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source: palm/trunk/SCRIPTS/palmrun @ 2938

Last change on this file since 2938 was 2906, checked in by Giersch, 7 years ago
new procedure for reading/writing svf data, initialization of local variable ids
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 96.3 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $
29	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
30	# the possible output or input of sky view factors
31	#
32	# 2718 2018-01-02 08:49:38Z maronga
33	# "fname" renamed to "jobname"
34	#
35	# 2718 2018-01-02 08:49:38Z maronga
36	# parameters are allowed in output commands (OC:)
37	#
38	# 2718 2018-01-02 08:49:38Z maronga
39	# bugfix: exit if no queue has been given neither with option -q nor in the
40	# configuration file
41	#
42	# 2718 2018-01-02 08:49:38Z maronga
43	# file connection file from trunk/SCRIPTS is taken by default
44	#
45	# 2718 2018-01-02 08:49:38Z maronga
46	# Corrected "Former revisions" section
47	#
48	# 2696 2017-12-14 17:12:51Z kanani
49	# Change in file header (GPL part)
50	#
51	# 2693 2017-12-13 12:33:49Z raasch
52	# replacement of variables given by {{<variable>}} in configuration file is now
53	# done in a more general way, variable names are written in small letters
54	#
55	# 2670 2017-12-06 16:32:19Z raasch
56	# test printouts removed
57	#
58	# 2669 2017-12-06 16:03:27Z raasch
59	# file attributes in .palm.iofiles restructured, "loc" attribute completely
60	# removed,
61	# wildcard (*) allowed in .palm.iofiles as file activation string for output
62	# files,
63	# informative messages in case of missing optional input files shortened
64	# bugfix: variable cycle explicitly interpreted with 10 as the number base
65	#
66	# 2638 2017-11-23 12:44:23Z raasch
67	# use of wildcards in file connection statements enabled
68	#
69	# 2605 2017-11-09 15:31:46Z raasch
70	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
71	# will not be sent with the job file any more, but copied into the
72	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
73	#
74	# 2600 2017-11-01 14:11:20Z raasch
75	# cycle numbers are made three digits wide
76	#
77	# 2566 2017-10-20 08:50:47Z raasch
78	# execute command for combine_plot_fields added
79	# "TEMPDIR" renamed "tempdir"
80	# temporary working directory for local batch jobs is created immediately within
81	# the user's palmrun call, due to a requirement of the "grid engine" batch
82	# system, where the working directory is given with batch directive -wd and must
83	# already exist when the job is submitted,
84	# informative messages in non-trace mode reduced and partly reformatted
85	#
86	# 2551 2017-10-18 07:25:11Z raasch
87	# TEMPDIR added as replacement string to be used in batch directives
88	#
89	# 2512 2017-10-04 08:26:59Z raasch
90	# bugfix for determining cycle numbers of NetCDF input files
91	#
92	# 2506 2017-09-29 08:30:37Z raasch
93	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
94	# host configuration added to SOURCES_FOR_RUN_... folder name
95	# host_identifier renamed host_configuration
96	# option -W added to allow for job dependencies
97	#
98	# 2501 2017-09-26 11:41:55Z raasch
99	# default value for number of cores (option -X) set to 1
100	# bugfix for mechanism which overwrites configuration file settings with values
101	# provided by palmrun options
102	#
103	# 2499 2017-09-22 16:47:58Z kanani
104	# option -h named configuration identifier
105	#
106	# 2480 2017-09-19 06:24:14Z maronga
107	# bugfix for last revision
108	#
109	# 2479 2017-09-19 06:12:16Z raasch
110	# option -A (project account number) added
111	#
112	# 2422 2017-09-08 08:25:41Z raasch
113	# initial revision
114	#
115	#--------------------------------------------------------------------------------#
116	# palmrun - script for running PALM jobs on local and remote hosts
117	#--------------------------------------------------------------------------------#
118
119
120
121	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
122
123	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
124	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
125	# (TOO MANY ARGUMENTS - PROBLEM)
126	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
127
128	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
129	typeset -i nr_of_output_files=0
130	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
131	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
132	# SCRIPT-OPTION ARGUMENTS
133	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
134	typeset -i icycle inode ival maxcycle mpi_tasks
135	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
136
137	activation_string_list=""
138	AddFilenames=""
139	combine_plot_fields=true
140	compiler_name=""
141	compiler_name_ser=""
142	compiler_options=""
143	cores=1
144	cores_atmos=0
145	cores_ocean=0
146	coupled_dist=""
147	cpp_options=""
148	cpumax=0
149	create_batch_job=false
150	create_jobfile_only=false
151	create_remote_batch_job=false
152	dashes=" ----------------------------------------------------------------------------"
153	defaultqueue=""
154	delete_temporary_catalog=true
155	do_compile=true
156	do_trace=false
157	executable=""
158	execute_command=""
159	execution_error=false
160	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
161	jobname=test
162	global_revision=""
163	host_configuration="default"
164	hostfile=""
165	hp=""
166	keep_data_from_previous_run=false
167	link_local_input=false
168	link_local_output=false
169	linker_options=""
170	local_jobcatalog=""
171	locat=normal
172	makefile=""
173	max_par_io_str=""
174	prc=$0
175	while [[ $(echo $prc \| grep -c "/") != 0 ]]
176	do
177	prc=`echo $prc \| cut -f2- -d"/"`
178	done
179	module_calls=""
180	palmrun_memory=""
181	palmrun_script_name=$prc
182	openmp=false
183	previous_job=""
184	project_account=""
185	queue=none
186	read_svf=""
187	restart_run=false
188	return_address=""
189	remote_jobcatalog=""
190	remote_username=""
191	running_in_batch_mode=false
192	run_coupled_model=false
193	run_id=""
194	silent=false
195	source_list=""
196	source_path=""
197	tasks_per_node=0
198	threads_per_task=1
199	transfer_problems=false
200	user_source_path=""
201	use_existing_sources_folder=""
202	use_openmp=false
203	version="palmrun 1.0 Rev$Rev: 2906 $"
204	working_directory=`pwd`
205	write_binary=""
206	write_svf=""
207	TOPT=""
208
209
210	# ERROR HANDLING IN CASE OF EXIT
211	trap 'if [[ $locat != normal && $locat != control_c ]]
212	then
213
214	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
215	(( i = 0 ))
216	while (( i < iec ))
217	do
218	(( i = i + 1 ))
219	printf "\n *** Execution of ERROR-command:\n"
220	printf " >>> ${err_command[$i]}\n"
221	eval ${err_command[$i]}
222	done
223	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
224	printf "\n\n+++ palmrun killed \n\n"
225	elif [[ $locat != control_c ]]
226	then
227	printf "\n --> palmrun finished\n\n"
228	fi' exit
229
230
231	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
232	trap 'cd; rm -rf $tempdir
233	printf "\n+++ palmrun killed by \"^C\" \n\n"
234	locat=control_c
235	exit
236	' 2
237
238
239	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
240	# WHICH WILL BE USED TO START RESTART-JOBS
241	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
242	do
243	case $option in
244	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
245	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
246	(b) create_batch_job=true; prc="$prc -b";;
247	(B) delete_temporary_catalog=false; prc="$prc -B";;
248	(C) restart_run=true; prc="$prc -C";;
249	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
250	(F) create_jobfile_only=true;;
251	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
252	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
253	(j) running_in_batch_mode=true;;
254	(k) keep_data_from_previous_run=true; prc="$prc -k";;
255	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
256	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
257	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
258	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
259	(r) run_id=$OPTARG;;
260	(R) return_address=$OPTARG;;
261	(s) source_list=$OPTARG;;
262	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
263	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
264	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
265	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
266	(v) silent=true; prc="$prc -v";;
267	(V) use_existing_sources_folder="-V";;
268	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
269	(W) previous_job=$OPTARG;;
270	(x) do_trace=true;set -x; prc="$prc -x";;
271	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
272	(y) ocean_file_appendix=true; prc="$prc -y";;
273	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
274	(Z) combine_plot_fields=false; prc="$prc -Z";;
275	(\?) printf "\n +++ unknown option $OPTARG \n"
276	printf "\n --> type \"$0 ?\" for available options \n"
277	locat=parameter;exit;;
278	esac
279	done
280
281
282	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
283	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
284	(( to_shift = $OPTIND - 1 ))
285	shift $to_shift
286
287	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
288	if [[ "$1" = "?" ]]
289	then
290	(printf "\n *** Description of available palmrun options:\n"
291	printf "\n Option Description Default-Value"
292	printf "\n -a activation string list \"\" "
293	printf "\n -A project account number ---"
294	printf "\n -b batch-job on local machine ---"
295	printf "\n -B do not delete temporary directory at end ---"
296	printf "\n -d base name of files attached to program test"
297	printf "\n -F create batch job file only ---"
298	printf "\n -h host configuration \"default\" "
299	printf "\n -k keep data from previous run"
300	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
301	printf "\n -M Makefile name Makefile"
302	printf "\n -O threads per openMP task ---"
303	printf "\n -q queue \"$queue\" "
304	printf "\n -s filenames of routines to be compiled \"\" "
305	printf "\n must end with .f, .f90, .F, or .c !"
