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source: palm/trunk/SCRIPTS/palmrun @ 2883

Last change on this file since 2883 was 2834, checked in by raasch, 7 years ago
fname renamed jobname
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.7 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	# "fname" renamed to "jobname"
30	#
31	# 2718 2018-01-02 08:49:38Z maronga
32	# parameters are allowed in output commands (OC:)
33	#
34	# 2718 2018-01-02 08:49:38Z maronga
35	# bugfix: exit if no queue has been given neither with option -q nor in the
36	# configuration file
37	#
38	# 2718 2018-01-02 08:49:38Z maronga
39	# file connection file from trunk/SCRIPTS is taken by default
40	#
41	# 2718 2018-01-02 08:49:38Z maronga
42	# Corrected "Former revisions" section
43	#
44	# 2696 2017-12-14 17:12:51Z kanani
45	# Change in file header (GPL part)
46	#
47	# 2693 2017-12-13 12:33:49Z raasch
48	# replacement of variables given by {{<variable>}} in configuration file is now
49	# done in a more general way, variable names are written in small letters
50	#
51	# 2670 2017-12-06 16:32:19Z raasch
52	# test printouts removed
53	#
54	# 2669 2017-12-06 16:03:27Z raasch
55	# file attributes in .palm.iofiles restructured, "loc" attribute completely
56	# removed,
57	# wildcard (*) allowed in .palm.iofiles as file activation string for output
58	# files,
59	# informative messages in case of missing optional input files shortened
60	# bugfix: variable cycle explicitly interpreted with 10 as the number base
61	#
62	# 2638 2017-11-23 12:44:23Z raasch
63	# use of wildcards in file connection statements enabled
64	#
65	# 2605 2017-11-09 15:31:46Z raasch
66	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
67	# will not be sent with the job file any more, but copied into the
68	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
69	#
70	# 2600 2017-11-01 14:11:20Z raasch
71	# cycle numbers are made three digits wide
72	#
73	# 2566 2017-10-20 08:50:47Z raasch
74	# execute command for combine_plot_fields added
75	# "TEMPDIR" renamed "tempdir"
76	# temporary working directory for local batch jobs is created immediately within
77	# the user's palmrun call, due to a requirement of the "grid engine" batch
78	# system, where the working directory is given with batch directive -wd and must
79	# already exist when the job is submitted,
80	# informative messages in non-trace mode reduced and partly reformatted
81	#
82	# 2551 2017-10-18 07:25:11Z raasch
83	# TEMPDIR added as replacement string to be used in batch directives
84	#
85	# 2512 2017-10-04 08:26:59Z raasch
86	# bugfix for determining cycle numbers of NetCDF input files
87	#
88	# 2506 2017-09-29 08:30:37Z raasch
89	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
90	# host configuration added to SOURCES_FOR_RUN_... folder name
91	# host_identifier renamed host_configuration
92	# option -W added to allow for job dependencies
93	#
94	# 2501 2017-09-26 11:41:55Z raasch
95	# default value for number of cores (option -X) set to 1
96	# bugfix for mechanism which overwrites configuration file settings with values
97	# provided by palmrun options
98	#
99	# 2499 2017-09-22 16:47:58Z kanani
100	# option -h named configuration identifier
101	#
102	# 2480 2017-09-19 06:24:14Z maronga
103	# bugfix for last revision
104	#
105	# 2479 2017-09-19 06:12:16Z raasch
106	# option -A (project account number) added
107	#
108	# 2422 2017-09-08 08:25:41Z raasch
109	# initial revision
110	#
111	#--------------------------------------------------------------------------------#
112	# palmrun - script for running PALM jobs on local and remote hosts
113	#--------------------------------------------------------------------------------#
114
115
116
117	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
118
119	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
120	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
121	# (TOO MANY ARGUMENTS - PROBLEM)
122	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
123
124	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
125	typeset -i nr_of_output_files=0
126	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
127	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
128	# SCRIPT-OPTION ARGUMENTS
129	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
130	typeset -i icycle inode ival maxcycle mpi_tasks
131	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
132
133	activation_string_list=""
134	AddFilenames=""
135	combine_plot_fields=true
136	compiler_name=""
137	compiler_name_ser=""
138	compiler_options=""
139	cores=1
140	cores_atmos=0
141	cores_ocean=0
142	coupled_dist=""
143	cpp_options=""
144	cpumax=0
145	create_batch_job=false
146	create_jobfile_only=false
147	create_remote_batch_job=false
148	dashes=" ----------------------------------------------------------------------------"
149	defaultqueue=""
150	delete_temporary_catalog=true
151	do_compile=true
152	do_trace=false
153	executable=""
154	execute_command=""
155	execution_error=false
156	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
157	jobname=test
158	global_revision=""
159	host_configuration="default"
160	hostfile=""
161	hp=""
162	keep_data_from_previous_run=false
163	link_local_input=false
164	link_local_output=false
165	linker_options=""
166	local_jobcatalog=""
167	locat=normal
168	makefile=""
169	max_par_io_str=""
170	prc=$0
171	while [[ $(echo $prc \| grep -c "/") != 0 ]]
172	do
173	prc=`echo $prc \| cut -f2- -d"/"`
174	done
175	module_calls=""
176	palmrun_memory=""
177	palmrun_script_name=$prc
178	openmp=false
179	previous_job=""
180	project_account=""
181	queue=none
182	restart_run=false
183	return_address=""
184	remote_jobcatalog=""
185	remote_username=""
186	running_in_batch_mode=false
187	run_coupled_model=false
188	run_id=""
189	silent=false
190	source_list=""
191	source_path=""
192	tasks_per_node=0
193	threads_per_task=1
194	transfer_problems=false
195	user_source_path=""
196	use_existing_sources_folder=""
197	use_openmp=false
198	version="palmrun 1.0 Rev$Rev: 2834 $"
199	working_directory=`pwd`
200	write_binary=""
201	TOPT=""
202
203
204	# ERROR HANDLING IN CASE OF EXIT
205	trap 'if [[ $locat != normal && $locat != control_c ]]
206	then
207
208	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
209	(( i = 0 ))
210	while (( i < iec ))
211	do
212	(( i = i + 1 ))
213	printf "\n *** Execution of ERROR-command:\n"
214	printf " >>> ${err_command[$i]}\n"
215	eval ${err_command[$i]}
216	done
217	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
218	printf "\n\n+++ palmrun killed \n\n"
219	elif [[ $locat != control_c ]]
220	then
221	printf "\n --> palmrun finished\n\n"
222	fi' exit
223
224
225	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
226	trap 'cd; rm -rf $tempdir
227	printf "\n+++ palmrun killed by \"^C\" \n\n"
228	locat=control_c
229	exit
230	' 2
231
232
233	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
234	# WHICH WILL BE USED TO START RESTART-JOBS
235	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
236	do
237	case $option in
238	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
239	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
240	(b) create_batch_job=true; prc="$prc -b";;
241	(B) delete_temporary_catalog=false; prc="$prc -B";;
242	(C) restart_run=true; prc="$prc -C";;
243	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
244	(F) create_jobfile_only=true;;
245	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
246	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
247	(j) running_in_batch_mode=true;;
248	(k) keep_data_from_previous_run=true; prc="$prc -k";;
249	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
250	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
251	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
252	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
253	(r) run_id=$OPTARG;;
254	(R) return_address=$OPTARG;;
255	(s) source_list=$OPTARG;;
256	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
257	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
258	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
259	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
260	(v) silent=true; prc="$prc -v";;
261	(V) use_existing_sources_folder="-V";;
262	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
263	(W) previous_job=$OPTARG;;
264	(x) do_trace=true;set -x; prc="$prc -x";;
265	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
266	(y) ocean_file_appendix=true; prc="$prc -y";;
267	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
268	(Z) combine_plot_fields=false; prc="$prc -Z";;
269	(\?) printf "\n +++ unknown option $OPTARG \n"
270	printf "\n --> type \"$0 ?\" for available options \n"
271	locat=parameter;exit;;
272	esac
273	done
274
275
276	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
277	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
278	(( to_shift = $OPTIND - 1 ))
279	shift $to_shift
280
281	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
282	if [[ "$1" = "?" ]]
283	then
284	(printf "\n *** Description of available palmrun options:\n"
285	printf "\n Option Description Default-Value"
286	printf "\n -a activation string list \"\" "
287	printf "\n -A project account number ---"
288	printf "\n -b batch-job on local machine ---"
289	printf "\n -B do not delete temporary directory at end ---"
290	printf "\n -d base name of files attached to program test"
291	printf "\n -F create batch job file only ---"
292	printf "\n -h host configuration \"default\" "
293	printf "\n -k keep data from previous run"
294	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
295	printf "\n -M Makefile name Makefile"
296	printf "\n -O threads per openMP task ---"
297	printf "\n -q queue \"$queue\" "
298	printf "\n -s filenames of routines to be compiled \"\" "
299	printf "\n must end with .f, .f90, .F, or .c !"
