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source: palm/trunk/SCRIPTS/palmrun @ 2608

Last change on this file since 2608 was 2605, checked in by raasch, 7 years ago
input files are not sent with remote batch job file any more
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 87.2 KB

Line
1	#!/bin/bash
2
3	# palmrun - script for running PALM jobs
4
5	#--------------------------------------------------------------------------------#
6	# This file is part of PALM.
7	#
8	# PALM is free software: you can redistribute it and/or modify it under the terms
9	# of the GNU General Public License as published by the Free Software Foundation,
10	# either version 3 of the License, or (at your option) any later version.
11	#
12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
15	#
16	# You should have received a copy of the GNU General Public License along with
17	# PALM. If not, see <http://www.gnu.org/licenses/>.
18	#
19	# Copyright 2017 Leibniz Universitaet Hannover
20	#--------------------------------------------------------------------------------#
21	#
22	# Current revisions:
23	# ------------------
24	#
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 2605 2017-11-09 15:31:46Z schwenkel $
29	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
30	# will not be sent with the job file any more, but copied into the
31	# SOURCES_FOR_RUN... folder on the remote host, before he job is submitted
32	#
33	# 2600 2017-11-01 14:11:20Z raasch
34	# cycle numbers are made three digits wide
35	#
36	# 2566 2017-10-20 08:50:47Z raasch
37	# execute command for combine_plot_fields added
38	# "TEMPDIR" renamed "tempdir"
39	# temporary working directory for local batch jobs is created immediately within
40	# the user's palmrun call, due to a requirement of the "grid engine" batch
41	# system, where the working directory is given with batch directive -wd and must
42	# already exist when the job is submitted,
43	# informative messages in non-trace mode reduced and partly reformatted
44	#
45	# 2551 2017-10-18 07:25:11Z raasch
46	# TEMPDIR added as replacement string to be used in batch directives
47	#
48	# 2512 2017-10-04 08:26:59Z raasch
49	# bugfix for determining cycle numbers of NetCDF input files
50	#
51	# 2506 2017-09-29 08:30:37Z raasch
52	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
53	# host configuration added to SOURCES_FOR_RUN_... folder name
54	# host_identifier renamed host_configuration
55	# option -W added to allow for job dependencies
56	#
57	# 2501 2017-09-26 11:41:55Z raasch
58	# default value for number of cores (option -X) set to 1
59	# bugfix for mechanism which overwrites configuration file settings with values
60	# provided by palmrun options
61	#
62	# 2499 2017-09-22 16:47:58Z kanani
63	# option -h named configuration identifier
64	#
65	# 2480 2017-09-19 06:24:14Z maronga
66	# bugfix for last revision
67	#
68	# 2479 2017-09-19 06:12:16Z raasch
69	# option -A (project account number) added
70	#
71	# 2422 2017-09-08 08:25:41Z raasch
72	# initial revision
73	#
74	#--------------------------------------------------------------------------------#
75	# palmrun - script for running PALM jobs on local and remote hosts
76	#--------------------------------------------------------------------------------#
77
78
79
80	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
81
82	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
83	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
84	# (TOO MANY ARGUMENTS - PROBLEM)
85	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
86
87	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
88	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
89	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
90	# SCRIPT-OPTION ARGUMENTS
91	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
92	typeset -i icycle inode ival maxcycle mpi_tasks
93	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
94
95	activation_string_list=""
96	AddFilenames=""
97	combine_plot_fields=true
98	compiler_name=""
99	compiler_name_ser=""
100	compiler_options=""
101	cores=1
102	cores_atmos=0
103	cores_ocean=0
104	coupled_dist=""
105	cpp_options=""
106	cpumax=0
107	create_batch_job=false
108	create_jobfile_only=false
109	create_remote_batch_job=false
110	dashes=" ----------------------------------------------------------------------------"
111	defaultqueue=""
112	delete_temporary_catalog=true
113	do_compile=true
114	do_trace=false
115	executable=""
116	execute_command=""
117	execution_error=false
118	fileconnection_file=.palm.iofiles
119	fname=test
120	global_revision=""
121	host_configuration="default"
122	hostfile=""
123	hp=""
124	keep_data_from_previous_run=false
125	link_local_input=false
126	link_local_output=false
127	linker_options=""
128	local_jobcatalog=""
129	locat=normal
130	makefile=""
131	max_par_io_str=""
132	prc=$0
133	while [[ $(echo $prc \| grep -c "/") != 0 ]]
134	do
135	prc=`echo $prc \| cut -f2- -d"/"`
136	done
137	module_calls=""
138	palmrun_memory=""
139	palmrun_script_name=$prc
140	openmp=false
141	previous_job=""
142	project_account=""
143	queue=none
144	restart_run=false
145	return_address=""
146	remote_jobcatalog=""
147	remote_username=""
148	running_in_batch_mode=false
149	run_coupled_model=false
150	run_id=""
151	silent=false
152	source_list=""
153	source_path=""
154	tasks_per_node=0
155	threads_per_task=1
156	transfer_problems=false
157	user_source_path=""
158	use_existing_sources_folder=""
159	use_openmp=false
160	version="palmrun 1.0 Rev$Rev: 2303 $"
161	working_directory=`pwd`
162	write_binary=""
163	TOPT=""
164
165
166	# ERROR HANDLING IN CASE OF EXIT
167	trap 'if [[ $locat != normal && $locat != control_c ]]
168	then
169
170	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
171	(( i = 0 ))
172	while (( i < iec ))
173	do
174	(( i = i + 1 ))
175	printf "\n *** Execution of ERROR-command:\n"
176	printf " >>> ${err_command[$i]}\n"
177	eval ${err_command[$i]}
178	done
179	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
180	printf "\n\n+++ palmrun killed \n\n"
181	elif [[ $locat != control_c ]]
182	then
183	printf "\n --> palmrun finished\n\n"
184	fi' exit
185
186
187	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
188	trap 'cd; rm -rf $tempdir
189	printf "\n+++ palmrun killed by \"^C\" \n\n"
190	locat=control_c
191	exit
192	' 2
193
194
195	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
196	# WHICH WILL BE USED TO START RESTART-JOBS
197	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
198	do
199	case $option in
200	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
201	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
202	(b) create_batch_job=true; prc="$prc -b";;
203	(B) delete_temporary_catalog=false; prc="$prc -B";;
204	(C) restart_run=true; prc="$prc -C";;
205	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
206	(F) create_jobfile_only=true;;
207	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
208	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
209	(j) running_in_batch_mode=true;;
210	(k) keep_data_from_previous_run=true; prc="$prc -k";;
211	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
212	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
213	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
214	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
215	(r) run_id=$OPTARG;;
216	(R) return_address=$OPTARG;;
217	(s) source_list=$OPTARG;;
218	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
219	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
220	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
221	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
222	(v) silent=true; prc="$prc -v";;
223	(V) use_existing_sources_folder="-V";;
224	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
225	(W) previous_job=$OPTARG;;
226	(x) do_trace=true;set -x; prc="$prc -x";;
227	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
228	(y) ocean_file_appendix=true; prc="$prc -y";;
229	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
230	(Z) combine_plot_fields=false; prc="$prc -Z";;
231	(\?) printf "\n +++ unknown option $OPTARG \n"
232	printf "\n --> type \"$0 ?\" for available options \n"
233	locat=parameter;exit;;
234	esac
235	done
236
237
238	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
239	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
240	(( to_shift = $OPTIND - 1 ))
241	shift $to_shift
242
243	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
244	if [[ "$1" = "?" ]]
245	then
246	(printf "\n *** Description of available palmrun options:\n"
247	printf "\n Option Description Default-Value"
248	printf "\n -a activation string list \"\" "
249	printf "\n -A project account number ---"
250	printf "\n -b batch-job on local machine ---"
251	printf "\n -B do not delete temporary directory at end ---"
252	printf "\n -d base name of files attached to program test"
253	printf "\n -F create batch job file only ---"
254	printf "\n -h host configuration \"default\" "
255	printf "\n -k keep data from previous run"
256	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
257	printf "\n -M Makefile name Makefile"
258	printf "\n -O threads per openMP task ---"
259	printf "\n -q queue \"$queue\" "
260	printf "\n -s filenames of routines to be compiled \"\" "
261	printf "\n must end with .f, .f90, .F, or .c !"
