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source: palm/trunk/SCRIPTS/palmrun @ 4442

Last change on this file since 4442 was 4425, checked in by raasch, 5 years ago
hard coded path to the fileconnection file replaced by a path that is based on the source path which has been given in the configuration file
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 105.6 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 4425 2020-02-26 15:35:00Z suehring $
29	# hard coded path to the fileconnection file replaced by a path that is based on
30	# the source path which has been given in the configuration file
31	#
32	# 4303 2019-11-25 08:55:18Z raasch
33	# Abort if temporary working catalog cannot be created
34	#
35	# 3982 2019-05-16 11:07:31Z raasch
36	# bugfix: -b is not added in automatically generated batch jobs for remote hosts
37	#
38	# 3917 2019-04-18 11:46:37Z raasch
39	# in case of batch jobs on remote machines, copying files from SOURCES_FOR_RUN folder has
40	# been rearranged to avoid that input files with original names (e.g. ..._p3d) are copied
41	# into the temporary working catalog
42	#
43	# 3860 2019-04-04 06:23:27Z raasch
44	# check added, that it is not allowed to set option -b if the configuration file has been setup
45	# for running batch jobs on remote hosts,
46	# local time added to terminal output before and after saving output files
47	#
48	# 3725 2019-02-07 10:11:02Z raasch
49	# error messages for failed restarts extended
50	#
51	# 3682 2019-01-18 17:01:54Z knoop
52	# ssh-call for submitting batch jobs on remote systems modified again to avoid output
53	# of login messages on specific systems
54	#
55	# 3574 2018-11-28 13:14:39Z raasch
56	# syntax-error in last commit fixed
57	#
58	# 3573 2018-11-28 13:03:44Z raasch
59	# bugfixes: don't check the .palm.iofiles in restart runs + wrong cd-command
60	# removed,
61	# r3570 reverted
62	#
63	# 3570 2018-11-27 17:44:21Z kanani
64	# Rename job-id by run_id
65	#
66	# 3555 2018-11-22 13:50:37Z raasch
67	# sed-command to remove repeated space-characters replaced by tr-command, to
68	# guarantee mac compatible
69	#
70	# 3549 2018-11-21 15:44:44Z raasch
71	# ssh-call for submitting batch jobs on remote systems modified to avoid output
72	# of login messages on specific systems
73	#
74	# 3534 2018-11-19 15:35:16Z raasch
75	# batch_scp for sending back the job protocol file is called via login-node if
76	# a login-node has been set in the config-file
77	# ssh-calls rearranged to avoid output of system/user-profile messages
78	#
79	# 3505 2018-11-08 09:14:30Z raasch
80	# job folders are created in case that they do not exist
81	#
82	# 3455 2018-10-30 14:12:31Z raasch
83	# options -h and -d renamed -c and -r, respectively
84	#
85	# 3402 2018-10-23 11:49:24Z knoop
86	# job_id is set for compatibility reasons with older versions of config files
87	#
88	# 3313 2018-10-06 15:22:48Z knoop
89	# more detailed error message for outdated fileconnection file
90	#
91	# 3236 2018-09-10 09:07:06Z raasch
92	# warning issued in case of file connection file version mismatch,
93	# host_configuration renamed configuration_identifier,
94	# "host identifier" in header output renamed "config. identifier",
95	# jobname renamed run_identifier,
96	# run_id renamed run_id_number
97	# job_id renamed run_id
98	# option -r renamed -i
99	#
100	# 3151 2018-07-19 08:45:38Z raasch
101	# removed additional listing of files to be compiled, print PALM code revision
102	# in header
103	#
104	# 3132 2018-07-16 11:44:58Z raasch
105	# create consistent error messages in case of failed restarts,
106	# check existence of remote job catalog
107	#
108	# 3043 2018-05-25 10:47:54Z raasch
109	# check for setting of fast_io_catalog
110	#
111	# 3033 2018-05-23 15:26:19Z raasch
112	# -T option not required for interactive runs (tasks per node =
113	# total number of cores is assumed as default, if option is not given),
114	# reformatting of a few messages,
115	# bugfix: destination output directory is created if attribute "pe" is set in
116	# .palm.iofiles
117	#
118	# 2718 2018-01-02 08:49:38Z maronga
119	# bugfix of r2990
120	#
121	# 2718 2018-01-02 08:49:38Z maronga
122	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
123	# not in the working directory from where palmrun is called
124	#
125	# 2718 2018-01-02 08:49:38Z maronga
126	# svfout in the activation string will be replaced now by svfin in case of
127	# automatic restarts
128	#
129	# 2718 2018-01-02 08:49:38Z maronga
130	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
131	# the possible output or input of sky view factors
132	#
133	# 2718 2018-01-02 08:49:38Z maronga
134	# "fname" renamed to "jobname"
135	#
136	# 2718 2018-01-02 08:49:38Z maronga
137	# parameters are allowed in output commands (OC:)
138	#
139	# 2718 2018-01-02 08:49:38Z maronga
140	# bugfix: exit if no queue has been given neither with option -q nor in the
141	# configuration file
142	#
143	# 2718 2018-01-02 08:49:38Z maronga
144	# file connection file from trunk/SCRIPTS is taken by default
145	#
146	# 2718 2018-01-02 08:49:38Z maronga
147	# Corrected "Former revisions" section
148	#
149	# 2696 2017-12-14 17:12:51Z kanani
150	# Change in file header (GPL part)
151	#
152	# 2693 2017-12-13 12:33:49Z raasch
153	# replacement of variables given by {{<variable>}} in configuration file is now
154	# done in a more general way, variable names are written in small letters
155	#
156	# 2670 2017-12-06 16:32:19Z raasch
157	# test printouts removed
158	#
159	# 2669 2017-12-06 16:03:27Z raasch
160	# file attributes in .palm.iofiles restructured, "loc" attribute completely
161	# removed,
162	# wildcard (*) allowed in .palm.iofiles as file activation string for output
163	# files,
164	# informative messages in case of missing optional input files shortened
165	# bugfix: variable cycle explicitly interpreted with 10 as the number base
166	#
167	# 2638 2017-11-23 12:44:23Z raasch
168	# use of wildcards in file connection statements enabled
169	#
170	# 2605 2017-11-09 15:31:46Z raasch
171	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
172	# will not be sent with the job file any more, but copied into the
173	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
174	#
175	# 2600 2017-11-01 14:11:20Z raasch
176	# cycle numbers are made three digits wide
177	#
178	# 2566 2017-10-20 08:50:47Z raasch
179	# execute command for combine_plot_fields added
180	# "TEMPDIR" renamed "tempdir"
181	# temporary working directory for local batch jobs is created immediately within
182	# the user's palmrun call, due to a requirement of the "grid engine" batch
183	# system, where the working directory is given with batch directive -wd and must
184	# already exist when the job is submitted,
185	# informative messages in non-trace mode reduced and partly reformatted
186	#
187	# 2551 2017-10-18 07:25:11Z raasch
188	# TEMPDIR added as replacement string to be used in batch directives
189	#
190	# 2512 2017-10-04 08:26:59Z raasch
191	# bugfix for determining cycle numbers of NetCDF input files
192	#
193	# 2506 2017-09-29 08:30:37Z raasch
194	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
195	# host configuration added to SOURCES_FOR_RUN_... folder name
196	# host_identifier renamed host_configuration
197	# option -W added to allow for job dependencies
198	#
199	# 2501 2017-09-26 11:41:55Z raasch
200	# default value for number of cores (option -X) set to 1
201	# bugfix for mechanism which overwrites configuration file settings with values
202	# provided by palmrun options
203	#
204	# 2499 2017-09-22 16:47:58Z kanani
205	# option -h named configuration identifier
206	#
207	# 2480 2017-09-19 06:24:14Z maronga
208	# bugfix for last revision
209	#
210	# 2479 2017-09-19 06:12:16Z raasch
211	# option -A (project account number) added
212	#
213	# 2422 2017-09-08 08:25:41Z raasch
214	# initial revision
215	#
216	#--------------------------------------------------------------------------------#
217	# palmrun - script for running PALM jobs on local and remote hosts
218	#--------------------------------------------------------------------------------#
219
220
221
222	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
223
224	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
225	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
226	# (TOO MANY ARGUMENTS - PROBLEM)
227	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
228
229	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
230	typeset -i nr_of_output_files=0
231	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
232	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
233	# SCRIPT-OPTION ARGUMENTS
234	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
235	typeset -i icycle inode ival maxcycle mpi_tasks
236	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
237
238	activation_string_list=""
239	AddFilenames=""
240	combine_plot_fields=true
241	compiler_name=""
242	compiler_name_ser=""
243	compiler_options=""
244	configuration_identifier="default"
245	cores=1
246	cores_atmos=0
247	cores_ocean=0
248	coupled_dist=""
249	cpp_options=""
250	cpumax=0
251	create_batch_job=false
252	create_jobfile_only=false
253	create_remote_batch_job=false
254	dashes=" ----------------------------------------------------------------------------"
255	defaultqueue=""
256	delete_temporary_catalog=true
257	do_compile=true
258	do_trace=false
259	executable=""
260	execute_command=""
261	execution_error=false
262	fileconnection_file=""
263	global_revision=""
264	hostfile=""
265	hp=""
266	keep_data_from_previous_run=false
267	link_local_input=false
268	link_local_output=false
269	linker_options=""
270	local_jobcatalog=""
271	locat=normal
272	makefile=""
273	max_par_io_str=""
274	prc=$0
275	while [[ $(echo $prc \| grep -c "/") != 0 ]]
276	do
277	prc=`echo $prc \| cut -f2- -d"/"`
278	done
279	module_calls=""
280	palmrun_memory=""
281	palmrun_script_name=$prc
282	openmp=false
283	previous_job=""
284	project_account=""
285	queue=none
286	read_svf=""
287	restart_run=false
288	return_address=""
289	remote_jobcatalog=""
290	remote_username=""
291	running_in_batch_mode=false
292	running_in_test_mode=false
293	run_coupled_model=false
294	run_id=""
295	run_id_number=""
296	run_identifier=test
297	silent=false
298	source_list=""
299	source_path=""
300	tasks_per_node=0
301	threads_per_task=1
302	transfer_problems=false
303	user_source_path=""
304	use_existing_sources_folder=""
305	use_openmp=false
306	version="palmrun 1.0 Rev$Rev: 4425 $"
307	working_directory=`pwd`
308	write_binary=""
309	write_svf=""
310
311
312	# ERROR HANDLING IN CASE OF EXIT
313	trap 'if [[ $locat != normal && $locat != control_c ]]
314	then
315
316	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
317	(( i = 0 ))
318	while (( i < iec ))
319	do
320	(( i = i + 1 ))
321	printf "\n *** Execution of ERROR-command:\n"
322	printf " >>> ${err_command[$i]}\n"
323	eval ${err_command[$i]}
324	done
325	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
326	printf "\n\n+++ palmrun crashed \n\n"
327	exit 1
328	elif [[ $locat != normal ]]
329	then
330	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
331	printf "\n+++ palmrun killed by \"^C\" \n\n"
332	exit 2
333	else
334	printf "\n --> palmrun finished\n\n"
335	exit 0
336	fi' exit
337
338
339	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
340	trap 'locat=control_c
