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source: palm/trunk/SCRIPTS/palmrun @ 2965

Last change on this file since 2965 was 2957, checked in by Giersch, 7 years ago
Sky view factors will always be read from file now in case of automatic restarts, corrected error message in case of writing sky view factors
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 96.7 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of the PALM model system.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017-2018 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $
29	# svfout in the activation string will be replaced now by svfin in case of
30	# automatic restarts
31	#
32	# 2718 2018-01-02 08:49:38Z maronga
33	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
34	# the possible output or input of sky view factors
35	#
36	# 2718 2018-01-02 08:49:38Z maronga
37	# "fname" renamed to "jobname"
38	#
39	# 2718 2018-01-02 08:49:38Z maronga
40	# parameters are allowed in output commands (OC:)
41	#
42	# 2718 2018-01-02 08:49:38Z maronga
43	# bugfix: exit if no queue has been given neither with option -q nor in the
44	# configuration file
45	#
46	# 2718 2018-01-02 08:49:38Z maronga
47	# file connection file from trunk/SCRIPTS is taken by default
48	#
49	# 2718 2018-01-02 08:49:38Z maronga
50	# Corrected "Former revisions" section
51	#
52	# 2696 2017-12-14 17:12:51Z kanani
53	# Change in file header (GPL part)
54	#
55	# 2693 2017-12-13 12:33:49Z raasch
56	# replacement of variables given by {{<variable>}} in configuration file is now
57	# done in a more general way, variable names are written in small letters
58	#
59	# 2670 2017-12-06 16:32:19Z raasch
60	# test printouts removed
61	#
62	# 2669 2017-12-06 16:03:27Z raasch
63	# file attributes in .palm.iofiles restructured, "loc" attribute completely
64	# removed,
65	# wildcard (*) allowed in .palm.iofiles as file activation string for output
66	# files,
67	# informative messages in case of missing optional input files shortened
68	# bugfix: variable cycle explicitly interpreted with 10 as the number base
69	#
70	# 2638 2017-11-23 12:44:23Z raasch
71	# use of wildcards in file connection statements enabled
72	#
73	# 2605 2017-11-09 15:31:46Z raasch
74	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
75	# will not be sent with the job file any more, but copied into the
76	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
77	#
78	# 2600 2017-11-01 14:11:20Z raasch
79	# cycle numbers are made three digits wide
80	#
81	# 2566 2017-10-20 08:50:47Z raasch
82	# execute command for combine_plot_fields added
83	# "TEMPDIR" renamed "tempdir"
84	# temporary working directory for local batch jobs is created immediately within
85	# the user's palmrun call, due to a requirement of the "grid engine" batch
86	# system, where the working directory is given with batch directive -wd and must
87	# already exist when the job is submitted,
88	# informative messages in non-trace mode reduced and partly reformatted
89	#
90	# 2551 2017-10-18 07:25:11Z raasch
91	# TEMPDIR added as replacement string to be used in batch directives
92	#
93	# 2512 2017-10-04 08:26:59Z raasch
94	# bugfix for determining cycle numbers of NetCDF input files
95	#
96	# 2506 2017-09-29 08:30:37Z raasch
97	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
98	# host configuration added to SOURCES_FOR_RUN_... folder name
99	# host_identifier renamed host_configuration
100	# option -W added to allow for job dependencies
101	#
102	# 2501 2017-09-26 11:41:55Z raasch
103	# default value for number of cores (option -X) set to 1
104	# bugfix for mechanism which overwrites configuration file settings with values
105	# provided by palmrun options
106	#
107	# 2499 2017-09-22 16:47:58Z kanani
108	# option -h named configuration identifier
109	#
110	# 2480 2017-09-19 06:24:14Z maronga
111	# bugfix for last revision
112	#
113	# 2479 2017-09-19 06:12:16Z raasch
114	# option -A (project account number) added
115	#
116	# 2422 2017-09-08 08:25:41Z raasch
117	# initial revision
118	#
119	#--------------------------------------------------------------------------------#
120	# palmrun - script for running PALM jobs on local and remote hosts
121	#--------------------------------------------------------------------------------#
122
123
124
125	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
126
127	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
128	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
129	# (TOO MANY ARGUMENTS - PROBLEM)
130	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
131
132	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
133	typeset -i nr_of_output_files=0
134	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
135	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
136	# SCRIPT-OPTION ARGUMENTS
137	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
138	typeset -i icycle inode ival maxcycle mpi_tasks
139	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
140
141	activation_string_list=""
142	AddFilenames=""
143	combine_plot_fields=true
144	compiler_name=""
145	compiler_name_ser=""
146	compiler_options=""
147	cores=1
148	cores_atmos=0
149	cores_ocean=0
150	coupled_dist=""
151	cpp_options=""
152	cpumax=0
153	create_batch_job=false
154	create_jobfile_only=false
155	create_remote_batch_job=false
156	dashes=" ----------------------------------------------------------------------------"
157	defaultqueue=""
158	delete_temporary_catalog=true
159	do_compile=true
160	do_trace=false
161	executable=""
162	execute_command=""
163	execution_error=false
164	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
165	jobname=test
166	global_revision=""
167	host_configuration="default"
168	hostfile=""
169	hp=""
170	keep_data_from_previous_run=false
171	link_local_input=false
172	link_local_output=false
173	linker_options=""
174	local_jobcatalog=""
175	locat=normal
176	makefile=""
177	max_par_io_str=""
178	prc=$0
179	while [[ $(echo $prc \| grep -c "/") != 0 ]]
180	do
181	prc=`echo $prc \| cut -f2- -d"/"`
182	done
183	module_calls=""
184	palmrun_memory=""
185	palmrun_script_name=$prc
186	openmp=false
187	previous_job=""
188	project_account=""
189	queue=none
190	read_svf=""
191	restart_run=false
192	return_address=""
193	remote_jobcatalog=""
194	remote_username=""
195	running_in_batch_mode=false
196	run_coupled_model=false
197	run_id=""
198	silent=false
199	source_list=""
200	source_path=""
201	tasks_per_node=0
202	threads_per_task=1
203	transfer_problems=false
204	user_source_path=""
205	use_existing_sources_folder=""
206	use_openmp=false
207	version="palmrun 1.0 Rev$Rev: 2957 $"
208	working_directory=`pwd`
209	write_binary=""
210	write_svf=""
211	TOPT=""
212
213
214	# ERROR HANDLING IN CASE OF EXIT
215	trap 'if [[ $locat != normal && $locat != control_c ]]
216	then
217
218	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
219	(( i = 0 ))
220	while (( i < iec ))
221	do
222	(( i = i + 1 ))
223	printf "\n *** Execution of ERROR-command:\n"
224	printf " >>> ${err_command[$i]}\n"
225	eval ${err_command[$i]}
226	done
227	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
228	printf "\n\n+++ palmrun killed \n\n"
229	elif [[ $locat != control_c ]]
230	then
231	printf "\n --> palmrun finished\n\n"
232	fi' exit
233
234
235	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
236	trap 'cd; rm -rf $tempdir
237	printf "\n+++ palmrun killed by \"^C\" \n\n"
238	locat=control_c
239	exit
240	' 2
241
242
243	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
244	# WHICH WILL BE USED TO START RESTART-JOBS
245	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
246	do
247	case $option in
248	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
249	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
250	(b) create_batch_job=true; prc="$prc -b";;
251	(B) delete_temporary_catalog=false; prc="$prc -B";;
252	(C) restart_run=true; prc="$prc -C";;
253	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
254	(F) create_jobfile_only=true;;
255	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
256	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
257	(j) running_in_batch_mode=true;;
258	(k) keep_data_from_previous_run=true; prc="$prc -k";;
259	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
260	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
261	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
262	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
263	(r) run_id=$OPTARG;;
264	(R) return_address=$OPTARG;;
265	(s) source_list=$OPTARG;;
266	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
267	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
268	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
269	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
270	(v) silent=true; prc="$prc -v";;
271	(V) use_existing_sources_folder="-V";;
272	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
273	(W) previous_job=$OPTARG;;
274	(x) do_trace=true;set -x; prc="$prc -x";;
275	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
276	(y) ocean_file_appendix=true; prc="$prc -y";;
277	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
278	(Z) combine_plot_fields=false; prc="$prc -Z";;
279	(\?) printf "\n +++ unknown option $OPTARG \n"
280	printf "\n --> type \"$0 ?\" for available options \n"
281	locat=parameter;exit;;
282	esac
283	done
284
285
286	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
287	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
288	(( to_shift = $OPTIND - 1 ))
289	shift $to_shift
290
291	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
292	if [[ "$1" = "?" ]]
293	then
294	(printf "\n *** Description of available palmrun options:\n"
295	printf "\n Option Description Default-Value"
296	printf "\n -a activation string list \"\" "
297	printf "\n -A project account number ---"
298	printf "\n -b batch-job on local machine ---"
299	printf "\n -B do not delete temporary directory at end ---"
300	printf "\n -d base name of files attached to program test"
301	printf "\n -F create batch job file only ---"
302	printf "\n -h host configuration \"default\" "
303	printf "\n -k keep data from previous run"
304	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
305	printf "\n -M Makefile name Makefile"
306	printf "\n -O threads per openMP task ---"
307	printf "\n -q queue \"$queue\" "
308	printf "\n -s filenames of routines to be compiled \"\" "
309	printf "\n must end with .f, .f90, .F, or .c !"
