source: palm/trunk/SCRIPTS/palmrun @ 3477

Last change on this file since 3477 was 3455, checked in by raasch, 6 years ago

options -h and -d renamed -c and -r, respectively, job_queue renamed job_logfiles in sveral configuration files

  • Property svn:executable set to *
  • Property svn:keywords set to Id Rev
File size: 100.8 KB
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[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 3455 2018-10-30 14:12:31Z maronga $
[3455]29# options -h and -d renamed -c and -r, respectively
30#
31# 3402 2018-10-23 11:49:24Z knoop
[3346]32# job_id is set for compatibility reasons with older versions of config files
33#
34# 3313 2018-10-06 15:22:48Z knoop
[3294]35# more detailed error message for outdated fileconnection file
36#
37# 3236 2018-09-10 09:07:06Z raasch
[3236]38# warning issued in case of file connection file version mismatch,
39# host_configuration renamed configuration_identifier,
40# "host identifier" in header output renamed "config. identifier",
41# jobname renamed run_identifier,
42# run_id renamed run_id_number
43# job_id renamed run_id
44# option -r renamed -i
45#
46# 3151 2018-07-19 08:45:38Z raasch
[3151]47# removed additional listing of files to be compiled, print PALM code revision
48# in header
49#
50# 3132 2018-07-16 11:44:58Z raasch
[3132]51# create consistent error messages in case of failed restarts,
52# check existence of remote job catalog
53#
54# 3043 2018-05-25 10:47:54Z raasch
[3043]55# check for setting of fast_io_catalog
56#
57# 3033 2018-05-23 15:26:19Z raasch
[3025]58# -T option not required for interactive runs (tasks per node =
59# total number of cores is assumed as default, if option is not given),
60# reformatting of a few messages,
61# bugfix: destination output directory is created if attribute "pe" is set in
62# .palm.iofiles
63#
64# 2718 2018-01-02 08:49:38Z maronga
[2993]65# bugfix of r2990
66#
67# 2718 2018-01-02 08:49:38Z maronga
[2990]68# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
69#         not in the working directory from where palmrun is called
70#
71# 2718 2018-01-02 08:49:38Z maronga
[2957]72# svfout in the activation string will be replaced now by svfin in case of
73# automatic restarts
74#
75# 2718 2018-01-02 08:49:38Z maronga
[2906]76# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
77# the possible output or input of sky view factors
78#
79# 2718 2018-01-02 08:49:38Z maronga
[2834]80# "fname" renamed to "jobname"
81#
82# 2718 2018-01-02 08:49:38Z maronga
[2799]83# parameters are allowed in output commands (OC:)
84#
85# 2718 2018-01-02 08:49:38Z maronga
[2789]86# bugfix: exit if no queue has been given neither with option -q nor in the
87# configuration file
88#
89# 2718 2018-01-02 08:49:38Z maronga
[2762]90# file connection file from trunk/SCRIPTS is taken by default
91#
92# 2718 2018-01-02 08:49:38Z maronga
[2716]93# Corrected "Former revisions" section
94#
95# 2696 2017-12-14 17:12:51Z kanani
96# Change in file header (GPL part)
97#
98# 2693 2017-12-13 12:33:49Z raasch
[2693]99# replacement of variables given by {{<variable>}} in configuration file is now
100# done in a more general way, variable names are written in small letters
101#
102# 2670 2017-12-06 16:32:19Z raasch
[2670]103# test printouts removed
104#
105# 2669 2017-12-06 16:03:27Z raasch
[2669]106# file attributes in .palm.iofiles restructured, "loc" attribute completely
107# removed,
108# wildcard (*) allowed in .palm.iofiles as file activation string for output
109# files,
110# informative messages in case of missing optional input files shortened
111# bugfix: variable cycle explicitly interpreted with 10 as the number base
112#
113# 2638 2017-11-23 12:44:23Z raasch
[2610]114# use of wildcards in file connection statements enabled
115#
116# 2605 2017-11-09 15:31:46Z raasch
[2605]117# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
118# will not be sent with the job file any more, but copied into the
[2610]119# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]120#
121# 2600 2017-11-01 14:11:20Z raasch
[2600]122# cycle numbers are made three digits wide
123#
124# 2566 2017-10-20 08:50:47Z raasch
[2566]125# execute command for combine_plot_fields added
126# "TEMPDIR" renamed "tempdir"
127# temporary working directory for local batch jobs is created immediately within
128# the user's palmrun call, due to a requirement of the "grid engine" batch
129# system, where the working directory is given with batch directive -wd and must
130# already exist when the job is submitted,
131# informative messages in non-trace mode reduced and partly reformatted
132#
133# 2551 2017-10-18 07:25:11Z raasch
[2551]134# TEMPDIR added as replacement string to be used in batch directives
135#
136# 2512 2017-10-04 08:26:59Z raasch
[2507]137# bugfix for determining cycle numbers of NetCDF input files
138#
139# 2506 2017-09-29 08:30:37Z raasch
[2506]140# option -V added to check for an existing SOURCES_FOR_RUN_... folder
141# host configuration added to SOURCES_FOR_RUN_... folder name
142# host_identifier renamed host_configuration
143# option -W added to allow for job dependencies
144#
145# 2501 2017-09-26 11:41:55Z raasch
[2501]146# default value for number of cores (option -X) set to 1
147# bugfix for mechanism which overwrites configuration file settings with values
148# provided by palmrun options
149#
150# 2499 2017-09-22 16:47:58Z kanani
[2499]151# option -h named configuration identifier
152#
153# 2480 2017-09-19 06:24:14Z maronga
[2480]154# bugfix for last revision
155#
156# 2479 2017-09-19 06:12:16Z raasch
[2479]157# option -A (project account number) added
158#
159# 2422 2017-09-08 08:25:41Z raasch
[2410]160# initial revision
[2380]161#
162#--------------------------------------------------------------------------------#
163# palmrun - script for running PALM jobs on local and remote hosts
164#--------------------------------------------------------------------------------#
165
166
167 
168    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
169
170 set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
171                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
172                     # (TOO MANY ARGUMENTS - PROBLEM)
173 set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
174
[2610]175 typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
176 typeset -i  nr_of_output_files=0
[2380]177 typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
178                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
179                           # SCRIPT-OPTION ARGUMENTS
180 typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
181 typeset -i  icycle inode ival maxcycle mpi_tasks
182 typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
183
184 activation_string_list=""
185 AddFilenames=""
186 combine_plot_fields=true
187 compiler_name=""
188 compiler_name_ser=""
189 compiler_options=""
[3236]190 configuration_identifier="default"
[2501]191 cores=1
[2380]192 cores_atmos=0
193 cores_ocean=0
194 coupled_dist=""
195 cpp_options=""
196 cpumax=0
[2506]197 create_batch_job=false
[2380]198 create_jobfile_only=false
199 create_remote_batch_job=false
200 dashes="  ----------------------------------------------------------------------------"
201 defaultqueue=""
[2506]202 delete_temporary_catalog=true
[2380]203 do_compile=true
204 do_trace=false
205 executable=""
206 execute_command=""
207 execution_error=false
[2762]208 fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]209 global_revision=""
210 hostfile=""
211 hp=""
212 keep_data_from_previous_run=false
213 link_local_input=false
214 link_local_output=false
[2388]215 linker_options=""
[2385]216 local_jobcatalog=""
[2380]217 locat=normal
218 makefile=""
219 max_par_io_str=""
220 prc=$0
221 while [[ $(echo $prc | grep -c "/") != 0 ]]
222 do
223    prc=`echo $prc | cut -f2- -d"/"`
224 done
225 module_calls=""
[2506]226 palmrun_memory=""
[2380]227 palmrun_script_name=$prc
228 openmp=false
[2506]229 previous_job=""
[2479]230 project_account=""
[2380]231 queue=none
[2906]232 read_svf=""
[2380]233 restart_run=false
234 return_address=""
[2385]235 remote_jobcatalog=""
[2380]236 remote_username=""
237 running_in_batch_mode=false
[3313]238 running_in_test_mode=false