341	exit 1
342	' 2
343
344
345	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
346	# WHICH WILL BE USED TO START RESTART-JOBS
347	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
348	do
349	case $option in
350	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
351	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
352	(b) create_batch_job=true; prc="$prc -b";;
353	(B) delete_temporary_catalog=false; prc="$prc -B";;
354	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
355	(C) restart_run=true; prc="$prc -C";;
356	(F) create_jobfile_only=true;;
357	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
358	(i) run_id_number=$OPTARG;;
359	(j) running_in_batch_mode=true;;
360	(k) keep_data_from_previous_run=true; prc="$prc -k";;
361	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
362	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
363	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
364	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
365	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
366	(R) return_address=$OPTARG;;
367	(s) source_list=$OPTARG;;
368	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
369	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
370	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
371	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
372	(v) silent=true; prc="$prc -v";;
373	(V) use_existing_sources_folder="-V";;
374	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
375	(W) previous_job=$OPTARG;;
376	(x) do_trace=true;set -x; prc="$prc -x";;
377	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
378	(y) ocean_file_appendix=true; prc="$prc -y";;
379	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
380	(z) running_in_test_mode=true;;
381	(Z) combine_plot_fields=false; prc="$prc -Z";;
382	(\?) printf "\n +++ unknown option $OPTARG \n"
383	printf "\n --> type \"$0 ?\" for available options \n"
384	locat=parameter;exit;;
385	esac
386	done
387
388
389	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
390	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
391	(( to_shift = $OPTIND - 1 ))
392	shift $to_shift
393
394	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
395	if [[ "$1" = "?" ]]
396	then
397	(printf "\n *** Description of available palmrun options:\n"
398	printf "\n Option Description Default-Value"
399	printf "\n -a activation string list \"\" "
400	printf "\n -A project account number ---"
401	printf "\n -b batch-job on local machine ---"
402	printf "\n -B do not delete temporary directory at end ---"
403	printf "\n -c configuration identifier \"default\" "
404	printf "\n -F create batch job file only ---"
405	printf "\n -k keep data from previous run"
406	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
407	printf "\n -M Makefile name Makefile"
408	printf "\n -O threads per openMP task ---"
409	printf "\n -q queue \"$queue\" "
410	printf "\n -r run identifier test"
411	printf "\n -s filenames of routines to be compiled \"\" "
412	printf "\n must end with .f, .f90, .F, or .c !"
413	printf "\n use \"..\" for more than one file and wildcards"
414	printf "\n -s LM compiles all locally modified files"
415	printf "\n -t allowed cpu-time in seconds (batch) 0"
416	printf "\n -T tasks per node ---"
417	printf "\n -u username on remote machine \"\" "
418	printf "\n -v no prompt for confirmation ---"
419	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
420	printf "\n -w maximum parallel io streams as given by -X"
421	printf "\n -W name of job to wait for ---"
422	printf "\n -x tracing of palmrun for debug purposes ---"
423	printf "\n -X # of processors (on parallel machines) 1"
424	printf "\n -y add appendix \"_O\" to all local output"
425	printf "\n files (ocean precursor runs followed by"
426	printf "\n coupled atmosphere-ocean runs) ---"
427	printf "\n -Y run coupled model, \"#1 #2\" with"
428	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
429	printf "\n -Z skip combine_plot_fields at the end of "
430	printf "\n the simulation ---"
431	printf "\n "
432	printf "\n Possible values of positional parameter <modus>:"
433	printf "\n \"?\" - this outline \n\n") \| more
434	exit
435	elif [[ "$1" != "" ]]
436	then
437	printf "\n +++ positional parameter $1 unknown \n"
438	locat=parameter; exit
439	fi
440
441
442
443	# SHORT STARTING MESSAGE
444	printf "\n*** $version "
445	printf "\n will be executed. Please wait ..."
446
447
448	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
449	config_file=.palm.config.$configuration_identifier
450	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
451
452
453	# CHECK, IF CONFIGURATION FILE EXISTS
454	if [[ ! -f $config_file ]]
455	then
456	printf "\n\n +++ configuration file: "
457	printf "\n $config_file"
458	printf "\n does not exist"
459	locat=connect; exit
460	fi
461
462
463	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
464	if [[ "$activation_string_list" = "" ]]
465	then
466	printf "\n\n +++ no activation string list given: "
467	printf "\n please set palmrun option \"-a\" "
468	locat=palmrun_option; exit
469	fi
470
471
472	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
473	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
474	then
475	write_binary=true
476	else
477	write_binary=false
478	fi
479
480	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
481	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
482	then
483	write_svf=true
484	else
485	write_svf=false
486	fi
487
488	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
489	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
490	then
491	read_svf=true
492	else
493	read_svf=false
494	fi
495
496
497	# READ AND EVALUATE THE CONFIGURATION-FILE
498	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
499
500	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
501	while read line
502	do
503
504	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
505	eval line=\"$line\"
506
507
508	# INTERPRET THE LINE
509	if [[ "$(echo $line)" = "" ]]
510	then
511
512	# EMPTY LINE, NO ACTION
513	continue
514
515	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
516	then
517
518	# LINE IS A COMMENT LINE
519	continue
520
521	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
522	then
523
524	# LINE DEFINES AN ENVIRONMENT-VARIABLE
525	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
526	value=`echo $line \| cut -d" " -s -f2-`
527
528
529	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
530	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
531	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
532	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
533	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
534	# CONFIGURATION-FILE.
535	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
536	then
537	eval export $var="\$value"
538
539	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
540	if [[ $do_trace = true ]]
541	then
542	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
543	fi
544	fi
545
546	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
547	then
548
549	# LINE DEFINES BATCH-DIRECTIVE
550	(( ibd = ibd + 1 ))
551	line=$(echo $line \| cut -c4-)
552	batch_directive[$ibd]="$line"
553
554	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
555	then
556
557	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
558	# REMOTE TO A LOCAL HOST
559	(( ibdt = ibdt + 1 ))
560	line=$(echo $line \| cut -c5-)
561	batch_directive_transfer[$ibdt]="$line"
562
563	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
564	then
565
566	# LINE DEFINES ERROR-COMMAND
567	(( iec = iec + 1 ))
568	line=$(echo $line \| cut -c4-)
569	err_command[$iec]="$line"
570
571	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
572	then
573
574	# LINE DEFINES INPUT-COMMAND
575	(( iic = iic + 1 ))
576	line=$(echo $line \| cut -c4-)
577	in_command[$iic]="$line"
578
579	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
580	then
581
582	# LINE DEFINES OUTPUT-COMMAND
583	(( ioc = ioc + 1 ))
584	line=$(echo $line \| cut -c4-)
585	out_command[$ioc]="$line"
586
587	else
588
589	# SKIP ALL OTHER LINES
590	continue
591
592	fi
593
594	done < $config_file
595
596
597	# CHECK SETTING OF REQUIRED PARAMETERS
598	if [[ "$fast_io_catalog" = "" ]]
599	then
600	printf "\n\n +++ no fast_io_catalog found in $config_file"
601	printf "\n Please add line \"fast_io_catalog ...\" to that file."
602	locat=config_file; exit
603	fi
604	if [[ "$compiler_name" = "" ]]
605	then
606	printf "\n\n +++ no compiler name found in $config_file"
607	printf "\n Please add line \"compiler_name ...\" to that file."
608	locat=config_file; exit
609	fi
610	if [[ "$compiler_name_ser" = "" ]]
611	then
612	printf "\n\n +++ no compiler name for non-paralle compilation found in $config_file"
613	printf "\n Please add line \"compiler_name_ser ...\" to that file."
614	locat=config_file; exit
615	fi
616	if [[ "$compiler_options" = "" ]]
617	then
618	printf "\n\n +++ no compiler options found in $config_file"
619	printf "\n Please add line \"compiler_options ...\" to that file."
620	locat=config_file; exit
621	fi
622	if [[ "$execute_command" = "" ]]
623	then
624	printf "\n\n +++ no execute command found in $config_file"
625	printf "\n Please add line \"execute_command ...\" to that file."
626	locat=config_file; exit
627	fi
628
629	if [[ "$hostfile" != "" ]]
630	then
631	if [[ $hostfile != auto && ! -f $hostfile ]]
632	then
633	printf "\n\n +++ no hostfile \"$hostfile\" found"
634	printf "\n Please check line \"hostfile ...\" in $config_file"
635	locat=config_file; exit
636	fi
637	fi
638
639
640	# DETERMINE THE CALL STATUS
641	if [[ "$return_address" != "" ]]
642	then
643
644	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
645	# BATCH MODE AND ...
646	running_on_remote=true
647
648	else
649
650	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
651	if [[ "$remote_ip" != "" ]]
652	then
653
654	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
655	create_remote_batch_job=true
656
657	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
658	if [[ "$remote_jobcatalog" = "" ]]
659	then
660	printf "\n\n +++ no remote jobcatalog found in $config_file"
661	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
662	locat=config_file; exit
663	fi
664
665	# CHECK THAT OPTION -b (SUBMITTING BATCH JOB ON LOCAL HOST) HASN'T BEEN SET
666	if [[ $create_batch_job = true ]]
667	then
668	printf "\n\n +++ option -b must not be set because configuration file has been setup"
669	printf "\n for running jobs on a remote host"
670	locat=config_file; exit
671	fi
672
673	fi
674	running_on_remote=false
675	fi
676
677
678	# SET THE DEFAULT FILE CONNECTION FILE (WHICH IS IN THE REPOSITORY)
679	fileconnection_file=${source_path}/../SCRIPTS/.palm.iofiles
680
681	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
682	if [[ -f .palm.iofiles ]]
683	then
684
685	# CHECK VERSION MISMATCH
686	# RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
687	# FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
688	if [[ $running_in_batch_mode != true && $restart_run != true ]]
689	then
690	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
691	then
692	printf "\n\n +++ WARNING: A file connection file has been found in your"
693	printf "\n working directory, but its revision does not match"
694	printf "\n the revision of the default (trunk) version."
