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source: palm/trunk/SCRIPTS/palmrun @ 2385

Last change on this file since 2385 was 2385, checked in by raasch, 7 years ago
job-catalog changes in palmrun
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 81.8 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	# initial revision
25	#
26	# Former revisions:
27	# -----------------
28	# $Id: palmrun 2385 2017-09-04 12:08:40Z raasch $
29	#
30	#
31	#--------------------------------------------------------------------------------#
32	# palmrun - script for running PALM jobs on local and remote hosts
33	#--------------------------------------------------------------------------------#
34
35
36
37	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
38
39	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
40	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
41	# (TOO MANY ARGUMENTS - PROBLEM)
42	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
43
44	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
45	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
46	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
47	# SCRIPT-OPTION ARGUMENTS
48	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
49	typeset -i icycle inode ival maxcycle mpi_tasks
50	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
51
52	activation_string_list=""
53	AddFilenames=""
54	combine_plot_fields=true
55	compiler_name=""
56	compiler_name_ser=""
57	compiler_options=""
58	config_file=""
59	cores=""
60	cores_atmos=0
61	cores_ocean=0
62	coupled_dist=""
63	cpp_options=""
64	cpumax=0
65	create_jobfile_only=false
66	delete_temporary_catalog=true
67	create_batch_job=false
68	create_remote_batch_job=false
69	dashes=" ----------------------------------------------------------------------------"
70	defaultqueue=""
71	do_compile=true
72	do_trace=false
73	executable=""
74	execute_command=""
75	execution_error=false
76	fileconnection_file=.palm.iofiles
77	fname=test
78	global_revision=""
79	host="default"
80	hostfile=""
81	hp=""
82	keep_data_from_previous_run=false
83	link_local_input=false
84	link_local_output=false
85	loader_options=""
86	local_jobcatalog=""
87	locat=normal
88	makefile=""
89	max_par_io_str=""
90	prc=$0
91	while [[ $(echo $prc \| grep -c "/") != 0 ]]
92	do
93	prc=`echo $prc \| cut -f2- -d"/"`
94	done
95	module_calls=""
96	palmrun_script_name=$prc
97	openmp=false
98	queue=none
99	restart_run=false
100	return_address=""
101	remote_jobcatalog=""
102	remote_username=""
103	running_in_batch_mode=false
104	run_coupled_model=false
105	run_id=""
106	silent=false
107	source_list=""
108	source_path=""
109	tasks_per_node=""
110	threads_per_task=1
111	tmpcreate=false
112	tmp_data_catalog=""
113	transfer_problems=false
114	user_source_path=""
115	use_openmp=false
116	version="palmrun 0.9 Rev$Rev: 2303 $"
117	working_directory=`pwd`
118	write_binary=""
119	TOPT=""
120
121
122	# ERROR HANDLING IN CASE OF EXIT
123	trap 'rm -rf $working_directory/tmp_mrun
124	if [[ $locat != normal && $locat != control_c ]]
125	then
126
127	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
128	(( i = 0 ))
129	while (( i < iec ))
130	do
131	(( i = i + 1 ))
132	printf "\n *** Execution of ERROR-command:\n"
133	printf " >>> ${err_command[$i]}\n"
134	eval ${err_command[$i]}
135	done
136	if [[ $tmpcreate = true ]]
137	then
138	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
139	fi
140	printf "\n\n+++ palmrun killed \n\n"
141	elif [[ $locat != control_c ]]
142	then
143	printf "\n\n --> palmrun finished\n\n"
144	if [[ $running_on_remote = true ]]
145	then
146	printf " Bye, bye $remote_username !!\n\n"
147	else
148	printf " Bye, bye $local_username !!\n\n"
149	fi
150	fi' exit
151
152
153	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
154	trap 'rm -rf $working_directory/tmp_mrun
155	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
156	printf "\n+++ palmrun killed by \"^C\" \n\n"
157	locat=control_c
158	exit
159	' 2
160
161
162	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
163	# BEEN SET
164	if [[ "$PALM_BIN" = "" ]]
165	then
166	printf "\n +++ environment variable PALM_BIN has not been set"
167	printf "\n please set it to the directory where the PALM scripts are located"
168	locat=palm_bin; exit
169	fi
170	export PATH=$PALM_BIN:$PATH
171
172
173
174	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
175	# WHICH WILL BE USED TO START RESTART-JOBS
176	while getopts :a:bBc:Cd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
177	do
178	case $option in
179	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
180	(b) create_batch_job=true; prc="$prc -b";;
181	(B) delete_temporary_catalog=false; prc="$prc -B";;
182	(c) config_file=$OPTARG; prc="$prc -c$OPTARG";;
183	(C) restart_run=true; prc="$prc -C";;
184	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
185	(F) create_jobfile_only=true;;
186	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
187	(h) host=$OPTARG; prc="$prc -h$OPTARG";;
188	(j) running_in_batch_mode=true;;
189	(k) keep_data_from_previous_run=true; prc="$prc -k";;
190	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
191	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
192	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
193	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
194	(r) run_id=$OPTARG;;
195	(R) return_address=$OPTARG;;
196	(s) source_list=$OPTARG;;
197	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
198	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
199	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
200	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
201	(v) silent=true; prc="$prc -v";;
202	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
203	(x) do_trace=true;set -x; prc="$prc -x";;
204	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
205	(y) ocean_file_appendix=true; prc="$prc -y";;
206	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
207	(Z) combine_plot_fields=false; prc="$prc -Z";;
208	(\?) printf "\n +++ unknown option $OPTARG \n"
209	printf "\n --> type \"$0 ?\" for available options \n"
210	locat=parameter;exit;;
211	esac
212	done
213
214
215	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
216	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
217	(( to_shift = $OPTIND - 1 ))
218	shift $to_shift
219
220	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
221	if [[ "$1" = "?" ]]
222	then
223	(printf "\n *** Description of available palmrun options:\n"
224	printf "\n Option Description Default-Value"
225	printf "\n -a activation string list \"\" "
226	printf "\n -b batch-job on local machine ---"
227	printf "\n -B do not delete temporary directory at end ---"
228	printf "\n -c configuration file .palm.config.default"
229	printf "\n -d base name of files attached to program test"
230	printf "\n -F create batch job file only ---"
231	printf "\n -h execution host \"default\" "
232	printf "\n -k keep data from previous run"
233	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
234	printf "\n -M Makefile name Makefile"
235	printf "\n -O threads per openMP task ---"
236	printf "\n -q queue \"$queue\" "
237	printf "\n -s filenames of routines to be compiled \"\" "
238	printf "\n must end with .f, .f90, .F, or .c !"
239	printf "\n use \"..\" for more than one file and wildcards"
240	printf "\n -s LM compiles all locally modified files"
241	printf "\n -t allowed cpu-time in seconds (batch) 0"
242	printf "\n -T tasks per node ---"
243	printf "\n -u username on remote machine \"\" "
244	printf "\n -v no prompt for confirmation ---"
245	printf "\n -w maximum parallel io streams as given by -X"
246	printf "\n -x tracing of palmrun for debug purposes ---"
247	printf "\n -X # of processors (on parallel machines) 1"
248	printf "\n -y add appendix \"_O\" to all local output"
249	printf "\n files (ocean precursor runs followed by"
250	printf "\n coupled atmosphere-ocean runs) ---"
251	printf "\n -Y run coupled model, \"#1 #2\" with"
252	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
253	printf "\n -Z skip combine_plot_fields at the end of "
254	printf "\n the simulation ---"
255	printf "\n "
256	printf "\n Possible values of positional parameter <modus>:"
257	printf "\n \"?\" - this outline \n\n") \| more
258	exit
259	elif [[ "$1" != "" ]]
260	then
261	printf "\n +++ positional parameter $1 unknown \n"
262	locat=parameter; exit
263	fi
264
265
266
267	# SHORT STARTING MESSAGE
268	printf "\n*** $version "
269	printf "\n will be executed. Please wait ..."
