source: palm/trunk/SCRIPTS/palmrun @ 3364

Last change on this file since 3364 was 3346, checked in by raasch, 6 years ago

job_id renamed run_id in configuration files, job_id is set for compatibility reasons with older versions of config files

  • Property svn:executable set to *
  • Property svn:keywords set to Id Rev
File size: 100.5 KB
RevLine 
[2380]1#!/bin/bash
2
3# palmrun - script for running PALM jobs
4
5#--------------------------------------------------------------------------------#
[2696]6# This file is part of the PALM model system.
[2380]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#
[2718]19# Copyright 2017-2018  Leibniz Universitaet Hannover
[2380]20#--------------------------------------------------------------------------------#
21#
22# Current revisions:
23# ------------------
24#
[2410]25#
[2380]26# Former revisions:
27# -----------------
[3032]28# $Id: palmrun 3346 2018-10-15 12:28:43Z suehring $
[3346]29# job_id is set for compatibility reasons with older versions of config files
30#
31# 3313 2018-10-06 15:22:48Z knoop
[3294]32# more detailed error message for outdated fileconnection file
33#
34# 3236 2018-09-10 09:07:06Z raasch
[3236]35# warning issued in case of file connection file version mismatch,
36# host_configuration renamed configuration_identifier,
37# "host identifier" in header output renamed "config. identifier",
38# jobname renamed run_identifier,
39# run_id renamed run_id_number
40# job_id renamed run_id
41# option -r renamed -i
42#
43# 3151 2018-07-19 08:45:38Z raasch
[3151]44# removed additional listing of files to be compiled, print PALM code revision
45# in header
46#
47# 3132 2018-07-16 11:44:58Z raasch
[3132]48# create consistent error messages in case of failed restarts,
49# check existence of remote job catalog
50#
51# 3043 2018-05-25 10:47:54Z raasch
[3043]52# check for setting of fast_io_catalog
53#
54# 3033 2018-05-23 15:26:19Z raasch
[3025]55# -T option not required for interactive runs (tasks per node =
56# total number of cores is assumed as default, if option is not given),
57# reformatting of a few messages,
58# bugfix: destination output directory is created if attribute "pe" is set in
59# .palm.iofiles
60#
61# 2718 2018-01-02 08:49:38Z maronga
[2993]62# bugfix of r2990
63#
64# 2718 2018-01-02 08:49:38Z maronga
[2990]65# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
66#         not in the working directory from where palmrun is called
67#
68# 2718 2018-01-02 08:49:38Z maronga
[2957]69# svfout in the activation string will be replaced now by svfin in case of
70# automatic restarts
71#
72# 2718 2018-01-02 08:49:38Z maronga
[2906]73# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
74# the possible output or input of sky view factors
75#
76# 2718 2018-01-02 08:49:38Z maronga
[2834]77# "fname" renamed to "jobname"
78#
79# 2718 2018-01-02 08:49:38Z maronga
[2799]80# parameters are allowed in output commands (OC:)
81#
82# 2718 2018-01-02 08:49:38Z maronga
[2789]83# bugfix: exit if no queue has been given neither with option -q nor in the
84# configuration file
85#
86# 2718 2018-01-02 08:49:38Z maronga
[2762]87# file connection file from trunk/SCRIPTS is taken by default
88#
89# 2718 2018-01-02 08:49:38Z maronga
[2716]90# Corrected "Former revisions" section
91#
92# 2696 2017-12-14 17:12:51Z kanani
93# Change in file header (GPL part)
94#
95# 2693 2017-12-13 12:33:49Z raasch
[2693]96# replacement of variables given by {{<variable>}} in configuration file is now
97# done in a more general way, variable names are written in small letters
98#
99# 2670 2017-12-06 16:32:19Z raasch
[2670]100# test printouts removed
101#
102# 2669 2017-12-06 16:03:27Z raasch
[2669]103# file attributes in .palm.iofiles restructured, "loc" attribute completely
104# removed,
105# wildcard (*) allowed in .palm.iofiles as file activation string for output
106# files,
107# informative messages in case of missing optional input files shortened
108# bugfix: variable cycle explicitly interpreted with 10 as the number base
109#
110# 2638 2017-11-23 12:44:23Z raasch
[2610]111# use of wildcards in file connection statements enabled
112#
113# 2605 2017-11-09 15:31:46Z raasch
[2605]114# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
115# will not be sent with the job file any more, but copied into the
[2610]116# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]117#
118# 2600 2017-11-01 14:11:20Z raasch
[2600]119# cycle numbers are made three digits wide
120#
121# 2566 2017-10-20 08:50:47Z raasch
[2566]122# execute command for combine_plot_fields added
123# "TEMPDIR" renamed "tempdir"
124# temporary working directory for local batch jobs is created immediately within
125# the user's palmrun call, due to a requirement of the "grid engine" batch
126# system, where the working directory is given with batch directive -wd and must
127# already exist when the job is submitted,
128# informative messages in non-trace mode reduced and partly reformatted
129#
130# 2551 2017-10-18 07:25:11Z raasch
[2551]131# TEMPDIR added as replacement string to be used in batch directives
132#
133# 2512 2017-10-04 08:26:59Z raasch
[2507]134# bugfix for determining cycle numbers of NetCDF input files
135#
136# 2506 2017-09-29 08:30:37Z raasch
[2506]137# option -V added to check for an existing SOURCES_FOR_RUN_... folder
138# host configuration added to SOURCES_FOR_RUN_... folder name
139# host_identifier renamed host_configuration
140# option -W added to allow for job dependencies
141#
142# 2501 2017-09-26 11:41:55Z raasch
[2501]143# default value for number of cores (option -X) set to 1
144# bugfix for mechanism which overwrites configuration file settings with values
145# provided by palmrun options
146#
147# 2499 2017-09-22 16:47:58Z kanani
[2499]148# option -h named configuration identifier
149#
150# 2480 2017-09-19 06:24:14Z maronga
[2480]151# bugfix for last revision
152#
153# 2479 2017-09-19 06:12:16Z raasch
[2479]154# option -A (project account number) added
155#
156# 2422 2017-09-08 08:25:41Z raasch
[2410]157# initial revision
[2380]158#
159#--------------------------------------------------------------------------------#
160# palmrun - script for running PALM jobs on local and remote hosts
161#--------------------------------------------------------------------------------#
162
163
164 
165    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
166
167 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
168                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
169                     # (TOO MANY ARGUMENTS - PROBLEM)
170 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
171
[2610]172 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
173 typeset -i  nr_of_output_files=0
[2380]174 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
175                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
176                           # SCRIPT-OPTION ARGUMENTS
177 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
178 typeset -i  icycle inode ival maxcycle mpi_tasks
179 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
180
181 activation_string_list=""
182 AddFilenames=""
183 combine_plot_fields=true
184 compiler_name=""
185 compiler_name_ser=""
186 compiler_options=""
[3236]187 configuration_identifier="default"
[2501]188 cores=1
[2380]189 cores_atmos=0
190 cores_ocean=0
191 coupled_dist=""
192 cpp_options=""
193 cpumax=0
[2506]194 create_batch_job=false
[2380]195 create_jobfile_only=false
196 create_remote_batch_job=false
197 dashes="  ----------------------------------------------------------------------------"
198 defaultqueue=""
[2506]199 delete_temporary_catalog=true
[2380]200 do_compile=true
201 do_trace=false
202 executable=""
203 execute_command=""
204 execution_error=false
[2762]205 fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]206 global_revision=""
207 hostfile=""
208 hp=""
209 keep_data_from_previous_run=false
210 link_local_input=false
211 link_local_output=false
[2388]212 linker_options=""
[2385]213 local_jobcatalog=""
[2380]214 locat=normal
215 makefile=""
216 max_par_io_str=""
217 prc=$0
218 while [[ $(echo $prc | grep -c "/") != 0 ]]
219 do
220    prc=`echo $prc | cut -f2- -d"/"`
221 done
222 module_calls=""
[2506]223 palmrun_memory=""
[2380]224 palmrun_script_name=$prc
225 openmp=false
[2506]226 previous_job=""
[2479]227 project_account=""
[2380]228 queue=none
[2906]229 read_svf=""
[2380]230 restart_run=false
231 return_address=""
[2385]232 remote_jobcatalog=""
[2380]233 remote_username=""
234 running_in_batch_mode=false
[3313]235 running_in_test_mode=false
[2380]236 run_coupled_model=false
237 run_id=""
[3236]238 run_id_number=""
239 run_identifier=test
[2380]240 silent=false
241 source_list=""
242 source_path=""
[2501]243 tasks_per_node=0
[2380]244 threads_per_task=1
245 transfer_problems=false
[2384]246 user_source_path=""
[2506]247 use_existing_sources_folder=""
[2380]248 use_openmp=false
[3033]249 version="palmrun  1.0 Rev$Rev: 3346 $"
[2380]250 working_directory=`pwd`
251 write_binary=""
[2906]252 write_svf=""
[2380]253
254
255    # ERROR HANDLING IN CASE OF EXIT
[2404]256 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
[2380]257       then
258
259              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
260          (( i = 0 ))
261          while (( i < iec ))
262          do
263             (( i = i + 1 ))
264             printf "\n  *** Execution of ERROR-command:\n"
265             printf "  >>> ${err_command[$i]}\n"
266             eval  ${err_command[$i]}
267          done
[2566]268          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
[3312]269          printf "\n\n+++ palmrun crashed \n\n"
270          exit 1
271       elif [[ $locat != normal ]]
[2380]272       then
[3312]273          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
274          printf "\n+++ palmrun killed by \"^C\" \n\n"
275          exit 2
276       else
[2566]277          printf "\n --> palmrun finished\n\n"
[3312]278          exit 0
[2380]279       fi' exit
280
281
282    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]283 trap 'locat=control_c
284       exit 1
[2380]285      ' 2
286
287
288    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
289    # WHICH WILL BE USED TO START RESTART-JOBS
[3313]290 while  getopts  :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]291 do
292   case  $option  in
293       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]294       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]295       (b)   create_batch_job=true; prc="$prc -b";;
296       (B)   delete_temporary_catalog=false; prc="$prc -B";;
297       (C)   restart_run=true; prc="$prc -C";;
[3236]298       (d)   run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
[2380]299       (F)   create_jobfile_only=true;;
300       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]301       (h)   configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
302       (i)   run_id_number=$OPTARG;;
[2380]303       (j)   running_in_batch_mode=true;;
304       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
[2501]305       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]306       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
307       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
308       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
309       (R)   return_address=$OPTARG;;
310       (s)   source_list=$OPTARG;;
[2501]311       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]312       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
313       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
314       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
315       (v)   silent=true; prc="$prc -v";;
[2506]316       (V)   use_existing_sources_folder="-V";;
[2380]317       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]318       (W)   previous_job=$OPTARG;;
[2380]319       (x)   do_trace=true;set -x; prc="$prc -x";;
[2501]320       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]321       (y)   ocean_file_appendix=true; prc="$prc -y";;
322       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]323       (z)   running_in_test_mode=true;;
[2380]324       (Z)   combine_plot_fields=false; prc="$prc -Z";;
325       (\?)  printf "\n  +++ unknown option $OPTARG \n"
326             printf "\n  --> type \"$0 ?\" for available options \n"
327             locat=parameter;exit;;
328   esac
329 done
330
331
332    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
333    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
334 (( to_shift = $OPTIND - 1 ))
335 shift $to_shift
336
337    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
338 if [[ "$1" = "?" ]]
339 then
340   (printf "\n  *** Description of available palmrun options:\n"
341    printf "\n      Option  Description                              Default-Value"
342    printf "\n        -a    activation string list                   \"\" "
[2479]343    printf "\n        -A    project account number                   ---"
[2380]344    printf "\n        -b    batch-job on local machine               ---"
345    printf "\n        -B    do not delete temporary directory at end ---"
[3025]346    printf "\n        -d    run identifier                           test"
[2380]347    printf "\n        -F    create batch job file only               ---"
[2506]348    printf "\n        -h    host configuration                       \"default\" "
[2380]349    printf "\n        -k    keep data from previous run"
350    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
351    printf "\n        -M    Makefile name                            Makefile"
352    printf "\n        -O    threads per openMP task                  ---"
353    printf "\n        -q    queue                                    \"$queue\" "
354    printf "\n        -s    filenames of routines to be compiled     \"\" "
355    printf "\n              must end with .f, .f90, .F, or .c !"
