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source: palm/trunk/SCRIPTS/palmrun @ 3196

Last change on this file since 3196 was 3151, checked in by raasch, 6 years ago
output of PALM code revision number in palmrun header, some preprocessor define strings removed, small revisions in configuration files
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 98.3 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 3151 2018-07-19 08:45:38Z maronga $
29	# removed additional listing of files to be compiled, print PALM code revision
30	# in header
31	#
32	# 3132 2018-07-16 11:44:58Z raasch
33	# create consistent error messages in case of failed restarts,
34	# check existence of remote job catalog
35	#
36	# 3043 2018-05-25 10:47:54Z raasch
37	# check for setting of fast_io_catalog
38	#
39	# 3033 2018-05-23 15:26:19Z raasch
40	# -T option not required for interactive runs (tasks per node =
41	# total number of cores is assumed as default, if option is not given),
42	# reformatting of a few messages,
43	# bugfix: destination output directory is created if attribute "pe" is set in
44	# .palm.iofiles
45	#
46	# 2718 2018-01-02 08:49:38Z maronga
47	# bugfix of r2990
48	#
49	# 2718 2018-01-02 08:49:38Z maronga
50	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
51	# not in the working directory from where palmrun is called
52	#
53	# 2718 2018-01-02 08:49:38Z maronga
54	# svfout in the activation string will be replaced now by svfin in case of
55	# automatic restarts
56	#
57	# 2718 2018-01-02 08:49:38Z maronga
58	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
59	# the possible output or input of sky view factors
60	#
61	# 2718 2018-01-02 08:49:38Z maronga
62	# "fname" renamed to "jobname"
63	#
64	# 2718 2018-01-02 08:49:38Z maronga
65	# parameters are allowed in output commands (OC:)
66	#
67	# 2718 2018-01-02 08:49:38Z maronga
68	# bugfix: exit if no queue has been given neither with option -q nor in the
69	# configuration file
70	#
71	# 2718 2018-01-02 08:49:38Z maronga
72	# file connection file from trunk/SCRIPTS is taken by default
73	#
74	# 2718 2018-01-02 08:49:38Z maronga
75	# Corrected "Former revisions" section
76	#
77	# 2696 2017-12-14 17:12:51Z kanani
78	# Change in file header (GPL part)
79	#
80	# 2693 2017-12-13 12:33:49Z raasch
81	# replacement of variables given by {{<variable>}} in configuration file is now
82	# done in a more general way, variable names are written in small letters
83	#
84	# 2670 2017-12-06 16:32:19Z raasch
85	# test printouts removed
86	#
87	# 2669 2017-12-06 16:03:27Z raasch
88	# file attributes in .palm.iofiles restructured, "loc" attribute completely
89	# removed,
90	# wildcard (*) allowed in .palm.iofiles as file activation string for output
91	# files,
92	# informative messages in case of missing optional input files shortened
93	# bugfix: variable cycle explicitly interpreted with 10 as the number base
94	#
95	# 2638 2017-11-23 12:44:23Z raasch
96	# use of wildcards in file connection statements enabled
97	#
98	# 2605 2017-11-09 15:31:46Z raasch
99	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
100	# will not be sent with the job file any more, but copied into the
101	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
102	#
103	# 2600 2017-11-01 14:11:20Z raasch
104	# cycle numbers are made three digits wide
105	#
106	# 2566 2017-10-20 08:50:47Z raasch
107	# execute command for combine_plot_fields added
108	# "TEMPDIR" renamed "tempdir"
109	# temporary working directory for local batch jobs is created immediately within
110	# the user's palmrun call, due to a requirement of the "grid engine" batch
111	# system, where the working directory is given with batch directive -wd and must
112	# already exist when the job is submitted,
113	# informative messages in non-trace mode reduced and partly reformatted
114	#
115	# 2551 2017-10-18 07:25:11Z raasch
116	# TEMPDIR added as replacement string to be used in batch directives
117	#
118	# 2512 2017-10-04 08:26:59Z raasch
119	# bugfix for determining cycle numbers of NetCDF input files
120	#
121	# 2506 2017-09-29 08:30:37Z raasch
122	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
123	# host configuration added to SOURCES_FOR_RUN_... folder name
124	# host_identifier renamed host_configuration
125	# option -W added to allow for job dependencies
126	#
127	# 2501 2017-09-26 11:41:55Z raasch
128	# default value for number of cores (option -X) set to 1
129	# bugfix for mechanism which overwrites configuration file settings with values
130	# provided by palmrun options
131	#
132	# 2499 2017-09-22 16:47:58Z kanani
133	# option -h named configuration identifier
134	#
135	# 2480 2017-09-19 06:24:14Z maronga
136	# bugfix for last revision
137	#
138	# 2479 2017-09-19 06:12:16Z raasch
139	# option -A (project account number) added
140	#
141	# 2422 2017-09-08 08:25:41Z raasch
142	# initial revision
143	#
144	#--------------------------------------------------------------------------------#
145	# palmrun - script for running PALM jobs on local and remote hosts
146	#--------------------------------------------------------------------------------#
147
148
149
150	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
151
152	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
153	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
154	# (TOO MANY ARGUMENTS - PROBLEM)
155	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
156
157	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
158	typeset -i nr_of_output_files=0
159	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
160	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
161	# SCRIPT-OPTION ARGUMENTS
162	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
163	typeset -i icycle inode ival maxcycle mpi_tasks
164	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
165
166	activation_string_list=""
167	AddFilenames=""
168	combine_plot_fields=true
169	compiler_name=""
170	compiler_name_ser=""
171	compiler_options=""
172	cores=1
173	cores_atmos=0
174	cores_ocean=0
175	coupled_dist=""
176	cpp_options=""
177	cpumax=0
178	create_batch_job=false
179	create_jobfile_only=false
180	create_remote_batch_job=false
181	dashes=" ----------------------------------------------------------------------------"
182	defaultqueue=""
183	delete_temporary_catalog=true
184	do_compile=true
185	do_trace=false
186	executable=""
187	execute_command=""
188	execution_error=false
189	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
190	jobname=test
191	global_revision=""
192	host_configuration="default"
193	hostfile=""
194	hp=""
195	keep_data_from_previous_run=false
196	link_local_input=false
197	link_local_output=false
198	linker_options=""
199	local_jobcatalog=""
200	locat=normal
201	makefile=""
202	max_par_io_str=""
203	prc=$0
204	while [[ $(echo $prc \| grep -c "/") != 0 ]]
205	do
206	prc=`echo $prc \| cut -f2- -d"/"`
207	done
208	module_calls=""
209	palmrun_memory=""
210	palmrun_script_name=$prc
211	openmp=false
212	previous_job=""
213	project_account=""
214	queue=none
215	read_svf=""
216	restart_run=false
217	return_address=""
218	remote_jobcatalog=""
219	remote_username=""
220	running_in_batch_mode=false
221	run_coupled_model=false
222	run_id=""
223	silent=false
224	source_list=""
225	source_path=""
226	tasks_per_node=0
227	threads_per_task=1
228	transfer_problems=false
229	user_source_path=""
230	use_existing_sources_folder=""
231	use_openmp=false
232	version="palmrun 1.0 Rev$Rev: 3151 $"
233	working_directory=`pwd`
234	write_binary=""
235	write_svf=""
236
237
238	# ERROR HANDLING IN CASE OF EXIT
239	trap 'if [[ $locat != normal && $locat != control_c ]]
240	then
241
242	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
243	(( i = 0 ))
244	while (( i < iec ))
245	do
246	(( i = i + 1 ))
247	printf "\n *** Execution of ERROR-command:\n"
248	printf " >>> ${err_command[$i]}\n"
249	eval ${err_command[$i]}
250	done
251	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
252	printf "\n\n+++ palmrun killed \n\n"
253	elif [[ $locat != control_c ]]
254	then
255	printf "\n --> palmrun finished\n\n"
256	fi' exit
257
258
259	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
260	trap 'cd; rm -rf $tempdir
261	printf "\n+++ palmrun killed by \"^C\" \n\n"
262	locat=control_c
263	exit
264	' 2
265
266
267	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
268	# WHICH WILL BE USED TO START RESTART-JOBS
269	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
270	do
271	case $option in
272	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
273	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
274	(b) create_batch_job=true; prc="$prc -b";;
275	(B) delete_temporary_catalog=false; prc="$prc -B";;
276	(C) restart_run=true; prc="$prc -C";;
277	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
278	(F) create_jobfile_only=true;;
279	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
280	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
281	(j) running_in_batch_mode=true;;
282	(k) keep_data_from_previous_run=true; prc="$prc -k";;
283	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
284	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
285	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
286	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
287	(r) run_id=$OPTARG;;
288	(R) return_address=$OPTARG;;
289	(s) source_list=$OPTARG;;
290	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
291	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
292	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
293	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
294	(v) silent=true; prc="$prc -v";;
295	(V) use_existing_sources_folder="-V";;
296	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
297	(W) previous_job=$OPTARG;;
298	(x) do_trace=true;set -x; prc="$prc -x";;
299	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
300	(y) ocean_file_appendix=true; prc="$prc -y";;
301	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
302	(Z) combine_plot_fields=false; prc="$prc -Z";;
303	(\?) printf "\n +++ unknown option $OPTARG \n"
304	printf "\n --> type \"$0 ?\" for available options \n"
305	locat=parameter;exit;;
306	esac
307	done
308
309
310	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
311	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
312	(( to_shift = $OPTIND - 1 ))
313	shift $to_shift
314
315	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
316	if [[ "$1" = "?" ]]
317	then
318	(printf "\n *** Description of available palmrun options:\n"
319	printf "\n Option Description Default-Value"
320	printf "\n -a activation string list \"\" "
321	printf "\n -A project account number ---"
322	printf "\n -b batch-job on local machine ---"
323	printf "\n -B do not delete temporary directory at end ---"
324	printf "\n -d run identifier test"
325	printf "\n -F create batch job file only ---"
326	printf "\n -h host configuration \"default\" "
327	printf "\n -k keep data from previous run"
328	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
329	printf "\n -M Makefile name Makefile"
330	printf "\n -O threads per openMP task ---"
331	printf "\n -q queue \"$queue\" "
332	printf "\n -s filenames of routines to be compiled \"\" "
333	printf "\n must end with .f, .f90, .F, or .c !"
