source: palm/trunk/SCRIPTS/palmrun @ 2638

Last change on this file since 2638 was 2638, checked in by raasch, 6 years ago

bugfix for cases with constant top momentumflux

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File size: 94.6 KB
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1#!/bin/bash
2
3# palmrun - script for running PALM jobs
4
5#--------------------------------------------------------------------------------#
6# This file is part of PALM.
7#
8# PALM is free software: you can redistribute it and/or modify it under the terms
9# of the GNU General Public License as published by the Free Software Foundation,
10# either version 3 of the License, or (at your option) any later version.
11#
12# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
13# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
14# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
15#
16# You should have received a copy of the GNU General Public License along with
17# PALM. If not, see <http://www.gnu.org/licenses/>.
18#
19# Copyright 2017  Leibniz Universitaet Hannover
20#--------------------------------------------------------------------------------#
21#
22# Current revisions:
23# ------------------
24#
25#
26# Former revisions:
27# -----------------
28# $Id: palmrun 2638 2017-11-23 12:44:23Z raasch $
29# use of wildcards in file connection statements enabled
30#
31# 2605 2017-11-09 15:31:46Z raasch
32# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
33# will not be sent with the job file any more, but copied into the
34# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
35#
36# 2600 2017-11-01 14:11:20Z raasch
37# cycle numbers are made three digits wide
38#
39# 2566 2017-10-20 08:50:47Z raasch
40# execute command for combine_plot_fields added
41# "TEMPDIR" renamed "tempdir"
42# temporary working directory for local batch jobs is created immediately within
43# the user's palmrun call, due to a requirement of the "grid engine" batch
44# system, where the working directory is given with batch directive -wd and must
45# already exist when the job is submitted,
46# informative messages in non-trace mode reduced and partly reformatted
47#
48# 2551 2017-10-18 07:25:11Z raasch
49# TEMPDIR added as replacement string to be used in batch directives
50#
51# 2512 2017-10-04 08:26:59Z raasch
52# bugfix for determining cycle numbers of NetCDF input files
53#
54# 2506 2017-09-29 08:30:37Z raasch
55# option -V added to check for an existing SOURCES_FOR_RUN_... folder
56# host configuration added to SOURCES_FOR_RUN_... folder name
57# host_identifier renamed host_configuration
58# option -W added to allow for job dependencies
59#
60# 2501 2017-09-26 11:41:55Z raasch
61# default value for number of cores (option -X) set to 1
62# bugfix for mechanism which overwrites configuration file settings with values
63# provided by palmrun options
64#
65# 2499 2017-09-22 16:47:58Z kanani
66# option -h named configuration identifier
67#
68# 2480 2017-09-19 06:24:14Z maronga
69# bugfix for last revision
70#
71# 2479 2017-09-19 06:12:16Z raasch
72# option -A (project account number) added
73#
74# 2422 2017-09-08 08:25:41Z raasch
75# initial revision
76#
77#--------------------------------------------------------------------------------#
78# palmrun - script for running PALM jobs on local and remote hosts
79#--------------------------------------------------------------------------------#
80
81
82 
83    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
84
85 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
86                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
87                     # (TOO MANY ARGUMENTS - PROBLEM)
88 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
89
90 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
91 typeset -i  nr_of_output_files=0
92 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
93                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
94                           # SCRIPT-OPTION ARGUMENTS
95 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
96 typeset -i  icycle inode ival maxcycle mpi_tasks
97 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
98
99 activation_string_list=""
100 AddFilenames=""
101 combine_plot_fields=true
102 compiler_name=""
103 compiler_name_ser=""
104 compiler_options=""
105 cores=1
106 cores_atmos=0
107 cores_ocean=0
108 coupled_dist=""
109 cpp_options=""
110 cpumax=0
111 create_batch_job=false
112 create_jobfile_only=false
113 create_remote_batch_job=false
114 dashes="  ----------------------------------------------------------------------------"
115 defaultqueue=""
116 delete_temporary_catalog=true
117 do_compile=true
118 do_trace=false
119 executable=""
120 execute_command=""
121 execution_error=false
122 fileconnection_file=.palm.iofiles
123 fname=test
124 global_revision=""
125 host_configuration="default"
126 hostfile=""
127 hp=""
128 keep_data_from_previous_run=false
129 link_local_input=false
130 link_local_output=false
131 linker_options=""
132 local_jobcatalog=""
133 locat=normal
134 makefile=""
135 max_par_io_str=""
136 prc=$0
137 while [[ $(echo $prc | grep -c "/") != 0 ]]
138 do
139    prc=`echo $prc | cut -f2- -d"/"`
140 done
141 module_calls=""
142 palmrun_memory=""
143 palmrun_script_name=$prc
144 openmp=false
145 previous_job=""
146 project_account=""
147 queue=none
148 restart_run=false
149 return_address=""
150 remote_jobcatalog=""
151 remote_username=""
152 running_in_batch_mode=false
153 run_coupled_model=false
154 run_id=""
155 silent=false
156 source_list=""
157 source_path=""
158 tasks_per_node=0
159 threads_per_task=1
160 transfer_problems=false
161 user_source_path=""
162 use_existing_sources_folder=""
163 use_openmp=false
164 version="palmrun  1.0 Rev$Rev: 2303 $"
165 working_directory=`pwd`
166 write_binary=""
167 TOPT=""
168
169
170    # ERROR HANDLING IN CASE OF EXIT
171 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
172       then
173
174              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
175          (( i = 0 ))
176          while (( i < iec ))
177          do
178             (( i = i + 1 ))
179             printf "\n  *** Execution of ERROR-command:\n"
180             printf "  >>> ${err_command[$i]}\n"
181             eval  ${err_command[$i]}
182          done
183          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
184          printf "\n\n+++ palmrun killed \n\n"
185       elif [[ $locat != control_c ]]
186       then
187          printf "\n --> palmrun finished\n\n"
188       fi' exit
189
190
191    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
192 trap 'cd; rm -rf $tempdir
193       printf "\n+++ palmrun killed by \"^C\" \n\n"
194       locat=control_c
195       exit
196      ' 2
197
198
199    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
200    # WHICH WILL BE USED TO START RESTART-JOBS
201 while  getopts  :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
202 do
203   case  $option  in
204       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
205       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
206       (b)   create_batch_job=true; prc="$prc -b";;
207       (B)   delete_temporary_catalog=false; prc="$prc -B";;
208       (C)   restart_run=true; prc="$prc -C";;
209       (d)   fname=$OPTARG; prc="$prc -d$OPTARG";;
210       (F)   create_jobfile_only=true;;
211       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
212       (h)   host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
213       (j)   running_in_batch_mode=true;;
214       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
215       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
216       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
217       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
218       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
219       (r)   run_id=$OPTARG;;
220       (R)   return_address=$OPTARG;;
221       (s)   source_list=$OPTARG;;
222       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
223       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
224       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
225       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
226       (v)   silent=true; prc="$prc -v";;
227       (V)   use_existing_sources_folder="-V";;
228       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
229       (W)   previous_job=$OPTARG;;
230       (x)   do_trace=true;set -x; prc="$prc -x";;
231       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
232       (y)   ocean_file_appendix=true; prc="$prc -y";;
233       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
234       (Z)   combine_plot_fields=false; prc="$prc -Z";;
235       (\?)  printf "\n  +++ unknown option $OPTARG \n"
236             printf "\n  --> type \"$0 ?\" for available options \n"
237             locat=parameter;exit;;
238   esac
239 done
240
241
242    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
243    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
244 (( to_shift = $OPTIND - 1 ))
245 shift $to_shift
246
247    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
248 if [[ "$1" = "?" ]]
249 then
250   (printf "\n  *** Description of available palmrun options:\n"
251    printf "\n      Option  Description                              Default-Value"
252    printf "\n        -a    activation string list                   \"\" "
253    printf "\n        -A    project account number                   ---"
254    printf "\n        -b    batch-job on local machine               ---"
255    printf "\n        -B    do not delete temporary directory at end ---"
256    printf "\n        -d    base name of files attached to program   test"
257    printf "\n        -F    create batch job file only               ---"
258    printf "\n        -h    host configuration                       \"default\" "
259    printf "\n        -k    keep data from previous run"
260    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
261    printf "\n        -M    Makefile name                            Makefile"
262    printf "\n        -O    threads per openMP task                  ---"
263    printf "\n        -q    queue                                    \"$queue\" "
264    printf "\n        -s    filenames of routines to be compiled     \"\" "
265    printf "\n              must end with .f, .f90, .F, or .c !"
266    printf "\n              use \"..\" for more than one file and wildcards"
267    printf "\n              -s LM compiles all locally modified files"
268    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
269    printf "\n        -T    tasks per node                           ---"
270    printf "\n        -u    username on remote machine               \"\" "
271    printf "\n        -v    no prompt for confirmation               ---"
272    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
273    printf "\n        -w    maximum parallel io streams              as given by -X"
274    printf "\n        -W    name of job to wait for                  ---"
275    printf "\n        -x    tracing of palmrun for debug purposes    ---"
276    printf "\n        -X    # of processors (on parallel machines)   1"
277    printf "\n        -y    add appendix \"_O\" to all local output"
278    printf "\n              files (ocean precursor runs followed by"
279    printf "\n              coupled atmosphere-ocean runs)           ---"
280    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
281    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
282    printf "\n        -Z    skip combine_plot_fields at the end of      "
283    printf "\n              the simulation                           ---"
284    printf "\n "
285    printf "\n      Possible values of positional parameter <modus>:"
286    printf "\n        \"?\"       -  this outline \n\n") | more
287    exit
288 elif [[ "$1" != "" ]]
289 then
290    printf "\n  +++ positional parameter $1 unknown \n"
291    locat=parameter; exit
292 fi
293
294
295
296    # SHORT STARTING MESSAGE
297 printf "\n*** $version "
298 printf "\n    will be executed.     Please wait ..."
