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source: palm/trunk/SCRIPTS/palmrun @ 2669

Last change on this file since 2669 was 2669, checked in by raasch, 7 years ago
file attributes and activation strings in .palm.iofiles revised, file extensions for nesting, masked output, wind turbine data, etc. changed
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 95.9 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
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 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 2669 2017-12-06 16:03:27Z raasch $
29	# file attributes in .palm.iofiles restructured, "loc" attribute completely
30	# removed,
31	# wildcard (*) allowed in .palm.iofiles as file activation string for output
32	# files,
33	# informative messages in case of missing optional input files shortened
34	# bugfix: variable cycle explicitly interpreted with 10 as the number base
35	#
36	# 2638 2017-11-23 12:44:23Z raasch
37	# use of wildcards in file connection statements enabled
38	#
39	# 2605 2017-11-09 15:31:46Z raasch
40	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
41	# will not be sent with the job file any more, but copied into the
42	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
43	#
44	# 2600 2017-11-01 14:11:20Z raasch
45	# cycle numbers are made three digits wide
46	#
47	# 2566 2017-10-20 08:50:47Z raasch
48	# execute command for combine_plot_fields added
49	# "TEMPDIR" renamed "tempdir"
50	# temporary working directory for local batch jobs is created immediately within
51	# the user's palmrun call, due to a requirement of the "grid engine" batch
52	# system, where the working directory is given with batch directive -wd and must
53	# already exist when the job is submitted,
54	# informative messages in non-trace mode reduced and partly reformatted
55	#
56	# 2551 2017-10-18 07:25:11Z raasch
57	# TEMPDIR added as replacement string to be used in batch directives
58	#
59	# 2512 2017-10-04 08:26:59Z raasch
60	# bugfix for determining cycle numbers of NetCDF input files
61	#
62	# 2506 2017-09-29 08:30:37Z raasch
63	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
64	# host configuration added to SOURCES_FOR_RUN_... folder name
65	# host_identifier renamed host_configuration
66	# option -W added to allow for job dependencies
67	#
68	# 2501 2017-09-26 11:41:55Z raasch
69	# default value for number of cores (option -X) set to 1
70	# bugfix for mechanism which overwrites configuration file settings with values
71	# provided by palmrun options
72	#
73	# 2499 2017-09-22 16:47:58Z kanani
74	# option -h named configuration identifier
75	#
76	# 2480 2017-09-19 06:24:14Z maronga
77	# bugfix for last revision
78	#
79	# 2479 2017-09-19 06:12:16Z raasch
80	# option -A (project account number) added
81	#
82	# 2422 2017-09-08 08:25:41Z raasch
83	# initial revision
84	#
85	#--------------------------------------------------------------------------------#
86	# palmrun - script for running PALM jobs on local and remote hosts
87	#--------------------------------------------------------------------------------#
88
89
90
91	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
92
93	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
94	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
95	# (TOO MANY ARGUMENTS - PROBLEM)
96	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
97
98	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
99	typeset -i nr_of_output_files=0
100	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
101	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
102	# SCRIPT-OPTION ARGUMENTS
103	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
104	typeset -i icycle inode ival maxcycle mpi_tasks
105	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
106
107	activation_string_list=""
108	AddFilenames=""
109	combine_plot_fields=true
110	compiler_name=""
111	compiler_name_ser=""
112	compiler_options=""
113	cores=1
114	cores_atmos=0
115	cores_ocean=0
116	coupled_dist=""
117	cpp_options=""
118	cpumax=0
119	create_batch_job=false
120	create_jobfile_only=false
121	create_remote_batch_job=false
122	dashes=" ----------------------------------------------------------------------------"
123	defaultqueue=""
124	delete_temporary_catalog=true
125	do_compile=true
126	do_trace=false
127	executable=""
128	execute_command=""
129	execution_error=false
130	fileconnection_file=.palm.iofiles
131	fname=test
132	global_revision=""
133	host_configuration="default"
134	hostfile=""
135	hp=""
136	keep_data_from_previous_run=false
137	link_local_input=false
138	link_local_output=false
139	linker_options=""
140	local_jobcatalog=""
141	locat=normal
142	makefile=""
143	max_par_io_str=""
144	prc=$0
145	while [[ $(echo $prc \| grep -c "/") != 0 ]]
146	do
147	prc=`echo $prc \| cut -f2- -d"/"`
148	done
149	module_calls=""
150	palmrun_memory=""
151	palmrun_script_name=$prc
152	openmp=false
153	previous_job=""
154	project_account=""
155	queue=none
156	restart_run=false
157	return_address=""
158	remote_jobcatalog=""
159	remote_username=""
160	running_in_batch_mode=false
161	run_coupled_model=false
162	run_id=""
163	silent=false
164	source_list=""
165	source_path=""
166	tasks_per_node=0
167	threads_per_task=1
168	transfer_problems=false
169	user_source_path=""
170	use_existing_sources_folder=""
171	use_openmp=false
172	version="palmrun 1.0 Rev$Rev: 2303 $"
173	working_directory=`pwd`
174	write_binary=""
175	TOPT=""
176
177
178	# ERROR HANDLING IN CASE OF EXIT
179	trap 'if [[ $locat != normal && $locat != control_c ]]
180	then
181
182	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
183	(( i = 0 ))
184	while (( i < iec ))
185	do
186	(( i = i + 1 ))
187	printf "\n *** Execution of ERROR-command:\n"
188	printf " >>> ${err_command[$i]}\n"
189	eval ${err_command[$i]}
190	done
191	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
192	printf "\n\n+++ palmrun killed \n\n"
193	elif [[ $locat != control_c ]]
194	then
195	printf "\n --> palmrun finished\n\n"
196	fi' exit
197
198
199	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
200	trap 'cd; rm -rf $tempdir
201	printf "\n+++ palmrun killed by \"^C\" \n\n"
202	locat=control_c
203	exit
204	' 2
205
206
207	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
208	# WHICH WILL BE USED TO START RESTART-JOBS
209	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
210	do
211	case $option in
212	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
213	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
214	(b) create_batch_job=true; prc="$prc -b";;
215	(B) delete_temporary_catalog=false; prc="$prc -B";;
216	(C) restart_run=true; prc="$prc -C";;
217	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
218	(F) create_jobfile_only=true;;
219	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
220	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
221	(j) running_in_batch_mode=true;;
222	(k) keep_data_from_previous_run=true; prc="$prc -k";;
223	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
224	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
225	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
226	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
227	(r) run_id=$OPTARG;;
228	(R) return_address=$OPTARG;;
229	(s) source_list=$OPTARG;;
230	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
231	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
232	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
233	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
234	(v) silent=true; prc="$prc -v";;
235	(V) use_existing_sources_folder="-V";;
236	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
237	(W) previous_job=$OPTARG;;
238	(x) do_trace=true;set -x; prc="$prc -x";;
239	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
240	(y) ocean_file_appendix=true; prc="$prc -y";;
241	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
242	(Z) combine_plot_fields=false; prc="$prc -Z";;
243	(\?) printf "\n +++ unknown option $OPTARG \n"
244	printf "\n --> type \"$0 ?\" for available options \n"
245	locat=parameter;exit;;
246	esac
247	done
248
249
250	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
251	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
252	(( to_shift = $OPTIND - 1 ))
253	shift $to_shift
254
255	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
256	if [[ "$1" = "?" ]]
257	then
258	(printf "\n *** Description of available palmrun options:\n"
259	printf "\n Option Description Default-Value"
260	printf "\n -a activation string list \"\" "
261	printf "\n -A project account number ---"
262	printf "\n -b batch-job on local machine ---"
263	printf "\n -B do not delete temporary directory at end ---"
264	printf "\n -d base name of files attached to program test"
265	printf "\n -F create batch job file only ---"
266	printf "\n -h host configuration \"default\" "
267	printf "\n -k keep data from previous run"
268	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
269	printf "\n -M Makefile name Makefile"
270	printf "\n -O threads per openMP task ---"
271	printf "\n -q queue \"$queue\" "
272	printf "\n -s filenames of routines to be compiled \"\" "
273	printf "\n must end with .f, .f90, .F, or .c !"
274	printf "\n use \"..\" for more than one file and wildcards"
275	printf "\n -s LM compiles all locally modified files"
276	printf "\n -t allowed cpu-time in seconds (batch) 0"
277	printf "\n -T tasks per node ---"
278	printf "\n -u username on remote machine \"\" "
279	printf "\n -v no prompt for confirmation ---"
280	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
281	printf "\n -w maximum parallel io streams as given by -X"
282	printf "\n -W name of job to wait for ---"
283	printf "\n -x tracing of palmrun for debug purposes ---"
284	printf "\n -X # of processors (on parallel machines) 1"
285	printf "\n -y add appendix \"_O\" to all local output"
286	printf "\n files (ocean precursor runs followed by"
287	printf "\n coupled atmosphere-ocean runs) ---"
288	printf "\n -Y run coupled model, \"#1 #2\" with"
289	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
290	printf "\n -Z skip combine_plot_fields at the end of "
291	printf "\n the simulation ---"
292	printf "\n "
293	printf "\n Possible values of positional parameter <modus>:"
294	printf "\n \"?\" - this outline \n\n") \| more
295	exit
296	elif [[ "$1" != "" ]]
297	then
298	printf "\n +++ positional parameter $1 unknown \n"
299	locat=parameter; exit
300	fi
301
302
303
304	# SHORT STARTING MESSAGE
305	printf "\n*** $version "
306	printf "\n will be executed. Please wait ..."