356    printf "\n              use \"..\" for more than one file and wildcards"
357    printf "\n              -s LM compiles all locally modified files"
358    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
[2384]359    printf "\n        -T    tasks per node                           ---"
[2380]360    printf "\n        -u    username on remote machine               \"\" "
361    printf "\n        -v    no prompt for confirmation               ---"
[2506]362    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
[2380]363    printf "\n        -w    maximum parallel io streams              as given by -X"
[2506]364    printf "\n        -W    name of job to wait for                  ---"
[2380]365    printf "\n        -x    tracing of palmrun for debug purposes    ---"
366    printf "\n        -X    # of processors (on parallel machines)   1"
367    printf "\n        -y    add appendix \"_O\" to all local output"
368    printf "\n              files (ocean precursor runs followed by"
369    printf "\n              coupled atmosphere-ocean runs)           ---"
370    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
371    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
372    printf "\n        -Z    skip combine_plot_fields at the end of      "
373    printf "\n              the simulation                           ---"
374    printf "\n "
375    printf "\n      Possible values of positional parameter <modus>:"
376    printf "\n        \"?\"       -  this outline \n\n") | more
377    exit
378 elif [[ "$1" != "" ]]
379 then
380    printf "\n  +++ positional parameter $1 unknown \n"
381    locat=parameter; exit
382 fi
383
384
385
386    # SHORT STARTING MESSAGE
387 printf "\n*** $version "
388 printf "\n    will be executed.     Please wait ..."
389
390
[3236]391    # FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
392 export fname=$run_identifier
393 export jobname=$run_identifier
[2834]394
395
[2506]396    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]397 config_file=.palm.config.$configuration_identifier
398 sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]399
400
401    # CHECK, IF CONFIGURATION FILE EXISTS
402 if [[ ! -f $config_file ]]
403 then
404    printf "\n\n  +++ configuration file: "
405    printf "\n           $config_file"
406    printf "\n      does not exist"
407    locat=connect; exit 
408 fi
409
410
[2762]411    # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
412 if [[ -f .palm.iofiles ]]
413 then
[3236]414
415       # CHECK VERSION MISMATCH
416    if [[ $running_in_batch_mode != true ]]
417    then
418       if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
419       then
420          printf "\n\n  +++ WARNING: A file connection file has been found in your"
421          printf "\n               working directory, but its revision does not match"
422          printf "\n               the revision of the default (trunk) version."
[3294]423          printf "\n               You may need to update your connection file"
424          printf "\n               \"${working_directory}/.palm.iofiles\" !"
[3236]425       fi
426    fi
427
[2762]428    fileconnection_file=.palm.iofiles
[3236]429
[2762]430 fi
431
432
[2380]433    # CHECK, IF FILE CONNECTION FILE EXISTS
434 if [[ ! -f $fileconnection_file ]]
435 then
436    printf "\n\n  +++ file connection file: "
437    printf "\n           $fileconnection_file"
438    printf "\n      does not exist"
439    locat=connect; exit 
440 fi
441
442
[2404]443    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
444 if [[ "$activation_string_list" = "" ]]
445 then
446    printf "\n\n  +++ no activation string list given: "
447    printf "\n        please set palmrun option \"-a\" "
448    locat=palmrun_option; exit 
449 fi
450
451
452    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
453 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
454 then
455    write_binary=true
456 else
457    write_binary=false
458 fi
459
[2906]460    # SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
461 if [[ $(echo $activation_string_list | grep -c "svfout") != 0 ]]
462 then
463    write_svf=true
464 else
465    write_svf=false
466 fi
[2404]467
[2906]468    # SET VARIABLE TO ACTIVATE READING OF SVF DATA
469 if [[ $(echo $activation_string_list | grep -c "svfin") != 0 ]]
470 then
471    read_svf=true
472 else
473    read_svf=false
474 fi
475
476
[2380]477    # READ AND EVALUATE THE CONFIGURATION-FILE
478 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
479
480    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
481 while  read line
482 do
483
484       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
485    eval  line=\"$line\"
486
487
488       # INTERPRET THE LINE
489    if [[ "$(echo $line)" = "" ]]
490    then
491
492          # EMPTY LINE, NO ACTION
493       continue
494
495    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
496    then
497
498          # LINE IS A COMMENT LINE
499       continue
500
501    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
502    then
503
504          # LINE DEFINES AN ENVIRONMENT-VARIABLE
505       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
506       value=`echo $line | cut -d" " -s -f2-`
507
508
509          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
510          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
511          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
512          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
513          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
514          # CONFIGURATION-FILE.
515       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
516       then
517          eval  export  $var="\$value"
518
519             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
520          if [[ $do_trace = true ]]
521          then
522             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
523          fi
524       fi
525
526    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
527    then
528
529          # LINE DEFINES BATCH-DIRECTIVE
530       (( ibd = ibd + 1 ))
531       line=$(echo $line | cut -c4-)
532       batch_directive[$ibd]="$line"
533
534    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
535    then
536
537          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
538          # REMOTE TO A LOCAL HOST
539       (( ibdt = ibdt + 1 ))
540       line=$(echo $line | cut -c5-)
541       batch_directive_transfer[$ibdt]="$line"
542
543    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
544    then
545
546          # LINE DEFINES ERROR-COMMAND
547       (( iec = iec + 1 ))
548       line=$(echo $line | cut -c4-)
549       err_command[$iec]="$line"
550
551    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
552    then
553
554          # LINE DEFINES INPUT-COMMAND
555       (( iic = iic + 1 ))
556       line=$(echo $line | cut -c4-)
557       in_command[$iic]="$line"
558
559    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
560    then
561
562          # LINE DEFINES OUTPUT-COMMAND
563       (( ioc = ioc + 1 ))
564       line=$(echo $line | cut -c4-)
565       out_command[$ioc]="$line"
566
567    else
568
569          # SKIP ALL OTHER LINES
570       continue
571
572    fi
573
574 done < $config_file
575
576
577    # CHECK SETTING OF REQUIRED PARAMETERS
[3043]578 if [[ "$fast_io_catalog" = "" ]]
579 then
580    printf "\n  +++ no fast_io_catalog found in $config_file"
581    printf "\n      Please add line \"fast_io_catalog ...\" to that file."
582    locat=config_file; exit
583 fi
[2380]584 if [[ "$compiler_name" = "" ]]
585 then
586    printf "\n  +++ no compiler name found in $config_file"
587    printf "\n      Please add line \"compiler_name ...\" to that file."
588    locat=config_file; exit
589 fi
590 if [[ "$compiler_name_ser" = "" ]]
591 then
592    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
593    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
594    locat=config_file; exit
595 fi
596 if [[ "$compiler_options" = "" ]]
597 then
598    printf "\n  +++ no compiler options found in $config_file"
599    printf "\n      Please add line \"compiler_options ...\" to that file."
600    locat=config_file; exit
601 fi
[2388]602 if [[ "$linker_options" = "" ]]
[2380]603 then
[2388]604    printf "\n  +++ no linker options found in $config_file"
605    printf "\n      Please add line \"linker_options ...\" to that file."
[2380]606    locat=config_file; exit
607 fi
608 if [[ "$execute_command" = "" ]]
609 then
610    printf "\n  +++ no execute command found in $config_file"
611    printf "\n      Please add line \"execute_command ...\" to that file."
612    locat=config_file; exit
613 fi
614
615 if [[ "$hostfile" != "" ]]
616 then
617    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
618    then
619       printf "\n  +++ no hostfile \"$hostfile\" found"
[3151]620       printf "\n      Please check line \"hostfile ...\" in $config_file"
[2380]621       locat=config_file; exit   
622    fi
623 fi
624
625
626    # DETERMINE THE CALL STATUS
627 if [[ "$return_address" != "" ]]
628 then
629 
630       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
631       # BATCH MODE AND ...
632    running_on_remote=true
633 
634 else
635
636       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
637     if [[ "$remote_ip" != "" ]]
638     then
639
640           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
641        create_remote_batch_job=true
642
[3132]643           # CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
644        if [[ "$remote_jobcatalog" = "" ]]
645        then
646           printf "\n  +++ no remote jobcatalog found in $config_file"
647           printf "\n      Please add line \"remote_jobcatalog ...\" to that file."
648           locat=config_file; exit
649        fi
650 
651
[2380]652     fi
653     running_on_remote=false
654 fi
655
656
657
658    # READ AND EVALUATE THE I/O-FILE LIST
659 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
660
661    # READ THE FILE CONNECTION FILE LINE BY LINE
662 while  read line
663 do
664
[2669]665       # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
666    line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"`
[2380]667
668       # INTERPRET THE LINE
669    if [[ "$(echo $line)" = "" ]]
670    then
671          # EMPTY LINE, NO ACTION
672       continue
673
674    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
675    then
676
677          # LINE IS A COMMENT LINE
678       true
679
680    else
681
682          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
683          # s2a: in/out - field
[2669]684          # s2b: action - field (optional)
685       s1=`echo "$line" | cut -d" " -f1`
686       s2=`echo "$line" | cut -d" " -s -f2`
[2380]687       if [[ $(echo $s2 | grep -c ":") = 0 ]]
688       then
[2669]689          s2a=$s2
[2380]690          s2b=""
691       else
[2669]692          s2a=`echo $s2 | cut -d":" -f1`
693          s2b=`echo $s2 | cut -d":" -f2`
[2380]694       fi
[2669]695       s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'`
696       s4=`echo "$line" | cut -d" " -s -f4`
697       eval s4=\"$s4\"    # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
698       s5=`echo "$line" | cut -d" " -s -f5`
699       s6=`echo "$line" | cut -d" " -s -f6`
[2380]700
701       
702          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
703          # INPUT- OR OUTPUT-LIST.
