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source: palm/trunk/SCRIPTS/palmrun @ 2733

Last change on this file since 2733 was 2732, checked in by raasch, 7 years ago
bugfix: keyword Rev set for scrpts palmrun and palmbuild
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 94.9 KB

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

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