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source: palm/trunk/SCRIPTS/palmrun @ 2404

Last change on this file since 2404 was 2404, checked in by raasch, 7 years ago
further simplifications in palmrun and palmbuild
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 82.3 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 2404 2017-09-05 09:33:14Z raasch $
29	#
30	#
31	#--------------------------------------------------------------------------------#
32	# palmrun - script for running PALM jobs on local and remote hosts
33	#--------------------------------------------------------------------------------#
34
35
36
37	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
38
39	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
40	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
41	# (TOO MANY ARGUMENTS - PROBLEM)
42	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
43
44	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
45	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
46	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
47	# SCRIPT-OPTION ARGUMENTS
48	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
49	typeset -i icycle inode ival maxcycle mpi_tasks
50	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
51
52	activation_string_list=""
53	AddFilenames=""
54	combine_plot_fields=true
55	compiler_name=""
56	compiler_name_ser=""
57	compiler_options=""
58	config_file=""
59	cores=""
60	cores_atmos=0
61	cores_ocean=0
62	coupled_dist=""
63	cpp_options=""
64	cpumax=0
65	create_jobfile_only=false
66	delete_temporary_catalog=true
67	create_batch_job=false
68	create_remote_batch_job=false
69	dashes=" ----------------------------------------------------------------------------"
70	defaultqueue=""
71	do_compile=true
72	do_trace=false
73	executable=""
74	execute_command=""
75	execution_error=false
76	fileconnection_file=.palm.iofiles
77	fname=test
78	global_revision=""
79	host="default"
80	hostfile=""
81	hp=""
82	keep_data_from_previous_run=false
83	link_local_input=false
84	link_local_output=false
85	linker_options=""
86	local_jobcatalog=""
87	locat=normal
88	makefile=""
89	max_par_io_str=""
90	prc=$0
91	while [[ $(echo $prc \| grep -c "/") != 0 ]]
92	do
93	prc=`echo $prc \| cut -f2- -d"/"`
94	done
95	module_calls=""
96	palmrun_script_name=$prc
97	openmp=false
98	queue=none
99	restart_run=false
100	return_address=""
101	remote_jobcatalog=""
102	remote_username=""
103	running_in_batch_mode=false
104	run_coupled_model=false
105	run_id=""
106	silent=false
107	source_list=""
108	source_path=""
109	tasks_per_node=""
110	threads_per_task=1
111	tmpcreate=false
112	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 'if [[ $locat != normal && $locat != control_c ]]
123	then
124
125	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
126	(( i = 0 ))
127	while (( i < iec ))
128	do
129	(( i = i + 1 ))
130	printf "\n *** Execution of ERROR-command:\n"
131	printf " >>> ${err_command[$i]}\n"
132	eval ${err_command[$i]}
133	done
134	if [[ $tmpcreate = true ]]
135	then
136	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
137	fi
138	printf "\n\n+++ palmrun killed \n\n"
139	elif [[ $locat != control_c ]]
140	then
141	printf "\n\n --> palmrun finished\n\n"
142	if [[ $running_on_remote = true ]]
143	then
144	printf " Bye, bye $remote_username !!\n\n"
145	else
146	printf " Bye, bye $local_username !!\n\n"
147	fi
148	fi' exit
149
150
151	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
152	trap '[[ $tmpcreate = true ]] && (cd; rm -rf $TEMPDIR)
153	printf "\n+++ palmrun killed by \"^C\" \n\n"
154	locat=control_c
155	exit
156	' 2
157
158
159	# CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
160	# BEEN SET
161	if [[ "$PALM_BIN" = "" ]]
162	then
163	printf "\n +++ environment variable PALM_BIN has not been set"
164	printf "\n please set it to the directory where the PALM scripts are located"
165	locat=palm_bin; exit
166	fi
167	export PATH=$PALM_BIN:$PATH
168
169
170
171	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
172	# WHICH WILL BE USED TO START RESTART-JOBS
173	while getopts :a:bBc:Cd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
174	do
175	case $option in
176	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
177	(b) create_batch_job=true; prc="$prc -b";;
178	(B) delete_temporary_catalog=false; prc="$prc -B";;
179	(c) config_file=$OPTARG; prc="$prc -c$OPTARG";;
180	(C) restart_run=true; prc="$prc -C";;
181	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
182	(F) create_jobfile_only=true;;
183	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
184	(h) host=$OPTARG; prc="$prc -h$OPTARG";;
185	(j) running_in_batch_mode=true;;
186	(k) keep_data_from_previous_run=true; prc="$prc -k";;
187	(m) memory=$OPTARG; prc="$prc -m$OPTARG";;
188	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
189	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
190	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
191	(r) run_id=$OPTARG;;
192	(R) return_address=$OPTARG;;
193	(s) source_list=$OPTARG;;
194	(t) cpumax=$OPTARG; prc="$prc -t$OPTARG";;
195	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
196	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
197	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
198	(v) silent=true; prc="$prc -v";;
199	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
200	(x) do_trace=true;set -x; prc="$prc -x";;
201	(X) cores=$OPTARG; prc="$prc -X$OPTARG";;
202	(y) ocean_file_appendix=true; prc="$prc -y";;
203	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
204	(Z) combine_plot_fields=false; prc="$prc -Z";;
205	(\?) printf "\n +++ unknown option $OPTARG \n"
206	printf "\n --> type \"$0 ?\" for available options \n"
207	locat=parameter;exit;;
208	esac
209	done
210
211
212	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
213	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
214	(( to_shift = $OPTIND - 1 ))
215	shift $to_shift
216
217	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
218	if [[ "$1" = "?" ]]
219	then
220	(printf "\n *** Description of available palmrun options:\n"
221	printf "\n Option Description Default-Value"
222	printf "\n -a activation string list \"\" "
223	printf "\n -b batch-job on local machine ---"
224	printf "\n -B do not delete temporary directory at end ---"
225	printf "\n -c configuration file .palm.config.default"
226	printf "\n -d base name of files attached to program test"
227	printf "\n -F create batch job file only ---"
228	printf "\n -h execution host \"default\" "
229	printf "\n -k keep data from previous run"
230	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
231	printf "\n -M Makefile name Makefile"
232	printf "\n -O threads per openMP task ---"
233	printf "\n -q queue \"$queue\" "
234	printf "\n -s filenames of routines to be compiled \"\" "
235	printf "\n must end with .f, .f90, .F, or .c !"
236	printf "\n use \"..\" for more than one file and wildcards"
237	printf "\n -s LM compiles all locally modified files"
238	printf "\n -t allowed cpu-time in seconds (batch) 0"
239	printf "\n -T tasks per node ---"
240	printf "\n -u username on remote machine \"\" "
241	printf "\n -v no prompt for confirmation ---"
242	printf "\n -w maximum parallel io streams as given by -X"
243	printf "\n -x tracing of palmrun for debug purposes ---"
244	printf "\n -X # of processors (on parallel machines) 1"
245	printf "\n -y add appendix \"_O\" to all local output"
246	printf "\n files (ocean precursor runs followed by"
247	printf "\n coupled atmosphere-ocean runs) ---"
248	printf "\n -Y run coupled model, \"#1 #2\" with"
249	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
250	printf "\n -Z skip combine_plot_fields at the end of "
251	printf "\n the simulation ---"
252	printf "\n "
253	printf "\n Possible values of positional parameter <modus>:"
254	printf "\n \"?\" - this outline \n\n") \| more
255	exit
256	elif [[ "$1" != "" ]]
257	then
258	printf "\n +++ positional parameter $1 unknown \n"
259	locat=parameter; exit
260	fi
261
262
263
264	# SHORT STARTING MESSAGE
265	printf "\n*** $version "
266	printf "\n will be executed. Please wait ..."
