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source: palm/trunk/SCRIPTS/palmrun @ 2381

Last change on this file since 2381 was 2381, checked in by raasch, 7 years ago
# in file connection statements replaced by r for restart runs
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 2381 2017-09-01 10:53:46Z 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	add_source_path=""
55	combine_plot_fields=true
56	compiler_name=""
57	compiler_name_ser=""
58	compiler_options=""
59	config_file=""
60	cores=""
61	cores_atmos=0
62	cores_ocean=0
63	coupled_dist=""
64	cpp_options=""
65	cpumax=0
66	create_jobfile_only=false
67	delete_temporary_catalog=true
68	create_batch_job=false
69	create_remote_batch_job=false
70	dashes=" ----------------------------------------------------------------------------"
71	defaultqueue=""
72	do_compile=true
73	do_trace=false
74	executable=""
75	execute_command=""
76	execution_error=false
77	fileconnection_file=.palm.iofiles
78	fname=test
79	global_revision=""
80	host="default"
81	hostfile=""
82	hp=""
83	job_directory=""
84	keep_data_from_previous_run=false
85	link_local_input=false
86	link_local_output=false
87	loader_options=""
88	locat=normal
89	makefile=""
90	max_par_io_str=""
91	prc=$0
92	while [[ $(echo $prc \| grep -c "/") != 0 ]]
93	do
94	prc=`echo $prc \| cut -f2- -d"/"`
95	done
96	module_calls=""
97	palmrun_script_name=$prc
98	openmp=false
99	queue=none
100	restart_run=false
101	return_address=""
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	use_openmp=false
115	version="palmrun 0.9 Rev$Rev: 2303 $"
116	working_directory=`pwd`
117	write_binary=""
118	TOPT=""
119
120
121	# ERROR HANDLING IN CASE OF EXIT
122	trap 'rm -rf $working_directory/tmp_mrun
123	if [[ $locat != normal && $locat != control_c ]]
124	then
125
126	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
127	(( i = 0 ))
128	while (( i < iec ))
129	do
130	(( i = i + 1 ))
131	printf "\n *** Execution of ERROR-command:\n"
132	printf " >>> ${err_command[$i]}\n"
133	eval ${err_command[$i]}
134	done
135	if [[ $tmpcreate = true ]]
136	then
137	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
138	fi
139	printf "\n\n+++ palmrun killed \n\n"
140	elif [[ $locat != control_c ]]
141	then
142	printf "\n\n --> palmrun finished\n\n"
143	if [[ $running_on_remote = true ]]
144	then
145	printf " Bye, bye $remote_username !!\n\n"
146	else
147	printf " Bye, bye $local_username !!\n\n"
148	fi
149	fi' exit
150
151
152	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
153	trap 'rm -rf $working_directory/tmp_mrun
154	[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
155	printf "\n+++ palmrun killed by \"^C\" \n\n"
156	locat=control_c
157	exit
158	' 2
159
160
161	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
162	# BEEN SET
163	if [[ "$PALM_BIN" = "" ]]
164	then
165	printf "\n +++ environment variable PALM_BIN has not been set"
166	printf "\n please set it to the directory where the PALM scripts are located"
167	locat=palm_bin; exit
168	fi
169	export PATH=$PALM_BIN:$PATH
170
171
172
173	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
174	# WHICH WILL BE USED TO START RESTART-JOBS
175	while getopts :a:bBc:Cd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
176	do
177	case $option in
178	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
179	(b) create_batch_job=true; prc="$prc -b";;
180	(B) delete_temporary_catalog=false; prc="$prc -B";;
181	(c) config_file=$OPTARG; prc="$prc -c$OPTARG";;
182	(C) restart_run=true; prc="$prc -C";;
183	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
184	(F) create_jobfile_only=true;;
185	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
186	(h) host=$OPTARG; prc="$prc -h$OPTARG";;
187	(j) running_in_batch_mode=true;;
188	(k) keep_data_from_previous_run=true; prc="$prc -k";;
189	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
190	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
191	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
192	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
193	(r) run_id=$OPTARG;;
194	(R) return_address=$OPTARG;;
195	(s) source_list=$OPTARG;;
196	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
197	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
198	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
199	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
200	(v) silent=true; prc="$prc -v";;
201	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
202	(x) do_trace=true;set -x; prc="$prc -x";;
203	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
204	(y) ocean_file_appendix=true; prc="$prc -y";;
205	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
206	(Z) combine_plot_fields=false; prc="$prc -Z";;
207	(\?) printf "\n +++ unknown option $OPTARG \n"
208	printf "\n --> type \"$0 ?\" for available options \n"
209	locat=parameter;exit;;
210	esac
211	done
212
213
214	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
215	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
216	(( to_shift = $OPTIND - 1 ))
217	shift $to_shift
218
219	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
220	if [[ "$1" = "?" ]]
221	then
222	(printf "\n *** Description of available palmrun options:\n"
223	printf "\n Option Description Default-Value"
224	printf "\n -a activation string list \"\" "
225	printf "\n -b batch-job on local machine ---"
226	printf "\n -B do not delete temporary directory at end ---"
227	printf "\n -c configuration file .mrun.config"
228	printf "\n -d base name of files attached to program test"
229	printf "\n -F create batch job file only ---"
230	printf "\n -h execution host \"default\" "
231	printf "\n -k keep data from previous run"
232	printf "\n -K additional conditions for controling"
233	printf "\n usage of conditional code and"
234	printf "\n env-variables in configuration file \"\" "
235	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
236	printf "\n -M Makefile name Makefile"
237	printf "\n -O threads per openMP task ---"
238	printf "\n -q queue \"$queue\" "
239	printf "\n -r run control list (combines -i -o) \"\" "
240	printf "\n -s filenames of routines to be compiled \"\" "
241	printf "\n must end with .f, .f90, .F, or .c !"
242	printf "\n use \"..\" for more than one file and wildcards"
243	printf "\n -s LM compiles all locally modified files"
244	printf "\n -t allowed cpu-time in seconds (batch) 0"
245	printf "\n -T tasks per node depending on -h"
246	printf "\n -u username on remote machine \"\" "
247	printf "\n -v no prompt for confirmation ---"
248	printf "\n -w maximum parallel io streams as given by -X"
249	printf "\n -x tracing of palmrun for debug purposes ---"
250	printf "\n -X # of processors (on parallel machines) 1"
251	printf "\n -y add appendix \"_O\" to all local output"
252	printf "\n files (ocean precursor runs followed by"
253	printf "\n coupled atmosphere-ocean runs) ---"
254	printf "\n -Y run coupled model, \"#1 #2\" with"
255	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
256	printf "\n -Z skip combine_plot_fields at the end of "
257	printf "\n the simulation ---"
258	printf "\n "
259	printf "\n Possible values of positional parameter <modus>:"
260	printf "\n \"?\" - this outline \n\n") \| more
261	exit
262	elif [[ "$1" != "" ]]
263	then
264	printf "\n +++ positional parameter $1 unknown \n"
265	locat=parameter; exit
266	fi
267
268
269
270	# SHORT STARTING MESSAGE
271	printf "\n*** $version "
272	printf "\n will be executed. Please wait ..."
273
274
275	# BUILD THE CONFIGURATION-FILE NAME
276	if [[ "$config_file" = "" ]]
277	then
278	config_file=.palm.config.$host
279	fi
280
281
282	# CHECK, IF CONFIGURATION FILE EXISTS
283	if [[ ! -f $config_file ]]
284	then
285	printf "\n\n +++ configuration file: "
286	printf "\n $config_file"
287	printf "\n does not exist"
288	locat=connect; exit
289	fi
290
291
292	# CHECK, IF FILE CONNECTION FILE EXISTS
293	if [[ ! -f $fileconnection_file ]]
294	then
295	printf "\n\n +++ file connection file: "
296	printf "\n $fileconnection_file"
297	printf "\n does not exist"
298	locat=connect; exit
299	fi
300
301
302	# READ AND EVALUATE THE CONFIGURATION-FILE
303	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
304
305	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
306	while read line
307	do
308
309	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
310	eval line=\"$line\"
311
312
313	# INTERPRET THE LINE
314	if [[ "$(echo $line)" = "" ]]
315	then
316
317	# EMPTY LINE, NO ACTION
318	continue
319
320	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
321	then
322
323	# LINE IS A COMMENT LINE
324	continue
325
326	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
327	then
328
329	# LINE DEFINES AN ENVIRONMENT-VARIABLE
330	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
331	value=`echo $line \| cut -d" " -s -f2-`
332
333
334	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
335	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
336	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
337	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
338	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
339	# CONFIGURATION-FILE.