307
308
309	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
310	config_file=.palm.config.$host_configuration
311	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
312
313
314	# CHECK, IF CONFIGURATION FILE EXISTS
315	if [[ ! -f $config_file ]]
316	then
317	printf "\n\n +++ configuration file: "
318	printf "\n $config_file"
319	printf "\n does not exist"
320	locat=connect; exit
321	fi
322
323
324	# CHECK, IF FILE CONNECTION FILE EXISTS
325	if [[ ! -f $fileconnection_file ]]
326	then
327	printf "\n\n +++ file connection file: "
328	printf "\n $fileconnection_file"
329	printf "\n does not exist"
330	locat=connect; exit
331	fi
332
333
334	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
335	if [[ "$activation_string_list" = "" ]]
336	then
337	printf "\n\n +++ no activation string list given: "
338	printf "\n please set palmrun option \"-a\" "
339	locat=palmrun_option; exit
340	fi
341
342
343	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
344	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
345	then
346	write_binary=true
347	else
348	write_binary=false
349	fi
350
351
352	# READ AND EVALUATE THE CONFIGURATION-FILE
353	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
354
355	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
356	while read line
357	do
358
359	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
360	eval line=\"$line\"
361
362
363	# INTERPRET THE LINE
364	if [[ "$(echo $line)" = "" ]]
365	then
366
367	# EMPTY LINE, NO ACTION
368	continue
369
370	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
371	then
372
373	# LINE IS A COMMENT LINE
374	continue
375
376	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
377	then
378
379	# LINE DEFINES AN ENVIRONMENT-VARIABLE
380	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
381	value=`echo $line \| cut -d" " -s -f2-`
382
383
384	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
385	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
386	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
387	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
388	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
389	# CONFIGURATION-FILE.
390	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
391	then
392	eval export $var="\$value"
393
394	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
395	if [[ $do_trace = true ]]
396	then
397	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
398	fi
399	fi
400
401	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
402	then
403
404	# LINE DEFINES BATCH-DIRECTIVE
405	(( ibd = ibd + 1 ))
406	line=$(echo $line \| cut -c4-)
407	batch_directive[$ibd]="$line"
408
409	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
410	then
411
412	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
413	# REMOTE TO A LOCAL HOST
414	(( ibdt = ibdt + 1 ))
415	line=$(echo $line \| cut -c5-)
416	batch_directive_transfer[$ibdt]="$line"
417
418	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
419	then
420
421	# LINE DEFINES ERROR-COMMAND
422	(( iec = iec + 1 ))
423	line=$(echo $line \| cut -c4-)
424	err_command[$iec]="$line"
425
426	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
427	then
428
429	# LINE DEFINES INPUT-COMMAND
430	(( iic = iic + 1 ))
431	line=$(echo $line \| cut -c4-)
432	in_command[$iic]="$line"
433
434	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
435	then
436
437	# LINE DEFINES OUTPUT-COMMAND
438	(( ioc = ioc + 1 ))
439	line=$(echo $line \| cut -c4-)
440	out_command[$ioc]="$line"
441
442	else
443
444	# SKIP ALL OTHER LINES
445	continue
446
447	fi
448
449	done < $config_file
450
451
452	# CHECK SETTING OF REQUIRED PARAMETERS
453	if [[ "$compiler_name" = "" ]]
454	then
455	printf "\n +++ no compiler name found in $config_file"
456	printf "\n Please add line \"compiler_name ...\" to that file."
457	locat=config_file; exit
458	fi
459	if [[ "$compiler_name_ser" = "" ]]
460	then
461	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
462	printf "\n Please add line \"compiler_name_ser ...\" to that file."
463	locat=config_file; exit
464	fi
465	if [[ "$compiler_options" = "" ]]
466	then
467	printf "\n +++ no compiler options found in $config_file"
468	printf "\n Please add line \"compiler_options ...\" to that file."
469	locat=config_file; exit
470	fi
471	if [[ "$linker_options" = "" ]]
472	then
473	printf "\n +++ no linker options found in $config_file"
474	printf "\n Please add line \"linker_options ...\" to that file."
475	locat=config_file; exit
476	fi
477	if [[ "$execute_command" = "" ]]
478	then
479	printf "\n +++ no execute command found in $config_file"
480	printf "\n Please add line \"execute_command ...\" to that file."
481	locat=config_file; exit
482	fi
483
484	if [[ "$hostfile" != "" ]]
485	then
486	if [[ $hostfile != auto && ! -f $hostfile ]]
487	then
488	printf "\n +++ no hostfile \"$hostfile\" found"
489	printf "\n Please check line \"hostfile ...\" in $config_file"
490	locat=config_file; exit
491	fi
492	fi
493
494
495	# DETERMINE THE CALL STATUS
496	if [[ "$return_address" != "" ]]
497	then
498
499	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
500	# BATCH MODE AND ...
501	running_on_remote=true
502
503	else
504
505	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
506	if [[ "$remote_ip" != "" ]]
507	then
508
509	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
510	create_remote_batch_job=true
511
512	fi
513	running_on_remote=false
514	fi
515
516
517
518	# READ AND EVALUATE THE I/O-FILE LIST
519	[[ $silent = false ]] && printf "\n Reading the I/O files... "
520
521	# READ THE FILE CONNECTION FILE LINE BY LINE
522	while read line
523	do
524
525	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
526	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
527
528	# INTERPRET THE LINE
529	if [[ "$(echo $line)" = "" ]]
530	then
531	# EMPTY LINE, NO ACTION
532	continue
533
534	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
535	then
536
537	# LINE IS A COMMENT LINE
538	true
539
540	else
541
542	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
543	# s2a: in/out - field
544	# s2b: action - field (optional)
545	s1=`echo "$line" \| cut -d" " -f1`
546	s2=`echo "$line" \| cut -d" " -s -f2`
547	# s2a=$(echo $s2 \| cut -d":" -f1)
548	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
549	then
550	s2a=$s2
551	s2b=""
552	else
553	s2a=`echo $s2 \| cut -d":" -f1`
554	s2b=`echo $s2 \| cut -d":" -f2`
555	fi
556	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
557	s4=`echo "$line" \| cut -d" " -s -f4`
558	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
559	echo "### s4=\"$s4\" "
560	s5=`echo "$line" \| cut -d" " -s -f5`
561	s6=`echo "$line" \| cut -d" " -s -f6`
562
563
564	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
565	# INPUT- OR OUTPUT-LIST.
566	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
567	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
568	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
569	# IS NOT CHECKED AND STORED.
570	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
571	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
572	then
573	found=false
574	for actual in $activation_string_list
575	do
576	for formal in $s3
577	do
578	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
579	done
580	done
581	if [[ $found = true ]]
582	then
583	(( iin = iin + 1 ))
584	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
585	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
586	if [[ "$s2a" = inopt ]]
587	then
588	optin_pre[$iin]=yes
589	else
590	optin_pre[$iin]=no
591	fi
592
593	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
594	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
595	if [[ $running_on_remote = true && "$s2b" = tr ]]
596	then
597	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
598	fi
599
600	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
601	# THE WILDCARD FROM THE ENDING
602	if [[ "${s5: -1}" = "*" ]]
603	then
604	if [[ "$s2b" = "di" ]]
605	then
606	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
607	printf "\n see file \"$fileconnection_file\", line"
608	printf "\n$line"
609	locat=iofiles_file; exit
610	fi
611	multin[$iin]=true
612	string=${endin_pre[$iin]}
613	endin_pre[$iin]="${string%?}"
614	else
615	multin[$iin]=false
616	fi
617	fi
618	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
619	then
620	found=false
621	echo "### line=\"$line\" "
622	for actual in $activation_string_list
623	do
624	for formal in $s3
625	do
626	echo "--- actual=\"$actual\" formal=\"$formal\" s3=\"$s3\" "
627	if [[ $actual = $formal \|\| $formal = wildcard ]]
628	then
629	found=true
630	echo "--- found"
631	else
632	echo "--- not found"
633	fi
634	done
635	done
636	if [[ $found = true ]]
637	then
638	(( iout = iout + 1 ))
639	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
640	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
641	echo "### pathout_pre[$iout]=\"${pathout_pre[$iout]}\" "
642
643	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
644	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
645	if [[ $formal = wildcard ]]
646	then
647	warnout_pre[$iout]=false
648	else
649	warnout_pre[$iout]=true
650	fi
651
652	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
653	# THE WILDCARD FROM THE LOCAL FILENAME
654	if [[ "${s1: -1}" = "*" ]]
655	then
656	if [[ "$s2b" = "di" ]]
657	then
658	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
659	printf "\n see file \"$fileconnection_file\", line"
660	printf "\n$line"
661	locat=iofiles_file; exit
662	fi
663	multout[$iout]=true
664	string=${localout_pre[$iout]}
665	localout_pre[$iout]="${string%?}"
666	else
667	multout[$iout]=false
668	fi
669	fi
670	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
671	then
672	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
673	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
674	locat=connect; exit
675	fi
676	IFS="$IFSALT"
677	fi
678
679	done < $fileconnection_file
680
681
682
683	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
684	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
685	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
686	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
687	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
688	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
689
690
691
692	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
693	if [[ $run_coupled_model = true ]]
694	then
695
696	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
697	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
698
699	if (( $cores_ocean + $cores_atmos != $cores ))
700	then
701
702	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
703	printf "\n PEs (total) : $cores"
704	printf "\n PEs (atmosphere): $cores_atmos"
705	printf "\n PEs (ocean) : $cores_ocean"
706	locat=coupling; exit
707
708	fi
709
710	fi
711
712
713	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
714	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
715	# FOLDER
716	if [[ $running_in_batch_mode = true ]]
717	then
718
719	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
720	then
721	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
722	printf "\n Please check the output of the palmrun-call"
723	printf "\n that you did on your local host."