299
300
301    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
302 config_file=.palm.config.$host_configuration
303 sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
304
305
306    # CHECK, IF CONFIGURATION FILE EXISTS
307 if [[ ! -f $config_file ]]
308 then
309    printf "\n\n  +++ configuration file: "
310    printf "\n           $config_file"
311    printf "\n      does not exist"
312    locat=connect; exit 
313 fi
314
315
316    # CHECK, IF FILE CONNECTION FILE EXISTS
317 if [[ ! -f $fileconnection_file ]]
318 then
319    printf "\n\n  +++ file connection file: "
320    printf "\n           $fileconnection_file"
321    printf "\n      does not exist"
322    locat=connect; exit 
323 fi
324
325
326    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
327 if [[ "$activation_string_list" = "" ]]
328 then
329    printf "\n\n  +++ no activation string list given: "
330    printf "\n        please set palmrun option \"-a\" "
331    locat=palmrun_option; exit 
332 fi
333
334
335    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
336 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
337 then
338    write_binary=true
339 else
340    write_binary=false
341 fi
342
343
344    # READ AND EVALUATE THE CONFIGURATION-FILE
345 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
346
347    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
348 while  read line
349 do
350
351       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
352    eval  line=\"$line\"
353
354
355       # INTERPRET THE LINE
356    if [[ "$(echo $line)" = "" ]]
357    then
358
359          # EMPTY LINE, NO ACTION
360       continue
361
362    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
363    then
364
365          # LINE IS A COMMENT LINE
366       continue
367
368    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
369    then
370
371          # LINE DEFINES AN ENVIRONMENT-VARIABLE
372       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
373       value=`echo $line | cut -d" " -s -f2-`
374
375
376          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
377          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
378          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
379          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
380          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
381          # CONFIGURATION-FILE.
382       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
383       then
384          eval  export  $var="\$value"
385
386             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
387          if [[ $do_trace = true ]]
388          then
389             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
390          fi
391       fi
392
393    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
394    then
395
396          # LINE DEFINES BATCH-DIRECTIVE
397       (( ibd = ibd + 1 ))
398       line=$(echo $line | cut -c4-)
399       batch_directive[$ibd]="$line"
400
401    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
402    then
403
404          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
405          # REMOTE TO A LOCAL HOST
406       (( ibdt = ibdt + 1 ))
407       line=$(echo $line | cut -c5-)
408       batch_directive_transfer[$ibdt]="$line"
409
410    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
411    then
412
413          # LINE DEFINES ERROR-COMMAND
414       (( iec = iec + 1 ))
415       line=$(echo $line | cut -c4-)
416       err_command[$iec]="$line"
417
418    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
419    then
420
421          # LINE DEFINES INPUT-COMMAND
422       (( iic = iic + 1 ))
423       line=$(echo $line | cut -c4-)
424       in_command[$iic]="$line"
425
426    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
427    then
428
429          # LINE DEFINES OUTPUT-COMMAND
430       (( ioc = ioc + 1 ))
431       line=$(echo $line | cut -c4-)
432       out_command[$ioc]="$line"
433
434    else
435
436          # SKIP ALL OTHER LINES
437       continue
438
439    fi
440
441 done < $config_file
442
443
444    # CHECK SETTING OF REQUIRED PARAMETERS
445 if [[ "$compiler_name" = "" ]]
446 then
447    printf "\n  +++ no compiler name found in $config_file"
448    printf "\n      Please add line \"compiler_name ...\" to that file."
449    locat=config_file; exit
450 fi
451 if [[ "$compiler_name_ser" = "" ]]
452 then
453    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
454    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
455    locat=config_file; exit
456 fi
457 if [[ "$compiler_options" = "" ]]
458 then
459    printf "\n  +++ no compiler options found in $config_file"
460    printf "\n      Please add line \"compiler_options ...\" to that file."
461    locat=config_file; exit
462 fi
463 if [[ "$linker_options" = "" ]]
464 then
465    printf "\n  +++ no linker options found in $config_file"
466    printf "\n      Please add line \"linker_options ...\" to that file."
467    locat=config_file; exit
468 fi
469 if [[ "$execute_command" = "" ]]
470 then
471    printf "\n  +++ no execute command found in $config_file"
472    printf "\n      Please add line \"execute_command ...\" to that file."
473    locat=config_file; exit
474 fi
475
476 if [[ "$hostfile" != "" ]]
477 then
478    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
479    then
480       printf "\n  +++ no hostfile \"$hostfile\" found"
481       printf "\n      Please check line \"hostfile ...\" in $config_file"
482       locat=config_file; exit   
483    fi
484 fi
485
486
487    # DETERMINE THE CALL STATUS
488 if [[ "$return_address" != "" ]]
489 then
490 
491       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
492       # BATCH MODE AND ...
493    running_on_remote=true
494 
495 else
496
497       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
498     if [[ "$remote_ip" != "" ]]
499     then
500
501           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
502        create_remote_batch_job=true
503
504     fi
505     running_on_remote=false
506 fi
507
508
509
510    # READ AND EVALUATE THE I/O-FILE LIST
511 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
512
513    # READ THE FILE CONNECTION FILE LINE BY LINE
514 while  read line
515 do
516
517       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
518    eval  line=\"$line\"
519
520
521       # INTERPRET THE LINE
522    if [[ "$(echo $line)" = "" ]]
523    then
524          # EMPTY LINE, NO ACTION
525       continue
526
527    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
528    then
529
530          # LINE IS A COMMENT LINE
531       true
532
533    else
534
535          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
536          # s2a: in/out - field
537          # s2b: action - field (optional)
538       s1=`echo $line | cut -d" " -f1`
539       s2=`echo $line | cut -d" " -s -f2`
540#       s2a=$(echo $s2 | cut -d":" -f1)
541       if [[ $(echo $s2 | grep -c ":") = 0 ]]
542       then
543          s2a=$s2
544          s2b=""
545       else
546          s2a=`echo $s2 | cut -d":" -f1`
547          s2b=`echo $s2 | cut -d":" -f2`
548       fi
549       s3=`echo $line | cut -d" " -f3`
550       s4=`echo $line | cut -d" " -s -f4`
551       s5=`echo $line | cut -d" " -s -f5`
552       s6=`echo $line | cut -d" " -s -f6`
553
554       
555          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
556          # INPUT- OR OUTPUT-LIST.
557          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
558          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
559          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
560          # IS NOT CHECKED AND STORED.
561       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
562       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
563       then
564          found=false
565          for  actual  in  $activation_string_list
566          do
567             for  formal  in  $s3
568             do
569                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
570             done
571          done
572          if [[ $found = true ]]
573          then
574             (( iin = iin + 1 ))
575             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
576             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
577             if [[ "$s2a" = inopt ]]
578             then
579                optin_pre[$iin]=yes
580             else
581                optin_pre[$iin]=no
582             fi 
583
584                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
585                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
586             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
587             then
588                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
589             fi
590
591                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
592                # THE WILDCARD FROM THE ENDING
593             if [[ "${s5: -1}" = "*" ]]
594             then
595                if [[ "$s2b" = "di" ]]
596                then
597                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
598                   printf "\n        see file \"$fileconnection_file\", line"
599                   printf "\n$line"
600                   locat=iofiles_file; exit
601                fi
602                multin[$iin]=true
603                string=${endin_pre[$iin]}
604                endin_pre[$iin]="${string%?}"
605             else
606                multin[$iin]=false
607             fi
608          fi
609       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
610       then
611          found=false
612          for  actual  in  $activation_string_list
613          do
614             for  formal  in  $s3 
615             do
616                [[ $actual = $formal  ||  "$formal" = "-"  ]]  &&  found=true
617             done
618          done
619          if [[ $found = true ]]
620          then
621             (( iout = iout + 1 ))
622             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b; typeout_pre[$iout]=$s3;
623             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
624
625                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
626                # THE WILDCARD FROM THE LOCAL FILENAME
627             if [[ "${s1: -1}" = "*" ]]
628             then
629                if [[ "$s2b" = "di" ]]
630                then
631                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
632                   printf "\n        see file \"$fileconnection_file\", line"
633                   printf "\n$line"
634                   locat=iofiles_file; exit
635                fi
636                multout[$iout]=true
637                string=${localout_pre[$iout]}
638                localout_pre[$iout]="${string%?}"
639             else
640                multout[$iout]=false
641             fi
642          fi
643       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
644       then
645          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
646          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
647          locat=connect; exit
648       fi
649       IFS="$IFSALT"
650    fi
651
652 done < $fileconnection_file
653
654
655
656    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
657 [[ $palmrun_memory     != ""   ]]  &&  memory=$palmrun_memory
658 [[ $palmrun_cpumax     != ""   ]]  &&  cpumax=$palmrun_cpumax
659 [[ "$palmrun_cores" != ""  ]]  &&  cores=$palmrun_cores
660 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
661 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
662
663
664
665      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
666 if [[ $run_coupled_model = true ]] 
667 then
668
669    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
670    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
671
672    if (( $cores_ocean + $cores_atmos != $cores ))
673    then
674
675       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
676       printf "\n      PEs (total)     : $cores"
677       printf "\n      PEs (atmosphere): $cores_atmos"
678       printf "\n      PEs (ocean)     : $cores_ocean"
679       locat=coupling; exit
680
681    fi
682
683 fi
684
685
686    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
687    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
688    # FOLDER
689 if [[ $running_in_batch_mode = true ]]
690 then
691 
692    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
693    then
694       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
695       printf "\n      Please check the output of the palmrun-call"
696       printf "\n      that you did on your local host."