270
271
272	# BUILD THE CONFIGURATION-FILE NAME
273	if [[ "$config_file" = "" ]]
274	then
275	config_file=.palm.config.$host
276	fi
277
278
279	# CHECK, IF CONFIGURATION FILE EXISTS
280	if [[ ! -f $config_file ]]
281	then
282	printf "\n\n +++ configuration file: "
283	printf "\n $config_file"
284	printf "\n does not exist"
285	locat=connect; exit
286	fi
287
288
289	# CHECK, IF FILE CONNECTION FILE EXISTS
290	if [[ ! -f $fileconnection_file ]]
291	then
292	printf "\n\n +++ file connection file: "
293	printf "\n $fileconnection_file"
294	printf "\n does not exist"
295	locat=connect; exit
296	fi
297
298
299	# READ AND EVALUATE THE CONFIGURATION-FILE
300	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
301
302	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
303	while read line
304	do
305
306	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
307	eval line=\"$line\"
308
309
310	# INTERPRET THE LINE
311	if [[ "$(echo $line)" = "" ]]
312	then
313
314	# EMPTY LINE, NO ACTION
315	continue
316
317	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
318	then
319
320	# LINE IS A COMMENT LINE
321	continue
322
323	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
324	then
325
326	# LINE DEFINES AN ENVIRONMENT-VARIABLE
327	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
328	value=`echo $line \| cut -d" " -s -f2-`
329
330
331	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
332	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
333	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
334	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
335	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
336	# CONFIGURATION-FILE.
337	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
338	then
339	eval export $var="\$value"
340
341	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
342	if [[ $do_trace = true ]]
343	then
344	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
345	fi
346	fi
347
348	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
349	then
350
351	# LINE DEFINES BATCH-DIRECTIVE
352	(( ibd = ibd + 1 ))
353	line=$(echo $line \| cut -c4-)
354	batch_directive[$ibd]="$line"
355
356	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
357	then
358
359	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
360	# REMOTE TO A LOCAL HOST
361	(( ibdt = ibdt + 1 ))
362	line=$(echo $line \| cut -c5-)
363	batch_directive_transfer[$ibdt]="$line"
364
365	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
366	then
367
368	# LINE DEFINES ERROR-COMMAND
369	(( iec = iec + 1 ))
370	line=$(echo $line \| cut -c4-)
371	err_command[$iec]="$line"
372
373	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
374	then
375
376	# LINE DEFINES INPUT-COMMAND
377	(( iic = iic + 1 ))
378	line=$(echo $line \| cut -c4-)
379	in_command[$iic]="$line"
380
381	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
382	then
383
384	# LINE DEFINES OUTPUT-COMMAND
385	(( ioc = ioc + 1 ))
386	line=$(echo $line \| cut -c4-)
387	out_command[$ioc]="$line"
388
389	else
390
391	# SKIP ALL OTHER LINES
392	continue
393
394	fi
395
396	done < $config_file
397
398
399	# CHECK SETTING OF REQUIRED PARAMETERS
400	if [[ "$compiler_name" = "" ]]
401	then
402	printf "\n +++ no compiler name found in $config_file"
403	printf "\n Please add line \"compiler_name ...\" to that file."
404	locat=config_file; exit
405	fi
406	if [[ "$compiler_name_ser" = "" ]]
407	then
408	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
409	printf "\n Please add line \"compiler_name_ser ...\" to that file."
410	locat=config_file; exit
411	fi
412	if [[ "$compiler_options" = "" ]]
413	then
414	printf "\n +++ no compiler options found in $config_file"
415	printf "\n Please add line \"compiler_options ...\" to that file."
416	locat=config_file; exit
417	fi
418	if [[ "$loader_options" = "" ]]
419	then
420	printf "\n +++ no loader options found in $config_file"
421	printf "\n Please add line \"loader_options ...\" to that file."
422	locat=config_file; exit
423	fi
424	if [[ "$execute_command" = "" ]]
425	then
426	printf "\n +++ no execute command found in $config_file"
427	printf "\n Please add line \"execute_command ...\" to that file."
428	locat=config_file; exit
429	fi
430
431	if [[ "$hostfile" != "" ]]
432	then
433	if [[ $hostfile != auto && ! -f $hostfile ]]
434	then
435	printf "\n +++ no hostfile \"$hostfile\" found"
436	printf "\n Please check line \"hostfile ...\" in $config_file"
437	locat=config_file; exit
438	fi
439	fi
440
441	if [[ "$write_binary" = "" ]]
442	then
443	write_binary=false
444	fi
445
446	# DETERMINE THE CALL STATUS
447	if [[ "$return_address" != "" ]]
448	then
449
450	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
451	# BATCH MODE AND ...
452	running_on_remote=true
453	host_name=$remote_hostname
454
455	else
456
457	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
458	if [[ "$remote_ip" != "" ]]
459	then
460
461	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
462	create_remote_batch_job=true
463
464	fi
465	host_name=$local_hostname
466	running_on_remote=false
467	fi
468
469
470
471	# READ AND EVALUATE THE I/O-FILE LIST
472	[[ $silent = false ]] && printf "\n Reading the I/O files... "
473
474	# READ THE FILE CONNECTION FILE LINE BY LINE
475	while read line
476	do
477
478	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
479	eval line=\"$line\"
480
481
482	# INTERPRET THE LINE
483	if [[ "$(echo $line)" = "" ]]
484	then
485	# EMPTY LINE, NO ACTION
486	continue
487
488	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
489	then
490
491	# LINE IS A COMMENT LINE
492	true
493
494	else
495
496	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
497	# s2a: in/out - field
498	# s2b: loc - field (optional)
499	# s2c: tr/ar - field (optional)
500	s1=`echo $line \| cut -d" " -f1`
501	s2=`echo $line \| cut -d" " -s -f2`
502	s2a=$(echo $s2 \| cut -d":" -f1)
503	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
504	then
505	s2b=""
506	s2c=""
507	else
508	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
509	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
510	fi
511	s3=`echo $line \| cut -d" " -f3`
512	s4=`echo $line \| cut -d" " -s -f4`
513	s5=`echo $line \| cut -d" " -s -f5`
514	s6=`echo $line \| cut -d" " -s -f6`
515
516
517	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
518	# INPUT- OR OUTPUT-LIST.
519	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
520	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
521	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
522	# IS NOT CHECKED AND STORED.
523	IFSALT="$IFS"; IFS="$IFS:"
524	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
525	then
526	found=false
527	for actual in $activation_string_list
528	do
529	for formal in $s3
530	do
531	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
532	done
533	done
534	if [[ $found = true ]]
535	then
536	(( iin = iin + 1 ))
537	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
538	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
539	extin[$iin]=$s6
540	fi
541	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
542	then
543	found=false
544	for actual in $activation_string_list
545	do
546	for formal in $s3
547	do
548	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
549	done
550	done
551	if [[ $found = true ]]
552	then
553	(( iout = iout + 1 ))
554	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
555	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
556	fi
557	elif [[ "$s2a" != in && "$s2a" != out ]]
558	then
559	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
560	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
561	locat=connect; exit
562	fi
563	IFS="$IFSALT"
564	fi
565
566	done < $fileconnection_file
567
568
569
570	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
571	if [[ $run_coupled_model = true ]]
572	then
573
574	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
575	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
576
577	if (( $cores_ocean + $cores_atmos != $cores ))
578	then
579
580	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
581	printf "\n PEs (total) : $cores"
582	printf "\n PEs (atmosphere): $cores_atmos"
583	printf "\n PEs (ocean) : $cores_ocean"
584	locat=coupling; exit
585
586	fi
587
588	fi
589
590
591	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
592	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
593	palmrun_memory=$memory
594	palmrun_cpumax=$cpumax
595	palmrun_cores=$cores
596
597
598	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
599	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
600	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
601	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
602	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
603	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
604
605
606
607	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
608	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
609	# FOLDER
610	if [[ $running_in_batch_mode = true ]]
611	then
612
613	if [[ ! -d ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname ]]
614	then
615	printf "\n +++ directory ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname is missing"
616	printf "\n Please check the output of the palmrun-call"
617	printf "\n that you did on your local host."
