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source: palm/trunk/SCRIPTS/palmrun @ 2602

Last change on this file since 2602 was 2600, checked in by raasch, 7 years ago
small changes concerning r2599, cycle number are now three digits wide
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 87.5 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 2600 2017-11-01 14:11:20Z hellstea $
29	# cycle numbers are made three digits wide
30	#
31	# 2566 2017-10-20 08:50:47Z raasch
32	# execute command for combine_plot_fields added
33	# "TEMPDIR" renamed "tempdir"
34	# temporary working directory for local batch jobs is created immediately within
35	# the user's palmrun call, due to a requirement of the "grid engine" batch
36	# system, where the working directory is given with batch directive -wd and must
37	# already exist when the job is submitted,
38	# informative messages in non-trace mode reduced and partly reformatted
39	#
40	# 2551 2017-10-18 07:25:11Z raasch
41	# TEMPDIR added as replacement string to be used in batch directives
42	#
43	# 2512 2017-10-04 08:26:59Z raasch
44	# bugfix for determining cycle numbers of NetCDF input files
45	#
46	# 2506 2017-09-29 08:30:37Z raasch
47	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
48	# host configuration added to SOURCES_FOR_RUN_... folder name
49	# host_identifier renamed host_configuration
50	# option -W added to allow for job dependencies
51	#
52	# 2501 2017-09-26 11:41:55Z raasch
53	# default value for number of cores (option -X) set to 1
54	# bugfix for mechanism which overwrites configuration file settings with values
55	# provided by palmrun options
56	#
57	# 2499 2017-09-22 16:47:58Z kanani
58	# option -h named configuration identifier
59	#
60	# 2480 2017-09-19 06:24:14Z maronga
61	# bugfix for last revision
62	#
63	# 2479 2017-09-19 06:12:16Z raasch
64	# option -A (project account number) added
65	#
66	# 2422 2017-09-08 08:25:41Z raasch
67	# initial revision
68	#
69	#--------------------------------------------------------------------------------#
70	# palmrun - script for running PALM jobs on local and remote hosts
71	#--------------------------------------------------------------------------------#
72
73
74
75	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
76
77	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
78	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
79	# (TOO MANY ARGUMENTS - PROBLEM)
80	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
81
82	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
83	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
84	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
85	# SCRIPT-OPTION ARGUMENTS
86	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
87	typeset -i icycle inode ival maxcycle mpi_tasks
88	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
89
90	activation_string_list=""
91	AddFilenames=""
92	combine_plot_fields=true
93	compiler_name=""
94	compiler_name_ser=""
95	compiler_options=""
96	cores=1
97	cores_atmos=0
98	cores_ocean=0
99	coupled_dist=""
100	cpp_options=""
101	cpumax=0
102	create_batch_job=false
103	create_jobfile_only=false
104	create_remote_batch_job=false
105	dashes=" ----------------------------------------------------------------------------"
106	defaultqueue=""
107	delete_temporary_catalog=true
108	do_compile=true
109	do_trace=false
110	executable=""
111	execute_command=""
112	execution_error=false
113	fileconnection_file=.palm.iofiles
114	fname=test
115	global_revision=""
116	host_configuration="default"
117	hostfile=""
118	hp=""
119	keep_data_from_previous_run=false
120	link_local_input=false
121	link_local_output=false
122	linker_options=""
123	local_jobcatalog=""
124	locat=normal
125	makefile=""
126	max_par_io_str=""
127	prc=$0
128	while [[ $(echo $prc \| grep -c "/") != 0 ]]
129	do
130	prc=`echo $prc \| cut -f2- -d"/"`
131	done
132	module_calls=""
133	palmrun_memory=""
134	palmrun_script_name=$prc
135	openmp=false
136	previous_job=""
137	project_account=""
138	queue=none
139	restart_run=false
140	return_address=""
141	remote_jobcatalog=""
142	remote_username=""
143	running_in_batch_mode=false
144	run_coupled_model=false
145	run_id=""
146	silent=false
147	source_list=""
148	source_path=""
149	tasks_per_node=0
150	threads_per_task=1
151	transfer_problems=false
152	user_source_path=""
153	use_existing_sources_folder=""
154	use_openmp=false
155	version="palmrun 1.0 Rev$Rev: 2303 $"
156	working_directory=`pwd`
157	write_binary=""
158	TOPT=""
159
160
161	# ERROR HANDLING IN CASE OF EXIT
162	trap 'if [[ $locat != normal && $locat != control_c ]]
163	then
164
165	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
166	(( i = 0 ))
167	while (( i < iec ))
168	do
169	(( i = i + 1 ))
170	printf "\n *** Execution of ERROR-command:\n"
171	printf " >>> ${err_command[$i]}\n"
172	eval ${err_command[$i]}
173	done
174	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
175	printf "\n\n+++ palmrun killed \n\n"
176	elif [[ $locat != control_c ]]
177	then
178	printf "\n --> palmrun finished\n\n"
179	fi' exit
180
181
182	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
183	trap 'cd; rm -rf $tempdir
184	printf "\n+++ palmrun killed by \"^C\" \n\n"
185	locat=control_c
186	exit
187	' 2
188
189
190	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
191	# WHICH WILL BE USED TO START RESTART-JOBS
192	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
193	do
194	case $option in
195	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
196	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
197	(b) create_batch_job=true; prc="$prc -b";;
198	(B) delete_temporary_catalog=false; prc="$prc -B";;
199	(C) restart_run=true; prc="$prc -C";;
200	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
201	(F) create_jobfile_only=true;;
202	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
203	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
204	(j) running_in_batch_mode=true;;
205	(k) keep_data_from_previous_run=true; prc="$prc -k";;
206	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
207	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
208	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
209	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
210	(r) run_id=$OPTARG;;
211	(R) return_address=$OPTARG;;
212	(s) source_list=$OPTARG;;
213	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
214	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
215	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
216	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
217	(v) silent=true; prc="$prc -v";;
218	(V) use_existing_sources_folder="-V";;
219	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
220	(W) previous_job=$OPTARG;;
221	(x) do_trace=true;set -x; prc="$prc -x";;
222	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
223	(y) ocean_file_appendix=true; prc="$prc -y";;
224	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
225	(Z) combine_plot_fields=false; prc="$prc -Z";;
226	(\?) printf "\n +++ unknown option $OPTARG \n"
227	printf "\n --> type \"$0 ?\" for available options \n"
228	locat=parameter;exit;;
229	esac
230	done
231
232
233	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
234	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
235	(( to_shift = $OPTIND - 1 ))
236	shift $to_shift
237
238	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
239	if [[ "$1" = "?" ]]
240	then
241	(printf "\n *** Description of available palmrun options:\n"
242	printf "\n Option Description Default-Value"
243	printf "\n -a activation string list \"\" "
244	printf "\n -A project account number ---"
245	printf "\n -b batch-job on local machine ---"
246	printf "\n -B do not delete temporary directory at end ---"
247	printf "\n -d base name of files attached to program test"
248	printf "\n -F create batch job file only ---"
249	printf "\n -h host configuration \"default\" "
250	printf "\n -k keep data from previous run"
251	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
252	printf "\n -M Makefile name Makefile"
253	printf "\n -O threads per openMP task ---"
254	printf "\n -q queue \"$queue\" "
255	printf "\n -s filenames of routines to be compiled \"\" "
256	printf "\n must end with .f, .f90, .F, or .c !"
257	printf "\n use \"..\" for more than one file and wildcards"
258	printf "\n -s LM compiles all locally modified files"
259	printf "\n -t allowed cpu-time in seconds (batch) 0"
260	printf "\n -T tasks per node ---"
261	printf "\n -u username on remote machine \"\" "
262	printf "\n -v no prompt for confirmation ---"
263	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
264	printf "\n -w maximum parallel io streams as given by -X"
265	printf "\n -W name of job to wait for ---"
266	printf "\n -x tracing of palmrun for debug purposes ---"
267	printf "\n -X # of processors (on parallel machines) 1"
268	printf "\n -y add appendix \"_O\" to all local output"
269	printf "\n files (ocean precursor runs followed by"
270	printf "\n coupled atmosphere-ocean runs) ---"
271	printf "\n -Y run coupled model, \"#1 #2\" with"
272	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
273	printf "\n -Z skip combine_plot_fields at the end of "
274	printf "\n the simulation ---"
275	printf "\n "
276	printf "\n Possible values of positional parameter <modus>:"
277	printf "\n \"?\" - this outline \n\n") \| more
278	exit
279	elif [[ "$1" != "" ]]
280	then
281	printf "\n +++ positional parameter $1 unknown \n"
282	locat=parameter; exit
283	fi
284
285
286
287	# SHORT STARTING MESSAGE
288	printf "\n*** $version "
289	printf "\n will be executed. Please wait ..."
