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source: palm/trunk/SCRIPTS/palmrun @ 2995

Last change on this file since 2995 was 2993, checked in by raasch, 7 years ago
bugfix of r2990
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 97.2 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	# bugfix of r2990
30	#
31	# 2718 2018-01-02 08:49:38Z maronga
32	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
33	# not in the working directory from where palmrun is called
34	#
35	# 2718 2018-01-02 08:49:38Z maronga
36	# svfout in the activation string will be replaced now by svfin in case of
37	# automatic restarts
38	#
39	# 2718 2018-01-02 08:49:38Z maronga
40	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
41	# the possible output or input of sky view factors
42	#
43	# 2718 2018-01-02 08:49:38Z maronga
44	# "fname" renamed to "jobname"
45	#
46	# 2718 2018-01-02 08:49:38Z maronga
47	# parameters are allowed in output commands (OC:)
48	#
49	# 2718 2018-01-02 08:49:38Z maronga
50	# bugfix: exit if no queue has been given neither with option -q nor in the
51	# configuration file
52	#
53	# 2718 2018-01-02 08:49:38Z maronga
54	# file connection file from trunk/SCRIPTS is taken by default
55	#
56	# 2718 2018-01-02 08:49:38Z maronga
57	# Corrected "Former revisions" section
58	#
59	# 2696 2017-12-14 17:12:51Z kanani
60	# Change in file header (GPL part)
61	#
62	# 2693 2017-12-13 12:33:49Z raasch
63	# replacement of variables given by {{<variable>}} in configuration file is now
64	# done in a more general way, variable names are written in small letters
65	#
66	# 2670 2017-12-06 16:32:19Z raasch
67	# test printouts removed
68	#
69	# 2669 2017-12-06 16:03:27Z raasch
70	# file attributes in .palm.iofiles restructured, "loc" attribute completely
71	# removed,
72	# wildcard (*) allowed in .palm.iofiles as file activation string for output
73	# files,
74	# informative messages in case of missing optional input files shortened
75	# bugfix: variable cycle explicitly interpreted with 10 as the number base
76	#
77	# 2638 2017-11-23 12:44:23Z raasch
78	# use of wildcards in file connection statements enabled
79	#
80	# 2605 2017-11-09 15:31:46Z raasch
81	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
82	# will not be sent with the job file any more, but copied into the
83	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
84	#
85	# 2600 2017-11-01 14:11:20Z raasch
86	# cycle numbers are made three digits wide
87	#
88	# 2566 2017-10-20 08:50:47Z raasch
89	# execute command for combine_plot_fields added
90	# "TEMPDIR" renamed "tempdir"
91	# temporary working directory for local batch jobs is created immediately within
92	# the user's palmrun call, due to a requirement of the "grid engine" batch
93	# system, where the working directory is given with batch directive -wd and must
94	# already exist when the job is submitted,
95	# informative messages in non-trace mode reduced and partly reformatted
96	#
97	# 2551 2017-10-18 07:25:11Z raasch
98	# TEMPDIR added as replacement string to be used in batch directives
99	#
100	# 2512 2017-10-04 08:26:59Z raasch
101	# bugfix for determining cycle numbers of NetCDF input files
102	#
103	# 2506 2017-09-29 08:30:37Z raasch
104	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
105	# host configuration added to SOURCES_FOR_RUN_... folder name
106	# host_identifier renamed host_configuration
107	# option -W added to allow for job dependencies
108	#
109	# 2501 2017-09-26 11:41:55Z raasch
110	# default value for number of cores (option -X) set to 1
111	# bugfix for mechanism which overwrites configuration file settings with values
112	# provided by palmrun options
113	#
114	# 2499 2017-09-22 16:47:58Z kanani
115	# option -h named configuration identifier
116	#
117	# 2480 2017-09-19 06:24:14Z maronga
118	# bugfix for last revision
119	#
120	# 2479 2017-09-19 06:12:16Z raasch
121	# option -A (project account number) added
122	#
123	# 2422 2017-09-08 08:25:41Z raasch
124	# initial revision
125	#
126	#--------------------------------------------------------------------------------#
127	# palmrun - script for running PALM jobs on local and remote hosts
128	#--------------------------------------------------------------------------------#
129
130
131
132	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
133
134	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
135	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
136	# (TOO MANY ARGUMENTS - PROBLEM)
137	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
138
139	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
140	typeset -i nr_of_output_files=0
141	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
142	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
143	# SCRIPT-OPTION ARGUMENTS
144	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
145	typeset -i icycle inode ival maxcycle mpi_tasks
146	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
147
148	activation_string_list=""
149	AddFilenames=""
150	combine_plot_fields=true
151	compiler_name=""
152	compiler_name_ser=""
153	compiler_options=""
154	cores=1
155	cores_atmos=0
156	cores_ocean=0
157	coupled_dist=""
158	cpp_options=""
159	cpumax=0
160	create_batch_job=false
161	create_jobfile_only=false
162	create_remote_batch_job=false
163	dashes=" ----------------------------------------------------------------------------"
164	defaultqueue=""
165	delete_temporary_catalog=true
166	do_compile=true
167	do_trace=false
168	executable=""
169	execute_command=""
170	execution_error=false
171	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
172	jobname=test
173	global_revision=""
174	host_configuration="default"
175	hostfile=""
176	hp=""
177	keep_data_from_previous_run=false
178	link_local_input=false
179	link_local_output=false
180	linker_options=""
181	local_jobcatalog=""
182	locat=normal
183	makefile=""
184	max_par_io_str=""
185	prc=$0
186	while [[ $(echo $prc \| grep -c "/") != 0 ]]
187	do
188	prc=`echo $prc \| cut -f2- -d"/"`
189	done
190	module_calls=""
191	palmrun_memory=""
192	palmrun_script_name=$prc
193	openmp=false
194	previous_job=""
195	project_account=""
196	queue=none
197	read_svf=""
198	restart_run=false
199	return_address=""
200	remote_jobcatalog=""
201	remote_username=""
202	running_in_batch_mode=false
203	run_coupled_model=false
204	run_id=""
205	silent=false
206	source_list=""
207	source_path=""
208	tasks_per_node=0
209	threads_per_task=1
210	transfer_problems=false
211	user_source_path=""
212	use_existing_sources_folder=""
213	use_openmp=false
214	version="palmrun 1.0 Rev$Rev: 2993 $"
215	working_directory=`pwd`
216	write_binary=""
217	write_svf=""
218	TOPT=""
219
220
221	# ERROR HANDLING IN CASE OF EXIT
222	trap 'if [[ $locat != normal && $locat != control_c ]]
223	then
224
225	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
226	(( i = 0 ))
227	while (( i < iec ))
228	do
229	(( i = i + 1 ))
230	printf "\n *** Execution of ERROR-command:\n"
231	printf " >>> ${err_command[$i]}\n"
232	eval ${err_command[$i]}
233	done
234	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
235	printf "\n\n+++ palmrun killed \n\n"
236	elif [[ $locat != control_c ]]
237	then
238	printf "\n --> palmrun finished\n\n"
239	fi' exit
240
241
242	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
243	trap 'cd; rm -rf $tempdir
244	printf "\n+++ palmrun killed by \"^C\" \n\n"
245	locat=control_c
246	exit
247	' 2
248
249
250	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
251	# WHICH WILL BE USED TO START RESTART-JOBS
252	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
253	do
254	case $option in
255	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
256	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
257	(b) create_batch_job=true; prc="$prc -b";;
258	(B) delete_temporary_catalog=false; prc="$prc -B";;
259	(C) restart_run=true; prc="$prc -C";;
260	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
261	(F) create_jobfile_only=true;;
262	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
263	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
264	(j) running_in_batch_mode=true;;
265	(k) keep_data_from_previous_run=true; prc="$prc -k";;
266	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
267	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
268	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
269	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
270	(r) run_id=$OPTARG;;
271	(R) return_address=$OPTARG;;
272	(s) source_list=$OPTARG;;
273	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
274	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
275	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
276	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
277	(v) silent=true; prc="$prc -v";;
278	(V) use_existing_sources_folder="-V";;
279	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
280	(W) previous_job=$OPTARG;;
281	(x) do_trace=true;set -x; prc="$prc -x";;
282	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
283	(y) ocean_file_appendix=true; prc="$prc -y";;
284	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
285	(Z) combine_plot_fields=false; prc="$prc -Z";;
286	(\?) printf "\n +++ unknown option $OPTARG \n"
287	printf "\n --> type \"$0 ?\" for available options \n"
288	locat=parameter;exit;;
289	esac
290	done
291
292
293	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
294	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
295	(( to_shift = $OPTIND - 1 ))
296	shift $to_shift
297
298	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
299	if [[ "$1" = "?" ]]
300	then
301	(printf "\n *** Description of available palmrun options:\n"
302	printf "\n Option Description Default-Value"
303	printf "\n -a activation string list \"\" "
304	printf "\n -A project account number ---"
305	printf "\n -b batch-job on local machine ---"
306	printf "\n -B do not delete temporary directory at end ---"
307	printf "\n -d base name of files attached to program test"
308	printf "\n -F create batch job file only ---"
309	printf "\n -h host configuration \"default\" "
310	printf "\n -k keep data from previous run"
311	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
312	printf "\n -M Makefile name Makefile"
313	printf "\n -O threads per openMP task ---"
314	printf "\n -q queue \"$queue\" "
315	printf "\n -s filenames of routines to be compiled \"\" "
316	printf "\n must end with .f, .f90, .F, or .c !"
