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source: palm/trunk/SCRIPTS/palmrun @ 2795

Last change on this file since 2795 was 2789, checked in by raasch, 7 years ago
bugfix: exit if no queue has been given neither with option -q nor in the configuration file
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.3 KB

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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 2718 2018-01-02 08:49:38Z maronga $
29	# bugfix: exit if no queue has been given neither with option -q nor in the
30	# configuration file
31	#
32	# 2718 2018-01-02 08:49:38Z maronga
33	# file connection file from trunk/SCRIPTS is taken by default
34	#
35	# 2718 2018-01-02 08:49:38Z maronga
36	# Corrected "Former revisions" section
37	#
38	# 2696 2017-12-14 17:12:51Z kanani
39	# Change in file header (GPL part)
40	#
41	# 2693 2017-12-13 12:33:49Z raasch
42	# replacement of variables given by {{<variable>}} in configuration file is now
43	# done in a more general way, variable names are written in small letters
44	#
45	# 2670 2017-12-06 16:32:19Z raasch
46	# test printouts removed
47	#
48	# 2669 2017-12-06 16:03:27Z raasch
49	# file attributes in .palm.iofiles restructured, "loc" attribute completely
50	# removed,
51	# wildcard (*) allowed in .palm.iofiles as file activation string for output
52	# files,
53	# informative messages in case of missing optional input files shortened
54	# bugfix: variable cycle explicitly interpreted with 10 as the number base
55	#
56	# 2638 2017-11-23 12:44:23Z raasch
57	# use of wildcards in file connection statements enabled
58	#
59	# 2605 2017-11-09 15:31:46Z raasch
60	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
61	# will not be sent with the job file any more, but copied into the
62	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
63	#
64	# 2600 2017-11-01 14:11:20Z raasch
65	# cycle numbers are made three digits wide
66	#
67	# 2566 2017-10-20 08:50:47Z raasch
68	# execute command for combine_plot_fields added
69	# "TEMPDIR" renamed "tempdir"
70	# temporary working directory for local batch jobs is created immediately within
71	# the user's palmrun call, due to a requirement of the "grid engine" batch
72	# system, where the working directory is given with batch directive -wd and must
73	# already exist when the job is submitted,
74	# informative messages in non-trace mode reduced and partly reformatted
75	#
76	# 2551 2017-10-18 07:25:11Z raasch
77	# TEMPDIR added as replacement string to be used in batch directives
78	#
79	# 2512 2017-10-04 08:26:59Z raasch
80	# bugfix for determining cycle numbers of NetCDF input files
81	#
82	# 2506 2017-09-29 08:30:37Z raasch
83	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
84	# host configuration added to SOURCES_FOR_RUN_... folder name
85	# host_identifier renamed host_configuration
86	# option -W added to allow for job dependencies
87	#
88	# 2501 2017-09-26 11:41:55Z raasch
89	# default value for number of cores (option -X) set to 1
90	# bugfix for mechanism which overwrites configuration file settings with values
91	# provided by palmrun options
92	#
93	# 2499 2017-09-22 16:47:58Z kanani
94	# option -h named configuration identifier
95	#
96	# 2480 2017-09-19 06:24:14Z maronga
97	# bugfix for last revision
98	#
99	# 2479 2017-09-19 06:12:16Z raasch
100	# option -A (project account number) added
101	#
102	# 2422 2017-09-08 08:25:41Z raasch
103	# initial revision
104	#
105	#--------------------------------------------------------------------------------#
106	# palmrun - script for running PALM jobs on local and remote hosts
107	#--------------------------------------------------------------------------------#
108
109
110
111	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
112
113	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
114	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
115	# (TOO MANY ARGUMENTS - PROBLEM)
116	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
117
118	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
119	typeset -i nr_of_output_files=0
120	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
121	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
122	# SCRIPT-OPTION ARGUMENTS
123	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
124	typeset -i icycle inode ival maxcycle mpi_tasks
125	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
126
127	activation_string_list=""
128	AddFilenames=""
129	combine_plot_fields=true
130	compiler_name=""
131	compiler_name_ser=""
132	compiler_options=""
133	cores=1
134	cores_atmos=0
135	cores_ocean=0
136	coupled_dist=""
137	cpp_options=""
138	cpumax=0
139	create_batch_job=false
140	create_jobfile_only=false
141	create_remote_batch_job=false
142	dashes=" ----------------------------------------------------------------------------"
143	defaultqueue=""
144	delete_temporary_catalog=true
145	do_compile=true
146	do_trace=false
147	executable=""
148	execute_command=""
149	execution_error=false
150	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
151	fname=test
152	global_revision=""
153	host_configuration="default"
154	hostfile=""
155	hp=""
156	keep_data_from_previous_run=false
157	link_local_input=false
158	link_local_output=false
159	linker_options=""
160	local_jobcatalog=""
161	locat=normal
162	makefile=""
163	max_par_io_str=""
164	prc=$0
165	while [[ $(echo $prc \| grep -c "/") != 0 ]]
166	do
167	prc=`echo $prc \| cut -f2- -d"/"`
168	done
169	module_calls=""
170	palmrun_memory=""
171	palmrun_script_name=$prc
172	openmp=false
173	previous_job=""
174	project_account=""
175	queue=none
176	restart_run=false
177	return_address=""
178	remote_jobcatalog=""
179	remote_username=""
180	running_in_batch_mode=false
181	run_coupled_model=false
182	run_id=""
183	silent=false
184	source_list=""
185	source_path=""
186	tasks_per_node=0
187	threads_per_task=1
188	transfer_problems=false
189	user_source_path=""
190	use_existing_sources_folder=""
191	use_openmp=false
192	version="palmrun 1.0 Rev$Rev: 2789 $"
193	working_directory=`pwd`
194	write_binary=""
195	TOPT=""
196
197
198	# ERROR HANDLING IN CASE OF EXIT
199	trap 'if [[ $locat != normal && $locat != control_c ]]
200	then
201
202	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
203	(( i = 0 ))
204	while (( i < iec ))
205	do
206	(( i = i + 1 ))
207	printf "\n *** Execution of ERROR-command:\n"
208	printf " >>> ${err_command[$i]}\n"
209	eval ${err_command[$i]}
210	done
211	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
212	printf "\n\n+++ palmrun killed \n\n"
213	elif [[ $locat != control_c ]]
214	then
215	printf "\n --> palmrun finished\n\n"
216	fi' exit
217
218
219	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
220	trap 'cd; rm -rf $tempdir
221	printf "\n+++ palmrun killed by \"^C\" \n\n"
222	locat=control_c
223	exit
224	' 2
225
226
227	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
228	# WHICH WILL BE USED TO START RESTART-JOBS
229	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
230	do
231	case $option in
232	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
233	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
234	(b) create_batch_job=true; prc="$prc -b";;
235	(B) delete_temporary_catalog=false; prc="$prc -B";;
236	(C) restart_run=true; prc="$prc -C";;
237	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
238	(F) create_jobfile_only=true;;
239	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
240	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
241	(j) running_in_batch_mode=true;;
242	(k) keep_data_from_previous_run=true; prc="$prc -k";;
243	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
244	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
245	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
246	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
247	(r) run_id=$OPTARG;;
248	(R) return_address=$OPTARG;;
249	(s) source_list=$OPTARG;;
250	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
251	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
252	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
253	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
254	(v) silent=true; prc="$prc -v";;
255	(V) use_existing_sources_folder="-V";;
256	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
257	(W) previous_job=$OPTARG;;
258	(x) do_trace=true;set -x; prc="$prc -x";;
259	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
260	(y) ocean_file_appendix=true; prc="$prc -y";;
261	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
262	(Z) combine_plot_fields=false; prc="$prc -Z";;
263	(\?) printf "\n +++ unknown option $OPTARG \n"
264	printf "\n --> type \"$0 ?\" for available options \n"
265	locat=parameter;exit;;
266	esac
267	done
268
269
270	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
271	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
272	(( to_shift = $OPTIND - 1 ))
273	shift $to_shift
274
275	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
276	if [[ "$1" = "?" ]]
277	then
278	(printf "\n *** Description of available palmrun options:\n"
279	printf "\n Option Description Default-Value"
280	printf "\n -a activation string list \"\" "
281	printf "\n -A project account number ---"
282	printf "\n -b batch-job on local machine ---"
283	printf "\n -B do not delete temporary directory at end ---"
284	printf "\n -d base name of files attached to program test"
285	printf "\n -F create batch job file only ---"
286	printf "\n -h host configuration \"default\" "
287	printf "\n -k keep data from previous run"
288	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
289	printf "\n -M Makefile name Makefile"
290	printf "\n -O threads per openMP task ---"
291	printf "\n -q queue \"$queue\" "
292	printf "\n -s filenames of routines to be compiled \"\" "
293	printf "\n must end with .f, .f90, .F, or .c !"