267
268
269	# BUILD THE CONFIGURATION-FILE NAME
270	if [[ "$config_file" = "" ]]
271	then
272	config_file=.palm.config.$host
273	fi
274
275
276	# CHECK, IF CONFIGURATION FILE EXISTS
277	if [[ ! -f $config_file ]]
278	then
279	printf "\n\n +++ configuration file: "
280	printf "\n $config_file"
281	printf "\n does not exist"
282	locat=connect; exit
283	fi
284
285
286	# CHECK, IF FILE CONNECTION FILE EXISTS
287	if [[ ! -f $fileconnection_file ]]
288	then
289	printf "\n\n +++ file connection file: "
290	printf "\n $fileconnection_file"
291	printf "\n does not exist"
292	locat=connect; exit
293	fi
294
295
296	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
297	if [[ "$activation_string_list" = "" ]]
298	then
299	printf "\n\n +++ no activation string list given: "
300	printf "\n please set palmrun option \"-a\" "
301	locat=palmrun_option; exit
302	fi
303
304
305	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
306	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
307	then
308	write_binary=true
309	else
310	write_binary=false
311	fi
312
313
314	# READ AND EVALUATE THE CONFIGURATION-FILE
315	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
316
317	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
318	while read line
319	do
320
321	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
322	eval line=\"$line\"
323
324
325	# INTERPRET THE LINE
326	if [[ "$(echo $line)" = "" ]]
327	then
328
329	# EMPTY LINE, NO ACTION
330	continue
331
332	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
333	then
334
335	# LINE IS A COMMENT LINE
336	continue
337
338	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
339	then
340
341	# LINE DEFINES AN ENVIRONMENT-VARIABLE
342	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
343	value=`echo $line \| cut -d" " -s -f2-`
344
345
346	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
347	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
348	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
349	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
350	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
351	# CONFIGURATION-FILE.
352	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
353	then
354	eval export $var="\$value"
355
356	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
357	if [[ $do_trace = true ]]
358	then
359	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
360	fi
361	fi
362
363	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
364	then
365
366	# LINE DEFINES BATCH-DIRECTIVE
367	(( ibd = ibd + 1 ))
368	line=$(echo $line \| cut -c4-)
369	batch_directive[$ibd]="$line"
370
371	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
372	then
373
374	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
375	# REMOTE TO A LOCAL HOST
376	(( ibdt = ibdt + 1 ))
377	line=$(echo $line \| cut -c5-)
378	batch_directive_transfer[$ibdt]="$line"
379
380	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
381	then
382
383	# LINE DEFINES ERROR-COMMAND
384	(( iec = iec + 1 ))
385	line=$(echo $line \| cut -c4-)
386	err_command[$iec]="$line"
387
388	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
389	then
390
391	# LINE DEFINES INPUT-COMMAND
392	(( iic = iic + 1 ))
393	line=$(echo $line \| cut -c4-)
394	in_command[$iic]="$line"
395
396	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
397	then
398
399	# LINE DEFINES OUTPUT-COMMAND
400	(( ioc = ioc + 1 ))
401	line=$(echo $line \| cut -c4-)
402	out_command[$ioc]="$line"
403
404	else
405
406	# SKIP ALL OTHER LINES
407	continue
408
409	fi
410
411	done < $config_file
412
413
414	# CHECK SETTING OF REQUIRED PARAMETERS
415	if [[ "$compiler_name" = "" ]]
416	then
417	printf "\n +++ no compiler name found in $config_file"
418	printf "\n Please add line \"compiler_name ...\" to that file."
419	locat=config_file; exit
420	fi
421	if [[ "$compiler_name_ser" = "" ]]
422	then
423	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
424	printf "\n Please add line \"compiler_name_ser ...\" to that file."
425	locat=config_file; exit
426	fi
427	if [[ "$compiler_options" = "" ]]
428	then
429	printf "\n +++ no compiler options found in $config_file"
430	printf "\n Please add line \"compiler_options ...\" to that file."
431	locat=config_file; exit
432	fi
433	if [[ "$linker_options" = "" ]]
434	then
435	printf "\n +++ no linker options found in $config_file"
436	printf "\n Please add line \"linker_options ...\" to that file."
437	locat=config_file; exit
438	fi
439	if [[ "$execute_command" = "" ]]
440	then
441	printf "\n +++ no execute command found in $config_file"
442	printf "\n Please add line \"execute_command ...\" to that file."
443	locat=config_file; exit
444	fi
445
446	if [[ "$hostfile" != "" ]]
447	then
448	if [[ $hostfile != auto && ! -f $hostfile ]]
449	then
450	printf "\n +++ no hostfile \"$hostfile\" found"
451	printf "\n Please check line \"hostfile ...\" in $config_file"
452	locat=config_file; exit
453	fi
454	fi
455
456
457	# DETERMINE THE CALL STATUS
458	if [[ "$return_address" != "" ]]
459	then
460
461	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
462	# BATCH MODE AND ...
463	running_on_remote=true
464	host_name=$remote_hostname
465
466	else
467
468	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
469	if [[ "$remote_ip" != "" ]]
470	then
471
472	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
473	create_remote_batch_job=true
474
475	fi
476	host_name=$local_hostname
477	running_on_remote=false
478	fi
479
480
481
482	# READ AND EVALUATE THE I/O-FILE LIST
483	[[ $silent = false ]] && printf "\n Reading the I/O files... "
484
485	# READ THE FILE CONNECTION FILE LINE BY LINE
486	while read line
487	do
488
489	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
490	eval line=\"$line\"
491
492
493	# INTERPRET THE LINE
494	if [[ "$(echo $line)" = "" ]]
495	then
496	# EMPTY LINE, NO ACTION
497	continue
498
499	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
500	then
501
502	# LINE IS A COMMENT LINE
503	true
504
505	else
506
507	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
508	# s2a: in/out - field
509	# s2b: loc - field (optional)
510	# s2c: tr/ar - field (optional)
511	s1=`echo $line \| cut -d" " -f1`
512	s2=`echo $line \| cut -d" " -s -f2`
513	s2a=$(echo $s2 \| cut -d":" -f1)
514	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
515	then
516	s2b=""
517	s2c=""
518	else
519	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
520	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
521	fi
522	s3=`echo $line \| cut -d" " -f3`
523	s4=`echo $line \| cut -d" " -s -f4`
524	s5=`echo $line \| cut -d" " -s -f5`
525	s6=`echo $line \| cut -d" " -s -f6`
526
527
528	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
529	# INPUT- OR OUTPUT-LIST.
530	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
531	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
532	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
533	# IS NOT CHECKED AND STORED.
534	IFSALT="$IFS"; IFS="$IFS:"
535	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
536	then
537	found=false
538	for actual in $activation_string_list
539	do
540	for formal in $s3
541	do
542	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
543	done
544	done
545	if [[ $found = true ]]
546	then
547	(( iin = iin + 1 ))
548	localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
549	typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
550	extin[$iin]=$s6
551	fi
552	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
553	then
554	found=false
555	for actual in $activation_string_list
556	do
557	for formal in $s3
558	do
559	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
560	done
561	done
562	if [[ $found = true ]]
563	then
564	(( iout = iout + 1 ))
565	localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
566	pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
567	fi
568	elif [[ "$s2a" != in && "$s2a" != out ]]
569	then
570	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
571	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
572	locat=connect; exit
573	fi
574	IFS="$IFSALT"
575	fi
576
577	done < $fileconnection_file
578
579
580
581	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
582	if [[ $run_coupled_model = true ]]
583	then
584
585	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
586	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
587
588	if (( $cores_ocean + $cores_atmos != $cores ))
589	then
590
591	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
592	printf "\n PEs (total) : $cores"
593	printf "\n PEs (atmosphere): $cores_atmos"
594	printf "\n PEs (ocean) : $cores_ocean"
595	locat=coupling; exit
596
597	fi
598
599	fi
600
601
602	# SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
603	# THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
604	palmrun_memory=$memory
605	palmrun_cpumax=$cpumax
606	palmrun_cores=$cores
607
608
609	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
610	[[ $palmrun_memory != 0 ]] && memory=$palmrun_memory
611	[[ $palmrun_cpumax != 0 ]] && cpumax=$palmrun_cpumax
612	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
613	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
614	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
615
616
617
618	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
619	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
620	# FOLDER
621	if [[ $running_in_batch_mode = true ]]
622	then
623
624	if [[ ! -d ${fast_io_catalog}/SOURCES_FOR_RUN_$fname ]]
625	then
626	printf "\n +++ directory ${fast_io_catalog}/SOURCES_FOR_RUN_$fname is missing"
627	printf "\n Please check the output of the palmrun-call"
628	printf "\n that you did on your local host."