306	printf "\n use \"..\" for more than one file and wildcards"
307	printf "\n -s LM compiles all locally modified files"
308	printf "\n -t allowed cpu-time in seconds (batch) 0"
309	printf "\n -T tasks per node ---"
310	printf "\n -u username on remote machine \"\" "
311	printf "\n -v no prompt for confirmation ---"
312	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
313	printf "\n -w maximum parallel io streams as given by -X"
314	printf "\n -W name of job to wait for ---"
315	printf "\n -x tracing of palmrun for debug purposes ---"
316	printf "\n -X # of processors (on parallel machines) 1"
317	printf "\n -y add appendix \"_O\" to all local output"
318	printf "\n files (ocean precursor runs followed by"
319	printf "\n coupled atmosphere-ocean runs) ---"
320	printf "\n -Y run coupled model, \"#1 #2\" with"
321	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
322	printf "\n -Z skip combine_plot_fields at the end of "
323	printf "\n the simulation ---"
324	printf "\n "
325	printf "\n Possible values of positional parameter <modus>:"
326	printf "\n \"?\" - this outline \n\n") \| more
327	exit
328	elif [[ "$1" != "" ]]
329	then
330	printf "\n +++ positional parameter $1 unknown \n"
331	locat=parameter; exit
332	fi
333
334
335
336	# SHORT STARTING MESSAGE
337	printf "\n*** $version "
338	printf "\n will be executed. Please wait ..."
339
340
341	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
342	export fname=$jobname
343
344
345	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
346	config_file=.palm.config.$host_configuration
347	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
348
349
350	# CHECK, IF CONFIGURATION FILE EXISTS
351	if [[ ! -f $config_file ]]
352	then
353	printf "\n\n +++ configuration file: "
354	printf "\n $config_file"
355	printf "\n does not exist"
356	locat=connect; exit
357	fi
358
359
360	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
361	if [[ -f .palm.iofiles ]]
362	then
363	fileconnection_file=.palm.iofiles
364	fi
365
366
367	# CHECK, IF FILE CONNECTION FILE EXISTS
368	if [[ ! -f $fileconnection_file ]]
369	then
370	printf "\n\n +++ file connection file: "
371	printf "\n $fileconnection_file"
372	printf "\n does not exist"
373	locat=connect; exit
374	fi
375
376
377	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
378	if [[ "$activation_string_list" = "" ]]
379	then
380	printf "\n\n +++ no activation string list given: "
381	printf "\n please set palmrun option \"-a\" "
382	locat=palmrun_option; exit
383	fi
384
385
386	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
387	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
388	then
389	write_binary=true
390	else
391	write_binary=false
392	fi
393
394	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
395	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
396	then
397	write_svf=true
398	else
399	write_svf=false
400	fi
401
402	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
403	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
404	then
405	read_svf=true
406	else
407	read_svf=false
408	fi
409
410
411	# READ AND EVALUATE THE CONFIGURATION-FILE
412	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
413
414	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
415	while read line
416	do
417
418	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
419	eval line=\"$line\"
420
421
422	# INTERPRET THE LINE
423	if [[ "$(echo $line)" = "" ]]
424	then
425
426	# EMPTY LINE, NO ACTION
427	continue
428
429	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
430	then
431
432	# LINE IS A COMMENT LINE
433	continue
434
435	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
436	then
437
438	# LINE DEFINES AN ENVIRONMENT-VARIABLE
439	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
440	value=`echo $line \| cut -d" " -s -f2-`
441
442
443	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
444	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
445	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
446	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
447	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
448	# CONFIGURATION-FILE.
449	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
450	then
451	eval export $var="\$value"
452
453	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
454	if [[ $do_trace = true ]]
455	then
456	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
457	fi
458	fi
459
460	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
461	then
462
463	# LINE DEFINES BATCH-DIRECTIVE
464	(( ibd = ibd + 1 ))
465	line=$(echo $line \| cut -c4-)
466	batch_directive[$ibd]="$line"
467
468	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
469	then
470
471	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
472	# REMOTE TO A LOCAL HOST
473	(( ibdt = ibdt + 1 ))
474	line=$(echo $line \| cut -c5-)
475	batch_directive_transfer[$ibdt]="$line"
476
477	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
478	then
479
480	# LINE DEFINES ERROR-COMMAND
481	(( iec = iec + 1 ))
482	line=$(echo $line \| cut -c4-)
483	err_command[$iec]="$line"
484
485	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
486	then
487
488	# LINE DEFINES INPUT-COMMAND
489	(( iic = iic + 1 ))
490	line=$(echo $line \| cut -c4-)
491	in_command[$iic]="$line"
492
493	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
494	then
495
496	# LINE DEFINES OUTPUT-COMMAND
497	(( ioc = ioc + 1 ))
498	line=$(echo $line \| cut -c4-)
499	out_command[$ioc]="$line"
500
501	else
502
503	# SKIP ALL OTHER LINES
504	continue
505
506	fi
507
508	done < $config_file
509
510
511	# CHECK SETTING OF REQUIRED PARAMETERS
512	if [[ "$compiler_name" = "" ]]
513	then
514	printf "\n +++ no compiler name found in $config_file"
515	printf "\n Please add line \"compiler_name ...\" to that file."
516	locat=config_file; exit
517	fi
518	if [[ "$compiler_name_ser" = "" ]]
519	then
520	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
521	printf "\n Please add line \"compiler_name_ser ...\" to that file."
522	locat=config_file; exit
523	fi
524	if [[ "$compiler_options" = "" ]]
525	then
526	printf "\n +++ no compiler options found in $config_file"
527	printf "\n Please add line \"compiler_options ...\" to that file."
528	locat=config_file; exit
529	fi
530	if [[ "$linker_options" = "" ]]
531	then
532	printf "\n +++ no linker options found in $config_file"
533	printf "\n Please add line \"linker_options ...\" to that file."
534	locat=config_file; exit
535	fi
536	if [[ "$execute_command" = "" ]]
537	then
538	printf "\n +++ no execute command found in $config_file"
539	printf "\n Please add line \"execute_command ...\" to that file."
540	locat=config_file; exit
541	fi
542
543	if [[ "$hostfile" != "" ]]
544	then
545	if [[ $hostfile != auto && ! -f $hostfile ]]
546	then
547	printf "\n +++ no hostfile \"$hostfile\" found"
548	printf "\n Please check line \"hostfile ...\" in $config_file"
549	locat=config_file; exit
550	fi
551	fi
552
553
554	# DETERMINE THE CALL STATUS
555	if [[ "$return_address" != "" ]]
556	then
557
558	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
559	# BATCH MODE AND ...
560	running_on_remote=true
561
562	else
563
564	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
565	if [[ "$remote_ip" != "" ]]
566	then
567
568	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
569	create_remote_batch_job=true
570
571	fi
572	running_on_remote=false
573	fi
574
575
576
577	# READ AND EVALUATE THE I/O-FILE LIST
578	[[ $silent = false ]] && printf "\n Reading the I/O files... "
579
580	# READ THE FILE CONNECTION FILE LINE BY LINE
581	while read line
582	do
583
584	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
585	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
586
587	# INTERPRET THE LINE
588	if [[ "$(echo $line)" = "" ]]
589	then
590	# EMPTY LINE, NO ACTION
591	continue
592
593	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
594	then
595
596	# LINE IS A COMMENT LINE
597	true
598
599	else
600
601	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
602	# s2a: in/out - field
603	# s2b: action - field (optional)
604	s1=`echo "$line" \| cut -d" " -f1`
605	s2=`echo "$line" \| cut -d" " -s -f2`
606	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
607	then
608	s2a=$s2
609	s2b=""
610	else
611	s2a=`echo $s2 \| cut -d":" -f1`
612	s2b=`echo $s2 \| cut -d":" -f2`
613	fi
614	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
615	s4=`echo "$line" \| cut -d" " -s -f4`
616	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
617	s5=`echo "$line" \| cut -d" " -s -f5`
618	s6=`echo "$line" \| cut -d" " -s -f6`
619
620
621	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
622	# INPUT- OR OUTPUT-LIST.
623	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
624	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
625	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
626	# IS NOT CHECKED AND STORED.