300	printf "\n use \"..\" for more than one file and wildcards"
301	printf "\n -s LM compiles all locally modified files"
302	printf "\n -t allowed cpu-time in seconds (batch) 0"
303	printf "\n -T tasks per node ---"
304	printf "\n -u username on remote machine \"\" "
305	printf "\n -v no prompt for confirmation ---"
306	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
307	printf "\n -w maximum parallel io streams as given by -X"
308	printf "\n -W name of job to wait for ---"
309	printf "\n -x tracing of palmrun for debug purposes ---"
310	printf "\n -X # of processors (on parallel machines) 1"
311	printf "\n -y add appendix \"_O\" to all local output"
312	printf "\n files (ocean precursor runs followed by"
313	printf "\n coupled atmosphere-ocean runs) ---"
314	printf "\n -Y run coupled model, \"#1 #2\" with"
315	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
316	printf "\n -Z skip combine_plot_fields at the end of "
317	printf "\n the simulation ---"
318	printf "\n "
319	printf "\n Possible values of positional parameter <modus>:"
320	printf "\n \"?\" - this outline \n\n") \| more
321	exit
322	elif [[ "$1" != "" ]]
323	then
324	printf "\n +++ positional parameter $1 unknown \n"
325	locat=parameter; exit
326	fi
327
328
329
330	# SHORT STARTING MESSAGE
331	printf "\n*** $version "
332	printf "\n will be executed. Please wait ..."
333
334
335	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
336	export fname=$jobname
337
338
339	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
340	config_file=.palm.config.$host_configuration
341	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
342
343
344	# CHECK, IF CONFIGURATION FILE EXISTS
345	if [[ ! -f $config_file ]]
346	then
347	printf "\n\n +++ configuration file: "
348	printf "\n $config_file"
349	printf "\n does not exist"
350	locat=connect; exit
351	fi
352
353
354	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
355	if [[ -f .palm.iofiles ]]
356	then
357	fileconnection_file=.palm.iofiles
358	fi
359
360
361	# CHECK, IF FILE CONNECTION FILE EXISTS
362	if [[ ! -f $fileconnection_file ]]
363	then
364	printf "\n\n +++ file connection file: "
365	printf "\n $fileconnection_file"
366	printf "\n does not exist"
367	locat=connect; exit
368	fi
369
370
371	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
372	if [[ "$activation_string_list" = "" ]]
373	then
374	printf "\n\n +++ no activation string list given: "
375	printf "\n please set palmrun option \"-a\" "
376	locat=palmrun_option; exit
377	fi
378
379
380	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
381	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
382	then
383	write_binary=true
384	else
385	write_binary=false
386	fi
387
388
389	# READ AND EVALUATE THE CONFIGURATION-FILE
390	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
391
392	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
393	while read line
394	do
395
396	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
397	eval line=\"$line\"
398
399
400	# INTERPRET THE LINE
401	if [[ "$(echo $line)" = "" ]]
402	then
403
404	# EMPTY LINE, NO ACTION
405	continue
406
407	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
408	then
409
410	# LINE IS A COMMENT LINE
411	continue
412
413	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
414	then
415
416	# LINE DEFINES AN ENVIRONMENT-VARIABLE
417	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
418	value=`echo $line \| cut -d" " -s -f2-`
419
420
421	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
422	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
423	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
424	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
425	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
426	# CONFIGURATION-FILE.
427	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
428	then
429	eval export $var="\$value"
430
431	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
432	if [[ $do_trace = true ]]
433	then
434	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
435	fi
436	fi
437
438	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
439	then
440
441	# LINE DEFINES BATCH-DIRECTIVE
442	(( ibd = ibd + 1 ))
443	line=$(echo $line \| cut -c4-)
444	batch_directive[$ibd]="$line"
445
446	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
447	then
448
449	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
450	# REMOTE TO A LOCAL HOST
451	(( ibdt = ibdt + 1 ))
452	line=$(echo $line \| cut -c5-)
453	batch_directive_transfer[$ibdt]="$line"
454
455	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
456	then
457
458	# LINE DEFINES ERROR-COMMAND
459	(( iec = iec + 1 ))
460	line=$(echo $line \| cut -c4-)
461	err_command[$iec]="$line"
462
463	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
464	then
465
466	# LINE DEFINES INPUT-COMMAND
467	(( iic = iic + 1 ))
468	line=$(echo $line \| cut -c4-)
469	in_command[$iic]="$line"
470
471	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
472	then
473
474	# LINE DEFINES OUTPUT-COMMAND
475	(( ioc = ioc + 1 ))
476	line=$(echo $line \| cut -c4-)
477	out_command[$ioc]="$line"
478
479	else
480
481	# SKIP ALL OTHER LINES
482	continue
483
484	fi
485
486	done < $config_file
487
488
489	# CHECK SETTING OF REQUIRED PARAMETERS
490	if [[ "$compiler_name" = "" ]]
491	then
492	printf "\n +++ no compiler name found in $config_file"
493	printf "\n Please add line \"compiler_name ...\" to that file."
494	locat=config_file; exit
495	fi
496	if [[ "$compiler_name_ser" = "" ]]
497	then
498	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
499	printf "\n Please add line \"compiler_name_ser ...\" to that file."
500	locat=config_file; exit
501	fi
502	if [[ "$compiler_options" = "" ]]
503	then
504	printf "\n +++ no compiler options found in $config_file"
505	printf "\n Please add line \"compiler_options ...\" to that file."
506	locat=config_file; exit
507	fi
508	if [[ "$linker_options" = "" ]]
509	then
510	printf "\n +++ no linker options found in $config_file"
511	printf "\n Please add line \"linker_options ...\" to that file."
512	locat=config_file; exit
513	fi
514	if [[ "$execute_command" = "" ]]
515	then
516	printf "\n +++ no execute command found in $config_file"
517	printf "\n Please add line \"execute_command ...\" to that file."
518	locat=config_file; exit
519	fi
520
521	if [[ "$hostfile" != "" ]]
522	then
523	if [[ $hostfile != auto && ! -f $hostfile ]]
524	then
525	printf "\n +++ no hostfile \"$hostfile\" found"
526	printf "\n Please check line \"hostfile ...\" in $config_file"
527	locat=config_file; exit
528	fi
529	fi
530
531
532	# DETERMINE THE CALL STATUS
533	if [[ "$return_address" != "" ]]
534	then
535
536	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
537	# BATCH MODE AND ...
538	running_on_remote=true
539
540	else
541
542	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
543	if [[ "$remote_ip" != "" ]]
544	then
545
546	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
547	create_remote_batch_job=true
548
549	fi
550	running_on_remote=false
551	fi
552
553
554
555	# READ AND EVALUATE THE I/O-FILE LIST
556	[[ $silent = false ]] && printf "\n Reading the I/O files... "
557
558	# READ THE FILE CONNECTION FILE LINE BY LINE
559	while read line
560	do
561
562	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
563	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
564
565	# INTERPRET THE LINE
566	if [[ "$(echo $line)" = "" ]]
567	then
568	# EMPTY LINE, NO ACTION
569	continue
570
571	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
572	then
573
574	# LINE IS A COMMENT LINE
575	true
576
577	else
578
579	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
580	# s2a: in/out - field
581	# s2b: action - field (optional)
582	s1=`echo "$line" \| cut -d" " -f1`
583	s2=`echo "$line" \| cut -d" " -s -f2`
584	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
585	then
586	s2a=$s2
587	s2b=""
588	else
589	s2a=`echo $s2 \| cut -d":" -f1`
590	s2b=`echo $s2 \| cut -d":" -f2`
591	fi
592	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
593	s4=`echo "$line" \| cut -d" " -s -f4`
594	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
595	s5=`echo "$line" \| cut -d" " -s -f5`
596	s6=`echo "$line" \| cut -d" " -s -f6`
597
598
599	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
600	# INPUT- OR OUTPUT-LIST.
601	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
602	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
603	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
604	# IS NOT CHECKED AND STORED.
