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source: palm/trunk/SCRIPTS/palmrun @ 3045

Last change on this file since 3045 was 3043, checked in by raasch, 6 years ago
check for setting of fast_io_catalog, update of default .palm.config.default
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 97.8 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 3043 2018-05-25 10:47:54Z Giersch $
29	# check for setting of fast_io_catalog
30	#
31	# 3033 2018-05-23 15:26:19Z raasch
32	# -T option not required for interactive runs (tasks per node =
33	# total number of cores is assumed as default, if option is not given),
34	# reformatting of a few messages,
35	# bugfix: destination output directory is created if attribute "pe" is set in
36	# .palm.iofiles
37	#
38	# 2718 2018-01-02 08:49:38Z maronga
39	# bugfix of r2990
40	#
41	# 2718 2018-01-02 08:49:38Z maronga
42	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
43	# not in the working directory from where palmrun is called
44	#
45	# 2718 2018-01-02 08:49:38Z maronga
46	# svfout in the activation string will be replaced now by svfin in case of
47	# automatic restarts
48	#
49	# 2718 2018-01-02 08:49:38Z maronga
50	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
51	# the possible output or input of sky view factors
52	#
53	# 2718 2018-01-02 08:49:38Z maronga
54	# "fname" renamed to "jobname"
55	#
56	# 2718 2018-01-02 08:49:38Z maronga
57	# parameters are allowed in output commands (OC:)
58	#
59	# 2718 2018-01-02 08:49:38Z maronga
60	# bugfix: exit if no queue has been given neither with option -q nor in the
61	# configuration file
62	#
63	# 2718 2018-01-02 08:49:38Z maronga
64	# file connection file from trunk/SCRIPTS is taken by default
65	#
66	# 2718 2018-01-02 08:49:38Z maronga
67	# Corrected "Former revisions" section
68	#
69	# 2696 2017-12-14 17:12:51Z kanani
70	# Change in file header (GPL part)
71	#
72	# 2693 2017-12-13 12:33:49Z raasch
73	# replacement of variables given by {{<variable>}} in configuration file is now
74	# done in a more general way, variable names are written in small letters
75	#
76	# 2670 2017-12-06 16:32:19Z raasch
77	# test printouts removed
78	#
79	# 2669 2017-12-06 16:03:27Z raasch
80	# file attributes in .palm.iofiles restructured, "loc" attribute completely
81	# removed,
82	# wildcard (*) allowed in .palm.iofiles as file activation string for output
83	# files,
84	# informative messages in case of missing optional input files shortened
85	# bugfix: variable cycle explicitly interpreted with 10 as the number base
86	#
87	# 2638 2017-11-23 12:44:23Z raasch
88	# use of wildcards in file connection statements enabled
89	#
90	# 2605 2017-11-09 15:31:46Z raasch
91	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
92	# will not be sent with the job file any more, but copied into the
93	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
94	#
95	# 2600 2017-11-01 14:11:20Z raasch
96	# cycle numbers are made three digits wide
97	#
98	# 2566 2017-10-20 08:50:47Z raasch
99	# execute command for combine_plot_fields added
100	# "TEMPDIR" renamed "tempdir"
101	# temporary working directory for local batch jobs is created immediately within
102	# the user's palmrun call, due to a requirement of the "grid engine" batch
103	# system, where the working directory is given with batch directive -wd and must
104	# already exist when the job is submitted,
105	# informative messages in non-trace mode reduced and partly reformatted
106	#
107	# 2551 2017-10-18 07:25:11Z raasch
108	# TEMPDIR added as replacement string to be used in batch directives
109	#
110	# 2512 2017-10-04 08:26:59Z raasch
111	# bugfix for determining cycle numbers of NetCDF input files
112	#
113	# 2506 2017-09-29 08:30:37Z raasch
114	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
115	# host configuration added to SOURCES_FOR_RUN_... folder name
116	# host_identifier renamed host_configuration
117	# option -W added to allow for job dependencies
118	#
119	# 2501 2017-09-26 11:41:55Z raasch
120	# default value for number of cores (option -X) set to 1
121	# bugfix for mechanism which overwrites configuration file settings with values
122	# provided by palmrun options
123	#
124	# 2499 2017-09-22 16:47:58Z kanani
125	# option -h named configuration identifier
126	#
127	# 2480 2017-09-19 06:24:14Z maronga
128	# bugfix for last revision
129	#
130	# 2479 2017-09-19 06:12:16Z raasch
131	# option -A (project account number) added
132	#
133	# 2422 2017-09-08 08:25:41Z raasch
134	# initial revision
135	#
136	#--------------------------------------------------------------------------------#
137	# palmrun - script for running PALM jobs on local and remote hosts
138	#--------------------------------------------------------------------------------#
139
140
141
142	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
143
144	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
145	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
146	# (TOO MANY ARGUMENTS - PROBLEM)
147	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
148
149	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
150	typeset -i nr_of_output_files=0
151	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
152	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
153	# SCRIPT-OPTION ARGUMENTS
154	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
155	typeset -i icycle inode ival maxcycle mpi_tasks
156	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
157
158	activation_string_list=""
159	AddFilenames=""
160	combine_plot_fields=true
161	compiler_name=""
162	compiler_name_ser=""
163	compiler_options=""
164	cores=1
165	cores_atmos=0
166	cores_ocean=0
167	coupled_dist=""
168	cpp_options=""
169	cpumax=0
170	create_batch_job=false
171	create_jobfile_only=false
172	create_remote_batch_job=false
173	dashes=" ----------------------------------------------------------------------------"
174	defaultqueue=""
175	delete_temporary_catalog=true
176	do_compile=true
177	do_trace=false
178	executable=""
179	execute_command=""
180	execution_error=false
181	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
182	jobname=test
183	global_revision=""
184	host_configuration="default"
185	hostfile=""
186	hp=""
187	keep_data_from_previous_run=false
188	link_local_input=false
189	link_local_output=false
190	linker_options=""
191	local_jobcatalog=""
192	locat=normal
193	makefile=""
194	max_par_io_str=""
195	prc=$0
196	while [[ $(echo $prc \| grep -c "/") != 0 ]]
197	do
198	prc=`echo $prc \| cut -f2- -d"/"`
199	done
200	module_calls=""
201	palmrun_memory=""
202	palmrun_script_name=$prc
203	openmp=false
204	previous_job=""
205	project_account=""
206	queue=none
207	read_svf=""
208	restart_run=false
209	return_address=""
210	remote_jobcatalog=""
211	remote_username=""
212	running_in_batch_mode=false
213	run_coupled_model=false
214	run_id=""
215	silent=false
216	source_list=""
217	source_path=""
218	tasks_per_node=0
219	threads_per_task=1
220	transfer_problems=false
221	user_source_path=""
222	use_existing_sources_folder=""
223	use_openmp=false
224	version="palmrun 1.0 Rev$Rev: 3043 $"
225	working_directory=`pwd`
226	write_binary=""
227	write_svf=""
228
229
230	# ERROR HANDLING IN CASE OF EXIT
231	trap 'if [[ $locat != normal && $locat != control_c ]]
232	then
233
234	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
235	(( i = 0 ))
236	while (( i < iec ))
237	do
238	(( i = i + 1 ))
239	printf "\n *** Execution of ERROR-command:\n"
240	printf " >>> ${err_command[$i]}\n"
241	eval ${err_command[$i]}
242	done
243	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
244	printf "\n\n+++ palmrun killed \n\n"
245	elif [[ $locat != control_c ]]
246	then
247	printf "\n --> palmrun finished\n\n"
248	fi' exit
249
250
251	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
252	trap 'cd; rm -rf $tempdir
253	printf "\n+++ palmrun killed by \"^C\" \n\n"
254	locat=control_c
255	exit
256	' 2
257
258
259	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
260	# WHICH WILL BE USED TO START RESTART-JOBS
261	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
262	do
263	case $option in
264	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
265	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
266	(b) create_batch_job=true; prc="$prc -b";;
267	(B) delete_temporary_catalog=false; prc="$prc -B";;
268	(C) restart_run=true; prc="$prc -C";;
269	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
270	(F) create_jobfile_only=true;;
271	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
272	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
273	(j) running_in_batch_mode=true;;
274	(k) keep_data_from_previous_run=true; prc="$prc -k";;
275	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
276	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
277	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
278	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
279	(r) run_id=$OPTARG;;
280	(R) return_address=$OPTARG;;
281	(s) source_list=$OPTARG;;
282	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
283	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
284	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
285	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
286	(v) silent=true; prc="$prc -v";;
287	(V) use_existing_sources_folder="-V";;
288	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
289	(W) previous_job=$OPTARG;;
290	(x) do_trace=true;set -x; prc="$prc -x";;
291	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
292	(y) ocean_file_appendix=true; prc="$prc -y";;
293	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
294	(Z) combine_plot_fields=false; prc="$prc -Z";;
295	(\?) printf "\n +++ unknown option $OPTARG \n"
296	printf "\n --> type \"$0 ?\" for available options \n"
297	locat=parameter;exit;;
298	esac
299	done
300
301
302	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
303	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
304	(( to_shift = $OPTIND - 1 ))
305	shift $to_shift
306
307	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
308	if [[ "$1" = "?" ]]
309	then
310	(printf "\n *** Description of available palmrun options:\n"
311	printf "\n Option Description Default-Value"
312	printf "\n -a activation string list \"\" "
313	printf "\n -A project account number ---"
314	printf "\n -b batch-job on local machine ---"
315	printf "\n -B do not delete temporary directory at end ---"
316	printf "\n -d run identifier test"
317	printf "\n -F create batch job file only ---"
318	printf "\n -h host configuration \"default\" "
319	printf "\n -k keep data from previous run"
320	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
321	printf "\n -M Makefile name Makefile"
322	printf "\n -O threads per openMP task ---"
323	printf "\n -q queue \"$queue\" "
324	printf "\n -s filenames of routines to be compiled \"\" "
325	printf "\n must end with .f, .f90, .F, or .c !"