724	locat=SOURCES_FOR_RUN; exit
725	fi
726
727	else
728
729	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
730	# AUTOMATIC RESTART RUN
731	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
732	if [[ $restart_run = false ]]
733	then
734
735	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
736	# THE LOCAL HOST
737	if [[ ! -d $source_path ]]
738	then
739	printf "\n\n +++ source path \"$source_path\" on local host"
740	printf "\n \"$(hostname)\" does not exist"
741	locat=source_path; exit
742	fi
743
744	rm -rf $sources_for_run_catalog
745	mkdir -p $sources_for_run_catalog
746
747	if [[ "$source_list" = LM ]]
748	then
749
750	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
751	source_list=""
752	cd $source_path
753
754
755	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
756	if [[ ! -d ../.svn ]]
757	then
758	printf "\n\n +++ source directory"
759	printf "\n \"$source_path\" "
760	printf "\n is not under control of \"subversion\"."
761	printf "\n Please do not use palmrun-option \"-s LM\"\n"
762	fi
763
764
765	# LIST ALL MODIFIED SOURCE CODE FILES
766	Filenames=""
767	svn status > tmp_svnstatus
768	while read line
769	do
770	firstc=`echo $line \| cut -c1`
771	if [[ $firstc = M \|\| $firstc = "?" ]]
772	then
773	Name=`echo "$line" \| cut -c8-`
774	extension=`echo $Name \| cut -d. -f2`
775	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
776	then
777	Filenames="$Filenames "$Name
778	fi
779	fi
780	done < tmp_svnstatus
781	rm -rf tmp_svnstatus
782
783
784	# COPY FILES TO SOURCES_FOR_RUN_...
785	for filename in $Filenames
786	do
787	cp $filename ${working_directory}/${sources_for_run_catalog}
788	source_list=$source_list"$filename "
789	done
790
791	cd - > /dev/null
792
793
794	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
795	elif [[ "$source_list" != "" ]]
796	then
797
798	cd $source_path
799
800	for filename in $source_list
801	do
802
803	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
804	if [[ $(echo $filename \| grep -c "/") != 0 ]]
805	then
806	printf "\n +++ source code file: $filename"
807	printf "\n must not contain (\"/\") "
808	locat=source; exit
809	fi
810
811	if [[ ! -f $filename ]]
812	then
813	printf "\n +++ source code file: $filename"
814	printf "\n does not exist"
815	locat=source; exit
816	else
817	cp $filename ${working_directory}/${sources_for_run_catalog}
818	fi
819
820	done
821
822	cd - > /dev/null
823
824	fi
825
826	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
827	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
828	if [[ ! -f $makefile ]]
829	then
830	printf "\n +++ file \"$makefile\" does not exist"
831	locat=make; exit
832	else
833	cp $makefile ${sources_for_run_catalog}/Makefile
834	fi
835
836
837	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
838	if [[ "$user_source_path" != "" ]]
839	then
840
841	# DOES THE DIRECTORY EXIST?
842	if [[ ! -d $user_source_path ]]
843	then
844
845	printf "\n\n *** INFORMATIVE: additional source code directory"
846	printf "\n \"$user_source_path\" "
847	printf "\n does not exist or is not a directory."
848	printf "\n No source code will be used from this directory!\n"
849	user_source_path=""
850	if [[ $silent == false ]]
851	then
852	sleep 2
853	fi
854
855	else
856
857	cd $user_source_path
858	found=false
859
860	Names=$(ls -1 *.f90 2>&1)
861	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
862	Names=$(ls -1 *.F90 2>&1)
863	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
864	Names=$(ls -1 *.F 2>&1)
865	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
866	Names=$(ls -1 *.f 2>&1)
867	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
868	Names=$(ls -1 *.c 2>&1)
869	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
870
871	cd - > /dev/null
872	cd $sources_for_run_catalog
873
874	# COPY MAKEFILE IF EXISTING
875	if [[ -f $user_source_path/Makefile ]]
876	then
877	printf "\n\n *** user Makefile from directory"
878	printf "\n \"$user_source_path\" is used \n"
879	if [[ $silent == false ]]
880	then
881	sleep 1
882	fi
883	cp $user_source_path/Makefile .
884	fi
885
886	for filename in $AddFilenames
887	do
888	if [[ -f $filename ]]
889	then
890	printf "\n +++ source code file \"$filename\" found in additional"
891	printf "\n source code directory \"$user_source_path\" "
892	printf "\n but was also given with option \"-s\" which means that it should be taken"
893	printf "\n from directory \"$source_path\"."
894	locat=source; exit
895	fi
896
897	cp $user_source_path/$filename .
898	source_list="$source_list $filename"
899
900	# CHECK IF FILE IS CONTAINED IN MAKEFILE
901	if [[ $(grep -c $filename Makefile) = 0 ]]
902	then
903	printf "\n\n +++ user file \"$filename\" "
904	printf "\n is not listed in Makefile \n"
905	locat=source; exit
906	else
907
908	if [[ $found = false ]]
909	then
910	found=true
911	printf "\n\n *** following user file(s) added to the"
912	printf " files to be translated:\n "
913	fi
914	printf "$filename "
915	if [[ $silent == false ]]
916	then
917	sleep 0.5
918	fi
919
920	fi
921	done
922	[[ $found = true ]] && printf "\n"
923	cd - > /dev/null
924	fi
925	fi
926
927	# COPY CONFIGURATION FILES
928	cp $config_file $sources_for_run_catalog
929	cp $fileconnection_file $sources_for_run_catalog
930
931	# COPY SHELLSCRIPTS
932	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
933	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
934
935	fi
936
937	fi
938
939
940	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
941	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
942	if [[ "$global_revision" = "" ]]
943	then
944	global_revision=`svnversion $source_path 2>/dev/null`
945	global_revision="Rev: $global_revision"
946	fi
947
948
949	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
950	if [[ -n $cores ]]
951	then
952
953	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
954	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
955	if [[ $tasks_per_node = 0 ]]
956	then
957	printf "\n"
958	printf "\n +++ option \"-T\" (tasks per node) is missing"
959	printf "\n set -T option or define tasks_per_node in the config file"
960	locat=tasks_per_node; (( iec = 0 )); exit
961	fi
962
963	if (( cores < tasks_per_node ))
964	then
965	printf "\n"
966	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
967	printf "\n given values: -T $tasks_per_node -X $cores"
968	locat=tasks_per_node; (( iec = 0 )); exit
969	fi
970
971	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
972	(( mpi_tasks = cores / threads_per_task ))
973	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
974	(( ii = cores / tasks_per_node ))
975	(( remaining_cores = cores - ii * tasks_per_node ))
976	if (( remaining_cores > 0 ))
977	then
978	printf "\n"
979	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
980	printf "\n divisor of the total number of cores (option \"-X\")"
981	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
982	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
983	(( nodes = nodes + 1 ))
984	fi
985
986	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
987	if [[ "$tasks_per_node" != "" ]]
988	then
989	TOPT="-T $tasks_per_node"
990	fi
991
992	fi
993
994
995	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
996	if [[ "$maximum_parallel_io_streams" = "" ]]
997	then
998	maximum_parallel_io_streams=$cores
999	fi
1000
1001
1002	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1003	if [[ "$scp_port" != "" ]]
1004	then
1005	PORTOPT="-P $scp_port"
1006	SSH_PORTOPT="-p $scp_port"
1007	fi
1008
1009
1010	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1011	# CONFIG-FILE
1012	if [[ "$ssh_key" != "" ]]
1013	then
1014	ssh_key="-i $HOME/.ssh/$ssh_key"
1015	fi
1016
1017
1018	# SET QUEUE, IF NOT GIVEN
1019	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1020	then
1021
1022	if [[ $queue = none && "$defaultqueue" = "" ]]
1023	then
1024	printf "\n"
1025	printf "\n +++ no default queue given in configuration file and no queue"
1026	printf "\n given with option -q"
1027	fi
1028	if [[ $queue = none ]]
1029	then
1030	queue=$defaultqueue
1031	fi
1032
1033	fi
1034
1035
1036	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1037	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1038	(( i = 0 ))
1039	(( nr_of_input_files = 0 ))
1040	while (( i < iin ))
1041	do
1042	(( i = i + 1 ))
1043
1044	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1045	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1046	if [[ "${actionin_pre[$i]}" = di ]]
1047	then
1048	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1049	else
1050	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
1051	fi
1052
1053
1054	# CHECK IF FILE EXISTS
1055	if ! ls $filename* 1>/dev/null 2>&1
1056	then
1057
1058	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1059	if [[ "${optin_pre[$i]}" != "yes" ]]
1060	then
1061	printf "\n\n +++ INPUT-file: "
1062	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1063	then
1064	printf "\n $filename"
1065	else
1066	printf "\n $filename.${extin_pre[$i]}"
1067	fi
1068	printf "\n does not exist\n"
1069	locat=input; exit
1070	else
1071	(( nr_of_input_files = nr_of_input_files + 1 ))
