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source: palm/trunk/SCRIPTS/palmrun @ 3272

Last change on this file since 3272 was 3236, checked in by raasch, 6 years ago
host identifier in header output renamed config. identifier, host_configuration renamed configuration_identifier, jobname renamed run_identifier, palmbuild: header output of PALM code revision, options -m, -s, and -S removed, palmrun: run_id renamed run_id_number, job_id renamed run_id, option -r renamed -i
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 99.7 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 3236 2018-09-10 09:07:06Z suehring $
29	# warning issued in case of file connection file version mismatch,
30	# host_configuration renamed configuration_identifier,
31	# "host identifier" in header output renamed "config. identifier",
32	# jobname renamed run_identifier,
33	# run_id renamed run_id_number
34	# job_id renamed run_id
35	# option -r renamed -i
36	#
37	# 3151 2018-07-19 08:45:38Z raasch
38	# removed additional listing of files to be compiled, print PALM code revision
39	# in header
40	#
41	# 3132 2018-07-16 11:44:58Z raasch
42	# create consistent error messages in case of failed restarts,
43	# check existence of remote job catalog
44	#
45	# 3043 2018-05-25 10:47:54Z raasch
46	# check for setting of fast_io_catalog
47	#
48	# 3033 2018-05-23 15:26:19Z raasch
49	# -T option not required for interactive runs (tasks per node =
50	# total number of cores is assumed as default, if option is not given),
51	# reformatting of a few messages,
52	# bugfix: destination output directory is created if attribute "pe" is set in
53	# .palm.iofiles
54	#
55	# 2718 2018-01-02 08:49:38Z maronga
56	# bugfix of r2990
57	#
58	# 2718 2018-01-02 08:49:38Z maronga
59	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
60	# not in the working directory from where palmrun is called
61	#
62	# 2718 2018-01-02 08:49:38Z maronga
63	# svfout in the activation string will be replaced now by svfin in case of
64	# automatic restarts
65	#
66	# 2718 2018-01-02 08:49:38Z maronga
67	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
68	# the possible output or input of sky view factors
69	#
70	# 2718 2018-01-02 08:49:38Z maronga
71	# "fname" renamed to "jobname"
72	#
73	# 2718 2018-01-02 08:49:38Z maronga
74	# parameters are allowed in output commands (OC:)
75	#
76	# 2718 2018-01-02 08:49:38Z maronga
77	# bugfix: exit if no queue has been given neither with option -q nor in the
78	# configuration file
79	#
80	# 2718 2018-01-02 08:49:38Z maronga
81	# file connection file from trunk/SCRIPTS is taken by default
82	#
83	# 2718 2018-01-02 08:49:38Z maronga
84	# Corrected "Former revisions" section
85	#
86	# 2696 2017-12-14 17:12:51Z kanani
87	# Change in file header (GPL part)
88	#
89	# 2693 2017-12-13 12:33:49Z raasch
90	# replacement of variables given by {{<variable>}} in configuration file is now
91	# done in a more general way, variable names are written in small letters
92	#
93	# 2670 2017-12-06 16:32:19Z raasch
94	# test printouts removed
95	#
96	# 2669 2017-12-06 16:03:27Z raasch
97	# file attributes in .palm.iofiles restructured, "loc" attribute completely
98	# removed,
99	# wildcard (*) allowed in .palm.iofiles as file activation string for output
100	# files,
101	# informative messages in case of missing optional input files shortened
102	# bugfix: variable cycle explicitly interpreted with 10 as the number base
103	#
104	# 2638 2017-11-23 12:44:23Z raasch
105	# use of wildcards in file connection statements enabled
106	#
107	# 2605 2017-11-09 15:31:46Z raasch
108	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
109	# will not be sent with the job file any more, but copied into the
110	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
111	#
112	# 2600 2017-11-01 14:11:20Z raasch
113	# cycle numbers are made three digits wide
114	#
115	# 2566 2017-10-20 08:50:47Z raasch
116	# execute command for combine_plot_fields added
117	# "TEMPDIR" renamed "tempdir"
118	# temporary working directory for local batch jobs is created immediately within
119	# the user's palmrun call, due to a requirement of the "grid engine" batch
120	# system, where the working directory is given with batch directive -wd and must
121	# already exist when the job is submitted,
122	# informative messages in non-trace mode reduced and partly reformatted
123	#
124	# 2551 2017-10-18 07:25:11Z raasch
125	# TEMPDIR added as replacement string to be used in batch directives
126	#
127	# 2512 2017-10-04 08:26:59Z raasch
128	# bugfix for determining cycle numbers of NetCDF input files
129	#
130	# 2506 2017-09-29 08:30:37Z raasch
131	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
132	# host configuration added to SOURCES_FOR_RUN_... folder name
133	# host_identifier renamed host_configuration
134	# option -W added to allow for job dependencies
135	#
136	# 2501 2017-09-26 11:41:55Z raasch
137	# default value for number of cores (option -X) set to 1
138	# bugfix for mechanism which overwrites configuration file settings with values
139	# provided by palmrun options
140	#
141	# 2499 2017-09-22 16:47:58Z kanani
142	# option -h named configuration identifier
143	#
144	# 2480 2017-09-19 06:24:14Z maronga
145	# bugfix for last revision
146	#
147	# 2479 2017-09-19 06:12:16Z raasch
148	# option -A (project account number) added
149	#
150	# 2422 2017-09-08 08:25:41Z raasch
151	# initial revision
152	#
153	#--------------------------------------------------------------------------------#
154	# palmrun - script for running PALM jobs on local and remote hosts
155	#--------------------------------------------------------------------------------#
156
157
158
159	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
160
161	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
162	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
163	# (TOO MANY ARGUMENTS - PROBLEM)
164	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
165
166	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
167	typeset -i nr_of_output_files=0
168	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
169	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
170	# SCRIPT-OPTION ARGUMENTS
171	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
172	typeset -i icycle inode ival maxcycle mpi_tasks
173	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
174
175	activation_string_list=""
176	AddFilenames=""
177	combine_plot_fields=true
178	compiler_name=""
179	compiler_name_ser=""
180	compiler_options=""
181	configuration_identifier="default"
182	cores=1
183	cores_atmos=0
184	cores_ocean=0
185	coupled_dist=""
186	cpp_options=""
187	cpumax=0
188	create_batch_job=false
189	create_jobfile_only=false
190	create_remote_batch_job=false
191	dashes=" ----------------------------------------------------------------------------"
192	defaultqueue=""
193	delete_temporary_catalog=true
194	do_compile=true
195	do_trace=false
196	executable=""
197	execute_command=""
198	execution_error=false
199	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
200	global_revision=""
201	hostfile=""
202	hp=""
203	keep_data_from_previous_run=false
204	link_local_input=false
205	link_local_output=false
206	linker_options=""
207	local_jobcatalog=""
208	locat=normal
209	makefile=""
210	max_par_io_str=""
211	prc=$0
212	while [[ $(echo $prc \| grep -c "/") != 0 ]]
213	do
214	prc=`echo $prc \| cut -f2- -d"/"`
215	done
216	module_calls=""
217	palmrun_memory=""
218	palmrun_script_name=$prc
219	openmp=false
220	previous_job=""
221	project_account=""
222	queue=none
223	read_svf=""
224	restart_run=false
225	return_address=""
226	remote_jobcatalog=""
227	remote_username=""
228	running_in_batch_mode=false
229	run_coupled_model=false
230	run_id=""
231	run_id_number=""
232	run_identifier=test
233	silent=false
234	source_list=""
235	source_path=""
236	tasks_per_node=0
237	threads_per_task=1
238	transfer_problems=false
239	user_source_path=""
240	use_existing_sources_folder=""
241	use_openmp=false
242	version="palmrun 1.0 Rev$Rev: 3236 $"
243	working_directory=`pwd`
244	write_binary=""
245	write_svf=""
246
247
248	# ERROR HANDLING IN CASE OF EXIT
249	trap 'if [[ $locat != normal && $locat != control_c ]]
250	then
251
252	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
253	(( i = 0 ))
254	while (( i < iec ))
255	do
256	(( i = i + 1 ))
257	printf "\n *** Execution of ERROR-command:\n"
258	printf " >>> ${err_command[$i]}\n"
259	eval ${err_command[$i]}
260	done
261	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
262	printf "\n\n+++ palmrun killed \n\n"
263	elif [[ $locat != control_c ]]
264	then
265	printf "\n --> palmrun finished\n\n"
266	fi' exit
267
268
269	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
270	trap 'cd; rm -rf $tempdir
271	printf "\n+++ palmrun killed by \"^C\" \n\n"
272	locat=control_c
273	exit
274	' 2
275
276
277	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
278	# WHICH WILL BE USED TO START RESTART-JOBS
279	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:Z option
280	do
281	case $option in
282	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
283	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
284	(b) create_batch_job=true; prc="$prc -b";;
285	(B) delete_temporary_catalog=false; prc="$prc -B";;
286	(C) restart_run=true; prc="$prc -C";;
287	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
288	(F) create_jobfile_only=true;;
289	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
290	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
291	(i) run_id_number=$OPTARG;;
292	(j) running_in_batch_mode=true;;
293	(k) keep_data_from_previous_run=true; prc="$prc -k";;
294	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
295	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
296	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
297	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
298	(R) return_address=$OPTARG;;
299	(s) source_list=$OPTARG;;
300	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
301	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
302	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
303	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
304	(v) silent=true; prc="$prc -v";;
305	(V) use_existing_sources_folder="-V";;
306	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
307	(W) previous_job=$OPTARG;;
308	(x) do_trace=true;set -x; prc="$prc -x";;
309	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
310	(y) ocean_file_appendix=true; prc="$prc -y";;
311	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
312	(Z) combine_plot_fields=false; prc="$prc -Z";;
313	(\?) printf "\n +++ unknown option $OPTARG \n"
314	printf "\n --> type \"$0 ?\" for available options \n"
315	locat=parameter;exit;;
316	esac
317	done
318
319
320	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
321	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
322	(( to_shift = $OPTIND - 1 ))
323	shift $to_shift
324
325	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
326	if [[ "$1" = "?" ]]
327	then
328	(printf "\n *** Description of available palmrun options:\n"
329	printf "\n Option Description Default-Value"
330	printf "\n -a activation string list \"\" "
331	printf "\n -A project account number ---"
332	printf "\n -b batch-job on local machine ---"
333	printf "\n -B do not delete temporary directory at end ---"
334	printf "\n -d run identifier test"
335	printf "\n -F create batch job file only ---"
336	printf "\n -h host configuration \"default\" "
337	printf "\n -k keep data from previous run"
338	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
339	printf "\n -M Makefile name Makefile"
340	printf "\n -O threads per openMP task ---"
341	printf "\n -q queue \"$queue\" "
342	printf "\n -s filenames of routines to be compiled \"\" "
343	printf "\n must end with .f, .f90, .F, or .c !"