326	printf "\n use \"..\" for more than one file and wildcards"
327	printf "\n -s LM compiles all locally modified files"
328	printf "\n -t allowed cpu-time in seconds (batch) 0"
329	printf "\n -T tasks per node ---"
330	printf "\n -u username on remote machine \"\" "
331	printf "\n -v no prompt for confirmation ---"
332	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
333	printf "\n -w maximum parallel io streams as given by -X"
334	printf "\n -W name of job to wait for ---"
335	printf "\n -x tracing of palmrun for debug purposes ---"
336	printf "\n -X # of processors (on parallel machines) 1"
337	printf "\n -y add appendix \"_O\" to all local output"
338	printf "\n files (ocean precursor runs followed by"
339	printf "\n coupled atmosphere-ocean runs) ---"
340	printf "\n -Y run coupled model, \"#1 #2\" with"
341	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
342	printf "\n -Z skip combine_plot_fields at the end of "
343	printf "\n the simulation ---"
344	printf "\n "
345	printf "\n Possible values of positional parameter <modus>:"
346	printf "\n \"?\" - this outline \n\n") \| more
347	exit
348	elif [[ "$1" != "" ]]
349	then
350	printf "\n +++ positional parameter $1 unknown \n"
351	locat=parameter; exit
352	fi
353
354
355
356	# SHORT STARTING MESSAGE
357	printf "\n*** $version "
358	printf "\n will be executed. Please wait ..."
359
360
361	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
362	export fname=$jobname
363
364
365	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
366	config_file=.palm.config.$host_configuration
367	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
368
369
370	# CHECK, IF CONFIGURATION FILE EXISTS
371	if [[ ! -f $config_file ]]
372	then
373	printf "\n\n +++ configuration file: "
374	printf "\n $config_file"
375	printf "\n does not exist"
376	locat=connect; exit
377	fi
378
379
380	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
381	if [[ -f .palm.iofiles ]]
382	then
383	fileconnection_file=.palm.iofiles
384	fi
385
386
387	# CHECK, IF FILE CONNECTION FILE EXISTS
388	if [[ ! -f $fileconnection_file ]]
389	then
390	printf "\n\n +++ file connection file: "
391	printf "\n $fileconnection_file"
392	printf "\n does not exist"
393	locat=connect; exit
394	fi
395
396
397	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
398	if [[ "$activation_string_list" = "" ]]
399	then
400	printf "\n\n +++ no activation string list given: "
401	printf "\n please set palmrun option \"-a\" "
402	locat=palmrun_option; exit
403	fi
404
405
406	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
407	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
408	then
409	write_binary=true
410	else
411	write_binary=false
412	fi
413
414	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
415	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
416	then
417	write_svf=true
418	else
419	write_svf=false
420	fi
421
422	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
423	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
424	then
425	read_svf=true
426	else
427	read_svf=false
428	fi
429
430
431	# READ AND EVALUATE THE CONFIGURATION-FILE
432	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
433
434	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
435	while read line
436	do
437
438	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
439	eval line=\"$line\"
440
441
442	# INTERPRET THE LINE
443	if [[ "$(echo $line)" = "" ]]
444	then
445
446	# EMPTY LINE, NO ACTION
447	continue
448
449	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
450	then
451
452	# LINE IS A COMMENT LINE
453	continue
454
455	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
456	then
457
458	# LINE DEFINES AN ENVIRONMENT-VARIABLE
459	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
460	value=`echo $line \| cut -d" " -s -f2-`
461
462
463	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
464	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
465	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
466	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
467	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
468	# CONFIGURATION-FILE.
469	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
470	then
471	eval export $var="\$value"
472
473	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
474	if [[ $do_trace = true ]]
475	then
476	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
477	fi
478	fi
479
480	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
481	then
482
483	# LINE DEFINES BATCH-DIRECTIVE
484	(( ibd = ibd + 1 ))
485	line=$(echo $line \| cut -c4-)
486	batch_directive[$ibd]="$line"
487
488	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
489	then
490
491	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
492	# REMOTE TO A LOCAL HOST
493	(( ibdt = ibdt + 1 ))
494	line=$(echo $line \| cut -c5-)
495	batch_directive_transfer[$ibdt]="$line"
496
497	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
498	then
499
500	# LINE DEFINES ERROR-COMMAND
501	(( iec = iec + 1 ))
502	line=$(echo $line \| cut -c4-)
503	err_command[$iec]="$line"
504
505	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
506	then
507
508	# LINE DEFINES INPUT-COMMAND
509	(( iic = iic + 1 ))
510	line=$(echo $line \| cut -c4-)
511	in_command[$iic]="$line"
512
513	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
514	then
515
516	# LINE DEFINES OUTPUT-COMMAND
517	(( ioc = ioc + 1 ))
518	line=$(echo $line \| cut -c4-)
519	out_command[$ioc]="$line"
520
521	else
522
523	# SKIP ALL OTHER LINES
524	continue
525
526	fi
527
528	done < $config_file
529
530
531	# CHECK SETTING OF REQUIRED PARAMETERS
532	if [[ "$fast_io_catalog" = "" ]]
533	then
534	printf "\n +++ no fast_io_catalog found in $config_file"
535	printf "\n Please add line \"fast_io_catalog ...\" to that file."
536	locat=config_file; exit
537	fi
538	if [[ "$compiler_name" = "" ]]
539	then
540	printf "\n +++ no compiler name found in $config_file"
541	printf "\n Please add line \"compiler_name ...\" to that file."
542	locat=config_file; exit
543	fi
544	if [[ "$compiler_name_ser" = "" ]]
545	then
546	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
547	printf "\n Please add line \"compiler_name_ser ...\" to that file."
548	locat=config_file; exit
549	fi
550	if [[ "$compiler_options" = "" ]]
551	then
552	printf "\n +++ no compiler options found in $config_file"
553	printf "\n Please add line \"compiler_options ...\" to that file."
554	locat=config_file; exit
555	fi
556	if [[ "$linker_options" = "" ]]
557	then
558	printf "\n +++ no linker options found in $config_file"
559	printf "\n Please add line \"linker_options ...\" to that file."
560	locat=config_file; exit
561	fi
562	if [[ "$execute_command" = "" ]]
563	then
564	printf "\n +++ no execute command found in $config_file"
565	printf "\n Please add line \"execute_command ...\" to that file."
566	locat=config_file; exit
567	fi
568
569	if [[ "$hostfile" != "" ]]
570	then
571	if [[ $hostfile != auto && ! -f $hostfile ]]
572	then
573	printf "\n +++ no hostfile \"$hostfile\" found"
574	printf "\n Please check line \"%hostfile ...\" in $config_file"
575	locat=config_file; exit
576	fi
577	fi
578
579
580	# DETERMINE THE CALL STATUS
581	if [[ "$return_address" != "" ]]
582	then
583
584	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
585	# BATCH MODE AND ...
586	running_on_remote=true
587
588	else
589
590	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
591	if [[ "$remote_ip" != "" ]]
592	then
593
594	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
595	create_remote_batch_job=true
596
597	fi
598	running_on_remote=false
599	fi
600
601
602
603	# READ AND EVALUATE THE I/O-FILE LIST
604	[[ $silent = false ]] && printf "\n Reading the I/O files... "
605
606	# READ THE FILE CONNECTION FILE LINE BY LINE
607	while read line
608	do
609
610	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
611	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
612
613	# INTERPRET THE LINE
614	if [[ "$(echo $line)" = "" ]]
615	then
616	# EMPTY LINE, NO ACTION
617	continue
618
619	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
620	then
621
622	# LINE IS A COMMENT LINE
623	true
624
625	else
626
627	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
628	# s2a: in/out - field
629	# s2b: action - field (optional)
630	s1=`echo "$line" \| cut -d" " -f1`
631	s2=`echo "$line" \| cut -d" " -s -f2`
632	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
633	then
634	s2a=$s2
635	s2b=""
636	else
637	s2a=`echo $s2 \| cut -d":" -f1`
638	s2b=`echo $s2 \| cut -d":" -f2`
639	fi
640	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
641	s4=`echo "$line" \| cut -d" " -s -f4`
642	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
643	s5=`echo "$line" \| cut -d" " -s -f5`
644	s6=`echo "$line" \| cut -d" " -s -f6`
645
646
647	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
648	# INPUT- OR OUTPUT-LIST.
649	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
650	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
651	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
652	# IS NOT CHECKED AND STORED.