317	printf "\n use \"..\" for more than one file and wildcards"
318	printf "\n -s LM compiles all locally modified files"
319	printf "\n -t allowed cpu-time in seconds (batch) 0"
320	printf "\n -T tasks per node ---"
321	printf "\n -u username on remote machine \"\" "
322	printf "\n -v no prompt for confirmation ---"
323	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
324	printf "\n -w maximum parallel io streams as given by -X"
325	printf "\n -W name of job to wait for ---"
326	printf "\n -x tracing of palmrun for debug purposes ---"
327	printf "\n -X # of processors (on parallel machines) 1"
328	printf "\n -y add appendix \"_O\" to all local output"
329	printf "\n files (ocean precursor runs followed by"
330	printf "\n coupled atmosphere-ocean runs) ---"
331	printf "\n -Y run coupled model, \"#1 #2\" with"
332	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
333	printf "\n -Z skip combine_plot_fields at the end of "
334	printf "\n the simulation ---"
335	printf "\n "
336	printf "\n Possible values of positional parameter <modus>:"
337	printf "\n \"?\" - this outline \n\n") \| more
338	exit
339	elif [[ "$1" != "" ]]
340	then
341	printf "\n +++ positional parameter $1 unknown \n"
342	locat=parameter; exit
343	fi
344
345
346
347	# SHORT STARTING MESSAGE
348	printf "\n*** $version "
349	printf "\n will be executed. Please wait ..."
350
351
352	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
353	export fname=$jobname
354
355
356	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
357	config_file=.palm.config.$host_configuration
358	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
359
360
361	# CHECK, IF CONFIGURATION FILE EXISTS
362	if [[ ! -f $config_file ]]
363	then
364	printf "\n\n +++ configuration file: "
365	printf "\n $config_file"
366	printf "\n does not exist"
367	locat=connect; exit
368	fi
369
370
371	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
372	if [[ -f .palm.iofiles ]]
373	then
374	fileconnection_file=.palm.iofiles
375	fi
376
377
378	# CHECK, IF FILE CONNECTION FILE EXISTS
379	if [[ ! -f $fileconnection_file ]]
380	then
381	printf "\n\n +++ file connection file: "
382	printf "\n $fileconnection_file"
383	printf "\n does not exist"
384	locat=connect; exit
385	fi
386
387
388	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
389	if [[ "$activation_string_list" = "" ]]
390	then
391	printf "\n\n +++ no activation string list given: "
392	printf "\n please set palmrun option \"-a\" "
393	locat=palmrun_option; exit
394	fi
395
396
397	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
398	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
399	then
400	write_binary=true
401	else
402	write_binary=false
403	fi
404
405	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
406	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
407	then
408	write_svf=true
409	else
410	write_svf=false
411	fi
412
413	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
414	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
415	then
416	read_svf=true
417	else
418	read_svf=false
419	fi
420
421
422	# READ AND EVALUATE THE CONFIGURATION-FILE
423	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
424
425	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
426	while read line
427	do
428
429	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
430	eval line=\"$line\"
431
432
433	# INTERPRET THE LINE
434	if [[ "$(echo $line)" = "" ]]
435	then
436
437	# EMPTY LINE, NO ACTION
438	continue
439
440	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
441	then
442
443	# LINE IS A COMMENT LINE
444	continue
445
446	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
447	then
448
449	# LINE DEFINES AN ENVIRONMENT-VARIABLE
450	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
451	value=`echo $line \| cut -d" " -s -f2-`
452
453
454	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
455	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
456	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
457	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
458	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
459	# CONFIGURATION-FILE.
460	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
461	then
462	eval export $var="\$value"
463
464	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
465	if [[ $do_trace = true ]]
466	then
467	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
468	fi
469	fi
470
471	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
472	then
473
474	# LINE DEFINES BATCH-DIRECTIVE
475	(( ibd = ibd + 1 ))
476	line=$(echo $line \| cut -c4-)
477	batch_directive[$ibd]="$line"
478
479	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
480	then
481
482	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
483	# REMOTE TO A LOCAL HOST
484	(( ibdt = ibdt + 1 ))
485	line=$(echo $line \| cut -c5-)
486	batch_directive_transfer[$ibdt]="$line"
487
488	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
489	then
490
491	# LINE DEFINES ERROR-COMMAND
492	(( iec = iec + 1 ))
493	line=$(echo $line \| cut -c4-)
494	err_command[$iec]="$line"
495
496	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
497	then
498
499	# LINE DEFINES INPUT-COMMAND
500	(( iic = iic + 1 ))
501	line=$(echo $line \| cut -c4-)
502	in_command[$iic]="$line"
503
504	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
505	then
506
507	# LINE DEFINES OUTPUT-COMMAND
508	(( ioc = ioc + 1 ))
509	line=$(echo $line \| cut -c4-)
510	out_command[$ioc]="$line"
511
512	else
513
514	# SKIP ALL OTHER LINES
515	continue
516
517	fi
518
519	done < $config_file
520
521
522	# CHECK SETTING OF REQUIRED PARAMETERS
523	if [[ "$compiler_name" = "" ]]
524	then
525	printf "\n +++ no compiler name found in $config_file"
526	printf "\n Please add line \"compiler_name ...\" to that file."
527	locat=config_file; exit
528	fi
529	if [[ "$compiler_name_ser" = "" ]]
530	then
531	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
532	printf "\n Please add line \"compiler_name_ser ...\" to that file."
533	locat=config_file; exit
534	fi
535	if [[ "$compiler_options" = "" ]]
536	then
537	printf "\n +++ no compiler options found in $config_file"
538	printf "\n Please add line \"compiler_options ...\" to that file."
539	locat=config_file; exit
540	fi
541	if [[ "$linker_options" = "" ]]
542	then
543	printf "\n +++ no linker options found in $config_file"
544	printf "\n Please add line \"linker_options ...\" to that file."
545	locat=config_file; exit
546	fi
547	if [[ "$execute_command" = "" ]]
548	then
549	printf "\n +++ no execute command found in $config_file"
550	printf "\n Please add line \"execute_command ...\" to that file."
551	locat=config_file; exit
552	fi
553
554	if [[ "$hostfile" != "" ]]
555	then
556	if [[ $hostfile != auto && ! -f $hostfile ]]
557	then
558	printf "\n +++ no hostfile \"$hostfile\" found"
559	printf "\n Please check line \"hostfile ...\" in $config_file"
560	locat=config_file; exit
561	fi
562	fi
563
564
565	# DETERMINE THE CALL STATUS
566	if [[ "$return_address" != "" ]]
567	then
568
569	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
570	# BATCH MODE AND ...
571	running_on_remote=true
572
573	else
574
575	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
576	if [[ "$remote_ip" != "" ]]
577	then
578
579	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
580	create_remote_batch_job=true
581
582	fi
583	running_on_remote=false
584	fi
585
586
587
588	# READ AND EVALUATE THE I/O-FILE LIST
589	[[ $silent = false ]] && printf "\n Reading the I/O files... "
590
591	# READ THE FILE CONNECTION FILE LINE BY LINE
592	while read line
593	do
594
595	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
596	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
597
598	# INTERPRET THE LINE
599	if [[ "$(echo $line)" = "" ]]
600	then
601	# EMPTY LINE, NO ACTION
602	continue
603
604	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
605	then
606
607	# LINE IS A COMMENT LINE
608	true
609
610	else
611
612	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
613	# s2a: in/out - field
614	# s2b: action - field (optional)
615	s1=`echo "$line" \| cut -d" " -f1`
616	s2=`echo "$line" \| cut -d" " -s -f2`
617	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
618	then
619	s2a=$s2
620	s2b=""
621	else
622	s2a=`echo $s2 \| cut -d":" -f1`
623	s2b=`echo $s2 \| cut -d":" -f2`
624	fi
625	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
626	s4=`echo "$line" \| cut -d" " -s -f4`
627	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
628	s5=`echo "$line" \| cut -d" " -s -f5`
629	s6=`echo "$line" \| cut -d" " -s -f6`
630
631
632	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
633	# INPUT- OR OUTPUT-LIST.
634	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
635	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
636	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
637	# IS NOT CHECKED AND STORED.
