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source: palm/trunk/SCRIPTS/palmrun @ 2675

Last change on this file since 2675 was 2670, checked in by raasch, 7 years ago
test printouts removed
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 95.5 KB

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

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