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source: palm/trunk/SCRIPTS/palmrun @ 2770

Last change on this file since 2770 was 2762, checked in by raasch, 7 years ago
file connection file is taken by default from trunk/SCRIPTS
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.1 KB

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

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