290
291
292	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
293	config_file=.palm.config.$host_configuration
294	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
295
296
297	# CHECK, IF CONFIGURATION FILE EXISTS
298	if [[ ! -f $config_file ]]
299	then
300	printf "\n\n +++ configuration file: "
301	printf "\n $config_file"
302	printf "\n does not exist"
303	locat=connect; exit
304	fi
305
306
307	# CHECK, IF FILE CONNECTION FILE EXISTS
308	if [[ ! -f $fileconnection_file ]]
309	then
310	printf "\n\n +++ file connection file: "
311	printf "\n $fileconnection_file"
312	printf "\n does not exist"
313	locat=connect; exit
314	fi
315
316
317	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
318	if [[ "$activation_string_list" = "" ]]
319	then
320	printf "\n\n +++ no activation string list given: "
321	printf "\n please set palmrun option \"-a\" "
322	locat=palmrun_option; exit
323	fi
324
325
326	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
327	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
328	then
329	write_binary=true
330	else
331	write_binary=false
332	fi
333
334
335	# READ AND EVALUATE THE CONFIGURATION-FILE
336	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
337
338	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
339	while read line
340	do
341
342	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
343	eval line=\"$line\"
344
345
346	# INTERPRET THE LINE
347	if [[ "$(echo $line)" = "" ]]
348	then
349
350	# EMPTY LINE, NO ACTION
351	continue
352
353	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
354	then
355
356	# LINE IS A COMMENT LINE
357	continue
358
359	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
360	then
361
362	# LINE DEFINES AN ENVIRONMENT-VARIABLE
363	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
364	value=`echo $line \| cut -d" " -s -f2-`
365
366
367	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
368	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
369	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
370	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
371	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
372	# CONFIGURATION-FILE.
373	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
374	then
375	eval export $var="\$value"
376
377	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
378	if [[ $do_trace = true ]]
379	then
380	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
381	fi
382	fi
383
384	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
385	then
386
387	# LINE DEFINES BATCH-DIRECTIVE
388	(( ibd = ibd + 1 ))
389	line=$(echo $line \| cut -c4-)
390	batch_directive[$ibd]="$line"
391
392	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
393	then
394
395	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
396	# REMOTE TO A LOCAL HOST
397	(( ibdt = ibdt + 1 ))
398	line=$(echo $line \| cut -c5-)
399	batch_directive_transfer[$ibdt]="$line"
400
401	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
402	then
403
404	# LINE DEFINES ERROR-COMMAND
405	(( iec = iec + 1 ))
406	line=$(echo $line \| cut -c4-)
407	err_command[$iec]="$line"
408
409	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
410	then
411
412	# LINE DEFINES INPUT-COMMAND
413	(( iic = iic + 1 ))
414	line=$(echo $line \| cut -c4-)
415	in_command[$iic]="$line"
416
417	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
418	then
419
420	# LINE DEFINES OUTPUT-COMMAND
421	(( ioc = ioc + 1 ))
422	line=$(echo $line \| cut -c4-)
423	out_command[$ioc]="$line"
424
425	else
426
427	# SKIP ALL OTHER LINES
428	continue
429
430	fi
431
432	done < $config_file
433
434
435	# CHECK SETTING OF REQUIRED PARAMETERS
436	if [[ "$compiler_name" = "" ]]
437	then
438	printf "\n +++ no compiler name found in $config_file"
439	printf "\n Please add line \"compiler_name ...\" to that file."
440	locat=config_file; exit
441	fi
442	if [[ "$compiler_name_ser" = "" ]]
443	then
444	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
445	printf "\n Please add line \"compiler_name_ser ...\" to that file."
446	locat=config_file; exit
447	fi
448	if [[ "$compiler_options" = "" ]]
449	then
450	printf "\n +++ no compiler options found in $config_file"
451	printf "\n Please add line \"compiler_options ...\" to that file."
452	locat=config_file; exit
453	fi
454	if [[ "$linker_options" = "" ]]
455	then
456	printf "\n +++ no linker options found in $config_file"
457	printf "\n Please add line \"linker_options ...\" to that file."
458	locat=config_file; exit
459	fi
460	if [[ "$execute_command" = "" ]]
461	then
462	printf "\n +++ no execute command found in $config_file"
463	printf "\n Please add line \"execute_command ...\" to that file."
464	locat=config_file; exit
465	fi
466
467	if [[ "$hostfile" != "" ]]
468	then
469	if [[ $hostfile != auto && ! -f $hostfile ]]
470	then
471	printf "\n +++ no hostfile \"$hostfile\" found"
472	printf "\n Please check line \"hostfile ...\" in $config_file"
473	locat=config_file; exit
474	fi
475	fi
476
477
478	# DETERMINE THE CALL STATUS
479	if [[ "$return_address" != "" ]]
480	then
481
482	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
483	# BATCH MODE AND ...
484	running_on_remote=true
485
486	else
487
488	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
489	if [[ "$remote_ip" != "" ]]
490	then
491
492	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
493	create_remote_batch_job=true
494
495	fi
496	running_on_remote=false
497	fi
498
499
500
501	# READ AND EVALUATE THE I/O-FILE LIST
502	[[ $silent = false ]] && printf "\n Reading the I/O files... "
503
504	# READ THE FILE CONNECTION FILE LINE BY LINE
505	while read line
506	do
507
508	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
509	eval line=\"$line\"
510
511
512	# INTERPRET THE LINE
513	if [[ "$(echo $line)" = "" ]]
514	then
515	# EMPTY LINE, NO ACTION
516	continue
517
518	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
519	then
520
521	# LINE IS A COMMENT LINE
522	true
523
524	else
525
526	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
527	# s2a: in/out - field
528	# s2b: loc - field (optional)
529	# s2c: tr/ar - field (optional)
530	s1=`echo $line \| cut -d" " -f1`
531	s2=`echo $line \| cut -d" " -s -f2`
532	s2a=$(echo $s2 \| cut -d":" -f1)
533	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
534	then
535	s2b=""
536	s2c=""
537	else
538	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
539	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
540	fi
541	s3=`echo $line \| cut -d" " -f3`
542	s4=`echo $line \| cut -d" " -s -f4`
543	s5=`echo $line \| cut -d" " -s -f5`
544	s6=`echo $line \| cut -d" " -s -f6`
545
546
547	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
548	# INPUT- OR OUTPUT-LIST.
549	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
550	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
551	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
552	# IS NOT CHECKED AND STORED.
553	IFSALT="$IFS"; IFS="$IFS:"
554	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
555	then
556	found=false
557	for actual in $activation_string_list
558	do
559	for formal in $s3
560	do
561	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
562	done
563	done
564	if [[ $found = true ]]
565	then
566	(( iin = iin + 1 ))
567	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
568	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
569	extin[$iin]=$s6
570	fi
571	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
572	then
573	found=false
574	for actual in $activation_string_list
575	do
576	for formal in $s3
577	do
578	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
579	done
580	done
581	if [[ $found = true ]]
582	then
583	(( iout = iout + 1 ))
584	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
585	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
586	fi
587	elif [[ "$s2a" != in && "$s2a" != out ]]
588	then
589	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
590	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
591	locat=connect; exit
592	fi
593	IFS="$IFSALT"
594	fi
595
596	done < $fileconnection_file
597
598
599
600	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
601	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
602	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
603	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
604	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
605	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
606
607
608
609	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
610	if [[ $run_coupled_model = true ]]
611	then
612
613	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
614	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
615
616	if (( $cores_ocean + $cores_atmos != $cores ))
617	then
618
619	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
620	printf "\n PEs (total) : $cores"
621	printf "\n PEs (atmosphere): $cores_atmos"
622	printf "\n PEs (ocean) : $cores_ocean"
623	locat=coupling; exit
624
625	fi
626
627	fi
628
629
630	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
631	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
632	# FOLDER
633	if [[ $running_in_batch_mode = true ]]
634	then
635
636	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
637	then
638	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
639	printf "\n Please check the output of the palmrun-call"
640	printf "\n that you did on your local host."