629	locat=SOURCES_FOR_RUN; exit
630	fi
631
632	else
633
634	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
635	# AUTOMATIC RESTART RUN
636	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
637	if [[ $restart_run = false ]]
638	then
639
640	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
641	# THE LOCAL HOST
642	if [[ ! -d $source_path ]]
643	then
644	printf "\n\n +++ source path \"$source_path\" on local host"
645	printf "\n \"$(hostname)\" does not exist"
646	locat=source_path; exit
647	fi
648
649	rm -rf SOURCES_FOR_RUN_$fname
650	mkdir -p SOURCES_FOR_RUN_$fname
651
652	if [[ "$source_list" = LM ]]
653	then
654
655	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
656	source_list=""
657	cd $source_path
658
659
660	# CHECK, IF DIRECTORY IS UNDER SVN CONTROL
661	if [[ ! -d .svn ]]
662	then
663	printf "\n\n +++ source directory"
664	printf "\n \"$source_path\" "
665	printf "\n is not under control of \"subversion\"."
666	printf "\n Please do not use palmmrun-option \"-s LM\"\n"
667	fi
668
669
670	# LIST ALL MODIFIED SOURCE CODE FILES
671	Filenames=""
672	svn status > tmp_svnstatus
673	while read line
674	do
675	firstc=`echo $line \| cut -c1`
676	if [[ $firstc = M \|\| $firstc = "?" ]]
677	then
678	Name=`echo "$line" \| cut -c8-`
679	extension=`echo $Name \| cut -d. -f2`
680	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
681	then
682	Filenames="$Filenames "$Name
683	fi
684	fi
685	done < tmp_svnstatus
686	rm -rf tmp_svnstatus
687
688
689	# COPY FILES TO SOURCES_FOR_RUN_...
690	for filename in $Filenames
691	do
692	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
693	source_list=$source_list"$filename "
694	done
695
696	cd - > /dev/null
697
698
699	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
700	elif [[ "$source_list" != "" ]]
701	then
702
703	cd $source_path
704
705	for filename in $source_list
706	do
707
708	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
709	if [[ $(echo $filename \| grep -c "/") != 0 ]]
710	then
711	printf "\n +++ source code file: $filename"
712	printf "\n must not contain (\"/\") "
713	locat=source; exit
714	fi
715
716	if [[ ! -f $filename ]]
717	then
718	printf "\n +++ source code file: $filename"
719	printf "\n does not exist"
720	locat=source; exit
721	else
722	cp $filename $working_directory/SOURCES_FOR_RUN_$fname
723	fi
724
725	done
726
727	cd - > /dev/null
728
729	fi
730
731	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
732	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
733	if [[ ! -f $makefile ]]
734	then
735	printf "\n +++ file \"$makefile\" does not exist"
736	locat=make; exit
737	else
738	cp $makefile SOURCES_FOR_RUN_$fname/Makefile
739	fi
740
741
742	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
743	if [[ "$user_source_path" != "" ]]
744	then
745
746	# DOES THE DIRECTORY EXIST?
747	if [[ ! -d $user_source_path ]]
748	then
749
750	printf "\n\n *** INFORMATIVE: additional source code directory"
751	printf "\n \"$user_source_path\" "
752	printf "\n does not exist or is not a directory."
753	printf "\n No source code will be used from this directory!\n"
754	user_source_path=""
755	if [[ $silent == false ]]
756	then
757	sleep 2
758	fi
759
760	else
761
762	cd $user_source_path
763	found=false
764
765	Names=$(ls -1 *.f90 2>&1)
766	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
767	Names=$(ls -1 *.F90 2>&1)
768	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
769	Names=$(ls -1 *.F 2>&1)
770	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
771	Names=$(ls -1 *.f 2>&1)
772	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
773	Names=$(ls -1 *.c 2>&1)
774	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
775
776	cd - > /dev/null
777	cd SOURCES_FOR_RUN_$fname
778
779	# COPY MAKEFILE IF EXISTING
780	if [[ -f $user_source_path/Makefile ]]
781	then
782	printf "\n\n *** user Makefile from directory"
783	printf "\n \"$user_source_path\" is used \n"
784	if [[ $silent == false ]]
785	then
786	sleep 1
787	fi
788	cp $user_source_path/Makefile .
789	fi
790
791	for filename in $AddFilenames
792	do
793	if [[ -f $filename ]]
794	then
795	printf "\n +++ source code file \"$filename\" found in additional"
796	printf "\n source code directory \"$user_source_path\" "
797	printf "\n but was also given with option \"-s\" which means that it should be taken"
798	printf "\n from directory \"$source_path\"."
799	locat=source; exit
800	fi
801
802	cp $user_source_path/$filename .
803	source_list="$source_list $filename"
804
805	# CHECK IF FILE IS CONTAINED IN MAKEFILE
806	if [[ $(grep -c $filename Makefile) = 0 ]]
807	then
808	printf "\n\n +++ user file \"$filename\" "
809	printf "\n is not listed in Makefile \n"
810	locat=source; exit
811	else
812
813	if [[ $found = false ]]
814	then
815	found=true
816	printf "\n\n *** following user file(s) added to the"
817	printf " files to be translated:\n "
818	fi
819	printf "$filename "
820	if [[ $silent == false ]]
821	then
822	sleep 0.5
823	fi
824
825	fi
826	done
827	[[ $found = true ]] && printf "\n"
828	cd - > /dev/null
829	fi
830	fi
831
832	# COPY CONFIGURATION FILES
833	cp $config_file SOURCES_FOR_RUN_$fname
834	cp $fileconnection_file SOURCES_FOR_RUN_$fname
835
836	# COPY SHELLSCRIPTS
837	cp ${source_path}/../SCRIPTS/palmrun SOURCES_FOR_RUN_$fname
838	cp ${source_path}/../SCRIPTS/batch_scp SOURCES_FOR_RUN_$fname
839
840	fi
841
842	fi
843
844	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
845	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
846	if [[ "$global_revision" = "" ]]
847	then
848	global_revision=`svnversion $source_path 2>/dev/null`
849	global_revision="Rev: $global_revision"
850	fi
851
852
853	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
854	if [[ -n $cores ]]
855	then
856
857	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
858	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
859	if [[ "$tasks_per_node" = "" ]]
860	then
861	printf "\n"
862	printf "\n +++ option \"-T\" (tasks per node) is missing"
863	printf "\n set -T option or define tasks_per_node in the config file"
864	locat=tasks_per_node; (( iec = 0 )); exit
865	fi
866
867	if (( cores < tasks_per_node ))
868	then
869	printf "\n"
870	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
871	printf "\n given values: -T $tasks_per_node -X $cores"
872	locat=tasks_per_node; (( iec = 0 )); exit
873	fi
874
875	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
876	(( mpi_tasks = cores / threads_per_task ))
877	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
878	(( ii = cores / tasks_per_node ))
879	(( remaining_cores = cores - ii * tasks_per_node ))
880	if (( remaining_cores > 0 ))
881	then
882	printf "\n"
883	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
884	printf "\n divisor of the total number of cores (option \"-X\")"
885	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
886	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
887	(( nodes = nodes + 1 ))
888	fi
889
890	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
891	if [[ "$tasks_per_node" != "" ]]
892	then
893	TOPT="-T $tasks_per_node"
894	fi
895
896	fi
897
898
899	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
900	if [[ "$maximum_parallel_io_streams" = "" ]]
901	then
902	maximum_parallel_io_streams=$cores
903	fi
904
905
906	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
907	if [[ "$scp_port" != "" ]]
908	then
909	PORTOPT="-P $scp_port"
910	SSH_PORTOPT="-p $scp_port"
911	fi
912
913
914	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
915	# CONFIG-FILE
916	if [[ "$ssh_key" != "" ]]
917	then
918	ssh_key="-i $HOME/.ssh/$ssh_key"
919	fi
920
921
922	# SET QUEUE, IF NOT GIVEN
923	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
924	then
925
926	if [[ $queue = none && "$defaultqueue" = "" ]]
927	then
928	printf "\n"
929	printf "\n +++ no default queue given in configuration file and no queue"
930	printf "\n given with option -q"
931	fi
932	if [[ $queue = none ]]
933	then
934	queue=$defaultqueue
935	fi
936
937	fi
938
939
940	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
941	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
942	(( i = 0 ))
943	while (( i < iin ))
944	do
945	(( i = i + 1 ))
946	(( maxcycle = 0 ))
947
948	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
949	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
950	if [[ "${actionin[$i]}" = di ]]
951	then
952	remotepathin[$i]=${pathin[$i]}/${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