697       locat=SOURCES_FOR_RUN; exit
698    fi
699
700 else
701
702       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
703       # AUTOMATIC RESTART RUN
704       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
705    if [[ $restart_run = false ]]
706    then
707
708          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
709          # THE LOCAL HOST
710       if [[ ! -d $source_path ]]
711       then
712          printf "\n\n  +++ source path \"$source_path\" on local host"
713          printf "\n      \"$(hostname)\" does not exist"
714          locat=source_path; exit
715       fi
716
717       rm -rf   $sources_for_run_catalog
718       mkdir -p $sources_for_run_catalog
719
720       if [[ "$source_list" = LM ]]
721       then
722
723             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
724          source_list=""
725          cd  $source_path
726
727
728             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
729          if [[ ! -d ../.svn ]]
730          then
731             printf "\n\n  +++ source directory"
732             printf "\n         \"$source_path\" "
733             printf "\n         is not under control of \"subversion\"."
734             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
735          fi
736
737
738             # LIST ALL MODIFIED SOURCE CODE FILES
739          Filenames=""
740          svn status  >  tmp_svnstatus
741          while  read line
742          do
743             firstc=`echo $line | cut -c1`
744             if [[ $firstc = M  ||  $firstc = "?" ]]
745             then
746                Name=`echo "$line" | cut -c8-`
747                extension=`echo $Name | cut -d. -f2`
748                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
749                then
750                   Filenames="$Filenames "$Name
751                fi
752             fi
753          done < tmp_svnstatus
754          rm -rf  tmp_svnstatus
755
756
757             # COPY FILES TO SOURCES_FOR_RUN_...
758          for  filename  in  $Filenames
759          do
760             cp  $filename  ${working_directory}/${sources_for_run_catalog}
761             source_list=$source_list"$filename "
762          done
763
764          cd -  > /dev/null
765
766
767          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
768       elif [[ "$source_list" != "" ]]
769       then
770
771          cd  $source_path
772
773          for  filename  in  $source_list
774          do
775
776                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
777             if [[ $(echo $filename | grep -c "/") != 0 ]]
778             then
779                printf "\n  +++ source code file:  $filename"
780                printf "\n      must not contain (\"/\") "
781                locat=source; exit
782             fi
783
784             if [[ ! -f $filename ]]
785             then
786                printf "\n  +++ source code file:  $filename"
787                printf "\n      does not exist"
788                locat=source; exit
789             else
790                cp  $filename  ${working_directory}/${sources_for_run_catalog}
791             fi
792
793          done
794
795          cd -  > /dev/null
796
797       fi
798
799          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
800       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
801       if [[ ! -f $makefile ]]
802       then
803          printf "\n  +++ file \"$makefile\" does not exist"
804          locat=make; exit
805       else
806          cp  $makefile  ${sources_for_run_catalog}/Makefile
807       fi
808
809
810          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
811       if [[ "$user_source_path" != "" ]]
812       then
813
814             # DOES THE DIRECTORY EXIST?
815          if [[ ! -d $user_source_path ]]
816          then
817
818             printf "\n\n  *** INFORMATIVE: additional source code directory"
819             printf "\n      \"$user_source_path\" "
820             printf "\n      does not exist or is not a directory."
821             printf "\n      No source code will be used from this directory!\n"
822             user_source_path=""
823             if [[ $silent == false ]]
824             then
825                sleep 2
826             fi
827
828          else
829
830             cd $user_source_path
831             found=false
832
833             Names=$(ls -1 *.f90 2>&1)
834             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
835             Names=$(ls -1 *.F90 2>&1)
836             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
837             Names=$(ls -1 *.F 2>&1)
838             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
839             Names=$(ls -1 *.f 2>&1)
840             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
841             Names=$(ls -1 *.c 2>&1)
842             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
843
844             cd -  > /dev/null
845             cd  $sources_for_run_catalog
846
847                # COPY MAKEFILE IF EXISTING
848             if [[ -f $user_source_path/Makefile ]]
849             then
850                printf "\n\n  *** user Makefile from directory"
851                printf "\n      \"$user_source_path\" is used \n"
852                if [[ $silent == false ]]
853                then
854                   sleep 1
855                fi
856                cp  $user_source_path/Makefile  .
857             fi
858
859             for  filename  in  $AddFilenames
860             do
861                if [[ -f $filename ]]
862                then
863                   printf "\n  +++ source code file \"$filename\" found in additional"
864                   printf "\n      source code directory \"$user_source_path\" "
865                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
866                   printf "\n      from directory \"$source_path\"."
867                   locat=source; exit
868                fi
869
870                cp  $user_source_path/$filename  .
871                source_list="$source_list $filename"
872
873                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
874                if [[ $(grep -c $filename Makefile) = 0 ]]
875                then
876                   printf "\n\n  +++ user file \"$filename\" "
877                   printf "\n      is not listed in Makefile \n"
878                   locat=source; exit
879                else
880
881                   if [[ $found = false ]]
882                   then
883                      found=true
884                      printf "\n\n  *** following user file(s) added to the"
885                      printf " files to be translated:\n      "
886                   fi
887                   printf "$filename  "
888                   if [[ $silent == false ]]
889                   then
890                      sleep 0.5
891                   fi
892
893                fi
894             done
895             [[ $found = true ]]  &&  printf "\n"
896             cd -  > /dev/null
897          fi
898       fi
899
900          # COPY CONFIGURATION FILES
901       cp  $config_file  $sources_for_run_catalog
902       cp  $fileconnection_file  $sources_for_run_catalog
903
904          # COPY SHELLSCRIPTS
905       cp  ${source_path}/../SCRIPTS/palmrun    $sources_for_run_catalog
906       cp  ${source_path}/../SCRIPTS/batch_scp  $sources_for_run_catalog
907
908    fi
909
910 fi
911
912
913    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
914    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
915 if [[ "$global_revision" = "" ]]
916 then
917    global_revision=`svnversion $source_path  2>/dev/null`
918    global_revision="Rev: $global_revision"
919 fi
920
921
922    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
923 if [[ -n $cores ]]
924 then
925
926       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
927       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
928    if [[ $tasks_per_node = 0 ]]
929    then
930       printf "\n"
931       printf "\n  +++ option \"-T\" (tasks per node) is missing"
932       printf "\n      set -T option or define tasks_per_node in the config file"
933       locat=tasks_per_node; (( iec = 0 )); exit
934    fi
935
936    if (( cores < tasks_per_node ))
937    then
938       printf "\n"
939       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
940       printf "\n      given values: -T $tasks_per_node  -X $cores"
941       locat=tasks_per_node; (( iec = 0 )); exit
942    fi
943
944    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
945    (( mpi_tasks = cores / threads_per_task ))
946    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
947    (( ii = cores / tasks_per_node ))
948    (( remaining_cores =  cores - ii * tasks_per_node ))
949    if (( remaining_cores > 0 ))
950    then
951       printf "\n"
952       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
953       printf "\n      divisor of the total number of cores (option \"-X\")"
954       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
955       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
956       (( nodes = nodes + 1 ))
957    fi
958
959       # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
960    if [[ "$tasks_per_node" != "" ]]
961    then
962       TOPT="-T $tasks_per_node"
963    fi
964
965 fi
966
967
968    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
969 if [[ "$maximum_parallel_io_streams" = "" ]]
970 then
971    maximum_parallel_io_streams=$cores
972 fi
973
974
975    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
976 if [[ "$scp_port" != "" ]]
977 then
978    PORTOPT="-P $scp_port"
979    SSH_PORTOPT="-p $scp_port"
980 fi
981
982
983    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
984    # CONFIG-FILE
985 if [[ "$ssh_key" != "" ]]
986 then
987    ssh_key="-i $HOME/.ssh/$ssh_key"
988 fi
989
990
991    # SET QUEUE, IF NOT GIVEN
992 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
993 then
994
995    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
996    then
997       printf "\n"
998       printf "\n  +++ no default queue given in configuration file and no queue"
999       printf "\n      given with option -q"
1000    fi
1001    if [[ $queue = none ]]
1002    then
1003       queue=$defaultqueue
1004    fi
1005
1006 fi
1007
1008
1009    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1010    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1011 (( i = 0 ))
1012 (( nr_of_input_files = 0 ))
1013 while (( i < iin ))
1014 do
1015    (( i = i + 1 ))
1016
1017       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1018       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1019    if [[ "${actionin_pre[$i]}" = di ]]
1020    then
1021       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
1022    else
1023       eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
1024    fi
1025
1026
1027       # CHECK IF FILE EXISTS
1028    if ! ls $filename* 1>/dev/null 2>&1
1029    then
1030
1031          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1032       if [[ "${optin_pre[$i]}" != "yes" ]]
1033       then
1034          printf "\n\n  +++ INPUT-file: "
1035          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
1036          then
1037             printf "\n           $filename"
1038          else
1039             printf "\n           $filename.${extin_pre[$i]}"