638	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
639	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
640	then
641	found=false
642	for actual in $activation_string_list
643	do
644	for formal in $s3
645	do
646	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
647	done
648	done
649	if [[ $found = true ]]
650	then
651	(( iin = iin + 1 ))
652	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
653	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
654	if [[ "$s2a" = inopt ]]
655	then
656	optin_pre[$iin]=yes
657	else
658	optin_pre[$iin]=no
659	fi
660
661	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
662	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
663	if [[ $running_on_remote = true && "$s2b" = tr ]]
664	then
665	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
666	fi
667
668	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
669	# THE WILDCARD FROM THE ENDING
670	if [[ "${s5: -1}" = "*" ]]
671	then
672	if [[ "$s2b" = "di" ]]
673	then
674	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
675	printf "\n see file \"$fileconnection_file\", line"
676	printf "\n$line"
677	locat=iofiles_file; exit
678	fi
679	multin[$iin]=true
680	string=${endin_pre[$iin]}
681	endin_pre[$iin]="${string%?}"
682	else
683	multin[$iin]=false
684	fi
685	fi
686	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
687	then
688	found=false
689	for actual in $activation_string_list
690	do
691	for formal in $s3
692	do
693	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
694	done
695	done
696	if [[ $found = true ]]
697	then
698	(( iout = iout + 1 ))
699	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
700	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
701
702	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
703	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
704	if [[ $formal = wildcard ]]
705	then
706	warnout_pre[$iout]=false
707	else
708	warnout_pre[$iout]=true
709	fi
710
711	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
712	# THE WILDCARD FROM THE LOCAL FILENAME
713	if [[ "${s1: -1}" = "*" ]]
714	then
715	if [[ "$s2b" = "di" ]]
716	then
717	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
718	printf "\n see file \"$fileconnection_file\", line"
719	printf "\n$line"
720	locat=iofiles_file; exit
721	fi
722	multout[$iout]=true
723	string=${localout_pre[$iout]}
724	localout_pre[$iout]="${string%?}"
725	else
726	multout[$iout]=false
727	fi
728	fi
729	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
730	then
731	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
732	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
733	locat=connect; exit
734	fi
735	IFS="$IFSALT"
736	fi
737
738	done < $fileconnection_file
739
740
741
742	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
743	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
744	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
745	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
746	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
747	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
748
749
750
751	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
752	if [[ $run_coupled_model = true ]]
753	then
754
755	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
756	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
757
758	if (( $cores_ocean + $cores_atmos != $cores ))
759	then
760
761	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
762	printf "\n PEs (total) : $cores"
763	printf "\n PEs (atmosphere): $cores_atmos"
764	printf "\n PEs (ocean) : $cores_ocean"
765	locat=coupling; exit
766
767	fi
768
769	fi
770
771
772	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
773	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
774	# FOLDER
775	if [[ $running_in_batch_mode = true ]]
776	then
777
778	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
779	then
780	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
781	printf "\n Please check the output of the palmrun-call"
782	printf "\n that you did on your local host."
783	locat=SOURCES_FOR_RUN; exit
784	fi
785
786	else
787
788	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
789	# AUTOMATIC RESTART RUN
790	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
791	if [[ $restart_run = false ]]
792	then
793
794	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
795	# THE LOCAL HOST
796	if [[ ! -d $source_path ]]
797	then
798	printf "\n\n +++ source path \"$source_path\" on local host"
799	printf "\n \"$(hostname)\" does not exist"
800	locat=source_path; exit
801	fi
802
803	rm -rf ${base_directory}/${sources_for_run_catalog}
804	mkdir -p ${base_directory}/${sources_for_run_catalog}
805
806	if [[ "$source_list" = LM ]]
807	then
808
809	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
810	source_list=""
811	cd $source_path
812
813
814	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
815	if [[ ! -d ../.svn ]]
816	then
817	printf "\n\n +++ source directory"
818	printf "\n \"$source_path\" "
819	printf "\n is not under control of \"subversion\"."
820	printf "\n Please do not use palmrun-option \"-s LM\"\n"
821	fi
822
823
824	# LIST ALL MODIFIED SOURCE CODE FILES
825	Filenames=""
826	svn status > tmp_svnstatus
827	while read line
828	do
829	firstc=`echo $line \| cut -c1`
830	if [[ $firstc = M \|\| $firstc = "?" ]]
831	then
832	Name=`echo "$line" \| cut -c8-`
833	extension=`echo $Name \| cut -d. -f2`
834	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
835	then
836	Filenames="$Filenames "$Name
837	fi
838	fi
839	done < tmp_svnstatus
840	rm -rf tmp_svnstatus
841
842
843	# COPY FILES TO SOURCES_FOR_RUN_...
844	for filename in $Filenames
845	do
846	cp $filename ${base_directory}/${sources_for_run_catalog}
847	source_list=$source_list"$filename "
848	done
849
850	cd - > /dev/null
851
852
853	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
854	elif [[ "$source_list" != "" ]]
855	then
856
857	cd $source_path
858
859	for filename in $source_list
860	do
861
862	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
863	if [[ $(echo $filename \| grep -c "/") != 0 ]]
864	then
865	printf "\n +++ source code file: $filename"
866	printf "\n must not contain (\"/\") "
867	locat=source; exit
868	fi
869
870	if [[ ! -f $filename ]]
871	then
872	printf "\n +++ source code file: $filename"
873	printf "\n does not exist"
874	locat=source; exit
875	else
876	cp $filename ${base_directory}/${sources_for_run_catalog}
877	fi
878
879	done
880
881	cd - > /dev/null
882
883	fi
884
885	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
886	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
887	if [[ ! -f $makefile ]]
888	then
889	printf "\n +++ file \"$makefile\" does not exist"
890	locat=make; exit
891	else
892	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
893	fi
894
895
896	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
897	if [[ "$user_source_path" != "" ]]
898	then
899
900	# DOES THE DIRECTORY EXIST?
901	if [[ ! -d $user_source_path ]]
902	then
903
904	printf "\n\n *** INFORMATIVE: additional source code directory"
905	printf "\n \"$user_source_path\" "
906	printf "\n does not exist or is not a directory."
907	printf "\n No source code will be used from this directory!\n"
908	user_source_path=""
909	if [[ $silent == false ]]
910	then
911	sleep 2
912	fi
913
914	else
915
916	cd $user_source_path
917	found=false
918
919	Names=$(ls -1 *.f90 2>&1)
920	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
921	Names=$(ls -1 *.F90 2>&1)
922	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
923	Names=$(ls -1 *.F 2>&1)
924	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
925	Names=$(ls -1 *.f 2>&1)
926	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
927	Names=$(ls -1 *.c 2>&1)
928	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
929
930	cd - > /dev/null
931	cd ${base_directory}/${sources_for_run_catalog}
932
933	# COPY MAKEFILE IF EXISTING
934	if [[ -f $user_source_path/Makefile ]]
935	then
936	printf "\n\n *** user Makefile from directory"
937	printf "\n \"$user_source_path\" is used \n"
938	if [[ $silent == false ]]
939	then
940	sleep 1
941	fi
942	cp $user_source_path/Makefile .
943	fi
944
945	for filename in $AddFilenames
946	do
947	if [[ -f $filename ]]
948	then
949	printf "\n +++ source code file \"$filename\" found in additional"
950	printf "\n source code directory \"$user_source_path\" "
951	printf "\n but was also given with option \"-s\" which means that it should be taken"
952	printf "\n from directory \"$source_path\"."
953	locat=source; exit
954	fi
955
956	cp $user_source_path/$filename .