653	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
654	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
655	then
656	found=false
657	for actual in $activation_string_list
658	do
659	for formal in $s3
660	do
661	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
662	done
663	done
664	if [[ $found = true ]]
665	then
666	(( iin = iin + 1 ))
667	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
668	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
669	if [[ "$s2a" = inopt ]]
670	then
671	optin_pre[$iin]=yes
672	else
673	optin_pre[$iin]=no
674	fi
675
676	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
677	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
678	if [[ $running_on_remote = true && "$s2b" = tr ]]
679	then
680	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
681	fi
682
683	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
684	# THE WILDCARD FROM THE ENDING
685	if [[ "${s5: -1}" = "*" ]]
686	then
687	if [[ "$s2b" = "di" ]]
688	then
689	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
690	printf "\n see file \"$fileconnection_file\", line"
691	printf "\n$line"
692	locat=iofiles_file; exit
693	fi
694	multin[$iin]=true
695	string=${endin_pre[$iin]}
696	endin_pre[$iin]="${string%?}"
697	else
698	multin[$iin]=false
699	fi
700	fi
701	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
702	then
703	found=false
704	for actual in $activation_string_list
705	do
706	for formal in $s3
707	do
708	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
709	done
710	done
711	if [[ $found = true ]]
712	then
713	(( iout = iout + 1 ))
714	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
715	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
716
717	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
718	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
719	if [[ $formal = wildcard ]]
720	then
721	warnout_pre[$iout]=false
722	else
723	warnout_pre[$iout]=true
724	fi
725
726	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
727	# THE WILDCARD FROM THE LOCAL FILENAME
728	if [[ "${s1: -1}" = "*" ]]
729	then
730	if [[ "$s2b" = "di" ]]
731	then
732	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
733	printf "\n see file \"$fileconnection_file\", line"
734	printf "\n$line"
735	locat=iofiles_file; exit
736	fi
737	multout[$iout]=true
738	string=${localout_pre[$iout]}
739	localout_pre[$iout]="${string%?}"
740	else
741	multout[$iout]=false
742	fi
743	fi
744	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
745	then
746	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
747	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
748	locat=connect; exit
749	fi
750	IFS="$IFSALT"
751	fi
752
753	done < $fileconnection_file
754
755
756
757	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
758	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
759	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
760	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
761	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
762	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
763
764
765
766	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
767	if [[ $run_coupled_model = true ]]
768	then
769
770	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
771	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
772
773	if (( $cores_ocean + $cores_atmos != $cores ))
774	then
775
776	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
777	printf "\n PEs (total) : $cores"
778	printf "\n PEs (atmosphere): $cores_atmos"
779	printf "\n PEs (ocean) : $cores_ocean"
780	locat=coupling; exit
781
782	fi
783
784	fi
785
786
787	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
788	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
789	# FOLDER
790	if [[ $running_in_batch_mode = true ]]
791	then
792
793	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
794	then
795	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
796	printf "\n Please check the output of the palmrun-call"
797	printf "\n that you did on your local host."
798	locat=SOURCES_FOR_RUN; exit
799	fi
800
801	else
802
803	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
804	# AUTOMATIC RESTART RUN
805	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
806	if [[ $restart_run = false ]]
807	then
808
809	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
810	# THE LOCAL HOST
811	if [[ ! -d $source_path ]]
812	then
813	printf "\n\n +++ source path \"$source_path\" on local host"
814	printf "\n \"$(hostname)\" does not exist"
815	locat=source_path; exit
816	fi
817
818	rm -rf ${base_directory}/${sources_for_run_catalog}
819	mkdir -p ${base_directory}/${sources_for_run_catalog}
820
821	if [[ "$source_list" = LM ]]
822	then
823
824	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
825	source_list=""
826	cd $source_path
827
828
829	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
830	if [[ ! -d ../.svn ]]
831	then
832	printf "\n\n +++ source directory"
833	printf "\n \"$source_path\" "
834	printf "\n is not under control of \"subversion\"."
835	printf "\n Please do not use palmrun-option \"-s LM\"\n"
836	fi
837
838
839	# LIST ALL MODIFIED SOURCE CODE FILES
840	Filenames=""
841	svn status > tmp_svnstatus
842	while read line
843	do
844	firstc=`echo $line \| cut -c1`
845	if [[ $firstc = M \|\| $firstc = "?" ]]
846	then
847	Name=`echo "$line" \| cut -c8-`
848	extension=`echo $Name \| cut -d. -f2`
849	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
850	then
851	Filenames="$Filenames "$Name
852	fi
853	fi
854	done < tmp_svnstatus
855	rm -rf tmp_svnstatus
856
857
858	# COPY FILES TO SOURCES_FOR_RUN_...
859	for filename in $Filenames
860	do
861	cp $filename ${base_directory}/${sources_for_run_catalog}
862	source_list=$source_list"$filename "
863	done
864
865	cd - > /dev/null
866
867
868	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
869	elif [[ "$source_list" != "" ]]
870	then
871
872	cd $source_path
873
874	for filename in $source_list
875	do
876
877	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
878	if [[ $(echo $filename \| grep -c "/") != 0 ]]
879	then
880	printf "\n +++ source code file: $filename"
881	printf "\n must not contain (\"/\") "
882	locat=source; exit
883	fi
884
885	if [[ ! -f $filename ]]
886	then
887	printf "\n +++ source code file: $filename"
888	printf "\n does not exist"
889	locat=source; exit
890	else
891	cp $filename ${base_directory}/${sources_for_run_catalog}
892	fi
893
894	done
895
896	cd - > /dev/null
897
898	fi
899
900	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
901	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
902	if [[ ! -f $makefile ]]
903	then
904	printf "\n +++ file \"$makefile\" does not exist"
905	locat=make; exit
906	else
907	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
908	fi
909
910
911	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
912	if [[ "$user_source_path" != "" ]]
913	then
914
915	# DOES THE DIRECTORY EXIST?
916	if [[ ! -d $user_source_path ]]
917	then
918
919	printf "\n\n *** INFORMATIVE: additional source code directory"
920	printf "\n \"$user_source_path\" "
921	printf "\n does not exist or is not a directory."
922	printf "\n No source code will be used from this directory!\n"
923	user_source_path=""
924	if [[ $silent == false ]]
925	then
926	sleep 2
927	fi
928
929	else
930
931	cd $user_source_path
932	found=false
933
934	Names=$(ls -1 *.f90 2>&1)
935	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
936	Names=$(ls -1 *.F90 2>&1)
937	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
938	Names=$(ls -1 *.F 2>&1)
939	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
940	Names=$(ls -1 *.f 2>&1)
941	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
942	Names=$(ls -1 *.c 2>&1)
943	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
944
945	cd - > /dev/null
946	cd ${base_directory}/${sources_for_run_catalog}
947
948	# COPY MAKEFILE IF EXISTING
949	if [[ -f $user_source_path/Makefile ]]
950	then
951	printf "\n\n *** user Makefile from directory"
952	printf "\n \"$user_source_path\" is used \n"
953	if [[ $silent == false ]]
954	then
955	sleep 1
956	fi
957	cp $user_source_path/Makefile .
958	fi
959
960	for filename in $AddFilenames
961	do
962	if [[ -f $filename ]]
963	then
964	printf "\n +++ source code file \"$filename\" found in additional"
965	printf "\n source code directory \"$user_source_path\" "
966	printf "\n but was also given with option \"-s\" which means that it should be taken"
967	printf "\n from directory \"$source_path\"."
968	locat=source; exit
969	fi
970
971	cp $user_source_path/$filename .