294	printf "\n use \"..\" for more than one file and wildcards"
295	printf "\n -s LM compiles all locally modified files"
296	printf "\n -t allowed cpu-time in seconds (batch) 0"
297	printf "\n -T tasks per node ---"
298	printf "\n -u username on remote machine \"\" "
299	printf "\n -v no prompt for confirmation ---"
300	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
301	printf "\n -w maximum parallel io streams as given by -X"
302	printf "\n -W name of job to wait for ---"
303	printf "\n -x tracing of palmrun for debug purposes ---"
304	printf "\n -X # of processors (on parallel machines) 1"
305	printf "\n -y add appendix \"_O\" to all local output"
306	printf "\n files (ocean precursor runs followed by"
307	printf "\n coupled atmosphere-ocean runs) ---"
308	printf "\n -Y run coupled model, \"#1 #2\" with"
309	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
310	printf "\n -Z skip combine_plot_fields at the end of "
311	printf "\n the simulation ---"
312	printf "\n "
313	printf "\n Possible values of positional parameter <modus>:"
314	printf "\n \"?\" - this outline \n\n") \| more
315	exit
316	elif [[ "$1" != "" ]]
317	then
318	printf "\n +++ positional parameter $1 unknown \n"
319	locat=parameter; exit
320	fi
321
322
323
324	# SHORT STARTING MESSAGE
325	printf "\n*** $version "
326	printf "\n will be executed. Please wait ..."
327
328
329	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
330	config_file=.palm.config.$host_configuration
331	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
332
333
334	# CHECK, IF CONFIGURATION FILE EXISTS
335	if [[ ! -f $config_file ]]
336	then
337	printf "\n\n +++ configuration file: "
338	printf "\n $config_file"
339	printf "\n does not exist"
340	locat=connect; exit
341	fi
342
343
344	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
345	if [[ -f .palm.iofiles ]]
346	then
347	fileconnection_file=.palm.iofiles
348	fi
349
350
351	# CHECK, IF FILE CONNECTION FILE EXISTS
352	if [[ ! -f $fileconnection_file ]]
353	then
354	printf "\n\n +++ file connection file: "
355	printf "\n $fileconnection_file"
356	printf "\n does not exist"
357	locat=connect; exit
358	fi
359
360
361	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
362	if [[ "$activation_string_list" = "" ]]
363	then
364	printf "\n\n +++ no activation string list given: "
365	printf "\n please set palmrun option \"-a\" "
366	locat=palmrun_option; exit
367	fi
368
369
370	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
371	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
372	then
373	write_binary=true
374	else
375	write_binary=false
376	fi
377
378
379	# READ AND EVALUATE THE CONFIGURATION-FILE
380	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
381
382	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
383	while read line
384	do
385
386	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
387	eval line=\"$line\"
388
389
390	# INTERPRET THE LINE
391	if [[ "$(echo $line)" = "" ]]
392	then
393
394	# EMPTY LINE, NO ACTION
395	continue
396
397	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
398	then
399
400	# LINE IS A COMMENT LINE
401	continue
402
403	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
404	then
405
406	# LINE DEFINES AN ENVIRONMENT-VARIABLE
407	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
408	value=`echo $line \| cut -d" " -s -f2-`
409
410
411	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
412	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
413	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
414	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
415	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
416	# CONFIGURATION-FILE.
417	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
418	then
419	eval export $var="\$value"
420
421	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
422	if [[ $do_trace = true ]]
423	then
424	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
425	fi
426	fi
427
428	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
429	then
430
431	# LINE DEFINES BATCH-DIRECTIVE
432	(( ibd = ibd + 1 ))
433	line=$(echo $line \| cut -c4-)
434	batch_directive[$ibd]="$line"
435
436	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
437	then
438
439	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
440	# REMOTE TO A LOCAL HOST
441	(( ibdt = ibdt + 1 ))
442	line=$(echo $line \| cut -c5-)
443	batch_directive_transfer[$ibdt]="$line"
444
445	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
446	then
447
448	# LINE DEFINES ERROR-COMMAND
449	(( iec = iec + 1 ))
450	line=$(echo $line \| cut -c4-)
451	err_command[$iec]="$line"
452
453	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
454	then
455
456	# LINE DEFINES INPUT-COMMAND
457	(( iic = iic + 1 ))
458	line=$(echo $line \| cut -c4-)
459	in_command[$iic]="$line"
460
461	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
462	then
463
464	# LINE DEFINES OUTPUT-COMMAND
465	(( ioc = ioc + 1 ))
466	line=$(echo $line \| cut -c4-)
467	out_command[$ioc]="$line"
468
469	else
470
471	# SKIP ALL OTHER LINES
472	continue
473
474	fi
475
476	done < $config_file
477
478
479	# CHECK SETTING OF REQUIRED PARAMETERS
480	if [[ "$compiler_name" = "" ]]
481	then
482	printf "\n +++ no compiler name found in $config_file"
483	printf "\n Please add line \"compiler_name ...\" to that file."
484	locat=config_file; exit
485	fi
486	if [[ "$compiler_name_ser" = "" ]]
487	then
488	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
489	printf "\n Please add line \"compiler_name_ser ...\" to that file."
490	locat=config_file; exit
491	fi
492	if [[ "$compiler_options" = "" ]]
493	then
494	printf "\n +++ no compiler options found in $config_file"
495	printf "\n Please add line \"compiler_options ...\" to that file."
496	locat=config_file; exit
497	fi
498	if [[ "$linker_options" = "" ]]
499	then
500	printf "\n +++ no linker options found in $config_file"
501	printf "\n Please add line \"linker_options ...\" to that file."
502	locat=config_file; exit
503	fi
504	if [[ "$execute_command" = "" ]]
505	then
506	printf "\n +++ no execute command found in $config_file"
507	printf "\n Please add line \"execute_command ...\" to that file."
508	locat=config_file; exit
509	fi
510
511	if [[ "$hostfile" != "" ]]
512	then
513	if [[ $hostfile != auto && ! -f $hostfile ]]
514	then
515	printf "\n +++ no hostfile \"$hostfile\" found"
516	printf "\n Please check line \"hostfile ...\" in $config_file"
517	locat=config_file; exit
518	fi
519	fi
520
521
522	# DETERMINE THE CALL STATUS
523	if [[ "$return_address" != "" ]]
524	then
525
526	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
527	# BATCH MODE AND ...
528	running_on_remote=true
529
530	else
531
532	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
533	if [[ "$remote_ip" != "" ]]
534	then
535
536	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
537	create_remote_batch_job=true
538
539	fi
540	running_on_remote=false
541	fi
542
543
544
545	# READ AND EVALUATE THE I/O-FILE LIST
546	[[ $silent = false ]] && printf "\n Reading the I/O files... "
547
548	# READ THE FILE CONNECTION FILE LINE BY LINE
549	while read line
550	do
551
552	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
553	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
554
555	# INTERPRET THE LINE
556	if [[ "$(echo $line)" = "" ]]
557	then
558	# EMPTY LINE, NO ACTION
559	continue
560
561	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
562	then
563
564	# LINE IS A COMMENT LINE
565	true
566
567	else
568
569	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
570	# s2a: in/out - field
571	# s2b: action - field (optional)
572	s1=`echo "$line" \| cut -d" " -f1`
573	s2=`echo "$line" \| cut -d" " -s -f2`
574	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
575	then
576	s2a=$s2
577	s2b=""
578	else
579	s2a=`echo $s2 \| cut -d":" -f1`
580	s2b=`echo $s2 \| cut -d":" -f2`
581	fi
582	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
583	s4=`echo "$line" \| cut -d" " -s -f4`
584	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
585	s5=`echo "$line" \| cut -d" " -s -f5`
586	s6=`echo "$line" \| cut -d" " -s -f6`
587
588
589	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
590	# INPUT- OR OUTPUT-LIST.
591	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
592	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
593	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
594	# IS NOT CHECKED AND STORED.
595	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
596	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
597	then
598	found=false
599	for actual in $activation_string_list
600	do
601	for formal in $s3
602	do
603	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
604	done
605	done
606	if [[ $found = true ]]
607	then
608	(( iin = iin + 1 ))
609	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
610	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
611	if [[ "$s2a" = inopt ]]
612	then
613	optin_pre[$iin]=yes
614	else
615	optin_pre[$iin]=no
616	fi
617
618	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
619	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
620	if [[ $running_on_remote = true && "$s2b" = tr ]]
621	then
622	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
623	fi
624
625	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
626	# THE WILDCARD FROM THE ENDING
627	if [[ "${s5: -1}" = "*" ]]
628	then
629	if [[ "$s2b" = "di" ]]
630	then
631	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
632	printf "\n see file \"$fileconnection_file\", line"
633	printf "\n$line"
634	locat=iofiles_file; exit
635	fi
636	multin[$iin]=true
637	string=${endin_pre[$iin]}
638	endin_pre[$iin]="${string%?}"
639	else
640	multin[$iin]=false
641	fi
642	fi
643	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
644	then
645	found=false
646	for actual in $activation_string_list
647	do
648	for formal in $s3
649	do
650	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
651	done
652	done
653	if [[ $found = true ]]
654	then
655	(( iout = iout + 1 ))
656	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
657	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
658
659	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
660	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
661	if [[ $formal = wildcard ]]
662	then
663	warnout_pre[$iout]=false
664	else
665	warnout_pre[$iout]=true
666	fi
667
668	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
669	# THE WILDCARD FROM THE LOCAL FILENAME
670	if [[ "${s1: -1}" = "*" ]]
671	then
672	if [[ "$s2b" = "di" ]]
673	then
674	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
675	printf "\n see file \"$fileconnection_file\", line"
676	printf "\n$line"
677	locat=iofiles_file; exit
678	fi
679	multout[$iout]=true
680	string=${localout_pre[$iout]}
681	localout_pre[$iout]="${string%?}"
682	else
683	multout[$iout]=false
684	fi
685	fi
686	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
687	then
688	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
689	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
690	locat=connect; exit
691	fi
692	IFS="$IFSALT"
693	fi
694
695	done < $fileconnection_file
696
697
698
699	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
700	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
701	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
702	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
703	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
704	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
705
706
707
708	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
709	if [[ $run_coupled_model = true ]]
710	then
711
712	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
713	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
714
715	if (( $cores_ocean + $cores_atmos != $cores ))
716	then
717
718	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
719	printf "\n PEs (total) : $cores"
720	printf "\n PEs (atmosphere): $cores_atmos"
721	printf "\n PEs (ocean) : $cores_ocean"
722	locat=coupling; exit
723
724	fi
725
726	fi
727
728
729	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
730	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
731	# FOLDER
732	if [[ $running_in_batch_mode = true ]]
733	then
734
735	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
736	then
737	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
738	printf "\n Please check the output of the palmrun-call"
739	printf "\n that you did on your local host."
