source: palm/trunk/SCRIPTS/palmrun @ 2670

Last change on this file since 2670 was 2670, checked in by raasch, 4 years ago

test printouts removed

  • Property svn:executable set to *
  • Property svn:keywords set to Id
File size: 95.5 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#
25#
26# Former revisions:
27# -----------------
28# $Id: palmrun 2670 2017-12-06 16:32:19Z raasch $
29# test printouts removed
30#
31# 2669 2017-12-06 16:03:27Z raasch
32# file attributes in .palm.iofiles restructured, "loc" attribute completely
33# removed,
34# wildcard (*) allowed in .palm.iofiles as file activation string for output
35# files,
36# informative messages in case of missing optional input files shortened
37# bugfix: variable cycle explicitly interpreted with 10 as the number base
38#
39# 2638 2017-11-23 12:44:23Z raasch
40# use of wildcards in file connection statements enabled
41#
42# 2605 2017-11-09 15:31:46Z raasch
43# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
44# will not be sent with the job file any more, but copied into the
45# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
46#
47# 2600 2017-11-01 14:11:20Z raasch
48# cycle numbers are made three digits wide
49#
50# 2566 2017-10-20 08:50:47Z raasch
51# execute command for combine_plot_fields added
52# "TEMPDIR" renamed "tempdir"
53# temporary working directory for local batch jobs is created immediately within
54# the user's palmrun call, due to a requirement of the "grid engine" batch
55# system, where the working directory is given with batch directive -wd and must
56# already exist when the job is submitted,
57# informative messages in non-trace mode reduced and partly reformatted
58#
59# 2551 2017-10-18 07:25:11Z raasch
60# TEMPDIR added as replacement string to be used in batch directives
61#
62# 2512 2017-10-04 08:26:59Z raasch
63# bugfix for determining cycle numbers of NetCDF input files
64#
65# 2506 2017-09-29 08:30:37Z raasch
66# option -V added to check for an existing SOURCES_FOR_RUN_... folder
67# host configuration added to SOURCES_FOR_RUN_... folder name
68# host_identifier renamed host_configuration
69# option -W added to allow for job dependencies
70#
71# 2501 2017-09-26 11:41:55Z raasch
72# default value for number of cores (option -X) set to 1
73# bugfix for mechanism which overwrites configuration file settings with values
74# provided by palmrun options
75#
76# 2499 2017-09-22 16:47:58Z kanani
77# option -h named configuration identifier
78#
79# 2480 2017-09-19 06:24:14Z maronga
80# bugfix for last revision
81#
82# 2479 2017-09-19 06:12:16Z raasch
83# option -A (project account number) added
84#
85# 2422 2017-09-08 08:25:41Z raasch
86# initial revision
87#
88#--------------------------------------------------------------------------------#
89# palmrun - script for running PALM jobs on local and remote hosts
90#--------------------------------------------------------------------------------#
91
92
93 
94    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
95
96 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
97                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
98                     # (TOO MANY ARGUMENTS - PROBLEM)
99 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
100
101 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
102 typeset -i  nr_of_output_files=0
103 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
104                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
105                           # SCRIPT-OPTION ARGUMENTS
106 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
107 typeset -i  icycle inode ival maxcycle mpi_tasks
108 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
109
110 activation_string_list=""
111 AddFilenames=""
112 combine_plot_fields=true
113 compiler_name=""
114 compiler_name_ser=""
115 compiler_options=""
116 cores=1
117 cores_atmos=0
118 cores_ocean=0
119 coupled_dist=""
120 cpp_options=""
121 cpumax=0
122 create_batch_job=false
123 create_jobfile_only=false
124 create_remote_batch_job=false
125 dashes="  ----------------------------------------------------------------------------"
126 defaultqueue=""
127 delete_temporary_catalog=true
128 do_compile=true
129 do_trace=false
130 executable=""
131 execute_command=""
132 execution_error=false
133 fileconnection_file=.palm.iofiles
134 fname=test
135 global_revision=""
136 host_configuration="default"
137 hostfile=""
138 hp=""
139 keep_data_from_previous_run=false
140 link_local_input=false
141 link_local_output=false
142 linker_options=""
143 local_jobcatalog=""
144 locat=normal
145 makefile=""
146 max_par_io_str=""
147 prc=$0
148 while [[ $(echo $prc | grep -c "/") != 0 ]]
149 do
150    prc=`echo $prc | cut -f2- -d"/"`
151 done
152 module_calls=""
153 palmrun_memory=""
154 palmrun_script_name=$prc
155 openmp=false
156 previous_job=""
157 project_account=""
158 queue=none
159 restart_run=false
160 return_address=""
161 remote_jobcatalog=""
162 remote_username=""
163 running_in_batch_mode=false
164 run_coupled_model=false
165 run_id=""
166 silent=false
167 source_list=""
168 source_path=""
169 tasks_per_node=0
170 threads_per_task=1
171 transfer_problems=false
172 user_source_path=""
173 use_existing_sources_folder=""
174 use_openmp=false
175 version="palmrun  1.0 Rev$Rev: 2303 $"
176 working_directory=`pwd`
177 write_binary=""
178 TOPT=""
179
180
181    # ERROR HANDLING IN CASE OF EXIT
182 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
183       then
184
185              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
186          (( i = 0 ))
187          while (( i < iec ))
188          do
189             (( i = i + 1 ))
190             printf "\n  *** Execution of ERROR-command:\n"
191             printf "  >>> ${err_command[$i]}\n"
192             eval  ${err_command[$i]}
193          done
194          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
195          printf "\n\n+++ palmrun killed \n\n"
196       elif [[ $locat != control_c ]]
197       then
198          printf "\n --> palmrun finished\n\n"
199       fi' exit
200
201
202    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
203 trap 'cd; rm -rf $tempdir
204       printf "\n+++ palmrun killed by \"^C\" \n\n"
205       locat=control_c
206       exit
207      ' 2
208
209
210    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
211    # WHICH WILL BE USED TO START RESTART-JOBS
212 while  getopts  :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
213 do
214   case  $option  in
215       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
216       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
217       (b)   create_batch_job=true; prc="$prc -b";;
218       (B)   delete_temporary_catalog=false; prc="$prc -B";;
219       (C)   restart_run=true; prc="$prc -C";;
220       (d)   fname=$OPTARG; prc="$prc -d$OPTARG";;
221       (F)   create_jobfile_only=true;;
222       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
223       (h)   host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
224       (j)   running_in_batch_mode=true;;
225       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
226       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
227       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
228       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
229       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
230       (r)   run_id=$OPTARG;;
231       (R)   return_address=$OPTARG;;
232       (s)   source_list=$OPTARG;;
233       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
234       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
235       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
236       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
237       (v)   silent=true; prc="$prc -v";;
238       (V)   use_existing_sources_folder="-V";;
239       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
240       (W)   previous_job=$OPTARG;;
241       (x)   do_trace=true;set -x; prc="$prc -x";;
242       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
243       (y)   ocean_file_appendix=true; prc="$prc -y";;
244       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
245       (Z)   combine_plot_fields=false; prc="$prc -Z";;
246       (\?)  printf "\n  +++ unknown option $OPTARG \n"
247             printf "\n  --> type \"$0 ?\" for available options \n"
248             locat=parameter;exit;;
249   esac
250 done
251
252
253    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
254    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
255 (( to_shift = $OPTIND - 1 ))
256 shift $to_shift
257
258    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
259 if [[ "$1" = "?" ]]
260 then
261   (printf "\n  *** Description of available palmrun options:\n"
262    printf "\n      Option  Description                              Default-Value"
263    printf "\n        -a    activation string list                   \"\" "
264    printf "\n        -A    project account number                   ---"
265    printf "\n        -b    batch-job on local machine               ---"
266    printf "\n        -B    do not delete temporary directory at end ---"
267    printf "\n        -d    base name of files attached to program   test"
268    printf "\n        -F    create batch job file only               ---"
269    printf "\n        -h    host configuration                       \"default\" "
270    printf "\n        -k    keep data from previous run"
271    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
272    printf "\n        -M    Makefile name                            Makefile"
273    printf "\n        -O    threads per openMP task                  ---"
274    printf "\n        -q    queue                                    \"$queue\" "
275    printf "\n        -s    filenames of routines to be compiled     \"\" "
276    printf "\n              must end with .f, .f90, .F, or .c !"
277    printf "\n              use \"..\" for more than one file and wildcards"
278    printf "\n              -s LM compiles all locally modified files"
279    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
280    printf "\n        -T    tasks per node                           ---"
281    printf "\n        -u    username on remote machine               \"\" "
282    printf "\n        -v    no prompt for confirmation               ---"
283    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
284    printf "\n        -w    maximum parallel io streams              as given by -X"
285    printf "\n        -W    name of job to wait for                  ---"
286    printf "\n        -x    tracing of palmrun for debug purposes    ---"
287    printf "\n        -X    # of processors (on parallel machines)   1"
288    printf "\n        -y    add appendix \"_O\" to all local output"
289    printf "\n              files (ocean precursor runs followed by"
290    printf "\n              coupled atmosphere-ocean runs)           ---"
291    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
292    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
293    printf "\n        -Z    skip combine_plot_fields at the end of      "
294    printf "\n              the simulation                           ---"
295    printf "\n "
296    printf "\n      Possible values of positional parameter <modus>:"
297    printf "\n        \"?\"       -  this outline \n\n") | more
298    exit
299 elif [[ "$1" != "" ]]
300 then
301    printf "\n  +++ positional parameter $1 unknown \n"
302    locat=parameter; exit
303 fi
304
305
306
307    # SHORT STARTING MESSAGE
308 printf "\n*** $version "
309 printf "\n    will be executed.     Please wait ..."