605	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
606	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
607	then
608	found=false
609	for actual in $activation_string_list
610	do
611	for formal in $s3
612	do
613	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
614	done
615	done
616	if [[ $found = true ]]
617	then
618	(( iin = iin + 1 ))
619	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
620	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
621	if [[ "$s2a" = inopt ]]
622	then
623	optin_pre[$iin]=yes
624	else
625	optin_pre[$iin]=no
626	fi
627
628	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
629	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
630	if [[ $running_on_remote = true && "$s2b" = tr ]]
631	then
632	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
633	fi
634
635	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
636	# THE WILDCARD FROM THE ENDING
637	if [[ "${s5: -1}" = "*" ]]
638	then
639	if [[ "$s2b" = "di" ]]
640	then
641	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
642	printf "\n see file \"$fileconnection_file\", line"
643	printf "\n$line"
644	locat=iofiles_file; exit
645	fi
646	multin[$iin]=true
647	string=${endin_pre[$iin]}
648	endin_pre[$iin]="${string%?}"
649	else
650	multin[$iin]=false
651	fi
652	fi
653	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
654	then
655	found=false
656	for actual in $activation_string_list
657	do
658	for formal in $s3
659	do
660	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
661	done
662	done
663	if [[ $found = true ]]
664	then
665	(( iout = iout + 1 ))
666	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
667	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
668
669	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
670	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
671	if [[ $formal = wildcard ]]
672	then
673	warnout_pre[$iout]=false
674	else
675	warnout_pre[$iout]=true
676	fi
677
678	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
679	# THE WILDCARD FROM THE LOCAL FILENAME
680	if [[ "${s1: -1}" = "*" ]]
681	then
682	if [[ "$s2b" = "di" ]]
683	then
684	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
685	printf "\n see file \"$fileconnection_file\", line"
686	printf "\n$line"
687	locat=iofiles_file; exit
688	fi
689	multout[$iout]=true
690	string=${localout_pre[$iout]}
691	localout_pre[$iout]="${string%?}"
692	else
693	multout[$iout]=false
694	fi
695	fi
696	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
697	then
698	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
699	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
700	locat=connect; exit
701	fi
702	IFS="$IFSALT"
703	fi
704
705	done < $fileconnection_file
706
707
708
709	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
710	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
711	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
712	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
713	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
714	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
715
716
717
718	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
719	if [[ $run_coupled_model = true ]]
720	then
721
722	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
723	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
724
725	if (( $cores_ocean + $cores_atmos != $cores ))
726	then
727
728	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
729	printf "\n PEs (total) : $cores"
730	printf "\n PEs (atmosphere): $cores_atmos"
731	printf "\n PEs (ocean) : $cores_ocean"
732	locat=coupling; exit
733
734	fi
735
736	fi
737
738
739	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
740	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
741	# FOLDER
742	if [[ $running_in_batch_mode = true ]]
743	then
744
745	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
746	then
747	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
748	printf "\n Please check the output of the palmrun-call"
749	printf "\n that you did on your local host."
750	locat=SOURCES_FOR_RUN; exit
751	fi
752
753	else
754
755	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
756	# AUTOMATIC RESTART RUN
757	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
758	if [[ $restart_run = false ]]
759	then
760
761	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
762	# THE LOCAL HOST
763	if [[ ! -d $source_path ]]
764	then
765	printf "\n\n +++ source path \"$source_path\" on local host"
766	printf "\n \"$(hostname)\" does not exist"
767	locat=source_path; exit
768	fi
769
770	rm -rf $sources_for_run_catalog
771	mkdir -p $sources_for_run_catalog
772
773	if [[ "$source_list" = LM ]]
774	then
775
776	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
777	source_list=""
778	cd $source_path
779
780
781	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
782	if [[ ! -d ../.svn ]]
783	then
784	printf "\n\n +++ source directory"
785	printf "\n \"$source_path\" "
786	printf "\n is not under control of \"subversion\"."
787	printf "\n Please do not use palmrun-option \"-s LM\"\n"
788	fi
789
790
791	# LIST ALL MODIFIED SOURCE CODE FILES
792	Filenames=""
793	svn status > tmp_svnstatus
794	while read line
795	do
796	firstc=`echo $line \| cut -c1`
797	if [[ $firstc = M \|\| $firstc = "?" ]]
798	then
799	Name=`echo "$line" \| cut -c8-`
800	extension=`echo $Name \| cut -d. -f2`
801	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
802	then
803	Filenames="$Filenames "$Name
804	fi
805	fi
806	done < tmp_svnstatus
807	rm -rf tmp_svnstatus
808
809
810	# COPY FILES TO SOURCES_FOR_RUN_...
811	for filename in $Filenames
812	do
813	cp $filename ${working_directory}/${sources_for_run_catalog}
814	source_list=$source_list"$filename "
815	done
816
817	cd - > /dev/null
818
819
820	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
821	elif [[ "$source_list" != "" ]]
822	then
823
824	cd $source_path
825
826	for filename in $source_list
827	do
828
829	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
830	if [[ $(echo $filename \| grep -c "/") != 0 ]]
831	then
832	printf "\n +++ source code file: $filename"
833	printf "\n must not contain (\"/\") "
834	locat=source; exit
835	fi
836
837	if [[ ! -f $filename ]]
838	then
839	printf "\n +++ source code file: $filename"
840	printf "\n does not exist"
841	locat=source; exit
842	else
843	cp $filename ${working_directory}/${sources_for_run_catalog}
844	fi
845
846	done
847
848	cd - > /dev/null
849
850	fi
851
852	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
853	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
854	if [[ ! -f $makefile ]]
855	then
856	printf "\n +++ file \"$makefile\" does not exist"
857	locat=make; exit
858	else
859	cp $makefile ${sources_for_run_catalog}/Makefile
860	fi
861
862
863	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
864	if [[ "$user_source_path" != "" ]]
865	then
866
867	# DOES THE DIRECTORY EXIST?
868	if [[ ! -d $user_source_path ]]
869	then
870
871	printf "\n\n *** INFORMATIVE: additional source code directory"
872	printf "\n \"$user_source_path\" "
873	printf "\n does not exist or is not a directory."
874	printf "\n No source code will be used from this directory!\n"
875	user_source_path=""
876	if [[ $silent == false ]]
877	then
878	sleep 2
879	fi
880
881	else
882
883	cd $user_source_path
884	found=false
885
886	Names=$(ls -1 *.f90 2>&1)
887	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
888	Names=$(ls -1 *.F90 2>&1)
889	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
890	Names=$(ls -1 *.F 2>&1)
891	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
892	Names=$(ls -1 *.f 2>&1)
893	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
894	Names=$(ls -1 *.c 2>&1)
895	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
896
897	cd - > /dev/null
898	cd $sources_for_run_catalog
899
900	# COPY MAKEFILE IF EXISTING
901	if [[ -f $user_source_path/Makefile ]]
902	then
903	printf "\n\n *** user Makefile from directory"
904	printf "\n \"$user_source_path\" is used \n"
905	if [[ $silent == false ]]
906	then
907	sleep 1
908	fi
909	cp $user_source_path/Makefile .
910	fi
911
912	for filename in $AddFilenames
913	do
914	if [[ -f $filename ]]
915	then
916	printf "\n +++ source code file \"$filename\" found in additional"
917	printf "\n source code directory \"$user_source_path\" "
918	printf "\n but was also given with option \"-s\" which means that it should be taken"
919	printf "\n from directory \"$source_path\"."
920	locat=source; exit
921	fi
922
923	cp $user_source_path/$filename .
924	source_list="$source_list $filename"
925
926	# CHECK IF FILE IS CONTAINED IN MAKEFILE
927	if [[ $(grep -c $filename Makefile) = 0 ]]
928	then
929	printf "\n\n +++ user file \"$filename\" "
930	printf "\n is not listed in Makefile \n"
931	locat=source; exit
932	else
933
934	if [[ $found = false ]]
935	then
936	found=true
937	printf "\n\n *** following user file(s) added to the"
938	printf " files to be translated:\n "
939	fi
940	printf "$filename "
941	if [[ $silent == false ]]
942	then
943	sleep 0.5
944	fi
945
946	fi
947	done
948	[[ $found = true ]] && printf "\n"
949	cd - > /dev/null
950	fi
951	fi
952
953	# COPY CONFIGURATION FILES
954	cp $config_file $sources_for_run_catalog
955	cp $fileconnection_file $sources_for_run_catalog
956
957	# COPY SHELLSCRIPTS
958	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
959	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
960
961	fi
962
963	fi
964
965
966	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
967	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
968	if [[ "$global_revision" = "" ]]
969	then
970	global_revision=`svnversion $source_path 2>/dev/null`
971	global_revision="Rev: $global_revision"
972	fi
973
974
975	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
976	if [[ -n $cores ]]
977	then
978
979	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
980	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
981	if [[ $tasks_per_node = 0 ]]
982	then
983	printf "\n"
984	printf "\n +++ option \"-T\" (tasks per node) is missing"
985	printf "\n set -T option or define tasks_per_node in the config file"
986	locat=tasks_per_node; (( iec = 0 )); exit
987	fi
988
989	if (( cores < tasks_per_node ))
990	then
991	printf "\n"
992	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
993	printf "\n given values: -T $tasks_per_node -X $cores"
994	locat=tasks_per_node; (( iec = 0 )); exit
995	fi
996