953	# HOST ONLY
954	eval filename=${pathin[$i]}/${endin[$i]}
955	else
956	remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]} # EVALUATE REMOTE-PATH ON THE REMOTE
957	# HOST ONLY
958	eval filename=${pathin[$i]}/${fname}${endin[$i]}
959	fi
960	eval pathname=${pathin[$i]}
961
962	# CHECK IF FILE EXISTS
963	if ! ls $filename* 1>/dev/null 2>&1
964	then
965
966	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
967	if [[ "${transin[$i]}" != "locopt" ]]
968	then
969	printf "\n\n +++ INPUT-file: "
970	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
971	then
972	printf "\n $filename"
973	else
974	printf "\n $filename.${extin[$i]}"
975	fi
976	printf "\n does not exist\n"
977	locat=input; exit
978	else
979	transin[$i]="unavailable"
980	fi
981	else
982
983	# DETERMINE THE FILE'S CYCLE NUMBER
984	ls -1 -d $filename > filelist 2>/dev/null
985	ls -1 -d $filename.* >> filelist 2>/dev/null
986	while read line
987	do
988	# filename without path (i.e. after the last "/")
989	basefilename=$(basename ${line})
990
991	# check if there is an extension
992	extension=${basefilename##*.}
993	if [[ "$extension" = "$extin[$i]" ]]
994	then
995	basefilename=${basefilename&.*}
996	fi
997
998	# check for an existing cycle number
999	cycle=${basefilename##*.}
1000	if [[ $cycle =~ ^-?[0-9]+$ ]]
1001	then
1002	(( icycle = $cycle ))
1003	else
1004	(( icycle = 0 ))
1005	fi
1006
1007	if (( icycle > maxcycle ))
1008	then
1009	(( maxcycle = icycle ))
1010	fi
1011
1012	done <filelist
1013	rm filelist
1014
1015	# APPEND CYCLE NUMBER TO FILENAME
1016	if (( maxcycle > 0 ))
1017	then
1018	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1019	then
1020	filename=${filename}.$maxcycle.${extin[$i]}
1021	else
1022	filename=${filename}.$maxcycle
1023	fi
1024	else
1025	if [[ "${extin[$i]}" != " " && "${extin[$i]}" != "" ]]
1026	then
1027	filename=${filename}.${extin[$i]}
1028	fi
1029	fi
1030
1031	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1032	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1033	absnamein[$i]=$filename
1034	if (( maxcycle > 0 ))
1035	then
1036	if [[ "${actionin[$i]}" = di ]]
1037	then
1038	frelin[$i]=${endin[$i]}.$maxcycle
1039	else
1040	frelin[$i]=${fname}${endin[$i]}.$maxcycle
1041	fi
1042	else
1043	if [[ "${actionin[$i]}" = di ]]
1044	then
1045	frelin[$i]=${endin[$i]}
1046	else
1047	frelin[$i]=${fname}${endin[$i]}
1048	fi
1049	fi
1050
1051	fi
1052	done
1053
1054
1055	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1056	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1057	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
1058	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
1059	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1060	# REMOTE HOST)
1061	(( i = 0 ))
1062	while (( i < iout ))
1063	do
1064	(( i = i + 1 ))
1065	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1066	then
1067	if [[ "${actionout[$i]}" = tr ]]
1068	then
1069	actionout[$i]=""
1070	elif [[ "${actionout[$i]}" = trpe ]]
1071	then
1072	actionout[$i]=pe
1073	elif [[ "${actionout[$i]}" = tra ]]
1074	then
1075	actionout[$i]=a
1076	fi
1077	(( maxcycle = 0 ))
1078	eval filename=${pathout[$i]}/${fname}${endout[$i]}
1079	eval catalogname=${pathout[$i]}
1080	if ! ls $filename* 1>/dev/null 2>&1
1081	then
1082
1083	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1084	if cat /dev/null > $filename
1085	then
1086	rm $filename
1087	else
1088
1089	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1090	# IF IT DOES NOT EXIST, TRY TO CREATE IT
1091	if [[ ! -d $catalogname ]]
1092	then
1093	if mkdir -p $catalogname
1094	then
1095	printf "\n\n *** directory:"
1096	printf "\n $catalogname"
1097	printf "\n was created\n"
1098	else
1099	printf "\n\n +++ OUTPUT-file:"
1100	printf "\n $filename"
1101	printf "\n cannot be created, because directory does not exist"
1102	printf "\n and cannot be created either"
1103	printf "\n"
1104	locat=output ; exit
1105	fi 2>/dev/null
1106	else
1107	printf "\n\n +++ OUTPUT-file:"
1108	printf "\n $filename"
1109	printf "\n cannot be created, although directory exists"
1110	printf "\n"
1111	locat=output ; exit
1112	fi
1113	fi 2>/dev/null
1114	else
1115
1116	# DETERMINE THE CYCLE NUMBER
1117	ls -1 -d $filename > filelist 2>/dev/null
1118	ls -1 -d $filename.* >> filelist 2>/dev/null
1119	while read line
1120	do
1121
1122	# filename without path (i.e. after the last "/")
1123	basefilename=$(basename ${line})
1124
1125	# check if there is an extension
1126	extension=${basefilename##*.}
1127	if [[ "$extension" = "${extout[$i]}" ]]
1128	then
1129	basefilename=${basefilename%.*}
1130	fi
1131
1132	# check for an existing cycle number
1133	cycle=${basefilename##*.}
1134	if [[ $cycle =~ ^-?[0-9]+$ ]]
1135	then
1136	(( icycle = $cycle + 1 ))
1137	else
1138	(( icycle = 1 ))
1139	fi
1140
1141	if (( icycle > maxcycle ))
1142	then
1143	(( maxcycle = icycle ))
1144	fi
1145
1146	done <filelist
1147	rm filelist
1148	fi
1149
1150	# APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
1151	# IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
1152	if [[ "${actionout[$i]}" != a ]]
1153	then
1154	if (( maxcycle > 0 ))
1155	then
1156	filename_tmp=${filename}.$maxcycle
1157	if cat /dev/null > $filename_tmp
1158	then
1159	rm $filename_tmp
1160	else
1161	printf "\n +++ OUTPUT-file:"
1162	printf "\n $filename_tmp"
1163	printf "\n cannot be created"
1164	locat=output ; exit
1165	fi
1166	fi
1167	else
1168	(( maxcycle = maxcycle - 1 ))
1169	fi
1170
1171	(( cycnum[$i] = maxcycle ))
1172	pathout[$i]=$filename
1173
1174	fi
1175	done
1176
1177
1178	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1179	if [[ $running_in_batch_mode = false ]]
1180	then
1181	run_id=$RANDOM
1182	job_id=${fname}.$run_id
1183
1184	TEMPDIR=$fast_io_catalog/$job_id
1185	fi
1186
1187
1188	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
1189	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1190	then
1191
1192	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1193	if [[ $ibd = 0 ]]
1194	then
1195	printf "\n"
1196	printf "\n +++ no batch directives found in configuration file"
1197	locat=config_file_batch_directives; (( iec = 0 )); exit
1198	fi
1199
1200	# CHECK IF CPUTIME IS GIVEN FOR JOB
1201	done=false
1202	cputime=$cpumax
1203	while [[ $done = false ]]
1204	do
1205	if (( cputime == 0 ))
1206	then
1207	printf "\n +++ cpu-time is undefined"
1208	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
1209	printf "\n >>> "
1210	read cputime 1>/dev/null 2>&1
1211	else
1212	done=true
1213	fi
1214	done
1215
1216	# CHECK THE MEMORY DEMAND
1217	done=false
1218	while [[ $done = false ]]
1219	do
1220	if (( memory == 0 ))
1221	then
1222	printf "\n +++ memory demand is undefined"
1223	printf "\n >>> Please type memory in MByte per process as INTEGER:"
1224	printf "\n >>> "
1225	read memory 1>/dev/null 2>&1
1226	else
1227	done=true
1228	fi
1229	done
1230
1231	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1232	if [[ $create_remote_batch_job = true && -z $remote_username ]]
1233	then
1234	while [[ -z $remote_username ]]
1235	do
1236	printf "\n +++ username on remote host \"$remote_ip\" is undefined"
1237	printf "\n >>> Please type username:"
1238	printf "\n >>> "
1239	read remote_username
1240	done
1241	fi
1242
1243	else
1244
1245	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
1246
1247	fi
1248	cpumax=$cputime
1249
1250
1251	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1252	(( cpu_hours = cputime / 3600 ))
1253	(( resttime = cputime - cpu_hours * 3600 ))
1254	(( cpu_minutes = resttime / 60 ))
1255	(( cpu_seconds = resttime - cpu_minutes * 60 ))
1256	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1257
1258
1259	# OUTPUT OF THE PALMRUN-HEADER
1260	calltime=$(date)
1261	printf "\n"
1262	printf "#------------------------------------------------------------------------# \n"
1263	printf "\| %-35s%35s \| \n" "$version" "$calltime"
1264	printf "\| \| \n"
1265	column1="called on:"; column2=$(hostname)
1266	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1267	if [[ $create_remote_batch_job = true ]]
1268	then
1269	column1="execution on:"; column2="$remote_hostname (username: $remote_username)"
1270	else
1271	if [[ $running_on_remote = true ]]
1272	then
1273	column1="execution on:"; column2="$remote_hostname"
1274	else
1275	column1="execution on:"; column2="$local_hostname"
1276	fi
1277	fi
1278	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1279
1280	column1="running in:"