704          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
705          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]706          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]707          # IS NOT CHECKED AND STORED.
[2610]708       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
[2669]709       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
[2380]710       then
711          found=false
712          for  actual  in  $activation_string_list
713          do
714             for  formal  in  $s3
715             do
716                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
717             done
718          done
719          if [[ $found = true ]]
720          then
721             (( iin = iin + 1 ))
[2669]722             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]723             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]724             if [[ "$s2a" = inopt ]]
725             then
726                optin_pre[$iin]=yes
727             else
728                optin_pre[$iin]=no
729             fi 
[2605]730
731                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
732                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]733             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
[2605]734             then
[2610]735                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]736             fi
737
[2610]738                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
739                # THE WILDCARD FROM THE ENDING
740             if [[ "${s5: -1}" = "*" ]]
741             then
[2669]742                if [[ "$s2b" = "di" ]]
[2610]743                then
744                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
745                   printf "\n        see file \"$fileconnection_file\", line"
746                   printf "\n$line"
747                   locat=iofiles_file; exit
748                fi
749                multin[$iin]=true
750                string=${endin_pre[$iin]}
751                endin_pre[$iin]="${string%?}"
752             else
753                multin[$iin]=false
754             fi
[2380]755          fi
[2669]756       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
[2380]757       then
758          found=false
759          for  actual  in  $activation_string_list
760          do
761             for  formal  in  $s3 
762             do
[2670]763                [[ $actual = $formal  ||  $formal = wildcard  ]]  &&  found=true
[2380]764             done
765          done
766          if [[ $found = true ]]
767          then
768             (( iout = iout + 1 ))
[2669]769             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]770             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
771
[2669]772                # CHECK IF WILDCARD IS USED AS ACTIVATION STRING
773                # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
774             if [[ $formal = wildcard  ]]
775             then
776                warnout_pre[$iout]=false
777             else
778                warnout_pre[$iout]=true
779             fi
780
[2610]781                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
782                # THE WILDCARD FROM THE LOCAL FILENAME
783             if [[ "${s1: -1}" = "*" ]]
784             then
[2669]785                if [[ "$s2b" = "di" ]]
[2610]786                then
787                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
788                   printf "\n        see file \"$fileconnection_file\", line"
789                   printf "\n$line"
790                   locat=iofiles_file; exit
791                fi
792                multout[$iout]=true
793                string=${localout_pre[$iout]}
794                localout_pre[$iout]="${string%?}"
795             else
796                multout[$iout]=false
797             fi
[2380]798          fi
[2669]799       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
[2380]800       then
[2669]801          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
802          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]803          locat=connect; exit
804       fi
805       IFS="$IFSALT"
806    fi
807
808 done < $fileconnection_file
809
810
811
[2501]812    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]813 [[ "$palmrun_memory" != "" ]]  &&  memory=$palmrun_memory
814 [[ "$palmrun_cpumax" != "" ]]  &&  cpumax=$palmrun_cpumax
815 [[ "$palmrun_cores"  != "" ]]  &&  cores=$palmrun_cores
[2501]816 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
817 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
818
819
820
[2380]821      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
822 if [[ $run_coupled_model = true ]] 
823 then
824
825    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
826    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
827
828    if (( $cores_ocean + $cores_atmos != $cores ))
829    then
830
831       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
832       printf "\n      PEs (total)     : $cores"
833       printf "\n      PEs (atmosphere): $cores_atmos"
834       printf "\n      PEs (ocean)     : $cores_ocean"
835       locat=coupling; exit
836
837    fi
838
839 fi
840
841
842    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
843    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
844    # FOLDER
845 if [[ $running_in_batch_mode = true ]]
846 then
847 
[2506]848    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]849    then
[2506]850       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]851       printf "\n      Please check the output of the palmrun-call"
852       printf "\n      that you did on your local host."
853       locat=SOURCES_FOR_RUN; exit
854    fi
855
856 else
857
858       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
859       # AUTOMATIC RESTART RUN
860       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
861    if [[ $restart_run = false ]]
862    then
863
864          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
865          # THE LOCAL HOST
866       if [[ ! -d $source_path ]]
867       then
868          printf "\n\n  +++ source path \"$source_path\" on local host"
869          printf "\n      \"$(hostname)\" does not exist"
870          locat=source_path; exit
871       fi
872
[2990]873       rm -rf   ${base_directory}/${sources_for_run_catalog}
874       mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]875
876       if [[ "$source_list" = LM ]]
877       then
878
879             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
880          source_list=""
881          cd  $source_path
882
883
[2512]884             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
885          if [[ ! -d ../.svn ]]
[2380]886          then
887             printf "\n\n  +++ source directory"
888             printf "\n         \"$source_path\" "
889             printf "\n         is not under control of \"subversion\"."
[2512]890             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
[2380]891          fi
892
893
894             # LIST ALL MODIFIED SOURCE CODE FILES
895          Filenames=""
[2404]896          svn status  >  tmp_svnstatus
[2380]897          while  read line
898          do
899             firstc=`echo $line | cut -c1`
900             if [[ $firstc = M  ||  $firstc = "?" ]]
901             then
902                Name=`echo "$line" | cut -c8-`
903                extension=`echo $Name | cut -d. -f2`
904                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
905                then
906                   Filenames="$Filenames "$Name
907                fi
908             fi
[2404]909          done < tmp_svnstatus
910          rm -rf  tmp_svnstatus
[2380]911
912
913             # COPY FILES TO SOURCES_FOR_RUN_...
914          for  filename  in  $Filenames
915          do
[2990]916             cp  $filename  ${base_directory}/${sources_for_run_catalog}
[2380]917             source_list=$source_list"$filename "
918          done
919
920          cd -  > /dev/null
921
922
923          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
924       elif [[ "$source_list" != "" ]]
925       then
926
927          cd  $source_path
928
929          for  filename  in  $source_list
930          do
931
932                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
933             if [[ $(echo $filename | grep -c "/") != 0 ]]
934             then
935                printf "\n  +++ source code file:  $filename"
936                printf "\n      must not contain (\"/\") "
937                locat=source; exit
938             fi
939
940             if [[ ! -f $filename ]]
941             then
942                printf "\n  +++ source code file:  $filename"
943                printf "\n      does not exist"
944                locat=source; exit
945             else
[2990]946                cp  $filename  ${base_directory}/${sources_for_run_catalog}
[2380]947             fi
948
949          done
950
951          cd -  > /dev/null
952
953       fi
954
955          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
956       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
957       if [[ ! -f $makefile ]]
958       then
959          printf "\n  +++ file \"$makefile\" does not exist"
960          locat=make; exit
961       else
[2990]962          cp  $makefile  ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]963       fi
964
965
966          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]967       if [[ "$user_source_path" != "" ]]
[2380]968       then
969
970             # DOES THE DIRECTORY EXIST?
[2384]971          if [[ ! -d $user_source_path ]]
[2380]972          then
973
974             printf "\n\n  *** INFORMATIVE: additional source code directory"
[2384]975             printf "\n      \"$user_source_path\" "
[2380]976             printf "\n      does not exist or is not a directory."
977             printf "\n      No source code will be used from this directory!\n"
[2384]978             user_source_path=""
[2380]979             if [[ $silent == false ]]
980             then
981                sleep 2
982             fi
983
984          else
985
[2384]986             cd $user_source_path
[2380]987
988             Names=$(ls -1 *.f90 2>&1)
989             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
990             Names=$(ls -1 *.F90 2>&1)
991             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
992             Names=$(ls -1 *.F 2>&1)
993             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
994             Names=$(ls -1 *.f 2>&1)
995             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
996             Names=$(ls -1 *.c 2>&1)
997             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
998
999             cd -  > /dev/null
[2990]1000             cd  ${base_directory}/${sources_for_run_catalog}
[2380]1001
1002                # COPY MAKEFILE IF EXISTING
[2384]1003             if [[ -f $user_source_path/Makefile ]]
[2380]1004             then
1005                printf "\n\n  *** user Makefile from directory"
[2384]1006                printf "\n      \"$user_source_path\" is used \n"
[2380]1007                if [[ $silent == false ]]
1008                then
1009                   sleep 1
1010                fi
[2384]1011                cp  $user_source_path/Makefile  .
[2380]1012             fi
1013
1014             for  filename  in  $AddFilenames
1015             do
1016                if [[ -f $filename ]]
1017                then
1018                   printf "\n  +++ source code file \"$filename\" found in additional"
[2384]1019                   printf "\n      source code directory \"$user_source_path\" "
[2380]1020                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
1021                   printf "\n      from directory \"$source_path\"."
1022                   locat=source; exit
1023                fi
1024
[2384]1025                cp  $user_source_path/$filename  .