310
311
312    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
313 config_file=.palm.config.$host_configuration
314 sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
315
316
317    # CHECK, IF CONFIGURATION FILE EXISTS
318 if [[ ! -f $config_file ]]
319 then
320    printf "\n\n  +++ configuration file: "
321    printf "\n           $config_file"
322    printf "\n      does not exist"
323    locat=connect; exit 
324 fi
325
326
327    # CHECK, IF FILE CONNECTION FILE EXISTS
328 if [[ ! -f $fileconnection_file ]]
329 then
330    printf "\n\n  +++ file connection file: "
331    printf "\n           $fileconnection_file"
332    printf "\n      does not exist"
333    locat=connect; exit 
334 fi
335
336
337    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
338 if [[ "$activation_string_list" = "" ]]
339 then
340    printf "\n\n  +++ no activation string list given: "
341    printf "\n        please set palmrun option \"-a\" "
342    locat=palmrun_option; exit 
343 fi
344
345
346    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
347 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
348 then
349    write_binary=true
350 else
351    write_binary=false
352 fi
353
354
355    # READ AND EVALUATE THE CONFIGURATION-FILE
356 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
357
358    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
359 while  read line
360 do
361
362       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
363    eval  line=\"$line\"
364
365
366       # INTERPRET THE LINE
367    if [[ "$(echo $line)" = "" ]]
368    then
369
370          # EMPTY LINE, NO ACTION
371       continue
372
373    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
374    then
375
376          # LINE IS A COMMENT LINE
377       continue
378
379    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
380    then
381
382          # LINE DEFINES AN ENVIRONMENT-VARIABLE
383       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
384       value=`echo $line | cut -d" " -s -f2-`
385
386
387          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
388          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
389          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
390          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
391          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
392          # CONFIGURATION-FILE.
393       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
394       then
395          eval  export  $var="\$value"
396
397             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
398          if [[ $do_trace = true ]]
399          then
400             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
401          fi
402       fi
403
404    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
405    then
406
407          # LINE DEFINES BATCH-DIRECTIVE
408       (( ibd = ibd + 1 ))
409       line=$(echo $line | cut -c4-)
410       batch_directive[$ibd]="$line"
411
412    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
413    then
414
415          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
416          # REMOTE TO A LOCAL HOST
417       (( ibdt = ibdt + 1 ))
418       line=$(echo $line | cut -c5-)
419       batch_directive_transfer[$ibdt]="$line"
420
421    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
422    then
423
424          # LINE DEFINES ERROR-COMMAND
425       (( iec = iec + 1 ))
426       line=$(echo $line | cut -c4-)
427       err_command[$iec]="$line"
428
429    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
430    then
431
432          # LINE DEFINES INPUT-COMMAND
433       (( iic = iic + 1 ))
434       line=$(echo $line | cut -c4-)
435       in_command[$iic]="$line"
436
437    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
438    then
439
440          # LINE DEFINES OUTPUT-COMMAND
441       (( ioc = ioc + 1 ))
442       line=$(echo $line | cut -c4-)
443       out_command[$ioc]="$line"
444
445    else
446
447          # SKIP ALL OTHER LINES
448       continue
449
450    fi
451
452 done < $config_file
453
454
455    # CHECK SETTING OF REQUIRED PARAMETERS
456 if [[ "$compiler_name" = "" ]]
457 then
458    printf "\n  +++ no compiler name found in $config_file"
459    printf "\n      Please add line \"compiler_name ...\" to that file."
460    locat=config_file; exit
461 fi
462 if [[ "$compiler_name_ser" = "" ]]
463 then
464    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
465    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
466    locat=config_file; exit
467 fi
468 if [[ "$compiler_options" = "" ]]
469 then
470    printf "\n  +++ no compiler options found in $config_file"
471    printf "\n      Please add line \"compiler_options ...\" to that file."
472    locat=config_file; exit
473 fi
474 if [[ "$linker_options" = "" ]]
475 then
476    printf "\n  +++ no linker options found in $config_file"
477    printf "\n      Please add line \"linker_options ...\" to that file."
478    locat=config_file; exit
479 fi
480 if [[ "$execute_command" = "" ]]
481 then
482    printf "\n  +++ no execute command found in $config_file"
483    printf "\n      Please add line \"execute_command ...\" to that file."
484    locat=config_file; exit
485 fi
486
487 if [[ "$hostfile" != "" ]]
488 then
489    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
490    then
491       printf "\n  +++ no hostfile \"$hostfile\" found"
492       printf "\n      Please check line \"hostfile ...\" in $config_file"
493       locat=config_file; exit   
494    fi
495 fi
496
497
498    # DETERMINE THE CALL STATUS
499 if [[ "$return_address" != "" ]]
500 then
501 
502       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
503       # BATCH MODE AND ...
504    running_on_remote=true
505 
506 else
507
508       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
509     if [[ "$remote_ip" != "" ]]
510     then
511
512           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
513        create_remote_batch_job=true
514
515     fi
516     running_on_remote=false
517 fi
518
519
520
521    # READ AND EVALUATE THE I/O-FILE LIST
522 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
523
524    # READ THE FILE CONNECTION FILE LINE BY LINE
525 while  read line
526 do
527
528       # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
529    line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"`
530
531       # INTERPRET THE LINE
532    if [[ "$(echo $line)" = "" ]]
533    then
534          # EMPTY LINE, NO ACTION
535       continue
536
537    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
538    then
539
540          # LINE IS A COMMENT LINE
541       true
542
543    else
544
545          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
546          # s2a: in/out - field
547          # s2b: action - field (optional)
548       s1=`echo "$line" | cut -d" " -f1`
549       s2=`echo "$line" | cut -d" " -s -f2`
550       if [[ $(echo $s2 | grep -c ":") = 0 ]]
551       then
552          s2a=$s2
553          s2b=""
554       else
555          s2a=`echo $s2 | cut -d":" -f1`
556          s2b=`echo $s2 | cut -d":" -f2`
557       fi
558       s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'`
559       s4=`echo "$line" | cut -d" " -s -f4`
560       eval s4=\"$s4\"    # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
561       s5=`echo "$line" | cut -d" " -s -f5`
562       s6=`echo "$line" | cut -d" " -s -f6`
563
564       
565          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
566          # INPUT- OR OUTPUT-LIST.
567          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
568          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
569          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
570          # IS NOT CHECKED AND STORED.
571       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
572       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
573       then
574          found=false
575          for  actual  in  $activation_string_list
576          do
577             for  formal  in  $s3
578             do
579                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
580             done
581          done
582          if [[ $found = true ]]
583          then
584             (( iin = iin + 1 ))
585             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
586             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
587             if [[ "$s2a" = inopt ]]
588             then
589                optin_pre[$iin]=yes
590             else
591                optin_pre[$iin]=no
592             fi 
593
594                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
595                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
596             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
597             then
598                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
599             fi
600
601                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
602                # THE WILDCARD FROM THE ENDING
603             if [[ "${s5: -1}" = "*" ]]
604             then
605                if [[ "$s2b" = "di" ]]
606                then
607                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
608                   printf "\n        see file \"$fileconnection_file\", line"
609                   printf "\n$line"
610                   locat=iofiles_file; exit
611                fi
612                multin[$iin]=true
613                string=${endin_pre[$iin]}
614                endin_pre[$iin]="${string%?}"
615             else
616                multin[$iin]=false
617             fi
618          fi
619       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
620       then
621          found=false
622          for  actual  in  $activation_string_list
623          do
624             for  formal  in  $s3 
625             do
626                [[ $actual = $formal  ||  $formal = wildcard  ]]  &&  found=true
627             done
628          done
629          if [[ $found = true ]]
630          then
631             (( iout = iout + 1 ))
632             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
633             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
634
635                # CHECK IF WILDCARD IS USED AS ACTIVATION STRING
636                # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
637             if [[ $formal = wildcard  ]]
638             then
639                warnout_pre[$iout]=false
640             else
641                warnout_pre[$iout]=true
642             fi
643
644                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
645                # THE WILDCARD FROM THE LOCAL FILENAME
646             if [[ "${s1: -1}" = "*" ]]
647             then
648                if [[ "$s2b" = "di" ]]
649                then
650                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
651                   printf "\n        see file \"$fileconnection_file\", line"
652                   printf "\n$line"
653                   locat=iofiles_file; exit
654                fi
655                multout[$iout]=true
656                string=${localout_pre[$iout]}
657                localout_pre[$iout]="${string%?}"
658             else
659                multout[$iout]=false
660             fi
661          fi
662       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
663       then
664          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
665          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
666          locat=connect; exit
667       fi
668       IFS="$IFSALT"
669    fi
670
671 done < $fileconnection_file
672
673
674
675    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
676 [[ $palmrun_memory     != ""   ]]  &&  memory=$palmrun_memory
677 [[ $palmrun_cpumax     != ""   ]]  &&  cpumax=$palmrun_cpumax
678 [[ "$palmrun_cores" != ""  ]]  &&  cores=$palmrun_cores
679 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
680 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
681
682
683
684      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
685 if [[ $run_coupled_model = true ]] 
686 then
687
688    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
689    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
690
691    if (( $cores_ocean + $cores_atmos != $cores ))
692    then
693
694       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
695       printf "\n      PEs (total)     : $cores"
696       printf "\n      PEs (atmosphere): $cores_atmos"
697       printf "\n      PEs (ocean)     : $cores_ocean"
698       locat=coupling; exit
699
700    fi
701
702 fi
703
704
705    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
706    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
707    # FOLDER
708 if [[ $running_in_batch_mode = true ]]
709 then
710 
711    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
712    then
713       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
714       printf "\n      Please check the output of the palmrun-call"
715       printf "\n      that you did on your local host."