957	source_list="$source_list $filename"
958
959	# CHECK IF FILE IS CONTAINED IN MAKEFILE
960	if [[ $(grep -c $filename Makefile) = 0 ]]
961	then
962	printf "\n\n +++ user file \"$filename\" "
963	printf "\n is not listed in Makefile \n"
964	locat=source; exit
965	else
966
967	if [[ $found = false ]]
968	then
969	found=true
970	printf "\n\n *** following user file(s) added to the"
971	printf " files to be translated:\n "
972	fi
973	printf "$filename "
974	if [[ $silent == false ]]
975	then
976	sleep 0.5
977	fi
978
979	fi
980	done
981	[[ $found = true ]] && printf "\n"
982	cd - > /dev/null
983	fi
984	fi
985
986	# COPY CONFIGURATION FILES
987	cp $config_file ${base_directory}/${sources_for_run_catalog}
988	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
989
990	# COPY SHELLSCRIPTS
991	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
992	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
993
994	fi
995
996	fi
997
998
999	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1000	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1001	if [[ "$global_revision" = "" ]]
1002	then
1003	global_revision=`svnversion $source_path 2>/dev/null`
1004	global_revision="Rev: $global_revision"
1005	fi
1006
1007
1008	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1009	if [[ -n $cores ]]
1010	then
1011
1012	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1013	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1014	if [[ $tasks_per_node = 0 ]]
1015	then
1016	printf "\n"
1017	printf "\n +++ option \"-T\" (tasks per node) is missing"
1018	printf "\n set -T option or define tasks_per_node in the config file"
1019	locat=tasks_per_node; (( iec = 0 )); exit
1020	fi
1021
1022	if (( cores < tasks_per_node ))
1023	then
1024	printf "\n"
1025	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1026	printf "\n given values: -T $tasks_per_node -X $cores"
1027	locat=tasks_per_node; (( iec = 0 )); exit
1028	fi
1029
1030	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1031	(( mpi_tasks = cores / threads_per_task ))
1032	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1033	(( ii = cores / tasks_per_node ))
1034	(( remaining_cores = cores - ii * tasks_per_node ))
1035	if (( remaining_cores > 0 ))
1036	then
1037	printf "\n"
1038	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1039	printf "\n divisor of the total number of cores (option \"-X\")"
1040	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1041	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1042	(( nodes = nodes + 1 ))
1043	fi
1044
1045	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
1046	if [[ "$tasks_per_node" != "" ]]
1047	then
1048	TOPT="-T $tasks_per_node"
1049	fi
1050
1051	fi
1052
1053
1054	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1055	if [[ "$maximum_parallel_io_streams" = "" ]]
1056	then
1057	maximum_parallel_io_streams=$cores
1058	fi
1059
1060
1061	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1062	if [[ "$scp_port" != "" ]]
1063	then
1064	PORTOPT="-P $scp_port"
1065	SSH_PORTOPT="-p $scp_port"
1066	fi
1067
1068
1069	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1070	# CONFIG-FILE
1071	if [[ "$ssh_key" != "" ]]
1072	then
1073	ssh_key="-i $HOME/.ssh/$ssh_key"
1074	fi
1075
1076
1077	# SET QUEUE, IF NOT GIVEN
1078	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1079	then
1080
1081	if [[ $queue = none && "$defaultqueue" = "" ]]
1082	then
1083	printf "\n"
1084	printf "\n +++ no default queue given in configuration file and no queue"
1085	printf "\n given with option -q"
1086	locat=queue; exit
1087	fi
1088	if [[ $queue = none ]]
1089	then
1090	queue=$defaultqueue
1091	fi
1092
1093	fi
1094
1095
1096	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1097	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1098	(( i = 0 ))
1099	(( nr_of_input_files = 0 ))
1100	while (( i < iin ))
1101	do
1102	(( i = i + 1 ))
1103
1104	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1105	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1106	if [[ "${actionin_pre[$i]}" = di ]]
1107	then
1108	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1109	else
1110	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1111	fi
1112
1113
1114	# CHECK IF FILE EXISTS
1115	if ! ls $filename* 1>/dev/null 2>&1
1116	then
1117
1118	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1119	if [[ "${optin_pre[$i]}" != "yes" ]]
1120	then
1121	printf "\n\n +++ INPUT-file: "
1122	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1123	then
1124	printf "\n $filename"
1125	else
1126	printf "\n $filename.${extin_pre[$i]}"
1127	fi
1128	printf "\n does not exist\n"
1129	locat=input; exit
1130	else
1131	(( nr_of_input_files = nr_of_input_files + 1 ))
1132	localin[$nr_of_input_files]="${localin_pre[$i]}"
1133	optin[$nr_of_input_files]="${optin_pre[$i]}"
1134	actionin[$nr_of_input_files]="unavailable"
1135	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1136	endin[$nr_of_input_files]="${endin_pre[$i]}"
1137	extin[$nr_of_input_files]="${extin_pre[$i]}"
1138	fi
1139
1140	else
1141
1142	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1143	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1144	if [[ "${multin[$i]}" = true ]]
1145	then
1146	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1147	ls -1 -d ${filename} > filelist 2>/dev/null
1148	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1149	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1150
1151	endings=""
1152	while read line
1153	do
1154	# filename without path (i.e. after the last "/")
1155	basefilename=$(basename ${line})
1156
1157	# check if there is an extension and remove it
1158	ext=${basefilename##*.}
1159	if [[ "$ext" = "${extin_pre[$i]}" ]]
1160	then
1161	basefilename=${basefilename%.*}
1162	fi
1163
1164	# check for an existing cycle number and remove it
1165	cycle=${basefilename##*.}
1166	if [[ $cycle =~ ^-?[0-9]+$ ]]
1167	then
1168	basefilename=${basefilename%.*}
1169	fi
1170
1171	# remove the jobname from the beginning
1172	length_jobname=${#jobname}
1173	ending=${basefilename:${length_jobname}}
1174
1175	# remove the ending given in the .iofiles from the beginning
1176	endingstring="${endin_pre[$i]}"
1177	length_ending=${#endingstring}
1178	ending=${ending:${length_ending}}
1179
1180	if [[ "$ending" = "" ]]
1181	then
1182	# standard ending as given in the .iofiles
1183	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1184	then
1185	endings="$endings DEFAULT"
1186	fi
1187	else
1188	# ending must start with "_", otherwise its a different file
1189	if [[ "${ending:0:1}" = "_" ]]
1190	then
1191	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1192	then
1193	endings="$endings $ending"
1194	fi
1195	fi
1196	fi
1197
1198	done <filelist
1199
1200	rm filelist
1201
1202	else
1203
1204	# SINGLE NAME
1205	endings=DEFAULT
1206
1207	fi
1208
1209	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1210	for ending in $endings
1211	do
1212
1213	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1214	if [[ $ending = DEFAULT ]]
1215	then
1216	ending=""
1217	fi
1218
1219	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1220	(( nr_of_input_files = nr_of_input_files + 1 ))
1221	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1222	optin[$nr_of_input_files]="${optin_pre[$i]}"
1223	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1224	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1225	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1226	extin[$nr_of_input_files]="${extin_pre[$i]}"
1227
1228
1229	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1230	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1231	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1232	then
1233	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1234	else
1235	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1236	fi
1237
1238	# DETERMINE THE FILE'S CYCLE NUMBER
1239	(( maxcycle = 0 ))
1240	ls -1 -d $filename > filelist 2>/dev/null
1241	ls -1 -d $filename.* >> filelist 2>/dev/null
1242	while read line
1243	do
1244	# filename without path (i.e. after the last "/")
1245	basefilename=$(basename ${line})
1246
1247	# check if there is an extension
1248	extension=${basefilename##*.}
1249	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1250	then
1251	basefilename=${basefilename%.*}
1252	fi
1253
1254	# check for an existing cycle number
1255	cycle=${basefilename##*.}
1256	if [[ $cycle =~ ^-?[0-9]+$ ]]
1257	then
1258	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1259	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1260	(( icycle = $((10#$cycle)) ))
1261	else
1262	(( icycle = 0 ))
1263	fi
1264
1265	if (( icycle > maxcycle ))
1266	then
1267	(( maxcycle = icycle ))
1268
1269	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1270	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1271	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1272	then
1273	leading_zero=true
1274	else
1275	leading_zero=false
1276	fi
1277	fi
1278
1279	done <filelist
1280	rm filelist
1281
1282	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1283	if [[ $leading_zero = true ]]
1284	then
1285	cyclestring=`printf "%03d" $maxcycle`
1286	else
1287	cyclestring=$maxcycle
1288	fi
1289
1290	# APPEND CYCLE NUMBER TO FILENAME
1291	if (( maxcycle > 0 ))
1292	then
1293	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1294	then
1295	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1296	else
1297	filename=${filename}.$cyclestring
1298	fi
1299	else
1300	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1301	then
1302	filename=${filename}.${extin[$nr_of_input_files]}
1303	fi
1304	fi
1305
1306	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1307	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1308	absnamein[$nr_of_input_files]=$filename
1309	if (( maxcycle > 0 ))
1310	then
1311	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1312	then
1313	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1314	else
1315	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1316	fi
1317	else
1318	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1319	then
1320	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1321	else
1322	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1323	fi
1324	fi
1325
1326	done
1327
1328	fi
1329
1330	done
1331
1332
1333	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1334	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1335	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1336	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1337	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1338	# REMOTE HOST)
1339	(( i = 0 ))
1340	while (( i < iout ))
1341	do
1342	(( i = i + 1 ))
1343	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1344	then
1345	if [[ "${actionout_pre[$i]}" = tr ]]
1346	then
1347	actionout_pre[$i]=""
1348	elif [[ "${actionout_pre[$i]}" = trpe ]]
1349	then
1350	actionout_pre[$i]=pe
1351	elif [[ "${actionout_pre[$i]}" = tra ]]
1352	then
1353	actionout_pre[$i]=a
1354	fi
1355	(( maxcycle = 0 ))
1356	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1357	eval catalogname=${pathout_pre[$i]}
1358	if ! ls $filename* 1>/dev/null 2>&1
1359	then
1360
1361	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1362	if cat /dev/null > $filename
1363	then
1364	rm $filename
1365	else
1366