627	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
628	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
629	then
630	found=false
631	for actual in $activation_string_list
632	do
633	for formal in $s3
634	do
635	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
636	done
637	done
638	if [[ $found = true ]]
639	then
640	(( iin = iin + 1 ))
641	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
642	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
643	if [[ "$s2a" = inopt ]]
644	then
645	optin_pre[$iin]=yes
646	else
647	optin_pre[$iin]=no
648	fi
649
650	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
651	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
652	if [[ $running_on_remote = true && "$s2b" = tr ]]
653	then
654	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
655	fi
656
657	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
658	# THE WILDCARD FROM THE ENDING
659	if [[ "${s5: -1}" = "*" ]]
660	then
661	if [[ "$s2b" = "di" ]]
662	then
663	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
664	printf "\n see file \"$fileconnection_file\", line"
665	printf "\n$line"
666	locat=iofiles_file; exit
667	fi
668	multin[$iin]=true
669	string=${endin_pre[$iin]}
670	endin_pre[$iin]="${string%?}"
671	else
672	multin[$iin]=false
673	fi
674	fi
675	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
676	then
677	found=false
678	for actual in $activation_string_list
679	do
680	for formal in $s3
681	do
682	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
683	done
684	done
685	if [[ $found = true ]]
686	then
687	(( iout = iout + 1 ))
688	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
689	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
690
691	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
692	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
693	if [[ $formal = wildcard ]]
694	then
695	warnout_pre[$iout]=false
696	else
697	warnout_pre[$iout]=true
698	fi
699
700	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
701	# THE WILDCARD FROM THE LOCAL FILENAME
702	if [[ "${s1: -1}" = "*" ]]
703	then
704	if [[ "$s2b" = "di" ]]
705	then
706	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
707	printf "\n see file \"$fileconnection_file\", line"
708	printf "\n$line"
709	locat=iofiles_file; exit
710	fi
711	multout[$iout]=true
712	string=${localout_pre[$iout]}
713	localout_pre[$iout]="${string%?}"
714	else
715	multout[$iout]=false
716	fi
717	fi
718	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
719	then
720	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
721	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
722	locat=connect; exit
723	fi
724	IFS="$IFSALT"
725	fi
726
727	done < $fileconnection_file
728
729
730
731	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
732	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
733	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
734	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
735	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
736	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
737
738
739
740	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
741	if [[ $run_coupled_model = true ]]
742	then
743
744	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
745	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
746
747	if (( $cores_ocean + $cores_atmos != $cores ))
748	then
749
750	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
751	printf "\n PEs (total) : $cores"
752	printf "\n PEs (atmosphere): $cores_atmos"
753	printf "\n PEs (ocean) : $cores_ocean"
754	locat=coupling; exit
755
756	fi
757
758	fi
759
760
761	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
762	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
763	# FOLDER
764	if [[ $running_in_batch_mode = true ]]
765	then
766
767	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
768	then
769	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
770	printf "\n Please check the output of the palmrun-call"
771	printf "\n that you did on your local host."
772	locat=SOURCES_FOR_RUN; exit
773	fi
774
775	else
776
777	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
778	# AUTOMATIC RESTART RUN
779	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
780	if [[ $restart_run = false ]]
781	then
782
783	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
784	# THE LOCAL HOST
785	if [[ ! -d $source_path ]]
786	then
787	printf "\n\n +++ source path \"$source_path\" on local host"
788	printf "\n \"$(hostname)\" does not exist"
789	locat=source_path; exit
790	fi
791
792	rm -rf $sources_for_run_catalog
793	mkdir -p $sources_for_run_catalog
794
795	if [[ "$source_list" = LM ]]
796	then
797
798	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
799	source_list=""
800	cd $source_path
801
802
803	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
804	if [[ ! -d ../.svn ]]
805	then
806	printf "\n\n +++ source directory"
807	printf "\n \"$source_path\" "
808	printf "\n is not under control of \"subversion\"."
809	printf "\n Please do not use palmrun-option \"-s LM\"\n"
810	fi
811
812
813	# LIST ALL MODIFIED SOURCE CODE FILES
814	Filenames=""
815	svn status > tmp_svnstatus
816	while read line
817	do
818	firstc=`echo $line \| cut -c1`
819	if [[ $firstc = M \|\| $firstc = "?" ]]
820	then
821	Name=`echo "$line" \| cut -c8-`
822	extension=`echo $Name \| cut -d. -f2`
823	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
824	then
825	Filenames="$Filenames "$Name
826	fi
827	fi
828	done < tmp_svnstatus
829	rm -rf tmp_svnstatus
830
831
832	# COPY FILES TO SOURCES_FOR_RUN_...
833	for filename in $Filenames
834	do
835	cp $filename ${working_directory}/${sources_for_run_catalog}
836	source_list=$source_list"$filename "
837	done
838
839	cd - > /dev/null
840
841
842	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
843	elif [[ "$source_list" != "" ]]
844	then
845
846	cd $source_path
847
848	for filename in $source_list
849	do
850
851	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
852	if [[ $(echo $filename \| grep -c "/") != 0 ]]
853	then
854	printf "\n +++ source code file: $filename"
855	printf "\n must not contain (\"/\") "
856	locat=source; exit
857	fi
858
859	if [[ ! -f $filename ]]
860	then
861	printf "\n +++ source code file: $filename"
862	printf "\n does not exist"
863	locat=source; exit
864	else
865	cp $filename ${working_directory}/${sources_for_run_catalog}
866	fi
867
868	done
869
870	cd - > /dev/null
871
872	fi
873
874	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
875	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
876	if [[ ! -f $makefile ]]
877	then
878	printf "\n +++ file \"$makefile\" does not exist"
879	locat=make; exit
880	else
881	cp $makefile ${sources_for_run_catalog}/Makefile
882	fi
883
884
885	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
886	if [[ "$user_source_path" != "" ]]
887	then
888
889	# DOES THE DIRECTORY EXIST?
890	if [[ ! -d $user_source_path ]]
891	then
892
893	printf "\n\n *** INFORMATIVE: additional source code directory"
894	printf "\n \"$user_source_path\" "
895	printf "\n does not exist or is not a directory."
896	printf "\n No source code will be used from this directory!\n"
897	user_source_path=""
898	if [[ $silent == false ]]
899	then
900	sleep 2
901	fi
902
903	else
904
905	cd $user_source_path
906	found=false
907
908	Names=$(ls -1 *.f90 2>&1)
909	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
910	Names=$(ls -1 *.F90 2>&1)
911	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
912	Names=$(ls -1 *.F 2>&1)
913	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
914	Names=$(ls -1 *.f 2>&1)
915	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
916	Names=$(ls -1 *.c 2>&1)
917	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
918
919	cd - > /dev/null
920	cd $sources_for_run_catalog
921
922	# COPY MAKEFILE IF EXISTING
923	if [[ -f $user_source_path/Makefile ]]
924	then
925	printf "\n\n *** user Makefile from directory"
926	printf "\n \"$user_source_path\" is used \n"
927	if [[ $silent == false ]]
928	then
929	sleep 1
930	fi
931	cp $user_source_path/Makefile .
932	fi
933
934	for filename in $AddFilenames
935	do
936	if [[ -f $filename ]]
937	then
938	printf "\n +++ source code file \"$filename\" found in additional"
939	printf "\n source code directory \"$user_source_path\" "
940	printf "\n but was also given with option \"-s\" which means that it should be taken"
941	printf "\n from directory \"$source_path\"."
942	locat=source; exit
943	fi
944
945	cp $user_source_path/$filename .
946	source_list="$source_list $filename"
947
948	# CHECK IF FILE IS CONTAINED IN MAKEFILE
949	if [[ $(grep -c $filename Makefile) = 0 ]]
950	then
951	printf "\n\n +++ user file \"$filename\" "
952	printf "\n is not listed in Makefile \n"
953	locat=source; exit
954	else
955
956	if [[ $found = false ]]
957	then
958	found=true
959	printf "\n\n *** following user file(s) added to the"
960	printf " files to be translated:\n "
961	fi
962	printf "$filename "
963	if [[ $silent == false ]]
964	then
965	sleep 0.5
966	fi
967
968	fi
969	done
970	[[ $found = true ]] && printf "\n"
971	cd - > /dev/null
972	fi
973	fi
974
975	# COPY CONFIGURATION FILES
976	cp $config_file $sources_for_run_catalog
977	cp $fileconnection_file $sources_for_run_catalog
978
979	# COPY SHELLSCRIPTS
980	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
981	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
982
983	fi
984
985	fi
986
987
988	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
989	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
990	if [[ "$global_revision" = "" ]]
991	then
992	global_revision=`svnversion $source_path 2>/dev/null`
993	global_revision="Rev: $global_revision"
994	fi
995
996
997	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
998	if [[ -n $cores ]]
999	then
1000
1001	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1002	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1003	if [[ $tasks_per_node = 0 ]]
1004	then
1005	printf "\n"
1006	printf "\n +++ option \"-T\" (tasks per node) is missing"
1007	printf "\n set -T option or define tasks_per_node in the config file"
1008	locat=tasks_per_node; (( iec = 0 )); exit
1009	fi
1010
1011	if (( cores < tasks_per_node ))
1012	then
1013	printf "\n"
1014	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1015	printf "\n given values: -T $tasks_per_node -X $cores"
1016	locat=tasks_per_node; (( iec = 0 )); exit
1017	fi