716       locat=SOURCES_FOR_RUN; exit
717    fi
718
719 else
720
721       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
722       # AUTOMATIC RESTART RUN
723       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
724    if [[ $restart_run = false ]]
725    then
726
727          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
728          # THE LOCAL HOST
729       if [[ ! -d $source_path ]]
730       then
731          printf "\n\n  +++ source path \"$source_path\" on local host"
732          printf "\n      \"$(hostname)\" does not exist"
733          locat=source_path; exit
734       fi
735
736       rm -rf   $sources_for_run_catalog
737       mkdir -p $sources_for_run_catalog
738
739       if [[ "$source_list" = LM ]]
740       then
741
742             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
743          source_list=""
744          cd  $source_path
745
746
747             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
748          if [[ ! -d ../.svn ]]
749          then
750             printf "\n\n  +++ source directory"
751             printf "\n         \"$source_path\" "
752             printf "\n         is not under control of \"subversion\"."
753             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
754          fi
755
756
757             # LIST ALL MODIFIED SOURCE CODE FILES
758          Filenames=""
759          svn status  >  tmp_svnstatus
760          while  read line
761          do
762             firstc=`echo $line | cut -c1`
763             if [[ $firstc = M  ||  $firstc = "?" ]]
764             then
765                Name=`echo "$line" | cut -c8-`
766                extension=`echo $Name | cut -d. -f2`
767                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
768                then
769                   Filenames="$Filenames "$Name
770                fi
771             fi
772          done < tmp_svnstatus
773          rm -rf  tmp_svnstatus
774
775
776             # COPY FILES TO SOURCES_FOR_RUN_...
777          for  filename  in  $Filenames
778          do
779             cp  $filename  ${working_directory}/${sources_for_run_catalog}
780             source_list=$source_list"$filename "
781          done
782
783          cd -  > /dev/null
784
785
786          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
787       elif [[ "$source_list" != "" ]]
788       then
789
790          cd  $source_path
791
792          for  filename  in  $source_list
793          do
794
795                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
796             if [[ $(echo $filename | grep -c "/") != 0 ]]
797             then
798                printf "\n  +++ source code file:  $filename"
799                printf "\n      must not contain (\"/\") "
800                locat=source; exit
801             fi
802
803             if [[ ! -f $filename ]]
804             then
805                printf "\n  +++ source code file:  $filename"
806                printf "\n      does not exist"
807                locat=source; exit
808             else
809                cp  $filename  ${working_directory}/${sources_for_run_catalog}
810             fi
811
812          done
813
814          cd -  > /dev/null
815
816       fi
817
818          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
819       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
820       if [[ ! -f $makefile ]]
821       then
822          printf "\n  +++ file \"$makefile\" does not exist"
823          locat=make; exit
824       else
825          cp  $makefile  ${sources_for_run_catalog}/Makefile
826       fi
827
828
829          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
830       if [[ "$user_source_path" != "" ]]
831       then
832
833             # DOES THE DIRECTORY EXIST?
834          if [[ ! -d $user_source_path ]]
835          then
836
837             printf "\n\n  *** INFORMATIVE: additional source code directory"
838             printf "\n      \"$user_source_path\" "
839             printf "\n      does not exist or is not a directory."
840             printf "\n      No source code will be used from this directory!\n"
841             user_source_path=""
842             if [[ $silent == false ]]
843             then
844                sleep 2
845             fi
846
847          else
848
849             cd $user_source_path
850             found=false
851
852             Names=$(ls -1 *.f90 2>&1)
853             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
854             Names=$(ls -1 *.F90 2>&1)
855             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
856             Names=$(ls -1 *.F 2>&1)
857             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
858             Names=$(ls -1 *.f 2>&1)
859             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
860             Names=$(ls -1 *.c 2>&1)
861             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
862
863             cd -  > /dev/null
864             cd  $sources_for_run_catalog
865
866                # COPY MAKEFILE IF EXISTING
867             if [[ -f $user_source_path/Makefile ]]
868             then
869                printf "\n\n  *** user Makefile from directory"
870                printf "\n      \"$user_source_path\" is used \n"
871                if [[ $silent == false ]]
872                then
873                   sleep 1
874                fi
875                cp  $user_source_path/Makefile  .
876             fi
877
878             for  filename  in  $AddFilenames
879             do
880                if [[ -f $filename ]]
881                then
882                   printf "\n  +++ source code file \"$filename\" found in additional"
883                   printf "\n      source code directory \"$user_source_path\" "
884                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
885                   printf "\n      from directory \"$source_path\"."
886                   locat=source; exit
887                fi
888
889                cp  $user_source_path/$filename  .
890                source_list="$source_list $filename"
891
892                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
893                if [[ $(grep -c $filename Makefile) = 0 ]]
894                then
895                   printf "\n\n  +++ user file \"$filename\" "
896                   printf "\n      is not listed in Makefile \n"
897                   locat=source; exit
898                else
899
900                   if [[ $found = false ]]
901                   then
902                      found=true
903                      printf "\n\n  *** following user file(s) added to the"
904                      printf " files to be translated:\n      "
905                   fi
906                   printf "$filename  "
907                   if [[ $silent == false ]]
908                   then
909                      sleep 0.5
910                   fi
911
912                fi
913             done
914             [[ $found = true ]]  &&  printf "\n"
915             cd -  > /dev/null
916          fi
917       fi
918
919          # COPY CONFIGURATION FILES
920       cp  $config_file  $sources_for_run_catalog
921       cp  $fileconnection_file  $sources_for_run_catalog
922
923          # COPY SHELLSCRIPTS
924       cp  ${source_path}/../SCRIPTS/palmrun    $sources_for_run_catalog
925       cp  ${source_path}/../SCRIPTS/batch_scp  $sources_for_run_catalog
926
927    fi
928
929 fi
930
931
932    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
933    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
934 if [[ "$global_revision" = "" ]]
935 then
936    global_revision=`svnversion $source_path  2>/dev/null`
937    global_revision="Rev: $global_revision"
938 fi
939
940
941    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
942 if [[ -n $cores ]]
943 then
944
945       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
946       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
947    if [[ $tasks_per_node = 0 ]]
948    then
949       printf "\n"
950       printf "\n  +++ option \"-T\" (tasks per node) is missing"
951       printf "\n      set -T option or define tasks_per_node in the config file"
952       locat=tasks_per_node; (( iec = 0 )); exit 
953    fi
954
955    if (( cores < tasks_per_node ))
956    then
957       printf "\n"
958       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
959       printf "\n      given values: -T $tasks_per_node  -X $cores"
960       locat=tasks_per_node; (( iec = 0 )); exit 
961    fi
962
963    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
964    (( mpi_tasks = cores / threads_per_task ))
965    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
966    (( ii = cores / tasks_per_node ))
967    (( remaining_cores =  cores - ii * tasks_per_node ))
968    if (( remaining_cores > 0 ))
969    then
970       printf "\n"
971       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
972       printf "\n      divisor of the total number of cores (option \"-X\")"
973       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
974       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
975       (( nodes = nodes + 1 ))
976    fi
977
978       # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
979    if [[ "$tasks_per_node" != "" ]]
980    then
981       TOPT="-T $tasks_per_node"
982    fi
983
984 fi
985
986
987    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
988 if [[ "$maximum_parallel_io_streams" = "" ]]
989 then
990    maximum_parallel_io_streams=$cores
991 fi
992
993
994    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
995 if [[ "$scp_port" != "" ]]
996 then
997    PORTOPT="-P $scp_port"
998    SSH_PORTOPT="-p $scp_port"
999 fi
1000
1001
1002    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1003    # CONFIG-FILE
1004 if [[ "$ssh_key" != "" ]]
1005 then
1006    ssh_key="-i $HOME/.ssh/$ssh_key"
1007 fi
1008
1009
1010    # SET QUEUE, IF NOT GIVEN
1011 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1012 then
1013
1014    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
1015    then
1016       printf "\n"
1017       printf "\n  +++ no default queue given in configuration file and no queue"
1018       printf "\n      given with option -q"
1019    fi
1020    if [[ $queue = none ]]
1021    then
1022       queue=$defaultqueue
1023    fi
1024
1025 fi
1026
1027
1028    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1029    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1030 (( i = 0 ))
1031 (( nr_of_input_files = 0 ))
1032 while (( i < iin ))
1033 do
1034    (( i = i + 1 ))
1035
1036       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1037       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1038    if [[ "${actionin_pre[$i]}" = di ]]
1039    then
1040       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1041    else
1042       eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
1043    fi
1044
1045
1046       # CHECK IF FILE EXISTS
1047    if ! ls $filename* 1>/dev/null 2>&1
1048    then
1049
1050          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1051       if [[ "${optin_pre[$i]}" != "yes" ]]
1052       then
1053          printf "\n\n  +++ INPUT-file: "
1054          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
1055          then
1056             printf "\n           $filename"
1057          else