[2380]239 run_coupled_model=false
240 run_id=""
[3236]241 run_id_number=""
242 run_identifier=test
[2380]243 silent=false
244 source_list=""
245 source_path=""
[2501]246 tasks_per_node=0
[2380]247 threads_per_task=1
248 transfer_problems=false
[2384]249 user_source_path=""
[2506]250 use_existing_sources_folder=""
[2380]251 use_openmp=false
[3033]252 version="palmrun  1.0 Rev$Rev: 3455 $"
[2380]253 working_directory=`pwd`
254 write_binary=""
[2906]255 write_svf=""
[2380]256
257
258    # ERROR HANDLING IN CASE OF EXIT
[2404]259 trap 'if [[ $locat != normal  &&  $locat != control_c ]]
[2380]260       then
261
262              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
263          (( i = 0 ))
264          while (( i < iec ))
265          do
266             (( i = i + 1 ))
267             printf "\n  *** Execution of ERROR-command:\n"
268             printf "  >>> ${err_command[$i]}\n"
269             eval  ${err_command[$i]}
270          done
[2566]271          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
[3312]272          printf "\n\n+++ palmrun crashed \n\n"
273          exit 1
274       elif [[ $locat != normal ]]
[2380]275       then
[3312]276          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
277          printf "\n+++ palmrun killed by \"^C\" \n\n"
278          exit 2
279       else
[2566]280          printf "\n --> palmrun finished\n\n"
[3312]281          exit 0
[2380]282       fi' exit
283
284
285    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]286 trap 'locat=control_c
287       exit 1
[2380]288      ' 2
289
290
291    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
292    # WHICH WILL BE USED TO START RESTART-JOBS
[3455]293 while  getopts  :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]294 do
295   case  $option  in
296       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]297       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]298       (b)   create_batch_job=true; prc="$prc -b";;
299       (B)   delete_temporary_catalog=false; prc="$prc -B";;
[3455]300       (c)   configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]301       (C)   restart_run=true; prc="$prc -C";;
302       (F)   create_jobfile_only=true;;
303       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]304       (i)   run_id_number=$OPTARG;;
[2380]305       (j)   running_in_batch_mode=true;;
306       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
[2501]307       (m)   palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]308       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
309       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
310       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]311       (r)   run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]312       (R)   return_address=$OPTARG;;
313       (s)   source_list=$OPTARG;;
[2501]314       (t)   palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]315       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
316       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
317       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
318       (v)   silent=true; prc="$prc -v";;
[2506]319       (V)   use_existing_sources_folder="-V";;
[2380]320       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]321       (W)   previous_job=$OPTARG;;
[2380]322       (x)   do_trace=true;set -x; prc="$prc -x";;
[2501]323       (X)   palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]324       (y)   ocean_file_appendix=true; prc="$prc -y";;
325       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]326       (z)   running_in_test_mode=true;;
[2380]327       (Z)   combine_plot_fields=false; prc="$prc -Z";;
328       (\?)  printf "\n  +++ unknown option $OPTARG \n"
329             printf "\n  --> type \"$0 ?\" for available options \n"
330             locat=parameter;exit;;
331   esac
332 done
333
334
335    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
336    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
337 (( to_shift = $OPTIND - 1 ))
338 shift $to_shift
339
340    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
341 if [[ "$1" = "?" ]]
342 then
343   (printf "\n  *** Description of available palmrun options:\n"
344    printf "\n      Option  Description                              Default-Value"
345    printf "\n        -a    activation string list                   \"\" "
[2479]346    printf "\n        -A    project account number                   ---"
[2380]347    printf "\n        -b    batch-job on local machine               ---"
348    printf "\n        -B    do not delete temporary directory at end ---"
[3455]349    printf "\n        -c    configuration identifier                 \"default\" "
[2380]350    printf "\n        -F    create batch job file only               ---"
351    printf "\n        -k    keep data from previous run"
352    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
353    printf "\n        -M    Makefile name                            Makefile"
354    printf "\n        -O    threads per openMP task                  ---"
355    printf "\n        -q    queue                                    \"$queue\" "
[3455]356    printf "\n        -r    run identifier                           test"
[2380]357    printf "\n        -s    filenames of routines to be compiled     \"\" "
358    printf "\n              must end with .f, .f90, .F, or .c !"
359    printf "\n              use \"..\" for more than one file and wildcards"
360    printf "\n              -s LM compiles all locally modified files"
361    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
[2384]362    printf "\n        -T    tasks per node                           ---"
[2380]363    printf "\n        -u    username on remote machine               \"\" "
364    printf "\n        -v    no prompt for confirmation               ---"
[2506]365    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
[2380]366    printf "\n        -w    maximum parallel io streams              as given by -X"
[2506]367    printf "\n        -W    name of job to wait for                  ---"
[2380]368    printf "\n        -x    tracing of palmrun for debug purposes    ---"
369    printf "\n        -X    # of processors (on parallel machines)   1"
370    printf "\n        -y    add appendix \"_O\" to all local output"
371    printf "\n              files (ocean precursor runs followed by"
372    printf "\n              coupled atmosphere-ocean runs)           ---"
373    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
374    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
375    printf "\n        -Z    skip combine_plot_fields at the end of      "
376    printf "\n              the simulation                           ---"
377    printf "\n "
378    printf "\n      Possible values of positional parameter <modus>:"
379    printf "\n        \"?\"       -  this outline \n\n") | more
380    exit
381 elif [[ "$1" != "" ]]
382 then
383    printf "\n  +++ positional parameter $1 unknown \n"
384    locat=parameter; exit
385 fi
386
387
388
389    # SHORT STARTING MESSAGE
390 printf "\n*** $version "
391 printf "\n    will be executed.     Please wait ..."
392
393
[2506]394    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]395 config_file=.palm.config.$configuration_identifier
396 sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]397
398
399    # CHECK, IF CONFIGURATION FILE EXISTS
400 if [[ ! -f $config_file ]]
401 then
402    printf "\n\n  +++ configuration file: "
403    printf "\n           $config_file"
404    printf "\n      does not exist"
405    locat=connect; exit 
406 fi
407
408
[2762]409    # CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
410 if [[ -f .palm.iofiles ]]
411 then
[3236]412
413       # CHECK VERSION MISMATCH
414    if [[ $running_in_batch_mode != true ]]
415    then
416       if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
417       then
418          printf "\n\n  +++ WARNING: A file connection file has been found in your"
419          printf "\n               working directory, but its revision does not match"
420          printf "\n               the revision of the default (trunk) version."