262	printf "\n use \"..\" for more than one file and wildcards"
263	printf "\n -s LM compiles all locally modified files"
264	printf "\n -t allowed cpu-time in seconds (batch) 0"
265	printf "\n -T tasks per node ---"
266	printf "\n -u username on remote machine \"\" "
267	printf "\n -v no prompt for confirmation ---"
268	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
269	printf "\n -w maximum parallel io streams as given by -X"
270	printf "\n -W name of job to wait for ---"
271	printf "\n -x tracing of palmrun for debug purposes ---"
272	printf "\n -X # of processors (on parallel machines) 1"
273	printf "\n -y add appendix \"_O\" to all local output"
274	printf "\n files (ocean precursor runs followed by"
275	printf "\n coupled atmosphere-ocean runs) ---"
276	printf "\n -Y run coupled model, \"#1 #2\" with"
277	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
278	printf "\n -Z skip combine_plot_fields at the end of "
279	printf "\n the simulation ---"
280	printf "\n "
281	printf "\n Possible values of positional parameter <modus>:"
282	printf "\n \"?\" - this outline \n\n") \| more
283	exit
284	elif [[ "$1" != "" ]]
285	then
286	printf "\n +++ positional parameter $1 unknown \n"
287	locat=parameter; exit
288	fi
289
290
291
292	# SHORT STARTING MESSAGE
293	printf "\n*** $version "
294	printf "\n will be executed. Please wait ..."
295
296
297	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
298	config_file=.palm.config.$host_configuration
299	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
300
301
302	# CHECK, IF CONFIGURATION FILE EXISTS
303	if [[ ! -f $config_file ]]
304	then
305	printf "\n\n +++ configuration file: "
306	printf "\n $config_file"
307	printf "\n does not exist"
308	locat=connect; exit
309	fi
310
311
312	# CHECK, IF FILE CONNECTION FILE EXISTS
313	if [[ ! -f $fileconnection_file ]]
314	then
315	printf "\n\n +++ file connection file: "
316	printf "\n $fileconnection_file"
317	printf "\n does not exist"
318	locat=connect; exit
319	fi
320
321
322	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
323	if [[ "$activation_string_list" = "" ]]
324	then
325	printf "\n\n +++ no activation string list given: "
326	printf "\n please set palmrun option \"-a\" "
327	locat=palmrun_option; exit
328	fi
329
330
331	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
332	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
333	then
334	write_binary=true
335	else
336	write_binary=false
337	fi
338
339
340	# READ AND EVALUATE THE CONFIGURATION-FILE
341	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
342
343	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
344	while read line
345	do
346
347	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
348	eval line=\"$line\"
349
350
351	# INTERPRET THE LINE
352	if [[ "$(echo $line)" = "" ]]
353	then
354
355	# EMPTY LINE, NO ACTION
356	continue
357
358	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
359	then
360
361	# LINE IS A COMMENT LINE
362	continue
363
364	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
365	then
366
367	# LINE DEFINES AN ENVIRONMENT-VARIABLE
368	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
369	value=`echo $line \| cut -d" " -s -f2-`
370
371
372	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
373	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
374	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
375	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
376	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
377	# CONFIGURATION-FILE.
378	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
379	then
380	eval export $var="\$value"
381
382	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
383	if [[ $do_trace = true ]]
384	then
385	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
386	fi
387	fi
388
389	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
390	then
391
392	# LINE DEFINES BATCH-DIRECTIVE
393	(( ibd = ibd + 1 ))
394	line=$(echo $line \| cut -c4-)
395	batch_directive[$ibd]="$line"
396
397	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
398	then
399
400	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
401	# REMOTE TO A LOCAL HOST
402	(( ibdt = ibdt + 1 ))
403	line=$(echo $line \| cut -c5-)
404	batch_directive_transfer[$ibdt]="$line"
405
406	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
407	then
408
409	# LINE DEFINES ERROR-COMMAND
410	(( iec = iec + 1 ))
411	line=$(echo $line \| cut -c4-)
412	err_command[$iec]="$line"
413
414	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
415	then
416
417	# LINE DEFINES INPUT-COMMAND
418	(( iic = iic + 1 ))
419	line=$(echo $line \| cut -c4-)
420	in_command[$iic]="$line"
421
422	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
423	then
424
425	# LINE DEFINES OUTPUT-COMMAND
426	(( ioc = ioc + 1 ))
427	line=$(echo $line \| cut -c4-)
428	out_command[$ioc]="$line"
429
430	else
431
432	# SKIP ALL OTHER LINES
433	continue
434
435	fi
436
437	done < $config_file
438
439
440	# CHECK SETTING OF REQUIRED PARAMETERS
441	if [[ "$compiler_name" = "" ]]
442	then
443	printf "\n +++ no compiler name found in $config_file"
444	printf "\n Please add line \"compiler_name ...\" to that file."
445	locat=config_file; exit
446	fi
447	if [[ "$compiler_name_ser" = "" ]]
448	then
449	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
450	printf "\n Please add line \"compiler_name_ser ...\" to that file."
451	locat=config_file; exit
452	fi
453	if [[ "$compiler_options" = "" ]]
454	then
455	printf "\n +++ no compiler options found in $config_file"
456	printf "\n Please add line \"compiler_options ...\" to that file."
457	locat=config_file; exit
458	fi
459	if [[ "$linker_options" = "" ]]
460	then
461	printf "\n +++ no linker options found in $config_file"
462	printf "\n Please add line \"linker_options ...\" to that file."
463	locat=config_file; exit
464	fi
465	if [[ "$execute_command" = "" ]]
466	then
467	printf "\n +++ no execute command found in $config_file"
468	printf "\n Please add line \"execute_command ...\" to that file."
469	locat=config_file; exit
470	fi
471
472	if [[ "$hostfile" != "" ]]
473	then
474	if [[ $hostfile != auto && ! -f $hostfile ]]
475	then
476	printf "\n +++ no hostfile \"$hostfile\" found"
477	printf "\n Please check line \"hostfile ...\" in $config_file"
478	locat=config_file; exit
479	fi
480	fi
481
482
483	# DETERMINE THE CALL STATUS
484	if [[ "$return_address" != "" ]]
485	then
486
487	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
488	# BATCH MODE AND ...
489	running_on_remote=true
490
491	else
492
493	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
494	if [[ "$remote_ip" != "" ]]
495	then
496
497	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
498	create_remote_batch_job=true
499
500	fi
501	running_on_remote=false
502	fi
503
504
505
506	# READ AND EVALUATE THE I/O-FILE LIST
507	[[ $silent = false ]] && printf "\n Reading the I/O files... "
508
509	# READ THE FILE CONNECTION FILE LINE BY LINE
510	while read line
511	do
512
513	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
514	eval line=\"$line\"
515
516
517	# INTERPRET THE LINE
518	if [[ "$(echo $line)" = "" ]]
519	then
520	# EMPTY LINE, NO ACTION
521	continue
522
523	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
524	then
525
526	# LINE IS A COMMENT LINE
527	true
528
529	else
530
531	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
532	# s2a: in/out - field
533	# s2b: loc - field (optional)
534	# s2c: tr/ar - field (optional)
535	s1=`echo $line \| cut -d" " -f1`
536	s2=`echo $line \| cut -d" " -s -f2`
537	s2a=$(echo $s2 \| cut -d":" -f1)
538	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
539	then
540	s2b=""
541	s2c=""
542	else
543	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
544	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
545	fi
546	s3=`echo $line \| cut -d" " -f3`
547	s4=`echo $line \| cut -d" " -s -f4`
548	s5=`echo $line \| cut -d" " -s -f5`
549	s6=`echo $line \| cut -d" " -s -f6`
550
551
552	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
553	# INPUT- OR OUTPUT-LIST.
554	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
555	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
556	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
557	# IS NOT CHECKED AND STORED.
558	IFSALT="$IFS"; IFS="$IFS:"
559	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
560	then
561	found=false
562	for actual in $activation_string_list
563	do
564	for formal in $s3
565	do
566	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
567	done
568	done
569	if [[ $found = true ]]
570	then
571	(( iin = iin + 1 ))
572	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
573	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
574	extin[$iin]=$s6
575
576	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
577	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
578	if [[ $running_on_remote = true && ( "$s2b" = job \|\| "$s2b" = jobopt ) ]]
579	then
580	pathin[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
581	fi
582
583	fi
584	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
585	then
586	found=false
587	for actual in $activation_string_list
588	do
589	for formal in $s3
590	do
591	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
592	done
593	done
594	if [[ $found = true ]]
595	then
596	(( iout = iout + 1 ))
597	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
598	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
599	fi
600	elif [[ "$s2a" != in && "$s2a" != out ]]
601	then
602	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
603	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
604	locat=connect; exit
605	fi
606	IFS="$IFSALT"
607	fi
608
609	done < $fileconnection_file
610
611
612
613	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
614	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
615	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
616	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
617	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
618	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
619
620
621
622	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
623	if [[ $run_coupled_model = true ]]
624	then
625
626	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
627	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
628
629	if (( $cores_ocean + $cores_atmos != $cores ))
630	then
631
632	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
633	printf "\n PEs (total) : $cores"
634	printf "\n PEs (atmosphere): $cores_atmos"
635	printf "\n PEs (ocean) : $cores_ocean"
636	locat=coupling; exit
637
638	fi
639
640	fi
641
642
643	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
644	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
645	# FOLDER
646	if [[ $running_in_batch_mode = true ]]
647	then
648
649	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
650	then
651	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
652	printf "\n Please check the output of the palmrun-call"
653	printf "\n that you did on your local host."