[2380]1026                source_list="$source_list $filename"
1027
1028                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
1029                if [[ $(grep -c $filename Makefile) = 0 ]]
1030                then
1031                   printf "\n\n  +++ user file \"$filename\" "
1032                   printf "\n      is not listed in Makefile \n"
1033                   locat=source; exit
1034                fi
1035             done
1036             cd -  > /dev/null
1037          fi
1038       fi
1039
1040          # COPY CONFIGURATION FILES
[2990]1041       cp  $config_file  ${base_directory}/${sources_for_run_catalog}
1042       cp  $fileconnection_file  ${base_directory}/${sources_for_run_catalog}
[2380]1043
1044          # COPY SHELLSCRIPTS
[2990]1045       cp  ${source_path}/../SCRIPTS/palmrun    ${base_directory}/${sources_for_run_catalog}
1046       cp  ${source_path}/../SCRIPTS/batch_scp  ${base_directory}/${sources_for_run_catalog}
[2380]1047
1048    fi
1049
1050 fi
1051
[2605]1052
[2380]1053    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1054    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1055 if [[ "$global_revision" = "" ]]
1056 then
1057    global_revision=`svnversion $source_path  2>/dev/null`
1058    global_revision="Rev: $global_revision"
1059 fi
1060
1061
1062    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1063 if [[ -n $cores ]]
1064 then
1065
1066       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1067       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]1068    if [[ $tasks_per_node = 0 ]]
[2380]1069    then
[3025]1070       if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1071       then
1072          printf "\n"
1073          printf "\n  +++ option \"-T\" (tasks per node) is missing"
1074          printf "\n      set -T option or define tasks_per_node in the config file"
1075          locat=tasks_per_node; (( iec = 0 )); exit
1076       else
1077             # DEFAULT FOR INTERACTIVE RUN
1078          tasks_per_node=$cores
1079       fi
[2380]1080    fi
1081
1082    if (( cores < tasks_per_node ))
1083    then
1084       printf "\n"
1085       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1086       printf "\n      given values: -T $tasks_per_node  -X $cores"
1087       locat=tasks_per_node; (( iec = 0 )); exit
1088    fi
1089
1090    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1091    (( mpi_tasks = cores / threads_per_task ))
1092    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
1093    (( ii = cores / tasks_per_node ))
1094    (( remaining_cores =  cores - ii * tasks_per_node ))
1095    if (( remaining_cores > 0 ))
1096    then
1097       printf "\n"
1098       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
1099       printf "\n      divisor of the total number of cores (option \"-X\")"
1100       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1101       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1102       (( nodes = nodes + 1 ))
1103    fi
1104
1105 fi
1106
1107
1108    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1109 if [[ "$maximum_parallel_io_streams" = "" ]]
1110 then
1111    maximum_parallel_io_streams=$cores
1112 fi
1113
1114
1115    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1116 if [[ "$scp_port" != "" ]]
1117 then
1118    PORTOPT="-P $scp_port"
1119    SSH_PORTOPT="-p $scp_port"
1120 fi
1121
1122
1123    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1124    # CONFIG-FILE
1125 if [[ "$ssh_key" != "" ]]
1126 then
1127    ssh_key="-i $HOME/.ssh/$ssh_key"
1128 fi
1129
1130
1131    # SET QUEUE, IF NOT GIVEN
1132 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1133 then
1134
1135    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
1136    then
1137       printf "\n"
1138       printf "\n  +++ no default queue given in configuration file and no queue"
1139       printf "\n      given with option -q"
[2789]1140       locat=queue; exit
[2380]1141    fi
1142    if [[ $queue = none ]]
1143    then
1144       queue=$defaultqueue
1145    fi
1146
1147 fi
1148
1149
1150    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1151    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1152 (( i = 0 ))
[2610]1153 (( nr_of_input_files = 0 ))
[2380]1154 while (( i < iin ))
1155 do
1156    (( i = i + 1 ))
1157
1158       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1159       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]1160    if [[ "${actionin_pre[$i]}" = di ]]
[2380]1161    then
[2610]1162       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]1163    else
[3236]1164       eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]1165    fi
1166
[2610]1167
[2380]1168       # CHECK IF FILE EXISTS
1169    if ! ls $filename* 1>/dev/null 2>&1
1170    then
1171
[2669]1172          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1173       if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]1174       then
1175          printf "\n\n  +++ INPUT-file: "
[2610]1176          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
[2380]1177          then
1178             printf "\n           $filename"
1179          else
[2610]1180             printf "\n           $filename.${extin_pre[$i]}"
[2380]1181          fi
1182          printf "\n      does not exist\n"
1183          locat=input; exit
1184       else
[2610]1185          (( nr_of_input_files = nr_of_input_files + 1 ))
1186          localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]1187          optin[$nr_of_input_files]="${optin_pre[$i]}"
1188          actionin[$nr_of_input_files]="unavailable"
[2610]1189          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1190          endin[$nr_of_input_files]="${endin_pre[$i]}"
1191          extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]1192       fi
[2605]1193
[2380]1194    else
1195
[3236]1196          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1197          # ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1198          # ENDINGS
[2610]1199       if [[ "${multin[$i]}" = true ]]
1200       then
1201             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1202          ls -1 -d ${filename}    >   filelist  2>/dev/null
1203          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
1204          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null
[2380]1205
[2610]1206          endings=""
1207          while  read line
1208          do
1209                 # filename without path (i.e. after the last "/")
1210              basefilename=$(basename ${line})
[2380]1211
[2610]1212                 # check if there is an extension and remove it
1213              ext=${basefilename##*.}
1214              if [[ "$ext" = "${extin_pre[$i]}" ]]
1215              then
1216                 basefilename=${basefilename%.*}
1217              fi
[2380]1218
[2610]1219                 # check for an existing cycle number and remove it
1220              cycle=${basefilename##*.}
1221              if [[ $cycle =~ ^-?[0-9]+$ ]]
1222              then
1223                 basefilename=${basefilename%.*}
1224              fi
[2600]1225
[3236]1226                 # remove the run_identifier from the beginning
1227              length_run_identifier=${#run_identifier}
1228              ending=${basefilename:${length_run_identifier}}
[2610]1229
1230                 # remove the ending given in the .iofiles from the beginning
1231              endingstring="${endin_pre[$i]}"
1232              length_ending=${#endingstring}
1233              ending=${ending:${length_ending}}
1234
1235              if [[ "$ending" = "" ]]
[2600]1236              then
[2610]1237                    # standard ending as given in the .iofiles
1238                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
1239                 then
1240                    endings="$endings DEFAULT"
1241                 fi
[2600]1242              else
[2610]1243                    # ending must start with "_", otherwise its a different file
1244                 if [[ "${ending:0:1}" = "_" ]]
1245                 then
1246                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
1247                    then
1248                       endings="$endings $ending"
1249                    fi
1250                 fi
[2600]1251              fi
[2610]1252 
1253          done <filelist
[2380]1254
[2610]1255          rm filelist
[2380]1256
[2600]1257       else
[2610]1258
1259             # SINGLE NAME
1260          endings=DEFAULT
1261
[2600]1262       fi
1263
[2610]1264          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1265       for  ending  in  $endings
1266       do
1267
1268             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1269          if [[ $ending = DEFAULT ]]
[2380]1270          then
[2610]1271             ending=""
1272          fi
1273
1274             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1275          (( nr_of_input_files = nr_of_input_files + 1 ))
1276          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]1277          optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]1278          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1279          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1280          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1281          extin[$nr_of_input_files]="${extin_pre[$i]}"
1282
1283
1284             # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1285             # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1286          if [[ "${actionin[$nr_of_input_files]}" = di ]]
1287          then
1288             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]1289          else
[3236]1290             eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]1291          fi
[2610]1292
1293             # DETERMINE THE FILE'S CYCLE NUMBER
1294          (( maxcycle = 0 ))
1295          ls -1 -d $filename    >   filelist  2>/dev/null
1296          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1297          while  read line
1298          do
1299                 # filename without path (i.e. after the last "/")
1300              basefilename=$(basename ${line})
1301   
1302                 # check if there is an extension
1303              extension=${basefilename##*.}
1304              if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1305              then
1306                 basefilename=${basefilename%.*}
1307              fi
1308   
1309                 # check for an existing cycle number
1310              cycle=${basefilename##*.}
1311              if [[ $cycle =~ ^-?[0-9]+$ ]]
1312              then
[2669]1313                    # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1314                    # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1315                 (( icycle = $((10#$cycle)) ))
[2610]1316              else
1317                 (( icycle = 0 ))
1318              fi
1319   
1320              if (( icycle > maxcycle ))
1321              then
1322                 (( maxcycle = icycle ))
1323   
1324                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1325                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1326                 if [[ $(echo $cycle | cut -c1) = 0 ]]
1327                 then
1328                    leading_zero=true
1329                 else
1330                    leading_zero=false
1331                 fi
1332              fi
1333   
1334          done <filelist
1335          rm filelist
1336   
1337             # MAKE CYCLE NUMBER THREE DIGITS WIDE
1338          if [[ $leading_zero = true ]]
[2380]1339          then
[2610]1340             cyclestring=`printf "%03d" $maxcycle`
1341          else
1342             cyclestring=$maxcycle
[2380]1343          fi
[2610]1344   
1345             # APPEND CYCLE NUMBER TO FILENAME
1346          if (( maxcycle > 0 ))
[2380]1347          then
[2610]1348             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1349             then
1350                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1351             else
1352                filename=${filename}.$cyclestring
1353             fi
[2380]1354          else
[2610]1355             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1356             then
1357                filename=${filename}.${extin[$nr_of_input_files]}
1358             fi
[2380]1359          fi
[2610]1360         
1361             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1362             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1363          absnamein[$nr_of_input_files]=$filename
1364          if (( maxcycle > 0 ))
[2380]1365          then
[2610]1366             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1367             then
1368                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1369             else
[3236]1370                frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]1371             fi
[2380]1372          else
[2610]1373             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1374             then
1375                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1376             else
[3236]1377                frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]1378             fi
[2380]1379          fi
1380
[2610]1381       done
1382
[2380]1383    fi
[2610]1384
[2380]1385 done
1386
[2610]1387
[2380]1388    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1389    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1390    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
[2610]1391    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]1392    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1393    # REMOTE HOST)
1394 (( i = 0 ))
1395 while (( i < iout ))
1396 do
1397    (( i = i + 1 ))
[2610]1398    if [[ ! ( $running_on_remote = true  &&  ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]1399    then
[2610]1400       if [[ "${actionout_pre[$i]}" = tr ]]
[2380]1401       then
[2610]1402          actionout_pre[$i]=""
1403       elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]1404       then
[2610]1405          actionout_pre[$i]=pe
1406       elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]1407       then