334	printf "\n use \"..\" for more than one file and wildcards"
335	printf "\n -s LM compiles all locally modified files"
336	printf "\n -t allowed cpu-time in seconds (batch) 0"
337	printf "\n -T tasks per node ---"
338	printf "\n -u username on remote machine \"\" "
339	printf "\n -v no prompt for confirmation ---"
340	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
341	printf "\n -w maximum parallel io streams as given by -X"
342	printf "\n -W name of job to wait for ---"
343	printf "\n -x tracing of palmrun for debug purposes ---"
344	printf "\n -X # of processors (on parallel machines) 1"
345	printf "\n -y add appendix \"_O\" to all local output"
346	printf "\n files (ocean precursor runs followed by"
347	printf "\n coupled atmosphere-ocean runs) ---"
348	printf "\n -Y run coupled model, \"#1 #2\" with"
349	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
350	printf "\n -Z skip combine_plot_fields at the end of "
351	printf "\n the simulation ---"
352	printf "\n "
353	printf "\n Possible values of positional parameter <modus>:"
354	printf "\n \"?\" - this outline \n\n") \| more
355	exit
356	elif [[ "$1" != "" ]]
357	then
358	printf "\n +++ positional parameter $1 unknown \n"
359	locat=parameter; exit
360	fi
361
362
363
364	# SHORT STARTING MESSAGE
365	printf "\n*** $version "
366	printf "\n will be executed. Please wait ..."
367
368
369	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
370	export fname=$jobname
371
372
373	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
374	config_file=.palm.config.$host_configuration
375	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
376
377
378	# CHECK, IF CONFIGURATION FILE EXISTS
379	if [[ ! -f $config_file ]]
380	then
381	printf "\n\n +++ configuration file: "
382	printf "\n $config_file"
383	printf "\n does not exist"
384	locat=connect; exit
385	fi
386
387
388	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
389	if [[ -f .palm.iofiles ]]
390	then
391	fileconnection_file=.palm.iofiles
392	fi
393
394
395	# CHECK, IF FILE CONNECTION FILE EXISTS
396	if [[ ! -f $fileconnection_file ]]
397	then
398	printf "\n\n +++ file connection file: "
399	printf "\n $fileconnection_file"
400	printf "\n does not exist"
401	locat=connect; exit
402	fi
403
404
405	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
406	if [[ "$activation_string_list" = "" ]]
407	then
408	printf "\n\n +++ no activation string list given: "
409	printf "\n please set palmrun option \"-a\" "
410	locat=palmrun_option; exit
411	fi
412
413
414	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
415	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
416	then
417	write_binary=true
418	else
419	write_binary=false
420	fi
421
422	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
423	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
424	then
425	write_svf=true
426	else
427	write_svf=false
428	fi
429
430	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
431	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
432	then
433	read_svf=true
434	else
435	read_svf=false
436	fi
437
438
439	# READ AND EVALUATE THE CONFIGURATION-FILE
440	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
441
442	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
443	while read line
444	do
445
446	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
447	eval line=\"$line\"
448
449
450	# INTERPRET THE LINE
451	if [[ "$(echo $line)" = "" ]]
452	then
453
454	# EMPTY LINE, NO ACTION
455	continue
456
457	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
458	then
459
460	# LINE IS A COMMENT LINE
461	continue
462
463	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
464	then
465
466	# LINE DEFINES AN ENVIRONMENT-VARIABLE
467	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
468	value=`echo $line \| cut -d" " -s -f2-`
469
470
471	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
472	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
473	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
474	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
475	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
476	# CONFIGURATION-FILE.
477	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
478	then
479	eval export $var="\$value"
480
481	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
482	if [[ $do_trace = true ]]
483	then
484	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
485	fi
486	fi
487
488	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
489	then
490
491	# LINE DEFINES BATCH-DIRECTIVE
492	(( ibd = ibd + 1 ))
493	line=$(echo $line \| cut -c4-)
494	batch_directive[$ibd]="$line"
495
496	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
497	then
498
499	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
500	# REMOTE TO A LOCAL HOST
501	(( ibdt = ibdt + 1 ))
502	line=$(echo $line \| cut -c5-)
503	batch_directive_transfer[$ibdt]="$line"
504
505	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
506	then
507
508	# LINE DEFINES ERROR-COMMAND
509	(( iec = iec + 1 ))
510	line=$(echo $line \| cut -c4-)
511	err_command[$iec]="$line"
512
513	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
514	then
515
516	# LINE DEFINES INPUT-COMMAND
517	(( iic = iic + 1 ))
518	line=$(echo $line \| cut -c4-)
519	in_command[$iic]="$line"
520
521	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
522	then
523
524	# LINE DEFINES OUTPUT-COMMAND
525	(( ioc = ioc + 1 ))
526	line=$(echo $line \| cut -c4-)
527	out_command[$ioc]="$line"
528
529	else
530
531	# SKIP ALL OTHER LINES
532	continue
533
534	fi
535
536	done < $config_file
537
538
539	# CHECK SETTING OF REQUIRED PARAMETERS
540	if [[ "$fast_io_catalog" = "" ]]
541	then
542	printf "\n +++ no fast_io_catalog found in $config_file"
543	printf "\n Please add line \"fast_io_catalog ...\" to that file."
544	locat=config_file; exit
545	fi
546	if [[ "$compiler_name" = "" ]]
547	then
548	printf "\n +++ no compiler name found in $config_file"
549	printf "\n Please add line \"compiler_name ...\" to that file."
550	locat=config_file; exit
551	fi
552	if [[ "$compiler_name_ser" = "" ]]
553	then
554	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
555	printf "\n Please add line \"compiler_name_ser ...\" to that file."
556	locat=config_file; exit
557	fi
558	if [[ "$compiler_options" = "" ]]
559	then
560	printf "\n +++ no compiler options found in $config_file"
561	printf "\n Please add line \"compiler_options ...\" to that file."
562	locat=config_file; exit
563	fi
564	if [[ "$linker_options" = "" ]]
565	then
566	printf "\n +++ no linker options found in $config_file"
567	printf "\n Please add line \"linker_options ...\" to that file."
568	locat=config_file; exit
569	fi
570	if [[ "$execute_command" = "" ]]
571	then
572	printf "\n +++ no execute command found in $config_file"
573	printf "\n Please add line \"execute_command ...\" to that file."
574	locat=config_file; exit
575	fi
576
577	if [[ "$hostfile" != "" ]]
578	then
579	if [[ $hostfile != auto && ! -f $hostfile ]]
580	then
581	printf "\n +++ no hostfile \"$hostfile\" found"
582	printf "\n Please check line \"hostfile ...\" in $config_file"
583	locat=config_file; exit
584	fi
585	fi
586
587
588	# DETERMINE THE CALL STATUS
589	if [[ "$return_address" != "" ]]
590	then
591
592	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
593	# BATCH MODE AND ...
594	running_on_remote=true
595
596	else
597
598	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
599	if [[ "$remote_ip" != "" ]]
600	then
601
602	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
603	create_remote_batch_job=true
604
605	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
606	if [[ "$remote_jobcatalog" = "" ]]
607	then
608	printf "\n +++ no remote jobcatalog found in $config_file"
609	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
610	locat=config_file; exit
611	fi
612
613
614	fi
615	running_on_remote=false
616	fi
617
618
619
620	# READ AND EVALUATE THE I/O-FILE LIST
621	[[ $silent = false ]] && printf "\n Reading the I/O files... "
622
623	# READ THE FILE CONNECTION FILE LINE BY LINE
624	while read line
625	do
626
627	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
628	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
629
630	# INTERPRET THE LINE
631	if [[ "$(echo $line)" = "" ]]
632	then
633	# EMPTY LINE, NO ACTION
634	continue
635
636	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
637	then
638
639	# LINE IS A COMMENT LINE
640	true
641
642	else
643
644	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
645	# s2a: in/out - field
646	# s2b: action - field (optional)
647	s1=`echo "$line" \| cut -d" " -f1`
648	s2=`echo "$line" \| cut -d" " -s -f2`
649	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
650	then
651	s2a=$s2
652	s2b=""
653	else
654	s2a=`echo $s2 \| cut -d":" -f1`
655	s2b=`echo $s2 \| cut -d":" -f2`
656	fi
657	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
658	s4=`echo "$line" \| cut -d" " -s -f4`
659	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
660	s5=`echo "$line" \| cut -d" " -s -f5`
661	s6=`echo "$line" \| cut -d" " -s -f6`
662
663
664	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
665	# INPUT- OR OUTPUT-LIST.