618	locat=SOURCES_FOR_RUN; exit
619	fi
620
621	else
622
623	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
624	# AUTOMATIC RESTART RUN
625	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
626	if [[ $restart_run = false ]]
627	then
628
629	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
630	# THE LOCAL HOST
631	if [[ ! -d $source_path ]]
632	then
633	printf "\n\n +++ source path \"$source_path\" on local host"
634	printf "\n \"$(hostname)\" does not exist"
635	locat=source_path; exit
636	fi
637
638	rm -rf SOURCES_FOR_RUN_$fname
639	mkdir SOURCES_FOR_RUN_$fname
640
641	if [[ "$source_list" = LM ]]
642	then
643
644	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
645	source_list=""
646	cd $source_path
647
648
649	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
650	if [[ ! -d .svn ]]
651	then
652	printf "\n\n +++ source directory"
653	printf "\n \"$source_path\" "
654	printf "\n is not under control of \"subversion\"."
655	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
656	fi
657
658
659	# LIST ALL MODIFIED SOURCE CODE FILES
660	Filenames=""
661	svn status > tmp_mrun
662	while read line
663	do
664	firstc=`echo $line \| cut -c1`
665	if [[ $firstc = M \|\| $firstc = "?" ]]
666	then
667	Name=`echo "$line" \| cut -c8-`
668	extension=`echo $Name \| cut -d. -f2`
669	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
670	then
671	Filenames="$Filenames "$Name
672	fi
673	fi
674	done < tmp_mrun
675
676
677	# COPY FILES TO SOURCES_FOR_RUN_...
678	for filename in $Filenames
679	do
680	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
681	source_list=$source_list"$filename "
682	done
683
684	cd - > /dev/null
685
686
687	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
688	elif [[ "$source_list" != "" ]]
689	then
690
691	cd $source_path
692
693	for filename in $source_list
694	do
695
696	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
697	if [[ $(echo $filename \| grep -c "/") != 0 ]]
698	then
699	printf "\n +++ source code file: $filename"
700	printf "\n must not contain (\"/\") "
701	locat=source; exit
702	fi
703
704	if [[ ! -f $filename ]]
705	then
706	printf "\n +++ source code file: $filename"
707	printf "\n does not exist"
708	locat=source; exit
709	else
710	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
711	fi
712
713	done
714
715	cd - > /dev/null
716
717	fi
718
719	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
720	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
721	if [[ ! -f $makefile ]]
722	then
723	printf "\n +++ file \"$makefile\" does not exist"
724	locat=make; exit
725	else
726	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
727	fi
728
729
730	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
731	if [[ "$user_source_path" != "" ]]
732	then
733
734	# DOES THE DIRECTORY EXIST?
735	if [[ ! -d $user_source_path ]]
736	then
737
738	printf "\n\n *** INFORMATIVE: additional source code directory"
739	printf "\n \"$user_source_path\" "
740	printf "\n does not exist or is not a directory."
741	printf "\n No source code will be used from this directory!\n"
742	user_source_path=""
743	if [[ $silent == false ]]
744	then
745	sleep 2
746	fi
747
748	else
749
750	cd $user_source_path
751	found=false
752
753	Names=$(ls -1 *.f90 2>&1)
754	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
755	Names=$(ls -1 *.F90 2>&1)
756	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
757	Names=$(ls -1 *.F 2>&1)
758	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
759	Names=$(ls -1 *.f 2>&1)
760	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
761	Names=$(ls -1 *.c 2>&1)
762	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
763
764	cd - > /dev/null
765	cd SOURCES_FOR_RUN_$fname
766
767	# COPY MAKEFILE IF EXISTING
768	if [[ -f $user_source_path/Makefile ]]
769	then
770	printf "\n\n *** user Makefile from directory"
771	printf "\n \"$user_source_path\" is used \n"
772	if [[ $silent == false ]]
773	then
774	sleep 1
775	fi
776	cp $user_source_path/Makefile .
777	fi
778
779	for filename in $AddFilenames
780	do
781	if [[ -f $filename ]]
782	then
783	printf "\n +++ source code file \"$filename\" found in additional"
784	printf "\n source code directory \"$user_source_path\" "
785	printf "\n but was also given with option \"-s\" which means that it should be taken"
786	printf "\n from directory \"$source_path\"."
787	locat=source; exit
788	fi
789
790	cp $user_source_path/$filename .
791	source_list="$source_list $filename"
792
793	# CHECK IF FILE IS CONTAINED IN MAKEFILE
794	if [[ $(grep -c $filename Makefile) = 0 ]]
795	then
796	printf "\n\n +++ user file \"$filename\" "
797	printf "\n is not listed in Makefile \n"
798	locat=source; exit
799	else
800
801	if [[ $found = false ]]
802	then
803	found=true
804	printf "\n\n *** following user file(s) added to the"
805	printf " files to be translated:\n "
806	fi
807	printf "$filename "
808	if [[ $silent == false ]]
809	then
810	sleep 0.5
811	fi
812
813	fi
814	done
815	[[ $found = true ]] && printf "\n"
816	cd - > /dev/null
817	fi
818	fi
819
820	# COPY CONFIGURATION FILES
821	cp $config_file SOURCES_FOR_RUN_$fname
822	cp $fileconnection_file SOURCES_FOR_RUN_$fname
823
824	# COPY SHELLSCRIPTS
825	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
826	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
827
828	fi
829
830	fi
831
832	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
833	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
834	if [[ "$global_revision" = "" ]]
835	then
836	global_revision=`svnversion $source_path 2>/dev/null`
837	global_revision="Rev: $global_revision"
838	fi
839
840
841	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
842	if [[ -n $cores ]]
843	then
844
845	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
846	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
847	if [[ "$tasks_per_node" = "" ]]
848	then
849	printf "\n"
850	printf "\n +++ option \"-T\" (tasks per node) is missing"
851	printf "\n set -T option or define tasks_per_node in the config file"
852	locat=tasks_per_node; (( iec = 0 )); exit
853	fi
854
855	if (( cores < tasks_per_node ))
856	then
857	printf "\n"
858	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
859	printf "\n given values: -T $tasks_per_node -X $cores"
860	locat=tasks_per_node; (( iec = 0 )); exit
861	fi
862
863	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
864	(( mpi_tasks = cores / threads_per_task ))
865	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
866	(( ii = cores / tasks_per_node ))
867	(( remaining_cores = cores - ii * tasks_per_node ))
868	if (( remaining_cores > 0 ))
869	then
870	printf "\n"
871	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
872	printf "\n divisor of the total number of cores (option \"-X\")"
873	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
874	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
875	(( nodes = nodes + 1 ))
876	fi
877
878	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
879	if [[ "$tasks_per_node" != "" ]]
880	then
881	TOPT="-T $tasks_per_node"
882	fi
883
884	fi
885
886
887	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
888	if [[ "$maximum_parallel_io_streams" = "" ]]
889	then
890	maximum_parallel_io_streams=$cores
891	fi
892
893
894	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
895	if [[ "$scp_port" != "" ]]
896	then
897	PORTOPT="-P $scp_port"
898	SSH_PORTOPT="-p $scp_port"
899	fi
900
901
902	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
903	# CONFIG-FILE
904	if [[ "$ssh_key" != "" ]]
905	then
906	ssh_key="-i $HOME/.ssh/$ssh_key"
907	fi
908
909
910	# SET QUEUE, IF NOT GIVEN
911	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
912	then
913
914	if [[ $queue = none && "$defaultqueue" = "" ]]
915	then
916	printf "\n"
917	printf "\n +++ no default queue given in configuration file and no queue"
918	printf "\n given with option -q"
919	fi
920	if [[ $queue = none ]]
921	then
922	queue=$defaultqueue
923	fi
924
925	fi
926
927
928	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
929	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
930	(( i = 0 ))
931	while (( i < iin ))
932	do
933	(( i = i + 1 ))
934	(( maxcycle = 0 ))
935
936	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
937	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
938	if [[ "${actionin[$i]}" = di ]]
939	then
940	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
941	# HOST ONLY
942	eval filename=${pathin[$i]}/${endin[$i]}
943	else
944	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