1058             printf "\n           $filename.${extin_pre[$i]}"
1059          fi
1060          printf "\n      does not exist\n"
1061          locat=input; exit
1062       else
1063          (( nr_of_input_files = nr_of_input_files + 1 ))
1064          localin[$nr_of_input_files]="${localin_pre[$i]}"
1065          optin[$nr_of_input_files]="${optin_pre[$i]}"
1066          actionin[$nr_of_input_files]="unavailable"
1067          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1068          endin[$nr_of_input_files]="${endin_pre[$i]}"
1069          extin[$nr_of_input_files]="${extin_pre[$i]}"
1070       fi
1071
1072    else
1073
1074          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
1075          # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1076       if [[ "${multin[$i]}" = true ]]
1077       then
1078             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1079          ls -1 -d ${filename}    >   filelist  2>/dev/null
1080          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
1081          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null
1082
1083          endings=""
1084          while  read line
1085          do
1086                 # filename without path (i.e. after the last "/")
1087              basefilename=$(basename ${line})
1088
1089                 # check if there is an extension and remove it
1090              ext=${basefilename##*.}
1091              if [[ "$ext" = "${extin_pre[$i]}" ]]
1092              then
1093                 basefilename=${basefilename%.*}
1094              fi
1095
1096                 # check for an existing cycle number and remove it
1097              cycle=${basefilename##*.}
1098              if [[ $cycle =~ ^-?[0-9]+$ ]]
1099              then
1100                 basefilename=${basefilename%.*}
1101              fi
1102
1103                 # remove the fname from the beginning
1104              length_fname=${#fname}
1105              ending=${basefilename:${length_fname}}
1106
1107                 # remove the ending given in the .iofiles from the beginning
1108              endingstring="${endin_pre[$i]}"
1109              length_ending=${#endingstring}
1110              ending=${ending:${length_ending}}
1111
1112              if [[ "$ending" = "" ]]
1113              then
1114                    # standard ending as given in the .iofiles
1115                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
1116                 then
1117                    endings="$endings DEFAULT"
1118                 fi
1119              else
1120                    # ending must start with "_", otherwise its a different file
1121                 if [[ "${ending:0:1}" = "_" ]]
1122                 then
1123                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
1124                    then
1125                       endings="$endings $ending"
1126                    fi
1127                 fi
1128              fi
1129 
1130          done <filelist
1131
1132          rm filelist
1133
1134       else
1135
1136             # SINGLE NAME
1137          endings=DEFAULT
1138
1139       fi
1140
1141          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1142       for  ending  in  $endings
1143       do
1144
1145             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1146          if [[ $ending = DEFAULT ]]
1147          then
1148             ending=""
1149          fi
1150
1151             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1152          (( nr_of_input_files = nr_of_input_files + 1 ))
1153          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1154          optin[$nr_of_input_files]="${optin_pre[$i]}"
1155          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1156          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1157          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1158          extin[$nr_of_input_files]="${extin_pre[$i]}"
1159
1160
1161             # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1162             # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1163          if [[ "${actionin[$nr_of_input_files]}" = di ]]
1164          then
1165             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1166          else
1167             eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
1168          fi
1169
1170             # DETERMINE THE FILE'S CYCLE NUMBER
1171          (( maxcycle = 0 ))
1172          ls -1 -d $filename    >   filelist  2>/dev/null
1173          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1174          while  read line
1175          do
1176                 # filename without path (i.e. after the last "/")
1177              basefilename=$(basename ${line})
1178   
1179                 # check if there is an extension
1180              extension=${basefilename##*.}
1181              if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1182              then
1183                 basefilename=${basefilename%.*}
1184              fi
1185   
1186                 # check for an existing cycle number
1187              cycle=${basefilename##*.}
1188              if [[ $cycle =~ ^-?[0-9]+$ ]]
1189              then
1190                    # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1191                    # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1192                 (( icycle = $((10#$cycle)) ))
1193              else
1194                 (( icycle = 0 ))
1195              fi
1196   
1197              if (( icycle > maxcycle ))
1198              then
1199                 (( maxcycle = icycle ))
1200   
1201                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1202                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1203                 if [[ $(echo $cycle | cut -c1) = 0 ]]
1204                 then
1205                    leading_zero=true
1206                 else
1207                    leading_zero=false
1208                 fi
1209              fi
1210   
1211          done <filelist
1212          rm filelist
1213   
1214             # MAKE CYCLE NUMBER THREE DIGITS WIDE
1215          if [[ $leading_zero = true ]]
1216          then
1217             cyclestring=`printf "%03d" $maxcycle`
1218          else
1219             cyclestring=$maxcycle
1220          fi
1221   
1222             # APPEND CYCLE NUMBER TO FILENAME
1223          if (( maxcycle > 0 ))
1224          then
1225             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1226             then
1227                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1228             else
1229                filename=${filename}.$cyclestring
1230             fi
1231          else
1232             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1233             then
1234                filename=${filename}.${extin[$nr_of_input_files]}
1235             fi
1236          fi
1237         
1238             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1239             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1240          absnamein[$nr_of_input_files]=$filename
1241          if (( maxcycle > 0 ))
1242          then
1243             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1244             then
1245                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1246             else
1247                frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
1248             fi
1249          else
1250             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1251             then
1252                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1253             else
1254                frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
1255             fi
1256          fi
1257
1258       done
1259
1260    fi
1261
1262 done
1263
1264
1265    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1266    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1267    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
1268    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1269    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1270    # REMOTE HOST)
1271 (( i = 0 ))
1272 while (( i < iout ))
1273 do
1274    (( i = i + 1 ))
1275    if [[ ! ( $running_on_remote = true  &&  ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
1276    then
1277       if [[ "${actionout_pre[$i]}" = tr ]]
1278       then
1279          actionout_pre[$i]=""
1280       elif [[ "${actionout_pre[$i]}" = trpe ]]
1281       then
1282          actionout_pre[$i]=pe
1283       elif [[ "${actionout_pre[$i]}" = tra ]]
1284       then
1285          actionout_pre[$i]=a
1286       fi
1287       (( maxcycle = 0 ))
1288       eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
1289       eval catalogname=${pathout_pre[$i]}
1290       if ! ls $filename* 1>/dev/null 2>&1
1291       then
1292     
1293             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1294          if  cat /dev/null > $filename 
1295          then
1296             rm  $filename
1297          else
1298
1299                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1300                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1301             if [[ ! -d $catalogname ]]
1302             then
1303                if  mkdir -p  $catalogname
1304                then
1305                   printf "\n\n  *** directory:"
1306                   printf "\n           $catalogname"
1307                   printf "\n      was created\n"
1308                else
1309                   printf "\n\n  +++ OUTPUT-file:"
1310                   printf "\n           $filename"
1311                   printf "\n      cannot be created, because directory does not exist"
1312                   printf "\n      and cannot be created either"
1313                   printf "\n"
1314                   locat=output  ; exit
1315                fi 2>/dev/null
1316             else
1317                printf "\n\n  +++ OUTPUT-file:"
1318                printf "\n           $filename"
1319                printf "\n      cannot be created, although directory exists"
1320                printf "\n"
1321                locat=output  ; exit
1322             fi
1323          fi 2>/dev/null
1324
1325       fi
1326
1327    fi
1328 done
1329
1330
1331    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1332 if [[ $running_in_batch_mode = false ]]
1333 then
1334    run_id=$RANDOM
1335    job_id=${fname}.$run_id
1336
1337    tempdir=$fast_io_catalog/$job_id
1338 fi
1339
1340
1341    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1342 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1343 then
1344
1345       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1346    if [[ $ibd = 0 ]]
1347    then
1348       printf "\n"
1349       printf "\n  +++ no batch directives found in configuration file"
1350       locat=config_file_batch_directives; (( iec = 0 )); exit 
1351    fi
1352
1353       # CHECK IF CPUTIME IS GIVEN FOR JOB
1354    done=false
1355    cputime=$cpumax
1356    while [[ $done = false ]]
1357    do
1358       if (( cputime == 0 ))
1359       then
1360          printf "\n  +++ cpu-time is undefined"
1361          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1362          printf "\n  >>> "
1363          read  cputime   1>/dev/null  2>&1
1364       else
1365          done=true
1366       fi
1367    done
1368    cpumax=$cputime