344	printf "\n use \"..\" for more than one file and wildcards"
345	printf "\n -s LM compiles all locally modified files"
346	printf "\n -t allowed cpu-time in seconds (batch) 0"
347	printf "\n -T tasks per node ---"
348	printf "\n -u username on remote machine \"\" "
349	printf "\n -v no prompt for confirmation ---"
350	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
351	printf "\n -w maximum parallel io streams as given by -X"
352	printf "\n -W name of job to wait for ---"
353	printf "\n -x tracing of palmrun for debug purposes ---"
354	printf "\n -X # of processors (on parallel machines) 1"
355	printf "\n -y add appendix \"_O\" to all local output"
356	printf "\n files (ocean precursor runs followed by"
357	printf "\n coupled atmosphere-ocean runs) ---"
358	printf "\n -Y run coupled model, \"#1 #2\" with"
359	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
360	printf "\n -Z skip combine_plot_fields at the end of "
361	printf "\n the simulation ---"
362	printf "\n "
363	printf "\n Possible values of positional parameter <modus>:"
364	printf "\n \"?\" - this outline \n\n") \| more
365	exit
366	elif [[ "$1" != "" ]]
367	then
368	printf "\n +++ positional parameter $1 unknown \n"
369	locat=parameter; exit
370	fi
371
372
373
374	# SHORT STARTING MESSAGE
375	printf "\n*** $version "
376	printf "\n will be executed. Please wait ..."
377
378
379	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
380	export fname=$run_identifier
381	export jobname=$run_identifier
382
383
384	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
385	config_file=.palm.config.$configuration_identifier
386	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
387
388
389	# CHECK, IF CONFIGURATION FILE EXISTS
390	if [[ ! -f $config_file ]]
391	then
392	printf "\n\n +++ configuration file: "
393	printf "\n $config_file"
394	printf "\n does not exist"
395	locat=connect; exit
396	fi
397
398
399	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
400	if [[ -f .palm.iofiles ]]
401	then
402
403	# CHECK VERSION MISMATCH
404	if [[ $running_in_batch_mode != true ]]
405	then
406	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
407	then
408	printf "\n\n +++ WARNING: A file connection file has been found in your"
409	printf "\n working directory, but its revision does not match"
410	printf "\n the revision of the default (trunk) version."
411	printf "\n You may need to update your connection file!"
412	fi
413	fi
414
415	fileconnection_file=.palm.iofiles
416
417	fi
418
419
420	# CHECK, IF FILE CONNECTION FILE EXISTS
421	if [[ ! -f $fileconnection_file ]]
422	then
423	printf "\n\n +++ file connection file: "
424	printf "\n $fileconnection_file"
425	printf "\n does not exist"
426	locat=connect; exit
427	fi
428
429
430	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
431	if [[ "$activation_string_list" = "" ]]
432	then
433	printf "\n\n +++ no activation string list given: "
434	printf "\n please set palmrun option \"-a\" "
435	locat=palmrun_option; exit
436	fi
437
438
439	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
440	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
441	then
442	write_binary=true
443	else
444	write_binary=false
445	fi
446
447	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
448	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
449	then
450	write_svf=true
451	else
452	write_svf=false
453	fi
454
455	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
456	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
457	then
458	read_svf=true
459	else
460	read_svf=false
461	fi
462
463
464	# READ AND EVALUATE THE CONFIGURATION-FILE
465	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
466
467	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
468	while read line
469	do
470
471	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
472	eval line=\"$line\"
473
474
475	# INTERPRET THE LINE
476	if [[ "$(echo $line)" = "" ]]
477	then
478
479	# EMPTY LINE, NO ACTION
480	continue
481
482	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
483	then
484
485	# LINE IS A COMMENT LINE
486	continue
487
488	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
489	then
490
491	# LINE DEFINES AN ENVIRONMENT-VARIABLE
492	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
493	value=`echo $line \| cut -d" " -s -f2-`
494
495
496	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
497	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
498	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
499	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
500	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
501	# CONFIGURATION-FILE.
502	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
503	then
504	eval export $var="\$value"
505
506	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
507	if [[ $do_trace = true ]]
508	then
509	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
510	fi
511	fi
512
513	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
514	then
515
516	# LINE DEFINES BATCH-DIRECTIVE
517	(( ibd = ibd + 1 ))
518	line=$(echo $line \| cut -c4-)
519	batch_directive[$ibd]="$line"
520
521	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
522	then
523
524	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
525	# REMOTE TO A LOCAL HOST
526	(( ibdt = ibdt + 1 ))
527	line=$(echo $line \| cut -c5-)
528	batch_directive_transfer[$ibdt]="$line"
529
530	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
531	then
532
533	# LINE DEFINES ERROR-COMMAND
534	(( iec = iec + 1 ))
535	line=$(echo $line \| cut -c4-)
536	err_command[$iec]="$line"
537
538	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
539	then
540
541	# LINE DEFINES INPUT-COMMAND
542	(( iic = iic + 1 ))
543	line=$(echo $line \| cut -c4-)
544	in_command[$iic]="$line"
545
546	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
547	then
548
549	# LINE DEFINES OUTPUT-COMMAND
550	(( ioc = ioc + 1 ))
551	line=$(echo $line \| cut -c4-)
552	out_command[$ioc]="$line"
553
554	else
555
556	# SKIP ALL OTHER LINES
557	continue
558
559	fi
560
561	done < $config_file
562
563
564	# CHECK SETTING OF REQUIRED PARAMETERS
565	if [[ "$fast_io_catalog" = "" ]]
566	then
567	printf "\n +++ no fast_io_catalog found in $config_file"
568	printf "\n Please add line \"fast_io_catalog ...\" to that file."
569	locat=config_file; exit
570	fi
571	if [[ "$compiler_name" = "" ]]
572	then
573	printf "\n +++ no compiler name found in $config_file"
574	printf "\n Please add line \"compiler_name ...\" to that file."
575	locat=config_file; exit
576	fi
577	if [[ "$compiler_name_ser" = "" ]]
578	then
579	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
580	printf "\n Please add line \"compiler_name_ser ...\" to that file."
581	locat=config_file; exit
582	fi
583	if [[ "$compiler_options" = "" ]]
584	then
585	printf "\n +++ no compiler options found in $config_file"
586	printf "\n Please add line \"compiler_options ...\" to that file."
587	locat=config_file; exit
588	fi
589	if [[ "$linker_options" = "" ]]
590	then
591	printf "\n +++ no linker options found in $config_file"
592	printf "\n Please add line \"linker_options ...\" to that file."
593	locat=config_file; exit
594	fi
595	if [[ "$execute_command" = "" ]]
596	then
597	printf "\n +++ no execute command found in $config_file"
598	printf "\n Please add line \"execute_command ...\" to that file."
599	locat=config_file; exit
600	fi
601
602	if [[ "$hostfile" != "" ]]
603	then
604	if [[ $hostfile != auto && ! -f $hostfile ]]
605	then
606	printf "\n +++ no hostfile \"$hostfile\" found"
607	printf "\n Please check line \"hostfile ...\" in $config_file"
608	locat=config_file; exit
609	fi
610	fi
611
612
613	# DETERMINE THE CALL STATUS
614	if [[ "$return_address" != "" ]]
615	then
616
617	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
618	# BATCH MODE AND ...
619	running_on_remote=true
620
621	else
622
623	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
624	if [[ "$remote_ip" != "" ]]
625	then
626
627	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
628	create_remote_batch_job=true
629
630	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
631	if [[ "$remote_jobcatalog" = "" ]]
632	then
633	printf "\n +++ no remote jobcatalog found in $config_file"
634	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
635	locat=config_file; exit
636	fi
637
638
639	fi
640	running_on_remote=false
641	fi
642
643
644
645	# READ AND EVALUATE THE I/O-FILE LIST
646	[[ $silent = false ]] && printf "\n Reading the I/O files... "
647
648	# READ THE FILE CONNECTION FILE LINE BY LINE
649	while read line
650	do
651
652	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
653	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
654
655	# INTERPRET THE LINE
656	if [[ "$(echo $line)" = "" ]]
657	then
658	# EMPTY LINE, NO ACTION
659	continue
660
661	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
662	then
663
664	# LINE IS A COMMENT LINE
665	true
666
667	else
668
669	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
670	# s2a: in/out - field
671	# s2b: action - field (optional)
672	s1=`echo "$line" \| cut -d" " -f1`
673	s2=`echo "$line" \| cut -d" " -s -f2`
674	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
675	then
676	s2a=$s2
677	s2b=""
678	else
679	s2a=`echo $s2 \| cut -d":" -f1`
680	s2b=`echo $s2 \| cut -d":" -f2`
681	fi
682	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
683	s4=`echo "$line" \| cut -d" " -s -f4`
684	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
685	s5=`echo "$line" \| cut -d" " -s -f5`
686	s6=`echo "$line" \| cut -d" " -s -f6`
687
688
689	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
690	# INPUT- OR OUTPUT-LIST.
