2819	# START THE RESTART JOB ON THE LOCAL HOST
2820	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2821
2822	fi
2823
2824	# CHECK, IF RESTART JOB HAS BEEN STARTED
2825	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
2826	then
2827	printf "\n$dashes\n +++ creating restart run failed \n"
2828	locat=create_restart
2829	rm palmrun_restart.log
2830	exit
2831	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
2832	then
2833	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
2834	locat=create_restart
2835	rm palmrun_restart.log
2836	exit
2837	else
2838	printf "\n$dashes\n *** restart run initiated \n"
2839	rm palmrun_restart.log
2840	fi
2841
2842
2843	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2844	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2845	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2846	# MAY BE VERY HUGE)
2847	(( i = 0 ))
2848	while (( i < nr_of_input_files ))
2849	do
2850	(( i = i + 1 ))
2851	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2852	then
2853	rm -r ${absnamein[$i]}
2854	fi
2855	done
2856
2857	fi
2858
2859
2860	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2861	cd $HOME
2862	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2863
2864
2865	else
2866
2867
2868	# PREPARING ACTIONS,
2869	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2870
2871	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2872	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2873	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2874	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2875	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2876	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2877	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2878	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2879	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2880	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2881	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2882	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2883	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2884	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2885	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2886	if [[ $create_remote_batch_job = true ]]
2887	then
2888	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2889	if [[ $do_trace = true ]]
2890	then
2891	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2892	fi
2893	elif [[ $create_batch_job = true ]]
2894	then
2895	palmrun_com=${palmrun_com}" -j"
2896	if [[ $do_trace = true ]]
2897	then
2898	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2899	fi
2900	fi
2901
2902
2903	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2904	# REMOTE HOST
2905	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2906	job_protocol_file=$job_protocol_file_local
2907	if [[ $create_remote_batch_job = true ]]
2908	then
2909	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2910	job_protocol_file=$job_protocol_file_remote
2911	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2912	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2913	fi
2914
2915
2916	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2917	jobfile=jobfile.$run_id_number
2918
2919
2920	# FIRST CREATE THE BATCH DIRECTIVES
2921	(( i = 0 ))
2922	while (( i < ibd ))
2923	do
2924	(( i = i + 1 ))
2925	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2926	eval line=\"$line\"
2927	echo "$line" >> $jobfile
2928	done
2929	echo " " >> $jobfile
2930
2931
2932	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2933	# PROTOCOL
2934	if [[ $create_remote_batch_job = true ]]
2935	then
2936	echo "set +vx" >> $jobfile
2937	echo "trap '" >> $jobfile
2938	echo "set +vx" >> $jobfile
2939	echo "cd ${remote_jobcatalog}" >> $jobfile
2940	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2941
2942	# ADD THE BATCH DIRECTIVES
2943	(( i = 0 ))
2944	while (( i < ibdt ))
2945	do
2946	(( i = i + 1 ))
2947	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2948	eval line=\"$line\"
2949	echo "$line" >> $jobfile
2950	done
2951	echo " " >> $jobfile
2952
2953	echo "set -x" >> $jobfile
2954	if [[ "$remote_loginnode" != "" ]]
2955	then
2956	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}\" " >> $jobfile
2957	else
2958	echo "${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
2959	fi
2960	echo "%%END%%" >> $jobfile
2961	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2962	echo "$submit_command $scpjob_file" >> $jobfile
2963	echo "rm $scpjob_file" >> $jobfile
2964	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2965	echo "set -x" >> $jobfile
2966	echo " ' exit" >> $jobfile
2967	fi
2968
2969
2970	# ACTIVATE ERROR-TRACEBACK
2971	if [[ $do_trace = true ]]
2972	then
2973	echo "set -x" >> $jobfile
2974	else
2975	echo "set +vx" >> $jobfile
2976	fi
2977
2978
2979	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2980	if [[ "$login_init_cmd" != "" ]]
2981	then
2982	echo "$login_init_cmd" >> $jobfile
2983	fi
2984	if [[ "$module_commands" != "" ]]
2985	then
2986	echo "$module_commands" >> $jobfile
2987	fi
2988
2989
2990	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2991	if [[ $create_remote_batch_job = true ]]
2992	then
2993	echo "mkdir $tempdir" >> $jobfile
2994	echo "chmod go+rx $tempdir" >> $jobfile
2995	else
2996	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2997	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2998	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2999	mkdir $tempdir
3000	chmod go+rx $tempdir
3001	fi
3002	echo "cd $tempdir" >> $jobfile
3003	echo "export tempdir=$tempdir" >> $jobfile
3004	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile
3005	echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile
3006	echo "export execute_palmrun=true" >> $jobfile
3007
3008
3009	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
3010	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
3011	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
3012	echo "LOCAL_PWD=$working_directory" >> $jobfile
3013	echo "export LOCAL_PWD" >> $jobfile
3014
3015
3016	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
3017	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
3018	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
3019
3020
3021	# CALL PALMRUN WITHIN THE JOB
3022	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
3023	echo "set -x" >> $jobfile
3024	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
3025
3026
3027	# TRANSFER JOBFILE TO THE TARGET HOST
3028	if [[ $create_jobfile_only = false ]]
3029	then
3030
3031	# CREATE LOCAL JOB FOLDER
3032	eval local_jobcatalog=$local_jobcatalog
3033	if [[ ! -d $local_jobcatalog ]]
3034	then
3035	echo " "
3036	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
3037	mkdir $local_jobcatalog
3038	fi
3039
3040	if [[ $create_remote_batch_job = true ]]
3041	then
3042
3043	echo " "
3044	echo " *** transfer of job to remote host via scp"
3045
3046	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3047	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
3048
3049	# COPY THE JOB FILE
3050	if [[ $do_trace = true ]]
3051	then
3052	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
3053	fi
3054	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
3055
3056	# SUBMIT THE JOB
3057	printf " *** submit the job (output of submit command, \n"
3058	printf " e.g. the job-id given by the batch-system, may follow) \n"
3059	if [[ $do_trace = true ]]
3060	then
3061	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}\" "
3062	fi
3063	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
3064
3065	elif [[ $create_batch_job = true ]]
3066	then
3067
3068	eval local_jobcatalog=$local_jobcatalog
3069	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3070	cd $local_jobcatalog
3071	echo " "
3072	echo " *** submit the job"
3073	if [[ $do_trace = true ]]
3074	then
3075	echo "$submit_command ${configuration_identifier}_${run_id}"
3076	fi
3077	$submit_command ${configuration_identifier}_${run_id}
3078	rm ${configuration_identifier}_${run_id}
3079	cd - > /dev/null
3080
3081	fi
3082
3083	rm -rf $jobfile
3084
3085	else
3086
3087	printf "\n *** jobfile created under name \"$jobfile\" "
3088	printf "\n no batch-job has been sent!"
3089
3090	fi
3091
3092	fi # END OF REMOTE-PART

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