340	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
341	then
342	eval export $var="\$value"
343
344	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
345	if [[ $do_trace = true ]]
346	then
347	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
348	fi
349	fi
350
351	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
352	then
353
354	# LINE DEFINES BATCH-DIRECTIVE
355	(( ibd = ibd + 1 ))
356	line=$(echo $line \| cut -c4-)
357	batch_directive[$ibd]="$line"
358
359	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
360	then
361
362	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
363	# REMOTE TO A LOCAL HOST
364	(( ibdt = ibdt + 1 ))
365	line=$(echo $line \| cut -c5-)
366	batch_directive_transfer[$ibdt]="$line"
367
368	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
369	then
370
371	# LINE DEFINES ERROR-COMMAND
372	(( iec = iec + 1 ))
373	line=$(echo $line \| cut -c4-)
374	err_command[$iec]="$line"
375
376	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
377	then
378
379	# LINE DEFINES INPUT-COMMAND
380	(( iic = iic + 1 ))
381	line=$(echo $line \| cut -c4-)
382	in_command[$iic]="$line"
383
384	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
385	then
386
387	# LINE DEFINES OUTPUT-COMMAND
388	(( ioc = ioc + 1 ))
389	line=$(echo $line \| cut -c4-)
390	out_command[$ioc]="$line"
391
392	else
393
394	# SKIP ALL OTHER LINES
395	continue
396
397	fi
398
399	done < $config_file
400
401
402	# CHECK SETTING OF REQUIRED PARAMETERS
403	if [[ "$compiler_name" = "" ]]
404	then
405	printf "\n +++ no compiler name found in $config_file"
406	printf "\n Please add line \"compiler_name ...\" to that file."
407	locat=config_file; exit
408	fi
409	if [[ "$compiler_name_ser" = "" ]]
410	then
411	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
412	printf "\n Please add line \"compiler_name_ser ...\" to that file."
413	locat=config_file; exit
414	fi
415	if [[ "$compiler_options" = "" ]]
416	then
417	printf "\n +++ no compiler options found in $config_file"
418	printf "\n Please add line \"compiler_options ...\" to that file."
419	locat=config_file; exit
420	fi
421	if [[ "$loader_options" = "" ]]
422	then
423	printf "\n +++ no loader options found in $config_file"
424	printf "\n Please add line \"loader_options ...\" to that file."
425	locat=config_file; exit
426	fi
427	if [[ "$execute_command" = "" ]]
428	then
429	printf "\n +++ no execute command found in $config_file"
430	printf "\n Please add line \"execute_command ...\" to that file."
431	locat=config_file; exit
432	fi
433
434	if [[ "$hostfile" != "" ]]
435	then
436	if [[ $hostfile != auto && ! -f $hostfile ]]
437	then
438	printf "\n +++ no hostfile \"$hostfile\" found"
439	printf "\n Please check line \"hostfile ...\" in $config_file"
440	locat=config_file; exit
441	fi
442	fi
443
444	if [[ "$write_binary" = "" ]]
445	then
446	write_binary=false
447	fi
448
449	# DETERMINE THE CALL STATUS
450	if [[ "$return_address" != "" ]]
451	then
452
453	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
454	# BATCH MODE AND ...
455	running_on_remote=true
456	host_name=$remote_hostname
457
458	else
459
460	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
461	if [[ "$remote_ip" != "" ]]
462	then
463
464	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
465	create_remote_batch_job=true
466
467	fi
468	host_name=$local_hostname
469	running_on_remote=false
470	fi
471
472
473
474	# READ AND EVALUATE THE I/O-FILE LIST
475	[[ $silent = false ]] && printf "\n Reading the I/O files... "
476
477	# READ THE FILE CONNECTION FILE LINE BY LINE
478	while read line
479	do
480
481	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
482	eval line=\"$line\"
483
484
485	# INTERPRET THE LINE
486	if [[ "$(echo $line)" = "" ]]
487	then
488	# EMPTY LINE, NO ACTION
489	continue
490
491	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
492	then
493
494	# LINE IS A COMMENT LINE
495	true
496
497	else
498
499	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
500	# s2a: in/out - field
501	# s2b: loc - field (optional)
502	# s2c: tr/ar - field (optional)
503	s1=`echo $line \| cut -d" " -f1`
504	s2=`echo $line \| cut -d" " -s -f2`
505	s2a=$(echo $s2 \| cut -d":" -f1)
506	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
507	then
508	s2b=""
509	s2c=""
510	else
511	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
512	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
513	fi
514	s3=`echo $line \| cut -d" " -f3`
515	s4=`echo $line \| cut -d" " -s -f4`
516	s5=`echo $line \| cut -d" " -s -f5`
517	s6=`echo $line \| cut -d" " -s -f6`
518
519
520	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
521	# INPUT- OR OUTPUT-LIST.
522	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
523	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
524	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
525	# IS NOT CHECKED AND STORED.
526	IFSALT="$IFS"; IFS="$IFS:"
527	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
528	then
529	found=false
530	for actual in $activation_string_list
531	do
532	for formal in $s3
533	do
534	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
535	done
536	done
537	if [[ $found = true ]]
538	then
539	(( iin = iin + 1 ))
540	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
541	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
542	extin[$iin]=$s6
543	fi
544	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
545	then
546	found=false
547	for actual in $activation_string_list
548	do
549	for formal in $s3
550	do
551	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
552	done
553	done
554	if [[ $found = true ]]
555	then
556	(( iout = iout + 1 ))
557	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
558	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
559	fi
560	elif [[ "$s2a" != in && "$s2a" != out ]]
561	then
562	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
563	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
564	locat=connect; exit
565	fi
566	IFS="$IFSALT"
567	fi
568
569	done < $fileconnection_file
570
571
572
573	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
574	if [[ $run_coupled_model = true ]]
575	then
576
577	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
578	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
579
580	if (( $cores_ocean + $cores_atmos != $cores ))
581	then
582
583	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
584	printf "\n PEs (total) : $cores"
585	printf "\n PEs (atmosphere): $cores_atmos"
586	printf "\n PEs (ocean) : $cores_ocean"
587	locat=coupling; exit
588
589	fi
590
591	fi
592
593
594	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
595	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
596	palmrun_memory=$memory
597	palmrun_cpumax=$cpumax
598	palmrun_cores=$cores
599
600
601	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
602	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
603	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
604	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
605	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
606	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
607
608
609
610	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
611	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
612	# FOLDER
613	if [[ $running_in_batch_mode = true ]]
614	then
615
616	if [[ ! -d ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname ]]
617	then
618	printf "\n +++ directory ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname is missing"
619	printf "\n Please check the output of the palmrun-call"
620	printf "\n that you did on your local host."
621	locat=SOURCES_FOR_RUN; exit
622	fi
623
624	else
625
626	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
627	# AUTOMATIC RESTART RUN
628	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
629	if [[ $restart_run = false ]]
630	then
631
632	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
633	# THE LOCAL HOST
634	if [[ ! -d $source_path ]]
635	then
636	printf "\n\n +++ source path \"$source_path\" on local host"
637	printf "\n \"$(hostname)\" does not exist"
638	locat=source_path; exit
639	fi
640
641	rm -rf SOURCES_FOR_RUN_$fname
642	mkdir SOURCES_FOR_RUN_$fname
643
644	if [[ "$source_list" = LM ]]
645	then
646
647	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
648	source_list=""
649	cd $source_path
650
651
652	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
653	if [[ ! -d .svn ]]
654	then
655	printf "\n\n +++ source directory"
656	printf "\n \"$source_path\" "
657	printf "\n is not under control of \"subversion\"."