654	locat=SOURCES_FOR_RUN; exit
655	fi
656
657	else
658
659	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
660	# AUTOMATIC RESTART RUN
661	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
662	if [[ $restart_run = false ]]
663	then
664
665	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
666	# THE LOCAL HOST
667	if [[ ! -d $source_path ]]
668	then
669	printf "\n\n +++ source path \"$source_path\" on local host"
670	printf "\n \"$(hostname)\" does not exist"
671	locat=source_path; exit
672	fi
673
674	rm -rf $sources_for_run_catalog
675	mkdir -p $sources_for_run_catalog
676
677	if [[ "$source_list" = LM ]]
678	then
679
680	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
681	source_list=""
682	cd $source_path
683
684
685	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
686	if [[ ! -d ../.svn ]]
687	then
688	printf "\n\n +++ source directory"
689	printf "\n \"$source_path\" "
690	printf "\n is not under control of \"subversion\"."
691	printf "\n Please do not use palmrun-option \"-s LM\"\n"
692	fi
693
694
695	# LIST ALL MODIFIED SOURCE CODE FILES
696	Filenames=""
697	svn status > tmp_svnstatus
698	while read line
699	do
700	firstc=`echo $line \| cut -c1`
701	if [[ $firstc = M \|\| $firstc = "?" ]]
702	then
703	Name=`echo "$line" \| cut -c8-`
704	extension=`echo $Name \| cut -d. -f2`
705	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
706	then
707	Filenames="$Filenames "$Name
708	fi
709	fi
710	done < tmp_svnstatus
711	rm -rf tmp_svnstatus
712
713
714	# COPY FILES TO SOURCES_FOR_RUN_...
715	for filename in $Filenames
716	do
717	cp $filename ${working_directory}/${sources_for_run_catalog}
718	source_list=$source_list"$filename "
719	done
720
721	cd - > /dev/null
722
723
724	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
725	elif [[ "$source_list" != "" ]]
726	then
727
728	cd $source_path
729
730	for filename in $source_list
731	do
732
733	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
734	if [[ $(echo $filename \| grep -c "/") != 0 ]]
735	then
736	printf "\n +++ source code file: $filename"
737	printf "\n must not contain (\"/\") "
738	locat=source; exit
739	fi
740
741	if [[ ! -f $filename ]]
742	then
743	printf "\n +++ source code file: $filename"
744	printf "\n does not exist"
745	locat=source; exit
746	else
747	cp $filename ${working_directory}/${sources_for_run_catalog}
748	fi
749
750	done
751
752	cd - > /dev/null
753
754	fi
755
756	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
757	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
758	if [[ ! -f $makefile ]]
759	then
760	printf "\n +++ file \"$makefile\" does not exist"
761	locat=make; exit
762	else
763	cp $makefile ${sources_for_run_catalog}/Makefile
764	fi
765
766
767	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
768	if [[ "$user_source_path" != "" ]]
769	then
770
771	# DOES THE DIRECTORY EXIST?
772	if [[ ! -d $user_source_path ]]
773	then
774
775	printf "\n\n *** INFORMATIVE: additional source code directory"
776	printf "\n \"$user_source_path\" "
777	printf "\n does not exist or is not a directory."
778	printf "\n No source code will be used from this directory!\n"
779	user_source_path=""
780	if [[ $silent == false ]]
781	then
782	sleep 2
783	fi
784
785	else
786
787	cd $user_source_path
788	found=false
789
790	Names=$(ls -1 *.f90 2>&1)
791	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
792	Names=$(ls -1 *.F90 2>&1)
793	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
794	Names=$(ls -1 *.F 2>&1)
795	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
796	Names=$(ls -1 *.f 2>&1)
797	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
798	Names=$(ls -1 *.c 2>&1)
799	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
800
801	cd - > /dev/null
802	cd $sources_for_run_catalog
803
804	# COPY MAKEFILE IF EXISTING
805	if [[ -f $user_source_path/Makefile ]]
806	then
807	printf "\n\n *** user Makefile from directory"
808	printf "\n \"$user_source_path\" is used \n"
809	if [[ $silent == false ]]
810	then
811	sleep 1
812	fi
813	cp $user_source_path/Makefile .
814	fi
815
816	for filename in $AddFilenames
817	do
818	if [[ -f $filename ]]
819	then
820	printf "\n +++ source code file \"$filename\" found in additional"
821	printf "\n source code directory \"$user_source_path\" "
822	printf "\n but was also given with option \"-s\" which means that it should be taken"
823	printf "\n from directory \"$source_path\"."
824	locat=source; exit
825	fi
826
827	cp $user_source_path/$filename .
828	source_list="$source_list $filename"
829
830	# CHECK IF FILE IS CONTAINED IN MAKEFILE
831	if [[ $(grep -c $filename Makefile) = 0 ]]
832	then
833	printf "\n\n +++ user file \"$filename\" "
834	printf "\n is not listed in Makefile \n"
835	locat=source; exit
836	else
837
838	if [[ $found = false ]]
839	then
840	found=true
841	printf "\n\n *** following user file(s) added to the"
842	printf " files to be translated:\n "
843	fi
844	printf "$filename "
845	if [[ $silent == false ]]
846	then
847	sleep 0.5
848	fi
849
850	fi
851	done
852	[[ $found = true ]] && printf "\n"
853	cd - > /dev/null
854	fi
855	fi
856
857	# COPY CONFIGURATION FILES
858	cp $config_file $sources_for_run_catalog
859	cp $fileconnection_file $sources_for_run_catalog
860
861	# COPY SHELLSCRIPTS
862	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
863	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
864
865	fi
866
867	fi
868
869
870	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
871	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
872	if [[ "$global_revision" = "" ]]
873	then
874	global_revision=`svnversion $source_path 2>/dev/null`
875	global_revision="Rev: $global_revision"
876	fi
877
878
879	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
880	if [[ -n $cores ]]
881	then
882
883	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
884	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
885	if [[ $tasks_per_node = 0 ]]
886	then
887	printf "\n"
888	printf "\n +++ option \"-T\" (tasks per node) is missing"
889	printf "\n set -T option or define tasks_per_node in the config file"
890	locat=tasks_per_node; (( iec = 0 )); exit
891	fi
892
893	if (( cores < tasks_per_node ))
894	then
895	printf "\n"
896	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
897	printf "\n given values: -T $tasks_per_node -X $cores"
898	locat=tasks_per_node; (( iec = 0 )); exit
899	fi
900
901	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
902	(( mpi_tasks = cores / threads_per_task ))
903	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
904	(( ii = cores / tasks_per_node ))
905	(( remaining_cores = cores - ii * tasks_per_node ))
906	if (( remaining_cores > 0 ))
907	then
908	printf "\n"
909	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
910	printf "\n divisor of the total number of cores (option \"-X\")"
911	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
912	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
913	(( nodes = nodes + 1 ))
914	fi
915
916	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
917	if [[ "$tasks_per_node" != "" ]]
918	then
919	TOPT="-T $tasks_per_node"
920	fi
921
922	fi
923
924
925	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
926	if [[ "$maximum_parallel_io_streams" = "" ]]
927	then
928	maximum_parallel_io_streams=$cores
929	fi
930
931
932	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
933	if [[ "$scp_port" != "" ]]
934	then
935	PORTOPT="-P $scp_port"
936	SSH_PORTOPT="-p $scp_port"
937	fi
938
939
940	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
941	# CONFIG-FILE
942	if [[ "$ssh_key" != "" ]]
943	then
944	ssh_key="-i $HOME/.ssh/$ssh_key"
945	fi
946
947
948	# SET QUEUE, IF NOT GIVEN
949	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
950	then
951
952	if [[ $queue = none && "$defaultqueue" = "" ]]
953	then
954	printf "\n"
955	printf "\n +++ no default queue given in configuration file and no queue"
956	printf "\n given with option -q"
957	fi
958	if [[ $queue = none ]]
959	then
960	queue=$defaultqueue
961	fi
962
963	fi
964
965
966	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
967	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
968	(( i = 0 ))
969	while (( i < iin ))
970	do
971	(( i = i + 1 ))
972	(( maxcycle = 0 ))
973
974	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
975	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
976	if [[ "${actionin[$i]}" = di ]]
977	then
978	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
979	# HOST ONLY
