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source: palm/trunk/SCRIPTS/palmrun @ 3138

Last change on this file since 3138 was 3132, checked in by raasch, 6 years ago
create consistent error messages in case of failed restarts, check existence of remote job catalog
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 98.7 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 3132 2018-07-16 11:44:58Z maronga $
29	# create consistent error messages in case of failed restarts,
30	# check existence of remote job catalog
31	#
32	# 3043 2018-05-25 10:47:54Z raasch
33	# check for setting of fast_io_catalog
34	#
35	# 3033 2018-05-23 15:26:19Z raasch
36	# -T option not required for interactive runs (tasks per node =
37	# total number of cores is assumed as default, if option is not given),
38	# reformatting of a few messages,
39	# bugfix: destination output directory is created if attribute "pe" is set in
40	# .palm.iofiles
41	#
42	# 2718 2018-01-02 08:49:38Z maronga
43	# bugfix of r2990
44	#
45	# 2718 2018-01-02 08:49:38Z maronga
46	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
47	# not in the working directory from where palmrun is called
48	#
49	# 2718 2018-01-02 08:49:38Z maronga
50	# svfout in the activation string will be replaced now by svfin in case of
51	# automatic restarts
52	#
53	# 2718 2018-01-02 08:49:38Z maronga
54	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
55	# the possible output or input of sky view factors
56	#
57	# 2718 2018-01-02 08:49:38Z maronga
58	# "fname" renamed to "jobname"
59	#
60	# 2718 2018-01-02 08:49:38Z maronga
61	# parameters are allowed in output commands (OC:)
62	#
63	# 2718 2018-01-02 08:49:38Z maronga
64	# bugfix: exit if no queue has been given neither with option -q nor in the
65	# configuration file
66	#
67	# 2718 2018-01-02 08:49:38Z maronga
68	# file connection file from trunk/SCRIPTS is taken by default
69	#
70	# 2718 2018-01-02 08:49:38Z maronga
71	# Corrected "Former revisions" section
72	#
73	# 2696 2017-12-14 17:12:51Z kanani
74	# Change in file header (GPL part)
75	#
76	# 2693 2017-12-13 12:33:49Z raasch
77	# replacement of variables given by {{<variable>}} in configuration file is now
78	# done in a more general way, variable names are written in small letters
79	#
80	# 2670 2017-12-06 16:32:19Z raasch
81	# test printouts removed
82	#
83	# 2669 2017-12-06 16:03:27Z raasch
84	# file attributes in .palm.iofiles restructured, "loc" attribute completely
85	# removed,
86	# wildcard (*) allowed in .palm.iofiles as file activation string for output
87	# files,
88	# informative messages in case of missing optional input files shortened
89	# bugfix: variable cycle explicitly interpreted with 10 as the number base
90	#
91	# 2638 2017-11-23 12:44:23Z raasch
92	# use of wildcards in file connection statements enabled
93	#
94	# 2605 2017-11-09 15:31:46Z raasch
95	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
96	# will not be sent with the job file any more, but copied into the
97	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
98	#
99	# 2600 2017-11-01 14:11:20Z raasch
100	# cycle numbers are made three digits wide
101	#
102	# 2566 2017-10-20 08:50:47Z raasch
103	# execute command for combine_plot_fields added
104	# "TEMPDIR" renamed "tempdir"
105	# temporary working directory for local batch jobs is created immediately within
106	# the user's palmrun call, due to a requirement of the "grid engine" batch
107	# system, where the working directory is given with batch directive -wd and must
108	# already exist when the job is submitted,
109	# informative messages in non-trace mode reduced and partly reformatted
110	#
111	# 2551 2017-10-18 07:25:11Z raasch
112	# TEMPDIR added as replacement string to be used in batch directives
113	#
114	# 2512 2017-10-04 08:26:59Z raasch
115	# bugfix for determining cycle numbers of NetCDF input files
116	#
117	# 2506 2017-09-29 08:30:37Z raasch
118	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
119	# host configuration added to SOURCES_FOR_RUN_... folder name
120	# host_identifier renamed host_configuration
121	# option -W added to allow for job dependencies
122	#
123	# 2501 2017-09-26 11:41:55Z raasch
124	# default value for number of cores (option -X) set to 1
125	# bugfix for mechanism which overwrites configuration file settings with values
126	# provided by palmrun options
127	#
128	# 2499 2017-09-22 16:47:58Z kanani
129	# option -h named configuration identifier
130	#
131	# 2480 2017-09-19 06:24:14Z maronga
132	# bugfix for last revision
133	#
134	# 2479 2017-09-19 06:12:16Z raasch
135	# option -A (project account number) added
136	#
137	# 2422 2017-09-08 08:25:41Z raasch
138	# initial revision
139	#
140	#--------------------------------------------------------------------------------#
141	# palmrun - script for running PALM jobs on local and remote hosts
142	#--------------------------------------------------------------------------------#
143
144
145
146	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
147
148	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
149	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
150	# (TOO MANY ARGUMENTS - PROBLEM)
151	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
152
153	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
154	typeset -i nr_of_output_files=0
155	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
156	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
157	# SCRIPT-OPTION ARGUMENTS
158	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
159	typeset -i icycle inode ival maxcycle mpi_tasks
160	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
161
162	activation_string_list=""
163	AddFilenames=""
164	combine_plot_fields=true
165	compiler_name=""
166	compiler_name_ser=""
167	compiler_options=""
168	cores=1
169	cores_atmos=0
170	cores_ocean=0
171	coupled_dist=""
172	cpp_options=""
173	cpumax=0
174	create_batch_job=false
175	create_jobfile_only=false
176	create_remote_batch_job=false
177	dashes=" ----------------------------------------------------------------------------"
178	defaultqueue=""
179	delete_temporary_catalog=true
180	do_compile=true
181	do_trace=false
182	executable=""
183	execute_command=""
184	execution_error=false
185	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
186	jobname=test
187	global_revision=""
188	host_configuration="default"
189	hostfile=""
190	hp=""
191	keep_data_from_previous_run=false
192	link_local_input=false
193	link_local_output=false
194	linker_options=""
195	local_jobcatalog=""
196	locat=normal
197	makefile=""
198	max_par_io_str=""
199	prc=$0
200	while [[ $(echo $prc \| grep -c "/") != 0 ]]
201	do
202	prc=`echo $prc \| cut -f2- -d"/"`
203	done
204	module_calls=""
205	palmrun_memory=""
206	palmrun_script_name=$prc
207	openmp=false
208	previous_job=""
209	project_account=""
210	queue=none
211	read_svf=""
212	restart_run=false
213	return_address=""
214	remote_jobcatalog=""
215	remote_username=""
216	running_in_batch_mode=false
217	run_coupled_model=false
218	run_id=""
219	silent=false
220	source_list=""
221	source_path=""
222	tasks_per_node=0
223	threads_per_task=1
224	transfer_problems=false
225	user_source_path=""
226	use_existing_sources_folder=""
227	use_openmp=false
228	version="palmrun 1.0 Rev$Rev: 3132 $"
229	working_directory=`pwd`
230	write_binary=""
231	write_svf=""
232
233
234	# ERROR HANDLING IN CASE OF EXIT
235	trap 'if [[ $locat != normal && $locat != control_c ]]
236	then
237
238	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
239	(( i = 0 ))
240	while (( i < iec ))
241	do
242	(( i = i + 1 ))
243	printf "\n *** Execution of ERROR-command:\n"
244	printf " >>> ${err_command[$i]}\n"
245	eval ${err_command[$i]}
246	done
247	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
248	printf "\n\n+++ palmrun killed \n\n"
249	elif [[ $locat != control_c ]]
250	then
251	printf "\n --> palmrun finished\n\n"
252	fi' exit
253
254
255	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
256	trap 'cd; rm -rf $tempdir
257	printf "\n+++ palmrun killed by \"^C\" \n\n"
258	locat=control_c
259	exit
260	' 2
261
262
263	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
264	# WHICH WILL BE USED TO START RESTART-JOBS
265	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
266	do
267	case $option in
268	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
269	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
270	(b) create_batch_job=true; prc="$prc -b";;
271	(B) delete_temporary_catalog=false; prc="$prc -B";;
272	(C) restart_run=true; prc="$prc -C";;
273	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
274	(F) create_jobfile_only=true;;
275	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
276	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
277	(j) running_in_batch_mode=true;;
278	(k) keep_data_from_previous_run=true; prc="$prc -k";;
279	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
280	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
281	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
282	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
283	(r) run_id=$OPTARG;;
284	(R) return_address=$OPTARG;;
285	(s) source_list=$OPTARG;;
286	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
287	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
288	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
289	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
290	(v) silent=true; prc="$prc -v";;
291	(V) use_existing_sources_folder="-V";;
292	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
293	(W) previous_job=$OPTARG;;
294	(x) do_trace=true;set -x; prc="$prc -x";;
295	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
296	(y) ocean_file_appendix=true; prc="$prc -y";;
297	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
298	(Z) combine_plot_fields=false; prc="$prc -Z";;
299	(\?) printf "\n +++ unknown option $OPTARG \n"
300	printf "\n --> type \"$0 ?\" for available options \n"
301	locat=parameter;exit;;
302	esac
303	done
304
305
306	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
307	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
308	(( to_shift = $OPTIND - 1 ))
309	shift $to_shift
310
311	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
312	if [[ "$1" = "?" ]]
313	then
314	(printf "\n *** Description of available palmrun options:\n"
315	printf "\n Option Description Default-Value"
316	printf "\n -a activation string list \"\" "
317	printf "\n -A project account number ---"
318	printf "\n -b batch-job on local machine ---"
319	printf "\n -B do not delete temporary directory at end ---"
320	printf "\n -d run identifier test"
321	printf "\n -F create batch job file only ---"
322	printf "\n -h host configuration \"default\" "
323	printf "\n -k keep data from previous run"
324	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
325	printf "\n -M Makefile name Makefile"
326	printf "\n -O threads per openMP task ---"
327	printf "\n -q queue \"$queue\" "
328	printf "\n -s filenames of routines to be compiled \"\" "
329	printf "\n must end with .f, .f90, .F, or .c !"