695	printf "\n You may need to update your connection file"
696	printf "\n \"${working_directory}/.palm.iofiles\" !"
697	fi
698	fi
699
700	fileconnection_file=.palm.iofiles
701
702	fi
703
704
705	# CHECK, IF FILE CONNECTION FILE EXISTS
706	if [[ ! -f $fileconnection_file ]]
707	then
708	printf "\n\n +++ file connection file: "
709	printf "\n $fileconnection_file"
710	printf "\n does not exist"
711	locat=connect; exit
712	fi
713
714
715	# READ AND EVALUATE THE I/O-FILE LIST
716	[[ $silent = false ]] && printf "\n Reading the I/O files... "
717
718	# READ THE FILE CONNECTION FILE LINE BY LINE
719	while read line
720	do
721
722	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
723	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
724	line=`echo "$line" \| tr -s " "`
725
726	# INTERPRET THE LINE
727	if [[ "$(echo $line)" = "" ]]
728	then
729	# EMPTY LINE, NO ACTION
730	continue
731
732	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
733	then
734
735	# LINE IS A COMMENT LINE
736	true
737
738	else
739
740	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
741	# s2a: in/out - field
742	# s2b: action - field (optional)
743	s1=`echo "$line" \| cut -d" " -f1`
744	s2=`echo "$line" \| cut -d" " -s -f2`
745	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
746	then
747	s2a=$s2
748	s2b=""
749	else
750	s2a=`echo $s2 \| cut -d":" -f1`
751	s2b=`echo $s2 \| cut -d":" -f2`
752	fi
753	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
754	s4=`echo "$line" \| cut -d" " -s -f4`
755	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
756	s5=`echo "$line" \| cut -d" " -s -f5`
757	s6=`echo "$line" \| cut -d" " -s -f6`
758
759
760	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
761	# INPUT- OR OUTPUT-LIST.
762	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
763	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
764	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
765	# IS NOT CHECKED AND STORED.
766	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
767	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
768	then
769	found=false
770	for actual in $activation_string_list
771	do
772	for formal in $s3
773	do
774	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
775	done
776	done
777	if [[ $found = true ]]
778	then
779	(( iin = iin + 1 ))
780	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
781	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
782	if [[ "$s2a" = inopt ]]
783	then
784	optin_pre[$iin]=yes
785	else
786	optin_pre[$iin]=no
787	fi
788
789	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
790	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
791	if [[ $running_on_remote = true && "$s2b" = tr ]]
792	then
793	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
794	fi
795
796	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
797	# THE WILDCARD FROM THE ENDING
798	if [[ "${s5: -1}" = "*" ]]
799	then
800	if [[ "$s2b" = "di" ]]
801	then
802	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
803	printf "\n see file \"$fileconnection_file\", line"
804	printf "\n$line"
805	locat=iofiles_file; exit
806	fi
807	multin[$iin]=true
808	string=${endin_pre[$iin]}
809	endin_pre[$iin]="${string%?}"
810	else
811	multin[$iin]=false
812	fi
813	fi
814	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
815	then
816	found=false
817	for actual in $activation_string_list
818	do
819	for formal in $s3
820	do
821	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
822	done
823	done
824	if [[ $found = true ]]
825	then
826	(( iout = iout + 1 ))
827	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
828	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
829
830	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
831	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
832	if [[ $formal = wildcard ]]
833	then
834	warnout_pre[$iout]=false
835	else
836	warnout_pre[$iout]=true
837	fi
838
839	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
840	# THE WILDCARD FROM THE LOCAL FILENAME
841	if [[ "${s1: -1}" = "*" ]]
842	then
843	if [[ "$s2b" = "di" ]]
844	then
845	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
846	printf "\n see file \"$fileconnection_file\", line"
847	printf "\n$line"
848	locat=iofiles_file; exit
849	fi
850	multout[$iout]=true
851	string=${localout_pre[$iout]}
852	localout_pre[$iout]="${string%?}"
853	else
854	multout[$iout]=false
855	fi
856	fi
857	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
858	then
859	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
860	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
861	locat=connect; exit
862	fi
863	IFS="$IFSALT"
864	fi
865
866	done < $fileconnection_file
867
868
869
870	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
871	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
872	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
873	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
874	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
875	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
876
877
878
879	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
880	if [[ $run_coupled_model = true ]]
881	then
882
883	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
884	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
885
886	if (( $cores_ocean + $cores_atmos != $cores ))
887	then
888
889	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
890	printf "\n PEs (total) : $cores"
891	printf "\n PEs (atmosphere): $cores_atmos"
892	printf "\n PEs (ocean) : $cores_ocean"
893	locat=coupling; exit
894
895	fi
896
897	fi
898
899
900	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
901	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
902	# FOLDER
903	if [[ $running_in_batch_mode = true ]]
904	then
905
906	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
907	then
908	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
909	printf "\n Please check the output of the palmrun-call"
910	printf "\n that you did on your local host."
911	locat=SOURCES_FOR_RUN; exit
912	fi
913
914	else
915
916	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
917	# AUTOMATIC RESTART RUN
918	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
919	if [[ $restart_run = false ]]
920	then
921
922	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
923	# THE LOCAL HOST
924	if [[ ! -d $source_path ]]
925	then
926	printf "\n\n +++ source path \"$source_path\" on local host"
927	printf "\n \"$(hostname)\" does not exist"
928	locat=source_path; exit
929	fi
930
931	rm -rf ${base_directory}/${sources_for_run_catalog}
932	mkdir -p ${base_directory}/${sources_for_run_catalog}
933
934	if [[ "$source_list" = LM ]]
935	then
936
937	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
938	source_list=""
939	cd $source_path
940
941
942	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
943	if [[ ! -d ../.svn ]]
944	then
945	printf "\n\n +++ source directory"
946	printf "\n \"$source_path\" "
947	printf "\n is not under control of \"subversion\"."
948	printf "\n Please do not use palmrun-option \"-s LM\"\n"
949	fi
950
951
952	# LIST ALL MODIFIED SOURCE CODE FILES
953	Filenames=""
954	svn status > tmp_svnstatus
955	while read line
956	do
957	firstc=`echo $line \| cut -c1`
958	if [[ $firstc = M \|\| $firstc = "?" ]]
959	then
960	Name=`echo "$line" \| cut -c8-`
961	extension=`echo $Name \| cut -d. -f2`
962	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
963	then
964	Filenames="$Filenames "$Name
965	fi
966	fi
967	done < tmp_svnstatus
968	rm -rf tmp_svnstatus
969
970
971	# COPY FILES TO SOURCES_FOR_RUN_...
972	for filename in $Filenames
973	do
974	cp $filename ${base_directory}/${sources_for_run_catalog}
975	source_list=$source_list"$filename "
976	done
977
978	cd - > /dev/null
979
980
981	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
982	elif [[ "$source_list" != "" ]]
983	then
984
985	cd $source_path
986
987	for filename in $source_list
988	do
989
990	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
991	if [[ $(echo $filename \| grep -c "/") != 0 ]]
992	then
993	printf "\n +++ source code file: $filename"
994	printf "\n must not contain (\"/\") "
995	locat=source; exit
996	fi
997
998	if [[ ! -f $filename ]]
999	then
1000	printf "\n +++ source code file: $filename"
1001	printf "\n does not exist"
1002	locat=source; exit
1003	else
1004	cp $filename ${base_directory}/${sources_for_run_catalog}
1005	fi
1006
1007	done
1008
1009	cd - > /dev/null
1010
1011	fi
1012
1013	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
1014	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
1015	if [[ ! -f $makefile ]]
1016	then
1017	printf "\n +++ file \"$makefile\" does not exist"
1018	locat=make; exit
1019	else
1020	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
1021	fi
1022
1023
1024	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
1025	if [[ "$user_source_path" != "" ]]
1026	then
1027
1028	# DOES THE DIRECTORY EXIST?
1029	if [[ ! -d $user_source_path ]]
1030	then
1031
1032	printf "\n\n *** INFORMATIVE: additional source code directory"
1033	printf "\n \"$user_source_path\" "
1034	printf "\n does not exist or is not a directory."
1035	printf "\n No source code will be used from this directory!\n"
1036	user_source_path=""
1037	if [[ $silent == false ]]
1038	then
1039	sleep 2
1040	fi
1041
1042	else
1043
1044	cd $user_source_path
1045
1046	Names=$(ls -1 *.f90 2>&1)
1047	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
1048	Names=$(ls -1 *.F90 2>&1)
1049	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
1050	Names=$(ls -1 *.F 2>&1)
1051	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
1052	Names=$(ls -1 *.f 2>&1)
1053	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
1054	Names=$(ls -1 *.c 2>&1)
1055	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
1056
1057	cd - > /dev/null
1058	cd ${base_directory}/${sources_for_run_catalog}
1059
1060	# COPY MAKEFILE IF EXISTING
1061	if [[ -f $user_source_path/Makefile ]]
1062	then
1063	printf "\n\n *** user Makefile from directory"
1064	printf "\n \"$user_source_path\" is used \n"
1065	if [[ $silent == false ]]
1066	then
1067	sleep 1
1068	fi
1069	cp $user_source_path/Makefile .
1070	fi
1071
1072	for filename in $AddFilenames
1073	do
1074	if [[ -f $filename ]]
1075	then
1076	printf "\n +++ source code file \"$filename\" found in additional"
1077	printf "\n source code directory \"$user_source_path\" "
1078	printf "\n but was also given with option \"-s\" which means that it should be taken"
1079	printf "\n from directory \"$source_path\"."
1080	locat=source; exit
1081	fi
1082
1083	cp $user_source_path/$filename .