[3294]421          printf "\n               You may need to update your connection file"
422          printf "\n               \"${working_directory}/.palm.iofiles\" !"
[3236]423       fi
424    fi
425
[2762]426    fileconnection_file=.palm.iofiles
[3236]427
[2762]428 fi
429
430
[2380]431    # CHECK, IF FILE CONNECTION FILE EXISTS
432 if [[ ! -f $fileconnection_file ]]
433 then
434    printf "\n\n  +++ file connection file: "
435    printf "\n           $fileconnection_file"
436    printf "\n      does not exist"
437    locat=connect; exit 
438 fi
439
440
[2404]441    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
442 if [[ "$activation_string_list" = "" ]]
443 then
444    printf "\n\n  +++ no activation string list given: "
445    printf "\n        please set palmrun option \"-a\" "
446    locat=palmrun_option; exit 
447 fi
448
449
450    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
451 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
452 then
453    write_binary=true
454 else
455    write_binary=false
456 fi
457
[2906]458    # SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
459 if [[ $(echo $activation_string_list | grep -c "svfout") != 0 ]]
460 then
461    write_svf=true
462 else
463    write_svf=false
464 fi
[2404]465
[2906]466    # SET VARIABLE TO ACTIVATE READING OF SVF DATA
467 if [[ $(echo $activation_string_list | grep -c "svfin") != 0 ]]
468 then
469    read_svf=true
470 else
471    read_svf=false
472 fi
473
474
[2380]475    # READ AND EVALUATE THE CONFIGURATION-FILE
476 [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
477
478    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
479 while  read line
480 do
481
482       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
483    eval  line=\"$line\"
484
485
486       # INTERPRET THE LINE
487    if [[ "$(echo $line)" = "" ]]
488    then
489
490          # EMPTY LINE, NO ACTION
491       continue
492
493    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
494    then
495
496          # LINE IS A COMMENT LINE
497       continue
498
499    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
500    then
501
502          # LINE DEFINES AN ENVIRONMENT-VARIABLE
503       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
504       value=`echo $line | cut -d" " -s -f2-`
505
506
507          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
508          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
509          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
510          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
511          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
512          # CONFIGURATION-FILE.
513       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
514       then
515          eval  export  $var="\$value"
516
517             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
518          if [[ $do_trace = true ]]
519          then
520             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
521          fi
522       fi
523
524    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
525    then
526
527          # LINE DEFINES BATCH-DIRECTIVE
528       (( ibd = ibd + 1 ))
529       line=$(echo $line | cut -c4-)
530       batch_directive[$ibd]="$line"
531
532    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
533    then
534
535          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
536          # REMOTE TO A LOCAL HOST
537       (( ibdt = ibdt + 1 ))
538       line=$(echo $line | cut -c5-)
539       batch_directive_transfer[$ibdt]="$line"
540
541    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
542    then
543
544          # LINE DEFINES ERROR-COMMAND
545       (( iec = iec + 1 ))
546       line=$(echo $line | cut -c4-)
547       err_command[$iec]="$line"
548
549    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
550    then
551
552          # LINE DEFINES INPUT-COMMAND
553       (( iic = iic + 1 ))
554       line=$(echo $line | cut -c4-)
555       in_command[$iic]="$line"
556
557    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
558    then
559
560          # LINE DEFINES OUTPUT-COMMAND
561       (( ioc = ioc + 1 ))
562       line=$(echo $line | cut -c4-)
563       out_command[$ioc]="$line"
564
565    else
566
567          # SKIP ALL OTHER LINES
568       continue
569
570    fi
571
572 done < $config_file
573
574
575    # CHECK SETTING OF REQUIRED PARAMETERS
[3043]576 if [[ "$fast_io_catalog" = "" ]]
577 then
578    printf "\n  +++ no fast_io_catalog found in $config_file"
579    printf "\n      Please add line \"fast_io_catalog ...\" to that file."
580    locat=config_file; exit
581 fi
[2380]582 if [[ "$compiler_name" = "" ]]
583 then
584    printf "\n  +++ no compiler name found in $config_file"
585    printf "\n      Please add line \"compiler_name ...\" to that file."
586    locat=config_file; exit
587 fi
588 if [[ "$compiler_name_ser" = "" ]]
589 then
590    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
591    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
592    locat=config_file; exit
593 fi
594 if [[ "$compiler_options" = "" ]]
595 then
596    printf "\n  +++ no compiler options found in $config_file"
597    printf "\n      Please add line \"compiler_options ...\" to that file."
598    locat=config_file; exit
599 fi
[2388]600 if [[ "$linker_options" = "" ]]
[2380]601 then
[2388]602    printf "\n  +++ no linker options found in $config_file"
603    printf "\n      Please add line \"linker_options ...\" to that file."
[2380]604    locat=config_file; exit
605 fi
606 if [[ "$execute_command" = "" ]]
607 then
608    printf "\n  +++ no execute command found in $config_file"
609    printf "\n      Please add line \"execute_command ...\" to that file."
610    locat=config_file; exit
611 fi
612
613 if [[ "$hostfile" != "" ]]
614 then
615    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
616    then
617       printf "\n  +++ no hostfile \"$hostfile\" found"
[3151]618       printf "\n      Please check line \"hostfile ...\" in $config_file"
[2380]619       locat=config_file; exit   
620    fi
621 fi
622
623
624    # DETERMINE THE CALL STATUS
625 if [[ "$return_address" != "" ]]
626 then
627 
628       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
629       # BATCH MODE AND ...
630    running_on_remote=true
631 
632 else
633
634       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
635     if [[ "$remote_ip" != "" ]]
636     then
637
638           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
639        create_remote_batch_job=true
640
[3132]641           # CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
642        if [[ "$remote_jobcatalog" = "" ]]
643        then
644           printf "\n  +++ no remote jobcatalog found in $config_file"
645           printf "\n      Please add line \"remote_jobcatalog ...\" to that file."
646           locat=config_file; exit
647        fi
648 
649
[2380]650     fi
651     running_on_remote=false
652 fi
653
654
655
656    # READ AND EVALUATE THE I/O-FILE LIST
657 [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
658
659    # READ THE FILE CONNECTION FILE LINE BY LINE
660 while  read line
661 do
662
[2669]663       # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
664    line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"`
[2380]665
666       # INTERPRET THE LINE
667    if [[ "$(echo $line)" = "" ]]
668    then
669          # EMPTY LINE, NO ACTION
670       continue
671
672    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
673    then
674
675          # LINE IS A COMMENT LINE
676       true
677
678    else
679
680          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
681          # s2a: in/out - field
[2669]682          # s2b: action - field (optional)
683       s1=`echo "$line" | cut -d" " -f1`
684       s2=`echo "$line" | cut -d" " -s -f2`
[2380]685       if [[ $(echo $s2 | grep -c ":") = 0 ]]
686       then
[2669]687          s2a=$s2
[2380]688          s2b=""
689       else
[2669]690          s2a=`echo $s2 | cut -d":" -f1`
691          s2b=`echo $s2 | cut -d":" -f2`
[2380]692       fi
[2669]693       s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'`
694       s4=`echo "$line" | cut -d" " -s -f4`
695       eval s4=\"$s4\"    # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
696       s5=`echo "$line" | cut -d" " -s -f5`
697       s6=`echo "$line" | cut -d" " -s -f6`
[2380]698
699       
700          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
701          # INPUT- OR OUTPUT-LIST.