980	eval filename=${pathin[$i]}/${endin[$i]}
981	else
982	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
983	# HOST ONLY
984	eval filename=${pathin[$i]}/${fname}${endin[$i]}
985	fi
986	eval pathname=${pathin[$i]}
987
988	# CHECK IF FILE EXISTS
989	if ! ls $filename* 1>/dev/null 2>&1
990	then
991
992	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
993	if [[ "${transin[$i]}" != "locopt" && "${transin[$i]}" != "jobopt" ]]
994	then
995	printf "\n\n +++ INPUT-file: "
996	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
997	then
998	printf "\n $filename"
999	else
1000	printf "\n $filename.${extin[$i]}"
1001	fi
1002	printf "\n does not exist\n"
1003	locat=input; exit
1004	else
1005	transin[$i]="unavailable"
1006	fi
1007
1008	else
1009
1010	# DETERMINE THE FILE'S CYCLE NUMBER
1011	ls -1 -d $filename > filelist 2>/dev/null
1012	ls -1 -d $filename.* >> filelist 2>/dev/null
1013	while read line
1014	do
1015	# filename without path (i.e. after the last "/")
1016	basefilename=$(basename ${line})
1017
1018	# check if there is an extension
1019	extension=${basefilename##*.}
1020	if [[ "$extension" = "${extin[$i]}" ]]
1021	then
1022	basefilename=${basefilename%.*}
1023	fi
1024
1025	# check for an existing cycle number
1026	cycle=${basefilename##*.}
1027	if [[ $cycle =~ ^-?[0-9]+$ ]]
1028	then
1029	(( icycle = $cycle ))
1030	else
1031	(( icycle = 0 ))
1032	fi
1033
1034	if (( icycle > maxcycle ))
1035	then
1036	(( maxcycle = icycle ))
1037
1038	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1039	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1040	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1041	then
1042	leading_zero=true
1043	else
1044	leading_zero=false
1045	fi
1046	fi
1047
1048	done <filelist
1049	rm filelist
1050
1051	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1052	if [[ $leading_zero = true ]]
1053	then
1054	cyclestring=`printf "%03d" $maxcycle`
1055	else
1056	cyclestring=$maxcycle
1057	fi
1058
1059	# APPEND CYCLE NUMBER TO FILENAME
1060	if (( maxcycle > 0 ))
1061	then
1062	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1063	then
1064	filename=${filename}.$cyclestring.${extin[$i]}
1065	else
1066	filename=${filename}.$cyclestring
1067	fi
1068	else
1069	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1070	then
1071	filename=${filename}.${extin[$i]}
1072	fi
1073	fi
1074
1075	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1076	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1077	absnamein[$i]=$filename
1078	if (( maxcycle > 0 ))
1079	then
1080	if [[ "${actionin[$i]}" = di ]]
1081	then
1082	frelin[$i]=${endin[$i]}.$cyclestring
1083	else
1084	frelin[$i]=${fname}${endin[$i]}.$cyclestring
1085	fi
1086	else
1087	if [[ "${actionin[$i]}" = di ]]
1088	then
1089	frelin[$i]=${endin[$i]}
1090	else
1091	frelin[$i]=${fname}${endin[$i]}
1092	fi
1093	fi
1094
1095	fi
1096	done
1097
1098
1099	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1100	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1101	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1102	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1103	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1104	# REMOTE HOST)
1105	(( i = 0 ))
1106	while (( i < iout ))
1107	do
1108	(( i = i + 1 ))
1109	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1110	then
1111	if [[ "${actionout[$i]}" = tr ]]
1112	then
1113	actionout[$i]=""
1114	elif [[ "${actionout[$i]}" = trpe ]]
1115	then
1116	actionout[$i]=pe
1117	elif [[ "${actionout[$i]}" = tra ]]
1118	then
1119	actionout[$i]=a
1120	fi
1121	(( maxcycle = 0 ))
1122	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1123	eval catalogname=${pathout[$i]}
1124	if ! ls $filename* 1>/dev/null 2>&1
1125	then
1126
1127	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1128	if cat /dev/null > $filename
1129	then
1130	rm $filename
1131	else
1132
1133	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1134	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1135	if [[ ! -d $catalogname ]]
1136	then
1137	if mkdir -p $catalogname
1138	then
1139	printf "\n\n *** directory:"
1140	printf "\n $catalogname"
1141	printf "\n was created\n"
1142	else
1143	printf "\n\n +++ OUTPUT-file:"
1144	printf "\n $filename"
1145	printf "\n cannot be created, because directory does not exist"
1146	printf "\n and cannot be created either"
1147	printf "\n"
1148	locat=output ; exit
1149	fi 2>/dev/null
1150	else
1151	printf "\n\n +++ OUTPUT-file:"
1152	printf "\n $filename"
1153	printf "\n cannot be created, although directory exists"
1154	printf "\n"
1155	locat=output ; exit
1156	fi
1157	fi 2>/dev/null
1158	else
1159
1160	# DETERMINE THE CYCLE NUMBER
1161	ls -1 -d $filename > filelist 2>/dev/null
1162	ls -1 -d $filename.* >> filelist 2>/dev/null
1163	while read line
1164	do
1165
1166	# filename without path (i.e. after the last "/")
1167	basefilename=$(basename ${line})
1168
1169	# check if there is an extension
1170	extension=${basefilename##*.}
1171	if [[ "$extension" = "${extout[$i]}" ]]
1172	then
1173	basefilename=${basefilename%.*}
1174	fi
1175
1176	# check for an existing cycle number
1177	cycle=${basefilename##*.}
1178	if [[ $cycle =~ ^-?[0-9]+$ ]]
1179	then
1180	(( icycle = $cycle + 1 ))
1181	else
1182	(( icycle = 1 ))
1183	fi
1184
1185	if (( icycle > maxcycle ))
1186	then
1187	(( maxcycle = icycle ))
1188	fi
1189
1190	done <filelist
1191	rm filelist
1192	fi
1193
1194	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1195	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1196	if [[ "${actionout[$i]}" != a ]]
1197	then
1198	cyclestring=`printf "%03d" $maxcycle`
1199	if (( maxcycle > 0 ))
1200	then
1201	filename_tmp=${filename}.$cyclestring
1202	if cat /dev/null > $filename_tmp
1203	then
1204	rm $filename_tmp
1205	else
1206	printf "\n +++ OUTPUT-file:"
1207	printf "\n $filename_tmp"
1208	printf "\n cannot be created"
1209	locat=output ; exit
1210	fi
1211	fi
1212	else
1213	(( maxcycle = maxcycle - 1 ))
1214	fi
1215
1216	(( cycnum[$i] = maxcycle ))
1217	pathout[$i]=$filename
1218
1219	fi
1220	done
1221
1222
1223	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1224	if [[ $running_in_batch_mode = false ]]
1225	then
1226	run_id=$RANDOM
1227	job_id=${fname}.$run_id
1228
1229	tempdir=$fast_io_catalog/$job_id
1230	fi
1231
1232
1233	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1234	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1235	then
1236
1237	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1238	if [[ $ibd = 0 ]]
1239	then
1240	printf "\n"
1241	printf "\n +++ no batch directives found in configuration file"
1242	locat=config_file_batch_directives; (( iec = 0 )); exit
1243	fi
1244
1245	# CHECK IF CPUTIME IS GIVEN FOR JOB
1246	done=false
1247	cputime=$cpumax
1248	while [[ $done = false ]]
1249	do
1250	if (( cputime == 0 ))
1251	then
1252	printf "\n +++ cpu-time is undefined"
1253	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1254	printf "\n >>> "
1255	read cputime 1>/dev/null 2>&1
1256	else
1257	done=true
1258	fi
1259	done
1260	cpumax=$cputime
1261
1262	# CHECK THE MEMORY DEMAND
1263	done=false
1264	while [[ $done = false ]]
1265	do
1266	if (( memory == 0 ))
1267	then
1268	printf "\n +++ memory demand is undefined"
1269	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1270	printf "\n >>> "
1271	read memory 1>/dev/null 2>&1
1272	else
1273	done=true
1274	fi
1275	done
1276
1277	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1278	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1279	then
1280	while [[ -z $remote_username ]]
1281	do
1282	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1283	printf "\n >>> Please type username:"
1284	printf "\n >>> "
1285	read remote_username
1286	done
1287	fi
1288
1289	else
1290
1291	if [[ $running_in_batch_mode = false ]]
1292	then
1293	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1294	cpumax=$cputime
1295	else
1296	cputime=$cpumax
1297	fi
1298
1299	fi
1300
1301
1302	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1303	(( cpu_hours = cputime / 3600 ))
1304	(( resttime = cputime - cpu_hours * 3600 ))
1305	(( cpu_minutes = resttime / 60 ))
1306	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1307	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1308
1309
1310	# OUTPUT OF THE PALMRUN-HEADER
1311	calltime=$(date)
1312	printf "\n"
1313	printf "#------------------------------------------------------------------------# \n"
1314	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1315	printf "\| \| \n"