1281	if [[ $running_in_batch_mode = true ]]
1282	then
1283	column2="batch job mode"
1284	else
1285	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1286	then
1287	column2="job creation mode"
1288	else
1289	column2="interactive run mode"
1290	fi
1291	fi
1292	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1293
1294	if [[ -n $cores ]]
1295	then
1296	if [[ $run_coupled_model = false ]]
1297	then
1298	column1="number of cores:"; column2=$cores
1299	else
1300	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1301	fi
1302	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1303	fi
1304	if [[ -n $tasks_per_node ]]
1305	then
1306	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1307	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1308	if (( remaining_cores > 0 ))
1309	then
1310	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1311	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1312	fi
1313	fi
1314	if [[ $maximum_parallel_io_streams != $cores ]]
1315	then
1316	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1317	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1318	fi
1319	if [[ $use_openmp = true ]]
1320	then
1321	column1="threads per task:"; column2="$threads_per_task"
1322	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1323	fi
1324	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
1325	then
1326	column1="job cpu time (h:m:s):"; column2="$timestring"
1327	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1328	fi
1329	printf "\| \| \n"
1330	if [[ "$source_list" != "" ]]
1331	then
1332	if [[ "$make_options" != "" ]]
1333	then
1334	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
1335	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1336	line=$(echo "$make_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 "$line" \| cut -c46-)
1343	done
1344	fi
1345	fi
1346
1347	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
1348	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1349	line=$(echo "$cpp_options" \| cut -c46-)
1350	while [[ "$line" != "" ]]
1351	do
1352	column1=""
1353	column2=$(echo "$line" \| cut -c-45)
1354	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1355	line=$(echo "$line" \| cut -c46-)
1356	done
1357
1358	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
1359	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1360	line=$(echo "$compiler_options" \| cut -c46-)
1361	while [[ "$line" != "" ]]
1362	do
1363	column1=""
1364	column2=$(echo "$line" \| cut -c-45)
1365	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1366	line=$(echo "$line" \| cut -c46-)
1367	done
1368
1369	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
1370	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1371	line=$(echo "$linker_options" \| cut -c46-)
1372	while [[ "$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
1380	if [[ "$login_init_cmd" != "" ]]
1381	then
1382	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
1383	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1384	line=$(echo "$login_init_cmd" \| cut -c46-)
1385	while [[ "$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
1394	if [[ "$module_commands" != "" ]]
1395	then
1396	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
1397	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1398	line=$(echo "$module_commands" \| cut -c46-)
1399	while [[ "$line" != "" ]]
1400	do
1401	column1=""
1402	column2=$(echo "$line" \| cut -c-45)
1403	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1404	line=$(echo "$line" \| cut -c46-)
1405	done
1406	fi
1407	printf "\| \| \n"
1408	column1="base name of files:"; column2=$fname
1409	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1410	column1="activation string list:"; column2=$(echo $activation_string_list)
1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1412
1413	if [[ "$ocean_file_appendix" = true ]]
1414	then
1415	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
1416	fi
1417
1418	if [[ $create_batch_job = true \|\| "$LOADLBATCH" = yes ]]
1419	then
1420	column1="memory demand / PE":; column2="$memory MB"
1421	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1422	column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
1423	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
1424	fi
1425
1426	if [[ "$source_list" != "" ]]
1427	then
1428	printf "\| \| \n"
1429	printf "\| Files to be compiled: \| \n"
1430	line=$source_list
1431	while [[ "$line" != "" ]]
1432	do
1433	linestart=$(echo $line \| cut -c-70)
1434	printf "\| %-70s \| \n" "$linestart"
1435	line=$(echo "$line" \| cut -c71-)
1436	done
1437	fi
1438	printf "#------------------------------------------------------------------------#"
1439
1440
1441
1442	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1443	if [[ $do_trace = true ]]
1444	then
1445	(( i = 0 ))
1446	while (( i < iin ))
1447	do
1448	(( i = i + 1 ))
1449	if (( i == 1 ))
1450	then
1451	printf "\n\n >>> INPUT-file assignments:\n"
1452	fi
1453	printf "\n ${localin[$i]} : ${absnamein[$i]}"
1454	done
1455	(( i = 0 ))
1456	while (( i < iout ))
1457	do
1458	(( i = i + 1 ))
1459	if (( i == 1 ))
1460	then
1461	printf "\n\n >>> OUTPUT-file assignments:\n"
1462	fi
1463	printf "\n ${localout[$i]} : ${pathout[$i]}"
1464	done
1465	(( i = 0 ))
1466	while (( i < iic ))
1467	do
1468	(( i = i + 1 ))
1469	if (( i == 1 ))
1470	then
1471	printf "\n\n >>> INPUT-commands:\n"
1472	fi
1473	printf "\n ${in_command[$i]}"
1474	done
1475	(( i = 0 ))
1476	while (( i < ioc ))
1477	do
1478	(( i = i + 1 ))
1479	if (( i == 1 ))
1480	then
1481	printf "\n\n >>> OUTPUT-commands:\n"
1482	fi
1483	printf "\n ${out_command[$i]}"
1484	done
1485	fi
1486
1487	# QUERY FOR CONTINUE
1488	if [[ $silent = false && $running_in_batch_mode = false ]]
1489	then
1490	antwort=dummy
1491	printf "\n\n"
1492	printf " >>> everything o.k. (y/n) ? "
1493	while read antwort
1494	do
1495	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
1496	then
1497	printf " >>> everything o.k. (y/n) ? "
1498	else
1499	break
1500	fi
1501	done
1502	if [[ $antwort = n \|\| $antwort = N ]]
1503	then
1504	locat=user_abort; (( iec = 0 )); exit
1505	fi
1506	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1507	then
1508	printf " *** batch-job will be created and submitted"
1509	else
1510	printf " *** PALMRUN will now continue to execute on this machine"
1511	fi
1512	fi
1513
1514
1515
1516	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1517	if [[ $restart_run = false && $running_in_batch_mode = false ]]
1518	then
1519
1520	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
1521	then
1522	printf "\n\n *** creating executable and other sources for the remote host"
1523	else
1524	printf "\n\n *** creating executable and other sources for the local host"
1525	fi
1526
1527	palmbuild -v -h $host -d $fname
1528	rm -rf SOURCES_FOR_RUN_$fname
1529
1530	if [[ $? != 0 ]]
1531	then
1532
1533	# ABORT IN CASE OF COMPILATION PROBLEMS
1534	printf "\n +++ error while creating executable and/or other sources"
1535	locat=execution
1536	exit
1537
1538	else
1539
1540	printf "\n$dashes\n *** executable and other sources created\n"
1541
1542	fi
1543
1544	fi
1545
1546
1547	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1548	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1549	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
1550	then
1551
1552	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
1553	if [[ $running_in_batch_mode = false ]]
1554	then
1555	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1556	# FOLDER
1557	mkdir -p $TEMPDIR
1558	chmod go+rx $TEMPDIR
1559	tmpcreate=true
1560	cd $TEMPDIR
1561	cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} $TEMPDIR
1562	printf "\n *** changed to temporary directory: $TEMPDIR"
1563
1564	else
1565
1566	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1567	printf "\n *** running in temporary directory: $TEMPDIR"
1568
1569	fi
1570
1571
1572	# PROVIDE THE INPUT FILES
1573	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1574	(( i = 0 ))
1575	while (( i < iin ))
1576	do
1577	(( i = i + 1 ))
1578	if (( i == 1 ))
1579	then
1580	printf "\n\n *** providing INPUT-files:\n$dashes"
1581	fi
1582
1583
1584	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1585	if [[ "${transin[$i]}" = unavailable ]]
1586	then
1587	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
1588	then
1589	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1590	printf "\n is not available!"
