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source: palm/trunk/SCRIPTS/palmrun @ 2644

Last change on this file since 2644 was 2639, checked in by raasch, 7 years ago
bugfix for r2638: switchback to palmrun r2636
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.4 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 2639 2017-11-23 13:09:53Z 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: loc - field (optional)
538	# s2c: tr/ar - field (optional)
539	s1=`echo $line \| cut -d" " -f1`
540	s2=`echo $line \| cut -d" " -s -f2`
541	s2a=$(echo $s2 \| cut -d":" -f1)
542	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
543	then
544	s2b=""
545	s2c=""
546	else
547	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
548	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
549	fi
550	s3=`echo $line \| cut -d" " -f3`
551	s4=`echo $line \| cut -d" " -s -f4`
552	s5=`echo $line \| cut -d" " -s -f5`
553	s6=`echo $line \| cut -d" " -s -f6`
554
555
556	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
557	# INPUT- OR OUTPUT-LIST.
558	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
559	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
560	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
561	# IS NOT CHECKED AND STORED.
562	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
563	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
564	then
565	found=false
566	for actual in $activation_string_list
567	do
568	for formal in $s3
569	do
570	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
571	done
572	done
573	if [[ $found = true ]]
574	then
575	(( iin = iin + 1 ))
576	localin_pre[$iin]=$s1; transin_pre[$iin]=$s2b; actionin_pre[$iin]=$s2c;
577	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
578
579	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
580	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
581	if [[ $running_on_remote = true && ( "$s2b" = job \|\| "$s2b" = jobopt ) ]]
582	then
583	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
584	fi
585
586	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
587	# THE WILDCARD FROM THE ENDING
588	if [[ "${s5: -1}" = "*" ]]
589	then
590	if [[ "$s2c" = "di" ]]
591	then
592	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
593	printf "\n see file \"$fileconnection_file\", line"
594	printf "\n$line"
595	locat=iofiles_file; exit
596	fi
597	multin[$iin]=true
598	string=${endin_pre[$iin]}
599	endin_pre[$iin]="${string%?}"
600	else
601	multin[$iin]=false
602	fi
603	fi
604	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
605	then
606	found=false
607	for actual in $activation_string_list
608	do
609	for formal in $s3
610	do
611	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
612	done
613	done
614	if [[ $found = true ]]
615	then
616	(( iout = iout + 1 ))
617	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2c; typeout_pre[$iout]=$s3;
618	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
619
620	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
621	# THE WILDCARD FROM THE LOCAL FILENAME
622	if [[ "${s1: -1}" = "*" ]]
623	then
624	if [[ "$s2c" = "di" ]]
625	then
626	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
627	printf "\n see file \"$fileconnection_file\", line"
628	printf "\n$line"
629	locat=iofiles_file; exit
630	fi
631	multout[$iout]=true
632	string=${localout_pre[$iout]}
633	localout_pre[$iout]="${string%?}"
634	else
635	multout[$iout]=false
636	fi
637	fi
638	elif [[ "$s2a" != in && "$s2a" != out ]]
639	then
640	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
641	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
642	locat=connect; exit
643	fi
644	IFS="$IFSALT"
645	fi
646
647	done < $fileconnection_file
648
649
650
651	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
652	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
653	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
654	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
655	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
656	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
657
658
659
660	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
661	if [[ $run_coupled_model = true ]]
662	then
663
664	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
665	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
666
667	if (( $cores_ocean + $cores_atmos != $cores ))
668	then
669
670	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
671	printf "\n PEs (total) : $cores"
672	printf "\n PEs (atmosphere): $cores_atmos"
673	printf "\n PEs (ocean) : $cores_ocean"
674	locat=coupling; exit
675
676	fi
677
678	fi
679
680
681	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
682	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
683	# FOLDER
684	if [[ $running_in_batch_mode = true ]]
685	then
686
687	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
688	then
689	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
690	printf "\n Please check the output of the palmrun-call"
691	printf "\n that you did on your local host."
692	locat=SOURCES_FOR_RUN; exit
693	fi
694
695	else
696
697	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
698	# AUTOMATIC RESTART RUN
699	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
700	if [[ $restart_run = false ]]
701	then
702
703	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
704	# THE LOCAL HOST
705	if [[ ! -d $source_path ]]
706	then
707	printf "\n\n +++ source path \"$source_path\" on local host"
708	printf "\n \"$(hostname)\" does not exist"
709	locat=source_path; exit
710	fi
711
712	rm -rf $sources_for_run_catalog
713	mkdir -p $sources_for_run_catalog
714
715	if [[ "$source_list" = LM ]]
716	then
717
718	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
719	source_list=""
720	cd $source_path
721
722
723	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
724	if [[ ! -d ../.svn ]]
725	then
726	printf "\n\n +++ source directory"
727	printf "\n \"$source_path\" "
728	printf "\n is not under control of \"subversion\"."
729	printf "\n Please do not use palmrun-option \"-s LM\"\n"
730	fi
731
732
733	# LIST ALL MODIFIED SOURCE CODE FILES
734	Filenames=""
735	svn status > tmp_svnstatus
736	while read line
737	do
738	firstc=`echo $line \| cut -c1`
739	if [[ $firstc = M \|\| $firstc = "?" ]]
740	then
741	Name=`echo "$line" \| cut -c8-`
742	extension=`echo $Name \| cut -d. -f2`
743	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
744	then
745	Filenames="$Filenames "$Name
746	fi
747	fi
748	done < tmp_svnstatus
749	rm -rf tmp_svnstatus
750
751
752	# COPY FILES TO SOURCES_FOR_RUN_...
753	for filename in $Filenames
754	do
755	cp $filename ${working_directory}/${sources_for_run_catalog}
756	source_list=$source_list"$filename "
757	done
758
759	cd - > /dev/null
760
761
762	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
763	elif [[ "$source_list" != "" ]]
764	then
765
766	cd $source_path
767
768	for filename in $source_list
769	do
770
771	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
772	if [[ $(echo $filename \| grep -c "/") != 0 ]]
773	then
774	printf "\n +++ source code file: $filename"
775	printf "\n must not contain (\"/\") "
776	locat=source; exit
777	fi
778
779	if [[ ! -f $filename ]]
780	then
781	printf "\n +++ source code file: $filename"
782	printf "\n does not exist"
783	locat=source; exit
784	else
785	cp $filename ${working_directory}/${sources_for_run_catalog}
786	fi
787
788	done
789
790	cd - > /dev/null
791
792	fi
793
794	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
795	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
796	if [[ ! -f $makefile ]]
797	then
798	printf "\n +++ file \"$makefile\" does not exist"
799	locat=make; exit
800	else
801	cp $makefile ${sources_for_run_catalog}/Makefile
802	fi
803
804
805	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
806	if [[ "$user_source_path" != "" ]]
807	then
808
809	# DOES THE DIRECTORY EXIST?
810	if [[ ! -d $user_source_path ]]
811	then
812
813	printf "\n\n *** INFORMATIVE: additional source code directory"
814	printf "\n \"$user_source_path\" "
815	printf "\n does not exist or is not a directory."