1316	column1="called on:"; column2=$(hostname)
1317	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1318	if [[ $create_remote_batch_job = true ]]
1319	then
1320	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1321	else
1322	if [[ $running_on_remote = true ]]
1323	then
1324	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1325	else
1326	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1327	fi
1328	fi
1329	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1330
1331	column1="running in:"
1332	if [[ $running_in_batch_mode = true ]]
1333	then
1334	column2="batch job mode"
1335	else
1336	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1337	then
1338	column2="job creation mode"
1339	else
1340	column2="interactive run mode"
1341	fi
1342	fi
1343	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1344
1345	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1346	then
1347	if [[ "$project_account" != "" ]]
1348	then
1349	column1="project account number:"
1350	column2="$project_account"
1351	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1352	fi
1353	fi
1354
1355	if [[ -n $cores ]]
1356	then
1357	if [[ $run_coupled_model = false ]]
1358	then
1359	column1="number of cores:"; column2=$cores
1360	else
1361	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1362	fi
1363	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1364	fi
1365	if [[ -n $tasks_per_node ]]
1366	then
1367	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1368	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1369	if (( remaining_cores > 0 ))
1370	then
1371	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1372	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1373	fi
1374	fi
1375	if [[ $maximum_parallel_io_streams != $cores ]]
1376	then
1377	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1378	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1379	fi
1380	if [[ $use_openmp = true ]]
1381	then
1382	column1="threads per task:"; column2="$threads_per_task"
1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1384	fi
1385	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1386	then
1387	column1="memory demand / PE":; column2="$memory MB"
1388	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1389	column1="job cpu time (h:m:s):"; column2="$timestring"
1390	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1391	fi
1392	printf "\| \| \n"
1393	if [[ "$source_list" != "" ]]
1394	then
1395	if [[ "$make_options" != "" ]]
1396	then
1397	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1398	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1399	line=$(echo "$make_options" \| cut -c46-)
1400	while [[ "$line" != "" ]]
1401	do
1402	column1=""
1403	column2=$(echo "$line" \| cut -c-45)
1404	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1405	line=$(echo "$line" \| cut -c46-)
1406	done
1407	fi
1408	fi
1409
1410	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1412	line=$(echo "$cpp_options" \| cut -c46-)
1413	while [[ "$line" != "" ]]
1414	do
1415	column1=""
1416	column2=$(echo "$line" \| cut -c-45)
1417	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1418	line=$(echo "$line" \| cut -c46-)
1419	done
1420
1421	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1422	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1423	line=$(echo "$compiler_options" \| cut -c46-)
1424	while [[ "$line" != "" ]]
1425	do
1426	column1=""
1427	column2=$(echo "$line" \| cut -c-45)
1428	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1429	line=$(echo "$line" \| cut -c46-)
1430	done
1431
1432	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1434	line=$(echo "$linker_options" \| cut -c46-)
1435	while [[ "$line" != "" ]]
1436	do
1437	column1=""
1438	column2=$(echo "$line" \| cut -c-45)
1439	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1440	line=$(echo "$line" \| cut -c46-)
1441	done
1442
1443	if [[ "$login_init_cmd" != "" ]]
1444	then
1445	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1446	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1447	line=$(echo "$login_init_cmd" \| cut -c46-)
1448	while [[ "$line" != "" ]]
1449	do
1450	column1=""
1451	column2=$(echo "$line" \| cut -c-45)
1452	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1453	line=$(echo "$line" \| cut -c46-)
1454	done
1455	fi
1456
1457	if [[ "$module_commands" != "" ]]
1458	then
1459	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1461	line=$(echo "$module_commands" \| cut -c46-)
1462	while [[ "$line" != "" ]]
1463	do
1464	column1=""
1465	column2=$(echo "$line" \| cut -c-45)
1466	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1467	line=$(echo "$line" \| cut -c46-)
1468	done
1469	fi
1470	printf "\| \| \n"
1471	column1="base name of files:"; column2=$fname
1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1473	column1="activation string list:"; column2=$(echo $activation_string_list)
1474	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1475
1476	if [[ "$ocean_file_appendix" = true ]]
1477	then
1478	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1479	fi
1480
1481	if [[ "$source_list" != "" ]]
1482	then
1483	printf "\| \| \n"
1484	printf "\| Files to be compiled: \| \n"
1485	line=$source_list
1486	while [[ "$line" != "" ]]
1487	do
1488	linestart=$(echo $line \| cut -c-70)
1489	printf "\| %-70s \| \n" "$linestart"
1490	line=$(echo "$line" \| cut -c71-)
1491	done
1492	fi
1493	printf "#------------------------------------------------------------------------#"
1494
1495
1496
1497	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1498	if [[ $do_trace = true ]]
1499	then
1500	(( i = 0 ))
1501	while (( i < iin ))
1502	do
1503	(( i = i + 1 ))
1504	if (( i == 1 ))
1505	then
1506	printf "\n\n >>> INPUT-file assignments:\n"
1507	fi
1508	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1509	done
1510	(( i = 0 ))
1511	while (( i < iout ))
1512	do
1513	(( i = i + 1 ))
1514	if (( i == 1 ))
1515	then
1516	printf "\n\n >>> OUTPUT-file assignments:\n"
1517	fi
1518	printf "\n ${localout[$i]} : ${pathout[$i]}"
1519	done
1520	(( i = 0 ))
1521	while (( i < iic ))
1522	do
1523	(( i = i + 1 ))
1524	if (( i == 1 ))
1525	then
1526	printf "\n\n >>> INPUT-commands:\n"
1527	fi
1528	printf "\n ${in_command[$i]}"
1529	done
1530	(( i = 0 ))
1531	while (( i < ioc ))
1532	do
1533	(( i = i + 1 ))
1534	if (( i == 1 ))
1535	then
1536	printf "\n\n >>> OUTPUT-commands:\n"
1537	fi
1538	printf "\n ${out_command[$i]}"
1539	done
1540	fi
1541
1542	# QUERY FOR CONTINUE
1543	if [[ $silent = false && $running_in_batch_mode = false ]]
1544	then
1545	antwort=dummy
1546	printf "\n\n"
1547	printf " >>> everything o.k. (y/n) ? "
1548	while read antwort
1549	do
1550	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1551	then
1552	printf " >>> everything o.k. (y/n) ? "
1553	else
1554	break
1555	fi
1556	done
1557	if [[ $antwort = n \|\| $antwort = N ]]
1558	then
1559	locat=user_abort; (( iec = 0 )); exit
1560	fi
1561	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1562	then
1563	printf "\n *** batch-job will be created and submitted"
1564	else
1565	printf "\n *** PALMRUN will now continue to execute on this machine"
1566	fi
1567	fi
1568
1569
1570
1571	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1572	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1573	then
1574
1575	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1576	then
1577	printf "\n\n *** creating executable and other sources for the remote host\n"
1578	else
1579	printf "\n\n *** creating executable and other sources for the local host\n"
1580	fi
1581
1582	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1583	# IT SHALL BE CREATED
1584	ask_for_make_depository=false
1585	if [[ $create_remote_batch_job = true ]]
1586	then
1587
1588	line=`grep %base_directory $config_file`
1589	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1590	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1591
1592	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1593	then
1594	printf "\n\n +++ make depository \"${make_depository}\""
1595	printf "\n on remote host not found!"
1596	ask_for_make_depository=true
1597	fi
1598	rm ${host_configuration}_last_make_protokoll
1599
1600	else
1601
1602	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1603	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1604	if [[ ! -d ${make_depository} ]]
1605	then
1606	printf "\n\n +++ make depository \"${make_depository}\""
1607	printf "\n on local host not found!"