310	printf "\n use \"..\" for more than one file and wildcards"
311	printf "\n -s LM compiles all locally modified files"
312	printf "\n -t allowed cpu-time in seconds (batch) 0"
313	printf "\n -T tasks per node ---"
314	printf "\n -u username on remote machine \"\" "
315	printf "\n -v no prompt for confirmation ---"
316	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
317	printf "\n -w maximum parallel io streams as given by -X"
318	printf "\n -W name of job to wait for ---"
319	printf "\n -x tracing of palmrun for debug purposes ---"
320	printf "\n -X # of processors (on parallel machines) 1"
321	printf "\n -y add appendix \"_O\" to all local output"
322	printf "\n files (ocean precursor runs followed by"
323	printf "\n coupled atmosphere-ocean runs) ---"
324	printf "\n -Y run coupled model, \"#1 #2\" with"
325	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
326	printf "\n -Z skip combine_plot_fields at the end of "
327	printf "\n the simulation ---"
328	printf "\n "
329	printf "\n Possible values of positional parameter <modus>:"
330	printf "\n \"?\" - this outline \n\n") \| more
331	exit
332	elif [[ "$1" != "" ]]
333	then
334	printf "\n +++ positional parameter $1 unknown \n"
335	locat=parameter; exit
336	fi
337
338
339
340	# SHORT STARTING MESSAGE
341	printf "\n*** $version "
342	printf "\n will be executed. Please wait ..."
343
344
345	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
346	export fname=$jobname
347
348
349	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
350	config_file=.palm.config.$host_configuration
351	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
352
353
354	# CHECK, IF CONFIGURATION FILE EXISTS
355	if [[ ! -f $config_file ]]
356	then
357	printf "\n\n +++ configuration file: "
358	printf "\n $config_file"
359	printf "\n does not exist"
360	locat=connect; exit
361	fi
362
363
364	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
365	if [[ -f .palm.iofiles ]]
366	then
367	fileconnection_file=.palm.iofiles
368	fi
369
370
371	# CHECK, IF FILE CONNECTION FILE EXISTS
372	if [[ ! -f $fileconnection_file ]]
373	then
374	printf "\n\n +++ file connection file: "
375	printf "\n $fileconnection_file"
376	printf "\n does not exist"
377	locat=connect; exit
378	fi
379
380
381	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
382	if [[ "$activation_string_list" = "" ]]
383	then
384	printf "\n\n +++ no activation string list given: "
385	printf "\n please set palmrun option \"-a\" "
386	locat=palmrun_option; exit
387	fi
388
389
390	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
391	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
392	then
393	write_binary=true
394	else
395	write_binary=false
396	fi
397
398	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
399	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
400	then
401	write_svf=true
402	else
403	write_svf=false
404	fi
405
406	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
407	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
408	then
409	read_svf=true
410	else
411	read_svf=false
412	fi
413
414
415	# READ AND EVALUATE THE CONFIGURATION-FILE
416	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
417
418	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
419	while read line
420	do
421
422	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
423	eval line=\"$line\"
424
425
426	# INTERPRET THE LINE
427	if [[ "$(echo $line)" = "" ]]
428	then
429
430	# EMPTY LINE, NO ACTION
431	continue
432
433	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
434	then
435
436	# LINE IS A COMMENT LINE
437	continue
438
439	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
440	then
441
442	# LINE DEFINES AN ENVIRONMENT-VARIABLE
443	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
444	value=`echo $line \| cut -d" " -s -f2-`
445
446
447	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
448	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
449	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
450	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
451	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
452	# CONFIGURATION-FILE.
453	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
454	then
455	eval export $var="\$value"
456
457	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
458	if [[ $do_trace = true ]]
459	then
460	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
461	fi
462	fi
463
464	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
465	then
466
467	# LINE DEFINES BATCH-DIRECTIVE
468	(( ibd = ibd + 1 ))
469	line=$(echo $line \| cut -c4-)
470	batch_directive[$ibd]="$line"
471
472	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
473	then
474
475	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
476	# REMOTE TO A LOCAL HOST
477	(( ibdt = ibdt + 1 ))
478	line=$(echo $line \| cut -c5-)
479	batch_directive_transfer[$ibdt]="$line"
480
481	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
482	then
483
484	# LINE DEFINES ERROR-COMMAND
485	(( iec = iec + 1 ))
486	line=$(echo $line \| cut -c4-)
487	err_command[$iec]="$line"
488
489	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
490	then
491
492	# LINE DEFINES INPUT-COMMAND
493	(( iic = iic + 1 ))
494	line=$(echo $line \| cut -c4-)
495	in_command[$iic]="$line"
496
497	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
498	then
499
500	# LINE DEFINES OUTPUT-COMMAND
501	(( ioc = ioc + 1 ))
502	line=$(echo $line \| cut -c4-)
503	out_command[$ioc]="$line"
504
505	else
506
507	# SKIP ALL OTHER LINES
508	continue
509
510	fi
511
512	done < $config_file
513
514
515	# CHECK SETTING OF REQUIRED PARAMETERS
516	if [[ "$compiler_name" = "" ]]
517	then
518	printf "\n +++ no compiler name found in $config_file"
519	printf "\n Please add line \"compiler_name ...\" to that file."
520	locat=config_file; exit
521	fi
522	if [[ "$compiler_name_ser" = "" ]]
523	then
524	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
525	printf "\n Please add line \"compiler_name_ser ...\" to that file."
526	locat=config_file; exit
527	fi
528	if [[ "$compiler_options" = "" ]]
529	then
530	printf "\n +++ no compiler options found in $config_file"
531	printf "\n Please add line \"compiler_options ...\" to that file."
532	locat=config_file; exit
533	fi
534	if [[ "$linker_options" = "" ]]
535	then
536	printf "\n +++ no linker options found in $config_file"
537	printf "\n Please add line \"linker_options ...\" to that file."
538	locat=config_file; exit
539	fi
540	if [[ "$execute_command" = "" ]]
541	then
542	printf "\n +++ no execute command found in $config_file"
543	printf "\n Please add line \"execute_command ...\" to that file."
544	locat=config_file; exit
545	fi
546
547	if [[ "$hostfile" != "" ]]
548	then
549	if [[ $hostfile != auto && ! -f $hostfile ]]
550	then
551	printf "\n +++ no hostfile \"$hostfile\" found"
552	printf "\n Please check line \"hostfile ...\" in $config_file"
553	locat=config_file; exit
554	fi
555	fi
556
557
558	# DETERMINE THE CALL STATUS
559	if [[ "$return_address" != "" ]]
560	then
561
562	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
563	# BATCH MODE AND ...
564	running_on_remote=true
565
566	else
567
568	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
569	if [[ "$remote_ip" != "" ]]
570	then
571
572	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
573	create_remote_batch_job=true
574
575	fi
576	running_on_remote=false
577	fi
578
579
580
581	# READ AND EVALUATE THE I/O-FILE LIST
582	[[ $silent = false ]] && printf "\n Reading the I/O files... "
583
584	# READ THE FILE CONNECTION FILE LINE BY LINE
585	while read line
586	do
587
588	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
589	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
590
591	# INTERPRET THE LINE
592	if [[ "$(echo $line)" = "" ]]
593	then
594	# EMPTY LINE, NO ACTION
595	continue
596
597	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
598	then
599
600	# LINE IS A COMMENT LINE
601	true
602
603	else
604
605	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
606	# s2a: in/out - field
607	# s2b: action - field (optional)
608	s1=`echo "$line" \| cut -d" " -f1`
609	s2=`echo "$line" \| cut -d" " -s -f2`
610	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
611	then
612	s2a=$s2
613	s2b=""
614	else
615	s2a=`echo $s2 \| cut -d":" -f1`
616	s2b=`echo $s2 \| cut -d":" -f2`
617	fi
618	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
619	s4=`echo "$line" \| cut -d" " -s -f4`
620	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
621	s5=`echo "$line" \| cut -d" " -s -f5`
622	s6=`echo "$line" \| cut -d" " -s -f6`
623
624
625	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
626	# INPUT- OR OUTPUT-LIST.
627	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
628	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
629	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
630	# IS NOT CHECKED AND STORED.
