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source: palm/trunk/SCRIPTS/palmrun @ 3034

Last change on this file since 3034 was 3033, checked in by raasch, 7 years ago
keyword correction
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 97.5 KB

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

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