666	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
667	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
668	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
669	# IS NOT CHECKED AND STORED.
670	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
671	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
672	then
673	found=false
674	for actual in $activation_string_list
675	do
676	for formal in $s3
677	do
678	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
679	done
680	done
681	if [[ $found = true ]]
682	then
683	(( iin = iin + 1 ))
684	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
685	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
686	if [[ "$s2a" = inopt ]]
687	then
688	optin_pre[$iin]=yes
689	else
690	optin_pre[$iin]=no
691	fi
692
693	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
694	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
695	if [[ $running_on_remote = true && "$s2b" = tr ]]
696	then
697	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
698	fi
699
700	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
701	# THE WILDCARD FROM THE ENDING
702	if [[ "${s5: -1}" = "*" ]]
703	then
704	if [[ "$s2b" = "di" ]]
705	then
706	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
707	printf "\n see file \"$fileconnection_file\", line"
708	printf "\n$line"
709	locat=iofiles_file; exit
710	fi
711	multin[$iin]=true
712	string=${endin_pre[$iin]}
713	endin_pre[$iin]="${string%?}"
714	else
715	multin[$iin]=false
716	fi
717	fi
718	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
719	then
720	found=false
721	for actual in $activation_string_list
722	do
723	for formal in $s3
724	do
725	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
726	done
727	done
728	if [[ $found = true ]]
729	then
730	(( iout = iout + 1 ))
731	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
732	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
733
734	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
735	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
736	if [[ $formal = wildcard ]]
737	then
738	warnout_pre[$iout]=false
739	else
740	warnout_pre[$iout]=true
741	fi
742
743	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
744	# THE WILDCARD FROM THE LOCAL FILENAME
745	if [[ "${s1: -1}" = "*" ]]
746	then
747	if [[ "$s2b" = "di" ]]
748	then
749	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
750	printf "\n see file \"$fileconnection_file\", line"
751	printf "\n$line"
752	locat=iofiles_file; exit
753	fi
754	multout[$iout]=true
755	string=${localout_pre[$iout]}
756	localout_pre[$iout]="${string%?}"
757	else
758	multout[$iout]=false
759	fi
760	fi
761	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
762	then
763	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
764	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
765	locat=connect; exit
766	fi
767	IFS="$IFSALT"
768	fi
769
770	done < $fileconnection_file
771
772
773
774	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
775	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
776	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
777	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
778	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
779	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
780
781
782
783	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
784	if [[ $run_coupled_model = true ]]
785	then
786
787	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
788	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
789
790	if (( $cores_ocean + $cores_atmos != $cores ))
791	then
792
793	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
794	printf "\n PEs (total) : $cores"
795	printf "\n PEs (atmosphere): $cores_atmos"
796	printf "\n PEs (ocean) : $cores_ocean"
797	locat=coupling; exit
798
799	fi
800
801	fi
802
803
804	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
805	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
806	# FOLDER
807	if [[ $running_in_batch_mode = true ]]
808	then
809
810	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
811	then
812	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
813	printf "\n Please check the output of the palmrun-call"
814	printf "\n that you did on your local host."
815	locat=SOURCES_FOR_RUN; exit
816	fi
817
818	else
819
820	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
821	# AUTOMATIC RESTART RUN
822	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
823	if [[ $restart_run = false ]]
824	then
825
826	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
827	# THE LOCAL HOST
828	if [[ ! -d $source_path ]]
829	then
830	printf "\n\n +++ source path \"$source_path\" on local host"
831	printf "\n \"$(hostname)\" does not exist"
832	locat=source_path; exit
833	fi
834
835	rm -rf ${base_directory}/${sources_for_run_catalog}
836	mkdir -p ${base_directory}/${sources_for_run_catalog}
837
838	if [[ "$source_list" = LM ]]
839	then
840
841	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
842	source_list=""
843	cd $source_path
844
845
846	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
847	if [[ ! -d ../.svn ]]
848	then
849	printf "\n\n +++ source directory"
850	printf "\n \"$source_path\" "
851	printf "\n is not under control of \"subversion\"."
852	printf "\n Please do not use palmrun-option \"-s LM\"\n"
853	fi
854
855
856	# LIST ALL MODIFIED SOURCE CODE FILES
857	Filenames=""
858	svn status > tmp_svnstatus
859	while read line
860	do
861	firstc=`echo $line \| cut -c1`
862	if [[ $firstc = M \|\| $firstc = "?" ]]
863	then
864	Name=`echo "$line" \| cut -c8-`
865	extension=`echo $Name \| cut -d. -f2`
866	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
867	then
868	Filenames="$Filenames "$Name
869	fi
870	fi
871	done < tmp_svnstatus
872	rm -rf tmp_svnstatus
873
874
875	# COPY FILES TO SOURCES_FOR_RUN_...
876	for filename in $Filenames
877	do
878	cp $filename ${base_directory}/${sources_for_run_catalog}
879	source_list=$source_list"$filename "
880	done
881
882	cd - > /dev/null
883
884
885	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
886	elif [[ "$source_list" != "" ]]
887	then
888
889	cd $source_path
890
891	for filename in $source_list
892	do
893
894	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
895	if [[ $(echo $filename \| grep -c "/") != 0 ]]
896	then
897	printf "\n +++ source code file: $filename"
898	printf "\n must not contain (\"/\") "
899	locat=source; exit
900	fi
901
902	if [[ ! -f $filename ]]
903	then
904	printf "\n +++ source code file: $filename"
905	printf "\n does not exist"
906	locat=source; exit
907	else
908	cp $filename ${base_directory}/${sources_for_run_catalog}
909	fi
910
911	done
912
913	cd - > /dev/null
914
915	fi
916
917	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
918	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
919	if [[ ! -f $makefile ]]
920	then
921	printf "\n +++ file \"$makefile\" does not exist"
922	locat=make; exit
923	else
924	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
925	fi
926
927
928	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
929	if [[ "$user_source_path" != "" ]]
930	then
931
932	# DOES THE DIRECTORY EXIST?
933	if [[ ! -d $user_source_path ]]
934	then
935
936	printf "\n\n *** INFORMATIVE: additional source code directory"
937	printf "\n \"$user_source_path\" "
938	printf "\n does not exist or is not a directory."
939	printf "\n No source code will be used from this directory!\n"
940	user_source_path=""
941	if [[ $silent == false ]]
942	then
943	sleep 2
944	fi
945
946	else
947
948	cd $user_source_path
949
950	Names=$(ls -1 *.f90 2>&1)
951	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
952	Names=$(ls -1 *.F90 2>&1)
953	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
954	Names=$(ls -1 *.F 2>&1)
955	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
956	Names=$(ls -1 *.f 2>&1)
957	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
958	Names=$(ls -1 *.c 2>&1)
959	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
960
961	cd - > /dev/null
962	cd ${base_directory}/${sources_for_run_catalog}
963
964	# COPY MAKEFILE IF EXISTING
965	if [[ -f $user_source_path/Makefile ]]
966	then
967	printf "\n\n *** user Makefile from directory"
968	printf "\n \"$user_source_path\" is used \n"
969	if [[ $silent == false ]]
970	then
971	sleep 1
972	fi
973	cp $user_source_path/Makefile .
974	fi
975
976	for filename in $AddFilenames
977	do
978	if [[ -f $filename ]]
979	then
980	printf "\n +++ source code file \"$filename\" found in additional"
981	printf "\n source code directory \"$user_source_path\" "
982	printf "\n but was also given with option \"-s\" which means that it should be taken"
983	printf "\n from directory \"$source_path\"."
984	locat=source; exit
985	fi
986
987	cp $user_source_path/$filename .