945	# HOST ONLY
946	eval filename=${pathin[$i]}/${fname}${endin[$i]}
947	fi
948	eval pathname=${pathin[$i]}
949
950	# CHECK IF FILE EXISTS
951	if ! ls $filename* 1>/dev/null 2>&1
952	then
953
954	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
955	if [[ "${transin[$i]}" != "locopt" ]]
956	then
957	printf "\n\n +++ INPUT-file: "
958	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
959	then
960	printf "\n $filename"
961	else
962	printf "\n $filename.${extin[$i]}"
963	fi
964	printf "\n does not exist\n"
965	locat=input; exit
966	else
967	transin[$i]="unavailable"
968	fi
969	else
970
971	# DETERMINE THE FILE'S CYCLE NUMBER
972	ls -1 -d $filename > filelist 2>/dev/null
973	ls -1 -d $filename.* >> filelist 2>/dev/null
974	while read line
975	do
976	# filename without path (i.e. after the last "/")
977	basefilename=$(basename ${line})
978
979	# check if there is an extension
980	extension=${basefilename##*.}
981	if [[ "$extension" = "$extin[$i]" ]]
982	then
983	basefilename=${basefilename&.*}
984	fi
985
986	# check for an existing cycle number
987	cycle=${basefilename##*.}
988	if [[ $cycle =~ ^-?[0-9]+$ ]]
989	then
990	(( icycle = $cycle ))
991	else
992	(( icycle = 0 ))
993	fi
994
995	if (( icycle > maxcycle ))
996	then
997	(( maxcycle = icycle ))
998	fi
999
1000	done <filelist
1001	rm filelist
1002
1003	# APPEND CYCLE NUMBER TO FILENAME
1004	if (( maxcycle > 0 ))
1005	then
1006	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1007	then
1008	filename=${filename}.$maxcycle.${extin[$i]}
1009	else
1010	filename=${filename}.$maxcycle
1011	fi
1012	else
1013	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1014	then
1015	filename=${filename}.${extin[$i]}
1016	fi
1017	fi
1018
1019	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1020	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1021	absnamein[$i]=$filename
1022	if (( maxcycle > 0 ))
1023	then
1024	if [[ "${actionin[$i]}" = di ]]
1025	then
1026	frelin[$i]=${endin[$i]}.$maxcycle
1027	else
1028	frelin[$i]=${fname}${endin[$i]}.$maxcycle
1029	fi
1030	else
1031	if [[ "${actionin[$i]}" = di ]]
1032	then
1033	frelin[$i]=${endin[$i]}
1034	else
1035	frelin[$i]=${fname}${endin[$i]}
1036	fi
1037	fi
1038
1039	fi
1040	done
1041
1042
1043	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1044	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1045	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1046	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1047	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1048	# REMOTE HOST)
1049	(( i = 0 ))
1050	while (( i < iout ))
1051	do
1052	(( i = i + 1 ))
1053	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1054	then
1055	if [[ "${actionout[$i]}" = tr ]]
1056	then
1057	actionout[$i]=""
1058	elif [[ "${actionout[$i]}" = trpe ]]
1059	then
1060	actionout[$i]=pe
1061	elif [[ "${actionout[$i]}" = tra ]]
1062	then
1063	actionout[$i]=a
1064	fi
1065	(( maxcycle = 0 ))
1066	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1067	eval catalogname=${pathout[$i]}
1068	if ! ls $filename* 1>/dev/null 2>&1
1069	then
1070
1071	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1072	if cat /dev/null > $filename
1073	then
1074	rm $filename
1075	else
1076
1077	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1078	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1079	if [[ ! -d $catalogname ]]
1080	then
1081	if mkdir -p $catalogname
1082	then
1083	printf "\n\n *** directory:"
1084	printf "\n $catalogname"
1085	printf "\n was created\n"
1086	else
1087	printf "\n\n +++ OUTPUT-file:"
1088	printf "\n $filename"
1089	printf "\n cannot be created, because directory does not exist"
1090	printf "\n and cannot be created either"
1091	printf "\n"
1092	locat=output ; exit
1093	fi 2>/dev/null
1094	else
1095	printf "\n\n +++ OUTPUT-file:"
1096	printf "\n $filename"
1097	printf "\n cannot be created, although directory exists"
1098	printf "\n"
1099	locat=output ; exit
1100	fi
1101	fi 2>/dev/null
1102	else
1103
1104	# DETERMINE THE CYCLE NUMBER
1105	ls -1 -d $filename > filelist 2>/dev/null
1106	ls -1 -d $filename.* >> filelist 2>/dev/null
1107	while read line
1108	do
1109
1110	# filename without path (i.e. after the last "/")
1111	basefilename=$(basename ${line})
1112
1113	# check if there is an extension
1114	extension=${basefilename##*.}
1115	if [[ "$extension" = "${extout[$i]}" ]]
1116	then
1117	basefilename=${basefilename%.*}
1118	fi
1119
1120	# check for an existing cycle number
1121	cycle=${basefilename##*.}
1122	if [[ $cycle =~ ^-?[0-9]+$ ]]
1123	then
1124	(( icycle = $cycle + 1 ))
1125	else
1126	(( icycle = 1 ))
1127	fi
1128
1129	if (( icycle > maxcycle ))
1130	then
1131	(( maxcycle = icycle ))
1132	fi
1133
1134	done <filelist
1135	rm filelist
1136	fi
1137
1138	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1139	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1140	if [[ "${actionout[$i]}" != a ]]
1141	then
1142	if (( maxcycle > 0 ))
1143	then
1144	filename_tmp=${filename}.$maxcycle
1145	if cat /dev/null > $filename_tmp
1146	then
1147	rm $filename_tmp
1148	else
1149	printf "\n +++ OUTPUT-file:"
1150	printf "\n $filename_tmp"
1151	printf "\n cannot be created"
1152	locat=output ; exit
1153	fi
1154	fi
1155	else
1156	(( maxcycle = maxcycle - 1 ))
1157	fi
1158
1159	(( cycnum[$i] = maxcycle ))
1160	pathout[$i]=$filename
1161
1162	fi
1163	done
1164
1165
1166	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1167	if [[ $running_in_batch_mode = false ]]
1168	then
1169	run_id=$RANDOM
1170	job_id=${fname}.$run_id
1171
1172	TEMPDIR=$tmp_user_catalog/$job_id
1173	fi
1174
1175
1176	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1177	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1178	then
1179
1180	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1181	if [[ $ibd = 0 ]]
1182	then
1183	printf "\n"
1184	printf "\n +++ no batch directives found in configuration file"
1185	locat=config_file_batch_directives; (( iec = 0 )); exit
1186	fi
1187
1188	# CHECK IF CPUTIME IS GIVEN FOR JOB
1189	done=false
1190	cputime=$cpumax
1191	while [[ $done = false ]]
1192	do
1193	if (( cputime == 0 ))
1194	then
1195	printf "\n +++ cpu-time is undefined"
1196	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1197	printf "\n >>> "
1198	read cputime 1>/dev/null 2>&1
1199	else
1200	done=true
1201	fi
1202	done
1203
1204	# CHECK THE MEMORY DEMAND
1205	done=false
1206	while [[ $done = false ]]
1207	do
1208	if (( memory == 0 ))
1209	then
1210	printf "\n +++ memory demand is undefined"
1211	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1212	printf "\n >>> "
1213	read memory 1>/dev/null 2>&1
1214	else
1215	done=true
1216	fi
1217	done
1218
1219	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1220	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1221	then
1222	while [[ -z $remote_username ]]
1223	do
1224	printf "\n +++ username on remote host \"$remote_ip\" is undefined"
1225	printf "\n >>> Please type username:"
1226	printf "\n >>> "
1227	read remote_username
1228	done
1229	fi
1230
1231	else
1232
1233	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1234
1235	fi
1236	cpumax=$cputime
1237
1238
1239	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1240	(( cpu_hours = cputime / 3600 ))
1241	(( resttime = cputime - cpu_hours * 3600 ))
1242	(( cpu_minutes = resttime / 60 ))
1243	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1244	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1245
1246
1247	# OUTPUT OF THE PALMRUN-HEADER
1248	calltime=$(date)
1249	printf "\n"
1250	printf "#------------------------------------------------------------------------# \n"
1251	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1252	printf "\| \| \n"
1253	column1="called on:"; column2=$(hostname)
1254	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1255	if [[ $create_remote_batch_job = true ]]
1256	then
1257	column1="execution on:"; column2="$remote_hostname (username: $remote_username)"
1258	else
1259	if [[ $running_on_remote = true ]]
1260	then
1261	column1="execution on:"; column2="$remote_hostname"
1262	else
1263	column1="execution on:"; column2="$local_hostname"
1264	fi
1265	fi
1266	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1267
1268	column1="running in:"
1269	if [[ $running_in_batch_mode = true ]]
1270	then
1271	column2="batch job mode"
1272	else
1273	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1274	then
1275	column2="job creation mode"
1276	else
1277	column2="interactive run mode"
1278	fi
1279	fi
