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source: palm/trunk/SCRIPTS/palmrun @ 3302

Last change on this file since 3302 was 3294, checked in by raasch, 6 years ago
modularization of the ocean code
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 99.9 KB

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1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 3294 2018-10-01 02:37:10Z raasch $
29	# more detailed error message for outdated fileconnection file
30	#
31	# 3236 2018-09-10 09:07:06Z raasch
32	# warning issued in case of file connection file version mismatch,
33	# host_configuration renamed configuration_identifier,
34	# "host identifier" in header output renamed "config. identifier",
35	# jobname renamed run_identifier,
36	# run_id renamed run_id_number
37	# job_id renamed run_id
38	# option -r renamed -i
39	#
40	# 3151 2018-07-19 08:45:38Z raasch
41	# removed additional listing of files to be compiled, print PALM code revision
42	# in header
43	#
44	# 3132 2018-07-16 11:44:58Z raasch
45	# create consistent error messages in case of failed restarts,
46	# check existence of remote job catalog
47	#
48	# 3043 2018-05-25 10:47:54Z raasch
49	# check for setting of fast_io_catalog
50	#
51	# 3033 2018-05-23 15:26:19Z raasch
52	# -T option not required for interactive runs (tasks per node =
53	# total number of cores is assumed as default, if option is not given),
54	# reformatting of a few messages,
55	# bugfix: destination output directory is created if attribute "pe" is set in
56	# .palm.iofiles
57	#
58	# 2718 2018-01-02 08:49:38Z maronga
59	# bugfix of r2990
60	#
61	# 2718 2018-01-02 08:49:38Z maronga
62	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
63	# not in the working directory from where palmrun is called
64	#
65	# 2718 2018-01-02 08:49:38Z maronga
66	# svfout in the activation string will be replaced now by svfin in case of
67	# automatic restarts
68	#
69	# 2718 2018-01-02 08:49:38Z maronga
70	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
71	# the possible output or input of sky view factors
72	#
73	# 2718 2018-01-02 08:49:38Z maronga
74	# "fname" renamed to "jobname"
75	#
76	# 2718 2018-01-02 08:49:38Z maronga
77	# parameters are allowed in output commands (OC:)
78	#
79	# 2718 2018-01-02 08:49:38Z maronga
80	# bugfix: exit if no queue has been given neither with option -q nor in the
81	# configuration file
82	#
83	# 2718 2018-01-02 08:49:38Z maronga
84	# file connection file from trunk/SCRIPTS is taken by default
85	#
86	# 2718 2018-01-02 08:49:38Z maronga
87	# Corrected "Former revisions" section
88	#
89	# 2696 2017-12-14 17:12:51Z kanani
90	# Change in file header (GPL part)
91	#
92	# 2693 2017-12-13 12:33:49Z raasch
93	# replacement of variables given by {{<variable>}} in configuration file is now
94	# done in a more general way, variable names are written in small letters
95	#
96	# 2670 2017-12-06 16:32:19Z raasch
97	# test printouts removed
98	#
99	# 2669 2017-12-06 16:03:27Z raasch
100	# file attributes in .palm.iofiles restructured, "loc" attribute completely
101	# removed,
102	# wildcard (*) allowed in .palm.iofiles as file activation string for output
103	# files,
104	# informative messages in case of missing optional input files shortened
105	# bugfix: variable cycle explicitly interpreted with 10 as the number base
106	#
107	# 2638 2017-11-23 12:44:23Z raasch
108	# use of wildcards in file connection statements enabled
109	#
110	# 2605 2017-11-09 15:31:46Z raasch
111	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
112	# will not be sent with the job file any more, but copied into the
113	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
114	#
115	# 2600 2017-11-01 14:11:20Z raasch
116	# cycle numbers are made three digits wide
117	#
118	# 2566 2017-10-20 08:50:47Z raasch
119	# execute command for combine_plot_fields added
120	# "TEMPDIR" renamed "tempdir"
121	# temporary working directory for local batch jobs is created immediately within
122	# the user's palmrun call, due to a requirement of the "grid engine" batch
123	# system, where the working directory is given with batch directive -wd and must
124	# already exist when the job is submitted,
125	# informative messages in non-trace mode reduced and partly reformatted
126	#
127	# 2551 2017-10-18 07:25:11Z raasch
128	# TEMPDIR added as replacement string to be used in batch directives
129	#
130	# 2512 2017-10-04 08:26:59Z raasch
131	# bugfix for determining cycle numbers of NetCDF input files
132	#
133	# 2506 2017-09-29 08:30:37Z raasch
134	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
135	# host configuration added to SOURCES_FOR_RUN_... folder name
136	# host_identifier renamed host_configuration
137	# option -W added to allow for job dependencies
138	#
139	# 2501 2017-09-26 11:41:55Z raasch
140	# default value for number of cores (option -X) set to 1
141	# bugfix for mechanism which overwrites configuration file settings with values
142	# provided by palmrun options
143	#
144	# 2499 2017-09-22 16:47:58Z kanani
145	# option -h named configuration identifier
146	#
147	# 2480 2017-09-19 06:24:14Z maronga
148	# bugfix for last revision
149	#
150	# 2479 2017-09-19 06:12:16Z raasch
151	# option -A (project account number) added
152	#
153	# 2422 2017-09-08 08:25:41Z raasch
154	# initial revision
155	#
156	#--------------------------------------------------------------------------------#
157	# palmrun - script for running PALM jobs on local and remote hosts
158	#--------------------------------------------------------------------------------#
159
160
161
162	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
163
164	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
165	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
166	# (TOO MANY ARGUMENTS - PROBLEM)
167	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
168
169	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
170	typeset -i nr_of_output_files=0
171	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
172	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
173	# SCRIPT-OPTION ARGUMENTS
174	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
175	typeset -i icycle inode ival maxcycle mpi_tasks
176	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
177
178	activation_string_list=""
179	AddFilenames=""
180	combine_plot_fields=true
181	compiler_name=""
182	compiler_name_ser=""
183	compiler_options=""
184	configuration_identifier="default"
185	cores=1
186	cores_atmos=0
187	cores_ocean=0
188	coupled_dist=""
189	cpp_options=""
190	cpumax=0
191	create_batch_job=false
192	create_jobfile_only=false
193	create_remote_batch_job=false
194	dashes=" ----------------------------------------------------------------------------"
195	defaultqueue=""
196	delete_temporary_catalog=true
197	do_compile=true
198	do_trace=false
199	executable=""
200	execute_command=""
201	execution_error=false
202	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
203	global_revision=""
204	hostfile=""
205	hp=""
206	keep_data_from_previous_run=false
207	link_local_input=false
208	link_local_output=false
209	linker_options=""
210	local_jobcatalog=""
211	locat=normal
212	makefile=""
213	max_par_io_str=""
214	prc=$0
215	while [[ $(echo $prc \| grep -c "/") != 0 ]]
216	do
217	prc=`echo $prc \| cut -f2- -d"/"`
218	done
219	module_calls=""
220	palmrun_memory=""
221	palmrun_script_name=$prc
222	openmp=false
223	previous_job=""
224	project_account=""
225	queue=none
226	read_svf=""
227	restart_run=false
228	return_address=""
229	remote_jobcatalog=""
230	remote_username=""
231	running_in_batch_mode=false
232	run_coupled_model=false
233	run_id=""
234	run_id_number=""
235	run_identifier=test
236	silent=false
237	source_list=""
238	source_path=""
239	tasks_per_node=0
240	threads_per_task=1
241	transfer_problems=false
242	user_source_path=""
243	use_existing_sources_folder=""
244	use_openmp=false
245	version="palmrun 1.0 Rev$Rev: 3294 $"
246	working_directory=`pwd`
247	write_binary=""
248	write_svf=""
249
250
251	# ERROR HANDLING IN CASE OF EXIT
252	trap 'if [[ $locat != normal && $locat != control_c ]]
253	then
254
255	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
256	(( i = 0 ))
257	while (( i < iec ))
258	do
259	(( i = i + 1 ))
260	printf "\n *** Execution of ERROR-command:\n"
261	printf " >>> ${err_command[$i]}\n"
262	eval ${err_command[$i]}
263	done
264	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
265	printf "\n\n+++ palmrun killed \n\n"
266	elif [[ $locat != control_c ]]
267	then
268	printf "\n --> palmrun finished\n\n"
269	fi' exit
270
271
272	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
273	trap 'cd; rm -rf $tempdir
274	printf "\n+++ palmrun killed by \"^C\" \n\n"
275	locat=control_c
276	exit
277	' 2
278
279
280	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
281	# WHICH WILL BE USED TO START RESTART-JOBS
282	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:Z option
283	do
284	case $option in
285	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
286	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
287	(b) create_batch_job=true; prc="$prc -b";;
288	(B) delete_temporary_catalog=false; prc="$prc -B";;
289	(C) restart_run=true; prc="$prc -C";;
290	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
291	(F) create_jobfile_only=true;;
292	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
293	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
294	(i) run_id_number=$OPTARG;;
295	(j) running_in_batch_mode=true;;
296	(k) keep_data_from_previous_run=true; prc="$prc -k";;
297	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
298	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
299	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
300	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
301	(R) return_address=$OPTARG;;
302	(s) source_list=$OPTARG;;
303	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
304	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
305	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
306	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
307	(v) silent=true; prc="$prc -v";;
308	(V) use_existing_sources_folder="-V";;
309	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
310	(W) previous_job=$OPTARG;;
311	(x) do_trace=true;set -x; prc="$prc -x";;
312	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
313	(y) ocean_file_appendix=true; prc="$prc -y";;
314	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
315	(Z) combine_plot_fields=false; prc="$prc -Z";;
316	(\?) printf "\n +++ unknown option $OPTARG \n"
317	printf "\n --> type \"$0 ?\" for available options \n"
318	locat=parameter;exit;;
319	esac
320	done
321
322
323	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
324	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
325	(( to_shift = $OPTIND - 1 ))
326	shift $to_shift
327
328	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
329	if [[ "$1" = "?" ]]
330	then
331	(printf "\n *** Description of available palmrun options:\n"
332	printf "\n Option Description Default-Value"
333	printf "\n -a activation string list \"\" "
334	printf "\n -A project account number ---"
335	printf "\n -b batch-job on local machine ---"
336	printf "\n -B do not delete temporary directory at end ---"
337	printf "\n -d run identifier test"
338	printf "\n -F create batch job file only ---"
339	printf "\n -h host configuration \"default\" "
340	printf "\n -k keep data from previous run"
341	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
342	printf "\n -M Makefile name Makefile"
343	printf "\n -O threads per openMP task ---"
344	printf "\n -q queue \"$queue\" "
345	printf "\n -s filenames of routines to be compiled \"\" "
346	printf "\n must end with .f, .f90, .F, or .c !"