1072	localin[$nr_of_input_files]="${localin_pre[$i]}"
1073	optin[$nr_of_input_files]="${optin_pre[$i]}"
1074	actionin[$nr_of_input_files]="unavailable"
1075	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1076	endin[$nr_of_input_files]="${endin_pre[$i]}"
1077	extin[$nr_of_input_files]="${extin_pre[$i]}"
1078	fi
1079
1080	else
1081
1082	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
1083	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1084	if [[ "${multin[$i]}" = true ]]
1085	then
1086	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1087	ls -1 -d ${filename} > filelist 2>/dev/null
1088	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1089	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1090
1091	endings=""
1092	while read line
1093	do
1094	# filename without path (i.e. after the last "/")
1095	basefilename=$(basename ${line})
1096
1097	# check if there is an extension and remove it
1098	ext=${basefilename##*.}
1099	if [[ "$ext" = "${extin_pre[$i]}" ]]
1100	then
1101	basefilename=${basefilename%.*}
1102	fi
1103
1104	# check for an existing cycle number and remove it
1105	cycle=${basefilename##*.}
1106	if [[ $cycle =~ ^-?[0-9]+$ ]]
1107	then
1108	basefilename=${basefilename%.*}
1109	fi
1110
1111	# remove the fname from the beginning
1112	length_fname=${#fname}
1113	ending=${basefilename:${length_fname}}
1114
1115	# remove the ending given in the .iofiles from the beginning
1116	endingstring="${endin_pre[$i]}"
1117	length_ending=${#endingstring}
1118	ending=${ending:${length_ending}}
1119
1120	if [[ "$ending" = "" ]]
1121	then
1122	# standard ending as given in the .iofiles
1123	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1124	then
1125	endings="$endings DEFAULT"
1126	fi
1127	else
1128	# ending must start with "_", otherwise its a different file
1129	if [[ "${ending:0:1}" = "_" ]]
1130	then
1131	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1132	then
1133	endings="$endings $ending"
1134	fi
1135	fi
1136	fi
1137
1138	done <filelist
1139
1140	rm filelist
1141
1142	else
1143
1144	# SINGLE NAME
1145	endings=DEFAULT
1146
1147	fi
1148
1149	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1150	for ending in $endings
1151	do
1152
1153	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1154	if [[ $ending = DEFAULT ]]
1155	then
1156	ending=""
1157	fi
1158
1159	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1160	(( nr_of_input_files = nr_of_input_files + 1 ))
1161	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1162	optin[$nr_of_input_files]="${optin_pre[$i]}"
1163	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1164	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1165	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1166	extin[$nr_of_input_files]="${extin_pre[$i]}"
1167
1168
1169	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1170	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1171	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1172	then
1173	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1174	else
1175	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
1176	fi
1177
1178	# DETERMINE THE FILE'S CYCLE NUMBER
1179	(( maxcycle = 0 ))
1180	ls -1 -d $filename > filelist 2>/dev/null
1181	ls -1 -d $filename.* >> filelist 2>/dev/null
1182	while read line
1183	do
1184	# filename without path (i.e. after the last "/")
1185	basefilename=$(basename ${line})
1186
1187	# check if there is an extension
1188	extension=${basefilename##*.}
1189	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1190	then
1191	basefilename=${basefilename%.*}
1192	fi
1193
1194	# check for an existing cycle number
1195	cycle=${basefilename##*.}
1196	if [[ $cycle =~ ^-?[0-9]+$ ]]
1197	then
1198	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1199	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1200	(( icycle = $((10#$cycle)) ))
1201	else
1202	(( icycle = 0 ))
1203	fi
1204
1205	if (( icycle > maxcycle ))
1206	then
1207	(( maxcycle = icycle ))
1208
1209	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1210	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1211	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1212	then
1213	leading_zero=true
1214	else
1215	leading_zero=false
1216	fi
1217	fi
1218
1219	done <filelist
1220	rm filelist
1221
1222	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1223	if [[ $leading_zero = true ]]
1224	then
1225	cyclestring=`printf "%03d" $maxcycle`
1226	else
1227	cyclestring=$maxcycle
1228	fi
1229
1230	# APPEND CYCLE NUMBER TO FILENAME
1231	if (( maxcycle > 0 ))
1232	then
1233	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1234	then
1235	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1236	else
1237	filename=${filename}.$cyclestring
1238	fi
1239	else
1240	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1241	then
1242	filename=${filename}.${extin[$nr_of_input_files]}
1243	fi
1244	fi
1245
1246	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1247	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1248	absnamein[$nr_of_input_files]=$filename
1249	if (( maxcycle > 0 ))
1250	then
1251	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1252	then
1253	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1254	else
1255	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
1256	fi
1257	else
1258	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1259	then
1260	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1261	else
1262	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
1263	fi
1264	fi
1265
1266	done
1267
1268	fi
1269
1270	done
1271
1272
1273	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1274	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1275	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1276	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1277	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1278	# REMOTE HOST)
1279	(( i = 0 ))
1280	while (( i < iout ))
1281	do
1282	(( i = i + 1 ))
1283	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1284	then
1285	if [[ "${actionout_pre[$i]}" = tr ]]
1286	then
1287	actionout_pre[$i]=""
1288	elif [[ "${actionout_pre[$i]}" = trpe ]]
1289	then
1290	actionout_pre[$i]=pe
1291	elif [[ "${actionout_pre[$i]}" = tra ]]
1292	then
1293	actionout_pre[$i]=a
1294	fi
1295	(( maxcycle = 0 ))
1296	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
1297	eval catalogname=${pathout_pre[$i]}
1298	if ! ls $filename* 1>/dev/null 2>&1
1299	then
1300
1301	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1302	if cat /dev/null > $filename
1303	then
1304	rm $filename
1305	else
1306
1307	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1308	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1309	if [[ ! -d $catalogname ]]
1310	then
1311	if mkdir -p $catalogname
1312	then
1313	printf "\n\n *** directory:"
1314	printf "\n $catalogname"
1315	printf "\n was created\n"
1316	else
1317	printf "\n\n +++ OUTPUT-file:"
1318	printf "\n $filename"
1319	printf "\n cannot be created, because directory does not exist"
1320	printf "\n and cannot be created either"
1321	printf "\n"
1322	locat=output ; exit
1323	fi 2>/dev/null
1324	else
1325	printf "\n\n +++ OUTPUT-file:"
1326	printf "\n $filename"
1327	printf "\n cannot be created, although directory exists"
1328	printf "\n"
1329	locat=output ; exit
1330	fi
1331	fi 2>/dev/null
1332
1333	fi
1334
1335	fi
1336	done
1337
1338
1339	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1340	if [[ $running_in_batch_mode = false ]]
1341	then
1342	run_id=$RANDOM
1343	job_id=${fname}.$run_id
1344
1345	tempdir=$fast_io_catalog/$job_id
1346	fi
1347
1348
1349	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1350	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1351	then
1352
1353	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1354	if [[ $ibd = 0 ]]
1355	then
1356	printf "\n"
1357	printf "\n +++ no batch directives found in configuration file"
1358	locat=config_file_batch_directives; (( iec = 0 )); exit
1359	fi
1360
1361	# CHECK IF CPUTIME IS GIVEN FOR JOB
1362	done=false
1363	cputime=$cpumax
1364	while [[ $done = false ]]
1365	do
1366	if (( cputime == 0 ))
1367	then
1368	printf "\n +++ cpu-time is undefined"
1369	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1370	printf "\n >>> "
1371	read cputime 1>/dev/null 2>&1
1372	else
1373	done=true
1374	fi
1375	done
1376	cpumax=$cputime
1377
1378	# CHECK THE MEMORY DEMAND
1379	done=false
1380	while [[ $done = false ]]
1381	do
1382	if (( memory == 0 ))
1383	then
1384	printf "\n +++ memory demand is undefined"
1385	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1386	printf "\n >>> "
1387	read memory 1>/dev/null 2>&1
1388	else
1389	done=true
1390	fi
1391	done
1392
1393	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1394	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1395	then
1396	while [[ -z $remote_username ]]
1397	do
1398	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1399	printf "\n >>> Please type username:"
1400	printf "\n >>> "
1401	read remote_username
1402	done
1403	fi
1404
1405	else
1406
1407	if [[ $running_in_batch_mode = false ]]
1408	then