1018
1019	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1020	(( mpi_tasks = cores / threads_per_task ))
1021	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1022	(( ii = cores / tasks_per_node ))
1023	(( remaining_cores = cores - ii * tasks_per_node ))
1024	if (( remaining_cores > 0 ))
1025	then
1026	printf "\n"
1027	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1028	printf "\n divisor of the total number of cores (option \"-X\")"
1029	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1030	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1031	(( nodes = nodes + 1 ))
1032	fi
1033
1034	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1035	if [[ "$tasks_per_node" != "" ]]
1036	then
1037	TOPT="-T $tasks_per_node"
1038	fi
1039
1040	fi
1041
1042
1043	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1044	if [[ "$maximum_parallel_io_streams" = "" ]]
1045	then
1046	maximum_parallel_io_streams=$cores
1047	fi
1048
1049
1050	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1051	if [[ "$scp_port" != "" ]]
1052	then
1053	PORTOPT="-P $scp_port"
1054	SSH_PORTOPT="-p $scp_port"
1055	fi
1056
1057
1058	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1059	# CONFIG-FILE
1060	if [[ "$ssh_key" != "" ]]
1061	then
1062	ssh_key="-i $HOME/.ssh/$ssh_key"
1063	fi
1064
1065
1066	# SET QUEUE, IF NOT GIVEN
1067	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1068	then
1069
1070	if [[ $queue = none && "$defaultqueue" = "" ]]
1071	then
1072	printf "\n"
1073	printf "\n +++ no default queue given in configuration file and no queue"
1074	printf "\n given with option -q"
1075	locat=queue; exit
1076	fi
1077	if [[ $queue = none ]]
1078	then
1079	queue=$defaultqueue
1080	fi
1081
1082	fi
1083
1084
1085	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1086	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1087	(( i = 0 ))
1088	(( nr_of_input_files = 0 ))
1089	while (( i < iin ))
1090	do
1091	(( i = i + 1 ))
1092
1093	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1094	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1095	if [[ "${actionin_pre[$i]}" = di ]]
1096	then
1097	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1098	else
1099	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1100	fi
1101
1102
1103	# CHECK IF FILE EXISTS
1104	if ! ls $filename* 1>/dev/null 2>&1
1105	then
1106
1107	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1108	if [[ "${optin_pre[$i]}" != "yes" ]]
1109	then
1110	printf "\n\n +++ INPUT-file: "
1111	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1112	then
1113	printf "\n $filename"
1114	else
1115	printf "\n $filename.${extin_pre[$i]}"
1116	fi
1117	printf "\n does not exist\n"
1118	locat=input; exit
1119	else
1120	(( nr_of_input_files = nr_of_input_files + 1 ))
1121	localin[$nr_of_input_files]="${localin_pre[$i]}"
1122	optin[$nr_of_input_files]="${optin_pre[$i]}"
1123	actionin[$nr_of_input_files]="unavailable"
1124	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1125	endin[$nr_of_input_files]="${endin_pre[$i]}"
1126	extin[$nr_of_input_files]="${extin_pre[$i]}"
1127	fi
1128
1129	else
1130
1131	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1132	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1133	if [[ "${multin[$i]}" = true ]]
1134	then
1135	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1136	ls -1 -d ${filename} > filelist 2>/dev/null
1137	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1138	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1139
1140	endings=""
1141	while read line
1142	do
1143	# filename without path (i.e. after the last "/")
1144	basefilename=$(basename ${line})
1145
1146	# check if there is an extension and remove it
1147	ext=${basefilename##*.}
1148	if [[ "$ext" = "${extin_pre[$i]}" ]]
1149	then
1150	basefilename=${basefilename%.*}
1151	fi
1152
1153	# check for an existing cycle number and remove it
1154	cycle=${basefilename##*.}
1155	if [[ $cycle =~ ^-?[0-9]+$ ]]
1156	then
1157	basefilename=${basefilename%.*}
1158	fi
1159
1160	# remove the jobname from the beginning
1161	length_jobname=${#jobname}
1162	ending=${basefilename:${length_jobname}}
1163
1164	# remove the ending given in the .iofiles from the beginning
1165	endingstring="${endin_pre[$i]}"
1166	length_ending=${#endingstring}
1167	ending=${ending:${length_ending}}
1168
1169	if [[ "$ending" = "" ]]
1170	then
1171	# standard ending as given in the .iofiles
1172	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1173	then
1174	endings="$endings DEFAULT"
1175	fi
1176	else
1177	# ending must start with "_", otherwise its a different file
1178	if [[ "${ending:0:1}" = "_" ]]
1179	then
1180	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1181	then
1182	endings="$endings $ending"
1183	fi
1184	fi
1185	fi
1186
1187	done <filelist
1188
1189	rm filelist
1190
1191	else
1192
1193	# SINGLE NAME
1194	endings=DEFAULT
1195
1196	fi
1197
1198	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1199	for ending in $endings
1200	do
1201
1202	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1203	if [[ $ending = DEFAULT ]]
1204	then
1205	ending=""
1206	fi
1207
1208	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1209	(( nr_of_input_files = nr_of_input_files + 1 ))
1210	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1211	optin[$nr_of_input_files]="${optin_pre[$i]}"
1212	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1213	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1214	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1215	extin[$nr_of_input_files]="${extin_pre[$i]}"
1216
1217
1218	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1219	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1220	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1221	then
1222	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1223	else
1224	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1225	fi
1226
1227	# DETERMINE THE FILE'S CYCLE NUMBER
1228	(( maxcycle = 0 ))
1229	ls -1 -d $filename > filelist 2>/dev/null
1230	ls -1 -d $filename.* >> filelist 2>/dev/null
1231	while read line
1232	do
1233	# filename without path (i.e. after the last "/")
1234	basefilename=$(basename ${line})
1235
1236	# check if there is an extension
1237	extension=${basefilename##*.}
1238	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1239	then
1240	basefilename=${basefilename%.*}
1241	fi
1242
1243	# check for an existing cycle number
1244	cycle=${basefilename##*.}
1245	if [[ $cycle =~ ^-?[0-9]+$ ]]
1246	then
1247	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1248	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1249	(( icycle = $((10#$cycle)) ))
1250	else
1251	(( icycle = 0 ))
1252	fi
1253
1254	if (( icycle > maxcycle ))
1255	then
1256	(( maxcycle = icycle ))
1257
1258	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1259	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1260	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1261	then
1262	leading_zero=true
1263	else
1264	leading_zero=false
1265	fi
1266	fi
1267
1268	done <filelist
1269	rm filelist
1270
1271	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1272	if [[ $leading_zero = true ]]
1273	then
1274	cyclestring=`printf "%03d" $maxcycle`
1275	else
1276	cyclestring=$maxcycle
1277	fi
1278
1279	# APPEND CYCLE NUMBER TO FILENAME
1280	if (( maxcycle > 0 ))
1281	then
1282	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1283	then
1284	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1285	else
1286	filename=${filename}.$cyclestring
1287	fi
1288	else
1289	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1290	then
1291	filename=${filename}.${extin[$nr_of_input_files]}
1292	fi
1293	fi
1294
1295	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1296	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1297	absnamein[$nr_of_input_files]=$filename
1298	if (( maxcycle > 0 ))
1299	then
1300	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1301	then
1302	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1303	else
1304	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1305	fi
1306	else
1307	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1308	then
1309	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1310	else
1311	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1312	fi
1313	fi
1314
1315	done
1316
1317	fi
1318
1319	done
1320
1321
1322	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1323	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1324	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1325	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1326	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1327	# REMOTE HOST)
1328	(( i = 0 ))
1329	while (( i < iout ))
1330	do
1331	(( i = i + 1 ))
1332	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1333	then
1334	if [[ "${actionout_pre[$i]}" = tr ]]
1335	then
1336	actionout_pre[$i]=""
1337	elif [[ "${actionout_pre[$i]}" = trpe ]]
1338	then
1339	actionout_pre[$i]=pe
1340	elif [[ "${actionout_pre[$i]}" = tra ]]
1341	then
1342	actionout_pre[$i]=a
1343	fi
1344	(( maxcycle = 0 ))
1345	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1346	eval catalogname=${pathout_pre[$i]}
1347	if ! ls $filename* 1>/dev/null 2>&1
1348	then
1349
1350	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1351	if cat /dev/null > $filename
1352	then
1353	rm $filename
1354	else
1355
1356	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1357	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1358	if [[ ! -d $catalogname ]]
1359	then
1360	if mkdir -p $catalogname
1361	then
1362	printf "\n\n *** directory:"
1363	printf "\n $catalogname"
1364	printf "\n was created\n"
1365	else
1366	printf "\n\n +++ OUTPUT-file:"
1367	printf "\n $filename"
1368	printf "\n cannot be created, because directory does not exist"
1369	printf "\n and cannot be created either"
1370	printf "\n"
1371	locat=output ; exit
1372	fi 2>/dev/null
1373	else
1374	printf "\n\n +++ OUTPUT-file:"
1375	printf "\n $filename"
1376	printf "\n cannot be created, although directory exists"
1377	printf "\n"
1378	locat=output ; exit
1379	fi
1380	fi 2>/dev/null
1381
1382	fi
1383
1384	fi
1385	done
1386
1387
1388	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1389	if [[ $running_in_batch_mode = false ]]
1390	then
1391	run_id=$RANDOM
1392	job_id=${jobname}.$run_id
1393
1394	tempdir=$fast_io_catalog/$job_id
1395	fi
1396
1397