702          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
703          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]704          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]705          # IS NOT CHECKED AND STORED.
[2610]706       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
[2669]707       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
[2380]708       then
709          found=false
710          for  actual  in  $activation_string_list
711          do
712             for  formal  in  $s3
713             do
714                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
715             done
716          done
717          if [[ $found = true ]]
718          then
719             (( iin = iin + 1 ))
[2669]720             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]721             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]722             if [[ "$s2a" = inopt ]]
723             then
724                optin_pre[$iin]=yes
725             else
726                optin_pre[$iin]=no
727             fi 
[2605]728
729                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
730                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]731             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
[2605]732             then
[2610]733                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]734             fi
735
[2610]736                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
737                # THE WILDCARD FROM THE ENDING
738             if [[ "${s5: -1}" = "*" ]]
739             then
[2669]740                if [[ "$s2b" = "di" ]]
[2610]741                then
742                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
743                   printf "\n        see file \"$fileconnection_file\", line"
744                   printf "\n$line"
745                   locat=iofiles_file; exit
746                fi
747                multin[$iin]=true
748                string=${endin_pre[$iin]}
749                endin_pre[$iin]="${string%?}"
750             else
751                multin[$iin]=false
752             fi
[2380]753          fi
[2669]754       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
[2380]755       then
756          found=false
757          for  actual  in  $activation_string_list
758          do
759             for  formal  in  $s3 
760             do
[2670]761                [[ $actual = $formal  ||  $formal = wildcard  ]]  &&  found=true
[2380]762             done
763          done
764          if [[ $found = true ]]
765          then
766             (( iout = iout + 1 ))
[2669]767             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]768             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
769
[2669]770                # CHECK IF WILDCARD IS USED AS ACTIVATION STRING
771                # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
772             if [[ $formal = wildcard  ]]
773             then
774                warnout_pre[$iout]=false
775             else
776                warnout_pre[$iout]=true
777             fi
778
[2610]779                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
780                # THE WILDCARD FROM THE LOCAL FILENAME
781             if [[ "${s1: -1}" = "*" ]]
782             then
[2669]783                if [[ "$s2b" = "di" ]]
[2610]784                then
785                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
786                   printf "\n        see file \"$fileconnection_file\", line"
787                   printf "\n$line"
788                   locat=iofiles_file; exit
789                fi
790                multout[$iout]=true
791                string=${localout_pre[$iout]}
792                localout_pre[$iout]="${string%?}"
793             else
794                multout[$iout]=false
795             fi
[2380]796          fi
[2669]797       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
[2380]798       then
[2669]799          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
800          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]801          locat=connect; exit
802       fi
803       IFS="$IFSALT"
804    fi
805
806 done < $fileconnection_file
807
808
809
[2501]810    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]811 [[ "$palmrun_memory" != "" ]]  &&  memory=$palmrun_memory
812 [[ "$palmrun_cpumax" != "" ]]  &&  cpumax=$palmrun_cpumax
813 [[ "$palmrun_cores"  != "" ]]  &&  cores=$palmrun_cores
[2501]814 [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
815 [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
816
817
818
[2380]819      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
820 if [[ $run_coupled_model = true ]] 
821 then
822
823    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
824    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
825
826    if (( $cores_ocean + $cores_atmos != $cores ))
827    then
828
829       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
830       printf "\n      PEs (total)     : $cores"
831       printf "\n      PEs (atmosphere): $cores_atmos"
832       printf "\n      PEs (ocean)     : $cores_ocean"
833       locat=coupling; exit
834
835    fi
836
837 fi
838
839
840    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
841    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
842    # FOLDER
843 if [[ $running_in_batch_mode = true ]]
844 then
845 
[2506]846    if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]847    then
[2506]848       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]849       printf "\n      Please check the output of the palmrun-call"
850       printf "\n      that you did on your local host."
851       locat=SOURCES_FOR_RUN; exit
852    fi
853
854 else
855
856       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
857       # AUTOMATIC RESTART RUN
858       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
859    if [[ $restart_run = false ]]
860    then
861
862          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
863          # THE LOCAL HOST
864       if [[ ! -d $source_path ]]
865       then
866          printf "\n\n  +++ source path \"$source_path\" on local host"
867          printf "\n      \"$(hostname)\" does not exist"
868          locat=source_path; exit
869       fi
870
[2990]871       rm -rf   ${base_directory}/${sources_for_run_catalog}
872       mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]873
874       if [[ "$source_list" = LM ]]
875       then
876
877             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
878          source_list=""
879          cd  $source_path
880
881
[2512]882             # CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
883          if [[ ! -d ../.svn ]]
[2380]884          then
885             printf "\n\n  +++ source directory"
886             printf "\n         \"$source_path\" "
887             printf "\n         is not under control of \"subversion\"."
[2512]888             printf "\n         Please do not use palmrun-option \"-s LM\"\n"
[2380]889          fi
890
891
892             # LIST ALL MODIFIED SOURCE CODE FILES
893          Filenames=""
[2404]894          svn status  >  tmp_svnstatus
[2380]895          while  read line
896          do
897             firstc=`echo $line | cut -c1`
898             if [[ $firstc = M  ||  $firstc = "?" ]]
899             then
900                Name=`echo "$line" | cut -c8-`
901                extension=`echo $Name | cut -d. -f2`
902                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
903                then
904                   Filenames="$Filenames "$Name
905                fi
906             fi
[2404]907          done < tmp_svnstatus
908          rm -rf  tmp_svnstatus
[2380]909
910
911             # COPY FILES TO SOURCES_FOR_RUN_...
912          for  filename  in  $Filenames
913          do
[2990]914             cp  $filename  ${base_directory}/${sources_for_run_catalog}
[2380]915             source_list=$source_list"$filename "
916          done
917
918          cd -  > /dev/null
919
920
921          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
922       elif [[ "$source_list" != "" ]]
923       then
924
925          cd  $source_path
926
927          for  filename  in  $source_list
928          do
929
930                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
931             if [[ $(echo $filename | grep -c "/") != 0 ]]
932             then
933                printf "\n  +++ source code file:  $filename"
934                printf "\n      must not contain (\"/\") "
935                locat=source; exit
936             fi
937
938             if [[ ! -f $filename ]]
939             then
940                printf "\n  +++ source code file:  $filename"
941                printf "\n      does not exist"
942                locat=source; exit
943             else
[2990]944                cp  $filename  ${base_directory}/${sources_for_run_catalog}
[2380]945             fi
946
947          done
948
949          cd -  > /dev/null
950
951       fi
952
953          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
954       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
955       if [[ ! -f $makefile ]]
956       then
957          printf "\n  +++ file \"$makefile\" does not exist"
958          locat=make; exit
959       else
[2990]960          cp  $makefile  ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]961       fi
962
963
964          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]965       if [[ "$user_source_path" != "" ]]
[2380]966       then
967
968             # DOES THE DIRECTORY EXIST?