347	printf "\n use \"..\" for more than one file and wildcards"
348	printf "\n -s LM compiles all locally modified files"
349	printf "\n -t allowed cpu-time in seconds (batch) 0"
350	printf "\n -T tasks per node ---"
351	printf "\n -u username on remote machine \"\" "
352	printf "\n -v no prompt for confirmation ---"
353	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
354	printf "\n -w maximum parallel io streams as given by -X"
355	printf "\n -W name of job to wait for ---"
356	printf "\n -x tracing of palmrun for debug purposes ---"
357	printf "\n -X # of processors (on parallel machines) 1"
358	printf "\n -y add appendix \"_O\" to all local output"
359	printf "\n files (ocean precursor runs followed by"
360	printf "\n coupled atmosphere-ocean runs) ---"
361	printf "\n -Y run coupled model, \"#1 #2\" with"
362	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
363	printf "\n -Z skip combine_plot_fields at the end of "
364	printf "\n the simulation ---"
365	printf "\n "
366	printf "\n Possible values of positional parameter <modus>:"
367	printf "\n \"?\" - this outline \n\n") \| more
368	exit
369	elif [[ "$1" != "" ]]
370	then
371	printf "\n +++ positional parameter $1 unknown \n"
372	locat=parameter; exit
373	fi
374
375
376
377	# SHORT STARTING MESSAGE
378	printf "\n*** $version "
379	printf "\n will be executed. Please wait ..."
380
381
382	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
383	export fname=$run_identifier
384	export jobname=$run_identifier
385
386
387	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
388	config_file=.palm.config.$configuration_identifier
389	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
390
391
392	# CHECK, IF CONFIGURATION FILE EXISTS
393	if [[ ! -f $config_file ]]
394	then
395	printf "\n\n +++ configuration file: "
396	printf "\n $config_file"
397	printf "\n does not exist"
398	locat=connect; exit
399	fi
400
401
402	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
403	if [[ -f .palm.iofiles ]]
404	then
405
406	# CHECK VERSION MISMATCH
407	if [[ $running_in_batch_mode != true ]]
408	then
409	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
410	then
411	printf "\n\n +++ WARNING: A file connection file has been found in your"
412	printf "\n working directory, but its revision does not match"
413	printf "\n the revision of the default (trunk) version."
414	printf "\n You may need to update your connection file"
415	printf "\n \"${working_directory}/.palm.iofiles\" !"
416	fi
417	fi
418
419	fileconnection_file=.palm.iofiles
420
421	fi
422
423
424	# CHECK, IF FILE CONNECTION FILE EXISTS
425	if [[ ! -f $fileconnection_file ]]
426	then
427	printf "\n\n +++ file connection file: "
428	printf "\n $fileconnection_file"
429	printf "\n does not exist"
430	locat=connect; exit
431	fi
432
433
434	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
435	if [[ "$activation_string_list" = "" ]]
436	then
437	printf "\n\n +++ no activation string list given: "
438	printf "\n please set palmrun option \"-a\" "
439	locat=palmrun_option; exit
440	fi
441
442
443	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
444	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
445	then
446	write_binary=true
447	else
448	write_binary=false
449	fi
450
451	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
452	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
453	then
454	write_svf=true
455	else
456	write_svf=false
457	fi
458
459	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
460	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
461	then
462	read_svf=true
463	else
464	read_svf=false
465	fi
466
467
468	# READ AND EVALUATE THE CONFIGURATION-FILE
469	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
470
471	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
472	while read line
473	do
474
475	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
476	eval line=\"$line\"
477
478
479	# INTERPRET THE LINE
480	if [[ "$(echo $line)" = "" ]]
481	then
482
483	# EMPTY LINE, NO ACTION
484	continue
485
486	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
487	then
488
489	# LINE IS A COMMENT LINE
490	continue
491
492	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
493	then
494
495	# LINE DEFINES AN ENVIRONMENT-VARIABLE
496	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
497	value=`echo $line \| cut -d" " -s -f2-`
498
499
500	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
501	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
502	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
503	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
504	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
505	# CONFIGURATION-FILE.
506	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
507	then
508	eval export $var="\$value"
509
510	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
511	if [[ $do_trace = true ]]
512	then
513	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
514	fi
515	fi
516
517	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
518	then
519
520	# LINE DEFINES BATCH-DIRECTIVE
521	(( ibd = ibd + 1 ))
522	line=$(echo $line \| cut -c4-)
523	batch_directive[$ibd]="$line"
524
525	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
526	then
527
528	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
529	# REMOTE TO A LOCAL HOST
530	(( ibdt = ibdt + 1 ))
531	line=$(echo $line \| cut -c5-)
532	batch_directive_transfer[$ibdt]="$line"
533
534	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
535	then
536
537	# LINE DEFINES ERROR-COMMAND
538	(( iec = iec + 1 ))
539	line=$(echo $line \| cut -c4-)
540	err_command[$iec]="$line"
541
542	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
543	then
544
545	# LINE DEFINES INPUT-COMMAND
546	(( iic = iic + 1 ))
547	line=$(echo $line \| cut -c4-)
548	in_command[$iic]="$line"
549
550	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
551	then
552
553	# LINE DEFINES OUTPUT-COMMAND
554	(( ioc = ioc + 1 ))
555	line=$(echo $line \| cut -c4-)
556	out_command[$ioc]="$line"
557
558	else
559
560	# SKIP ALL OTHER LINES
561	continue
562
563	fi
564
565	done < $config_file
566
567
568	# CHECK SETTING OF REQUIRED PARAMETERS
569	if [[ "$fast_io_catalog" = "" ]]
570	then
571	printf "\n +++ no fast_io_catalog found in $config_file"
572	printf "\n Please add line \"fast_io_catalog ...\" to that file."
573	locat=config_file; exit
574	fi
575	if [[ "$compiler_name" = "" ]]
576	then
577	printf "\n +++ no compiler name found in $config_file"
578	printf "\n Please add line \"compiler_name ...\" to that file."
579	locat=config_file; exit
580	fi
581	if [[ "$compiler_name_ser" = "" ]]
582	then
583	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
584	printf "\n Please add line \"compiler_name_ser ...\" to that file."
585	locat=config_file; exit
586	fi
587	if [[ "$compiler_options" = "" ]]
588	then
589	printf "\n +++ no compiler options found in $config_file"
590	printf "\n Please add line \"compiler_options ...\" to that file."
591	locat=config_file; exit
592	fi
593	if [[ "$linker_options" = "" ]]
594	then
595	printf "\n +++ no linker options found in $config_file"
596	printf "\n Please add line \"linker_options ...\" to that file."
597	locat=config_file; exit
598	fi
599	if [[ "$execute_command" = "" ]]
600	then
601	printf "\n +++ no execute command found in $config_file"
602	printf "\n Please add line \"execute_command ...\" to that file."
603	locat=config_file; exit
604	fi
605
606	if [[ "$hostfile" != "" ]]
607	then
608	if [[ $hostfile != auto && ! -f $hostfile ]]
609	then
610	printf "\n +++ no hostfile \"$hostfile\" found"
611	printf "\n Please check line \"hostfile ...\" in $config_file"
612	locat=config_file; exit
613	fi
614	fi
615
616
617	# DETERMINE THE CALL STATUS
618	if [[ "$return_address" != "" ]]
619	then
620
621	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
622	# BATCH MODE AND ...
623	running_on_remote=true
624
625	else
626
627	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
628	if [[ "$remote_ip" != "" ]]
629	then
630
631	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
632	create_remote_batch_job=true
633
634	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
635	if [[ "$remote_jobcatalog" = "" ]]
636	then
637	printf "\n +++ no remote jobcatalog found in $config_file"
638	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
639	locat=config_file; exit
640	fi
641
642
643	fi
644	running_on_remote=false
645	fi
646
647
648
649	# READ AND EVALUATE THE I/O-FILE LIST
650	[[ $silent = false ]] && printf "\n Reading the I/O files... "
651
652	# READ THE FILE CONNECTION FILE LINE BY LINE
653	while read line
654	do
655
656	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
657	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
658
659	# INTERPRET THE LINE
660	if [[ "$(echo $line)" = "" ]]
661	then
662	# EMPTY LINE, NO ACTION
663	continue
664
665	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
666	then
667
668	# LINE IS A COMMENT LINE
669	true
670
671	else
672
673	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
674	# s2a: in/out - field
675	# s2b: action - field (optional)
676	s1=`echo "$line" \| cut -d" " -f1`
677	s2=`echo "$line" \| cut -d" " -s -f2`
678	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
679	then
680	s2a=$s2
681	s2b=""
682	else
683	s2a=`echo $s2 \| cut -d":" -f1`
684	s2b=`echo $s2 \| cut -d":" -f2`
685	fi
686	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
687	s4=`echo "$line" \| cut -d" " -s -f4`
688	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
689	s5=`echo "$line" \| cut -d" " -s -f5`
690	s6=`echo "$line" \| cut -d" " -s -f6`
691
692
693	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
694	# INPUT- OR OUTPUT-LIST.