997	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
998	(( mpi_tasks = cores / threads_per_task ))
999	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1000	(( ii = cores / tasks_per_node ))
1001	(( remaining_cores = cores - ii * tasks_per_node ))
1002	if (( remaining_cores > 0 ))
1003	then
1004	printf "\n"
1005	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1006	printf "\n divisor of the total number of cores (option \"-X\")"
1007	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1008	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1009	(( nodes = nodes + 1 ))
1010	fi
1011
1012	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1013	if [[ "$tasks_per_node" != "" ]]
1014	then
1015	TOPT="-T $tasks_per_node"
1016	fi
1017
1018	fi
1019
1020
1021	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1022	if [[ "$maximum_parallel_io_streams" = "" ]]
1023	then
1024	maximum_parallel_io_streams=$cores
1025	fi
1026
1027
1028	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1029	if [[ "$scp_port" != "" ]]
1030	then
1031	PORTOPT="-P $scp_port"
1032	SSH_PORTOPT="-p $scp_port"
1033	fi
1034
1035
1036	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1037	# CONFIG-FILE
1038	if [[ "$ssh_key" != "" ]]
1039	then
1040	ssh_key="-i $HOME/.ssh/$ssh_key"
1041	fi
1042
1043
1044	# SET QUEUE, IF NOT GIVEN
1045	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1046	then
1047
1048	if [[ $queue = none && "$defaultqueue" = "" ]]
1049	then
1050	printf "\n"
1051	printf "\n +++ no default queue given in configuration file and no queue"
1052	printf "\n given with option -q"
1053	locat=queue; exit
1054	fi
1055	if [[ $queue = none ]]
1056	then
1057	queue=$defaultqueue
1058	fi
1059
1060	fi
1061
1062
1063	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1064	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1065	(( i = 0 ))
1066	(( nr_of_input_files = 0 ))
1067	while (( i < iin ))
1068	do
1069	(( i = i + 1 ))
1070
1071	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1072	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1073	if [[ "${actionin_pre[$i]}" = di ]]
1074	then
1075	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1076	else
1077	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1078	fi
1079
1080
1081	# CHECK IF FILE EXISTS
1082	if ! ls $filename* 1>/dev/null 2>&1
1083	then
1084
1085	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1086	if [[ "${optin_pre[$i]}" != "yes" ]]
1087	then
1088	printf "\n\n +++ INPUT-file: "
1089	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1090	then
1091	printf "\n $filename"
1092	else
1093	printf "\n $filename.${extin_pre[$i]}"
1094	fi
1095	printf "\n does not exist\n"
1096	locat=input; exit
1097	else
1098	(( nr_of_input_files = nr_of_input_files + 1 ))
1099	localin[$nr_of_input_files]="${localin_pre[$i]}"
1100	optin[$nr_of_input_files]="${optin_pre[$i]}"
1101	actionin[$nr_of_input_files]="unavailable"
1102	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1103	endin[$nr_of_input_files]="${endin_pre[$i]}"
1104	extin[$nr_of_input_files]="${extin_pre[$i]}"
1105	fi
1106
1107	else
1108
1109	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1110	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1111	if [[ "${multin[$i]}" = true ]]
1112	then
1113	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1114	ls -1 -d ${filename} > filelist 2>/dev/null
1115	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1116	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1117
1118	endings=""
1119	while read line
1120	do
1121	# filename without path (i.e. after the last "/")
1122	basefilename=$(basename ${line})
1123
1124	# check if there is an extension and remove it
1125	ext=${basefilename##*.}
1126	if [[ "$ext" = "${extin_pre[$i]}" ]]
1127	then
1128	basefilename=${basefilename%.*}
1129	fi
1130
1131	# check for an existing cycle number and remove it
1132	cycle=${basefilename##*.}
1133	if [[ $cycle =~ ^-?[0-9]+$ ]]
1134	then
1135	basefilename=${basefilename%.*}
1136	fi
1137
1138	# remove the jobname from the beginning
1139	length_jobname=${#jobname}
1140	ending=${basefilename:${length_jobname}}
1141
1142	# remove the ending given in the .iofiles from the beginning
1143	endingstring="${endin_pre[$i]}"
1144	length_ending=${#endingstring}
1145	ending=${ending:${length_ending}}
1146
1147	if [[ "$ending" = "" ]]
1148	then
1149	# standard ending as given in the .iofiles
1150	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1151	then
1152	endings="$endings DEFAULT"
1153	fi
1154	else
1155	# ending must start with "_", otherwise its a different file
1156	if [[ "${ending:0:1}" = "_" ]]
1157	then
1158	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1159	then
1160	endings="$endings $ending"
1161	fi
1162	fi
1163	fi
1164
1165	done <filelist
1166
1167	rm filelist
1168
1169	else
1170
1171	# SINGLE NAME
1172	endings=DEFAULT
1173
1174	fi
1175
1176	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1177	for ending in $endings
1178	do
1179
1180	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1181	if [[ $ending = DEFAULT ]]
1182	then
1183	ending=""
1184	fi
1185
1186	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1187	(( nr_of_input_files = nr_of_input_files + 1 ))
1188	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1189	optin[$nr_of_input_files]="${optin_pre[$i]}"
1190	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1191	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1192	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1193	extin[$nr_of_input_files]="${extin_pre[$i]}"
1194
1195
1196	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1197	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1198	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1199	then
1200	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1201	else
1202	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1203	fi
1204
1205	# DETERMINE THE FILE'S CYCLE NUMBER
1206	(( maxcycle = 0 ))
1207	ls -1 -d $filename > filelist 2>/dev/null
1208	ls -1 -d $filename.* >> filelist 2>/dev/null
1209	while read line
1210	do
1211	# filename without path (i.e. after the last "/")
1212	basefilename=$(basename ${line})
1213
1214	# check if there is an extension
1215	extension=${basefilename##*.}
1216	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1217	then
1218	basefilename=${basefilename%.*}
1219	fi
1220
1221	# check for an existing cycle number
1222	cycle=${basefilename##*.}
1223	if [[ $cycle =~ ^-?[0-9]+$ ]]
1224	then
1225	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1226	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1227	(( icycle = $((10#$cycle)) ))
1228	else
1229	(( icycle = 0 ))
1230	fi
1231
1232	if (( icycle > maxcycle ))
1233	then
1234	(( maxcycle = icycle ))
1235
1236	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1237	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1238	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1239	then
1240	leading_zero=true
1241	else
1242	leading_zero=false
1243	fi
1244	fi
1245
1246	done <filelist
1247	rm filelist
1248
1249	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1250	if [[ $leading_zero = true ]]
1251	then
1252	cyclestring=`printf "%03d" $maxcycle`
1253	else
1254	cyclestring=$maxcycle
1255	fi
1256
1257	# APPEND CYCLE NUMBER TO FILENAME
1258	if (( maxcycle > 0 ))
1259	then
1260	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1261	then
1262	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1263	else
1264	filename=${filename}.$cyclestring
1265	fi
1266	else
1267	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1268	then
1269	filename=${filename}.${extin[$nr_of_input_files]}
1270	fi
1271	fi
1272
1273	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1274	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1275	absnamein[$nr_of_input_files]=$filename
1276	if (( maxcycle > 0 ))
1277	then
1278	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1279	then
1280	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1281	else
1282	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1283	fi
1284	else
1285	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1286	then
1287	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1288	else
1289	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1290	fi
1291	fi
1292
1293	done
1294
1295	fi
1296
1297	done
1298
1299
1300	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1301	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1302	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1303	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1304	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1305	# REMOTE HOST)
1306	(( i = 0 ))
1307	while (( i < iout ))
1308	do
1309	(( i = i + 1 ))
1310	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1311	then
1312	if [[ "${actionout_pre[$i]}" = tr ]]
1313	then
1314	actionout_pre[$i]=""
1315	elif [[ "${actionout_pre[$i]}" = trpe ]]
1316	then
1317	actionout_pre[$i]=pe
1318	elif [[ "${actionout_pre[$i]}" = tra ]]
1319	then
1320	actionout_pre[$i]=a
1321	fi
1322	(( maxcycle = 0 ))
1323	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1324	eval catalogname=${pathout_pre[$i]}
1325	if ! ls $filename* 1>/dev/null 2>&1
1326	then
1327
1328	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1329	if cat /dev/null > $filename
1330	then
1331	rm $filename
1332	else
1333
1334	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1335	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1336	if [[ ! -d $catalogname ]]
1337	then
1338	if mkdir -p $catalogname
1339	then
1340	printf "\n\n *** directory:"
1341	printf "\n $catalogname"
1342	printf "\n was created\n"
1343	else
1344	printf "\n\n +++ OUTPUT-file:"
1345	printf "\n $filename"
1346	printf "\n cannot be created, because directory does not exist"
1347	printf "\n and cannot be created either"
1348	printf "\n"
1349	locat=output ; exit
1350	fi 2>/dev/null
1351	else
1352	printf "\n\n +++ OUTPUT-file:"
1353	printf "\n $filename"
1354	printf "\n cannot be created, although directory exists"
1355	printf "\n"
1356	locat=output ; exit
1357	fi
1358	fi 2>/dev/null
1359
1360	fi
1361
1362	fi
1363	done
1364
1365
1366	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1367	if [[ $running_in_batch_mode = false ]]
1368	then
1369	run_id=$RANDOM
1370	job_id=${jobname}.$run_id
1371
1372	tempdir=$fast_io_catalog/$job_id
1373	fi
1374
1375
1376	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1377	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1378	then