972	source_list="$source_list $filename"
973
974	# CHECK IF FILE IS CONTAINED IN MAKEFILE
975	if [[ $(grep -c $filename Makefile) = 0 ]]
976	then
977	printf "\n\n +++ user file \"$filename\" "
978	printf "\n is not listed in Makefile \n"
979	locat=source; exit
980	else
981
982	if [[ $found = false ]]
983	then
984	found=true
985	printf "\n\n *** following user file(s) added to the"
986	printf " files to be translated:\n "
987	fi
988	printf "$filename "
989	if [[ $silent == false ]]
990	then
991	sleep 0.5
992	fi
993
994	fi
995	done
996	[[ $found = true ]] && printf "\n"
997	cd - > /dev/null
998	fi
999	fi
1000
1001	# COPY CONFIGURATION FILES
1002	cp $config_file ${base_directory}/${sources_for_run_catalog}
1003	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1004
1005	# COPY SHELLSCRIPTS
1006	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1007	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1008
1009	fi
1010
1011	fi
1012
1013
1014	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1015	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1016	if [[ "$global_revision" = "" ]]
1017	then
1018	global_revision=`svnversion $source_path 2>/dev/null`
1019	global_revision="Rev: $global_revision"
1020	fi
1021
1022
1023	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1024	if [[ -n $cores ]]
1025	then
1026
1027	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1028	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1029	if [[ $tasks_per_node = 0 ]]
1030	then
1031	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1032	then
1033	printf "\n"
1034	printf "\n +++ option \"-T\" (tasks per node) is missing"
1035	printf "\n set -T option or define tasks_per_node in the config file"
1036	locat=tasks_per_node; (( iec = 0 )); exit
1037	else
1038	# DEFAULT FOR INTERACTIVE RUN
1039	tasks_per_node=$cores
1040	fi
1041	fi
1042
1043	if (( cores < tasks_per_node ))
1044	then
1045	printf "\n"
1046	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1047	printf "\n given values: -T $tasks_per_node -X $cores"
1048	locat=tasks_per_node; (( iec = 0 )); exit
1049	fi
1050
1051	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1052	(( mpi_tasks = cores / threads_per_task ))
1053	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1054	(( ii = cores / tasks_per_node ))
1055	(( remaining_cores = cores - ii * tasks_per_node ))
1056	if (( remaining_cores > 0 ))
1057	then
1058	printf "\n"
1059	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1060	printf "\n divisor of the total number of cores (option \"-X\")"
1061	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1062	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1063	(( nodes = nodes + 1 ))
1064	fi
1065
1066	fi
1067
1068
1069	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1070	if [[ "$maximum_parallel_io_streams" = "" ]]
1071	then
1072	maximum_parallel_io_streams=$cores
1073	fi
1074
1075
1076	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1077	if [[ "$scp_port" != "" ]]
1078	then
1079	PORTOPT="-P $scp_port"
1080	SSH_PORTOPT="-p $scp_port"
1081	fi
1082
1083
1084	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1085	# CONFIG-FILE
1086	if [[ "$ssh_key" != "" ]]
1087	then
1088	ssh_key="-i $HOME/.ssh/$ssh_key"
1089	fi
1090
1091
1092	# SET QUEUE, IF NOT GIVEN
1093	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1094	then
1095
1096	if [[ $queue = none && "$defaultqueue" = "" ]]
1097	then
1098	printf "\n"
1099	printf "\n +++ no default queue given in configuration file and no queue"
1100	printf "\n given with option -q"
1101	locat=queue; exit
1102	fi
1103	if [[ $queue = none ]]
1104	then
1105	queue=$defaultqueue
1106	fi
1107
1108	fi
1109
1110
1111	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1112	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1113	(( i = 0 ))
1114	(( nr_of_input_files = 0 ))
1115	while (( i < iin ))
1116	do
1117	(( i = i + 1 ))
1118
1119	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1120	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1121	if [[ "${actionin_pre[$i]}" = di ]]
1122	then
1123	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1124	else
1125	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1126	fi
1127
1128
1129	# CHECK IF FILE EXISTS
1130	if ! ls $filename* 1>/dev/null 2>&1
1131	then
1132
1133	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1134	if [[ "${optin_pre[$i]}" != "yes" ]]
1135	then
1136	printf "\n\n +++ INPUT-file: "
1137	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1138	then
1139	printf "\n $filename"
1140	else
1141	printf "\n $filename.${extin_pre[$i]}"
1142	fi
1143	printf "\n does not exist\n"
1144	locat=input; exit
1145	else
1146	(( nr_of_input_files = nr_of_input_files + 1 ))
1147	localin[$nr_of_input_files]="${localin_pre[$i]}"
1148	optin[$nr_of_input_files]="${optin_pre[$i]}"
1149	actionin[$nr_of_input_files]="unavailable"
1150	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1151	endin[$nr_of_input_files]="${endin_pre[$i]}"
1152	extin[$nr_of_input_files]="${extin_pre[$i]}"
1153	fi
1154
1155	else
1156
1157	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1158	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1159	if [[ "${multin[$i]}" = true ]]
1160	then
1161	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1162	ls -1 -d ${filename} > filelist 2>/dev/null
1163	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1164	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1165
1166	endings=""
1167	while read line
1168	do
1169	# filename without path (i.e. after the last "/")
1170	basefilename=$(basename ${line})
1171
1172	# check if there is an extension and remove it
1173	ext=${basefilename##*.}
1174	if [[ "$ext" = "${extin_pre[$i]}" ]]
1175	then
1176	basefilename=${basefilename%.*}
1177	fi
1178
1179	# check for an existing cycle number and remove it
1180	cycle=${basefilename##*.}
1181	if [[ $cycle =~ ^-?[0-9]+$ ]]
1182	then
1183	basefilename=${basefilename%.*}
1184	fi
1185
1186	# remove the jobname from the beginning
1187	length_jobname=${#jobname}
1188	ending=${basefilename:${length_jobname}}
1189
1190	# remove the ending given in the .iofiles from the beginning
1191	endingstring="${endin_pre[$i]}"
1192	length_ending=${#endingstring}
1193	ending=${ending:${length_ending}}
1194
1195	if [[ "$ending" = "" ]]
1196	then
1197	# standard ending as given in the .iofiles
1198	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1199	then
1200	endings="$endings DEFAULT"
1201	fi
1202	else
1203	# ending must start with "_", otherwise its a different file
1204	if [[ "${ending:0:1}" = "_" ]]
1205	then
1206	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1207	then
1208	endings="$endings $ending"
1209	fi
1210	fi
1211	fi
1212
1213	done <filelist
1214
1215	rm filelist
1216
1217	else
1218
1219	# SINGLE NAME
1220	endings=DEFAULT
1221
1222	fi
1223
1224	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1225	for ending in $endings
1226	do
1227
1228	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1229	if [[ $ending = DEFAULT ]]
1230	then
1231	ending=""
1232	fi
1233
1234	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1235	(( nr_of_input_files = nr_of_input_files + 1 ))
1236	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1237	optin[$nr_of_input_files]="${optin_pre[$i]}"
1238	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1239	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1240	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1241	extin[$nr_of_input_files]="${extin_pre[$i]}"
1242
1243
1244	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1245	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1246	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1247	then
1248	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1249	else
1250	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1251	fi
1252
1253	# DETERMINE THE FILE'S CYCLE NUMBER
1254	(( maxcycle = 0 ))
1255	ls -1 -d $filename > filelist 2>/dev/null
1256	ls -1 -d $filename.* >> filelist 2>/dev/null
1257	while read line
1258	do
1259	# filename without path (i.e. after the last "/")
1260	basefilename=$(basename ${line})
1261
1262	# check if there is an extension
1263	extension=${basefilename##*.}
1264	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1265	then
1266	basefilename=${basefilename%.*}
1267	fi
1268
1269	# check for an existing cycle number
1270	cycle=${basefilename##*.}
1271	if [[ $cycle =~ ^-?[0-9]+$ ]]
1272	then
1273	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1274	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1275	(( icycle = $((10#$cycle)) ))
1276	else
1277	(( icycle = 0 ))
1278	fi
1279
1280	if (( icycle > maxcycle ))
1281	then
1282	(( maxcycle = icycle ))
1283
1284	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1285	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1286	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1287	then
1288	leading_zero=true
1289	else
1290	leading_zero=false
1291	fi
1292	fi
1293
1294	done <filelist
1295	rm filelist
1296
1297	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1298	if [[ $leading_zero = true ]]
1299	then
1300	cyclestring=`printf "%03d" $maxcycle`
1301	else
1302	cyclestring=$maxcycle
1303	fi
1304
1305	# APPEND CYCLE NUMBER TO FILENAME
1306	if (( maxcycle > 0 ))
1307	then
1308	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1309	then
1310	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1311	else
1312	filename=${filename}.$cyclestring
1313	fi
1314	else
1315	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1316	then
1317	filename=${filename}.${extin[$nr_of_input_files]}
1318	fi
1319	fi
1320
1321	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1322	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1323	absnamein[$nr_of_input_files]=$filename
1324	if (( maxcycle > 0 ))
1325	then
1326	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1327	then
1328	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1329	else
1330	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1331	fi
1332	else
1333	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1334	then
1335	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1336	else
1337	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1338	fi
1339	fi
1340
1341	done
1342
1343	fi
1344
1345	done
1346
1347
1348	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1349	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1350	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1351	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1352	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1353	# REMOTE HOST)
1354	(( i = 0 ))
1355	while (( i < iout ))
1356	do
1357	(( i = i + 1 ))
1358	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1359	then
1360	if [[ "${actionout_pre[$i]}" = tr ]]
1361	then
1362	actionout_pre[$i]=""
1363	elif [[ "${actionout_pre[$i]}" = trpe ]]
1364	then
1365	actionout_pre[$i]=pe
1366	elif [[ "${actionout_pre[$i]}" = tra ]]
1367	then
1368	actionout_pre[$i]=a
1369	fi
1370	(( maxcycle = 0 ))
1371	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1372	eval catalogname=${pathout_pre[$i]}
1373	if ! ls $filename* 1>/dev/null 2>&1
1374	then
1375
1376	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1377	if cat /dev/null > $filename
1378	then
1379	rm $filename
1380	else
1381