695	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
696	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
697	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
698	# IS NOT CHECKED AND STORED.
699	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
700	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
701	then
702	found=false
703	for actual in $activation_string_list
704	do
705	for formal in $s3
706	do
707	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
708	done
709	done
710	if [[ $found = true ]]
711	then
712	(( iin = iin + 1 ))
713	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
714	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
715	if [[ "$s2a" = inopt ]]
716	then
717	optin_pre[$iin]=yes
718	else
719	optin_pre[$iin]=no
720	fi
721
722	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
723	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
724	if [[ $running_on_remote = true && "$s2b" = tr ]]
725	then
726	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
727	fi
728
729	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
730	# THE WILDCARD FROM THE ENDING
731	if [[ "${s5: -1}" = "*" ]]
732	then
733	if [[ "$s2b" = "di" ]]
734	then
735	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
736	printf "\n see file \"$fileconnection_file\", line"
737	printf "\n$line"
738	locat=iofiles_file; exit
739	fi
740	multin[$iin]=true
741	string=${endin_pre[$iin]}
742	endin_pre[$iin]="${string%?}"
743	else
744	multin[$iin]=false
745	fi
746	fi
747	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
748	then
749	found=false
750	for actual in $activation_string_list
751	do
752	for formal in $s3
753	do
754	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
755	done
756	done
757	if [[ $found = true ]]
758	then
759	(( iout = iout + 1 ))
760	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
761	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
762
763	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
764	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
765	if [[ $formal = wildcard ]]
766	then
767	warnout_pre[$iout]=false
768	else
769	warnout_pre[$iout]=true
770	fi
771
772	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
773	# THE WILDCARD FROM THE LOCAL FILENAME
774	if [[ "${s1: -1}" = "*" ]]
775	then
776	if [[ "$s2b" = "di" ]]
777	then
778	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
779	printf "\n see file \"$fileconnection_file\", line"
780	printf "\n$line"
781	locat=iofiles_file; exit
782	fi
783	multout[$iout]=true
784	string=${localout_pre[$iout]}
785	localout_pre[$iout]="${string%?}"
786	else
787	multout[$iout]=false
788	fi
789	fi
790	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
791	then
792	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
793	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
794	locat=connect; exit
795	fi
796	IFS="$IFSALT"
797	fi
798
799	done < $fileconnection_file
800
801
802
803	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
804	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
805	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
806	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
807	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
808	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
809
810
811
812	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
813	if [[ $run_coupled_model = true ]]
814	then
815
816	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
817	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
818
819	if (( $cores_ocean + $cores_atmos != $cores ))
820	then
821
822	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
823	printf "\n PEs (total) : $cores"
824	printf "\n PEs (atmosphere): $cores_atmos"
825	printf "\n PEs (ocean) : $cores_ocean"
826	locat=coupling; exit
827
828	fi
829
830	fi
831
832
833	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
834	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
835	# FOLDER
836	if [[ $running_in_batch_mode = true ]]
837	then
838
839	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
840	then
841	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
842	printf "\n Please check the output of the palmrun-call"
843	printf "\n that you did on your local host."
844	locat=SOURCES_FOR_RUN; exit
845	fi
846
847	else
848
849	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
850	# AUTOMATIC RESTART RUN
851	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
852	if [[ $restart_run = false ]]
853	then
854
855	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
856	# THE LOCAL HOST
857	if [[ ! -d $source_path ]]
858	then
859	printf "\n\n +++ source path \"$source_path\" on local host"
860	printf "\n \"$(hostname)\" does not exist"
861	locat=source_path; exit
862	fi
863
864	rm -rf ${base_directory}/${sources_for_run_catalog}
865	mkdir -p ${base_directory}/${sources_for_run_catalog}
866
867	if [[ "$source_list" = LM ]]
868	then
869
870	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
871	source_list=""
872	cd $source_path
873
874
875	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
876	if [[ ! -d ../.svn ]]
877	then
878	printf "\n\n +++ source directory"
879	printf "\n \"$source_path\" "
880	printf "\n is not under control of \"subversion\"."
881	printf "\n Please do not use palmrun-option \"-s LM\"\n"
882	fi
883
884
885	# LIST ALL MODIFIED SOURCE CODE FILES
886	Filenames=""
887	svn status > tmp_svnstatus
888	while read line
889	do
890	firstc=`echo $line \| cut -c1`
891	if [[ $firstc = M \|\| $firstc = "?" ]]
892	then
893	Name=`echo "$line" \| cut -c8-`
894	extension=`echo $Name \| cut -d. -f2`
895	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
896	then
897	Filenames="$Filenames "$Name
898	fi
899	fi
900	done < tmp_svnstatus
901	rm -rf tmp_svnstatus
902
903
904	# COPY FILES TO SOURCES_FOR_RUN_...
905	for filename in $Filenames
906	do
907	cp $filename ${base_directory}/${sources_for_run_catalog}
908	source_list=$source_list"$filename "
909	done
910
911	cd - > /dev/null
912
913
914	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
915	elif [[ "$source_list" != "" ]]
916	then
917
918	cd $source_path
919
920	for filename in $source_list
921	do
922
923	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
924	if [[ $(echo $filename \| grep -c "/") != 0 ]]
925	then
926	printf "\n +++ source code file: $filename"
927	printf "\n must not contain (\"/\") "
928	locat=source; exit
929	fi
930
931	if [[ ! -f $filename ]]
932	then
933	printf "\n +++ source code file: $filename"
934	printf "\n does not exist"
935	locat=source; exit
936	else
937	cp $filename ${base_directory}/${sources_for_run_catalog}
938	fi
939
940	done
941
942	cd - > /dev/null
943
944	fi
945
946	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
947	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
948	if [[ ! -f $makefile ]]
949	then
950	printf "\n +++ file \"$makefile\" does not exist"
951	locat=make; exit
952	else
953	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
954	fi
955
956
957	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
958	if [[ "$user_source_path" != "" ]]
959	then
960
961	# DOES THE DIRECTORY EXIST?
962	if [[ ! -d $user_source_path ]]
963	then
964
965	printf "\n\n *** INFORMATIVE: additional source code directory"
966	printf "\n \"$user_source_path\" "
967	printf "\n does not exist or is not a directory."
968	printf "\n No source code will be used from this directory!\n"
969	user_source_path=""
970	if [[ $silent == false ]]
971	then
972	sleep 2
973	fi
974
975	else
976
977	cd $user_source_path
978
979	Names=$(ls -1 *.f90 2>&1)
980	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
981	Names=$(ls -1 *.F90 2>&1)
982	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
983	Names=$(ls -1 *.F 2>&1)
984	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
985	Names=$(ls -1 *.f 2>&1)
986	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
987	Names=$(ls -1 *.c 2>&1)
988	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
989
990	cd - > /dev/null
991	cd ${base_directory}/${sources_for_run_catalog}
992
993	# COPY MAKEFILE IF EXISTING
994	if [[ -f $user_source_path/Makefile ]]
995	then
996	printf "\n\n *** user Makefile from directory"
997	printf "\n \"$user_source_path\" is used \n"
998	if [[ $silent == false ]]
999	then
1000	sleep 1
1001	fi
1002	cp $user_source_path/Makefile .
1003	fi
1004
1005	for filename in $AddFilenames
1006	do
1007	if [[ -f $filename ]]
1008	then
1009	printf "\n +++ source code file \"$filename\" found in additional"
1010	printf "\n source code directory \"$user_source_path\" "
1011	printf "\n but was also given with option \"-s\" which means that it should be taken"
1012	printf "\n from directory \"$source_path\"."
1013	locat=source; exit
1014	fi
1015
1016	cp $user_source_path/$filename .