988	source_list="$source_list $filename"
989
990	# CHECK IF FILE IS CONTAINED IN MAKEFILE
991	if [[ $(grep -c $filename Makefile) = 0 ]]
992	then
993	printf "\n\n +++ user file \"$filename\" "
994	printf "\n is not listed in Makefile \n"
995	locat=source; exit
996	fi
997	done
998	cd - > /dev/null
999	fi
1000	fi
1001
1002	# COPY CONFIGURATION FILES
1003	cp $config_file ${base_directory}/${sources_for_run_catalog}
1004	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1005
1006	# COPY SHELLSCRIPTS
1007	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1008	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1009
1010	fi
1011
1012	fi
1013
1014
1015	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1016	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1017	if [[ "$global_revision" = "" ]]
1018	then
1019	global_revision=`svnversion $source_path 2>/dev/null`
1020	global_revision="Rev: $global_revision"
1021	fi
1022
1023
1024	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1025	if [[ -n $cores ]]
1026	then
1027
1028	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1029	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1030	if [[ $tasks_per_node = 0 ]]
1031	then
1032	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1033	then
1034	printf "\n"
1035	printf "\n +++ option \"-T\" (tasks per node) is missing"
1036	printf "\n set -T option or define tasks_per_node in the config file"
1037	locat=tasks_per_node; (( iec = 0 )); exit
1038	else
1039	# DEFAULT FOR INTERACTIVE RUN
1040	tasks_per_node=$cores
1041	fi
1042	fi
1043
1044	if (( cores < tasks_per_node ))
1045	then
1046	printf "\n"
1047	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1048	printf "\n given values: -T $tasks_per_node -X $cores"
1049	locat=tasks_per_node; (( iec = 0 )); exit
1050	fi
1051
1052	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1053	(( mpi_tasks = cores / threads_per_task ))
1054	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1055	(( ii = cores / tasks_per_node ))
1056	(( remaining_cores = cores - ii * tasks_per_node ))
1057	if (( remaining_cores > 0 ))
1058	then
1059	printf "\n"
1060	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1061	printf "\n divisor of the total number of cores (option \"-X\")"
1062	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1063	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1064	(( nodes = nodes + 1 ))
1065	fi
1066
1067	fi
1068
1069
1070	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1071	if [[ "$maximum_parallel_io_streams" = "" ]]
1072	then
1073	maximum_parallel_io_streams=$cores
1074	fi
1075
1076
1077	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1078	if [[ "$scp_port" != "" ]]
1079	then
1080	PORTOPT="-P $scp_port"
1081	SSH_PORTOPT="-p $scp_port"
1082	fi
1083
1084
1085	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1086	# CONFIG-FILE
1087	if [[ "$ssh_key" != "" ]]
1088	then
1089	ssh_key="-i $HOME/.ssh/$ssh_key"
1090	fi
1091
1092
1093	# SET QUEUE, IF NOT GIVEN
1094	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1095	then
1096
1097	if [[ $queue = none && "$defaultqueue" = "" ]]
1098	then
1099	printf "\n"
1100	printf "\n +++ no default queue given in configuration file and no queue"
1101	printf "\n given with option -q"
1102	locat=queue; exit
1103	fi
1104	if [[ $queue = none ]]
1105	then
1106	queue=$defaultqueue
1107	fi
1108
1109	fi
1110
1111
1112	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1113	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1114	(( i = 0 ))
1115	(( nr_of_input_files = 0 ))
1116	while (( i < iin ))
1117	do
1118	(( i = i + 1 ))
1119
1120	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1121	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1122	if [[ "${actionin_pre[$i]}" = di ]]
1123	then
1124	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1125	else
1126	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
1127	fi
1128
1129
1130	# CHECK IF FILE EXISTS
1131	if ! ls $filename* 1>/dev/null 2>&1
1132	then
1133
1134	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1135	if [[ "${optin_pre[$i]}" != "yes" ]]
1136	then
1137	printf "\n\n +++ INPUT-file: "
1138	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1139	then
1140	printf "\n $filename"
1141	else
1142	printf "\n $filename.${extin_pre[$i]}"
1143	fi
1144	printf "\n does not exist\n"
1145	locat=input; exit
1146	else
1147	(( nr_of_input_files = nr_of_input_files + 1 ))
1148	localin[$nr_of_input_files]="${localin_pre[$i]}"
1149	optin[$nr_of_input_files]="${optin_pre[$i]}"
1150	actionin[$nr_of_input_files]="unavailable"
1151	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1152	endin[$nr_of_input_files]="${endin_pre[$i]}"
1153	extin[$nr_of_input_files]="${extin_pre[$i]}"
1154	fi
1155
1156	else
1157
1158	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
1159	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1160	if [[ "${multin[$i]}" = true ]]
1161	then
1162	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1163	ls -1 -d ${filename} > filelist 2>/dev/null
1164	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1165	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1166
1167	endings=""
1168	while read line
1169	do
1170	# filename without path (i.e. after the last "/")
1171	basefilename=$(basename ${line})
1172
1173	# check if there is an extension and remove it
1174	ext=${basefilename##*.}
1175	if [[ "$ext" = "${extin_pre[$i]}" ]]
1176	then
1177	basefilename=${basefilename%.*}
1178	fi
1179
1180	# check for an existing cycle number and remove it
1181	cycle=${basefilename##*.}
1182	if [[ $cycle =~ ^-?[0-9]+$ ]]
1183	then
1184	basefilename=${basefilename%.*}
1185	fi
1186
1187	# remove the jobname from the beginning
1188	length_jobname=${#jobname}
1189	ending=${basefilename:${length_jobname}}
1190
1191	# remove the ending given in the .iofiles from the beginning
1192	endingstring="${endin_pre[$i]}"
1193	length_ending=${#endingstring}
1194	ending=${ending:${length_ending}}
1195
1196	if [[ "$ending" = "" ]]
1197	then
1198	# standard ending as given in the .iofiles
1199	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1200	then
1201	endings="$endings DEFAULT"
1202	fi
1203	else
1204	# ending must start with "_", otherwise its a different file
1205	if [[ "${ending:0:1}" = "_" ]]
1206	then
1207	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1208	then
1209	endings="$endings $ending"
1210	fi
1211	fi
1212	fi
1213
1214	done <filelist
1215
1216	rm filelist
1217
1218	else
1219
1220	# SINGLE NAME
1221	endings=DEFAULT
1222
1223	fi
1224
1225	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1226	for ending in $endings
1227	do
1228
1229	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1230	if [[ $ending = DEFAULT ]]
1231	then
1232	ending=""
1233	fi
1234
1235	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1236	(( nr_of_input_files = nr_of_input_files + 1 ))
1237	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1238	optin[$nr_of_input_files]="${optin_pre[$i]}"
1239	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1240	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1241	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1242	extin[$nr_of_input_files]="${extin_pre[$i]}"
1243
1244
1245	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1246	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1247	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1248	then
1249	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1250	else
1251	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
1252	fi
1253
1254	# DETERMINE THE FILE'S CYCLE NUMBER
1255	(( maxcycle = 0 ))
1256	ls -1 -d $filename > filelist 2>/dev/null
1257	ls -1 -d $filename.* >> filelist 2>/dev/null
1258	while read line
1259	do
1260	# filename without path (i.e. after the last "/")
1261	basefilename=$(basename ${line})
1262
1263	# check if there is an extension
1264	extension=${basefilename##*.}
1265	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1266	then
1267	basefilename=${basefilename%.*}
1268	fi
1269
1270	# check for an existing cycle number
1271	cycle=${basefilename##*.}
1272	if [[ $cycle =~ ^-?[0-9]+$ ]]
1273	then
1274	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1275	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1276	(( icycle = $((10#$cycle)) ))
1277	else
1278	(( icycle = 0 ))
1279	fi
1280
1281	if (( icycle > maxcycle ))
1282	then
1283	(( maxcycle = icycle ))
1284
1285	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1286	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1287	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1288	then
1289	leading_zero=true
1290	else
1291	leading_zero=false
1292	fi
1293	fi
1294
1295	done <filelist
1296	rm filelist
1297
1298	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1299	if [[ $leading_zero = true ]]
1300	then
1301	cyclestring=`printf "%03d" $maxcycle`
1302	else
1303	cyclestring=$maxcycle
1304	fi
1305
1306	# APPEND CYCLE NUMBER TO FILENAME
1307	if (( maxcycle > 0 ))
1308	then
1309	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1310	then
1311	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1312	else
1313	filename=${filename}.$cyclestring
1314	fi
1315	else
1316	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1317	then
1318	filename=${filename}.${extin[$nr_of_input_files]}
1319	fi
1320	fi
1321
1322	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1323	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1324	absnamein[$nr_of_input_files]=$filename
1325	if (( maxcycle > 0 ))
1326	then
1327	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1328	then
1329	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1330	else
1331	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
1332	fi
1333	else
1334	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1335	then
1336	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1337	else
1338	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
1339	fi
1340	fi
1341
1342	done
1343
1344	fi
1345
1346	done
1347
1348
1349	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1350	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1351	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1352	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1353	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1354	# REMOTE HOST)
1355	(( i = 0 ))
1356	while (( i < iout ))
1357	do
1358	(( i = i + 1 ))
1359	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1360	then
1361	if [[ "${actionout_pre[$i]}" = tr ]]
1362	then
1363	actionout_pre[$i]=""
1364	elif [[ "${actionout_pre[$i]}" = trpe ]]
1365	then
1366	actionout_pre[$i]=pe
1367	elif [[ "${actionout_pre[$i]}" = tra ]]
1368	then
1369	actionout_pre[$i]=a
1370	fi
1371	(( maxcycle = 0 ))
1372	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
1373	eval catalogname=${pathout_pre[$i]}
1374	if ! ls $filename* 1>/dev/null 2>&1
1375	then
1376
1377	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1378	if cat /dev/null > $filename
1379	then
1380	rm $filename
1381	else
1382
1383	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1384	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1385	if [[ ! -d $catalogname ]]
1386	then
1387	if mkdir -p $catalogname
1388	then
1389	printf "\n\n *** directory:"
1390	printf "\n $catalogname"
