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source: palm/trunk/SCRIPTS/palmrun @ 2384

Last change on this file since 2384 was 2384, checked in by raasch, 7 years ago
small changes and bugfixes for new palm-scripts
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 81.8 KB

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

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