740	locat=SOURCES_FOR_RUN; exit
741	fi
742
743	else
744
745	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
746	# AUTOMATIC RESTART RUN
747	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
748	if [[ $restart_run = false ]]
749	then
750
751	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
752	# THE LOCAL HOST
753	if [[ ! -d $source_path ]]
754	then
755	printf "\n\n +++ source path \"$source_path\" on local host"
756	printf "\n \"$(hostname)\" does not exist"
757	locat=source_path; exit
758	fi
759
760	rm -rf $sources_for_run_catalog
761	mkdir -p $sources_for_run_catalog
762
763	if [[ "$source_list" = LM ]]
764	then
765
766	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
767	source_list=""
768	cd $source_path
769
770
771	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
772	if [[ ! -d ../.svn ]]
773	then
774	printf "\n\n +++ source directory"
775	printf "\n \"$source_path\" "
776	printf "\n is not under control of \"subversion\"."
777	printf "\n Please do not use palmrun-option \"-s LM\"\n"
778	fi
779
780
781	# LIST ALL MODIFIED SOURCE CODE FILES
782	Filenames=""
783	svn status > tmp_svnstatus
784	while read line
785	do
786	firstc=`echo $line \| cut -c1`
787	if [[ $firstc = M \|\| $firstc = "?" ]]
788	then
789	Name=`echo "$line" \| cut -c8-`
790	extension=`echo $Name \| cut -d. -f2`
791	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
792	then
793	Filenames="$Filenames "$Name
794	fi
795	fi
796	done < tmp_svnstatus
797	rm -rf tmp_svnstatus
798
799
800	# COPY FILES TO SOURCES_FOR_RUN_...
801	for filename in $Filenames
802	do
803	cp $filename ${working_directory}/${sources_for_run_catalog}
804	source_list=$source_list"$filename "
805	done
806
807	cd - > /dev/null
808
809
810	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
811	elif [[ "$source_list" != "" ]]
812	then
813
814	cd $source_path
815
816	for filename in $source_list
817	do
818
819	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
820	if [[ $(echo $filename \| grep -c "/") != 0 ]]
821	then
822	printf "\n +++ source code file: $filename"
823	printf "\n must not contain (\"/\") "
824	locat=source; exit
825	fi
826
827	if [[ ! -f $filename ]]
828	then
829	printf "\n +++ source code file: $filename"
830	printf "\n does not exist"
831	locat=source; exit
832	else
833	cp $filename ${working_directory}/${sources_for_run_catalog}
834	fi
835
836	done
837
838	cd - > /dev/null
839
840	fi
841
842	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
843	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
844	if [[ ! -f $makefile ]]
845	then
846	printf "\n +++ file \"$makefile\" does not exist"
847	locat=make; exit
848	else
849	cp $makefile ${sources_for_run_catalog}/Makefile
850	fi
851
852
853	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
854	if [[ "$user_source_path" != "" ]]
855	then
856
857	# DOES THE DIRECTORY EXIST?
858	if [[ ! -d $user_source_path ]]
859	then
860
861	printf "\n\n *** INFORMATIVE: additional source code directory"
862	printf "\n \"$user_source_path\" "
863	printf "\n does not exist or is not a directory."
864	printf "\n No source code will be used from this directory!\n"
865	user_source_path=""
866	if [[ $silent == false ]]
867	then
868	sleep 2
869	fi
870
871	else
872
873	cd $user_source_path
874	found=false
875
876	Names=$(ls -1 *.f90 2>&1)
877	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
878	Names=$(ls -1 *.F90 2>&1)
879	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
880	Names=$(ls -1 *.F 2>&1)
881	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
882	Names=$(ls -1 *.f 2>&1)
883	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
884	Names=$(ls -1 *.c 2>&1)
885	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
886
887	cd - > /dev/null
888	cd $sources_for_run_catalog
889
890	# COPY MAKEFILE IF EXISTING
891	if [[ -f $user_source_path/Makefile ]]
892	then
893	printf "\n\n *** user Makefile from directory"
894	printf "\n \"$user_source_path\" is used \n"
895	if [[ $silent == false ]]
896	then
897	sleep 1
898	fi
899	cp $user_source_path/Makefile .
900	fi
901
902	for filename in $AddFilenames
903	do
904	if [[ -f $filename ]]
905	then
906	printf "\n +++ source code file \"$filename\" found in additional"
907	printf "\n source code directory \"$user_source_path\" "
908	printf "\n but was also given with option \"-s\" which means that it should be taken"
909	printf "\n from directory \"$source_path\"."
910	locat=source; exit
911	fi
912
913	cp $user_source_path/$filename .
914	source_list="$source_list $filename"
915
916	# CHECK IF FILE IS CONTAINED IN MAKEFILE
917	if [[ $(grep -c $filename Makefile) = 0 ]]
918	then
919	printf "\n\n +++ user file \"$filename\" "
920	printf "\n is not listed in Makefile \n"
921	locat=source; exit
922	else
923
924	if [[ $found = false ]]
925	then
926	found=true
927	printf "\n\n *** following user file(s) added to the"
928	printf " files to be translated:\n "
929	fi
930	printf "$filename "
931	if [[ $silent == false ]]
932	then
933	sleep 0.5
934	fi
935
936	fi
937	done
938	[[ $found = true ]] && printf "\n"
939	cd - > /dev/null
940	fi
941	fi
942
943	# COPY CONFIGURATION FILES
944	cp $config_file $sources_for_run_catalog
945	cp $fileconnection_file $sources_for_run_catalog
946
947	# COPY SHELLSCRIPTS
948	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
949	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
950
951	fi
952
953	fi
954
955
956	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
957	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
958	if [[ "$global_revision" = "" ]]
959	then
960	global_revision=`svnversion $source_path 2>/dev/null`
961	global_revision="Rev: $global_revision"
962	fi
963
964
965	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
966	if [[ -n $cores ]]
967	then
968
969	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
970	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
971	if [[ $tasks_per_node = 0 ]]
972	then
973	printf "\n"
974	printf "\n +++ option \"-T\" (tasks per node) is missing"
975	printf "\n set -T option or define tasks_per_node in the config file"
976	locat=tasks_per_node; (( iec = 0 )); exit
977	fi
978
979	if (( cores < tasks_per_node ))
980	then
981	printf "\n"
982	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
983	printf "\n given values: -T $tasks_per_node -X $cores"
984	locat=tasks_per_node; (( iec = 0 )); exit
985	fi
986
987	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
988	(( mpi_tasks = cores / threads_per_task ))
989	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
990	(( ii = cores / tasks_per_node ))
991	(( remaining_cores = cores - ii * tasks_per_node ))
992	if (( remaining_cores > 0 ))
993	then
994	printf "\n"
995	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
996	printf "\n divisor of the total number of cores (option \"-X\")"
997	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
998	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
999	(( nodes = nodes + 1 ))
1000	fi
1001
1002	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1003	if [[ "$tasks_per_node" != "" ]]
1004	then
1005	TOPT="-T $tasks_per_node"
1006	fi
1007
1008	fi
1009
1010
1011	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1012	if [[ "$maximum_parallel_io_streams" = "" ]]
1013	then
1014	maximum_parallel_io_streams=$cores
1015	fi
1016
1017
1018	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1019	if [[ "$scp_port" != "" ]]
1020	then
1021	PORTOPT="-P $scp_port"
1022	SSH_PORTOPT="-p $scp_port"
1023	fi
1024
1025
1026	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1027	# CONFIG-FILE
1028	if [[ "$ssh_key" != "" ]]
1029	then
1030	ssh_key="-i $HOME/.ssh/$ssh_key"
1031	fi
1032
1033
1034	# SET QUEUE, IF NOT GIVEN
1035	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1036	then
1037
1038	if [[ $queue = none && "$defaultqueue" = "" ]]
1039	then
1040	printf "\n"
1041	printf "\n +++ no default queue given in configuration file and no queue"
1042	printf "\n given with option -q"
1043	locat=queue; exit
1044	fi
1045	if [[ $queue = none ]]
1046	then
1047	queue=$defaultqueue
1048	fi
1049
1050	fi
1051
1052
1053	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1054	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1055	(( i = 0 ))
1056	(( nr_of_input_files = 0 ))
1057	while (( i < iin ))
1058	do
1059	(( i = i + 1 ))
1060
1061	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1062	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1063	if [[ "${actionin_pre[$i]}" = di ]]
1064	then
1065	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1066	else
1067	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
1068	fi
1069
1070
1071	# CHECK IF FILE EXISTS
1072	if ! ls $filename* 1>/dev/null 2>&1
1073	then
1074
1075	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1076	if [[ "${optin_pre[$i]}" != "yes" ]]
1077	then
1078	printf "\n\n +++ INPUT-file: "
1079	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1080	then
1081	printf "\n $filename"
1082	else
1083	printf "\n $filename.${extin_pre[$i]}"
1084	fi
1085	printf "\n does not exist\n"
1086	locat=input; exit
1087	else
