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source: palm/trunk/SCRIPTS/palmrun @ 2699

Last change on this file since 2699 was 2696, checked in by kanani, 7 years ago
Merge of branch palm4u into trunk
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.7 KB

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

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