1591	else
1592	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1593	printf "\n is not available!"
1594	fi
1595	continue
1596	fi
1597
1598	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1599	files_for_cores=false; filetype=file
1600	if [[ "${actionin[$i]}" = pe && -n $cores ]]
1601	then
1602	files_for_cores=true; filetype=files
1603	actionin[$i]=""
1604	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
1605	then
1606	actionin[$i]=""
1607	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
1608	then
1609	files_for_cores=true; filetype=files
1610	actionin[$i]="ln"
1611	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
1612	then
1613	actionin[$i]="ln"
1614	fi
1615
1616	if [[ $files_for_cores = true ]]
1617	then
1618	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
1619	else
1620	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
1621	fi
1622
1623	# INPUT-FILES TO BE LINKED
1624	if [[ "${actionin[$i]}" = ln ]]
1625	then
1626
1627	printf "\n $filetype will be linked"
1628	if [[ $files_for_cores = false ]]
1629	then
1630	if [[ -f "${absnamein[$i]}" ]]
1631	then
1632	ln ${absnamein[$i]} ${localin[$i]}
1633	got_tmp[$i]=true
1634	fi
1635	else
1636	if [[ -d "${absnamein[$i]}" ]]
1637	then
1638	mkdir -p ${localin[$i]}
1639	cd ${absnamein[$i]}
1640	for file in $(ls *)
1641	do
1642	ln $file $TEMPDIR/${localin[$i]}
1643	done >\|/dev/null 2>&1
1644	cd $TEMPDIR
1645	fi
1646
1647	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1648	if [[ ! -f "${localin[$i]}/_000000" ]]
1649	then
1650	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1651	cp -r ${absnamein[$i]}/* ${localin[$i]}
1652	fi
1653
1654	got_tmp[$i]=true
1655	fi
1656	fi
1657
1658	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1659	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
1660	then
1661
1662	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
1663	then
1664
1665	# FILE COPIES ARE PROVIDED FOR ALL CORES
1666	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1667	printf "\n file will be provided for $cores processors"
1668	mkdir -p ${localin[$i]}
1669	ival=$cores
1670	(( ii = 0 ))
1671	while (( ii <= ival-1 ))
1672	do
1673	if (( ii < 10 ))
1674	then
1675	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
1676	elif (( ii < 100 ))
1677	then
1678	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
1679	elif (( ii < 1000 ))
1680	then
1681	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
1682	else
1683	cp ${absnamein[$i]} ${localin[$i]}/_$ii
1684	fi
1685	(( ii = ii + 1 ))
1686	done
1687
1688	else
1689
1690	if [[ $files_for_cores = true ]]
1691	then
1692
1693	# PROVIDE FILES FOR EACH CORE
1694	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1695	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1696	printf "\n providing $cores files for the respective cores"
1697	mkdir -p ${localin[$i]}
1698	if [[ $link_local_input = true ]]
1699	then
1700	printf " files will be linked\n"
1701	cd ${absnamein[$i]}
1702	for file in $(ls *)
1703	do
1704	ln -f $file ${localin[$i]}
1705	done
1706	cd $TEMPDIR
1707	fi
1708
1709	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1710	if [[ ! -f "${localin[$i]}/_000000" ]]
1711	then
1712	if [[ $link_local_input = true ]]
1713	then
1714	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1715	fi
1716	cp -r ${absnamein[$i]}/* ${localin[$i]}
1717	fi
1718
1719	else
1720
1721	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
1722	if [[ $link_local_input = true ]]
1723	then
1724	printf " file will be linked\n"
1725	ln -f ${absnamein[$i]} ${localin[$i]}
1726	fi
1727	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
1728	if [[ ! -f "${localin[$i]}" ]]
1729	then
1730	if [[ $link_local_input = true ]]
1731	then
1732	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
1733	fi
1734	cp ${absnamein[$i]} ${localin[$i]}
1735	fi
1736	fi
1737	fi
1738	fi
1739
1740	done
1741	if (( i != 0 ))
1742	then
1743	printf "\n$dashes\n *** all INPUT-files provided \n"
1744	fi
1745
1746
1747	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1748	(( i = 0 ))
1749	while (( i < iic ))
1750	do
1751	(( i = i + 1 ))
1752	if (( i == 1 ))
1753	then
1754	printf "\n\n *** execution of INPUT-commands:\n$dashes"
1755	fi
1756	printf "\n >>> ${in_command[$i]}"
1757	eval ${in_command[$i]}
1758	if (( i == iic ))
1759	then
1760	printf "\n$dashes\n"
1761	fi
1762	done
1763
1764
1765	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
1766	# (FILE ENVPAR WILL BE READ BY PALM)
1767	cat > ENVPAR << EOF
1768	&envpar run_identifier = '$fname', host = '$host',
1769	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
1770	maximum_parallel_io_streams = $maximum_parallel_io_streams,
1771	maximum_cpu_time_allowed = ${cpumax}.,
1772	revision = '$global_revision',
1773	batch_job = .${running_in_batch_mode}. /
1774
1775	EOF
1776
1777
1778	# STARTING THE EXECUTABLE
1779	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
1780	PATH=$PATH:$TEMPDIR
1781
1782
1783	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
1784	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
1785	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
1786	eval line=\"$line\"
1787	execute_command="$line"
1788
1789
1790	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
1791	eval line2=\"$line2\"
1792	execute_command_for_combine="$line2"
1793
1794
1795	# PROVIDE A HOSTFILE, IF REQUIRED
1796	if [[ "$hostfile" != "" ]]
1797	then
1798
1799	if [[ $hostfile = auto ]]
1800	then
1801	# CREATE A NEW HOSTFILE
1802	(( ii = 1 ))
1803	while (( ii <= cores / threads_per_task ))
1804	do
1805	echo $(hostname) >> hostfile
1806	(( ii = ii + 1 ))
1807	done
1808	if (( cores / threads_per_task == 0 ))
1809	then
1810	echo $(hostname) >> hostfile
1811	fi
1812
1813	else
1814	cp $hostfile hostfile
1815	fi
1816	eval line=\"`head -n $ii hostfile`\"
1817	printf "\n *** running on: $line"
1818	fi
1819
1820
1821
1822	# SET THE NUMBER OF OPENMP-THREADS
1823	if [[ $use_openmp = true ]]
1824	then
1825	export OMP_NUM_THREADS=$threads_per_task
1826	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
1827	else
1828	export OMP_NUM_THREADS=1
1829	fi
1830
1831
1832	# PROVIDE DATA FOR
1833	if [[ $run_coupled_model = false ]]
1834	then
1835	if [[ "$ocean_file_appendix" = true ]]
1836	then
1837	echo "precursor_ocean" > coupling_steering
1838	else
1839	echo "precursor_atmos" > coupling_steering
1840	fi
1841	else
1842	(( iia = $cores_atmos / $threads_per_task ))
1843	(( iio = $cores_ocean / $threads_per_task ))
1844	printf "\n coupled run ($iia atmosphere, $iio ocean)"
1845	printf "\n\n"
1846	echo "coupled_run $iia $iio" > coupling_steering
1847	fi
1848
1849	printf "\n *** execute command:"
1850	printf "\n \"$execute_command\" \n\n"
1851
1852	$execute_command < coupling_steering
1853
1854	if [[ $? != 0 ]]
1855	then
1856
1857	# ABORT IN CASE OF RUNTIME ERRORS
1858	printf "\n +++ runtime error occured"
1859	locat=execution
1860	exit
1861
1862	else
1863
1864	printf "\n$dashes\n *** execution finished \n"
1865
1866	fi
1867
1868
1869	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
1870	# BY EACH CORE INTO ONE FILE
1871	if [[ ! -f combine_plot_fields.x ]]
1872	then
1873
1874	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
1875	printf "\n 2d- and/or 3d-data may be incomplete!"