1088	(( nr_of_input_files = nr_of_input_files + 1 ))
1089	localin[$nr_of_input_files]="${localin_pre[$i]}"
1090	optin[$nr_of_input_files]="${optin_pre[$i]}"
1091	actionin[$nr_of_input_files]="unavailable"
1092	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1093	endin[$nr_of_input_files]="${endin_pre[$i]}"
1094	extin[$nr_of_input_files]="${extin_pre[$i]}"
1095	fi
1096
1097	else
1098
1099	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
1100	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1101	if [[ "${multin[$i]}" = true ]]
1102	then
1103	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1104	ls -1 -d ${filename} > filelist 2>/dev/null
1105	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1106	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1107
1108	endings=""
1109	while read line
1110	do
1111	# filename without path (i.e. after the last "/")
1112	basefilename=$(basename ${line})
1113
1114	# check if there is an extension and remove it
1115	ext=${basefilename##*.}
1116	if [[ "$ext" = "${extin_pre[$i]}" ]]
1117	then
1118	basefilename=${basefilename%.*}
1119	fi
1120
1121	# check for an existing cycle number and remove it
1122	cycle=${basefilename##*.}
1123	if [[ $cycle =~ ^-?[0-9]+$ ]]
1124	then
1125	basefilename=${basefilename%.*}
1126	fi
1127
1128	# remove the fname from the beginning
1129	length_fname=${#fname}
1130	ending=${basefilename:${length_fname}}
1131
1132	# remove the ending given in the .iofiles from the beginning
1133	endingstring="${endin_pre[$i]}"
1134	length_ending=${#endingstring}
1135	ending=${ending:${length_ending}}
1136
1137	if [[ "$ending" = "" ]]
1138	then
1139	# standard ending as given in the .iofiles
1140	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1141	then
1142	endings="$endings DEFAULT"
1143	fi
1144	else
1145	# ending must start with "_", otherwise its a different file
1146	if [[ "${ending:0:1}" = "_" ]]
1147	then
1148	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1149	then
1150	endings="$endings $ending"
1151	fi
1152	fi
1153	fi
1154
1155	done <filelist
1156
1157	rm filelist
1158
1159	else
1160
1161	# SINGLE NAME
1162	endings=DEFAULT
1163
1164	fi
1165
1166	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1167	for ending in $endings
1168	do
1169
1170	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1171	if [[ $ending = DEFAULT ]]
1172	then
1173	ending=""
1174	fi
1175
1176	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1177	(( nr_of_input_files = nr_of_input_files + 1 ))
1178	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1179	optin[$nr_of_input_files]="${optin_pre[$i]}"
1180	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1181	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1182	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1183	extin[$nr_of_input_files]="${extin_pre[$i]}"
1184
1185
1186	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1187	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1188	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1189	then
1190	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1191	else
1192	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
1193	fi
1194
1195	# DETERMINE THE FILE'S CYCLE NUMBER
1196	(( maxcycle = 0 ))
1197	ls -1 -d $filename > filelist 2>/dev/null
1198	ls -1 -d $filename.* >> filelist 2>/dev/null
1199	while read line
1200	do
1201	# filename without path (i.e. after the last "/")
1202	basefilename=$(basename ${line})
1203
1204	# check if there is an extension
1205	extension=${basefilename##*.}
1206	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1207	then
1208	basefilename=${basefilename%.*}
1209	fi
1210
1211	# check for an existing cycle number
1212	cycle=${basefilename##*.}
1213	if [[ $cycle =~ ^-?[0-9]+$ ]]
1214	then
1215	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1216	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1217	(( icycle = $((10#$cycle)) ))
1218	else
1219	(( icycle = 0 ))
1220	fi
1221
1222	if (( icycle > maxcycle ))
1223	then
1224	(( maxcycle = icycle ))
1225
1226	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1227	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1228	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1229	then
1230	leading_zero=true
1231	else
1232	leading_zero=false
1233	fi
1234	fi
1235
1236	done <filelist
1237	rm filelist
1238
1239	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1240	if [[ $leading_zero = true ]]
1241	then
1242	cyclestring=`printf "%03d" $maxcycle`
1243	else
1244	cyclestring=$maxcycle
1245	fi
1246
1247	# APPEND CYCLE NUMBER TO FILENAME
1248	if (( maxcycle > 0 ))
1249	then
1250	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1251	then
1252	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1253	else
1254	filename=${filename}.$cyclestring
1255	fi
1256	else
1257	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1258	then
1259	filename=${filename}.${extin[$nr_of_input_files]}
1260	fi
1261	fi
1262
1263	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1264	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1265	absnamein[$nr_of_input_files]=$filename
1266	if (( maxcycle > 0 ))
1267	then
1268	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1269	then
1270	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1271	else
1272	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
1273	fi
1274	else
1275	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1276	then
1277	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1278	else
1279	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
1280	fi
1281	fi
1282
1283	done
1284
1285	fi
1286
1287	done
1288
1289
1290	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1291	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1292	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1293	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1294	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1295	# REMOTE HOST)
1296	(( i = 0 ))
1297	while (( i < iout ))
1298	do
1299	(( i = i + 1 ))
1300	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1301	then
1302	if [[ "${actionout_pre[$i]}" = tr ]]
1303	then
1304	actionout_pre[$i]=""
1305	elif [[ "${actionout_pre[$i]}" = trpe ]]
1306	then
1307	actionout_pre[$i]=pe
1308	elif [[ "${actionout_pre[$i]}" = tra ]]
1309	then
1310	actionout_pre[$i]=a
1311	fi
1312	(( maxcycle = 0 ))
1313	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
1314	eval catalogname=${pathout_pre[$i]}
1315	if ! ls $filename* 1>/dev/null 2>&1
1316	then
1317
1318	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1319	if cat /dev/null > $filename
1320	then
1321	rm $filename
1322	else
1323
1324	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1325	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1326	if [[ ! -d $catalogname ]]
1327	then
1328	if mkdir -p $catalogname
1329	then
1330	printf "\n\n *** directory:"
1331	printf "\n $catalogname"
1332	printf "\n was created\n"
1333	else
1334	printf "\n\n +++ OUTPUT-file:"
1335	printf "\n $filename"
1336	printf "\n cannot be created, because directory does not exist"
1337	printf "\n and cannot be created either"
1338	printf "\n"
1339	locat=output ; exit
1340	fi 2>/dev/null
1341	else
1342	printf "\n\n +++ OUTPUT-file:"
1343	printf "\n $filename"
1344	printf "\n cannot be created, although directory exists"
1345	printf "\n"
1346	locat=output ; exit
1347	fi
1348	fi 2>/dev/null
1349
1350	fi
1351
1352	fi
1353	done
1354
1355
1356	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1357	if [[ $running_in_batch_mode = false ]]
1358	then
1359	run_id=$RANDOM
1360	job_id=${fname}.$run_id
1361
1362	tempdir=$fast_io_catalog/$job_id
1363	fi
1364
1365
1366	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1367	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1368	then
1369
1370	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1371	if [[ $ibd = 0 ]]
1372	then
1373	printf "\n"
1374	printf "\n +++ no batch directives found in configuration file"
1375	locat=config_file_batch_directives; (( iec = 0 )); exit
1376	fi
1377
1378	# CHECK IF CPUTIME IS GIVEN FOR JOB
1379	done=false
1380	cputime=$cpumax
1381	while [[ $done = false ]]
1382	do
1383	if (( cputime == 0 ))
1384	then
1385	printf "\n +++ cpu-time is undefined"
1386	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1387	printf "\n >>> "
1388	read cputime 1>/dev/null 2>&1
1389	else
1390	done=true
1391	fi
1392	done
1393	cpumax=$cputime
1394
1395	# CHECK THE MEMORY DEMAND
1396	done=false
1397	while [[ $done = false ]]
1398	do
1399	if (( memory == 0 ))
1400	then
1401	printf "\n +++ memory demand is undefined"
1402	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1403	printf "\n >>> "
1404	read memory 1>/dev/null 2>&1
1405	else
1406	done=true
1407	fi
1408	done
1409
1410	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1411	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1412	then
1413	while [[ -z $remote_username ]]
1414	do
1415	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1416	printf "\n >>> Please type username:"
1417	printf "\n >>> "
1418	read remote_username
1419	done
1420	fi
1421
1422	else