[2384]969          if [[ ! -d $user_source_path ]]
[2380]970          then
971
972             printf "\n\n  *** INFORMATIVE: additional source code directory"
[2384]973             printf "\n      \"$user_source_path\" "
[2380]974             printf "\n      does not exist or is not a directory."
975             printf "\n      No source code will be used from this directory!\n"
[2384]976             user_source_path=""
[2380]977             if [[ $silent == false ]]
978             then
979                sleep 2
980             fi
981
982          else
983
[2384]984             cd $user_source_path
[2380]985
986             Names=$(ls -1 *.f90 2>&1)
987             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
988             Names=$(ls -1 *.F90 2>&1)
989             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
990             Names=$(ls -1 *.F 2>&1)
991             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
992             Names=$(ls -1 *.f 2>&1)
993             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
994             Names=$(ls -1 *.c 2>&1)
995             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
996
997             cd -  > /dev/null
[2990]998             cd  ${base_directory}/${sources_for_run_catalog}
[2380]999
1000                # COPY MAKEFILE IF EXISTING
[2384]1001             if [[ -f $user_source_path/Makefile ]]
[2380]1002             then
1003                printf "\n\n  *** user Makefile from directory"
[2384]1004                printf "\n      \"$user_source_path\" is used \n"
[2380]1005                if [[ $silent == false ]]
1006                then
1007                   sleep 1
1008                fi
[2384]1009                cp  $user_source_path/Makefile  .
[2380]1010             fi
1011
1012             for  filename  in  $AddFilenames
1013             do
1014                if [[ -f $filename ]]
1015                then
1016                   printf "\n  +++ source code file \"$filename\" found in additional"
[2384]1017                   printf "\n      source code directory \"$user_source_path\" "
[2380]1018                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
1019                   printf "\n      from directory \"$source_path\"."
1020                   locat=source; exit
1021                fi
1022
[2384]1023                cp  $user_source_path/$filename  .
[2380]1024                source_list="$source_list $filename"
1025
1026                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
1027                if [[ $(grep -c $filename Makefile) = 0 ]]
1028                then
1029                   printf "\n\n  +++ user file \"$filename\" "
1030                   printf "\n      is not listed in Makefile \n"
1031                   locat=source; exit
1032                fi
1033             done
1034             cd -  > /dev/null
1035          fi
1036       fi
1037
1038          # COPY CONFIGURATION FILES
[2990]1039       cp  $config_file  ${base_directory}/${sources_for_run_catalog}
1040       cp  $fileconnection_file  ${base_directory}/${sources_for_run_catalog}
[2380]1041
1042          # COPY SHELLSCRIPTS
[2990]1043       cp  ${source_path}/../SCRIPTS/palmrun    ${base_directory}/${sources_for_run_catalog}
1044       cp  ${source_path}/../SCRIPTS/batch_scp  ${base_directory}/${sources_for_run_catalog}
[2380]1045
1046    fi
1047
1048 fi
1049
[2605]1050
[2380]1051    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
1052    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
1053 if [[ "$global_revision" = "" ]]
1054 then
1055    global_revision=`svnversion $source_path  2>/dev/null`
1056    global_revision="Rev: $global_revision"
1057 fi
1058
1059
1060    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
1061 if [[ -n $cores ]]
1062 then
1063
1064       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
1065       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]1066    if [[ $tasks_per_node = 0 ]]
[2380]1067    then
[3025]1068       if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1069       then
1070          printf "\n"
1071          printf "\n  +++ option \"-T\" (tasks per node) is missing"
1072          printf "\n      set -T option or define tasks_per_node in the config file"
1073          locat=tasks_per_node; (( iec = 0 )); exit
1074       else
1075             # DEFAULT FOR INTERACTIVE RUN
1076          tasks_per_node=$cores
1077       fi
[2380]1078    fi
1079
1080    if (( cores < tasks_per_node ))
1081    then
1082       printf "\n"
1083       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
1084       printf "\n      given values: -T $tasks_per_node  -X $cores"
1085       locat=tasks_per_node; (( iec = 0 )); exit
1086    fi
1087
1088    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
1089    (( mpi_tasks = cores / threads_per_task ))
1090    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
1091    (( ii = cores / tasks_per_node ))
1092    (( remaining_cores =  cores - ii * tasks_per_node ))
1093    if (( remaining_cores > 0 ))
1094    then
1095       printf "\n"
1096       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
1097       printf "\n      divisor of the total number of cores (option \"-X\")"
1098       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
1099       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
1100       (( nodes = nodes + 1 ))
1101    fi
1102
1103 fi
1104
1105
1106    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
1107 if [[ "$maximum_parallel_io_streams" = "" ]]
1108 then
1109    maximum_parallel_io_streams=$cores
1110 fi
1111
1112
1113    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
1114 if [[ "$scp_port" != "" ]]
1115 then
1116    PORTOPT="-P $scp_port"
1117    SSH_PORTOPT="-p $scp_port"
1118 fi
1119
1120
1121    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
1122    # CONFIG-FILE
1123 if [[ "$ssh_key" != "" ]]
1124 then
1125    ssh_key="-i $HOME/.ssh/$ssh_key"
1126 fi
1127
1128
1129    # SET QUEUE, IF NOT GIVEN
1130 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1131 then
1132
1133    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
1134    then
1135       printf "\n"
1136       printf "\n  +++ no default queue given in configuration file and no queue"
1137       printf "\n      given with option -q"
[2789]1138       locat=queue; exit
[2380]1139    fi
1140    if [[ $queue = none ]]
1141    then
1142       queue=$defaultqueue
1143    fi
1144
1145 fi
1146
1147
1148    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
1149    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
1150 (( i = 0 ))
[2610]1151 (( nr_of_input_files = 0 ))
[2380]1152 while (( i < iin ))
1153 do
1154    (( i = i + 1 ))
1155
1156       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1157       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]1158    if [[ "${actionin_pre[$i]}" = di ]]
[2380]1159    then
[2610]1160       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]1161    else
[3236]1162       eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]1163    fi
1164
[2610]1165
[2380]1166       # CHECK IF FILE EXISTS
1167    if ! ls $filename* 1>/dev/null 2>&1
1168    then
1169
[2669]1170          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
1171       if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]1172       then
1173          printf "\n\n  +++ INPUT-file: "
[2610]1174          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
[2380]1175          then
1176             printf "\n           $filename"
1177          else
[2610]1178             printf "\n           $filename.${extin_pre[$i]}"
[2380]1179          fi
1180          printf "\n      does not exist\n"
1181          locat=input; exit
1182       else
[2610]1183          (( nr_of_input_files = nr_of_input_files + 1 ))
1184          localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]1185          optin[$nr_of_input_files]="${optin_pre[$i]}"
1186          actionin[$nr_of_input_files]="unavailable"
[2610]1187          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1188          endin[$nr_of_input_files]="${endin_pre[$i]}"
1189          extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]1190       fi
[2605]1191
[2380]1192    else
1193
[3236]1194          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
1195          # ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
1196          # ENDINGS