1280	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1281
1282	if [[ -n $cores ]]
1283	then
1284	if [[ $run_coupled_model = false ]]
1285	then
1286	column1="number of cores:"; column2=$cores
1287	else
1288	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1289	fi
1290	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1291	fi
1292	if [[ -n $tasks_per_node ]]
1293	then
1294	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1295	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1296	if (( remaining_cores > 0 ))
1297	then
1298	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1299	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1300	fi
1301	fi
1302	if [[ $maximum_parallel_io_streams != $cores ]]
1303	then
1304	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1305	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1306	fi
1307	if [[ $use_openmp = true ]]
1308	then
1309	column1="threads per task:"; column2="$threads_per_task"
1310	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1311	fi
1312	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1313	then
1314	column1="job cpu time (h:m:s):"; column2="$timestring"
1315	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1316	fi
1317	printf "\| \| \n"
1318	if [[ "$source_list" != "" ]]
1319	then
1320	if [[ "$make_options" != "" ]]
1321	then
1322	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1323	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1324	line=$(echo "$make_options" \| cut -c46-)
1325	while [[ "$line" != "" ]]
1326	do
1327	column1=""
1328	column2=$(echo "$line" \| cut -c-45)
1329	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1330	line=$(echo "$line" \| cut -c46-)
1331	done
1332	fi
1333	fi
1334
1335	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1336	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1337	line=$(echo "$cpp_options" \| cut -c46-)
1338	while [[ "$line" != "" ]]
1339	do
1340	column1=""
1341	column2=$(echo "$line" \| cut -c-45)
1342	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1343	line=$(echo "$line" \| cut -c46-)
1344	done
1345
1346	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1347	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1348	line=$(echo "$compiler_options" \| cut -c46-)
1349	while [[ "$line" != "" ]]
1350	do
1351	column1=""
1352	column2=$(echo "$line" \| cut -c-45)
1353	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1354	line=$(echo "$line" \| cut -c46-)
1355	done
1356
1357	column1="loader options:"; column2=$(echo "$loader_options" \| cut -c-45)
1358	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1359	line=$(echo "$loader_options" \| cut -c46-)
1360	while [[ "$line" != "" ]]
1361	do
1362	column1=""
1363	column2=$(echo "$line" \| cut -c-45)
1364	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1365	line=$(echo "$line" \| cut -c46-)
1366	done
1367
1368	if [[ "$login_init_cmd" != "" ]]
1369	then
1370	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1371	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1372	line=$(echo "$login_init_cmd" \| cut -c46-)
1373	while [[ "$line" != "" ]]
1374	do
1375	column1=""
1376	column2=$(echo "$line" \| cut -c-45)
1377	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1378	line=$(echo "$line" \| cut -c46-)
1379	done
1380	fi
1381
1382	if [[ "$module_commands" != "" ]]
1383	then
1384	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1385	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1386	line=$(echo "$module_commands" \| cut -c46-)
1387	while [[ "$line" != "" ]]
1388	do
1389	column1=""
1390	column2=$(echo "$line" \| cut -c-45)
1391	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1392	line=$(echo "$line" \| cut -c46-)
1393	done
1394	fi
1395	printf "\| \| \n"
1396	column1="base name of files:"; column2=$fname
1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1398	column1="activation string list:"; column2=$(echo $activation_string_list)
1399	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1400
1401	if [[ "$ocean_file_appendix" = true ]]
1402	then
1403	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1404	fi
1405
1406	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
1407	then
1408	column1="memory demand / PE":; column2="$memory MB"
1409	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1410	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1412	fi
1413
1414	if [[ "$source_list" != "" ]]
1415	then
1416	printf "\| \| \n"
1417	printf "\| Files to be compiled: \| \n"
1418	line=$source_list
1419	while [[ "$line" != "" ]]
1420	do
1421	linestart=$(echo $line \| cut -c-70)
1422	printf "\| %-70s \| \n" "$linestart"
1423	line=$(echo "$line" \| cut -c71-)
1424	done
1425	fi
1426	printf "#------------------------------------------------------------------------#"
1427
1428
1429
1430	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1431	if [[ $do_trace = true ]]
1432	then
1433	(( i = 0 ))
1434	while (( i < iin ))
1435	do
1436	(( i = i + 1 ))
1437	if (( i == 1 ))
1438	then
1439	printf "\n\n >>> INPUT-file assignments:\n"
1440	fi
1441	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1442	done
1443	(( i = 0 ))
1444	while (( i < iout ))
1445	do
1446	(( i = i + 1 ))
1447	if (( i == 1 ))
1448	then
1449	printf "\n\n >>> OUTPUT-file assignments:\n"
1450	fi
1451	printf "\n ${localout[$i]} : ${pathout[$i]}"
1452	done
1453	(( i = 0 ))
1454	while (( i < iic ))
1455	do
1456	(( i = i + 1 ))
1457	if (( i == 1 ))
1458	then
1459	printf "\n\n >>> INPUT-commands:\n"
1460	fi
1461	printf "\n ${in_command[$i]}"
1462	done
1463	(( i = 0 ))
1464	while (( i < ioc ))
1465	do
1466	(( i = i + 1 ))
1467	if (( i == 1 ))
1468	then
1469	printf "\n\n >>> OUTPUT-commands:\n"
1470	fi
1471	printf "\n ${out_command[$i]}"
1472	done
1473	fi
1474
1475	# QUERY FOR CONTINUE
1476	if [[ $silent = false && $running_in_batch_mode = false ]]
1477	then
1478	antwort=dummy
1479	printf "\n\n"
1480	printf " >>> everything o.k. (y/n) ? "
1481	while read antwort
1482	do
1483	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1484	then
1485	printf " >>> everything o.k. (y/n) ? "
1486	else
1487	break
1488	fi
1489	done
1490	if [[ $antwort = n \|\| $antwort = N ]]
1491	then
1492	locat=user_abort; (( iec = 0 )); exit
1493	fi
1494	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1495	then
1496	printf " *** batch-job will be created and submitted"
1497	else
1498	printf " *** PALMRUN will now continue to execute on this machine"
1499	fi
1500	fi
1501
1502
1503
1504	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1505	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1506	then
1507
1508	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1509	then
1510	printf "\n\n *** creating executable and other sources for the remote host"
1511	else
1512	printf "\n\n *** creating executable and other sources for the local host"
1513	fi
1514
1515	palmbuild -v -h $host -d $fname
1516	rm -rf SOURCES_FOR_RUN_$fname
1517
1518	if [[ $? != 0 ]]
1519	then
1520
1521	# ABORT IN CASE OF COMPILATION PROBLEMS
1522	printf "\n +++ error while creating executable and/or other sources"
1523	locat=execution
1524	exit
1525
1526	else
1527
1528	printf "\n$dashes\n *** executable and other sources created\n"
1529
1530	fi
1531
1532	fi
1533
1534
1535	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1536	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1537	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1538	then
1539
1540	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1541	if [[ $running_in_batch_mode = false ]]
1542	then
1543	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1544	# FOLDER
1545	mkdir -p $TEMPDIR
1546	chmod go+rx $TEMPDIR
1547	tmpcreate=true
1548	cd $TEMPDIR
1549	cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
1550	printf "\n *** changed to temporary directory: $TEMPDIR"
1551
1552	else
1553
1554	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1555	printf "\n *** running in temporary directory: $TEMPDIR"
1556
1557	fi
1558
1559
1560	# PROVIDE THE INPUT FILES
1561	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1562	(( i = 0 ))
1563	while (( i < iin ))
1564	do
1565	(( i = i + 1 ))
1566	if (( i == 1 ))
1567	then
1568	printf "\n\n *** providing INPUT-files:\n$dashes"
1569	fi
1570
1571
1572	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1573	if [[ "${transin[$i]}" = unavailable ]]
1574	then
1575	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1576	then
1577	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1578	printf "\n is not available!"