1423
1424	if [[ $running_in_batch_mode = false ]]
1425	then
1426	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1427	cpumax=$cputime
1428	else
1429	cputime=$cpumax
1430	fi
1431
1432	fi
1433
1434
1435	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1436	(( cpu_hours = cputime / 3600 ))
1437	(( resttime = cputime - cpu_hours * 3600 ))
1438	(( cpu_minutes = resttime / 60 ))
1439	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1440	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1441
1442
1443	# OUTPUT OF THE PALMRUN-HEADER
1444	calltime=$(date)
1445	printf "\n"
1446	printf "#------------------------------------------------------------------------# \n"
1447	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1448	printf "\| \| \n"
1449	column1="called on:"; column2=$(hostname)
1450	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1451	if [[ $create_remote_batch_job = true ]]
1452	then
1453	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1454	else
1455	if [[ $running_on_remote = true ]]
1456	then
1457	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1458	else
1459	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1460	fi
1461	fi
1462	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1463
1464	column1="running in:"
1465	if [[ $running_in_batch_mode = true ]]
1466	then
1467	column2="batch job mode"
1468	else
1469	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1470	then
1471	column2="job creation mode"
1472	else
1473	column2="interactive run mode"
1474	fi
1475	fi
1476	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1477
1478	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1479	then
1480	if [[ "$project_account" != "" ]]
1481	then
1482	column1="project account number:"
1483	column2="$project_account"
1484	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1485	fi
1486	fi
1487
1488	if [[ -n $cores ]]
1489	then
1490	if [[ $run_coupled_model = false ]]
1491	then
1492	column1="number of cores:"; column2=$cores
1493	else
1494	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1495	fi
1496	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1497	fi
1498	if [[ -n $tasks_per_node ]]
1499	then
1500	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1501	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1502	if (( remaining_cores > 0 ))
1503	then
1504	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1505	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1506	fi
1507	fi
1508	if [[ $maximum_parallel_io_streams != $cores ]]
1509	then
1510	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1512	fi
1513	if [[ $use_openmp = true ]]
1514	then
1515	column1="threads per task:"; column2="$threads_per_task"
1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1517	fi
1518	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1519	then
1520	column1="memory demand / PE":; column2="$memory MB"
1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1522	column1="job cpu time (h:m:s):"; column2="$timestring"
1523	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1524	fi
1525	printf "\| \| \n"
1526	if [[ "$source_list" != "" ]]
1527	then
1528	if [[ "$make_options" != "" ]]
1529	then
1530	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1531	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1532	line=$(echo "$make_options" \| cut -c46-)
1533	while [[ "$line" != "" ]]
1534	do
1535	column1=""
1536	column2=$(echo "$line" \| cut -c-45)
1537	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1538	line=$(echo "$line" \| cut -c46-)
1539	done
1540	fi
1541	fi
1542
1543	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1545	line=$(echo "$cpp_options" \| cut -c46-)
1546	while [[ "$line" != "" ]]
1547	do
1548	column1=""
1549	column2=$(echo "$line" \| cut -c-45)
1550	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1551	line=$(echo "$line" \| cut -c46-)
1552	done
1553
1554	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1555	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1556	line=$(echo "$compiler_options" \| cut -c46-)
1557	while [[ "$line" != "" ]]
1558	do
1559	column1=""
1560	column2=$(echo "$line" \| cut -c-45)
1561	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1562	line=$(echo "$line" \| cut -c46-)
1563	done
1564
1565	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1567	line=$(echo "$linker_options" \| cut -c46-)
1568	while [[ "$line" != "" ]]
1569	do
1570	column1=""
1571	column2=$(echo "$line" \| cut -c-45)
1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1573	line=$(echo "$line" \| cut -c46-)
1574	done
1575
1576	if [[ "$login_init_cmd" != "" ]]
1577	then
1578	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1580	line=$(echo "$login_init_cmd" \| cut -c46-)
1581	while [[ "$line" != "" ]]
1582	do
1583	column1=""
1584	column2=$(echo "$line" \| cut -c-45)
1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1586	line=$(echo "$line" \| cut -c46-)
1587	done
1588	fi
1589
1590	if [[ "$module_commands" != "" ]]
1591	then
1592	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1594	line=$(echo "$module_commands" \| cut -c46-)
1595	while [[ "$line" != "" ]]
1596	do
1597	column1=""
1598	column2=$(echo "$line" \| cut -c-45)
1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1600	line=$(echo "$line" \| cut -c46-)
1601	done
1602	fi
1603	printf "\| \| \n"
1604	column1="base name of files:"; column2=$fname
1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1606	column1="activation string list:"; column2=$(echo $activation_string_list)
1607	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1608
1609	if [[ "$ocean_file_appendix" = true ]]
1610	then
1611	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1612	fi
1613
1614	if [[ "$source_list" != "" ]]
1615	then
1616	printf "\| \| \n"
1617	printf "\| Files to be compiled: \| \n"
1618	line=$source_list
1619	while [[ "$line" != "" ]]
1620	do
1621	linestart=$(echo $line \| cut -c-70)
1622	printf "\| %-70s \| \n" "$linestart"
1623	line=$(echo "$line" \| cut -c71-)
1624	done
1625	fi
1626	printf "#------------------------------------------------------------------------#"
1627
1628
1629
1630	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1631	if [[ $do_trace = true ]]
1632	then
1633	(( i = 0 ))
1634	while (( i < nr_of_input_files ))
1635	do
1636	(( i = i + 1 ))
1637	if (( i == 1 ))
1638	then
1639	printf "\n\n >>> INPUT-file assignments:\n"
1640	fi
1641	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1642	done
1643	(( i = 0 ))
1644	while (( i < iout ))
1645	do
1646	(( i = i + 1 ))
1647	if (( i == 1 ))
1648	then
1649	printf "\n\n >>> OUTPUT-file assignments:\n"
1650	fi
1651	printf "\n ${localout[$i]} : ${pathout[$i]}"
1652	done
1653	(( i = 0 ))
1654	while (( i < iic ))
1655	do
1656	(( i = i + 1 ))
1657	if (( i == 1 ))
1658	then
1659	printf "\n\n >>> INPUT-commands:\n"
1660	fi
1661	printf "\n ${in_command[$i]}"
1662	done
1663	(( i = 0 ))
1664	while (( i < ioc ))
1665	do
1666	(( i = i + 1 ))
1667	if (( i == 1 ))
1668	then
1669	printf "\n\n >>> OUTPUT-commands:\n"
1670	fi
1671	printf "\n ${out_command[$i]}"
1672	done
1673	fi
1674
1675	# QUERY FOR CONTINUE
1676	if [[ $silent = false && $running_in_batch_mode = false ]]
1677	then
1678	antwort=dummy
1679	printf "\n\n"
1680	printf " >>> everything o.k. (y/n) ? "
1681	while read antwort
1682	do
1683	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1684	then
1685	printf " >>> everything o.k. (y/n) ? "
1686	else
1687	break
1688	fi
1689	done
1690	if [[ $antwort = n \|\| $antwort = N ]]
1691	then
1692	locat=user_abort; (( iec = 0 )); exit
1693	fi
1694	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1695	then
1696	printf "\n *** batch-job will be created and submitted"
1697	else
1698	printf "\n *** PALMRUN will now continue to execute on this machine"
1699	fi
1700	fi
1701
1702
1703
1704	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1705	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1706	then
1707
1708	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1709	then
1710	printf "\n\n *** creating executable and other sources for the remote host\n"
1711	else
1712	printf "\n\n *** creating executable and other sources for the local host\n"
1713	fi
1714
1715	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1716	# IT SHALL BE CREATED
1717	ask_for_make_depository=false
1718	if [[ $create_remote_batch_job = true ]]
1719	then
1720
1721	line=`grep %base_directory $config_file`
1722	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1723	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1724
1725	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1726	then
1727	printf "\n\n +++ make depository \"${make_depository}\""
1728	printf "\n on remote host not found!"
1729	ask_for_make_depository=true
1730	fi
1731	rm ${host_configuration}_last_make_protokoll
1732
1733	else
1734
1735	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1736	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1737	if [[ ! -d ${make_depository} ]]
1738	then
1739	printf "\n\n +++ make depository \"${make_depository}\""
1740	printf "\n on local host not found!"