1608	ask_for_make_depository=true
1609	fi
1610
1611	fi
1612
1613	if [[ $ask_for_make_depository = true ]]
1614	then
1615
1616	antwort=dummy
1617	printf "\n\n"
1618	printf " >>> Create a new one (y/n) ? "
1619	while read antwort
1620	do
1621	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1622	then
1623	printf " >>> Create a new one (y/n) ? "
1624	else
1625	break
1626	fi
1627	done
1628	if [[ $antwort = n \|\| $antwort = N ]]
1629	then
1630	locat=user_abort; (( iec = 0 )); exit
1631	fi
1632
1633	if [[ $do_trace = true ]]
1634	then
1635	palmbuild -h $host_configuration
1636	else
1637	palmbuild -v -h $host_configuration
1638	fi
1639
1640	if [[ $? != 0 ]]
1641	then
1642
1643	# ABORT IN CASE OF COMPILATION PROBLEMS
1644	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1645	locat=make_depository
1646	exit
1647	else
1648	echo " *** now continue with creating executable and other sources"
1649	fi
1650
1651	fi
1652
1653	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1654	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
1655
1656	if [[ $? != 0 ]]
1657	then
1658
1659	# ABORT IN CASE OF COMPILATION PROBLEMS
1660	printf "\n +++ error while creating executable and/or other sources"
1661	locat=execution
1662	rm -rf $sources_for_run_catalog
1663	exit
1664
1665	else
1666
1667	printf " *** executable and other sources created\n"
1668	rm -rf $sources_for_run_catalog
1669
1670	fi
1671
1672	fi
1673
1674
1675	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH JOB-ATTRIBUT WILL
1676	# BE COPIED TO THE REMOTE HOST
1677	if [[ $create_remote_batch_job = true ]]
1678	then
1679	(( i = 0 ))
1680	while (( i < iin ))
1681	do
1682	(( i = i + 1 ))
1683	if [[ "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ]]
1684	then
1685	eval inputfile=${pathin[$i]}/${frelin[$i]}
1686	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1687	fi
1688	done
1689	if (( i > 0 ))
1690	then
1691	printf " *** input files have been copied to the remote host\n"
1692	fi
1693	fi
1694
1695
1696	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1697	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1698	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1699	then
1700
1701	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1702	if [[ $running_in_batch_mode = false ]]
1703	then
1704	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1705	# FOLDER
1706	mkdir -p $tempdir
1707	chmod go+rx $tempdir
1708	cd $tempdir
1709	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1710	printf "\n *** changed to temporary directory: $tempdir"
1711
1712	else
1713
1714	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1715	printf "\n *** running in temporary directory: $tempdir"
1716
1717	fi
1718
1719
1720	# PROVIDE THE INPUT FILES
1721	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1722	(( i = 0 ))
1723	while (( i < iin ))
1724	do
1725	(( i = i + 1 ))
1726	if (( i == 1 ))
1727	then
1728	printf "\n\n *** providing INPUT-files:\n$dashes"
1729	fi
1730
1731
1732	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1733	if [[ "${transin[$i]}" = unavailable ]]
1734	then
1735	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1736	then
1737	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1738	printf "\n is not available!"
1739	else
1740	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1741	printf "\n is not available!"
1742	fi
1743	continue
1744	fi
1745
1746	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1747	files_for_cores=false; filetype=file
1748	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1749	then
1750	files_for_cores=true; filetype=files
1751	actionin[$i]=""
1752	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1753	then
1754	actionin[$i]=""
1755	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1756	then
1757	files_for_cores=true; filetype=files
1758	actionin[$i]="ln"
1759	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1760	then
1761	actionin[$i]="ln"
1762	fi
1763
1764	if [[ $files_for_cores = true ]]
1765	then
1766	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1767	else
1768	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1769	fi
1770
1771	# INPUT-FILES TO BE LINKED
1772	if [[ "${actionin[$i]}" = ln ]]
1773	then
1774
1775	printf "\n $filetype will be linked"
1776	if [[ $files_for_cores = false ]]
1777	then
1778	if [[ -f "${absnamein[$i]}" ]]
1779	then
1780	ln ${absnamein[$i]} ${localin[$i]}
1781	got_tmp[$i]=true
1782	fi
1783	else
1784	if [[ -d "${absnamein[$i]}" ]]
1785	then
1786	mkdir -p ${localin[$i]}
1787	cd ${absnamein[$i]}
1788	for file in $(ls *)
1789	do
1790	ln $file $tempdir/${localin[$i]}
1791	done >\|/dev/null 2>&1
1792	cd $tempdir
1793	fi
1794
1795	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1796	if [[ ! -f "${localin[$i]}/_000000" ]]
1797	then
1798	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1799	cp -r ${absnamein[$i]}/* ${localin[$i]}
1800	fi
1801
1802	got_tmp[$i]=true
1803	fi
1804	fi
1805
1806	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1807	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1808	then
1809
1810	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1811	then
1812
1813	# FILE COPIES ARE PROVIDED FOR ALL CORES
1814	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1815	printf "\n file will be provided for $cores processors"
1816	mkdir -p ${localin[$i]}
1817	ival=$cores
1818	(( ii = 0 ))
1819	while (( ii <= ival-1 ))
1820	do
1821	if (( ii < 10 ))
1822	then
1823	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1824	elif (( ii < 100 ))
1825	then
1826	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1827	elif (( ii < 1000 ))
1828	then
1829	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1830	else
1831	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1832	fi
1833	(( ii = ii + 1 ))
1834	done
1835
1836	else
1837
1838	if [[ $files_for_cores = true ]]
1839	then
1840
1841	# PROVIDE FILES FOR EACH CORE
1842	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1843	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1844	printf "\n providing $cores files for the respective cores"
1845	mkdir -p ${localin[$i]}
1846	if [[ $link_local_input = true ]]
1847	then
1848	printf " files will be linked\n"
1849	cd ${absnamein[$i]}
1850	for file in $(ls *)
1851	do
1852	ln -f $file ${localin[$i]}
1853	done
1854	cd $tempdir
1855	fi
1856
1857	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1858	if [[ ! -f "${localin[$i]}/_000000" ]]
1859	then
1860	if [[ $link_local_input = true ]]
1861	then
1862	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1863	fi
1864	cp -r ${absnamein[$i]}/* ${localin[$i]}
1865	fi
1866
1867	else
1868
1869	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1870	if [[ $link_local_input = true ]]
1871	then
1872	printf " file will be linked\n"
1873	ln -f ${absnamein[$i]} ${localin[$i]}
1874	fi
1875	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
1876	if [[ ! -f "${localin[$i]}" ]]
1877	then
1878	if [[ $link_local_input = true ]]
1879	then
1880	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1881	fi
1882	if [[ $running_on_remote = true && ( "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ) ]]
1883	then
1884	mv ${absnamein[$i]} ${localin[$i]}
1885	else
1886	cp ${absnamein[$i]} ${localin[$i]}
1887	fi
1888	fi
1889	fi
1890	fi
1891	fi
1892
1893	done
1894	if (( i != 0 ))
1895	then
1896	printf "\n$dashes\n *** all INPUT-files provided \n"
1897	fi
1898
1899
1900	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1901	(( i = 0 ))
1902	while (( i < iic ))
1903	do
1904	(( i = i + 1 ))
1905	if (( i == 1 ))
1906	then
1907	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1908	fi
1909	printf "\n >>> ${in_command[$i]}"
1910	eval ${in_command[$i]}
1911	if (( i == iic ))
1912	then
1913	printf "\n$dashes\n"
1914	fi
1915	done
1916
1917
1918	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1919	# (FILE ENVPAR WILL BE READ BY PALM)
1920	cat > ENVPAR << EOF
1921	&envpar run_identifier = '$fname', host = '$host_configuration',
1922	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1923	maximum_parallel_io_streams = $maximum_parallel_io_streams,
1924	maximum_cpu_time_allowed = ${cpumax}.,
1925	revision = '$global_revision',
1926	batch_job = .${running_in_batch_mode}. /
1927
1928	EOF
1929
1930
1931	# STARTING THE EXECUTABLE
1932	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
1933	PATH=$PATH:$tempdir
1934
1935
1936	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1937	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
1938	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
1939	eval line=\"$line\"
1940	execute_command="$line"
1941
1942
1943	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1944	if [[ "$execute_command_for_combine" = "" ]]
1945	then
1946	eval line2=\"$line2\"
1947	execute_command_for_combine="$line2"
1948	fi
1949
1950
1951
1952	# PROVIDE A HOSTFILE, IF REQUIRED
1953	if [[ "$hostfile" != "" ]]
1954	then
1955
1956	if [[ $hostfile = auto ]]
1957	then
1958	# CREATE A NEW HOSTFILE
1959	(( ii = 1 ))
1960	while (( ii <= cores / threads_per_task ))
1961	do
1962	echo $(hostname) >> hostfile
1963	(( ii = ii + 1 ))
1964	done
1965	if (( cores / threads_per_task == 0 ))
1966	then
1967	echo $(hostname) >> hostfile
1968	fi
1969
1970	else
1971	cp $hostfile hostfile
1972	fi
1973	eval line=\"`head -n $ii hostfile`\"
1974	printf "\n *** running on: $line"
1975	fi
1976
1977
1978
1979	# SET THE NUMBER OF OPENMP-THREADS
1980	if [[ $use_openmp = true ]]
1981	then
1982	export OMP_NUM_THREADS=$threads_per_task
1983	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1984	else
1985	export OMP_NUM_THREADS=1
1986	fi
1987
1988
1989	# PROVIDE DATA FOR
1990	if [[ $run_coupled_model = false ]]
1991	then
1992	if [[ "$ocean_file_appendix" = true ]]
1993	then
1994	echo "precursor_ocean" > coupling_steering
1995	else
1996	echo "precursor_atmos" > coupling_steering
1997	fi
1998	else
1999	(( iia = $cores_atmos / $threads_per_task ))
2000	(( iio = $cores_ocean / $threads_per_task ))
2001	printf "\n coupled run ($iia atmosphere, $iio ocean)"
2002	printf "\n\n"
2003	echo "coupled_run $iia $iio" > coupling_steering
2004	fi
2005
2006	printf "\n *** execute command:"
2007	printf "\n \"$execute_command\" \n\n"
2008
2009	$execute_command < coupling_steering
2010
2011	if [[ $? != 0 ]]
2012	then
2013
2014	# ABORT IN CASE OF RUNTIME ERRORS
2015	printf "\n +++ runtime error occured"
2016	locat=execution
2017	exit
2018
2019	else
2020
2021	printf "\n$dashes\n *** execution finished \n"
2022
2023	fi
2024
2025
2026	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2027	# BY EACH CORE INTO ONE FILE
2028	if [[ ! -f combine_plot_fields.x ]]
2029	then
2030
2031	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
2032	printf "\n 2d- and/or 3d-data may be incomplete!"