631	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
632	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
633	then
634	found=false
635	for actual in $activation_string_list
636	do
637	for formal in $s3
638	do
639	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
640	done
641	done
642	if [[ $found = true ]]
643	then
644	(( iin = iin + 1 ))
645	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
646	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
647	if [[ "$s2a" = inopt ]]
648	then
649	optin_pre[$iin]=yes
650	else
651	optin_pre[$iin]=no
652	fi
653
654	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
655	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
656	if [[ $running_on_remote = true && "$s2b" = tr ]]
657	then
658	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
659	fi
660
661	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
662	# THE WILDCARD FROM THE ENDING
663	if [[ "${s5: -1}" = "*" ]]
664	then
665	if [[ "$s2b" = "di" ]]
666	then
667	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
668	printf "\n see file \"$fileconnection_file\", line"
669	printf "\n$line"
670	locat=iofiles_file; exit
671	fi
672	multin[$iin]=true
673	string=${endin_pre[$iin]}
674	endin_pre[$iin]="${string%?}"
675	else
676	multin[$iin]=false
677	fi
678	fi
679	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
680	then
681	found=false
682	for actual in $activation_string_list
683	do
684	for formal in $s3
685	do
686	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
687	done
688	done
689	if [[ $found = true ]]
690	then
691	(( iout = iout + 1 ))
692	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
693	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
694
695	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
696	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
697	if [[ $formal = wildcard ]]
698	then
699	warnout_pre[$iout]=false
700	else
701	warnout_pre[$iout]=true
702	fi
703
704	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
705	# THE WILDCARD FROM THE LOCAL FILENAME
706	if [[ "${s1: -1}" = "*" ]]
707	then
708	if [[ "$s2b" = "di" ]]
709	then
710	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
711	printf "\n see file \"$fileconnection_file\", line"
712	printf "\n$line"
713	locat=iofiles_file; exit
714	fi
715	multout[$iout]=true
716	string=${localout_pre[$iout]}
717	localout_pre[$iout]="${string%?}"
718	else
719	multout[$iout]=false
720	fi
721	fi
722	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
723	then
724	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
725	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
726	locat=connect; exit
727	fi
728	IFS="$IFSALT"
729	fi
730
731	done < $fileconnection_file
732
733
734
735	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
736	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
737	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
738	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
739	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
740	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
741
742
743
744	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
745	if [[ $run_coupled_model = true ]]
746	then
747
748	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
749	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
750
751	if (( $cores_ocean + $cores_atmos != $cores ))
752	then
753
754	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
755	printf "\n PEs (total) : $cores"
756	printf "\n PEs (atmosphere): $cores_atmos"
757	printf "\n PEs (ocean) : $cores_ocean"
758	locat=coupling; exit
759
760	fi
761
762	fi
763
764
765	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
766	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
767	# FOLDER
768	if [[ $running_in_batch_mode = true ]]
769	then
770
771	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
772	then
773	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
774	printf "\n Please check the output of the palmrun-call"
775	printf "\n that you did on your local host."
776	locat=SOURCES_FOR_RUN; exit
777	fi
778
779	else
780
781	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
782	# AUTOMATIC RESTART RUN
783	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
784	if [[ $restart_run = false ]]
785	then
786
787	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
788	# THE LOCAL HOST
789	if [[ ! -d $source_path ]]
790	then
791	printf "\n\n +++ source path \"$source_path\" on local host"
792	printf "\n \"$(hostname)\" does not exist"
793	locat=source_path; exit
794	fi
795
796	rm -rf $sources_for_run_catalog
797	mkdir -p $sources_for_run_catalog
798
799	if [[ "$source_list" = LM ]]
800	then
801
802	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
803	source_list=""
804	cd $source_path
805
806
807	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
808	if [[ ! -d ../.svn ]]
809	then
810	printf "\n\n +++ source directory"
811	printf "\n \"$source_path\" "
812	printf "\n is not under control of \"subversion\"."
813	printf "\n Please do not use palmrun-option \"-s LM\"\n"
814	fi
815
816
817	# LIST ALL MODIFIED SOURCE CODE FILES
818	Filenames=""
819	svn status > tmp_svnstatus
820	while read line
821	do
822	firstc=`echo $line \| cut -c1`
823	if [[ $firstc = M \|\| $firstc = "?" ]]
824	then
825	Name=`echo "$line" \| cut -c8-`
826	extension=`echo $Name \| cut -d. -f2`
827	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
828	then
829	Filenames="$Filenames "$Name
830	fi
831	fi
832	done < tmp_svnstatus
833	rm -rf tmp_svnstatus
834
835
836	# COPY FILES TO SOURCES_FOR_RUN_...
837	for filename in $Filenames
838	do
839	cp $filename ${working_directory}/${sources_for_run_catalog}
840	source_list=$source_list"$filename "
841	done
842
843	cd - > /dev/null
844
845
846	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
847	elif [[ "$source_list" != "" ]]
848	then
849
850	cd $source_path
851
852	for filename in $source_list
853	do
854
855	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
856	if [[ $(echo $filename \| grep -c "/") != 0 ]]
857	then
858	printf "\n +++ source code file: $filename"
859	printf "\n must not contain (\"/\") "
860	locat=source; exit
861	fi
862
863	if [[ ! -f $filename ]]
864	then
865	printf "\n +++ source code file: $filename"
866	printf "\n does not exist"
867	locat=source; exit
868	else
869	cp $filename ${working_directory}/${sources_for_run_catalog}
870	fi
871
872	done
873
874	cd - > /dev/null
875
876	fi
877
878	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
879	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
880	if [[ ! -f $makefile ]]
881	then
882	printf "\n +++ file \"$makefile\" does not exist"
883	locat=make; exit
884	else
885	cp $makefile ${sources_for_run_catalog}/Makefile
886	fi
887
888
889	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
890	if [[ "$user_source_path" != "" ]]
891	then
892
893	# DOES THE DIRECTORY EXIST?
894	if [[ ! -d $user_source_path ]]
895	then
896
897	printf "\n\n *** INFORMATIVE: additional source code directory"
898	printf "\n \"$user_source_path\" "
899	printf "\n does not exist or is not a directory."
900	printf "\n No source code will be used from this directory!\n"
901	user_source_path=""
902	if [[ $silent == false ]]
903	then
904	sleep 2
905	fi
906
907	else
908
909	cd $user_source_path
910	found=false
911
912	Names=$(ls -1 *.f90 2>&1)
913	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
914	Names=$(ls -1 *.F90 2>&1)
915	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
916	Names=$(ls -1 *.F 2>&1)
917	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
918	Names=$(ls -1 *.f 2>&1)
919	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
920	Names=$(ls -1 *.c 2>&1)
921	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
922
923	cd - > /dev/null
924	cd $sources_for_run_catalog
925
926	# COPY MAKEFILE IF EXISTING
927	if [[ -f $user_source_path/Makefile ]]
928	then
929	printf "\n\n *** user Makefile from directory"
930	printf "\n \"$user_source_path\" is used \n"
931	if [[ $silent == false ]]
932	then
933	sleep 1
934	fi
935	cp $user_source_path/Makefile .
936	fi
937
938	for filename in $AddFilenames
939	do
940	if [[ -f $filename ]]
941	then
942	printf "\n +++ source code file \"$filename\" found in additional"
943	printf "\n source code directory \"$user_source_path\" "
944	printf "\n but was also given with option \"-s\" which means that it should be taken"
945	printf "\n from directory \"$source_path\"."
946	locat=source; exit
947	fi
948
949	cp $user_source_path/$filename .