1741	ask_for_make_depository=true
1742	fi
1743
1744	fi
1745
1746	if [[ $ask_for_make_depository = true ]]
1747	then
1748
1749	antwort=dummy
1750	printf "\n\n"
1751	printf " >>> Create a new one (y/n) ? "
1752	while read antwort
1753	do
1754	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1755	then
1756	printf " >>> Create a new one (y/n) ? "
1757	else
1758	break
1759	fi
1760	done
1761	if [[ $antwort = n \|\| $antwort = N ]]
1762	then
1763	locat=user_abort; (( iec = 0 )); exit
1764	fi
1765
1766	if [[ $do_trace = true ]]
1767	then
1768	palmbuild -h $host_configuration
1769	else
1770	palmbuild -v -h $host_configuration
1771	fi
1772
1773	if [[ $? != 0 ]]
1774	then
1775
1776	# ABORT IN CASE OF COMPILATION PROBLEMS
1777	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1778	locat=make_depository
1779	exit
1780	else
1781	echo " *** now continue with creating executable and other sources"
1782	fi
1783
1784	fi
1785
1786	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1787	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
1788
1789	if [[ $? != 0 ]]
1790	then
1791
1792	# ABORT IN CASE OF COMPILATION PROBLEMS
1793	printf "\n +++ error while creating executable and/or other sources"
1794	locat=execution
1795	rm -rf $sources_for_run_catalog
1796	exit
1797
1798	else
1799
1800	printf " *** executable and other sources created\n"
1801	rm -rf $sources_for_run_catalog
1802
1803	fi
1804
1805	fi
1806
1807
1808	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1809	# WILL BE COPIED TO THE REMOTE HOST
1810	if [[ $create_remote_batch_job = true ]]
1811	then
1812	(( i = 0 ))
1813	while (( i < nr_of_input_files ))
1814	do
1815	(( i = i + 1 ))
1816	if [[ "${actionin[$i]}" = tr ]]
1817	then
1818	eval inputfile=${pathin[$i]}/${frelin[$i]}
1819	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1820	fi
1821	done
1822	if (( i > 0 ))
1823	then
1824	printf " *** input files have been copied to the remote host\n"
1825	fi
1826	fi
1827
1828
1829	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1830	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1831	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1832	then
1833
1834	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1835	if [[ $running_in_batch_mode = false ]]
1836	then
1837	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1838	# FOLDER
1839	mkdir -p $tempdir
1840	chmod go+rx $tempdir
1841	cd $tempdir
1842	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1843	printf "\n *** changed to temporary directory: $tempdir"
1844
1845	else
1846
1847	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1848	printf "\n *** running in temporary directory: $tempdir"
1849
1850	fi
1851
1852
1853	# PROVIDE THE INPUT FILES
1854	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1855	optional_files_missing=false
1856	(( i = 0 ))
1857	while (( i < nr_of_input_files ))
1858	do
1859	(( i = i + 1 ))
1860	if (( i == 1 ))
1861	then
1862	printf "\n\n *** providing INPUT-files:\n$dashes"
1863	fi
1864
1865
1866	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1867	if [[ "${actionin[$i]}" = unavailable ]]
1868	then
1869	optional_files_missing=true
1870	continue
1871	fi
1872
1873	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1874	files_for_cores=false; filetype=file
1875	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1876	then
1877	files_for_cores=true; filetype=files
1878	actionin[$i]=""
1879	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1880	then
1881	actionin[$i]=""
1882	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1883	then
1884	files_for_cores=true; filetype=files
1885	actionin[$i]="ln"
1886	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1887	then
1888	actionin[$i]="ln"
1889	fi
1890
1891	if [[ $files_for_cores = true ]]
1892	then
1893	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1894	else
1895	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1896	fi
1897
1898	# INPUT-FILES TO BE LINKED
1899	if [[ "${actionin[$i]}" = ln ]]
1900	then
1901
1902	printf "\n $filetype will be linked"
1903	if [[ $files_for_cores = false ]]
1904	then
1905	if [[ -f "${absnamein[$i]}" ]]
1906	then
1907	ln ${absnamein[$i]} ${localin[$i]}
1908	got_tmp[$i]=true
1909	fi
1910	else
1911	if [[ -d "${absnamein[$i]}" ]]
1912	then
1913	mkdir -p ${localin[$i]}
1914	cd ${absnamein[$i]}
1915	for file in $(ls *)
1916	do
1917	ln $file $tempdir/${localin[$i]}
1918	done >\|/dev/null 2>&1
1919	cd $tempdir
1920	fi
1921
1922	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1923	if [[ ! -f "${localin[$i]}/_000000" ]]
1924	then
1925	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1926	cp -r ${absnamein[$i]}/* ${localin[$i]}
1927	fi
1928
1929	got_tmp[$i]=true
1930	fi
1931	fi
1932
1933	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1934	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1935	then
1936
1937	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1938	then
1939
1940	# FILE COPIES ARE PROVIDED FOR ALL CORES
1941	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1942	printf "\n file will be provided for $cores processors"
1943	mkdir -p ${localin[$i]}
1944	ival=$cores
1945	(( ii = 0 ))
1946	while (( ii <= ival-1 ))
1947	do
1948	if (( ii < 10 ))
1949	then
1950	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1951	elif (( ii < 100 ))
1952	then
1953	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1954	elif (( ii < 1000 ))
1955	then
1956	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1957	else
1958	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1959	fi
1960	(( ii = ii + 1 ))
1961	done
1962
1963	else
1964
1965	if [[ $files_for_cores = true ]]
1966	then
1967
1968	# PROVIDE FILES FOR EACH CORE
1969	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1970	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1971	printf "\n providing $cores files for the respective cores"
1972	mkdir -p ${localin[$i]}
1973	if [[ $link_local_input = true ]]
1974	then
1975	printf " files will be linked\n"
1976	cd ${absnamein[$i]}
1977	for file in $(ls *)
1978	do
1979	ln -f $file ${localin[$i]}
1980	done
1981	cd $tempdir
1982	fi
1983
1984	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1985	if [[ ! -f "${localin[$i]}/_000000" ]]
1986	then
1987	if [[ $link_local_input = true ]]
1988	then
1989	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1990	fi
1991	cp -r ${absnamein[$i]}/* ${localin[$i]}
1992	fi
1993
1994	else
1995
1996	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1997	if [[ $link_local_input = true ]]
1998	then
1999	printf " file will be linked\n"
2000	ln -f ${absnamein[$i]} ${localin[$i]}
2001	fi
2002	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2003	if [[ ! -f "${localin[$i]}" ]]
2004	then
2005	if [[ $link_local_input = true ]]
2006	then
2007	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2008	fi
2009	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2010	then
2011	mv ${absnamein[$i]} ${localin[$i]}
2012	else
2013	cp ${absnamein[$i]} ${localin[$i]}
2014	fi
2015	fi
2016	fi
2017	fi
2018	fi
2019
2020	done
2021	if (( i != 0 ))
2022	then
2023	if [[ $optional_files_missing = true ]]
2024	then
2025	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2026	fi
2027	printf "\n$dashes\n *** all INPUT-files provided \n"
2028	fi
2029
2030
2031	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2032	(( i = 0 ))
2033	while (( i < iic ))
2034	do
2035	(( i = i + 1 ))
2036	if (( i == 1 ))
2037	then
2038	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2039	fi
2040	printf "\n >>> ${in_command[$i]}"
2041	eval ${in_command[$i]}
2042	if (( i == iic ))
2043	then
2044	printf "\n$dashes\n"
2045	fi
2046	done
2047
2048
2049	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2050	# (FILE ENVPAR WILL BE READ BY PALM)
2051	cat > ENVPAR << EOF
2052	&envpar run_identifier = '$fname', host = '$host_configuration',
2053	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2054	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2055	maximum_cpu_time_allowed = ${cpumax}.,
2056	revision = '$global_revision',
2057	batch_job = .${running_in_batch_mode}. /
2058
2059	EOF
2060
2061
2062	# STARTING THE EXECUTABLE
2063	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2064	PATH=$PATH:$tempdir
2065
2066
2067	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2068	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2069	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2070	eval line=\"$line\"
2071	execute_command="$line"
2072
2073
2074	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2075	if [[ "$execute_command_for_combine" = "" ]]
2076	then
2077	eval line2=\"$line2\"
2078	execute_command_for_combine="$line2"
2079	fi
2080
2081
2082
2083	# PROVIDE A HOSTFILE, IF REQUIRED
2084	if [[ "$hostfile" != "" ]]
2085	then
2086
2087	if [[ $hostfile = auto ]]
2088	then
2089	# CREATE A NEW HOSTFILE
2090	(( ii = 1 ))
2091	while (( ii <= cores / threads_per_task ))
2092	do
2093	echo $(hostname) >> hostfile
2094	(( ii = ii + 1 ))
2095	done
2096	if (( cores / threads_per_task == 0 ))
2097	then
2098	echo $(hostname) >> hostfile
2099	fi
2100
2101	else
2102	cp $hostfile hostfile
2103	fi
2104	eval line=\"`head -n $ii hostfile`\"
2105	printf "\n *** running on: $line"
2106	fi
2107
2108
2109
2110	# SET THE NUMBER OF OPENMP-THREADS
2111	if [[ $use_openmp = true ]]
2112	then
2113	export OMP_NUM_THREADS=$threads_per_task
2114	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2115	else
2116	export OMP_NUM_THREADS=1
2117	fi
2118
2119
2120	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2121	if [[ $run_coupled_model = false ]]
2122	then
2123	if [[ "$ocean_file_appendix" = true ]]
2124	then
2125	echo "precursor_ocean" > coupling_steering
2126	else
2127	echo "precursor_atmos" > coupling_steering
2128	fi
2129	else
2130	(( iia = $cores_atmos / $threads_per_task ))
2131	(( iio = $cores_ocean / $threads_per_task ))
2132	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2133	printf "\n\n"
2134	echo "coupled_run $iia $iio" > coupling_steering
2135	fi
2136
2137	printf "\n *** execute command:"
2138	printf "\n \"$execute_command\" \n\n"
2139
2140	$execute_command < coupling_steering
2141
2142	if [[ $? != 0 ]]
2143	then
2144
2145	# ABORT IN CASE OF RUNTIME ERRORS
2146	printf "\n +++ runtime error occured"
2147	locat=execution
2148	exit
2149
2150	else
2151
2152	printf "\n$dashes\n *** execution finished \n"
2153
2154	fi
2155
2156
2157	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2158	# BY EACH CORE INTO ONE FILE
2159	if [[ ! -f combine_plot_fields.x ]]
2160	then
2161
2162	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2163	printf "\n 2d- and/or 3d-data may be incomplete!"