691	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
692	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
693	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
694	# IS NOT CHECKED AND STORED.
695	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
696	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
697	then
698	found=false
699	for actual in $activation_string_list
700	do
701	for formal in $s3
702	do
703	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
704	done
705	done
706	if [[ $found = true ]]
707	then
708	(( iin = iin + 1 ))
709	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
710	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
711	if [[ "$s2a" = inopt ]]
712	then
713	optin_pre[$iin]=yes
714	else
715	optin_pre[$iin]=no
716	fi
717
718	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
719	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
720	if [[ $running_on_remote = true && "$s2b" = tr ]]
721	then
722	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
723	fi
724
725	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
726	# THE WILDCARD FROM THE ENDING
727	if [[ "${s5: -1}" = "*" ]]
728	then
729	if [[ "$s2b" = "di" ]]
730	then
731	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
732	printf "\n see file \"$fileconnection_file\", line"
733	printf "\n$line"
734	locat=iofiles_file; exit
735	fi
736	multin[$iin]=true
737	string=${endin_pre[$iin]}
738	endin_pre[$iin]="${string%?}"
739	else
740	multin[$iin]=false
741	fi
742	fi
743	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
744	then
745	found=false
746	for actual in $activation_string_list
747	do
748	for formal in $s3
749	do
750	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
751	done
752	done
753	if [[ $found = true ]]
754	then
755	(( iout = iout + 1 ))
756	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
757	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
758
759	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
760	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
761	if [[ $formal = wildcard ]]
762	then
763	warnout_pre[$iout]=false
764	else
765	warnout_pre[$iout]=true
766	fi
767
768	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
769	# THE WILDCARD FROM THE LOCAL FILENAME
770	if [[ "${s1: -1}" = "*" ]]
771	then
772	if [[ "$s2b" = "di" ]]
773	then
774	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
775	printf "\n see file \"$fileconnection_file\", line"
776	printf "\n$line"
777	locat=iofiles_file; exit
778	fi
779	multout[$iout]=true
780	string=${localout_pre[$iout]}
781	localout_pre[$iout]="${string%?}"
782	else
783	multout[$iout]=false
784	fi
785	fi
786	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
787	then
788	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
789	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
790	locat=connect; exit
791	fi
792	IFS="$IFSALT"
793	fi
794
795	done < $fileconnection_file
796
797
798
799	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
800	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
801	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
802	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
803	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
804	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
805
806
807
808	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
809	if [[ $run_coupled_model = true ]]
810	then
811
812	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
813	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
814
815	if (( $cores_ocean + $cores_atmos != $cores ))
816	then
817
818	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
819	printf "\n PEs (total) : $cores"
820	printf "\n PEs (atmosphere): $cores_atmos"
821	printf "\n PEs (ocean) : $cores_ocean"
822	locat=coupling; exit
823
824	fi
825
826	fi
827
828
829	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
830	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
831	# FOLDER
832	if [[ $running_in_batch_mode = true ]]
833	then
834
835	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
836	then
837	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
838	printf "\n Please check the output of the palmrun-call"
839	printf "\n that you did on your local host."
840	locat=SOURCES_FOR_RUN; exit
841	fi
842
843	else
844
845	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
846	# AUTOMATIC RESTART RUN
847	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
848	if [[ $restart_run = false ]]
849	then
850
851	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
852	# THE LOCAL HOST
853	if [[ ! -d $source_path ]]
854	then
855	printf "\n\n +++ source path \"$source_path\" on local host"
856	printf "\n \"$(hostname)\" does not exist"
857	locat=source_path; exit
858	fi
859
860	rm -rf ${base_directory}/${sources_for_run_catalog}
861	mkdir -p ${base_directory}/${sources_for_run_catalog}
862
863	if [[ "$source_list" = LM ]]
864	then
865
866	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
867	source_list=""
868	cd $source_path
869
870
871	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
872	if [[ ! -d ../.svn ]]
873	then
874	printf "\n\n +++ source directory"
875	printf "\n \"$source_path\" "
876	printf "\n is not under control of \"subversion\"."
877	printf "\n Please do not use palmrun-option \"-s LM\"\n"
878	fi
879
880
881	# LIST ALL MODIFIED SOURCE CODE FILES
882	Filenames=""
883	svn status > tmp_svnstatus
884	while read line
885	do
886	firstc=`echo $line \| cut -c1`
887	if [[ $firstc = M \|\| $firstc = "?" ]]
888	then
889	Name=`echo "$line" \| cut -c8-`
890	extension=`echo $Name \| cut -d. -f2`
891	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
892	then
893	Filenames="$Filenames "$Name
894	fi
895	fi
896	done < tmp_svnstatus
897	rm -rf tmp_svnstatus
898
899
900	# COPY FILES TO SOURCES_FOR_RUN_...
901	for filename in $Filenames
902	do
903	cp $filename ${base_directory}/${sources_for_run_catalog}
904	source_list=$source_list"$filename "
905	done
906
907	cd - > /dev/null
908
909
910	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
911	elif [[ "$source_list" != "" ]]
912	then
913
914	cd $source_path
915
916	for filename in $source_list
917	do
918
919	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
920	if [[ $(echo $filename \| grep -c "/") != 0 ]]
921	then
922	printf "\n +++ source code file: $filename"
923	printf "\n must not contain (\"/\") "
924	locat=source; exit
925	fi
926
927	if [[ ! -f $filename ]]
928	then
929	printf "\n +++ source code file: $filename"
930	printf "\n does not exist"
931	locat=source; exit
932	else
933	cp $filename ${base_directory}/${sources_for_run_catalog}
934	fi
935
936	done
937
938	cd - > /dev/null
939
940	fi
941
942	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
943	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
944	if [[ ! -f $makefile ]]
945	then
946	printf "\n +++ file \"$makefile\" does not exist"
947	locat=make; exit
948	else
949	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
950	fi
951
952
953	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
954	if [[ "$user_source_path" != "" ]]
955	then
956
957	# DOES THE DIRECTORY EXIST?
958	if [[ ! -d $user_source_path ]]
959	then
960
961	printf "\n\n *** INFORMATIVE: additional source code directory"
962	printf "\n \"$user_source_path\" "
963	printf "\n does not exist or is not a directory."
964	printf "\n No source code will be used from this directory!\n"
965	user_source_path=""
966	if [[ $silent == false ]]
967	then
968	sleep 2
969	fi
970
971	else
972
973	cd $user_source_path
974
975	Names=$(ls -1 *.f90 2>&1)
976	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
977	Names=$(ls -1 *.F90 2>&1)
978	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
979	Names=$(ls -1 *.F 2>&1)
980	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
981	Names=$(ls -1 *.f 2>&1)
982	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
983	Names=$(ls -1 *.c 2>&1)
984	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
985
986	cd - > /dev/null
987	cd ${base_directory}/${sources_for_run_catalog}
988
989	# COPY MAKEFILE IF EXISTING
990	if [[ -f $user_source_path/Makefile ]]
991	then
992	printf "\n\n *** user Makefile from directory"
993	printf "\n \"$user_source_path\" is used \n"
994	if [[ $silent == false ]]
995	then
996	sleep 1
997	fi
998	cp $user_source_path/Makefile .
999	fi
1000
1001	for filename in $AddFilenames
1002	do
1003	if [[ -f $filename ]]
1004	then
1005	printf "\n +++ source code file \"$filename\" found in additional"
1006	printf "\n source code directory \"$user_source_path\" "
1007	printf "\n but was also given with option \"-s\" which means that it should be taken"
1008	printf "\n from directory \"$source_path\"."
1009	locat=source; exit
1010	fi
1011
1012	cp $user_source_path/$filename .