816	printf "\n No source code will be used from this directory!\n"
817	user_source_path=""
818	if [[ $silent == false ]]
819	then
820	sleep 2
821	fi
822
823	else
824
825	cd $user_source_path
826	found=false
827
828	Names=$(ls -1 *.f90 2>&1)
829	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
830	Names=$(ls -1 *.F90 2>&1)
831	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
832	Names=$(ls -1 *.F 2>&1)
833	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
834	Names=$(ls -1 *.f 2>&1)
835	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
836	Names=$(ls -1 *.c 2>&1)
837	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
838
839	cd - > /dev/null
840	cd $sources_for_run_catalog
841
842	# COPY MAKEFILE IF EXISTING
843	if [[ -f $user_source_path/Makefile ]]
844	then
845	printf "\n\n *** user Makefile from directory"
846	printf "\n \"$user_source_path\" is used \n"
847	if [[ $silent == false ]]
848	then
849	sleep 1
850	fi
851	cp $user_source_path/Makefile .
852	fi
853
854	for filename in $AddFilenames
855	do
856	if [[ -f $filename ]]
857	then
858	printf "\n +++ source code file \"$filename\" found in additional"
859	printf "\n source code directory \"$user_source_path\" "
860	printf "\n but was also given with option \"-s\" which means that it should be taken"
861	printf "\n from directory \"$source_path\"."
862	locat=source; exit
863	fi
864
865	cp $user_source_path/$filename .
866	source_list="$source_list $filename"
867
868	# CHECK IF FILE IS CONTAINED IN MAKEFILE
869	if [[ $(grep -c $filename Makefile) = 0 ]]
870	then
871	printf "\n\n +++ user file \"$filename\" "
872	printf "\n is not listed in Makefile \n"
873	locat=source; exit
874	else
875
876	if [[ $found = false ]]
877	then
878	found=true
879	printf "\n\n *** following user file(s) added to the"
880	printf " files to be translated:\n "
881	fi
882	printf "$filename "
883	if [[ $silent == false ]]
884	then
885	sleep 0.5
886	fi
887
888	fi
889	done
890	[[ $found = true ]] && printf "\n"
891	cd - > /dev/null
892	fi
893	fi
894
895	# COPY CONFIGURATION FILES
896	cp $config_file $sources_for_run_catalog
897	cp $fileconnection_file $sources_for_run_catalog
898
899	# COPY SHELLSCRIPTS
900	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
901	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
902
903	fi
904
905	fi
906
907
908	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
909	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
910	if [[ "$global_revision" = "" ]]
911	then
912	global_revision=`svnversion $source_path 2>/dev/null`
913	global_revision="Rev: $global_revision"
914	fi
915
916
917	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
918	if [[ -n $cores ]]
919	then
920
921	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
922	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
923	if [[ $tasks_per_node = 0 ]]
924	then
925	printf "\n"
926	printf "\n +++ option \"-T\" (tasks per node) is missing"
927	printf "\n set -T option or define tasks_per_node in the config file"
928	locat=tasks_per_node; (( iec = 0 )); exit
929	fi
930
931	if (( cores < tasks_per_node ))
932	then
933	printf "\n"
934	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
935	printf "\n given values: -T $tasks_per_node -X $cores"
936	locat=tasks_per_node; (( iec = 0 )); exit
937	fi
938
939	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
940	(( mpi_tasks = cores / threads_per_task ))
941	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
942	(( ii = cores / tasks_per_node ))
943	(( remaining_cores = cores - ii * tasks_per_node ))
944	if (( remaining_cores > 0 ))
945	then
946	printf "\n"
947	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
948	printf "\n divisor of the total number of cores (option \"-X\")"
949	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
950	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
951	(( nodes = nodes + 1 ))
952	fi
953
954	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
955	if [[ "$tasks_per_node" != "" ]]
956	then
957	TOPT="-T $tasks_per_node"
958	fi
959
960	fi
961
962
963	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
964	if [[ "$maximum_parallel_io_streams" = "" ]]
965	then
966	maximum_parallel_io_streams=$cores
967	fi
968
969
970	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
971	if [[ "$scp_port" != "" ]]
972	then
973	PORTOPT="-P $scp_port"
974	SSH_PORTOPT="-p $scp_port"
975	fi
976
977
978	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
979	# CONFIG-FILE
980	if [[ "$ssh_key" != "" ]]
981	then
982	ssh_key="-i $HOME/.ssh/$ssh_key"
983	fi
984
985
986	# SET QUEUE, IF NOT GIVEN
987	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
988	then
989
990	if [[ $queue = none && "$defaultqueue" = "" ]]
991	then
992	printf "\n"
993	printf "\n +++ no default queue given in configuration file and no queue"
994	printf "\n given with option -q"
995	fi
996	if [[ $queue = none ]]
997	then
998	queue=$defaultqueue
999	fi
1000
1001	fi
1002
1003
1004	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1005	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1006	(( i = 0 ))
1007	(( nr_of_input_files = 0 ))
1008	while (( i < iin ))
1009	do
1010	(( i = i + 1 ))
1011
1012	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1013	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1014	if [[ "${actionin_pre[$i]}" = di ]]
1015	then
1016	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1017	else
1018	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
1019	fi
1020
1021
1022	# CHECK IF FILE EXISTS
1023	if ! ls $filename* 1>/dev/null 2>&1
1024	then
1025
1026	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1027	if [[ "${transin_pre[$i]}" != "locopt" && "${transin_pre[$i]}" != "jobopt" ]]
1028	then
1029	printf "\n\n +++ INPUT-file: "
1030	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1031	then
1032	printf "\n $filename"
1033	else
1034	printf "\n $filename.${extin_pre[$i]}"
1035	fi
1036	printf "\n does not exist\n"
1037	locat=input; exit
1038	else
1039	(( nr_of_input_files = nr_of_input_files + 1 ))
1040	localin[$nr_of_input_files]="${localin_pre[$i]}"
1041	transin[$nr_of_input_files]="unavailable"
1042	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1043	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1044	endin[$nr_of_input_files]="${endin_pre[$i]}"
1045	extin[$nr_of_input_files]="${extin_pre[$i]}"
1046	fi
1047
1048	else
1049
1050	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
1051	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1052	if [[ "${multin[$i]}" = true ]]
1053	then
1054	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1055	ls -1 -d ${filename} > filelist 2>/dev/null
1056	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1057	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1058
1059	endings=""
1060	while read line
1061	do
1062	# filename without path (i.e. after the last "/")
1063	basefilename=$(basename ${line})
1064
1065	# check if there is an extension and remove it
1066	ext=${basefilename##*.}
1067	if [[ "$ext" = "${extin_pre[$i]}" ]]
1068	then
1069	basefilename=${basefilename%.*}
1070	fi
1071
1072	# check for an existing cycle number and remove it
1073	cycle=${basefilename##*.}
1074	if [[ $cycle =~ ^-?[0-9]+$ ]]
1075	then
1076	basefilename=${basefilename%.*}
1077	fi
1078
1079	# remove the fname from the beginning
1080	length_fname=${#fname}
1081	ending=${basefilename:${length_fname}}
1082
1083	# remove the ending given in the .iofiles from the beginning
1084	endingstring="${endin_pre[$i]}"
1085	length_ending=${#endingstring}
1086	ending=${ending:${length_ending}}
1087
1088	if [[ "$ending" = "" ]]
1089	then
1090	# standard ending as given in the .iofiles
1091	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1092	then
1093	endings="$endings DEFAULT"
1094	fi
1095	else
1096	# ending must start with "_", otherwise its a different file
1097	if [[ "${ending:0:1}" = "_" ]]
1098	then
1099	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1100	then