1409	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1410	cpumax=$cputime
1411	else
1412	cputime=$cpumax
1413	fi
1414
1415	fi
1416
1417
1418	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1419	(( cpu_hours = cputime / 3600 ))
1420	(( resttime = cputime - cpu_hours * 3600 ))
1421	(( cpu_minutes = resttime / 60 ))
1422	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1423	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1424
1425
1426	# OUTPUT OF THE PALMRUN-HEADER
1427	calltime=$(date)
1428	printf "\n"
1429	printf "#------------------------------------------------------------------------# \n"
1430	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1431	printf "\| \| \n"
1432	column1="called on:"; column2=$(hostname)
1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1434	if [[ $create_remote_batch_job = true ]]
1435	then
1436	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1437	else
1438	if [[ $running_on_remote = true ]]
1439	then
1440	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1441	else
1442	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1443	fi
1444	fi
1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1446
1447	column1="running in:"
1448	if [[ $running_in_batch_mode = true ]]
1449	then
1450	column2="batch job mode"
1451	else
1452	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1453	then
1454	column2="job creation mode"
1455	else
1456	column2="interactive run mode"
1457	fi
1458	fi
1459	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1460
1461	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1462	then
1463	if [[ "$project_account" != "" ]]
1464	then
1465	column1="project account number:"
1466	column2="$project_account"
1467	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1468	fi
1469	fi
1470
1471	if [[ -n $cores ]]
1472	then
1473	if [[ $run_coupled_model = false ]]
1474	then
1475	column1="number of cores:"; column2=$cores
1476	else
1477	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1478	fi
1479	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1480	fi
1481	if [[ -n $tasks_per_node ]]
1482	then
1483	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1484	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1485	if (( remaining_cores > 0 ))
1486	then
1487	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1488	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1489	fi
1490	fi
1491	if [[ $maximum_parallel_io_streams != $cores ]]
1492	then
1493	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1494	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1495	fi
1496	if [[ $use_openmp = true ]]
1497	then
1498	column1="threads per task:"; column2="$threads_per_task"
1499	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1500	fi
1501	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1502	then
1503	column1="memory demand / PE":; column2="$memory MB"
1504	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1505	column1="job cpu time (h:m:s):"; column2="$timestring"
1506	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1507	fi
1508	printf "\| \| \n"
1509	if [[ "$source_list" != "" ]]
1510	then
1511	if [[ "$make_options" != "" ]]
1512	then
1513	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1514	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1515	line=$(echo "$make_options" \| cut -c46-)
1516	while [[ "$line" != "" ]]
1517	do
1518	column1=""
1519	column2=$(echo "$line" \| cut -c-45)
1520	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1521	line=$(echo "$line" \| cut -c46-)
1522	done
1523	fi
1524	fi
1525
1526	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1527	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1528	line=$(echo "$cpp_options" \| cut -c46-)
1529	while [[ "$line" != "" ]]
1530	do
1531	column1=""
1532	column2=$(echo "$line" \| cut -c-45)
1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1534	line=$(echo "$line" \| cut -c46-)
1535	done
1536
1537	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1538	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1539	line=$(echo "$compiler_options" \| cut -c46-)
1540	while [[ "$line" != "" ]]
1541	do
1542	column1=""
1543	column2=$(echo "$line" \| cut -c-45)
1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1545	line=$(echo "$line" \| cut -c46-)
1546	done
1547
1548	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1549	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1550	line=$(echo "$linker_options" \| cut -c46-)
1551	while [[ "$line" != "" ]]
1552	do
1553	column1=""
1554	column2=$(echo "$line" \| cut -c-45)
1555	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1556	line=$(echo "$line" \| cut -c46-)
1557	done
1558
1559	if [[ "$login_init_cmd" != "" ]]
1560	then
1561	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1562	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1563	line=$(echo "$login_init_cmd" \| cut -c46-)
1564	while [[ "$line" != "" ]]
1565	do
1566	column1=""
1567	column2=$(echo "$line" \| cut -c-45)
1568	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1569	line=$(echo "$line" \| cut -c46-)
1570	done
1571	fi
1572
1573	if [[ "$module_commands" != "" ]]
1574	then
1575	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1577	line=$(echo "$module_commands" \| 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 "$line" \| cut -c46-)
1584	done
1585	fi
1586	printf "\| \| \n"
1587	column1="base name of files:"; column2=$fname
1588	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1589	column1="activation string list:"; column2=$(echo $activation_string_list)
1590	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1591
1592	if [[ "$ocean_file_appendix" = true ]]
1593	then
1594	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1595	fi
1596
1597	if [[ "$source_list" != "" ]]
1598	then
1599	printf "\| \| \n"
1600	printf "\| Files to be compiled: \| \n"
1601	line=$source_list
1602	while [[ "$line" != "" ]]
1603	do
1604	linestart=$(echo $line \| cut -c-70)
1605	printf "\| %-70s \| \n" "$linestart"
1606	line=$(echo "$line" \| cut -c71-)
1607	done
1608	fi
1609	printf "#------------------------------------------------------------------------#"
1610
1611
1612
1613	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1614	if [[ $do_trace = true ]]
1615	then
1616	(( i = 0 ))
1617	while (( i < nr_of_input_files ))
1618	do
1619	(( i = i + 1 ))
1620	if (( i == 1 ))
1621	then
1622	printf "\n\n >>> INPUT-file assignments:\n"
1623	fi
1624	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1625	done
1626	(( i = 0 ))
1627	while (( i < iout ))
1628	do
1629	(( i = i + 1 ))
1630	if (( i == 1 ))
1631	then
1632	printf "\n\n >>> OUTPUT-file assignments:\n"
1633	fi
1634	printf "\n ${localout[$i]} : ${pathout[$i]}"
1635	done
1636	(( i = 0 ))
1637	while (( i < iic ))
1638	do
1639	(( i = i + 1 ))
1640	if (( i == 1 ))
1641	then
1642	printf "\n\n >>> INPUT-commands:\n"
1643	fi
1644	printf "\n ${in_command[$i]}"
1645	done
1646	(( i = 0 ))
1647	while (( i < ioc ))
1648	do
1649	(( i = i + 1 ))
1650	if (( i == 1 ))
1651	then
1652	printf "\n\n >>> OUTPUT-commands:\n"
1653	fi
1654	printf "\n ${out_command[$i]}"
1655	done
1656	fi
1657
1658	# QUERY FOR CONTINUE
1659	if [[ $silent = false && $running_in_batch_mode = false ]]
1660	then
1661	antwort=dummy
1662	printf "\n\n"
1663	printf " >>> everything o.k. (y/n) ? "
1664	while read antwort
1665	do
1666	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1667	then
1668	printf " >>> everything o.k. (y/n) ? "
1669	else
1670	break
1671	fi
1672	done
1673	if [[ $antwort = n \|\| $antwort = N ]]
1674	then
1675	locat=user_abort; (( iec = 0 )); exit
1676	fi
1677	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1678	then
1679	printf "\n *** batch-job will be created and submitted"
1680	else
1681	printf "\n *** PALMRUN will now continue to execute on this machine"
1682	fi
1683	fi
1684
1685
1686
1687	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1688	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1689	then
1690
1691	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1692	then
1693	printf "\n\n *** creating executable and other sources for the remote host\n"
1694	else
1695	printf "\n\n *** creating executable and other sources for the local host\n"
1696	fi
1697
1698	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1699	# IT SHALL BE CREATED
1700	ask_for_make_depository=false
1701	if [[ $create_remote_batch_job = true ]]
1702	then
1703
1704	line=`grep %base_directory $config_file`
1705	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1706	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1707
1708	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1709	then
1710	printf "\n\n +++ make depository \"${make_depository}\""
1711	printf "\n on remote host not found!"
1712	ask_for_make_depository=true
1713	fi
1714	rm ${host_configuration}_last_make_protokoll
1715
1716	else
1717
1718	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1719	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1720	if [[ ! -d ${make_depository} ]]
1721	then
1722	printf "\n\n +++ make depository \"${make_depository}\""
1723	printf "\n on local host not found!"