1084	source_list="$source_list $filename"
1085
1086	# CHECK IF FILE IS CONTAINED IN MAKEFILE
1087	if [[ $(grep -c $filename Makefile) = 0 ]]
1088	then
1089	printf "\n\n +++ user file \"$filename\" "
1090	printf "\n is not listed in Makefile \n"
1091	locat=source; exit
1092	fi
1093	done
1094	cd - > /dev/null
1095	fi
1096	fi
1097
1098	# COPY CONFIGURATION FILES
1099	cp $config_file ${base_directory}/${sources_for_run_catalog}
1100	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
1101
1102	# COPY SHELLSCRIPTS
1103	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
1104	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
1105
1106	fi
1107
1108	fi
1109
1110
1111	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1112	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1113	if [[ "$global_revision" = "" ]]
1114	then
1115	global_revision=`svnversion $source_path 2>/dev/null`
1116	global_revision="Rev: $global_revision"
1117	fi
1118
1119
1120	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1121	if [[ -n $cores ]]
1122	then
1123
1124	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1125	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
1126	if [[ $tasks_per_node = 0 ]]
1127	then
1128	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1129	then
1130	printf "\n"
1131	printf "\n +++ option \"-T\" (tasks per node) is missing"
1132	printf "\n set -T option or define tasks_per_node in the config file"
1133	locat=tasks_per_node; (( iec = 0 )); exit
1134	else
1135	# DEFAULT FOR INTERACTIVE RUN
1136	tasks_per_node=$cores
1137	fi
1138	fi
1139
1140	if (( cores < tasks_per_node ))
1141	then
1142	printf "\n"
1143	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1144	printf "\n given values: -T $tasks_per_node -X $cores"
1145	locat=tasks_per_node; (( iec = 0 )); exit
1146	fi
1147
1148	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1149	(( mpi_tasks = cores / threads_per_task ))
1150	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
1151	(( ii = cores / tasks_per_node ))
1152	(( remaining_cores = cores - ii * tasks_per_node ))
1153	if (( remaining_cores > 0 ))
1154	then
1155	printf "\n"
1156	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
1157	printf "\n divisor of the total number of cores (option \"-X\")"
1158	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1159	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1160	(( nodes = nodes + 1 ))
1161	fi
1162
1163	fi
1164
1165
1166	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1167	if [[ "$maximum_parallel_io_streams" = "" ]]
1168	then
1169	maximum_parallel_io_streams=$cores
1170	fi
1171
1172
1173	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1174	if [[ "$scp_port" != "" ]]
1175	then
1176	PORTOPT="-P $scp_port"
1177	SSH_PORTOPT="-p $scp_port"
1178	fi
1179
1180
1181	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1182	# CONFIG-FILE
1183	if [[ "$ssh_key" != "" ]]
1184	then
1185	ssh_key="-i $HOME/.ssh/$ssh_key"
1186	fi
1187
1188
1189	# SET QUEUE, IF NOT GIVEN
1190	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1191	then
1192
1193	if [[ $queue = none && "$defaultqueue" = "" ]]
1194	then
1195	printf "\n"
1196	printf "\n +++ no default queue given in configuration file and no queue"
1197	printf "\n given with option -q"
1198	locat=queue; exit
1199	fi
1200	if [[ $queue = none ]]
1201	then
1202	queue=$defaultqueue
1203	fi
1204
1205	fi
1206
1207
1208	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1209	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1210	(( i = 0 ))
1211	(( nr_of_input_files = 0 ))
1212	while (( i < iin ))
1213	do
1214	(( i = i + 1 ))
1215
1216	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1217	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1218	if [[ "${actionin_pre[$i]}" = di ]]
1219	then
1220	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1221	else
1222	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
1223	fi
1224
1225
1226	# CHECK IF FILE EXISTS
1227	if ! ls $filename* 1>/dev/null 2>&1
1228	then
1229
1230	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1231	if [[ "${optin_pre[$i]}" != "yes" ]]
1232	then
1233	printf "\n\n +++ INPUT-file: "
1234	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
1235	then
1236	printf "\n $filename"
1237	else
1238	printf "\n $filename.${extin_pre[$i]}"
1239	fi
1240	printf "\n does not exist\n"
1241	locat=input; exit
1242	else
1243	(( nr_of_input_files = nr_of_input_files + 1 ))
1244	localin[$nr_of_input_files]="${localin_pre[$i]}"
1245	optin[$nr_of_input_files]="${optin_pre[$i]}"
1246	actionin[$nr_of_input_files]="unavailable"
1247	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1248	endin[$nr_of_input_files]="${endin_pre[$i]}"
1249	extin[$nr_of_input_files]="${extin_pre[$i]}"
1250	fi
1251
1252	else
1253
1254	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1255	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1256	# ENDINGS
1257	if [[ "${multin[$i]}" = true ]]
1258	then
1259	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1260	ls -1 -d ${filename} > filelist 2>/dev/null
1261	ls -1 -d ${filename}.* >> filelist 2>/dev/null
1262	ls -1 -d ${filename}_* >> filelist 2>/dev/null
1263
1264	endings=""
1265	while read line
1266	do
1267	# filename without path (i.e. after the last "/")
1268	basefilename=$(basename ${line})
1269
1270	# check if there is an extension and remove it
1271	ext=${basefilename##*.}
1272	if [[ "$ext" = "${extin_pre[$i]}" ]]
1273	then
1274	basefilename=${basefilename%.*}
1275	fi
1276
1277	# check for an existing cycle number and remove it
1278	cycle=${basefilename##*.}
1279	if [[ $cycle =~ ^-?[0-9]+$ ]]
1280	then
1281	basefilename=${basefilename%.*}
1282	fi
1283
1284	# remove the run_identifier from the beginning
1285	length_run_identifier=${#run_identifier}
1286	ending=${basefilename:${length_run_identifier}}
1287
1288	# remove the ending given in the .iofiles from the beginning
1289	endingstring="${endin_pre[$i]}"
1290	length_ending=${#endingstring}
1291	ending=${ending:${length_ending}}
1292
1293	if [[ "$ending" = "" ]]
1294	then
1295	# standard ending as given in the .iofiles
1296	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
1297	then
1298	endings="$endings DEFAULT"
1299	fi
1300	else
1301	# ending must start with "_", otherwise its a different file
1302	if [[ "${ending:0:1}" = "_" ]]
1303	then
1304	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
1305	then
1306	endings="$endings $ending"
1307	fi
1308	fi
1309	fi
1310
1311	done <filelist
1312
1313	rm filelist
1314
1315	else
1316
1317	# SINGLE NAME
1318	endings=DEFAULT
1319
1320	fi
1321
1322	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1323	for ending in $endings
1324	do
1325
1326	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1327	if [[ $ending = DEFAULT ]]
1328	then
1329	ending=""
1330	fi
1331
1332	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1333	(( nr_of_input_files = nr_of_input_files + 1 ))
1334	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1335	optin[$nr_of_input_files]="${optin_pre[$i]}"
1336	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1337	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1338	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1339	extin[$nr_of_input_files]="${extin_pre[$i]}"
1340
1341
1342	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1343	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1344	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1345	then
1346	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1347	else
1348	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
1349	fi
1350
1351	# DETERMINE THE FILE'S CYCLE NUMBER
1352	(( maxcycle = 0 ))
1353	ls -1 -d $filename > filelist 2>/dev/null
1354	ls -1 -d $filename.* >> filelist 2>/dev/null
1355	while read line
1356	do
1357	# filename without path (i.e. after the last "/")
1358	basefilename=$(basename ${line})
1359
1360	# check if there is an extension
1361	extension=${basefilename##*.}
1362	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1363	then
1364	basefilename=${basefilename%.*}
1365	fi
1366
1367	# check for an existing cycle number
1368	cycle=${basefilename##*.}
1369	if [[ $cycle =~ ^-?[0-9]+$ ]]
1370	then
1371	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1372	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1373	(( icycle = $((10#$cycle)) ))
1374	else
1375	(( icycle = 0 ))
1376	fi
1377
1378	if (( icycle > maxcycle ))
1379	then
1380	(( maxcycle = icycle ))
1381
1382	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1383	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1384	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1385	then
1386	leading_zero=true
1387	else
1388	leading_zero=false
1389	fi
1390	fi
1391
1392	done <filelist
1393	rm filelist
1394
1395	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1396	if [[ $leading_zero = true ]]
1397	then
1398	cyclestring=`printf "%03d" $maxcycle`
1399	else
1400	cyclestring=$maxcycle
1401	fi
1402
1403	# APPEND CYCLE NUMBER TO FILENAME
1404	if (( maxcycle > 0 ))
1405	then
1406	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1407	then
1408	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1409	else
1410	filename=${filename}.$cyclestring
1411	fi
1412	else
1413	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
1414	then
1415	filename=${filename}.${extin[$nr_of_input_files]}
1416	fi
1417	fi
1418
1419	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1420	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1421	absnamein[$nr_of_input_files]=$filename
1422	if (( maxcycle > 0 ))
1423	then
1424	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1425	then
1426	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1427	else
1428	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
1429	fi
1430	else
1431	if [[ "${actionin[$nr_of_input_files]}" = di ]]
1432	then
1433	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1434	else
1435	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
1436	fi
1437	fi
1438
1439	done
1440
1441	fi
1442
1443	done
1444
1445
1446	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1447	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1448	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1449	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1450	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1451	# REMOTE HOST)
1452	(( i = 0 ))
1453	while (( i < iout ))
1454	do
1455	(( i = i + 1 ))
1456	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
1457	then
1458	if [[ "${actionout_pre[$i]}" = tr ]]
1459	then
1460	actionout_pre[$i]=""
1461	elif [[ "${actionout_pre[$i]}" = trpe ]]
1462	then
1463	actionout_pre[$i]=pe
1464	elif [[ "${actionout_pre[$i]}" = tra ]]
1465	then
1466	actionout_pre[$i]=a
1467	fi
1468	(( maxcycle = 0 ))
1469	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
1470	eval catalogname=${pathout_pre[$i]}
1471	if ! ls $filename* 1>/dev/null 2>&1
1472	then
1473
1474	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1475	if cat /dev/null > $filename
1476	then
1477	rm $filename
1478	else
1479
1480	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1481	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1482	if [[ ! -d $catalogname ]]
1483	then
1484	if mkdir -p $catalogname
1485	then
1486	printf "\n\n *** directory:"
1487	printf "\n $catalogname"
1488	printf "\n was created\n"
1489	else
1490	printf "\n\n +++ OUTPUT-file:"
1491	printf "\n $filename"
1492	printf "\n cannot be created, because directory does not exist"
