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source: palm/trunk/SCRIPTS/palmrun @ 2638

Last change on this file since 2638 was 2638, checked in by raasch, 7 years ago
bugfix for cases with constant top momentumflux
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.6 KB

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

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