[2610]1408          actionout_pre[$i]=a
[2380]1409       fi
1410       (( maxcycle = 0 ))
[3236]1411       eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]1412       eval catalogname=${pathout_pre[$i]}
[2380]1413       if ! ls $filename* 1>/dev/null 2>&1
1414       then
1415     
1416             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1417          if  cat /dev/null > $filename 
1418          then
1419             rm  $filename
1420          else
1421
1422                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1423                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1424             if [[ ! -d $catalogname ]]
1425             then
1426                if  mkdir -p  $catalogname
1427                then
1428                   printf "\n\n  *** directory:"
1429                   printf "\n           $catalogname"
1430                   printf "\n      was created\n"
1431                else
1432                   printf "\n\n  +++ OUTPUT-file:"
1433                   printf "\n           $filename"
1434                   printf "\n      cannot be created, because directory does not exist"
1435                   printf "\n      and cannot be created either"
1436                   printf "\n"
1437                   locat=output  ; exit
1438                fi 2>/dev/null
1439             else
1440                printf "\n\n  +++ OUTPUT-file:"
1441                printf "\n           $filename"
1442                printf "\n      cannot be created, although directory exists"
1443                printf "\n"
1444                locat=output  ; exit
1445             fi
1446          fi 2>/dev/null
1447
1448       fi
1449
1450    fi
1451 done
1452
1453
1454    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1455 if [[ $running_in_batch_mode = false ]]
1456 then
[3236]1457    run_id_number=$RANDOM
1458    run_id=${run_identifier}.$run_id_number
[2380]1459
[3236]1460    tempdir=$fast_io_catalog/$run_id
[3346]1461
1462       # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1463    export job_id=$run_id
1464
[2380]1465 fi
1466
1467
1468    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1469 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1470 then
1471
1472       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1473    if [[ $ibd = 0 ]]
1474    then
1475       printf "\n"
1476       printf "\n  +++ no batch directives found in configuration file"
1477       locat=config_file_batch_directives; (( iec = 0 )); exit
1478    fi
1479
1480       # CHECK IF CPUTIME IS GIVEN FOR JOB
1481    done=false
[2384]1482    cputime=$cpumax
[2380]1483    while [[ $done = false ]]
1484    do
[2384]1485       if (( cputime == 0 ))
[2380]1486       then
1487          printf "\n  +++ cpu-time is undefined"
1488          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1489          printf "\n  >>> "
[2384]1490          read  cputime   1>/dev/null  2>&1
[2380]1491       else
1492          done=true
1493       fi
1494    done
[2420]1495    cpumax=$cputime
[2380]1496
1497       # CHECK THE MEMORY DEMAND
1498    done=false
1499    while [[ $done = false ]]
1500    do
1501       if (( memory == 0 ))
1502       then
1503          printf "\n  +++ memory demand is undefined"
1504          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1505          printf "\n  >>> "
1506          read  memory  1>/dev/null  2>&1
1507       else
1508          done=true
1509       fi
1510    done
1511
1512       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1513    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1514    then
1515       while [[ -z $remote_username ]]
1516       do
[2420]1517          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]1518          printf "\n  >>> Please type username:"
1519          printf "\n  >>> "
1520          read  remote_username
1521       done
1522    fi
1523
1524 else
1525
[2420]1526    if [[ $running_in_batch_mode = false ]]
1527    then
1528       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1529       cpumax=$cputime
1530    else
1531       cputime=$cpumax
1532    fi
[2380]1533
1534 fi
1535
1536
1537    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1538 (( cpu_hours  = cputime / 3600 ))
1539 (( resttime = cputime - cpu_hours * 3600 ))
1540 (( cpu_minutes  = resttime / 60 ))
1541 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1542 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1543
1544
1545    # OUTPUT OF THE PALMRUN-HEADER
1546 calltime=$(date)
1547 printf "\n"
1548 printf "#------------------------------------------------------------------------# \n"
1549 printf "| %-35s%35s | \n" "$version" "$calltime"
[3151]1550 printf "| %-35s%35s | \n" "PALM code    $global_revision" " "
[2380]1551 printf "|                                                                        | \n"
1552 column1="called on:"; column2=$(hostname)
1553 printf "| %-25s%-45s | \n" "$column1" "$column2"
1554 if [[ $create_remote_batch_job = true ]]
1555 then
[3236]1556    column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]1557 else
1558    if [[ $running_on_remote = true ]]
1559    then
[3236]1560       column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]1561    else
[3236]1562       column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]1563    fi
1564 fi
1565 printf "| %-25s%-45s | \n" "$column1" "$column2"
1566
1567 column1="running in:"
1568 if [[ $running_in_batch_mode = true ]]
1569 then
1570    column2="batch job mode"
1571 else
1572    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1573    then
1574       column2="job creation mode"
1575    else
1576       column2="interactive run mode"
1577    fi
1578 fi
1579 printf "| %-25s%-45s | \n" "$column1" "$column2"
1580
[2479]1581 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1582 then
[2480]1583    if [[ "$project_account" != "" ]]
[2479]1584    then
1585       column1="project account number:"
1586       column2="$project_account"
1587       printf "| %-25s%-45s | \n" "$column1" "$column2"
1588    fi
1589 fi
1590
[2380]1591 if [[ -n $cores ]]
1592 then
1593    if [[ $run_coupled_model = false ]]
1594    then
1595       column1="number of cores:"; column2=$cores
1596    else
1597       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1598    fi
1599    printf "| %-25s%-45s | \n" "$column1" "$column2"
1600 fi
1601 if [[ -n $tasks_per_node ]]
1602 then
1603    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1604    printf "| %-25s%-45s | \n" "$column1" "$column2"
1605    if (( remaining_cores > 0 ))
1606    then
1607       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1608       printf "| %-25s%-45s | \n" "$column1" "$column2"
1609    fi
1610 fi
1611 if [[ $maximum_parallel_io_streams != $cores ]]
1612 then
1613    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1614    printf "| %-25s%-45s | \n" "$column1" "$column2"
1615 fi
1616 if [[ $use_openmp = true ]]
1617 then
1618    column1="threads per task:"; column2="$threads_per_task"
1619    printf "| %-25s%-45s | \n" "$column1" "$column2"
1620 fi
[2384]1621 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1622 then
[2506]1623    column1="memory demand / PE":; column2="$memory MB"
1624    printf "| %-25s%-45s | \n" "$column1" "$column2"
[2384]1625    column1="job cpu time (h:m:s):"; column2="$timestring"
1626    printf "| %-25s%-45s | \n" "$column1" "$column2"
1627 fi
[2380]1628 printf "|                                                                        | \n"
1629 if [[ "$source_list" != "" ]]
1630 then
1631    if [[ "$make_options" != "" ]]
1632    then
1633       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1634       printf "| %-25s%-45s | \n" "$column1" "$column2"
1635       line=$(echo "$make_options" | cut -c46-)
1636       while [[ "$line" != "" ]]
1637       do
1638          column1=""
1639          column2=$(echo "$line" | cut -c-45)
1640          printf "| %-25s%-45s | \n" "$column1" "$column2"
1641          line=$(echo "$line" | cut -c46-)
1642       done
1643    fi
1644 fi
1645
1646 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1647 printf "| %-25s%-45s | \n" "$column1" "$column2"
1648 line=$(echo "$cpp_options" | cut -c46-)
1649 while [[ "$line" != "" ]]
1650 do
1651    column1=""
1652    column2=$(echo "$line" | cut -c-45)
1653    printf "| %-25s%-45s | \n" "$column1" "$column2"
1654    line=$(echo "$line" | cut -c46-)
1655 done
1656
1657 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1658 printf "| %-25s%-45s | \n" "$column1" "$column2"
1659 line=$(echo "$compiler_options" | cut -c46-)
1660 while [[ "$line" != "" ]]
1661 do
1662    column1=""
1663    column2=$(echo "$line" | cut -c-45)
1664    printf "| %-25s%-45s | \n" "$column1" "$column2"
1665    line=$(echo "$line" | cut -c46-)
1666 done
1667
[2388]1668 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
[2380]1669 printf "| %-25s%-45s | \n" "$column1" "$column2"
[2388]1670 line=$(echo "$linker_options" | cut -c46-)
[2380]1671 while [[ "$line" != "" ]]
1672 do
1673    column1=""
1674    column2=$(echo "$line" | cut -c-45)
1675    printf "| %-25s%-45s | \n" "$column1" "$column2"
1676    line=$(echo "$line" | cut -c46-)
1677 done
1678
1679 if [[ "$login_init_cmd" != "" ]]
1680 then
1681    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1682    printf "| %-25s%-45s | \n" "$column1" "$column2"
1683    line=$(echo "$login_init_cmd" | cut -c46-)
1684    while [[ "$line" != "" ]]
1685    do
1686       column1=""
1687       column2=$(echo "$line" | cut -c-45)
1688       printf "| %-25s%-45s | \n" "$column1" "$column2"
1689       line=$(echo "$line" | cut -c46-)
1690    done
1691 fi
1692
1693 if [[ "$module_commands" != "" ]]
1694 then
1695    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1696    printf "| %-25s%-45s | \n" "$column1" "$column2"
1697    line=$(echo "$module_commands" | cut -c46-)
1698    while [[ "$line" != "" ]]
1699    do
1700       column1=""
1701       column2=$(echo "$line" | cut -c-45)
1702       printf "| %-25s%-45s | \n" "$column1" "$column2"
1703       line=$(echo "$line" | cut -c46-)
1704    done
1705 fi
1706 printf "|                                                                        | \n"
[3236]1707 column1="run identifier:"; column2=$run_identifier
[2380]1708 printf "| %-25s%-45s | \n" "$column1" "$column2"
1709 column1="activation string list:"; column2=$(echo $activation_string_list)
1710 printf "| %-25s%-45s | \n" "$column1" "$column2"
1711
1712 if [[ "$ocean_file_appendix" = true ]]
1713 then
1714    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1715 fi
1716
1717 if [[ "$source_list" != "" ]]
1718 then
1719    printf "|                                                                        | \n"
1720    printf "| Files to be compiled:                                                  | \n"
1721    line=$source_list
1722    while [[ "$line" != "" ]]
1723    do
1724       linestart=$(echo $line | cut -c-70)
1725       printf "| %-70s | \n" "$linestart"
1726       line=$(echo "$line" | cut -c71-)
1727    done
1728 fi
1729 printf "#------------------------------------------------------------------------#"
1730
1731
1732
1733    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1734 if [[ $do_trace = true ]]
1735 then
1736    (( i = 0 ))
[2610]1737    while (( i < nr_of_input_files ))
[2380]1738    do
1739       (( i = i + 1 ))
1740       if (( i == 1 ))
1741       then
1742          printf "\n\n >>> INPUT-file assignments:\n"
1743       fi
1744       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1745    done
1746    (( i = 0 ))
1747    while (( i < iout ))
1748    do
1749       (( i = i + 1 ))
1750       if (( i == 1 ))
1751       then
1752          printf "\n\n >>> OUTPUT-file assignments:\n"
1753       fi
1754       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1755    done
1756    (( i = 0 ))
1757    while (( i < iic ))
1758    do
1759       (( i = i + 1 ))
1760       if (( i == 1 ))
1761       then
1762          printf "\n\n >>> INPUT-commands:\n"
1763       fi
1764       printf "\n     ${in_command[$i]}" 
1765    done
1766    (( i = 0 ))
1767    while (( i < ioc ))
1768    do
1769       (( i = i + 1 ))
1770       if (( i == 1 ))
1771       then
1772          printf "\n\n >>> OUTPUT-commands:\n"
1773       fi
1774       printf "\n     ${out_command[$i]}" 
1775    done
1776 fi
1777
1778    # QUERY FOR CONTINUE
1779 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1780 then
1781    antwort=dummy
1782    printf "\n\n"
1783    printf " >>> everything o.k. (y/n) ?  "
1784    while  read antwort
1785    do
1786       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1787       then
1788          printf " >>> everything o.k. (y/n) ?  "
1789       else
1790          break
1791       fi
1792    done
1793    if [[ $antwort = n  ||  $antwort = N ]]
1794    then
1795       locat=user_abort; (( iec = 0 )); exit
1796    fi
1797    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1798    then
[2566]1799       printf "\n ***  batch-job will be created and submitted"
[2380]1800    else
[2566]1801       printf "\n ***  PALMRUN will now continue to execute on this machine"
[2380]1802    fi
1803 fi
1804
1805 
1806
1807    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1808 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1809 then
1810
1811    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1812    then
[2566]1813       printf "\n\n  *** creating executable and other sources for the remote host\n"
[2380]1814    else
[2566]1815       printf "\n\n  *** creating executable and other sources for the local host\n"
[2380]1816    fi
1817
[2422]1818       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1819       # IT SHALL BE CREATED
1820    ask_for_make_depository=false
1821    if [[ $create_remote_batch_job = true ]]
1822    then
1823
1824       line=`grep %base_directory $config_file`
[3236]1825       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1826       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${configuration_identifier}_last_make_protokoll
[2422]1827
[3236]1828       if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]1829       then
1830          printf "\n\n  +++ make depository \"${make_depository}\""
1831          printf "\n      on remote host not found!"