1493	printf "\n and cannot be created either"
1494	printf "\n"
1495	locat=output ; exit
1496	fi 2>/dev/null
1497	else
1498	printf "\n\n +++ OUTPUT-file:"
1499	printf "\n $filename"
1500	printf "\n cannot be created, although directory exists"
1501	printf "\n"
1502	locat=output ; exit
1503	fi
1504	fi 2>/dev/null
1505
1506	fi
1507
1508	fi
1509	done
1510
1511
1512	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1513	if [[ $running_in_batch_mode = false ]]
1514	then
1515	run_id_number=$RANDOM
1516	run_id=${run_identifier}.$run_id_number
1517
1518	tempdir=$fast_io_catalog/$run_id
1519
1520	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1521	export job_id=$run_id
1522
1523	fi
1524
1525
1526	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1527	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1528	then
1529
1530	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1531	if [[ $ibd = 0 ]]
1532	then
1533	printf "\n"
1534	printf "\n +++ no batch directives found in configuration file"
1535	locat=config_file_batch_directives; (( iec = 0 )); exit
1536	fi
1537
1538	# CHECK IF CPUTIME IS GIVEN FOR JOB
1539	done=false
1540	cputime=$cpumax
1541	while [[ $done = false ]]
1542	do
1543	if (( cputime == 0 ))
1544	then
1545	printf "\n +++ cpu-time is undefined"
1546	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1547	printf "\n >>> "
1548	read cputime 1>/dev/null 2>&1
1549	else
1550	done=true
1551	fi
1552	done
1553	cpumax=$cputime
1554
1555	# CHECK THE MEMORY DEMAND
1556	done=false
1557	while [[ $done = false ]]
1558	do
1559	if (( memory == 0 ))
1560	then
1561	printf "\n +++ memory demand is undefined"
1562	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1563	printf "\n >>> "
1564	read memory 1>/dev/null 2>&1
1565	else
1566	done=true
1567	fi
1568	done
1569
1570	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1571	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1572	then
1573	while [[ -z $remote_username ]]
1574	do
1575	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1576	printf "\n >>> Please type username:"
1577	printf "\n >>> "
1578	read remote_username
1579	done
1580	fi
1581
1582	else
1583
1584	if [[ $running_in_batch_mode = false ]]
1585	then
1586	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1587	cpumax=$cputime
1588	else
1589	cputime=$cpumax
1590	fi
1591
1592	fi
1593
1594
1595	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1596	(( cpu_hours = cputime / 3600 ))
1597	(( resttime = cputime - cpu_hours * 3600 ))
1598	(( cpu_minutes = resttime / 60 ))
1599	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1600	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1601
1602
1603	# OUTPUT OF THE PALMRUN-HEADER
1604	calltime=$(date)
1605	printf "\n"
1606	printf "#------------------------------------------------------------------------# \n"
1607	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1608	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
1609	printf "\| \| \n"
1610	column1="called on:"; column2=$(hostname)
1611	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1612	if [[ $create_remote_batch_job = true ]]
1613	then
1614	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
1615	else
1616	if [[ $running_on_remote = true ]]
1617	then
1618	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
1619	else
1620	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
1621	fi
1622	fi
1623	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1624
1625	column1="running in:"
1626	if [[ $running_in_batch_mode = true ]]
1627	then
1628	column2="batch job mode"
1629	else
1630	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1631	then
1632	column2="job creation mode"
1633	else
1634	column2="interactive run mode"
1635	fi
1636	fi
1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1638
1639	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1640	then
1641	if [[ "$project_account" != "" ]]
1642	then
1643	column1="project account number:"
1644	column2="$project_account"
1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1646	fi
1647	fi
1648
1649	if [[ -n $cores ]]
1650	then
1651	if [[ $run_coupled_model = false ]]
1652	then
1653	column1="number of cores:"; column2=$cores
1654	else
1655	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1656	fi
1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1658	fi
1659	if [[ -n $tasks_per_node ]]
1660	then
1661	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1663	if (( remaining_cores > 0 ))
1664	then
1665	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1666	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1667	fi
1668	fi
1669	if [[ $maximum_parallel_io_streams != $cores ]]
1670	then
1671	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1672	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1673	fi
1674	if [[ $use_openmp = true ]]
1675	then
1676	column1="threads per task:"; column2="$threads_per_task"
1677	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1678	fi
1679	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1680	then
1681	column1="memory demand / PE":; column2="$memory MB"
1682	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1683	column1="job cpu time (h:m:s):"; column2="$timestring"
1684	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1685	fi
1686	printf "\| \| \n"
1687	if [[ "$source_list" != "" ]]
1688	then
1689	if [[ "$make_options" != "" ]]
1690	then
1691	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1692	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1693	line=$(echo "$make_options" \| cut -c46-)
1694	while [[ "$line" != "" ]]
1695	do
1696	column1=""
1697	column2=$(echo "$line" \| cut -c-45)
1698	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1699	line=$(echo "$line" \| cut -c46-)
1700	done
1701	fi
1702	fi
1703
1704	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1705	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1706	line=$(echo "$cpp_options" \| cut -c46-)
1707	while [[ "$line" != "" ]]
1708	do
1709	column1=""
1710	column2=$(echo "$line" \| cut -c-45)
1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1712	line=$(echo "$line" \| cut -c46-)
1713	done
1714
1715	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1717	line=$(echo "$compiler_options" \| cut -c46-)
1718	while [[ "$line" != "" ]]
1719	do
1720	column1=""
1721	column2=$(echo "$line" \| cut -c-45)
1722	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1723	line=$(echo "$line" \| cut -c46-)
1724	done
1725
1726	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1727	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1728	line=$(echo "$linker_options" \| cut -c46-)
1729	while [[ "$line" != "" ]]
1730	do
1731	column1=""
1732	column2=$(echo "$line" \| cut -c-45)
1733	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1734	line=$(echo "$line" \| cut -c46-)
1735	done
1736
1737	if [[ "$login_init_cmd" != "" ]]
1738	then
1739	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1740	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1741	line=$(echo "$login_init_cmd" \| cut -c46-)
1742	while [[ "$line" != "" ]]
1743	do
1744	column1=""
1745	column2=$(echo "$line" \| cut -c-45)
1746	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1747	line=$(echo "$line" \| cut -c46-)
1748	done
1749	fi
1750
1751	if [[ "$module_commands" != "" ]]
1752	then
1753	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1754	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1755	line=$(echo "$module_commands" \| cut -c46-)
1756	while [[ "$line" != "" ]]
1757	do
1758	column1=""
1759	column2=$(echo "$line" \| cut -c-45)
1760	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1761	line=$(echo "$line" \| cut -c46-)
1762	done
1763	fi
1764	printf "\| \| \n"
1765	column1="run identifier:"; column2=$run_identifier
1766	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1767	column1="activation string list:"; column2=$(echo $activation_string_list)
1768	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1769
1770	if [[ "$ocean_file_appendix" = true ]]
1771	then
1772	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1773	fi
1774
1775	if [[ "$source_list" != "" ]]
1776	then
1777	printf "\| \| \n"
1778	printf "\| Files to be compiled: \| \n"
1779	line=$source_list
1780	while [[ "$line" != "" ]]
1781	do
1782	linestart=$(echo $line \| cut -c-70)
1783	printf "\| %-70s \| \n" "$linestart"
1784	line=$(echo "$line" \| cut -c71-)
1785	done
1786	fi
1787	printf "#------------------------------------------------------------------------#"
1788
1789
1790
1791	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1792	if [[ $do_trace = true ]]
1793	then
1794	(( i = 0 ))
1795	while (( i < nr_of_input_files ))
1796	do
1797	(( i = i + 1 ))
1798	if (( i == 1 ))
1799	then
1800	printf "\n\n >>> INPUT-file assignments:\n"
1801	fi
1802	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1803	done
1804	(( i = 0 ))
1805	while (( i < iout ))
1806	do
1807	(( i = i + 1 ))
1808	if (( i == 1 ))
1809	then
1810	printf "\n\n >>> OUTPUT-file assignments:\n"
1811	fi
1812	printf "\n ${localout[$i]} : ${pathout[$i]}"
1813	done
1814	(( i = 0 ))
1815	while (( i < iic ))
1816	do
1817	(( i = i + 1 ))
1818	if (( i == 1 ))
1819	then
1820	printf "\n\n >>> INPUT-commands:\n"
1821	fi
1822	printf "\n ${in_command[$i]}"
1823	done
1824	(( i = 0 ))
1825	while (( i < ioc ))
1826	do
1827	(( i = i + 1 ))
1828	if (( i == 1 ))
1829	then
1830	printf "\n\n >>> OUTPUT-commands:\n"
1831	fi
1832	printf "\n ${out_command[$i]}"
1833	done
1834	fi
1835
1836	# QUERY FOR CONTINUE
1837	if [[ $silent = false && $running_in_batch_mode = false ]]
1838	then
1839	antwort=dummy
1840	printf "\n\n"
1841	printf " >>> everything o.k. (y/n) ? "
1842	while read antwort
1843	do
1844	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1845	then
1846	printf " >>> everything o.k. (y/n) ? "
1847	else
1848	break
1849	fi
1850	done
1851	if [[ $antwort = n \|\| $antwort = N ]]
1852	then
1853	locat=user_abort; (( iec = 0 )); exit
1854	fi
1855	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1856	then
1857	printf "\n *** batch-job will be created and submitted"
1858	else
1859	printf "\n *** PALMRUN will now continue to execute on this machine"
1860	fi
1861	fi
1862
1863
1864
1865	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1866	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1867	then
1868
1869	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1870	then
1871	printf "\n\n *** creating executable and other sources for the remote host\n"
1872	else
1873	printf "\n\n *** creating executable and other sources for the local host\n"
1874	fi
1875
1876	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1877	# IT SHALL BE CREATED
1878	ask_for_make_depository=false
1879	if [[ $create_remote_batch_job = true ]]
1880	then
1881
1882	line=`grep %base_directory $config_file`
1883	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1884	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
1885
1886	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
1887	then
1888	printf "\n\n +++ make depository \"${make_depository}\""
1889	printf "\n on remote host not found!"
1890	ask_for_make_depository=true
1891	fi
1892	rm ${configuration_identifier}_last_make_protokoll
1893
1894	else
1895
1896	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1897	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
1898	if [[ ! -d ${make_depository} ]]
1899	then
1900	printf "\n\n +++ make depository \"${make_depository}\""
1901	printf "\n on local host not found!"