641	locat=SOURCES_FOR_RUN; exit
642	fi
643
644	else
645
646	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
647	# AUTOMATIC RESTART RUN
648	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
649	if [[ $restart_run = false ]]
650	then
651
652	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
653	# THE LOCAL HOST
654	if [[ ! -d $source_path ]]
655	then
656	printf "\n\n +++ source path \"$source_path\" on local host"
657	printf "\n \"$(hostname)\" does not exist"
658	locat=source_path; exit
659	fi
660
661	rm -rf $sources_for_run_catalog
662	mkdir -p $sources_for_run_catalog
663
664	if [[ "$source_list" = LM ]]
665	then
666
667	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
668	source_list=""
669	cd $source_path
670
671
672	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
673	if [[ ! -d ../.svn ]]
674	then
675	printf "\n\n +++ source directory"
676	printf "\n \"$source_path\" "
677	printf "\n is not under control of \"subversion\"."
678	printf "\n Please do not use palmrun-option \"-s LM\"\n"
679	fi
680
681
682	# LIST ALL MODIFIED SOURCE CODE FILES
683	Filenames=""
684	svn status > tmp_svnstatus
685	while read line
686	do
687	firstc=`echo $line \| cut -c1`
688	if [[ $firstc = M \|\| $firstc = "?" ]]
689	then
690	Name=`echo "$line" \| cut -c8-`
691	extension=`echo $Name \| cut -d. -f2`
692	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
693	then
694	Filenames="$Filenames "$Name
695	fi
696	fi
697	done < tmp_svnstatus
698	rm -rf tmp_svnstatus
699
700
701	# COPY FILES TO SOURCES_FOR_RUN_...
702	for filename in $Filenames
703	do
704	cp $filename ${working_directory}/${sources_for_run_catalog}
705	source_list=$source_list"$filename "
706	done
707
708	cd - > /dev/null
709
710
711	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
712	elif [[ "$source_list" != "" ]]
713	then
714
715	cd $source_path
716
717	for filename in $source_list
718	do
719
720	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
721	if [[ $(echo $filename \| grep -c "/") != 0 ]]
722	then
723	printf "\n +++ source code file: $filename"
724	printf "\n must not contain (\"/\") "
725	locat=source; exit
726	fi
727
728	if [[ ! -f $filename ]]
729	then
730	printf "\n +++ source code file: $filename"
731	printf "\n does not exist"
732	locat=source; exit
733	else
734	cp $filename ${working_directory}/${sources_for_run_catalog}
735	fi
736
737	done
738
739	cd - > /dev/null
740
741	fi
742
743	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
744	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
745	if [[ ! -f $makefile ]]
746	then
747	printf "\n +++ file \"$makefile\" does not exist"
748	locat=make; exit
749	else
750	cp $makefile ${sources_for_run_catalog}/Makefile
751	fi
752
753
754	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
755	if [[ "$user_source_path" != "" ]]
756	then
757
758	# DOES THE DIRECTORY EXIST?
759	if [[ ! -d $user_source_path ]]
760	then
761
762	printf "\n\n *** INFORMATIVE: additional source code directory"
763	printf "\n \"$user_source_path\" "
764	printf "\n does not exist or is not a directory."
765	printf "\n No source code will be used from this directory!\n"
766	user_source_path=""
767	if [[ $silent == false ]]
768	then
769	sleep 2
770	fi
771
772	else
773
774	cd $user_source_path
775	found=false
776
777	Names=$(ls -1 *.f90 2>&1)
778	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
779	Names=$(ls -1 *.F90 2>&1)
780	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
781	Names=$(ls -1 *.F 2>&1)
782	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
783	Names=$(ls -1 *.f 2>&1)
784	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
785	Names=$(ls -1 *.c 2>&1)
786	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
787
788	cd - > /dev/null
789	cd $sources_for_run_catalog
790
791	# COPY MAKEFILE IF EXISTING
792	if [[ -f $user_source_path/Makefile ]]
793	then
794	printf "\n\n *** user Makefile from directory"
795	printf "\n \"$user_source_path\" is used \n"
796	if [[ $silent == false ]]
797	then
798	sleep 1
799	fi
800	cp $user_source_path/Makefile .
801	fi
802
803	for filename in $AddFilenames
804	do
805	if [[ -f $filename ]]
806	then
807	printf "\n +++ source code file \"$filename\" found in additional"
808	printf "\n source code directory \"$user_source_path\" "
809	printf "\n but was also given with option \"-s\" which means that it should be taken"
810	printf "\n from directory \"$source_path\"."
811	locat=source; exit
812	fi
813
814	cp $user_source_path/$filename .
815	source_list="$source_list $filename"
816
817	# CHECK IF FILE IS CONTAINED IN MAKEFILE
818	if [[ $(grep -c $filename Makefile) = 0 ]]
819	then
820	printf "\n\n +++ user file \"$filename\" "
821	printf "\n is not listed in Makefile \n"
822	locat=source; exit
823	else
824
825	if [[ $found = false ]]
826	then
827	found=true
828	printf "\n\n *** following user file(s) added to the"
829	printf " files to be translated:\n "
830	fi
831	printf "$filename "
832	if [[ $silent == false ]]
833	then
834	sleep 0.5
835	fi
836
837	fi
838	done
839	[[ $found = true ]] && printf "\n"
840	cd - > /dev/null
841	fi
842	fi
843
844	# COPY CONFIGURATION FILES
845	cp $config_file $sources_for_run_catalog
846	cp $fileconnection_file $sources_for_run_catalog
847
848	# COPY SHELLSCRIPTS
849	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
850	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
851
852	fi
853
854	fi
855
856	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
857	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
858	if [[ "$global_revision" = "" ]]
859	then
860	global_revision=`svnversion $source_path 2>/dev/null`
861	global_revision="Rev: $global_revision"
862	fi
863
864
865	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
866	if [[ -n $cores ]]
867	then
868
869	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
870	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
871	if [[ $tasks_per_node = 0 ]]
872	then
873	printf "\n"
874	printf "\n +++ option \"-T\" (tasks per node) is missing"
875	printf "\n set -T option or define tasks_per_node in the config file"
876	locat=tasks_per_node; (( iec = 0 )); exit
877	fi
878
879	if (( cores < tasks_per_node ))
880	then
881	printf "\n"
882	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
883	printf "\n given values: -T $tasks_per_node -X $cores"
884	locat=tasks_per_node; (( iec = 0 )); exit
885	fi
886
887	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
888	(( mpi_tasks = cores / threads_per_task ))
889	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
890	(( ii = cores / tasks_per_node ))
891	(( remaining_cores = cores - ii * tasks_per_node ))
892	if (( remaining_cores > 0 ))
893	then
894	printf "\n"
895	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
896	printf "\n divisor of the total number of cores (option \"-X\")"
897	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
898	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
899	(( nodes = nodes + 1 ))
900	fi
901
902	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
903	if [[ "$tasks_per_node" != "" ]]
904	then
905	TOPT="-T $tasks_per_node"
906	fi
907
908	fi
909
910
911	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
912	if [[ "$maximum_parallel_io_streams" = "" ]]
913	then
914	maximum_parallel_io_streams=$cores
915	fi
916
917
918	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
919	if [[ "$scp_port" != "" ]]
920	then
921	PORTOPT="-P $scp_port"
922	SSH_PORTOPT="-p $scp_port"
923	fi
924
925
926	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
927	# CONFIG-FILE
928	if [[ "$ssh_key" != "" ]]
929	then
930	ssh_key="-i $HOME/.ssh/$ssh_key"
931	fi
932
933
934	# SET QUEUE, IF NOT GIVEN
935	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
936	then
937
938	if [[ $queue = none && "$defaultqueue" = "" ]]
939	then
940	printf "\n"
941	printf "\n +++ no default queue given in configuration file and no queue"
942	printf "\n given with option -q"
943	fi
944	if [[ $queue = none ]]
945	then
946	queue=$defaultqueue
947	fi
948
949	fi
950
951
952	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
953	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
954	(( i = 0 ))
955	while (( i < iin ))
956	do
957	(( i = i + 1 ))
958	(( maxcycle = 0 ))
959
960	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
961	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
962	if [[ "${actionin[$i]}" = di ]]
963	then
964	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
965	# HOST ONLY