1369
1370       # CHECK THE MEMORY DEMAND
1371    done=false
1372    while [[ $done = false ]]
1373    do
1374       if (( memory == 0 ))
1375       then
1376          printf "\n  +++ memory demand is undefined"
1377          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1378          printf "\n  >>> "
1379          read  memory  1>/dev/null  2>&1
1380       else
1381          done=true
1382       fi
1383    done
1384
1385       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1386    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1387    then
1388       while [[ -z $remote_username ]]
1389       do
1390          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
1391          printf "\n  >>> Please type username:"
1392          printf "\n  >>> "
1393          read  remote_username
1394       done
1395    fi
1396
1397 else
1398
1399    if [[ $running_in_batch_mode = false ]]
1400    then
1401       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1402       cpumax=$cputime
1403    else
1404       cputime=$cpumax
1405    fi
1406
1407 fi
1408
1409
1410    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1411 (( cpu_hours  = cputime / 3600 ))
1412 (( resttime = cputime - cpu_hours * 3600 ))
1413 (( cpu_minutes  = resttime / 60 ))
1414 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1415 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1416
1417
1418    # OUTPUT OF THE PALMRUN-HEADER
1419 calltime=$(date)
1420 printf "\n"
1421 printf "#------------------------------------------------------------------------# \n"
1422 printf "| %-35s%35s | \n" "$version" "$calltime"
1423 printf "|                                                                        | \n"
1424 column1="called on:"; column2=$(hostname)
1425 printf "| %-25s%-45s | \n" "$column1" "$column2"
1426 if [[ $create_remote_batch_job = true ]]
1427 then
1428    column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1429 else
1430    if [[ $running_on_remote = true ]]
1431    then
1432       column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1433    else
1434       column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1435    fi
1436 fi
1437 printf "| %-25s%-45s | \n" "$column1" "$column2"
1438
1439 column1="running in:"
1440 if [[ $running_in_batch_mode = true ]]
1441 then
1442    column2="batch job mode"
1443 else
1444    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1445    then
1446       column2="job creation mode"
1447    else
1448       column2="interactive run mode"
1449    fi
1450 fi
1451 printf "| %-25s%-45s | \n" "$column1" "$column2"
1452
1453 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1454 then
1455    if [[ "$project_account" != "" ]]
1456    then
1457       column1="project account number:"
1458       column2="$project_account"
1459       printf "| %-25s%-45s | \n" "$column1" "$column2"
1460    fi
1461 fi
1462
1463 if [[ -n $cores ]]
1464 then
1465    if [[ $run_coupled_model = false ]]
1466    then
1467       column1="number of cores:"; column2=$cores
1468    else
1469       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1470    fi
1471    printf "| %-25s%-45s | \n" "$column1" "$column2"
1472 fi
1473 if [[ -n $tasks_per_node ]]
1474 then
1475    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1476    printf "| %-25s%-45s | \n" "$column1" "$column2"
1477    if (( remaining_cores > 0 ))
1478    then
1479       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1480       printf "| %-25s%-45s | \n" "$column1" "$column2"
1481    fi
1482 fi
1483 if [[ $maximum_parallel_io_streams != $cores ]]
1484 then
1485    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1486    printf "| %-25s%-45s | \n" "$column1" "$column2"
1487 fi
1488 if [[ $use_openmp = true ]]
1489 then
1490    column1="threads per task:"; column2="$threads_per_task"
1491    printf "| %-25s%-45s | \n" "$column1" "$column2"
1492 fi
1493 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1494 then
1495    column1="memory demand / PE":; column2="$memory MB"
1496    printf "| %-25s%-45s | \n" "$column1" "$column2"
1497    column1="job cpu time (h:m:s):"; column2="$timestring"
1498    printf "| %-25s%-45s | \n" "$column1" "$column2"
1499 fi
1500 printf "|                                                                        | \n"
1501 if [[ "$source_list" != "" ]]
1502 then
1503    if [[ "$make_options" != "" ]]
1504    then
1505       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1506       printf "| %-25s%-45s | \n" "$column1" "$column2"
1507       line=$(echo "$make_options" | cut -c46-)
1508       while [[ "$line" != "" ]]
1509       do
1510          column1=""
1511          column2=$(echo "$line" | cut -c-45)
1512          printf "| %-25s%-45s | \n" "$column1" "$column2"
1513          line=$(echo "$line" | cut -c46-)
1514       done
1515    fi
1516 fi
1517
1518 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1519 printf "| %-25s%-45s | \n" "$column1" "$column2"
1520 line=$(echo "$cpp_options" | cut -c46-)
1521 while [[ "$line" != "" ]]
1522 do
1523    column1=""
1524    column2=$(echo "$line" | cut -c-45)
1525    printf "| %-25s%-45s | \n" "$column1" "$column2"
1526    line=$(echo "$line" | cut -c46-)
1527 done
1528
1529 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1530 printf "| %-25s%-45s | \n" "$column1" "$column2"
1531 line=$(echo "$compiler_options" | cut -c46-)
1532 while [[ "$line" != "" ]]
1533 do
1534    column1=""
1535    column2=$(echo "$line" | cut -c-45)
1536    printf "| %-25s%-45s | \n" "$column1" "$column2"
1537    line=$(echo "$line" | cut -c46-)
1538 done
1539
1540 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
1541 printf "| %-25s%-45s | \n" "$column1" "$column2"
1542 line=$(echo "$linker_options" | cut -c46-)
1543 while [[ "$line" != "" ]]
1544 do
1545    column1=""
1546    column2=$(echo "$line" | cut -c-45)
1547    printf "| %-25s%-45s | \n" "$column1" "$column2"
1548    line=$(echo "$line" | cut -c46-)
1549 done
1550
1551 if [[ "$login_init_cmd" != "" ]]
1552 then
1553    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1554    printf "| %-25s%-45s | \n" "$column1" "$column2"
1555    line=$(echo "$login_init_cmd" | cut -c46-)
1556    while [[ "$line" != "" ]]
1557    do
1558       column1=""
1559       column2=$(echo "$line" | cut -c-45)
1560       printf "| %-25s%-45s | \n" "$column1" "$column2"
1561       line=$(echo "$line" | cut -c46-)
1562    done
1563 fi
1564
1565 if [[ "$module_commands" != "" ]]
1566 then
1567    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1568    printf "| %-25s%-45s | \n" "$column1" "$column2"
1569    line=$(echo "$module_commands" | cut -c46-)
1570    while [[ "$line" != "" ]]
1571    do
1572       column1=""
1573       column2=$(echo "$line" | cut -c-45)
1574       printf "| %-25s%-45s | \n" "$column1" "$column2"
1575       line=$(echo "$line" | cut -c46-)
1576    done
1577 fi
1578 printf "|                                                                        | \n"
1579 column1="base name of files:"; column2=$fname
1580 printf "| %-25s%-45s | \n" "$column1" "$column2"
1581 column1="activation string list:"; column2=$(echo $activation_string_list)
1582 printf "| %-25s%-45s | \n" "$column1" "$column2"
1583
1584 if [[ "$ocean_file_appendix" = true ]]
1585 then
1586    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1587 fi
1588
1589 if [[ "$source_list" != "" ]]
1590 then
1591    printf "|                                                                        | \n"
1592    printf "| Files to be compiled:                                                  | \n"
1593    line=$source_list
1594    while [[ "$line" != "" ]]
1595    do
1596       linestart=$(echo $line | cut -c-70)
1597       printf "| %-70s | \n" "$linestart"
1598       line=$(echo "$line" | cut -c71-)
1599    done
1600 fi
1601 printf "#------------------------------------------------------------------------#"
1602
1603
1604
1605    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1606 if [[ $do_trace = true ]]
1607 then
1608    (( i = 0 ))
1609    while (( i < nr_of_input_files ))
1610    do
1611       (( i = i + 1 ))
1612       if (( i == 1 ))
1613       then
1614          printf "\n\n >>> INPUT-file assignments:\n"
1615       fi
1616       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1617    done
1618    (( i = 0 ))
1619    while (( i < iout ))
1620    do
1621       (( i = i + 1 ))
1622       if (( i == 1 ))
1623       then
1624          printf "\n\n >>> OUTPUT-file assignments:\n"
1625       fi
1626       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1627    done
1628    (( i = 0 ))
1629    while (( i < iic ))
1630    do
1631       (( i = i + 1 ))
1632       if (( i == 1 ))
1633       then
1634          printf "\n\n >>> INPUT-commands:\n"
1635       fi
1636       printf "\n     ${in_command[$i]}" 
1637    done
1638    (( i = 0 ))
1639    while (( i < ioc ))
1640    do
1641       (( i = i + 1 ))
1642       if (( i == 1 ))
1643       then
1644          printf "\n\n >>> OUTPUT-commands:\n"
1645       fi
1646       printf "\n     ${out_command[$i]}" 
1647    done
1648 fi
1649
1650    # QUERY FOR CONTINUE
1651 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1652 then
1653    antwort=dummy
1654    printf "\n\n"
1655    printf " >>> everything o.k. (y/n) ?  "
1656    while  read antwort
1657    do
1658       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1659       then
1660          printf " >>> everything o.k. (y/n) ?  "
1661       else
1662          break
1663       fi
1664    done
1665    if [[ $antwort = n  ||  $antwort = N ]]
1666    then
1667       locat=user_abort; (( iec = 0 )); exit
1668    fi
1669    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1670    then
1671       printf "\n ***  batch-job will be created and submitted"
1672    else
1673       printf "\n ***  PALMRUN will now continue to execute on this machine"
1674    fi
1675 fi
1676
1677 
1678
1679    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1680 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1681 then
1682
1683    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1684    then
1685       printf "\n\n  *** creating executable and other sources for the remote host\n"
1686    else
1687       printf "\n\n  *** creating executable and other sources for the local host\n"
1688    fi
1689
1690       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1691       # IT SHALL BE CREATED
1692    ask_for_make_depository=false
1693    if [[ $create_remote_batch_job = true ]]
1694    then
1695
1696       line=`grep %base_directory $config_file`
1697       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1698       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${host_configuration}_last_make_protokoll
1699
1700       if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1701       then
1702          printf "\n\n  +++ make depository \"${make_depository}\""
1703          printf "\n      on remote host not found!"
1704          ask_for_make_depository=true
1705       fi
1706       rm ${host_configuration}_last_make_protokoll
1707
1708    else
1709
1710          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1711       make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1712       if [[ ! -d ${make_depository} ]]
1713       then
1714          printf "\n\n  +++ make depository \"${make_depository}\""
1715          printf "\n      on local host not found!"