950	source_list="$source_list $filename"
951
952	# CHECK IF FILE IS CONTAINED IN MAKEFILE
953	if [[ $(grep -c $filename Makefile) = 0 ]]
954	then
955	printf "\n\n +++ user file \"$filename\" "
956	printf "\n is not listed in Makefile \n"
957	locat=source; exit
958	else
959
960	if [[ $found = false ]]
961	then
962	found=true
963	printf "\n\n *** following user file(s) added to the"
964	printf " files to be translated:\n "
965	fi
966	printf "$filename "
967	if [[ $silent == false ]]
968	then
969	sleep 0.5
970	fi
971
972	fi
973	done
974	[[ $found = true ]] && printf "\n"
975	cd - > /dev/null
976	fi
977	fi
978
979	# COPY CONFIGURATION FILES
980	cp $config_file $sources_for_run_catalog
981	cp $fileconnection_file $sources_for_run_catalog
982
983	# COPY SHELLSCRIPTS
984	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
985	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
986
987	fi
988
989	fi
990
991
992	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
993	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
994	if [[ "$global_revision" = "" ]]
995	then
996	global_revision=`svnversion $source_path 2>/dev/null`
997	global_revision="Rev: $global_revision"
998	fi
999
1000
1001	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1002	if [[ -n $cores ]]
1003	then
1004
1005	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1006	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1007	if [[ $tasks_per_node = 0 ]]
1008	then
1009	printf "\n"
1010	printf "\n +++ option \"-T\" (tasks per node) is missing"
1011	printf "\n set -T option or define tasks_per_node in the config file"
1012	locat=tasks_per_node; (( iec = 0 )); exit
1013	fi
1014
1015	if (( cores < tasks_per_node ))
1016	then
1017	printf "\n"
1018	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1019	printf "\n given values: -T $tasks_per_node -X $cores"
1020	locat=tasks_per_node; (( iec = 0 )); exit
1021	fi
1022
1023	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1024	(( mpi_tasks = cores / threads_per_task ))
1025	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1026	(( ii = cores / tasks_per_node ))
1027	(( remaining_cores = cores - ii * tasks_per_node ))
1028	if (( remaining_cores > 0 ))
1029	then
1030	printf "\n"
1031	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1032	printf "\n divisor of the total number of cores (option \"-X\")"
1033	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1034	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1035	(( nodes = nodes + 1 ))
1036	fi
1037
1038	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1039	if [[ "$tasks_per_node" != "" ]]
1040	then
1041	TOPT="-T $tasks_per_node"
1042	fi
1043
1044	fi
1045
1046
1047	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1048	if [[ "$maximum_parallel_io_streams" = "" ]]
1049	then
1050	maximum_parallel_io_streams=$cores
1051	fi
1052
1053
1054	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1055	if [[ "$scp_port" != "" ]]
1056	then
1057	PORTOPT="-P $scp_port"
1058	SSH_PORTOPT="-p $scp_port"
1059	fi
1060
1061
1062	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1063	# CONFIG-FILE
1064	if [[ "$ssh_key" != "" ]]
1065	then
1066	ssh_key="-i $HOME/.ssh/$ssh_key"
1067	fi
1068
1069
1070	# SET QUEUE, IF NOT GIVEN
1071	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1072	then
1073
1074	if [[ $queue = none && "$defaultqueue" = "" ]]
1075	then
1076	printf "\n"
1077	printf "\n +++ no default queue given in configuration file and no queue"
1078	printf "\n given with option -q"
1079	locat=queue; exit
1080	fi
1081	if [[ $queue = none ]]
1082	then
1083	queue=$defaultqueue
1084	fi
1085
1086	fi
1087
1088
1089	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1090	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1091	(( i = 0 ))
1092	(( nr_of_input_files = 0 ))
1093	while (( i < iin ))
1094	do
1095	(( i = i + 1 ))
1096
1097	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1098	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1099	if [[ "${actionin_pre[$i]}" = di ]]
1100	then
1101	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1102	else
1103	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1104	fi
1105
1106
1107	# CHECK IF FILE EXISTS
1108	if ! ls $filename* 1>/dev/null 2>&1
1109	then
1110
1111	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1112	if [[ "${optin_pre[$i]}" != "yes" ]]
1113	then
1114	printf "\n\n +++ INPUT-file: "
1115	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1116	then
1117	printf "\n $filename"
1118	else
1119	printf "\n $filename.${extin_pre[$i]}"
1120	fi
1121	printf "\n does not exist\n"
1122	locat=input; exit
1123	else
1124	(( nr_of_input_files = nr_of_input_files + 1 ))
1125	localin[$nr_of_input_files]="${localin_pre[$i]}"
1126	optin[$nr_of_input_files]="${optin_pre[$i]}"
1127	actionin[$nr_of_input_files]="unavailable"
1128	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1129	endin[$nr_of_input_files]="${endin_pre[$i]}"
1130	extin[$nr_of_input_files]="${extin_pre[$i]}"
1131	fi
1132
1133	else
1134
1135	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1136	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1137	if [[ "${multin[$i]}" = true ]]
1138	then
1139	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1140	ls -1 -d ${filename} > filelist 2>/dev/null
1141	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1142	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1143
1144	endings=""
1145	while read line
1146	do
1147	# filename without path (i.e. after the last "/")
1148	basefilename=$(basename ${line})
1149
1150	# check if there is an extension and remove it
1151	ext=${basefilename##*.}
1152	if [[ "$ext" = "${extin_pre[$i]}" ]]
1153	then
1154	basefilename=${basefilename%.*}
1155	fi
1156
1157	# check for an existing cycle number and remove it
1158	cycle=${basefilename##*.}
1159	if [[ $cycle =~ ^-?[0-9]+$ ]]
1160	then
1161	basefilename=${basefilename%.*}
1162	fi
1163
1164	# remove the jobname from the beginning
1165	length_jobname=${#jobname}
1166	ending=${basefilename:${length_jobname}}
1167
1168	# remove the ending given in the .iofiles from the beginning
1169	endingstring="${endin_pre[$i]}"
1170	length_ending=${#endingstring}
1171	ending=${ending:${length_ending}}
1172
1173	if [[ "$ending" = "" ]]
1174	then
1175	# standard ending as given in the .iofiles
1176	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1177	then
1178	endings="$endings DEFAULT"
1179	fi
1180	else
1181	# ending must start with "_", otherwise its a different file
1182	if [[ "${ending:0:1}" = "_" ]]
1183	then
1184	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1185	then
1186	endings="$endings $ending"
1187	fi
1188	fi
1189	fi
1190
1191	done <filelist
1192
1193	rm filelist
1194
1195	else
1196
1197	# SINGLE NAME
1198	endings=DEFAULT
1199
1200	fi
1201
1202	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1203	for ending in $endings
1204	do
1205
1206	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1207	if [[ $ending = DEFAULT ]]
1208	then
1209	ending=""
1210	fi
1211
1212	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1213	(( nr_of_input_files = nr_of_input_files + 1 ))
1214	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1215	optin[$nr_of_input_files]="${optin_pre[$i]}"
1216	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1217	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1218	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1219	extin[$nr_of_input_files]="${extin_pre[$i]}"
1220
1221
1222	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1223	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1224	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1225	then
1226	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1227	else
1228	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1229	fi
1230
1231	# DETERMINE THE FILE'S CYCLE NUMBER
1232	(( maxcycle = 0 ))
1233	ls -1 -d $filename > filelist 2>/dev/null
1234	ls -1 -d $filename.* >> filelist 2>/dev/null
1235	while read line
1236	do
1237	# filename without path (i.e. after the last "/")
1238	basefilename=$(basename ${line})
1239
1240	# check if there is an extension
1241	extension=${basefilename##*.}
1242	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1243	then
1244	basefilename=${basefilename%.*}
1245	fi
1246
1247	# check for an existing cycle number
1248	cycle=${basefilename##*.}
1249	if [[ $cycle =~ ^-?[0-9]+$ ]]
1250	then
1251	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1252	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1253	(( icycle = $((10#$cycle)) ))
1254	else
1255	(( icycle = 0 ))
1256	fi
1257
1258	if (( icycle > maxcycle ))
1259	then
1260	(( maxcycle = icycle ))
1261
1262	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1263	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1264	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1265	then
1266	leading_zero=true
1267	else
1268	leading_zero=false
1269	fi
1270	fi
1271
1272	done <filelist
1273	rm filelist
1274
1275	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1276	if [[ $leading_zero = true ]]
1277	then
1278	cyclestring=`printf "%03d" $maxcycle`
1279	else
1280	cyclestring=$maxcycle
1281	fi
1282
1283	# APPEND CYCLE NUMBER TO FILENAME
1284	if (( maxcycle > 0 ))
1285	then
1286	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1287	then
1288	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1289	else
1290	filename=${filename}.$cyclestring
1291	fi
1292	else
1293	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1294	then
1295	filename=${filename}.${extin[$nr_of_input_files]}
1296	fi
1297	fi
1298
1299	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1300	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1301	absnamein[$nr_of_input_files]=$filename
1302	if (( maxcycle > 0 ))
1303	then
1304	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1305	then
1306	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1307	else
1308	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1309	fi
1310	else
1311	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1312	then
1313	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1314	else
1315	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1316	fi
1317	fi
1318
1319	done
1320
1321	fi
1322
1323	done
1324
1325
1326	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1327	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1328	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1329	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1330	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1331	# REMOTE HOST)
1332	(( i = 0 ))
1333	while (( i < iout ))
1334	do
1335	(( i = i + 1 ))
1336	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1337	then
1338	if [[ "${actionout_pre[$i]}" = tr ]]
1339	then
1340	actionout_pre[$i]=""
1341	elif [[ "${actionout_pre[$i]}" = trpe ]]
1342	then
1343	actionout_pre[$i]=pe
1344	elif [[ "${actionout_pre[$i]}" = tra ]]
1345	then
1346	actionout_pre[$i]=a
1347	fi
1348	(( maxcycle = 0 ))
1349	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1350	eval catalogname=${pathout_pre[$i]}
1351	if ! ls $filename* 1>/dev/null 2>&1
1352	then
1353
1354	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1355	if cat /dev/null > $filename
1356	then
1357	rm $filename
1358	else
1359