966	eval filename=${pathin[$i]}/${endin[$i]}
967	else
968	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
969	# HOST ONLY
970	eval filename=${pathin[$i]}/${fname}${endin[$i]}
971	fi
972	eval pathname=${pathin[$i]}
973
974	# CHECK IF FILE EXISTS
975	if ! ls $filename* 1>/dev/null 2>&1
976	then
977
978	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
979	if [[ "${transin[$i]}" != "locopt" ]]
980	then
981	printf "\n\n +++ INPUT-file: "
982	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
983	then
984	printf "\n $filename"
985	else
986	printf "\n $filename.${extin[$i]}"
987	fi
988	printf "\n does not exist\n"
989	locat=input; exit
990	else
991	transin[$i]="unavailable"
992	fi
993	else
994
995	# DETERMINE THE FILE'S CYCLE NUMBER
996	ls -1 -d $filename > filelist 2>/dev/null
997	ls -1 -d $filename.* >> filelist 2>/dev/null
998	while read line
999	do
1000	# filename without path (i.e. after the last "/")
1001	basefilename=$(basename ${line})
1002
1003	# check if there is an extension
1004	extension=${basefilename##*.}
1005	if [[ "$extension" = "${extin[$i]}" ]]
1006	then
1007	basefilename=${basefilename%.*}
1008	fi
1009
1010	# check for an existing cycle number
1011	cycle=${basefilename##*.}
1012	if [[ $cycle =~ ^-?[0-9]+$ ]]
1013	then
1014	(( icycle = $cycle ))
1015	else
1016	(( icycle = 0 ))
1017	fi
1018
1019	if (( icycle > maxcycle ))
1020	then
1021	(( maxcycle = icycle ))
1022
1023	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1024	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1025	if [[ $(echo $cycle \| cut -c1) = 0 ]]
1026	then
1027	leading_zero=true
1028	else
1029	leading_zero=false
1030	fi
1031	fi
1032
1033	done <filelist
1034	rm filelist
1035
1036	# MAKE CYCLE NUMBER THREE DIGITS WIDE
1037	if [[ $leading_zero = true ]]
1038	then
1039	cyclestring=`printf "%03d" $maxcycle`
1040	else
1041	cyclestring=$maxcycle
1042	fi
1043
1044	# APPEND CYCLE NUMBER TO FILENAME
1045	if (( maxcycle > 0 ))
1046	then
1047	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1048	then
1049	filename=${filename}.$cyclestring.${extin[$i]}
1050	else
1051	filename=${filename}.$cyclestring
1052	fi
1053	else
1054	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1055	then
1056	filename=${filename}.${extin[$i]}
1057	fi
1058	fi
1059
1060	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1061	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1062	absnamein[$i]=$filename
1063	if (( maxcycle > 0 ))
1064	then
1065	if [[ "${actionin[$i]}" = di ]]
1066	then
1067	frelin[$i]=${endin[$i]}.$cyclestring
1068	else
1069	frelin[$i]=${fname}${endin[$i]}.$cyclestring
1070	fi
1071	else
1072	if [[ "${actionin[$i]}" = di ]]
1073	then
1074	frelin[$i]=${endin[$i]}
1075	else
1076	frelin[$i]=${fname}${endin[$i]}
1077	fi
1078	fi
1079
1080	fi
1081	done
1082
1083
1084	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1085	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1086	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1087	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1088	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1089	# REMOTE HOST)
1090	(( i = 0 ))
1091	while (( i < iout ))
1092	do
1093	(( i = i + 1 ))
1094	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1095	then
1096	if [[ "${actionout[$i]}" = tr ]]
1097	then
1098	actionout[$i]=""
1099	elif [[ "${actionout[$i]}" = trpe ]]
1100	then
1101	actionout[$i]=pe
1102	elif [[ "${actionout[$i]}" = tra ]]
1103	then
1104	actionout[$i]=a
1105	fi
1106	(( maxcycle = 0 ))
1107	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1108	eval catalogname=${pathout[$i]}
1109	if ! ls $filename* 1>/dev/null 2>&1
1110	then
1111
1112	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1113	if cat /dev/null > $filename
1114	then
1115	rm $filename
1116	else
1117
1118	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1119	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1120	if [[ ! -d $catalogname ]]
1121	then
1122	if mkdir -p $catalogname
1123	then
1124	printf "\n\n *** directory:"
1125	printf "\n $catalogname"
1126	printf "\n was created\n"
1127	else
1128	printf "\n\n +++ OUTPUT-file:"
1129	printf "\n $filename"
1130	printf "\n cannot be created, because directory does not exist"
1131	printf "\n and cannot be created either"
1132	printf "\n"
1133	locat=output ; exit
1134	fi 2>/dev/null
1135	else
1136	printf "\n\n +++ OUTPUT-file:"
1137	printf "\n $filename"
1138	printf "\n cannot be created, although directory exists"
1139	printf "\n"
1140	locat=output ; exit
1141	fi
1142	fi 2>/dev/null
1143	else
1144
1145	# DETERMINE THE CYCLE NUMBER
1146	ls -1 -d $filename > filelist 2>/dev/null
1147	ls -1 -d $filename.* >> filelist 2>/dev/null
1148	while read line
1149	do
1150
1151	# filename without path (i.e. after the last "/")
1152	basefilename=$(basename ${line})
1153
1154	# check if there is an extension
1155	extension=${basefilename##*.}
1156	if [[ "$extension" = "${extout[$i]}" ]]
1157	then
1158	basefilename=${basefilename%.*}
1159	fi
1160
1161	# check for an existing cycle number
1162	cycle=${basefilename##*.}
1163	if [[ $cycle =~ ^-?[0-9]+$ ]]
1164	then
1165	(( icycle = $cycle + 1 ))
1166	else
1167	(( icycle = 1 ))
1168	fi
1169
1170	if (( icycle > maxcycle ))
1171	then
1172	(( maxcycle = icycle ))
1173	fi
1174
1175	done <filelist
1176	rm filelist
1177	fi
1178
1179	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1180	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1181	if [[ "${actionout[$i]}" != a ]]
1182	then
1183	cyclestring=`printf "%03d" $maxcycle`
1184	if (( maxcycle > 0 ))
1185	then
1186	filename_tmp=${filename}.$cyclestring
1187	if cat /dev/null > $filename_tmp
1188	then
1189	rm $filename_tmp
1190	else
1191	printf "\n +++ OUTPUT-file:"
1192	printf "\n $filename_tmp"
1193	printf "\n cannot be created"
1194	locat=output ; exit
1195	fi
1196	fi
1197	else
1198	(( maxcycle = maxcycle - 1 ))
1199	fi
1200
1201	(( cycnum[$i] = maxcycle ))
1202	pathout[$i]=$filename
1203
1204	fi
1205	done
1206
1207
1208	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1209	if [[ $running_in_batch_mode = false ]]
1210	then
1211	run_id=$RANDOM
1212	job_id=${fname}.$run_id
1213
1214	tempdir=$fast_io_catalog/$job_id
1215	fi
1216
1217
1218	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1219	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1220	then
1221
1222	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1223	if [[ $ibd = 0 ]]
1224	then
1225	printf "\n"
1226	printf "\n +++ no batch directives found in configuration file"
1227	locat=config_file_batch_directives; (( iec = 0 )); exit
1228	fi
1229
1230	# CHECK IF CPUTIME IS GIVEN FOR JOB
1231	done=false
1232	cputime=$cpumax
1233	while [[ $done = false ]]
1234	do
1235	if (( cputime == 0 ))
1236	then
1237	printf "\n +++ cpu-time is undefined"
1238	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1239	printf "\n >>> "
1240	read cputime 1>/dev/null 2>&1
1241	else
1242	done=true
1243	fi
1244	done
1245	cpumax=$cputime
1246
1247	# CHECK THE MEMORY DEMAND
1248	done=false
1249	while [[ $done = false ]]
1250	do
1251	if (( memory == 0 ))
1252	then
1253	printf "\n +++ memory demand is undefined"
1254	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1255	printf "\n >>> "
1256	read memory 1>/dev/null 2>&1
1257	else
1258	done=true
1259	fi
1260	done
1261
1262	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1263	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1264	then
1265	while [[ -z $remote_username ]]
1266	do
1267	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
1268	printf "\n >>> Please type username:"
1269	printf "\n >>> "
1270	read remote_username
1271	done
1272	fi
1273
1274	else
1275
1276	if [[ $running_in_batch_mode = false ]]
1277	then
1278	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1279	cpumax=$cputime
1280	else
1281	cputime=$cpumax
1282	fi
1283
1284	fi
1285
1286
1287	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1288	(( cpu_hours = cputime / 3600 ))
1289	(( resttime = cputime - cpu_hours * 3600 ))
1290	(( cpu_minutes = resttime / 60 ))
1291	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1292	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1293
1294
1295	# OUTPUT OF THE PALMRUN-HEADER
1296	calltime=$(date)
1297	printf "\n"
1298	printf "#------------------------------------------------------------------------# \n"
1299	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1300	printf "\| \| \n"
1301	column1="called on:"; column2=$(hostname)