1017	source_list="$source_list $filename"
1018
1019	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1020	if [[ $(grep -c $filename Makefile) = 0 ]]
1021	then
1022	printf "\n\n +++ user file \"$filename\" "
1023	printf "\n is not listed in Makefile \n"
1024	locat=source; exit
1025	fi
1026	done
1027	cd - > /dev/null
1028	fi
1029	fi
1030
1031	# COPY CONFIGURATION FILES
1032	cp $config_file ${base_directory}/${sources_for_run_catalog}
1033	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1034
1035	# COPY SHELLSCRIPTS
1036	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1037	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1038
1039	fi
1040
1041	fi
1042
1043
1044	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1045	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1046	if [[ "$global_revision" = "" ]]
1047	then
1048	global_revision=`svnversion $source_path 2>/dev/null`
1049	global_revision="Rev: $global_revision"
1050	fi
1051
1052
1053	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1054	if [[ -n $cores ]]
1055	then
1056
1057	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1058	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1059	if [[ $tasks_per_node = 0 ]]
1060	then
1061	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1062	then
1063	printf "\n"
1064	printf "\n +++ option \"-T\" (tasks per node) is missing"
1065	printf "\n set -T option or define tasks_per_node in the config file"
1066	locat=tasks_per_node; (( iec = 0 )); exit
1067	else
1068	# DEFAULT FOR INTERACTIVE RUN
1069	tasks_per_node=$cores
1070	fi
1071	fi
1072
1073	if (( cores < tasks_per_node ))
1074	then
1075	printf "\n"
1076	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1077	printf "\n given values: -T $tasks_per_node -X $cores"
1078	locat=tasks_per_node; (( iec = 0 )); exit
1079	fi
1080
1081	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1082	(( mpi_tasks = cores / threads_per_task ))
1083	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1084	(( ii = cores / tasks_per_node ))
1085	(( remaining_cores = cores - ii * tasks_per_node ))
1086	if (( remaining_cores > 0 ))
1087	then
1088	printf "\n"
1089	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1090	printf "\n divisor of the total number of cores (option \"-X\")"
1091	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1092	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1093	(( nodes = nodes + 1 ))
1094	fi
1095
1096	fi
1097
1098
1099	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1100	if [[ "$maximum_parallel_io_streams" = "" ]]
1101	then
1102	maximum_parallel_io_streams=$cores
1103	fi
1104
1105
1106	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1107	if [[ "$scp_port" != "" ]]
1108	then
1109	PORTOPT="-P $scp_port"
1110	SSH_PORTOPT="-p $scp_port"
1111	fi
1112
1113
1114	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1115	# CONFIG-FILE
1116	if [[ "$ssh_key" != "" ]]
1117	then
1118	ssh_key="-i $HOME/.ssh/$ssh_key"
1119	fi
1120
1121
1122	# SET QUEUE, IF NOT GIVEN
1123	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1124	then
1125
1126	if [[ $queue = none && "$defaultqueue" = "" ]]
1127	then
1128	printf "\n"
1129	printf "\n +++ no default queue given in configuration file and no queue"
1130	printf "\n given with option -q"
1131	locat=queue; exit
1132	fi
1133	if [[ $queue = none ]]
1134	then
1135	queue=$defaultqueue
1136	fi
1137
1138	fi
1139
1140
1141	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1142	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1143	(( i = 0 ))
1144	(( nr_of_input_files = 0 ))
1145	while (( i < iin ))
1146	do
1147	(( i = i + 1 ))
1148
1149	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1150	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1151	if [[ "${actionin_pre[$i]}" = di ]]
1152	then
1153	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1154	else
1155	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1156	fi
1157
1158
1159	# CHECK IF FILE EXISTS
1160	if ! ls $filename* 1>/dev/null 2>&1
1161	then
1162
1163	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1164	if [[ "${optin_pre[$i]}" != "yes" ]]
1165	then
1166	printf "\n\n +++ INPUT-file: "
1167	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1168	then
1169	printf "\n $filename"
1170	else
1171	printf "\n $filename.${extin_pre[$i]}"
1172	fi
1173	printf "\n does not exist\n"
1174	locat=input; exit
1175	else
1176	(( nr_of_input_files = nr_of_input_files + 1 ))
1177	localin[$nr_of_input_files]="${localin_pre[$i]}"
1178	optin[$nr_of_input_files]="${optin_pre[$i]}"
1179	actionin[$nr_of_input_files]="unavailable"
1180	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1181	endin[$nr_of_input_files]="${endin_pre[$i]}"
1182	extin[$nr_of_input_files]="${extin_pre[$i]}"
1183	fi
1184
1185	else
1186
1187	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1188	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1189	# ENDINGS
1190	if [[ "${multin[$i]}" = true ]]
1191	then
1192	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1193	ls -1 -d ${filename} > filelist 2>/dev/null
1194	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1195	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1196
1197	endings=""
1198	while read line
1199	do
1200	# filename without path (i.e. after the last "/")
1201	basefilename=$(basename ${line})
1202
1203	# check if there is an extension and remove it
1204	ext=${basefilename##*.}
1205	if [[ "$ext" = "${extin_pre[$i]}" ]]
1206	then
1207	basefilename=${basefilename%.*}
1208	fi
1209
1210	# check for an existing cycle number and remove it
1211	cycle=${basefilename##*.}
1212	if [[ $cycle =~ ^-?[0-9]+$ ]]
1213	then
1214	basefilename=${basefilename%.*}
1215	fi
1216
1217	# remove the run_identifier from the beginning
1218	length_run_identifier=${#run_identifier}
1219	ending=${basefilename:${length_run_identifier}}
1220
1221	# remove the ending given in the .iofiles from the beginning
1222	endingstring="${endin_pre[$i]}"
1223	length_ending=${#endingstring}
1224	ending=${ending:${length_ending}}
1225
1226	if [[ "$ending" = "" ]]
1227	then
1228	# standard ending as given in the .iofiles
1229	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1230	then
1231	endings="$endings DEFAULT"
1232	fi
1233	else
1234	# ending must start with "_", otherwise its a different file
1235	if [[ "${ending:0:1}" = "_" ]]
1236	then
1237	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1238	then
1239	endings="$endings $ending"
1240	fi
1241	fi
1242	fi
1243
1244	done <filelist
1245
1246	rm filelist
1247
1248	else
1249
1250	# SINGLE NAME
1251	endings=DEFAULT
1252
1253	fi
1254
1255	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1256	for ending in $endings
1257	do
1258
1259	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1260	if [[ $ending = DEFAULT ]]
1261	then
1262	ending=""
1263	fi
1264
1265	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1266	(( nr_of_input_files = nr_of_input_files + 1 ))
1267	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1268	optin[$nr_of_input_files]="${optin_pre[$i]}"
1269	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1270	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1271	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1272	extin[$nr_of_input_files]="${extin_pre[$i]}"
1273
1274
1275	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1276	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1277	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1278	then
1279	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1280	else
1281	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1282	fi
1283
1284	# DETERMINE THE FILE'S CYCLE NUMBER
1285	(( maxcycle = 0 ))
1286	ls -1 -d $filename > filelist 2>/dev/null
1287	ls -1 -d $filename.* >> filelist 2>/dev/null
1288	while read line
1289	do
1290	# filename without path (i.e. after the last "/")
1291	basefilename=$(basename ${line})
1292
1293	# check if there is an extension
1294	extension=${basefilename##*.}
1295	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1296	then
1297	basefilename=${basefilename%.*}
1298	fi
1299
1300	# check for an existing cycle number
1301	cycle=${basefilename##*.}
1302	if [[ $cycle =~ ^-?[0-9]+$ ]]
1303	then
1304	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1305	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1306	(( icycle = $((10#$cycle)) ))
1307	else
1308	(( icycle = 0 ))
1309	fi
1310
1311	if (( icycle > maxcycle ))
1312	then
1313	(( maxcycle = icycle ))
1314
1315	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1316	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1317	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1318	then
1319	leading_zero=true
1320	else
1321	leading_zero=false
1322	fi
1323	fi
1324
1325	done <filelist
1326	rm filelist
1327
1328	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1329	if [[ $leading_zero = true ]]
1330	then
1331	cyclestring=`printf "%03d" $maxcycle`
1332	else
1333	cyclestring=$maxcycle
1334	fi
1335
1336	# APPEND CYCLE NUMBER TO FILENAME
1337	if (( maxcycle > 0 ))
1338	then
1339	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1340	then
1341	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1342	else
1343	filename=${filename}.$cyclestring
1344	fi
1345	else
1346	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1347	then
1348	filename=${filename}.${extin[$nr_of_input_files]}
1349	fi
1350	fi
1351
1352	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1353	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1354	absnamein[$nr_of_input_files]=$filename
1355	if (( maxcycle > 0 ))
1356	then
1357	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1358	then
1359	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1360	else
1361	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1362	fi
1363	else
1364	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1365	then
1366	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1367	else
1368	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1369	fi
1370	fi
1371
1372	done
1373
1374	fi
1375
1376	done
1377
1378
1379	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1380	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1381	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1382	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1383	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1384	# REMOTE HOST)
1385	(( i = 0 ))
1386	while (( i < iout ))
1387	do
1388	(( i = i + 1 ))
1389	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1390	then
1391	if [[ "${actionout_pre[$i]}" = tr ]]
1392	then
1393	actionout_pre[$i]=""
1394	elif [[ "${actionout_pre[$i]}" = trpe ]]
1395	then
1396	actionout_pre[$i]=pe
1397	elif [[ "${actionout_pre[$i]}" = tra ]]
1398	then
1399	actionout_pre[$i]=a
1400	fi
1401	(( maxcycle = 0 ))
1402	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1403	eval catalogname=${pathout_pre[$i]}
1404	if ! ls $filename* 1>/dev/null 2>&1
1405	then
1406
1407	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1408	if cat /dev/null > $filename
1409	then
1410	rm $filename
1411	else
1412