1013	source_list="$source_list $filename"
1014
1015	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1016	if [[ $(grep -c $filename Makefile) = 0 ]]
1017	then
1018	printf "\n\n +++ user file \"$filename\" "
1019	printf "\n is not listed in Makefile \n"
1020	locat=source; exit
1021	fi
1022	done
1023	cd - > /dev/null
1024	fi
1025	fi
1026
1027	# COPY CONFIGURATION FILES
1028	cp $config_file ${base_directory}/${sources_for_run_catalog}
1029	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1030
1031	# COPY SHELLSCRIPTS
1032	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1033	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1034
1035	fi
1036
1037	fi
1038
1039
1040	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1041	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1042	if [[ "$global_revision" = "" ]]
1043	then
1044	global_revision=`svnversion $source_path 2>/dev/null`
1045	global_revision="Rev: $global_revision"
1046	fi
1047
1048
1049	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1050	if [[ -n $cores ]]
1051	then
1052
1053	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1054	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1055	if [[ $tasks_per_node = 0 ]]
1056	then
1057	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1058	then
1059	printf "\n"
1060	printf "\n +++ option \"-T\" (tasks per node) is missing"
1061	printf "\n set -T option or define tasks_per_node in the config file"
1062	locat=tasks_per_node; (( iec = 0 )); exit
1063	else
1064	# DEFAULT FOR INTERACTIVE RUN
1065	tasks_per_node=$cores
1066	fi
1067	fi
1068
1069	if (( cores < tasks_per_node ))
1070	then
1071	printf "\n"
1072	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1073	printf "\n given values: -T $tasks_per_node -X $cores"
1074	locat=tasks_per_node; (( iec = 0 )); exit
1075	fi
1076
1077	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1078	(( mpi_tasks = cores / threads_per_task ))
1079	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1080	(( ii = cores / tasks_per_node ))
1081	(( remaining_cores = cores - ii * tasks_per_node ))
1082	if (( remaining_cores > 0 ))
1083	then
1084	printf "\n"
1085	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1086	printf "\n divisor of the total number of cores (option \"-X\")"
1087	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1088	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1089	(( nodes = nodes + 1 ))
1090	fi
1091
1092	fi
1093
1094
1095	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1096	if [[ "$maximum_parallel_io_streams" = "" ]]
1097	then
1098	maximum_parallel_io_streams=$cores
1099	fi
1100
1101
1102	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1103	if [[ "$scp_port" != "" ]]
1104	then
1105	PORTOPT="-P $scp_port"
1106	SSH_PORTOPT="-p $scp_port"
1107	fi
1108
1109
1110	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1111	# CONFIG-FILE
1112	if [[ "$ssh_key" != "" ]]
1113	then
1114	ssh_key="-i $HOME/.ssh/$ssh_key"
1115	fi
1116
1117
1118	# SET QUEUE, IF NOT GIVEN
1119	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1120	then
1121
1122	if [[ $queue = none && "$defaultqueue" = "" ]]
1123	then
1124	printf "\n"
1125	printf "\n +++ no default queue given in configuration file and no queue"
1126	printf "\n given with option -q"
1127	locat=queue; exit
1128	fi
1129	if [[ $queue = none ]]
1130	then
1131	queue=$defaultqueue
1132	fi
1133
1134	fi
1135
1136
1137	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1138	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1139	(( i = 0 ))
1140	(( nr_of_input_files = 0 ))
1141	while (( i < iin ))
1142	do
1143	(( i = i + 1 ))
1144
1145	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1146	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1147	if [[ "${actionin_pre[$i]}" = di ]]
1148	then
1149	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1150	else
1151	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1152	fi
1153
1154
1155	# CHECK IF FILE EXISTS
1156	if ! ls $filename* 1>/dev/null 2>&1
1157	then
1158
1159	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1160	if [[ "${optin_pre[$i]}" != "yes" ]]
1161	then
1162	printf "\n\n +++ INPUT-file: "
1163	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1164	then
1165	printf "\n $filename"
1166	else
1167	printf "\n $filename.${extin_pre[$i]}"
1168	fi
1169	printf "\n does not exist\n"
1170	locat=input; exit
1171	else
1172	(( nr_of_input_files = nr_of_input_files + 1 ))
1173	localin[$nr_of_input_files]="${localin_pre[$i]}"
1174	optin[$nr_of_input_files]="${optin_pre[$i]}"
1175	actionin[$nr_of_input_files]="unavailable"
1176	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1177	endin[$nr_of_input_files]="${endin_pre[$i]}"
1178	extin[$nr_of_input_files]="${extin_pre[$i]}"
1179	fi
1180
1181	else
1182
1183	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1184	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1185	# ENDINGS
1186	if [[ "${multin[$i]}" = true ]]
1187	then
1188	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1189	ls -1 -d ${filename} > filelist 2>/dev/null
1190	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1191	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1192
1193	endings=""
1194	while read line
1195	do
1196	# filename without path (i.e. after the last "/")
1197	basefilename=$(basename ${line})
1198
1199	# check if there is an extension and remove it
1200	ext=${basefilename##*.}
1201	if [[ "$ext" = "${extin_pre[$i]}" ]]
1202	then
1203	basefilename=${basefilename%.*}
1204	fi
1205
1206	# check for an existing cycle number and remove it
1207	cycle=${basefilename##*.}
1208	if [[ $cycle =~ ^-?[0-9]+$ ]]
1209	then
1210	basefilename=${basefilename%.*}
1211	fi
1212
1213	# remove the run_identifier from the beginning
1214	length_run_identifier=${#run_identifier}
1215	ending=${basefilename:${length_run_identifier}}
1216
1217	# remove the ending given in the .iofiles from the beginning
1218	endingstring="${endin_pre[$i]}"
1219	length_ending=${#endingstring}
1220	ending=${ending:${length_ending}}
1221
1222	if [[ "$ending" = "" ]]
1223	then
1224	# standard ending as given in the .iofiles
1225	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1226	then
1227	endings="$endings DEFAULT"
1228	fi
1229	else
1230	# ending must start with "_", otherwise its a different file
1231	if [[ "${ending:0:1}" = "_" ]]
1232	then
1233	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1234	then
1235	endings="$endings $ending"
1236	fi
1237	fi
1238	fi
1239
1240	done <filelist
1241
1242	rm filelist
1243
1244	else
1245
1246	# SINGLE NAME
1247	endings=DEFAULT
1248
1249	fi
1250
1251	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1252	for ending in $endings
1253	do
1254
1255	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1256	if [[ $ending = DEFAULT ]]
1257	then
1258	ending=""
1259	fi
1260
1261	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1262	(( nr_of_input_files = nr_of_input_files + 1 ))
1263	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1264	optin[$nr_of_input_files]="${optin_pre[$i]}"
1265	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1266	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1267	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1268	extin[$nr_of_input_files]="${extin_pre[$i]}"
1269
1270
1271	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1272	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1273	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1274	then
1275	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1276	else
1277	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1278	fi
1279
1280	# DETERMINE THE FILE'S CYCLE NUMBER
1281	(( maxcycle = 0 ))
1282	ls -1 -d $filename > filelist 2>/dev/null
1283	ls -1 -d $filename.* >> filelist 2>/dev/null
1284	while read line
1285	do
1286	# filename without path (i.e. after the last "/")
1287	basefilename=$(basename ${line})
1288
1289	# check if there is an extension
1290	extension=${basefilename##*.}
1291	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1292	then
1293	basefilename=${basefilename%.*}
1294	fi
1295
1296	# check for an existing cycle number
1297	cycle=${basefilename##*.}
1298	if [[ $cycle =~ ^-?[0-9]+$ ]]
1299	then
1300	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1301	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1302	(( icycle = $((10#$cycle)) ))
1303	else
1304	(( icycle = 0 ))
1305	fi
1306
1307	if (( icycle > maxcycle ))
1308	then
1309	(( maxcycle = icycle ))
1310
1311	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1312	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1313	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1314	then
1315	leading_zero=true
1316	else
1317	leading_zero=false
1318	fi
1319	fi
1320
1321	done <filelist
1322	rm filelist
1323
1324	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1325	if [[ $leading_zero = true ]]
1326	then
1327	cyclestring=`printf "%03d" $maxcycle`
1328	else
1329	cyclestring=$maxcycle
1330	fi
1331
1332	# APPEND CYCLE NUMBER TO FILENAME
1333	if (( maxcycle > 0 ))
1334	then
1335	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1336	then
1337	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1338	else
1339	filename=${filename}.$cyclestring
1340	fi
1341	else
1342	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1343	then
1344	filename=${filename}.${extin[$nr_of_input_files]}
1345	fi
1346	fi
1347
1348	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1349	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1350	absnamein[$nr_of_input_files]=$filename
1351	if (( maxcycle > 0 ))
1352	then
1353	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1354	then
1355	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1356	else
1357	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1358	fi
1359	else
1360	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1361	then
1362	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1363	else
1364	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1365	fi
1366	fi
1367
1368	done
1369
1370	fi
1371
1372	done
1373
1374
1375	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1376	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1377	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1378	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1379	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1380	# REMOTE HOST)
1381	(( i = 0 ))
1382	while (( i < iout ))
1383	do
1384	(( i = i + 1 ))
1385	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1386	then
1387	if [[ "${actionout_pre[$i]}" = tr ]]
1388	then
1389	actionout_pre[$i]=""
1390	elif [[ "${actionout_pre[$i]}" = trpe ]]
1391	then
1392	actionout_pre[$i]=pe
1393	elif [[ "${actionout_pre[$i]}" = tra ]]
1394	then
1395	actionout_pre[$i]=a
1396	fi
1397	(( maxcycle = 0 ))
1398	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1399	eval catalogname=${pathout_pre[$i]}
1400	if ! ls $filename* 1>/dev/null 2>&1
1401	then
1402
1403	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1404	if cat /dev/null > $filename
1405	then
1406	rm $filename
1407	else
1408
