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source: palm/trunk/SCRIPTS/palmrun @ 2566

Last change on this file since 2566 was 2566, checked in by raasch, 7 years ago
palmrun adjusted for grid engine batch systems, informative messages reduced and reformatted
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 86.8 KB

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

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