1367	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1368	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1369	if [[ ! -d $catalogname ]]
1370	then
1371	if mkdir -p $catalogname
1372	then
1373	printf "\n\n *** directory:"
1374	printf "\n $catalogname"
1375	printf "\n was created\n"
1376	else
1377	printf "\n\n +++ OUTPUT-file:"
1378	printf "\n $filename"
1379	printf "\n cannot be created, because directory does not exist"
1380	printf "\n and cannot be created either"
1381	printf "\n"
1382	locat=output ; exit
1383	fi 2>/dev/null
1384	else
1385	printf "\n\n +++ OUTPUT-file:"
1386	printf "\n $filename"
1387	printf "\n cannot be created, although directory exists"
1388	printf "\n"
1389	locat=output ; exit
1390	fi
1391	fi 2>/dev/null
1392
1393	fi
1394
1395	fi
1396	done
1397
1398
1399	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1400	if [[ $running_in_batch_mode = false ]]
1401	then
1402	run_id=$RANDOM
1403	job_id=${jobname}.$run_id
1404
1405	tempdir=$fast_io_catalog/$job_id
1406	fi
1407
1408
1409	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1410	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1411	then
1412
1413	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1414	if [[ $ibd = 0 ]]
1415	then
1416	printf "\n"
1417	printf "\n +++ no batch directives found in configuration file"
1418	locat=config_file_batch_directives; (( iec = 0 )); exit
1419	fi
1420
1421	# CHECK IF CPUTIME IS GIVEN FOR JOB
1422	done=false
1423	cputime=$cpumax
1424	while [[ $done = false ]]
1425	do
1426	if (( cputime == 0 ))
1427	then
1428	printf "\n +++ cpu-time is undefined"
1429	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1430	printf "\n >>> "
1431	read cputime 1>/dev/null 2>&1
1432	else
1433	done=true
1434	fi
1435	done
1436	cpumax=$cputime
1437
1438	# CHECK THE MEMORY DEMAND
1439	done=false
1440	while [[ $done = false ]]
1441	do
1442	if (( memory == 0 ))
1443	then
1444	printf "\n +++ memory demand is undefined"
1445	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1446	printf "\n >>> "
1447	read memory 1>/dev/null 2>&1
1448	else
1449	done=true
1450	fi
1451	done
1452
1453	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1454	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1455	then
1456	while [[ -z $remote_username ]]
1457	do
1458	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1459	printf "\n >>> Please type username:"
1460	printf "\n >>> "
1461	read remote_username
1462	done
1463	fi
1464
1465	else
1466
1467	if [[ $running_in_batch_mode = false ]]
1468	then
1469	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1470	cpumax=$cputime
1471	else
1472	cputime=$cpumax
1473	fi
1474
1475	fi
1476
1477
1478	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1479	(( cpu_hours = cputime / 3600 ))
1480	(( resttime = cputime - cpu_hours * 3600 ))
1481	(( cpu_minutes = resttime / 60 ))
1482	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1483	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1484
1485
1486	# OUTPUT OF THE PALMRUN-HEADER
1487	calltime=$(date)
1488	printf "\n"
1489	printf "#------------------------------------------------------------------------# \n"
1490	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1491	printf "\| \| \n"
1492	column1="called on:"; column2=$(hostname)
1493	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1494	if [[ $create_remote_batch_job = true ]]
1495	then
1496	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1497	else
1498	if [[ $running_on_remote = true ]]
1499	then
1500	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1501	else
1502	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1503	fi
1504	fi
1505	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1506
1507	column1="running in:"
1508	if [[ $running_in_batch_mode = true ]]
1509	then
1510	column2="batch job mode"
1511	else
1512	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1513	then
1514	column2="job creation mode"
1515	else
1516	column2="interactive run mode"
1517	fi
1518	fi
1519	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1520
1521	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1522	then
1523	if [[ "$project_account" != "" ]]
1524	then
1525	column1="project account number:"
1526	column2="$project_account"
1527	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1528	fi
1529	fi
1530
1531	if [[ -n $cores ]]
1532	then
1533	if [[ $run_coupled_model = false ]]
1534	then
1535	column1="number of cores:"; column2=$cores
1536	else
1537	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1538	fi
1539	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1540	fi
1541	if [[ -n $tasks_per_node ]]
1542	then
1543	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1545	if (( remaining_cores > 0 ))
1546	then
1547	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1549	fi
1550	fi
1551	if [[ $maximum_parallel_io_streams != $cores ]]
1552	then
1553	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1555	fi
1556	if [[ $use_openmp = true ]]
1557	then
1558	column1="threads per task:"; column2="$threads_per_task"
1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1560	fi
1561	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1562	then
1563	column1="memory demand / PE":; column2="$memory MB"
1564	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1565	column1="job cpu time (h:m:s):"; column2="$timestring"
1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1567	fi
1568	printf "\| \| \n"
1569	if [[ "$source_list" != "" ]]
1570	then
1571	if [[ "$make_options" != "" ]]
1572	then
1573	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1575	line=$(echo "$make_options" \| cut -c46-)
1576	while [[ "$line" != "" ]]
1577	do
1578	column1=""
1579	column2=$(echo "$line" \| cut -c-45)
1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1581	line=$(echo "$line" \| cut -c46-)
1582	done
1583	fi
1584	fi
1585
1586	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1588	line=$(echo "$cpp_options" \| cut -c46-)
1589	while [[ "$line" != "" ]]
1590	do
1591	column1=""
1592	column2=$(echo "$line" \| cut -c-45)
1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1594	line=$(echo "$line" \| cut -c46-)
1595	done
1596
1597	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1598	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1599	line=$(echo "$compiler_options" \| cut -c46-)
1600	while [[ "$line" != "" ]]
1601	do
1602	column1=""
1603	column2=$(echo "$line" \| cut -c-45)
1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1605	line=$(echo "$line" \| cut -c46-)
1606	done
1607
1608	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1610	line=$(echo "$linker_options" \| cut -c46-)
1611	while [[ "$line" != "" ]]
1612	do
1613	column1=""
1614	column2=$(echo "$line" \| cut -c-45)
1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1616	line=$(echo "$line" \| cut -c46-)
1617	done
1618
1619	if [[ "$login_init_cmd" != "" ]]
1620	then
1621	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1622	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1623	line=$(echo "$login_init_cmd" \| cut -c46-)
1624	while [[ "$line" != "" ]]
1625	do
1626	column1=""
1627	column2=$(echo "$line" \| cut -c-45)
1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1629	line=$(echo "$line" \| cut -c46-)
1630	done
1631	fi
1632
1633	if [[ "$module_commands" != "" ]]
1634	then
1635	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1637	line=$(echo "$module_commands" \| cut -c46-)
1638	while [[ "$line" != "" ]]
1639	do
1640	column1=""
1641	column2=$(echo "$line" \| cut -c-45)
1642	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1643	line=$(echo "$line" \| cut -c46-)
1644	done
1645	fi
1646	printf "\| \| \n"
1647	column1="base name of files:"; column2=$jobname
1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1649	column1="activation string list:"; column2=$(echo $activation_string_list)
1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1651
1652	if [[ "$ocean_file_appendix" = true ]]
1653	then
1654	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1655	fi
1656
1657	if [[ "$source_list" != "" ]]
1658	then
1659	printf "\| \| \n"
1660	printf "\| Files to be compiled: \| \n"
1661	line=$source_list
1662	while [[ "$line" != "" ]]
1663	do
1664	linestart=$(echo $line \| cut -c-70)
1665	printf "\| %-70s \| \n" "$linestart"
1666	line=$(echo "$line" \| cut -c71-)
1667	done
1668	fi
1669	printf "#------------------------------------------------------------------------#"
1670
1671
1672
1673	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1674	if [[ $do_trace = true ]]
1675	then
1676	(( i = 0 ))
1677	while (( i < nr_of_input_files ))
1678	do
1679	(( i = i + 1 ))
1680	if (( i == 1 ))
1681	then
1682	printf "\n\n >>> INPUT-file assignments:\n"
1683	fi
1684	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1685	done
1686	(( i = 0 ))
1687	while (( i < iout ))
1688	do
1689	(( i = i + 1 ))
1690	if (( i == 1 ))
1691	then
1692	printf "\n\n >>> OUTPUT-file assignments:\n"
1693	fi
1694	printf "\n ${localout[$i]} : ${pathout[$i]}"
1695	done
1696	(( i = 0 ))
1697	while (( i < iic ))
1698	do
1699	(( i = i + 1 ))
1700	if (( i == 1 ))
1701	then
1702	printf "\n\n >>> INPUT-commands:\n"
1703	fi
1704	printf "\n ${in_command[$i]}"
1705	done
1706	(( i = 0 ))
1707	while (( i < ioc ))
1708	do
1709	(( i = i + 1 ))
1710	if (( i == 1 ))
1711	then
1712	printf "\n\n >>> OUTPUT-commands:\n"
1713	fi
1714	printf "\n ${out_command[$i]}"
1715	done
1716	fi
1717
1718	# QUERY FOR CONTINUE
1719	if [[ $silent = false && $running_in_batch_mode = false ]]
1720	then
1721	antwort=dummy
1722	printf "\n\n"
1723	printf " >>> everything o.k. (y/n) ? "
1724	while read antwort
1725	do
1726	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1727	then
1728	printf " >>> everything o.k. (y/n) ? "
1729	else
1730	break
1731	fi
1732	done
1733	if [[ $antwort = n \|\| $antwort = N ]]
1734	then
1735	locat=user_abort; (( iec = 0 )); exit
1736	fi
1737	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1738	then
1739	printf "\n *** batch-job will be created and submitted"
1740	else
1741	printf "\n *** PALMRUN will now continue to execute on this machine"
1742	fi
1743	fi
1744
1745
1746
1747	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1748	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1749	then
1750
1751	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1752	then
1753	printf "\n\n *** creating executable and other sources for the remote host\n"
1754	else
1755	printf "\n\n *** creating executable and other sources for the local host\n"
1756	fi
1757
1758	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1759	# IT SHALL BE CREATED
1760	ask_for_make_depository=false
1761	if [[ $create_remote_batch_job = true ]]
1762	then
1763
1764	line=`grep %base_directory $config_file`
1765	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1766	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1767
1768	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1769	then
1770	printf "\n\n +++ make depository \"${make_depository}\""
1771	printf "\n on remote host not found!"
1772	ask_for_make_depository=true
1773	fi
1774	rm ${host_configuration}_last_make_protokoll
1775
1776	else
1777
1778	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1779	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1780	if [[ ! -d ${make_depository} ]]
1781	then
1782	printf "\n\n +++ make depository \"${make_depository}\""
1783	printf "\n on local host not found!"