658	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
659	fi
660
661
662	# LIST ALL MODIFIED SOURCE CODE FILES
663	Filenames=""
664	svn status > tmp_mrun
665	while read line
666	do
667	firstc=`echo $line \| cut -c1`
668	if [[ $firstc = M \|\| $firstc = "?" ]]
669	then
670	Name=`echo "$line" \| cut -c8-`
671	extension=`echo $Name \| cut -d. -f2`
672	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
673	then
674	Filenames="$Filenames "$Name
675	fi
676	fi
677	done < tmp_mrun
678
679
680	# COPY FILES TO SOURCES_FOR_RUN_...
681	for filename in $Filenames
682	do
683	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
684	source_list=$source_list"$filename "
685	done
686
687	cd - > /dev/null
688
689
690	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
691	elif [[ "$source_list" != "" ]]
692	then
693
694	cd $source_path
695
696	for filename in $source_list
697	do
698
699	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
700	if [[ $(echo $filename \| grep -c "/") != 0 ]]
701	then
702	printf "\n +++ source code file: $filename"
703	printf "\n must not contain (\"/\") "
704	locat=source; exit
705	fi
706
707	if [[ ! -f $filename ]]
708	then
709	printf "\n +++ source code file: $filename"
710	printf "\n does not exist"
711	locat=source; exit
712	else
713	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
714	fi
715
716	done
717
718	cd - > /dev/null
719
720	fi
721
722	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
723	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
724	if [[ ! -f $makefile ]]
725	then
726	printf "\n +++ file \"$makefile\" does not exist"
727	locat=make; exit
728	else
729	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
730	fi
731
732
733	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
734	if [[ "$add_source_path" != "" ]]
735	then
736
737	# DOES THE DIRECTORY EXIST?
738	if [[ ! -d $add_source_path ]]
739	then
740
741	printf "\n\n *** INFORMATIVE: additional source code directory"
742	printf "\n \"$add_source_path\" "
743	printf "\n does not exist or is not a directory."
744	printf "\n No source code will be used from this directory!\n"
745	add_source_path=""
746	if [[ $silent == false ]]
747	then
748	sleep 2
749	fi
750
751	else
752
753	cd $add_source_path
754	found=false
755
756	Names=$(ls -1 *.f90 2>&1)
757	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
758	Names=$(ls -1 *.F90 2>&1)
759	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
760	Names=$(ls -1 *.F 2>&1)
761	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
762	Names=$(ls -1 *.f 2>&1)
763	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
764	Names=$(ls -1 *.c 2>&1)
765	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
766
767	cd - > /dev/null
768	cd SOURCES_FOR_RUN_$fname
769
770	# COPY MAKEFILE IF EXISTING
771	if [[ -f $add_source_path/Makefile ]]
772	then
773	printf "\n\n *** user Makefile from directory"
774	printf "\n \"$add_source_path\" is used \n"
775	if [[ $silent == false ]]
776	then
777	sleep 1
778	fi
779	cp $add_source_path/Makefile .
780	fi
781
782	for filename in $AddFilenames
783	do
784	if [[ -f $filename ]]
785	then
786	printf "\n +++ source code file \"$filename\" found in additional"
787	printf "\n source code directory \"$add_source_path\" "
788	printf "\n but was also given with option \"-s\" which means that it should be taken"
789	printf "\n from directory \"$source_path\"."
790	locat=source; exit
791	fi
792
793	cp $add_source_path/$filename .
794	source_list="$source_list $filename"
795
796	# CHECK IF FILE IS CONTAINED IN MAKEFILE
797	if [[ $(grep -c $filename Makefile) = 0 ]]
798	then
799	printf "\n\n +++ user file \"$filename\" "
800	printf "\n is not listed in Makefile \n"
801	locat=source; exit
802	else
803
804	if [[ $found = false ]]
805	then
806	found=true
807	printf "\n\n *** following user file(s) added to the"
808	printf " files to be translated:\n "
809	fi
810	printf "$filename "
811	if [[ $silent == false ]]
812	then
813	sleep 0.5
814	fi
815
816	fi
817	done
818	[[ $found = true ]] && printf "\n"
819	cd - > /dev/null
820	fi
821	fi
822
823	# COPY CONFIGURATION FILES
824	cp $config_file SOURCES_FOR_RUN_$fname
825	cp $fileconnection_file SOURCES_FOR_RUN_$fname
826
827	# COPY SHELLSCRIPTS
828	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
829	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
830
831	fi
832
833	fi
834
835	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
836	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
837	if [[ "$global_revision" = "" ]]
838	then
839	global_revision=`svnversion $source_path 2>/dev/null`
840	global_revision="Rev: $global_revision"
841	fi
842
843
844	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
845	if [[ -n $cores ]]
846	then
847
848	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
849	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
850	if [[ "$tasks_per_node" = "" && $host != lcxt5m ]]
851	then
852	printf "\n"
853	printf "\n +++ option \"-T\" (tasks per node) is missing"
854	printf "\n set -T option or define tasks_per_node in the config file"
855	locat=tasks_per_node; (( iec = 0 )); exit
856	fi
857
858	if (( cores < tasks_per_node ))
859	then
860	printf "\n"
861	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
862	printf "\n given values: -T $tasks_per_node -X $cores"
863	locat=tasks_per_node; (( iec = 0 )); exit
864	fi
865
866	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
867	(( mpi_tasks = cores / threads_per_task ))
868	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
869	(( ii = cores / tasks_per_node ))
870	(( remaining_cores = cores - ii * tasks_per_node ))
871	if (( remaining_cores > 0 ))
872	then
873	printf "\n"
874	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
875	printf "\n divisor of the total number of cores (option \"-X\")"
876	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
877	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
878	(( nodes = nodes + 1 ))
879	fi
880
881	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
882	if [[ "$tasks_per_node" != "" ]]
883	then
884	TOPT="-T $tasks_per_node"
885	fi
886
887	fi
888
889
890	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
891	if [[ "$maximum_parallel_io_streams" = "" ]]
892	then
893	maximum_parallel_io_streams=$cores
894	fi
895
896
897	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
898	if [[ "$scp_port" != "" ]]
899	then
900	PORTOPT="-P $scp_port"
901	SSH_PORTOPT="-p $scp_port"
902	fi
903
904
905	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
906	# CONFIG-FILE
907	if [[ "$ssh_key" != "" ]]
908	then
909	ssh_key="-i $HOME/.ssh/$ssh_key"
910	fi
911
912
913	# SET QUEUE, IF NOT GIVEN
914	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
915	then
916
917	if [[ $queue = none && "$defaultqueue" = "" ]]
918	then
919	printf "\n"
920	printf "\n +++ no default queue given in configuration file and no queue"
921	printf "\n given with option -q"
922	fi
923	if [[ $queue = none ]]
924	then
925	queue=$defaultqueue
926	fi
927
928	fi
929
930
931	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
932	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
933	(( i = 0 ))
934	while (( i < iin ))
935	do
936	(( i = i + 1 ))
937	(( maxcycle = 0 ))
938
939	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
940	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
941	if [[ "${actionin[$i]}" = di ]]
942	then
943	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
944	# HOST ONLY
945	eval filename=${pathin[$i]}/${endin[$i]}
946	else
947	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
948	# HOST ONLY
949	eval filename=${pathin[$i]}/${fname}${endin[$i]}
950	fi
951	eval pathname=${pathin[$i]}
952
953	# CHECK IF FILE EXISTS
954	if ! ls $filename* 1>/dev/null 2>&1
955	then
956
957	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
958	if [[ "${transin[$i]}" != "locopt" ]]
959	then
960	printf "\n\n +++ INPUT-file: "
961	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
962	then
963	printf "\n $filename"
964	else
965	printf "\n $filename.${extin[$i]}"
966	fi
967	printf "\n does not exist\n"
968	locat=input; exit
969	else