330	printf "\n use \"..\" for more than one file and wildcards"
331	printf "\n -s LM compiles all locally modified files"
332	printf "\n -t allowed cpu-time in seconds (batch) 0"
333	printf "\n -T tasks per node ---"
334	printf "\n -u username on remote machine \"\" "
335	printf "\n -v no prompt for confirmation ---"
336	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
337	printf "\n -w maximum parallel io streams as given by -X"
338	printf "\n -W name of job to wait for ---"
339	printf "\n -x tracing of palmrun for debug purposes ---"
340	printf "\n -X # of processors (on parallel machines) 1"
341	printf "\n -y add appendix \"_O\" to all local output"
342	printf "\n files (ocean precursor runs followed by"
343	printf "\n coupled atmosphere-ocean runs) ---"
344	printf "\n -Y run coupled model, \"#1 #2\" with"
345	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
346	printf "\n -Z skip combine_plot_fields at the end of "
347	printf "\n the simulation ---"
348	printf "\n "
349	printf "\n Possible values of positional parameter <modus>:"
350	printf "\n \"?\" - this outline \n\n") \| more
351	exit
352	elif [[ "$1" != "" ]]
353	then
354	printf "\n +++ positional parameter $1 unknown \n"
355	locat=parameter; exit
356	fi
357
358
359
360	# SHORT STARTING MESSAGE
361	printf "\n*** $version "
362	printf "\n will be executed. Please wait ..."
363
364
365	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
366	export fname=$jobname
367
368
369	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
370	config_file=.palm.config.$host_configuration
371	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
372
373
374	# CHECK, IF CONFIGURATION FILE EXISTS
375	if [[ ! -f $config_file ]]
376	then
377	printf "\n\n +++ configuration file: "
378	printf "\n $config_file"
379	printf "\n does not exist"
380	locat=connect; exit
381	fi
382
383
384	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
385	if [[ -f .palm.iofiles ]]
386	then
387	fileconnection_file=.palm.iofiles
388	fi
389
390
391	# CHECK, IF FILE CONNECTION FILE EXISTS
392	if [[ ! -f $fileconnection_file ]]
393	then
394	printf "\n\n +++ file connection file: "
395	printf "\n $fileconnection_file"
396	printf "\n does not exist"
397	locat=connect; exit
398	fi
399
400
401	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
402	if [[ "$activation_string_list" = "" ]]
403	then
404	printf "\n\n +++ no activation string list given: "
405	printf "\n please set palmrun option \"-a\" "
406	locat=palmrun_option; exit
407	fi
408
409
410	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
411	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
412	then
413	write_binary=true
414	else
415	write_binary=false
416	fi
417
418	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
419	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
420	then
421	write_svf=true
422	else
423	write_svf=false
424	fi
425
426	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
427	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
428	then
429	read_svf=true
430	else
431	read_svf=false
432	fi
433
434
435	# READ AND EVALUATE THE CONFIGURATION-FILE
436	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
437
438	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
439	while read line
440	do
441
442	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
443	eval line=\"$line\"
444
445
446	# INTERPRET THE LINE
447	if [[ "$(echo $line)" = "" ]]
448	then
449
450	# EMPTY LINE, NO ACTION
451	continue
452
453	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
454	then
455
456	# LINE IS A COMMENT LINE
457	continue
458
459	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
460	then
461
462	# LINE DEFINES AN ENVIRONMENT-VARIABLE
463	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
464	value=`echo $line \| cut -d" " -s -f2-`
465
466
467	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
468	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
469	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
470	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
471	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
472	# CONFIGURATION-FILE.
473	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
474	then
475	eval export $var="\$value"
476
477	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
478	if [[ $do_trace = true ]]
479	then
480	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
481	fi
482	fi
483
484	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
485	then
486
487	# LINE DEFINES BATCH-DIRECTIVE
488	(( ibd = ibd + 1 ))
489	line=$(echo $line \| cut -c4-)
490	batch_directive[$ibd]="$line"
491
492	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
493	then
494
495	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
496	# REMOTE TO A LOCAL HOST
497	(( ibdt = ibdt + 1 ))
498	line=$(echo $line \| cut -c5-)
499	batch_directive_transfer[$ibdt]="$line"
500
501	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
502	then
503
504	# LINE DEFINES ERROR-COMMAND
505	(( iec = iec + 1 ))
506	line=$(echo $line \| cut -c4-)
507	err_command[$iec]="$line"
508
509	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
510	then
511
512	# LINE DEFINES INPUT-COMMAND
513	(( iic = iic + 1 ))
514	line=$(echo $line \| cut -c4-)
515	in_command[$iic]="$line"
516
517	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
518	then
519
520	# LINE DEFINES OUTPUT-COMMAND
521	(( ioc = ioc + 1 ))
522	line=$(echo $line \| cut -c4-)
523	out_command[$ioc]="$line"
524
525	else
526
527	# SKIP ALL OTHER LINES
528	continue
529
530	fi
531
532	done < $config_file
533
534
535	# CHECK SETTING OF REQUIRED PARAMETERS
536	if [[ "$fast_io_catalog" = "" ]]
537	then
538	printf "\n +++ no fast_io_catalog found in $config_file"
539	printf "\n Please add line \"fast_io_catalog ...\" to that file."
540	locat=config_file; exit
541	fi
542	if [[ "$compiler_name" = "" ]]
543	then
544	printf "\n +++ no compiler name found in $config_file"
545	printf "\n Please add line \"compiler_name ...\" to that file."
546	locat=config_file; exit
547	fi
548	if [[ "$compiler_name_ser" = "" ]]
549	then
550	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
551	printf "\n Please add line \"compiler_name_ser ...\" to that file."
552	locat=config_file; exit
553	fi
554	if [[ "$compiler_options" = "" ]]
555	then
556	printf "\n +++ no compiler options found in $config_file"
557	printf "\n Please add line \"compiler_options ...\" to that file."
558	locat=config_file; exit
559	fi
560	if [[ "$linker_options" = "" ]]
561	then
562	printf "\n +++ no linker options found in $config_file"
563	printf "\n Please add line \"linker_options ...\" to that file."
564	locat=config_file; exit
565	fi
566	if [[ "$execute_command" = "" ]]
567	then
568	printf "\n +++ no execute command found in $config_file"
569	printf "\n Please add line \"execute_command ...\" to that file."
570	locat=config_file; exit
571	fi
572
573	if [[ "$hostfile" != "" ]]
574	then
575	if [[ $hostfile != auto && ! -f $hostfile ]]
576	then
577	printf "\n +++ no hostfile \"$hostfile\" found"
578	printf "\n Please check line \"%hostfile ...\" in $config_file"
579	locat=config_file; exit
580	fi
581	fi
582
583
584	# DETERMINE THE CALL STATUS
585	if [[ "$return_address" != "" ]]
586	then
587
588	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
589	# BATCH MODE AND ...
590	running_on_remote=true
591
592	else
593
594	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
595	if [[ "$remote_ip" != "" ]]
596	then
597
598	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
599	create_remote_batch_job=true
600
601	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
602	if [[ "$remote_jobcatalog" = "" ]]
603	then
604	printf "\n +++ no remote jobcatalog found in $config_file"
605	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
606	locat=config_file; exit
607	fi
608
609
610	fi
611	running_on_remote=false
612	fi
613
614
615
616	# READ AND EVALUATE THE I/O-FILE LIST
617	[[ $silent = false ]] && printf "\n Reading the I/O files... "
618
619	# READ THE FILE CONNECTION FILE LINE BY LINE
620	while read line
621	do
622
623	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
624	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
625
626	# INTERPRET THE LINE
627	if [[ "$(echo $line)" = "" ]]
628	then
629	# EMPTY LINE, NO ACTION
630	continue
631
632	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
633	then
634
635	# LINE IS A COMMENT LINE
636	true
637
638	else
639
640	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
641	# s2a: in/out - field
642	# s2b: action - field (optional)
643	s1=`echo "$line" \| cut -d" " -f1`
644	s2=`echo "$line" \| cut -d" " -s -f2`
645	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
646	then
647	s2a=$s2
648	s2b=""
649	else
650	s2a=`echo $s2 \| cut -d":" -f1`
651	s2b=`echo $s2 \| cut -d":" -f2`
652	fi
653	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
654	s4=`echo "$line" \| cut -d" " -s -f4`
655	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
656	s5=`echo "$line" \| cut -d" " -s -f5`
657	s6=`echo "$line" \| cut -d" " -s -f6`
658
659
660	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
661	# INPUT- OR OUTPUT-LIST.
662	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
663	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
664	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
665	# IS NOT CHECKED AND STORED.