1398	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1399	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1400	then
1401
1402	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1403	if [[ $ibd = 0 ]]
1404	then
1405	printf "\n"
1406	printf "\n +++ no batch directives found in configuration file"
1407	locat=config_file_batch_directives; (( iec = 0 )); exit
1408	fi
1409
1410	# CHECK IF CPUTIME IS GIVEN FOR JOB
1411	done=false
1412	cputime=$cpumax
1413	while [[ $done = false ]]
1414	do
1415	if (( cputime == 0 ))
1416	then
1417	printf "\n +++ cpu-time is undefined"
1418	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1419	printf "\n >>> "
1420	read cputime 1>/dev/null 2>&1
1421	else
1422	done=true
1423	fi
1424	done
1425	cpumax=$cputime
1426
1427	# CHECK THE MEMORY DEMAND
1428	done=false
1429	while [[ $done = false ]]
1430	do
1431	if (( memory == 0 ))
1432	then
1433	printf "\n +++ memory demand is undefined"
1434	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1435	printf "\n >>> "
1436	read memory 1>/dev/null 2>&1
1437	else
1438	done=true
1439	fi
1440	done
1441
1442	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1443	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1444	then
1445	while [[ -z $remote_username ]]
1446	do
1447	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1448	printf "\n >>> Please type username:"
1449	printf "\n >>> "
1450	read remote_username
1451	done
1452	fi
1453
1454	else
1455
1456	if [[ $running_in_batch_mode = false ]]
1457	then
1458	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1459	cpumax=$cputime
1460	else
1461	cputime=$cpumax
1462	fi
1463
1464	fi
1465
1466
1467	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1468	(( cpu_hours = cputime / 3600 ))
1469	(( resttime = cputime - cpu_hours * 3600 ))
1470	(( cpu_minutes = resttime / 60 ))
1471	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1472	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1473
1474
1475	# OUTPUT OF THE PALMRUN-HEADER
1476	calltime=$(date)
1477	printf "\n"
1478	printf "#------------------------------------------------------------------------# \n"
1479	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1480	printf "\| \| \n"
1481	column1="called on:"; column2=$(hostname)
1482	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1483	if [[ $create_remote_batch_job = true ]]
1484	then
1485	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1486	else
1487	if [[ $running_on_remote = true ]]
1488	then
1489	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1490	else
1491	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1492	fi
1493	fi
1494	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1495
1496	column1="running in:"
1497	if [[ $running_in_batch_mode = true ]]
1498	then
1499	column2="batch job mode"
1500	else
1501	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1502	then
1503	column2="job creation mode"
1504	else
1505	column2="interactive run mode"
1506	fi
1507	fi
1508	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1509
1510	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1511	then
1512	if [[ "$project_account" != "" ]]
1513	then
1514	column1="project account number:"
1515	column2="$project_account"
1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1517	fi
1518	fi
1519
1520	if [[ -n $cores ]]
1521	then
1522	if [[ $run_coupled_model = false ]]
1523	then
1524	column1="number of cores:"; column2=$cores
1525	else
1526	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1527	fi
1528	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1529	fi
1530	if [[ -n $tasks_per_node ]]
1531	then
1532	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1534	if (( remaining_cores > 0 ))
1535	then
1536	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1537	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1538	fi
1539	fi
1540	if [[ $maximum_parallel_io_streams != $cores ]]
1541	then
1542	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1543	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1544	fi
1545	if [[ $use_openmp = true ]]
1546	then
1547	column1="threads per task:"; column2="$threads_per_task"
1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1549	fi
1550	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1551	then
1552	column1="memory demand / PE":; column2="$memory MB"
1553	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1554	column1="job cpu time (h:m:s):"; column2="$timestring"
1555	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1556	fi
1557	printf "\| \| \n"
1558	if [[ "$source_list" != "" ]]
1559	then
1560	if [[ "$make_options" != "" ]]
1561	then
1562	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1564	line=$(echo "$make_options" \| cut -c46-)
1565	while [[ "$line" != "" ]]
1566	do
1567	column1=""
1568	column2=$(echo "$line" \| cut -c-45)
1569	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1570	line=$(echo "$line" \| cut -c46-)
1571	done
1572	fi
1573	fi
1574
1575	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1577	line=$(echo "$cpp_options" \| cut -c46-)
1578	while [[ "$line" != "" ]]
1579	do
1580	column1=""
1581	column2=$(echo "$line" \| cut -c-45)
1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1583	line=$(echo "$line" \| cut -c46-)
1584	done
1585
1586	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1588	line=$(echo "$compiler_options" \| cut -c46-)
1589	while [[ "$line" != "" ]]
1590	do
1591	column1=""
1592	column2=$(echo "$line" \| cut -c-45)
1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1594	line=$(echo "$line" \| cut -c46-)
1595	done
1596
1597	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1598	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1599	line=$(echo "$linker_options" \| cut -c46-)
1600	while [[ "$line" != "" ]]
1601	do
1602	column1=""
1603	column2=$(echo "$line" \| cut -c-45)
1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1605	line=$(echo "$line" \| cut -c46-)
1606	done
1607
1608	if [[ "$login_init_cmd" != "" ]]
1609	then
1610	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1612	line=$(echo "$login_init_cmd" \| cut -c46-)
1613	while [[ "$line" != "" ]]
1614	do
1615	column1=""
1616	column2=$(echo "$line" \| cut -c-45)
1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1618	line=$(echo "$line" \| cut -c46-)
1619	done
1620	fi
1621
1622	if [[ "$module_commands" != "" ]]
1623	then
1624	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1626	line=$(echo "$module_commands" \| cut -c46-)
1627	while [[ "$line" != "" ]]
1628	do
1629	column1=""
1630	column2=$(echo "$line" \| cut -c-45)
1631	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1632	line=$(echo "$line" \| cut -c46-)
1633	done
1634	fi
1635	printf "\| \| \n"
1636	column1="base name of files:"; column2=$jobname
1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1638	column1="activation string list:"; column2=$(echo $activation_string_list)
1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1640
1641	if [[ "$ocean_file_appendix" = true ]]
1642	then
1643	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1644	fi
1645
1646	if [[ "$source_list" != "" ]]
1647	then
1648	printf "\| \| \n"
1649	printf "\| Files to be compiled: \| \n"
1650	line=$source_list
1651	while [[ "$line" != "" ]]
1652	do
1653	linestart=$(echo $line \| cut -c-70)
1654	printf "\| %-70s \| \n" "$linestart"
1655	line=$(echo "$line" \| cut -c71-)
1656	done
1657	fi
1658	printf "#------------------------------------------------------------------------#"
1659
1660
1661
1662	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1663	if [[ $do_trace = true ]]
1664	then
1665	(( i = 0 ))
1666	while (( i < nr_of_input_files ))
1667	do
1668	(( i = i + 1 ))
1669	if (( i == 1 ))
1670	then
1671	printf "\n\n >>> INPUT-file assignments:\n"
1672	fi
1673	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1674	done
1675	(( i = 0 ))
1676	while (( i < iout ))
1677	do
1678	(( i = i + 1 ))
1679	if (( i == 1 ))
1680	then
1681	printf "\n\n >>> OUTPUT-file assignments:\n"
1682	fi
1683	printf "\n ${localout[$i]} : ${pathout[$i]}"
1684	done
1685	(( i = 0 ))
1686	while (( i < iic ))
1687	do
1688	(( i = i + 1 ))
1689	if (( i == 1 ))
1690	then
1691	printf "\n\n >>> INPUT-commands:\n"
1692	fi
1693	printf "\n ${in_command[$i]}"
1694	done
1695	(( i = 0 ))
1696	while (( i < ioc ))
1697	do
1698	(( i = i + 1 ))
1699	if (( i == 1 ))
1700	then
1701	printf "\n\n >>> OUTPUT-commands:\n"
1702	fi
1703	printf "\n ${out_command[$i]}"
1704	done
1705	fi
1706
1707	# QUERY FOR CONTINUE
1708	if [[ $silent = false && $running_in_batch_mode = false ]]
1709	then
1710	antwort=dummy
1711	printf "\n\n"
1712	printf " >>> everything o.k. (y/n) ? "
1713	while read antwort
1714	do
1715	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1716	then
1717	printf " >>> everything o.k. (y/n) ? "
1718	else
1719	break
1720	fi
1721	done
1722	if [[ $antwort = n \|\| $antwort = N ]]
1723	then
1724	locat=user_abort; (( iec = 0 )); exit
1725	fi
1726	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1727	then
1728	printf "\n *** batch-job will be created and submitted"
1729	else
1730	printf "\n *** PALMRUN will now continue to execute on this machine"
1731	fi
1732	fi
1733
1734
1735
1736	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1737	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1738	then
1739
1740	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1741	then
1742	printf "\n\n *** creating executable and other sources for the remote host\n"
1743	else
1744	printf "\n\n *** creating executable and other sources for the local host\n"
1745	fi
1746
1747	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1748	# IT SHALL BE CREATED
1749	ask_for_make_depository=false
1750	if [[ $create_remote_batch_job = true ]]
1751	then
1752
1753	line=`grep %base_directory $config_file`
1754	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1755	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1756
1757	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1758	then
1759	printf "\n\n +++ make depository \"${make_depository}\""
1760	printf "\n on remote host not found!"
1761	ask_for_make_depository=true
1762	fi
1763	rm ${host_configuration}_last_make_protokoll
1764
1765	else
1766
1767	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1768	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1769	if [[ ! -d ${make_depository} ]]
1770	then
1771	printf "\n\n +++ make depository \"${make_depository}\""
1772	printf "\n on local host not found!"