1040          fi
1041          printf "\n      does not exist\n"
1042          locat=input; exit
1043       else
1044          (( nr_of_input_files = nr_of_input_files + 1 ))
1045          localin[$nr_of_input_files]="${localin_pre[$i]}"
1046          optin[$nr_of_input_files]="${optin_pre[$i]}"
1047#          transin[$nr_of_input_files]="unavailable"
1048#          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1049          actionin[$nr_of_input_files]="unavailable"
1050          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1051          endin[$nr_of_input_files]="${endin_pre[$i]}"
1052          extin[$nr_of_input_files]="${extin_pre[$i]}"
1053       fi
1054
1055    else
1056
1057          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
1058          # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
1059       if [[ "${multin[$i]}" = true ]]
1060       then
1061             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1062          ls -1 -d ${filename}    >   filelist  2>/dev/null
1063          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
1064          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null
1065
1066          endings=""
1067          while  read line
1068          do
1069                 # filename without path (i.e. after the last "/")
1070              basefilename=$(basename ${line})
1071
1072                 # check if there is an extension and remove it
1073              ext=${basefilename##*.}
1074              if [[ "$ext" = "${extin_pre[$i]}" ]]
1075              then
1076                 basefilename=${basefilename%.*}
1077              fi
1078
1079                 # check for an existing cycle number and remove it
1080              cycle=${basefilename##*.}
1081              if [[ $cycle =~ ^-?[0-9]+$ ]]
1082              then
1083                 basefilename=${basefilename%.*}
1084              fi
1085
1086                 # remove the fname from the beginning
1087              length_fname=${#fname}
1088              ending=${basefilename:${length_fname}}
1089
1090                 # remove the ending given in the .iofiles from the beginning
1091              endingstring="${endin_pre[$i]}"
1092              length_ending=${#endingstring}
1093              ending=${ending:${length_ending}}
1094
1095              if [[ "$ending" = "" ]]
1096              then
1097                    # standard ending as given in the .iofiles
1098                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
1099                 then
1100                    endings="$endings DEFAULT"
1101                 fi
1102              else
1103                    # ending must start with "_", otherwise its a different file
1104                 if [[ "${ending:0:1}" = "_" ]]
1105                 then
1106                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
1107                    then
1108                       endings="$endings $ending"
1109                    fi
1110                 fi
1111              fi
1112 
1113          done <filelist
1114
1115          rm filelist
1116
1117       else
1118
1119             # SINGLE NAME
1120          endings=DEFAULT
1121
1122       fi
1123
1124          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1125       for  ending  in  $endings
1126       do
1127
1128             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1129          if [[ $ending = DEFAULT ]]
1130          then
1131             ending=""
1132          fi
1133
1134             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1135          (( nr_of_input_files = nr_of_input_files + 1 ))
1136          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
1137          optin[$nr_of_input_files]="${optin_pre[$i]}"
1138#          transin[$nr_of_input_files]="${transin_pre[$i]}"
1139          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1140          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1141          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1142          extin[$nr_of_input_files]="${extin_pre[$i]}"
1143
1144
1145             # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1146             # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1147          if [[ "${actionin[$nr_of_input_files]}" = di ]]
1148          then
1149             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
1150          else
1151             eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
1152          fi
1153
1154             # DETERMINE THE FILE'S CYCLE NUMBER
1155          (( maxcycle = 0 ))
1156          ls -1 -d $filename    >   filelist  2>/dev/null
1157          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1158          while  read line
1159          do
1160                 # filename without path (i.e. after the last "/")
1161              basefilename=$(basename ${line})
1162   
1163                 # check if there is an extension
1164              extension=${basefilename##*.}
1165              if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1166              then
1167                 basefilename=${basefilename%.*}
1168              fi
1169   
1170                 # check for an existing cycle number
1171              cycle=${basefilename##*.}
1172              if [[ $cycle =~ ^-?[0-9]+$ ]]
1173              then
1174                 (( icycle = $cycle ))
1175              else
1176                 (( icycle = 0 ))
1177              fi
1178   
1179              if (( icycle > maxcycle ))
1180              then
1181                 (( maxcycle = icycle ))
1182   
1183                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1184                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1185                 if [[ $(echo $cycle | cut -c1) = 0 ]]
1186                 then
1187                    leading_zero=true
1188                 else
1189                    leading_zero=false
1190                 fi
1191              fi
1192   
1193          done <filelist
1194          rm filelist
1195   
1196             # MAKE CYCLE NUMBER THREE DIGITS WIDE
1197          if [[ $leading_zero = true ]]
1198          then
1199             cyclestring=`printf "%03d" $maxcycle`
1200          else
1201             cyclestring=$maxcycle
1202          fi
1203   
1204             # APPEND CYCLE NUMBER TO FILENAME
1205          if (( maxcycle > 0 ))
1206          then
1207             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1208             then
1209                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1210             else
1211                filename=${filename}.$cyclestring
1212             fi
1213          else
1214             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1215             then
1216                filename=${filename}.${extin[$nr_of_input_files]}
1217             fi
1218          fi
1219         
1220             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1221             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1222          absnamein[$nr_of_input_files]=$filename
1223          if (( maxcycle > 0 ))
1224          then
1225             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1226             then
1227                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1228             else
1229                frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
1230             fi
1231          else
1232             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1233             then
1234                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1235             else
1236                frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
1237             fi
1238          fi
1239
1240       done
1241
1242    fi
1243
1244 done
1245
1246
1247    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1248    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1249    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
1250    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
1251    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1252    # REMOTE HOST)
1253 (( i = 0 ))
1254 while (( i < iout ))
1255 do
1256    (( i = i + 1 ))
1257    if [[ ! ( $running_on_remote = true  &&  ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
1258    then
1259       if [[ "${actionout_pre[$i]}" = tr ]]
1260       then
1261          actionout_pre[$i]=""
1262       elif [[ "${actionout_pre[$i]}" = trpe ]]
1263       then
1264          actionout_pre[$i]=pe
1265       elif [[ "${actionout_pre[$i]}" = tra ]]
1266       then
1267          actionout_pre[$i]=a
1268       fi
1269       (( maxcycle = 0 ))
1270       eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
1271       eval catalogname=${pathout_pre[$i]}
1272       if ! ls $filename* 1>/dev/null 2>&1
1273       then
1274     
1275             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1276          if  cat /dev/null > $filename 
1277          then
1278             rm  $filename
1279          else
1280
1281                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1282                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1283             if [[ ! -d $catalogname ]]
1284             then
1285                if  mkdir -p  $catalogname
1286                then
1287                   printf "\n\n  *** directory:"
1288                   printf "\n           $catalogname"
1289                   printf "\n      was created\n"
1290                else
1291                   printf "\n\n  +++ OUTPUT-file:"
1292                   printf "\n           $filename"
1293                   printf "\n      cannot be created, because directory does not exist"
1294                   printf "\n      and cannot be created either"
1295                   printf "\n"
1296                   locat=output  ; exit
1297                fi 2>/dev/null
1298             else
1299                printf "\n\n  +++ OUTPUT-file:"
1300                printf "\n           $filename"
1301                printf "\n      cannot be created, although directory exists"
1302                printf "\n"
1303                locat=output  ; exit
1304             fi
1305          fi 2>/dev/null
1306
1307       fi
1308
1309    fi
1310 done
1311
1312
1313    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1314 if [[ $running_in_batch_mode = false ]]
1315 then
1316    run_id=$RANDOM
1317    job_id=${fname}.$run_id
1318
1319    tempdir=$fast_io_catalog/$job_id
1320 fi
1321
1322
1323    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1324 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1325 then
1326
1327       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1328    if [[ $ibd = 0 ]]
1329    then
1330       printf "\n"
1331       printf "\n  +++ no batch directives found in configuration file"
1332       locat=config_file_batch_directives; (( iec = 0 )); exit
1333    fi
1334
1335       # CHECK IF CPUTIME IS GIVEN FOR JOB
1336    done=false
1337    cputime=$cpumax
1338    while [[ $done = false ]]
1339    do
1340       if (( cputime == 0 ))
1341       then
1342          printf "\n  +++ cpu-time is undefined"
1343          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1344          printf "\n  >>> "
1345          read  cputime   1>/dev/null  2>&1
1346       else
1347          done=true
1348       fi
1349    done
1350    cpumax=$cputime
1351