666	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
667	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
668	then
669	found=false
670	for actual in $activation_string_list
671	do
672	for formal in $s3
673	do
674	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
675	done
676	done
677	if [[ $found = true ]]
678	then
679	(( iin = iin + 1 ))
680	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
681	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
682	if [[ "$s2a" = inopt ]]
683	then
684	optin_pre[$iin]=yes
685	else
686	optin_pre[$iin]=no
687	fi
688
689	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
690	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
691	if [[ $running_on_remote = true && "$s2b" = tr ]]
692	then
693	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
694	fi
695
696	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
697	# THE WILDCARD FROM THE ENDING
698	if [[ "${s5: -1}" = "*" ]]
699	then
700	if [[ "$s2b" = "di" ]]
701	then
702	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
703	printf "\n see file \"$fileconnection_file\", line"
704	printf "\n$line"
705	locat=iofiles_file; exit
706	fi
707	multin[$iin]=true
708	string=${endin_pre[$iin]}
709	endin_pre[$iin]="${string%?}"
710	else
711	multin[$iin]=false
712	fi
713	fi
714	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
715	then
716	found=false
717	for actual in $activation_string_list
718	do
719	for formal in $s3
720	do
721	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
722	done
723	done
724	if [[ $found = true ]]
725	then
726	(( iout = iout + 1 ))
727	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
728	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
729
730	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
731	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
732	if [[ $formal = wildcard ]]
733	then
734	warnout_pre[$iout]=false
735	else
736	warnout_pre[$iout]=true
737	fi
738
739	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
740	# THE WILDCARD FROM THE LOCAL FILENAME
741	if [[ "${s1: -1}" = "*" ]]
742	then
743	if [[ "$s2b" = "di" ]]
744	then
745	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
746	printf "\n see file \"$fileconnection_file\", line"
747	printf "\n$line"
748	locat=iofiles_file; exit
749	fi
750	multout[$iout]=true
751	string=${localout_pre[$iout]}
752	localout_pre[$iout]="${string%?}"
753	else
754	multout[$iout]=false
755	fi
756	fi
757	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
758	then
759	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
760	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
761	locat=connect; exit
762	fi
763	IFS="$IFSALT"
764	fi
765
766	done < $fileconnection_file
767
768
769
770	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
771	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
772	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
773	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
774	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
775	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
776
777
778
779	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
780	if [[ $run_coupled_model = true ]]
781	then
782
783	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
784	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
785
786	if (( $cores_ocean + $cores_atmos != $cores ))
787	then
788
789	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
790	printf "\n PEs (total) : $cores"
791	printf "\n PEs (atmosphere): $cores_atmos"
792	printf "\n PEs (ocean) : $cores_ocean"
793	locat=coupling; exit
794
795	fi
796
797	fi
798
799
800	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
801	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
802	# FOLDER
803	if [[ $running_in_batch_mode = true ]]
804	then
805
806	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
807	then
808	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
809	printf "\n Please check the output of the palmrun-call"
810	printf "\n that you did on your local host."
811	locat=SOURCES_FOR_RUN; exit
812	fi
813
814	else
815
816	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
817	# AUTOMATIC RESTART RUN
818	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
819	if [[ $restart_run = false ]]
820	then
821
822	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
823	# THE LOCAL HOST
824	if [[ ! -d $source_path ]]
825	then
826	printf "\n\n +++ source path \"$source_path\" on local host"
827	printf "\n \"$(hostname)\" does not exist"
828	locat=source_path; exit
829	fi
830
831	rm -rf ${base_directory}/${sources_for_run_catalog}
832	mkdir -p ${base_directory}/${sources_for_run_catalog}
833
834	if [[ "$source_list" = LM ]]
835	then
836
837	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
838	source_list=""
839	cd $source_path
840
841
842	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
843	if [[ ! -d ../.svn ]]
844	then
845	printf "\n\n +++ source directory"
846	printf "\n \"$source_path\" "
847	printf "\n is not under control of \"subversion\"."
848	printf "\n Please do not use palmrun-option \"-s LM\"\n"
849	fi
850
851
852	# LIST ALL MODIFIED SOURCE CODE FILES
853	Filenames=""
854	svn status > tmp_svnstatus
855	while read line
856	do
857	firstc=`echo $line \| cut -c1`
858	if [[ $firstc = M \|\| $firstc = "?" ]]
859	then
860	Name=`echo "$line" \| cut -c8-`
861	extension=`echo $Name \| cut -d. -f2`
862	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
863	then
864	Filenames="$Filenames "$Name
865	fi
866	fi
867	done < tmp_svnstatus
868	rm -rf tmp_svnstatus
869
870
871	# COPY FILES TO SOURCES_FOR_RUN_...
872	for filename in $Filenames
873	do
874	cp $filename ${base_directory}/${sources_for_run_catalog}
875	source_list=$source_list"$filename "
876	done
877
878	cd - > /dev/null
879
880
881	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
882	elif [[ "$source_list" != "" ]]
883	then
884
885	cd $source_path
886
887	for filename in $source_list
888	do
889
890	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
891	if [[ $(echo $filename \| grep -c "/") != 0 ]]
892	then
893	printf "\n +++ source code file: $filename"
894	printf "\n must not contain (\"/\") "
895	locat=source; exit
896	fi
897
898	if [[ ! -f $filename ]]
899	then
900	printf "\n +++ source code file: $filename"
901	printf "\n does not exist"
902	locat=source; exit
903	else
904	cp $filename ${base_directory}/${sources_for_run_catalog}
905	fi
906
907	done
908
909	cd - > /dev/null
910
911	fi
912
913	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
914	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
915	if [[ ! -f $makefile ]]
916	then
917	printf "\n +++ file \"$makefile\" does not exist"
918	locat=make; exit
919	else
920	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
921	fi
922
923
924	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
925	if [[ "$user_source_path" != "" ]]
926	then
927
928	# DOES THE DIRECTORY EXIST?
929	if [[ ! -d $user_source_path ]]
930	then
931
932	printf "\n\n *** INFORMATIVE: additional source code directory"
933	printf "\n \"$user_source_path\" "
934	printf "\n does not exist or is not a directory."
935	printf "\n No source code will be used from this directory!\n"
936	user_source_path=""
937	if [[ $silent == false ]]
938	then
939	sleep 2
940	fi
941
942	else
943
944	cd $user_source_path
945	found=false
946
947	Names=$(ls -1 *.f90 2>&1)
948	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
949	Names=$(ls -1 *.F90 2>&1)
950	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
951	Names=$(ls -1 *.F 2>&1)
952	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
953	Names=$(ls -1 *.f 2>&1)
954	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
955	Names=$(ls -1 *.c 2>&1)
956	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
957
958	cd - > /dev/null
959	cd ${base_directory}/${sources_for_run_catalog}
960
961	# COPY MAKEFILE IF EXISTING
962	if [[ -f $user_source_path/Makefile ]]
963	then
964	printf "\n\n *** user Makefile from directory"
965	printf "\n \"$user_source_path\" is used \n"
966	if [[ $silent == false ]]
967	then
968	sleep 1
969	fi
970	cp $user_source_path/Makefile .
971	fi
972
973	for filename in $AddFilenames
974	do
975	if [[ -f $filename ]]
976	then
977	printf "\n +++ source code file \"$filename\" found in additional"
978	printf "\n source code directory \"$user_source_path\" "
979	printf "\n but was also given with option \"-s\" which means that it should be taken"
980	printf "\n from directory \"$source_path\"."
981	locat=source; exit
982	fi
983
984	cp $user_source_path/$filename .