1360	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1361	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1362	if [[ ! -d $catalogname ]]
1363	then
1364	if mkdir -p $catalogname
1365	then
1366	printf "\n\n *** directory:"
1367	printf "\n $catalogname"
1368	printf "\n was created\n"
1369	else
1370	printf "\n\n +++ OUTPUT-file:"
1371	printf "\n $filename"
1372	printf "\n cannot be created, because directory does not exist"
1373	printf "\n and cannot be created either"
1374	printf "\n"
1375	locat=output ; exit
1376	fi 2>/dev/null
1377	else
1378	printf "\n\n +++ OUTPUT-file:"
1379	printf "\n $filename"
1380	printf "\n cannot be created, although directory exists"
1381	printf "\n"
1382	locat=output ; exit
1383	fi
1384	fi 2>/dev/null
1385
1386	fi
1387
1388	fi
1389	done
1390
1391
1392	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1393	if [[ $running_in_batch_mode = false ]]
1394	then
1395	run_id=$RANDOM
1396	job_id=${jobname}.$run_id
1397
1398	tempdir=$fast_io_catalog/$job_id
1399	fi
1400
1401
1402	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1403	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1404	then
1405
1406	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1407	if [[ $ibd = 0 ]]
1408	then
1409	printf "\n"
1410	printf "\n +++ no batch directives found in configuration file"
1411	locat=config_file_batch_directives; (( iec = 0 )); exit
1412	fi
1413
1414	# CHECK IF CPUTIME IS GIVEN FOR JOB
1415	done=false
1416	cputime=$cpumax
1417	while [[ $done = false ]]
1418	do
1419	if (( cputime == 0 ))
1420	then
1421	printf "\n +++ cpu-time is undefined"
1422	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1423	printf "\n >>> "
1424	read cputime 1>/dev/null 2>&1
1425	else
1426	done=true
1427	fi
1428	done
1429	cpumax=$cputime
1430
1431	# CHECK THE MEMORY DEMAND
1432	done=false
1433	while [[ $done = false ]]
1434	do
1435	if (( memory == 0 ))
1436	then
1437	printf "\n +++ memory demand is undefined"
1438	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1439	printf "\n >>> "
1440	read memory 1>/dev/null 2>&1
1441	else
1442	done=true
1443	fi
1444	done
1445
1446	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1447	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1448	then
1449	while [[ -z $remote_username ]]
1450	do
1451	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1452	printf "\n >>> Please type username:"
1453	printf "\n >>> "
1454	read remote_username
1455	done
1456	fi
1457
1458	else
1459
1460	if [[ $running_in_batch_mode = false ]]
1461	then
1462	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1463	cpumax=$cputime
1464	else
1465	cputime=$cpumax
1466	fi
1467
1468	fi
1469
1470
1471	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1472	(( cpu_hours = cputime / 3600 ))
1473	(( resttime = cputime - cpu_hours * 3600 ))
1474	(( cpu_minutes = resttime / 60 ))
1475	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1476	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1477
1478
1479	# OUTPUT OF THE PALMRUN-HEADER
1480	calltime=$(date)
1481	printf "\n"
1482	printf "#------------------------------------------------------------------------# \n"
1483	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1484	printf "\| \| \n"
1485	column1="called on:"; column2=$(hostname)
1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1487	if [[ $create_remote_batch_job = true ]]
1488	then
1489	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1490	else
1491	if [[ $running_on_remote = true ]]
1492	then
1493	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1494	else
1495	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1496	fi
1497	fi
1498	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1499
1500	column1="running in:"
1501	if [[ $running_in_batch_mode = true ]]
1502	then
1503	column2="batch job mode"
1504	else
1505	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1506	then
1507	column2="job creation mode"
1508	else
1509	column2="interactive run mode"
1510	fi
1511	fi
1512	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1513
1514	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1515	then
1516	if [[ "$project_account" != "" ]]
1517	then
1518	column1="project account number:"
1519	column2="$project_account"
1520	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1521	fi
1522	fi
1523
1524	if [[ -n $cores ]]
1525	then
1526	if [[ $run_coupled_model = false ]]
1527	then
1528	column1="number of cores:"; column2=$cores
1529	else
1530	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1531	fi
1532	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1533	fi
1534	if [[ -n $tasks_per_node ]]
1535	then
1536	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1537	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1538	if (( remaining_cores > 0 ))
1539	then
1540	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1541	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1542	fi
1543	fi
1544	if [[ $maximum_parallel_io_streams != $cores ]]
1545	then
1546	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1548	fi
1549	if [[ $use_openmp = true ]]
1550	then
1551	column1="threads per task:"; column2="$threads_per_task"
1552	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1553	fi
1554	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1555	then
1556	column1="memory demand / PE":; column2="$memory MB"
1557	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1558	column1="job cpu time (h:m:s):"; column2="$timestring"
1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1560	fi
1561	printf "\| \| \n"
1562	if [[ "$source_list" != "" ]]
1563	then
1564	if [[ "$make_options" != "" ]]
1565	then
1566	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1567	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1568	line=$(echo "$make_options" \| cut -c46-)
1569	while [[ "$line" != "" ]]
1570	do
1571	column1=""
1572	column2=$(echo "$line" \| cut -c-45)
1573	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1574	line=$(echo "$line" \| cut -c46-)
1575	done
1576	fi
1577	fi
1578
1579	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1581	line=$(echo "$cpp_options" \| cut -c46-)
1582	while [[ "$line" != "" ]]
1583	do
1584	column1=""
1585	column2=$(echo "$line" \| cut -c-45)
1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1587	line=$(echo "$line" \| cut -c46-)
1588	done
1589
1590	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1592	line=$(echo "$compiler_options" \| cut -c46-)
1593	while [[ "$line" != "" ]]
1594	do
1595	column1=""
1596	column2=$(echo "$line" \| cut -c-45)
1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1598	line=$(echo "$line" \| cut -c46-)
1599	done
1600
1601	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1603	line=$(echo "$linker_options" \| cut -c46-)
1604	while [[ "$line" != "" ]]
1605	do
1606	column1=""
1607	column2=$(echo "$line" \| cut -c-45)
1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1609	line=$(echo "$line" \| cut -c46-)
1610	done
1611
1612	if [[ "$login_init_cmd" != "" ]]
1613	then
1614	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1616	line=$(echo "$login_init_cmd" \| 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 "$line" \| cut -c46-)
1623	done
1624	fi
1625
1626	if [[ "$module_commands" != "" ]]
1627	then
1628	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1630	line=$(echo "$module_commands" \| cut -c46-)
1631	while [[ "$line" != "" ]]
1632	do
1633	column1=""
1634	column2=$(echo "$line" \| cut -c-45)
1635	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1636	line=$(echo "$line" \| cut -c46-)
1637	done
1638	fi
1639	printf "\| \| \n"
1640	column1="base name of files:"; column2=$jobname
1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1642	column1="activation string list:"; column2=$(echo $activation_string_list)
1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1644
1645	if [[ "$ocean_file_appendix" = true ]]
1646	then
1647	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1648	fi
1649
1650	if [[ "$source_list" != "" ]]
1651	then
1652	printf "\| \| \n"
1653	printf "\| Files to be compiled: \| \n"
1654	line=$source_list
1655	while [[ "$line" != "" ]]
1656	do
1657	linestart=$(echo $line \| cut -c-70)
1658	printf "\| %-70s \| \n" "$linestart"
1659	line=$(echo "$line" \| cut -c71-)
1660	done
1661	fi
1662	printf "#------------------------------------------------------------------------#"
1663
1664
1665
1666	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1667	if [[ $do_trace = true ]]
1668	then
1669	(( i = 0 ))
1670	while (( i < nr_of_input_files ))
1671	do
1672	(( i = i + 1 ))
1673	if (( i == 1 ))
1674	then
1675	printf "\n\n >>> INPUT-file assignments:\n"
1676	fi
1677	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1678	done
1679	(( i = 0 ))
1680	while (( i < iout ))
1681	do
1682	(( i = i + 1 ))
1683	if (( i == 1 ))
1684	then
1685	printf "\n\n >>> OUTPUT-file assignments:\n"
1686	fi
1687	printf "\n ${localout[$i]} : ${pathout[$i]}"
1688	done
1689	(( i = 0 ))
1690	while (( i < iic ))
1691	do
1692	(( i = i + 1 ))
1693	if (( i == 1 ))
1694	then
1695	printf "\n\n >>> INPUT-commands:\n"
1696	fi
1697	printf "\n ${in_command[$i]}"
1698	done
1699	(( i = 0 ))
1700	while (( i < ioc ))
1701	do
1702	(( i = i + 1 ))
1703	if (( i == 1 ))
1704	then
1705	printf "\n\n >>> OUTPUT-commands:\n"
1706	fi
1707	printf "\n ${out_command[$i]}"
1708	done
1709	fi
1710
1711	# QUERY FOR CONTINUE
1712	if [[ $silent = false && $running_in_batch_mode = false ]]
1713	then
1714	antwort=dummy
1715	printf "\n\n"
1716	printf " >>> everything o.k. (y/n) ? "
1717	while read antwort
1718	do
1719	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1720	then
1721	printf " >>> everything o.k. (y/n) ? "
1722	else
1723	break
1724	fi
1725	done
1726	if [[ $antwort = n \|\| $antwort = N ]]
1727	then
1728	locat=user_abort; (( iec = 0 )); exit
1729	fi
1730	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1731	then
1732	printf "\n *** batch-job will be created and submitted"
1733	else
1734	printf "\n *** PALMRUN will now continue to execute on this machine"
1735	fi
1736	fi
1737
1738
1739
1740	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1741	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1742	then
1743
1744	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1745	then
1746	printf "\n\n *** creating executable and other sources for the remote host\n"
1747	else
1748	printf "\n\n *** creating executable and other sources for the local host\n"
1749	fi
1750
1751	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1752	# IT SHALL BE CREATED
1753	ask_for_make_depository=false
1754	if [[ $create_remote_batch_job = true ]]
1755	then
1756
1757	line=`grep %base_directory $config_file`
1758	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1759	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1760
1761	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1762	then
1763	printf "\n\n +++ make depository \"${make_depository}\""
1764	printf "\n on remote host not found!"
1765	ask_for_make_depository=true
1766	fi
1767	rm ${host_configuration}_last_make_protokoll
1768
1769	else
1770
1771	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1772	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1773	if [[ ! -d ${make_depository} ]]
1774	then
1775	printf "\n\n +++ make depository \"${make_depository}\""
1776	printf "\n on local host not found!"