1409	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1410	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1411	if [[ ! -d $catalogname ]]
1412	then
1413	if mkdir -p $catalogname
1414	then
1415	printf "\n\n *** directory:"
1416	printf "\n $catalogname"
1417	printf "\n was created\n"
1418	else
1419	printf "\n\n +++ OUTPUT-file:"
1420	printf "\n $filename"
1421	printf "\n cannot be created, because directory does not exist"
1422	printf "\n and cannot be created either"
1423	printf "\n"
1424	locat=output ; exit
1425	fi 2>/dev/null
1426	else
1427	printf "\n\n +++ OUTPUT-file:"
1428	printf "\n $filename"
1429	printf "\n cannot be created, although directory exists"
1430	printf "\n"
1431	locat=output ; exit
1432	fi
1433	fi 2>/dev/null
1434
1435	fi
1436
1437	fi
1438	done
1439
1440
1441	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1442	if [[ $running_in_batch_mode = false ]]
1443	then
1444	run_id_number=$RANDOM
1445	run_id=${run_identifier}.$run_id_number
1446
1447	tempdir=$fast_io_catalog/$run_id
1448	fi
1449
1450
1451	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1452	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1453	then
1454
1455	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1456	if [[ $ibd = 0 ]]
1457	then
1458	printf "\n"
1459	printf "\n +++ no batch directives found in configuration file"
1460	locat=config_file_batch_directives; (( iec = 0 )); exit
1461	fi
1462
1463	# CHECK IF CPUTIME IS GIVEN FOR JOB
1464	done=false
1465	cputime=$cpumax
1466	while [[ $done = false ]]
1467	do
1468	if (( cputime == 0 ))
1469	then
1470	printf "\n +++ cpu-time is undefined"
1471	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1472	printf "\n >>> "
1473	read cputime 1>/dev/null 2>&1
1474	else
1475	done=true
1476	fi
1477	done
1478	cpumax=$cputime
1479
1480	# CHECK THE MEMORY DEMAND
1481	done=false
1482	while [[ $done = false ]]
1483	do
1484	if (( memory == 0 ))
1485	then
1486	printf "\n +++ memory demand is undefined"
1487	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1488	printf "\n >>> "
1489	read memory 1>/dev/null 2>&1
1490	else
1491	done=true
1492	fi
1493	done
1494
1495	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1496	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1497	then
1498	while [[ -z $remote_username ]]
1499	do
1500	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1501	printf "\n >>> Please type username:"
1502	printf "\n >>> "
1503	read remote_username
1504	done
1505	fi
1506
1507	else
1508
1509	if [[ $running_in_batch_mode = false ]]
1510	then
1511	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1512	cpumax=$cputime
1513	else
1514	cputime=$cpumax
1515	fi
1516
1517	fi
1518
1519
1520	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1521	(( cpu_hours = cputime / 3600 ))
1522	(( resttime = cputime - cpu_hours * 3600 ))
1523	(( cpu_minutes = resttime / 60 ))
1524	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1525	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1526
1527
1528	# OUTPUT OF THE PALMRUN-HEADER
1529	calltime=$(date)
1530	printf "\n"
1531	printf "#------------------------------------------------------------------------# \n"
1532	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1533	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1534	printf "\| \| \n"
1535	column1="called on:"; column2=$(hostname)
1536	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1537	if [[ $create_remote_batch_job = true ]]
1538	then
1539	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1540	else
1541	if [[ $running_on_remote = true ]]
1542	then
1543	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1544	else
1545	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1546	fi
1547	fi
1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1549
1550	column1="running in:"
1551	if [[ $running_in_batch_mode = true ]]
1552	then
1553	column2="batch job mode"
1554	else
1555	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1556	then
1557	column2="job creation mode"
1558	else
1559	column2="interactive run mode"
1560	fi
1561	fi
1562	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1563
1564	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1565	then
1566	if [[ "$project_account" != "" ]]
1567	then
1568	column1="project account number:"
1569	column2="$project_account"
1570	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1571	fi
1572	fi
1573
1574	if [[ -n $cores ]]
1575	then
1576	if [[ $run_coupled_model = false ]]
1577	then
1578	column1="number of cores:"; column2=$cores
1579	else
1580	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1581	fi
1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1583	fi
1584	if [[ -n $tasks_per_node ]]
1585	then
1586	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1588	if (( remaining_cores > 0 ))
1589	then
1590	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1592	fi
1593	fi
1594	if [[ $maximum_parallel_io_streams != $cores ]]
1595	then
1596	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1598	fi
1599	if [[ $use_openmp = true ]]
1600	then
1601	column1="threads per task:"; column2="$threads_per_task"
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	fi
1604	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1605	then
1606	column1="memory demand / PE":; column2="$memory MB"
1607	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1608	column1="job cpu time (h:m:s):"; column2="$timestring"
1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1610	fi
1611	printf "\| \| \n"
1612	if [[ "$source_list" != "" ]]
1613	then
1614	if [[ "$make_options" != "" ]]
1615	then
1616	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1618	line=$(echo "$make_options" \| cut -c46-)
1619	while [[ "$line" != "" ]]
1620	do
1621	column1=""
1622	column2=$(echo "$line" \| cut -c-45)
1623	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1624	line=$(echo "$line" \| cut -c46-)
1625	done
1626	fi
1627	fi
1628
1629	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1631	line=$(echo "$cpp_options" \| cut -c46-)
1632	while [[ "$line" != "" ]]
1633	do
1634	column1=""
1635	column2=$(echo "$line" \| cut -c-45)
1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1637	line=$(echo "$line" \| cut -c46-)
1638	done
1639
1640	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1642	line=$(echo "$compiler_options" \| cut -c46-)
1643	while [[ "$line" != "" ]]
1644	do
1645	column1=""
1646	column2=$(echo "$line" \| cut -c-45)
1647	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1648	line=$(echo "$line" \| cut -c46-)
1649	done
1650
1651	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1652	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1653	line=$(echo "$linker_options" \| cut -c46-)
1654	while [[ "$line" != "" ]]
1655	do
1656	column1=""
1657	column2=$(echo "$line" \| cut -c-45)
1658	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1659	line=$(echo "$line" \| cut -c46-)
1660	done
1661
1662	if [[ "$login_init_cmd" != "" ]]
1663	then
1664	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1666	line=$(echo "$login_init_cmd" \| cut -c46-)
1667	while [[ "$line" != "" ]]
1668	do
1669	column1=""
1670	column2=$(echo "$line" \| cut -c-45)
1671	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1672	line=$(echo "$line" \| cut -c46-)
1673	done
1674	fi
1675
1676	if [[ "$module_commands" != "" ]]
1677	then
1678	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1680	line=$(echo "$module_commands" \| cut -c46-)
1681	while [[ "$line" != "" ]]
1682	do
1683	column1=""
1684	column2=$(echo "$line" \| cut -c-45)
1685	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1686	line=$(echo "$line" \| cut -c46-)
1687	done
1688	fi
1689	printf "\| \| \n"
1690	column1="run identifier:"; column2=$run_identifier
1691	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1692	column1="activation string list:"; column2=$(echo $activation_string_list)
1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1694
1695	if [[ "$ocean_file_appendix" = true ]]
1696	then
1697	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1698	fi
1699
1700	if [[ "$source_list" != "" ]]
1701	then
1702	printf "\| \| \n"
1703	printf "\| Files to be compiled: \| \n"
1704	line=$source_list
1705	while [[ "$line" != "" ]]
1706	do
1707	linestart=$(echo $line \| cut -c-70)
1708	printf "\| %-70s \| \n" "$linestart"
1709	line=$(echo "$line" \| cut -c71-)
1710	done
1711	fi
1712	printf "#------------------------------------------------------------------------#"
1713
1714
1715
1716	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1717	if [[ $do_trace = true ]]
1718	then
1719	(( i = 0 ))
1720	while (( i < nr_of_input_files ))
1721	do
1722	(( i = i + 1 ))
1723	if (( i == 1 ))
1724	then
1725	printf "\n\n >>> INPUT-file assignments:\n"
1726	fi
1727	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1728	done
1729	(( i = 0 ))
1730	while (( i < iout ))
1731	do
1732	(( i = i + 1 ))
1733	if (( i == 1 ))
1734	then
1735	printf "\n\n >>> OUTPUT-file assignments:\n"
1736	fi
1737	printf "\n ${localout[$i]} : ${pathout[$i]}"
1738	done
1739	(( i = 0 ))
1740	while (( i < iic ))
1741	do
1742	(( i = i + 1 ))
1743	if (( i == 1 ))
1744	then
1745	printf "\n\n >>> INPUT-commands:\n"
1746	fi
1747	printf "\n ${in_command[$i]}"
1748	done
1749	(( i = 0 ))
1750	while (( i < ioc ))
1751	do
1752	(( i = i + 1 ))
1753	if (( i == 1 ))
1754	then
1755	printf "\n\n >>> OUTPUT-commands:\n"
1756	fi
1757	printf "\n ${out_command[$i]}"
1758	done
1759	fi
1760
1761	# QUERY FOR CONTINUE
1762	if [[ $silent = false && $running_in_batch_mode = false ]]
1763	then
1764	antwort=dummy
1765	printf "\n\n"
1766	printf " >>> everything o.k. (y/n) ? "
1767	while read antwort
1768	do
1769	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1770	then
1771	printf " >>> everything o.k. (y/n) ? "
1772	else
1773	break
1774	fi
1775	done
1776	if [[ $antwort = n \|\| $antwort = N ]]
1777	then
1778	locat=user_abort; (( iec = 0 )); exit
1779	fi
1780	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1781	then
1782	printf "\n *** batch-job will be created and submitted"
1783	else
1784	printf "\n *** PALMRUN will now continue to execute on this machine"
1785	fi
1786	fi
1787
1788
1789
1790	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1791	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1792	then
1793
1794	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1795	then
1796	printf "\n\n *** creating executable and other sources for the remote host\n"
1797	else
1798	printf "\n\n *** creating executable and other sources for the local host\n"
1799	fi
1800
1801	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1802	# IT SHALL BE CREATED
1803	ask_for_make_depository=false
1804	if [[ $create_remote_batch_job = true ]]
1805	then
1806
1807	line=`grep %base_directory $config_file`
1808	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1809	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1810
1811	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1812	then
1813	printf "\n\n +++ make depository \"${make_depository}\""
1814	printf "\n on remote host not found!"