1352       # CHECK THE MEMORY DEMAND
1353    done=false
1354    while [[ $done = false ]]
1355    do
1356       if (( memory == 0 ))
1357       then
1358          printf "\n  +++ memory demand is undefined"
1359          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1360          printf "\n  >>> "
1361          read  memory  1>/dev/null  2>&1
1362       else
1363          done=true
1364       fi
1365    done
1366
1367       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1368    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1369    then
1370       while [[ -z $remote_username ]]
1371       do
1372          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
1373          printf "\n  >>> Please type username:"
1374          printf "\n  >>> "
1375          read  remote_username
1376       done
1377    fi
1378
1379 else
1380
1381    if [[ $running_in_batch_mode = false ]]
1382    then
1383       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1384       cpumax=$cputime
1385    else
1386       cputime=$cpumax
1387    fi
1388
1389 fi
1390
1391
1392    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1393 (( cpu_hours  = cputime / 3600 ))
1394 (( resttime = cputime - cpu_hours * 3600 ))
1395 (( cpu_minutes  = resttime / 60 ))
1396 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1397 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1398
1399
1400    # OUTPUT OF THE PALMRUN-HEADER
1401 calltime=$(date)
1402 printf "\n"
1403 printf "#------------------------------------------------------------------------# \n"
1404 printf "| %-35s%35s | \n" "$version" "$calltime"
1405 printf "|                                                                        | \n"
1406 column1="called on:"; column2=$(hostname)
1407 printf "| %-25s%-45s | \n" "$column1" "$column2"
1408 if [[ $create_remote_batch_job = true ]]
1409 then
1410    column1="execution on:"; column2="$host_configuration (username: $remote_username)"
1411 else
1412    if [[ $running_on_remote = true ]]
1413    then
1414       column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
1415    else
1416       column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
1417    fi
1418 fi
1419 printf "| %-25s%-45s | \n" "$column1" "$column2"
1420
1421 column1="running in:"
1422 if [[ $running_in_batch_mode = true ]]
1423 then
1424    column2="batch job mode"
1425 else
1426    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1427    then
1428       column2="job creation mode"
1429    else
1430       column2="interactive run mode"
1431    fi
1432 fi
1433 printf "| %-25s%-45s | \n" "$column1" "$column2"
1434
1435 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1436 then
1437    if [[ "$project_account" != "" ]]
1438    then
1439       column1="project account number:"
1440       column2="$project_account"
1441       printf "| %-25s%-45s | \n" "$column1" "$column2"
1442    fi
1443 fi
1444
1445 if [[ -n $cores ]]
1446 then
1447    if [[ $run_coupled_model = false ]]
1448    then
1449       column1="number of cores:"; column2=$cores
1450    else
1451       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1452    fi
1453    printf "| %-25s%-45s | \n" "$column1" "$column2"
1454 fi
1455 if [[ -n $tasks_per_node ]]
1456 then
1457    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1458    printf "| %-25s%-45s | \n" "$column1" "$column2"
1459    if (( remaining_cores > 0 ))
1460    then
1461       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1462       printf "| %-25s%-45s | \n" "$column1" "$column2"
1463    fi
1464 fi
1465 if [[ $maximum_parallel_io_streams != $cores ]]
1466 then
1467    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1468    printf "| %-25s%-45s | \n" "$column1" "$column2"
1469 fi
1470 if [[ $use_openmp = true ]]
1471 then
1472    column1="threads per task:"; column2="$threads_per_task"
1473    printf "| %-25s%-45s | \n" "$column1" "$column2"
1474 fi
1475 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1476 then
1477    column1="memory demand / PE":; column2="$memory MB"
1478    printf "| %-25s%-45s | \n" "$column1" "$column2"
1479    column1="job cpu time (h:m:s):"; column2="$timestring"
1480    printf "| %-25s%-45s | \n" "$column1" "$column2"
1481 fi
1482 printf "|                                                                        | \n"
1483 if [[ "$source_list" != "" ]]
1484 then
1485    if [[ "$make_options" != "" ]]
1486    then
1487       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1488       printf "| %-25s%-45s | \n" "$column1" "$column2"
1489       line=$(echo "$make_options" | cut -c46-)
1490       while [[ "$line" != "" ]]
1491       do
1492          column1=""
1493          column2=$(echo "$line" | cut -c-45)
1494          printf "| %-25s%-45s | \n" "$column1" "$column2"
1495          line=$(echo "$line" | cut -c46-)
1496       done
1497    fi
1498 fi
1499
1500 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1501 printf "| %-25s%-45s | \n" "$column1" "$column2"
1502 line=$(echo "$cpp_options" | cut -c46-)
1503 while [[ "$line" != "" ]]
1504 do
1505    column1=""
1506    column2=$(echo "$line" | cut -c-45)
1507    printf "| %-25s%-45s | \n" "$column1" "$column2"
1508    line=$(echo "$line" | cut -c46-)
1509 done
1510
1511 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1512 printf "| %-25s%-45s | \n" "$column1" "$column2"
1513 line=$(echo "$compiler_options" | cut -c46-)
1514 while [[ "$line" != "" ]]
1515 do
1516    column1=""
1517    column2=$(echo "$line" | cut -c-45)
1518    printf "| %-25s%-45s | \n" "$column1" "$column2"
1519    line=$(echo "$line" | cut -c46-)
1520 done
1521
1522 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
1523 printf "| %-25s%-45s | \n" "$column1" "$column2"
1524 line=$(echo "$linker_options" | cut -c46-)
1525 while [[ "$line" != "" ]]
1526 do
1527    column1=""
1528    column2=$(echo "$line" | cut -c-45)
1529    printf "| %-25s%-45s | \n" "$column1" "$column2"
1530    line=$(echo "$line" | cut -c46-)
1531 done
1532
1533 if [[ "$login_init_cmd" != "" ]]
1534 then
1535    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1536    printf "| %-25s%-45s | \n" "$column1" "$column2"
1537    line=$(echo "$login_init_cmd" | cut -c46-)
1538    while [[ "$line" != "" ]]
1539    do
1540       column1=""
1541       column2=$(echo "$line" | cut -c-45)
1542       printf "| %-25s%-45s | \n" "$column1" "$column2"
1543       line=$(echo "$line" | cut -c46-)
1544    done
1545 fi
1546
1547 if [[ "$module_commands" != "" ]]
1548 then
1549    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1550    printf "| %-25s%-45s | \n" "$column1" "$column2"
1551    line=$(echo "$module_commands" | cut -c46-)
1552    while [[ "$line" != "" ]]
1553    do
1554       column1=""
1555       column2=$(echo "$line" | cut -c-45)
1556       printf "| %-25s%-45s | \n" "$column1" "$column2"
1557       line=$(echo "$line" | cut -c46-)
1558    done
1559 fi
1560 printf "|                                                                        | \n"
1561 column1="base name of files:"; column2=$fname
1562 printf "| %-25s%-45s | \n" "$column1" "$column2"
1563 column1="activation string list:"; column2=$(echo $activation_string_list)
1564 printf "| %-25s%-45s | \n" "$column1" "$column2"
1565
1566 if [[ "$ocean_file_appendix" = true ]]
1567 then
1568    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1569 fi
1570
1571 if [[ "$source_list" != "" ]]
1572 then
1573    printf "|                                                                        | \n"
1574    printf "| Files to be compiled:                                                  | \n"
1575    line=$source_list
1576    while [[ "$line" != "" ]]
1577    do
1578       linestart=$(echo $line | cut -c-70)
1579       printf "| %-70s | \n" "$linestart"
1580       line=$(echo "$line" | cut -c71-)
1581    done
1582 fi
1583 printf "#------------------------------------------------------------------------#"
1584
1585
1586
1587    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1588 if [[ $do_trace = true ]]
1589 then
1590    (( i = 0 ))
1591    while (( i < nr_of_input_files ))
1592    do
1593       (( i = i + 1 ))
1594       if (( i == 1 ))
1595       then
1596          printf "\n\n >>> INPUT-file assignments:\n"
1597       fi
1598       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1599    done
1600    (( i = 0 ))
1601    while (( i < iout ))
1602    do
1603       (( i = i + 1 ))
1604       if (( i == 1 ))
1605       then
1606          printf "\n\n >>> OUTPUT-file assignments:\n"
1607       fi
1608       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1609    done
1610    (( i = 0 ))
1611    while (( i < iic ))
1612    do
1613       (( i = i + 1 ))
1614       if (( i == 1 ))
1615       then
1616          printf "\n\n >>> INPUT-commands:\n"
1617       fi
1618       printf "\n     ${in_command[$i]}" 
1619    done
1620    (( i = 0 ))
1621    while (( i < ioc ))
1622    do
1623       (( i = i + 1 ))
1624       if (( i == 1 ))
1625       then
1626          printf "\n\n >>> OUTPUT-commands:\n"
1627       fi
1628       printf "\n     ${out_command[$i]}" 
1629    done
1630 fi
1631
1632    # QUERY FOR CONTINUE
1633 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1634 then
1635    antwort=dummy
1636    printf "\n\n"
1637    printf " >>> everything o.k. (y/n) ?  "
1638    while  read antwort
1639    do
1640       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1641       then
1642          printf " >>> everything o.k. (y/n) ?  "
1643       else
1644          break
1645       fi
1646    done
1647    if [[ $antwort = n  ||  $antwort = N ]]
1648    then
1649       locat=user_abort; (( iec = 0 )); exit
1650    fi
1651    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1652    then
1653       printf "\n ***  batch-job will be created and submitted"
1654    else
1655       printf "\n ***  PALMRUN will now continue to execute on this machine"
1656    fi
1657 fi
1658
1659 
1660
1661    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1662 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1663 then
1664
1665    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1666    then
1667       printf "\n\n  *** creating executable and other sources for the remote host\n"
1668    else
1669       printf "\n\n  *** creating executable and other sources for the local host\n"
1670    fi
1671
1672       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1673       # IT SHALL BE CREATED
1674    ask_for_make_depository=false
1675    if [[ $create_remote_batch_job = true ]]
1676    then
1677
1678       line=`grep %base_directory $config_file`
1679       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
1680       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${host_configuration}_last_make_protokoll
1681
1682       if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
1683       then
1684          printf "\n\n  +++ make depository \"${make_depository}\""
1685          printf "\n      on remote host not found!"
1686          ask_for_make_depository=true
1687       fi
1688       rm ${host_configuration}_last_make_protokoll
1689
1690    else
1691
1692          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
1693       make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
1694       if [[ ! -d ${make_depository} ]]
1695       then
1696          printf "\n\n  +++ make depository \"${make_depository}\""
1697          printf "\n      on local host not found!"