1777	ask_for_make_depository=true
1778	fi
1779
1780	fi
1781
1782	if [[ $ask_for_make_depository = true ]]
1783	then
1784
1785	antwort=dummy
1786	printf "\n\n"
1787	printf " >>> Create a new one (y/n) ? "
1788	while read antwort
1789	do
1790	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1791	then
1792	printf " >>> Create a new one (y/n) ? "
1793	else
1794	break
1795	fi
1796	done
1797	if [[ $antwort = n \|\| $antwort = N ]]
1798	then
1799	locat=user_abort; (( iec = 0 )); exit
1800	fi
1801
1802	if [[ $do_trace = true ]]
1803	then
1804	palmbuild -h $host_configuration
1805	else
1806	palmbuild -v -h $host_configuration
1807	fi
1808
1809	if [[ $? != 0 ]]
1810	then
1811
1812	# ABORT IN CASE OF COMPILATION PROBLEMS
1813	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1814	locat=make_depository
1815	exit
1816	else
1817	echo " *** now continue with creating executable and other sources"
1818	fi
1819
1820	fi
1821
1822	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1823	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1824
1825	if [[ $? != 0 ]]
1826	then
1827
1828	# ABORT IN CASE OF COMPILATION PROBLEMS
1829	printf "\n +++ error while creating executable and/or other sources"
1830	locat=execution
1831	rm -rf $sources_for_run_catalog
1832	exit
1833
1834	else
1835
1836	printf " *** executable and other sources created\n"
1837	rm -rf $sources_for_run_catalog
1838
1839	fi
1840
1841	fi
1842
1843
1844	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1845	# WILL BE COPIED TO THE REMOTE HOST
1846	if [[ $create_remote_batch_job = true ]]
1847	then
1848	(( i = 0 ))
1849	while (( i < nr_of_input_files ))
1850	do
1851	(( i = i + 1 ))
1852	if [[ "${actionin[$i]}" = tr ]]
1853	then
1854	eval inputfile=${pathin[$i]}/${frelin[$i]}
1855	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1856	fi
1857	done
1858	if (( i > 0 ))
1859	then
1860	printf " *** input files have been copied to the remote host\n"
1861	fi
1862	fi
1863
1864
1865	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1866	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1867	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1868	then
1869
1870	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1871	if [[ $running_in_batch_mode = false ]]
1872	then
1873	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1874	# FOLDER
1875	mkdir -p $tempdir
1876	chmod go+rx $tempdir
1877	cd $tempdir
1878	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1879	printf "\n *** changed to temporary directory: $tempdir"
1880
1881	else
1882
1883	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1884	printf "\n *** running in temporary directory: $tempdir"
1885
1886	fi
1887
1888
1889	# PROVIDE THE INPUT FILES
1890	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1891	optional_files_missing=false
1892	(( i = 0 ))
1893	while (( i < nr_of_input_files ))
1894	do
1895	(( i = i + 1 ))
1896	if (( i == 1 ))
1897	then
1898	printf "\n\n *** providing INPUT-files:\n$dashes"
1899	fi
1900
1901
1902	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1903	if [[ "${actionin[$i]}" = unavailable ]]
1904	then
1905	optional_files_missing=true
1906	continue
1907	fi
1908
1909	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1910	files_for_cores=false; filetype=file
1911	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1912	then
1913	files_for_cores=true; filetype=files
1914	actionin[$i]=""
1915	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1916	then
1917	actionin[$i]=""
1918	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1919	then
1920	files_for_cores=true; filetype=files
1921	actionin[$i]="ln"
1922	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1923	then
1924	actionin[$i]="ln"
1925	fi
1926
1927	if [[ $files_for_cores = true ]]
1928	then
1929	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1930	else
1931	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1932	fi
1933
1934	# INPUT-FILES TO BE LINKED
1935	if [[ "${actionin[$i]}" = ln ]]
1936	then
1937
1938	printf "\n $filetype will be linked"
1939	if [[ $files_for_cores = false ]]
1940	then
1941	if [[ -f "${absnamein[$i]}" ]]
1942	then
1943	ln ${absnamein[$i]} ${localin[$i]}
1944	got_tmp[$i]=true
1945	fi
1946	else
1947	if [[ -d "${absnamein[$i]}" ]]
1948	then
1949	mkdir -p ${localin[$i]}
1950	cd ${absnamein[$i]}
1951	for file in $(ls *)
1952	do
1953	ln $file $tempdir/${localin[$i]}
1954	done >\|/dev/null 2>&1
1955	cd $tempdir
1956	fi
1957
1958	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1959	if [[ ! -f "${localin[$i]}/_000000" ]]
1960	then
1961	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1962	cp -r ${absnamein[$i]}/* ${localin[$i]}
1963	fi
1964
1965	got_tmp[$i]=true
1966	fi
1967	fi
1968
1969	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1970	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1971	then
1972
1973	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1974	then
1975
1976	# FILE COPIES ARE PROVIDED FOR ALL CORES
1977	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1978	printf "\n file will be provided for $cores processors"
1979	mkdir -p ${localin[$i]}
1980	ival=$cores
1981	(( ii = 0 ))
1982	while (( ii <= ival-1 ))
1983	do
1984	if (( ii < 10 ))
1985	then
1986	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1987	elif (( ii < 100 ))
1988	then
1989	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1990	elif (( ii < 1000 ))
1991	then
1992	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1993	else
1994	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1995	fi
1996	(( ii = ii + 1 ))
1997	done
1998
1999	else
2000
2001	if [[ $files_for_cores = true ]]
2002	then
2003
2004	# PROVIDE FILES FOR EACH CORE
2005	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2006	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2007	printf "\n providing $cores files for the respective cores"
2008	mkdir -p ${localin[$i]}
2009	if [[ $link_local_input = true ]]
2010	then
2011	printf " files will be linked\n"
2012	cd ${absnamein[$i]}
2013	for file in $(ls *)
2014	do
2015	ln -f $file ${localin[$i]}
2016	done
2017	cd $tempdir
2018	fi
2019
2020	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2021	if [[ ! -f "${localin[$i]}/_000000" ]]
2022	then
2023	if [[ $link_local_input = true ]]
2024	then
2025	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2026	fi
2027	cp -r ${absnamein[$i]}/* ${localin[$i]}
2028	fi
2029
2030	else
2031
2032	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2033	if [[ $link_local_input = true ]]
2034	then
2035	printf " file will be linked\n"
2036	ln -f ${absnamein[$i]} ${localin[$i]}
2037	fi
2038	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2039	if [[ ! -f "${localin[$i]}" ]]
2040	then
2041	if [[ $link_local_input = true ]]
2042	then
2043	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2044	fi
2045	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2046	then
2047	mv ${absnamein[$i]} ${localin[$i]}
2048	else
2049	cp ${absnamein[$i]} ${localin[$i]}
2050	fi
2051	fi
2052	fi
2053	fi
2054	fi
2055
2056	done
2057	if (( i != 0 ))
2058	then
2059	if [[ $optional_files_missing = true ]]
2060	then
2061	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2062	fi
2063	printf "\n$dashes\n *** all INPUT-files provided \n"
2064	fi
2065
2066
2067	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2068	(( i = 0 ))
2069	while (( i < iic ))
2070	do
2071	(( i = i + 1 ))
2072	if (( i == 1 ))
2073	then
2074	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2075	fi
2076	printf "\n >>> ${in_command[$i]}"
2077	eval ${in_command[$i]}
2078	if (( i == iic ))
2079	then
2080	printf "\n$dashes\n"
2081	fi
2082	done
2083
2084
2085	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2086	# (FILE ENVPAR WILL BE READ BY PALM)
2087	cat > ENVPAR << EOF
2088	&envpar run_identifier = '$jobname', host = '$host_configuration',
2089	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2090	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2091	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2092	maximum_cpu_time_allowed = ${cpumax}.,
2093	revision = '$global_revision',
2094	batch_job = .${running_in_batch_mode}. /
2095
2096	EOF
2097
2098
2099	# STARTING THE EXECUTABLE
2100	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2101	PATH=$PATH:$tempdir
2102
2103
2104	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2105	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2106	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2107	eval line=\"$line\"
2108	execute_command="$line"
2109
2110
2111	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2112	if [[ "$execute_command_for_combine" = "" ]]
2113	then
2114	eval line2=\"$line2\"
2115	execute_command_for_combine="$line2"
2116	fi
2117
2118
2119
2120	# PROVIDE A HOSTFILE, IF REQUIRED
2121	if [[ "$hostfile" != "" ]]
2122	then
2123
2124	if [[ $hostfile = auto ]]
2125	then
2126	# CREATE A NEW HOSTFILE
2127	(( ii = 1 ))
2128	while (( ii <= cores / threads_per_task ))
2129	do
2130	echo $(hostname) >> hostfile
2131	(( ii = ii + 1 ))
2132	done
2133	if (( cores / threads_per_task == 0 ))
2134	then
2135	echo $(hostname) >> hostfile
2136	fi
2137
2138	else
2139	cp $hostfile hostfile
2140	fi
2141	eval line=\"`head -n $ii hostfile`\"
2142	printf "\n *** running on: $line"
2143	fi
2144
2145
2146
2147	# SET THE NUMBER OF OPENMP-THREADS
2148	if [[ $use_openmp = true ]]
2149	then
2150	export OMP_NUM_THREADS=$threads_per_task
2151	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2152	else
2153	export OMP_NUM_THREADS=1
2154	fi
2155
2156
2157	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2158	if [[ $run_coupled_model = false ]]
2159	then
2160	if [[ "$ocean_file_appendix" = true ]]
2161	then
2162	echo "precursor_ocean" > coupling_steering
2163	else
2164	echo "precursor_atmos" > coupling_steering
2165	fi
2166	else
2167	(( iia = $cores_atmos / $threads_per_task ))
2168	(( iio = $cores_ocean / $threads_per_task ))
2169	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2170	printf "\n\n"
2171	echo "coupled_run $iia $iio" > coupling_steering
2172	fi
2173
2174	printf "\n *** execute command:"
2175	printf "\n \"$execute_command\" \n\n"
2176
2177	$execute_command < coupling_steering
2178
2179	if [[ $? != 0 ]]
2180	then
2181
2182	# ABORT IN CASE OF RUNTIME ERRORS
2183	printf "\n +++ runtime error occured"
2184	locat=execution
2185	exit
2186
2187	else
2188
2189	printf "\n$dashes\n *** execution finished \n"
2190
2191	fi
2192
2193
2194	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2195	# BY EACH CORE INTO ONE FILE
2196	if [[ ! -f combine_plot_fields.x ]]
2197	then
2198
2199	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2200	printf "\n 2d- and/or 3d-data may be incomplete!"