1815	ask_for_make_depository=true
1816	fi
1817	rm ${configuration_identifier}_last_make_protokoll
1818
1819	else
1820
1821	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1822	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1823	if [[ ! -d ${make_depository} ]]
1824	then
1825	printf "\n\n +++ make depository \"${make_depository}\""
1826	printf "\n on local host not found!"
1827	ask_for_make_depository=true
1828	fi
1829
1830	fi
1831
1832	if [[ $ask_for_make_depository = true ]]
1833	then
1834
1835	antwort=dummy
1836	printf "\n\n"
1837	printf " >>> Create a new one (y/n) ? "
1838	while read antwort
1839	do
1840	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1841	then
1842	printf " >>> Create a new one (y/n) ? "
1843	else
1844	break
1845	fi
1846	done
1847	if [[ $antwort = n \|\| $antwort = N ]]
1848	then
1849	locat=user_abort; (( iec = 0 )); exit
1850	fi
1851
1852	if [[ $do_trace = true ]]
1853	then
1854	palmbuild -h $configuration_identifier
1855	else
1856	palmbuild -v -h $configuration_identifier
1857	fi
1858
1859	if [[ $? != 0 ]]
1860	then
1861
1862	# ABORT IN CASE OF COMPILATION PROBLEMS
1863	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1864	locat=make_depository
1865	exit
1866	else
1867	echo " *** now continue with creating executable and other sources"
1868	fi
1869
1870	fi
1871
1872	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1873	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
1874
1875	if [[ $? != 0 ]]
1876	then
1877
1878	# ABORT IN CASE OF COMPILATION PROBLEMS
1879	printf "\n +++ error while creating executable and/or other sources"
1880	locat=execution
1881	rm -rf ${base_directory}/${sources_for_run_catalog}
1882	exit
1883
1884	else
1885
1886	printf " *** executable and other sources created\n"
1887	rm -rf ${base_directory}/${sources_for_run_catalog}
1888
1889	fi
1890
1891	fi
1892
1893
1894	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1895	# WILL BE COPIED TO THE REMOTE HOST
1896	if [[ $create_remote_batch_job = true ]]
1897	then
1898	(( i = 0 ))
1899	while (( i < nr_of_input_files ))
1900	do
1901	(( i = i + 1 ))
1902	if [[ "${actionin[$i]}" = tr ]]
1903	then
1904	eval inputfile=${pathin[$i]}/${frelin[$i]}
1905	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1906	fi
1907	done
1908	if (( i > 0 ))
1909	then
1910	printf "\n\n *** input files have been copied to the remote host\n"
1911	fi
1912	fi
1913
1914
1915	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1916	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1917	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1918	then
1919
1920	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1921	if [[ $running_in_batch_mode = false ]]
1922	then
1923	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1924	# FOLDER
1925	mkdir -p $tempdir
1926	chmod go+rx $tempdir
1927	cd $tempdir
1928	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1929	printf "\n *** changed to temporary directory: $tempdir"
1930
1931	else
1932
1933	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1934	printf "\n *** running in temporary directory: $tempdir"
1935
1936	fi
1937
1938
1939	# PROVIDE THE INPUT FILES
1940	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1941	optional_files_missing=false
1942	(( i = 0 ))
1943	while (( i < nr_of_input_files ))
1944	do
1945	(( i = i + 1 ))
1946	if (( i == 1 ))
1947	then
1948	printf "\n\n *** providing INPUT-files:\n$dashes"
1949	fi
1950
1951
1952	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1953	if [[ "${actionin[$i]}" = unavailable ]]
1954	then
1955	optional_files_missing=true
1956	continue
1957	fi
1958
1959	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1960	files_for_cores=false; filetype=file
1961	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1962	then
1963	files_for_cores=true; filetype=files
1964	actionin[$i]=""
1965	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1966	then
1967	actionin[$i]=""
1968	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1969	then
1970	files_for_cores=true; filetype=files
1971	actionin[$i]="ln"
1972	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1973	then
1974	actionin[$i]="ln"
1975	fi
1976
1977	if [[ $files_for_cores = true ]]
1978	then
1979	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1980	else
1981	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1982	fi
1983
1984	# INPUT-FILES TO BE LINKED
1985	if [[ "${actionin[$i]}" = ln ]]
1986	then
1987
1988	printf "\n $filetype will be linked"
1989	if [[ $files_for_cores = false ]]
1990	then
1991	if [[ -f "${absnamein[$i]}" ]]
1992	then
1993	ln ${absnamein[$i]} ${localin[$i]}
1994	got_tmp[$i]=true
1995	fi
1996	else
1997	if [[ -d "${absnamein[$i]}" ]]
1998	then
1999	mkdir -p ${localin[$i]}
2000	cd ${absnamein[$i]}
2001	for file in $(ls *)
2002	do
2003	ln $file $tempdir/${localin[$i]}
2004	done >\|/dev/null 2>&1
2005	cd $tempdir
2006	fi
2007
2008	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2009	if [[ ! -f "${localin[$i]}/_000000" ]]
2010	then
2011	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2012	cp -r ${absnamein[$i]}/* ${localin[$i]}
2013	fi
2014
2015	got_tmp[$i]=true
2016	fi
2017	fi
2018
2019	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2020	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2021	then
2022
2023	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2024	then
2025
2026	# FILE COPIES ARE PROVIDED FOR ALL CORES
2027	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2028	printf "\n file will be provided for $cores processors"
2029	mkdir -p ${localin[$i]}
2030	ival=$cores
2031	(( ii = 0 ))
2032	while (( ii <= ival-1 ))
2033	do
2034	if (( ii < 10 ))
2035	then
2036	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2037	elif (( ii < 100 ))
2038	then
2039	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2040	elif (( ii < 1000 ))
2041	then
2042	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2043	else
2044	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2045	fi
2046	(( ii = ii + 1 ))
2047	done
2048
2049	else
2050
2051	if [[ $files_for_cores = true ]]
2052	then
2053
2054	# PROVIDE FILES FOR EACH CORE
2055	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2056	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2057	printf "\n providing $cores files for the respective cores"
2058	mkdir -p ${localin[$i]}
2059	if [[ $link_local_input = true ]]
2060	then
2061	printf " files will be linked\n"
2062	cd ${absnamein[$i]}
2063	for file in $(ls *)
2064	do
2065	ln -f $file ${localin[$i]}
2066	done
2067	cd $tempdir
2068	fi
2069
2070	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2071	if [[ ! -f "${localin[$i]}/_000000" ]]
2072	then
2073	if [[ $link_local_input = true ]]
2074	then
2075	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2076	fi
2077	cp -r ${absnamein[$i]}/* ${localin[$i]}
2078	fi
2079
2080	else
2081
2082	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2083	if [[ $link_local_input = true ]]
2084	then
2085	printf " file will be linked\n"
2086	ln -f ${absnamein[$i]} ${localin[$i]}
2087	fi
2088	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2089	if [[ ! -f "${localin[$i]}" ]]
2090	then
2091	if [[ $link_local_input = true ]]
2092	then
2093	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2094	fi
2095	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2096	then
2097	mv ${absnamein[$i]} ${localin[$i]}
2098	else
2099	cp ${absnamein[$i]} ${localin[$i]}
2100	fi
2101	fi
2102	fi
2103	fi
2104	fi
2105
2106	done
2107	if (( i != 0 ))
2108	then
2109	if [[ $optional_files_missing = true ]]
2110	then
2111	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2112	fi
2113	printf "\n$dashes\n *** all INPUT-files provided \n"
2114	fi
2115
2116
2117	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2118	(( i = 0 ))
2119	while (( i < iic ))
2120	do
2121	(( i = i + 1 ))
2122	if (( i == 1 ))
2123	then
2124	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2125	fi
2126	printf "\n >>> ${in_command[$i]}"
2127	eval ${in_command[$i]}
2128	if (( i == iic ))
2129	then
2130	printf "\n$dashes\n"
2131	fi
2132	done
2133
2134
2135	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2136	# (FILE ENVPAR WILL BE READ BY PALM)
2137	cat > ENVPAR << EOF
2138	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2139	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2140	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2141	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2142	maximum_cpu_time_allowed = ${cpumax}.,
2143	revision = '$global_revision',
2144	batch_job = .${running_in_batch_mode}. /
2145
2146	EOF
2147
2148
2149	# STARTING THE EXECUTABLE
2150	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2151	PATH=$PATH:$tempdir
2152
2153
2154	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2155	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2156	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2157	eval line=\"$line\"
2158	execute_command="$line"
2159
2160
2161	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2162	if [[ "$execute_command_for_combine" = "" ]]
2163	then
2164	eval line2=\"$line2\"
2165	execute_command_for_combine="$line2"
2166	fi
2167
2168
2169
2170	# PROVIDE A HOSTFILE, IF REQUIRED
2171	if [[ "$hostfile" != "" ]]
2172	then
2173
2174	if [[ $hostfile = auto ]]
2175	then
2176	# CREATE A NEW HOSTFILE
2177	(( ii = 1 ))
2178	while (( ii <= cores / threads_per_task ))
2179	do
2180	echo $(hostname) >> hostfile
2181	(( ii = ii + 1 ))
2182	done
2183	if (( cores / threads_per_task == 0 ))
2184	then
2185	echo $(hostname) >> hostfile
2186	fi
2187
2188	else
2189	cp $hostfile hostfile
2190	fi
2191	eval line=\"`head -n $ii hostfile`\"
2192	printf "\n *** running on: $line"
2193	fi
2194
2195
2196
2197	# SET THE NUMBER OF OPENMP-THREADS
2198	if [[ $use_openmp = true ]]
2199	then
2200	export OMP_NUM_THREADS=$threads_per_task
2201	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2202	else
2203	export OMP_NUM_THREADS=1
2204	fi
2205
2206
2207	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2208	if [[ $run_coupled_model = false ]]
2209	then
2210	if [[ "$ocean_file_appendix" = true ]]
2211	then
2212	echo "precursor_ocean" > coupling_steering
2213	else
2214	echo "precursor_atmos" > coupling_steering
2215	fi
2216	else
2217	(( iia = $cores_atmos / $threads_per_task ))
2218	(( iio = $cores_ocean / $threads_per_task ))
2219	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2220	printf "\n\n"
2221	echo "coupled_run $iia $iio" > coupling_steering
2222	fi
2223
2224	printf "\n *** execute command:"
2225	printf "\n \"$execute_command\" \n\n"
2226
2227	$execute_command < coupling_steering
2228
2229	if [[ $? != 0 ]]
2230	then
2231
2232	# ABORT IN CASE OF RUNTIME ERRORS
2233	printf "\n +++ runtime error occured"
2234	locat=execution
2235	exit
2236
2237	else
2238
2239	printf "\n$dashes\n *** execution finished \n"
2240
2241	fi
2242
2243
2244	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2245	# BY EACH CORE INTO ONE FILE
2246	if [[ ! -f combine_plot_fields.x ]]
2247	then
2248
2249	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2250	printf "\n 2d- and/or 3d-data may be incomplete!"