1379
1380	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1381	if [[ $ibd = 0 ]]
1382	then
1383	printf "\n"
1384	printf "\n +++ no batch directives found in configuration file"
1385	locat=config_file_batch_directives; (( iec = 0 )); exit
1386	fi
1387
1388	# CHECK IF CPUTIME IS GIVEN FOR JOB
1389	done=false
1390	cputime=$cpumax
1391	while [[ $done = false ]]
1392	do
1393	if (( cputime == 0 ))
1394	then
1395	printf "\n +++ cpu-time is undefined"
1396	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1397	printf "\n >>> "
1398	read cputime 1>/dev/null 2>&1
1399	else
1400	done=true
1401	fi
1402	done
1403	cpumax=$cputime
1404
1405	# CHECK THE MEMORY DEMAND
1406	done=false
1407	while [[ $done = false ]]
1408	do
1409	if (( memory == 0 ))
1410	then
1411	printf "\n +++ memory demand is undefined"
1412	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1413	printf "\n >>> "
1414	read memory 1>/dev/null 2>&1
1415	else
1416	done=true
1417	fi
1418	done
1419
1420	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1421	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1422	then
1423	while [[ -z $remote_username ]]
1424	do
1425	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1426	printf "\n >>> Please type username:"
1427	printf "\n >>> "
1428	read remote_username
1429	done
1430	fi
1431
1432	else
1433
1434	if [[ $running_in_batch_mode = false ]]
1435	then
1436	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1437	cpumax=$cputime
1438	else
1439	cputime=$cpumax
1440	fi
1441
1442	fi
1443
1444
1445	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1446	(( cpu_hours = cputime / 3600 ))
1447	(( resttime = cputime - cpu_hours * 3600 ))
1448	(( cpu_minutes = resttime / 60 ))
1449	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1450	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1451
1452
1453	# OUTPUT OF THE PALMRUN-HEADER
1454	calltime=$(date)
1455	printf "\n"
1456	printf "#------------------------------------------------------------------------# \n"
1457	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1458	printf "\| \| \n"
1459	column1="called on:"; column2=$(hostname)
1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1461	if [[ $create_remote_batch_job = true ]]
1462	then
1463	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1464	else
1465	if [[ $running_on_remote = true ]]
1466	then
1467	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1468	else
1469	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1470	fi
1471	fi
1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1473
1474	column1="running in:"
1475	if [[ $running_in_batch_mode = true ]]
1476	then
1477	column2="batch job mode"
1478	else
1479	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1480	then
1481	column2="job creation mode"
1482	else
1483	column2="interactive run mode"
1484	fi
1485	fi
1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1487
1488	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1489	then
1490	if [[ "$project_account" != "" ]]
1491	then
1492	column1="project account number:"
1493	column2="$project_account"
1494	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1495	fi
1496	fi
1497
1498	if [[ -n $cores ]]
1499	then
1500	if [[ $run_coupled_model = false ]]
1501	then
1502	column1="number of cores:"; column2=$cores
1503	else
1504	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1505	fi
1506	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1507	fi
1508	if [[ -n $tasks_per_node ]]
1509	then
1510	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1512	if (( remaining_cores > 0 ))
1513	then
1514	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1515	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1516	fi
1517	fi
1518	if [[ $maximum_parallel_io_streams != $cores ]]
1519	then
1520	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1522	fi
1523	if [[ $use_openmp = true ]]
1524	then
1525	column1="threads per task:"; column2="$threads_per_task"
1526	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1527	fi
1528	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1529	then
1530	column1="memory demand / PE":; column2="$memory MB"
1531	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1532	column1="job cpu time (h:m:s):"; column2="$timestring"
1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1534	fi
1535	printf "\| \| \n"
1536	if [[ "$source_list" != "" ]]
1537	then
1538	if [[ "$make_options" != "" ]]
1539	then
1540	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1541	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1542	line=$(echo "$make_options" \| cut -c46-)
1543	while [[ "$line" != "" ]]
1544	do
1545	column1=""
1546	column2=$(echo "$line" \| cut -c-45)
1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1548	line=$(echo "$line" \| cut -c46-)
1549	done
1550	fi
1551	fi
1552
1553	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1555	line=$(echo "$cpp_options" \| cut -c46-)
1556	while [[ "$line" != "" ]]
1557	do
1558	column1=""
1559	column2=$(echo "$line" \| cut -c-45)
1560	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1561	line=$(echo "$line" \| cut -c46-)
1562	done
1563
1564	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1565	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1566	line=$(echo "$compiler_options" \| cut -c46-)
1567	while [[ "$line" != "" ]]
1568	do
1569	column1=""
1570	column2=$(echo "$line" \| cut -c-45)
1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1572	line=$(echo "$line" \| cut -c46-)
1573	done
1574
1575	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1577	line=$(echo "$linker_options" \| cut -c46-)
1578	while [[ "$line" != "" ]]
1579	do
1580	column1=""
1581	column2=$(echo "$line" \| cut -c-45)
1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1583	line=$(echo "$line" \| cut -c46-)
1584	done
1585
1586	if [[ "$login_init_cmd" != "" ]]
1587	then
1588	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1590	line=$(echo "$login_init_cmd" \| cut -c46-)
1591	while [[ "$line" != "" ]]
1592	do
1593	column1=""
1594	column2=$(echo "$line" \| cut -c-45)
1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1596	line=$(echo "$line" \| cut -c46-)
1597	done
1598	fi
1599
1600	if [[ "$module_commands" != "" ]]
1601	then
1602	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1603	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1604	line=$(echo "$module_commands" \| cut -c46-)
1605	while [[ "$line" != "" ]]
1606	do
1607	column1=""
1608	column2=$(echo "$line" \| cut -c-45)
1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1610	line=$(echo "$line" \| cut -c46-)
1611	done
1612	fi
1613	printf "\| \| \n"
1614	column1="base name of files:"; column2=$jobname
1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1616	column1="activation string list:"; column2=$(echo $activation_string_list)
1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1618
1619	if [[ "$ocean_file_appendix" = true ]]
1620	then
1621	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1622	fi
1623
1624	if [[ "$source_list" != "" ]]
1625	then
1626	printf "\| \| \n"
1627	printf "\| Files to be compiled: \| \n"
1628	line=$source_list
1629	while [[ "$line" != "" ]]
1630	do
1631	linestart=$(echo $line \| cut -c-70)
1632	printf "\| %-70s \| \n" "$linestart"
1633	line=$(echo "$line" \| cut -c71-)
1634	done
1635	fi
1636	printf "#------------------------------------------------------------------------#"
1637
1638
1639
1640	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1641	if [[ $do_trace = true ]]
1642	then
1643	(( i = 0 ))
1644	while (( i < nr_of_input_files ))
1645	do
1646	(( i = i + 1 ))
1647	if (( i == 1 ))
1648	then
1649	printf "\n\n >>> INPUT-file assignments:\n"
1650	fi
1651	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1652	done
1653	(( i = 0 ))
1654	while (( i < iout ))
1655	do
1656	(( i = i + 1 ))
1657	if (( i == 1 ))
1658	then
1659	printf "\n\n >>> OUTPUT-file assignments:\n"
1660	fi
1661	printf "\n ${localout[$i]} : ${pathout[$i]}"
1662	done
1663	(( i = 0 ))
1664	while (( i < iic ))
1665	do
1666	(( i = i + 1 ))
1667	if (( i == 1 ))
1668	then
1669	printf "\n\n >>> INPUT-commands:\n"
1670	fi
1671	printf "\n ${in_command[$i]}"
1672	done
1673	(( i = 0 ))
1674	while (( i < ioc ))
1675	do
1676	(( i = i + 1 ))
1677	if (( i == 1 ))
1678	then
1679	printf "\n\n >>> OUTPUT-commands:\n"
1680	fi
1681	printf "\n ${out_command[$i]}"
1682	done
1683	fi
1684
1685	# QUERY FOR CONTINUE
1686	if [[ $silent = false && $running_in_batch_mode = false ]]
1687	then
1688	antwort=dummy
1689	printf "\n\n"
1690	printf " >>> everything o.k. (y/n) ? "
1691	while read antwort
1692	do
1693	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1694	then
1695	printf " >>> everything o.k. (y/n) ? "
1696	else
1697	break
1698	fi
1699	done
1700	if [[ $antwort = n \|\| $antwort = N ]]
1701	then
1702	locat=user_abort; (( iec = 0 )); exit
1703	fi
1704	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1705	then
1706	printf "\n *** batch-job will be created and submitted"
1707	else
1708	printf "\n *** PALMRUN will now continue to execute on this machine"
1709	fi
1710	fi
1711
1712
1713
1714	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1715	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1716	then
1717
1718	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1719	then
1720	printf "\n\n *** creating executable and other sources for the remote host\n"
1721	else
1722	printf "\n\n *** creating executable and other sources for the local host\n"
1723	fi
1724
1725	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1726	# IT SHALL BE CREATED
1727	ask_for_make_depository=false
1728	if [[ $create_remote_batch_job = true ]]
1729	then
1730
1731	line=`grep %base_directory $config_file`
1732	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1733	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1734
1735	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1736	then
1737	printf "\n\n +++ make depository \"${make_depository}\""
1738	printf "\n on remote host not found!"
1739	ask_for_make_depository=true
1740	fi
1741	rm ${host_configuration}_last_make_protokoll
1742
1743	else
1744
1745	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1746	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1747	if [[ ! -d ${make_depository} ]]
1748	then
1749	printf "\n\n +++ make depository \"${make_depository}\""
1750	printf "\n on local host not found!"