1832          ask_for_make_depository=true
1833       fi
[3236]1834       rm ${configuration_identifier}_last_make_protokoll
[2422]1835
1836    else
1837
1838          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]1839       make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]1840       if [[ ! -d ${make_depository} ]]
1841       then
1842          printf "\n\n  +++ make depository \"${make_depository}\""
1843          printf "\n      on local host not found!"
1844          ask_for_make_depository=true
1845       fi
1846
1847    fi
1848
1849    if [[ $ask_for_make_depository = true ]]
1850    then
1851
1852       antwort=dummy
1853       printf "\n\n"
1854       printf "  >>> Create a new one (y/n) ?  "
1855       while  read antwort
1856       do
1857          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1858          then
1859             printf "  >>> Create a new one (y/n) ?  "
1860          else
1861             break
1862          fi
1863       done
1864       if [[ $antwort = n  ||  $antwort = N ]]
1865       then
1866          locat=user_abort; (( iec = 0 )); exit
1867       fi
1868
[2566]1869       if [[ $do_trace = true ]]
1870       then
[3236]1871          palmbuild  -h $configuration_identifier
[2566]1872       else
[3236]1873          palmbuild  -v  -h $configuration_identifier
[2566]1874       fi
[2422]1875
[3312]1876       if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]1877       then
1878   
1879              # ABORT IN CASE OF COMPILATION PROBLEMS
1880          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1881          locat=make_depository
1882          exit
1883       else
1884          echo "  *** now continue with creating executable and other sources"
1885       fi
1886
1887    fi
1888
[2566]1889       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3236]1890    palmbuild  -v  $use_existing_sources_folder  -h $configuration_identifier  -d $run_identifier
[2380]1891
[3312]1892    if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]1893    then
1894
1895           # ABORT IN CASE OF COMPILATION PROBLEMS
1896       printf "\n  +++ error while creating executable and/or other sources"
1897       locat=execution
[2990]1898       rm -rf  ${base_directory}/${sources_for_run_catalog}
[2380]1899       exit
1900
1901    else
1902
[2566]1903       printf "  *** executable and other sources created\n"
[2990]1904       rm -rf  ${base_directory}/${sources_for_run_catalog}
[2380]1905
1906    fi
1907
1908 fi
1909
1910
[2669]1911    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1912    # WILL BE COPIED TO THE REMOTE HOST
[2605]1913 if [[ $create_remote_batch_job = true ]]
1914 then
1915    (( i = 0 ))
[2610]1916    while (( i < nr_of_input_files ))
[2605]1917    do
1918       (( i = i + 1 ))
[2669]1919       if [[ "${actionin[$i]}" = tr ]]
[2605]1920       then
1921          eval inputfile=${pathin[$i]}/${frelin[$i]}
1922          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1923       fi
1924    done
1925    if (( i > 0 ))
1926    then
[3025]1927       printf "\n\n  *** input files have been copied to the remote host\n"
[2605]1928    fi
1929 fi
1930 
1931
[2380]1932    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1933    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1934 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1935 then
1936
1937       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1938    if [[ $running_in_batch_mode = false ]]
1939    then
1940          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1941          # FOLDER
[2566]1942       mkdir -p  $tempdir
1943       chmod  go+rx  $tempdir
1944       cd  $tempdir
1945       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $tempdir
1946       printf "\n  *** changed to temporary directory: $tempdir"
[2380]1947
1948    else
1949
1950          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]1951       printf "\n  *** running in temporary directory: $tempdir"
[2380]1952
1953    fi
1954
1955
1956       # PROVIDE THE INPUT FILES
1957       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]1958    optional_files_missing=false
[2380]1959    (( i = 0 ))
[2610]1960    while (( i < nr_of_input_files ))
[2380]1961    do
1962       (( i = i + 1 ))
1963       if (( i == 1 ))
1964       then
1965          printf "\n\n  *** providing INPUT-files:\n$dashes"
1966       fi
1967
1968
1969          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]1970       if [[ "${actionin[$i]}" = unavailable ]]
[2380]1971       then
[2669]1972          optional_files_missing=true
[2380]1973          continue
1974       fi
1975
1976          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1977       files_for_cores=false; filetype=file
1978       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1979       then
1980          files_for_cores=true; filetype=files
1981          actionin[$i]=""
1982       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1983       then
1984          actionin[$i]=""
1985       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1986       then
1987          files_for_cores=true; filetype=files
1988          actionin[$i]="ln"
1989       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1990       then
1991          actionin[$i]="ln"
1992       fi
1993
1994       if [[ $files_for_cores = true ]]
1995       then
1996          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1997       else
1998          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1999       fi
2000
2001          # INPUT-FILES TO BE LINKED
2002       if [[ "${actionin[$i]}" = ln ]]
2003       then
2004
2005          printf "\n      $filetype will be linked"
2006          if [[ $files_for_cores = false ]]
2007          then
2008             if [[ -f "${absnamein[$i]}" ]]
2009             then
2010                ln  ${absnamein[$i]}  ${localin[$i]}
2011                got_tmp[$i]=true
2012             fi
2013          else
2014             if [[ -d "${absnamein[$i]}" ]]
2015             then
[2396]2016                mkdir -p ${localin[$i]}
[2380]2017                cd ${absnamein[$i]}
2018                for file in $(ls *)
2019                do
[2566]2020                   ln $file $tempdir/${localin[$i]}
[2380]2021                done >|/dev/null 2>&1
[2566]2022                cd $tempdir
[2380]2023             fi
2024
2025                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2026             if [[ ! -f "${localin[$i]}/_000000" ]]
2027             then
2028                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2029                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
2030             fi
2031
2032             got_tmp[$i]=true
2033          fi
2034       fi
2035
2036          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]2037       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "tr"  ||  "${actionin[$i]}" = "npe" ]]
[2380]2038       then
2039
2040          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
2041          then
2042
2043                # FILE COPIES ARE PROVIDED FOR ALL CORES
2044                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2045             printf "\n      file will be provided for $cores processors"
[2396]2046             mkdir -p ${localin[$i]}
[2380]2047             ival=$cores
2048             (( ii = 0 ))
2049             while (( ii <= ival-1 ))
2050             do
2051                if (( ii < 10 ))
2052                then
2053                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
2054                elif (( ii < 100 ))
2055                then
2056                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
2057                elif (( ii < 1000 ))
2058                then
2059                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
2060                else
2061                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
2062                fi
2063                (( ii = ii + 1 ))
2064             done
2065
2066          else
2067
2068             if [[ $files_for_cores = true ]]
2069             then
2070
2071                   # PROVIDE FILES FOR EACH CORE
2072                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2073                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2074                printf "\n      providing $cores files for the respective cores"
[2396]2075                mkdir -p ${localin[$i]}
[2380]2076                        if [[ $link_local_input = true ]]
2077                              then
2078                                 printf "      files will be linked\n"
2079                                 cd ${absnamein[$i]}
2080                                 for file in $(ls *)
2081                                 do
2082                                    ln -f $file  ${localin[$i]}
2083                                 done
[2566]2084                                 cd $tempdir
[2380]2085                              fi
2086
2087                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2088                              if [[ ! -f "${localin[$i]}/_000000" ]]
2089                              then
2090                                 if [[ $link_local_input = true ]]
2091                                        then
2092                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2093                                 fi
2094                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
2095                              fi
2096
2097             else
2098
2099                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
2100                        if [[ $link_local_input = true ]]
2101                        then
2102                                 printf "      file will be linked\n"
2103                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
2104                        fi
[2605]2105                                # If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]2106                        if [[ ! -f "${localin[$i]}" ]]
2107                then
2108                                 if [[ $link_local_input = true ]]
2109                          then
2110                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2111                                 fi
[2669]2112                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
[2605]2113                   then
2114                      mv  ${absnamein[$i]}  ${localin[$i]}
2115                   else
2116                                 cp  ${absnamein[$i]}  ${localin[$i]}
2117                   fi
[2380]2118                fi
2119             fi
2120          fi
2121       fi
2122
2123    done
2124    if (( i != 0 ))
2125    then
[2669]2126       if [[ $optional_files_missing = true ]]
2127       then
2128          printf "\n  *** INFORMATIVE: some optional INPUT-files are not present"
2129       fi
[2380]2130       printf "\n$dashes\n  *** all INPUT-files provided \n"
2131    fi
2132
2133
2134       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2135    (( i = 0 ))
2136    while (( i < iic ))
2137    do
2138       (( i = i + 1 ))
2139       if (( i == 1 ))
2140       then
2141          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
2142       fi
2143       printf "\n  >>> ${in_command[$i]}"
2144       eval  ${in_command[$i]}
2145       if (( i == iic ))
2146       then
2147          printf "\n$dashes\n"
2148       fi
2149    done
2150
2151
[3313]2152    # CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2153    if [[ $running_in_batch_mode = true  ||  $running_in_test_mode = true ]]
2154    then
2155       progress_bar_disabled=true
2156    else
2157       progress_bar_disabled=false
2158    fi
2159
2160
[2380]2161       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2162       # (FILE ENVPAR WILL BE READ BY PALM)
2163    cat  >  ENVPAR  <<  EOF
[3236]2164 &envpar  run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]2165          write_svf = .${write_svf}., write_binary = .${write_binary}.,
2166          read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]2167          maximum_parallel_io_streams = $maximum_parallel_io_streams,
2168          maximum_cpu_time_allowed = ${cpumax}.,
2169          revision = '$global_revision',
[3313]2170          progress_bar_disabled = .${progress_bar_disabled}. /
[2380]2171
2172EOF
2173
2174
2175       # STARTING THE EXECUTABLE
2176    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
[2566]2177    PATH=$PATH:$tempdir
[2380]2178
2179
2180       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]2181    line=`echo  "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//g'`
2182    line2=`echo  "${execute_command}" | sed 's/{{mpi_tasks}}/1/g' | sed 's/{{tasks_per_node}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
[2380]2183    eval line=\"$line\"
2184    execute_command="$line"
2185
2186
2187       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]2188    if [[ "$execute_command_for_combine" = "" ]]
2189    then
2190       eval line2=\"$line2\"
2191       execute_command_for_combine="$line2"
2192    fi
2193   
[2380]2194
2195
2196       # PROVIDE A HOSTFILE, IF REQUIRED
2197    if [[ "$hostfile" != "" ]]
2198    then
2199
2200       if [[ $hostfile = auto ]]
2201       then
2202             # CREATE A NEW HOSTFILE
2203          (( ii = 1 ))
2204          while (( ii <= cores / threads_per_task ))
2205          do
2206             echo  $(hostname)  >>  hostfile
2207             (( ii = ii + 1 ))
2208          done
2209          if (( cores / threads_per_task == 0 ))
2210          then
2211             echo  $(hostname)  >>  hostfile
2212          fi
2213       
2214       else
2215          cp  $hostfile  hostfile
2216       fi
2217       eval line=\"`head -n $ii  hostfile`\"
2218       printf "\n  *** running on: $line"
2219    fi
2220
2221
2222
2223       # SET THE NUMBER OF OPENMP-THREADS
2224    if [[ $use_openmp = true ]]
2225    then
2226       export OMP_NUM_THREADS=$threads_per_task
2227       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2228    else
2229       export OMP_NUM_THREADS=1
2230    fi
2231
2232
[2610]2233       # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]2234    if [[ $run_coupled_model = false ]]
2235    then
2236       if [[ "$ocean_file_appendix" = true ]]
2237       then
2238          echo "precursor_ocean"  >  coupling_steering
2239       else
2240          echo "precursor_atmos"  >  coupling_steering
2241      fi
2242    else
2243       (( iia = $cores_atmos / $threads_per_task ))
2244       (( iio = $cores_ocean / $threads_per_task ))
2245       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
2246       printf "\n\n"
2247       echo "coupled_run $iia $iio"  >  coupling_steering
2248    fi
2249
2250    printf "\n  *** execute command:"
2251    printf "\n      \"$execute_command\" \n\n"
2252
2253    $execute_command  <  coupling_steering
2254
[3312]2255    if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]2256    then
2257
2258           # ABORT IN CASE OF RUNTIME ERRORS
2259       printf "\n  +++ runtime error occured"
2260       locat=execution
2261       exit
2262
2263    else
2264
2265       printf "\n$dashes\n  *** execution finished \n"
2266
2267    fi
2268
2269
2270       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2271       # BY EACH CORE INTO ONE FILE
2272   if [[ ! -f combine_plot_fields.x ]]
2273   then
2274
2275      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
2276      printf "\n      2d- and/or 3d-data may be incomplete!"