2251	printf "\n Your previous palmbuild may have failed. Please check.\n"
2252
2253	elif [[ "$combine_plot_fields" == true ]]
2254	then
2255
2256	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2257	$execute_command_for_combine
2258
2259	else
2260
2261	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2262	# DATA OUTPUT
2263	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2264	fi
2265
2266
2267
2268	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2269	(( i = 0 ))
2270	while (( i < ioc ))
2271	do
2272	(( i = i + 1 ))
2273	if (( i == 1 ))
2274	then
2275	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2276	fi
2277
2278	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2279	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2280
2281	printf "\n >>> ${out_command[$i]}"
2282	eval ${out_command[$i]}
2283	if (( i == ioc ))
2284	then
2285	printf "\n$dashes\n"
2286	fi
2287	done
2288
2289
2290	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2291	# WILDCARDS
2292	(( i = 0 ))
2293	(( nr_of_output_files = 0 ))
2294
2295	while (( i < iout ))
2296	do
2297
2298	(( i = i + 1 ))
2299
2300	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2301	# CREATE A LIST FOR THE DETECTED ENDINGS
2302	if [[ "${multout[$i]}" = true ]]
2303	then
2304	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2305	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2306	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2307
2308	endings="DEFAULT"
2309	while read line
2310	do
2311	# remove the local name from the beginning
2312	localnamestring="${localout_pre[$i]}"
2313	length_localname=${#localnamestring}
2314	ending=${line:${length_localname}}
2315
2316	if [[ "$ending" != "" ]]
2317	then
2318	endings="$endings $ending"
2319	fi
2320
2321	done <filelist
2322
2323	rm filelist
2324
2325	else
2326
2327	# SINGLE NAME
2328	endings=DEFAULT
2329
2330	fi
2331
2332	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2333	for ending in $endings
2334	do
2335
2336	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2337	if [[ $ending = DEFAULT ]]
2338	then
2339	ending=""
2340	fi
2341
2342	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2343	(( nr_of_output_files = nr_of_output_files + 1 ))
2344	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2345	transout[$nr_of_output_files]="${transout_pre[$i]}"
2346	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2347	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2348	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2349	extout[$nr_of_output_files]="${extout_pre[$i]}"
2350	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2351
2352	done
2353
2354	done
2355
2356
2357
2358
2359	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2360	(( i = 0 ))
2361	while (( i < nr_of_output_files ))
2362	do
2363	(( i = i + 1 ))
2364	if (( i == 1 ))
2365	then
2366	printf "\n\n *** saving OUTPUT-files:"
2367
2368	# GET RUN NUMBER ASSIGNED BY PALM
2369	if [[ -f RUN_NUMBER ]]
2370	then
2371	read run_number < RUN_NUMBER
2372	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2373	usecycle_option="-U $run_number"
2374	else
2375	run_number=0
2376	usecycle_option=""
2377	fi
2378	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2379	then
2380	printf "\n *** in case of SCP transfers to local host"
2381	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2382	fi
2383	printf "\n$dashes"
2384	fi
2385
2386	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2387	then
2388
2389	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2390
2391	# DETERMINE THE CYCLE NUMBER
2392	ls -1 -d $filename > filelist 2>/dev/null
2393	ls -1 -d $filename.* >> filelist 2>/dev/null
2394	while read line
2395	do
2396
2397	# filename without path (i.e. after the last "/")
2398	basefilename=$(basename ${line})
2399
2400	# check if there is an extension
2401	extension=${basefilename##*.}
2402	if [[ "$extension" = "${extout[$i]}" ]]
2403	then
2404	basefilename=${basefilename%.*}
2405	fi
2406
2407	# check for an existing cycle number
2408	cycle=${basefilename##*.}
2409	if [[ $cycle =~ ^-?[0-9]+$ ]]
2410	then
2411	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2412	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2413	(( icycle = $((10#$cycle)) + 1 ))
2414	else
2415	(( icycle = 1 ))
2416	fi
2417
2418	if (( icycle > maxcycle ))
2419	then
2420	(( maxcycle = icycle ))
2421	fi
2422
2423	done <filelist
2424	rm filelist
2425
2426
2427	# SET THE CYCLE NUMBER
2428	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2429	if [[ "${actionout[$i]}" = a ]]
2430	then
2431	(( maxcycle = maxcycle - 1 ))
2432	fi
2433
2434	(( cycnum[$i] = maxcycle ))
2435	pathout[$i]=$filename
2436
2437
2438	# ADD CYCLE NUMBER TO FILENAME
2439	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2440	if [[ "${actionout[$i]}" != "a" ]]
2441	then
2442	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2443	# WITH AN EXISTING CYCLE NUMBER
2444	if (( run_number >= cycnum[$i] ))
2445	then
2446	(( cycnum[$i] = run_number ))
2447	else
2448	if (( run_number > 0 ))
2449	then
2450	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2451	fi
2452	fi
2453	fi
2454	if (( cycnum[$i] > 0 ))
2455	then
2456	cyclestring=`printf "%03d" ${cycnum[$i]}`
2457	pathout[$i]=${pathout[$i]}.$cyclestring
2458	fi
2459	fi
2460
2461	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2462	files_for_cores=false; filetype=file
2463	link_local_output=false
2464	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2465	then
2466	files_for_cores=true; filetype=directory
2467	actionout[$i]=""
2468	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2469	then
2470	actionout[$i]=""
2471	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2472	then
2473	files_for_cores=true; filetype=directory
2474	link_local_output=true
2475	actionout[$i]=""
2476	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2477	then
2478	link_local_output
2479	actionout[$i]=""
2480	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2481	then
2482	files_for_cores=true; filetype=directory
2483	actionout[$i]="tr"
2484	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2485	then
2486	actionout[$i]="tr"
2487	fi
2488
2489	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2490	then
2491	if [[ ${warnout[$i]} = true ]]
2492	then
2493	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2494	fi
2495	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2496	then
2497	if [[ ${warnout[$i]} = true ]]
2498	then
2499	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2500	fi
2501	else
2502
2503
2504	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2505	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2506	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2507	then
2508	if [[ $running_on_remote = true ]]
2509	then
2510
2511	# SET OPTIONS FOR TRANSFER
2512	if [[ "${actionout[$i]}" = tr ]]
2513	then
2514	if [[ $files_for_cores = false ]]
2515	then
2516	catalog_option=""
2517	catalog_string=""
2518	else
2519	catalog_option="-c"
2520	catalog_string="/"
2521	fi
2522	append_option=""
2523	append_string=""
2524	else
2525	append_option="-A"
2526	append_string="append"
2527	fi
2528
2529	transfer_failed=false
2530	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2531	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2532
2533	# TRANSFER VIA SCP
2534	if [[ "$remote_loginnode" != "" ]]
2535	then
2536	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]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2537	else
2538	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
2539	fi
2540	[[ $? != 0 ]] && transfer_failed=true
2541
2542
2543	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2544	if [[ $transfer_failed = true ]]
2545	then
2546	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2547	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2548
2549	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2550	eval local_catalog=${pathout[$i]}
2551	if [[ ! -d $local_catalog ]]
2552	then
2553	printf " *** local directory does not exist. Trying to create:\n"
2554	printf " $local_catalog \n"
2555	mkdir -p $local_catalog
2556	fi
2557	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2558	transfer_problems=true
2559	fi
2560
2561	else
2562
2563	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2564	# BE COPIED OR APPENDED ON THIS MACHINE
2565	if [[ "${actionout[$i]}" = tr ]]
2566	then
2567	actionout[$i]=""
2568	else
2569	actionout[$i]="a"
2570	fi
2571	fi
2572	fi
2573
2574
2575	# APPEND ON THIS MACHINE
2576	if [[ "${actionout[$i]}" = "a" ]]
2577	then
2578	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2579	then
2580	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2581	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2582	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2583	else
2584	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2585	printf "\n ${pathout[$i]}\n"
2586	cat ${localout[$i]} >> ${pathout[$i]}
2587	fi
2588	fi
2589
2590	# COPY ON THIS MACHINE
2591	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2592	# ON DIFFERENT FILE-SYSTEMS
2593	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2594	then
2595
2596	# COPY IN CASE OF RUNS ON SINGLE CORES
2597	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2598	then
2599	printf "\n >>> OUTPUT: ${localout[$i]} to"
2600	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2601	if [[ $link_local_output = true ]]
2602	then
2603	printf " file will be linked\n"
2604	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2605	fi
2606	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2607	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2608	then
2609	if [[ $link_local_output = true ]]
2610	then
2611	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2612	fi
2613	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2614	else
2615	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2616	fi
2617	else
2618	printf "\n >>> OUTPUT: ${localout[$i]} to"
2619	printf "\n ${pathout[$i]}\n"
2620	if [[ $link_local_output = true ]]
2621	then
2622	printf " file will be linked\n"
2623	ln -f ${localout[$i]} ${pathout[$i]}
2624	fi
2625	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2626	if [[ ! -f "${pathout[$i]}" ]]
2627	then
2628	if [[ $link_local_output = true ]]
2629	then
2630	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2631	fi
2632	cp ${localout[$i]} ${pathout[$i]}
2633	else