1101	endings="$endings $ending"
1102	fi
1103	fi
1104	fi
1105
1106	done <filelist
1107
1108	rm filelist
1109
1110	else
1111
1112	# SINGLE NAME
1113	endings=DEFAULT
1114
1115	fi
1116
1117	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1118	for ending in $endings
1119	do
1120
1121	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1122	if [[ $ending = DEFAULT ]]
1123	then
1124	ending=""
1125	fi
1126
1127	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1128	(( nr_of_input_files = nr_of_input_files + 1 ))
1129	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1130	transin[$nr_of_input_files]="${transin_pre[$i]}"
1131	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1132	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1133	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1134	extin[$nr_of_input_files]="${extin_pre[$i]}"
1135
1136
1137	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1138	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1139	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1140	then
1141	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1142	else
1143	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
1144	fi
1145
1146	# DETERMINE THE FILE'S CYCLE NUMBER
1147	(( maxcycle = 0 ))
1148	ls -1 -d $filename > filelist 2>/dev/null
1149	ls -1 -d $filename.* >> filelist 2>/dev/null
1150	while read line
1151	do
1152	# filename without path (i.e. after the last "/")
1153	basefilename=$(basename ${line})
1154
1155	# check if there is an extension
1156	extension=${basefilename##*.}
1157	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1158	then
1159	basefilename=${basefilename%.*}
1160	fi
1161
1162	# check for an existing cycle number
1163	cycle=${basefilename##*.}
1164	if [[ $cycle =~ ^-?[0-9]+$ ]]
1165	then
1166	(( icycle = $cycle ))
1167	else
1168	(( icycle = 0 ))
1169	fi
1170
1171	if (( icycle > maxcycle ))
1172	then
1173	(( maxcycle = icycle ))
1174
1175	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1176	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1177	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1178	then
1179	leading_zero=true
1180	else
1181	leading_zero=false
1182	fi
1183	fi
1184
1185	done <filelist
1186	rm filelist
1187
1188	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1189	if [[ $leading_zero = true ]]
1190	then
1191	cyclestring=`printf "%03d" $maxcycle`
1192	else
1193	cyclestring=$maxcycle
1194	fi
1195
1196	# APPEND CYCLE NUMBER TO FILENAME
1197	if (( maxcycle > 0 ))
1198	then
1199	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1200	then
1201	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1202	else
1203	filename=${filename}.$cyclestring
1204	fi
1205	else
1206	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1207	then
1208	filename=${filename}.${extin[$nr_of_input_files]}
1209	fi
1210	fi
1211
1212	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1213	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1214	absnamein[$nr_of_input_files]=$filename
1215	if (( maxcycle > 0 ))
1216	then
1217	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1218	then
1219	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1220	else
1221	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
1222	fi
1223	else
1224	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1225	then
1226	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1227	else
1228	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
1229	fi
1230	fi
1231
1232	done
1233
1234	fi
1235
1236	done
1237
1238
1239	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1240	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1241	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1242	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1243	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1244	# REMOTE HOST)
1245	(( i = 0 ))
1246	while (( i < iout ))
1247	do
1248	(( i = i + 1 ))
1249	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1250	then
1251	if [[ "${actionout_pre[$i]}" = tr ]]
1252	then
1253	actionout_pre[$i]=""
1254	elif [[ "${actionout_pre[$i]}" = trpe ]]
1255	then
1256	actionout_pre[$i]=pe
1257	elif [[ "${actionout_pre[$i]}" = tra ]]
1258	then
1259	actionout_pre[$i]=a
1260	fi
1261	(( maxcycle = 0 ))
1262	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
1263	eval catalogname=${pathout_pre[$i]}
1264	if ! ls $filename* 1>/dev/null 2>&1
1265	then
1266
1267	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1268	if cat /dev/null > $filename
1269	then
1270	rm $filename
1271	else
1272
1273	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1274	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1275	if [[ ! -d $catalogname ]]
1276	then
1277	if mkdir -p $catalogname
1278	then
1279	printf "\n\n *** directory:"
1280	printf "\n $catalogname"
1281	printf "\n was created\n"
1282	else
1283	printf "\n\n +++ OUTPUT-file:"
1284	printf "\n $filename"
1285	printf "\n cannot be created, because directory does not exist"
1286	printf "\n and cannot be created either"
1287	printf "\n"
1288	locat=output ; exit
1289	fi 2>/dev/null
1290	else
1291	printf "\n\n +++ OUTPUT-file:"
1292	printf "\n $filename"
1293	printf "\n cannot be created, although directory exists"
1294	printf "\n"
1295	locat=output ; exit
1296	fi
1297	fi 2>/dev/null
1298
1299	fi
1300
1301	fi
1302	done
1303
1304
1305	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1306	if [[ $running_in_batch_mode = false ]]
1307	then
1308	run_id=$RANDOM
1309	job_id=${fname}.$run_id
1310
1311	tempdir=$fast_io_catalog/$job_id
1312	fi
1313
1314
1315	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1316	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1317	then
1318
1319	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1320	if [[ $ibd = 0 ]]
1321	then
1322	printf "\n"
1323	printf "\n +++ no batch directives found in configuration file"
1324	locat=config_file_batch_directives; (( iec = 0 )); exit
1325	fi
1326
1327	# CHECK IF CPUTIME IS GIVEN FOR JOB
1328	done=false
1329	cputime=$cpumax
1330	while [[ $done = false ]]
1331	do
1332	if (( cputime == 0 ))
1333	then
1334	printf "\n +++ cpu-time is undefined"
1335	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1336	printf "\n >>> "
1337	read cputime 1>/dev/null 2>&1
1338	else
1339	done=true
1340	fi
1341	done
1342	cpumax=$cputime
1343
1344	# CHECK THE MEMORY DEMAND
1345	done=false
1346	while [[ $done = false ]]
1347	do
1348	if (( memory == 0 ))
1349	then
1350	printf "\n +++ memory demand is undefined"
1351	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1352	printf "\n >>> "
1353	read memory 1>/dev/null 2>&1
1354	else
1355	done=true
1356	fi
1357	done
1358
1359	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1360	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1361	then
1362	while [[ -z $remote_username ]]
1363	do
1364	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1365	printf "\n >>> Please type username:"
1366	printf "\n >>> "
1367	read remote_username
1368	done
1369	fi
1370
1371	else
1372
1373	if [[ $running_in_batch_mode = false ]]
1374	then
1375	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1376	cpumax=$cputime
1377	else
1378	cputime=$cpumax
1379	fi
1380
1381	fi
1382
1383
1384	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1385	(( cpu_hours = cputime / 3600 ))
1386	(( resttime = cputime - cpu_hours * 3600 ))
1387	(( cpu_minutes = resttime / 60 ))
1388	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1389	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1390
1391
1392	# OUTPUT OF THE PALMRUN-HEADER
1393	calltime=$(date)
1394	printf "\n"
1395	printf "#------------------------------------------------------------------------# \n"
1396	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1397	printf "\| \| \n"
1398	column1="called on:"; column2=$(hostname)
1399	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1400	if [[ $create_remote_batch_job = true ]]
1401	then
1402	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1403	else