2033	printf "\n Your previous palmbuild may have failed. Please check.\n"
2034
2035	elif [[ "$combine_plot_fields" == true ]]
2036	then
2037
2038	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2039	$execute_command_for_combine
2040
2041	else
2042
2043	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2044	# DATA OUTPUT
2045	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2046	fi
2047
2048
2049
2050	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2051	(( i = 0 ))
2052	while (( i < ioc ))
2053	do
2054	(( i = i + 1 ))
2055	if (( i == 1 ))
2056	then
2057	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2058	fi
2059	printf "\n >>> ${out_command[$i]}"
2060	eval ${out_command[$i]}
2061	if (( i == ioc ))
2062	then
2063	printf "\n$dashes\n"
2064	fi
2065	done
2066
2067
2068	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2069	(( i = 0 ))
2070	while (( i < iout ))
2071	do
2072	(( i = i + 1 ))
2073	if (( i == 1 ))
2074	then
2075	printf "\n\n *** saving OUTPUT-files:"
2076
2077	# GET RUN NUMBER ASSIGNED BY PALM
2078	if [[ -f RUN_NUMBER ]]
2079	then
2080	read run_number < RUN_NUMBER
2081	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2082	usecycle_option="-U $run_number"
2083	else
2084	run_number=0
2085	usecycle_option=""
2086	fi
2087	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2088	then
2089	printf "\n *** in case of SCP transfers to local host"
2090	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2091	fi
2092	printf "\n$dashes"
2093	fi
2094
2095	# ADD CYCLE NUMBER TO FILENAME
2096	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2097	then
2098
2099	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2100	if [[ "${actionout[$i]}" != "a" ]]
2101	then
2102	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2103	# WITH AN EXISTING CYCLE NUMBER
2104	if (( run_number >= cycnum[$i] ))
2105	then
2106	(( cycnum[$i] = run_number ))
2107	else
2108	if (( run_number > 0 ))
2109	then
2110	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2111	fi
2112	fi
2113	fi
2114	if (( cycnum[$i] > 0 ))
2115	then
2116	cyclestring=`printf "%03d" ${cycnum[$i]}`
2117	pathout[$i]=${pathout[$i]}.$cyclestring
2118	fi
2119	fi
2120
2121	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2122	files_for_cores=false; filetype=file
2123	link_local_output=false
2124	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2125	then
2126	files_for_cores=true; filetype=directory
2127	actionout[$i]=""
2128	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2129	then
2130	actionout[$i]=""
2131	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2132	then
2133	files_for_cores=true; filetype=directory
2134	link_local_output=true
2135	actionout[$i]=""
2136	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2137	then
2138	link_local_output
2139	actionout[$i]=""
2140	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2141	then
2142	files_for_cores=true; filetype=directory
2143	actionout[$i]="tr"
2144	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2145	then
2146	actionout[$i]="tr"
2147	fi
2148
2149	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2150	then
2151	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2152	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2153	then
2154	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2155	else
2156
2157
2158	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2159	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2160	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2161	then
2162	if [[ $running_on_remote = true ]]
2163	then
2164
2165	# SET OPTIONS FOR TRANSFER
2166	if [[ "${actionout[$i]}" = tr ]]
2167	then
2168	if [[ $files_for_cores = false ]]
2169	then
2170	catalog_option=""
2171	catalog_string=""
2172	else
2173	catalog_option="-c"
2174	catalog_string="/"
2175	fi
2176	append_option=""
2177	append_string=""
2178	else
2179	append_option="-A"
2180	append_string="append"
2181	fi
2182
2183	transfer_failed=false
2184	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2185	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2186
2187	# TRANSFER VIA SCP
2188	if [[ "$remote_loginnode" != "" ]]
2189	then
2190	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2191	else
2192	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
2193	fi
2194	[[ $? != 0 ]] && transfer_failed=true
2195
2196
2197	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2198	if [[ $transfer_failed = true ]]
2199	then
2200	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2201	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2202
2203	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2204	eval local_catalog=${pathout[$i]}
2205	if [[ ! -d $local_catalog ]]
2206	then
2207	printf " *** local directory does not exist. Trying to create:\n"
2208	printf " $local_catalog \n"
2209	mkdir -p $local_catalog
2210	fi
2211	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2212	transfer_problems=true
2213	fi
2214
2215	else
2216
2217	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2218	# BE COPIED OR APPENDED ON THIS MACHINE
2219	if [[ "${actionout[$i]}" = tr ]]
2220	then
2221	actionout[$i]=""
2222	else
2223	actionout[$i]="a"
2224	fi
2225	fi
2226	fi
2227
2228
2229	# APPEND ON THIS MACHINE
2230	if [[ "${actionout[$i]}" = "a" ]]
2231	then
2232	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2233	then
2234	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2235	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2236	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2237	else
2238	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2239	printf "\n ${pathout[$i]}\n"
2240	cat ${localout[$i]} >> ${pathout[$i]}
2241	fi
2242	fi
2243
2244	# COPY ON THIS MACHINE
2245	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2246	# ON DIFFERENT FILE-SYSTEMS
2247	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2248	then
2249
2250	# COPY IN CASE OF RUNS ON SINGLE CORES
2251	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2252	then
2253	printf "\n >>> OUTPUT: ${localout[$i]} to"
2254	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2255	if [[ $link_local_output = true ]]
2256	then
2257	printf " file will be linked\n"
2258	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2259	fi
2260	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2261	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2262	then
2263	if [[ $link_local_output = true ]]
2264	then
2265	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2266	fi
2267	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2268	else
2269	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2270	fi
2271	else
2272	printf "\n >>> OUTPUT: ${localout[$i]} to"
2273	printf "\n ${pathout[$i]}\n"
2274	if [[ $link_local_output = true ]]
2275	then
2276	printf " file will be linked\n"
2277	ln -f ${localout[$i]} ${pathout[$i]}
2278	fi
2279	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2280	if [[ ! -f "${pathout[$i]}" ]]
2281	then
2282	if [[ $link_local_output = true ]]
2283	then
2284	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2285	fi
2286	cp ${localout[$i]} ${pathout[$i]}
2287	else
2288	printf "+++ no copy because file ${pathout[$i]} exists\n"
2289	fi
2290	fi
2291
2292	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2293	then
2294
2295	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2296	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2297	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2298	printf "\n ${pathout[$i]}\n"
2299	if [[ $link_local_output = true ]]
2300	then
2301	printf " files will be linked\n"
2302	mkdir -p ${pathout[$i]}
2303	cd ${localout[$i]}
2304	for file in $(ls *)
2305	do
2306	ln -f $file ${pathout[$i]}
2307	done >\|/dev/null 2>&1
2308	cd $tempdir
2309	fi
2310
2311	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2312	if [[ ! -f "${pathout[$i]}/_000000" ]]
2313	then
2314	if [[ $link_local_output = true ]]
2315	then
2316	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2317	fi
2318	cp -r ${localout[$i]}/* ${pathout[$i]}
2319	fi
2320
2321	fi
2322	fi
2323	done
2324
2325	if (( i != 0 ))
2326	then
2327	if [[ $transfer_problems = true ]]
2328	then
2329	printf "\n$dashes\n *** OUTPUT-files saved"
2330	printf "\n +++ WARNING: some data transfers failed! \n"
2331	else
2332	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2333	fi
2334	fi
2335
2336
2337	# IF REQUIRED, START A RESTART-JOB
2338	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2339	if [[ -f CONTINUE_RUN ]]
2340	then
2341
2342	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2343	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2344	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2345	# -b START A BATCH JOB
2346	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2347	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2348	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2349
2350
2351	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2352	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2353	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2354	then
2355	prc=`echo $prc \| sed 's/#/r/g'`
2356	fi
2357
2358
2359	# START THE RESTART-JOB
2360	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2361	echo " $prc"
2362	printf "\n$dashes\n"
2363	if [[ $running_on_remote = true ]]
2364	then
2365
2366	echo "*** ssh will be used to initiate restart-runs!"