1902	ask_for_make_depository=true
1903	fi
1904
1905	fi
1906
1907	if [[ $ask_for_make_depository = true ]]
1908	then
1909
1910	antwort=dummy
1911	printf "\n\n"
1912	printf " >>> Create a new one (y/n) ? "
1913	while read antwort
1914	do
1915	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1916	then
1917	printf " >>> Create a new one (y/n) ? "
1918	else
1919	break
1920	fi
1921	done
1922	if [[ $antwort = n \|\| $antwort = N ]]
1923	then
1924	locat=user_abort; (( iec = 0 )); exit
1925	fi
1926
1927	if [[ $do_trace = true ]]
1928	then
1929	palmbuild -c $configuration_identifier
1930	else
1931	palmbuild -v -c $configuration_identifier
1932	fi
1933
1934	if [[ ${PIPESTATUS[0]} != 0 ]]
1935	then
1936
1937	# ABORT IN CASE OF COMPILATION PROBLEMS
1938	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1939	locat=make_depository
1940	exit
1941	else
1942	echo " *** now continue with creating executable and other sources"
1943	fi
1944
1945	fi
1946
1947	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1948	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
1949
1950	if [[ ${PIPESTATUS[0]} != 0 ]]
1951	then
1952
1953	# ABORT IN CASE OF COMPILATION PROBLEMS
1954	printf "\n +++ error while creating executable and/or other sources"
1955	locat=execution
1956	rm -rf ${base_directory}/${sources_for_run_catalog}
1957	exit
1958
1959	else
1960
1961	printf " *** executable and other sources created\n"
1962	rm -rf ${base_directory}/${sources_for_run_catalog}
1963
1964	fi
1965
1966	fi
1967
1968
1969	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1970	# WILL BE COPIED TO THE REMOTE HOST
1971	if [[ $create_remote_batch_job = true ]]
1972	then
1973	(( i = 0 ))
1974	while (( i < nr_of_input_files ))
1975	do
1976	(( i = i + 1 ))
1977	if [[ "${actionin[$i]}" = tr ]]
1978	then
1979	eval inputfile=${pathin[$i]}/${frelin[$i]}
1980	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1981	fi
1982	done
1983	if (( i > 0 ))
1984	then
1985	printf "\n\n *** input files have been copied to the remote host\n"
1986	fi
1987	fi
1988
1989
1990	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1991	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1992	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1993	then
1994
1995	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1996	if [[ $running_in_batch_mode = false ]]
1997	then
1998	# CREATE THE DIRECTORY
1999	mkdir -p $tempdir
2000	if [[ $? != 0 ]]
2001	then
2002	printf "\n +++ temporary working directory cannot be created."
2003	printf "\n Check setting of variable fast_io_catalog in your config file."
2004	locat=execution
2005	exit
2006	fi
2007	chmod go+rx $tempdir
2008	cd $tempdir
2009	printf "\n *** changed to temporary directory: $tempdir"
2010
2011	else
2012
2013	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
2014	printf "\n *** running in temporary directory: $tempdir"
2015
2016	fi
2017
2018
2019	# PROVIDE THE INPUT FILES
2020	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
2021	optional_files_missing=false
2022	(( i = 0 ))
2023	while (( i < nr_of_input_files ))
2024	do
2025	(( i = i + 1 ))
2026	if (( i == 1 ))
2027	then
2028	printf "\n\n *** providing INPUT-files:\n$dashes"
2029	fi
2030
2031
2032	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
2033	if [[ "${actionin[$i]}" = unavailable ]]
2034	then
2035	optional_files_missing=true
2036	continue
2037	fi
2038
2039	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2040	files_for_cores=false; filetype=file
2041	if [[ "${actionin[$i]}" = pe && -n $cores ]]
2042	then
2043	files_for_cores=true; filetype=files
2044	actionin[$i]=""
2045	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
2046	then
2047	actionin[$i]=""
2048	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
2049	then
2050	files_for_cores=true; filetype=files
2051	actionin[$i]="ln"
2052	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
2053	then
2054	actionin[$i]="ln"
2055	fi
2056
2057	if [[ $files_for_cores = true ]]
2058	then
2059	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
2060	else
2061	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
2062	fi
2063
2064	# INPUT-FILES TO BE LINKED
2065	if [[ "${actionin[$i]}" = ln ]]
2066	then
2067
2068	printf "\n $filetype will be linked"
2069	if [[ $files_for_cores = false ]]
2070	then
2071	if [[ -f "${absnamein[$i]}" ]]
2072	then
2073	ln ${absnamein[$i]} ${localin[$i]}
2074	got_tmp[$i]=true
2075	fi
2076	else
2077	if [[ -d "${absnamein[$i]}" ]]
2078	then
2079	mkdir -p ${localin[$i]}
2080	cd ${absnamein[$i]}
2081	for file in $(ls *)
2082	do
2083	ln $file $tempdir/${localin[$i]}
2084	done >\|/dev/null 2>&1
2085	cd $tempdir
2086	fi
2087
2088	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2089	if [[ ! -f "${localin[$i]}/_000000" ]]
2090	then
2091	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2092	cp -r ${absnamein[$i]}/* ${localin[$i]}
2093	fi
2094
2095	got_tmp[$i]=true
2096	fi
2097	fi
2098
2099	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
2100	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
2101	then
2102
2103	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
2104	then
2105
2106	# FILE COPIES ARE PROVIDED FOR ALL CORES
2107	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2108	printf "\n file will be provided for $cores processors"
2109	mkdir -p ${localin[$i]}
2110	ival=$cores
2111	(( ii = 0 ))
2112	while (( ii <= ival-1 ))
2113	do
2114	if (( ii < 10 ))
2115	then
2116	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
2117	elif (( ii < 100 ))
2118	then
2119	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
2120	elif (( ii < 1000 ))
2121	then
2122	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
2123	else
2124	cp ${absnamein[$i]} ${localin[$i]}/_$ii
2125	fi
2126	(( ii = ii + 1 ))
2127	done
2128
2129	else
2130
2131	if [[ $files_for_cores = true ]]
2132	then
2133
2134	# PROVIDE FILES FOR EACH CORE
2135	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2136	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2137	printf "\n providing $cores files for the respective cores"
2138	mkdir -p ${localin[$i]}
2139	if [[ $link_local_input = true ]]
2140	then
2141	printf " files will be linked\n"
2142	cd ${absnamein[$i]}
2143	for file in $(ls *)
2144	do
2145	ln -f $file ${localin[$i]}
2146	done
2147	cd $tempdir
2148	fi
2149
2150	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2151	if [[ ! -f "${localin[$i]}/_000000" ]]
2152	then
2153	if [[ $link_local_input = true ]]
2154	then
2155	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2156	fi
2157	cp -r ${absnamein[$i]}/* ${localin[$i]}
2158	fi
2159
2160	else
2161
2162	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
2163	if [[ $link_local_input = true ]]
2164	then
2165	printf " file will be linked\n"
2166	ln -f ${absnamein[$i]} ${localin[$i]}
2167	fi
2168	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
2169	if [[ ! -f "${localin[$i]}" ]]
2170	then
2171	if [[ $link_local_input = true ]]
2172	then
2173	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
2174	fi
2175	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
2176	then
2177	mv ${absnamein[$i]} ${localin[$i]}
2178	else
2179	cp ${absnamein[$i]} ${localin[$i]}
2180	fi
2181	fi
2182	fi
2183	fi
2184	fi
2185
2186	done
2187	if (( i != 0 ))
2188	then
2189	if [[ $optional_files_missing = true ]]
2190	then
2191	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
2192	fi
2193	printf "\n$dashes\n *** all INPUT-files provided \n"
2194	fi
2195
2196	# NOW COPY FILES (.f90, .o, config files, etc.) FROM SOURCES_FOR_RUN_... TO THE TEMPORARY
2197	# WORKING DIRECTORY
2198	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
2199
2200
2201	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2202	(( i = 0 ))
2203	while (( i < iic ))
2204	do
2205	(( i = i + 1 ))
2206	if (( i == 1 ))
2207	then
2208	printf "\n\n *** execution of INPUT-commands:\n$dashes"
2209	fi
2210	printf "\n >>> ${in_command[$i]}"
2211	eval ${in_command[$i]}
2212	if (( i == iic ))
2213	then
2214	printf "\n$dashes\n"
2215	fi
2216	done
2217
2218
2219	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2220	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
2221	then
2222	progress_bar_disabled=true
2223	else
2224	progress_bar_disabled=false
2225	fi
2226
2227
2228	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2229	# (FILE ENVPAR WILL BE READ BY PALM)
2230	cat > ENVPAR << EOF
2231	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
2232	write_svf = .${write_svf}., write_binary = .${write_binary}.,
2233	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
2234	maximum_parallel_io_streams = $maximum_parallel_io_streams,
2235	maximum_cpu_time_allowed = ${cpumax}.,
2236	revision = '$global_revision',
2237	progress_bar_disabled = .${progress_bar_disabled}. /
2238
2239	EOF
2240
2241
2242	# STARTING THE EXECUTABLE
2243	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
2244	PATH=$PATH:$tempdir
2245
2246
2247	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2248	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2249	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
2250	eval line=\"$line\"
2251	execute_command="$line"
2252
2253
2254	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2255	if [[ "$execute_command_for_combine" = "" ]]
2256	then
2257	eval line2=\"$line2\"
2258	execute_command_for_combine="$line2"
2259	fi
2260
2261
2262
2263	# PROVIDE A HOSTFILE, IF REQUIRED
2264	if [[ "$hostfile" != "" ]]
2265	then
2266
2267	if [[ $hostfile = auto ]]
2268	then
2269	# CREATE A NEW HOSTFILE
2270	(( ii = 1 ))
2271	while (( ii <= cores / threads_per_task ))
2272	do
2273	echo $(hostname) >> hostfile
2274	(( ii = ii + 1 ))
2275	done
2276	if (( cores / threads_per_task == 0 ))
2277	then
2278	echo $(hostname) >> hostfile
2279	fi
2280
2281	else
2282	cp $hostfile hostfile
2283	fi
2284	eval line=\"`head -n $ii hostfile`\"
2285	printf "\n *** running on: $line"
2286	fi
2287
2288
2289
2290	# SET THE NUMBER OF OPENMP-THREADS
2291	if [[ $use_openmp = true ]]
2292	then
2293	export OMP_NUM_THREADS=$threads_per_task
2294	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2295	else
2296	export OMP_NUM_THREADS=1
2297	fi
2298
2299
2300	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2301	if [[ $run_coupled_model = false ]]
2302	then
2303	if [[ "$ocean_file_appendix" = true ]]
2304	then
2305	echo "precursor_ocean" > coupling_steering
2306	else
2307	echo "precursor_atmos" > coupling_steering
2308	fi
2309	else
2310	(( iia = $cores_atmos / $threads_per_task ))
2311	(( iio = $cores_ocean / $threads_per_task ))
2312	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2313	printf "\n\n"
2314	echo "coupled_run $iia $iio" > coupling_steering
2315	fi
2316
2317	printf "\n *** execute command:"
2318	printf "\n \"$execute_command\" \n\n"
2319
2320
2321	if [[ $progress_bar_disabled = true ]]
2322	then
2323	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
2324	exit_code=${PIPESTATUS[0]}
2325	else
2326	$execute_command < coupling_steering &> >(tee STDOUT)
2327	exit_code=${PIPESTATUS[0]}
2328	fi
2329
2330	if [[ ${exit_code} != 0 ]]
2331	then
2332
2333	# ABORT IN CASE OF RUNTIME ERRORS
2334	printf "\n +++ runtime error occured"
2335	locat=execution
2336	exit
2337
2338	else
2339
2340	printf "\n$dashes\n *** execution finished \n"
2341
2342	fi
2343
2344
2345	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2346	# BY EACH CORE INTO ONE FILE
2347	if [[ ! -f combine_plot_fields.x ]]
2348	then
2349
2350	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2351	printf "\n 2d- and/or 3d-data may be incomplete!"