1382	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1383	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1384	if [[ ! -d $catalogname ]]
1385	then
1386	if mkdir -p $catalogname
1387	then
1388	printf "\n\n *** directory:"
1389	printf "\n $catalogname"
1390	printf "\n was created\n"
1391	else
1392	printf "\n\n +++ OUTPUT-file:"
1393	printf "\n $filename"
1394	printf "\n cannot be created, because directory does not exist"
1395	printf "\n and cannot be created either"
1396	printf "\n"
1397	locat=output ; exit
1398	fi 2>/dev/null
1399	else
1400	printf "\n\n +++ OUTPUT-file:"
1401	printf "\n $filename"
1402	printf "\n cannot be created, although directory exists"
1403	printf "\n"
1404	locat=output ; exit
1405	fi
1406	fi 2>/dev/null
1407
1408	fi
1409
1410	fi
1411	done
1412
1413
1414	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1415	if [[ $running_in_batch_mode = false ]]
1416	then
1417	run_id=$RANDOM
1418	job_id=${jobname}.$run_id
1419
1420	tempdir=$fast_io_catalog/$job_id
1421	fi
1422
1423
1424	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1425	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1426	then
1427
1428	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1429	if [[ $ibd = 0 ]]
1430	then
1431	printf "\n"
1432	printf "\n +++ no batch directives found in configuration file"
1433	locat=config_file_batch_directives; (( iec = 0 )); exit
1434	fi
1435
1436	# CHECK IF CPUTIME IS GIVEN FOR JOB
1437	done=false
1438	cputime=$cpumax
1439	while [[ $done = false ]]
1440	do
1441	if (( cputime == 0 ))
1442	then
1443	printf "\n +++ cpu-time is undefined"
1444	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1445	printf "\n >>> "
1446	read cputime 1>/dev/null 2>&1
1447	else
1448	done=true
1449	fi
1450	done
1451	cpumax=$cputime
1452
1453	# CHECK THE MEMORY DEMAND
1454	done=false
1455	while [[ $done = false ]]
1456	do
1457	if (( memory == 0 ))
1458	then
1459	printf "\n +++ memory demand is undefined"
1460	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1461	printf "\n >>> "
1462	read memory 1>/dev/null 2>&1
1463	else
1464	done=true
1465	fi
1466	done
1467
1468	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1469	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1470	then
1471	while [[ -z $remote_username ]]
1472	do
1473	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1474	printf "\n >>> Please type username:"
1475	printf "\n >>> "
1476	read remote_username
1477	done
1478	fi
1479
1480	else
1481
1482	if [[ $running_in_batch_mode = false ]]
1483	then
1484	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1485	cpumax=$cputime
1486	else
1487	cputime=$cpumax
1488	fi
1489
1490	fi
1491
1492
1493	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1494	(( cpu_hours = cputime / 3600 ))
1495	(( resttime = cputime - cpu_hours * 3600 ))
1496	(( cpu_minutes = resttime / 60 ))
1497	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1498	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1499
1500
1501	# OUTPUT OF THE PALMRUN-HEADER
1502	calltime=$(date)
1503	printf "\n"
1504	printf "#------------------------------------------------------------------------# \n"
1505	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1506	printf "\| \| \n"
1507	column1="called on:"; column2=$(hostname)
1508	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1509	if [[ $create_remote_batch_job = true ]]
1510	then
1511	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1512	else
1513	if [[ $running_on_remote = true ]]
1514	then
1515	column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
1516	else
1517	column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
1518	fi
1519	fi
1520	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1521
1522	column1="running in:"
1523	if [[ $running_in_batch_mode = true ]]
1524	then
1525	column2="batch job mode"
1526	else
1527	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1528	then
1529	column2="job creation mode"
1530	else
1531	column2="interactive run mode"
1532	fi
1533	fi
1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1535
1536	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1537	then
1538	if [[ "$project_account" != "" ]]
1539	then
1540	column1="project account number:"
1541	column2="$project_account"
1542	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1543	fi
1544	fi
1545
1546	if [[ -n $cores ]]
1547	then
1548	if [[ $run_coupled_model = false ]]
1549	then
1550	column1="number of cores:"; column2=$cores
1551	else
1552	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1553	fi
1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1555	fi
1556	if [[ -n $tasks_per_node ]]
1557	then
1558	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1560	if (( remaining_cores > 0 ))
1561	then
1562	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1564	fi
1565	fi
1566	if [[ $maximum_parallel_io_streams != $cores ]]
1567	then
1568	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1569	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1570	fi
1571	if [[ $use_openmp = true ]]
1572	then
1573	column1="threads per task:"; column2="$threads_per_task"
1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1575	fi
1576	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1577	then
1578	column1="memory demand / PE":; column2="$memory MB"
1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1580	column1="job cpu time (h:m:s):"; column2="$timestring"
1581	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1582	fi
1583	printf "\| \| \n"
1584	if [[ "$source_list" != "" ]]
1585	then
1586	if [[ "$make_options" != "" ]]
1587	then
1588	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1590	line=$(echo "$make_options" \| cut -c46-)
1591	while [[ "$line" != "" ]]
1592	do
1593	column1=""
1594	column2=$(echo "$line" \| cut -c-45)
1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1596	line=$(echo "$line" \| cut -c46-)
1597	done
1598	fi
1599	fi
1600
1601	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	line=$(echo "$cpp_options" \| cut -c46-)
1604	while [[ "$line" != "" ]]
1605	do
1606	column1=""
1607	column2=$(echo "$line" \| cut -c-45)
1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1609	line=$(echo "$line" \| cut -c46-)
1610	done
1611
1612	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1613	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1614	line=$(echo "$compiler_options" \| cut -c46-)
1615	while [[ "$line" != "" ]]
1616	do
1617	column1=""
1618	column2=$(echo "$line" \| cut -c-45)
1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1620	line=$(echo "$line" \| cut -c46-)
1621	done
1622
1623	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1625	line=$(echo "$linker_options" \| cut -c46-)
1626	while [[ "$line" != "" ]]
1627	do
1628	column1=""
1629	column2=$(echo "$line" \| cut -c-45)
1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1631	line=$(echo "$line" \| cut -c46-)
1632	done
1633
1634	if [[ "$login_init_cmd" != "" ]]
1635	then
1636	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1638	line=$(echo "$login_init_cmd" \| cut -c46-)
1639	while [[ "$line" != "" ]]
1640	do
1641	column1=""
1642	column2=$(echo "$line" \| cut -c-45)
1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1644	line=$(echo "$line" \| cut -c46-)
1645	done
1646	fi
1647
1648	if [[ "$module_commands" != "" ]]
1649	then
1650	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1652	line=$(echo "$module_commands" \| cut -c46-)
1653	while [[ "$line" != "" ]]
1654	do
1655	column1=""
1656	column2=$(echo "$line" \| cut -c-45)
1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1658	line=$(echo "$line" \| cut -c46-)
1659	done
1660	fi
1661	printf "\| \| \n"
1662	column1="run identifier:"; column2=$jobname
1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1664	column1="activation string list:"; column2=$(echo $activation_string_list)
1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1666
1667	if [[ "$ocean_file_appendix" = true ]]
1668	then
1669	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1670	fi
1671
1672	if [[ "$source_list" != "" ]]
1673	then
1674	printf "\| \| \n"
1675	printf "\| Files to be compiled: \| \n"
1676	line=$source_list
1677	while [[ "$line" != "" ]]
1678	do
1679	linestart=$(echo $line \| cut -c-70)
1680	printf "\| %-70s \| \n" "$linestart"
1681	line=$(echo "$line" \| cut -c71-)
1682	done
1683	fi
1684	printf "#------------------------------------------------------------------------#"
1685
1686
1687
1688	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1689	if [[ $do_trace = true ]]
1690	then
1691	(( i = 0 ))
1692	while (( i < nr_of_input_files ))
1693	do
1694	(( i = i + 1 ))
1695	if (( i == 1 ))
1696	then
1697	printf "\n\n >>> INPUT-file assignments:\n"
1698	fi
1699	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1700	done
1701	(( i = 0 ))
1702	while (( i < iout ))
1703	do
1704	(( i = i + 1 ))
1705	if (( i == 1 ))
1706	then
1707	printf "\n\n >>> OUTPUT-file assignments:\n"
1708	fi
1709	printf "\n ${localout[$i]} : ${pathout[$i]}"
1710	done
1711	(( i = 0 ))
1712	while (( i < iic ))
1713	do
1714	(( i = i + 1 ))
1715	if (( i == 1 ))
1716	then
1717	printf "\n\n >>> INPUT-commands:\n"
1718	fi
1719	printf "\n ${in_command[$i]}"
1720	done
1721	(( i = 0 ))
1722	while (( i < ioc ))
1723	do
1724	(( i = i + 1 ))
1725	if (( i == 1 ))
1726	then
1727	printf "\n\n >>> OUTPUT-commands:\n"
1728	fi
1729	printf "\n ${out_command[$i]}"
1730	done
1731	fi
1732
1733	# QUERY FOR CONTINUE
1734	if [[ $silent = false && $running_in_batch_mode = false ]]
1735	then
1736	antwort=dummy
1737	printf "\n\n"
1738	printf " >>> everything o.k. (y/n) ? "
1739	while read antwort
1740	do
1741	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1742	then
1743	printf " >>> everything o.k. (y/n) ? "
1744	else
1745	break
1746	fi
1747	done
1748	if [[ $antwort = n \|\| $antwort = N ]]
1749	then
1750	locat=user_abort; (( iec = 0 )); exit
1751	fi
1752	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1753	then
1754	printf "\n *** batch-job will be created and submitted"
1755	else
1756	printf "\n *** PALMRUN will now continue to execute on this machine"
1757	fi
1758	fi
1759
1760
1761
1762	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1763	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1764	then
1765
1766	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1767	then
1768	printf "\n\n *** creating executable and other sources for the remote host\n"
1769	else
1770	printf "\n\n *** creating executable and other sources for the local host\n"
1771	fi
1772
1773	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1774	# IT SHALL BE CREATED
1775	ask_for_make_depository=false
1776	if [[ $create_remote_batch_job = true ]]
1777	then
1778
1779	line=`grep %base_directory $config_file`
1780	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1781	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1782
1783	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1784	then
1785	printf "\n\n +++ make depository \"${make_depository}\""
1786	printf "\n on remote host not found!"
1787	ask_for_make_depository=true
1788	fi
1789	rm ${host_configuration}_last_make_protokoll
1790
1791	else
1792
1793	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1794	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1795	if [[ ! -d ${make_depository} ]]
1796	then
1797	printf "\n\n +++ make depository \"${make_depository}\""
1798	printf "\n on local host not found!"