985	source_list="$source_list $filename"
986
987	# CHECK IF FILE IS CONTAINED IN MAKEFILE
988	if [[ $(grep -c $filename Makefile) = 0 ]]
989	then
990	printf "\n\n +++ user file \"$filename\" "
991	printf "\n is not listed in Makefile \n"
992	locat=source; exit
993	else
994
995	if [[ $found = false ]]
996	then
997	found=true
998	printf "\n\n *** following user file(s) added to the"
999	printf " files to be translated:\n "
1000	fi
1001	printf "$filename "
1002	if [[ $silent == false ]]
1003	then
1004	sleep 0.5
1005	fi
1006
1007	fi
1008	done
1009	[[ $found = true ]] && printf "\n"
1010	cd - > /dev/null
1011	fi
1012	fi
1013
1014	# COPY CONFIGURATION FILES
1015	cp $config_file ${base_directory}/${sources_for_run_catalog}
1016	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1017
1018	# COPY SHELLSCRIPTS
1019	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1020	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1021
1022	fi
1023
1024	fi
1025
1026
1027	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1028	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1029	if [[ "$global_revision" = "" ]]
1030	then
1031	global_revision=`svnversion $source_path 2>/dev/null`
1032	global_revision="Rev: $global_revision"
1033	fi
1034
1035
1036	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1037	if [[ -n $cores ]]
1038	then
1039
1040	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1041	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1042	if [[ $tasks_per_node = 0 ]]
1043	then
1044	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1045	then
1046	printf "\n"
1047	printf "\n +++ option \"-T\" (tasks per node) is missing"
1048	printf "\n set -T option or define tasks_per_node in the config file"
1049	locat=tasks_per_node; (( iec = 0 )); exit
1050	else
1051	# DEFAULT FOR INTERACTIVE RUN
1052	tasks_per_node=$cores
1053	fi
1054	fi
1055
1056	if (( cores < tasks_per_node ))
1057	then
1058	printf "\n"
1059	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1060	printf "\n given values: -T $tasks_per_node -X $cores"
1061	locat=tasks_per_node; (( iec = 0 )); exit
1062	fi
1063
1064	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1065	(( mpi_tasks = cores / threads_per_task ))
1066	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1067	(( ii = cores / tasks_per_node ))
1068	(( remaining_cores = cores - ii * tasks_per_node ))
1069	if (( remaining_cores > 0 ))
1070	then
1071	printf "\n"
1072	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1073	printf "\n divisor of the total number of cores (option \"-X\")"
1074	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1075	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1076	(( nodes = nodes + 1 ))
1077	fi
1078
1079	fi
1080
1081
1082	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1083	if [[ "$maximum_parallel_io_streams" = "" ]]
1084	then
1085	maximum_parallel_io_streams=$cores
1086	fi
1087
1088
1089	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1090	if [[ "$scp_port" != "" ]]
1091	then
1092	PORTOPT="-P $scp_port"
1093	SSH_PORTOPT="-p $scp_port"
1094	fi
1095
1096
1097	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1098	# CONFIG-FILE
1099	if [[ "$ssh_key" != "" ]]
1100	then
1101	ssh_key="-i $HOME/.ssh/$ssh_key"
1102	fi
1103
1104
1105	# SET QUEUE, IF NOT GIVEN
1106	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1107	then
1108
1109	if [[ $queue = none && "$defaultqueue" = "" ]]
1110	then
1111	printf "\n"
1112	printf "\n +++ no default queue given in configuration file and no queue"
1113	printf "\n given with option -q"
1114	locat=queue; exit
1115	fi
1116	if [[ $queue = none ]]
1117	then
1118	queue=$defaultqueue
1119	fi
1120
1121	fi
1122
1123
1124	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1125	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1126	(( i = 0 ))
1127	(( nr_of_input_files = 0 ))
1128	while (( i < iin ))
1129	do
1130	(( i = i + 1 ))
1131
1132	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1133	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1134	if [[ "${actionin_pre[$i]}" = di ]]
1135	then
1136	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1137	else
1138	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1139	fi
1140
1141
1142	# CHECK IF FILE EXISTS
1143	if ! ls $filename* 1>/dev/null 2>&1
1144	then
1145
1146	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1147	if [[ "${optin_pre[$i]}" != "yes" ]]
1148	then
1149	printf "\n\n +++ INPUT-file: "
1150	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1151	then
1152	printf "\n $filename"
1153	else
1154	printf "\n $filename.${extin_pre[$i]}"
1155	fi
1156	printf "\n does not exist\n"
1157	locat=input; exit
1158	else
1159	(( nr_of_input_files = nr_of_input_files + 1 ))
1160	localin[$nr_of_input_files]="${localin_pre[$i]}"
1161	optin[$nr_of_input_files]="${optin_pre[$i]}"
1162	actionin[$nr_of_input_files]="unavailable"
1163	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1164	endin[$nr_of_input_files]="${endin_pre[$i]}"
1165	extin[$nr_of_input_files]="${extin_pre[$i]}"
1166	fi
1167
1168	else
1169
1170	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1171	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1172	if [[ "${multin[$i]}" = true ]]
1173	then
1174	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1175	ls -1 -d ${filename} > filelist 2>/dev/null
1176	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1177	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1178
1179	endings=""
1180	while read line
1181	do
1182	# filename without path (i.e. after the last "/")
1183	basefilename=$(basename ${line})
1184
1185	# check if there is an extension and remove it
1186	ext=${basefilename##*.}
1187	if [[ "$ext" = "${extin_pre[$i]}" ]]
1188	then
1189	basefilename=${basefilename%.*}
1190	fi
1191
1192	# check for an existing cycle number and remove it
1193	cycle=${basefilename##*.}
1194	if [[ $cycle =~ ^-?[0-9]+$ ]]
1195	then
1196	basefilename=${basefilename%.*}
1197	fi
1198
1199	# remove the jobname from the beginning
1200	length_jobname=${#jobname}
1201	ending=${basefilename:${length_jobname}}
1202
1203	# remove the ending given in the .iofiles from the beginning
1204	endingstring="${endin_pre[$i]}"
1205	length_ending=${#endingstring}
1206	ending=${ending:${length_ending}}
1207
1208	if [[ "$ending" = "" ]]
1209	then
1210	# standard ending as given in the .iofiles
1211	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1212	then
1213	endings="$endings DEFAULT"
1214	fi
1215	else
1216	# ending must start with "_", otherwise its a different file
1217	if [[ "${ending:0:1}" = "_" ]]
1218	then
1219	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1220	then
1221	endings="$endings $ending"
1222	fi
1223	fi
1224	fi
1225
1226	done <filelist
1227
1228	rm filelist
1229
1230	else
1231
1232	# SINGLE NAME
1233	endings=DEFAULT
1234
1235	fi
1236
1237	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1238	for ending in $endings
1239	do
1240
1241	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1242	if [[ $ending = DEFAULT ]]
1243	then
1244	ending=""
1245	fi
1246
1247	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1248	(( nr_of_input_files = nr_of_input_files + 1 ))
1249	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1250	optin[$nr_of_input_files]="${optin_pre[$i]}"
1251	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1252	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1253	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1254	extin[$nr_of_input_files]="${extin_pre[$i]}"
1255
1256
1257	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1258	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1259	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1260	then
1261	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1262	else
1263	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1264	fi
1265
1266	# DETERMINE THE FILE'S CYCLE NUMBER
1267	(( maxcycle = 0 ))
1268	ls -1 -d $filename > filelist 2>/dev/null
1269	ls -1 -d $filename.* >> filelist 2>/dev/null
1270	while read line
1271	do
1272	# filename without path (i.e. after the last "/")
1273	basefilename=$(basename ${line})
1274
1275	# check if there is an extension
1276	extension=${basefilename##*.}
1277	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1278	then
1279	basefilename=${basefilename%.*}
1280	fi
1281
1282	# check for an existing cycle number
1283	cycle=${basefilename##*.}
1284	if [[ $cycle =~ ^-?[0-9]+$ ]]
1285	then
1286	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1287	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1288	(( icycle = $((10#$cycle)) ))
1289	else
1290	(( icycle = 0 ))
1291	fi
1292
1293	if (( icycle > maxcycle ))
1294	then
1295	(( maxcycle = icycle ))
1296
1297	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1298	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1299	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1300	then
1301	leading_zero=true
1302	else
1303	leading_zero=false
1304	fi
1305	fi
1306
1307	done <filelist
1308	rm filelist
1309
1310	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1311	if [[ $leading_zero = true ]]
1312	then
1313	cyclestring=`printf "%03d" $maxcycle`
1314	else
1315	cyclestring=$maxcycle
1316	fi
1317
1318	# APPEND CYCLE NUMBER TO FILENAME
1319	if (( maxcycle > 0 ))
1320	then
1321	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1322	then
1323	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1324	else
1325	filename=${filename}.$cyclestring
1326	fi
1327	else
1328	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1329	then
1330	filename=${filename}.${extin[$nr_of_input_files]}
1331	fi
1332	fi
1333
1334	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1335	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1336	absnamein[$nr_of_input_files]=$filename
1337	if (( maxcycle > 0 ))
1338	then
1339	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1340	then
1341	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1342	else
1343	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1344	fi
1345	else
1346	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1347	then
1348	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1349	else
1350	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1351	fi
1352	fi
1353
1354	done
1355
1356	fi
1357
1358	done
1359
1360
1361	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1362	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1363	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1364	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1365	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1366	# REMOTE HOST)
1367	(( i = 0 ))
1368	while (( i < iout ))
1369	do
1370	(( i = i + 1 ))
1371	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1372	then
1373	if [[ "${actionout_pre[$i]}" = tr ]]
1374	then
1375	actionout_pre[$i]=""
1376	elif [[ "${actionout_pre[$i]}" = trpe ]]
1377	then
1378	actionout_pre[$i]=pe
1379	elif [[ "${actionout_pre[$i]}" = tra ]]
1380	then
1381	actionout_pre[$i]=a
1382	fi
1383	(( maxcycle = 0 ))
1384	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1385	eval catalogname=${pathout_pre[$i]}
1386	if ! ls $filename* 1>/dev/null 2>&1
1387	then
1388
1389	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1390	if cat /dev/null > $filename
1391	then
1392	rm $filename
1393	else
1394