1404	if [[ $running_on_remote = true ]]
1405	then
1406	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1407	else
1408	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1409	fi
1410	fi
1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1412
1413	column1="running in:"
1414	if [[ $running_in_batch_mode = true ]]
1415	then
1416	column2="batch job mode"
1417	else
1418	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1419	then
1420	column2="job creation mode"
1421	else
1422	column2="interactive run mode"
1423	fi
1424	fi
1425	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1426
1427	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1428	then
1429	if [[ "$project_account" != "" ]]
1430	then
1431	column1="project account number:"
1432	column2="$project_account"
1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1434	fi
1435	fi
1436
1437	if [[ -n $cores ]]
1438	then
1439	if [[ $run_coupled_model = false ]]
1440	then
1441	column1="number of cores:"; column2=$cores
1442	else
1443	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1444	fi
1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1446	fi
1447	if [[ -n $tasks_per_node ]]
1448	then
1449	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1450	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1451	if (( remaining_cores > 0 ))
1452	then
1453	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1454	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1455	fi
1456	fi
1457	if [[ $maximum_parallel_io_streams != $cores ]]
1458	then
1459	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1461	fi
1462	if [[ $use_openmp = true ]]
1463	then
1464	column1="threads per task:"; column2="$threads_per_task"
1465	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1466	fi
1467	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1468	then
1469	column1="memory demand / PE":; column2="$memory MB"
1470	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1471	column1="job cpu time (h:m:s):"; column2="$timestring"
1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1473	fi
1474	printf "\| \| \n"
1475	if [[ "$source_list" != "" ]]
1476	then
1477	if [[ "$make_options" != "" ]]
1478	then
1479	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1480	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1481	line=$(echo "$make_options" \| cut -c46-)
1482	while [[ "$line" != "" ]]
1483	do
1484	column1=""
1485	column2=$(echo "$line" \| cut -c-45)
1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1487	line=$(echo "$line" \| cut -c46-)
1488	done
1489	fi
1490	fi
1491
1492	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1493	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1494	line=$(echo "$cpp_options" \| cut -c46-)
1495	while [[ "$line" != "" ]]
1496	do
1497	column1=""
1498	column2=$(echo "$line" \| cut -c-45)
1499	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1500	line=$(echo "$line" \| cut -c46-)
1501	done
1502
1503	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1504	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1505	line=$(echo "$compiler_options" \| cut -c46-)
1506	while [[ "$line" != "" ]]
1507	do
1508	column1=""
1509	column2=$(echo "$line" \| cut -c-45)
1510	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1511	line=$(echo "$line" \| cut -c46-)
1512	done
1513
1514	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1515	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1516	line=$(echo "$linker_options" \| cut -c46-)
1517	while [[ "$line" != "" ]]
1518	do
1519	column1=""
1520	column2=$(echo "$line" \| cut -c-45)
1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1522	line=$(echo "$line" \| cut -c46-)
1523	done
1524
1525	if [[ "$login_init_cmd" != "" ]]
1526	then
1527	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1528	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1529	line=$(echo "$login_init_cmd" \| cut -c46-)
1530	while [[ "$line" != "" ]]
1531	do
1532	column1=""
1533	column2=$(echo "$line" \| cut -c-45)
1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1535	line=$(echo "$line" \| cut -c46-)
1536	done
1537	fi
1538
1539	if [[ "$module_commands" != "" ]]
1540	then
1541	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1542	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1543	line=$(echo "$module_commands" \| cut -c46-)
1544	while [[ "$line" != "" ]]
1545	do
1546	column1=""
1547	column2=$(echo "$line" \| cut -c-45)
1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1549	line=$(echo "$line" \| cut -c46-)
1550	done
1551	fi
1552	printf "\| \| \n"
1553	column1="base name of files:"; column2=$fname
1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1555	column1="activation string list:"; column2=$(echo $activation_string_list)
1556	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1557
1558	if [[ "$ocean_file_appendix" = true ]]
1559	then
1560	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1561	fi
1562
1563	if [[ "$source_list" != "" ]]
1564	then
1565	printf "\| \| \n"
1566	printf "\| Files to be compiled: \| \n"
1567	line=$source_list
1568	while [[ "$line" != "" ]]
1569	do
1570	linestart=$(echo $line \| cut -c-70)
1571	printf "\| %-70s \| \n" "$linestart"
1572	line=$(echo "$line" \| cut -c71-)
1573	done
1574	fi
1575	printf "#------------------------------------------------------------------------#"
1576
1577
1578
1579	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1580	if [[ $do_trace = true ]]
1581	then
1582	(( i = 0 ))
1583	while (( i < nr_of_input_files ))
1584	do
1585	(( i = i + 1 ))
1586	if (( i == 1 ))
1587	then
1588	printf "\n\n >>> INPUT-file assignments:\n"
1589	fi
1590	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1591	done
1592	(( i = 0 ))
1593	while (( i < iout ))
1594	do
1595	(( i = i + 1 ))
1596	if (( i == 1 ))
1597	then
1598	printf "\n\n >>> OUTPUT-file assignments:\n"
1599	fi
1600	printf "\n ${localout[$i]} : ${pathout[$i]}"
1601	done
1602	(( i = 0 ))
1603	while (( i < iic ))
1604	do
1605	(( i = i + 1 ))
1606	if (( i == 1 ))
1607	then
1608	printf "\n\n >>> INPUT-commands:\n"
1609	fi
1610	printf "\n ${in_command[$i]}"
1611	done
1612	(( i = 0 ))
1613	while (( i < ioc ))
1614	do
1615	(( i = i + 1 ))
1616	if (( i == 1 ))
1617	then
1618	printf "\n\n >>> OUTPUT-commands:\n"
1619	fi
1620	printf "\n ${out_command[$i]}"
1621	done
1622	fi
1623
1624	# QUERY FOR CONTINUE
1625	if [[ $silent = false && $running_in_batch_mode = false ]]
1626	then
1627	antwort=dummy
1628	printf "\n\n"
1629	printf " >>> everything o.k. (y/n) ? "
1630	while read antwort
1631	do
1632	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1633	then
1634	printf " >>> everything o.k. (y/n) ? "
1635	else
1636	break
1637	fi
1638	done
1639	if [[ $antwort = n \|\| $antwort = N ]]
1640	then
1641	locat=user_abort; (( iec = 0 )); exit
1642	fi
1643	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1644	then
1645	printf "\n *** batch-job will be created and submitted"
1646	else
1647	printf "\n *** PALMRUN will now continue to execute on this machine"
1648	fi
1649	fi
1650
1651
1652
1653	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1654	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1655	then
1656
1657	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1658	then
1659	printf "\n\n *** creating executable and other sources for the remote host\n"
1660	else
1661	printf "\n\n *** creating executable and other sources for the local host\n"
1662	fi
1663
1664	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1665	# IT SHALL BE CREATED
1666	ask_for_make_depository=false
1667	if [[ $create_remote_batch_job = true ]]
1668	then
1669
1670	line=`grep %base_directory $config_file`
1671	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1672	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1673
1674	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1675	then
1676	printf "\n\n +++ make depository \"${make_depository}\""
1677	printf "\n on remote host not found!"