2277      printf "\n      Your previous palmbuild may have failed. Please check.\n"
2278
2279   elif [[ "$combine_plot_fields" == true ]]
2280   then
2281
2282      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2283      $execute_command_for_combine
2284
2285   else
2286
2287         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]2288         # DATA OUTPUT
[2380]2289      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2290   fi
2291
2292
2293
2294       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2295    (( i = 0 ))
2296    while (( i < ioc ))
2297    do
2298       (( i = i + 1 ))
2299       if (( i == 1 ))
2300       then
2301          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
2302       fi
[2799]2303
2304          # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2305       out_command[$i]=`echo  "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
2306
[2380]2307       printf "\n  >>> ${out_command[$i]}"
2308       eval  ${out_command[$i]}
2309       if (( i == ioc ))
2310       then
2311          printf "\n$dashes\n"
2312       fi
2313    done
2314
2315
[2610]2316       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2317       # WILDCARDS
[2380]2318    (( i = 0 ))
[2610]2319    (( nr_of_output_files = 0 ))
2320
[2380]2321    while (( i < iout ))
2322    do
[2610]2323
[2380]2324       (( i = i + 1 ))
[2610]2325
2326          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2327          # CREATE A LIST FOR THE DETECTED ENDINGS
2328       if [[ "${multout[$i]}" = true ]]
2329       then
2330             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2331          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
2332          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null
2333
2334          endings="DEFAULT"
2335          while  read line
2336          do
2337                 # remove the local name from the beginning
2338              localnamestring="${localout_pre[$i]}"
2339              length_localname=${#localnamestring}
2340              ending=${line:${length_localname}}
2341
2342              if [[ "$ending" != "" ]]
2343              then
2344                 endings="$endings $ending"
2345              fi
2346 
2347          done <filelist
2348
2349          rm filelist
2350
2351       else
2352
2353             # SINGLE NAME
2354          endings=DEFAULT
2355
2356       fi
2357
2358          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2359       for  ending  in  $endings
2360       do
2361
2362             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2363          if [[ $ending = DEFAULT ]]
2364          then
2365             ending=""
2366          fi
2367
2368             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2369          (( nr_of_output_files = nr_of_output_files + 1 ))
2370          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2371          transout[$nr_of_output_files]="${transout_pre[$i]}"
2372          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2373          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2374          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2375          extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]2376          warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]2377
2378       done
2379
2380    done
2381
2382
2383
2384
2385       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2386    (( i = 0 ))
2387    while (( i < nr_of_output_files ))
2388    do
2389       (( i = i + 1 ))
[2380]2390       if (( i == 1 ))
2391       then
2392          printf "\n\n  *** saving OUTPUT-files:"
2393
2394             # GET RUN NUMBER ASSIGNED BY PALM
2395          if [[ -f RUN_NUMBER ]]
2396          then
2397              read  run_number  <  RUN_NUMBER
2398              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2399              usecycle_option="-U $run_number"
2400          else
2401              run_number=0
2402              usecycle_option=""
2403          fi
2404          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2405          then
[2404]2406             printf "\n  *** in case of SCP transfers to local host"
2407             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
[2380]2408          fi
2409          printf "\n$dashes"
2410       fi
2411
2412       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2413       then
2414
[3236]2415          eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]2416
2417             # DETERMINE THE CYCLE NUMBER
2418          ls -1 -d $filename    >   filelist  2>/dev/null
2419          ls -1 -d $filename.*  >>  filelist  2>/dev/null
2420          while  read line
2421          do
2422   
2423                # filename without path (i.e. after the last "/")
2424             basefilename=$(basename ${line})
2425   
2426                # check if there is an extension
2427             extension=${basefilename##*.}
2428             if [[ "$extension" = "${extout[$i]}" ]]
2429             then
2430                basefilename=${basefilename%.*}
2431             fi
2432   
2433                # check for an existing cycle number
2434             cycle=${basefilename##*.}
2435             if [[ $cycle =~ ^-?[0-9]+$ ]]
2436             then
[2669]2437                   # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2438                   # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2439                (( icycle = $((10#$cycle)) + 1 ))
[2610]2440             else
2441                (( icycle = 1 ))
2442             fi
2443   
2444             if (( icycle > maxcycle ))
2445             then
2446                (( maxcycle = icycle ))
2447             fi
2448   
2449          done <filelist
2450          rm filelist
2451
2452   
2453             # SET THE CYCLE NUMBER
2454             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2455          if [[ "${actionout[$i]}" = a ]]
2456          then
2457             (( maxcycle = maxcycle - 1 ))
2458          fi
2459         
2460          (( cycnum[$i] = maxcycle ))
2461          pathout[$i]=$filename
2462
2463
2464             # ADD CYCLE NUMBER TO FILENAME
2465             # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]2466          if [[ "${actionout[$i]}" != "a" ]]
2467          then
2468                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2469                # WITH AN EXISTING CYCLE NUMBER
2470             if (( run_number >= cycnum[$i] ))
2471             then
2472                (( cycnum[$i] = run_number ))
2473             else
2474                if (( run_number > 0 ))
2475                then
2476                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2477                fi
2478             fi
2479          fi
2480          if (( cycnum[$i] > 0 ))
2481          then
[2600]2482             cyclestring=`printf "%03d" ${cycnum[$i]}`
2483             pathout[$i]=${pathout[$i]}.$cyclestring
[2380]2484          fi
2485       fi           
2486
2487          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2488       files_for_cores=false; filetype=file
2489       link_local_output=false
2490       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2491       then
2492          files_for_cores=true; filetype=directory
2493          actionout[$i]=""
2494       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2495       then
2496          actionout[$i]=""
2497       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2498       then
2499          files_for_cores=true; filetype=directory
2500          link_local_output=true
2501          actionout[$i]=""
2502       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2503       then
2504          link_local_output
2505          actionout[$i]=""
2506       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2507       then
2508          files_for_cores=true; filetype=directory
2509          actionout[$i]="tr"
2510       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2511       then
2512          actionout[$i]="tr"
2513       fi
2514
2515       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
2516       then
[2669]2517          if [[ ${warnout[$i]} = true ]]
2518          then
2519             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
2520          fi
[2380]2521       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2522       then
[2669]2523          if [[ ${warnout[$i]} = true ]]
2524          then
2525             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2526          fi
[2380]2527       else
2528
2529
2530             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2531             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2532          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2533          then
2534             if [[ $running_on_remote = true ]]
2535             then
2536
2537                   # SET OPTIONS FOR TRANSFER
2538                if [[ "${actionout[$i]}" = tr ]]
2539                then
2540                   if [[ $files_for_cores = false ]]
2541                   then
2542                      catalog_option=""
2543                      catalog_string=""
2544                   else
2545                      catalog_option="-c"
2546                      catalog_string="/"
2547                   fi
2548                   append_option=""
2549                   append_string=""
2550                else
2551                   append_option="-A"
2552                   append_string="append"
2553                fi
2554
2555                transfer_failed=false
2556                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
[3236]2557                printf "\n              ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]2558
2559                   # TRANSFER VIA SCP
2560                if [[ "$remote_loginnode" != "" ]]
2561                then
[3236]2562                   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]}\" ${configuration_identifier}_${run_identifier}${endout[$i]}  ${extout[$i]}"  |  ssh -q $remote_username@$remote_loginnode
[2380]2563                else
[3236]2564                   batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]}  ${extout[$i]}
[2380]2565                fi
[3312]2566                [[ ${PIPESTATUS[0]} != 0 ]]  &&  transfer_failed=true
[2380]2567
2568
2569                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2570                if [[ $transfer_failed = true ]]
2571                then
2572                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]2573                   printf "      ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]2574
2575                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2576                   eval  local_catalog=${pathout[$i]}
2577                   if [[ ! -d $local_catalog ]]
2578                   then
2579                      printf "  *** local directory does not exist. Trying to create:\n"
2580                      printf "      $local_catalog \n"
2581                      mkdir -p  $local_catalog
2582                   fi
[3236]2583                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]2584                   transfer_problems=true
2585                fi
2586
2587             else
2588
2589                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2590                   # BE COPIED OR APPENDED ON THIS MACHINE
2591                if [[ "${actionout[$i]}" = tr ]]
2592                then
2593                   actionout[$i]=""
2594                else
2595                   actionout[$i]="a"
2596                fi
2597             fi
2598          fi
2599
2600
2601             # APPEND ON THIS MACHINE
2602          if [[ "${actionout[$i]}" = "a" ]]
2603          then
2604             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2605             then
2606                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2607                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2608                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2609             else
2610                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2611                printf "\n              ${pathout[$i]}\n"
2612                cat  ${localout[$i]}  >>  ${pathout[$i]}
2613             fi
2614          fi
2615
2616             # COPY ON THIS MACHINE
2617             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2618             # ON DIFFERENT FILE-SYSTEMS
2619          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2620          then
2621
2622                # COPY IN CASE OF RUNS ON SINGLE CORES
2623             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2624             then
2625                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2626                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2627                              if [[ $link_local_output = true ]]
2628                              then
2629                                 printf "      file will be linked\n"
2630                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2631                              fi
2632                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2633                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2634                then
2635                                 if [[ $link_local_output = true ]]
2636                          then
2637                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2638                                 fi
2639                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2640                              else
2641                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2642                fi
2643             else
2644                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2645                printf "\n              ${pathout[$i]}\n"
2646                              if [[ $link_local_output = true ]]
2647                              then
2648                                 printf "      file will be linked\n"
2649                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2650                              fi
2651                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2652                        if [[ ! -f "${pathout[$i]}" ]]
2653                then
2654                                 if [[ $link_local_output = true ]]
2655                          then
2656                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2657                                 fi
2658                                 cp  ${localout[$i]}  ${pathout[$i]}
2659                              else
2660                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2661                fi
2662             fi
2663
2664          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2665          then
2666
2667                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2668                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2669             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2670             printf "\n              ${pathout[$i]}\n"
2671                    if [[ $link_local_output = true ]]
2672                    then
2673                              printf "      files will be linked\n"
[2396]2674                              mkdir -p ${pathout[$i]}
[2380]2675                              cd ${localout[$i]}
2676                              for file in $(ls *)
2677                              do
2678                                 ln -f $file  ${pathout[$i]}
2679                              done >|/dev/null 2>&1
[2566]2680                              cd $tempdir
[2380]2681                    fi
2682
2683                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2684                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2685             then
2686                              if [[ $link_local_output = true ]]
2687                              then
2688                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2689                              fi
[3025]2690                              [[ ! -d "${pathout[$i]}" ]]  &&  mkdir  ${pathout[$i]}
[2380]2691                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2692             fi
2693
2694          fi
2695       fi
2696    done
2697
2698    if (( i != 0 ))
2699    then
2700       if [[ $transfer_problems = true ]]
2701       then
2702          printf "\n$dashes\n  *** OUTPUT-files saved"
2703          printf "\n  +++ WARNING: some data transfers failed! \n"
2704       else
2705          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2706       fi
2707    fi
2708
2709
2710       # IF REQUIRED, START A RESTART-JOB
2711       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2712    if [[ -f CONTINUE_RUN ]]
2713    then
2714
2715          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2716          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2717          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2718          # -b START A BATCH JOB
2719       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2720       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2721       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2722
[2957]2723          # REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2724          # SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2725       if [[ $(echo $prc | grep -c "svfout") != 0 ]]
2726       then
2727          prc=`echo $prc | sed 's/svfout/svfin/g'`
2728       fi
[2380]2729
2730          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2731          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2732       if [[ $(echo $prc | grep -c "#") != 0 ]]
2733       then
[2381]2734          prc=`echo $prc | sed 's/#/r/g'`
[2380]2735       fi
2736
2737
2738          # START THE RESTART-JOB
2739       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2740       echo "      $prc"
2741       printf "\n$dashes\n"
2742       if [[ $running_on_remote = true ]]
2743       then
2744
2745          echo "*** ssh will be used to initiate restart-runs!"