1391	printf "\n was created\n"
1392	else
1393	printf "\n\n +++ OUTPUT-file:"
1394	printf "\n $filename"
1395	printf "\n cannot be created, because directory does not exist"
1396	printf "\n and cannot be created either"
1397	printf "\n"
1398	locat=output ; exit
1399	fi 2>/dev/null
1400	else
1401	printf "\n\n +++ OUTPUT-file:"
1402	printf "\n $filename"
1403	printf "\n cannot be created, although directory exists"
1404	printf "\n"
1405	locat=output ; exit
1406	fi
1407	fi 2>/dev/null
1408
1409	fi
1410
1411	fi
1412	done
1413
1414
1415	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1416	if [[ $running_in_batch_mode = false ]]
1417	then
1418	run_id=$RANDOM
1419	job_id=${jobname}.$run_id
1420
1421	tempdir=$fast_io_catalog/$job_id
1422	fi
1423
1424
1425	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1426	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1427	then
1428
1429	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1430	if [[ $ibd = 0 ]]
1431	then
1432	printf "\n"
1433	printf "\n +++ no batch directives found in configuration file"
1434	locat=config_file_batch_directives; (( iec = 0 )); exit
1435	fi
1436
1437	# CHECK IF CPUTIME IS GIVEN FOR JOB
1438	done=false
1439	cputime=$cpumax
1440	while [[ $done = false ]]
1441	do
1442	if (( cputime == 0 ))
1443	then
1444	printf "\n +++ cpu-time is undefined"
1445	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1446	printf "\n >>> "
1447	read cputime 1>/dev/null 2>&1
1448	else
1449	done=true
1450	fi
1451	done
1452	cpumax=$cputime
1453
1454	# CHECK THE MEMORY DEMAND
1455	done=false
1456	while [[ $done = false ]]
1457	do
1458	if (( memory == 0 ))
1459	then
1460	printf "\n +++ memory demand is undefined"
1461	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1462	printf "\n >>> "
1463	read memory 1>/dev/null 2>&1
1464	else
1465	done=true
1466	fi
1467	done
1468
1469	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1470	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1471	then
1472	while [[ -z $remote_username ]]
1473	do
1474	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1475	printf "\n >>> Please type username:"
1476	printf "\n >>> "
1477	read remote_username
1478	done
1479	fi
1480
1481	else
1482
1483	if [[ $running_in_batch_mode = false ]]
1484	then
1485	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1486	cpumax=$cputime
1487	else
1488	cputime=$cpumax
1489	fi
1490
1491	fi
1492
1493
1494	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1495	(( cpu_hours = cputime / 3600 ))
1496	(( resttime = cputime - cpu_hours * 3600 ))
1497	(( cpu_minutes = resttime / 60 ))
1498	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1499	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1500
1501
1502	# OUTPUT OF THE PALMRUN-HEADER
1503	calltime=$(date)
1504	printf "\n"
1505	printf "#------------------------------------------------------------------------# \n"
1506	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1507	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1508	printf "\| \| \n"
1509	column1="called on:"; column2=$(hostname)
1510	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1511	if [[ $create_remote_batch_job = true ]]
1512	then
1513	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1514	else
1515	if [[ $running_on_remote = true ]]
1516	then
1517	column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
1518	else
1519	column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
1520	fi
1521	fi
1522	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1523
1524	column1="running in:"
1525	if [[ $running_in_batch_mode = true ]]
1526	then
1527	column2="batch job mode"
1528	else
1529	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1530	then
1531	column2="job creation mode"
1532	else
1533	column2="interactive run mode"
1534	fi
1535	fi
1536	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1537
1538	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1539	then
1540	if [[ "$project_account" != "" ]]
1541	then
1542	column1="project account number:"
1543	column2="$project_account"
1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1545	fi
1546	fi
1547
1548	if [[ -n $cores ]]
1549	then
1550	if [[ $run_coupled_model = false ]]
1551	then
1552	column1="number of cores:"; column2=$cores
1553	else
1554	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1555	fi
1556	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1557	fi
1558	if [[ -n $tasks_per_node ]]
1559	then
1560	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1561	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1562	if (( remaining_cores > 0 ))
1563	then
1564	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1565	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1566	fi
1567	fi
1568	if [[ $maximum_parallel_io_streams != $cores ]]
1569	then
1570	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1572	fi
1573	if [[ $use_openmp = true ]]
1574	then
1575	column1="threads per task:"; column2="$threads_per_task"
1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1577	fi
1578	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1579	then
1580	column1="memory demand / PE":; column2="$memory MB"
1581	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1582	column1="job cpu time (h:m:s):"; column2="$timestring"
1583	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1584	fi
1585	printf "\| \| \n"
1586	if [[ "$source_list" != "" ]]
1587	then
1588	if [[ "$make_options" != "" ]]
1589	then
1590	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1592	line=$(echo "$make_options" \| cut -c46-)
1593	while [[ "$line" != "" ]]
1594	do
1595	column1=""
1596	column2=$(echo "$line" \| cut -c-45)
1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1598	line=$(echo "$line" \| cut -c46-)
1599	done
1600	fi
1601	fi
1602
1603	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1605	line=$(echo "$cpp_options" \| cut -c46-)
1606	while [[ "$line" != "" ]]
1607	do
1608	column1=""
1609	column2=$(echo "$line" \| cut -c-45)
1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1611	line=$(echo "$line" \| cut -c46-)
1612	done
1613
1614	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1616	line=$(echo "$compiler_options" \| cut -c46-)
1617	while [[ "$line" != "" ]]
1618	do
1619	column1=""
1620	column2=$(echo "$line" \| cut -c-45)
1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1622	line=$(echo "$line" \| cut -c46-)
1623	done
1624
1625	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1626	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1627	line=$(echo "$linker_options" \| cut -c46-)
1628	while [[ "$line" != "" ]]
1629	do
1630	column1=""
1631	column2=$(echo "$line" \| cut -c-45)
1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1633	line=$(echo "$line" \| cut -c46-)
1634	done
1635
1636	if [[ "$login_init_cmd" != "" ]]
1637	then
1638	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1640	line=$(echo "$login_init_cmd" \| cut -c46-)
1641	while [[ "$line" != "" ]]
1642	do
1643	column1=""
1644	column2=$(echo "$line" \| cut -c-45)
1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1646	line=$(echo "$line" \| cut -c46-)
1647	done
1648	fi
1649
1650	if [[ "$module_commands" != "" ]]
1651	then
1652	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1654	line=$(echo "$module_commands" \| cut -c46-)
1655	while [[ "$line" != "" ]]
1656	do
1657	column1=""
1658	column2=$(echo "$line" \| cut -c-45)
1659	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1660	line=$(echo "$line" \| cut -c46-)
1661	done
1662	fi
1663	printf "\| \| \n"
1664	column1="run identifier:"; column2=$jobname
1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1666	column1="activation string list:"; column2=$(echo $activation_string_list)
1667	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1668
1669	if [[ "$ocean_file_appendix" = true ]]
1670	then
1671	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1672	fi
1673
1674	if [[ "$source_list" != "" ]]
1675	then
1676	printf "\| \| \n"
1677	printf "\| Files to be compiled: \| \n"
1678	line=$source_list
1679	while [[ "$line" != "" ]]
1680	do
1681	linestart=$(echo $line \| cut -c-70)
1682	printf "\| %-70s \| \n" "$linestart"
1683	line=$(echo "$line" \| cut -c71-)
1684	done
1685	fi
1686	printf "#------------------------------------------------------------------------#"
1687
1688
1689
1690	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1691	if [[ $do_trace = true ]]
1692	then
1693	(( i = 0 ))
1694	while (( i < nr_of_input_files ))
1695	do
1696	(( i = i + 1 ))
1697	if (( i == 1 ))
1698	then
1699	printf "\n\n >>> INPUT-file assignments:\n"
1700	fi
1701	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1702	done
1703	(( i = 0 ))
1704	while (( i < iout ))
1705	do
1706	(( i = i + 1 ))
1707	if (( i == 1 ))
1708	then
1709	printf "\n\n >>> OUTPUT-file assignments:\n"
1710	fi
1711	printf "\n ${localout[$i]} : ${pathout[$i]}"
1712	done
1713	(( i = 0 ))
1714	while (( i < iic ))
1715	do
1716	(( i = i + 1 ))
1717	if (( i == 1 ))
1718	then
1719	printf "\n\n >>> INPUT-commands:\n"
1720	fi
1721	printf "\n ${in_command[$i]}"
1722	done
1723	(( i = 0 ))
1724	while (( i < ioc ))
1725	do
1726	(( i = i + 1 ))
1727	if (( i == 1 ))
1728	then
1729	printf "\n\n >>> OUTPUT-commands:\n"
1730	fi
1731	printf "\n ${out_command[$i]}"
1732	done
1733	fi
1734
1735	# QUERY FOR CONTINUE
1736	if [[ $silent = false && $running_in_batch_mode = false ]]
1737	then
1738	antwort=dummy
1739	printf "\n\n"
1740	printf " >>> everything o.k. (y/n) ? "
1741	while read antwort
1742	do
1743	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1744	then
1745	printf " >>> everything o.k. (y/n) ? "
1746	else
1747	break
1748	fi
1749	done
1750	if [[ $antwort = n \|\| $antwort = N ]]
1751	then
1752	locat=user_abort; (( iec = 0 )); exit
1753	fi
1754	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1755	then
1756	printf "\n *** batch-job will be created and submitted"
1757	else
1758	printf "\n *** PALMRUN will now continue to execute on this machine"
1759	fi
1760	fi
1761
1762
1763
1764	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1765	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1766	then
1767
1768	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1769	then
1770	printf "\n\n *** creating executable and other sources for the remote host\n"
1771	else
1772	printf "\n\n *** creating executable and other sources for the local host\n"
1773	fi
1774
1775	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1776	# IT SHALL BE CREATED
1777	ask_for_make_depository=false
1778	if [[ $create_remote_batch_job = true ]]
1779	then
1780
1781	line=`grep %base_directory $config_file`
1782	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1783	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1784
1785	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1786	then
1787	printf "\n\n +++ make depository \"${make_depository}\""
1788	printf "\n on remote host not found!"
1789	ask_for_make_depository=true
1790	fi
1791	rm ${host_configuration}_last_make_protokoll
1792
1793	else
1794
1795	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1796	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1797	if [[ ! -d ${make_depository} ]]
1798	then
1799	printf "\n\n +++ make depository \"${make_depository}\""
1800	printf "\n on local host not found!"