1395	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1396	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1397	if [[ ! -d $catalogname ]]
1398	then
1399	if mkdir -p $catalogname
1400	then
1401	printf "\n\n *** directory:"
1402	printf "\n $catalogname"
1403	printf "\n was created\n"
1404	else
1405	printf "\n\n +++ OUTPUT-file:"
1406	printf "\n $filename"
1407	printf "\n cannot be created, because directory does not exist"
1408	printf "\n and cannot be created either"
1409	printf "\n"
1410	locat=output ; exit
1411	fi 2>/dev/null
1412	else
1413	printf "\n\n +++ OUTPUT-file:"
1414	printf "\n $filename"
1415	printf "\n cannot be created, although directory exists"
1416	printf "\n"
1417	locat=output ; exit
1418	fi
1419	fi 2>/dev/null
1420
1421	fi
1422
1423	fi
1424	done
1425
1426
1427	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1428	if [[ $running_in_batch_mode = false ]]
1429	then
1430	run_id=$RANDOM
1431	job_id=${jobname}.$run_id
1432
1433	tempdir=$fast_io_catalog/$job_id
1434	fi
1435
1436
1437	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1438	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1439	then
1440
1441	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1442	if [[ $ibd = 0 ]]
1443	then
1444	printf "\n"
1445	printf "\n +++ no batch directives found in configuration file"
1446	locat=config_file_batch_directives; (( iec = 0 )); exit
1447	fi
1448
1449	# CHECK IF CPUTIME IS GIVEN FOR JOB
1450	done=false
1451	cputime=$cpumax
1452	while [[ $done = false ]]
1453	do
1454	if (( cputime == 0 ))
1455	then
1456	printf "\n +++ cpu-time is undefined"
1457	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1458	printf "\n >>> "
1459	read cputime 1>/dev/null 2>&1
1460	else
1461	done=true
1462	fi
1463	done
1464	cpumax=$cputime
1465
1466	# CHECK THE MEMORY DEMAND
1467	done=false
1468	while [[ $done = false ]]
1469	do
1470	if (( memory == 0 ))
1471	then
1472	printf "\n +++ memory demand is undefined"
1473	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1474	printf "\n >>> "
1475	read memory 1>/dev/null 2>&1
1476	else
1477	done=true
1478	fi
1479	done
1480
1481	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1482	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1483	then
1484	while [[ -z $remote_username ]]
1485	do
1486	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1487	printf "\n >>> Please type username:"
1488	printf "\n >>> "
1489	read remote_username
1490	done
1491	fi
1492
1493	else
1494
1495	if [[ $running_in_batch_mode = false ]]
1496	then
1497	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1498	cpumax=$cputime
1499	else
1500	cputime=$cpumax
1501	fi
1502
1503	fi
1504
1505
1506	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1507	(( cpu_hours = cputime / 3600 ))
1508	(( resttime = cputime - cpu_hours * 3600 ))
1509	(( cpu_minutes = resttime / 60 ))
1510	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1511	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1512
1513
1514	# OUTPUT OF THE PALMRUN-HEADER
1515	calltime=$(date)
1516	printf "\n"
1517	printf "#------------------------------------------------------------------------# \n"
1518	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1519	printf "\| \| \n"
1520	column1="called on:"; column2=$(hostname)
1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1522	if [[ $create_remote_batch_job = true ]]
1523	then
1524	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1525	else
1526	if [[ $running_on_remote = true ]]
1527	then
1528	column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
1529	else
1530	column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
1531	fi
1532	fi
1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1534
1535	column1="running in:"
1536	if [[ $running_in_batch_mode = true ]]
1537	then
1538	column2="batch job mode"
1539	else
1540	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1541	then
1542	column2="job creation mode"
1543	else
1544	column2="interactive run mode"
1545	fi
1546	fi
1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1548
1549	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1550	then
1551	if [[ "$project_account" != "" ]]
1552	then
1553	column1="project account number:"
1554	column2="$project_account"
1555	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1556	fi
1557	fi
1558
1559	if [[ -n $cores ]]
1560	then
1561	if [[ $run_coupled_model = false ]]
1562	then
1563	column1="number of cores:"; column2=$cores
1564	else
1565	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1566	fi
1567	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1568	fi
1569	if [[ -n $tasks_per_node ]]
1570	then
1571	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1573	if (( remaining_cores > 0 ))
1574	then
1575	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1577	fi
1578	fi
1579	if [[ $maximum_parallel_io_streams != $cores ]]
1580	then
1581	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1583	fi
1584	if [[ $use_openmp = true ]]
1585	then
1586	column1="threads per task:"; column2="$threads_per_task"
1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1588	fi
1589	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1590	then
1591	column1="memory demand / PE":; column2="$memory MB"
1592	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1593	column1="job cpu time (h:m:s):"; column2="$timestring"
1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1595	fi
1596	printf "\| \| \n"
1597	if [[ "$source_list" != "" ]]
1598	then
1599	if [[ "$make_options" != "" ]]
1600	then
1601	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	line=$(echo "$make_options" \| cut -c46-)
1604	while [[ "$line" != "" ]]
1605	do
1606	column1=""
1607	column2=$(echo "$line" \| cut -c-45)
1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1609	line=$(echo "$line" \| cut -c46-)
1610	done
1611	fi
1612	fi
1613
1614	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1616	line=$(echo "$cpp_options" \| cut -c46-)
1617	while [[ "$line" != "" ]]
1618	do
1619	column1=""
1620	column2=$(echo "$line" \| cut -c-45)
1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1622	line=$(echo "$line" \| cut -c46-)
1623	done
1624
1625	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1626	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1627	line=$(echo "$compiler_options" \| cut -c46-)
1628	while [[ "$line" != "" ]]
1629	do
1630	column1=""
1631	column2=$(echo "$line" \| cut -c-45)
1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1633	line=$(echo "$line" \| cut -c46-)
1634	done
1635
1636	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1638	line=$(echo "$linker_options" \| cut -c46-)
1639	while [[ "$line" != "" ]]
1640	do
1641	column1=""
1642	column2=$(echo "$line" \| cut -c-45)
1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1644	line=$(echo "$line" \| cut -c46-)
1645	done
1646
1647	if [[ "$login_init_cmd" != "" ]]
1648	then
1649	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1651	line=$(echo "$login_init_cmd" \| cut -c46-)
1652	while [[ "$line" != "" ]]
1653	do
1654	column1=""
1655	column2=$(echo "$line" \| cut -c-45)
1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1657	line=$(echo "$line" \| cut -c46-)
1658	done
1659	fi
1660
1661	if [[ "$module_commands" != "" ]]
1662	then
1663	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1664	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1665	line=$(echo "$module_commands" \| cut -c46-)
1666	while [[ "$line" != "" ]]
1667	do
1668	column1=""
1669	column2=$(echo "$line" \| cut -c-45)
1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1671	line=$(echo "$line" \| cut -c46-)
1672	done
1673	fi
1674	printf "\| \| \n"
1675	column1="run identifier:"; column2=$jobname
1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1677	column1="activation string list:"; column2=$(echo $activation_string_list)
1678	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1679
1680	if [[ "$ocean_file_appendix" = true ]]
1681	then
1682	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1683	fi
1684
1685	if [[ "$source_list" != "" ]]
1686	then
1687	printf "\| \| \n"
1688	printf "\| Files to be compiled: \| \n"
1689	line=$source_list
1690	while [[ "$line" != "" ]]
1691	do
1692	linestart=$(echo $line \| cut -c-70)
1693	printf "\| %-70s \| \n" "$linestart"
1694	line=$(echo "$line" \| cut -c71-)
1695	done
1696	fi
1697	printf "#------------------------------------------------------------------------#"
1698
1699
1700
1701	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1702	if [[ $do_trace = true ]]
1703	then
1704	(( i = 0 ))
1705	while (( i < nr_of_input_files ))
1706	do
1707	(( i = i + 1 ))
1708	if (( i == 1 ))
1709	then
1710	printf "\n\n >>> INPUT-file assignments:\n"
1711	fi
1712	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1713	done
1714	(( i = 0 ))
1715	while (( i < iout ))
1716	do
1717	(( i = i + 1 ))
1718	if (( i == 1 ))
1719	then
1720	printf "\n\n >>> OUTPUT-file assignments:\n"
1721	fi
1722	printf "\n ${localout[$i]} : ${pathout[$i]}"
1723	done
1724	(( i = 0 ))
1725	while (( i < iic ))
1726	do
1727	(( i = i + 1 ))
1728	if (( i == 1 ))
1729	then
1730	printf "\n\n >>> INPUT-commands:\n"
1731	fi
1732	printf "\n ${in_command[$i]}"
1733	done
1734	(( i = 0 ))
1735	while (( i < ioc ))
1736	do
1737	(( i = i + 1 ))
1738	if (( i == 1 ))
1739	then
1740	printf "\n\n >>> OUTPUT-commands:\n"
1741	fi
1742	printf "\n ${out_command[$i]}"
1743	done
1744	fi
1745
1746	# QUERY FOR CONTINUE
1747	if [[ $silent = false && $running_in_batch_mode = false ]]
1748	then
1749	antwort=dummy
1750	printf "\n\n"
1751	printf " >>> everything o.k. (y/n) ? "
1752	while read antwort
1753	do
1754	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1755	then
1756	printf " >>> everything o.k. (y/n) ? "
1757	else
1758	break
1759	fi
1760	done
1761	if [[ $antwort = n \|\| $antwort = N ]]
1762	then
1763	locat=user_abort; (( iec = 0 )); exit
1764	fi
1765	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1766	then
1767	printf "\n *** batch-job will be created and submitted"
1768	else
1769	printf "\n *** PALMRUN will now continue to execute on this machine"
1770	fi
1771	fi
1772
1773
1774
1775	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1776	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1777	then
1778
1779	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1780	then
1781	printf "\n\n *** creating executable and other sources for the remote host\n"
1782	else
1783	printf "\n\n *** creating executable and other sources for the local host\n"
1784	fi
1785
1786	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1787	# IT SHALL BE CREATED
1788	ask_for_make_depository=false
1789	if [[ $create_remote_batch_job = true ]]
1790	then
1791
1792	line=`grep %base_directory $config_file`
1793	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1794	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1795
1796	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1797	then
1798	printf "\n\n +++ make depository \"${make_depository}\""
1799	printf "\n on remote host not found!"
1800	ask_for_make_depository=true
1801	fi
1802	rm ${host_configuration}_last_make_protokoll
1803
1804	else
1805
1806	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1807	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1808	if [[ ! -d ${make_depository} ]]
1809	then
1810	printf "\n\n +++ make depository \"${make_depository}\""
1811	printf "\n on local host not found!"