1784	ask_for_make_depository=true
1785	fi
1786
1787	fi
1788
1789	if [[ $ask_for_make_depository = true ]]
1790	then
1791
1792	antwort=dummy
1793	printf "\n\n"
1794	printf " >>> Create a new one (y/n) ? "
1795	while read antwort
1796	do
1797	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1798	then
1799	printf " >>> Create a new one (y/n) ? "
1800	else
1801	break
1802	fi
1803	done
1804	if [[ $antwort = n \|\| $antwort = N ]]
1805	then
1806	locat=user_abort; (( iec = 0 )); exit
1807	fi
1808
1809	if [[ $do_trace = true ]]
1810	then
1811	palmbuild -h $host_configuration
1812	else
1813	palmbuild -v -h $host_configuration
1814	fi
1815
1816	if [[ $? != 0 ]]
1817	then
1818
1819	# ABORT IN CASE OF COMPILATION PROBLEMS
1820	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1821	locat=make_depository
1822	exit
1823	else
1824	echo " *** now continue with creating executable and other sources"
1825	fi
1826
1827	fi
1828
1829	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1830	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1831
1832	if [[ $? != 0 ]]
1833	then
1834
1835	# ABORT IN CASE OF COMPILATION PROBLEMS
1836	printf "\n +++ error while creating executable and/or other sources"
1837	locat=execution
1838	rm -rf ${base_directory}/${sources_for_run_catalog}
1839	exit
1840
1841	else
1842
1843	printf " *** executable and other sources created\n"
1844	rm -rf ${base_directory}/${sources_for_run_catalog}
1845
1846	fi
1847
1848	fi
1849
1850
1851	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1852	# WILL BE COPIED TO THE REMOTE HOST
1853	if [[ $create_remote_batch_job = true ]]
1854	then
1855	(( i = 0 ))
1856	while (( i < nr_of_input_files ))
1857	do
1858	(( i = i + 1 ))
1859	if [[ "${actionin[$i]}" = tr ]]
1860	then
1861	eval inputfile=${pathin[$i]}/${frelin[$i]}
1862	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1863	fi
1864	done
1865	if (( i > 0 ))
1866	then
1867	printf " *** input files have been copied to the remote host\n"
1868	fi
1869	fi
1870
1871
1872	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1873	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1874	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1875	then
1876
1877	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1878	if [[ $running_in_batch_mode = false ]]
1879	then
1880	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1881	# FOLDER
1882	mkdir -p $tempdir
1883	chmod go+rx $tempdir
1884	cd $tempdir
1885	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1886	printf "\n *** changed to temporary directory: $tempdir"
1887
1888	else
1889
1890	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1891	printf "\n *** running in temporary directory: $tempdir"
1892
1893	fi
1894
1895
1896	# PROVIDE THE INPUT FILES
1897	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1898	optional_files_missing=false
1899	(( i = 0 ))
1900	while (( i < nr_of_input_files ))
1901	do
1902	(( i = i + 1 ))
1903	if (( i == 1 ))
1904	then
1905	printf "\n\n *** providing INPUT-files:\n$dashes"
1906	fi
1907
1908
1909	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1910	if [[ "${actionin[$i]}" = unavailable ]]
1911	then
1912	optional_files_missing=true
1913	continue
1914	fi
1915
1916	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1917	files_for_cores=false; filetype=file
1918	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1919	then
1920	files_for_cores=true; filetype=files
1921	actionin[$i]=""
1922	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1923	then
1924	actionin[$i]=""
1925	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1926	then
1927	files_for_cores=true; filetype=files
1928	actionin[$i]="ln"
1929	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1930	then
1931	actionin[$i]="ln"
1932	fi
1933
1934	if [[ $files_for_cores = true ]]
1935	then
1936	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1937	else
1938	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1939	fi
1940
1941	# INPUT-FILES TO BE LINKED
1942	if [[ "${actionin[$i]}" = ln ]]
1943	then
1944
1945	printf "\n $filetype will be linked"
1946	if [[ $files_for_cores = false ]]
1947	then
1948	if [[ -f "${absnamein[$i]}" ]]
1949	then
1950	ln ${absnamein[$i]} ${localin[$i]}
1951	got_tmp[$i]=true
1952	fi
1953	else
1954	if [[ -d "${absnamein[$i]}" ]]
1955	then
1956	mkdir -p ${localin[$i]}
1957	cd ${absnamein[$i]}
1958	for file in $(ls *)
1959	do
1960	ln $file $tempdir/${localin[$i]}
1961	done >\|/dev/null 2>&1
1962	cd $tempdir
1963	fi
1964
1965	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1966	if [[ ! -f "${localin[$i]}/_000000" ]]
1967	then
1968	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1969	cp -r ${absnamein[$i]}/* ${localin[$i]}
1970	fi
1971
1972	got_tmp[$i]=true
1973	fi
1974	fi
1975
1976	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1977	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1978	then
1979
1980	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1981	then
1982
1983	# FILE COPIES ARE PROVIDED FOR ALL CORES
1984	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1985	printf "\n file will be provided for $cores processors"
1986	mkdir -p ${localin[$i]}
1987	ival=$cores
1988	(( ii = 0 ))
1989	while (( ii <= ival-1 ))
1990	do
1991	if (( ii < 10 ))
1992	then
1993	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1994	elif (( ii < 100 ))
1995	then
1996	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1997	elif (( ii < 1000 ))
1998	then
1999	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2000	else
2001	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2002	fi
2003	(( ii = ii + 1 ))
2004	done
2005
2006	else
2007
2008	if [[ $files_for_cores = true ]]
2009	then
2010
2011	# PROVIDE FILES FOR EACH CORE
2012	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2013	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2014	printf "\n providing $cores files for the respective cores"
2015	mkdir -p ${localin[$i]}
2016	if [[ $link_local_input = true ]]
2017	then
2018	printf " files will be linked\n"
2019	cd ${absnamein[$i]}
2020	for file in $(ls *)
2021	do
2022	ln -f $file ${localin[$i]}
2023	done
2024	cd $tempdir
2025	fi
2026
2027	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2028	if [[ ! -f "${localin[$i]}/_000000" ]]
2029	then
2030	if [[ $link_local_input = true ]]
2031	then
2032	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2033	fi
2034	cp -r ${absnamein[$i]}/* ${localin[$i]}
2035	fi
2036
2037	else
2038
2039	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2040	if [[ $link_local_input = true ]]
2041	then
2042	printf " file will be linked\n"
2043	ln -f ${absnamein[$i]} ${localin[$i]}
2044	fi
2045	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2046	if [[ ! -f "${localin[$i]}" ]]
2047	then
2048	if [[ $link_local_input = true ]]
2049	then
2050	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2051	fi
2052	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2053	then
2054	mv ${absnamein[$i]} ${localin[$i]}
2055	else
2056	cp ${absnamein[$i]} ${localin[$i]}
2057	fi
2058	fi
2059	fi
2060	fi
2061	fi
2062
2063	done
2064	if (( i != 0 ))
2065	then
2066	if [[ $optional_files_missing = true ]]
2067	then
2068	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2069	fi
2070	printf "\n$dashes\n *** all INPUT-files provided \n"
2071	fi
2072
2073
2074	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2075	(( i = 0 ))
2076	while (( i < iic ))
2077	do
2078	(( i = i + 1 ))
2079	if (( i == 1 ))
2080	then
2081	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2082	fi
2083	printf "\n >>> ${in_command[$i]}"
2084	eval ${in_command[$i]}
2085	if (( i == iic ))
2086	then
2087	printf "\n$dashes\n"
2088	fi
2089	done
2090
2091
2092	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2093	# (FILE ENVPAR WILL BE READ BY PALM)
2094	cat > ENVPAR << EOF
2095	&envpar run_identifier = '$jobname', host = '$host_configuration',
2096	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2097	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2098	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2099	maximum_cpu_time_allowed = ${cpumax}.,
2100	revision = '$global_revision',
2101	batch_job = .${running_in_batch_mode}. /
2102
2103	EOF
2104
2105
2106	# STARTING THE EXECUTABLE
2107	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2108	PATH=$PATH:$tempdir
2109
2110
2111	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2112	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2113	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2114	eval line=\"$line\"
2115	execute_command="$line"
2116
2117
2118	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2119	if [[ "$execute_command_for_combine" = "" ]]
2120	then
2121	eval line2=\"$line2\"
2122	execute_command_for_combine="$line2"
2123	fi
2124
2125
2126
2127	# PROVIDE A HOSTFILE, IF REQUIRED
2128	if [[ "$hostfile" != "" ]]
2129	then
2130
2131	if [[ $hostfile = auto ]]
2132	then
2133	# CREATE A NEW HOSTFILE
2134	(( ii = 1 ))
2135	while (( ii <= cores / threads_per_task ))
2136	do
2137	echo $(hostname) >> hostfile
2138	(( ii = ii + 1 ))
2139	done
2140	if (( cores / threads_per_task == 0 ))
2141	then
2142	echo $(hostname) >> hostfile
2143	fi
2144
2145	else
2146	cp $hostfile hostfile
2147	fi
2148	eval line=\"`head -n $ii hostfile`\"
2149	printf "\n *** running on: $line"
2150	fi
2151
2152
2153
2154	# SET THE NUMBER OF OPENMP-THREADS
2155	if [[ $use_openmp = true ]]
2156	then
2157	export OMP_NUM_THREADS=$threads_per_task
2158	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2159	else
2160	export OMP_NUM_THREADS=1
2161	fi
2162
2163
2164	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2165	if [[ $run_coupled_model = false ]]
2166	then
2167	if [[ "$ocean_file_appendix" = true ]]
2168	then
2169	echo "precursor_ocean" > coupling_steering
2170	else
2171	echo "precursor_atmos" > coupling_steering
2172	fi
2173	else
2174	(( iia = $cores_atmos / $threads_per_task ))
2175	(( iio = $cores_ocean / $threads_per_task ))
2176	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2177	printf "\n\n"
2178	echo "coupled_run $iia $iio" > coupling_steering
2179	fi
2180
2181	printf "\n *** execute command:"
2182	printf "\n \"$execute_command\" \n\n"
2183
2184	$execute_command < coupling_steering
2185
2186	if [[ $? != 0 ]]
2187	then
2188
2189	# ABORT IN CASE OF RUNTIME ERRORS
2190	printf "\n +++ runtime error occured"
2191	locat=execution
2192	exit
2193
2194	else
2195
2196	printf "\n$dashes\n *** execution finished \n"
2197
2198	fi
2199
2200
2201	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2202	# BY EACH CORE INTO ONE FILE
2203	if [[ ! -f combine_plot_fields.x ]]
2204	then
2205
2206	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2207	printf "\n 2d- and/or 3d-data may be incomplete!"