2201	printf "\n Your previous palmbuild may have failed. Please check.\n"
2202
2203	elif [[ "$combine_plot_fields" == true ]]
2204	then
2205
2206	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2207	$execute_command_for_combine
2208
2209	else
2210
2211	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2212	# DATA OUTPUT
2213	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2214	fi
2215
2216
2217
2218	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2219	(( i = 0 ))
2220	while (( i < ioc ))
2221	do
2222	(( i = i + 1 ))
2223	if (( i == 1 ))
2224	then
2225	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2226	fi
2227
2228	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2229	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2230
2231	printf "\n >>> ${out_command[$i]}"
2232	eval ${out_command[$i]}
2233	if (( i == ioc ))
2234	then
2235	printf "\n$dashes\n"
2236	fi
2237	done
2238
2239
2240	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2241	# WILDCARDS
2242	(( i = 0 ))
2243	(( nr_of_output_files = 0 ))
2244
2245	while (( i < iout ))
2246	do
2247
2248	(( i = i + 1 ))
2249
2250	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2251	# CREATE A LIST FOR THE DETECTED ENDINGS
2252	if [[ "${multout[$i]}" = true ]]
2253	then
2254	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2255	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2256	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2257
2258	endings="DEFAULT"
2259	while read line
2260	do
2261	# remove the local name from the beginning
2262	localnamestring="${localout_pre[$i]}"
2263	length_localname=${#localnamestring}
2264	ending=${line:${length_localname}}
2265
2266	if [[ "$ending" != "" ]]
2267	then
2268	endings="$endings $ending"
2269	fi
2270
2271	done <filelist
2272
2273	rm filelist
2274
2275	else
2276
2277	# SINGLE NAME
2278	endings=DEFAULT
2279
2280	fi
2281
2282	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2283	for ending in $endings
2284	do
2285
2286	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2287	if [[ $ending = DEFAULT ]]
2288	then
2289	ending=""
2290	fi
2291
2292	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2293	(( nr_of_output_files = nr_of_output_files + 1 ))
2294	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2295	transout[$nr_of_output_files]="${transout_pre[$i]}"
2296	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2297	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2298	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2299	extout[$nr_of_output_files]="${extout_pre[$i]}"
2300	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2301
2302	done
2303
2304	done
2305
2306
2307
2308
2309	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2310	(( i = 0 ))
2311	while (( i < nr_of_output_files ))
2312	do
2313	(( i = i + 1 ))
2314	if (( i == 1 ))
2315	then
2316	printf "\n\n *** saving OUTPUT-files:"
2317
2318	# GET RUN NUMBER ASSIGNED BY PALM
2319	if [[ -f RUN_NUMBER ]]
2320	then
2321	read run_number < RUN_NUMBER
2322	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2323	usecycle_option="-U $run_number"
2324	else
2325	run_number=0
2326	usecycle_option=""
2327	fi
2328	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2329	then
2330	printf "\n *** in case of SCP transfers to local host"
2331	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2332	fi
2333	printf "\n$dashes"
2334	fi
2335
2336	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2337	then
2338
2339	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2340
2341	# DETERMINE THE CYCLE NUMBER
2342	ls -1 -d $filename > filelist 2>/dev/null
2343	ls -1 -d $filename.* >> filelist 2>/dev/null
2344	while read line
2345	do
2346
2347	# filename without path (i.e. after the last "/")
2348	basefilename=$(basename ${line})
2349
2350	# check if there is an extension
2351	extension=${basefilename##*.}
2352	if [[ "$extension" = "${extout[$i]}" ]]
2353	then
2354	basefilename=${basefilename%.*}
2355	fi
2356
2357	# check for an existing cycle number
2358	cycle=${basefilename##*.}
2359	if [[ $cycle =~ ^-?[0-9]+$ ]]
2360	then
2361	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2362	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2363	(( icycle = $((10#$cycle)) + 1 ))
2364	else
2365	(( icycle = 1 ))
2366	fi
2367
2368	if (( icycle > maxcycle ))
2369	then
2370	(( maxcycle = icycle ))
2371	fi
2372
2373	done <filelist
2374	rm filelist
2375
2376
2377	# SET THE CYCLE NUMBER
2378	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2379	if [[ "${actionout[$i]}" = a ]]
2380	then
2381	(( maxcycle = maxcycle - 1 ))
2382	fi
2383
2384	(( cycnum[$i] = maxcycle ))
2385	pathout[$i]=$filename
2386
2387
2388	# ADD CYCLE NUMBER TO FILENAME
2389	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2390	if [[ "${actionout[$i]}" != "a" ]]
2391	then
2392	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2393	# WITH AN EXISTING CYCLE NUMBER
2394	if (( run_number >= cycnum[$i] ))
2395	then
2396	(( cycnum[$i] = run_number ))
2397	else
2398	if (( run_number > 0 ))
2399	then
2400	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2401	fi
2402	fi
2403	fi
2404	if (( cycnum[$i] > 0 ))
2405	then
2406	cyclestring=`printf "%03d" ${cycnum[$i]}`
2407	pathout[$i]=${pathout[$i]}.$cyclestring
2408	fi
2409	fi
2410
2411	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2412	files_for_cores=false; filetype=file
2413	link_local_output=false
2414	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2415	then
2416	files_for_cores=true; filetype=directory
2417	actionout[$i]=""
2418	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2419	then
2420	actionout[$i]=""
2421	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2422	then
2423	files_for_cores=true; filetype=directory
2424	link_local_output=true
2425	actionout[$i]=""
2426	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2427	then
2428	link_local_output
2429	actionout[$i]=""
2430	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2431	then
2432	files_for_cores=true; filetype=directory
2433	actionout[$i]="tr"
2434	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2435	then
2436	actionout[$i]="tr"
2437	fi
2438
2439	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2440	then
2441	if [[ ${warnout[$i]} = true ]]
2442	then
2443	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2444	fi
2445	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2446	then
2447	if [[ ${warnout[$i]} = true ]]
2448	then
2449	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2450	fi
2451	else
2452
2453
2454	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2455	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2456	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2457	then
2458	if [[ $running_on_remote = true ]]
2459	then
2460
2461	# SET OPTIONS FOR TRANSFER
2462	if [[ "${actionout[$i]}" = tr ]]
2463	then
2464	if [[ $files_for_cores = false ]]
2465	then
2466	catalog_option=""
2467	catalog_string=""
2468	else
2469	catalog_option="-c"
2470	catalog_string="/"
2471	fi
2472	append_option=""
2473	append_string=""
2474	else
2475	append_option="-A"
2476	append_string="append"
2477	fi
2478
2479	transfer_failed=false
2480	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2481	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2482
2483	# TRANSFER VIA SCP
2484	if [[ "$remote_loginnode" != "" ]]
2485	then
2486	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
2487	else
2488	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]}
2489	fi
2490	[[ $? != 0 ]] && transfer_failed=true
2491
2492
2493	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2494	if [[ $transfer_failed = true ]]
2495	then
2496	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2497	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2498
2499	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2500	eval local_catalog=${pathout[$i]}
2501	if [[ ! -d $local_catalog ]]
2502	then
2503	printf " *** local directory does not exist. Trying to create:\n"
2504	printf " $local_catalog \n"
2505	mkdir -p $local_catalog
2506	fi
2507	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2508	transfer_problems=true
2509	fi
2510
2511	else
2512
2513	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2514	# BE COPIED OR APPENDED ON THIS MACHINE
2515	if [[ "${actionout[$i]}" = tr ]]
2516	then
2517	actionout[$i]=""
2518	else
2519	actionout[$i]="a"
2520	fi
2521	fi
2522	fi
2523
2524
2525	# APPEND ON THIS MACHINE
2526	if [[ "${actionout[$i]}" = "a" ]]
2527	then
2528	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2529	then
2530	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2531	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2532	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2533	else
2534	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2535	printf "\n ${pathout[$i]}\n"
2536	cat ${localout[$i]} >> ${pathout[$i]}
2537	fi
2538	fi
2539
2540	# COPY ON THIS MACHINE
2541	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2542	# ON DIFFERENT FILE-SYSTEMS
2543	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2544	then
2545
2546	# COPY IN CASE OF RUNS ON SINGLE CORES
2547	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2548	then
2549	printf "\n >>> OUTPUT: ${localout[$i]} to"
2550	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2551	if [[ $link_local_output = true ]]
2552	then
2553	printf " file will be linked\n"
2554	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2555	fi
2556	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2557	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2558	then
2559	if [[ $link_local_output = true ]]
2560	then
2561	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2562	fi
2563	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2564	else
2565	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2566	fi
2567	else
2568	printf "\n >>> OUTPUT: ${localout[$i]} to"
2569	printf "\n ${pathout[$i]}\n"
2570	if [[ $link_local_output = true ]]
2571	then
2572	printf " file will be linked\n"
2573	ln -f ${localout[$i]} ${pathout[$i]}
2574	fi
2575	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2576	if [[ ! -f "${pathout[$i]}" ]]
2577	then