1812	ask_for_make_depository=true
1813	fi
1814
1815	fi
1816
1817	if [[ $ask_for_make_depository = true ]]
1818	then
1819
1820	antwort=dummy
1821	printf "\n\n"
1822	printf " >>> Create a new one (y/n) ? "
1823	while read antwort
1824	do
1825	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1826	then
1827	printf " >>> Create a new one (y/n) ? "
1828	else
1829	break
1830	fi
1831	done
1832	if [[ $antwort = n \|\| $antwort = N ]]
1833	then
1834	locat=user_abort; (( iec = 0 )); exit
1835	fi
1836
1837	if [[ $do_trace = true ]]
1838	then
1839	palmbuild -h $host_configuration
1840	else
1841	palmbuild -v -h $host_configuration
1842	fi
1843
1844	if [[ $? != 0 ]]
1845	then
1846
1847	# ABORT IN CASE OF COMPILATION PROBLEMS
1848	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1849	locat=make_depository
1850	exit
1851	else
1852	echo " *** now continue with creating executable and other sources"
1853	fi
1854
1855	fi
1856
1857	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1858	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1859
1860	if [[ $? != 0 ]]
1861	then
1862
1863	# ABORT IN CASE OF COMPILATION PROBLEMS
1864	printf "\n +++ error while creating executable and/or other sources"
1865	locat=execution
1866	rm -rf ${base_directory}/${sources_for_run_catalog}
1867	exit
1868
1869	else
1870
1871	printf " *** executable and other sources created\n"
1872	rm -rf ${base_directory}/${sources_for_run_catalog}
1873
1874	fi
1875
1876	fi
1877
1878
1879	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1880	# WILL BE COPIED TO THE REMOTE HOST
1881	if [[ $create_remote_batch_job = true ]]
1882	then
1883	(( i = 0 ))
1884	while (( i < nr_of_input_files ))
1885	do
1886	(( i = i + 1 ))
1887	if [[ "${actionin[$i]}" = tr ]]
1888	then
1889	eval inputfile=${pathin[$i]}/${frelin[$i]}
1890	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1891	fi
1892	done
1893	if (( i > 0 ))
1894	then
1895	printf "\n\n *** input files have been copied to the remote host\n"
1896	fi
1897	fi
1898
1899
1900	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1901	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1902	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1903	then
1904
1905	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1906	if [[ $running_in_batch_mode = false ]]
1907	then
1908	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1909	# FOLDER
1910	mkdir -p $tempdir
1911	chmod go+rx $tempdir
1912	cd $tempdir
1913	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1914	printf "\n *** changed to temporary directory: $tempdir"
1915
1916	else
1917
1918	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1919	printf "\n *** running in temporary directory: $tempdir"
1920
1921	fi
1922
1923
1924	# PROVIDE THE INPUT FILES
1925	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1926	optional_files_missing=false
1927	(( i = 0 ))
1928	while (( i < nr_of_input_files ))
1929	do
1930	(( i = i + 1 ))
1931	if (( i == 1 ))
1932	then
1933	printf "\n\n *** providing INPUT-files:\n$dashes"
1934	fi
1935
1936
1937	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1938	if [[ "${actionin[$i]}" = unavailable ]]
1939	then
1940	optional_files_missing=true
1941	continue
1942	fi
1943
1944	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1945	files_for_cores=false; filetype=file
1946	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1947	then
1948	files_for_cores=true; filetype=files
1949	actionin[$i]=""
1950	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1951	then
1952	actionin[$i]=""
1953	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1954	then
1955	files_for_cores=true; filetype=files
1956	actionin[$i]="ln"
1957	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1958	then
1959	actionin[$i]="ln"
1960	fi
1961
1962	if [[ $files_for_cores = true ]]
1963	then
1964	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1965	else
1966	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1967	fi
1968
1969	# INPUT-FILES TO BE LINKED
1970	if [[ "${actionin[$i]}" = ln ]]
1971	then
1972
1973	printf "\n $filetype will be linked"
1974	if [[ $files_for_cores = false ]]
1975	then
1976	if [[ -f "${absnamein[$i]}" ]]
1977	then
1978	ln ${absnamein[$i]} ${localin[$i]}
1979	got_tmp[$i]=true
1980	fi
1981	else
1982	if [[ -d "${absnamein[$i]}" ]]
1983	then
1984	mkdir -p ${localin[$i]}
1985	cd ${absnamein[$i]}
1986	for file in $(ls *)
1987	do
1988	ln $file $tempdir/${localin[$i]}
1989	done >\|/dev/null 2>&1
1990	cd $tempdir
1991	fi
1992
1993	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1994	if [[ ! -f "${localin[$i]}/_000000" ]]
1995	then
1996	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1997	cp -r ${absnamein[$i]}/* ${localin[$i]}
1998	fi
1999
2000	got_tmp[$i]=true
2001	fi
2002	fi
2003
2004	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2005	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2006	then
2007
2008	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2009	then
2010
2011	# FILE COPIES ARE PROVIDED FOR ALL CORES
2012	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2013	printf "\n file will be provided for $cores processors"
2014	mkdir -p ${localin[$i]}
2015	ival=$cores
2016	(( ii = 0 ))
2017	while (( ii <= ival-1 ))
2018	do
2019	if (( ii < 10 ))
2020	then
2021	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2022	elif (( ii < 100 ))
2023	then
2024	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2025	elif (( ii < 1000 ))
2026	then
2027	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2028	else
2029	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2030	fi
2031	(( ii = ii + 1 ))
2032	done
2033
2034	else
2035
2036	if [[ $files_for_cores = true ]]
2037	then
2038
2039	# PROVIDE FILES FOR EACH CORE
2040	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2041	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2042	printf "\n providing $cores files for the respective cores"
2043	mkdir -p ${localin[$i]}
2044	if [[ $link_local_input = true ]]
2045	then
2046	printf " files will be linked\n"
2047	cd ${absnamein[$i]}
2048	for file in $(ls *)
2049	do
2050	ln -f $file ${localin[$i]}
2051	done
2052	cd $tempdir
2053	fi
2054
2055	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2056	if [[ ! -f "${localin[$i]}/_000000" ]]
2057	then
2058	if [[ $link_local_input = true ]]
2059	then
2060	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2061	fi
2062	cp -r ${absnamein[$i]}/* ${localin[$i]}
2063	fi
2064
2065	else
2066
2067	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2068	if [[ $link_local_input = true ]]
2069	then
2070	printf " file will be linked\n"
2071	ln -f ${absnamein[$i]} ${localin[$i]}
2072	fi
2073	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2074	if [[ ! -f "${localin[$i]}" ]]
2075	then
2076	if [[ $link_local_input = true ]]
2077	then
2078	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2079	fi
2080	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2081	then
2082	mv ${absnamein[$i]} ${localin[$i]}
2083	else
2084	cp ${absnamein[$i]} ${localin[$i]}
2085	fi
2086	fi
2087	fi
2088	fi
2089	fi
2090
2091	done
2092	if (( i != 0 ))
2093	then
2094	if [[ $optional_files_missing = true ]]
2095	then
2096	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2097	fi
2098	printf "\n$dashes\n *** all INPUT-files provided \n"
2099	fi
2100
2101
2102	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2103	(( i = 0 ))
2104	while (( i < iic ))
2105	do
2106	(( i = i + 1 ))
2107	if (( i == 1 ))
2108	then
2109	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2110	fi
2111	printf "\n >>> ${in_command[$i]}"
2112	eval ${in_command[$i]}
2113	if (( i == iic ))
2114	then
2115	printf "\n$dashes\n"
2116	fi
2117	done
2118
2119
2120	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2121	# (FILE ENVPAR WILL BE READ BY PALM)
2122	cat > ENVPAR << EOF
2123	&envpar run_identifier = '$jobname', host = '$host_configuration',
2124	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2125	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2126	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2127	maximum_cpu_time_allowed = ${cpumax}.,
2128	revision = '$global_revision',
2129	batch_job = .${running_in_batch_mode}. /
2130
2131	EOF
2132
2133
2134	# STARTING THE EXECUTABLE
2135	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2136	PATH=$PATH:$tempdir
2137
2138
2139	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2140	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2141	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2142	eval line=\"$line\"
2143	execute_command="$line"
2144
2145
2146	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2147	if [[ "$execute_command_for_combine" = "" ]]
2148	then
2149	eval line2=\"$line2\"
2150	execute_command_for_combine="$line2"
2151	fi
2152
2153
2154
2155	# PROVIDE A HOSTFILE, IF REQUIRED
2156	if [[ "$hostfile" != "" ]]
2157	then
2158
2159	if [[ $hostfile = auto ]]
2160	then
2161	# CREATE A NEW HOSTFILE
2162	(( ii = 1 ))
2163	while (( ii <= cores / threads_per_task ))
2164	do
2165	echo $(hostname) >> hostfile
2166	(( ii = ii + 1 ))
2167	done
2168	if (( cores / threads_per_task == 0 ))
2169	then
2170	echo $(hostname) >> hostfile
2171	fi
2172
2173	else
2174	cp $hostfile hostfile
2175	fi
2176	eval line=\"`head -n $ii hostfile`\"
2177	printf "\n *** running on: $line"
2178	fi
2179
2180
2181
2182	# SET THE NUMBER OF OPENMP-THREADS
2183	if [[ $use_openmp = true ]]
2184	then
2185	export OMP_NUM_THREADS=$threads_per_task
2186	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2187	else
2188	export OMP_NUM_THREADS=1
2189	fi
2190
2191
2192	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2193	if [[ $run_coupled_model = false ]]
2194	then
2195	if [[ "$ocean_file_appendix" = true ]]
2196	then
2197	echo "precursor_ocean" > coupling_steering
2198	else
2199	echo "precursor_atmos" > coupling_steering
2200	fi
2201	else
2202	(( iia = $cores_atmos / $threads_per_task ))
2203	(( iio = $cores_ocean / $threads_per_task ))
2204	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2205	printf "\n\n"
2206	echo "coupled_run $iia $iio" > coupling_steering
2207	fi
2208
2209	printf "\n *** execute command:"
2210	printf "\n \"$execute_command\" \n\n"
2211
2212	$execute_command < coupling_steering
2213
2214	if [[ $? != 0 ]]
2215	then
2216
2217	# ABORT IN CASE OF RUNTIME ERRORS
2218	printf "\n +++ runtime error occured"
2219	locat=execution
2220	exit
2221
2222	else
2223
2224	printf "\n$dashes\n *** execution finished \n"
2225
2226	fi
2227
2228
2229	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2230	# BY EACH CORE INTO ONE FILE
2231	if [[ ! -f combine_plot_fields.x ]]
2232	then
2233
2234	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2235	printf "\n 2d- and/or 3d-data may be incomplete!"