1724	ask_for_make_depository=true
1725	fi
1726
1727	fi
1728
1729	if [[ $ask_for_make_depository = true ]]
1730	then
1731
1732	antwort=dummy
1733	printf "\n\n"
1734	printf " >>> Create a new one (y/n) ? "
1735	while read antwort
1736	do
1737	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1738	then
1739	printf " >>> Create a new one (y/n) ? "
1740	else
1741	break
1742	fi
1743	done
1744	if [[ $antwort = n \|\| $antwort = N ]]
1745	then
1746	locat=user_abort; (( iec = 0 )); exit
1747	fi
1748
1749	if [[ $do_trace = true ]]
1750	then
1751	palmbuild -h $host_configuration
1752	else
1753	palmbuild -v -h $host_configuration
1754	fi
1755
1756	if [[ $? != 0 ]]
1757	then
1758
1759	# ABORT IN CASE OF COMPILATION PROBLEMS
1760	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1761	locat=make_depository
1762	exit
1763	else
1764	echo " *** now continue with creating executable and other sources"
1765	fi
1766
1767	fi
1768
1769	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1770	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
1771
1772	if [[ $? != 0 ]]
1773	then
1774
1775	# ABORT IN CASE OF COMPILATION PROBLEMS
1776	printf "\n +++ error while creating executable and/or other sources"
1777	locat=execution
1778	rm -rf $sources_for_run_catalog
1779	exit
1780
1781	else
1782
1783	printf " *** executable and other sources created\n"
1784	rm -rf $sources_for_run_catalog
1785
1786	fi
1787
1788	fi
1789
1790
1791	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1792	# WILL BE COPIED TO THE REMOTE HOST
1793	if [[ $create_remote_batch_job = true ]]
1794	then
1795	(( i = 0 ))
1796	while (( i < nr_of_input_files ))
1797	do
1798	(( i = i + 1 ))
1799	if [[ "${actionin[$i]}" = tr ]]
1800	then
1801	eval inputfile=${pathin[$i]}/${frelin[$i]}
1802	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1803	fi
1804	done
1805	if (( i > 0 ))
1806	then
1807	printf " *** input files have been copied to the remote host\n"
1808	fi
1809	fi
1810
1811
1812	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1813	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1814	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1815	then
1816
1817	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1818	if [[ $running_in_batch_mode = false ]]
1819	then
1820	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1821	# FOLDER
1822	mkdir -p $tempdir
1823	chmod go+rx $tempdir
1824	cd $tempdir
1825	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1826	printf "\n *** changed to temporary directory: $tempdir"
1827
1828	else
1829
1830	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1831	printf "\n *** running in temporary directory: $tempdir"
1832
1833	fi
1834
1835
1836	# PROVIDE THE INPUT FILES
1837	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1838	optional_files_missing=false
1839	(( i = 0 ))
1840	while (( i < nr_of_input_files ))
1841	do
1842	(( i = i + 1 ))
1843	if (( i == 1 ))
1844	then
1845	printf "\n\n *** providing INPUT-files:\n$dashes"
1846	fi
1847
1848
1849	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1850	if [[ "${actionin[$i]}" = unavailable ]]
1851	then
1852	optional_files_missing=true
1853	continue
1854	fi
1855
1856	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1857	files_for_cores=false; filetype=file
1858	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1859	then
1860	files_for_cores=true; filetype=files
1861	actionin[$i]=""
1862	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1863	then
1864	actionin[$i]=""
1865	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1866	then
1867	files_for_cores=true; filetype=files
1868	actionin[$i]="ln"
1869	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1870	then
1871	actionin[$i]="ln"
1872	fi
1873
1874	if [[ $files_for_cores = true ]]
1875	then
1876	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1877	else
1878	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1879	fi
1880
1881	# INPUT-FILES TO BE LINKED
1882	if [[ "${actionin[$i]}" = ln ]]
1883	then
1884
1885	printf "\n $filetype will be linked"
1886	if [[ $files_for_cores = false ]]
1887	then
1888	if [[ -f "${absnamein[$i]}" ]]
1889	then
1890	ln ${absnamein[$i]} ${localin[$i]}
1891	got_tmp[$i]=true
1892	fi
1893	else
1894	if [[ -d "${absnamein[$i]}" ]]
1895	then
1896	mkdir -p ${localin[$i]}
1897	cd ${absnamein[$i]}
1898	for file in $(ls *)
1899	do
1900	ln $file $tempdir/${localin[$i]}
1901	done >\|/dev/null 2>&1
1902	cd $tempdir
1903	fi
1904
1905	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1906	if [[ ! -f "${localin[$i]}/_000000" ]]
1907	then
1908	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1909	cp -r ${absnamein[$i]}/* ${localin[$i]}
1910	fi
1911
1912	got_tmp[$i]=true
1913	fi
1914	fi
1915
1916	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1917	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1918	then
1919
1920	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1921	then
1922
1923	# FILE COPIES ARE PROVIDED FOR ALL CORES
1924	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1925	printf "\n file will be provided for $cores processors"
1926	mkdir -p ${localin[$i]}
1927	ival=$cores
1928	(( ii = 0 ))
1929	while (( ii <= ival-1 ))
1930	do
1931	if (( ii < 10 ))
1932	then
1933	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1934	elif (( ii < 100 ))
1935	then
1936	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1937	elif (( ii < 1000 ))
1938	then
1939	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1940	else
1941	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1942	fi
1943	(( ii = ii + 1 ))
1944	done
1945
1946	else
1947
1948	if [[ $files_for_cores = true ]]
1949	then
1950
1951	# PROVIDE FILES FOR EACH CORE
1952	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1953	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1954	printf "\n providing $cores files for the respective cores"
1955	mkdir -p ${localin[$i]}
1956	if [[ $link_local_input = true ]]
1957	then
1958	printf " files will be linked\n"
1959	cd ${absnamein[$i]}
1960	for file in $(ls *)
1961	do
1962	ln -f $file ${localin[$i]}
1963	done
1964	cd $tempdir
1965	fi
1966
1967	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1968	if [[ ! -f "${localin[$i]}/_000000" ]]
1969	then
1970	if [[ $link_local_input = true ]]
1971	then
1972	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1973	fi
1974	cp -r ${absnamein[$i]}/* ${localin[$i]}
1975	fi
1976
1977	else
1978
1979	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1980	if [[ $link_local_input = true ]]
1981	then
1982	printf " file will be linked\n"
1983	ln -f ${absnamein[$i]} ${localin[$i]}
1984	fi
1985	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
1986	if [[ ! -f "${localin[$i]}" ]]
1987	then
1988	if [[ $link_local_input = true ]]
1989	then
1990	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1991	fi
1992	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
1993	then
1994	mv ${absnamein[$i]} ${localin[$i]}
1995	else
1996	cp ${absnamein[$i]} ${localin[$i]}
1997	fi
1998	fi
1999	fi
2000	fi
2001	fi
2002
2003	done
2004	if (( i != 0 ))
2005	then
2006	if [[ $optional_files_missing = true ]]
2007	then
2008	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2009	fi
2010	printf "\n$dashes\n *** all INPUT-files provided \n"
2011	fi
2012
2013
2014	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2015	(( i = 0 ))
2016	while (( i < iic ))
2017	do
2018	(( i = i + 1 ))
2019	if (( i == 1 ))
2020	then
2021	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2022	fi
2023	printf "\n >>> ${in_command[$i]}"
2024	eval ${in_command[$i]}
2025	if (( i == iic ))
2026	then
2027	printf "\n$dashes\n"
2028	fi
2029	done
2030
2031
2032	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2033	# (FILE ENVPAR WILL BE READ BY PALM)
2034	cat > ENVPAR << EOF
2035	&envpar run_identifier = '$fname', host = '$host_configuration',
2036	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2037	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2038	maximum_cpu_time_allowed = ${cpumax}.,
2039	revision = '$global_revision',
2040	batch_job = .${running_in_batch_mode}. /
2041
2042	EOF
2043
2044
2045	# STARTING THE EXECUTABLE
2046	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2047	PATH=$PATH:$tempdir
2048
2049
2050	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2051	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
2052	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2053	eval line=\"$line\"
2054	execute_command="$line"
2055
2056
2057	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2058	if [[ "$execute_command_for_combine" = "" ]]
2059	then
2060	eval line2=\"$line2\"
2061	execute_command_for_combine="$line2"
2062	fi
2063
2064
2065
2066	# PROVIDE A HOSTFILE, IF REQUIRED
2067	if [[ "$hostfile" != "" ]]
2068	then
2069
2070	if [[ $hostfile = auto ]]
2071	then
2072	# CREATE A NEW HOSTFILE
2073	(( ii = 1 ))
2074	while (( ii <= cores / threads_per_task ))
2075	do
2076	echo $(hostname) >> hostfile
2077	(( ii = ii + 1 ))
2078	done
2079	if (( cores / threads_per_task == 0 ))
2080	then
2081	echo $(hostname) >> hostfile
2082	fi
2083
2084	else
2085	cp $hostfile hostfile
2086	fi
2087	eval line=\"`head -n $ii hostfile`\"
2088	printf "\n *** running on: $line"
2089	fi
2090
2091
2092
2093	# SET THE NUMBER OF OPENMP-THREADS
2094	if [[ $use_openmp = true ]]
2095	then
2096	export OMP_NUM_THREADS=$threads_per_task
2097	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2098	else
2099	export OMP_NUM_THREADS=1
2100	fi
2101
2102
2103	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2104	if [[ $run_coupled_model = false ]]
2105	then
2106	if [[ "$ocean_file_appendix" = true ]]
2107	then
2108	echo "precursor_ocean" > coupling_steering
2109	else
2110	echo "precursor_atmos" > coupling_steering
2111	fi
2112	else
2113	(( iia = $cores_atmos / $threads_per_task ))
2114	(( iio = $cores_ocean / $threads_per_task ))
2115	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2116	printf "\n\n"
2117	echo "coupled_run $iia $iio" > coupling_steering
2118	fi
2119
2120	printf "\n *** execute command:"
2121	printf "\n \"$execute_command\" \n\n"
2122
2123	$execute_command < coupling_steering
2124
2125	if [[ $? != 0 ]]
2126	then
2127
2128	# ABORT IN CASE OF RUNTIME ERRORS
2129	printf "\n +++ runtime error occured"
2130	locat=execution
2131	exit
2132
2133	else
2134
2135	printf "\n$dashes\n *** execution finished \n"
2136
2137	fi
2138
2139
2140	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2141	# BY EACH CORE INTO ONE FILE
2142	if [[ ! -f combine_plot_fields.x ]]
2143	then
2144
2145	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2146	printf "\n 2d- and/or 3d-data may be incomplete!"