1801	ask_for_make_depository=true
1802	fi
1803
1804	fi
1805
1806	if [[ $ask_for_make_depository = true ]]
1807	then
1808
1809	antwort=dummy
1810	printf "\n\n"
1811	printf " >>> Create a new one (y/n) ? "
1812	while read antwort
1813	do
1814	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1815	then
1816	printf " >>> Create a new one (y/n) ? "
1817	else
1818	break
1819	fi
1820	done
1821	if [[ $antwort = n \|\| $antwort = N ]]
1822	then
1823	locat=user_abort; (( iec = 0 )); exit
1824	fi
1825
1826	if [[ $do_trace = true ]]
1827	then
1828	palmbuild -h $host_configuration
1829	else
1830	palmbuild -v -h $host_configuration
1831	fi
1832
1833	if [[ $? != 0 ]]
1834	then
1835
1836	# ABORT IN CASE OF COMPILATION PROBLEMS
1837	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1838	locat=make_depository
1839	exit
1840	else
1841	echo " *** now continue with creating executable and other sources"
1842	fi
1843
1844	fi
1845
1846	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1847	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
1848
1849	if [[ $? != 0 ]]
1850	then
1851
1852	# ABORT IN CASE OF COMPILATION PROBLEMS
1853	printf "\n +++ error while creating executable and/or other sources"
1854	locat=execution
1855	rm -rf ${base_directory}/${sources_for_run_catalog}
1856	exit
1857
1858	else
1859
1860	printf " *** executable and other sources created\n"
1861	rm -rf ${base_directory}/${sources_for_run_catalog}
1862
1863	fi
1864
1865	fi
1866
1867
1868	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1869	# WILL BE COPIED TO THE REMOTE HOST
1870	if [[ $create_remote_batch_job = true ]]
1871	then
1872	(( i = 0 ))
1873	while (( i < nr_of_input_files ))
1874	do
1875	(( i = i + 1 ))
1876	if [[ "${actionin[$i]}" = tr ]]
1877	then
1878	eval inputfile=${pathin[$i]}/${frelin[$i]}
1879	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1880	fi
1881	done
1882	if (( i > 0 ))
1883	then
1884	printf "\n\n *** input files have been copied to the remote host\n"
1885	fi
1886	fi
1887
1888
1889	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1890	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1891	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1892	then
1893
1894	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1895	if [[ $running_in_batch_mode = false ]]
1896	then
1897	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1898	# FOLDER
1899	mkdir -p $tempdir
1900	chmod go+rx $tempdir
1901	cd $tempdir
1902	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1903	printf "\n *** changed to temporary directory: $tempdir"
1904
1905	else
1906
1907	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1908	printf "\n *** running in temporary directory: $tempdir"
1909
1910	fi
1911
1912
1913	# PROVIDE THE INPUT FILES
1914	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1915	optional_files_missing=false
1916	(( i = 0 ))
1917	while (( i < nr_of_input_files ))
1918	do
1919	(( i = i + 1 ))
1920	if (( i == 1 ))
1921	then
1922	printf "\n\n *** providing INPUT-files:\n$dashes"
1923	fi
1924
1925
1926	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1927	if [[ "${actionin[$i]}" = unavailable ]]
1928	then
1929	optional_files_missing=true
1930	continue
1931	fi
1932
1933	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1934	files_for_cores=false; filetype=file
1935	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1936	then
1937	files_for_cores=true; filetype=files
1938	actionin[$i]=""
1939	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1940	then
1941	actionin[$i]=""
1942	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1943	then
1944	files_for_cores=true; filetype=files
1945	actionin[$i]="ln"
1946	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1947	then
1948	actionin[$i]="ln"
1949	fi
1950
1951	if [[ $files_for_cores = true ]]
1952	then
1953	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1954	else
1955	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1956	fi
1957
1958	# INPUT-FILES TO BE LINKED
1959	if [[ "${actionin[$i]}" = ln ]]
1960	then
1961
1962	printf "\n $filetype will be linked"
1963	if [[ $files_for_cores = false ]]
1964	then
1965	if [[ -f "${absnamein[$i]}" ]]
1966	then
1967	ln ${absnamein[$i]} ${localin[$i]}
1968	got_tmp[$i]=true
1969	fi
1970	else
1971	if [[ -d "${absnamein[$i]}" ]]
1972	then
1973	mkdir -p ${localin[$i]}
1974	cd ${absnamein[$i]}
1975	for file in $(ls *)
1976	do
1977	ln $file $tempdir/${localin[$i]}
1978	done >\|/dev/null 2>&1
1979	cd $tempdir
1980	fi
1981
1982	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1983	if [[ ! -f "${localin[$i]}/_000000" ]]
1984	then
1985	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1986	cp -r ${absnamein[$i]}/* ${localin[$i]}
1987	fi
1988
1989	got_tmp[$i]=true
1990	fi
1991	fi
1992
1993	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1994	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
1995	then
1996
1997	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1998	then
1999
2000	# FILE COPIES ARE PROVIDED FOR ALL CORES
2001	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2002	printf "\n file will be provided for $cores processors"
2003	mkdir -p ${localin[$i]}
2004	ival=$cores
2005	(( ii = 0 ))
2006	while (( ii <= ival-1 ))
2007	do
2008	if (( ii < 10 ))
2009	then
2010	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2011	elif (( ii < 100 ))
2012	then
2013	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2014	elif (( ii < 1000 ))
2015	then
2016	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2017	else
2018	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2019	fi
2020	(( ii = ii + 1 ))
2021	done
2022
2023	else
2024
2025	if [[ $files_for_cores = true ]]
2026	then
2027
2028	# PROVIDE FILES FOR EACH CORE
2029	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2030	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2031	printf "\n providing $cores files for the respective cores"
2032	mkdir -p ${localin[$i]}
2033	if [[ $link_local_input = true ]]
2034	then
2035	printf " files will be linked\n"
2036	cd ${absnamein[$i]}
2037	for file in $(ls *)
2038	do
2039	ln -f $file ${localin[$i]}
2040	done
2041	cd $tempdir
2042	fi
2043
2044	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2045	if [[ ! -f "${localin[$i]}/_000000" ]]
2046	then
2047	if [[ $link_local_input = true ]]
2048	then
2049	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2050	fi
2051	cp -r ${absnamein[$i]}/* ${localin[$i]}
2052	fi
2053
2054	else
2055
2056	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2057	if [[ $link_local_input = true ]]
2058	then
2059	printf " file will be linked\n"
2060	ln -f ${absnamein[$i]} ${localin[$i]}
2061	fi
2062	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2063	if [[ ! -f "${localin[$i]}" ]]
2064	then
2065	if [[ $link_local_input = true ]]
2066	then
2067	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2068	fi
2069	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2070	then
2071	mv ${absnamein[$i]} ${localin[$i]}
2072	else
2073	cp ${absnamein[$i]} ${localin[$i]}
2074	fi
2075	fi
2076	fi
2077	fi
2078	fi
2079
2080	done
2081	if (( i != 0 ))
2082	then
2083	if [[ $optional_files_missing = true ]]
2084	then
2085	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2086	fi
2087	printf "\n$dashes\n *** all INPUT-files provided \n"
2088	fi
2089
2090
2091	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2092	(( i = 0 ))
2093	while (( i < iic ))
2094	do
2095	(( i = i + 1 ))
2096	if (( i == 1 ))
2097	then
2098	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2099	fi
2100	printf "\n >>> ${in_command[$i]}"
2101	eval ${in_command[$i]}
2102	if (( i == iic ))
2103	then
2104	printf "\n$dashes\n"
2105	fi
2106	done
2107
2108
2109	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2110	# (FILE ENVPAR WILL BE READ BY PALM)
2111	cat > ENVPAR << EOF
2112	&envpar run_identifier = '$jobname', host = '$host_configuration',
2113	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2114	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2115	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2116	maximum_cpu_time_allowed = ${cpumax}.,
2117	revision = '$global_revision',
2118	batch_job = .${running_in_batch_mode}. /
2119
2120	EOF
2121
2122
2123	# STARTING THE EXECUTABLE
2124	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2125	PATH=$PATH:$tempdir
2126
2127
2128	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2129	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2130	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2131	eval line=\"$line\"
2132	execute_command="$line"
2133
2134
2135	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2136	if [[ "$execute_command_for_combine" = "" ]]
2137	then
2138	eval line2=\"$line2\"
2139	execute_command_for_combine="$line2"
2140	fi
2141
2142
2143
2144	# PROVIDE A HOSTFILE, IF REQUIRED
2145	if [[ "$hostfile" != "" ]]
2146	then
2147
2148	if [[ $hostfile = auto ]]
2149	then
2150	# CREATE A NEW HOSTFILE
2151	(( ii = 1 ))
2152	while (( ii <= cores / threads_per_task ))
2153	do
2154	echo $(hostname) >> hostfile
2155	(( ii = ii + 1 ))
2156	done
2157	if (( cores / threads_per_task == 0 ))
2158	then
2159	echo $(hostname) >> hostfile
2160	fi
2161
2162	else
2163	cp $hostfile hostfile
2164	fi
2165	eval line=\"`head -n $ii hostfile`\"
2166	printf "\n *** running on: $line"
2167	fi
2168
2169
2170
2171	# SET THE NUMBER OF OPENMP-THREADS
2172	if [[ $use_openmp = true ]]
2173	then
2174	export OMP_NUM_THREADS=$threads_per_task
2175	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2176	else
2177	export OMP_NUM_THREADS=1
2178	fi
2179
2180
2181	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2182	if [[ $run_coupled_model = false ]]
2183	then
2184	if [[ "$ocean_file_appendix" = true ]]
2185	then
2186	echo "precursor_ocean" > coupling_steering
2187	else
2188	echo "precursor_atmos" > coupling_steering
2189	fi
2190	else
2191	(( iia = $cores_atmos / $threads_per_task ))
2192	(( iio = $cores_ocean / $threads_per_task ))
2193	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2194	printf "\n\n"
2195	echo "coupled_run $iia $iio" > coupling_steering
2196	fi
2197
2198	printf "\n *** execute command:"
2199	printf "\n \"$execute_command\" \n\n"
2200
2201	$execute_command < coupling_steering
2202
2203	if [[ $? != 0 ]]
2204	then
2205
2206	# ABORT IN CASE OF RUNTIME ERRORS
2207	printf "\n +++ runtime error occured"
2208	locat=execution
2209	exit
2210
2211	else
2212
2213	printf "\n$dashes\n *** execution finished \n"
2214
2215	fi
2216
2217
2218	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2219	# BY EACH CORE INTO ONE FILE
2220	if [[ ! -f combine_plot_fields.x ]]
2221	then
2222
2223	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2224	printf "\n 2d- and/or 3d-data may be incomplete!"