2208	printf "\n Your previous palmbuild may have failed. Please check.\n"
2209
2210	elif [[ "$combine_plot_fields" == true ]]
2211	then
2212
2213	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2214	$execute_command_for_combine
2215
2216	else
2217
2218	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2219	# DATA OUTPUT
2220	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2221	fi
2222
2223
2224
2225	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2226	(( i = 0 ))
2227	while (( i < ioc ))
2228	do
2229	(( i = i + 1 ))
2230	if (( i == 1 ))
2231	then
2232	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2233	fi
2234
2235	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2236	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2237
2238	printf "\n >>> ${out_command[$i]}"
2239	eval ${out_command[$i]}
2240	if (( i == ioc ))
2241	then
2242	printf "\n$dashes\n"
2243	fi
2244	done
2245
2246
2247	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2248	# WILDCARDS
2249	(( i = 0 ))
2250	(( nr_of_output_files = 0 ))
2251
2252	while (( i < iout ))
2253	do
2254
2255	(( i = i + 1 ))
2256
2257	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2258	# CREATE A LIST FOR THE DETECTED ENDINGS
2259	if [[ "${multout[$i]}" = true ]]
2260	then
2261	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2262	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2263	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2264
2265	endings="DEFAULT"
2266	while read line
2267	do
2268	# remove the local name from the beginning
2269	localnamestring="${localout_pre[$i]}"
2270	length_localname=${#localnamestring}
2271	ending=${line:${length_localname}}
2272
2273	if [[ "$ending" != "" ]]
2274	then
2275	endings="$endings $ending"
2276	fi
2277
2278	done <filelist
2279
2280	rm filelist
2281
2282	else
2283
2284	# SINGLE NAME
2285	endings=DEFAULT
2286
2287	fi
2288
2289	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2290	for ending in $endings
2291	do
2292
2293	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2294	if [[ $ending = DEFAULT ]]
2295	then
2296	ending=""
2297	fi
2298
2299	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2300	(( nr_of_output_files = nr_of_output_files + 1 ))
2301	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2302	transout[$nr_of_output_files]="${transout_pre[$i]}"
2303	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2304	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2305	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2306	extout[$nr_of_output_files]="${extout_pre[$i]}"
2307	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2308
2309	done
2310
2311	done
2312
2313
2314
2315
2316	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2317	(( i = 0 ))
2318	while (( i < nr_of_output_files ))
2319	do
2320	(( i = i + 1 ))
2321	if (( i == 1 ))
2322	then
2323	printf "\n\n *** saving OUTPUT-files:"
2324
2325	# GET RUN NUMBER ASSIGNED BY PALM
2326	if [[ -f RUN_NUMBER ]]
2327	then
2328	read run_number < RUN_NUMBER
2329	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2330	usecycle_option="-U $run_number"
2331	else
2332	run_number=0
2333	usecycle_option=""
2334	fi
2335	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2336	then
2337	printf "\n *** in case of SCP transfers to local host"
2338	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2339	fi
2340	printf "\n$dashes"
2341	fi
2342
2343	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2344	then
2345
2346	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2347
2348	# DETERMINE THE CYCLE NUMBER
2349	ls -1 -d $filename > filelist 2>/dev/null
2350	ls -1 -d $filename.* >> filelist 2>/dev/null
2351	while read line
2352	do
2353
2354	# filename without path (i.e. after the last "/")
2355	basefilename=$(basename ${line})
2356
2357	# check if there is an extension
2358	extension=${basefilename##*.}
2359	if [[ "$extension" = "${extout[$i]}" ]]
2360	then
2361	basefilename=${basefilename%.*}
2362	fi
2363
2364	# check for an existing cycle number
2365	cycle=${basefilename##*.}
2366	if [[ $cycle =~ ^-?[0-9]+$ ]]
2367	then
2368	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2369	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2370	(( icycle = $((10#$cycle)) + 1 ))
2371	else
2372	(( icycle = 1 ))
2373	fi
2374
2375	if (( icycle > maxcycle ))
2376	then
2377	(( maxcycle = icycle ))
2378	fi
2379
2380	done <filelist
2381	rm filelist
2382
2383
2384	# SET THE CYCLE NUMBER
2385	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2386	if [[ "${actionout[$i]}" = a ]]
2387	then
2388	(( maxcycle = maxcycle - 1 ))
2389	fi
2390
2391	(( cycnum[$i] = maxcycle ))
2392	pathout[$i]=$filename
2393
2394
2395	# ADD CYCLE NUMBER TO FILENAME
2396	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2397	if [[ "${actionout[$i]}" != "a" ]]
2398	then
2399	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2400	# WITH AN EXISTING CYCLE NUMBER
2401	if (( run_number >= cycnum[$i] ))
2402	then
2403	(( cycnum[$i] = run_number ))
2404	else
2405	if (( run_number > 0 ))
2406	then
2407	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2408	fi
2409	fi
2410	fi
2411	if (( cycnum[$i] > 0 ))
2412	then
2413	cyclestring=`printf "%03d" ${cycnum[$i]}`
2414	pathout[$i]=${pathout[$i]}.$cyclestring
2415	fi
2416	fi
2417
2418	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2419	files_for_cores=false; filetype=file
2420	link_local_output=false
2421	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2422	then
2423	files_for_cores=true; filetype=directory
2424	actionout[$i]=""
2425	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2426	then
2427	actionout[$i]=""
2428	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2429	then
2430	files_for_cores=true; filetype=directory
2431	link_local_output=true
2432	actionout[$i]=""
2433	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2434	then
2435	link_local_output
2436	actionout[$i]=""
2437	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2438	then
2439	files_for_cores=true; filetype=directory
2440	actionout[$i]="tr"
2441	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2442	then
2443	actionout[$i]="tr"
2444	fi
2445
2446	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2447	then
2448	if [[ ${warnout[$i]} = true ]]
2449	then
2450	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2451	fi
2452	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2453	then
2454	if [[ ${warnout[$i]} = true ]]
2455	then
2456	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2457	fi
2458	else
2459
2460
2461	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2462	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2463	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2464	then
2465	if [[ $running_on_remote = true ]]
2466	then
2467
2468	# SET OPTIONS FOR TRANSFER
2469	if [[ "${actionout[$i]}" = tr ]]
2470	then
2471	if [[ $files_for_cores = false ]]
2472	then
2473	catalog_option=""
2474	catalog_string=""
2475	else
2476	catalog_option="-c"
2477	catalog_string="/"
2478	fi
2479	append_option=""
2480	append_string=""
2481	else
2482	append_option="-A"
2483	append_string="append"
2484	fi
2485
2486	transfer_failed=false
2487	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2488	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2489
2490	# TRANSFER VIA SCP
2491	if [[ "$remote_loginnode" != "" ]]
2492	then
2493	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
2494	else
2495	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]}
2496	fi
2497	[[ $? != 0 ]] && transfer_failed=true
2498
2499
2500	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2501	if [[ $transfer_failed = true ]]
2502	then
2503	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2504	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2505
2506	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2507	eval local_catalog=${pathout[$i]}
2508	if [[ ! -d $local_catalog ]]
2509	then
2510	printf " *** local directory does not exist. Trying to create:\n"
2511	printf " $local_catalog \n"
2512	mkdir -p $local_catalog
2513	fi
2514	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2515	transfer_problems=true
2516	fi
2517
2518	else
2519
2520	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2521	# BE COPIED OR APPENDED ON THIS MACHINE
2522	if [[ "${actionout[$i]}" = tr ]]
2523	then
2524	actionout[$i]=""
2525	else
2526	actionout[$i]="a"
2527	fi
2528	fi
2529	fi
2530
2531
2532	# APPEND ON THIS MACHINE
2533	if [[ "${actionout[$i]}" = "a" ]]
2534	then
2535	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2536	then
2537	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2538	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2539	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2540	else
2541	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2542	printf "\n ${pathout[$i]}\n"
2543	cat ${localout[$i]} >> ${pathout[$i]}
2544	fi
2545	fi
2546
2547	# COPY ON THIS MACHINE
2548	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2549	# ON DIFFERENT FILE-SYSTEMS
2550	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2551	then
2552
2553	# COPY IN CASE OF RUNS ON SINGLE CORES
2554	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2555	then
2556	printf "\n >>> OUTPUT: ${localout[$i]} to"
2557	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2558	if [[ $link_local_output = true ]]
2559	then
2560	printf " file will be linked\n"
2561	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2562	fi
2563	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2564	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2565	then
2566	if [[ $link_local_output = true ]]
2567	then
2568	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2569	fi
2570	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2571	else
2572	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2573	fi
2574	else
2575	printf "\n >>> OUTPUT: ${localout[$i]} to"
2576	printf "\n ${pathout[$i]}\n"
2577	if [[ $link_local_output = true ]]
2578	then
2579	printf " file will be linked\n"
2580	ln -f ${localout[$i]} ${pathout[$i]}
2581	fi
2582	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2583	if [[ ! -f "${pathout[$i]}" ]]
2584	then