1876	printf "\n Your previous palmbuild may have failed. Please check.\n"
1877
1878	elif [[ "$combine_plot_fields" == true ]]
1879	then
1880
1881	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
1882	$execute_command_for_combine
1883
1884	else
1885
1886	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
1887	# DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
1888	# ??? koennen wir das streichen ???
1889	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
1890	fi
1891
1892
1893
1894	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1895	(( i = 0 ))
1896	while (( i < ioc ))
1897	do
1898	(( i = i + 1 ))
1899	if (( i == 1 ))
1900	then
1901	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
1902	fi
1903	printf "\n >>> ${out_command[$i]}"
1904	eval ${out_command[$i]}
1905	if (( i == ioc ))
1906	then
1907	printf "\n$dashes\n"
1908	fi
1909	done
1910
1911
1912	# IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
1913	if [[ $do_trace = true ]]
1914	then
1915	printf "\n\n"
1916	ls -al
1917	fi
1918
1919
1920	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
1921	(( i = 0 ))
1922	while (( i < iout ))
1923	do
1924	(( i = i + 1 ))
1925	if (( i == 1 ))
1926	then
1927	printf "\n\n *** saving OUTPUT-files:"
1928
1929	# GET RUN NUMBER ASSIGNED BY PALM
1930	if [[ -f RUN_NUMBER ]]
1931	then
1932	read run_number < RUN_NUMBER
1933	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
1934	usecycle_option="-U $run_number"
1935	else
1936	run_number=0
1937	usecycle_option=""
1938	fi
1939	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
1940	then
1941	printf "\n *** in case of SCP transfers to local host"
1942	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
1943	fi
1944	printf "\n$dashes"
1945	fi
1946
1947	# ADD CYCLE NUMBER TO FILENAME
1948	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
1949	then
1950
1951	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
1952	if [[ "${actionout[$i]}" != "a" ]]
1953	then
1954	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
1955	# WITH AN EXISTING CYCLE NUMBER
1956	if (( run_number >= cycnum[$i] ))
1957	then
1958	(( cycnum[$i] = run_number ))
1959	else
1960	if (( run_number > 0 ))
1961	then
1962	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
1963	fi
1964	fi
1965	fi
1966	if (( cycnum[$i] > 0 ))
1967	then
1968	pathout[$i]=${pathout[$i]}.${cycnum[$i]}
1969	fi
1970	fi
1971
1972	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1973	files_for_cores=false; filetype=file
1974	link_local_output=false
1975	if [[ "${actionout[$i]}" = pe && -n $cores ]]
1976	then
1977	files_for_cores=true; filetype=directory
1978	actionout[$i]=""
1979	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
1980	then
1981	actionout[$i]=""
1982	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
1983	then
1984	files_for_cores=true; filetype=directory
1985	link_local_output=true
1986	actionout[$i]=""
1987	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
1988	then
1989	link_local_output
1990	actionout[$i]=""
1991	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
1992	then
1993	files_for_cores=true; filetype=directory
1994	actionout[$i]="tr"
1995	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
1996	then
1997	actionout[$i]="tr"
1998	fi
1999
2000	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
2001	then
2002	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
2003	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
2004	then
2005	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
2006	else
2007
2008
2009	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2010	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2011	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
2012	then
2013	if [[ $running_on_remote = true ]]
2014	then
2015
2016	# SET OPTIONS FOR TRANSFER
2017	if [[ "${actionout[$i]}" = tr ]]
2018	then
2019	if [[ $files_for_cores = false ]]
2020	then
2021	catalog_option=""
2022	catalog_string=""
2023	else
2024	catalog_option="-c"
2025	catalog_string="/"
2026	fi
2027	append_option=""
2028	append_string=""
2029	else
2030	append_option="-A"
2031	append_string="append"
2032	fi
2033
2034	transfer_failed=false
2035	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
2036	printf "\n ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}$catalog_string\n"
2037
2038	# TRANSFER VIA SCP
2039	if [[ "$remote_loginnode" != "" ]]
2040	then
2041	echo "cd $TEMPDIR; ${fast_io_catalog}/SOURCES_FOR_RUN_${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
2042	else
2043	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]}
2044	fi
2045	[[ $? != 0 ]] && transfer_failed=true
2046
2047
2048	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2049	if [[ $transfer_failed = true ]]
2050	then
2051	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
2052	printf " ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id\n"
2053
2054	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2055	eval local_catalog=${pathout[$i]}
2056	if [[ ! -d $local_catalog ]]
2057	then
2058	printf " *** local directory does not exist. Trying to create:\n"
2059	printf " $local_catalog \n"
2060	mkdir -p $local_catalog
2061	fi
2062	eval cp ${localout[$i]} ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id
2063	transfer_problems=true
2064	fi
2065
2066	else
2067
2068	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2069	# BE COPIED OR APPENDED ON THIS MACHINE
2070	if [[ "${actionout[$i]}" = tr ]]
2071	then
2072	actionout[$i]=""
2073	else
2074	actionout[$i]="a"
2075	fi
2076	fi
2077	fi
2078
2079
2080	# APPEND ON THIS MACHINE
2081	if [[ "${actionout[$i]}" = "a" ]]
2082	then
2083	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2084	then
2085	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2086	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2087	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
2088	else
2089	printf "\n >>> OUTPUT: ${localout[$i]} append to"
2090	printf "\n ${pathout[$i]}\n"
2091	cat ${localout[$i]} >> ${pathout[$i]}
2092	fi
2093	fi
2094
2095	# COPY ON THIS MACHINE
2096	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2097	# ON DIFFERENT FILE-SYSTEMS
2098	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
2099	then
2100
2101	# COPY IN CASE OF RUNS ON SINGLE CORES
2102	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
2103	then
2104	printf "\n >>> OUTPUT: ${localout[$i]} to"
2105	printf "\n ${pathout[$i]}.${extout[$i]}\n"
2106	if [[ $link_local_output = true ]]
2107	then
2108	printf " file will be linked\n"
2109	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2110	fi
2111	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2112	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2113	then
2114	if [[ $link_local_output = true ]]
2115	then
2116	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2117	fi
2118	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
2119	else
2120	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2121	fi
2122	else
2123	printf "\n >>> OUTPUT: ${localout[$i]} to"
2124	printf "\n ${pathout[$i]}\n"
2125	if [[ $link_local_output = true ]]
2126	then
2127	printf " file will be linked\n"
2128	ln -f ${localout[$i]} ${pathout[$i]}
2129	fi
2130	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2131	if [[ ! -f "${pathout[$i]}" ]]
2132	then
2133	if [[ $link_local_output = true ]]
2134	then
2135	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2136	fi
2137	cp ${localout[$i]} ${pathout[$i]}
2138	else
2139	printf "+++ no copy because file ${pathout[$i]} exists\n"
2140	fi
2141	fi
2142
2143	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
2144	then
2145
2146	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2147	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2148	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
2149	printf "\n ${pathout[$i]}\n"
2150	if [[ $link_local_output = true ]]
2151	then
2152	printf " files will be linked\n"
2153	mkdir -p ${pathout[$i]}
2154	cd ${localout[$i]}
2155	for file in $(ls *)
2156	do
2157	ln -f $file ${pathout[$i]}
2158	done >\|/dev/null 2>&1
2159	cd $TEMPDIR
2160	fi
2161
2162	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2163	if [[ ! -f "${pathout[$i]}/_000000" ]]
2164	then
2165	if [[ $link_local_output = true ]]
2166	then
2167	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2168	fi
2169	cp -r ${localout[$i]}/* ${pathout[$i]}
2170	fi
2171
2172	fi
2173	fi
2174	done
2175
2176	if (( i != 0 ))
2177	then
2178	if [[ $transfer_problems = true ]]
2179	then
2180	printf "\n$dashes\n *** OUTPUT-files saved"
2181	printf "\n +++ WARNING: some data transfers failed! \n"
2182	else
2183	printf "\n$dashes\n *** all OUTPUT-files saved \n"
2184	fi
2185	fi
2186
2187
2188	# IF REQUIRED, START A RESTART-JOB
2189	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2190	if [[ -f CONTINUE_RUN ]]
2191	then
2192
2193	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2194	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2195	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2196	# -b START A BATCH JOB
2197	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
2198	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
2199	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
2200
2201
2202	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2203	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2204	if [[ $(echo $prc \| grep -c "#") != 0 ]]
2205	then
2206	prc=`echo $prc \| sed 's/#/r/g'`
2207	fi
2208
2209
2210	# START THE RESTART-JOB
2211	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
2212	echo " $prc"
2213	printf "\n$dashes\n"
2214	if [[ $running_on_remote = true ]]
2215	then
2216
2217	echo "*** ssh will be used to initiate restart-runs!"