2746          echo "    return_address=\"$return_address\" "
2747          echo "    return_username=\"$local_username\" "
2748
2749          if [[ "$remote_loginnode" != "" ]]
2750          then
[3132]2751             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  |  tee palmrun_restart.log
[2380]2752          else
[3132]2753             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  |  tee palmrun_restart.log
[2380]2754          fi
2755
2756             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2757          sleep 30
2758
2759       else
2760
2761             # START THE RESTART JOB ON THE LOCAL HOST
[3132]2762          eval  $prc  |  tee palmrun_restart.log              # THE ' MUST BE EVALUATED
[2380]2763          cd -  > /dev/null
2764
2765       fi
2766
[3132]2767          # CHECK, IF RESTART JOB HAS BEEN STARTED
2768       if [[ $( grep -c "+++ palmrun killed"  palmrun_restart.log ) != 0 ]]
2769       then
2770          printf "\n$dashes\n  +++ creating restart run failed \n"
2771          locat=create_restart
2772          exit
2773          rm  palmrun_restart.log
2774       else
2775          printf "\n$dashes\n  *** restart run initiated \n"
2776          rm  palmrun_restart.log
2777       fi
[2380]2778
[3132]2779
[2380]2780          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2781          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2782          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2783          # MAY BE VERY HUGE)
2784       (( i = 0 ))
[2610]2785       while (( i < nr_of_input_files ))
[2380]2786       do
2787          (( i = i + 1 ))
2788          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2789          then
2790             rm -r  ${absnamein[$i]}
2791          fi
2792       done
2793
2794    fi
2795
2796
2797       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2798    cd  $HOME
[2566]2799    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $tempdir
[2380]2800
2801
2802 else
2803
2804
2805       # PREPARING ACTIONS,
2806       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2807
2808       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3236]2809    palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]2810    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2811    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2812    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2813    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2814    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2815    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]2816    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]2817    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2818    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2819    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2820    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2821    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]2822    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
[2380]2823    if [[ $create_remote_batch_job = true ]]
2824    then
2825       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]2826       if [[ $do_trace = true ]]
2827       then
2828          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2829       fi
[2380]2830    elif [[ $create_batch_job = true ]]
2831    then
2832       palmrun_com=${palmrun_com}" -j"
[2420]2833       if [[ $do_trace = true ]]
2834       then
2835          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2836       fi
[2380]2837    fi
2838
2839
2840       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2841       # REMOTE HOST
[3236]2842    job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]2843    job_protocol_file=$job_protocol_file_local
2844    if [[ $create_remote_batch_job = true ]]
2845    then
[3236]2846       job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]2847       job_protocol_file=$job_protocol_file_remote
2848       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]2849       scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]2850    fi
2851
2852
2853       # BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]2854    jobfile=jobfile.$run_id_number
[2380]2855
2856
2857       # FIRST CREATE THE BATCH DIRECTIVES
2858    (( i = 0 ))
2859    while (( i < ibd ))
2860    do
2861       (( i = i + 1 ))
[2693]2862       line=`echo  "${batch_directive[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
[2380]2863       eval line=\"$line\"
2864       echo  "$line"                               >>  $jobfile
2865    done
2866    echo " "                                       >>  $jobfile
2867
2868
2869       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2870       # PROTOCOL
2871    if [[ $create_remote_batch_job = true ]]
2872    then
[3236]2873       echo "set +vx"                                   >>  $jobfile
2874       echo "trap '"                                    >>  $jobfile
2875       echo "set +vx"                                   >>  $jobfile
2876       echo "cd ${remote_jobcatalog}"                   >>  $jobfile
2877       echo "cat >  scpjob.$run_id_number << %%END%%"   >>  $jobfile
[2380]2878
2879          # ADD THE BATCH DIRECTIVES
2880       (( i = 0 ))
2881       while (( i < ibdt ))
2882       do
2883          (( i = i + 1 ))
[2693]2884          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
[2380]2885          eval line=\"$line\"
2886          echo  "$line"                            >>  $jobfile
2887       done
2888       echo " "                                    >>  $jobfile
2889
2890       echo "set -x"                               >>  $jobfile
[3236]2891       echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${configuration_identifier}_${run_identifier}"  >>  $jobfile
[2380]2892       echo "%%END%%"                              >>  $jobfile
2893       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2894       echo "$submit_command  $scpjob_file"        >>  $jobfile
2895       echo "rm $scpjob_file"                      >>  $jobfile
[2404]2896       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
[2380]2897       echo "set -x"                               >>  $jobfile
2898       echo "     ' exit"                          >>  $jobfile
2899    fi
2900
2901
2902       # ACTIVATE ERROR-TRACEBACK
2903    if [[ $do_trace = true ]]
2904    then
2905       echo  "set -x"                                    >>  $jobfile
2906    else
2907       echo  "set +vx"                                   >>  $jobfile
2908    fi
2909
2910
2911       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2912    if [[ "$login_init_cmd" != "" ]]
2913    then
2914       echo  "$login_init_cmd"        >>  $jobfile
2915    fi
2916    if [[ "$module_commands" != "" ]]
2917    then
2918       echo  "$module_commands"     >>  $jobfile
2919    fi
2920
2921
2922       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]2923    if [[ $create_remote_batch_job = true ]]
2924    then
2925       echo  "mkdir  $tempdir"           >>  $jobfile
2926       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
2927    else
2928          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2929          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2930          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2931       mkdir  $tempdir
2932       chmod  go+rx  $tempdir
2933    fi
2934    echo  "cd  $tempdir"                 >>  $jobfile
2935    echo  "export tempdir=$tempdir"      >>  $jobfile
[2506]2936    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
[2380]2937    echo  "export PATH=.:\$PATH"         >>  $jobfile
2938    echo  "export execute_palmrun=true"  >>  $jobfile
2939
2940
2941       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2942       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2943       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2944    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2945    echo  "export LOCAL_PWD"                            >>  $jobfile
2946
2947
2948       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]2949    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
[2380]2950    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2951
2952
2953       # CALL PALMRUN WITHIN THE JOB
2954       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2955    echo  "set -x"                                              >>  $jobfile
2956    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2957
2958
2959       # TRANSFER JOBFILE TO THE TARGET HOST
2960    if [[ $create_jobfile_only = false ]]
2961    then
2962
2963       if [[ $create_remote_batch_job = true ]]
2964       then
2965
[2420]2966          echo " "
[2566]2967          echo " *** transfer of job to remote host via scp"
[2420]2968          if [[ $do_trace = true ]]
2969          then
[3236]2970             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]2971          fi
[3236]2972          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}  >  /dev/null
[2380]2973
[2566]2974          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]2975          if [[ $do_trace = true ]]
2976          then
[3236]2977             echo "     cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1"
[2420]2978          fi
[3236]2979          echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1
[2380]2980
2981       elif [[ $create_batch_job = true ]]
2982       then
2983
[2385]2984          eval  local_jobcatalog=$local_jobcatalog
[3236]2985          cp  $jobfile  ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]2986          cd $local_jobcatalog
[2380]2987          echo " "
[2420]2988          echo " *** submit the job"
2989          if [[ $do_trace = true ]]
2990          then
[3236]2991             echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]2992          fi
[3236]2993          $submit_command ${configuration_identifier}_${run_id}
2994          rm ${configuration_identifier}_${run_id}
[2380]2995          cd -  > /dev/null
2996
2997       fi
2998
2999       rm -rf  $jobfile
3000
3001    else
3002
3003       printf "\n *** jobfile created under name \"$jobfile\" "
3004       printf "\n     no batch-job has been sent!"
3005
3006    fi
3007
3008 fi  # END OF REMOTE-PART
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