[2610]1197       if [[ "${multin[$i]}" = true ]]
1198       then
1199             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
1200          ls -1 -d ${filename}    >   filelist  2>/dev/null
1201          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
1202          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null
[2380]1203
[2610]1204          endings=""
1205          while  read line
1206          do
1207                 # filename without path (i.e. after the last "/")
1208              basefilename=$(basename ${line})
[2380]1209
[2610]1210                 # check if there is an extension and remove it
1211              ext=${basefilename##*.}
1212              if [[ "$ext" = "${extin_pre[$i]}" ]]
1213              then
1214                 basefilename=${basefilename%.*}
1215              fi
[2380]1216
[2610]1217                 # check for an existing cycle number and remove it
1218              cycle=${basefilename##*.}
1219              if [[ $cycle =~ ^-?[0-9]+$ ]]
1220              then
1221                 basefilename=${basefilename%.*}
1222              fi
[2600]1223
[3236]1224                 # remove the run_identifier from the beginning
1225              length_run_identifier=${#run_identifier}
1226              ending=${basefilename:${length_run_identifier}}
[2610]1227
1228                 # remove the ending given in the .iofiles from the beginning
1229              endingstring="${endin_pre[$i]}"
1230              length_ending=${#endingstring}
1231              ending=${ending:${length_ending}}
1232
1233              if [[ "$ending" = "" ]]
[2600]1234              then
[2610]1235                    # standard ending as given in the .iofiles
1236                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
1237                 then
1238                    endings="$endings DEFAULT"
1239                 fi
[2600]1240              else
[2610]1241                    # ending must start with "_", otherwise its a different file
1242                 if [[ "${ending:0:1}" = "_" ]]
1243                 then
1244                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
1245                    then
1246                       endings="$endings $ending"
1247                    fi
1248                 fi
[2600]1249              fi
[2610]1250 
1251          done <filelist
[2380]1252
[2610]1253          rm filelist
[2380]1254
[2600]1255       else
[2610]1256
1257             # SINGLE NAME
1258          endings=DEFAULT
1259
[2600]1260       fi
1261
[2610]1262          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
1263       for  ending  in  $endings
1264       do
1265
1266             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
1267          if [[ $ending = DEFAULT ]]
[2380]1268          then
[2610]1269             ending=""
1270          fi
1271
1272             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
1273          (( nr_of_input_files = nr_of_input_files + 1 ))
1274          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]1275          optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]1276          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
1277          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
1278          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
1279          extin[$nr_of_input_files]="${extin_pre[$i]}"
1280
1281
1282             # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
1283             # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
1284          if [[ "${actionin[$nr_of_input_files]}" = di ]]
1285          then
1286             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]1287          else
[3236]1288             eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]1289          fi
[2610]1290
1291             # DETERMINE THE FILE'S CYCLE NUMBER
1292          (( maxcycle = 0 ))
1293          ls -1 -d $filename    >   filelist  2>/dev/null
1294          ls -1 -d $filename.*  >>  filelist  2>/dev/null
1295          while  read line
1296          do
1297                 # filename without path (i.e. after the last "/")
1298              basefilename=$(basename ${line})
1299   
1300                 # check if there is an extension
1301              extension=${basefilename##*.}
1302              if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
1303              then
1304                 basefilename=${basefilename%.*}
1305              fi
1306   
1307                 # check for an existing cycle number
1308              cycle=${basefilename##*.}
1309              if [[ $cycle =~ ^-?[0-9]+$ ]]
1310              then
[2669]1311                    # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
1312                    # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
1313                 (( icycle = $((10#$cycle)) ))
[2610]1314              else
1315                 (( icycle = 0 ))
1316              fi
1317   
1318              if (( icycle > maxcycle ))
1319              then
1320                 (( maxcycle = icycle ))
1321   
1322                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
1323                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
1324                 if [[ $(echo $cycle | cut -c1) = 0 ]]
1325                 then
1326                    leading_zero=true
1327                 else
1328                    leading_zero=false
1329                 fi
1330              fi
1331   
1332          done <filelist
1333          rm filelist
1334   
1335             # MAKE CYCLE NUMBER THREE DIGITS WIDE
1336          if [[ $leading_zero = true ]]
[2380]1337          then
[2610]1338             cyclestring=`printf "%03d" $maxcycle`
1339          else
1340             cyclestring=$maxcycle
[2380]1341          fi
[2610]1342   
1343             # APPEND CYCLE NUMBER TO FILENAME
1344          if (( maxcycle > 0 ))
[2380]1345          then
[2610]1346             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1347             then
1348                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
1349             else
1350                filename=${filename}.$cyclestring
1351             fi
[2380]1352          else
[2610]1353             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
1354             then
1355                filename=${filename}.${extin[$nr_of_input_files]}
1356             fi
[2380]1357          fi
[2610]1358         
1359             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
1360             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
1361          absnamein[$nr_of_input_files]=$filename
1362          if (( maxcycle > 0 ))
[2380]1363          then
[2610]1364             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1365             then
1366                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
1367             else
[3236]1368                frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]1369             fi
[2380]1370          else
[2610]1371             if [[ "${actionin[$nr_of_input_files]}" = di ]]
1372             then
1373                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
1374             else
[3236]1375                frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]1376             fi
[2380]1377          fi
1378
[2610]1379       done
1380
[2380]1381    fi
[2610]1382
[2380]1383 done
1384
[2610]1385
[2380]1386    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
1387    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
1388    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED 
[2610]1389    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]1390    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
1391    # REMOTE HOST)
1392 (( i = 0 ))
1393 while (( i < iout ))
1394 do
1395    (( i = i + 1 ))
[2610]1396    if [[ ! ( $running_on_remote = true  &&  ( "${actionout_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]1397    then
[2610]1398       if [[ "${actionout_pre[$i]}" = tr ]]
[2380]1399       then
[2610]1400          actionout_pre[$i]=""
1401       elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]1402       then
[2610]1403          actionout_pre[$i]=pe
1404       elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]1405       then
[2610]1406          actionout_pre[$i]=a
[2380]1407       fi
1408       (( maxcycle = 0 ))