2634	printf "+++ no copy because file ${pathout[$i]} exists\n"
2635	fi
2636	fi
2637
2638	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2639	then
2640
2641	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2642	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2643	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2644	printf "\n ${pathout[$i]}\n"
2645	if [[ $link_local_output = true ]]
2646	then
2647	printf " files will be linked\n"
2648	mkdir -p ${pathout[$i]}
2649	cd ${localout[$i]}
2650	for file in $(ls *)
2651	do
2652	ln -f $file ${pathout[$i]}
2653	done >\|/dev/null 2>&1
2654	cd $tempdir
2655	fi
2656
2657	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2658	if [[ ! -f "${pathout[$i]}/_000000" ]]
2659	then
2660	if [[ $link_local_output = true ]]
2661	then
2662	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2663	fi
2664	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2665	cp -r ${localout[$i]}/* ${pathout[$i]}
2666	fi
2667
2668	fi
2669	fi
2670	done
2671
2672	if (( i != 0 ))
2673	then
2674	if [[ $transfer_problems = true ]]
2675	then
2676	printf "\n$dashes\n *** OUTPUT-files saved"
2677	printf "\n +++ WARNING: some data transfers failed! \n"
2678	else
2679	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2680	fi
2681	fi
2682
2683
2684	# IF REQUIRED, START A RESTART-JOB
2685	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2686	if [[ -f CONTINUE_RUN ]]
2687	then
2688
2689	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2690	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2691	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2692	# -b START A BATCH JOB
2693	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2694	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2695	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2696
2697	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2698	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2699	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2700	then
2701	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2702	fi
2703
2704	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2705	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2706	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2707	then
2708	prc=`echo $prc \| sed 's/#/r/g'`
2709	fi
2710
2711
2712	# START THE RESTART-JOB
2713	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2714	echo " $prc"
2715	printf "\n$dashes\n"
2716	if [[ $running_on_remote = true ]]
2717	then
2718
2719	echo "*** ssh will be used to initiate restart-runs!"
2720	echo " return_address=\"$return_address\" "
2721	echo " return_username=\"$local_username\" "
2722
2723	if [[ "$remote_loginnode" != "" ]]
2724	then
2725	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 \| tee palmrun_restart.log
2726	else
2727	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2728	fi
2729
2730	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2731	sleep 30
2732
2733	else
2734
2735	# START THE RESTART JOB ON THE LOCAL HOST
2736	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2737	cd - > /dev/null
2738
2739	fi
2740
2741	# CHECK, IF RESTART JOB HAS BEEN STARTED
2742	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2743	then
2744	printf "\n$dashes\n +++ creating restart run failed \n"
2745	locat=create_restart
2746	exit
2747	rm palmrun_restart.log
2748	else
2749	printf "\n$dashes\n *** restart run initiated \n"
2750	rm palmrun_restart.log
2751	fi
2752
2753
2754	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2755	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2756	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2757	# MAY BE VERY HUGE)
2758	(( i = 0 ))
2759	while (( i < nr_of_input_files ))
2760	do
2761	(( i = i + 1 ))
2762	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2763	then
2764	rm -r ${absnamein[$i]}
2765	fi
2766	done
2767
2768	fi
2769
2770
2771	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2772	cd $HOME
2773	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2774
2775
2776	else
2777
2778
2779	# PREPARING ACTIONS,
2780	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2781
2782	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2783	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2784	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2785	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2786	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2787	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2788	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2789	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2790	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2791	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2792	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2793	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2794	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2795	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2796	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2797	if [[ $create_remote_batch_job = true ]]
2798	then
2799	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2800	if [[ $do_trace = true ]]
2801	then
2802	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2803	fi
2804	elif [[ $create_batch_job = true ]]
2805	then
2806	palmrun_com=${palmrun_com}" -j"
2807	if [[ $do_trace = true ]]
2808	then
2809	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2810	fi
2811	fi
2812
2813
2814	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2815	# REMOTE HOST
2816	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2817	job_protocol_file=$job_protocol_file_local
2818	if [[ $create_remote_batch_job = true ]]
2819	then
2820	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2821	job_protocol_file=$job_protocol_file_remote
2822	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2823	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2824	fi
2825
2826
2827	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2828	jobfile=jobfile.$run_id_number
2829
2830
2831	# FIRST CREATE THE BATCH DIRECTIVES
2832	(( i = 0 ))
2833	while (( i < ibd ))
2834	do
2835	(( i = i + 1 ))
2836	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2837	eval line=\"$line\"
2838	echo "$line" >> $jobfile
2839	done
2840	echo " " >> $jobfile
2841
2842
2843	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2844	# PROTOCOL
2845	if [[ $create_remote_batch_job = true ]]
2846	then
2847	echo "set +vx" >> $jobfile
2848	echo "trap '" >> $jobfile
2849	echo "set +vx" >> $jobfile
2850	echo "cd ${remote_jobcatalog}" >> $jobfile
2851	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2852
2853	# ADD THE BATCH DIRECTIVES
2854	(( i = 0 ))
2855	while (( i < ibdt ))
2856	do
2857	(( i = i + 1 ))
2858	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2859	eval line=\"$line\"
2860	echo "$line" >> $jobfile
2861	done
2862	echo " " >> $jobfile
2863
2864	echo "set -x" >> $jobfile
2865	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
2866	echo "%%END%%" >> $jobfile
2867	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2868	echo "$submit_command $scpjob_file" >> $jobfile
2869	echo "rm $scpjob_file" >> $jobfile
2870	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2871	echo "set -x" >> $jobfile
2872	echo " ' exit" >> $jobfile
2873	fi
2874
2875
2876	# ACTIVATE ERROR-TRACEBACK
2877	if [[ $do_trace = true ]]
2878	then
2879	echo "set -x" >> $jobfile
2880	else
2881	echo "set +vx" >> $jobfile
2882	fi
2883
2884
2885	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2886	if [[ "$login_init_cmd" != "" ]]
2887	then
2888	echo "$login_init_cmd" >> $jobfile
2889	fi
2890	if [[ "$module_commands" != "" ]]
2891	then
2892	echo "$module_commands" >> $jobfile
2893	fi
2894
2895
2896	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2897	if [[ $create_remote_batch_job = true ]]
2898	then
2899	echo "mkdir $tempdir" >> $jobfile
2900	echo "chmod go+rx $tempdir" >> $jobfile
2901	else
2902	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2903	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2904	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2905	mkdir $tempdir
2906	chmod go+rx $tempdir
2907	fi
2908	echo "cd $tempdir" >> $jobfile
2909	echo "export tempdir=$tempdir" >> $jobfile
2910	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2911	echo "export PATH=.:\$PATH" >> $jobfile
2912	echo "export execute_palmrun=true" >> $jobfile
2913
2914
2915	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2916	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2917	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2918	echo "LOCAL_PWD=$working_directory" >> $jobfile
2919	echo "export LOCAL_PWD" >> $jobfile
2920
2921
2922	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2923	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2924	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2925
2926
2927	# CALL PALMRUN WITHIN THE JOB
2928	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2929	echo "set -x" >> $jobfile
2930	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2931
2932
2933	# TRANSFER JOBFILE TO THE TARGET HOST
2934	if [[ $create_jobfile_only = false ]]
2935	then
2936
2937	if [[ $create_remote_batch_job = true ]]
2938	then
2939
2940	echo " "
2941	echo " *** transfer of job to remote host via scp"
2942	if [[ $do_trace = true ]]
2943	then
2944	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
2945	fi
2946	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
2947
2948	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2949	if [[ $do_trace = true ]]
2950	then
2951	echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2952	fi
2953	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2954
2955	elif [[ $create_batch_job = true ]]
2956	then
2957
2958	eval local_jobcatalog=$local_jobcatalog
2959	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
2960	cd $local_jobcatalog
2961	echo " "
2962	echo " *** submit the job"
2963	if [[ $do_trace = true ]]
2964	then
2965	echo "$submit_command ${configuration_identifier}_${run_id}"
2966	fi
2967	$submit_command ${configuration_identifier}_${run_id}
2968	rm ${configuration_identifier}_${run_id}
2969	cd - > /dev/null
2970
2971	fi
2972
2973	rm -rf $jobfile
2974
2975	else
2976
2977	printf "\n *** jobfile created under name \"$jobfile\" "
2978	printf "\n no batch-job has been sent!"
2979
2980	fi
2981
2982	fi # END OF REMOTE-PART

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