2578	if [[ $link_local_output = true ]]
2579	then
2580	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2581	fi
2582	cp ${localout[$i]} ${pathout[$i]}
2583	else
2584	printf "+++ no copy because file ${pathout[$i]} exists\n"
2585	fi
2586	fi
2587
2588	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2589	then
2590
2591	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2592	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2593	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2594	printf "\n ${pathout[$i]}\n"
2595	if [[ $link_local_output = true ]]
2596	then
2597	printf " files will be linked\n"
2598	mkdir -p ${pathout[$i]}
2599	cd ${localout[$i]}
2600	for file in $(ls *)
2601	do
2602	ln -f $file ${pathout[$i]}
2603	done >\|/dev/null 2>&1
2604	cd $tempdir
2605	fi
2606
2607	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2608	if [[ ! -f "${pathout[$i]}/_000000" ]]
2609	then
2610	if [[ $link_local_output = true ]]
2611	then
2612	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2613	fi
2614	cp -r ${localout[$i]}/* ${pathout[$i]}
2615	fi
2616
2617	fi
2618	fi
2619	done
2620
2621	if (( i != 0 ))
2622	then
2623	if [[ $transfer_problems = true ]]
2624	then
2625	printf "\n$dashes\n *** OUTPUT-files saved"
2626	printf "\n +++ WARNING: some data transfers failed! \n"
2627	else
2628	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2629	fi
2630	fi
2631
2632
2633	# IF REQUIRED, START A RESTART-JOB
2634	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2635	if [[ -f CONTINUE_RUN ]]
2636	then
2637
2638	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2639	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2640	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2641	# -b START A BATCH JOB
2642	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2643	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2644	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2645
2646	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2647	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2648	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2649	then
2650	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2651	fi
2652
2653	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2654	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2655	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2656	then
2657	prc=`echo $prc \| sed 's/#/r/g'`
2658	fi
2659
2660
2661	# START THE RESTART-JOB
2662	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2663	echo " $prc"
2664	printf "\n$dashes\n"
2665	if [[ $running_on_remote = true ]]
2666	then
2667
2668	echo "*** ssh will be used to initiate restart-runs!"
2669	echo " return_address=\"$return_address\" "
2670	echo " return_username=\"$local_username\" "
2671
2672	if [[ "$remote_loginnode" != "" ]]
2673	then
2674	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
2675	else
2676	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2677	fi
2678
2679	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2680	sleep 30
2681
2682	else
2683
2684	# START THE RESTART JOB ON THE LOCAL HOST
2685	eval $prc # THE ' MUST BE EVALUATED
2686	cd - > /dev/null
2687
2688	fi
2689	printf "\n$dashes\n *** restart-run initiated \n"
2690
2691
2692	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2693	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2694	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2695	# MAY BE VERY HUGE)
2696	(( i = 0 ))
2697	while (( i < nr_of_input_files ))
2698	do
2699	(( i = i + 1 ))
2700	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2701	then
2702	rm -r ${absnamein[$i]}
2703	fi
2704	done
2705
2706	fi
2707
2708
2709	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2710	cd $HOME
2711	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2712
2713
2714	else
2715
2716
2717	# PREPARING ACTIONS,
2718	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2719
2720	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2721	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2722	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2723	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2724	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2725	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2726	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2727	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2728	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2729	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2730	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2731	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2732	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2733	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2734	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2735	if [[ $create_remote_batch_job = true ]]
2736	then
2737	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2738	if [[ $do_trace = true ]]
2739	then
2740	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2741	fi
2742	elif [[ $create_batch_job = true ]]
2743	then
2744	palmrun_com=${palmrun_com}" -j"
2745	if [[ $do_trace = true ]]
2746	then
2747	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2748	fi
2749	fi
2750
2751
2752	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2753	# REMOTE HOST
2754	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2755	job_protocol_file=$job_protocol_file_local
2756	if [[ $create_remote_batch_job = true ]]
2757	then
2758	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2759	job_protocol_file=$job_protocol_file_remote
2760	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2761	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2762	fi
2763
2764
2765	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2766	jobfile=jobfile.$run_id
2767
2768
2769	# FIRST CREATE THE BATCH DIRECTIVES
2770	(( i = 0 ))
2771	while (( i < ibd ))
2772	do
2773	(( i = i + 1 ))
2774	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2775	eval line=\"$line\"
2776	echo "$line" >> $jobfile
2777	done
2778	echo " " >> $jobfile
2779
2780
2781	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2782	# PROTOCOL
2783	if [[ $create_remote_batch_job = true ]]
2784	then
2785	echo "set +vx" >> $jobfile
2786	echo "trap '" >> $jobfile
2787	echo "set +vx" >> $jobfile
2788	echo "cd ${remote_jobcatalog}" >> $jobfile
2789	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2790
2791	# ADD THE BATCH DIRECTIVES
2792	(( i = 0 ))
2793	while (( i < ibdt ))
2794	do
2795	(( i = i + 1 ))
2796	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2797	eval line=\"$line\"
2798	echo "$line" >> $jobfile
2799	done
2800	echo " " >> $jobfile
2801
2802	echo "set -x" >> $jobfile
2803	echo "${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
2804	echo "%%END%%" >> $jobfile
2805	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2806	echo "$submit_command $scpjob_file" >> $jobfile
2807	echo "rm $scpjob_file" >> $jobfile
2808	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2809	echo "set -x" >> $jobfile
2810	echo " ' exit" >> $jobfile
2811	fi
2812
2813
2814	# ACTIVATE ERROR-TRACEBACK
2815	if [[ $do_trace = true ]]
2816	then
2817	echo "set -x" >> $jobfile
2818	else
2819	echo "set +vx" >> $jobfile
2820	fi
2821
2822
2823	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2824	if [[ "$login_init_cmd" != "" ]]
2825	then
2826	echo "$login_init_cmd" >> $jobfile
2827	fi
2828	if [[ "$module_commands" != "" ]]
2829	then
2830	echo "$module_commands" >> $jobfile
2831	fi
2832
2833
2834	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2835	if [[ $create_remote_batch_job = true ]]
2836	then
2837	echo "mkdir $tempdir" >> $jobfile
2838	echo "chmod go+rx $tempdir" >> $jobfile
2839	else
2840	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2841	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2842	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2843	mkdir $tempdir
2844	chmod go+rx $tempdir
2845	fi
2846	echo "cd $tempdir" >> $jobfile
2847	echo "export tempdir=$tempdir" >> $jobfile
2848	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2849	echo "export PATH=.:\$PATH" >> $jobfile
2850	echo "export execute_palmrun=true" >> $jobfile
2851
2852
2853	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2854	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2855	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2856	echo "LOCAL_PWD=$working_directory" >> $jobfile
2857	echo "export LOCAL_PWD" >> $jobfile
2858
2859
2860	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2861	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2862	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2863
2864
2865	# CALL PALMRUN WITHIN THE JOB
2866	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2867	echo "set -x" >> $jobfile
2868	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2869
2870
2871	# TRANSFER JOBFILE TO THE TARGET HOST
2872	if [[ $create_jobfile_only = false ]]
2873	then
2874
2875	if [[ $create_remote_batch_job = true ]]
2876	then
2877
2878	echo " "
2879	echo " *** transfer of job to remote host via scp"
2880	if [[ $do_trace = true ]]
2881	then
2882	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2883	fi
2884	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2885
2886	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2887	if [[ $do_trace = true ]]
2888	then
2889	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"
2890	fi
2891	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
2892
2893	elif [[ $create_batch_job = true ]]
2894	then
2895
2896	eval local_jobcatalog=$local_jobcatalog
2897	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2898	cd $local_jobcatalog
2899	echo " "
2900	echo " *** submit the job"
2901	if [[ $do_trace = true ]]
2902	then
2903	echo "$submit_command ${host_configuration}_${job_id}"
2904	fi
2905	$submit_command ${host_configuration}_${job_id}
2906	rm ${host_configuration}_${job_id}
2907	cd - > /dev/null
2908
2909	fi
2910
2911	rm -rf $jobfile
2912
2913	else
2914
2915	printf "\n *** jobfile created under name \"$jobfile\" "
2916	printf "\n no batch-job has been sent!"
2917
2918	fi
2919
2920	fi # END OF REMOTE-PART

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