1678	ask_for_make_depository=true
1679	fi
1680	rm ${host_configuration}_last_make_protokoll
1681
1682	else
1683
1684	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1685	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1686	if [[ ! -d ${make_depository} ]]
1687	then
1688	printf "\n\n +++ make depository \"${make_depository}\""
1689	printf "\n on local host not found!"
1690	ask_for_make_depository=true
1691	fi
1692
1693	fi
1694
1695	if [[ $ask_for_make_depository = true ]]
1696	then
1697
1698	antwort=dummy
1699	printf "\n\n"
1700	printf " >>> Create a new one (y/n) ? "
1701	while read antwort
1702	do
1703	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1704	then
1705	printf " >>> Create a new one (y/n) ? "
1706	else
1707	break
1708	fi
1709	done
1710	if [[ $antwort = n \|\| $antwort = N ]]
1711	then
1712	locat=user_abort; (( iec = 0 )); exit
1713	fi
1714
1715	if [[ $do_trace = true ]]
1716	then
1717	palmbuild -h $host_configuration
1718	else
1719	palmbuild -v -h $host_configuration
1720	fi
1721
1722	if [[ $? != 0 ]]
1723	then
1724
1725	# ABORT IN CASE OF COMPILATION PROBLEMS
1726	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1727	locat=make_depository
1728	exit
1729	else
1730	echo " *** now continue with creating executable and other sources"
1731	fi
1732
1733	fi
1734
1735	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1736	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
1737
1738	if [[ $? != 0 ]]
1739	then
1740
1741	# ABORT IN CASE OF COMPILATION PROBLEMS
1742	printf "\n +++ error while creating executable and/or other sources"
1743	locat=execution
1744	rm -rf $sources_for_run_catalog
1745	exit
1746
1747	else
1748
1749	printf " *** executable and other sources created\n"
1750	rm -rf $sources_for_run_catalog
1751
1752	fi
1753
1754	fi
1755
1756
1757	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH JOB-ATTRIBUT WILL
1758	# BE COPIED TO THE REMOTE HOST
1759	if [[ $create_remote_batch_job = true ]]
1760	then
1761	(( i = 0 ))
1762	while (( i < nr_of_input_files ))
1763	do
1764	(( i = i + 1 ))
1765	if [[ "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ]]
1766	then
1767	eval inputfile=${pathin[$i]}/${frelin[$i]}
1768	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1769	fi
1770	done
1771	if (( i > 0 ))
1772	then
1773	printf " *** input files have been copied to the remote host\n"
1774	fi
1775	fi
1776
1777
1778	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1779	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1780	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1781	then
1782
1783	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1784	if [[ $running_in_batch_mode = false ]]
1785	then
1786	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1787	# FOLDER
1788	mkdir -p $tempdir
1789	chmod go+rx $tempdir
1790	cd $tempdir
1791	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1792	printf "\n *** changed to temporary directory: $tempdir"
1793
1794	else
1795
1796	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1797	printf "\n *** running in temporary directory: $tempdir"
1798
1799	fi
1800
1801
1802	# PROVIDE THE INPUT FILES
1803	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1804	(( i = 0 ))
1805	while (( i < nr_of_input_files ))
1806	do
1807	(( i = i + 1 ))
1808	if (( i == 1 ))
1809	then
1810	printf "\n\n *** providing INPUT-files:\n$dashes"
1811	fi
1812
1813
1814	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1815	if [[ "${transin[$i]}" = unavailable ]]
1816	then
1817	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1818	then
1819	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1820	printf "\n is not available!"
1821	else
1822	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1823	printf "\n is not available!"
1824	fi
1825	continue
1826	fi
1827
1828	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1829	files_for_cores=false; filetype=file
1830	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1831	then
1832	files_for_cores=true; filetype=files
1833	actionin[$i]=""
1834	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1835	then
1836	actionin[$i]=""
1837	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1838	then
1839	files_for_cores=true; filetype=files
1840	actionin[$i]="ln"
1841	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1842	then
1843	actionin[$i]="ln"
1844	fi
1845
1846	if [[ $files_for_cores = true ]]
1847	then
1848	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1849	else
1850	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1851	fi
1852
1853	# INPUT-FILES TO BE LINKED
1854	if [[ "${actionin[$i]}" = ln ]]
1855	then
1856
1857	printf "\n $filetype will be linked"
1858	if [[ $files_for_cores = false ]]
1859	then
1860	if [[ -f "${absnamein[$i]}" ]]
1861	then
1862	ln ${absnamein[$i]} ${localin[$i]}
1863	got_tmp[$i]=true
1864	fi
1865	else
1866	if [[ -d "${absnamein[$i]}" ]]
1867	then
1868	mkdir -p ${localin[$i]}
1869	cd ${absnamein[$i]}
1870	for file in $(ls *)
1871	do
1872	ln $file $tempdir/${localin[$i]}
1873	done >\|/dev/null 2>&1
1874	cd $tempdir
1875	fi
1876
1877	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1878	if [[ ! -f "${localin[$i]}/_000000" ]]
1879	then
1880	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1881	cp -r ${absnamein[$i]}/* ${localin[$i]}
1882	fi
1883
1884	got_tmp[$i]=true
1885	fi
1886	fi
1887
1888	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1889	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1890	then
1891
1892	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1893	then
1894
1895	# FILE COPIES ARE PROVIDED FOR ALL CORES
1896	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1897	printf "\n file will be provided for $cores processors"
1898	mkdir -p ${localin[$i]}
1899	ival=$cores
1900	(( ii = 0 ))
1901	while (( ii <= ival-1 ))
1902	do
1903	if (( ii < 10 ))
1904	then
1905	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1906	elif (( ii < 100 ))
1907	then
1908	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1909	elif (( ii < 1000 ))
1910	then
1911	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1912	else
1913	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1914	fi
1915	(( ii = ii + 1 ))
1916	done
1917
1918	else
1919
1920	if [[ $files_for_cores = true ]]
1921	then
1922
1923	# PROVIDE FILES FOR EACH CORE
1924	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1925	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1926	printf "\n providing $cores files for the respective cores"
1927	mkdir -p ${localin[$i]}
1928	if [[ $link_local_input = true ]]
1929	then
1930	printf " files will be linked\n"
1931	cd ${absnamein[$i]}
1932	for file in $(ls *)
1933	do
1934	ln -f $file ${localin[$i]}
1935	done
1936	cd $tempdir
1937	fi
1938
1939	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1940	if [[ ! -f "${localin[$i]}/_000000" ]]
1941	then
1942	if [[ $link_local_input = true ]]
1943	then
1944	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1945	fi
1946	cp -r ${absnamein[$i]}/* ${localin[$i]}
1947	fi
1948
1949	else
1950
1951	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1952	if [[ $link_local_input = true ]]
1953	then
1954	printf " file will be linked\n"
1955	ln -f ${absnamein[$i]} ${localin[$i]}
1956	fi
1957	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
1958	if [[ ! -f "${localin[$i]}" ]]
1959	then
1960	if [[ $link_local_input = true ]]
1961	then
1962	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1963	fi
1964	if [[ $running_on_remote = true && ( "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ) ]]
1965	then
1966	mv ${absnamein[$i]} ${localin[$i]}
1967	else
1968	cp ${absnamein[$i]} ${localin[$i]}
1969	fi
1970	fi
1971	fi
1972	fi
1973	fi
1974
1975	done
1976	if (( i != 0 ))
1977	then
1978	printf "\n$dashes\n *** all INPUT-files provided \n"