2147	printf "\n Your previous palmbuild may have failed. Please check.\n"
2148
2149	elif [[ "$combine_plot_fields" == true ]]
2150	then
2151
2152	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2153	$execute_command_for_combine
2154
2155	else
2156
2157	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2158	# DATA OUTPUT
2159	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2160	fi
2161
2162
2163
2164	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2165	(( i = 0 ))
2166	while (( i < ioc ))
2167	do
2168	(( i = i + 1 ))
2169	if (( i == 1 ))
2170	then
2171	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2172	fi
2173	printf "\n >>> ${out_command[$i]}"
2174	eval ${out_command[$i]}
2175	if (( i == ioc ))
2176	then
2177	printf "\n$dashes\n"
2178	fi
2179	done
2180
2181
2182	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2183	# WILDCARDS
2184	(( i = 0 ))
2185	(( nr_of_output_files = 0 ))
2186
2187	while (( i < iout ))
2188	do
2189
2190	(( i = i + 1 ))
2191
2192	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2193	# CREATE A LIST FOR THE DETECTED ENDINGS
2194	if [[ "${multout[$i]}" = true ]]
2195	then
2196	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2197	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2198	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2199
2200	endings="DEFAULT"
2201	while read line
2202	do
2203	# remove the local name from the beginning
2204	localnamestring="${localout_pre[$i]}"
2205	length_localname=${#localnamestring}
2206	ending=${line:${length_localname}}
2207
2208	if [[ "$ending" != "" ]]
2209	then
2210	endings="$endings $ending"
2211	fi
2212
2213	done <filelist
2214
2215	rm filelist
2216
2217	else
2218
2219	# SINGLE NAME
2220	endings=DEFAULT
2221
2222	fi
2223
2224	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2225	for ending in $endings
2226	do
2227
2228	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2229	if [[ $ending = DEFAULT ]]
2230	then
2231	ending=""
2232	fi
2233
2234	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2235	(( nr_of_output_files = nr_of_output_files + 1 ))
2236	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2237	transout[$nr_of_output_files]="${transout_pre[$i]}"
2238	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2239	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2240	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2241	extout[$nr_of_output_files]="${extout_pre[$i]}"
2242	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2243
2244	done
2245
2246	done
2247
2248
2249
2250
2251	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2252	(( i = 0 ))
2253	while (( i < nr_of_output_files ))
2254	do
2255	(( i = i + 1 ))
2256	if (( i == 1 ))
2257	then
2258	printf "\n\n *** saving OUTPUT-files:"
2259
2260	# GET RUN NUMBER ASSIGNED BY PALM
2261	if [[ -f RUN_NUMBER ]]
2262	then
2263	read run_number < RUN_NUMBER
2264	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2265	usecycle_option="-U $run_number"
2266	else
2267	run_number=0
2268	usecycle_option=""
2269	fi
2270	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2271	then
2272	printf "\n *** in case of SCP transfers to local host"
2273	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2274	fi
2275	printf "\n$dashes"
2276	fi
2277
2278	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2279	then
2280
2281	eval filename=${pathout[$i]}/${fname}${endout[$i]}
2282
2283	# DETERMINE THE CYCLE NUMBER
2284	ls -1 -d $filename > filelist 2>/dev/null
2285	ls -1 -d $filename.* >> filelist 2>/dev/null
2286	while read line
2287	do
2288
2289	# filename without path (i.e. after the last "/")
2290	basefilename=$(basename ${line})
2291
2292	# check if there is an extension
2293	extension=${basefilename##*.}
2294	if [[ "$extension" = "${extout[$i]}" ]]
2295	then
2296	basefilename=${basefilename%.*}
2297	fi
2298
2299	# check for an existing cycle number
2300	cycle=${basefilename##*.}
2301	if [[ $cycle =~ ^-?[0-9]+$ ]]
2302	then
2303	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2304	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2305	(( icycle = $((10#$cycle)) + 1 ))
2306	else
2307	(( icycle = 1 ))
2308	fi
2309
2310	if (( icycle > maxcycle ))
2311	then
2312	(( maxcycle = icycle ))
2313	fi
2314
2315	done <filelist
2316	rm filelist
2317
2318
2319	# SET THE CYCLE NUMBER
2320	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2321	if [[ "${actionout[$i]}" = a ]]
2322	then
2323	(( maxcycle = maxcycle - 1 ))
2324	fi
2325
2326	(( cycnum[$i] = maxcycle ))
2327	pathout[$i]=$filename
2328
2329
2330	# ADD CYCLE NUMBER TO FILENAME
2331	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2332	if [[ "${actionout[$i]}" != "a" ]]
2333	then
2334	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2335	# WITH AN EXISTING CYCLE NUMBER
2336	if (( run_number >= cycnum[$i] ))
2337	then
2338	(( cycnum[$i] = run_number ))
2339	else
2340	if (( run_number > 0 ))
2341	then
2342	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2343	fi
2344	fi
2345	fi
2346	if (( cycnum[$i] > 0 ))
2347	then
2348	cyclestring=`printf "%03d" ${cycnum[$i]}`
2349	pathout[$i]=${pathout[$i]}.$cyclestring
2350	fi
2351	fi
2352
2353	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2354	files_for_cores=false; filetype=file
2355	link_local_output=false
2356	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2357	then
2358	files_for_cores=true; filetype=directory
2359	actionout[$i]=""
2360	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2361	then
2362	actionout[$i]=""
2363	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2364	then
2365	files_for_cores=true; filetype=directory
2366	link_local_output=true
2367	actionout[$i]=""
2368	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2369	then
2370	link_local_output
2371	actionout[$i]=""
2372	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2373	then
2374	files_for_cores=true; filetype=directory
2375	actionout[$i]="tr"
2376	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2377	then
2378	actionout[$i]="tr"
2379	fi
2380
2381	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2382	then
2383	if [[ ${warnout[$i]} = true ]]
2384	then
2385	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2386	fi
2387	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2388	then
2389	if [[ ${warnout[$i]} = true ]]
2390	then
2391	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2392	fi
2393	else
2394
2395
2396	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2397	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2398	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2399	then
2400	if [[ $running_on_remote = true ]]
2401	then
2402
2403	# SET OPTIONS FOR TRANSFER
2404	if [[ "${actionout[$i]}" = tr ]]
2405	then
2406	if [[ $files_for_cores = false ]]
2407	then
2408	catalog_option=""
2409	catalog_string=""
2410	else
2411	catalog_option="-c"
2412	catalog_string="/"
2413	fi
2414	append_option=""
2415	append_string=""
2416	else
2417	append_option="-A"
2418	append_string="append"
2419	fi
2420
2421	transfer_failed=false
2422	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2423	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2424
2425	# TRANSFER VIA SCP
2426	if [[ "$remote_loginnode" != "" ]]
2427	then
2428	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]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2429	else
2430	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
2431	fi
2432	[[ $? != 0 ]] && transfer_failed=true
2433
2434
2435	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2436	if [[ $transfer_failed = true ]]
2437	then
2438	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2439	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2440
2441	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2442	eval local_catalog=${pathout[$i]}
2443	if [[ ! -d $local_catalog ]]
2444	then
2445	printf " *** local directory does not exist. Trying to create:\n"
2446	printf " $local_catalog \n"
2447	mkdir -p $local_catalog
2448	fi
2449	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2450	transfer_problems=true
2451	fi
2452
2453	else
2454
2455	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2456	# BE COPIED OR APPENDED ON THIS MACHINE
2457	if [[ "${actionout[$i]}" = tr ]]
2458	then
2459	actionout[$i]=""
2460	else
2461	actionout[$i]="a"
2462	fi
2463	fi
2464	fi
2465
2466
2467	# APPEND ON THIS MACHINE
2468	if [[ "${actionout[$i]}" = "a" ]]
2469	then
2470	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2471	then
2472	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2473	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2474	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2475	else
2476	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2477	printf "\n ${pathout[$i]}\n"
2478	cat ${localout[$i]} >> ${pathout[$i]}
2479	fi
2480	fi
2481
2482	# COPY ON THIS MACHINE
2483	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2484	# ON DIFFERENT FILE-SYSTEMS
2485	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2486	then
2487
2488	# COPY IN CASE OF RUNS ON SINGLE CORES
2489	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2490	then
2491	printf "\n >>> OUTPUT: ${localout[$i]} to"
2492	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2493	if [[ $link_local_output = true ]]
2494	then
2495	printf " file will be linked\n"
2496	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2497	fi
2498	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2499	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2500	then
2501	if [[ $link_local_output = true ]]
2502	then
2503	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2504	fi
2505	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2506	else
2507	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2508	fi
2509	else
2510	printf "\n >>> OUTPUT: ${localout[$i]} to"
2511	printf "\n ${pathout[$i]}\n"
2512	if [[ $link_local_output = true ]]
2513	then
2514	printf " file will be linked\n"
2515	ln -f ${localout[$i]} ${pathout[$i]}
2516	fi
2517	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2518	if [[ ! -f "${pathout[$i]}" ]]