2218	echo " return_address=\"$return_address\" "
2219	echo " return_username=\"$local_username\" "
2220
2221	if [[ "$remote_loginnode" != "" ]]
2222	then
2223	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
2224	else
2225	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
2226	fi
2227
2228	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2229	sleep 30
2230
2231	else
2232
2233	# START THE RESTART JOB ON THE LOCAL HOST
2234	eval $prc # THE ' MUST BE EVALUATED
2235	cd - > /dev/null
2236
2237	fi
2238	printf "\n$dashes\n *** restart-run initiated \n"
2239
2240
2241	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2242	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2243	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2244	# MAY BE VERY HUGE)
2245	(( i = 0 ))
2246	while (( i < iin ))
2247	do
2248	(( i = i + 1 ))
2249	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
2250	then
2251	rm -r ${absnamein[$i]}
2252	fi
2253	done
2254
2255	fi
2256
2257
2258	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2259	cd $HOME
2260	[[ $delete_temporary_catalog = true ]] && rm -rf $TEMPDIR
2261
2262
2263	else
2264
2265
2266	# PREPARING ACTIONS,
2267	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2268
2269	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2270	palmrun_com="$palmrun_script_name -c $config_file -d $fname -h $host -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2271	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2272	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
2273	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
2274	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
2275	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
2276	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
2277	[[ "$tasks_per_node" != "" ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
2278	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
2279	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
2280	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2281	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
2282	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
2283	if [[ $create_remote_batch_job = true ]]
2284	then
2285	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2286	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
2287	elif [[ $create_batch_job = true ]]
2288	then
2289	palmrun_com=${palmrun_com}" -j"
2290	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
2291	fi
2292
2293
2294	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2295	# REMOTE HOST
2296	job_protocol_file_local=${local_jobcatalog}/${host}_${job_id}
2297	job_protocol_file=$job_protocol_file_local
2298	if [[ $create_remote_batch_job = true ]]
2299	then
2300	job_protocol_file_remote=${remote_jobcatalog}/${host}_${job_id}
2301	job_protocol_file=$job_protocol_file_remote
2302	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2303	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2304	fi
2305
2306
2307	# BUILD THE JOB-SCRIPTS ON FILE jobfile
2308	jobfile=jobfile.$run_id
2309
2310
2311	# FIRST CREATE THE BATCH DIRECTIVES
2312	(( i = 0 ))
2313	while (( i < ibd ))
2314	do
2315	(( i = i + 1 ))
2316	line=`echo "${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}}/$queue/g' \| sed 's/{{MEMORY}}/$memory/g'`
2317	eval line=\"$line\"
2318	echo "$line" >> $jobfile
2319	done
2320	echo " " >> $jobfile
2321
2322
2323	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2324	# PROTOCOL
2325	if [[ $create_remote_batch_job = true ]]
2326	then
2327	echo "set +vx" >> $jobfile
2328	echo "trap '" >> $jobfile
2329	echo "set +vx" >> $jobfile
2330	echo "cd ${remote_jobcatalog}" >> $jobfile
2331	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
2332
2333	# ADD THE BATCH DIRECTIVES
2334	(( i = 0 ))
2335	while (( i < ibdt ))
2336	do
2337	(( i = i + 1 ))
2338	line=`echo "${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'`
2339	eval line=\"$line\"
2340	echo "$line" >> $jobfile
2341	done
2342	echo " " >> $jobfile
2343
2344	echo "set -x" >> $jobfile
2345	echo "${fast_io_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
2346	echo "%%END%%" >> $jobfile
2347	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
2348	echo "$submit_command $scpjob_file" >> $jobfile
2349	echo "rm $scpjob_file" >> $jobfile
2350	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
2351	echo "set -x" >> $jobfile
2352	echo " ' exit" >> $jobfile
2353	fi
2354
2355
2356	# ACTIVATE ERROR-TRACEBACK
2357	if [[ $do_trace = true ]]
2358	then
2359	echo "set -x" >> $jobfile
2360	else
2361	echo "set +vx" >> $jobfile
2362	fi
2363
2364
2365	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2366	if [[ "$login_init_cmd" != "" ]]
2367	then
2368	echo "$login_init_cmd" >> $jobfile
2369	fi
2370	if [[ "$module_commands" != "" ]]
2371	then
2372	echo "$module_commands" >> $jobfile
2373	fi
2374
2375
2376	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2377	echo "mkdir $TEMPDIR" >> $jobfile
2378	echo "cd $TEMPDIR" >> $jobfile
2379	echo "export TEMPDIR=$TEMPDIR" >> $jobfile
2380	echo "cp $fast_io_catalog/SOURCES_FOR_RUN_$fname/{,.[!.]} ." >> $jobfile
2381	echo "export PATH=.:\$PATH" >> $jobfile
2382	echo "export execute_palmrun=true" >> $jobfile
2383
2384
2385	# GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
2386	# PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
2387	# IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
2388	if [[ $create_remote_batch_job = true ]]
2389	then
2390	(( i = 0 ))
2391	while (( i < iin ))
2392	do
2393	(( i = i + 1 ))
2394	echo "[[ ! -d ${pathin[$i]} ]] && mkdir -p ${pathin[$i]}" >> $jobfile
2395	if [[ "${transin[$i]}" = job ]]
2396	then
2397	echo "cat > ${remotepathin[$i]} <<\"%END%\"" >> $jobfile
2398	eval cat ${pathin[$i]}/${frelin[$i]} >> $jobfile
2399	echo " " >> $jobfile
2400	echo "%END%" >> $jobfile
2401	else
2402	echo "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >> $jobfile
2403	fi
2404
2405	# CHECK, IF FILE COULD BE CREATED
2406	echo "if [[ \$? = 1 ]]" >> $jobfile
2407	echo "then" >> $jobfile
2408	echo " echo \" \" " >> $jobfile
2409	echo " echo \"+++ file ${remotepathin[$i]} could not be created\" " >> $jobfile
2410	echo " echo \" please check, if directory exists on $host!\" " >> $jobfile
2411	echo " echo \"+++ PALMRUN will not be continued\" " >> $jobfile
2412	echo " execute_palmrun=false" >> $jobfile
2413	echo "fi" >> $jobfile
2414	done
2415	fi
2416
2417
2418	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2419	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2420	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2421	echo "LOCAL_PWD=$working_directory" >> $jobfile
2422	echo "export LOCAL_PWD" >> $jobfile
2423
2424
2425	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2426	echo "LOCAL_PALMRUN_PATH=$PALM_BIN" >> $jobfile
2427	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
2428
2429
2430	# CALL PALMRUN WITHIN THE JOB
2431	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2432	echo "set -x" >> $jobfile
2433	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
2434
2435
2436	# TRANSFER JOBFILE TO THE TARGET HOST
2437	if [[ $create_jobfile_only = false ]]
2438	then
2439
2440	if [[ $create_remote_batch_job = true ]]
2441	then
2442
2443	echo " *** transfer of job to remote host via scp"
2444	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}"
2445	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host}_${job_id}
2446
2447	echo " "
2448	echo " *** submit the job"
2449	echo " cd $remote_jobcatalog; $submit_command ${host}_${job_id}; rm ${host}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
2450	echo "cd $remote_jobcatalog; $submit_command ${host}_${job_id}; rm ${host}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
2451
2452	elif [[ $create_batch_job = true ]]
2453	then
2454
2455	eval local_jobcatalog=$local_jobcatalog
2456	cp $jobfile ${local_jobcatalog}/${host}_${job_id}
2457	cd $local_jobcatalog
2458	echo " "
2459	echo "--- submit the job"
2460	echo "$submit_command ${host}_${job_id}"
2461	$submit_command ${host}_${job_id}
2462	rm ${host}_${job_id}
2463	cd - > /dev/null
2464
2465	fi
2466
2467	rm -rf $jobfile
2468
2469	else
2470
2471	printf "\n *** jobfile created under name \"$jobfile\" "
2472	printf "\n no batch-job has been sent!"
2473
2474	fi
2475
2476	fi # END OF REMOTE-PART

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