970	transin[$i]="unavailable"
971	fi
972	else
973
974	# DETERMINE THE FILE'S CYCLE NUMBER
975	ls -1 -d $filename > filelist 2>/dev/null
976	ls -1 -d $filename.* >> filelist 2>/dev/null
977	while read line
978	do
979	# filename without path (i.e. after the last "/")
980	basefilename=$(basename ${line})
981
982	# check if there is an extension
983	extension=${basefilename##*.}
984	if [[ "$extension" = "$extin[$i]" ]]
985	then
986	basefilename=${basefilename&.*}
987	fi
988
989	# check for an existing cycle number
990	cycle=${basefilename##*.}
991	if [[ $cycle =~ ^-?[0-9]+$ ]]
992	then
993	(( icycle = $cycle ))
994	else
995	(( icycle = 0 ))
996	fi
997
998	if (( icycle > maxcycle ))
999	then
1000	(( maxcycle = icycle ))
1001	fi
1002
1003	done <filelist
1004	rm filelist
1005
1006	# APPEND CYCLE NUMBER TO FILENAME
1007	if (( maxcycle > 0 ))
1008	then
1009	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1010	then
1011	filename=${filename}.$maxcycle.${extin[$i]}
1012	else
1013	filename=${filename}.$maxcycle
1014	fi
1015	else
1016	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1017	then
1018	filename=${filename}.${extin[$i]}
1019	fi
1020	fi
1021
1022	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1023	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1024	absnamein[$i]=$filename
1025	if (( maxcycle > 0 ))
1026	then
1027	if [[ "${actionin[$i]}" = di ]]
1028	then
1029	frelin[$i]=${endin[$i]}.$maxcycle
1030	else
1031	frelin[$i]=${fname}${endin[$i]}.$maxcycle
1032	fi
1033	else
1034	if [[ "${actionin[$i]}" = di ]]
1035	then
1036	frelin[$i]=${endin[$i]}
1037	else
1038	frelin[$i]=${fname}${endin[$i]}
1039	fi
1040	fi
1041
1042	fi
1043	done
1044
1045
1046	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1047	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1048	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1049	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1050	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1051	# REMOTE HOST)
1052	(( i = 0 ))
1053	while (( i < iout ))
1054	do
1055	(( i = i + 1 ))
1056	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1057	then
1058	if [[ "${actionout[$i]}" = tr ]]
1059	then
1060	actionout[$i]=""
1061	elif [[ "${actionout[$i]}" = trpe ]]
1062	then
1063	actionout[$i]=pe
1064	elif [[ "${actionout[$i]}" = tra ]]
1065	then
1066	actionout[$i]=a
1067	fi
1068	(( maxcycle = 0 ))
1069	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1070	eval catalogname=${pathout[$i]}
1071	if ! ls $filename* 1>/dev/null 2>&1
1072	then
1073
1074	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1075	if cat /dev/null > $filename
1076	then
1077	rm $filename
1078	else
1079
1080	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1081	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1082	if [[ ! -d $catalogname ]]
1083	then
1084	if mkdir -p $catalogname
1085	then
1086	printf "\n\n *** directory:"
1087	printf "\n $catalogname"
1088	printf "\n was created\n"
1089	else
1090	printf "\n\n +++ OUTPUT-file:"
1091	printf "\n $filename"
1092	printf "\n cannot be created, because directory does not exist"
1093	printf "\n and cannot be created either"
1094	printf "\n"
1095	locat=output ; exit
1096	fi 2>/dev/null
1097	else
1098	printf "\n\n +++ OUTPUT-file:"
1099	printf "\n $filename"
1100	printf "\n cannot be created, although directory exists"
1101	printf "\n"
1102	locat=output ; exit
1103	fi
1104	fi 2>/dev/null
1105	else
1106
1107	# DETERMINE THE CYCLE NUMBER
1108	ls -1 -d $filename > filelist 2>/dev/null
1109	ls -1 -d $filename.* >> filelist 2>/dev/null
1110	while read line
1111	do
1112
1113	# filename without path (i.e. after the last "/")
1114	basefilename=$(basename ${line})
1115
1116	# check if there is an extension
1117	extension=${basefilename##*.}
1118	if [[ "$extension" = "${extout[$i]}" ]]
1119	then
1120	basefilename=${basefilename%.*}
1121	fi
1122
1123	# check for an existing cycle number
1124	cycle=${basefilename##*.}
1125	if [[ $cycle =~ ^-?[0-9]+$ ]]
1126	then
1127	(( icycle = $cycle + 1 ))
1128	else
1129	(( icycle = 1 ))
1130	fi
1131
1132	if (( icycle > maxcycle ))
1133	then
1134	(( maxcycle = icycle ))
1135	fi
1136
1137	done <filelist
1138	rm filelist
1139	fi
1140
1141	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1142	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1143	if [[ "${actionout[$i]}" != a ]]
1144	then
1145	if (( maxcycle > 0 ))
1146	then
1147	filename_tmp=${filename}.$maxcycle
1148	if cat /dev/null > $filename_tmp
1149	then
1150	rm $filename_tmp
1151	else
1152	printf "\n +++ OUTPUT-file:"
1153	printf "\n $filename_tmp"
1154	printf "\n cannot be created"
1155	locat=output ; exit
1156	fi
1157	fi
1158	else
1159	(( maxcycle = maxcycle - 1 ))
1160	fi
1161
1162	(( cycnum[$i] = maxcycle ))
1163	pathout[$i]=$filename
1164
1165	fi
1166	done
1167
1168
1169	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1170	if [[ $running_in_batch_mode = false ]]
1171	then
1172	run_id=$RANDOM
1173	job_id=${fname}.$run_id
1174
1175	TEMPDIR=$tmp_user_catalog/$job_id
1176	fi
1177
1178
1179	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1180	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1181	then
1182
1183	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1184	if [[ $ibd = 0 ]]
1185	then
1186	printf "\n"
1187	printf "\n +++ no batch directives found in configuration file"
1188	locat=config_file_batch_directives; (( iec = 0 )); exit
1189	fi
1190
1191	# CHECK IF CPUTIME IS GIVEN FOR JOB
1192	done=false
1193	while [[ $done = false ]]
1194	do
1195	cputime=$cpumax
1196	if (( $cputime == 0 ))
1197	then
1198	printf "\n +++ cpu-time is undefined"
1199	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1200	printf "\n >>> "
1201	read cputime 1>/dev/null 2>&1
1202	else
1203	done=true
1204	fi
1205	done
1206
1207	# CHECK THE MEMORY DEMAND
1208	done=false
1209	while [[ $done = false ]]
1210	do
1211	if (( memory == 0 ))
1212	then
1213	printf "\n +++ memory demand is undefined"
1214	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1215	printf "\n >>> "
1216	read memory 1>/dev/null 2>&1
1217	else
1218	done=true
1219	fi
1220	done
1221
1222	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1223	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1224	then
1225	while [[ -z $remote_username ]]
1226	do
1227	printf "\n +++ username on remote host \"$remote_ip\" is undefined"
1228	printf "\n >>> Please type username:"
1229	printf "\n >>> "
1230	read remote_username
1231	done
1232	fi
1233
1234	else
1235
1236	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1237
1238	fi
1239	cpumax=$cputime
1240
1241
1242	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1243	(( cpu_hours = cputime / 3600 ))
1244	(( resttime = cputime - cpu_hours * 3600 ))
1245	(( cpu_minutes = resttime / 60 ))
1246	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1247	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1248
1249
1250	# OUTPUT OF THE PALMRUN-HEADER
1251	calltime=$(date)
1252	printf "\n"
1253	printf "#------------------------------------------------------------------------# \n"
1254	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1255	printf "\| \| \n"
1256	column1="called on:"; column2=$(hostname)
1257	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1258	if [[ $create_remote_batch_job = true ]]
1259	then
1260	column1="execution on:"; column2="$remote_hostname (username: $remote_username)"
1261	else
1262	if [[ $running_on_remote = true ]]
1263	then
1264	column1="execution on:"; column2="$remote_hostname"
1265	else
1266	column1="execution on:"; column2="$local_hostname"
1267	fi
1268	fi
1269	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1270
1271	column1="running in:"
1272	if [[ $running_in_batch_mode = true ]]
1273	then
1274	column2="batch job mode"
1275	else
1276	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1277	then
1278	column2="job creation mode"
1279	else
1280	column2="interactive run mode"
1281	fi
1282	fi
1283	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1284
1285	if [[ -n $cores ]]
1286	then
1287	if [[ $run_coupled_model = false ]]
1288	then
1289	column1="number of cores:"; column2=$cores