2519	then
2520	if [[ $link_local_output = true ]]
2521	then
2522	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2523	fi
2524	cp ${localout[$i]} ${pathout[$i]}
2525	else
2526	printf "+++ no copy because file ${pathout[$i]} exists\n"
2527	fi
2528	fi
2529
2530	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2531	then
2532
2533	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2534	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2535	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2536	printf "\n ${pathout[$i]}\n"
2537	if [[ $link_local_output = true ]]
2538	then
2539	printf " files will be linked\n"
2540	mkdir -p ${pathout[$i]}
2541	cd ${localout[$i]}
2542	for file in $(ls *)
2543	do
2544	ln -f $file ${pathout[$i]}
2545	done >\|/dev/null 2>&1
2546	cd $tempdir
2547	fi
2548
2549	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2550	if [[ ! -f "${pathout[$i]}/_000000" ]]
2551	then
2552	if [[ $link_local_output = true ]]
2553	then
2554	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2555	fi
2556	cp -r ${localout[$i]}/* ${pathout[$i]}
2557	fi
2558
2559	fi
2560	fi
2561	done
2562
2563	if (( i != 0 ))
2564	then
2565	if [[ $transfer_problems = true ]]
2566	then
2567	printf "\n$dashes\n *** OUTPUT-files saved"
2568	printf "\n +++ WARNING: some data transfers failed! \n"
2569	else
2570	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2571	fi
2572	fi
2573
2574
2575	# IF REQUIRED, START A RESTART-JOB
2576	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2577	if [[ -f CONTINUE_RUN ]]
2578	then
2579
2580	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2581	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2582	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2583	# -b START A BATCH JOB
2584	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2585	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2586	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2587
2588
2589	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2590	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2591	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2592	then
2593	prc=`echo $prc \| sed 's/#/r/g'`
2594	fi
2595
2596
2597	# START THE RESTART-JOB
2598	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2599	echo " $prc"
2600	printf "\n$dashes\n"
2601	if [[ $running_on_remote = true ]]
2602	then
2603
2604	echo "*** ssh will be used to initiate restart-runs!"
2605	echo " return_address=\"$return_address\" "
2606	echo " return_username=\"$local_username\" "
2607
2608	if [[ "$remote_loginnode" != "" ]]
2609	then
2610	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
2611	else
2612	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2613	fi
2614
2615	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2616	sleep 30
2617
2618	else
2619
2620	# START THE RESTART JOB ON THE LOCAL HOST
2621	eval $prc # THE ' MUST BE EVALUATED
2622	cd - > /dev/null
2623
2624	fi
2625	printf "\n$dashes\n *** restart-run initiated \n"
2626
2627
2628	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2629	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2630	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2631	# MAY BE VERY HUGE)
2632	(( i = 0 ))
2633	while (( i < nr_of_input_files ))
2634	do
2635	(( i = i + 1 ))
2636	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2637	then
2638	rm -r ${absnamein[$i]}
2639	fi
2640	done
2641
2642	fi
2643
2644
2645	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2646	cd $HOME
2647	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2648
2649
2650	else
2651
2652
2653	# PREPARING ACTIONS,
2654	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2655
2656	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2657	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2658	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2659	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2660	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2661	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2662	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2663	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2664	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2665	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2666	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2667	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2668	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2669	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2670	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2671	if [[ $create_remote_batch_job = true ]]
2672	then
2673	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2674	if [[ $do_trace = true ]]
2675	then
2676	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2677	fi
2678	elif [[ $create_batch_job = true ]]
2679	then
2680	palmrun_com=${palmrun_com}" -j"
2681	if [[ $do_trace = true ]]
2682	then
2683	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2684	fi
2685	fi
2686
2687
2688	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2689	# REMOTE HOST
2690	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2691	job_protocol_file=$job_protocol_file_local
2692	if [[ $create_remote_batch_job = true ]]
2693	then
2694	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2695	job_protocol_file=$job_protocol_file_remote
2696	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2697	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2698	fi
2699
2700
2701	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2702	jobfile=jobfile.$run_id
2703
2704
2705	# FIRST CREATE THE BATCH DIRECTIVES
2706	(( i = 0 ))
2707	while (( i < ibd ))
2708	do
2709	(( i = i + 1 ))
2710	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' \| sed 's/{{PREVIOUS_JOB}}/$previous_job/g' \| sed 's/{{TEMPDIR}}/$tempdir/g'`
2711	eval line=\"$line\"
2712	echo "$line" >> $jobfile
2713	done
2714	echo " " >> $jobfile
2715
2716
2717	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2718	# PROTOCOL
2719	if [[ $create_remote_batch_job = true ]]
2720	then
2721	echo "set +vx" >> $jobfile
2722	echo "trap '" >> $jobfile
2723	echo "set +vx" >> $jobfile
2724	echo "cd ${remote_jobcatalog}" >> $jobfile
2725	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2726
2727	# ADD THE BATCH DIRECTIVES
2728	(( i = 0 ))
2729	while (( i < ibdt ))
2730	do
2731	(( i = i + 1 ))
2732	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
2733	eval line=\"$line\"
2734	echo "$line" >> $jobfile
2735	done
2736	echo " " >> $jobfile
2737
2738	echo "set -x" >> $jobfile
2739	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
2740	echo "%%END%%" >> $jobfile
2741	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2742	echo "$submit_command $scpjob_file" >> $jobfile
2743	echo "rm $scpjob_file" >> $jobfile
2744	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2745	echo "set -x" >> $jobfile
2746	echo " ' exit" >> $jobfile
2747	fi
2748
2749
2750	# ACTIVATE ERROR-TRACEBACK
2751	if [[ $do_trace = true ]]
2752	then
2753	echo "set -x" >> $jobfile
2754	else
2755	echo "set +vx" >> $jobfile
2756	fi
2757
2758
2759	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2760	if [[ "$login_init_cmd" != "" ]]
2761	then
2762	echo "$login_init_cmd" >> $jobfile
2763	fi
2764	if [[ "$module_commands" != "" ]]
2765	then
2766	echo "$module_commands" >> $jobfile
2767	fi
2768
2769
2770	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2771	if [[ $create_remote_batch_job = true ]]
2772	then
2773	echo "mkdir $tempdir" >> $jobfile
2774	echo "chmod go+rx $tempdir" >> $jobfile
2775	else
2776	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2777	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2778	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2779	mkdir $tempdir
2780	chmod go+rx $tempdir
2781	fi
2782	echo "cd $tempdir" >> $jobfile
2783	echo "export tempdir=$tempdir" >> $jobfile
2784	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2785	echo "export PATH=.:\$PATH" >> $jobfile
2786	echo "export execute_palmrun=true" >> $jobfile
2787
2788
2789	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2790	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2791	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2792	echo "LOCAL_PWD=$working_directory" >> $jobfile
2793	echo "export LOCAL_PWD" >> $jobfile
2794
2795
2796	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2797	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2798	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2799
2800
2801	# CALL PALMRUN WITHIN THE JOB
2802	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2803	echo "set -x" >> $jobfile
2804	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2805
2806
2807	# TRANSFER JOBFILE TO THE TARGET HOST
2808	if [[ $create_jobfile_only = false ]]
2809	then
2810
2811	if [[ $create_remote_batch_job = true ]]
2812	then
2813
2814	echo " "
2815	echo " *** transfer of job to remote host via scp"
2816	if [[ $do_trace = true ]]
2817	then
2818	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2819	fi
2820	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2821
2822	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2823	if [[ $do_trace = true ]]
2824	then
2825	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"
2826	fi
2827	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
2828
2829	elif [[ $create_batch_job = true ]]
2830	then
2831
2832	eval local_jobcatalog=$local_jobcatalog
2833	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2834	cd $local_jobcatalog
2835	echo " "
2836	echo " *** submit the job"
2837	if [[ $do_trace = true ]]
2838	then
2839	echo "$submit_command ${host_configuration}_${job_id}"
2840	fi
2841	$submit_command ${host_configuration}_${job_id}
2842	rm ${host_configuration}_${job_id}
2843	cd - > /dev/null
2844
2845	fi
2846
2847	rm -rf $jobfile
2848
2849	else
2850
2851	printf "\n *** jobfile created under name \"$jobfile\" "
2852	printf "\n no batch-job has been sent!"
2853
2854	fi
2855
2856	fi # END OF REMOTE-PART

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