1799	ask_for_make_depository=true
1800	fi
1801
1802	fi
1803
1804	if [[ $ask_for_make_depository = true ]]
1805	then
1806
1807	antwort=dummy
1808	printf "\n\n"
1809	printf " >>> Create a new one (y/n) ? "
1810	while read antwort
1811	do
1812	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1813	then
1814	printf " >>> Create a new one (y/n) ? "
1815	else
1816	break
1817	fi
1818	done
1819	if [[ $antwort = n \|\| $antwort = N ]]
1820	then
1821	locat=user_abort; (( iec = 0 )); exit
1822	fi
1823
1824	if [[ $do_trace = true ]]
1825	then
1826	palmbuild -h $host_configuration
1827	else
1828	palmbuild -v -h $host_configuration
1829	fi
1830
1831	if [[ $? != 0 ]]
1832	then
1833
1834	# ABORT IN CASE OF COMPILATION PROBLEMS
1835	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1836	locat=make_depository
1837	exit
1838	else
1839	echo " *** now continue with creating executable and other sources"
1840	fi
1841
1842	fi
1843
1844	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1845	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1846
1847	if [[ $? != 0 ]]
1848	then
1849
1850	# ABORT IN CASE OF COMPILATION PROBLEMS
1851	printf "\n +++ error while creating executable and/or other sources"
1852	locat=execution
1853	rm -rf ${base_directory}/${sources_for_run_catalog}
1854	exit
1855
1856	else
1857
1858	printf " *** executable and other sources created\n"
1859	rm -rf ${base_directory}/${sources_for_run_catalog}
1860
1861	fi
1862
1863	fi
1864
1865
1866	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1867	# WILL BE COPIED TO THE REMOTE HOST
1868	if [[ $create_remote_batch_job = true ]]
1869	then
1870	(( i = 0 ))
1871	while (( i < nr_of_input_files ))
1872	do
1873	(( i = i + 1 ))
1874	if [[ "${actionin[$i]}" = tr ]]
1875	then
1876	eval inputfile=${pathin[$i]}/${frelin[$i]}
1877	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1878	fi
1879	done
1880	if (( i > 0 ))
1881	then
1882	printf "\n\n *** input files have been copied to the remote host\n"
1883	fi
1884	fi
1885
1886
1887	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1888	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1889	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1890	then
1891
1892	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1893	if [[ $running_in_batch_mode = false ]]
1894	then
1895	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1896	# FOLDER
1897	mkdir -p $tempdir
1898	chmod go+rx $tempdir
1899	cd $tempdir
1900	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1901	printf "\n *** changed to temporary directory: $tempdir"
1902
1903	else
1904
1905	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1906	printf "\n *** running in temporary directory: $tempdir"
1907
1908	fi
1909
1910
1911	# PROVIDE THE INPUT FILES
1912	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1913	optional_files_missing=false
1914	(( i = 0 ))
1915	while (( i < nr_of_input_files ))
1916	do
1917	(( i = i + 1 ))
1918	if (( i == 1 ))
1919	then
1920	printf "\n\n *** providing INPUT-files:\n$dashes"
1921	fi
1922
1923
1924	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1925	if [[ "${actionin[$i]}" = unavailable ]]
1926	then
1927	optional_files_missing=true
1928	continue
1929	fi
1930
1931	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1932	files_for_cores=false; filetype=file
1933	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1934	then
1935	files_for_cores=true; filetype=files
1936	actionin[$i]=""
1937	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1938	then
1939	actionin[$i]=""
1940	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1941	then
1942	files_for_cores=true; filetype=files
1943	actionin[$i]="ln"
1944	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1945	then
1946	actionin[$i]="ln"
1947	fi
1948
1949	if [[ $files_for_cores = true ]]
1950	then
1951	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1952	else
1953	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1954	fi
1955
1956	# INPUT-FILES TO BE LINKED
1957	if [[ "${actionin[$i]}" = ln ]]
1958	then
1959
1960	printf "\n $filetype will be linked"
1961	if [[ $files_for_cores = false ]]
1962	then
1963	if [[ -f "${absnamein[$i]}" ]]
1964	then
1965	ln ${absnamein[$i]} ${localin[$i]}
1966	got_tmp[$i]=true
1967	fi
1968	else
1969	if [[ -d "${absnamein[$i]}" ]]
1970	then
1971	mkdir -p ${localin[$i]}
1972	cd ${absnamein[$i]}
1973	for file in $(ls *)
1974	do
1975	ln $file $tempdir/${localin[$i]}
1976	done >\|/dev/null 2>&1
1977	cd $tempdir
1978	fi
1979
1980	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1981	if [[ ! -f "${localin[$i]}/_000000" ]]
1982	then
1983	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1984	cp -r ${absnamein[$i]}/* ${localin[$i]}
1985	fi
1986
1987	got_tmp[$i]=true
1988	fi
1989	fi
1990
1991	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1992	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1993	then
1994
1995	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1996	then
1997
1998	# FILE COPIES ARE PROVIDED FOR ALL CORES
1999	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2000	printf "\n file will be provided for $cores processors"
2001	mkdir -p ${localin[$i]}
2002	ival=$cores
2003	(( ii = 0 ))
2004	while (( ii <= ival-1 ))
2005	do
2006	if (( ii < 10 ))
2007	then
2008	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2009	elif (( ii < 100 ))
2010	then
2011	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2012	elif (( ii < 1000 ))
2013	then
2014	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2015	else
2016	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2017	fi
2018	(( ii = ii + 1 ))
2019	done
2020
2021	else
2022
2023	if [[ $files_for_cores = true ]]
2024	then
2025
2026	# PROVIDE FILES FOR EACH CORE
2027	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2028	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2029	printf "\n providing $cores files for the respective cores"
2030	mkdir -p ${localin[$i]}
2031	if [[ $link_local_input = true ]]
2032	then
2033	printf " files will be linked\n"
2034	cd ${absnamein[$i]}
2035	for file in $(ls *)
2036	do
2037	ln -f $file ${localin[$i]}
2038	done
2039	cd $tempdir
2040	fi
2041
2042	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2043	if [[ ! -f "${localin[$i]}/_000000" ]]
2044	then
2045	if [[ $link_local_input = true ]]
2046	then
2047	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2048	fi
2049	cp -r ${absnamein[$i]}/* ${localin[$i]}
2050	fi
2051
2052	else
2053
2054	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2055	if [[ $link_local_input = true ]]
2056	then
2057	printf " file will be linked\n"
2058	ln -f ${absnamein[$i]} ${localin[$i]}
2059	fi
2060	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2061	if [[ ! -f "${localin[$i]}" ]]
2062	then
2063	if [[ $link_local_input = true ]]
2064	then
2065	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2066	fi
2067	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2068	then
2069	mv ${absnamein[$i]} ${localin[$i]}
2070	else
2071	cp ${absnamein[$i]} ${localin[$i]}
2072	fi
2073	fi
2074	fi
2075	fi
2076	fi
2077
2078	done
2079	if (( i != 0 ))
2080	then
2081	if [[ $optional_files_missing = true ]]
2082	then
2083	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2084	fi
2085	printf "\n$dashes\n *** all INPUT-files provided \n"
2086	fi
2087
2088
2089	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2090	(( i = 0 ))
2091	while (( i < iic ))
2092	do
2093	(( i = i + 1 ))
2094	if (( i == 1 ))
2095	then
2096	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2097	fi
2098	printf "\n >>> ${in_command[$i]}"
2099	eval ${in_command[$i]}
2100	if (( i == iic ))
2101	then
2102	printf "\n$dashes\n"
2103	fi
2104	done
2105
2106
2107	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2108	# (FILE ENVPAR WILL BE READ BY PALM)
2109	cat > ENVPAR << EOF
2110	&envpar run_identifier = '$jobname', host = '$host_configuration',
2111	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2112	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2113	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2114	maximum_cpu_time_allowed = ${cpumax}.,
2115	revision = '$global_revision',
2116	batch_job = .${running_in_batch_mode}. /
2117
2118	EOF
2119
2120
2121	# STARTING THE EXECUTABLE
2122	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2123	PATH=$PATH:$tempdir
2124
2125
2126	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2127	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2128	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2129	eval line=\"$line\"
2130	execute_command="$line"
2131
2132
2133	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2134	if [[ "$execute_command_for_combine" = "" ]]
2135	then
2136	eval line2=\"$line2\"
2137	execute_command_for_combine="$line2"
2138	fi
2139
2140
2141
2142	# PROVIDE A HOSTFILE, IF REQUIRED
2143	if [[ "$hostfile" != "" ]]
2144	then
2145
2146	if [[ $hostfile = auto ]]
2147	then
2148	# CREATE A NEW HOSTFILE
2149	(( ii = 1 ))
2150	while (( ii <= cores / threads_per_task ))
2151	do
2152	echo $(hostname) >> hostfile
2153	(( ii = ii + 1 ))
2154	done
2155	if (( cores / threads_per_task == 0 ))
2156	then
2157	echo $(hostname) >> hostfile
2158	fi
2159
2160	else
2161	cp $hostfile hostfile
2162	fi
2163	eval line=\"`head -n $ii hostfile`\"
2164	printf "\n *** running on: $line"
2165	fi
2166
2167
2168
2169	# SET THE NUMBER OF OPENMP-THREADS
2170	if [[ $use_openmp = true ]]
2171	then
2172	export OMP_NUM_THREADS=$threads_per_task
2173	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2174	else
2175	export OMP_NUM_THREADS=1
2176	fi
2177
2178
2179	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2180	if [[ $run_coupled_model = false ]]
2181	then
2182	if [[ "$ocean_file_appendix" = true ]]
2183	then
2184	echo "precursor_ocean" > coupling_steering
2185	else
2186	echo "precursor_atmos" > coupling_steering
2187	fi
2188	else
2189	(( iia = $cores_atmos / $threads_per_task ))
2190	(( iio = $cores_ocean / $threads_per_task ))
2191	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2192	printf "\n\n"
2193	echo "coupled_run $iia $iio" > coupling_steering
2194	fi
2195
2196	printf "\n *** execute command:"
2197	printf "\n \"$execute_command\" \n\n"
2198
2199	$execute_command < coupling_steering
2200
2201	if [[ $? != 0 ]]
2202	then
2203
2204	# ABORT IN CASE OF RUNTIME ERRORS
2205	printf "\n +++ runtime error occured"
2206	locat=execution
2207	exit
2208
2209	else
2210
2211	printf "\n$dashes\n *** execution finished \n"
2212
2213	fi
2214
2215
2216	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2217	# BY EACH CORE INTO ONE FILE
2218	if [[ ! -f combine_plot_fields.x ]]
2219	then
2220
2221	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2222	printf "\n 2d- and/or 3d-data may be incomplete!"