1751	ask_for_make_depository=true
1752	fi
1753
1754	fi
1755
1756	if [[ $ask_for_make_depository = true ]]
1757	then
1758
1759	antwort=dummy
1760	printf "\n\n"
1761	printf " >>> Create a new one (y/n) ? "
1762	while read antwort
1763	do
1764	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1765	then
1766	printf " >>> Create a new one (y/n) ? "
1767	else
1768	break
1769	fi
1770	done
1771	if [[ $antwort = n \|\| $antwort = N ]]
1772	then
1773	locat=user_abort; (( iec = 0 )); exit
1774	fi
1775
1776	if [[ $do_trace = true ]]
1777	then
1778	palmbuild -h $host_configuration
1779	else
1780	palmbuild -v -h $host_configuration
1781	fi
1782
1783	if [[ $? != 0 ]]
1784	then
1785
1786	# ABORT IN CASE OF COMPILATION PROBLEMS
1787	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1788	locat=make_depository
1789	exit
1790	else
1791	echo " *** now continue with creating executable and other sources"
1792	fi
1793
1794	fi
1795
1796	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1797	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1798
1799	if [[ $? != 0 ]]
1800	then
1801
1802	# ABORT IN CASE OF COMPILATION PROBLEMS
1803	printf "\n +++ error while creating executable and/or other sources"
1804	locat=execution
1805	rm -rf $sources_for_run_catalog
1806	exit
1807
1808	else
1809
1810	printf " *** executable and other sources created\n"
1811	rm -rf $sources_for_run_catalog
1812
1813	fi
1814
1815	fi
1816
1817
1818	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1819	# WILL BE COPIED TO THE REMOTE HOST
1820	if [[ $create_remote_batch_job = true ]]
1821	then
1822	(( i = 0 ))
1823	while (( i < nr_of_input_files ))
1824	do
1825	(( i = i + 1 ))
1826	if [[ "${actionin[$i]}" = tr ]]
1827	then
1828	eval inputfile=${pathin[$i]}/${frelin[$i]}
1829	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1830	fi
1831	done
1832	if (( i > 0 ))
1833	then
1834	printf " *** input files have been copied to the remote host\n"
1835	fi
1836	fi
1837
1838
1839	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1840	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1841	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1842	then
1843
1844	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1845	if [[ $running_in_batch_mode = false ]]
1846	then
1847	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1848	# FOLDER
1849	mkdir -p $tempdir
1850	chmod go+rx $tempdir
1851	cd $tempdir
1852	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1853	printf "\n *** changed to temporary directory: $tempdir"
1854
1855	else
1856
1857	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1858	printf "\n *** running in temporary directory: $tempdir"
1859
1860	fi
1861
1862
1863	# PROVIDE THE INPUT FILES
1864	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1865	optional_files_missing=false
1866	(( i = 0 ))
1867	while (( i < nr_of_input_files ))
1868	do
1869	(( i = i + 1 ))
1870	if (( i == 1 ))
1871	then
1872	printf "\n\n *** providing INPUT-files:\n$dashes"
1873	fi
1874
1875
1876	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1877	if [[ "${actionin[$i]}" = unavailable ]]
1878	then
1879	optional_files_missing=true
1880	continue
1881	fi
1882
1883	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1884	files_for_cores=false; filetype=file
1885	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1886	then
1887	files_for_cores=true; filetype=files
1888	actionin[$i]=""
1889	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1890	then
1891	actionin[$i]=""
1892	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1893	then
1894	files_for_cores=true; filetype=files
1895	actionin[$i]="ln"
1896	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1897	then
1898	actionin[$i]="ln"
1899	fi
1900
1901	if [[ $files_for_cores = true ]]
1902	then
1903	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1904	else
1905	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1906	fi
1907
1908	# INPUT-FILES TO BE LINKED
1909	if [[ "${actionin[$i]}" = ln ]]
1910	then
1911
1912	printf "\n $filetype will be linked"
1913	if [[ $files_for_cores = false ]]
1914	then
1915	if [[ -f "${absnamein[$i]}" ]]
1916	then
1917	ln ${absnamein[$i]} ${localin[$i]}
1918	got_tmp[$i]=true
1919	fi
1920	else
1921	if [[ -d "${absnamein[$i]}" ]]
1922	then
1923	mkdir -p ${localin[$i]}
1924	cd ${absnamein[$i]}
1925	for file in $(ls *)
1926	do
1927	ln $file $tempdir/${localin[$i]}
1928	done >\|/dev/null 2>&1
1929	cd $tempdir
1930	fi
1931
1932	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1933	if [[ ! -f "${localin[$i]}/_000000" ]]
1934	then
1935	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1936	cp -r ${absnamein[$i]}/* ${localin[$i]}
1937	fi
1938
1939	got_tmp[$i]=true
1940	fi
1941	fi
1942
1943	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1944	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1945	then
1946
1947	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1948	then
1949
1950	# FILE COPIES ARE PROVIDED FOR ALL CORES
1951	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1952	printf "\n file will be provided for $cores processors"
1953	mkdir -p ${localin[$i]}
1954	ival=$cores
1955	(( ii = 0 ))
1956	while (( ii <= ival-1 ))
1957	do
1958	if (( ii < 10 ))
1959	then
1960	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1961	elif (( ii < 100 ))
1962	then
1963	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1964	elif (( ii < 1000 ))
1965	then
1966	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1967	else
1968	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1969	fi
1970	(( ii = ii + 1 ))
1971	done
1972
1973	else
1974
1975	if [[ $files_for_cores = true ]]
1976	then
1977
1978	# PROVIDE FILES FOR EACH CORE
1979	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1980	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1981	printf "\n providing $cores files for the respective cores"
1982	mkdir -p ${localin[$i]}
1983	if [[ $link_local_input = true ]]
1984	then
1985	printf " files will be linked\n"
1986	cd ${absnamein[$i]}
1987	for file in $(ls *)
1988	do
1989	ln -f $file ${localin[$i]}
1990	done
1991	cd $tempdir
1992	fi
1993
1994	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1995	if [[ ! -f "${localin[$i]}/_000000" ]]
1996	then
1997	if [[ $link_local_input = true ]]
1998	then
1999	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2000	fi
2001	cp -r ${absnamein[$i]}/* ${localin[$i]}
2002	fi
2003
2004	else
2005
2006	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2007	if [[ $link_local_input = true ]]
2008	then
2009	printf " file will be linked\n"
2010	ln -f ${absnamein[$i]} ${localin[$i]}
2011	fi
2012	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2013	if [[ ! -f "${localin[$i]}" ]]
2014	then
2015	if [[ $link_local_input = true ]]
2016	then
2017	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2018	fi
2019	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2020	then
2021	mv ${absnamein[$i]} ${localin[$i]}
2022	else
2023	cp ${absnamein[$i]} ${localin[$i]}
2024	fi
2025	fi
2026	fi
2027	fi
2028	fi
2029
2030	done
2031	if (( i != 0 ))
2032	then
2033	if [[ $optional_files_missing = true ]]
2034	then
2035	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2036	fi
2037	printf "\n$dashes\n *** all INPUT-files provided \n"
2038	fi
2039
2040
2041	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2042	(( i = 0 ))
2043	while (( i < iic ))
2044	do
2045	(( i = i + 1 ))
2046	if (( i == 1 ))
2047	then
2048	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2049	fi
2050	printf "\n >>> ${in_command[$i]}"
2051	eval ${in_command[$i]}
2052	if (( i == iic ))
2053	then
2054	printf "\n$dashes\n"
2055	fi
2056	done
2057
2058
2059	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2060	# (FILE ENVPAR WILL BE READ BY PALM)
2061	cat > ENVPAR << EOF
2062	&envpar run_identifier = '$jobname', host = '$host_configuration',
2063	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2064	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2065	maximum_cpu_time_allowed = ${cpumax}.,
2066	revision = '$global_revision',
2067	batch_job = .${running_in_batch_mode}. /
2068
2069	EOF
2070
2071
2072	# STARTING THE EXECUTABLE
2073	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2074	PATH=$PATH:$tempdir
2075
2076
2077	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2078	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2079	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2080	eval line=\"$line\"
2081	execute_command="$line"
2082
2083
2084	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2085	if [[ "$execute_command_for_combine" = "" ]]
2086	then
2087	eval line2=\"$line2\"
2088	execute_command_for_combine="$line2"
2089	fi
2090
2091
2092
2093	# PROVIDE A HOSTFILE, IF REQUIRED
2094	if [[ "$hostfile" != "" ]]
2095	then
2096
2097	if [[ $hostfile = auto ]]
2098	then
2099	# CREATE A NEW HOSTFILE
2100	(( ii = 1 ))
2101	while (( ii <= cores / threads_per_task ))
2102	do
2103	echo $(hostname) >> hostfile
2104	(( ii = ii + 1 ))
2105	done
2106	if (( cores / threads_per_task == 0 ))
2107	then
2108	echo $(hostname) >> hostfile
2109	fi
2110
2111	else
2112	cp $hostfile hostfile
2113	fi
2114	eval line=\"`head -n $ii hostfile`\"
2115	printf "\n *** running on: $line"
2116	fi
2117
2118
2119
2120	# SET THE NUMBER OF OPENMP-THREADS
2121	if [[ $use_openmp = true ]]
2122	then
2123	export OMP_NUM_THREADS=$threads_per_task
2124	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2125	else
2126	export OMP_NUM_THREADS=1
2127	fi
2128
2129
2130	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2131	if [[ $run_coupled_model = false ]]
2132	then
2133	if [[ "$ocean_file_appendix" = true ]]
2134	then
2135	echo "precursor_ocean" > coupling_steering
2136	else
2137	echo "precursor_atmos" > coupling_steering
2138	fi
2139	else
2140	(( iia = $cores_atmos / $threads_per_task ))
2141	(( iio = $cores_ocean / $threads_per_task ))
2142	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2143	printf "\n\n"
2144	echo "coupled_run $iia $iio" > coupling_steering
2145	fi
2146
2147	printf "\n *** execute command:"
2148	printf "\n \"$execute_command\" \n\n"
2149
2150	$execute_command < coupling_steering
2151
2152	if [[ $? != 0 ]]
2153	then
2154
2155	# ABORT IN CASE OF RUNTIME ERRORS
2156	printf "\n +++ runtime error occured"
2157	locat=execution
2158	exit
2159
2160	else
2161
2162	printf "\n$dashes\n *** execution finished \n"
2163
2164	fi
2165
2166
2167	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2168	# BY EACH CORE INTO ONE FILE
2169	if [[ ! -f combine_plot_fields.x ]]
2170	then
2171
2172	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2173	printf "\n 2d- and/or 3d-data may be incomplete!"