1290	else
1291	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1292	fi
1293	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1294	fi
1295	if [[ -n $tasks_per_node ]]
1296	then
1297	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1298	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1299	if (( remaining_cores > 0 ))
1300	then
1301	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1302	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1303	fi
1304	fi
1305	if [[ $maximum_parallel_io_streams != $cores ]]
1306	then
1307	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1308	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1309	fi
1310	if [[ $use_openmp = true ]]
1311	then
1312	column1="threads per task:"; column2="$threads_per_task"
1313	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1314	fi
1315	printf "\| \| \n"
1316	if [[ "$source_list" != "" ]]
1317	then
1318	if [[ "$make_options" != "" ]]
1319	then
1320	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1321	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1322	line=$(echo "$make_options" \| cut -c46-)
1323	while [[ "$line" != "" ]]
1324	do
1325	column1=""
1326	column2=$(echo "$line" \| cut -c-45)
1327	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1328	line=$(echo "$line" \| cut -c46-)
1329	done
1330	fi
1331	fi
1332
1333	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1334	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1335	line=$(echo "$cpp_options" \| cut -c46-)
1336	while [[ "$line" != "" ]]
1337	do
1338	column1=""
1339	column2=$(echo "$line" \| cut -c-45)
1340	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1341	line=$(echo "$line" \| cut -c46-)
1342	done
1343
1344	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1345	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1346	line=$(echo "$compiler_options" \| cut -c46-)
1347	while [[ "$line" != "" ]]
1348	do
1349	column1=""
1350	column2=$(echo "$line" \| cut -c-45)
1351	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1352	line=$(echo "$line" \| cut -c46-)
1353	done
1354
1355	column1="loader options:"; column2=$(echo "$loader_options" \| cut -c-45)
1356	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1357	line=$(echo "$loader_options" \| cut -c46-)
1358	while [[ "$line" != "" ]]
1359	do
1360	column1=""
1361	column2=$(echo "$line" \| cut -c-45)
1362	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1363	line=$(echo "$line" \| cut -c46-)
1364	done
1365
1366	if [[ "$login_init_cmd" != "" ]]
1367	then
1368	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1369	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1370	line=$(echo "$login_init_cmd" \| cut -c46-)
1371	while [[ "$line" != "" ]]
1372	do
1373	column1=""
1374	column2=$(echo "$line" \| cut -c-45)
1375	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1376	line=$(echo "$line" \| cut -c46-)
1377	done
1378	fi
1379
1380	if [[ "$module_commands" != "" ]]
1381	then
1382	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1384	line=$(echo "$module_commands" \| cut -c46-)
1385	while [[ "$line" != "" ]]
1386	do
1387	column1=""
1388	column2=$(echo "$line" \| cut -c-45)
1389	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1390	line=$(echo "$line" \| cut -c46-)
1391	done
1392	fi
1393	printf "\| \| \n"
1394	column1="base name of files:"; column2=$fname
1395	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1396	column1="activation string list:"; column2=$(echo $activation_string_list)
1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1398
1399	if [[ "$ocean_file_appendix" = true ]]
1400	then
1401	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1402	fi
1403
1404	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
1405	then
1406	column1="memory demand / PE":; column2="$memory MB"
1407	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1408	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
1409	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1410	fi
1411
1412	if [[ "$source_list" != "" ]]
1413	then
1414	printf "\| \| \n"
1415	printf "\| Files to be compiled: \| \n"
1416	line=$source_list
1417	while [[ "$line" != "" ]]
1418	do
1419	linestart=$(echo $line \| cut -c-70)
1420	printf "\| %-70s \| \n" "$linestart"
1421	line=$(echo "$line" \| cut -c71-)
1422	done
1423	fi
1424	printf "#------------------------------------------------------------------------#"
1425
1426
1427
1428	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1429	if [[ $do_trace = true ]]
1430	then
1431	(( i = 0 ))
1432	while (( i < iin ))
1433	do
1434	(( i = i + 1 ))
1435	if (( i == 1 ))
1436	then
1437	printf "\n\n >>> INPUT-file assignments:\n"
1438	fi
1439	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1440	done
1441	(( i = 0 ))
1442	while (( i < iout ))
1443	do
1444	(( i = i + 1 ))
1445	if (( i == 1 ))
1446	then
1447	printf "\n\n >>> OUTPUT-file assignments:\n"
1448	fi
1449	printf "\n ${localout[$i]} : ${pathout[$i]}"
1450	done
1451	(( i = 0 ))
1452	while (( i < iic ))
1453	do
1454	(( i = i + 1 ))
1455	if (( i == 1 ))
1456	then
1457	printf "\n\n >>> INPUT-commands:\n"
1458	fi
1459	printf "\n ${in_command[$i]}"
1460	done
1461	(( i = 0 ))
1462	while (( i < ioc ))
1463	do
1464	(( i = i + 1 ))
1465	if (( i == 1 ))
1466	then
1467	printf "\n\n >>> OUTPUT-commands:\n"
1468	fi
1469	printf "\n ${out_command[$i]}"
1470	done
1471	fi
1472
1473	# QUERY FOR CONTINUE
1474	if [[ $silent = false && $running_in_batch_mode = false ]]
1475	then
1476	antwort=dummy
1477	printf "\n\n"
1478	printf " >>> everything o.k. (y/n) ? "
1479	while read antwort
1480	do
1481	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1482	then
1483	printf " >>> everything o.k. (y/n) ? "
1484	else
1485	break
1486	fi
1487	done
1488	if [[ $antwort = n \|\| $antwort = N ]]
1489	then
1490	locat=user_abort; (( iec = 0 )); exit
1491	fi
1492	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1493	then
1494	printf " *** batch-job will be created and submitted"
1495	else
1496	printf " *** PALMRUN will now continue to execute on this machine"
1497	fi
1498	fi
1499
1500
1501
1502	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1503	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1504	then
1505
1506	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1507	then
1508	printf "\n\n *** creating executable and other sources for the remote host"
1509	else
1510	printf "\n\n *** creating executable and other sources for the local host"
1511	fi
1512
1513	palmbuild -v -h $host -d $fname
1514	rm -rf SOURCES_FOR_RUN_$fname
1515
1516	if [[ $? != 0 ]]
1517	then
1518
1519	# ABORT IN CASE OF COMPILATION PROBLEMS
1520	printf "\n +++ error while creating executable and/or other sources"
1521	locat=execution
1522	exit
1523
1524	else
1525
1526	printf "\n$dashes\n *** executable and other sources created\n"
1527
1528	fi
1529
1530	fi
1531
1532
1533	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1534	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1535	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1536	then
1537
1538	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1539	if [[ $running_in_batch_mode = false ]]
1540	then
1541	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1542	# FOLDER
1543	mkdir -p $TEMPDIR
1544	chmod go+rx $TEMPDIR
1545	tmpcreate=true
1546	cd $TEMPDIR
1547	cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
1548	printf "\n *** changed to temporary directory: $TEMPDIR"
1549
1550	else
1551
1552	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1553	printf "\n *** running in temporary directory: $TEMPDIR"
1554
1555	fi
1556
1557
1558	# PROVIDE THE INPUT FILES
1559	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1560	(( i = 0 ))
1561	while (( i < iin ))
1562	do
1563	(( i = i + 1 ))
1564	if (( i == 1 ))
1565	then
1566	printf "\n\n *** providing INPUT-files:\n$dashes"
1567	fi
1568
1569
1570	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1571	if [[ "${transin[$i]}" = unavailable ]]
1572	then
1573	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1574	then
1575	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1576	printf "\n is not available!"