1579	else
1580	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1581	printf "\n is not available!"
1582	fi
1583	continue
1584	fi
1585
1586	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1587	files_for_cores=false; filetype=file
1588	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1589	then
1590	files_for_cores=true; filetype=files
1591	actionin[$i]=""
1592	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1593	then
1594	actionin[$i]=""
1595	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1596	then
1597	files_for_cores=true; filetype=files
1598	actionin[$i]="ln"
1599	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1600	then
1601	actionin[$i]="ln"
1602	fi
1603
1604	if [[ $files_for_cores = true ]]
1605	then
1606	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1607	else
1608	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1609	fi
1610
1611	# INPUT-FILES TO BE LINKED
1612	if [[ "${actionin[$i]}" = ln ]]
1613	then
1614
1615	printf "\n $filetype will be linked"
1616	if [[ $files_for_cores = false ]]
1617	then
1618	if [[ -f "${absnamein[$i]}" ]]
1619	then
1620	ln ${absnamein[$i]} ${localin[$i]}
1621	got_tmp[$i]=true
1622	fi
1623	else
1624	if [[ -d "${absnamein[$i]}" ]]
1625	then
1626	mkdir ${localin[$i]}
1627	cd ${absnamein[$i]}
1628	for file in $(ls *)
1629	do
1630	ln $file $TEMPDIR/${localin[$i]}
1631	done >\|/dev/null 2>&1
1632	cd $TEMPDIR
1633	fi
1634
1635	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1636	if [[ ! -f "${localin[$i]}/_000000" ]]
1637	then
1638	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1639	cp -r ${absnamein[$i]}/* ${localin[$i]}
1640	fi
1641
1642	got_tmp[$i]=true
1643	fi
1644	fi
1645
1646	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1647	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1648	then
1649
1650	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1651	then
1652
1653	# FILE COPIES ARE PROVIDED FOR ALL CORES
1654	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1655	printf "\n file will be provided for $cores processors"
1656	mkdir ${localin[$i]}
1657	ival=$cores
1658	(( ii = 0 ))
1659	while (( ii <= ival-1 ))
1660	do
1661	if (( ii < 10 ))
1662	then
1663	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1664	elif (( ii < 100 ))
1665	then
1666	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1667	elif (( ii < 1000 ))
1668	then
1669	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1670	else
1671	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1672	fi
1673	(( ii = ii + 1 ))
1674	done
1675
1676	else
1677
1678	if [[ $files_for_cores = true ]]
1679	then
1680
1681	# PROVIDE FILES FOR EACH CORE
1682	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1683	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1684	printf "\n providing $cores files for the respective cores"
1685	mkdir ${localin[$i]}
1686	if [[ $link_local_input = true ]]
1687	then
1688	printf " files will be linked\n"
1689	cd ${absnamein[$i]}
1690	for file in $(ls *)
1691	do
1692	ln -f $file ${localin[$i]}
1693	done
1694	cd $TEMPDIR
1695	fi
1696
1697	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1698	if [[ ! -f "${localin[$i]}/_000000" ]]
1699	then
1700	if [[ $link_local_input = true ]]
1701	then
1702	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1703	fi
1704	cp -r ${absnamein[$i]}/* ${localin[$i]}
1705	fi
1706
1707	else
1708
1709	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1710	if [[ $link_local_input = true ]]
1711	then
1712	printf " file will be linked\n"
1713	ln -f ${absnamein[$i]} ${localin[$i]}
1714	fi
1715	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
1716	if [[ ! -f "${localin[$i]}" ]]
1717	then
1718	if [[ $link_local_input = true ]]
1719	then
1720	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1721	fi
1722	cp ${absnamein[$i]} ${localin[$i]}
1723	fi
1724	fi
1725	fi
1726	fi
1727
1728	done
1729	if (( i != 0 ))
1730	then
1731	printf "\n$dashes\n *** all INPUT-files provided \n"
1732	fi
1733
1734
1735	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1736	(( i = 0 ))
1737	while (( i < iic ))
1738	do
1739	(( i = i + 1 ))
1740	if (( i == 1 ))
1741	then
1742	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1743	fi
1744	printf "\n >>> ${in_command[$i]}"
1745	eval ${in_command[$i]}
1746	if (( i == iic ))
1747	then
1748	printf "\n$dashes\n"
1749	fi
1750	done
1751
1752
1753	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1754	# (FILE ENVPAR WILL BE READ BY PALM)
1755	cat > ENVPAR << EOF
1756	&envpar run_identifier = '$fname', host = '$host',
1757	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1758	maximum_parallel_io_streams = $maximum_parallel_io_streams,
1759	maximum_cpu_time_allowed = ${cpumax}.,
1760	revision = '$global_revision',
1761	batch_job = .${running_in_batch_mode}. /
1762
1763	EOF
1764
1765
1766	# STARTING THE EXECUTABLE
1767	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
1768	PATH=$PATH:$TEMPDIR
1769
1770
1771	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1772	line=`echo "${execute_command}" \| sed 's/@MPI_TASKS@/$mpi_tasks/g' \| sed 's/@TASKS_PER_NODE@/$tasks_per_node/g'`
1773	line2=`echo "${execute_command}" \| sed 's/@MPI_TASKS@/1/g' \| sed 's/@TASKS_PER_NODE@/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
1774	eval line=\"$line\"
1775	execute_command="$line"
1776
1777
1778	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1779	eval line2=\"$line2\"
1780	execute_command_for_combine="$line2"
1781
1782
1783	# PROVIDE A HOSTFILE, IF REQUIRED
1784	if [[ "$hostfile" != "" ]]
1785	then
1786
1787	if [[ $hostfile = auto ]]
1788	then
1789	# CREATE A NEW HOSTFILE
1790	(( ii = 1 ))
1791	while (( ii <= cores / threads_per_task ))
1792	do
1793	echo $(hostname) >> hostfile
1794	(( ii = ii + 1 ))
1795	done
1796	if (( cores / threads_per_task == 0 ))
1797	then
1798	echo $(hostname) >> hostfile
1799	fi
1800
1801	else
1802	cp $hostfile hostfile
1803	fi
1804	eval line=\"`head -n $ii hostfile`\"
1805	printf "\n *** running on: $line"
1806	fi
1807
1808
1809
1810	# SET THE NUMBER OF OPENMP-THREADS
1811	if [[ $use_openmp = true ]]
1812	then
1813	export OMP_NUM_THREADS=$threads_per_task
1814	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1815	else
1816	export OMP_NUM_THREADS=1
1817	fi
1818
1819
1820	# PROVIDE DATA FOR
1821	if [[ $run_coupled_model = false ]]
1822	then
1823	if [[ "$ocean_file_appendix" = true ]]
1824	then
1825	echo "precursor_ocean" > coupling_steering
1826	else
1827	echo "precursor_atmos" > coupling_steering
1828	fi
1829	else
1830	(( iia = $cores_atmos / $threads_per_task ))
1831	(( iio = $cores_ocean / $threads_per_task ))
1832	printf "\n coupled run ($iia atmosphere, $iio ocean)"
1833	printf "\n\n"
1834	echo "coupled_run $iia $iio" > coupling_steering
1835	fi
1836
1837	printf "\n *** execute command:"
1838	printf "\n \"$execute_command\" \n\n"
1839
1840	$execute_command < coupling_steering
1841
1842	if [[ $? != 0 ]]
1843	then
1844
1845	# ABORT IN CASE OF RUNTIME ERRORS
1846	printf "\n +++ runtime error occured"
1847	locat=execution
1848	exit
1849
1850	else
1851
1852	printf "\n$dashes\n *** execution finished \n"
1853
1854	fi
1855
1856
1857	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
1858	# BY EACH CORE INTO ONE FILE
1859	if [[ ! -f combine_plot_fields.x ]]
1860	then
1861
1862	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
1863	printf "\n 2d- and/or 3d-data may be incomplete!"