2164	printf "\n Your previous palmbuild may have failed. Please check.\n"
2165
2166	elif [[ "$combine_plot_fields" == true ]]
2167	then
2168
2169	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2170	$execute_command_for_combine
2171
2172	else
2173
2174	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2175	# DATA OUTPUT
2176	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2177	fi
2178
2179
2180
2181	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2182	(( i = 0 ))
2183	while (( i < ioc ))
2184	do
2185	(( i = i + 1 ))
2186	if (( i == 1 ))
2187	then
2188	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2189	fi
2190	printf "\n >>> ${out_command[$i]}"
2191	eval ${out_command[$i]}
2192	if (( i == ioc ))
2193	then
2194	printf "\n$dashes\n"
2195	fi
2196	done
2197
2198
2199	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2200	# WILDCARDS
2201	(( i = 0 ))
2202	(( nr_of_output_files = 0 ))
2203
2204	while (( i < iout ))
2205	do
2206
2207	(( i = i + 1 ))
2208
2209	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2210	# CREATE A LIST FOR THE DETECTED ENDINGS
2211	if [[ "${multout[$i]}" = true ]]
2212	then
2213	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2214	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2215	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2216
2217	endings="DEFAULT"
2218	while read line
2219	do
2220	# remove the local name from the beginning
2221	localnamestring="${localout_pre[$i]}"
2222	length_localname=${#localnamestring}
2223	ending=${line:${length_localname}}
2224
2225	if [[ "$ending" != "" ]]
2226	then
2227	endings="$endings $ending"
2228	fi
2229
2230	done <filelist
2231
2232	rm filelist
2233
2234	else
2235
2236	# SINGLE NAME
2237	endings=DEFAULT
2238
2239	fi
2240
2241	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2242	for ending in $endings
2243	do
2244
2245	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2246	if [[ $ending = DEFAULT ]]
2247	then
2248	ending=""
2249	fi
2250
2251	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2252	(( nr_of_output_files = nr_of_output_files + 1 ))
2253	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2254	transout[$nr_of_output_files]="${transout_pre[$i]}"
2255	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2256	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2257	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2258	extout[$nr_of_output_files]="${extout_pre[$i]}"
2259	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2260
2261	done
2262
2263	done
2264
2265
2266
2267
2268	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2269	(( i = 0 ))
2270	while (( i < nr_of_output_files ))
2271	do
2272	(( i = i + 1 ))
2273	if (( i == 1 ))
2274	then
2275	printf "\n\n *** saving OUTPUT-files:"
2276
2277	# GET RUN NUMBER ASSIGNED BY PALM
2278	if [[ -f RUN_NUMBER ]]
2279	then
2280	read run_number < RUN_NUMBER
2281	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2282	usecycle_option="-U $run_number"
2283	else
2284	run_number=0
2285	usecycle_option=""
2286	fi
2287	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2288	then
2289	printf "\n *** in case of SCP transfers to local host"
2290	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2291	fi
2292	printf "\n$dashes"
2293	fi
2294
2295	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2296	then
2297
2298	eval filename=${pathout[$i]}/${fname}${endout[$i]}
2299
2300	# DETERMINE THE CYCLE NUMBER
2301	ls -1 -d $filename > filelist 2>/dev/null
2302	ls -1 -d $filename.* >> filelist 2>/dev/null
2303	while read line
2304	do
2305
2306	# filename without path (i.e. after the last "/")
2307	basefilename=$(basename ${line})
2308
2309	# check if there is an extension
2310	extension=${basefilename##*.}
2311	if [[ "$extension" = "${extout[$i]}" ]]
2312	then
2313	basefilename=${basefilename%.*}
2314	fi
2315
2316	# check for an existing cycle number
2317	cycle=${basefilename##*.}
2318	if [[ $cycle =~ ^-?[0-9]+$ ]]
2319	then
2320	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2321	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2322	(( icycle = $((10#$cycle)) + 1 ))
2323	else
2324	(( icycle = 1 ))
2325	fi
2326
2327	if (( icycle > maxcycle ))
2328	then
2329	(( maxcycle = icycle ))
2330	fi
2331
2332	done <filelist
2333	rm filelist
2334
2335
2336	# SET THE CYCLE NUMBER
2337	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2338	if [[ "${actionout[$i]}" = a ]]
2339	then
2340	(( maxcycle = maxcycle - 1 ))
2341	fi
2342
2343	(( cycnum[$i] = maxcycle ))
2344	pathout[$i]=$filename
2345
2346
2347	# ADD CYCLE NUMBER TO FILENAME
2348	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2349	if [[ "${actionout[$i]}" != "a" ]]
2350	then
2351	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2352	# WITH AN EXISTING CYCLE NUMBER
2353	if (( run_number >= cycnum[$i] ))
2354	then
2355	(( cycnum[$i] = run_number ))
2356	else
2357	if (( run_number > 0 ))
2358	then
2359	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2360	fi
2361	fi
2362	fi
2363	if (( cycnum[$i] > 0 ))
2364	then
2365	cyclestring=`printf "%03d" ${cycnum[$i]}`
2366	pathout[$i]=${pathout[$i]}.$cyclestring
2367	fi
2368	fi
2369
2370	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2371	files_for_cores=false; filetype=file
2372	link_local_output=false
2373	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2374	then
2375	files_for_cores=true; filetype=directory
2376	actionout[$i]=""
2377	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2378	then
2379	actionout[$i]=""
2380	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2381	then
2382	files_for_cores=true; filetype=directory
2383	link_local_output=true
2384	actionout[$i]=""
2385	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2386	then
2387	link_local_output
2388	actionout[$i]=""
2389	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2390	then
2391	files_for_cores=true; filetype=directory
2392	actionout[$i]="tr"
2393	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2394	then
2395	actionout[$i]="tr"
2396	fi
2397
2398	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2399	then
2400	if [[ ${warnout[$i]} = true ]]
2401	then
2402	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2403	fi
2404	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2405	then
2406	if [[ ${warnout[$i]} = true ]]
2407	then
2408	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2409	fi
2410	else
2411
2412
2413	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2414	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2415	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2416	then
2417	if [[ $running_on_remote = true ]]
2418	then
2419
2420	# SET OPTIONS FOR TRANSFER
2421	if [[ "${actionout[$i]}" = tr ]]
2422	then
2423	if [[ $files_for_cores = false ]]
2424	then
2425	catalog_option=""
2426	catalog_string=""
2427	else
2428	catalog_option="-c"
2429	catalog_string="/"
2430	fi
2431	append_option=""
2432	append_string=""
2433	else
2434	append_option="-A"
2435	append_string="append"
2436	fi
2437
2438	transfer_failed=false
2439	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2440	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2441
2442	# TRANSFER VIA SCP
2443	if [[ "$remote_loginnode" != "" ]]
2444	then
2445	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2446	else
2447	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
2448	fi
2449	[[ $? != 0 ]] && transfer_failed=true
2450
2451
2452	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2453	if [[ $transfer_failed = true ]]
2454	then
2455	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2456	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2457
2458	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2459	eval local_catalog=${pathout[$i]}
2460	if [[ ! -d $local_catalog ]]
2461	then
2462	printf " *** local directory does not exist. Trying to create:\n"
2463	printf " $local_catalog \n"
2464	mkdir -p $local_catalog
2465	fi
2466	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2467	transfer_problems=true
2468	fi
2469
2470	else
2471
2472	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2473	# BE COPIED OR APPENDED ON THIS MACHINE
2474	if [[ "${actionout[$i]}" = tr ]]
2475	then
2476	actionout[$i]=""
2477	else
2478	actionout[$i]="a"
2479	fi
2480	fi
2481	fi
2482
2483
2484	# APPEND ON THIS MACHINE
2485	if [[ "${actionout[$i]}" = "a" ]]
2486	then
2487	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2488	then
2489	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2490	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2491	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2492	else
2493	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2494	printf "\n ${pathout[$i]}\n"
2495	cat ${localout[$i]} >> ${pathout[$i]}
2496	fi
2497	fi
2498
2499	# COPY ON THIS MACHINE
2500	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2501	# ON DIFFERENT FILE-SYSTEMS
2502	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2503	then
2504
2505	# COPY IN CASE OF RUNS ON SINGLE CORES
2506	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2507	then
2508	printf "\n >>> OUTPUT: ${localout[$i]} to"
2509	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2510	if [[ $link_local_output = true ]]
2511	then
2512	printf " file will be linked\n"
2513	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2514	fi
2515	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2516	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2517	then
2518	if [[ $link_local_output = true ]]
2519	then
2520	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2521	fi
2522	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2523	else
2524	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2525	fi
2526	else
2527	printf "\n >>> OUTPUT: ${localout[$i]} to"
2528	printf "\n ${pathout[$i]}\n"
2529	if [[ $link_local_output = true ]]
2530	then
2531	printf " file will be linked\n"
2532	ln -f ${localout[$i]} ${pathout[$i]}
2533	fi
2534	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2535	if [[ ! -f "${pathout[$i]}" ]]