1413	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1414	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1415	if [[ ! -d $catalogname ]]
1416	then
1417	if mkdir -p $catalogname
1418	then
1419	printf "\n\n *** directory:"
1420	printf "\n $catalogname"
1421	printf "\n was created\n"
1422	else
1423	printf "\n\n +++ OUTPUT-file:"
1424	printf "\n $filename"
1425	printf "\n cannot be created, because directory does not exist"
1426	printf "\n and cannot be created either"
1427	printf "\n"
1428	locat=output ; exit
1429	fi 2>/dev/null
1430	else
1431	printf "\n\n +++ OUTPUT-file:"
1432	printf "\n $filename"
1433	printf "\n cannot be created, although directory exists"
1434	printf "\n"
1435	locat=output ; exit
1436	fi
1437	fi 2>/dev/null
1438
1439	fi
1440
1441	fi
1442	done
1443
1444
1445	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1446	if [[ $running_in_batch_mode = false ]]
1447	then
1448	run_id_number=$RANDOM
1449	run_id=${run_identifier}.$run_id_number
1450
1451	tempdir=$fast_io_catalog/$run_id
1452	fi
1453
1454
1455	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1456	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1457	then
1458
1459	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1460	if [[ $ibd = 0 ]]
1461	then
1462	printf "\n"
1463	printf "\n +++ no batch directives found in configuration file"
1464	locat=config_file_batch_directives; (( iec = 0 )); exit
1465	fi
1466
1467	# CHECK IF CPUTIME IS GIVEN FOR JOB
1468	done=false
1469	cputime=$cpumax
1470	while [[ $done = false ]]
1471	do
1472	if (( cputime == 0 ))
1473	then
1474	printf "\n +++ cpu-time is undefined"
1475	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1476	printf "\n >>> "
1477	read cputime 1>/dev/null 2>&1
1478	else
1479	done=true
1480	fi
1481	done
1482	cpumax=$cputime
1483
1484	# CHECK THE MEMORY DEMAND
1485	done=false
1486	while [[ $done = false ]]
1487	do
1488	if (( memory == 0 ))
1489	then
1490	printf "\n +++ memory demand is undefined"
1491	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1492	printf "\n >>> "
1493	read memory 1>/dev/null 2>&1
1494	else
1495	done=true
1496	fi
1497	done
1498
1499	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1500	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1501	then
1502	while [[ -z $remote_username ]]
1503	do
1504	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1505	printf "\n >>> Please type username:"
1506	printf "\n >>> "
1507	read remote_username
1508	done
1509	fi
1510
1511	else
1512
1513	if [[ $running_in_batch_mode = false ]]
1514	then
1515	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1516	cpumax=$cputime
1517	else
1518	cputime=$cpumax
1519	fi
1520
1521	fi
1522
1523
1524	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1525	(( cpu_hours = cputime / 3600 ))
1526	(( resttime = cputime - cpu_hours * 3600 ))
1527	(( cpu_minutes = resttime / 60 ))
1528	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1529	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1530
1531
1532	# OUTPUT OF THE PALMRUN-HEADER
1533	calltime=$(date)
1534	printf "\n"
1535	printf "#------------------------------------------------------------------------# \n"
1536	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1537	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1538	printf "\| \| \n"
1539	column1="called on:"; column2=$(hostname)
1540	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1541	if [[ $create_remote_batch_job = true ]]
1542	then
1543	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1544	else
1545	if [[ $running_on_remote = true ]]
1546	then
1547	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1548	else
1549	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1550	fi
1551	fi
1552	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1553
1554	column1="running in:"
1555	if [[ $running_in_batch_mode = true ]]
1556	then
1557	column2="batch job mode"
1558	else
1559	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1560	then
1561	column2="job creation mode"
1562	else
1563	column2="interactive run mode"
1564	fi
1565	fi
1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1567
1568	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1569	then
1570	if [[ "$project_account" != "" ]]
1571	then
1572	column1="project account number:"
1573	column2="$project_account"
1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1575	fi
1576	fi
1577
1578	if [[ -n $cores ]]
1579	then
1580	if [[ $run_coupled_model = false ]]
1581	then
1582	column1="number of cores:"; column2=$cores
1583	else
1584	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1585	fi
1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1587	fi
1588	if [[ -n $tasks_per_node ]]
1589	then
1590	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1592	if (( remaining_cores > 0 ))
1593	then
1594	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1596	fi
1597	fi
1598	if [[ $maximum_parallel_io_streams != $cores ]]
1599	then
1600	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1601	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1602	fi
1603	if [[ $use_openmp = true ]]
1604	then
1605	column1="threads per task:"; column2="$threads_per_task"
1606	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1607	fi
1608	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1609	then
1610	column1="memory demand / PE":; column2="$memory MB"
1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1612	column1="job cpu time (h:m:s):"; column2="$timestring"
1613	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1614	fi
1615	printf "\| \| \n"
1616	if [[ "$source_list" != "" ]]
1617	then
1618	if [[ "$make_options" != "" ]]
1619	then
1620	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1622	line=$(echo "$make_options" \| cut -c46-)
1623	while [[ "$line" != "" ]]
1624	do
1625	column1=""
1626	column2=$(echo "$line" \| cut -c-45)
1627	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1628	line=$(echo "$line" \| cut -c46-)
1629	done
1630	fi
1631	fi
1632
1633	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1635	line=$(echo "$cpp_options" \| cut -c46-)
1636	while [[ "$line" != "" ]]
1637	do
1638	column1=""
1639	column2=$(echo "$line" \| cut -c-45)
1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1641	line=$(echo "$line" \| cut -c46-)
1642	done
1643
1644	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1646	line=$(echo "$compiler_options" \| cut -c46-)
1647	while [[ "$line" != "" ]]
1648	do
1649	column1=""
1650	column2=$(echo "$line" \| cut -c-45)
1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1652	line=$(echo "$line" \| cut -c46-)
1653	done
1654
1655	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1657	line=$(echo "$linker_options" \| cut -c46-)
1658	while [[ "$line" != "" ]]
1659	do
1660	column1=""
1661	column2=$(echo "$line" \| cut -c-45)
1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1663	line=$(echo "$line" \| cut -c46-)
1664	done
1665
1666	if [[ "$login_init_cmd" != "" ]]
1667	then
1668	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1669	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1670	line=$(echo "$login_init_cmd" \| cut -c46-)
1671	while [[ "$line" != "" ]]
1672	do
1673	column1=""
1674	column2=$(echo "$line" \| cut -c-45)
1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1676	line=$(echo "$line" \| cut -c46-)
1677	done
1678	fi
1679
1680	if [[ "$module_commands" != "" ]]
1681	then
1682	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1683	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1684	line=$(echo "$module_commands" \| cut -c46-)
1685	while [[ "$line" != "" ]]
1686	do
1687	column1=""
1688	column2=$(echo "$line" \| cut -c-45)
1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1690	line=$(echo "$line" \| cut -c46-)
1691	done
1692	fi
1693	printf "\| \| \n"
1694	column1="run identifier:"; column2=$run_identifier
1695	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1696	column1="activation string list:"; column2=$(echo $activation_string_list)
1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1698
1699	if [[ "$ocean_file_appendix" = true ]]
1700	then
1701	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1702	fi
1703
1704	if [[ "$source_list" != "" ]]
1705	then
1706	printf "\| \| \n"
1707	printf "\| Files to be compiled: \| \n"
1708	line=$source_list
1709	while [[ "$line" != "" ]]
1710	do
1711	linestart=$(echo $line \| cut -c-70)
1712	printf "\| %-70s \| \n" "$linestart"
1713	line=$(echo "$line" \| cut -c71-)
1714	done
1715	fi
1716	printf "#------------------------------------------------------------------------#"
1717
1718
1719
1720	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1721	if [[ $do_trace = true ]]
1722	then
1723	(( i = 0 ))
1724	while (( i < nr_of_input_files ))
1725	do
1726	(( i = i + 1 ))
1727	if (( i == 1 ))
1728	then
1729	printf "\n\n >>> INPUT-file assignments:\n"
1730	fi
1731	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1732	done
1733	(( i = 0 ))
1734	while (( i < iout ))
1735	do
1736	(( i = i + 1 ))
1737	if (( i == 1 ))
1738	then
1739	printf "\n\n >>> OUTPUT-file assignments:\n"
1740	fi
1741	printf "\n ${localout[$i]} : ${pathout[$i]}"
1742	done
1743	(( i = 0 ))
1744	while (( i < iic ))
1745	do
1746	(( i = i + 1 ))
1747	if (( i == 1 ))
1748	then
1749	printf "\n\n >>> INPUT-commands:\n"
1750	fi
1751	printf "\n ${in_command[$i]}"
1752	done
1753	(( i = 0 ))
1754	while (( i < ioc ))
1755	do
1756	(( i = i + 1 ))
1757	if (( i == 1 ))
1758	then
1759	printf "\n\n >>> OUTPUT-commands:\n"
1760	fi
1761	printf "\n ${out_command[$i]}"
1762	done
1763	fi
1764
1765	# QUERY FOR CONTINUE
1766	if [[ $silent = false && $running_in_batch_mode = false ]]
1767	then
1768	antwort=dummy
1769	printf "\n\n"
1770	printf " >>> everything o.k. (y/n) ? "
1771	while read antwort
1772	do
1773	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1774	then
1775	printf " >>> everything o.k. (y/n) ? "
1776	else
1777	break
1778	fi
1779	done
1780	if [[ $antwort = n \|\| $antwort = N ]]
1781	then
1782	locat=user_abort; (( iec = 0 )); exit
1783	fi
1784	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1785	then
1786	printf "\n *** batch-job will be created and submitted"
1787	else
1788	printf "\n *** PALMRUN will now continue to execute on this machine"
1789	fi
1790	fi
1791
1792
1793
1794	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1795	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1796	then
1797
1798	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1799	then
1800	printf "\n\n *** creating executable and other sources for the remote host\n"
1801	else
1802	printf "\n\n *** creating executable and other sources for the local host\n"
1803	fi
1804
1805	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1806	# IT SHALL BE CREATED
1807	ask_for_make_depository=false
1808	if [[ $create_remote_batch_job = true ]]
1809	then
1810
1811	line=`grep %base_directory $config_file`
1812	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1813	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1814
1815	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1816	then
1817	printf "\n\n +++ make depository \"${make_depository}\""
1818	printf "\n on remote host not found!"