1864	printf "\n Your previous palmbuild may have failed. Please check.\n"
1865
1866	elif [[ "$combine_plot_fields" == true ]]
1867	then
1868
1869	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
1870	$execute_command_for_combine
1871
1872	else
1873
1874	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
1875	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
1876	# ??? koennen wir das streichen ???
1877	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
1878	fi
1879
1880
1881
1882	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1883	(( i = 0 ))
1884	while (( i < ioc ))
1885	do
1886	(( i = i + 1 ))
1887	if (( i == 1 ))
1888	then
1889	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
1890	fi
1891	printf "\n >>> ${out_command[$i]}"
1892	eval ${out_command[$i]}
1893	if (( i == ioc ))
1894	then
1895	printf "\n$dashes\n"
1896	fi
1897	done
1898
1899
1900	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
1901	if [[ $do_trace = true ]]
1902	then
1903	printf "\n\n"
1904	ls -al
1905	fi
1906
1907
1908	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
1909	(( i = 0 ))
1910	while (( i < iout ))
1911	do
1912	(( i = i + 1 ))
1913	if (( i == 1 ))
1914	then
1915	printf "\n\n *** saving OUTPUT-files:"
1916
1917	# GET RUN NUMBER ASSIGNED BY PALM
1918	if [[ -f RUN_NUMBER ]]
1919	then
1920	read run_number < RUN_NUMBER
1921	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
1922	usecycle_option="-U $run_number"
1923	else
1924	run_number=0
1925	usecycle_option=""
1926	fi
1927	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
1928	then
1929	printf "\n *** SCP transfers to local host via remote login-node \"$remote_loginnode\" "
1930	fi
1931	printf "\n$dashes"
1932	fi
1933
1934	# ADD CYCLE NUMBER TO FILENAME
1935	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1936	then
1937
1938	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
1939	if [[ "${actionout[$i]}" != "a" ]]
1940	then
1941	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
1942	# WITH AN EXISTING CYCLE NUMBER
1943	if (( run_number >= cycnum[$i] ))
1944	then
1945	(( cycnum[$i] = run_number ))
1946	else
1947	if (( run_number > 0 ))
1948	then
1949	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
1950	fi
1951	fi
1952	fi
1953	if (( cycnum[$i] > 0 ))
1954	then
1955	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
1956	fi
1957	fi
1958
1959	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1960	files_for_cores=false; filetype=file
1961	link_local_output=false
1962	if [[ "${actionout[$i]}" = pe && -n $cores ]]
1963	then
1964	files_for_cores=true; filetype=directory
1965	actionout[$i]=""
1966	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
1967	then
1968	actionout[$i]=""
1969	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
1970	then
1971	files_for_cores=true; filetype=directory
1972	link_local_output=true
1973	actionout[$i]=""
1974	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
1975	then
1976	link_local_output
1977	actionout[$i]=""
1978	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
1979	then
1980	files_for_cores=true; filetype=directory
1981	actionout[$i]="tr"
1982	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
1983	then
1984	actionout[$i]="tr"
1985	fi
1986
1987	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
1988	then
1989	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
1990	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
1991	then
1992	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
1993	else
1994
1995
1996	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
1997	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
1998	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
1999	then
2000	if [[ $running_on_remote = true ]]
2001	then
2002
2003	# SET OPTIONS FOR TRANSFER
2004	if [[ "${actionout[$i]}" = tr ]]
2005	then
2006	if [[ $files_for_cores = false ]]
2007	then
2008	catalog_option=""
2009	catalog_string=""
2010	else
2011	catalog_option="-c"
2012	catalog_string="/"
2013	fi
2014	append_option=""
2015	append_string=""
2016	else
2017	append_option="-A"
2018	append_string="append"
2019	fi
2020
2021	transfer_failed=false
2022	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2023	printf "\n ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}$catalog_string\n"
2024
2025	# TRANSFER VIA SCP
2026	if [[ "$remote_loginnode" != "" ]]
2027	then
2028	echo "cd $TEMPDIR; ${tmp_user_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${remote_hostname}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
2029	else
2030	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${remote_hostname}_${fname}${endout[$i]} ${extout[$i]}
2031	fi
2032	[[ $? != 0 ]] && transfer_failed=true
2033
2034
2035	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2036	if [[ $transfer_failed = true ]]
2037	then
2038	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2039	printf " ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id\n"
2040
2041	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2042	eval local_catalog=${pathout[$i]}
2043	if [[ ! -d $local_catalog ]]
2044	then
2045	printf " *** local directory does not exist. Trying to create:\n"
2046	printf " $local_catalog \n"
2047	mkdir -p $local_catalog
2048	fi
2049	eval cp ${localout[$i]} ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id
2050	transfer_problems=true
2051	fi
2052
2053	else
2054
2055	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2056	# BE COPIED OR APPENDED ON THIS MACHINE
2057	if [[ "${actionout[$i]}" = tr ]]
2058	then
2059	actionout[$i]=""
2060	else
2061	actionout[$i]="a"
2062	fi
2063	fi
2064	fi
2065
2066
2067	# APPEND ON THIS MACHINE
2068	if [[ "${actionout[$i]}" = "a" ]]
2069	then
2070	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2071	then
2072	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2073	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2074	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2075	else
2076	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2077	printf "\n ${pathout[$i]}\n"
2078	cat ${localout[$i]} >> ${pathout[$i]}
2079	fi
2080	fi
2081
2082	# COPY ON THIS MACHINE
2083	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2084	# ON DIFFERENT FILE-SYSTEMS
2085	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2086	then
2087
2088	# COPY IN CASE OF RUNS ON SINGLE CORES
2089	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2090	then
2091	printf "\n >>> OUTPUT: ${localout[$i]} to"
2092	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2093	if [[ $link_local_output = true ]]
2094	then
2095	printf " file will be linked\n"
2096	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2097	fi
2098	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2099	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2100	then
2101	if [[ $link_local_output = true ]]
2102	then
2103	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2104	fi
2105	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2106	else
2107	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2108	fi
2109	else
2110	printf "\n >>> OUTPUT: ${localout[$i]} to"
2111	printf "\n ${pathout[$i]}\n"
2112	if [[ $link_local_output = true ]]
2113	then
2114	printf " file will be linked\n"
2115	ln -f ${localout[$i]} ${pathout[$i]}
2116	fi
2117	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2118	if [[ ! -f "${pathout[$i]}" ]]
2119	then
2120	if [[ $link_local_output = true ]]
2121	then
2122	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2123	fi
2124	cp ${localout[$i]} ${pathout[$i]}
2125	else
2126	printf "+++ no copy because file ${pathout[$i]} exists\n"
2127	fi
2128	fi
2129
2130	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2131	then
2132
2133	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2134	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2135	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2136	printf "\n ${pathout[$i]}\n"
2137	if [[ $link_local_output = true ]]
2138	then
2139	printf " files will be linked\n"
2140	mkdir ${pathout[$i]}
2141	cd ${localout[$i]}
2142	for file in $(ls *)
2143	do
2144	ln -f $file ${pathout[$i]}
2145	done >\|/dev/null 2>&1
2146	cd $TEMPDIR
2147	fi
2148
2149	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2150	if [[ ! -f "${pathout[$i]}/_000000" ]]
2151	then
2152	if [[ $link_local_output = true ]]
2153	then
2154	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2155	fi
2156	cp -r ${localout[$i]}/* ${pathout[$i]}
2157	fi
2158
2159	fi
2160	fi
2161	done
2162
2163	if (( i != 0 ))
2164	then
2165	if [[ $transfer_problems = true ]]
2166	then
2167	printf "\n$dashes\n *** OUTPUT-files saved"
2168	printf "\n +++ WARNING: some data transfers failed! \n"
2169	else
2170	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2171	fi
2172	fi
2173
2174
2175	# IF REQUIRED, START A RESTART-JOB
2176	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2177	if [[ -f CONTINUE_RUN ]]
2178	then
2179
2180	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2181	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2182	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2183	# -b START A BATCH JOB
2184	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2185	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2186	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2187
2188
2189	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2190	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2191	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2192	then
2193	prc=`echo $prc \| sed 's/#/r/g'`
2194	fi
2195
2196
2197	# START THE RESTART-JOB
2198	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2199	echo " $prc"
2200	printf "\n$dashes\n"
2201	if [[ $running_on_remote = true ]]
2202	then
2203
2204	echo "*** ssh will be used to initiate restart-runs!"