2174	printf "\n Your previous palmbuild may have failed. Please check.\n"
2175
2176	elif [[ "$combine_plot_fields" == true ]]
2177	then
2178
2179	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2180	$execute_command_for_combine
2181
2182	else
2183
2184	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2185	# DATA OUTPUT
2186	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2187	fi
2188
2189
2190
2191	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2192	(( i = 0 ))
2193	while (( i < ioc ))
2194	do
2195	(( i = i + 1 ))
2196	if (( i == 1 ))
2197	then
2198	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2199	fi
2200
2201	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2202	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2203
2204	printf "\n >>> ${out_command[$i]}"
2205	eval ${out_command[$i]}
2206	if (( i == ioc ))
2207	then
2208	printf "\n$dashes\n"
2209	fi
2210	done
2211
2212
2213	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2214	# WILDCARDS
2215	(( i = 0 ))
2216	(( nr_of_output_files = 0 ))
2217
2218	while (( i < iout ))
2219	do
2220
2221	(( i = i + 1 ))
2222
2223	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2224	# CREATE A LIST FOR THE DETECTED ENDINGS
2225	if [[ "${multout[$i]}" = true ]]
2226	then
2227	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2228	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2229	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2230
2231	endings="DEFAULT"
2232	while read line
2233	do
2234	# remove the local name from the beginning
2235	localnamestring="${localout_pre[$i]}"
2236	length_localname=${#localnamestring}
2237	ending=${line:${length_localname}}
2238
2239	if [[ "$ending" != "" ]]
2240	then
2241	endings="$endings $ending"
2242	fi
2243
2244	done <filelist
2245
2246	rm filelist
2247
2248	else
2249
2250	# SINGLE NAME
2251	endings=DEFAULT
2252
2253	fi
2254
2255	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2256	for ending in $endings
2257	do
2258
2259	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2260	if [[ $ending = DEFAULT ]]
2261	then
2262	ending=""
2263	fi
2264
2265	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2266	(( nr_of_output_files = nr_of_output_files + 1 ))
2267	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2268	transout[$nr_of_output_files]="${transout_pre[$i]}"
2269	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2270	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2271	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2272	extout[$nr_of_output_files]="${extout_pre[$i]}"
2273	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2274
2275	done
2276
2277	done
2278
2279
2280
2281
2282	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2283	(( i = 0 ))
2284	while (( i < nr_of_output_files ))
2285	do
2286	(( i = i + 1 ))
2287	if (( i == 1 ))
2288	then
2289	printf "\n\n *** saving OUTPUT-files:"
2290
2291	# GET RUN NUMBER ASSIGNED BY PALM
2292	if [[ -f RUN_NUMBER ]]
2293	then
2294	read run_number < RUN_NUMBER
2295	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2296	usecycle_option="-U $run_number"
2297	else
2298	run_number=0
2299	usecycle_option=""
2300	fi
2301	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2302	then
2303	printf "\n *** in case of SCP transfers to local host"
2304	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2305	fi
2306	printf "\n$dashes"
2307	fi
2308
2309	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2310	then
2311
2312	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2313
2314	# DETERMINE THE CYCLE NUMBER
2315	ls -1 -d $filename > filelist 2>/dev/null
2316	ls -1 -d $filename.* >> filelist 2>/dev/null
2317	while read line
2318	do
2319
2320	# filename without path (i.e. after the last "/")
2321	basefilename=$(basename ${line})
2322
2323	# check if there is an extension
2324	extension=${basefilename##*.}
2325	if [[ "$extension" = "${extout[$i]}" ]]
2326	then
2327	basefilename=${basefilename%.*}
2328	fi
2329
2330	# check for an existing cycle number
2331	cycle=${basefilename##*.}
2332	if [[ $cycle =~ ^-?[0-9]+$ ]]
2333	then
2334	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2335	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2336	(( icycle = $((10#$cycle)) + 1 ))
2337	else
2338	(( icycle = 1 ))
2339	fi
2340
2341	if (( icycle > maxcycle ))
2342	then
2343	(( maxcycle = icycle ))
2344	fi
2345
2346	done <filelist
2347	rm filelist
2348
2349
2350	# SET THE CYCLE NUMBER
2351	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2352	if [[ "${actionout[$i]}" = a ]]
2353	then
2354	(( maxcycle = maxcycle - 1 ))
2355	fi
2356
2357	(( cycnum[$i] = maxcycle ))
2358	pathout[$i]=$filename
2359
2360
2361	# ADD CYCLE NUMBER TO FILENAME
2362	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2363	if [[ "${actionout[$i]}" != "a" ]]
2364	then
2365	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2366	# WITH AN EXISTING CYCLE NUMBER
2367	if (( run_number >= cycnum[$i] ))
2368	then
2369	(( cycnum[$i] = run_number ))
2370	else
2371	if (( run_number > 0 ))
2372	then
2373	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2374	fi
2375	fi
2376	fi
2377	if (( cycnum[$i] > 0 ))
2378	then
2379	cyclestring=`printf "%03d" ${cycnum[$i]}`
2380	pathout[$i]=${pathout[$i]}.$cyclestring
2381	fi
2382	fi
2383
2384	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2385	files_for_cores=false; filetype=file
2386	link_local_output=false
2387	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2388	then
2389	files_for_cores=true; filetype=directory
2390	actionout[$i]=""
2391	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2392	then
2393	actionout[$i]=""
2394	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2395	then
2396	files_for_cores=true; filetype=directory
2397	link_local_output=true
2398	actionout[$i]=""
2399	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2400	then
2401	link_local_output
2402	actionout[$i]=""
2403	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2404	then
2405	files_for_cores=true; filetype=directory
2406	actionout[$i]="tr"
2407	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2408	then
2409	actionout[$i]="tr"
2410	fi
2411
2412	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2413	then
2414	if [[ ${warnout[$i]} = true ]]
2415	then
2416	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2417	fi
2418	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2419	then
2420	if [[ ${warnout[$i]} = true ]]
2421	then
2422	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2423	fi
2424	else
2425
2426
2427	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2428	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2429	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2430	then
2431	if [[ $running_on_remote = true ]]
2432	then
2433
2434	# SET OPTIONS FOR TRANSFER
2435	if [[ "${actionout[$i]}" = tr ]]
2436	then
2437	if [[ $files_for_cores = false ]]
2438	then
2439	catalog_option=""
2440	catalog_string=""
2441	else
2442	catalog_option="-c"
2443	catalog_string="/"
2444	fi
2445	append_option=""
2446	append_string=""
2447	else
2448	append_option="-A"
2449	append_string="append"
2450	fi
2451
2452	transfer_failed=false
2453	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2454	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2455
2456	# TRANSFER VIA SCP
2457	if [[ "$remote_loginnode" != "" ]]
2458	then
2459	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
2460	else
2461	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]}
2462	fi
2463	[[ $? != 0 ]] && transfer_failed=true
2464
2465
2466	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2467	if [[ $transfer_failed = true ]]
2468	then
2469	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2470	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2471
2472	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2473	eval local_catalog=${pathout[$i]}
2474	if [[ ! -d $local_catalog ]]
2475	then
2476	printf " *** local directory does not exist. Trying to create:\n"
2477	printf " $local_catalog \n"
2478	mkdir -p $local_catalog
2479	fi
2480	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2481	transfer_problems=true
2482	fi
2483
2484	else
2485
2486	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2487	# BE COPIED OR APPENDED ON THIS MACHINE
2488	if [[ "${actionout[$i]}" = tr ]]
2489	then
2490	actionout[$i]=""
2491	else
2492	actionout[$i]="a"
2493	fi
2494	fi
2495	fi
2496
2497
2498	# APPEND ON THIS MACHINE
2499	if [[ "${actionout[$i]}" = "a" ]]
2500	then
2501	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2502	then
2503	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2504	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2505	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2506	else
2507	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2508	printf "\n ${pathout[$i]}\n"
2509	cat ${localout[$i]} >> ${pathout[$i]}
2510	fi
2511	fi
2512
2513	# COPY ON THIS MACHINE
2514	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2515	# ON DIFFERENT FILE-SYSTEMS
2516	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2517	then
2518
2519	# COPY IN CASE OF RUNS ON SINGLE CORES
2520	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2521	then
2522	printf "\n >>> OUTPUT: ${localout[$i]} to"
2523	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2524	if [[ $link_local_output = true ]]
2525	then
2526	printf " file will be linked\n"
2527	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2528	fi
2529	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2530	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2531	then
2532	if [[ $link_local_output = true ]]
2533	then
2534	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2535	fi
2536	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2537	else
2538	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2539	fi
2540	else
2541	printf "\n >>> OUTPUT: ${localout[$i]} to"
2542	printf "\n ${pathout[$i]}\n"
2543	if [[ $link_local_output = true ]]
2544	then
2545	printf " file will be linked\n"
2546	ln -f ${localout[$i]} ${pathout[$i]}