[3236]1409       eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]1410       eval catalogname=${pathout_pre[$i]}
[2380]1411       if ! ls $filename* 1>/dev/null 2>&1
1412       then
1413     
1414             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
1415          if  cat /dev/null > $filename 
1416          then
1417             rm  $filename
1418          else
1419
1420                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
1421                # IF IT DOES NOT EXIST, TRY TO CREATE IT
1422             if [[ ! -d $catalogname ]]
1423             then
1424                if  mkdir -p  $catalogname
1425                then
1426                   printf "\n\n  *** directory:"
1427                   printf "\n           $catalogname"
1428                   printf "\n      was created\n"
1429                else
1430                   printf "\n\n  +++ OUTPUT-file:"
1431                   printf "\n           $filename"
1432                   printf "\n      cannot be created, because directory does not exist"
1433                   printf "\n      and cannot be created either"
1434                   printf "\n"
1435                   locat=output  ; exit
1436                fi 2>/dev/null
1437             else
1438                printf "\n\n  +++ OUTPUT-file:"
1439                printf "\n           $filename"
1440                printf "\n      cannot be created, although directory exists"
1441                printf "\n"
1442                locat=output  ; exit
1443             fi
1444          fi 2>/dev/null
1445
1446       fi
1447
1448    fi
1449 done
1450
1451
1452    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
1453 if [[ $running_in_batch_mode = false ]]
1454 then
[3236]1455    run_id_number=$RANDOM
1456    run_id=${run_identifier}.$run_id_number
[2380]1457
[3236]1458    tempdir=$fast_io_catalog/$run_id
[3346]1459
1460       # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
1461    export job_id=$run_id
1462
[2380]1463 fi
1464
1465
1466    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
1467 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1468 then
1469
1470       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
1471    if [[ $ibd = 0 ]]
1472    then
1473       printf "\n"
1474       printf "\n  +++ no batch directives found in configuration file"
1475       locat=config_file_batch_directives; (( iec = 0 )); exit
1476    fi
1477
1478       # CHECK IF CPUTIME IS GIVEN FOR JOB
1479    done=false
[2384]1480    cputime=$cpumax
[2380]1481    while [[ $done = false ]]
1482    do
[2384]1483       if (( cputime == 0 ))
[2380]1484       then
1485          printf "\n  +++ cpu-time is undefined"
1486          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
1487          printf "\n  >>> "
[2384]1488          read  cputime   1>/dev/null  2>&1
[2380]1489       else
1490          done=true
1491       fi
1492    done
[2420]1493    cpumax=$cputime
[2380]1494
1495       # CHECK THE MEMORY DEMAND
1496    done=false
1497    while [[ $done = false ]]
1498    do
1499       if (( memory == 0 ))
1500       then
1501          printf "\n  +++ memory demand is undefined"
1502          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
1503          printf "\n  >>> "
1504          read  memory  1>/dev/null  2>&1
1505       else
1506          done=true
1507       fi
1508    done
1509
1510       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
1511    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
1512    then
1513       while [[ -z $remote_username ]]
1514       do
[2420]1515          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]1516          printf "\n  >>> Please type username:"
1517          printf "\n  >>> "
1518          read  remote_username
1519       done
1520    fi
1521
1522 else
1523
[2420]1524    if [[ $running_in_batch_mode = false ]]
1525    then
1526       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
1527       cpumax=$cputime
1528    else
1529       cputime=$cpumax
1530    fi
[2380]1531
1532 fi
1533
1534
1535    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
1536 (( cpu_hours  = cputime / 3600 ))
1537 (( resttime = cputime - cpu_hours * 3600 ))
1538 (( cpu_minutes  = resttime / 60 ))
1539 (( cpu_seconds = resttime - cpu_minutes * 60 ))
1540 timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
1541
1542
1543    # OUTPUT OF THE PALMRUN-HEADER
1544 calltime=$(date)
1545 printf "\n"
1546 printf "#------------------------------------------------------------------------# \n"
1547 printf "| %-35s%35s | \n" "$version" "$calltime"
[3151]1548 printf "| %-35s%35s | \n" "PALM code    $global_revision" " "
[2380]1549 printf "|                                                                        | \n"
1550 column1="called on:"; column2=$(hostname)
1551 printf "| %-25s%-45s | \n" "$column1" "$column2"
1552 if [[ $create_remote_batch_job = true ]]
1553 then
[3236]1554    column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]1555 else
1556    if [[ $running_on_remote = true ]]
1557    then
[3236]1558       column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]1559    else
[3236]1560       column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]1561    fi
1562 fi
1563 printf "| %-25s%-45s | \n" "$column1" "$column2"
1564
1565 column1="running in:"
1566 if [[ $running_in_batch_mode = true ]]
1567 then
1568    column2="batch job mode"
1569 else
1570    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1571    then
1572       column2="job creation mode"
1573    else
1574       column2="interactive run mode"
1575    fi
1576 fi
1577 printf "| %-25s%-45s | \n" "$column1" "$column2"
1578
[2479]1579 if  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1580 then
[2480]1581    if [[ "$project_account" != "" ]]
[2479]1582    then
1583       column1="project account number:"
1584       column2="$project_account"
1585       printf "| %-25s%-45s | \n" "$column1" "$column2"
1586    fi
1587 fi
1588
[2380]1589 if [[ -n $cores ]]
1590 then
1591    if [[ $run_coupled_model = false ]]
1592    then
1593       column1="number of cores:"; column2=$cores
1594    else
1595       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
1596    fi
1597    printf "| %-25s%-45s | \n" "$column1" "$column2"
1598 fi
1599 if [[ -n $tasks_per_node ]]
1600 then
1601    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
1602    printf "| %-25s%-45s | \n" "$column1" "$column2"
1603    if (( remaining_cores > 0 ))
1604    then
1605       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
1606       printf "| %-25s%-45s | \n" "$column1" "$column2"
1607    fi
1608 fi
1609 if [[ $maximum_parallel_io_streams != $cores ]]
1610 then
1611    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
1612    printf "| %-25s%-45s | \n" "$column1" "$column2"
1613 fi
1614 if [[ $use_openmp = true ]]
1615 then
1616    column1="threads per task:"; column2="$threads_per_task"
1617    printf "| %-25s%-45s | \n" "$column1" "$column2"
1618 fi
[2384]1619 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
1620 then
[2506]1621    column1="memory demand / PE":; column2="$memory MB"
1622    printf "| %-25s%-45s | \n" "$column1" "$column2"
[2384]1623    column1="job cpu time (h:m:s):"; column2="$timestring"
1624    printf "| %-25s%-45s | \n" "$column1" "$column2"
1625 fi
[2380]1626 printf "|                                                                        | \n"
1627 if [[ "$source_list" != "" ]]
1628 then
1629    if [[ "$make_options" != "" ]]
1630    then
1631       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
1632       printf "| %-25s%-45s | \n" "$column1" "$column2"
1633       line=$(echo "$make_options" | cut -c46-)
1634       while [[ "$line" != "" ]]
1635       do
1636          column1=""
1637          column2=$(echo "$line" | cut -c-45)
1638          printf "| %-25s%-45s | \n" "$column1" "$column2"
1639          line=$(echo "$line" | cut -c46-)
1640       done
1641    fi
1642 fi
1643
1644 column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
1645 printf "| %-25s%-45s | \n" "$column1" "$column2"
1646 line=$(echo "$cpp_options" | cut -c46-)
1647 while [[ "$line" != "" ]]
1648 do
1649    column1=""
1650    column2=$(echo "$line" | cut -c-45)
1651    printf "| %-25s%-45s | \n" "$column1" "$column2"
1652    line=$(echo "$line" | cut -c46-)
1653 done
1654
1655 column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
1656 printf "| %-25s%-45s | \n" "$column1" "$column2"
1657 line=$(echo "$compiler_options" | cut -c46-)