2205	echo " return_address=\"$return_address\" "
2206	echo " return_username=\"$local_username\" "
2207
2208	if [[ "$remote_loginnode" != "" ]]
2209	then
2210	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
2211	else
2212	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2213	fi
2214
2215	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2216	sleep 30
2217
2218	else
2219
2220	# START THE RESTART JOB ON THE LOCAL HOST
2221	eval $prc # THE ' MUST BE EVALUATED
2222	cd - > /dev/null
2223
2224	fi
2225	printf "\n$dashes\n *** restart-run initiated \n"
2226
2227
2228	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2229	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2230	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2231	# MAY BE VERY HUGE)
2232	(( i = 0 ))
2233	while (( i < iin ))
2234	do
2235	(( i = i + 1 ))
2236	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2237	then
2238	rm -r ${absnamein[$i]}
2239	fi
2240	done
2241
2242	fi
2243
2244
2245	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2246	cd $HOME
2247	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
2248
2249
2250	else
2251
2252
2253	# PREPARING ACTIONS,
2254	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2255
2256	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2257	palmrun_com="$palmrun_script_name -c $config_file -d $fname -h $host -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2258	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2259	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2260	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2261	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2262	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2263	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2264	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2265	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2266	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2267	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2268	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2269	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2270	if [[ $create_remote_batch_job = true ]]
2271	then
2272	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2273	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2274	elif [[ $create_batch_job = true ]]
2275	then
2276	palmrun_com=${palmrun_com}" -j"
2277	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2278	fi
2279
2280
2281	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2282	# REMOTE HOST
2283	job_protocol_file_local=${local_jobcatalog}/${host}_${job_id}
2284	job_protocol_file=$job_protocol_file_local
2285	if [[ $create_remote_batch_job = true ]]
2286	then
2287	job_protocol_file_remote=${remote_jobcatalog}/${host}_${job_id}
2288	job_protocol_file=$job_protocol_file_remote
2289	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2290	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2291	fi
2292
2293
2294	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2295	jobfile=jobfile.$run_id
2296
2297
2298	# FIRST CREATE THE BATCH DIRECTIVES
2299	(( i = 0 ))
2300	while (( i < ibd ))
2301	do
2302	(( i = i + 1 ))
2303	line=`echo "${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@/$tasks_per_node/g' \| sed 's/@LOCAL_HOSTNAME@/${local_hostname}/g' \| sed 's/@HOST@/${host}/g' \| sed 's/@FNAME@/$fname/g' \| sed 's/@QUEUE@/$queue/g'`
2304	eval line=\"$line\"
2305	echo "$line" >> $jobfile
2306	done
2307	echo " " >> $jobfile
2308
2309
2310	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2311	# PROTOCOL
2312	if [[ $create_remote_batch_job = true ]]
2313	then
2314	echo "set +vx" >> $jobfile
2315	echo "trap '" >> $jobfile
2316	echo "set +vx" >> $jobfile
2317	echo "cd ${remote_jobcatalog}" >> $jobfile
2318	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2319
2320	# ADD THE BATCH DIRECTIVES
2321	(( i = 0 ))
2322	while (( i < ibdt ))
2323	do
2324	(( i = i + 1 ))
2325	line=`echo "${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@/$tasks_per_node/g' \| sed 's/@LOCAL_HOSTNAME@/${local_hostname}/g' \| sed 's/@HOST@/${host}/g' \| sed 's/@FNAME@/$fname/g'`
2326	eval line=\"$line\"
2327	echo "$line" >> $jobfile
2328	done
2329	echo " " >> $jobfile
2330
2331	echo "set -x" >> $jobfile
2332	echo "${tmp_user_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host}_${fname}" >> $jobfile
2333	echo "%%END%%" >> $jobfile
2334	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2335	echo "$submit_command $scpjob_file" >> $jobfile
2336	echo "rm $scpjob_file" >> $jobfile
2337	echo "rm $job_transfer_protocol_file" >> $jobfile
2338	echo "set -x" >> $jobfile
2339	echo " ' exit" >> $jobfile
2340	fi
2341
2342
2343	# ACTIVATE ERROR-TRACEBACK
2344	if [[ $do_trace = true ]]
2345	then
2346	echo "set -x" >> $jobfile
2347	else
2348	echo "set +vx" >> $jobfile
2349	fi
2350
2351
2352	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2353	if [[ "$login_init_cmd" != "" ]]
2354	then
2355	echo "$login_init_cmd" >> $jobfile
2356	fi
2357	if [[ "$module_commands" != "" ]]
2358	then
2359	echo "$module_commands" >> $jobfile
2360	fi
2361
2362
2363	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2364	echo "mkdir $TEMPDIR" >> $jobfile
2365	echo "cd $TEMPDIR" >> $jobfile
2366	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
2367	echo "cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
2368	echo "export PATH=.:\$PATH" >> $jobfile
2369	echo "export execute_palmrun=true" >> $jobfile
2370
2371
2372	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
2373	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
2374	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
2375	if [[ $create_remote_batch_job = true ]]
2376	then
2377	(( i = 0 ))
2378	while (( i < iin ))
2379	do
2380	(( i = i + 1 ))
2381	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
2382	if [[ "${transin[$i]}" = job ]]
2383	then
2384	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
2385	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
2386	echo " " >> $jobfile
2387	echo "%END%" >> $jobfile
2388	else
2389	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
2390	fi
2391
2392	# CHECK, IF FILE COULD BE CREATED
2393	echo "if [[ \$? = 1 ]]" >> $jobfile
2394	echo "then" >> $jobfile
2395	echo " echo \" \" " >> $jobfile
2396	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
2397	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
2398	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
2399	echo " execute_palmrun=false" >> $jobfile
2400	echo "fi" >> $jobfile
2401	done
2402	fi
2403
2404
2405	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2406	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2407	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2408	echo "LOCAL_PWD=$working_directory" >> $jobfile
2409	echo "export LOCAL_PWD" >> $jobfile
2410
2411
2412	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2413	echo "LOCAL_PALMRUN_PATH=$PALM_BIN" >> $jobfile
2414	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2415
2416
2417	# CALL PALMRUN WITHIN THE JOB
2418	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2419	echo "set -x" >> $jobfile
2420	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2421
2422
2423	# TRANSFER JOBFILE TO THE TARGET HOST
2424	if [[ $create_jobfile_only = false ]]
2425	then
2426
2427	if [[ $create_remote_batch_job = true ]]
2428	then
2429
2430	echo " *** transfer of job to remote host via scp"
2431	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}"
2432	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}
2433
2434	echo " "
2435	echo " *** submit the job"
2436	echo " cd $remote_jobcatalog; $submit_command ${host}_${job_id}; rm ${host}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2437	echo "cd $remote_jobcatalog; $submit_command ${host}_${job_id}; rm ${host}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2438
2439	elif [[ $create_batch_job = true ]]
2440	then
2441
2442	eval local_jobcatalog=$local_jobcatalog
2443	cp $jobfile ${local_jobcatalog}/${host}_${job_id}
2444	cd $local_jobcatalog
2445	echo " "
2446	echo "--- submit the job"
2447	echo "$submit_command ${host}_${job_id}"
2448	$submit_command ${host}_${job_id}
2449	rm ${host}_${job_id}
2450	cd - > /dev/null
2451
2452	fi
2453
2454	rm -rf $jobfile
2455
2456	else
2457
2458	printf "\n *** jobfile created under name \"$jobfile\" "
2459	printf "\n no batch-job has been sent!"
2460
2461	fi
2462
2463	fi # END OF REMOTE-PART

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