1773	ask_for_make_depository=true
1774	fi
1775
1776	fi
1777
1778	if [[ $ask_for_make_depository = true ]]
1779	then
1780
1781	antwort=dummy
1782	printf "\n\n"
1783	printf " >>> Create a new one (y/n) ? "
1784	while read antwort
1785	do
1786	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1787	then
1788	printf " >>> Create a new one (y/n) ? "
1789	else
1790	break
1791	fi
1792	done
1793	if [[ $antwort = n \|\| $antwort = N ]]
1794	then
1795	locat=user_abort; (( iec = 0 )); exit
1796	fi
1797
1798	if [[ $do_trace = true ]]
1799	then
1800	palmbuild -h $host_configuration
1801	else
1802	palmbuild -v -h $host_configuration
1803	fi
1804
1805	if [[ $? != 0 ]]
1806	then
1807
1808	# ABORT IN CASE OF COMPILATION PROBLEMS
1809	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1810	locat=make_depository
1811	exit
1812	else
1813	echo " *** now continue with creating executable and other sources"
1814	fi
1815
1816	fi
1817
1818	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1819	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1820
1821	if [[ $? != 0 ]]
1822	then
1823
1824	# ABORT IN CASE OF COMPILATION PROBLEMS
1825	printf "\n +++ error while creating executable and/or other sources"
1826	locat=execution
1827	rm -rf $sources_for_run_catalog
1828	exit
1829
1830	else
1831
1832	printf " *** executable and other sources created\n"
1833	rm -rf $sources_for_run_catalog
1834
1835	fi
1836
1837	fi
1838
1839
1840	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1841	# WILL BE COPIED TO THE REMOTE HOST
1842	if [[ $create_remote_batch_job = true ]]
1843	then
1844	(( i = 0 ))
1845	while (( i < nr_of_input_files ))
1846	do
1847	(( i = i + 1 ))
1848	if [[ "${actionin[$i]}" = tr ]]
1849	then
1850	eval inputfile=${pathin[$i]}/${frelin[$i]}
1851	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1852	fi
1853	done
1854	if (( i > 0 ))
1855	then
1856	printf " *** input files have been copied to the remote host\n"
1857	fi
1858	fi
1859
1860
1861	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1862	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1863	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1864	then
1865
1866	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1867	if [[ $running_in_batch_mode = false ]]
1868	then
1869	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1870	# FOLDER
1871	mkdir -p $tempdir
1872	chmod go+rx $tempdir
1873	cd $tempdir
1874	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1875	printf "\n *** changed to temporary directory: $tempdir"
1876
1877	else
1878
1879	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1880	printf "\n *** running in temporary directory: $tempdir"
1881
1882	fi
1883
1884
1885	# PROVIDE THE INPUT FILES
1886	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1887	optional_files_missing=false
1888	(( i = 0 ))
1889	while (( i < nr_of_input_files ))
1890	do
1891	(( i = i + 1 ))
1892	if (( i == 1 ))
1893	then
1894	printf "\n\n *** providing INPUT-files:\n$dashes"
1895	fi
1896
1897
1898	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1899	if [[ "${actionin[$i]}" = unavailable ]]
1900	then
1901	optional_files_missing=true
1902	continue
1903	fi
1904
1905	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1906	files_for_cores=false; filetype=file
1907	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1908	then
1909	files_for_cores=true; filetype=files
1910	actionin[$i]=""
1911	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1912	then
1913	actionin[$i]=""
1914	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1915	then
1916	files_for_cores=true; filetype=files
1917	actionin[$i]="ln"
1918	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1919	then
1920	actionin[$i]="ln"
1921	fi
1922
1923	if [[ $files_for_cores = true ]]
1924	then
1925	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1926	else
1927	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1928	fi
1929
1930	# INPUT-FILES TO BE LINKED
1931	if [[ "${actionin[$i]}" = ln ]]
1932	then
1933
1934	printf "\n $filetype will be linked"
1935	if [[ $files_for_cores = false ]]
1936	then
1937	if [[ -f "${absnamein[$i]}" ]]
1938	then
1939	ln ${absnamein[$i]} ${localin[$i]}
1940	got_tmp[$i]=true
1941	fi
1942	else
1943	if [[ -d "${absnamein[$i]}" ]]
1944	then
1945	mkdir -p ${localin[$i]}
1946	cd ${absnamein[$i]}
1947	for file in $(ls *)
1948	do
1949	ln $file $tempdir/${localin[$i]}
1950	done >\|/dev/null 2>&1
1951	cd $tempdir
1952	fi
1953
1954	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1955	if [[ ! -f "${localin[$i]}/_000000" ]]
1956	then
1957	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1958	cp -r ${absnamein[$i]}/* ${localin[$i]}
1959	fi
1960
1961	got_tmp[$i]=true
1962	fi
1963	fi
1964
1965	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1966	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1967	then
1968
1969	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1970	then
1971
1972	# FILE COPIES ARE PROVIDED FOR ALL CORES
1973	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1974	printf "\n file will be provided for $cores processors"
1975	mkdir -p ${localin[$i]}
1976	ival=$cores
1977	(( ii = 0 ))
1978	while (( ii <= ival-1 ))
1979	do
1980	if (( ii < 10 ))
1981	then
1982	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1983	elif (( ii < 100 ))
1984	then
1985	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1986	elif (( ii < 1000 ))
1987	then
1988	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1989	else
1990	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1991	fi
1992	(( ii = ii + 1 ))
1993	done
1994
1995	else
1996
1997	if [[ $files_for_cores = true ]]
1998	then
1999
2000	# PROVIDE FILES FOR EACH CORE
2001	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2002	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2003	printf "\n providing $cores files for the respective cores"
2004	mkdir -p ${localin[$i]}
2005	if [[ $link_local_input = true ]]
2006	then
2007	printf " files will be linked\n"
2008	cd ${absnamein[$i]}
2009	for file in $(ls *)
2010	do
2011	ln -f $file ${localin[$i]}
2012	done
2013	cd $tempdir
2014	fi
2015
2016	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2017	if [[ ! -f "${localin[$i]}/_000000" ]]
2018	then
2019	if [[ $link_local_input = true ]]
2020	then
2021	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2022	fi
2023	cp -r ${absnamein[$i]}/* ${localin[$i]}
2024	fi
2025
2026	else
2027
2028	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2029	if [[ $link_local_input = true ]]
2030	then
2031	printf " file will be linked\n"
2032	ln -f ${absnamein[$i]} ${localin[$i]}
2033	fi
2034	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2035	if [[ ! -f "${localin[$i]}" ]]
2036	then
2037	if [[ $link_local_input = true ]]
2038	then
2039	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2040	fi
2041	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2042	then
2043	mv ${absnamein[$i]} ${localin[$i]}
2044	else
2045	cp ${absnamein[$i]} ${localin[$i]}
2046	fi
2047	fi
2048	fi
2049	fi
2050	fi
2051
2052	done
2053	if (( i != 0 ))
2054	then
2055	if [[ $optional_files_missing = true ]]
2056	then
2057	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2058	fi
2059	printf "\n$dashes\n *** all INPUT-files provided \n"
2060	fi
2061
2062
2063	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2064	(( i = 0 ))
2065	while (( i < iic ))
2066	do
2067	(( i = i + 1 ))
2068	if (( i == 1 ))
2069	then
2070	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2071	fi
2072	printf "\n >>> ${in_command[$i]}"
2073	eval ${in_command[$i]}
2074	if (( i == iic ))
2075	then
2076	printf "\n$dashes\n"
2077	fi
2078	done
2079
2080
2081	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2082	# (FILE ENVPAR WILL BE READ BY PALM)
2083	cat > ENVPAR << EOF
2084	&envpar run_identifier = '$jobname', host = '$host_configuration',
2085	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2086	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2087	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2088	maximum_cpu_time_allowed = ${cpumax}.,
2089	revision = '$global_revision',
2090	batch_job = .${running_in_batch_mode}. /
2091
2092	EOF
2093
2094
2095	# STARTING THE EXECUTABLE
2096	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2097	PATH=$PATH:$tempdir
2098
2099
2100	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2101	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2102	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2103	eval line=\"$line\"
2104	execute_command="$line"
2105
2106
2107	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2108	if [[ "$execute_command_for_combine" = "" ]]
2109	then
2110	eval line2=\"$line2\"
2111	execute_command_for_combine="$line2"
2112	fi
2113
2114
2115
2116	# PROVIDE A HOSTFILE, IF REQUIRED
2117	if [[ "$hostfile" != "" ]]
2118	then
2119
2120	if [[ $hostfile = auto ]]
2121	then
2122	# CREATE A NEW HOSTFILE
2123	(( ii = 1 ))
2124	while (( ii <= cores / threads_per_task ))
2125	do
2126	echo $(hostname) >> hostfile
2127	(( ii = ii + 1 ))
2128	done
2129	if (( cores / threads_per_task == 0 ))
2130	then
2131	echo $(hostname) >> hostfile
2132	fi
2133
2134	else
2135	cp $hostfile hostfile
2136	fi
2137	eval line=\"`head -n $ii hostfile`\"
2138	printf "\n *** running on: $line"
2139	fi
2140
2141
2142
2143	# SET THE NUMBER OF OPENMP-THREADS
2144	if [[ $use_openmp = true ]]
2145	then
2146	export OMP_NUM_THREADS=$threads_per_task
2147	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2148	else
2149	export OMP_NUM_THREADS=1
2150	fi
2151
2152
2153	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2154	if [[ $run_coupled_model = false ]]
2155	then
2156	if [[ "$ocean_file_appendix" = true ]]
2157	then
2158	echo "precursor_ocean" > coupling_steering
2159	else
2160	echo "precursor_atmos" > coupling_steering
2161	fi
2162	else
2163	(( iia = $cores_atmos / $threads_per_task ))
2164	(( iio = $cores_ocean / $threads_per_task ))
2165	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2166	printf "\n\n"
2167	echo "coupled_run $iia $iio" > coupling_steering
2168	fi
2169
2170	printf "\n *** execute command:"
2171	printf "\n \"$execute_command\" \n\n"
2172
2173	$execute_command < coupling_steering
2174
2175	if [[ $? != 0 ]]
2176	then
2177
2178	# ABORT IN CASE OF RUNTIME ERRORS
2179	printf "\n +++ runtime error occured"
2180	locat=execution
2181	exit
2182
2183	else
2184
2185	printf "\n$dashes\n *** execution finished \n"
2186
2187	fi
2188
2189
2190	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2191	# BY EACH CORE INTO ONE FILE
2192	if [[ ! -f combine_plot_fields.x ]]
2193	then
2194
2195	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2196	printf "\n 2d- and/or 3d-data may be incomplete!"