1819	ask_for_make_depository=true
1820	fi
1821	rm ${configuration_identifier}_last_make_protokoll
1822
1823	else
1824
1825	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1826	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1827	if [[ ! -d ${make_depository} ]]
1828	then
1829	printf "\n\n +++ make depository \"${make_depository}\""
1830	printf "\n on local host not found!"
1831	ask_for_make_depository=true
1832	fi
1833
1834	fi
1835
1836	if [[ $ask_for_make_depository = true ]]
1837	then
1838
1839	antwort=dummy
1840	printf "\n\n"
1841	printf " >>> Create a new one (y/n) ? "
1842	while read antwort
1843	do
1844	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1845	then
1846	printf " >>> Create a new one (y/n) ? "
1847	else
1848	break
1849	fi
1850	done
1851	if [[ $antwort = n \|\| $antwort = N ]]
1852	then
1853	locat=user_abort; (( iec = 0 )); exit
1854	fi
1855
1856	if [[ $do_trace = true ]]
1857	then
1858	palmbuild -h $configuration_identifier
1859	else
1860	palmbuild -v -h $configuration_identifier
1861	fi
1862
1863	if [[ $? != 0 ]]
1864	then
1865
1866	# ABORT IN CASE OF COMPILATION PROBLEMS
1867	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1868	locat=make_depository
1869	exit
1870	else
1871	echo " *** now continue with creating executable and other sources"
1872	fi
1873
1874	fi
1875
1876	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1877	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
1878
1879	if [[ $? != 0 ]]
1880	then
1881
1882	# ABORT IN CASE OF COMPILATION PROBLEMS
1883	printf "\n +++ error while creating executable and/or other sources"
1884	locat=execution
1885	rm -rf ${base_directory}/${sources_for_run_catalog}
1886	exit
1887
1888	else
1889
1890	printf " *** executable and other sources created\n"
1891	rm -rf ${base_directory}/${sources_for_run_catalog}
1892
1893	fi
1894
1895	fi
1896
1897
1898	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1899	# WILL BE COPIED TO THE REMOTE HOST
1900	if [[ $create_remote_batch_job = true ]]
1901	then
1902	(( i = 0 ))
1903	while (( i < nr_of_input_files ))
1904	do
1905	(( i = i + 1 ))
1906	if [[ "${actionin[$i]}" = tr ]]
1907	then
1908	eval inputfile=${pathin[$i]}/${frelin[$i]}
1909	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1910	fi
1911	done
1912	if (( i > 0 ))
1913	then
1914	printf "\n\n *** input files have been copied to the remote host\n"
1915	fi
1916	fi
1917
1918
1919	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1920	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1921	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1922	then
1923
1924	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1925	if [[ $running_in_batch_mode = false ]]
1926	then
1927	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1928	# FOLDER
1929	mkdir -p $tempdir
1930	chmod go+rx $tempdir
1931	cd $tempdir
1932	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1933	printf "\n *** changed to temporary directory: $tempdir"
1934
1935	else
1936
1937	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1938	printf "\n *** running in temporary directory: $tempdir"
1939
1940	fi
1941
1942
1943	# PROVIDE THE INPUT FILES
1944	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1945	optional_files_missing=false
1946	(( i = 0 ))
1947	while (( i < nr_of_input_files ))
1948	do
1949	(( i = i + 1 ))
1950	if (( i == 1 ))
1951	then
1952	printf "\n\n *** providing INPUT-files:\n$dashes"
1953	fi
1954
1955
1956	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1957	if [[ "${actionin[$i]}" = unavailable ]]
1958	then
1959	optional_files_missing=true
1960	continue
1961	fi
1962
1963	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1964	files_for_cores=false; filetype=file
1965	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1966	then
1967	files_for_cores=true; filetype=files
1968	actionin[$i]=""
1969	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1970	then
1971	actionin[$i]=""
1972	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1973	then
1974	files_for_cores=true; filetype=files
1975	actionin[$i]="ln"
1976	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1977	then
1978	actionin[$i]="ln"
1979	fi
1980
1981	if [[ $files_for_cores = true ]]
1982	then
1983	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1984	else
1985	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1986	fi
1987
1988	# INPUT-FILES TO BE LINKED
1989	if [[ "${actionin[$i]}" = ln ]]
1990	then
1991
1992	printf "\n $filetype will be linked"
1993	if [[ $files_for_cores = false ]]
1994	then
1995	if [[ -f "${absnamein[$i]}" ]]
1996	then
1997	ln ${absnamein[$i]} ${localin[$i]}
1998	got_tmp[$i]=true
1999	fi
2000	else
2001	if [[ -d "${absnamein[$i]}" ]]
2002	then
2003	mkdir -p ${localin[$i]}
2004	cd ${absnamein[$i]}
2005	for file in $(ls *)
2006	do
2007	ln $file $tempdir/${localin[$i]}
2008	done >\|/dev/null 2>&1
2009	cd $tempdir
2010	fi
2011
2012	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2013	if [[ ! -f "${localin[$i]}/_000000" ]]
2014	then
2015	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2016	cp -r ${absnamein[$i]}/* ${localin[$i]}
2017	fi
2018
2019	got_tmp[$i]=true
2020	fi
2021	fi
2022
2023	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2024	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2025	then
2026
2027	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2028	then
2029
2030	# FILE COPIES ARE PROVIDED FOR ALL CORES
2031	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2032	printf "\n file will be provided for $cores processors"
2033	mkdir -p ${localin[$i]}
2034	ival=$cores
2035	(( ii = 0 ))
2036	while (( ii <= ival-1 ))
2037	do
2038	if (( ii < 10 ))
2039	then
2040	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2041	elif (( ii < 100 ))
2042	then
2043	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2044	elif (( ii < 1000 ))
2045	then
2046	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2047	else
2048	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2049	fi
2050	(( ii = ii + 1 ))
2051	done
2052
2053	else
2054
2055	if [[ $files_for_cores = true ]]
2056	then
2057
2058	# PROVIDE FILES FOR EACH CORE
2059	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2060	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2061	printf "\n providing $cores files for the respective cores"
2062	mkdir -p ${localin[$i]}
2063	if [[ $link_local_input = true ]]
2064	then
2065	printf " files will be linked\n"
2066	cd ${absnamein[$i]}
2067	for file in $(ls *)
2068	do
2069	ln -f $file ${localin[$i]}
2070	done
2071	cd $tempdir
2072	fi
2073
2074	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2075	if [[ ! -f "${localin[$i]}/_000000" ]]
2076	then
2077	if [[ $link_local_input = true ]]
2078	then
2079	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2080	fi
2081	cp -r ${absnamein[$i]}/* ${localin[$i]}
2082	fi
2083
2084	else
2085
2086	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2087	if [[ $link_local_input = true ]]
2088	then
2089	printf " file will be linked\n"
2090	ln -f ${absnamein[$i]} ${localin[$i]}
2091	fi
2092	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2093	if [[ ! -f "${localin[$i]}" ]]
2094	then
2095	if [[ $link_local_input = true ]]
2096	then
2097	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2098	fi
2099	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2100	then
2101	mv ${absnamein[$i]} ${localin[$i]}
2102	else
2103	cp ${absnamein[$i]} ${localin[$i]}
2104	fi
2105	fi
2106	fi
2107	fi
2108	fi
2109
2110	done
2111	if (( i != 0 ))
2112	then
2113	if [[ $optional_files_missing = true ]]
2114	then
2115	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2116	fi
2117	printf "\n$dashes\n *** all INPUT-files provided \n"
2118	fi
2119
2120
2121	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2122	(( i = 0 ))
2123	while (( i < iic ))
2124	do
2125	(( i = i + 1 ))
2126	if (( i == 1 ))
2127	then
2128	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2129	fi
2130	printf "\n >>> ${in_command[$i]}"
2131	eval ${in_command[$i]}
2132	if (( i == iic ))
2133	then
2134	printf "\n$dashes\n"
2135	fi
2136	done
2137
2138
2139	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2140	# (FILE ENVPAR WILL BE READ BY PALM)
2141	cat > ENVPAR << EOF
2142	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2143	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2144	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2145	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2146	maximum_cpu_time_allowed = ${cpumax}.,
2147	revision = '$global_revision',
2148	batch_job = .${running_in_batch_mode}. /
2149
2150	EOF
2151
2152
2153	# STARTING THE EXECUTABLE
2154	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2155	PATH=$PATH:$tempdir
2156
2157
2158	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2159	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2160	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2161	eval line=\"$line\"
2162	execute_command="$line"
2163
2164
2165	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2166	if [[ "$execute_command_for_combine" = "" ]]
2167	then
2168	eval line2=\"$line2\"
2169	execute_command_for_combine="$line2"
2170	fi
2171
2172
2173
2174	# PROVIDE A HOSTFILE, IF REQUIRED
2175	if [[ "$hostfile" != "" ]]
2176	then
2177
2178	if [[ $hostfile = auto ]]
2179	then
2180	# CREATE A NEW HOSTFILE
2181	(( ii = 1 ))
2182	while (( ii <= cores / threads_per_task ))
2183	do
2184	echo $(hostname) >> hostfile
2185	(( ii = ii + 1 ))
2186	done
2187	if (( cores / threads_per_task == 0 ))
2188	then
2189	echo $(hostname) >> hostfile
2190	fi
2191
2192	else
2193	cp $hostfile hostfile
2194	fi
2195	eval line=\"`head -n $ii hostfile`\"
2196	printf "\n *** running on: $line"
2197	fi
2198
2199
2200
2201	# SET THE NUMBER OF OPENMP-THREADS
2202	if [[ $use_openmp = true ]]
2203	then
2204	export OMP_NUM_THREADS=$threads_per_task
2205	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2206	else
2207	export OMP_NUM_THREADS=1
2208	fi
2209
2210
2211	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2212	if [[ $run_coupled_model = false ]]
2213	then
2214	if [[ "$ocean_file_appendix" = true ]]
2215	then
2216	echo "precursor_ocean" > coupling_steering
2217	else
2218	echo "precursor_atmos" > coupling_steering
2219	fi
2220	else
2221	(( iia = $cores_atmos / $threads_per_task ))
2222	(( iio = $cores_ocean / $threads_per_task ))
2223	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2224	printf "\n\n"
2225	echo "coupled_run $iia $iio" > coupling_steering
2226	fi
2227
2228	printf "\n *** execute command:"
2229	printf "\n \"$execute_command\" \n\n"
2230
2231	$execute_command < coupling_steering
2232
2233	if [[ $? != 0 ]]
2234	then
2235
2236	# ABORT IN CASE OF RUNTIME ERRORS
2237	printf "\n +++ runtime error occured"
2238	locat=execution
2239	exit
2240
2241	else
2242
2243	printf "\n$dashes\n *** execution finished \n"
2244
2245	fi
2246
2247
2248	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2249	# BY EACH CORE INTO ONE FILE
2250	if [[ ! -f combine_plot_fields.x ]]
2251	then
2252
2253	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2254	printf "\n 2d- and/or 3d-data may be incomplete!"