1577	else
1578	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1579	printf "\n is not available!"
1580	fi
1581	continue
1582	fi
1583
1584	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1585	files_for_cores=false; filetype=file
1586	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1587	then
1588	files_for_cores=true; filetype=files
1589	actionin[$i]=""
1590	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1591	then
1592	actionin[$i]=""
1593	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1594	then
1595	files_for_cores=true; filetype=files
1596	actionin[$i]="ln"
1597	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1598	then
1599	actionin[$i]="ln"
1600	fi
1601
1602	if [[ $files_for_cores = true ]]
1603	then
1604	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1605	else
1606	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1607	fi
1608
1609	# INPUT-FILES TO BE LINKED
1610	if [[ "${actionin[$i]}" = ln ]]
1611	then
1612
1613	printf "\n $filetype will be linked"
1614	if [[ $files_for_cores = false ]]
1615	then
1616	if [[ -f "${absnamein[$i]}" ]]
1617	then
1618	ln ${absnamein[$i]} ${localin[$i]}
1619	got_tmp[$i]=true
1620	fi
1621	else
1622	if [[ -d "${absnamein[$i]}" ]]
1623	then
1624	mkdir ${localin[$i]}
1625	cd ${absnamein[$i]}
1626	for file in $(ls *)
1627	do
1628	ln $file $TEMPDIR/${localin[$i]}
1629	done >\|/dev/null 2>&1
1630	cd $TEMPDIR
1631	fi
1632
1633	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1634	if [[ ! -f "${localin[$i]}/_000000" ]]
1635	then
1636	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1637	cp -r ${absnamein[$i]}/* ${localin[$i]}
1638	fi
1639
1640	got_tmp[$i]=true
1641	fi
1642	fi
1643
1644	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1645	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1646	then
1647
1648	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1649	then
1650
1651	# FILE COPIES ARE PROVIDED FOR ALL CORES
1652	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1653	printf "\n file will be provided for $cores processors"
1654	mkdir ${localin[$i]}
1655	ival=$cores
1656	(( ii = 0 ))
1657	while (( ii <= ival-1 ))
1658	do
1659	if (( ii < 10 ))
1660	then
1661	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1662	elif (( ii < 100 ))
1663	then
1664	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1665	elif (( ii < 1000 ))
1666	then
1667	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1668	else
1669	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1670	fi
1671	(( ii = ii + 1 ))
1672	done
1673
1674	else
1675
1676	if [[ $files_for_cores = true ]]
1677	then
1678
1679	# PROVIDE FILES FOR EACH CORE
1680	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1681	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1682	printf "\n providing $cores files for the respective cores"
1683	mkdir ${localin[$i]}
1684	if [[ $link_local_input = true ]]
1685	then
1686	printf " files will be linked\n"
1687	cd ${absnamein[$i]}
1688	for file in $(ls *)
1689	do
1690	ln -f $file ${localin[$i]}
1691	done
1692	cd $TEMPDIR
1693	fi
1694
1695	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1696	if [[ ! -f "${localin[$i]}/_000000" ]]
1697	then
1698	if [[ $link_local_input = true ]]
1699	then
1700	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1701	fi
1702	cp -r ${absnamein[$i]}/* ${localin[$i]}
1703	fi
1704
1705	else
1706
1707	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1708	if [[ $link_local_input = true ]]
1709	then
1710	printf " file will be linked\n"
1711	ln -f ${absnamein[$i]} ${localin[$i]}
1712	fi
1713	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
1714	if [[ ! -f "${localin[$i]}" ]]
1715	then
1716	if [[ $link_local_input = true ]]
1717	then
1718	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1719	fi
1720	cp ${absnamein[$i]} ${localin[$i]}
1721	fi
1722	fi
1723	fi
1724	fi
1725
1726	done
1727	if (( i != 0 ))
1728	then
1729	printf "\n$dashes\n *** all INPUT-files provided \n"
1730	fi
1731
1732
1733	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1734	(( i = 0 ))
1735	while (( i < iic ))
1736	do
1737	(( i = i + 1 ))
1738	if (( i == 1 ))
1739	then
1740	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1741	fi
1742	printf "\n >>> ${in_command[$i]}"
1743	eval ${in_command[$i]}
1744	if (( i == iic ))
1745	then
1746	printf "\n$dashes\n"
1747	fi
1748	done
1749
1750
1751	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1752	# (FILE ENVPAR WILL BE READ BY PALM)
1753	cat > ENVPAR << EOF
1754	&envpar run_identifier = '$fname', host = '$host',
1755	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1756	maximum_parallel_io_streams = $maximum_parallel_io_streams,
1757	maximum_cpu_time_allowed = ${cpumax}.,
1758	revision = '$global_revision',
1759	batch_job = .${running_in_batch_mode}. /
1760
1761	EOF
1762
1763
1764	# STARTING THE EXECUTABLE
1765	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
1766	PATH=$PATH:$TEMPDIR
1767
1768
1769	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1770	line=`echo "${execute_command}" \| sed 's/@MPI_TASKS@/$mpi_tasks/g' \| sed 's/@TASKS_PER_NODE@/$tasks_per_node/g'`
1771	line2=`echo "${execute_command}" \| sed 's/@MPI_TASKS@/1/g' \| sed 's/@TASKS_PER_NODE@/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
1772	eval line=\"$line\"
1773	execute_command="$line"
1774
1775
1776	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1777	eval line2=\"$line2\"
1778	execute_command_for_combine="$line2"
1779
1780
1781	# PROVIDE A HOSTFILE, IF REQUIRED
1782	if [[ "$hostfile" != "" ]]
1783	then
1784
1785	if [[ $hostfile = auto ]]
1786	then
1787	# CREATE A NEW HOSTFILE
1788	(( ii = 1 ))
1789	while (( ii <= cores / threads_per_task ))
1790	do
1791	echo $(hostname) >> hostfile
1792	(( ii = ii + 1 ))
1793	done
1794	if (( cores / threads_per_task == 0 ))
1795	then
1796	echo $(hostname) >> hostfile
1797	fi
1798
1799	else
1800	cp $hostfile hostfile
1801	fi
1802	eval line=\"`head -n $ii hostfile`\"
1803	printf "\n *** running on: $line"
1804	fi
1805
1806
1807
1808	# SET THE NUMBER OF OPENMP-THREADS
1809	if [[ $use_openmp = true ]]
1810	then
1811	export OMP_NUM_THREADS=$threads_per_task
1812	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1813	else
1814	export OMP_NUM_THREADS=1
1815	fi
1816
1817
1818	# PROVIDE DATA FOR
1819	if [[ $run_coupled_model = false ]]
1820	then
1821	if [[ "$ocean_file_appendix" = true ]]
1822	then
1823	echo "precursor_ocean" > coupling_steering
1824	else
1825	echo "precursor_atmos" > coupling_steering
1826	fi
1827	else
1828	(( iia = $cores_atmos / $threads_per_task ))
1829	(( iio = $cores_ocean / $threads_per_task ))
1830	printf "\n coupled run ($iia atmosphere, $iio ocean)"
1831	printf "\n\n"
1832	echo "coupled_run $iia $iio" > coupling_steering
1833	fi
1834
1835	printf "\n *** execute command:"
1836	printf "\n \"$execute_command\" \n\n"
1837
1838	$execute_command < coupling_steering
1839
1840	if [[ $? != 0 ]]
1841	then
1842
1843	# ABORT IN CASE OF RUNTIME ERRORS
1844	printf "\n +++ runtime error occured"
1845	locat=execution
1846	exit
1847
1848	else
1849
1850	printf "\n$dashes\n *** execution finished \n"
1851
1852	fi
1853
1854
1855	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
1856	# BY EACH CORE INTO ONE FILE
1857	if [[ ! -f combine_plot_fields.x ]]
1858	then
1859
1860	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
1861	printf "\n 2d- and/or 3d-data may be incomplete!"