1698          ask_for_make_depository=true
1699       fi
1700
1701    fi
1702
1703    if [[ $ask_for_make_depository = true ]]
1704    then
1705
1706       antwort=dummy
1707       printf "\n\n"
1708       printf "  >>> Create a new one (y/n) ?  "
1709       while  read antwort
1710       do
1711          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1712          then
1713             printf "  >>> Create a new one (y/n) ?  "
1714          else
1715             break
1716          fi
1717       done
1718       if [[ $antwort = n  ||  $antwort = N ]]
1719       then
1720          locat=user_abort; (( iec = 0 )); exit
1721       fi
1722
1723       if [[ $do_trace = true ]]
1724       then
1725          palmbuild  -h $host_configuration
1726       else
1727          palmbuild  -v  -h $host_configuration
1728       fi
1729
1730       if [[ $? != 0 ]]
1731       then
1732   
1733              # ABORT IN CASE OF COMPILATION PROBLEMS
1734          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1735          locat=make_depository
1736          exit
1737       else
1738          echo "  *** now continue with creating executable and other sources"
1739       fi
1740
1741    fi
1742
1743       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
1744    palmbuild  -v  $use_existing_sources_folder  -h $host_configuration  -d $fname
1745
1746    if [[ $? != 0 ]]
1747    then
1748
1749           # ABORT IN CASE OF COMPILATION PROBLEMS
1750       printf "\n  +++ error while creating executable and/or other sources"
1751       locat=execution
1752       rm -rf  $sources_for_run_catalog
1753       exit
1754
1755    else
1756
1757       printf "  *** executable and other sources created\n"
1758       rm -rf  $sources_for_run_catalog
1759
1760    fi
1761
1762 fi
1763
1764
1765    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1766    # WILL BE COPIED TO THE REMOTE HOST
1767 if [[ $create_remote_batch_job = true ]]
1768 then
1769    (( i = 0 ))
1770    while (( i < nr_of_input_files ))
1771    do
1772       (( i = i + 1 ))
1773       if [[ "${actionin[$i]}" = tr ]]
1774       then
1775          eval inputfile=${pathin[$i]}/${frelin[$i]}
1776          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1777       fi
1778    done
1779    if (( i > 0 ))
1780    then
1781       printf "  *** input files have been copied to the remote host\n"
1782    fi
1783 fi
1784 
1785
1786    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1787    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1788 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1789 then
1790
1791       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1792    if [[ $running_in_batch_mode = false ]]
1793    then
1794          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1795          # FOLDER
1796       mkdir -p  $tempdir
1797       chmod  go+rx  $tempdir
1798       cd  $tempdir
1799       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $tempdir
1800       printf "\n  *** changed to temporary directory: $tempdir"
1801
1802    else
1803
1804          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
1805       printf "\n  *** running in temporary directory: $tempdir"
1806
1807    fi
1808
1809
1810       # PROVIDE THE INPUT FILES
1811       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
1812    (( i = 0 ))
1813    while (( i < nr_of_input_files ))
1814    do
1815       (( i = i + 1 ))
1816       if (( i == 1 ))
1817       then
1818          printf "\n\n  *** providing INPUT-files:\n$dashes"
1819       fi
1820
1821
1822          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
1823       if [[ "${actionin[$i]}" = unavailable ]]
1824       then
1825          if [[ "${extin[$i]}" = ""  ||  "${extin[$i]}" = " " ]]
1826          then
1827             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
1828             printf "\n                   is not available!"
1829          else
1830             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
1831             printf "\n                   is not available!"
1832          fi
1833          continue
1834       fi
1835
1836          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1837       files_for_cores=false; filetype=file
1838       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1839       then
1840          files_for_cores=true; filetype=files
1841          actionin[$i]=""
1842       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1843       then
1844          actionin[$i]=""
1845       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1846       then
1847          files_for_cores=true; filetype=files
1848          actionin[$i]="ln"
1849       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1850       then
1851          actionin[$i]="ln"
1852       fi
1853
1854       if [[ $files_for_cores = true ]]
1855       then
1856          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1857       else
1858          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1859       fi
1860
1861          # INPUT-FILES TO BE LINKED
1862       if [[ "${actionin[$i]}" = ln ]]
1863       then
1864
1865          printf "\n      $filetype will be linked"
1866          if [[ $files_for_cores = false ]]
1867          then
1868             if [[ -f "${absnamein[$i]}" ]]
1869             then
1870                ln  ${absnamein[$i]}  ${localin[$i]}
1871                got_tmp[$i]=true
1872             fi
1873          else
1874             if [[ -d "${absnamein[$i]}" ]]
1875             then
1876                mkdir -p ${localin[$i]}
1877                cd ${absnamein[$i]}
1878                for file in $(ls *)
1879                do
1880                   ln $file $tempdir/${localin[$i]}
1881                done >|/dev/null 2>&1
1882                cd $tempdir
1883             fi
1884
1885                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
1886             if [[ ! -f "${localin[$i]}/_000000" ]]
1887             then
1888                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1889                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1890             fi
1891
1892             got_tmp[$i]=true
1893          fi
1894       fi
1895
1896          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
1897       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "tr"  ||  "${actionin[$i]}" = "npe" ]]
1898       then
1899
1900          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
1901          then
1902
1903                # FILE COPIES ARE PROVIDED FOR ALL CORES
1904                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
1905             printf "\n      file will be provided for $cores processors"
1906             mkdir -p ${localin[$i]}
1907             ival=$cores
1908             (( ii = 0 ))
1909             while (( ii <= ival-1 ))
1910             do
1911                if (( ii < 10 ))
1912                then
1913                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
1914                elif (( ii < 100 ))
1915                then
1916                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
1917                elif (( ii < 1000 ))
1918                then
1919                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
1920                else
1921                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
1922                fi
1923                (( ii = ii + 1 ))
1924             done
1925
1926          else
1927
1928             if [[ $files_for_cores = true ]]
1929             then
1930
1931                   # PROVIDE FILES FOR EACH CORE
1932                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
1933                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
1934                printf "\n      providing $cores files for the respective cores"
1935                mkdir -p ${localin[$i]}
1936                        if [[ $link_local_input = true ]]
1937                              then
1938                                 printf "      files will be linked\n"
1939                                 cd ${absnamein[$i]}
1940                                 for file in $(ls *)
1941                                 do
1942                                    ln -f $file  ${localin[$i]}
1943                                 done
1944                                 cd $tempdir
1945                              fi
1946
1947                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
1948                              if [[ ! -f "${localin[$i]}/_000000" ]]
1949                              then
1950                                 if [[ $link_local_input = true ]]
1951                                        then
1952                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1953                                 fi
1954                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
1955                              fi
1956
1957             else
1958
1959                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
1960                        if [[ $link_local_input = true ]]
1961                        then
1962                                 printf "      file will be linked\n"
1963                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
1964                        fi
1965                                # If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
1966                        if [[ ! -f "${localin[$i]}" ]]
1967                then
1968                                 if [[ $link_local_input = true ]]
1969                          then
1970                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
1971                                 fi
1972                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
1973                   then
1974                      mv  ${absnamein[$i]}  ${localin[$i]}
1975                   else
1976                                 cp  ${absnamein[$i]}  ${localin[$i]}
1977                   fi
1978                fi
1979             fi
1980          fi
1981       fi
1982
1983    done
1984    if (( i != 0 ))
1985    then
1986       printf "\n$dashes\n  *** all INPUT-files provided \n"
1987    fi
1988
1989
1990       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
1991    (( i = 0 ))
1992    while (( i < iic ))
1993    do
1994       (( i = i + 1 ))
1995       if (( i == 1 ))
1996       then
1997          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
1998       fi
1999       printf "\n  >>> ${in_command[$i]}"
2000       eval  ${in_command[$i]}
2001       if (( i == iic ))
2002       then
2003          printf "\n$dashes\n"
2004       fi
2005    done
2006
2007
2008       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2009       # (FILE ENVPAR WILL BE READ BY PALM)
2010    cat  >  ENVPAR  <<  EOF
2011 &envpar  run_identifier = '$fname', host = '$host_configuration',
2012          write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
2013          maximum_parallel_io_streams = $maximum_parallel_io_streams,
2014          maximum_cpu_time_allowed = ${cpumax}.,
2015          revision = '$global_revision',
2016          batch_job = .${running_in_batch_mode}. /
2017
2018EOF
2019
2020
2021       # STARTING THE EXECUTABLE
2022    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
2023    PATH=$PATH:$tempdir
2024
2025
2026       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
2027    line=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/$mpi_tasks/g' | sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
2028    line2=`echo  "${execute_command}" | sed 's/{{MPI_TASKS}}/1/g' | sed 's/{{TASKS_PER_NODE}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
2029    eval line=\"$line\"
2030    execute_command="$line"
2031
2032
2033       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
2034    if [[ "$execute_command_for_combine" = "" ]]
2035    then
2036       eval line2=\"$line2\"
2037       execute_command_for_combine="$line2"
2038    fi
2039   
2040
2041
2042       # PROVIDE A HOSTFILE, IF REQUIRED
2043    if [[ "$hostfile" != "" ]]
2044    then
2045
2046       if [[ $hostfile = auto ]]
2047       then
2048             # CREATE A NEW HOSTFILE
2049          (( ii = 1 ))
2050          while (( ii <= cores / threads_per_task ))
2051          do
2052             echo  $(hostname)  >>  hostfile
2053             (( ii = ii + 1 ))
2054          done
2055          if (( cores / threads_per_task == 0 ))
2056          then
2057             echo  $(hostname)  >>  hostfile
2058          fi
2059       
2060       else
2061          cp  $hostfile  hostfile
2062       fi
2063       eval line=\"`head -n $ii  hostfile`\"
2064       printf "\n  *** running on: $line"
2065    fi
2066
2067
2068
2069       # SET THE NUMBER OF OPENMP-THREADS
2070    if [[ $use_openmp = true ]]
2071    then
2072       export OMP_NUM_THREADS=$threads_per_task
2073       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2074    else
2075       export OMP_NUM_THREADS=1
2076    fi
2077
2078
2079       # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
2080    if [[ $run_coupled_model = false ]]
2081    then
2082       if [[ "$ocean_file_appendix" = true ]]
2083       then
2084          echo "precursor_ocean"  >  coupling_steering
2085       else
2086          echo "precursor_atmos"  >  coupling_steering
2087      fi
2088    else
2089       (( iia = $cores_atmos / $threads_per_task ))
2090       (( iio = $cores_ocean / $threads_per_task ))
2091       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
2092       printf "\n\n"
2093       echo "coupled_run $iia $iio"  >  coupling_steering
2094    fi
2095
2096    printf "\n  *** execute command:"
2097    printf "\n      \"$execute_command\" \n\n"
2098
2099    $execute_command  <  coupling_steering
2100
2101    if [[ $? != 0 ]]
2102    then
2103
2104           # ABORT IN CASE OF RUNTIME ERRORS
2105       printf "\n  +++ runtime error occured"
2106       locat=execution
2107       exit
2108
2109    else
2110
2111       printf "\n$dashes\n  *** execution finished \n"
2112
2113    fi
2114
2115
2116       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2117       # BY EACH CORE INTO ONE FILE
2118   if [[ ! -f combine_plot_fields.x ]]
2119   then
2120
2121      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
2122      printf "\n      2d- and/or 3d-data may be incomplete!"