2367	echo " return_address=\"$return_address\" "
2368	echo " return_username=\"$local_username\" "
2369
2370	if [[ "$remote_loginnode" != "" ]]
2371	then
2372	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
2373	else
2374	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2375	fi
2376
2377	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2378	sleep 30
2379
2380	else
2381
2382	# START THE RESTART JOB ON THE LOCAL HOST
2383	eval $prc # THE ' MUST BE EVALUATED
2384	cd - > /dev/null
2385
2386	fi
2387	printf "\n$dashes\n *** restart-run initiated \n"
2388
2389
2390	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2391	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2392	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2393	# MAY BE VERY HUGE)
2394	(( i = 0 ))
2395	while (( i < iin ))
2396	do
2397	(( i = i + 1 ))
2398	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2399	then
2400	rm -r ${absnamein[$i]}
2401	fi
2402	done
2403
2404	fi
2405
2406
2407	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2408	cd $HOME
2409	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2410
2411
2412	else
2413
2414
2415	# PREPARING ACTIONS,
2416	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2417
2418	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2419	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2420	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2421	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2422	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2423	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2424	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2425	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2426	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2427	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2428	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2429	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2430	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2431	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2432	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2433	if [[ $create_remote_batch_job = true ]]
2434	then
2435	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2436	if [[ $do_trace = true ]]
2437	then
2438	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2439	fi
2440	elif [[ $create_batch_job = true ]]
2441	then
2442	palmrun_com=${palmrun_com}" -j"
2443	if [[ $do_trace = true ]]
2444	then
2445	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2446	fi
2447	fi
2448
2449
2450	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2451	# REMOTE HOST
2452	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2453	job_protocol_file=$job_protocol_file_local
2454	if [[ $create_remote_batch_job = true ]]
2455	then
2456	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2457	job_protocol_file=$job_protocol_file_remote
2458	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2459	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2460	fi
2461
2462
2463	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2464	jobfile=jobfile.$run_id
2465
2466
2467	# FIRST CREATE THE BATCH DIRECTIVES
2468	(( i = 0 ))
2469	while (( i < ibd ))
2470	do
2471	(( i = i + 1 ))
2472	line=`echo "${batch_directive[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{CORES}}/$cores/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{QUEUE}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' \| sed 's/{{PREVIOUS_JOB}}/$previous_job/g' \| sed 's/{{TEMPDIR}}/$tempdir/g'`
2473	eval line=\"$line\"
2474	echo "$line" >> $jobfile
2475	done
2476	echo " " >> $jobfile
2477
2478
2479	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2480	# PROTOCOL
2481	if [[ $create_remote_batch_job = true ]]
2482	then
2483	echo "set +vx" >> $jobfile
2484	echo "trap '" >> $jobfile
2485	echo "set +vx" >> $jobfile
2486	echo "cd ${remote_jobcatalog}" >> $jobfile
2487	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2488
2489	# ADD THE BATCH DIRECTIVES
2490	(( i = 0 ))
2491	while (( i < ibdt ))
2492	do
2493	(( i = i + 1 ))
2494	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{JOB_ID}}/$job_id/g' \| sed 's/{{JOBFILE}}/$job_protocol_file/g' \| sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' \| sed 's/{{CPU_HOURS}}/$cpu_hours/g' \| sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' \| sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' \| sed 's/{{NODES}}/$nodes/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' \| sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' \| sed 's/{{FNAME}}/$fname/g' \| sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
2495	eval line=\"$line\"
2496	echo "$line" >> $jobfile
2497	done
2498	echo " " >> $jobfile
2499
2500	echo "set -x" >> $jobfile
2501	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
2502	echo "%%END%%" >> $jobfile
2503	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2504	echo "$submit_command $scpjob_file" >> $jobfile
2505	echo "rm $scpjob_file" >> $jobfile
2506	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2507	echo "set -x" >> $jobfile
2508	echo " ' exit" >> $jobfile
2509	fi
2510
2511
2512	# ACTIVATE ERROR-TRACEBACK
2513	if [[ $do_trace = true ]]
2514	then
2515	echo "set -x" >> $jobfile
2516	else
2517	echo "set +vx" >> $jobfile
2518	fi
2519
2520
2521	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2522	if [[ "$login_init_cmd" != "" ]]
2523	then
2524	echo "$login_init_cmd" >> $jobfile
2525	fi
2526	if [[ "$module_commands" != "" ]]
2527	then
2528	echo "$module_commands" >> $jobfile
2529	fi
2530
2531
2532	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2533	if [[ $create_remote_batch_job = true ]]
2534	then
2535	echo "mkdir $tempdir" >> $jobfile
2536	echo "chmod go+rx $tempdir" >> $jobfile
2537	else
2538	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2539	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2540	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2541	mkdir $tempdir
2542	chmod go+rx $tempdir
2543	fi
2544	echo "cd $tempdir" >> $jobfile
2545	echo "export tempdir=$tempdir" >> $jobfile
2546	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2547	echo "export PATH=.:\$PATH" >> $jobfile
2548	echo "export execute_palmrun=true" >> $jobfile
2549
2550
2551	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2552	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2553	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2554	echo "LOCAL_PWD=$working_directory" >> $jobfile
2555	echo "export LOCAL_PWD" >> $jobfile
2556
2557
2558	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2559	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2560	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2561
2562
2563	# CALL PALMRUN WITHIN THE JOB
2564	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2565	echo "set -x" >> $jobfile
2566	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2567
2568
2569	# TRANSFER JOBFILE TO THE TARGET HOST
2570	if [[ $create_jobfile_only = false ]]
2571	then
2572
2573	if [[ $create_remote_batch_job = true ]]
2574	then
2575
2576	echo " "
2577	echo " *** transfer of job to remote host via scp"
2578	if [[ $do_trace = true ]]
2579	then
2580	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2581	fi
2582	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2583
2584	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2585	if [[ $do_trace = true ]]
2586	then
2587	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2588	fi
2589	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2590
2591	elif [[ $create_batch_job = true ]]
2592	then
2593
2594	eval local_jobcatalog=$local_jobcatalog
2595	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2596	cd $local_jobcatalog
2597	echo " "
2598	echo " *** submit the job"
2599	if [[ $do_trace = true ]]
2600	then
2601	echo "$submit_command ${host_configuration}_${job_id}"
2602	fi
2603	$submit_command ${host_configuration}_${job_id}
2604	rm ${host_configuration}_${job_id}
2605	cd - > /dev/null
2606
2607	fi
2608
2609	rm -rf $jobfile
2610
2611	else
2612
2613	printf "\n *** jobfile created under name \"$jobfile\" "
2614	printf "\n no batch-job has been sent!"
2615
2616	fi
2617
2618	fi # END OF REMOTE-PART

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