2236	printf "\n Your previous palmbuild may have failed. Please check.\n"
2237
2238	elif [[ "$combine_plot_fields" == true ]]
2239	then
2240
2241	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2242	$execute_command_for_combine
2243
2244	else
2245
2246	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2247	# DATA OUTPUT
2248	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2249	fi
2250
2251
2252
2253	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2254	(( i = 0 ))
2255	while (( i < ioc ))
2256	do
2257	(( i = i + 1 ))
2258	if (( i == 1 ))
2259	then
2260	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2261	fi
2262
2263	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2264	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2265
2266	printf "\n >>> ${out_command[$i]}"
2267	eval ${out_command[$i]}
2268	if (( i == ioc ))
2269	then
2270	printf "\n$dashes\n"
2271	fi
2272	done
2273
2274
2275	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2276	# WILDCARDS
2277	(( i = 0 ))
2278	(( nr_of_output_files = 0 ))
2279
2280	while (( i < iout ))
2281	do
2282
2283	(( i = i + 1 ))
2284
2285	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2286	# CREATE A LIST FOR THE DETECTED ENDINGS
2287	if [[ "${multout[$i]}" = true ]]
2288	then
2289	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2290	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2291	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2292
2293	endings="DEFAULT"
2294	while read line
2295	do
2296	# remove the local name from the beginning
2297	localnamestring="${localout_pre[$i]}"
2298	length_localname=${#localnamestring}
2299	ending=${line:${length_localname}}
2300
2301	if [[ "$ending" != "" ]]
2302	then
2303	endings="$endings $ending"
2304	fi
2305
2306	done <filelist
2307
2308	rm filelist
2309
2310	else
2311
2312	# SINGLE NAME
2313	endings=DEFAULT
2314
2315	fi
2316
2317	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2318	for ending in $endings
2319	do
2320
2321	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2322	if [[ $ending = DEFAULT ]]
2323	then
2324	ending=""
2325	fi
2326
2327	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2328	(( nr_of_output_files = nr_of_output_files + 1 ))
2329	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2330	transout[$nr_of_output_files]="${transout_pre[$i]}"
2331	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2332	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2333	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2334	extout[$nr_of_output_files]="${extout_pre[$i]}"
2335	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2336
2337	done
2338
2339	done
2340
2341
2342
2343
2344	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2345	(( i = 0 ))
2346	while (( i < nr_of_output_files ))
2347	do
2348	(( i = i + 1 ))
2349	if (( i == 1 ))
2350	then
2351	printf "\n\n *** saving OUTPUT-files:"
2352
2353	# GET RUN NUMBER ASSIGNED BY PALM
2354	if [[ -f RUN_NUMBER ]]
2355	then
2356	read run_number < RUN_NUMBER
2357	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2358	usecycle_option="-U $run_number"
2359	else
2360	run_number=0
2361	usecycle_option=""
2362	fi
2363	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2364	then
2365	printf "\n *** in case of SCP transfers to local host"
2366	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2367	fi
2368	printf "\n$dashes"
2369	fi
2370
2371	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2372	then
2373
2374	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2375
2376	# DETERMINE THE CYCLE NUMBER
2377	ls -1 -d $filename > filelist 2>/dev/null
2378	ls -1 -d $filename.* >> filelist 2>/dev/null
2379	while read line
2380	do
2381
2382	# filename without path (i.e. after the last "/")
2383	basefilename=$(basename ${line})
2384
2385	# check if there is an extension
2386	extension=${basefilename##*.}
2387	if [[ "$extension" = "${extout[$i]}" ]]
2388	then
2389	basefilename=${basefilename%.*}
2390	fi
2391
2392	# check for an existing cycle number
2393	cycle=${basefilename##*.}
2394	if [[ $cycle =~ ^-?[0-9]+$ ]]
2395	then
2396	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2397	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2398	(( icycle = $((10#$cycle)) + 1 ))
2399	else
2400	(( icycle = 1 ))
2401	fi
2402
2403	if (( icycle > maxcycle ))
2404	then
2405	(( maxcycle = icycle ))
2406	fi
2407
2408	done <filelist
2409	rm filelist
2410
2411
2412	# SET THE CYCLE NUMBER
2413	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2414	if [[ "${actionout[$i]}" = a ]]
2415	then
2416	(( maxcycle = maxcycle - 1 ))
2417	fi
2418
2419	(( cycnum[$i] = maxcycle ))
2420	pathout[$i]=$filename
2421
2422
2423	# ADD CYCLE NUMBER TO FILENAME
2424	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2425	if [[ "${actionout[$i]}" != "a" ]]
2426	then
2427	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2428	# WITH AN EXISTING CYCLE NUMBER
2429	if (( run_number >= cycnum[$i] ))
2430	then
2431	(( cycnum[$i] = run_number ))
2432	else
2433	if (( run_number > 0 ))
2434	then
2435	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2436	fi
2437	fi
2438	fi
2439	if (( cycnum[$i] > 0 ))
2440	then
2441	cyclestring=`printf "%03d" ${cycnum[$i]}`
2442	pathout[$i]=${pathout[$i]}.$cyclestring
2443	fi
2444	fi
2445
2446	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2447	files_for_cores=false; filetype=file
2448	link_local_output=false
2449	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2450	then
2451	files_for_cores=true; filetype=directory
2452	actionout[$i]=""
2453	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2454	then
2455	actionout[$i]=""
2456	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2457	then
2458	files_for_cores=true; filetype=directory
2459	link_local_output=true
2460	actionout[$i]=""
2461	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2462	then
2463	link_local_output
2464	actionout[$i]=""
2465	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2466	then
2467	files_for_cores=true; filetype=directory
2468	actionout[$i]="tr"
2469	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2470	then
2471	actionout[$i]="tr"
2472	fi
2473
2474	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2475	then
2476	if [[ ${warnout[$i]} = true ]]
2477	then
2478	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2479	fi
2480	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2481	then
2482	if [[ ${warnout[$i]} = true ]]
2483	then
2484	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2485	fi
2486	else
2487
2488
2489	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2490	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2491	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2492	then
2493	if [[ $running_on_remote = true ]]
2494	then
2495
2496	# SET OPTIONS FOR TRANSFER
2497	if [[ "${actionout[$i]}" = tr ]]
2498	then
2499	if [[ $files_for_cores = false ]]
2500	then
2501	catalog_option=""
2502	catalog_string=""
2503	else
2504	catalog_option="-c"
2505	catalog_string="/"
2506	fi
2507	append_option=""
2508	append_string=""
2509	else
2510	append_option="-A"
2511	append_string="append"
2512	fi
2513
2514	transfer_failed=false
2515	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2516	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2517
2518	# TRANSFER VIA SCP
2519	if [[ "$remote_loginnode" != "" ]]
2520	then
2521	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2522	else
2523	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}
2524	fi
2525	[[ $? != 0 ]] && transfer_failed=true
2526
2527
2528	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2529	if [[ $transfer_failed = true ]]
2530	then
2531	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2532	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2533
2534	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2535	eval local_catalog=${pathout[$i]}
2536	if [[ ! -d $local_catalog ]]
2537	then
2538	printf " *** local directory does not exist. Trying to create:\n"
2539	printf " $local_catalog \n"
2540	mkdir -p $local_catalog
2541	fi
2542	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2543	transfer_problems=true
2544	fi
2545
2546	else
2547
2548	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2549	# BE COPIED OR APPENDED ON THIS MACHINE
2550	if [[ "${actionout[$i]}" = tr ]]
2551	then
2552	actionout[$i]=""
2553	else
2554	actionout[$i]="a"
2555	fi
2556	fi
2557	fi
2558
2559
2560	# APPEND ON THIS MACHINE
2561	if [[ "${actionout[$i]}" = "a" ]]
2562	then
2563	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2564	then
2565	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2566	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2567	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2568	else
2569	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2570	printf "\n ${pathout[$i]}\n"
2571	cat ${localout[$i]} >> ${pathout[$i]}
2572	fi
2573	fi
2574
2575	# COPY ON THIS MACHINE
2576	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2577	# ON DIFFERENT FILE-SYSTEMS
2578	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2579	then
2580
2581	# COPY IN CASE OF RUNS ON SINGLE CORES
2582	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2583	then
2584	printf "\n >>> OUTPUT: ${localout[$i]} to"
2585	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2586	if [[ $link_local_output = true ]]
2587	then
2588	printf " file will be linked\n"
2589	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2590	fi
2591	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2592	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2593	then
2594	if [[ $link_local_output = true ]]
2595	then
2596	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2597	fi
2598	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2599	else
2600	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2601	fi
2602	else
2603	printf "\n >>> OUTPUT: ${localout[$i]} to"
2604	printf "\n ${pathout[$i]}\n"
2605	if [[ $link_local_output = true ]]
2606	then
2607	printf " file will be linked\n"
2608	ln -f ${localout[$i]} ${pathout[$i]}
2609	fi
2610	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2611	if [[ ! -f "${pathout[$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]}
2618	else
2619	printf "+++ no copy because file ${pathout[$i]} exists\n"
2620	fi
2621	fi
2622