2352	printf "\n Your previous palmbuild may have failed. Please check.\n"
2353
2354	elif [[ "$combine_plot_fields" == true ]]
2355	then
2356
2357	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2358	$execute_command_for_combine
2359
2360	else
2361
2362	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2363	# DATA OUTPUT
2364	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2365	fi
2366
2367
2368
2369	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2370	(( i = 0 ))
2371	while (( i < ioc ))
2372	do
2373	(( i = i + 1 ))
2374	if (( i == 1 ))
2375	then
2376	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2377	fi
2378
2379	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2380	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2381
2382	printf "\n >>> ${out_command[$i]}"
2383	eval ${out_command[$i]}
2384	if (( i == ioc ))
2385	then
2386	printf "\n$dashes\n"
2387	fi
2388	done
2389
2390
2391	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2392	# WILDCARDS
2393	(( i = 0 ))
2394	(( nr_of_output_files = 0 ))
2395
2396	while (( i < iout ))
2397	do
2398
2399	(( i = i + 1 ))
2400
2401	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2402	# CREATE A LIST FOR THE DETECTED ENDINGS
2403	if [[ "${multout[$i]}" = true ]]
2404	then
2405	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2406	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
2407	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
2408
2409	endings="DEFAULT"
2410	while read line
2411	do
2412	# remove the local name from the beginning
2413	localnamestring="${localout_pre[$i]}"
2414	length_localname=${#localnamestring}
2415	ending=${line:${length_localname}}
2416
2417	if [[ "$ending" != "" ]]
2418	then
2419	endings="$endings $ending"
2420	fi
2421
2422	done <filelist
2423
2424	rm filelist
2425
2426	else
2427
2428	# SINGLE NAME
2429	endings=DEFAULT
2430
2431	fi
2432
2433	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2434	for ending in $endings
2435	do
2436
2437	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2438	if [[ $ending = DEFAULT ]]
2439	then
2440	ending=""
2441	fi
2442
2443	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2444	(( nr_of_output_files = nr_of_output_files + 1 ))
2445	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2446	transout[$nr_of_output_files]="${transout_pre[$i]}"
2447	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2448	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2449	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2450	extout[$nr_of_output_files]="${extout_pre[$i]}"
2451	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2452
2453	done
2454
2455	done
2456
2457
2458
2459
2460	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2461	(( i = 0 ))
2462	while (( i < nr_of_output_files ))
2463	do
2464	(( i = i + 1 ))
2465	if (( i == 1 ))
2466	then
2467	timestring=`date +%H:%M:%S`
2468	printf "\n\n *** saving OUTPUT-files: local time: $timestring"
2469
2470	# GET RUN NUMBER ASSIGNED BY PALM
2471	if [[ -f RUN_NUMBER ]]
2472	then
2473	read run_number < RUN_NUMBER
2474	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2475	usecycle_option="-U $run_number"
2476	else
2477	run_number=0
2478	usecycle_option=""
2479	fi
2480	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2481	then
2482	printf "\n *** in case of SCP transfers to local host"
2483	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2484	fi
2485	printf "\n$dashes"
2486	fi
2487
2488	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2489	then
2490
2491	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
2492
2493	# DETERMINE THE CYCLE NUMBER
2494	ls -1 -d $filename > filelist 2>/dev/null
2495	ls -1 -d $filename.* >> filelist 2>/dev/null
2496	while read line
2497	do
2498
2499	# filename without path (i.e. after the last "/")
2500	basefilename=$(basename ${line})
2501
2502	# check if there is an extension
2503	extension=${basefilename##*.}
2504	if [[ "$extension" = "${extout[$i]}" ]]
2505	then
2506	basefilename=${basefilename%.*}
2507	fi
2508
2509	# check for an existing cycle number
2510	cycle=${basefilename##*.}
2511	if [[ $cycle =~ ^-?[0-9]+$ ]]
2512	then
2513	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2514	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2515	(( icycle = $((10#$cycle)) + 1 ))
2516	else
2517	(( icycle = 1 ))
2518	fi
2519
2520	if (( icycle > maxcycle ))
2521	then
2522	(( maxcycle = icycle ))
2523	fi
2524
2525	done <filelist
2526	rm filelist
2527
2528
2529	# SET THE CYCLE NUMBER
2530	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2531	if [[ "${actionout[$i]}" = a ]]
2532	then
2533	(( maxcycle = maxcycle - 1 ))
2534	fi
2535
2536	(( cycnum[$i] = maxcycle ))
2537	pathout[$i]=$filename
2538
2539
2540	# ADD CYCLE NUMBER TO FILENAME
2541	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2542	if [[ "${actionout[$i]}" != "a" ]]
2543	then
2544	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2545	# WITH AN EXISTING CYCLE NUMBER
2546	if (( run_number >= cycnum[$i] ))
2547	then
2548	(( cycnum[$i] = run_number ))
2549	else
2550	if (( run_number > 0 ))
2551	then
2552	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2553	fi
2554	fi
2555	fi
2556	if (( cycnum[$i] > 0 ))
2557	then
2558	cyclestring=`printf "%03d" ${cycnum[$i]}`
2559	pathout[$i]=${pathout[$i]}.$cyclestring
2560	fi
2561	fi
2562
2563	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2564	files_for_cores=false; filetype=file
2565	link_local_output=false
2566	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2567	then
2568	files_for_cores=true; filetype=directory
2569	actionout[$i]=""
2570	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2571	then
2572	actionout[$i]=""
2573	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2574	then
2575	files_for_cores=true; filetype=directory
2576	link_local_output=true
2577	actionout[$i]=""
2578	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2579	then
2580	link_local_output
2581	actionout[$i]=""
2582	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2583	then
2584	files_for_cores=true; filetype=directory
2585	actionout[$i]="tr"
2586	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2587	then
2588	actionout[$i]="tr"
2589	fi
2590
2591	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2592	then
2593	if [[ ${warnout[$i]} = true ]]
2594	then
2595	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2596	fi
2597	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2598	then
2599	if [[ ${warnout[$i]} = true ]]
2600	then
2601	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2602	fi
2603	else
2604
2605
2606	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2607	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2608	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2609	then
2610	if [[ $running_on_remote = true ]]
2611	then
2612
2613	# SET OPTIONS FOR TRANSFER
2614	if [[ "${actionout[$i]}" = tr ]]
2615	then
2616	if [[ $files_for_cores = false ]]
2617	then
2618	catalog_option=""
2619	catalog_string=""
2620	else
2621	catalog_option="-c"
2622	catalog_string="/"
2623	fi
2624	append_option=""
2625	append_string=""
2626	else
2627	append_option="-A"
2628	append_string="append"
2629	fi
2630
2631	transfer_failed=false
2632	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2633	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
2634
2635	# TRANSFER VIA SCP
2636	if [[ "$remote_loginnode" != "" ]]
2637	then
2638	ssh -q $remote_username@$remote_loginnode "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]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}"
2639	else
2640	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
2641	fi
2642	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
2643
2644
2645	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2646	if [[ $transfer_failed = true ]]
2647	then
2648	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2649	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
2650
2651	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2652	eval local_catalog=${pathout[$i]}
2653	if [[ ! -d $local_catalog ]]
2654	then
2655	printf " *** local directory does not exist. Trying to create:\n"
2656	printf " $local_catalog \n"
2657	mkdir -p $local_catalog
2658	fi
2659	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
2660	transfer_problems=true
2661	fi
2662
2663	else
2664
2665	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2666	# BE COPIED OR APPENDED ON THIS MACHINE
2667	if [[ "${actionout[$i]}" = tr ]]
2668	then
2669	actionout[$i]=""
2670	else
2671	actionout[$i]="a"
2672	fi
2673	fi
2674	fi
2675
2676
2677	# APPEND ON THIS MACHINE
2678	if [[ "${actionout[$i]}" = "a" ]]
2679	then
2680	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2681	then
2682	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2683	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2684	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2685	else
2686	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2687	printf "\n ${pathout[$i]}\n"
2688	cat ${localout[$i]} >> ${pathout[$i]}
2689	fi
2690	fi
2691
2692	# COPY ON THIS MACHINE
2693	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2694	# ON DIFFERENT FILE-SYSTEMS
2695	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2696	then
2697
2698	# COPY IN CASE OF RUNS ON SINGLE CORES
2699	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2700	then
2701	printf "\n >>> OUTPUT: ${localout[$i]} to"
2702	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2703	if [[ $link_local_output = true ]]
2704	then
2705	printf " file will be linked\n"
2706	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2707	fi
2708	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2709	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2710	then
2711	if [[ $link_local_output = true ]]
2712	then
2713	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2714	fi
2715	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2716	else
2717	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2718	fi
2719	else
2720	printf "\n >>> OUTPUT: ${localout[$i]} to"
2721	printf "\n ${pathout[$i]}\n"
2722	if [[ $link_local_output = true ]]
2723	then
2724	printf " file will be linked\n"
2725	ln -f ${localout[$i]} ${pathout[$i]}
2726	fi
2727	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2728	if [[ ! -f "${pathout[$i]}" ]]
2729	then
2730	if [[ $link_local_output = true ]]
2731	then
2732	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2733	fi
2734	cp ${localout[$i]} ${pathout[$i]}
2735	else
2736	printf "+++ no copy because file ${pathout[$i]} exists\n"
2737	fi
2738	fi
2739
2740	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2741	then
2742
2743	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2744	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2745	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2746	printf "\n ${pathout[$i]}\n"
2747	if [[ $link_local_output = true ]]
2748	then
2749	printf " files will be linked\n"
2750	mkdir -p ${pathout[$i]}
2751	cd ${localout[$i]}
2752	for file in $(ls *)
2753	do
2754	ln -f $file ${pathout[$i]}
2755	done >\|/dev/null 2>&1
2756	cd $tempdir
2757	fi
2758
2759	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2760	if [[ ! -f "${pathout[$i]}/_000000" ]]
2761	then
2762	if [[ $link_local_output = true ]]
2763	then
2764	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2765	fi
2766	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
2767	cp -r ${localout[$i]}/* ${pathout[$i]}
2768	fi
2769
2770	fi
2771	fi
2772	done
2773
2774	if (( i != 0 ))
2775	then
2776	timestring=`date +%H:%M:%S`
2777	if [[ $transfer_problems = true ]]
2778	then
2779	printf "\n$dashes\n *** OUTPUT-files saved local time: $timestring"
2780	printf "\n +++ WARNING: some data transfers failed! \n"
2781	else
2782	printf "\n$dashes\n *** all OUTPUT-files saved local time: $timestring \n"
2783	fi
2784	fi
2785
2786
2787	# IF REQUIRED, START A RESTART-JOB
2788	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2789	if [[ -f CONTINUE_RUN ]]
2790	then
2791
2792	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2793	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2794	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2795	# -b START A BATCH JOB
2796	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2797	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2798	[[ $(echo $prc \| grep -c "\-b") = 0 && $running_on_remote = false ]] && prc="$prc -b"
2799
2800	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2801	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2802	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
2803	then
2804	prc=`echo $prc \| sed 's/svfout/svfin/g'`
2805	fi
2806
2807	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2808	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2809	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2810	then
2811	prc=`echo $prc \| sed 's/#/r/g'`
2812	fi
2813
2814
2815	# START THE RESTART-JOB
2816	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2817	echo " $prc"
2818	printf "\n$dashes\n"
2819	if [[ $running_on_remote = true ]]
2820	then
2821
2822	echo "*** ssh will be used to initiate restart-runs!"