2255	printf "\n Your previous palmbuild may have failed. Please check.\n"
2256
2257	elif [[ "$combine_plot_fields" == true ]]
2258	then
2259
2260	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2261	$execute_command_for_combine
2262
2263	else
2264
2265	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2266	# DATA OUTPUT
2267	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2268	fi
2269
2270
2271
2272	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2273	(( i = 0 ))
2274	while (( i < ioc ))
2275	do
2276	(( i = i + 1 ))
2277	if (( i == 1 ))
2278	then
2279	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2280	fi
2281
2282	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2283	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2284
2285	printf "\n >>> ${out_command[$i]}"
2286	eval ${out_command[$i]}
2287	if (( i == ioc ))
2288	then
2289	printf "\n$dashes\n"
2290	fi
2291	done
2292
2293
2294	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2295	# WILDCARDS
2296	(( i = 0 ))
2297	(( nr_of_output_files = 0 ))
2298
2299	while (( i < iout ))
2300	do
2301
2302	(( i = i + 1 ))
2303
2304	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2305	# CREATE A LIST FOR THE DETECTED ENDINGS
2306	if [[ "${multout[$i]}" = true ]]
2307	then
2308	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2309	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2310	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2311
2312	endings="DEFAULT"
2313	while read line
2314	do
2315	# remove the local name from the beginning
2316	localnamestring="${localout_pre[$i]}"
2317	length_localname=${#localnamestring}
2318	ending=${line:${length_localname}}
2319
2320	if [[ "$ending" != "" ]]
2321	then
2322	endings="$endings $ending"
2323	fi
2324
2325	done <filelist
2326
2327	rm filelist
2328
2329	else
2330
2331	# SINGLE NAME
2332	endings=DEFAULT
2333
2334	fi
2335
2336	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2337	for ending in $endings
2338	do
2339
2340	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2341	if [[ $ending = DEFAULT ]]
2342	then
2343	ending=""
2344	fi
2345
2346	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2347	(( nr_of_output_files = nr_of_output_files + 1 ))
2348	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2349	transout[$nr_of_output_files]="${transout_pre[$i]}"
2350	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2351	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2352	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2353	extout[$nr_of_output_files]="${extout_pre[$i]}"
2354	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2355
2356	done
2357
2358	done
2359
2360
2361
2362
2363	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2364	(( i = 0 ))
2365	while (( i < nr_of_output_files ))
2366	do
2367	(( i = i + 1 ))
2368	if (( i == 1 ))
2369	then
2370	printf "\n\n *** saving OUTPUT-files:"
2371
2372	# GET RUN NUMBER ASSIGNED BY PALM
2373	if [[ -f RUN_NUMBER ]]
2374	then
2375	read run_number < RUN_NUMBER
2376	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2377	usecycle_option="-U $run_number"
2378	else
2379	run_number=0
2380	usecycle_option=""
2381	fi
2382	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2383	then
2384	printf "\n *** in case of SCP transfers to local host"
2385	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2386	fi
2387	printf "\n$dashes"
2388	fi
2389
2390	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2391	then
2392
2393	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2394
2395	# DETERMINE THE CYCLE NUMBER
2396	ls -1 -d $filename > filelist 2>/dev/null
2397	ls -1 -d $filename.* >> filelist 2>/dev/null
2398	while read line
2399	do
2400
2401	# filename without path (i.e. after the last "/")
2402	basefilename=$(basename ${line})
2403
2404	# check if there is an extension
2405	extension=${basefilename##*.}
2406	if [[ "$extension" = "${extout[$i]}" ]]
2407	then
2408	basefilename=${basefilename%.*}
2409	fi
2410
2411	# check for an existing cycle number
2412	cycle=${basefilename##*.}
2413	if [[ $cycle =~ ^-?[0-9]+$ ]]
2414	then
2415	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2416	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2417	(( icycle = $((10#$cycle)) + 1 ))
2418	else
2419	(( icycle = 1 ))
2420	fi
2421
2422	if (( icycle > maxcycle ))
2423	then
2424	(( maxcycle = icycle ))
2425	fi
2426
2427	done <filelist
2428	rm filelist
2429
2430
2431	# SET THE CYCLE NUMBER
2432	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2433	if [[ "${actionout[$i]}" = a ]]
2434	then
2435	(( maxcycle = maxcycle - 1 ))
2436	fi
2437
2438	(( cycnum[$i] = maxcycle ))
2439	pathout[$i]=$filename
2440
2441
2442	# ADD CYCLE NUMBER TO FILENAME
2443	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2444	if [[ "${actionout[$i]}" != "a" ]]
2445	then
2446	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2447	# WITH AN EXISTING CYCLE NUMBER
2448	if (( run_number >= cycnum[$i] ))
2449	then
2450	(( cycnum[$i] = run_number ))
2451	else
2452	if (( run_number > 0 ))
2453	then
2454	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2455	fi
2456	fi
2457	fi
2458	if (( cycnum[$i] > 0 ))
2459	then
2460	cyclestring=`printf "%03d" ${cycnum[$i]}`
2461	pathout[$i]=${pathout[$i]}.$cyclestring
2462	fi
2463	fi
2464
2465	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2466	files_for_cores=false; filetype=file
2467	link_local_output=false
2468	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2469	then
2470	files_for_cores=true; filetype=directory
2471	actionout[$i]=""
2472	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2473	then
2474	actionout[$i]=""
2475	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2476	then
2477	files_for_cores=true; filetype=directory
2478	link_local_output=true
2479	actionout[$i]=""
2480	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2481	then
2482	link_local_output
2483	actionout[$i]=""
2484	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2485	then
2486	files_for_cores=true; filetype=directory
2487	actionout[$i]="tr"
2488	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2489	then
2490	actionout[$i]="tr"
2491	fi
2492
2493	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2494	then
2495	if [[ ${warnout[$i]} = true ]]
2496	then
2497	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2498	fi
2499	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2500	then
2501	if [[ ${warnout[$i]} = true ]]
2502	then
2503	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2504	fi
2505	else
2506
2507
2508	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2509	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2510	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2511	then
2512	if [[ $running_on_remote = true ]]
2513	then
2514
2515	# SET OPTIONS FOR TRANSFER
2516	if [[ "${actionout[$i]}" = tr ]]
2517	then
2518	if [[ $files_for_cores = false ]]
2519	then
2520	catalog_option=""
2521	catalog_string=""
2522	else
2523	catalog_option="-c"
2524	catalog_string="/"
2525	fi
2526	append_option=""
2527	append_string=""
2528	else
2529	append_option="-A"
2530	append_string="append"
2531	fi
2532
2533	transfer_failed=false
2534	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2535	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2536
2537	# TRANSFER VIA SCP
2538	if [[ "$remote_loginnode" != "" ]]
2539	then
2540	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
2541	else
2542	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]}
2543	fi
2544	[[ $? != 0 ]] && transfer_failed=true
2545
2546
2547	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2548	if [[ $transfer_failed = true ]]
2549	then
2550	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2551	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2552
2553	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2554	eval local_catalog=${pathout[$i]}
2555	if [[ ! -d $local_catalog ]]
2556	then
2557	printf " *** local directory does not exist. Trying to create:\n"
2558	printf " $local_catalog \n"
2559	mkdir -p $local_catalog
2560	fi
2561	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2562	transfer_problems=true
2563	fi
2564
2565	else
2566
2567	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2568	# BE COPIED OR APPENDED ON THIS MACHINE
2569	if [[ "${actionout[$i]}" = tr ]]
2570	then
2571	actionout[$i]=""
2572	else
2573	actionout[$i]="a"
2574	fi
2575	fi
2576	fi
2577
2578
2579	# APPEND ON THIS MACHINE
2580	if [[ "${actionout[$i]}" = "a" ]]
2581	then
2582	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2583	then
2584	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2585	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2586	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2587	else
2588	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2589	printf "\n ${pathout[$i]}\n"
2590	cat ${localout[$i]} >> ${pathout[$i]}
2591	fi
2592	fi
2593
2594	# COPY ON THIS MACHINE
2595	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2596	# ON DIFFERENT FILE-SYSTEMS
2597	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2598	then
2599
2600	# COPY IN CASE OF RUNS ON SINGLE CORES
2601	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2602	then
2603	printf "\n >>> OUTPUT: ${localout[$i]} to"
2604	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2605	if [[ $link_local_output = true ]]
2606	then
2607	printf " file will be linked\n"
2608	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2609	fi
2610	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2611	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2612	then
2613	if [[ $link_local_output = true ]]
2614	then
2615	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2616	fi
2617	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2618	else
2619	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2620	fi
2621	else
2622	printf "\n >>> OUTPUT: ${localout[$i]} to"
2623	printf "\n ${pathout[$i]}\n"
2624	if [[ $link_local_output = true ]]
2625	then
2626	printf " file will be linked\n"
2627	ln -f ${localout[$i]} ${pathout[$i]}
2628	fi
2629	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2630	if [[ ! -f "${pathout[$i]}" ]]
2631	then
2632	if [[ $link_local_output = true ]]
2633	then
2634	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2635	fi
2636	cp ${localout[$i]} ${pathout[$i]}
2637	else
2638	printf "+++ no copy because file ${pathout[$i]} exists\n"