1302	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1303	if [[ $create_remote_batch_job = true ]]
1304	then
1305	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1306	else
1307	if [[ $running_on_remote = true ]]
1308	then
1309	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1310	else
1311	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1312	fi
1313	fi
1314	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1315
1316	column1="running in:"
1317	if [[ $running_in_batch_mode = true ]]
1318	then
1319	column2="batch job mode"
1320	else
1321	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1322	then
1323	column2="job creation mode"
1324	else
1325	column2="interactive run mode"
1326	fi
1327	fi
1328	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1329
1330	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1331	then
1332	if [[ "$project_account" != "" ]]
1333	then
1334	column1="project account number:"
1335	column2="$project_account"
1336	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1337	fi
1338	fi
1339
1340	if [[ -n $cores ]]
1341	then
1342	if [[ $run_coupled_model = false ]]
1343	then
1344	column1="number of cores:"; column2=$cores
1345	else
1346	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1347	fi
1348	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1349	fi
1350	if [[ -n $tasks_per_node ]]
1351	then
1352	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1353	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1354	if (( remaining_cores > 0 ))
1355	then
1356	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1357	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1358	fi
1359	fi
1360	if [[ $maximum_parallel_io_streams != $cores ]]
1361	then
1362	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1363	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1364	fi
1365	if [[ $use_openmp = true ]]
1366	then
1367	column1="threads per task:"; column2="$threads_per_task"
1368	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1369	fi
1370	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1371	then
1372	column1="memory demand / PE":; column2="$memory MB"
1373	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1374	column1="job cpu time (h:m:s):"; column2="$timestring"
1375	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1376	fi
1377	printf "\| \| \n"
1378	if [[ "$source_list" != "" ]]
1379	then
1380	if [[ "$make_options" != "" ]]
1381	then
1382	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1384	line=$(echo "$make_options" \| cut -c46-)
1385	while [[ "$line" != "" ]]
1386	do
1387	column1=""
1388	column2=$(echo "$line" \| cut -c-45)
1389	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1390	line=$(echo "$line" \| cut -c46-)
1391	done
1392	fi
1393	fi
1394
1395	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1396	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1397	line=$(echo "$cpp_options" \| cut -c46-)
1398	while [[ "$line" != "" ]]
1399	do
1400	column1=""
1401	column2=$(echo "$line" \| cut -c-45)
1402	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1403	line=$(echo "$line" \| cut -c46-)
1404	done
1405
1406	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1407	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1408	line=$(echo "$compiler_options" \| cut -c46-)
1409	while [[ "$line" != "" ]]
1410	do
1411	column1=""
1412	column2=$(echo "$line" \| cut -c-45)
1413	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1414	line=$(echo "$line" \| cut -c46-)
1415	done
1416
1417	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1418	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1419	line=$(echo "$linker_options" \| cut -c46-)
1420	while [[ "$line" != "" ]]
1421	do
1422	column1=""
1423	column2=$(echo "$line" \| cut -c-45)
1424	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1425	line=$(echo "$line" \| cut -c46-)
1426	done
1427
1428	if [[ "$login_init_cmd" != "" ]]
1429	then
1430	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1431	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1432	line=$(echo "$login_init_cmd" \| cut -c46-)
1433	while [[ "$line" != "" ]]
1434	do
1435	column1=""
1436	column2=$(echo "$line" \| cut -c-45)
1437	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1438	line=$(echo "$line" \| cut -c46-)
1439	done
1440	fi
1441
1442	if [[ "$module_commands" != "" ]]
1443	then
1444	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1446	line=$(echo "$module_commands" \| cut -c46-)
1447	while [[ "$line" != "" ]]
1448	do
1449	column1=""
1450	column2=$(echo "$line" \| cut -c-45)
1451	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1452	line=$(echo "$line" \| cut -c46-)
1453	done
1454	fi
1455	printf "\| \| \n"
1456	column1="base name of files:"; column2=$fname
1457	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1458	column1="activation string list:"; column2=$(echo $activation_string_list)
1459	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1460
1461	if [[ "$ocean_file_appendix" = true ]]
1462	then
1463	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1464	fi
1465
1466	if [[ "$source_list" != "" ]]
1467	then
1468	printf "\| \| \n"
1469	printf "\| Files to be compiled: \| \n"
1470	line=$source_list
1471	while [[ "$line" != "" ]]
1472	do
1473	linestart=$(echo $line \| cut -c-70)
1474	printf "\| %-70s \| \n" "$linestart"
1475	line=$(echo "$line" \| cut -c71-)
1476	done
1477	fi
1478	printf "#------------------------------------------------------------------------#"
1479
1480
1481
1482	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1483	if [[ $do_trace = true ]]
1484	then
1485	(( i = 0 ))
1486	while (( i < iin ))
1487	do
1488	(( i = i + 1 ))
1489	if (( i == 1 ))
1490	then
1491	printf "\n\n >>> INPUT-file assignments:\n"
1492	fi
1493	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1494	done
1495	(( i = 0 ))
1496	while (( i < iout ))
1497	do
1498	(( i = i + 1 ))
1499	if (( i == 1 ))
1500	then
1501	printf "\n\n >>> OUTPUT-file assignments:\n"
1502	fi
1503	printf "\n ${localout[$i]} : ${pathout[$i]}"
1504	done
1505	(( i = 0 ))
1506	while (( i < iic ))
1507	do
1508	(( i = i + 1 ))
1509	if (( i == 1 ))
1510	then
1511	printf "\n\n >>> INPUT-commands:\n"
1512	fi
1513	printf "\n ${in_command[$i]}"
1514	done
1515	(( i = 0 ))
1516	while (( i < ioc ))
1517	do
1518	(( i = i + 1 ))
1519	if (( i == 1 ))
1520	then
1521	printf "\n\n >>> OUTPUT-commands:\n"
1522	fi
1523	printf "\n ${out_command[$i]}"
1524	done
1525	fi
1526
1527	# QUERY FOR CONTINUE
1528	if [[ $silent = false && $running_in_batch_mode = false ]]
1529	then
1530	antwort=dummy
1531	printf "\n\n"
1532	printf " >>> everything o.k. (y/n) ? "
1533	while read antwort
1534	do
1535	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1536	then
1537	printf " >>> everything o.k. (y/n) ? "
1538	else
1539	break
1540	fi
1541	done
1542	if [[ $antwort = n \|\| $antwort = N ]]
1543	then
1544	locat=user_abort; (( iec = 0 )); exit
1545	fi
1546	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1547	then
1548	printf "\n *** batch-job will be created and submitted"
1549	else
1550	printf "\n *** PALMRUN will now continue to execute on this machine"
1551	fi
1552	fi
1553
1554
1555
1556	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1557	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1558	then
1559
1560	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1561	then
1562	printf "\n\n *** creating executable and other sources for the remote host\n"
1563	else
1564	printf "\n\n *** creating executable and other sources for the local host\n"
1565	fi
1566
1567	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1568	# IT SHALL BE CREATED
1569	ask_for_make_depository=false
1570	if [[ $create_remote_batch_job = true ]]
1571	then
1572
1573	line=`grep %base_directory $config_file`
1574	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1575	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
1576
1577	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1578	then
1579	printf "\n\n +++ make depository \"${make_depository}\""
1580	printf "\n on remote host not found!"
1581	ask_for_make_depository=true
1582	fi
1583	rm ${host_configuration}_last_make_protokoll
1584
1585	else
1586
1587	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1588	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1589	if [[ ! -d ${make_depository} ]]
1590	then
1591	printf "\n\n +++ make depository \"${make_depository}\""
1592	printf "\n on local host not found!"