2823	echo " return_address=\"$return_address\" "
2824	echo " return_username=\"$local_username\" "
2825
2826	if [[ "$remote_loginnode" != "" ]]
2827	then
2828	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
2829	else
2830	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
2831	fi
2832
2833	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2834	sleep 30
2835
2836	else
2837
2838	# START THE RESTART JOB ON THE LOCAL HOST
2839	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
2840
2841	fi
2842
2843	# CHECK, IF RESTART JOB HAS BEEN STARTED
2844	if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
2845	then
2846	printf "\n$dashes\n +++ creating restart run failed \n"
2847	locat=create_restart
2848	rm palmrun_restart.log
2849	exit
2850	elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
2851	then
2852	printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
2853	locat=create_restart
2854	rm palmrun_restart.log
2855	exit
2856	else
2857	printf "\n$dashes\n *** restart run initiated \n"
2858	rm palmrun_restart.log
2859	fi
2860
2861
2862	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2863	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2864	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2865	# MAY BE VERY HUGE)
2866	(( i = 0 ))
2867	while (( i < nr_of_input_files ))
2868	do
2869	(( i = i + 1 ))
2870	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2871	then
2872	rm -r ${absnamein[$i]}
2873	fi
2874	done
2875
2876	fi
2877
2878
2879	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2880	cd $HOME
2881	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2882
2883
2884	else
2885
2886
2887	# PREPARING ACTIONS,
2888	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2889
2890	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2891	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
2892	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2893	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2894	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2895	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2896	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2897	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2898	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2899	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2900	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2901	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2902	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2903	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2904	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2905	if [[ $create_remote_batch_job = true ]]
2906	then
2907	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2908	if [[ $do_trace = true ]]
2909	then
2910	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2911	fi
2912	elif [[ $create_batch_job = true ]]
2913	then
2914	palmrun_com=${palmrun_com}" -j"
2915	if [[ $do_trace = true ]]
2916	then
2917	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2918	fi
2919	fi
2920
2921
2922	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2923	# REMOTE HOST
2924	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
2925	job_protocol_file=$job_protocol_file_local
2926	if [[ $create_remote_batch_job = true ]]
2927	then
2928	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
2929	job_protocol_file=$job_protocol_file_remote
2930	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2931	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
2932	fi
2933
2934
2935	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2936	jobfile=jobfile.$run_id_number
2937
2938
2939	# FIRST CREATE THE BATCH DIRECTIVES
2940	(( i = 0 ))
2941	while (( i < ibd ))
2942	do
2943	(( i = i + 1 ))
2944	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2945	eval line=\"$line\"
2946	echo "$line" >> $jobfile
2947	done
2948	echo " " >> $jobfile
2949
2950
2951	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2952	# PROTOCOL
2953	if [[ $create_remote_batch_job = true ]]
2954	then
2955	echo "set +vx" >> $jobfile
2956	echo "trap '" >> $jobfile
2957	echo "set +vx" >> $jobfile
2958	echo "cd ${remote_jobcatalog}" >> $jobfile
2959	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
2960
2961	# ADD THE BATCH DIRECTIVES
2962	(( i = 0 ))
2963	while (( i < ibdt ))
2964	do
2965	(( i = i + 1 ))
2966	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
2967	eval line=\"$line\"
2968	echo "$line" >> $jobfile
2969	done
2970	echo " " >> $jobfile
2971
2972	echo "set -x" >> $jobfile
2973	if [[ "$remote_loginnode" != "" ]]
2974	then
2975	echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \\\"$local_jobcatalog\\\" ${configuration_identifier}_${run_identifier}\" " >> $jobfile
2976	else
2977	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
2978	fi
2979	echo "%%END%%" >> $jobfile
2980	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2981	echo "$submit_command $scpjob_file" >> $jobfile
2982	echo "rm $scpjob_file" >> $jobfile
2983	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2984	echo "set -x" >> $jobfile
2985	echo " ' exit" >> $jobfile
2986	fi
2987
2988
2989	# ACTIVATE ERROR-TRACEBACK
2990	if [[ $do_trace = true ]]
2991	then
2992	echo "set -x" >> $jobfile
2993	else
2994	echo "set +vx" >> $jobfile
2995	fi
2996
2997
2998	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2999	if [[ "$login_init_cmd" != "" ]]
3000	then
3001	echo "$login_init_cmd" >> $jobfile
3002	fi
3003	if [[ "$module_commands" != "" ]]
3004	then
3005	echo "$module_commands" >> $jobfile
3006	fi
3007
3008
3009	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
3010	if [[ $create_remote_batch_job = true ]]
3011	then
3012	echo "mkdir $tempdir" >> $jobfile
3013	echo "if [[ \$? != 0 ]]" >> $jobfile
3014	echo "then" >> $jobfile
3015	echo " echo \"+++ temporary working directory cannot be created.\" " >> $jobfile
3016	echo " echo \" Check setting of variable fast_io_catalog in your config file.\" " >> $jobfile
3017	echo " exit" >> $jobfile
3018	echo "fi" >> $jobfile
3019	echo "chmod go+rx $tempdir" >> $jobfile
3020	else
3021	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
3022	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
3023	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
3024	mkdir $tempdir
3025	if [[ $? != 0 ]]
3026	then
3027	printf "\n +++ temporary working directory cannot be created."
3028	printf "\n Check setting of variable fast_io_catalog in your config file."
3029	locat=execution
3030	exit
3031	fi
3032	chmod go+rx $tempdir
3033	fi
3034	echo "cd $tempdir" >> $jobfile
3035	echo "export tempdir=$tempdir" >> $jobfile
3036	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/.[!.]* ." >> $jobfile
3037	echo "export PATH=.:${fast_io_catalog}/${sources_for_run_catalog}:\$PATH" >> $jobfile
3038	echo "export execute_palmrun=true" >> $jobfile
3039
3040
3041	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
3042	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
3043	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
3044	echo "LOCAL_PWD=$working_directory" >> $jobfile
3045	echo "export LOCAL_PWD" >> $jobfile
3046
3047
3048	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
3049	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
3050	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
3051
3052
3053	# CALL PALMRUN WITHIN THE JOB
3054	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
3055	echo "set -x" >> $jobfile
3056	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
3057
3058
3059	# TRANSFER JOBFILE TO THE TARGET HOST
3060	if [[ $create_jobfile_only = false ]]
3061	then
3062
3063	# CREATE LOCAL JOB FOLDER
3064	eval local_jobcatalog=$local_jobcatalog
3065	if [[ ! -d $local_jobcatalog ]]
3066	then
3067	echo " "
3068	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
3069	mkdir $local_jobcatalog
3070	fi
3071
3072	if [[ $create_remote_batch_job = true ]]
3073	then
3074
3075	echo " "
3076	echo " *** transfer of job to remote host via scp"
3077
3078	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
3079	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
3080
3081	# COPY THE JOB FILE
3082	if [[ $do_trace = true ]]
3083	then
3084	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
3085	fi
3086	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
3087
3088	# SUBMIT THE JOB
3089	printf " *** submit the job (output of submit command, \n"
3090	printf " e.g. the job-id given by the batch-system, may follow) \n"
3091	if [[ $do_trace = true ]]
3092	then
3093	echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" "
3094	fi
3095	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
3096
3097	elif [[ $create_batch_job = true ]]
3098	then
3099
3100	eval local_jobcatalog=$local_jobcatalog
3101	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
3102	cd $local_jobcatalog
3103	echo " "
3104	echo " *** submit the job"
3105	if [[ $do_trace = true ]]
3106	then
3107	echo "$submit_command ${configuration_identifier}_${run_id}"
3108	fi
3109	$submit_command ${configuration_identifier}_${run_id}
3110	rm ${configuration_identifier}_${run_id}
3111	cd - > /dev/null
3112
3113	fi
3114
3115	rm -rf $jobfile
3116
3117	else
3118
3119	printf "\n *** jobfile created under name \"$jobfile\" "
3120	printf "\n no batch-job has been sent!"
3121
3122	fi
3123
3124	fi # END OF REMOTE-PART

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