2536	then
2537	if [[ $link_local_output = true ]]
2538	then
2539	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2540	fi
2541	cp ${localout[$i]} ${pathout[$i]}
2542	else
2543	printf "+++ no copy because file ${pathout[$i]} exists\n"
2544	fi
2545	fi
2546
2547	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2548	then
2549
2550	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2551	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2552	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2553	printf "\n ${pathout[$i]}\n"
2554	if [[ $link_local_output = true ]]
2555	then
2556	printf " files will be linked\n"
2557	mkdir -p ${pathout[$i]}
2558	cd ${localout[$i]}
2559	for file in $(ls *)
2560	do
2561	ln -f $file ${pathout[$i]}
2562	done >\|/dev/null 2>&1
2563	cd $tempdir
2564	fi
2565
2566	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2567	if [[ ! -f "${pathout[$i]}/_000000" ]]
2568	then
2569	if [[ $link_local_output = true ]]
2570	then
2571	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2572	fi
2573	cp -r ${localout[$i]}/* ${pathout[$i]}
2574	fi
2575
2576	fi
2577	fi
2578	done
2579
2580	if (( i != 0 ))
2581	then
2582	if [[ $transfer_problems = true ]]
2583	then
2584	printf "\n$dashes\n *** OUTPUT-files saved"
2585	printf "\n +++ WARNING: some data transfers failed! \n"
2586	else
2587	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2588	fi
2589	fi
2590
2591
2592	# IF REQUIRED, START A RESTART-JOB
2593	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2594	if [[ -f CONTINUE_RUN ]]
2595	then
2596
2597	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2598	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2599	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2600	# -b START A BATCH JOB
2601	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2602	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2603	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2604
2605
2606	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2607	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2608	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2609	then
2610	prc=`echo $prc \| sed 's/#/r/g'`
2611	fi
2612
2613
2614	# START THE RESTART-JOB
2615	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2616	echo " $prc"
2617	printf "\n$dashes\n"
2618	if [[ $running_on_remote = true ]]
2619	then
2620
2621	echo "*** ssh will be used to initiate restart-runs!"
2622	echo " return_address=\"$return_address\" "
2623	echo " return_username=\"$local_username\" "
2624
2625	if [[ "$remote_loginnode" != "" ]]
2626	then
2627	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
2628	else
2629	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2630	fi
2631
2632	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2633	sleep 30
2634
2635	else
2636
2637	# START THE RESTART JOB ON THE LOCAL HOST
2638	eval $prc # THE ' MUST BE EVALUATED
2639	cd - > /dev/null
2640
2641	fi
2642	printf "\n$dashes\n *** restart-run initiated \n"
2643
2644
2645	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2646	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2647	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2648	# MAY BE VERY HUGE)
2649	(( i = 0 ))
2650	while (( i < nr_of_input_files ))
2651	do
2652	(( i = i + 1 ))
2653	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2654	then
2655	rm -r ${absnamein[$i]}
2656	fi
2657	done
2658
2659	fi
2660
2661
2662	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2663	cd $HOME
2664	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2665
2666
2667	else
2668
2669
2670	# PREPARING ACTIONS,
2671	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2672
2673	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2674	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2675	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2676	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2677	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2678	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2679	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2680	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2681	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2682	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2683	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2684	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2685	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2686	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2687	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2688	if [[ $create_remote_batch_job = true ]]
2689	then
2690	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2691	if [[ $do_trace = true ]]
2692	then
2693	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2694	fi
2695	elif [[ $create_batch_job = true ]]
2696	then
2697	palmrun_com=${palmrun_com}" -j"
2698	if [[ $do_trace = true ]]
2699	then
2700	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2701	fi
2702	fi
2703
2704
2705	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2706	# REMOTE HOST
2707	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2708	job_protocol_file=$job_protocol_file_local
2709	if [[ $create_remote_batch_job = true ]]
2710	then
2711	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2712	job_protocol_file=$job_protocol_file_remote
2713	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2714	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2715	fi
2716
2717
2718	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2719	jobfile=jobfile.$run_id
2720
2721
2722	# FIRST CREATE THE BATCH DIRECTIVES
2723	(( i = 0 ))
2724	while (( i < ibd ))
2725	do
2726	(( i = i + 1 ))
2727	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2728	eval line=\"$line\"
2729	echo "$line" >> $jobfile
2730	done
2731	echo " " >> $jobfile
2732
2733
2734	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2735	# PROTOCOL
2736	if [[ $create_remote_batch_job = true ]]
2737	then
2738	echo "set +vx" >> $jobfile
2739	echo "trap '" >> $jobfile
2740	echo "set +vx" >> $jobfile
2741	echo "cd ${remote_jobcatalog}" >> $jobfile
2742	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2743
2744	# ADD THE BATCH DIRECTIVES
2745	(( i = 0 ))
2746	while (( i < ibdt ))
2747	do
2748	(( i = i + 1 ))
2749	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2750	eval line=\"$line\"
2751	echo "$line" >> $jobfile
2752	done
2753	echo " " >> $jobfile
2754
2755	echo "set -x" >> $jobfile
2756	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
2757	echo "%%END%%" >> $jobfile
2758	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2759	echo "$submit_command $scpjob_file" >> $jobfile
2760	echo "rm $scpjob_file" >> $jobfile
2761	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2762	echo "set -x" >> $jobfile
2763	echo " ' exit" >> $jobfile
2764	fi
2765
2766
2767	# ACTIVATE ERROR-TRACEBACK
2768	if [[ $do_trace = true ]]
2769	then
2770	echo "set -x" >> $jobfile
2771	else
2772	echo "set +vx" >> $jobfile
2773	fi
2774
2775
2776	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2777	if [[ "$login_init_cmd" != "" ]]
2778	then
2779	echo "$login_init_cmd" >> $jobfile
2780	fi
2781	if [[ "$module_commands" != "" ]]
2782	then
2783	echo "$module_commands" >> $jobfile
2784	fi
2785
2786
2787	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2788	if [[ $create_remote_batch_job = true ]]
2789	then
2790	echo "mkdir $tempdir" >> $jobfile
2791	echo "chmod go+rx $tempdir" >> $jobfile
2792	else
2793	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2794	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2795	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2796	mkdir $tempdir
2797	chmod go+rx $tempdir
2798	fi
2799	echo "cd $tempdir" >> $jobfile
2800	echo "export tempdir=$tempdir" >> $jobfile
2801	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2802	echo "export PATH=.:\$PATH" >> $jobfile
2803	echo "export execute_palmrun=true" >> $jobfile
2804
2805
2806	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2807	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2808	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2809	echo "LOCAL_PWD=$working_directory" >> $jobfile
2810	echo "export LOCAL_PWD" >> $jobfile
2811
2812
2813	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2814	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2815	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2816
2817
2818	# CALL PALMRUN WITHIN THE JOB
2819	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2820	echo "set -x" >> $jobfile
2821	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2822
2823
2824	# TRANSFER JOBFILE TO THE TARGET HOST
2825	if [[ $create_jobfile_only = false ]]
2826	then
2827
2828	if [[ $create_remote_batch_job = true ]]
2829	then
2830
2831	echo " "
2832	echo " *** transfer of job to remote host via scp"
2833	if [[ $do_trace = true ]]
2834	then
2835	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2836	fi
2837	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2838
2839	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2840	if [[ $do_trace = true ]]
2841	then
2842	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2843	fi
2844	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2845
2846	elif [[ $create_batch_job = true ]]
2847	then
2848
2849	eval local_jobcatalog=$local_jobcatalog
2850	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2851	cd $local_jobcatalog
2852	echo " "
2853	echo " *** submit the job"
2854	if [[ $do_trace = true ]]
2855	then
2856	echo "$submit_command ${host_configuration}_${job_id}"
2857	fi
2858	$submit_command ${host_configuration}_${job_id}
2859	rm ${host_configuration}_${job_id}
2860	cd - > /dev/null
2861
2862	fi
2863
2864	rm -rf $jobfile
2865
2866	else
2867
2868	printf "\n *** jobfile created under name \"$jobfile\" "
2869	printf "\n no batch-job has been sent!"
2870
2871	fi
2872
2873	fi # END OF REMOTE-PART

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