2223	printf "\n Your previous palmbuild may have failed. Please check.\n"
2224
2225	elif [[ "$combine_plot_fields" == true ]]
2226	then
2227
2228	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2229	$execute_command_for_combine
2230
2231	else
2232
2233	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2234	# DATA OUTPUT
2235	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2236	fi
2237
2238
2239
2240	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2241	(( i = 0 ))
2242	while (( i < ioc ))
2243	do
2244	(( i = i + 1 ))
2245	if (( i == 1 ))
2246	then
2247	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2248	fi
2249
2250	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2251	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2252
2253	printf "\n >>> ${out_command[$i]}"
2254	eval ${out_command[$i]}
2255	if (( i == ioc ))
2256	then
2257	printf "\n$dashes\n"
2258	fi
2259	done
2260
2261
2262	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2263	# WILDCARDS
2264	(( i = 0 ))
2265	(( nr_of_output_files = 0 ))
2266
2267	while (( i < iout ))
2268	do
2269
2270	(( i = i + 1 ))
2271
2272	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2273	# CREATE A LIST FOR THE DETECTED ENDINGS
2274	if [[ "${multout[$i]}" = true ]]
2275	then
2276	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2277	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2278	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2279
2280	endings="DEFAULT"
2281	while read line
2282	do
2283	# remove the local name from the beginning
2284	localnamestring="${localout_pre[$i]}"
2285	length_localname=${#localnamestring}
2286	ending=${line:${length_localname}}
2287
2288	if [[ "$ending" != "" ]]
2289	then
2290	endings="$endings $ending"
2291	fi
2292
2293	done <filelist
2294
2295	rm filelist
2296
2297	else
2298
2299	# SINGLE NAME
2300	endings=DEFAULT
2301
2302	fi
2303
2304	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2305	for ending in $endings
2306	do
2307
2308	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2309	if [[ $ending = DEFAULT ]]
2310	then
2311	ending=""
2312	fi
2313
2314	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2315	(( nr_of_output_files = nr_of_output_files + 1 ))
2316	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2317	transout[$nr_of_output_files]="${transout_pre[$i]}"
2318	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2319	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2320	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2321	extout[$nr_of_output_files]="${extout_pre[$i]}"
2322	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2323
2324	done
2325
2326	done
2327
2328
2329
2330
2331	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2332	(( i = 0 ))
2333	while (( i < nr_of_output_files ))
2334	do
2335	(( i = i + 1 ))
2336	if (( i == 1 ))
2337	then
2338	printf "\n\n *** saving OUTPUT-files:"
2339
2340	# GET RUN NUMBER ASSIGNED BY PALM
2341	if [[ -f RUN_NUMBER ]]
2342	then
2343	read run_number < RUN_NUMBER
2344	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2345	usecycle_option="-U $run_number"
2346	else
2347	run_number=0
2348	usecycle_option=""
2349	fi
2350	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2351	then
2352	printf "\n *** in case of SCP transfers to local host"
2353	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2354	fi
2355	printf "\n$dashes"
2356	fi
2357
2358	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2359	then
2360
2361	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2362
2363	# DETERMINE THE CYCLE NUMBER
2364	ls -1 -d $filename > filelist 2>/dev/null
2365	ls -1 -d $filename.* >> filelist 2>/dev/null
2366	while read line
2367	do
2368
2369	# filename without path (i.e. after the last "/")
2370	basefilename=$(basename ${line})
2371
2372	# check if there is an extension
2373	extension=${basefilename##*.}
2374	if [[ "$extension" = "${extout[$i]}" ]]
2375	then
2376	basefilename=${basefilename%.*}
2377	fi
2378
2379	# check for an existing cycle number
2380	cycle=${basefilename##*.}
2381	if [[ $cycle =~ ^-?[0-9]+$ ]]
2382	then
2383	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2384	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2385	(( icycle = $((10#$cycle)) + 1 ))
2386	else
2387	(( icycle = 1 ))
2388	fi
2389
2390	if (( icycle > maxcycle ))
2391	then
2392	(( maxcycle = icycle ))
2393	fi
2394
2395	done <filelist
2396	rm filelist
2397
2398
2399	# SET THE CYCLE NUMBER
2400	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2401	if [[ "${actionout[$i]}" = a ]]
2402	then
2403	(( maxcycle = maxcycle - 1 ))
2404	fi
2405
2406	(( cycnum[$i] = maxcycle ))
2407	pathout[$i]=$filename
2408
2409
2410	# ADD CYCLE NUMBER TO FILENAME
2411	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2412	if [[ "${actionout[$i]}" != "a" ]]
2413	then
2414	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2415	# WITH AN EXISTING CYCLE NUMBER
2416	if (( run_number >= cycnum[$i] ))
2417	then
2418	(( cycnum[$i] = run_number ))
2419	else
2420	if (( run_number > 0 ))
2421	then
2422	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2423	fi
2424	fi
2425	fi
2426	if (( cycnum[$i] > 0 ))
2427	then
2428	cyclestring=`printf "%03d" ${cycnum[$i]}`
2429	pathout[$i]=${pathout[$i]}.$cyclestring
2430	fi
2431	fi
2432
2433	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2434	files_for_cores=false; filetype=file
2435	link_local_output=false
2436	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2437	then
2438	files_for_cores=true; filetype=directory
2439	actionout[$i]=""
2440	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2441	then
2442	actionout[$i]=""
2443	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2444	then
2445	files_for_cores=true; filetype=directory
2446	link_local_output=true
2447	actionout[$i]=""
2448	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2449	then
2450	link_local_output
2451	actionout[$i]=""
2452	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2453	then
2454	files_for_cores=true; filetype=directory
2455	actionout[$i]="tr"
2456	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2457	then
2458	actionout[$i]="tr"
2459	fi
2460
2461	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2462	then
2463	if [[ ${warnout[$i]} = true ]]
2464	then
2465	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2466	fi
2467	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2468	then
2469	if [[ ${warnout[$i]} = true ]]
2470	then
2471	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2472	fi
2473	else
2474
2475
2476	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2477	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2478	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2479	then
2480	if [[ $running_on_remote = true ]]
2481	then
2482
2483	# SET OPTIONS FOR TRANSFER
2484	if [[ "${actionout[$i]}" = tr ]]
2485	then
2486	if [[ $files_for_cores = false ]]
2487	then
2488	catalog_option=""
2489	catalog_string=""
2490	else
2491	catalog_option="-c"
2492	catalog_string="/"
2493	fi
2494	append_option=""
2495	append_string=""
2496	else
2497	append_option="-A"
2498	append_string="append"
2499	fi
2500
2501	transfer_failed=false
2502	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2503	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2504
2505	# TRANSFER VIA SCP
2506	if [[ "$remote_loginnode" != "" ]]
2507	then
2508	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]}\" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2509	else
2510	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}
2511	fi
2512	[[ $? != 0 ]] && transfer_failed=true
2513
2514
2515	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2516	if [[ $transfer_failed = true ]]
2517	then
2518	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2519	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2520
2521	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2522	eval local_catalog=${pathout[$i]}
2523	if [[ ! -d $local_catalog ]]
2524	then
2525	printf " *** local directory does not exist. Trying to create:\n"
2526	printf " $local_catalog \n"
2527	mkdir -p $local_catalog
2528	fi
2529	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2530	transfer_problems=true
2531	fi
2532
2533	else
2534
2535	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2536	# BE COPIED OR APPENDED ON THIS MACHINE
2537	if [[ "${actionout[$i]}" = tr ]]
2538	then
2539	actionout[$i]=""
2540	else
2541	actionout[$i]="a"
2542	fi
2543	fi
2544	fi
2545
2546
2547	# APPEND ON THIS MACHINE
2548	if [[ "${actionout[$i]}" = "a" ]]
2549	then
2550	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2551	then
2552	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2553	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2554	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2555	else
2556	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2557	printf "\n ${pathout[$i]}\n"
2558	cat ${localout[$i]} >> ${pathout[$i]}
2559	fi
2560	fi
2561
2562	# COPY ON THIS MACHINE
2563	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2564	# ON DIFFERENT FILE-SYSTEMS
2565	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2566	then
2567
2568	# COPY IN CASE OF RUNS ON SINGLE CORES
2569	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2570	then
2571	printf "\n >>> OUTPUT: ${localout[$i]} to"
2572	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2573	if [[ $link_local_output = true ]]
2574	then
2575	printf " file will be linked\n"
2576	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2577	fi
2578	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2579	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2580	then
2581	if [[ $link_local_output = true ]]
2582	then
2583	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2584	fi
2585	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2586	else
2587	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2588	fi
2589	else
2590	printf "\n >>> OUTPUT: ${localout[$i]} to"
2591	printf "\n ${pathout[$i]}\n"
2592	if [[ $link_local_output = true ]]
2593	then
2594	printf " file will be linked\n"
2595	ln -f ${localout[$i]} ${pathout[$i]}
2596	fi
2597	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2598	if [[ ! -f "${pathout[$i]}" ]]
2599	then
2600	if [[ $link_local_output = true ]]