2225	printf "\n Your previous palmbuild may have failed. Please check.\n"
2226
2227	elif [[ "$combine_plot_fields" == true ]]
2228	then
2229
2230	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2231	$execute_command_for_combine
2232
2233	else
2234
2235	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2236	# DATA OUTPUT
2237	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2238	fi
2239
2240
2241
2242	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2243	(( i = 0 ))
2244	while (( i < ioc ))
2245	do
2246	(( i = i + 1 ))
2247	if (( i == 1 ))
2248	then
2249	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2250	fi
2251
2252	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2253	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2254
2255	printf "\n >>> ${out_command[$i]}"
2256	eval ${out_command[$i]}
2257	if (( i == ioc ))
2258	then
2259	printf "\n$dashes\n"
2260	fi
2261	done
2262
2263
2264	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2265	# WILDCARDS
2266	(( i = 0 ))
2267	(( nr_of_output_files = 0 ))
2268
2269	while (( i < iout ))
2270	do
2271
2272	(( i = i + 1 ))
2273
2274	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2275	# CREATE A LIST FOR THE DETECTED ENDINGS
2276	if [[ "${multout[$i]}" = true ]]
2277	then
2278	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2279	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2280	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2281
2282	endings="DEFAULT"
2283	while read line
2284	do
2285	# remove the local name from the beginning
2286	localnamestring="${localout_pre[$i]}"
2287	length_localname=${#localnamestring}
2288	ending=${line:${length_localname}}
2289
2290	if [[ "$ending" != "" ]]
2291	then
2292	endings="$endings $ending"
2293	fi
2294
2295	done <filelist
2296
2297	rm filelist
2298
2299	else
2300
2301	# SINGLE NAME
2302	endings=DEFAULT
2303
2304	fi
2305
2306	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2307	for ending in $endings
2308	do
2309
2310	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2311	if [[ $ending = DEFAULT ]]
2312	then
2313	ending=""
2314	fi
2315
2316	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2317	(( nr_of_output_files = nr_of_output_files + 1 ))
2318	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2319	transout[$nr_of_output_files]="${transout_pre[$i]}"
2320	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2321	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2322	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2323	extout[$nr_of_output_files]="${extout_pre[$i]}"
2324	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2325
2326	done
2327
2328	done
2329
2330
2331
2332
2333	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2334	(( i = 0 ))
2335	while (( i < nr_of_output_files ))
2336	do
2337	(( i = i + 1 ))
2338	if (( i == 1 ))
2339	then
2340	printf "\n\n *** saving OUTPUT-files:"
2341
2342	# GET RUN NUMBER ASSIGNED BY PALM
2343	if [[ -f RUN_NUMBER ]]
2344	then
2345	read run_number < RUN_NUMBER
2346	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2347	usecycle_option="-U $run_number"
2348	else
2349	run_number=0
2350	usecycle_option=""
2351	fi
2352	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2353	then
2354	printf "\n *** in case of SCP transfers to local host"
2355	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2356	fi
2357	printf "\n$dashes"
2358	fi
2359
2360	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2361	then
2362
2363	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
2364
2365	# DETERMINE THE CYCLE NUMBER
2366	ls -1 -d $filename > filelist 2>/dev/null
2367	ls -1 -d $filename.* >> filelist 2>/dev/null
2368	while read line
2369	do
2370
2371	# filename without path (i.e. after the last "/")
2372	basefilename=$(basename ${line})
2373
2374	# check if there is an extension
2375	extension=${basefilename##*.}
2376	if [[ "$extension" = "${extout[$i]}" ]]
2377	then
2378	basefilename=${basefilename%.*}
2379	fi
2380
2381	# check for an existing cycle number
2382	cycle=${basefilename##*.}
2383	if [[ $cycle =~ ^-?[0-9]+$ ]]
2384	then
2385	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2386	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2387	(( icycle = $((10#$cycle)) + 1 ))
2388	else
2389	(( icycle = 1 ))
2390	fi
2391
2392	if (( icycle > maxcycle ))
2393	then
2394	(( maxcycle = icycle ))
2395	fi
2396
2397	done <filelist
2398	rm filelist
2399
2400
2401	# SET THE CYCLE NUMBER
2402	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2403	if [[ "${actionout[$i]}" = a ]]
2404	then
2405	(( maxcycle = maxcycle - 1 ))
2406	fi
2407
2408	(( cycnum[$i] = maxcycle ))
2409	pathout[$i]=$filename
2410
2411
2412	# ADD CYCLE NUMBER TO FILENAME
2413	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2414	if [[ "${actionout[$i]}" != "a" ]]
2415	then
2416	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2417	# WITH AN EXISTING CYCLE NUMBER
2418	if (( run_number >= cycnum[$i] ))
2419	then
2420	(( cycnum[$i] = run_number ))
2421	else
2422	if (( run_number > 0 ))
2423	then
2424	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2425	fi
2426	fi
2427	fi
2428	if (( cycnum[$i] > 0 ))
2429	then
2430	cyclestring=`printf "%03d" ${cycnum[$i]}`
2431	pathout[$i]=${pathout[$i]}.$cyclestring
2432	fi
2433	fi
2434
2435	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2436	files_for_cores=false; filetype=file
2437	link_local_output=false
2438	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2439	then
2440	files_for_cores=true; filetype=directory
2441	actionout[$i]=""
2442	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2443	then
2444	actionout[$i]=""
2445	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2446	then
2447	files_for_cores=true; filetype=directory
2448	link_local_output=true
2449	actionout[$i]=""
2450	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2451	then
2452	link_local_output
2453	actionout[$i]=""
2454	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2455	then
2456	files_for_cores=true; filetype=directory
2457	actionout[$i]="tr"
2458	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2459	then
2460	actionout[$i]="tr"
2461	fi
2462
2463	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2464	then
2465	if [[ ${warnout[$i]} = true ]]
2466	then
2467	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2468	fi
2469	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2470	then
2471	if [[ ${warnout[$i]} = true ]]
2472	then
2473	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2474	fi
2475	else
2476
2477
2478	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2479	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2480	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2481	then
2482	if [[ $running_on_remote = true ]]
2483	then
2484
2485	# SET OPTIONS FOR TRANSFER
2486	if [[ "${actionout[$i]}" = tr ]]
2487	then
2488	if [[ $files_for_cores = false ]]
2489	then
2490	catalog_option=""
2491	catalog_string=""
2492	else
2493	catalog_option="-c"
2494	catalog_string="/"
2495	fi
2496	append_option=""
2497	append_string=""
2498	else
2499	append_option="-A"
2500	append_string="append"
2501	fi
2502
2503	transfer_failed=false
2504	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2505	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
2506
2507	# TRANSFER VIA SCP
2508	if [[ "$remote_loginnode" != "" ]]
2509	then
2510	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
2511	else
2512	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]}
2513	fi
2514	[[ $? != 0 ]] && transfer_failed=true
2515
2516
2517	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2518	if [[ $transfer_failed = true ]]
2519	then
2520	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2521	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
2522
2523	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2524	eval local_catalog=${pathout[$i]}
2525	if [[ ! -d $local_catalog ]]
2526	then
2527	printf " *** local directory does not exist. Trying to create:\n"
2528	printf " $local_catalog \n"
2529	mkdir -p $local_catalog
2530	fi
2531	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
2532	transfer_problems=true
2533	fi
2534
2535	else
2536
2537	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2538	# BE COPIED OR APPENDED ON THIS MACHINE
2539	if [[ "${actionout[$i]}" = tr ]]
2540	then
2541	actionout[$i]=""
2542	else
2543	actionout[$i]="a"
2544	fi
2545	fi
2546	fi
2547
2548
2549	# APPEND ON THIS MACHINE
2550	if [[ "${actionout[$i]}" = "a" ]]
2551	then
2552	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2553	then
2554	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2555	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2556	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2557	else
2558	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2559	printf "\n ${pathout[$i]}\n"
2560	cat ${localout[$i]} >> ${pathout[$i]}
2561	fi
2562	fi
2563
2564	# COPY ON THIS MACHINE
2565	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2566	# ON DIFFERENT FILE-SYSTEMS
2567	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2568	then
2569
2570	# COPY IN CASE OF RUNS ON SINGLE CORES
2571	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2572	then
2573	printf "\n >>> OUTPUT: ${localout[$i]} to"
2574	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2575	if [[ $link_local_output = true ]]
2576	then
2577	printf " file will be linked\n"
2578	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2579	fi
2580	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2581	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2582	then
2583	if [[ $link_local_output = true ]]
2584	then
2585	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2586	fi
2587	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2588	else
2589	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2590	fi
2591	else
2592	printf "\n >>> OUTPUT: ${localout[$i]} to"
2593	printf "\n ${pathout[$i]}\n"
2594	if [[ $link_local_output = true ]]
2595	then
2596	printf " file will be linked\n"
2597	ln -f ${localout[$i]} ${pathout[$i]}
2598	fi
2599	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2600	if [[ ! -f "${pathout[$i]}" ]]
2601	then
2602	if [[ $link_local_output = true ]]
2603	then
2604	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2605	fi
2606	cp ${localout[$i]} ${pathout[$i]}
2607	else
2608	printf "+++ no copy because file ${pathout[$i]} exists\n"