2547	fi
2548	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2549	if [[ ! -f "${pathout[$i]}" ]]
2550	then
2551	if [[ $link_local_output = true ]]
2552	then
2553	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2554	fi
2555	cp ${localout[$i]} ${pathout[$i]}
2556	else
2557	printf "+++ no copy because file ${pathout[$i]} exists\n"
2558	fi
2559	fi
2560
2561	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2562	then
2563
2564	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2565	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2566	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2567	printf "\n ${pathout[$i]}\n"
2568	if [[ $link_local_output = true ]]
2569	then
2570	printf " files will be linked\n"
2571	mkdir -p ${pathout[$i]}
2572	cd ${localout[$i]}
2573	for file in $(ls *)
2574	do
2575	ln -f $file ${pathout[$i]}
2576	done >\|/dev/null 2>&1
2577	cd $tempdir
2578	fi
2579
2580	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2581	if [[ ! -f "${pathout[$i]}/_000000" ]]
2582	then
2583	if [[ $link_local_output = true ]]
2584	then
2585	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2586	fi
2587	cp -r ${localout[$i]}/* ${pathout[$i]}
2588	fi
2589
2590	fi
2591	fi
2592	done
2593
2594	if (( i != 0 ))
2595	then
2596	if [[ $transfer_problems = true ]]
2597	then
2598	printf "\n$dashes\n *** OUTPUT-files saved"
2599	printf "\n +++ WARNING: some data transfers failed! \n"
2600	else
2601	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2602	fi
2603	fi
2604
2605
2606	# IF REQUIRED, START A RESTART-JOB
2607	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2608	if [[ -f CONTINUE_RUN ]]
2609	then
2610
2611	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2612	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2613	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2614	# -b START A BATCH JOB
2615	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2616	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2617	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2618
2619
2620	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2621	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2622	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2623	then
2624	prc=`echo $prc \| sed 's/#/r/g'`
2625	fi
2626
2627
2628	# START THE RESTART-JOB
2629	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2630	echo " $prc"
2631	printf "\n$dashes\n"
2632	if [[ $running_on_remote = true ]]
2633	then
2634
2635	echo "*** ssh will be used to initiate restart-runs!"
2636	echo " return_address=\"$return_address\" "
2637	echo " return_username=\"$local_username\" "
2638
2639	if [[ "$remote_loginnode" != "" ]]
2640	then
2641	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
2642	else
2643	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2644	fi
2645
2646	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2647	sleep 30
2648
2649	else
2650
2651	# START THE RESTART JOB ON THE LOCAL HOST
2652	eval $prc # THE ' MUST BE EVALUATED
2653	cd - > /dev/null
2654
2655	fi
2656	printf "\n$dashes\n *** restart-run initiated \n"
2657
2658
2659	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2660	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2661	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2662	# MAY BE VERY HUGE)
2663	(( i = 0 ))
2664	while (( i < nr_of_input_files ))
2665	do
2666	(( i = i + 1 ))
2667	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2668	then
2669	rm -r ${absnamein[$i]}
2670	fi
2671	done
2672
2673	fi
2674
2675
2676	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2677	cd $HOME
2678	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2679
2680
2681	else
2682
2683
2684	# PREPARING ACTIONS,
2685	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2686
2687	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2688	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2689	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2690	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2691	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2692	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2693	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2694	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2695	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2696	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2697	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2698	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2699	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2700	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2701	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2702	if [[ $create_remote_batch_job = true ]]
2703	then
2704	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2705	if [[ $do_trace = true ]]
2706	then
2707	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2708	fi
2709	elif [[ $create_batch_job = true ]]
2710	then
2711	palmrun_com=${palmrun_com}" -j"
2712	if [[ $do_trace = true ]]
2713	then
2714	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2715	fi
2716	fi
2717
2718
2719	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2720	# REMOTE HOST
2721	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2722	job_protocol_file=$job_protocol_file_local
2723	if [[ $create_remote_batch_job = true ]]
2724	then
2725	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2726	job_protocol_file=$job_protocol_file_remote
2727	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2728	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2729	fi
2730
2731
2732	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2733	jobfile=jobfile.$run_id
2734
2735
2736	# FIRST CREATE THE BATCH DIRECTIVES
2737	(( i = 0 ))
2738	while (( i < ibd ))
2739	do
2740	(( i = i + 1 ))
2741	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2742	eval line=\"$line\"
2743	echo "$line" >> $jobfile
2744	done
2745	echo " " >> $jobfile
2746
2747
2748	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2749	# PROTOCOL
2750	if [[ $create_remote_batch_job = true ]]
2751	then
2752	echo "set +vx" >> $jobfile
2753	echo "trap '" >> $jobfile
2754	echo "set +vx" >> $jobfile
2755	echo "cd ${remote_jobcatalog}" >> $jobfile
2756	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2757
2758	# ADD THE BATCH DIRECTIVES
2759	(( i = 0 ))
2760	while (( i < ibdt ))
2761	do
2762	(( i = i + 1 ))
2763	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2764	eval line=\"$line\"
2765	echo "$line" >> $jobfile
2766	done
2767	echo " " >> $jobfile
2768
2769	echo "set -x" >> $jobfile
2770	echo "${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
2771	echo "%%END%%" >> $jobfile
2772	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2773	echo "$submit_command $scpjob_file" >> $jobfile
2774	echo "rm $scpjob_file" >> $jobfile
2775	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2776	echo "set -x" >> $jobfile
2777	echo " ' exit" >> $jobfile
2778	fi
2779
2780
2781	# ACTIVATE ERROR-TRACEBACK
2782	if [[ $do_trace = true ]]
2783	then
2784	echo "set -x" >> $jobfile
2785	else
2786	echo "set +vx" >> $jobfile
2787	fi
2788
2789
2790	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2791	if [[ "$login_init_cmd" != "" ]]
2792	then
2793	echo "$login_init_cmd" >> $jobfile
2794	fi
2795	if [[ "$module_commands" != "" ]]
2796	then
2797	echo "$module_commands" >> $jobfile
2798	fi
2799
2800
2801	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2802	if [[ $create_remote_batch_job = true ]]
2803	then
2804	echo "mkdir $tempdir" >> $jobfile
2805	echo "chmod go+rx $tempdir" >> $jobfile
2806	else
2807	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2808	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2809	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2810	mkdir $tempdir
2811	chmod go+rx $tempdir
2812	fi
2813	echo "cd $tempdir" >> $jobfile
2814	echo "export tempdir=$tempdir" >> $jobfile
2815	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2816	echo "export PATH=.:\$PATH" >> $jobfile
2817	echo "export execute_palmrun=true" >> $jobfile
2818
2819
2820	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2821	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2822	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2823	echo "LOCAL_PWD=$working_directory" >> $jobfile
2824	echo "export LOCAL_PWD" >> $jobfile
2825
2826
2827	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2828	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2829	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2830
2831
2832	# CALL PALMRUN WITHIN THE JOB
2833	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2834	echo "set -x" >> $jobfile
2835	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2836
2837
2838	# TRANSFER JOBFILE TO THE TARGET HOST
2839	if [[ $create_jobfile_only = false ]]
2840	then
2841
2842	if [[ $create_remote_batch_job = true ]]
2843	then
2844
2845	echo " "
2846	echo " *** transfer of job to remote host via scp"
2847	if [[ $do_trace = true ]]
2848	then
2849	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2850	fi
2851	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2852
2853	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2854	if [[ $do_trace = true ]]
2855	then
2856	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"
2857	fi
2858	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
2859
2860	elif [[ $create_batch_job = true ]]
2861	then
2862
2863	eval local_jobcatalog=$local_jobcatalog
2864	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2865	cd $local_jobcatalog
2866	echo " "
2867	echo " *** submit the job"
2868	if [[ $do_trace = true ]]
2869	then
2870	echo "$submit_command ${host_configuration}_${job_id}"
2871	fi
2872	$submit_command ${host_configuration}_${job_id}
2873	rm ${host_configuration}_${job_id}
2874	cd - > /dev/null
2875
2876	fi
2877
2878	rm -rf $jobfile
2879
2880	else
2881
2882	printf "\n *** jobfile created under name \"$jobfile\" "
2883	printf "\n no batch-job has been sent!"
2884
2885	fi
2886
2887	fi # END OF REMOTE-PART

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