1593	ask_for_make_depository=true
1594	fi
1595
1596	fi
1597
1598	if [[ $ask_for_make_depository = true ]]
1599	then
1600
1601	antwort=dummy
1602	printf "\n\n"
1603	printf " >>> Create a new one (y/n) ? "
1604	while read antwort
1605	do
1606	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1607	then
1608	printf " >>> Create a new one (y/n) ? "
1609	else
1610	break
1611	fi
1612	done
1613	if [[ $antwort = n \|\| $antwort = N ]]
1614	then
1615	locat=user_abort; (( iec = 0 )); exit
1616	fi
1617
1618	if [[ $do_trace = true ]]
1619	then
1620	palmbuild -h $host_configuration
1621	else
1622	palmbuild -v -h $host_configuration
1623	fi
1624
1625	if [[ $? != 0 ]]
1626	then
1627
1628	# ABORT IN CASE OF COMPILATION PROBLEMS
1629	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
1630	locat=make_depository
1631	exit
1632	else
1633	echo " *** now continue with creating executable and other sources"
1634	fi
1635
1636	fi
1637
1638	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
1639	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
1640
1641	if [[ $? != 0 ]]
1642	then
1643
1644	# ABORT IN CASE OF COMPILATION PROBLEMS
1645	printf "\n +++ error while creating executable and/or other sources"
1646	locat=execution
1647	rm -rf $sources_for_run_catalog
1648	exit
1649
1650	else
1651
1652	printf " *** executable and other sources created\n"
1653	rm -rf $sources_for_run_catalog
1654
1655	fi
1656
1657	fi
1658
1659
1660	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1661	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1662	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1663	then
1664
1665	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1666	if [[ $running_in_batch_mode = false ]]
1667	then
1668	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1669	# FOLDER
1670	mkdir -p $tempdir
1671	chmod go+rx $tempdir
1672	cd $tempdir
1673	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
1674	printf "\n *** changed to temporary directory: $tempdir"
1675
1676	else
1677
1678	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1679	printf "\n *** running in temporary directory: $tempdir"
1680
1681	fi
1682
1683
1684	# PROVIDE THE INPUT FILES
1685	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1686	(( i = 0 ))
1687	while (( i < iin ))
1688	do
1689	(( i = i + 1 ))
1690	if (( i == 1 ))
1691	then
1692	printf "\n\n *** providing INPUT-files:\n$dashes"
1693	fi
1694
1695
1696	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1697	if [[ "${transin[$i]}" = unavailable ]]
1698	then
1699	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1700	then
1701	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1702	printf "\n is not available!"
1703	else
1704	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1705	printf "\n is not available!"
1706	fi
1707	continue
1708	fi
1709
1710	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1711	files_for_cores=false; filetype=file
1712	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1713	then
1714	files_for_cores=true; filetype=files
1715	actionin[$i]=""
1716	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1717	then
1718	actionin[$i]=""
1719	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1720	then
1721	files_for_cores=true; filetype=files
1722	actionin[$i]="ln"
1723	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1724	then
1725	actionin[$i]="ln"
1726	fi
1727
1728	if [[ $files_for_cores = true ]]
1729	then
1730	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1731	else
1732	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1733	fi
1734
1735	# INPUT-FILES TO BE LINKED
1736	if [[ "${actionin[$i]}" = ln ]]
1737	then
1738
1739	printf "\n $filetype will be linked"
1740	if [[ $files_for_cores = false ]]
1741	then
1742	if [[ -f "${absnamein[$i]}" ]]
1743	then
1744	ln ${absnamein[$i]} ${localin[$i]}
1745	got_tmp[$i]=true
1746	fi
1747	else
1748	if [[ -d "${absnamein[$i]}" ]]
1749	then
1750	mkdir -p ${localin[$i]}
1751	cd ${absnamein[$i]}
1752	for file in $(ls *)
1753	do
1754	ln $file $tempdir/${localin[$i]}
1755	done >\|/dev/null 2>&1
1756	cd $tempdir
1757	fi
1758
1759	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1760	if [[ ! -f "${localin[$i]}/_000000" ]]
1761	then
1762	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1763	cp -r ${absnamein[$i]}/* ${localin[$i]}
1764	fi
1765
1766	got_tmp[$i]=true
1767	fi
1768	fi
1769
1770	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1771	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1772	then
1773
1774	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1775	then
1776
1777	# FILE COPIES ARE PROVIDED FOR ALL CORES
1778	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1779	printf "\n file will be provided for $cores processors"
1780	mkdir -p ${localin[$i]}
1781	ival=$cores
1782	(( ii = 0 ))
1783	while (( ii <= ival-1 ))
1784	do
1785	if (( ii < 10 ))
1786	then
1787	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1788	elif (( ii < 100 ))
1789	then
1790	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1791	elif (( ii < 1000 ))
1792	then
1793	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1794	else
1795	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1796	fi
1797	(( ii = ii + 1 ))
1798	done
1799
1800	else
1801
1802	if [[ $files_for_cores = true ]]
1803	then
1804
1805	# PROVIDE FILES FOR EACH CORE
1806	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1807	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1808	printf "\n providing $cores files for the respective cores"
1809	mkdir -p ${localin[$i]}
1810	if [[ $link_local_input = true ]]
1811	then
1812	printf " files will be linked\n"
1813	cd ${absnamein[$i]}
1814	for file in $(ls *)
1815	do
1816	ln -f $file ${localin[$i]}
1817	done
1818	cd $tempdir
1819	fi
1820
1821	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1822	if [[ ! -f "${localin[$i]}/_000000" ]]
1823	then
1824	if [[ $link_local_input = true ]]
1825	then
1826	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1827	fi
1828	cp -r ${absnamein[$i]}/* ${localin[$i]}
1829	fi
1830
1831	else
1832
1833	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1834	if [[ $link_local_input = true ]]
1835	then
1836	printf " file will be linked\n"
1837	ln -f ${absnamein[$i]} ${localin[$i]}
1838	fi
1839	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
1840	if [[ ! -f "${localin[$i]}" ]]
1841	then
1842	if [[ $link_local_input = true ]]
1843	then
1844	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1845	fi
1846	cp ${absnamein[$i]} ${localin[$i]}
1847	fi
1848	fi
1849	fi
1850	fi
1851
1852	done
1853	if (( i != 0 ))
1854	then
1855	printf "\n$dashes\n *** all INPUT-files provided \n"
1856	fi
1857
1858
1859	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1860	(( i = 0 ))
1861	while (( i < iic ))
1862	do
1863	(( i = i + 1 ))
1864	if (( i == 1 ))
1865	then
1866	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1867	fi
1868	printf "\n >>> ${in_command[$i]}"
1869	eval ${in_command[$i]}
1870	if (( i == iic ))
1871	then
1872	printf "\n$dashes\n"
1873	fi
1874	done
1875
1876
1877	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1878	# (FILE ENVPAR WILL BE READ BY PALM)
1879	cat > ENVPAR << EOF
1880	&envpar run_identifier = '$fname', host = '$host_configuration',
1881	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1882	maximum_parallel_io_streams = $maximum_parallel_io_streams,
1883	maximum_cpu_time_allowed = ${cpumax}.,
1884	revision = '$global_revision',
1885	batch_job = .${running_in_batch_mode}. /
1886
1887	EOF
1888
1889
1890	# STARTING THE EXECUTABLE
1891	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
1892	PATH=$PATH:$tempdir
1893
1894
1895	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1896	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
1897	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
1898	eval line=\"$line\"
1899	execute_command="$line"
1900
1901
1902	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1903	if [[ "$execute_command_for_combine" = "" ]]
1904	then
1905	eval line2=\"$line2\"
1906	execute_command_for_combine="$line2"
1907	fi
1908
1909
1910
1911	# PROVIDE A HOSTFILE, IF REQUIRED
1912	if [[ "$hostfile" != "" ]]
1913	then
1914
1915	if [[ $hostfile = auto ]]
1916	then
1917	# CREATE A NEW HOSTFILE
1918	(( ii = 1 ))
1919	while (( ii <= cores / threads_per_task ))
1920	do
1921	echo $(hostname) >> hostfile
1922	(( ii = ii + 1 ))
1923	done
1924	if (( cores / threads_per_task == 0 ))
1925	then
1926	echo $(hostname) >> hostfile
1927	fi
1928
1929	else
1930	cp $hostfile hostfile
1931	fi
1932	eval line=\"`head -n $ii hostfile`\"
1933	printf "\n *** running on: $line"
1934	fi
1935
1936
1937
1938	# SET THE NUMBER OF OPENMP-THREADS
1939	if [[ $use_openmp = true ]]
1940	then
1941	export OMP_NUM_THREADS=$threads_per_task
1942	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1943	else
1944	export OMP_NUM_THREADS=1
1945	fi
1946
1947
1948	# PROVIDE DATA FOR
1949	if [[ $run_coupled_model = false ]]
1950	then
1951	if [[ "$ocean_file_appendix" = true ]]
1952	then
1953	echo "precursor_ocean" > coupling_steering
1954	else
1955	echo "precursor_atmos" > coupling_steering
1956	fi
1957	else
1958	(( iia = $cores_atmos / $threads_per_task ))
1959	(( iio = $cores_ocean / $threads_per_task ))
1960	printf "\n coupled run ($iia atmosphere, $iio ocean)"
1961	printf "\n\n"
1962	echo "coupled_run $iia $iio" > coupling_steering
1963	fi
1964
1965	printf "\n *** execute command:"
1966	printf "\n \"$execute_command\" \n\n"
1967
1968	$execute_command < coupling_steering
1969
1970	if [[ $? != 0 ]]
1971	then
1972
1973	# ABORT IN CASE OF RUNTIME ERRORS
1974	printf "\n +++ runtime error occured"
1975	locat=execution
1976	exit
1977
1978	else
1979
1980	printf "\n$dashes\n *** execution finished \n"
1981
1982	fi
1983
1984
1985	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
1986	# BY EACH CORE INTO ONE FILE
1987	if [[ ! -f combine_plot_fields.x ]]
1988	then
1989
1990	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
1991	printf "\n 2d- and/or 3d-data may be incomplete!"