2123      printf "\n      Your previous palmbuild may have failed. Please check.\n"
2124
2125   elif [[ "$combine_plot_fields" == true ]]
2126   then
2127
2128      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2129      $execute_command_for_combine
2130
2131   else
2132
2133         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
2134         # DATA OUTPUT
2135      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2136   fi
2137
2138
2139
2140       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2141    (( i = 0 ))
2142    while (( i < ioc ))
2143    do
2144       (( i = i + 1 ))
2145       if (( i == 1 ))
2146       then
2147          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
2148       fi
2149       printf "\n  >>> ${out_command[$i]}"
2150       eval  ${out_command[$i]}
2151       if (( i == ioc ))
2152       then
2153          printf "\n$dashes\n"
2154       fi
2155    done
2156
2157
2158       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2159       # WILDCARDS
2160    (( i = 0 ))
2161    (( nr_of_output_files = 0 ))
2162
2163    while (( i < iout ))
2164    do
2165
2166       (( i = i + 1 ))
2167
2168          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2169          # CREATE A LIST FOR THE DETECTED ENDINGS
2170       if [[ "${multout[$i]}" = true ]]
2171       then
2172             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2173          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
2174          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null
2175
2176          endings="DEFAULT"
2177          while  read line
2178          do
2179                 # remove the local name from the beginning
2180              localnamestring="${localout_pre[$i]}"
2181              length_localname=${#localnamestring}
2182              ending=${line:${length_localname}}
2183
2184              if [[ "$ending" != "" ]]
2185              then
2186                 endings="$endings $ending"
2187              fi
2188 
2189          done <filelist
2190
2191          rm filelist
2192
2193       else
2194
2195             # SINGLE NAME
2196          endings=DEFAULT
2197
2198       fi
2199
2200          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2201       for  ending  in  $endings
2202       do
2203
2204             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2205          if [[ $ending = DEFAULT ]]
2206          then
2207             ending=""
2208          fi
2209
2210             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2211          (( nr_of_output_files = nr_of_output_files + 1 ))
2212          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2213          transout[$nr_of_output_files]="${transout_pre[$i]}"
2214          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2215          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2216          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2217          extout[$nr_of_output_files]="${extout_pre[$i]}"
2218
2219       done
2220
2221    done
2222
2223
2224
2225
2226       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2227    (( i = 0 ))
2228    while (( i < nr_of_output_files ))
2229    do
2230       (( i = i + 1 ))
2231       if (( i == 1 ))
2232       then
2233          printf "\n\n  *** saving OUTPUT-files:"
2234
2235             # GET RUN NUMBER ASSIGNED BY PALM
2236          if [[ -f RUN_NUMBER ]]
2237          then
2238              read  run_number  <  RUN_NUMBER
2239              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2240              usecycle_option="-U $run_number"
2241          else
2242              run_number=0
2243              usecycle_option=""
2244          fi
2245          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2246          then
2247             printf "\n  *** in case of SCP transfers to local host"
2248             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
2249          fi
2250          printf "\n$dashes"
2251       fi
2252
2253       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2254       then
2255
2256          eval filename=${pathout[$i]}/${fname}${endout[$i]}
2257
2258             # DETERMINE THE CYCLE NUMBER
2259          ls -1 -d $filename    >   filelist  2>/dev/null
2260          ls -1 -d $filename.*  >>  filelist  2>/dev/null
2261          while  read line
2262          do
2263   
2264                # filename without path (i.e. after the last "/")
2265             basefilename=$(basename ${line})
2266   
2267                # check if there is an extension
2268             extension=${basefilename##*.}
2269             if [[ "$extension" = "${extout[$i]}" ]]
2270             then
2271                basefilename=${basefilename%.*}
2272             fi
2273   
2274                # check for an existing cycle number
2275             cycle=${basefilename##*.}
2276             if [[ $cycle =~ ^-?[0-9]+$ ]]
2277             then
2278                (( icycle = $cycle + 1 ))
2279             else
2280                (( icycle = 1 ))
2281             fi
2282   
2283             if (( icycle > maxcycle ))
2284             then
2285                (( maxcycle = icycle ))
2286             fi
2287   
2288          done <filelist
2289          rm filelist
2290
2291   
2292             # SET THE CYCLE NUMBER
2293             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2294          if [[ "${actionout[$i]}" = a ]]
2295          then
2296             (( maxcycle = maxcycle - 1 ))
2297          fi
2298         
2299          (( cycnum[$i] = maxcycle ))
2300          pathout[$i]=$filename
2301
2302
2303             # ADD CYCLE NUMBER TO FILENAME
2304             # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
2305          if [[ "${actionout[$i]}" != "a" ]]
2306          then
2307                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2308                # WITH AN EXISTING CYCLE NUMBER
2309             if (( run_number >= cycnum[$i] ))
2310             then
2311                (( cycnum[$i] = run_number ))
2312             else
2313                if (( run_number > 0 ))
2314                then
2315                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2316                fi
2317             fi
2318          fi
2319          if (( cycnum[$i] > 0 ))
2320          then
2321             cyclestring=`printf "%03d" ${cycnum[$i]}`
2322             pathout[$i]=${pathout[$i]}.$cyclestring
2323          fi
2324       fi           
2325
2326          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2327       files_for_cores=false; filetype=file
2328       link_local_output=false
2329       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2330       then
2331          files_for_cores=true; filetype=directory
2332          actionout[$i]=""
2333       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2334       then
2335          actionout[$i]=""
2336       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2337       then
2338          files_for_cores=true; filetype=directory
2339          link_local_output=true
2340          actionout[$i]=""
2341       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2342       then
2343          link_local_output
2344          actionout[$i]=""
2345       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2346       then
2347          files_for_cores=true; filetype=directory
2348          actionout[$i]="tr"
2349       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2350       then
2351          actionout[$i]="tr"
2352       fi
2353
2354       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
2355       then
2356          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
2357       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2358       then
2359          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2360       else
2361
2362
2363             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2364             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2365          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2366          then
2367             if [[ $running_on_remote = true ]]
2368             then
2369
2370                   # SET OPTIONS FOR TRANSFER
2371                if [[ "${actionout[$i]}" = tr ]]
2372                then
2373                   if [[ $files_for_cores = false ]]
2374                   then
2375                      catalog_option=""
2376                      catalog_string=""
2377                   else
2378                      catalog_option="-c"
2379                      catalog_string="/"
2380                   fi
2381                   append_option=""
2382                   append_string=""
2383                else
2384                   append_option="-A"
2385                   append_string="append"
2386                fi
2387
2388                transfer_failed=false
2389                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
2390                printf "\n              ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
2391
2392                   # TRANSFER VIA SCP
2393                if [[ "$remote_loginnode" != "" ]]
2394                then
2395                   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
2396                else
2397                   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]}
2398                fi
2399                [[ $? != 0 ]]  &&  transfer_failed=true
2400
2401
2402                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2403                if [[ $transfer_failed = true ]]
2404                then
2405                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
2406                   printf "      ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
2407
2408                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2409                   eval  local_catalog=${pathout[$i]}
2410                   if [[ ! -d $local_catalog ]]
2411                   then
2412                      printf "  *** local directory does not exist. Trying to create:\n"
2413                      printf "      $local_catalog \n"
2414                      mkdir -p  $local_catalog
2415                   fi
2416                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
2417                   transfer_problems=true
2418                fi
2419
2420             else
2421
2422                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2423                   # BE COPIED OR APPENDED ON THIS MACHINE
2424                if [[ "${actionout[$i]}" = tr ]]
2425                then
2426                   actionout[$i]=""
2427                else
2428                   actionout[$i]="a"
2429                fi
2430             fi
2431          fi
2432
2433
2434             # APPEND ON THIS MACHINE
2435          if [[ "${actionout[$i]}" = "a" ]]
2436          then
2437             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2438             then
2439                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2440                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2441                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2442             else
2443                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2444                printf "\n              ${pathout[$i]}\n"
2445                cat  ${localout[$i]}  >>  ${pathout[$i]}
2446             fi
2447          fi
2448
2449             # COPY ON THIS MACHINE
2450             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2451             # ON DIFFERENT FILE-SYSTEMS
2452          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2453          then
2454
2455                # COPY IN CASE OF RUNS ON SINGLE CORES
2456             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2457             then
2458                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2459                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2460                              if [[ $link_local_output = true ]]
2461                              then
2462                                 printf "      file will be linked\n"
2463                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2464                              fi
2465                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2466                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2467                then
2468                                 if [[ $link_local_output = true ]]
2469                          then
2470                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2471                                 fi
2472                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2473                              else
2474                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2475                fi
2476             else
2477                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2478                printf "\n              ${pathout[$i]}\n"
2479                              if [[ $link_local_output = true ]]
2480                              then
2481                                 printf "      file will be linked\n"
2482                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2483                              fi
2484                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2485                        if [[ ! -f "${pathout[$i]}" ]]
2486                then
2487                                 if [[ $link_local_output = true ]]
2488                          then
2489                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2490                                 fi
2491                                 cp  ${localout[$i]}  ${pathout[$i]}
2492                              else
2493                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2494                fi
2495             fi
2496
2497          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2498          then
2499
2500                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2501                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2502             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2503             printf "\n              ${pathout[$i]}\n"
2504                    if [[ $link_local_output = true ]]
2505                    then
2506                              printf "      files will be linked\n"
2507                              mkdir -p ${pathout[$i]}
2508                              cd ${localout[$i]}
2509                              for file in $(ls *)
2510                              do
2511                                 ln -f $file  ${pathout[$i]}
2512                              done >|/dev/null 2>&1
2513                              cd $tempdir
2514                    fi
2515
2516                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2517                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2518             then
2519                              if [[ $link_local_output = true ]]
2520                              then
2521                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2522                              fi
2523                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2524             fi
2525
2526          fi
2527       fi
2528    done
2529
2530    if (( i != 0 ))
2531    then
2532       if [[ $transfer_problems = true ]]
2533       then
2534          printf "\n$dashes\n  *** OUTPUT-files saved"
2535          printf "\n  +++ WARNING: some data transfers failed! \n"
2536       else
2537          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2538       fi
2539    fi
2540
2541
2542       # IF REQUIRED, START A RESTART-JOB
2543       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2544    if [[ -f CONTINUE_RUN ]]
2545    then
2546
2547          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2548          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2549          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2550          # -b START A BATCH JOB
2551       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2552       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2553       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2554
2555
2556          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2557          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2558       if [[ $(echo $prc | grep -c "#") != 0 ]]
2559       then
2560          prc=`echo $prc | sed 's/#/r/g'`
2561       fi
2562
2563
2564          # START THE RESTART-JOB
2565       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2566       echo "      $prc"
2567       printf "\n$dashes\n"
2568       if [[ $running_on_remote = true ]]
2569       then
2570
2571          echo "*** ssh will be used to initiate restart-runs!"