1716          ask_for_make_depository=true
1717       fi
1718
1719    fi
1720
1721    if [[ $ask_for_make_depository = true ]]
1722    then
1723
1724       antwort=dummy
1725       printf "\n\n"
1726       printf "  >>> Create a new one (y/n) ?  "
1727       while  read antwort
1728       do
1729          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1730          then
1731             printf "  >>> Create a new one (y/n) ?  "
1732          else
1733             break
1734          fi
1735       done
1736       if [[ $antwort = n  ||  $antwort = N ]]
1737       then
1738          locat=user_abort; (( iec = 0 )); exit
1739       fi
1740
1741       if [[ $do_trace = true ]]
1742       then
1743          palmbuild  -h $host_configuration
1744       else
1745          palmbuild  -v  -h $host_configuration
1746       fi
1747
1748       if [[ $? != 0 ]]
1749       then
1750   
1751              # ABORT IN CASE OF COMPILATION PROBLEMS
1752          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1753          locat=make_depository
1754          exit
1755       else
1756          echo "  *** now continue with creating executable and other sources"
1757       fi
1758
1759    fi
1760
1761       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
1762    palmbuild  -v  $use_existing_sources_folder  -h $host_configuration  -d $fname
1763
1764    if [[ $? != 0 ]]
1765    then
1766
1767           # ABORT IN CASE OF COMPILATION PROBLEMS
1768       printf "\n  +++ error while creating executable and/or other sources"
1769       locat=execution
1770       rm -rf  $sources_for_run_catalog
1771       exit
1772
1773    else
1774
1775       printf "  *** executable and other sources created\n"
1776       rm -rf  $sources_for_run_catalog
1777
1778    fi
1779
1780 fi
1781
1782
1783    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1784    # WILL BE COPIED TO THE REMOTE HOST
1785 if [[ $create_remote_batch_job = true ]]
1786 then
1787    (( i = 0 ))
1788    while (( i < nr_of_input_files ))
1789    do
1790       (( i = i + 1 ))
1791       if [[ "${actionin[$i]}" = tr ]]
1792       then
1793          eval inputfile=${pathin[$i]}/${frelin[$i]}
1794          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1795       fi
1796    done
1797    if (( i > 0 ))
1798    then
1799       printf "  *** input files have been copied to the remote host\n"
1800    fi
1801 fi
1802 
1803
1804    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1805    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1806 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1807 then
1808
1809       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1810    if [[ $running_in_batch_mode = false ]]
1811    then
1812          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1813          # FOLDER
1814       mkdir -p  $tempdir
1815       chmod  go+rx  $tempdir
1816       cd  $tempdir
1817       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $tempdir
1818       printf "\n  *** changed to temporary directory: $tempdir"
1819
1820    else
1821
1822          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1823       printf "\n  *** running in temporary directory: $tempdir"
1824
1825    fi
1826
1827
1828       # PROVIDE THE INPUT FILES
1829       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1830    optional_files_missing=false
1831    (( i = 0 ))
1832    while (( i < nr_of_input_files ))
1833    do
1834       (( i = i + 1 ))
1835       if (( i == 1 ))
1836       then
1837          printf "\n\n  *** providing INPUT-files:\n$dashes"
1838       fi
1839
1840
1841          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1842       if [[ "${actionin[$i]}" = unavailable ]]
1843       then
1844          optional_files_missing=true
1845          continue
1846       fi
1847
1848          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1849       files_for_cores=false; filetype=file
1850       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1851       then
1852          files_for_cores=true; filetype=files
1853          actionin[$i]=""
1854       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1855       then
1856          actionin[$i]=""
1857       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1858       then
1859          files_for_cores=true; filetype=files
1860          actionin[$i]="ln"
1861       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1862       then
1863          actionin[$i]="ln"
1864       fi
1865
1866       if [[ $files_for_cores = true ]]
1867       then
1868          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1869       else
1870          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1871       fi
1872
1873          # INPUT-FILES TO BE LINKED
1874       if [[ "${actionin[$i]}" = ln ]]
1875       then
1876
1877          printf "\n      $filetype will be linked"
1878          if [[ $files_for_cores = false ]]
1879          then
1880             if [[ -f "${absnamein[$i]}" ]]
1881             then
1882                ln  ${absnamein[$i]}  ${localin[$i]}
1883                got_tmp[$i]=true
1884             fi
1885          else
1886             if [[ -d "${absnamein[$i]}" ]]
1887             then
1888                mkdir -p ${localin[$i]}
1889                cd ${absnamein[$i]}
1890                for file in $(ls *)
1891                do
1892                   ln $file $tempdir/${localin[$i]}
1893                done >|/dev/null 2>&1
1894                cd $tempdir
1895             fi
1896
1897                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1898             if [[ ! -f "${localin[$i]}/_000000" ]]
1899             then
1900                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1901                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1902             fi
1903
1904             got_tmp[$i]=true
1905          fi
1906       fi
1907
1908          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1909       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "tr"  ||  "${actionin[$i]}" = "npe" ]]
1910       then
1911
1912          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
1913          then
1914
1915                # FILE COPIES ARE PROVIDED FOR ALL CORES
1916                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1917             printf "\n      file will be provided for $cores processors"
1918             mkdir -p ${localin[$i]}
1919             ival=$cores
1920             (( ii = 0 ))
1921             while (( ii <= ival-1 ))
1922             do
1923                if (( ii < 10 ))
1924                then
1925                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
1926                elif (( ii < 100 ))
1927                then
1928                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
1929                elif (( ii < 1000 ))
1930                then
1931                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
1932                else
1933                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
1934                fi
1935                (( ii = ii + 1 ))
1936             done
1937
1938          else
1939
1940             if [[ $files_for_cores = true ]]
1941             then
1942
1943                   # PROVIDE FILES FOR EACH CORE
1944                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1945                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1946                printf "\n      providing $cores files for the respective cores"
1947                mkdir -p ${localin[$i]}
1948                        if [[ $link_local_input = true ]]
1949                              then
1950                                 printf "      files will be linked\n"
1951                                 cd ${absnamein[$i]}
1952                                 for file in $(ls *)
1953                                 do
1954                                    ln -f $file  ${localin[$i]}
1955                                 done
1956                                 cd $tempdir
1957                              fi
1958
1959                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1960                              if [[ ! -f "${localin[$i]}/_000000" ]]
1961                              then
1962                                 if [[ $link_local_input = true ]]
1963                                        then
1964                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1965                                 fi
1966                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1967                              fi
1968
1969             else
1970
1971                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
1972                        if [[ $link_local_input = true ]]
1973                        then
1974                                 printf "      file will be linked\n"
1975                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
1976                        fi
1977                                # If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
1978                        if [[ ! -f "${localin[$i]}" ]]
1979                then
1980                                 if [[ $link_local_input = true ]]
1981                          then
1982                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1983                                 fi
1984                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
1985                   then
1986                      mv  ${absnamein[$i]}  ${localin[$i]}
1987                   else
1988                                 cp  ${absnamein[$i]}  ${localin[$i]}
1989                   fi
1990                fi
1991             fi
1992          fi
1993       fi
1994
1995    done
1996    if (( i != 0 ))
1997    then
1998       if [[ $optional_files_missing = true ]]
1999       then
2000          printf "\n  *** INFORMATIVE: some optional INPUT-files are not present"
2001       fi
2002       printf "\n$dashes\n  *** all INPUT-files provided \n"
2003    fi
2004
2005
2006       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2007    (( i = 0 ))
2008    while (( i < iic ))
2009    do
2010       (( i = i + 1 ))
2011       if (( i == 1 ))
2012       then
2013          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
2014       fi
2015       printf "\n  >>> ${in_command[$i]}"
2016       eval  ${in_command[$i]}
2017       if (( i == iic ))
2018       then
2019          printf "\n$dashes\n"
2020       fi
2021    done
2022
2023
2024       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2025       # (FILE ENVPAR WILL BE READ BY PALM)
2026    cat  >  ENVPAR  <<  EOF
2027 &envpar  run_identifier = '$fname', host = '$host_configuration',
2028          write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2029          maximum_parallel_io_streams = $maximum_parallel_io_streams,
2030          maximum_cpu_time_allowed = ${cpumax}.,
2031          revision = '$global_revision',
2032          batch_job = .${running_in_batch_mode}. /
2033
2034EOF
2035
2036
2037       # STARTING THE EXECUTABLE
2038    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
2039    PATH=$PATH:$tempdir
2040
2041
2042       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2043    line=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/$mpi_tasks/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
2044    line2=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/1/g' | sed 's/{{TASKS_PER_NODE}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
2045    eval line=\"$line\"
2046    execute_command="$line"
2047
2048
2049       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2050    if [[ "$execute_command_for_combine" = "" ]]
2051    then
2052       eval line2=\"$line2\"
2053       execute_command_for_combine="$line2"
2054    fi
2055   
2056
2057
2058       # PROVIDE A HOSTFILE, IF REQUIRED
2059    if [[ "$hostfile" != "" ]]
2060    then
2061
2062       if [[ $hostfile = auto ]]
2063       then
2064             # CREATE A NEW HOSTFILE
2065          (( ii = 1 ))
2066          while (( ii <= cores / threads_per_task ))
2067          do
2068             echo  $(hostname)  >>  hostfile
2069             (( ii = ii + 1 ))
2070          done
2071          if (( cores / threads_per_task == 0 ))
2072          then
2073             echo  $(hostname)  >>  hostfile
2074          fi
2075       
2076       else
2077          cp  $hostfile  hostfile
2078       fi
2079       eval line=\"`head -n $ii  hostfile`\"
2080       printf "\n  *** running on: $line"
2081    fi
2082
2083
2084
2085       # SET THE NUMBER OF OPENMP-THREADS
2086    if [[ $use_openmp = true ]]
2087    then
2088       export OMP_NUM_THREADS=$threads_per_task
2089       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2090    else
2091       export OMP_NUM_THREADS=1
2092    fi
2093
2094
2095       # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2096    if [[ $run_coupled_model = false ]]
2097    then
2098       if [[ "$ocean_file_appendix" = true ]]
2099       then
2100          echo "precursor_ocean"  >  coupling_steering
2101       else
2102          echo "precursor_atmos"  >  coupling_steering
2103      fi
2104    else
2105       (( iia = $cores_atmos / $threads_per_task ))
2106       (( iio = $cores_ocean / $threads_per_task ))
2107       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
2108       printf "\n\n"
2109       echo "coupled_run $iia $iio"  >  coupling_steering
2110    fi
2111
2112    printf "\n  *** execute command:"
2113    printf "\n      \"$execute_command\" \n\n"
2114
2115    $execute_command  <  coupling_steering
2116
2117    if [[ $? != 0 ]]
2118    then
2119
2120           # ABORT IN CASE OF RUNTIME ERRORS
2121       printf "\n  +++ runtime error occured"
2122       locat=execution
2123       exit
2124
2125    else
2126
2127       printf "\n$dashes\n  *** execution finished \n"
2128
2129    fi
2130
2131
2132       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2133       # BY EACH CORE INTO ONE FILE
2134   if [[ ! -f combine_plot_fields.x ]]
2135   then
2136
2137      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
2138      printf "\n      2d- and/or 3d-data may be incomplete!"