1979	fi
1980
1981
1982	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1983	(( i = 0 ))
1984	while (( i < iic ))
1985	do
1986	(( i = i + 1 ))
1987	if (( i == 1 ))
1988	then
1989	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1990	fi
1991	printf "\n >>> ${in_command[$i]}"
1992	eval ${in_command[$i]}
1993	if (( i == iic ))
1994	then
1995	printf "\n$dashes\n"
1996	fi
1997	done
1998
1999
2000	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2001	# (FILE ENVPAR WILL BE READ BY PALM)
2002	cat > ENVPAR << EOF
2003	&envpar run_identifier = '$fname', host = '$host_configuration',
2004	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2005	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2006	maximum_cpu_time_allowed = ${cpumax}.,
2007	revision = '$global_revision',
2008	batch_job = .${running_in_batch_mode}. /
2009
2010	EOF
2011
2012
2013	# STARTING THE EXECUTABLE
2014	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2015	PATH=$PATH:$tempdir
2016
2017
2018	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2019	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
2020	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2021	eval line=\"$line\"
2022	execute_command="$line"
2023
2024
2025	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2026	if [[ "$execute_command_for_combine" = "" ]]
2027	then
2028	eval line2=\"$line2\"
2029	execute_command_for_combine="$line2"
2030	fi
2031
2032
2033
2034	# PROVIDE A HOSTFILE, IF REQUIRED
2035	if [[ "$hostfile" != "" ]]
2036	then
2037
2038	if [[ $hostfile = auto ]]
2039	then
2040	# CREATE A NEW HOSTFILE
2041	(( ii = 1 ))
2042	while (( ii <= cores / threads_per_task ))
2043	do
2044	echo $(hostname) >> hostfile
2045	(( ii = ii + 1 ))
2046	done
2047	if (( cores / threads_per_task == 0 ))
2048	then
2049	echo $(hostname) >> hostfile
2050	fi
2051
2052	else
2053	cp $hostfile hostfile
2054	fi
2055	eval line=\"`head -n $ii hostfile`\"
2056	printf "\n *** running on: $line"
2057	fi
2058
2059
2060
2061	# SET THE NUMBER OF OPENMP-THREADS
2062	if [[ $use_openmp = true ]]
2063	then
2064	export OMP_NUM_THREADS=$threads_per_task
2065	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2066	else
2067	export OMP_NUM_THREADS=1
2068	fi
2069
2070
2071	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2072	if [[ $run_coupled_model = false ]]
2073	then
2074	if [[ "$ocean_file_appendix" = true ]]
2075	then
2076	echo "precursor_ocean" > coupling_steering
2077	else
2078	echo "precursor_atmos" > coupling_steering
2079	fi
2080	else
2081	(( iia = $cores_atmos / $threads_per_task ))
2082	(( iio = $cores_ocean / $threads_per_task ))
2083	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2084	printf "\n\n"
2085	echo "coupled_run $iia $iio" > coupling_steering
2086	fi
2087
2088	printf "\n *** execute command:"
2089	printf "\n \"$execute_command\" \n\n"
2090
2091	$execute_command < coupling_steering
2092
2093	if [[ $? != 0 ]]
2094	then
2095
2096	# ABORT IN CASE OF RUNTIME ERRORS
2097	printf "\n +++ runtime error occured"
2098	locat=execution
2099	exit
2100
2101	else
2102
2103	printf "\n$dashes\n *** execution finished \n"
2104
2105	fi
2106
2107
2108	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2109	# BY EACH CORE INTO ONE FILE
2110	if [[ ! -f combine_plot_fields.x ]]
2111	then
2112
2113	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2114	printf "\n 2d- and/or 3d-data may be incomplete!"
2115	printf "\n Your previous palmbuild may have failed. Please check.\n"
2116
2117	elif [[ "$combine_plot_fields" == true ]]
2118	then
2119
2120	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2121	$execute_command_for_combine
2122
2123	else
2124
2125	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2126	# DATA OUTPUT
2127	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2128	fi
2129
2130
2131
2132	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2133	(( i = 0 ))
2134	while (( i < ioc ))
2135	do
2136	(( i = i + 1 ))
2137	if (( i == 1 ))
2138	then
2139	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2140	fi
2141	printf "\n >>> ${out_command[$i]}"
2142	eval ${out_command[$i]}
2143	if (( i == ioc ))
2144	then
2145	printf "\n$dashes\n"
2146	fi
2147	done
2148
2149
2150	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2151	# WILDCARDS
2152	(( i = 0 ))
2153	(( nr_of_output_files = 0 ))
2154
2155	while (( i < iout ))
2156	do
2157
2158	(( i = i + 1 ))
2159
2160	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2161	# CREATE A LIST FOR THE DETECTED ENDINGS
2162	if [[ "${multout[$i]}" = true ]]
2163	then
2164	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2165	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2166	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2167
2168	endings="DEFAULT"
2169	while read line
2170	do
2171	# remove the local name from the beginning
2172	localnamestring="${localout_pre[$i]}"
2173	length_localname=${#localnamestring}
2174	ending=${line:${length_localname}}
2175
2176	if [[ "$ending" != "" ]]
2177	then
2178	endings="$endings $ending"
2179	fi
2180
2181	done <filelist
2182
2183	rm filelist
2184
2185	else
2186
2187	# SINGLE NAME
2188	endings=DEFAULT
2189
2190	fi
2191
2192	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2193	for ending in $endings
2194	do
2195
2196	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2197	if [[ $ending = DEFAULT ]]
2198	then
2199	ending=""
2200	fi
2201
2202	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2203	(( nr_of_output_files = nr_of_output_files + 1 ))
2204	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2205	transout[$nr_of_output_files]="${transout_pre[$i]}"
2206	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2207	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2208	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2209	extout[$nr_of_output_files]="${extout_pre[$i]}"
2210
2211	done
2212
2213	done
2214
2215
2216
2217
2218	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2219	(( i = 0 ))
2220	while (( i < nr_of_output_files ))
2221	do
2222	(( i = i + 1 ))
2223	if (( i == 1 ))
2224	then
2225	printf "\n\n *** saving OUTPUT-files:"
2226
2227	# GET RUN NUMBER ASSIGNED BY PALM
2228	if [[ -f RUN_NUMBER ]]
2229	then
2230	read run_number < RUN_NUMBER
2231	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2232	usecycle_option="-U $run_number"
2233	else
2234	run_number=0
2235	usecycle_option=""
2236	fi
2237	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2238	then
2239	printf "\n *** in case of SCP transfers to local host"
2240	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2241	fi
2242	printf "\n$dashes"
2243	fi
2244
2245	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2246	then
2247
2248	eval filename=${pathout[$i]}/${fname}${endout[$i]}
2249
2250	# DETERMINE THE CYCLE NUMBER
2251	ls -1 -d $filename > filelist 2>/dev/null
2252	ls -1 -d $filename.* >> filelist 2>/dev/null
2253	while read line
2254	do
2255
2256	# filename without path (i.e. after the last "/")
2257	basefilename=$(basename ${line})
2258
2259	# check if there is an extension
2260	extension=${basefilename##*.}
2261	if [[ "$extension" = "${extout[$i]}" ]]
2262	then
2263	basefilename=${basefilename%.*}
2264	fi
2265
2266	# check for an existing cycle number
2267	cycle=${basefilename##*.}
2268	if [[ $cycle =~ ^-?[0-9]+$ ]]
2269	then
2270	(( icycle = $cycle + 1 ))
2271	else
2272	(( icycle = 1 ))
2273	fi
2274
2275	if (( icycle > maxcycle ))
2276	then
2277	(( maxcycle = icycle ))
2278	fi
2279
2280	done <filelist
2281	rm filelist
2282
2283
2284	# SET THE CYCLE NUMBER
2285	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2286	if [[ "${actionout[$i]}" = a ]]
2287	then
2288	(( maxcycle = maxcycle - 1 ))
2289	fi
2290
2291	(( cycnum[$i] = maxcycle ))
2292	pathout[$i]=$filename
2293
2294