2572          echo "    return_address=\"$return_address\" "
2573          echo "    return_username=\"$local_username\" "
2574
2575          if [[ "$remote_loginnode" != "" ]]
2576          then
2577             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
2578          else
2579             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address
2580          fi
2581
2582             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2583          sleep 30
2584
2585       else
2586
2587             # START THE RESTART JOB ON THE LOCAL HOST
2588          eval  $prc                # THE ' MUST BE EVALUATED
2589          cd -  > /dev/null
2590
2591       fi
2592       printf "\n$dashes\n  *** restart-run initiated \n"
2593
2594
2595          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2596          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2597          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2598          # MAY BE VERY HUGE)
2599       (( i = 0 ))
2600       while (( i < nr_of_input_files ))
2601       do
2602          (( i = i + 1 ))
2603          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2604          then
2605             rm -r  ${absnamein[$i]}
2606          fi
2607       done
2608
2609    fi
2610
2611
2612       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2613    cd  $HOME
2614    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $tempdir
2615
2616
2617 else
2618
2619
2620       # PREPARING ACTIONS,
2621       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2622
2623       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
2624    palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
2625    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2626    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2627    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2628    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2629    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2630    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
2631    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
2632    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2633    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2634    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2635    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2636    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
2637    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
2638    if [[ $create_remote_batch_job = true ]]
2639    then
2640       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
2641       if [[ $do_trace = true ]]
2642       then
2643          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2644       fi
2645    elif [[ $create_batch_job = true ]]
2646    then
2647       palmrun_com=${palmrun_com}" -j"
2648       if [[ $do_trace = true ]]
2649       then
2650          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2651       fi
2652    fi
2653
2654
2655       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2656       # REMOTE HOST
2657    job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
2658    job_protocol_file=$job_protocol_file_local
2659    if [[ $create_remote_batch_job = true ]]
2660    then
2661       job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
2662       job_protocol_file=$job_protocol_file_remote
2663       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
2664       scpjob_file=${remote_jobcatalog}/scpjob.$run_id
2665    fi
2666
2667
2668       # BUILD THE JOB-SCRIPTS ON FILE jobfile
2669    jobfile=jobfile.$run_id
2670
2671
2672       # FIRST CREATE THE BATCH DIRECTIVES
2673    (( i = 0 ))
2674    while (( i < ibd ))
2675    do
2676       (( i = i + 1 ))
2677       line=`echo  "${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'`
2678       eval line=\"$line\"
2679       echo  "$line"                               >>  $jobfile
2680    done
2681    echo " "                                       >>  $jobfile
2682
2683
2684       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2685       # PROTOCOL
2686    if [[ $create_remote_batch_job = true ]]
2687    then
2688       echo "set +vx"                              >>  $jobfile
2689       echo "trap '"                               >>  $jobfile
2690       echo "set +vx"                              >>  $jobfile
2691       echo "cd ${remote_jobcatalog}"              >>  $jobfile
2692       echo "cat >  scpjob.$run_id << %%END%%"     >>  $jobfile
2693
2694          # ADD THE BATCH DIRECTIVES
2695       (( i = 0 ))
2696       while (( i < ibdt ))
2697       do
2698          (( i = i + 1 ))
2699          line=`echo  "${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'`
2700          eval line=\"$line\"
2701          echo  "$line"                            >>  $jobfile
2702       done
2703       echo " "                                    >>  $jobfile
2704
2705       echo "set -x"                               >>  $jobfile
2706       echo "${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
2707       echo "%%END%%"                              >>  $jobfile
2708       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2709       echo "$submit_command  $scpjob_file"        >>  $jobfile
2710       echo "rm $scpjob_file"                      >>  $jobfile
2711       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
2712       echo "set -x"                               >>  $jobfile
2713       echo "     ' exit"                          >>  $jobfile
2714    fi
2715
2716
2717       # ACTIVATE ERROR-TRACEBACK
2718    if [[ $do_trace = true ]]
2719    then
2720       echo  "set -x"                                    >>  $jobfile
2721    else
2722       echo  "set +vx"                                   >>  $jobfile
2723    fi
2724
2725
2726       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2727    if [[ "$login_init_cmd" != "" ]]
2728    then
2729       echo  "$login_init_cmd"        >>  $jobfile
2730    fi
2731    if [[ "$module_commands" != "" ]]
2732    then
2733       echo  "$module_commands"     >>  $jobfile
2734    fi
2735
2736
2737       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
2738    if [[ $create_remote_batch_job = true ]]
2739    then
2740       echo  "mkdir  $tempdir"           >>  $jobfile
2741       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
2742    else
2743          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2744          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2745          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2746       mkdir  $tempdir
2747       chmod  go+rx  $tempdir
2748    fi
2749    echo  "cd  $tempdir"                 >>  $jobfile
2750    echo  "export tempdir=$tempdir"      >>  $jobfile
2751    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
2752    echo  "export PATH=.:\$PATH"         >>  $jobfile
2753    echo  "export execute_palmrun=true"  >>  $jobfile
2754
2755
2756       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2757       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2758       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2759    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2760    echo  "export LOCAL_PWD"                            >>  $jobfile
2761
2762
2763       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
2764    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
2765    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2766
2767
2768       # CALL PALMRUN WITHIN THE JOB
2769       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2770    echo  "set -x"                                              >>  $jobfile
2771    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2772
2773
2774       # TRANSFER JOBFILE TO THE TARGET HOST
2775    if [[ $create_jobfile_only = false ]]
2776    then
2777
2778       if [[ $create_remote_batch_job = true ]]
2779       then
2780
2781          echo " "
2782          echo " *** transfer of job to remote host via scp"
2783          if [[ $do_trace = true ]]
2784          then
2785             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
2786          fi
2787          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}  >  /dev/null
2788
2789          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
2790          if [[ $do_trace = true ]]
2791          then
2792             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"
2793          fi
2794          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
2795
2796       elif [[ $create_batch_job = true ]]
2797       then
2798
2799          eval  local_jobcatalog=$local_jobcatalog
2800          cp  $jobfile  ${local_jobcatalog}/${host_configuration}_${job_id}
2801          cd $local_jobcatalog
2802          echo " "
2803          echo " *** submit the job"
2804          if [[ $do_trace = true ]]
2805          then
2806             echo "$submit_command ${host_configuration}_${job_id}"
2807          fi
2808          $submit_command ${host_configuration}_${job_id}
2809          rm ${host_configuration}_${job_id}
2810          cd -  > /dev/null
2811
2812       fi
2813
2814       rm -rf  $jobfile
2815
2816    else
2817
2818       printf "\n *** jobfile created under name \"$jobfile\" "
2819       printf "\n     no batch-job has been sent!"
2820
2821    fi
2822
2823 fi  # END OF REMOTE-PART
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