2639	fi
2640	fi
2641
2642	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2643	then
2644
2645	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2646	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2647	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2648	printf "\n ${pathout[$i]}\n"
2649	if [[ $link_local_output = true ]]
2650	then
2651	printf " files will be linked\n"
2652	mkdir -p ${pathout[$i]}
2653	cd ${localout[$i]}
2654	for file in $(ls *)
2655	do
2656	ln -f $file ${pathout[$i]}
2657	done >\|/dev/null 2>&1
2658	cd $tempdir
2659	fi
2660
2661	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2662	if [[ ! -f "${pathout[$i]}/_000000" ]]
2663	then
2664	if [[ $link_local_output = true ]]
2665	then
2666	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2667	fi
2668	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2669	cp -r ${localout[$i]}/* ${pathout[$i]}
2670	fi
2671
2672	fi
2673	fi
2674	done
2675
2676	if (( i != 0 ))
2677	then
2678	if [[ $transfer_problems = true ]]
2679	then
2680	printf "\n$dashes\n *** OUTPUT-files saved"
2681	printf "\n +++ WARNING: some data transfers failed! \n"
2682	else
2683	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2684	fi
2685	fi
2686
2687
2688	# IF REQUIRED, START A RESTART-JOB
2689	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2690	if [[ -f CONTINUE_RUN ]]
2691	then
2692
2693	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2694	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2695	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2696	# -b START A BATCH JOB
2697	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2698	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2699	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2700
2701	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2702	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2703	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2704	then
2705	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2706	fi
2707
2708	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2709	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2710	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2711	then
2712	prc=`echo $prc \| sed 's/#/r/g'`
2713	fi
2714
2715
2716	# START THE RESTART-JOB
2717	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2718	echo " $prc"
2719	printf "\n$dashes\n"
2720	if [[ $running_on_remote = true ]]
2721	then
2722
2723	echo "*** ssh will be used to initiate restart-runs!"
2724	echo " return_address=\"$return_address\" "
2725	echo " return_username=\"$local_username\" "
2726
2727	if [[ "$remote_loginnode" != "" ]]
2728	then
2729	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
2730	else
2731	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2732	fi
2733
2734	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2735	sleep 30
2736
2737	else
2738
2739	# START THE RESTART JOB ON THE LOCAL HOST
2740	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2741	cd - > /dev/null
2742
2743	fi
2744
2745	# CHECK, IF RESTART JOB HAS BEEN STARTED
2746	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2747	then
2748	printf "\n$dashes\n +++ creating restart run failed \n"
2749	locat=create_restart
2750	exit
2751	rm palmrun_restart.log
2752	else
2753	printf "\n$dashes\n *** restart run initiated \n"
2754	rm palmrun_restart.log
2755	fi
2756
2757
2758	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2759	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2760	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2761	# MAY BE VERY HUGE)
2762	(( i = 0 ))
2763	while (( i < nr_of_input_files ))
2764	do
2765	(( i = i + 1 ))
2766	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2767	then
2768	rm -r ${absnamein[$i]}
2769	fi
2770	done
2771
2772	fi
2773
2774
2775	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2776	cd $HOME
2777	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2778
2779
2780	else
2781
2782
2783	# PREPARING ACTIONS,
2784	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2785
2786	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2787	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2788	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2789	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2790	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2791	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2792	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2793	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2794	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2795	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2796	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2797	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2798	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2799	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2800	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2801	if [[ $create_remote_batch_job = true ]]
2802	then
2803	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2804	if [[ $do_trace = true ]]
2805	then
2806	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2807	fi
2808	elif [[ $create_batch_job = true ]]
2809	then
2810	palmrun_com=${palmrun_com}" -j"
2811	if [[ $do_trace = true ]]
2812	then
2813	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2814	fi
2815	fi
2816
2817
2818	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2819	# REMOTE HOST
2820	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2821	job_protocol_file=$job_protocol_file_local
2822	if [[ $create_remote_batch_job = true ]]
2823	then
2824	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2825	job_protocol_file=$job_protocol_file_remote
2826	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2827	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2828	fi
2829
2830
2831	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2832	jobfile=jobfile.$run_id_number
2833
2834
2835	# FIRST CREATE THE BATCH DIRECTIVES
2836	(( i = 0 ))
2837	while (( i < ibd ))
2838	do
2839	(( i = i + 1 ))
2840	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2841	eval line=\"$line\"
2842	echo "$line" >> $jobfile
2843	done
2844	echo " " >> $jobfile
2845
2846
2847	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2848	# PROTOCOL
2849	if [[ $create_remote_batch_job = true ]]
2850	then
2851	echo "set +vx" >> $jobfile
2852	echo "trap '" >> $jobfile
2853	echo "set +vx" >> $jobfile
2854	echo "cd ${remote_jobcatalog}" >> $jobfile
2855	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2856
2857	# ADD THE BATCH DIRECTIVES
2858	(( i = 0 ))
2859	while (( i < ibdt ))
2860	do
2861	(( i = i + 1 ))
2862	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2863	eval line=\"$line\"
2864	echo "$line" >> $jobfile
2865	done
2866	echo " " >> $jobfile
2867
2868	echo "set -x" >> $jobfile
2869	echo "${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
2870	echo "%%END%%" >> $jobfile
2871	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2872	echo "$submit_command $scpjob_file" >> $jobfile
2873	echo "rm $scpjob_file" >> $jobfile
2874	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2875	echo "set -x" >> $jobfile
2876	echo " ' exit" >> $jobfile
2877	fi
2878
2879
2880	# ACTIVATE ERROR-TRACEBACK
2881	if [[ $do_trace = true ]]
2882	then
2883	echo "set -x" >> $jobfile
2884	else
2885	echo "set +vx" >> $jobfile
2886	fi
2887
2888
2889	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2890	if [[ "$login_init_cmd" != "" ]]
2891	then
2892	echo "$login_init_cmd" >> $jobfile
2893	fi
2894	if [[ "$module_commands" != "" ]]
2895	then
2896	echo "$module_commands" >> $jobfile
2897	fi
2898
2899
2900	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2901	if [[ $create_remote_batch_job = true ]]
2902	then
2903	echo "mkdir $tempdir" >> $jobfile
2904	echo "chmod go+rx $tempdir" >> $jobfile
2905	else
2906	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2907	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2908	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2909	mkdir $tempdir
2910	chmod go+rx $tempdir
2911	fi
2912	echo "cd $tempdir" >> $jobfile
2913	echo "export tempdir=$tempdir" >> $jobfile
2914	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2915	echo "export PATH=.:\$PATH" >> $jobfile
2916	echo "export execute_palmrun=true" >> $jobfile
2917
2918
2919	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2920	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2921	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2922	echo "LOCAL_PWD=$working_directory" >> $jobfile
2923	echo "export LOCAL_PWD" >> $jobfile
2924
2925
2926	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2927	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2928	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2929
2930
2931	# CALL PALMRUN WITHIN THE JOB
2932	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2933	echo "set -x" >> $jobfile
2934	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2935
2936
2937	# TRANSFER JOBFILE TO THE TARGET HOST
2938	if [[ $create_jobfile_only = false ]]
2939	then
2940
2941	if [[ $create_remote_batch_job = true ]]
2942	then
2943
2944	echo " "
2945	echo " *** transfer of job to remote host via scp"
2946	if [[ $do_trace = true ]]
2947	then
2948	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
2949	fi
2950	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
2951
2952	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2953	if [[ $do_trace = true ]]
2954	then
2955	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"
2956	fi
2957	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
2958
2959	elif [[ $create_batch_job = true ]]
2960	then
2961
2962	eval local_jobcatalog=$local_jobcatalog
2963	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
2964	cd $local_jobcatalog
2965	echo " "
2966	echo " *** submit the job"
2967	if [[ $do_trace = true ]]
2968	then
2969	echo "$submit_command ${configuration_identifier}_${run_id}"
2970	fi
2971	$submit_command ${configuration_identifier}_${run_id}
2972	rm ${configuration_identifier}_${run_id}
2973	cd - > /dev/null
2974
2975	fi
2976
2977	rm -rf $jobfile
2978
2979	else
2980
2981	printf "\n *** jobfile created under name \"$jobfile\" "
2982	printf "\n no batch-job has been sent!"
2983
2984	fi
2985
2986	fi # END OF REMOTE-PART

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