2295	# ADD CYCLE NUMBER TO FILENAME
2296	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2297	if [[ "${actionout[$i]}" != "a" ]]
2298	then
2299	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2300	# WITH AN EXISTING CYCLE NUMBER
2301	if (( run_number >= cycnum[$i] ))
2302	then
2303	(( cycnum[$i] = run_number ))
2304	else
2305	if (( run_number > 0 ))
2306	then
2307	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2308	fi
2309	fi
2310	fi
2311	if (( cycnum[$i] > 0 ))
2312	then
2313	cyclestring=`printf "%03d" ${cycnum[$i]}`
2314	pathout[$i]=${pathout[$i]}.$cyclestring
2315	fi
2316	fi
2317
2318	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2319	files_for_cores=false; filetype=file
2320	link_local_output=false
2321	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2322	then
2323	files_for_cores=true; filetype=directory
2324	actionout[$i]=""
2325	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2326	then
2327	actionout[$i]=""
2328	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2329	then
2330	files_for_cores=true; filetype=directory
2331	link_local_output=true
2332	actionout[$i]=""
2333	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2334	then
2335	link_local_output
2336	actionout[$i]=""
2337	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2338	then
2339	files_for_cores=true; filetype=directory
2340	actionout[$i]="tr"
2341	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2342	then
2343	actionout[$i]="tr"
2344	fi
2345
2346	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2347	then
2348	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2349	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2350	then
2351	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2352	else
2353
2354
2355	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2356	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2357	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2358	then
2359	if [[ $running_on_remote = true ]]
2360	then
2361
2362	# SET OPTIONS FOR TRANSFER
2363	if [[ "${actionout[$i]}" = tr ]]
2364	then
2365	if [[ $files_for_cores = false ]]
2366	then
2367	catalog_option=""
2368	catalog_string=""
2369	else
2370	catalog_option="-c"
2371	catalog_string="/"
2372	fi
2373	append_option=""
2374	append_string=""
2375	else
2376	append_option="-A"
2377	append_string="append"
2378	fi
2379
2380	transfer_failed=false
2381	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2382	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2383
2384	# TRANSFER VIA SCP
2385	if [[ "$remote_loginnode" != "" ]]
2386	then
2387	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
2388	else
2389	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]}
2390	fi
2391	[[ $? != 0 ]] && transfer_failed=true
2392
2393
2394	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2395	if [[ $transfer_failed = true ]]
2396	then
2397	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2398	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2399
2400	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2401	eval local_catalog=${pathout[$i]}
2402	if [[ ! -d $local_catalog ]]
2403	then
2404	printf " *** local directory does not exist. Trying to create:\n"
2405	printf " $local_catalog \n"
2406	mkdir -p $local_catalog
2407	fi
2408	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2409	transfer_problems=true
2410	fi
2411
2412	else
2413
2414	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2415	# BE COPIED OR APPENDED ON THIS MACHINE
2416	if [[ "${actionout[$i]}" = tr ]]
2417	then
2418	actionout[$i]=""
2419	else
2420	actionout[$i]="a"
2421	fi
2422	fi
2423	fi
2424
2425
2426	# APPEND ON THIS MACHINE
2427	if [[ "${actionout[$i]}" = "a" ]]
2428	then
2429	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2430	then
2431	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2432	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2433	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2434	else
2435	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2436	printf "\n ${pathout[$i]}\n"
2437	cat ${localout[$i]} >> ${pathout[$i]}
2438	fi
2439	fi
2440
2441	# COPY ON THIS MACHINE
2442	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2443	# ON DIFFERENT FILE-SYSTEMS
2444	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2445	then
2446
2447	# COPY IN CASE OF RUNS ON SINGLE CORES
2448	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2449	then
2450	printf "\n >>> OUTPUT: ${localout[$i]} to"
2451	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2452	if [[ $link_local_output = true ]]
2453	then
2454	printf " file will be linked\n"
2455	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2456	fi
2457	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2458	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2459	then
2460	if [[ $link_local_output = true ]]
2461	then
2462	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2463	fi
2464	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2465	else
2466	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2467	fi
2468	else
2469	printf "\n >>> OUTPUT: ${localout[$i]} to"
2470	printf "\n ${pathout[$i]}\n"
2471	if [[ $link_local_output = true ]]
2472	then
2473	printf " file will be linked\n"
2474	ln -f ${localout[$i]} ${pathout[$i]}
2475	fi
2476	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2477	if [[ ! -f "${pathout[$i]}" ]]
2478	then
2479	if [[ $link_local_output = true ]]
2480	then
2481	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2482	fi
2483	cp ${localout[$i]} ${pathout[$i]}
2484	else
2485	printf "+++ no copy because file ${pathout[$i]} exists\n"
2486	fi
2487	fi
2488
2489	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2490	then
2491
2492	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2493	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2494	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2495	printf "\n ${pathout[$i]}\n"
2496	if [[ $link_local_output = true ]]
2497	then
2498	printf " files will be linked\n"
2499	mkdir -p ${pathout[$i]}
2500	cd ${localout[$i]}
2501	for file in $(ls *)
2502	do
2503	ln -f $file ${pathout[$i]}
2504	done >\|/dev/null 2>&1
2505	cd $tempdir
2506	fi
2507
2508	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2509	if [[ ! -f "${pathout[$i]}/_000000" ]]
2510	then
2511	if [[ $link_local_output = true ]]
2512	then
2513	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2514	fi
2515	cp -r ${localout[$i]}/* ${pathout[$i]}
2516	fi
2517
2518	fi
2519	fi
2520	done
2521
2522	if (( i != 0 ))
2523	then
2524	if [[ $transfer_problems = true ]]
2525	then
2526	printf "\n$dashes\n *** OUTPUT-files saved"
2527	printf "\n +++ WARNING: some data transfers failed! \n"
2528	else
2529	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2530	fi
2531	fi
2532
2533
2534	# IF REQUIRED, START A RESTART-JOB
2535	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2536	if [[ -f CONTINUE_RUN ]]
2537	then
2538
2539	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2540	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2541	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2542	# -b START A BATCH JOB
2543	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2544	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2545	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2546
2547
2548	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2549	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2550	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2551	then
2552	prc=`echo $prc \| sed 's/#/r/g'`
2553	fi
2554
2555
2556	# START THE RESTART-JOB
2557	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2558	echo " $prc"
2559	printf "\n$dashes\n"
2560	if [[ $running_on_remote = true ]]
2561	then
2562
2563	echo "*** ssh will be used to initiate restart-runs!"