2601	then
2602	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2603	fi
2604	cp ${localout[$i]} ${pathout[$i]}
2605	else
2606	printf "+++ no copy because file ${pathout[$i]} exists\n"
2607	fi
2608	fi
2609
2610	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2611	then
2612
2613	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2614	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2615	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2616	printf "\n ${pathout[$i]}\n"
2617	if [[ $link_local_output = true ]]
2618	then
2619	printf " files will be linked\n"
2620	mkdir -p ${pathout[$i]}
2621	cd ${localout[$i]}
2622	for file in $(ls *)
2623	do
2624	ln -f $file ${pathout[$i]}
2625	done >\|/dev/null 2>&1
2626	cd $tempdir
2627	fi
2628
2629	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2630	if [[ ! -f "${pathout[$i]}/_000000" ]]
2631	then
2632	if [[ $link_local_output = true ]]
2633	then
2634	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2635	fi
2636	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2637	cp -r ${localout[$i]}/* ${pathout[$i]}
2638	fi
2639
2640	fi
2641	fi
2642	done
2643
2644	if (( i != 0 ))
2645	then
2646	if [[ $transfer_problems = true ]]
2647	then
2648	printf "\n$dashes\n *** OUTPUT-files saved"
2649	printf "\n +++ WARNING: some data transfers failed! \n"
2650	else
2651	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2652	fi
2653	fi
2654
2655
2656	# IF REQUIRED, START A RESTART-JOB
2657	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2658	if [[ -f CONTINUE_RUN ]]
2659	then
2660
2661	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2662	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2663	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2664	# -b START A BATCH JOB
2665	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2666	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2667	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2668
2669	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2670	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2671	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2672	then
2673	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2674	fi
2675
2676	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2677	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2678	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2679	then
2680	prc=`echo $prc \| sed 's/#/r/g'`
2681	fi
2682
2683
2684	# START THE RESTART-JOB
2685	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2686	echo " $prc"
2687	printf "\n$dashes\n"
2688	if [[ $running_on_remote = true ]]
2689	then
2690
2691	echo "*** ssh will be used to initiate restart-runs!"
2692	echo " return_address=\"$return_address\" "
2693	echo " return_username=\"$local_username\" "
2694
2695	if [[ "$remote_loginnode" != "" ]]
2696	then
2697	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
2698	else
2699	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2700	fi
2701
2702	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2703	sleep 30
2704
2705	else
2706
2707	# START THE RESTART JOB ON THE LOCAL HOST
2708	eval $prc # THE ' MUST BE EVALUATED
2709	cd - > /dev/null
2710
2711	fi
2712	printf "\n$dashes\n *** restart-run initiated \n"
2713
2714
2715	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2716	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2717	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2718	# MAY BE VERY HUGE)
2719	(( i = 0 ))
2720	while (( i < nr_of_input_files ))
2721	do
2722	(( i = i + 1 ))
2723	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2724	then
2725	rm -r ${absnamein[$i]}
2726	fi
2727	done
2728
2729	fi
2730
2731
2732	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2733	cd $HOME
2734	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2735
2736
2737	else
2738
2739
2740	# PREPARING ACTIONS,
2741	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2742
2743	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2744	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2745	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2746	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2747	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2748	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2749	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2750	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2751	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2752	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2753	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2754	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2755	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2756	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2757	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2758	if [[ $create_remote_batch_job = true ]]
2759	then
2760	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2761	if [[ $do_trace = true ]]
2762	then
2763	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2764	fi
2765	elif [[ $create_batch_job = true ]]
2766	then
2767	palmrun_com=${palmrun_com}" -j"
2768	if [[ $do_trace = true ]]
2769	then
2770	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2771	fi
2772	fi
2773
2774
2775	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2776	# REMOTE HOST
2777	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2778	job_protocol_file=$job_protocol_file_local
2779	if [[ $create_remote_batch_job = true ]]
2780	then
2781	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2782	job_protocol_file=$job_protocol_file_remote
2783	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2784	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2785	fi
2786
2787
2788	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2789	jobfile=jobfile.$run_id
2790
2791
2792	# FIRST CREATE THE BATCH DIRECTIVES
2793	(( i = 0 ))
2794	while (( i < ibd ))
2795	do
2796	(( i = i + 1 ))
2797	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2798	eval line=\"$line\"
2799	echo "$line" >> $jobfile
2800	done
2801	echo " " >> $jobfile
2802
2803
2804	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2805	# PROTOCOL
2806	if [[ $create_remote_batch_job = true ]]
2807	then
2808	echo "set +vx" >> $jobfile
2809	echo "trap '" >> $jobfile
2810	echo "set +vx" >> $jobfile
2811	echo "cd ${remote_jobcatalog}" >> $jobfile
2812	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2813
2814	# ADD THE BATCH DIRECTIVES
2815	(( i = 0 ))
2816	while (( i < ibdt ))
2817	do
2818	(( i = i + 1 ))
2819	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2820	eval line=\"$line\"
2821	echo "$line" >> $jobfile
2822	done
2823	echo " " >> $jobfile
2824
2825	echo "set -x" >> $jobfile
2826	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${jobname}" >> $jobfile
2827	echo "%%END%%" >> $jobfile
2828	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2829	echo "$submit_command $scpjob_file" >> $jobfile
2830	echo "rm $scpjob_file" >> $jobfile
2831	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2832	echo "set -x" >> $jobfile
2833	echo " ' exit" >> $jobfile
2834	fi
2835
2836
2837	# ACTIVATE ERROR-TRACEBACK
2838	if [[ $do_trace = true ]]
2839	then
2840	echo "set -x" >> $jobfile
2841	else
2842	echo "set +vx" >> $jobfile
2843	fi
2844
2845
2846	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2847	if [[ "$login_init_cmd" != "" ]]
2848	then
2849	echo "$login_init_cmd" >> $jobfile
2850	fi
2851	if [[ "$module_commands" != "" ]]
2852	then
2853	echo "$module_commands" >> $jobfile
2854	fi
2855
2856
2857	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2858	if [[ $create_remote_batch_job = true ]]
2859	then
2860	echo "mkdir $tempdir" >> $jobfile
2861	echo "chmod go+rx $tempdir" >> $jobfile
2862	else
2863	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2864	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2865	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2866	mkdir $tempdir
2867	chmod go+rx $tempdir
2868	fi
2869	echo "cd $tempdir" >> $jobfile
2870	echo "export tempdir=$tempdir" >> $jobfile
2871	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2872	echo "export PATH=.:\$PATH" >> $jobfile
2873	echo "export execute_palmrun=true" >> $jobfile
2874
2875
2876	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2877	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2878	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2879	echo "LOCAL_PWD=$working_directory" >> $jobfile
2880	echo "export LOCAL_PWD" >> $jobfile
2881
2882
2883	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2884	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2885	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2886
2887
2888	# CALL PALMRUN WITHIN THE JOB
2889	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2890	echo "set -x" >> $jobfile
2891	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2892
2893
2894	# TRANSFER JOBFILE TO THE TARGET HOST
2895	if [[ $create_jobfile_only = false ]]
2896	then
2897
2898	if [[ $create_remote_batch_job = true ]]
2899	then
2900
2901	echo " "
2902	echo " *** transfer of job to remote host via scp"
2903	if [[ $do_trace = true ]]
2904	then
2905	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2906	fi
2907	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2908
2909	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2910	if [[ $do_trace = true ]]
2911	then
2912	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"
2913	fi
2914	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
2915
2916	elif [[ $create_batch_job = true ]]
2917	then
2918
2919	eval local_jobcatalog=$local_jobcatalog
2920	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2921	cd $local_jobcatalog
2922	echo " "
2923	echo " *** submit the job"
2924	if [[ $do_trace = true ]]
2925	then
2926	echo "$submit_command ${host_configuration}_${job_id}"
2927	fi
2928	$submit_command ${host_configuration}_${job_id}
2929	rm ${host_configuration}_${job_id}
2930	cd - > /dev/null
2931
2932	fi
2933
2934	rm -rf $jobfile
2935
2936	else
2937
2938	printf "\n *** jobfile created under name \"$jobfile\" "
2939	printf "\n no batch-job has been sent!"
2940
2941	fi
2942
2943	fi # END OF REMOTE-PART

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