2139      printf "\n      Your previous palmbuild may have failed. Please check.\n"
2140
2141   elif [[ "$combine_plot_fields" == true ]]
2142   then
2143
2144      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2145      $execute_command_for_combine
2146
2147   else
2148
2149         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2150         # DATA OUTPUT
2151      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2152   fi
2153
2154
2155
2156       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2157    (( i = 0 ))
2158    while (( i < ioc ))
2159    do
2160       (( i = i + 1 ))
2161       if (( i == 1 ))
2162       then
2163          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
2164       fi
2165       printf "\n  >>> ${out_command[$i]}"
2166       eval  ${out_command[$i]}
2167       if (( i == ioc ))
2168       then
2169          printf "\n$dashes\n"
2170       fi
2171    done
2172
2173
2174       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2175       # WILDCARDS
2176    (( i = 0 ))
2177    (( nr_of_output_files = 0 ))
2178
2179    while (( i < iout ))
2180    do
2181
2182       (( i = i + 1 ))
2183
2184          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2185          # CREATE A LIST FOR THE DETECTED ENDINGS
2186       if [[ "${multout[$i]}" = true ]]
2187       then
2188             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2189          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
2190          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null
2191
2192          endings="DEFAULT"
2193          while  read line
2194          do
2195                 # remove the local name from the beginning
2196              localnamestring="${localout_pre[$i]}"
2197              length_localname=${#localnamestring}
2198              ending=${line:${length_localname}}
2199
2200              if [[ "$ending" != "" ]]
2201              then
2202                 endings="$endings $ending"
2203              fi
2204 
2205          done <filelist
2206
2207          rm filelist
2208
2209       else
2210
2211             # SINGLE NAME
2212          endings=DEFAULT
2213
2214       fi
2215
2216          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2217       for  ending  in  $endings
2218       do
2219
2220             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2221          if [[ $ending = DEFAULT ]]
2222          then
2223             ending=""
2224          fi
2225
2226             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2227          (( nr_of_output_files = nr_of_output_files + 1 ))
2228          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2229          transout[$nr_of_output_files]="${transout_pre[$i]}"
2230          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2231          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2232          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2233          extout[$nr_of_output_files]="${extout_pre[$i]}"
2234          warnout[$nr_of_output_files]="${warnout_pre[$i]}"
2235
2236       done
2237
2238    done
2239
2240
2241
2242
2243       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2244    (( i = 0 ))
2245    while (( i < nr_of_output_files ))
2246    do
2247       (( i = i + 1 ))
2248       if (( i == 1 ))
2249       then
2250          printf "\n\n  *** saving OUTPUT-files:"
2251
2252             # GET RUN NUMBER ASSIGNED BY PALM
2253          if [[ -f RUN_NUMBER ]]
2254          then
2255              read  run_number  <  RUN_NUMBER
2256              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2257              usecycle_option="-U $run_number"
2258          else
2259              run_number=0
2260              usecycle_option=""
2261          fi
2262          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2263          then
2264             printf "\n  *** in case of SCP transfers to local host"
2265             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
2266          fi
2267          printf "\n$dashes"
2268       fi
2269
2270       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2271       then
2272
2273          eval filename=${pathout[$i]}/${fname}${endout[$i]}
2274
2275             # DETERMINE THE CYCLE NUMBER
2276          ls -1 -d $filename    >   filelist  2>/dev/null
2277          ls -1 -d $filename.*  >>  filelist  2>/dev/null
2278          while  read line
2279          do
2280   
2281                # filename without path (i.e. after the last "/")
2282             basefilename=$(basename ${line})
2283   
2284                # check if there is an extension
2285             extension=${basefilename##*.}
2286             if [[ "$extension" = "${extout[$i]}" ]]
2287             then
2288                basefilename=${basefilename%.*}
2289             fi
2290   
2291                # check for an existing cycle number
2292             cycle=${basefilename##*.}
2293             if [[ $cycle =~ ^-?[0-9]+$ ]]
2294             then
2295                   # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2296                   # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2297                (( icycle = $((10#$cycle)) + 1 ))
2298             else
2299                (( icycle = 1 ))
2300             fi
2301   
2302             if (( icycle > maxcycle ))
2303             then
2304                (( maxcycle = icycle ))
2305             fi
2306   
2307          done <filelist
2308          rm filelist
2309
2310   
2311             # SET THE CYCLE NUMBER
2312             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2313          if [[ "${actionout[$i]}" = a ]]
2314          then
2315             (( maxcycle = maxcycle - 1 ))
2316          fi
2317         
2318          (( cycnum[$i] = maxcycle ))
2319          pathout[$i]=$filename
2320
2321
2322             # ADD CYCLE NUMBER TO FILENAME
2323             # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2324          if [[ "${actionout[$i]}" != "a" ]]
2325          then
2326                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2327                # WITH AN EXISTING CYCLE NUMBER
2328             if (( run_number >= cycnum[$i] ))
2329             then
2330                (( cycnum[$i] = run_number ))
2331             else
2332                if (( run_number > 0 ))
2333                then
2334                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2335                fi
2336             fi
2337          fi
2338          if (( cycnum[$i] > 0 ))
2339          then
2340             cyclestring=`printf "%03d" ${cycnum[$i]}`
2341             pathout[$i]=${pathout[$i]}.$cyclestring
2342          fi
2343       fi           
2344
2345          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2346       files_for_cores=false; filetype=file
2347       link_local_output=false
2348       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2349       then
2350          files_for_cores=true; filetype=directory
2351          actionout[$i]=""
2352       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2353       then
2354          actionout[$i]=""
2355       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2356       then
2357          files_for_cores=true; filetype=directory
2358          link_local_output=true
2359          actionout[$i]=""
2360       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2361       then
2362          link_local_output
2363          actionout[$i]=""
2364       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2365       then
2366          files_for_cores=true; filetype=directory
2367          actionout[$i]="tr"
2368       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2369       then
2370          actionout[$i]="tr"
2371       fi
2372
2373       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
2374       then
2375          if [[ ${warnout[$i]} = true ]]
2376          then
2377             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
2378          fi
2379       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2380       then
2381          if [[ ${warnout[$i]} = true ]]
2382          then
2383             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2384          fi
2385       else
2386
2387
2388             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2389             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2390          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2391          then
2392             if [[ $running_on_remote = true ]]
2393             then
2394
2395                   # SET OPTIONS FOR TRANSFER
2396                if [[ "${actionout[$i]}" = tr ]]
2397                then
2398                   if [[ $files_for_cores = false ]]
2399                   then
2400                      catalog_option=""
2401                      catalog_string=""
2402                   else
2403                      catalog_option="-c"
2404                      catalog_string="/"
2405                   fi
2406                   append_option=""
2407                   append_string=""
2408                else
2409                   append_option="-A"
2410                   append_string="append"
2411                fi
2412
2413                transfer_failed=false
2414                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
2415                printf "\n              ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2416
2417                   # TRANSFER VIA SCP
2418                if [[ "$remote_loginnode" != "" ]]
2419                then
2420                   echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]}  ${extout[$i]}"  |  ssh -q $remote_username@$remote_loginnode
2421                else
2422                   batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]}  ${extout[$i]}
2423                fi
2424                [[ $? != 0 ]]  &&  transfer_failed=true
2425
2426
2427                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2428                if [[ $transfer_failed = true ]]
2429                then
2430                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
2431                   printf "      ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2432
2433                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2434                   eval  local_catalog=${pathout[$i]}
2435                   if [[ ! -d $local_catalog ]]
2436                   then
2437                      printf "  *** local directory does not exist. Trying to create:\n"
2438                      printf "      $local_catalog \n"
2439                      mkdir -p  $local_catalog
2440                   fi
2441                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2442                   transfer_problems=true
2443                fi
2444
2445             else
2446
2447                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2448                   # BE COPIED OR APPENDED ON THIS MACHINE
2449                if [[ "${actionout[$i]}" = tr ]]
2450                then
2451                   actionout[$i]=""
2452                else
2453                   actionout[$i]="a"
2454                fi
2455             fi
2456          fi
2457
2458
2459             # APPEND ON THIS MACHINE
2460          if [[ "${actionout[$i]}" = "a" ]]
2461          then
2462             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2463             then
2464                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2465                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2466                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2467             else
2468                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2469                printf "\n              ${pathout[$i]}\n"
2470                cat  ${localout[$i]}  >>  ${pathout[$i]}
2471             fi
2472          fi
2473
2474             # COPY ON THIS MACHINE
2475             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2476             # ON DIFFERENT FILE-SYSTEMS
2477          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2478          then
2479
2480                # COPY IN CASE OF RUNS ON SINGLE CORES
2481             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2482             then
2483                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2484                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2485                              if [[ $link_local_output = true ]]
2486                              then
2487                                 printf "      file will be linked\n"
2488                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2489                              fi
2490                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2491                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2492                then
2493                                 if [[ $link_local_output = true ]]
2494                          then
2495                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2496                                 fi
2497                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2498                              else
2499                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2500                fi
2501             else
2502                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2503                printf "\n              ${pathout[$i]}\n"
2504                              if [[ $link_local_output = true ]]
2505                              then
2506                                 printf "      file will be linked\n"
2507                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2508                              fi
2509                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2510                        if [[ ! -f "${pathout[$i]}" ]]
2511                then
2512                                 if [[ $link_local_output = true ]]
2513                          then
2514                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2515                                 fi
2516                                 cp  ${localout[$i]}  ${pathout[$i]}
2517                              else
2518                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2519                fi
2520             fi
2521
2522          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2523          then
2524
2525                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2526                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2527             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2528             printf "\n              ${pathout[$i]}\n"
2529                    if [[ $link_local_output = true ]]
2530                    then
2531                              printf "      files will be linked\n"
2532                              mkdir -p ${pathout[$i]}
2533                              cd ${localout[$i]}
2534                              for file in $(ls *)
2535                              do
2536                                 ln -f $file  ${pathout[$i]}
2537                              done >|/dev/null 2>&1
2538                              cd $tempdir
2539                    fi
2540
2541                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2542                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2543             then
2544                              if [[ $link_local_output = true ]]
2545                              then
2546                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2547                              fi
2548                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2549             fi
2550
2551          fi
2552       fi
2553    done
2554
2555    if (( i != 0 ))
2556    then
2557       if [[ $transfer_problems = true ]]
2558       then
2559          printf "\n$dashes\n  *** OUTPUT-files saved"
2560          printf "\n  +++ WARNING: some data transfers failed! \n"
2561       else
2562          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2563       fi
2564    fi
2565
2566
2567       # IF REQUIRED, START A RESTART-JOB
2568       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2569    if [[ -f CONTINUE_RUN ]]
2570    then
2571
2572          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2573          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2574          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2575          # -b START A BATCH JOB
2576       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2577       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2578       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2579
2580
2581          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2582          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2583       if [[ $(echo $prc | grep -c "#") != 0 ]]
2584       then
2585          prc=`echo $prc | sed 's/#/r/g'`
2586       fi
2587
2588
2589          # START THE RESTART-JOB
2590       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2591       echo "      $prc"
2592       printf "\n$dashes\n"
2593       if [[ $running_on_remote = true ]]
2594       then
2595
2596          echo "*** ssh will be used to initiate restart-runs!"