2564	echo " return_address=\"$return_address\" "
2565	echo " return_username=\"$local_username\" "
2566
2567	if [[ "$remote_loginnode" != "" ]]
2568	then
2569	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
2570	else
2571	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2572	fi
2573
2574	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2575	sleep 30
2576
2577	else
2578
2579	# START THE RESTART JOB ON THE LOCAL HOST
2580	eval $prc # THE ' MUST BE EVALUATED
2581	cd - > /dev/null
2582
2583	fi
2584	printf "\n$dashes\n *** restart-run initiated \n"
2585
2586
2587	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2588	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2589	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2590	# MAY BE VERY HUGE)
2591	(( i = 0 ))
2592	while (( i < nr_of_input_files ))
2593	do
2594	(( i = i + 1 ))
2595	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2596	then
2597	rm -r ${absnamein[$i]}
2598	fi
2599	done
2600
2601	fi
2602
2603
2604	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2605	cd $HOME
2606	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2607
2608
2609	else
2610
2611
2612	# PREPARING ACTIONS,
2613	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2614
2615	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2616	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2617	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2618	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2619	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2620	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2621	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2622	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2623	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2624	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2625	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2626	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2627	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2628	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2629	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2630	if [[ $create_remote_batch_job = true ]]
2631	then
2632	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2633	if [[ $do_trace = true ]]
2634	then
2635	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2636	fi
2637	elif [[ $create_batch_job = true ]]
2638	then
2639	palmrun_com=${palmrun_com}" -j"
2640	if [[ $do_trace = true ]]
2641	then
2642	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2643	fi
2644	fi
2645
2646
2647	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2648	# REMOTE HOST
2649	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2650	job_protocol_file=$job_protocol_file_local
2651	if [[ $create_remote_batch_job = true ]]
2652	then
2653	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2654	job_protocol_file=$job_protocol_file_remote
2655	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2656	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2657	fi
2658
2659
2660	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2661	jobfile=jobfile.$run_id
2662
2663
2664	# FIRST CREATE THE BATCH DIRECTIVES
2665	(( i = 0 ))
2666	while (( i < ibd ))
2667	do
2668	(( i = i + 1 ))
2669	line=`echo "${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'`
2670	eval line=\"$line\"
2671	echo "$line" >> $jobfile
2672	done
2673	echo " " >> $jobfile
2674
2675
2676	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2677	# PROTOCOL
2678	if [[ $create_remote_batch_job = true ]]
2679	then
2680	echo "set +vx" >> $jobfile
2681	echo "trap '" >> $jobfile
2682	echo "set +vx" >> $jobfile
2683	echo "cd ${remote_jobcatalog}" >> $jobfile
2684	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2685
2686	# ADD THE BATCH DIRECTIVES
2687	(( i = 0 ))
2688	while (( i < ibdt ))
2689	do
2690	(( i = i + 1 ))
2691	line=`echo "${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'`
2692	eval line=\"$line\"
2693	echo "$line" >> $jobfile
2694	done
2695	echo " " >> $jobfile
2696
2697	echo "set -x" >> $jobfile
2698	echo "${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
2699	echo "%%END%%" >> $jobfile
2700	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2701	echo "$submit_command $scpjob_file" >> $jobfile
2702	echo "rm $scpjob_file" >> $jobfile
2703	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2704	echo "set -x" >> $jobfile
2705	echo " ' exit" >> $jobfile
2706	fi
2707
2708
2709	# ACTIVATE ERROR-TRACEBACK
2710	if [[ $do_trace = true ]]
2711	then
2712	echo "set -x" >> $jobfile
2713	else
2714	echo "set +vx" >> $jobfile
2715	fi
2716
2717
2718	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2719	if [[ "$login_init_cmd" != "" ]]
2720	then
2721	echo "$login_init_cmd" >> $jobfile
2722	fi
2723	if [[ "$module_commands" != "" ]]
2724	then
2725	echo "$module_commands" >> $jobfile
2726	fi
2727
2728
2729	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2730	if [[ $create_remote_batch_job = true ]]
2731	then
2732	echo "mkdir $tempdir" >> $jobfile
2733	echo "chmod go+rx $tempdir" >> $jobfile
2734	else
2735	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2736	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2737	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2738	mkdir $tempdir
2739	chmod go+rx $tempdir
2740	fi
2741	echo "cd $tempdir" >> $jobfile
2742	echo "export tempdir=$tempdir" >> $jobfile
2743	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2744	echo "export PATH=.:\$PATH" >> $jobfile
2745	echo "export execute_palmrun=true" >> $jobfile
2746
2747
2748	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2749	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2750	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2751	echo "LOCAL_PWD=$working_directory" >> $jobfile
2752	echo "export LOCAL_PWD" >> $jobfile
2753
2754
2755	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2756	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2757	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2758
2759
2760	# CALL PALMRUN WITHIN THE JOB
2761	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2762	echo "set -x" >> $jobfile
2763	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2764
2765
2766	# TRANSFER JOBFILE TO THE TARGET HOST
2767	if [[ $create_jobfile_only = false ]]
2768	then
2769
2770	if [[ $create_remote_batch_job = true ]]
2771	then
2772
2773	echo " "
2774	echo " *** transfer of job to remote host via scp"
2775	if [[ $do_trace = true ]]
2776	then
2777	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2778	fi
2779	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2780
2781	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2782	if [[ $do_trace = true ]]
2783	then
2784	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"
2785	fi
2786	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
2787
2788	elif [[ $create_batch_job = true ]]
2789	then
2790
2791	eval local_jobcatalog=$local_jobcatalog
2792	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2793	cd $local_jobcatalog
2794	echo " "
2795	echo " *** submit the job"
2796	if [[ $do_trace = true ]]
2797	then
2798	echo "$submit_command ${host_configuration}_${job_id}"
2799	fi
2800	$submit_command ${host_configuration}_${job_id}
2801	rm ${host_configuration}_${job_id}
2802	cd - > /dev/null
2803
2804	fi
2805
2806	rm -rf $jobfile
2807
2808	else
2809
2810	printf "\n *** jobfile created under name \"$jobfile\" "
2811	printf "\n no batch-job has been sent!"
2812
2813	fi
2814
2815	fi # END OF REMOTE-PART

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