2623	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2624	then
2625
2626	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2627	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2628	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2629	printf "\n ${pathout[$i]}\n"
2630	if [[ $link_local_output = true ]]
2631	then
2632	printf " files will be linked\n"
2633	mkdir -p ${pathout[$i]}
2634	cd ${localout[$i]}
2635	for file in $(ls *)
2636	do
2637	ln -f $file ${pathout[$i]}
2638	done >\|/dev/null 2>&1
2639	cd $tempdir
2640	fi
2641
2642	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2643	if [[ ! -f "${pathout[$i]}/_000000" ]]
2644	then
2645	if [[ $link_local_output = true ]]
2646	then
2647	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2648	fi
2649	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2650	cp -r ${localout[$i]}/* ${pathout[$i]}
2651	fi
2652
2653	fi
2654	fi
2655	done
2656
2657	if (( i != 0 ))
2658	then
2659	if [[ $transfer_problems = true ]]
2660	then
2661	printf "\n$dashes\n *** OUTPUT-files saved"
2662	printf "\n +++ WARNING: some data transfers failed! \n"
2663	else
2664	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2665	fi
2666	fi
2667
2668
2669	# IF REQUIRED, START A RESTART-JOB
2670	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2671	if [[ -f CONTINUE_RUN ]]
2672	then
2673
2674	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2675	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2676	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2677	# -b START A BATCH JOB
2678	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2679	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2680	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2681
2682	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2683	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2684	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2685	then
2686	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2687	fi
2688
2689	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2690	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2691	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2692	then
2693	prc=`echo $prc \| sed 's/#/r/g'`
2694	fi
2695
2696
2697	# START THE RESTART-JOB
2698	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2699	echo " $prc"
2700	printf "\n$dashes\n"
2701	if [[ $running_on_remote = true ]]
2702	then
2703
2704	echo "*** ssh will be used to initiate restart-runs!"
2705	echo " return_address=\"$return_address\" "
2706	echo " return_username=\"$local_username\" "
2707
2708	if [[ "$remote_loginnode" != "" ]]
2709	then
2710	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
2711	else
2712	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2713	fi
2714
2715	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2716	sleep 30
2717
2718	else
2719
2720	# START THE RESTART JOB ON THE LOCAL HOST
2721	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2722	cd - > /dev/null
2723
2724	fi
2725
2726	# CHECK, IF RESTART JOB HAS BEEN STARTED
2727	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2728	then
2729	printf "\n$dashes\n +++ creating restart run failed \n"
2730	locat=create_restart
2731	exit
2732	rm palmrun_restart.log
2733	else
2734	printf "\n$dashes\n *** restart run initiated \n"
2735	rm palmrun_restart.log
2736	fi
2737
2738
2739	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2740	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2741	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2742	# MAY BE VERY HUGE)
2743	(( i = 0 ))
2744	while (( i < nr_of_input_files ))
2745	do
2746	(( i = i + 1 ))
2747	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2748	then
2749	rm -r ${absnamein[$i]}
2750	fi
2751	done
2752
2753	fi
2754
2755
2756	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2757	cd $HOME
2758	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2759
2760
2761	else
2762
2763
2764	# PREPARING ACTIONS,
2765	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2766
2767	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2768	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2769	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2770	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2771	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2772	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2773	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2774	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2775	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2776	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2777	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2778	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2779	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2780	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2781	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2782	if [[ $create_remote_batch_job = true ]]
2783	then
2784	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2785	if [[ $do_trace = true ]]
2786	then
2787	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2788	fi
2789	elif [[ $create_batch_job = true ]]
2790	then
2791	palmrun_com=${palmrun_com}" -j"
2792	if [[ $do_trace = true ]]
2793	then
2794	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2795	fi
2796	fi
2797
2798
2799	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2800	# REMOTE HOST
2801	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2802	job_protocol_file=$job_protocol_file_local
2803	if [[ $create_remote_batch_job = true ]]
2804	then
2805	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2806	job_protocol_file=$job_protocol_file_remote
2807	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2808	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2809	fi
2810
2811
2812	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2813	jobfile=jobfile.$run_id
2814
2815
2816	# FIRST CREATE THE BATCH DIRECTIVES
2817	(( i = 0 ))
2818	while (( i < ibd ))
2819	do
2820	(( i = i + 1 ))
2821	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2822	eval line=\"$line\"
2823	echo "$line" >> $jobfile
2824	done
2825	echo " " >> $jobfile
2826
2827
2828	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2829	# PROTOCOL
2830	if [[ $create_remote_batch_job = true ]]
2831	then
2832	echo "set +vx" >> $jobfile
2833	echo "trap '" >> $jobfile
2834	echo "set +vx" >> $jobfile
2835	echo "cd ${remote_jobcatalog}" >> $jobfile
2836	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2837
2838	# ADD THE BATCH DIRECTIVES
2839	(( i = 0 ))
2840	while (( i < ibdt ))
2841	do
2842	(( i = i + 1 ))
2843	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2844	eval line=\"$line\"
2845	echo "$line" >> $jobfile
2846	done
2847	echo " " >> $jobfile
2848
2849	echo "set -x" >> $jobfile
2850	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${jobname}" >> $jobfile
2851	echo "%%END%%" >> $jobfile
2852	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2853	echo "$submit_command $scpjob_file" >> $jobfile
2854	echo "rm $scpjob_file" >> $jobfile
2855	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2856	echo "set -x" >> $jobfile
2857	echo " ' exit" >> $jobfile
2858	fi
2859
2860
2861	# ACTIVATE ERROR-TRACEBACK
2862	if [[ $do_trace = true ]]
2863	then
2864	echo "set -x" >> $jobfile
2865	else
2866	echo "set +vx" >> $jobfile
2867	fi
2868
2869
2870	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2871	if [[ "$login_init_cmd" != "" ]]
2872	then
2873	echo "$login_init_cmd" >> $jobfile
2874	fi
2875	if [[ "$module_commands" != "" ]]
2876	then
2877	echo "$module_commands" >> $jobfile
2878	fi
2879
2880
2881	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2882	if [[ $create_remote_batch_job = true ]]
2883	then
2884	echo "mkdir $tempdir" >> $jobfile
2885	echo "chmod go+rx $tempdir" >> $jobfile
2886	else
2887	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2888	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2889	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2890	mkdir $tempdir
2891	chmod go+rx $tempdir
2892	fi
2893	echo "cd $tempdir" >> $jobfile
2894	echo "export tempdir=$tempdir" >> $jobfile
2895	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2896	echo "export PATH=.:\$PATH" >> $jobfile
2897	echo "export execute_palmrun=true" >> $jobfile
2898
2899
2900	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2901	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2902	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2903	echo "LOCAL_PWD=$working_directory" >> $jobfile
2904	echo "export LOCAL_PWD" >> $jobfile
2905
2906
2907	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2908	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2909	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2910
2911
2912	# CALL PALMRUN WITHIN THE JOB
2913	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2914	echo "set -x" >> $jobfile
2915	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2916
2917
2918	# TRANSFER JOBFILE TO THE TARGET HOST
2919	if [[ $create_jobfile_only = false ]]
2920	then
2921
2922	if [[ $create_remote_batch_job = true ]]
2923	then
2924
2925	echo " "
2926	echo " *** transfer of job to remote host via scp"
2927	if [[ $do_trace = true ]]
2928	then
2929	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2930	fi
2931	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2932
2933	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2934	if [[ $do_trace = true ]]
2935	then
2936	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2937	fi
2938	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2939
2940	elif [[ $create_batch_job = true ]]
2941	then
2942
2943	eval local_jobcatalog=$local_jobcatalog
2944	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2945	cd $local_jobcatalog
2946	echo " "
2947	echo " *** submit the job"
2948	if [[ $do_trace = true ]]
2949	then
2950	echo "$submit_command ${host_configuration}_${job_id}"
2951	fi
2952	$submit_command ${host_configuration}_${job_id}
2953	rm ${host_configuration}_${job_id}
2954	cd - > /dev/null
2955
2956	fi
2957
2958	rm -rf $jobfile
2959
2960	else
2961
2962	printf "\n *** jobfile created under name \"$jobfile\" "
2963	printf "\n no batch-job has been sent!"
2964
2965	fi
2966
2967	fi # END OF REMOTE-PART

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