1992	printf "\n Your previous palmbuild may have failed. Please check.\n"
1993
1994	elif [[ "$combine_plot_fields" == true ]]
1995	then
1996
1997	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
1998	$execute_command_for_combine
1999
2000	else
2001
2002	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2003	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
2004	# ??? koennen wir das streichen ???
2005	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2006	fi
2007
2008
2009
2010	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2011	(( i = 0 ))
2012	while (( i < ioc ))
2013	do
2014	(( i = i + 1 ))
2015	if (( i == 1 ))
2016	then
2017	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
2018	fi
2019	printf "\n >>> ${out_command[$i]}"
2020	eval ${out_command[$i]}
2021	if (( i == ioc ))
2022	then
2023	printf "\n$dashes\n"
2024	fi
2025	done
2026
2027
2028	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2029	(( i = 0 ))
2030	while (( i < iout ))
2031	do
2032	(( i = i + 1 ))
2033	if (( i == 1 ))
2034	then
2035	printf "\n\n *** saving OUTPUT-files:"
2036
2037	# GET RUN NUMBER ASSIGNED BY PALM
2038	if [[ -f RUN_NUMBER ]]
2039	then
2040	read run_number < RUN_NUMBER
2041	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2042	usecycle_option="-U $run_number"
2043	else
2044	run_number=0
2045	usecycle_option=""
2046	fi
2047	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
2048	then
2049	printf "\n *** in case of SCP transfers to local host"
2050	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
2051	fi
2052	printf "\n$dashes"
2053	fi
2054
2055	# ADD CYCLE NUMBER TO FILENAME
2056	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
2057	then
2058
2059	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2060	if [[ "${actionout[$i]}" != "a" ]]
2061	then
2062	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2063	# WITH AN EXISTING CYCLE NUMBER
2064	if (( run_number >= cycnum[$i] ))
2065	then
2066	(( cycnum[$i] = run_number ))
2067	else
2068	if (( run_number > 0 ))
2069	then
2070	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
2071	fi
2072	fi
2073	fi
2074	if (( cycnum[$i] > 0 ))
2075	then
2076	cyclestring=`printf "%03d" ${cycnum[$i]}`
2077	pathout[$i]=${pathout[$i]}.$cyclestring
2078	fi
2079	fi
2080
2081	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2082	files_for_cores=false; filetype=file
2083	link_local_output=false
2084	if [[ "${actionout[$i]}" = pe && -n $cores ]]
2085	then
2086	files_for_cores=true; filetype=directory
2087	actionout[$i]=""
2088	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
2089	then
2090	actionout[$i]=""
2091	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
2092	then
2093	files_for_cores=true; filetype=directory
2094	link_local_output=true
2095	actionout[$i]=""
2096	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
2097	then
2098	link_local_output
2099	actionout[$i]=""
2100	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
2101	then
2102	files_for_cores=true; filetype=directory
2103	actionout[$i]="tr"
2104	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
2105	then
2106	actionout[$i]="tr"
2107	fi
2108
2109	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2110	then
2111	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2112	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2113	then
2114	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2115	else
2116
2117
2118	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2119	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2120	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2121	then
2122	if [[ $running_on_remote = true ]]
2123	then
2124
2125	# SET OPTIONS FOR TRANSFER
2126	if [[ "${actionout[$i]}" = tr ]]
2127	then
2128	if [[ $files_for_cores = false ]]
2129	then
2130	catalog_option=""
2131	catalog_string=""
2132	else
2133	catalog_option="-c"
2134	catalog_string="/"
2135	fi
2136	append_option=""
2137	append_string=""
2138	else
2139	append_option="-A"
2140	append_string="append"
2141	fi
2142
2143	transfer_failed=false
2144	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2145	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2146
2147	# TRANSFER VIA SCP
2148	if [[ "$remote_loginnode" != "" ]]
2149	then
2150	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
2151	else
2152	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]}
2153	fi
2154	[[ $? != 0 ]] && transfer_failed=true
2155
2156
2157	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2158	if [[ $transfer_failed = true ]]
2159	then
2160	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2161	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2162
2163	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2164	eval local_catalog=${pathout[$i]}
2165	if [[ ! -d $local_catalog ]]
2166	then
2167	printf " *** local directory does not exist. Trying to create:\n"
2168	printf " $local_catalog \n"
2169	mkdir -p $local_catalog
2170	fi
2171	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2172	transfer_problems=true
2173	fi
2174
2175	else
2176
2177	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2178	# BE COPIED OR APPENDED ON THIS MACHINE
2179	if [[ "${actionout[$i]}" = tr ]]
2180	then
2181	actionout[$i]=""
2182	else
2183	actionout[$i]="a"
2184	fi
2185	fi
2186	fi
2187
2188
2189	# APPEND ON THIS MACHINE
2190	if [[ "${actionout[$i]}" = "a" ]]
2191	then
2192	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2193	then
2194	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2195	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2196	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2197	else
2198	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2199	printf "\n ${pathout[$i]}\n"
2200	cat ${localout[$i]} >> ${pathout[$i]}
2201	fi
2202	fi
2203
2204	# COPY ON THIS MACHINE
2205	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2206	# ON DIFFERENT FILE-SYSTEMS
2207	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2208	then
2209
2210	# COPY IN CASE OF RUNS ON SINGLE CORES
2211	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2212	then
2213	printf "\n >>> OUTPUT: ${localout[$i]} to"
2214	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2215	if [[ $link_local_output = true ]]
2216	then
2217	printf " file will be linked\n"
2218	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2219	fi
2220	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2221	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2222	then
2223	if [[ $link_local_output = true ]]
2224	then
2225	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2226	fi
2227	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2228	else
2229	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2230	fi
2231	else
2232	printf "\n >>> OUTPUT: ${localout[$i]} to"
2233	printf "\n ${pathout[$i]}\n"
2234	if [[ $link_local_output = true ]]
2235	then
2236	printf " file will be linked\n"
2237	ln -f ${localout[$i]} ${pathout[$i]}
2238	fi
2239	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2240	if [[ ! -f "${pathout[$i]}" ]]
2241	then
2242	if [[ $link_local_output = true ]]
2243	then
2244	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2245	fi
2246	cp ${localout[$i]} ${pathout[$i]}
2247	else
2248	printf "+++ no copy because file ${pathout[$i]} exists\n"
2249	fi
2250	fi
2251
2252	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2253	then
2254
2255	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2256	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2257	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2258	printf "\n ${pathout[$i]}\n"
2259	if [[ $link_local_output = true ]]
2260	then
2261	printf " files will be linked\n"
2262	mkdir -p ${pathout[$i]}
2263	cd ${localout[$i]}
2264	for file in $(ls *)
2265	do
2266	ln -f $file ${pathout[$i]}
2267	done >\|/dev/null 2>&1
2268	cd $tempdir
2269	fi
2270
2271	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2272	if [[ ! -f "${pathout[$i]}/_000000" ]]
2273	then
2274	if [[ $link_local_output = true ]]
2275	then
2276	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2277	fi
2278	cp -r ${localout[$i]}/* ${pathout[$i]}
2279	fi
2280
2281	fi
2282	fi
2283	done
2284
2285	if (( i != 0 ))
2286	then
2287	if [[ $transfer_problems = true ]]
2288	then
2289	printf "\n$dashes\n *** OUTPUT-files saved"
2290	printf "\n +++ WARNING: some data transfers failed! \n"
2291	else
2292	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2293	fi
2294	fi
2295
2296
2297	# IF REQUIRED, START A RESTART-JOB
2298	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2299	if [[ -f CONTINUE_RUN ]]
2300	then
2301
2302	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2303	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2304	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2305	# -b START A BATCH JOB
2306	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2307	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2308	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2309
2310
2311	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2312	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2313	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2314	then
2315	prc=`echo $prc \| sed 's/#/r/g'`
2316	fi
2317
2318
2319	# START THE RESTART-JOB
2320	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2321	echo " $prc"
2322	printf "\n$dashes\n"
2323	if [[ $running_on_remote = true ]]
2324	then
2325
2326	echo "*** ssh will be used to initiate restart-runs!"