2197	printf "\n Your previous palmbuild may have failed. Please check.\n"
2198
2199	elif [[ "$combine_plot_fields" == true ]]
2200	then
2201
2202	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2203	$execute_command_for_combine
2204
2205	else
2206
2207	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2208	# DATA OUTPUT
2209	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2210	fi
2211
2212
2213
2214	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2215	(( i = 0 ))
2216	while (( i < ioc ))
2217	do
2218	(( i = i + 1 ))
2219	if (( i == 1 ))
2220	then
2221	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2222	fi
2223
2224	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2225	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2226
2227	printf "\n >>> ${out_command[$i]}"
2228	eval ${out_command[$i]}
2229	if (( i == ioc ))
2230	then
2231	printf "\n$dashes\n"
2232	fi
2233	done
2234
2235
2236	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2237	# WILDCARDS
2238	(( i = 0 ))
2239	(( nr_of_output_files = 0 ))
2240
2241	while (( i < iout ))
2242	do
2243
2244	(( i = i + 1 ))
2245
2246	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2247	# CREATE A LIST FOR THE DETECTED ENDINGS
2248	if [[ "${multout[$i]}" = true ]]
2249	then
2250	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2251	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2252	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2253
2254	endings="DEFAULT"
2255	while read line
2256	do
2257	# remove the local name from the beginning
2258	localnamestring="${localout_pre[$i]}"
2259	length_localname=${#localnamestring}
2260	ending=${line:${length_localname}}
2261
2262	if [[ "$ending" != "" ]]
2263	then
2264	endings="$endings $ending"
2265	fi
2266
2267	done <filelist
2268
2269	rm filelist
2270
2271	else
2272
2273	# SINGLE NAME
2274	endings=DEFAULT
2275
2276	fi
2277
2278	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2279	for ending in $endings
2280	do
2281
2282	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2283	if [[ $ending = DEFAULT ]]
2284	then
2285	ending=""
2286	fi
2287
2288	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2289	(( nr_of_output_files = nr_of_output_files + 1 ))
2290	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2291	transout[$nr_of_output_files]="${transout_pre[$i]}"
2292	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2293	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2294	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2295	extout[$nr_of_output_files]="${extout_pre[$i]}"
2296	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2297
2298	done
2299
2300	done
2301
2302
2303
2304
2305	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2306	(( i = 0 ))
2307	while (( i < nr_of_output_files ))
2308	do
2309	(( i = i + 1 ))
2310	if (( i == 1 ))
2311	then
2312	printf "\n\n *** saving OUTPUT-files:"
2313
2314	# GET RUN NUMBER ASSIGNED BY PALM
2315	if [[ -f RUN_NUMBER ]]
2316	then
2317	read run_number < RUN_NUMBER
2318	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2319	usecycle_option="-U $run_number"
2320	else
2321	run_number=0
2322	usecycle_option=""
2323	fi
2324	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2325	then
2326	printf "\n *** in case of SCP transfers to local host"
2327	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2328	fi
2329	printf "\n$dashes"
2330	fi
2331
2332	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2333	then
2334
2335	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2336
2337	# DETERMINE THE CYCLE NUMBER
2338	ls -1 -d $filename > filelist 2>/dev/null
2339	ls -1 -d $filename.* >> filelist 2>/dev/null
2340	while read line
2341	do
2342
2343	# filename without path (i.e. after the last "/")
2344	basefilename=$(basename ${line})
2345
2346	# check if there is an extension
2347	extension=${basefilename##*.}
2348	if [[ "$extension" = "${extout[$i]}" ]]
2349	then
2350	basefilename=${basefilename%.*}
2351	fi
2352
2353	# check for an existing cycle number
2354	cycle=${basefilename##*.}
2355	if [[ $cycle =~ ^-?[0-9]+$ ]]
2356	then
2357	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2358	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2359	(( icycle = $((10#$cycle)) + 1 ))
2360	else
2361	(( icycle = 1 ))
2362	fi
2363
2364	if (( icycle > maxcycle ))
2365	then
2366	(( maxcycle = icycle ))
2367	fi
2368
2369	done <filelist
2370	rm filelist
2371
2372
2373	# SET THE CYCLE NUMBER
2374	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2375	if [[ "${actionout[$i]}" = a ]]
2376	then
2377	(( maxcycle = maxcycle - 1 ))
2378	fi
2379
2380	(( cycnum[$i] = maxcycle ))
2381	pathout[$i]=$filename
2382
2383
2384	# ADD CYCLE NUMBER TO FILENAME
2385	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2386	if [[ "${actionout[$i]}" != "a" ]]
2387	then
2388	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2389	# WITH AN EXISTING CYCLE NUMBER
2390	if (( run_number >= cycnum[$i] ))
2391	then
2392	(( cycnum[$i] = run_number ))
2393	else
2394	if (( run_number > 0 ))
2395	then
2396	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2397	fi
2398	fi
2399	fi
2400	if (( cycnum[$i] > 0 ))
2401	then
2402	cyclestring=`printf "%03d" ${cycnum[$i]}`
2403	pathout[$i]=${pathout[$i]}.$cyclestring
2404	fi
2405	fi
2406
2407	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2408	files_for_cores=false; filetype=file
2409	link_local_output=false
2410	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2411	then
2412	files_for_cores=true; filetype=directory
2413	actionout[$i]=""
2414	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2415	then
2416	actionout[$i]=""
2417	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2418	then
2419	files_for_cores=true; filetype=directory
2420	link_local_output=true
2421	actionout[$i]=""
2422	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2423	then
2424	link_local_output
2425	actionout[$i]=""
2426	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2427	then
2428	files_for_cores=true; filetype=directory
2429	actionout[$i]="tr"
2430	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2431	then
2432	actionout[$i]="tr"
2433	fi
2434
2435	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2436	then
2437	if [[ ${warnout[$i]} = true ]]
2438	then
2439	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2440	fi
2441	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2442	then
2443	if [[ ${warnout[$i]} = true ]]
2444	then
2445	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2446	fi
2447	else
2448
2449
2450	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2451	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2452	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2453	then
2454	if [[ $running_on_remote = true ]]
2455	then
2456
2457	# SET OPTIONS FOR TRANSFER
2458	if [[ "${actionout[$i]}" = tr ]]
2459	then
2460	if [[ $files_for_cores = false ]]
2461	then
2462	catalog_option=""
2463	catalog_string=""
2464	else
2465	catalog_option="-c"
2466	catalog_string="/"
2467	fi
2468	append_option=""
2469	append_string=""
2470	else
2471	append_option="-A"
2472	append_string="append"
2473	fi
2474
2475	transfer_failed=false
2476	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2477	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2478
2479	# TRANSFER VIA SCP
2480	if [[ "$remote_loginnode" != "" ]]
2481	then
2482	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]}\" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2483	else
2484	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}
2485	fi
2486	[[ $? != 0 ]] && transfer_failed=true
2487
2488
2489	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2490	if [[ $transfer_failed = true ]]
2491	then
2492	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2493	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2494
2495	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2496	eval local_catalog=${pathout[$i]}
2497	if [[ ! -d $local_catalog ]]
2498	then
2499	printf " *** local directory does not exist. Trying to create:\n"
2500	printf " $local_catalog \n"
2501	mkdir -p $local_catalog
2502	fi
2503	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2504	transfer_problems=true
2505	fi
2506
2507	else
2508
2509	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2510	# BE COPIED OR APPENDED ON THIS MACHINE
2511	if [[ "${actionout[$i]}" = tr ]]
2512	then
2513	actionout[$i]=""
2514	else
2515	actionout[$i]="a"
2516	fi
2517	fi
2518	fi
2519
2520
2521	# APPEND ON THIS MACHINE
2522	if [[ "${actionout[$i]}" = "a" ]]
2523	then
2524	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2525	then
2526	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2527	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2528	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2529	else
2530	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2531	printf "\n ${pathout[$i]}\n"
2532	cat ${localout[$i]} >> ${pathout[$i]}
2533	fi
2534	fi
2535
2536	# COPY ON THIS MACHINE
2537	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2538	# ON DIFFERENT FILE-SYSTEMS
2539	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2540	then
2541
2542	# COPY IN CASE OF RUNS ON SINGLE CORES
2543	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2544	then
2545	printf "\n >>> OUTPUT: ${localout[$i]} to"
2546	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2547	if [[ $link_local_output = true ]]
2548	then
2549	printf " file will be linked\n"
2550	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2551	fi
2552	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2553	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2554	then
2555	if [[ $link_local_output = true ]]
2556	then
2557	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2558	fi
2559	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2560	else
2561	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2562	fi
2563	else
2564	printf "\n >>> OUTPUT: ${localout[$i]} to"
2565	printf "\n ${pathout[$i]}\n"
2566	if [[ $link_local_output = true ]]
2567	then
2568	printf " file will be linked\n"