1862	printf "\n Your previous palmbuild may have failed. Please check.\n"
1863
1864	elif [[ "$combine_plot_fields" == true ]]
1865	then
1866
1867	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
1868	$execute_command_for_combine
1869
1870	else
1871
1872	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
1873	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
1874	# ??? koennen wir das streichen ???
1875	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
1876	fi
1877
1878
1879
1880	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1881	(( i = 0 ))
1882	while (( i < ioc ))
1883	do
1884	(( i = i + 1 ))
1885	if (( i == 1 ))
1886	then
1887	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
1888	fi
1889	printf "\n >>> ${out_command[$i]}"
1890	eval ${out_command[$i]}
1891	if (( i == ioc ))
1892	then
1893	printf "\n$dashes\n"
1894	fi
1895	done
1896
1897
1898	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
1899	if [[ $do_trace = true ]]
1900	then
1901	printf "\n\n"
1902	ls -al
1903	fi
1904
1905
1906	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
1907	(( i = 0 ))
1908	while (( i < iout ))
1909	do
1910	(( i = i + 1 ))
1911	if (( i == 1 ))
1912	then
1913	printf "\n\n *** saving OUTPUT-files:"
1914
1915	# GET RUN NUMBER ASSIGNED BY PALM
1916	if [[ -f RUN_NUMBER ]]
1917	then
1918	read run_number < RUN_NUMBER
1919	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
1920	usecycle_option="-U $run_number"
1921	else
1922	run_number=0
1923	usecycle_option=""
1924	fi
1925	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
1926	then
1927	printf "\n *** SCP transfers to local host via remote login-node \"$remote_loginnode\" "
1928	fi
1929	printf "\n$dashes"
1930	fi
1931
1932	# ADD CYCLE NUMBER TO FILENAME
1933	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1934	then
1935
1936	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
1937	if [[ "${actionout[$i]}" != "a" ]]
1938	then
1939	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
1940	# WITH AN EXISTING CYCLE NUMBER
1941	if (( run_number >= cycnum[$i] ))
1942	then
1943	(( cycnum[$i] = run_number ))
1944	else
1945	if (( run_number > 0 ))
1946	then
1947	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
1948	fi
1949	fi
1950	fi
1951	if (( cycnum[$i] > 0 ))
1952	then
1953	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
1954	fi
1955	fi
1956
1957	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1958	files_for_cores=false; filetype=file
1959	link_local_output=false
1960	if [[ "${actionout[$i]}" = pe && -n $cores ]]
1961	then
1962	files_for_cores=true; filetype=directory
1963	actionout[$i]=""
1964	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
1965	then
1966	actionout[$i]=""
1967	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
1968	then
1969	files_for_cores=true; filetype=directory
1970	link_local_output=true
1971	actionout[$i]=""
1972	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
1973	then
1974	link_local_output
1975	actionout[$i]=""
1976	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
1977	then
1978	files_for_cores=true; filetype=directory
1979	actionout[$i]="tr"
1980	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
1981	then
1982	actionout[$i]="tr"
1983	fi
1984
1985	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
1986	then
1987	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
1988	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
1989	then
1990	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
1991	else
1992
1993
1994	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
1995	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
1996	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
1997	then
1998	if [[ $running_on_remote = true ]]
1999	then
2000
2001	# SET OPTIONS FOR TRANSFER
2002	if [[ "${actionout[$i]}" = tr ]]
2003	then
2004	if [[ $files_for_cores = false ]]
2005	then
2006	catalog_option=""
2007	catalog_string=""
2008	else
2009	catalog_option="-c"
2010	catalog_string="/"
2011	fi
2012	append_option=""
2013	append_string=""
2014	else
2015	append_option="-A"
2016	append_string="append"
2017	fi
2018
2019	transfer_failed=false
2020	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2021	printf "\n ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}$catalog_string\n"
2022
2023	# TRANSFER VIA SCP
2024	if [[ "$remote_loginnode" != "" ]]
2025	then
2026	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
2027	else
2028	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]}
2029	fi
2030	[[ $? != 0 ]] && transfer_failed=true
2031
2032
2033	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2034	if [[ $transfer_failed = true ]]
2035	then
2036	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2037	printf " ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id\n"
2038
2039	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2040	eval local_catalog=${pathout[$i]}
2041	if [[ ! -d $local_catalog ]]
2042	then
2043	printf " *** local directory does not exist. Trying to create:\n"
2044	printf " $local_catalog \n"
2045	mkdir -p $local_catalog
2046	fi
2047	eval cp ${localout[$i]} ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id
2048	transfer_problems=true
2049	fi
2050
2051	else
2052
2053	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2054	# BE COPIED OR APPENDED ON THIS MACHINE
2055	if [[ "${actionout[$i]}" = tr ]]
2056	then
2057	actionout[$i]=""
2058	else
2059	actionout[$i]="a"
2060	fi
2061	fi
2062	fi
2063
2064
2065	# APPEND ON THIS MACHINE
2066	if [[ "${actionout[$i]}" = "a" ]]
2067	then
2068	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2069	then
2070	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2071	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2072	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2073	else
2074	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2075	printf "\n ${pathout[$i]}\n"
2076	cat ${localout[$i]} >> ${pathout[$i]}
2077	fi
2078	fi
2079
2080	# COPY ON THIS MACHINE
2081	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2082	# ON DIFFERENT FILE-SYSTEMS
2083	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2084	then
2085
2086	# COPY IN CASE OF RUNS ON SINGLE CORES
2087	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2088	then
2089	printf "\n >>> OUTPUT: ${localout[$i]} to"
2090	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2091	if [[ $link_local_output = true ]]
2092	then
2093	printf " file will be linked\n"
2094	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2095	fi
2096	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2097	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2098	then
2099	if [[ $link_local_output = true ]]
2100	then
2101	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2102	fi
2103	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2104	else
2105	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2106	fi
2107	else
2108	printf "\n >>> OUTPUT: ${localout[$i]} to"
2109	printf "\n ${pathout[$i]}\n"
2110	if [[ $link_local_output = true ]]
2111	then
2112	printf " file will be linked\n"
2113	ln -f ${localout[$i]} ${pathout[$i]}
2114	fi
2115	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2116	if [[ ! -f "${pathout[$i]}" ]]
2117	then
2118	if [[ $link_local_output = true ]]
2119	then
2120	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2121	fi
2122	cp ${localout[$i]} ${pathout[$i]}
2123	else
2124	printf "+++ no copy because file ${pathout[$i]} exists\n"
2125	fi
2126	fi
2127
2128	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2129	then
2130
2131	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2132	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2133	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2134	printf "\n ${pathout[$i]}\n"
2135	if [[ $link_local_output = true ]]
2136	then
2137	printf " files will be linked\n"
2138	mkdir ${pathout[$i]}
2139	cd ${localout[$i]}
2140	for file in $(ls *)
2141	do
2142	ln -f $file ${pathout[$i]}
2143	done >\|/dev/null 2>&1
2144	cd $TEMPDIR
2145	fi
2146
2147	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2148	if [[ ! -f "${pathout[$i]}/_000000" ]]
2149	then
2150	if [[ $link_local_output = true ]]
2151	then
2152	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2153	fi
2154	cp -r ${localout[$i]}/* ${pathout[$i]}
2155	fi
2156
2157	fi
2158	fi
2159	done
2160
2161	if (( i != 0 ))
2162	then
2163	if [[ $transfer_problems = true ]]
2164	then
2165	printf "\n$dashes\n *** OUTPUT-files saved"
2166	printf "\n +++ WARNING: some data transfers failed! \n"
2167	else
2168	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2169	fi
2170	fi
2171
2172
2173	# IF REQUIRED, START A RESTART-JOB
2174	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2175	if [[ -f CONTINUE_RUN ]]
2176	then
2177
2178	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2179	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2180	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2181	# -b START A BATCH JOB
2182	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2183	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2184	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2185
2186
2187	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2188	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2189	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2190	then
2191	prc=`echo $prc \| sed 's/#/r/g'`
2192	fi
2193
2194
2195	# START THE RESTART-JOB
2196	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2197	echo " $prc"
2198	printf "\n$dashes\n"
2199	if [[ $running_on_remote = true ]]
2200	then
2201
2202	echo "*** ssh will be used to initiate restart-runs!"