2327	echo " return_address=\"$return_address\" "
2328	echo " return_username=\"$local_username\" "
2329
2330	if [[ "$remote_loginnode" != "" ]]
2331	then
2332	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
2333	else
2334	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2335	fi
2336
2337	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2338	sleep 30
2339
2340	else
2341
2342	# START THE RESTART JOB ON THE LOCAL HOST
2343	eval $prc # THE ' MUST BE EVALUATED
2344	cd - > /dev/null
2345
2346	fi
2347	printf "\n$dashes\n *** restart-run initiated \n"
2348
2349
2350	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2351	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2352	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2353	# MAY BE VERY HUGE)
2354	(( i = 0 ))
2355	while (( i < iin ))
2356	do
2357	(( i = i + 1 ))
2358	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2359	then
2360	rm -r ${absnamein[$i]}
2361	fi
2362	done
2363
2364	fi
2365
2366
2367	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2368	cd $HOME
2369	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
2370
2371
2372	else
2373
2374
2375	# PREPARING ACTIONS,
2376	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2377
2378	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2379	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2380	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2381	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2382	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2383	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2384	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2385	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2386	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2387	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2388	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2389	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2390	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2391	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2392	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
2393	if [[ $create_remote_batch_job = true ]]
2394	then
2395	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2396	if [[ $do_trace = true ]]
2397	then
2398	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2399	fi
2400	elif [[ $create_batch_job = true ]]
2401	then
2402	palmrun_com=${palmrun_com}" -j"
2403	if [[ $do_trace = true ]]
2404	then
2405	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2406	fi
2407	fi
2408
2409
2410	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2411	# REMOTE HOST
2412	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2413	job_protocol_file=$job_protocol_file_local
2414	if [[ $create_remote_batch_job = true ]]
2415	then
2416	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2417	job_protocol_file=$job_protocol_file_remote
2418	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2419	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2420	fi
2421
2422
2423	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2424	jobfile=jobfile.$run_id
2425
2426
2427	# FIRST CREATE THE BATCH DIRECTIVES
2428	(( i = 0 ))
2429	while (( i < ibd ))
2430	do
2431	(( i = i + 1 ))
2432	line=`echo "${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'`
2433	eval line=\"$line\"
2434	echo "$line" >> $jobfile
2435	done
2436	echo " " >> $jobfile
2437
2438
2439	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2440	# PROTOCOL
2441	if [[ $create_remote_batch_job = true ]]
2442	then
2443	echo "set +vx" >> $jobfile
2444	echo "trap '" >> $jobfile
2445	echo "set +vx" >> $jobfile
2446	echo "cd ${remote_jobcatalog}" >> $jobfile
2447	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2448
2449	# ADD THE BATCH DIRECTIVES
2450	(( i = 0 ))
2451	while (( i < ibdt ))
2452	do
2453	(( i = i + 1 ))
2454	line=`echo "${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'`
2455	eval line=\"$line\"
2456	echo "$line" >> $jobfile
2457	done
2458	echo " " >> $jobfile
2459
2460	echo "set -x" >> $jobfile
2461	echo "${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
2462	echo "%%END%%" >> $jobfile
2463	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2464	echo "$submit_command $scpjob_file" >> $jobfile
2465	echo "rm $scpjob_file" >> $jobfile
2466	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2467	echo "set -x" >> $jobfile
2468	echo " ' exit" >> $jobfile
2469	fi
2470
2471
2472	# ACTIVATE ERROR-TRACEBACK
2473	if [[ $do_trace = true ]]
2474	then
2475	echo "set -x" >> $jobfile
2476	else
2477	echo "set +vx" >> $jobfile
2478	fi
2479
2480
2481	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2482	if [[ "$login_init_cmd" != "" ]]
2483	then
2484	echo "$login_init_cmd" >> $jobfile
2485	fi
2486	if [[ "$module_commands" != "" ]]
2487	then
2488	echo "$module_commands" >> $jobfile
2489	fi
2490
2491
2492	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2493	if [[ $create_remote_batch_job = true ]]
2494	then
2495	echo "mkdir $tempdir" >> $jobfile
2496	echo "chmod go+rx $tempdir" >> $jobfile
2497	else
2498	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2499	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2500	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2501	mkdir $tempdir
2502	chmod go+rx $tempdir
2503	fi
2504	echo "cd $tempdir" >> $jobfile
2505	echo "export tempdir=$tempdir" >> $jobfile
2506	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
2507	echo "export PATH=.:\$PATH" >> $jobfile
2508	echo "export execute_palmrun=true" >> $jobfile
2509
2510
2511	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
2512	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
2513	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
2514	if [[ $create_remote_batch_job = true ]]
2515	then
2516	(( i = 0 ))
2517	while (( i < iin ))
2518	do
2519	(( i = i + 1 ))
2520	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
2521	if [[ "${transin[$i]}" = job ]]
2522	then
2523	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
2524	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
2525	echo " " >> $jobfile
2526	echo "%END%" >> $jobfile
2527	else
2528	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
2529	fi
2530
2531	# CHECK, IF FILE COULD BE CREATED
2532	echo "if [[ \$? = 1 ]]" >> $jobfile
2533	echo "then" >> $jobfile
2534	echo " echo \" \" " >> $jobfile
2535	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
2536	echo " echo \" please check, if directory exists on $host_configuration!\" " >> $jobfile
2537	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
2538	echo " execute_palmrun=false" >> $jobfile
2539	echo "fi" >> $jobfile
2540	done
2541	fi
2542
2543
2544	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2545	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2546	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2547	echo "LOCAL_PWD=$working_directory" >> $jobfile
2548	echo "export LOCAL_PWD" >> $jobfile
2549
2550
2551	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2552	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
2553	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2554
2555
2556	# CALL PALMRUN WITHIN THE JOB
2557	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2558	echo "set -x" >> $jobfile
2559	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2560
2561
2562	# TRANSFER JOBFILE TO THE TARGET HOST
2563	if [[ $create_jobfile_only = false ]]
2564	then
2565
2566	if [[ $create_remote_batch_job = true ]]
2567	then
2568
2569	echo " "
2570	echo " *** transfer of job to remote host via scp"
2571	if [[ $do_trace = true ]]
2572	then
2573	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2574	fi
2575	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
2576
2577	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2578	if [[ $do_trace = true ]]
2579	then
2580	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"
2581	fi
2582	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
2583
2584	elif [[ $create_batch_job = true ]]
2585	then
2586
2587	eval local_jobcatalog=$local_jobcatalog
2588	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
2589	cd $local_jobcatalog
2590	echo " "
2591	echo " *** submit the job"
2592	if [[ $do_trace = true ]]
2593	then
2594	echo "$submit_command ${host_configuration}_${job_id}"
2595	fi
2596	$submit_command ${host_configuration}_${job_id}
2597	rm ${host_configuration}_${job_id}
2598	cd - > /dev/null
2599
2600	fi
2601
2602	rm -rf $jobfile
2603
2604	else
2605
2606	printf "\n *** jobfile created under name \"$jobfile\" "
2607	printf "\n no batch-job has been sent!"
2608
2609	fi
2610
2611	fi # END OF REMOTE-PART

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