2569	ln -f ${localout[$i]} ${pathout[$i]}
2570	fi
2571	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2572	if [[ ! -f "${pathout[$i]}" ]]
2573	then
2574	if [[ $link_local_output = true ]]
2575	then
2576	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2577	fi
2578	cp ${localout[$i]} ${pathout[$i]}
2579	else
2580	printf "+++ no copy because file ${pathout[$i]} exists\n"
2581	fi
2582	fi
2583
2584	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2585	then
2586
2587	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2588	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2589	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2590	printf "\n ${pathout[$i]}\n"
2591	if [[ $link_local_output = true ]]
2592	then
2593	printf " files will be linked\n"
2594	mkdir -p ${pathout[$i]}
2595	cd ${localout[$i]}
2596	for file in $(ls *)
2597	do
2598	ln -f $file ${pathout[$i]}
2599	done >\|/dev/null 2>&1
2600	cd $tempdir
2601	fi
2602
2603	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2604	if [[ ! -f "${pathout[$i]}/_000000" ]]
2605	then
2606	if [[ $link_local_output = true ]]
2607	then
2608	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2609	fi
2610	cp -r ${localout[$i]}/* ${pathout[$i]}
2611	fi
2612
2613	fi
2614	fi
2615	done
2616
2617	if (( i != 0 ))
2618	then
2619	if [[ $transfer_problems = true ]]
2620	then
2621	printf "\n$dashes\n *** OUTPUT-files saved"
2622	printf "\n +++ WARNING: some data transfers failed! \n"
2623	else
2624	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2625	fi
2626	fi
2627
2628
2629	# IF REQUIRED, START A RESTART-JOB
2630	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2631	if [[ -f CONTINUE_RUN ]]
2632	then
2633
2634	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2635	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2636	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2637	# -b START A BATCH JOB
2638	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2639	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2640	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2641
2642
2643	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2644	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2645	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2646	then
2647	prc=`echo $prc \| sed 's/#/r/g'`
2648	fi
2649
2650
2651	# START THE RESTART-JOB
2652	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2653	echo " $prc"
2654	printf "\n$dashes\n"
2655	if [[ $running_on_remote = true ]]
2656	then
2657
2658	echo "*** ssh will be used to initiate restart-runs!"
2659	echo " return_address=\"$return_address\" "
2660	echo " return_username=\"$local_username\" "
2661
2662	if [[ "$remote_loginnode" != "" ]]
2663	then
2664	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
2665	else
2666	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2667	fi
2668
2669	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2670	sleep 30
2671
2672	else
2673
2674	# START THE RESTART JOB ON THE LOCAL HOST
2675	eval $prc # THE ' MUST BE EVALUATED
2676	cd - > /dev/null
2677
2678	fi
2679	printf "\n$dashes\n *** restart-run initiated \n"
2680
2681
2682	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2683	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2684	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2685	# MAY BE VERY HUGE)
2686	(( i = 0 ))
2687	while (( i < nr_of_input_files ))
2688	do
2689	(( i = i + 1 ))
2690	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2691	then
2692	rm -r ${absnamein[$i]}
2693	fi
2694	done
2695
2696	fi
2697
2698
2699	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2700	cd $HOME
2701	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2702
2703
2704	else
2705
2706
2707	# PREPARING ACTIONS,
2708	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2709
2710	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2711	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2712	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2713	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2714	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2715	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2716	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2717	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2718	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2719	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2720	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2721	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2722	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2723	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2724	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2725	if [[ $create_remote_batch_job = true ]]
2726	then
2727	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2728	if [[ $do_trace = true ]]
2729	then
2730	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2731	fi
2732	elif [[ $create_batch_job = true ]]
2733	then
2734	palmrun_com=${palmrun_com}" -j"
2735	if [[ $do_trace = true ]]
2736	then
2737	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2738	fi
2739	fi
2740
2741
2742	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2743	# REMOTE HOST
2744	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2745	job_protocol_file=$job_protocol_file_local
2746	if [[ $create_remote_batch_job = true ]]
2747	then
2748	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2749	job_protocol_file=$job_protocol_file_remote
2750	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2751	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2752	fi
2753
2754
2755	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2756	jobfile=jobfile.$run_id
2757
2758
2759	# FIRST CREATE THE BATCH DIRECTIVES
2760	(( i = 0 ))
2761	while (( i < ibd ))
2762	do
2763	(( i = i + 1 ))
2764	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2765	eval line=\"$line\"
2766	echo "$line" >> $jobfile
2767	done
2768	echo " " >> $jobfile
2769
2770
2771	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2772	# PROTOCOL
2773	if [[ $create_remote_batch_job = true ]]
2774	then
2775	echo "set +vx" >> $jobfile
2776	echo "trap '" >> $jobfile
2777	echo "set +vx" >> $jobfile
2778	echo "cd ${remote_jobcatalog}" >> $jobfile
2779	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2780
2781	# ADD THE BATCH DIRECTIVES
2782	(( i = 0 ))
2783	while (( i < ibdt ))
2784	do
2785	(( i = i + 1 ))
2786	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2787	eval line=\"$line\"
2788	echo "$line" >> $jobfile
2789	done
2790	echo " " >> $jobfile
2791
2792	echo "set -x" >> $jobfile
2793	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${jobname}" >> $jobfile
2794	echo "%%END%%" >> $jobfile
2795	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2796	echo "$submit_command $scpjob_file" >> $jobfile
2797	echo "rm $scpjob_file" >> $jobfile
2798	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2799	echo "set -x" >> $jobfile
2800	echo " ' exit" >> $jobfile
2801	fi
2802
2803
2804	# ACTIVATE ERROR-TRACEBACK
2805	if [[ $do_trace = true ]]
2806	then
2807	echo "set -x" >> $jobfile
2808	else
2809	echo "set +vx" >> $jobfile
2810	fi
2811
2812
2813	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2814	if [[ "$login_init_cmd" != "" ]]
2815	then
2816	echo "$login_init_cmd" >> $jobfile
2817	fi
2818	if [[ "$module_commands" != "" ]]
2819	then
2820	echo "$module_commands" >> $jobfile
2821	fi
2822
2823
2824	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2825	if [[ $create_remote_batch_job = true ]]
2826	then
2827	echo "mkdir $tempdir" >> $jobfile
2828	echo "chmod go+rx $tempdir" >> $jobfile
2829	else
2830	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2831	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2832	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2833	mkdir $tempdir
2834	chmod go+rx $tempdir
2835	fi
2836	echo "cd $tempdir" >> $jobfile
2837	echo "export tempdir=$tempdir" >> $jobfile
2838	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2839	echo "export PATH=.:\$PATH" >> $jobfile
2840	echo "export execute_palmrun=true" >> $jobfile
2841
2842
2843	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2844	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2845	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2846	echo "LOCAL_PWD=$working_directory" >> $jobfile
2847	echo "export LOCAL_PWD" >> $jobfile
2848
2849
2850	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2851	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2852	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2853
2854
2855	# CALL PALMRUN WITHIN THE JOB
2856	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2857	echo "set -x" >> $jobfile
2858	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2859
2860
2861	# TRANSFER JOBFILE TO THE TARGET HOST
2862	if [[ $create_jobfile_only = false ]]
2863	then
2864
2865	if [[ $create_remote_batch_job = true ]]
2866	then
2867
2868	echo " "
2869	echo " *** transfer of job to remote host via scp"
2870	if [[ $do_trace = true ]]
2871	then
2872	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2873	fi
2874	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2875
2876	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2877	if [[ $do_trace = true ]]
2878	then
2879	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"
2880	fi
2881	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
2882
2883	elif [[ $create_batch_job = true ]]
2884	then
2885
2886	eval local_jobcatalog=$local_jobcatalog
2887	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2888	cd $local_jobcatalog
2889	echo " "
2890	echo " *** submit the job"
2891	if [[ $do_trace = true ]]
2892	then
2893	echo "$submit_command ${host_configuration}_${job_id}"
2894	fi
2895	$submit_command ${host_configuration}_${job_id}
2896	rm ${host_configuration}_${job_id}
2897	cd - > /dev/null
2898
2899	fi
2900
2901	rm -rf $jobfile
2902
2903	else
2904
2905	printf "\n *** jobfile created under name \"$jobfile\" "
2906	printf "\n no batch-job has been sent!"
2907
2908	fi
2909
2910	fi # END OF REMOTE-PART

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