2597          echo "    return_address=\"$return_address\" "
2598          echo "    return_username=\"$local_username\" "
2599
2600          if [[ "$remote_loginnode" != "" ]]
2601          then
2602             echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  " |  ssh -q $remote_username@$remote_loginnode
2603          else
2604             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address
2605          fi
2606
2607             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2608          sleep 30
2609
2610       else
2611
2612             # START THE RESTART JOB ON THE LOCAL HOST
2613          eval  $prc                # THE ' MUST BE EVALUATED
2614          cd -  > /dev/null
2615
2616       fi
2617       printf "\n$dashes\n  *** restart-run initiated \n"
2618
2619
2620          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2621          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2622          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2623          # MAY BE VERY HUGE)
2624       (( i = 0 ))
2625       while (( i < nr_of_input_files ))
2626       do
2627          (( i = i + 1 ))
2628          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2629          then
2630             rm -r  ${absnamein[$i]}
2631          fi
2632       done
2633
2634    fi
2635
2636
2637       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2638    cd  $HOME
2639    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $tempdir
2640
2641
2642 else
2643
2644
2645       # PREPARING ACTIONS,
2646       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2647
2648       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2649    palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2650    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2651    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2652    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2653    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2654    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2655    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
2656    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
2657    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2658    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2659    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2660    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2661    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
2662    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
2663    if [[ $create_remote_batch_job = true ]]
2664    then
2665       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2666       if [[ $do_trace = true ]]
2667       then
2668          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2669       fi
2670    elif [[ $create_batch_job = true ]]
2671    then
2672       palmrun_com=${palmrun_com}" -j"
2673       if [[ $do_trace = true ]]
2674       then
2675          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2676       fi
2677    fi
2678
2679
2680       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2681       # REMOTE HOST
2682    job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2683    job_protocol_file=$job_protocol_file_local
2684    if [[ $create_remote_batch_job = true ]]
2685    then
2686       job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2687       job_protocol_file=$job_protocol_file_remote
2688       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2689       scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2690    fi
2691
2692
2693       # BUILD THE JOB-SCRIPTS ON FILE jobfile
2694    jobfile=jobfile.$run_id
2695
2696
2697       # FIRST CREATE THE BATCH DIRECTIVES
2698    (( i = 0 ))
2699    while (( i < ibd ))
2700    do
2701       (( i = i + 1 ))
2702       line=`echo  "${batch_directive[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{CORES}}/$cores/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{QUEUE}}/$queue/g' | sed 's/{{MEMORY}}/$memory/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g' | sed 's/{{PREVIOUS_JOB}}/$previous_job/g' | sed 's/{{TEMPDIR}}/$tempdir/g'`
2703       eval line=\"$line\"
2704       echo  "$line"                               >>  $jobfile
2705    done
2706    echo " "                                       >>  $jobfile
2707
2708
2709       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2710       # PROTOCOL
2711    if [[ $create_remote_batch_job = true ]]
2712    then
2713       echo "set +vx"                              >>  $jobfile
2714       echo "trap '"                               >>  $jobfile
2715       echo "set +vx"                              >>  $jobfile
2716       echo "cd ${remote_jobcatalog}"              >>  $jobfile
2717       echo "cat >  scpjob.$run_id << %%END%%"     >>  $jobfile
2718
2719          # ADD THE BATCH DIRECTIVES
2720       (( i = 0 ))
2721       while (( i < ibdt ))
2722       do
2723          (( i = i + 1 ))
2724          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/{{JOB_ID}}/$job_id/g' | sed 's/{{JOBFILE}}/$job_protocol_file/g' | sed 's/{{JOB_TRANSFER_PROTOCOL_FILE}}/$job_transfer_protocol_file/g' | sed 's/{{CPU_HOURS}}/$cpu_hours/g' | sed 's/{{CPU_MINUTES}}/$cpu_minutes/g' | sed 's/{{CPU_SECONDS}}/$cpu_seconds/g' | sed 's/{{NODES}}/$nodes/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g' | sed 's/{{HOST_CONFIGURATION}}/${host_configuration}/g' | sed 's/{{FNAME}}/$fname/g' | sed 's/{{PROJECT_ACCOUNT}}/$project_account/g'`
2725          eval line=\"$line\"
2726          echo  "$line"                            >>  $jobfile
2727       done
2728       echo " "                                    >>  $jobfile
2729
2730       echo "set -x"                               >>  $jobfile
2731       echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${host_configuration}_${fname}"  >>  $jobfile
2732       echo "%%END%%"                              >>  $jobfile
2733       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2734       echo "$submit_command  $scpjob_file"        >>  $jobfile
2735       echo "rm $scpjob_file"                      >>  $jobfile
2736       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
2737       echo "set -x"                               >>  $jobfile
2738       echo "     ' exit"                          >>  $jobfile
2739    fi
2740
2741
2742       # ACTIVATE ERROR-TRACEBACK
2743    if [[ $do_trace = true ]]
2744    then
2745       echo  "set -x"                                    >>  $jobfile
2746    else
2747       echo  "set +vx"                                   >>  $jobfile
2748    fi
2749
2750
2751       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2752    if [[ "$login_init_cmd" != "" ]]
2753    then
2754       echo  "$login_init_cmd"        >>  $jobfile
2755    fi
2756    if [[ "$module_commands" != "" ]]
2757    then
2758       echo  "$module_commands"     >>  $jobfile
2759    fi
2760
2761
2762       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2763    if [[ $create_remote_batch_job = true ]]
2764    then
2765       echo  "mkdir  $tempdir"           >>  $jobfile
2766       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
2767    else
2768          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2769          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2770          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2771       mkdir  $tempdir
2772       chmod  go+rx  $tempdir
2773    fi
2774    echo  "cd  $tempdir"                 >>  $jobfile
2775    echo  "export tempdir=$tempdir"      >>  $jobfile
2776    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
2777    echo  "export PATH=.:\$PATH"         >>  $jobfile
2778    echo  "export execute_palmrun=true"  >>  $jobfile
2779
2780
2781       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2782       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2783       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2784    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2785    echo  "export LOCAL_PWD"                            >>  $jobfile
2786
2787
2788       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2789    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
2790    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2791
2792
2793       # CALL PALMRUN WITHIN THE JOB
2794       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2795    echo  "set -x"                                              >>  $jobfile
2796    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2797
2798
2799       # TRANSFER JOBFILE TO THE TARGET HOST
2800    if [[ $create_jobfile_only = false ]]
2801    then
2802
2803       if [[ $create_remote_batch_job = true ]]
2804       then
2805
2806          echo " "
2807          echo " *** transfer of job to remote host via scp"
2808          if [[ $do_trace = true ]]
2809          then
2810             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2811          fi
2812          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}  >  /dev/null
2813
2814          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2815          if [[ $do_trace = true ]]
2816          then
2817             echo "     cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1"
2818          fi
2819          echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}"  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1
2820
2821       elif [[ $create_batch_job = true ]]
2822       then
2823
2824          eval  local_jobcatalog=$local_jobcatalog
2825          cp  $jobfile  ${local_jobcatalog}/${host_configuration}_${job_id}
2826          cd $local_jobcatalog
2827          echo " "
2828          echo " *** submit the job"
2829          if [[ $do_trace = true ]]
2830          then
2831             echo "$submit_command ${host_configuration}_${job_id}"
2832          fi
2833          $submit_command ${host_configuration}_${job_id}
2834          rm ${host_configuration}_${job_id}
2835          cd -  > /dev/null
2836
2837       fi
2838
2839       rm -rf  $jobfile
2840
2841    else
2842
2843       printf "\n *** jobfile created under name \"$jobfile\" "
2844       printf "\n     no batch-job has been sent!"
2845
2846    fi
2847
2848 fi  # END OF REMOTE-PART
Note: See TracBrowser for help on using the repository browser.