2585	if [[ $link_local_output = true ]]
2586	then
2587	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2588	fi
2589	cp ${localout[$i]} ${pathout[$i]}
2590	else
2591	printf "+++ no copy because file ${pathout[$i]} exists\n"
2592	fi
2593	fi
2594
2595	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2596	then
2597
2598	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2599	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2600	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2601	printf "\n ${pathout[$i]}\n"
2602	if [[ $link_local_output = true ]]
2603	then
2604	printf " files will be linked\n"
2605	mkdir -p ${pathout[$i]}
2606	cd ${localout[$i]}
2607	for file in $(ls *)
2608	do
2609	ln -f $file ${pathout[$i]}
2610	done >\|/dev/null 2>&1
2611	cd $tempdir
2612	fi
2613
2614	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2615	if [[ ! -f "${pathout[$i]}/_000000" ]]
2616	then
2617	if [[ $link_local_output = true ]]
2618	then
2619	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2620	fi
2621	cp -r ${localout[$i]}/* ${pathout[$i]}
2622	fi
2623
2624	fi
2625	fi
2626	done
2627
2628	if (( i != 0 ))
2629	then
2630	if [[ $transfer_problems = true ]]
2631	then
2632	printf "\n$dashes\n *** OUTPUT-files saved"
2633	printf "\n +++ WARNING: some data transfers failed! \n"
2634	else
2635	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2636	fi
2637	fi
2638
2639
2640	# IF REQUIRED, START A RESTART-JOB
2641	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2642	if [[ -f CONTINUE_RUN ]]
2643	then
2644
2645	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2646	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2647	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2648	# -b START A BATCH JOB
2649	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2650	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2651	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2652
2653	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2654	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2655	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2656	then
2657	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2658	fi
2659
2660	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2661	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2662	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2663	then
2664	prc=`echo $prc \| sed 's/#/r/g'`
2665	fi
2666
2667
2668	# START THE RESTART-JOB
2669	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2670	echo " $prc"
2671	printf "\n$dashes\n"
2672	if [[ $running_on_remote = true ]]
2673	then
2674
2675	echo "*** ssh will be used to initiate restart-runs!"
2676	echo " return_address=\"$return_address\" "
2677	echo " return_username=\"$local_username\" "
2678
2679	if [[ "$remote_loginnode" != "" ]]
2680	then
2681	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
2682	else
2683	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2684	fi
2685
2686	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2687	sleep 30
2688
2689	else
2690
2691	# START THE RESTART JOB ON THE LOCAL HOST
2692	eval $prc # THE ' MUST BE EVALUATED
2693	cd - > /dev/null
2694
2695	fi
2696	printf "\n$dashes\n *** restart-run initiated \n"
2697
2698
2699	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2700	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2701	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2702	# MAY BE VERY HUGE)
2703	(( i = 0 ))
2704	while (( i < nr_of_input_files ))
2705	do
2706	(( i = i + 1 ))
2707	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2708	then
2709	rm -r ${absnamein[$i]}
2710	fi
2711	done
2712
2713	fi
2714
2715
2716	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2717	cd $HOME
2718	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2719
2720
2721	else
2722
2723
2724	# PREPARING ACTIONS,
2725	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2726
2727	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2728	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2729	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2730	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2731	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2732	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2733	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2734	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2735	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2736	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2737	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2738	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2739	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2740	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2741	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2742	if [[ $create_remote_batch_job = true ]]
2743	then
2744	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2745	if [[ $do_trace = true ]]
2746	then
2747	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2748	fi
2749	elif [[ $create_batch_job = true ]]
2750	then
2751	palmrun_com=${palmrun_com}" -j"
2752	if [[ $do_trace = true ]]
2753	then
2754	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2755	fi
2756	fi
2757
2758
2759	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2760	# REMOTE HOST
2761	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2762	job_protocol_file=$job_protocol_file_local
2763	if [[ $create_remote_batch_job = true ]]
2764	then
2765	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2766	job_protocol_file=$job_protocol_file_remote
2767	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2768	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2769	fi
2770
2771
2772	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2773	jobfile=jobfile.$run_id
2774
2775
2776	# FIRST CREATE THE BATCH DIRECTIVES
2777	(( i = 0 ))
2778	while (( i < ibd ))
2779	do
2780	(( i = i + 1 ))
2781	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2782	eval line=\"$line\"
2783	echo "$line" >> $jobfile
2784	done
2785	echo " " >> $jobfile
2786
2787
2788	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2789	# PROTOCOL
2790	if [[ $create_remote_batch_job = true ]]
2791	then
2792	echo "set +vx" >> $jobfile
2793	echo "trap '" >> $jobfile
2794	echo "set +vx" >> $jobfile
2795	echo "cd ${remote_jobcatalog}" >> $jobfile
2796	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2797
2798	# ADD THE BATCH DIRECTIVES
2799	(( i = 0 ))
2800	while (( i < ibdt ))
2801	do
2802	(( i = i + 1 ))
2803	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2804	eval line=\"$line\"
2805	echo "$line" >> $jobfile
2806	done
2807	echo " " >> $jobfile
2808
2809	echo "set -x" >> $jobfile
2810	echo "${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
2811	echo "%%END%%" >> $jobfile
2812	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2813	echo "$submit_command $scpjob_file" >> $jobfile
2814	echo "rm $scpjob_file" >> $jobfile
2815	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2816	echo "set -x" >> $jobfile
2817	echo " ' exit" >> $jobfile
2818	fi
2819
2820
2821	# ACTIVATE ERROR-TRACEBACK
2822	if [[ $do_trace = true ]]
2823	then
2824	echo "set -x" >> $jobfile
2825	else
2826	echo "set +vx" >> $jobfile
2827	fi
2828
2829
2830	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2831	if [[ "$login_init_cmd" != "" ]]
2832	then
2833	echo "$login_init_cmd" >> $jobfile
2834	fi
2835	if [[ "$module_commands" != "" ]]
2836	then
2837	echo "$module_commands" >> $jobfile
2838	fi
2839
2840
2841	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2842	if [[ $create_remote_batch_job = true ]]
2843	then
2844	echo "mkdir $tempdir" >> $jobfile
2845	echo "chmod go+rx $tempdir" >> $jobfile
2846	else
2847	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2848	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2849	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2850	mkdir $tempdir
2851	chmod go+rx $tempdir
2852	fi
2853	echo "cd $tempdir" >> $jobfile
2854	echo "export tempdir=$tempdir" >> $jobfile
2855	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2856	echo "export PATH=.:\$PATH" >> $jobfile
2857	echo "export execute_palmrun=true" >> $jobfile
2858
2859
2860	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2861	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2862	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2863	echo "LOCAL_PWD=$working_directory" >> $jobfile
2864	echo "export LOCAL_PWD" >> $jobfile
2865
2866
2867	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2868	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2869	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2870
2871
2872	# CALL PALMRUN WITHIN THE JOB
2873	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2874	echo "set -x" >> $jobfile
2875	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2876
2877
2878	# TRANSFER JOBFILE TO THE TARGET HOST
2879	if [[ $create_jobfile_only = false ]]
2880	then
2881
2882	if [[ $create_remote_batch_job = true ]]
2883	then
2884
2885	echo " "
2886	echo " *** transfer of job to remote host via scp"
2887	if [[ $do_trace = true ]]
2888	then
2889	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2890	fi
2891	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2892
2893	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2894	if [[ $do_trace = true ]]
2895	then
2896	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"
2897	fi
2898	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
2899
2900	elif [[ $create_batch_job = true ]]
2901	then
2902
2903	eval local_jobcatalog=$local_jobcatalog
2904	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2905	cd $local_jobcatalog
2906	echo " "
2907	echo " *** submit the job"
2908	if [[ $do_trace = true ]]
2909	then
2910	echo "$submit_command ${host_configuration}_${job_id}"
2911	fi
2912	$submit_command ${host_configuration}_${job_id}
2913	rm ${host_configuration}_${job_id}
2914	cd - > /dev/null
2915
2916	fi
2917
2918	rm -rf $jobfile
2919
2920	else
2921
2922	printf "\n *** jobfile created under name \"$jobfile\" "
2923	printf "\n no batch-job has been sent!"
2924
2925	fi
2926
2927	fi # END OF REMOTE-PART

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