2609	fi
2610	fi
2611
2612	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2613	then
2614
2615	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2616	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2617	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2618	printf "\n ${pathout[$i]}\n"
2619	if [[ $link_local_output = true ]]
2620	then
2621	printf " files will be linked\n"
2622	mkdir -p ${pathout[$i]}
2623	cd ${localout[$i]}
2624	for file in $(ls *)
2625	do
2626	ln -f $file ${pathout[$i]}
2627	done >\|/dev/null 2>&1
2628	cd $tempdir
2629	fi
2630
2631	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2632	if [[ ! -f "${pathout[$i]}/_000000" ]]
2633	then
2634	if [[ $link_local_output = true ]]
2635	then
2636	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2637	fi
2638	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2639	cp -r ${localout[$i]}/* ${pathout[$i]}
2640	fi
2641
2642	fi
2643	fi
2644	done
2645
2646	if (( i != 0 ))
2647	then
2648	if [[ $transfer_problems = true ]]
2649	then
2650	printf "\n$dashes\n *** OUTPUT-files saved"
2651	printf "\n +++ WARNING: some data transfers failed! \n"
2652	else
2653	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2654	fi
2655	fi
2656
2657
2658	# IF REQUIRED, START A RESTART-JOB
2659	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2660	if [[ -f CONTINUE_RUN ]]
2661	then
2662
2663	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2664	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2665	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2666	# -b START A BATCH JOB
2667	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2668	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2669	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2670
2671	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2672	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2673	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2674	then
2675	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2676	fi
2677
2678	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2679	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2680	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2681	then
2682	prc=`echo $prc \| sed 's/#/r/g'`
2683	fi
2684
2685
2686	# START THE RESTART-JOB
2687	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2688	echo " $prc"
2689	printf "\n$dashes\n"
2690	if [[ $running_on_remote = true ]]
2691	then
2692
2693	echo "*** ssh will be used to initiate restart-runs!"
2694	echo " return_address=\"$return_address\" "
2695	echo " return_username=\"$local_username\" "
2696
2697	if [[ "$remote_loginnode" != "" ]]
2698	then
2699	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode \| tee palmrun_restart.log
2700	else
2701	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
2702	fi
2703
2704	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2705	sleep 30
2706
2707	else
2708
2709	# START THE RESTART JOB ON THE LOCAL HOST
2710	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2711	cd - > /dev/null
2712
2713	fi
2714
2715	# CHECK, IF RESTART JOB HAS BEEN STARTED
2716	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
2717	then
2718	printf "\n$dashes\n +++ creating restart run failed \n"
2719	locat=create_restart
2720	exit
2721	rm palmrun_restart.log
2722	else
2723	printf "\n$dashes\n *** restart run initiated \n"
2724	rm palmrun_restart.log
2725	fi
2726
2727
2728	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2729	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2730	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2731	# MAY BE VERY HUGE)
2732	(( i = 0 ))
2733	while (( i < nr_of_input_files ))
2734	do
2735	(( i = i + 1 ))
2736	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2737	then
2738	rm -r ${absnamein[$i]}
2739	fi
2740	done
2741
2742	fi
2743
2744
2745	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2746	cd $HOME
2747	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2748
2749
2750	else
2751
2752
2753	# PREPARING ACTIONS,
2754	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2755
2756	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2757	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2758	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2759	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2760	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2761	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2762	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2763	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2764	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2765	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2766	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2767	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2768	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2769	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2770	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2771	if [[ $create_remote_batch_job = true ]]
2772	then
2773	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2774	if [[ $do_trace = true ]]
2775	then
2776	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2777	fi
2778	elif [[ $create_batch_job = true ]]
2779	then
2780	palmrun_com=${palmrun_com}" -j"
2781	if [[ $do_trace = true ]]
2782	then
2783	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2784	fi
2785	fi
2786
2787
2788	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2789	# REMOTE HOST
2790	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2791	job_protocol_file=$job_protocol_file_local
2792	if [[ $create_remote_batch_job = true ]]
2793	then
2794	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2795	job_protocol_file=$job_protocol_file_remote
2796	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2797	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2798	fi
2799
2800
2801	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2802	jobfile=jobfile.$run_id
2803
2804
2805	# FIRST CREATE THE BATCH DIRECTIVES
2806	(( i = 0 ))
2807	while (( i < ibd ))
2808	do
2809	(( i = i + 1 ))
2810	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2811	eval line=\"$line\"
2812	echo "$line" >> $jobfile
2813	done
2814	echo " " >> $jobfile
2815
2816
2817	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2818	# PROTOCOL
2819	if [[ $create_remote_batch_job = true ]]
2820	then
2821	echo "set +vx" >> $jobfile
2822	echo "trap '" >> $jobfile
2823	echo "set +vx" >> $jobfile
2824	echo "cd ${remote_jobcatalog}" >> $jobfile
2825	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2826
2827	# ADD THE BATCH DIRECTIVES
2828	(( i = 0 ))
2829	while (( i < ibdt ))
2830	do
2831	(( i = i + 1 ))
2832	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2833	eval line=\"$line\"
2834	echo "$line" >> $jobfile
2835	done
2836	echo " " >> $jobfile
2837
2838	echo "set -x" >> $jobfile
2839	echo "${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
2840	echo "%%END%%" >> $jobfile
2841	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2842	echo "$submit_command $scpjob_file" >> $jobfile
2843	echo "rm $scpjob_file" >> $jobfile
2844	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2845	echo "set -x" >> $jobfile
2846	echo " ' exit" >> $jobfile
2847	fi
2848
2849
2850	# ACTIVATE ERROR-TRACEBACK
2851	if [[ $do_trace = true ]]
2852	then
2853	echo "set -x" >> $jobfile
2854	else
2855	echo "set +vx" >> $jobfile
2856	fi
2857
2858
2859	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2860	if [[ "$login_init_cmd" != "" ]]
2861	then
2862	echo "$login_init_cmd" >> $jobfile
2863	fi
2864	if [[ "$module_commands" != "" ]]
2865	then
2866	echo "$module_commands" >> $jobfile
2867	fi
2868
2869
2870	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2871	if [[ $create_remote_batch_job = true ]]
2872	then
2873	echo "mkdir $tempdir" >> $jobfile
2874	echo "chmod go+rx $tempdir" >> $jobfile
2875	else
2876	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2877	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2878	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2879	mkdir $tempdir
2880	chmod go+rx $tempdir
2881	fi
2882	echo "cd $tempdir" >> $jobfile
2883	echo "export tempdir=$tempdir" >> $jobfile
2884	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2885	echo "export PATH=.:\$PATH" >> $jobfile
2886	echo "export execute_palmrun=true" >> $jobfile
2887
2888
2889	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2890	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2891	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2892	echo "LOCAL_PWD=$working_directory" >> $jobfile
2893	echo "export LOCAL_PWD" >> $jobfile
2894
2895
2896	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2897	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2898	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2899
2900
2901	# CALL PALMRUN WITHIN THE JOB
2902	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2903	echo "set -x" >> $jobfile
2904	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2905
2906
2907	# TRANSFER JOBFILE TO THE TARGET HOST
2908	if [[ $create_jobfile_only = false ]]
2909	then
2910
2911	if [[ $create_remote_batch_job = true ]]
2912	then
2913
2914	echo " "
2915	echo " *** transfer of job to remote host via scp"
2916	if [[ $do_trace = true ]]
2917	then
2918	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2919	fi
2920	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2921
2922	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2923	if [[ $do_trace = true ]]
2924	then
2925	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"
2926	fi
2927	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
2928
2929	elif [[ $create_batch_job = true ]]
2930	then
2931
2932	eval local_jobcatalog=$local_jobcatalog
2933	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2934	cd $local_jobcatalog
2935	echo " "
2936	echo " *** submit the job"
2937	if [[ $do_trace = true ]]
2938	then
2939	echo "$submit_command ${host_configuration}_${job_id}"
2940	fi
2941	$submit_command ${host_configuration}_${job_id}
2942	rm ${host_configuration}_${job_id}
2943	cd - > /dev/null
2944
2945	fi
2946
2947	rm -rf $jobfile
2948
2949	else
2950
2951	printf "\n *** jobfile created under name \"$jobfile\" "
2952	printf "\n no batch-job has been sent!"
2953
2954	fi
2955
2956	fi # END OF REMOTE-PART

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