2203	echo " return_address=\"$return_address\" "
2204	echo " return_username=\"$local_username\" "
2205
2206	if [[ "$remote_loginnode" != "" ]]
2207	then
2208	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
2209	else
2210	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2211	fi
2212
2213	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2214	sleep 30
2215
2216	else
2217
2218	# START THE RESTART JOB ON THE LOCAL HOST
2219	eval $prc # THE ' MUST BE EVALUATED
2220	cd - > /dev/null
2221
2222	fi
2223	printf "\n$dashes\n *** restart-run initiated \n"
2224
2225
2226	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2227	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2228	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2229	# MAY BE VERY HUGE)
2230	(( i = 0 ))
2231	while (( i < iin ))
2232	do
2233	(( i = i + 1 ))
2234	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2235	then
2236	rm -r ${absnamein[$i]}
2237	fi
2238	done
2239
2240	fi
2241
2242
2243	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2244	cd $HOME
2245	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
2246
2247
2248	else
2249
2250
2251	# PREPARING ACTIONS,
2252	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2253
2254	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2255	palmrun_com="$palmrun_script_name -c $config_file -d $fname -h $host -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2256	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2257	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2258	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2259	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2260	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2261	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2262	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2263	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2264	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2265	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2266	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2267	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2268	if [[ $create_remote_batch_job = true ]]
2269	then
2270	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2271	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2272	elif [[ $create_batch_job = true ]]
2273	then
2274	palmrun_com=${palmrun_com}" -j"
2275	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2276	fi
2277
2278
2279	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2280	# REMOTE HOST
2281	job_protocol_file_local=${local_jobcatalog}/${host}_${job_id}
2282	job_protocol_file=$job_protocol_file_local
2283	if [[ $create_remote_batch_job = true ]]
2284	then
2285	job_protocol_file_remote=${remote_jobcatalog}/${host}_${job_id}
2286	job_protocol_file=$job_protocol_file_remote
2287	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2288	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2289	fi
2290
2291
2292	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2293	jobfile=jobfile.$run_id
2294
2295
2296	# FIRST CREATE THE BATCH DIRECTIVES
2297	(( i = 0 ))
2298	while (( i < ibd ))
2299	do
2300	(( i = i + 1 ))
2301	line=`echo "${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@/$queue/g'`
2302	eval line=\"$line\"
2303	echo "$line" >> $jobfile
2304	done
2305	echo " " >> $jobfile
2306
2307
2308	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2309	# PROTOCOL
2310	if [[ $create_remote_batch_job = true ]]
2311	then
2312	echo "set +vx" >> $jobfile
2313	echo "trap '" >> $jobfile
2314	echo "set +vx" >> $jobfile
2315	echo "cd ${remote_jobcatalog}" >> $jobfile
2316	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2317
2318	# ADD THE BATCH DIRECTIVES
2319	(( i = 0 ))
2320	while (( i < ibdt ))
2321	do
2322	(( i = i + 1 ))
2323	line=`echo "${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'`
2324	eval line=\"$line\"
2325	echo "$line" >> $jobfile
2326	done
2327	echo " " >> $jobfile
2328
2329	echo "set -x" >> $jobfile
2330	echo "${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
2331	echo "%%END%%" >> $jobfile
2332	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2333	echo "$submit_command $scpjob_file" >> $jobfile
2334	echo "rm $scpjob_file" >> $jobfile
2335	echo "rm $job_transfer_protocol_file" >> $jobfile
2336	echo "set -x" >> $jobfile
2337	echo " ' exit" >> $jobfile
2338	fi
2339
2340
2341	# ACTIVATE ERROR-TRACEBACK
2342	if [[ $do_trace = true ]]
2343	then
2344	echo "set -x" >> $jobfile
2345	else
2346	echo "set +vx" >> $jobfile
2347	fi
2348
2349
2350	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2351	if [[ "$login_init_cmd" != "" ]]
2352	then
2353	echo "$login_init_cmd" >> $jobfile
2354	fi
2355	if [[ "$module_commands" != "" ]]
2356	then
2357	echo "$module_commands" >> $jobfile
2358	fi
2359
2360
2361	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2362	echo "mkdir $TEMPDIR" >> $jobfile
2363	echo "cd $TEMPDIR" >> $jobfile
2364	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
2365	echo "cp $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
2366	echo "export PATH=.:\$PATH" >> $jobfile
2367	echo "export execute_palmrun=true" >> $jobfile
2368
2369
2370	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
2371	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
2372	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
2373	if [[ $create_remote_batch_job = true ]]
2374	then
2375	(( i = 0 ))
2376	while (( i < iin ))
2377	do
2378	(( i = i + 1 ))
2379	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
2380	if [[ "${transin[$i]}" = job ]]
2381	then
2382	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
2383	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
2384	echo " " >> $jobfile
2385	echo "%END%" >> $jobfile
2386	else
2387	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
2388	fi
2389
2390	# CHECK, IF FILE COULD BE CREATED
2391	echo "if [[ \$? = 1 ]]" >> $jobfile
2392	echo "then" >> $jobfile
2393	echo " echo \" \" " >> $jobfile
2394	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
2395	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
2396	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
2397	echo " execute_palmrun=false" >> $jobfile
2398	echo "fi" >> $jobfile
2399	done
2400	fi
2401
2402
2403	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2404	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2405	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2406	echo "LOCAL_PWD=$working_directory" >> $jobfile
2407	echo "export LOCAL_PWD" >> $jobfile
2408
2409
2410	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2411	echo "LOCAL_PALMRUN_PATH=$PALM_BIN" >> $jobfile
2412	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2413
2414
2415	# CALL PALMRUN WITHIN THE JOB
2416	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2417	echo "set -x" >> $jobfile
2418	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2419
2420
2421	# TRANSFER JOBFILE TO THE TARGET HOST
2422	if [[ $create_jobfile_only = false ]]
2423	then
2424
2425	if [[ $create_remote_batch_job = true ]]
2426	then
2427
2428	echo " *** transfer of job to remote host via scp"
2429	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${job_directory}/${host}_${job_id}"
2430	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${job_directory}/${host}_${job_id}
2431
2432	echo " "
2433	echo " *** submit the job"
2434	echo " cd $job_directory; $submit_command ${host}_${job_id}; rm ${host}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2435	echo "cd $job_directory; $submit_command ${host}_${job_id}; rm ${host}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2436
2437	elif [[ $create_batch_job = true ]]
2438	then
2439
2440	eval job_directory=$job_directory
2441	cp $jobfile ${job_directory}/${host}_${job_id}
2442	cd $job_directory
2443	echo " "
2444	echo "--- submit the job"
2445	echo "$submit_command ${host}_${job_id}"
2446	$submit_command ${host}_${job_id}
2447	rm ${host}_${job_id}
2448	cd - > /dev/null
2449
2450	fi
2451
2452	rm -rf $jobfile
2453
2454	else
2455
2456	printf "\n *** jobfile created under name \"$jobfile\" "
2457	printf "\n no batch-job has been sent!"
2458
2459	fi
2460
2461	fi # END OF REMOTE-PART

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