1658 while [[ "$line" != "" ]]
1659 do
1660    column1=""
1661    column2=$(echo "$line" | cut -c-45)
1662    printf "| %-25s%-45s | \n" "$column1" "$column2"
1663    line=$(echo "$line" | cut -c46-)
1664 done
1665
[2388]1666 column1="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
[2380]1667 printf "| %-25s%-45s | \n" "$column1" "$column2"
[2388]1668 line=$(echo "$linker_options" | cut -c46-)
[2380]1669 while [[ "$line" != "" ]]
1670 do
1671    column1=""
1672    column2=$(echo "$line" | cut -c-45)
1673    printf "| %-25s%-45s | \n" "$column1" "$column2"
1674    line=$(echo "$line" | cut -c46-)
1675 done
1676
1677 if [[ "$login_init_cmd" != "" ]]
1678 then
1679    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
1680    printf "| %-25s%-45s | \n" "$column1" "$column2"
1681    line=$(echo "$login_init_cmd" | cut -c46-)
1682    while [[ "$line" != "" ]]
1683    do
1684       column1=""
1685       column2=$(echo "$line" | cut -c-45)
1686       printf "| %-25s%-45s | \n" "$column1" "$column2"
1687       line=$(echo "$line" | cut -c46-)
1688    done
1689 fi
1690
1691 if [[ "$module_commands" != "" ]]
1692 then
1693    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
1694    printf "| %-25s%-45s | \n" "$column1" "$column2"
1695    line=$(echo "$module_commands" | cut -c46-)
1696    while [[ "$line" != "" ]]
1697    do
1698       column1=""
1699       column2=$(echo "$line" | cut -c-45)
1700       printf "| %-25s%-45s | \n" "$column1" "$column2"
1701       line=$(echo "$line" | cut -c46-)
1702    done
1703 fi
1704 printf "|                                                                        | \n"
[3236]1705 column1="run identifier:"; column2=$run_identifier
[2380]1706 printf "| %-25s%-45s | \n" "$column1" "$column2"
1707 column1="activation string list:"; column2=$(echo $activation_string_list)
1708 printf "| %-25s%-45s | \n" "$column1" "$column2"
1709
1710 if [[ "$ocean_file_appendix" = true ]]
1711 then
1712    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
1713 fi
1714
1715 if [[ "$source_list" != "" ]]
1716 then
1717    printf "|                                                                        | \n"
1718    printf "| Files to be compiled:                                                  | \n"
1719    line=$source_list
1720    while [[ "$line" != "" ]]
1721    do
1722       linestart=$(echo $line | cut -c-70)
1723       printf "| %-70s | \n" "$linestart"
1724       line=$(echo "$line" | cut -c71-)
1725    done
1726 fi
1727 printf "#------------------------------------------------------------------------#"
1728
1729
1730
1731    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
1732 if [[ $do_trace = true ]]
1733 then
1734    (( i = 0 ))
[2610]1735    while (( i < nr_of_input_files ))
[2380]1736    do
1737       (( i = i + 1 ))
1738       if (( i == 1 ))
1739       then
1740          printf "\n\n >>> INPUT-file assignments:\n"
1741       fi
1742       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
1743    done
1744    (( i = 0 ))
1745    while (( i < iout ))
1746    do
1747       (( i = i + 1 ))
1748       if (( i == 1 ))
1749       then
1750          printf "\n\n >>> OUTPUT-file assignments:\n"
1751       fi
1752       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
1753    done
1754    (( i = 0 ))
1755    while (( i < iic ))
1756    do
1757       (( i = i + 1 ))
1758       if (( i == 1 ))
1759       then
1760          printf "\n\n >>> INPUT-commands:\n"
1761       fi
1762       printf "\n     ${in_command[$i]}" 
1763    done
1764    (( i = 0 ))
1765    while (( i < ioc ))
1766    do
1767       (( i = i + 1 ))
1768       if (( i == 1 ))
1769       then
1770          printf "\n\n >>> OUTPUT-commands:\n"
1771       fi
1772       printf "\n     ${out_command[$i]}" 
1773    done
1774 fi
1775
1776    # QUERY FOR CONTINUE
1777 if [[ $silent = false  &&  $running_in_batch_mode = false ]]
1778 then
1779    antwort=dummy
1780    printf "\n\n"
1781    printf " >>> everything o.k. (y/n) ?  "
1782    while  read antwort
1783    do
1784       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1785       then
1786          printf " >>> everything o.k. (y/n) ?  "
1787       else
1788          break
1789       fi
1790    done
1791    if [[ $antwort = n  ||  $antwort = N ]]
1792    then
1793       locat=user_abort; (( iec = 0 )); exit
1794    fi
1795    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
1796    then
[2566]1797       printf "\n ***  batch-job will be created and submitted"
[2380]1798    else
[2566]1799       printf "\n ***  PALMRUN will now continue to execute on this machine"
[2380]1800    fi
1801 fi
1802
1803 
1804
1805    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
1806 if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
1807 then
1808
1809    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
1810    then
[2566]1811       printf "\n\n  *** creating executable and other sources for the remote host\n"
[2380]1812    else
[2566]1813       printf "\n\n  *** creating executable and other sources for the local host\n"
[2380]1814    fi
1815
[2422]1816       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
1817       # IT SHALL BE CREATED
1818    ask_for_make_depository=false
1819    if [[ $create_remote_batch_job = true ]]
1820    then
1821
1822       line=`grep %base_directory $config_file`
[3236]1823       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
1824       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]1825
[3236]1826       if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]1827       then
1828          printf "\n\n  +++ make depository \"${make_depository}\""
1829          printf "\n      on remote host not found!"
1830          ask_for_make_depository=true
1831       fi
[3236]1832       rm ${configuration_identifier}_last_make_protokoll
[2422]1833
1834    else
1835
1836          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]1837       make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]1838       if [[ ! -d ${make_depository} ]]
1839       then
1840          printf "\n\n  +++ make depository \"${make_depository}\""
1841          printf "\n      on local host not found!"
1842          ask_for_make_depository=true
1843       fi
1844
1845    fi
1846
1847    if [[ $ask_for_make_depository = true ]]
1848    then
1849
1850       antwort=dummy
1851       printf "\n\n"
1852       printf "  >>> Create a new one (y/n) ?  "
1853       while  read antwort
1854       do
1855          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
1856          then
1857             printf "  >>> Create a new one (y/n) ?  "
1858          else
1859             break
1860          fi
1861       done
1862       if [[ $antwort = n  ||  $antwort = N ]]
1863       then
1864          locat=user_abort; (( iec = 0 )); exit
1865       fi
1866
[2566]1867       if [[ $do_trace = true ]]
1868       then
[3455]1869          palmbuild  -c $configuration_identifier
[2566]1870       else
[3455]1871          palmbuild  -v  -c $configuration_identifier
[2566]1872       fi
[2422]1873
[3312]1874       if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]1875       then
1876   
1877              # ABORT IN CASE OF COMPILATION PROBLEMS
1878          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
1879          locat=make_depository
1880          exit
1881       else
1882          echo "  *** now continue with creating executable and other sources"
1883       fi
1884
1885    fi
1886
[2566]1887       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]1888    palmbuild  -v  $use_existing_sources_folder  -c $configuration_identifier  -r $run_identifier
[2380]1889
[3312]1890    if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]1891    then
1892
1893           # ABORT IN CASE OF COMPILATION PROBLEMS
1894       printf "\n  +++ error while creating executable and/or other sources"
1895       locat=execution
[2990]1896       rm -rf  ${base_directory}/${sources_for_run_catalog}
[2380]1897       exit
1898
1899    else
1900
[2566]1901       printf "  *** executable and other sources created\n"
[2990]1902       rm -rf  ${base_directory}/${sources_for_run_catalog}
[2380]1903
1904    fi
1905
1906 fi
1907
1908
[2669]1909    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
1910    # WILL BE COPIED TO THE REMOTE HOST
[2605]1911 if [[ $create_remote_batch_job = true ]]
1912 then
1913    (( i = 0 ))
[2610]1914    while (( i < nr_of_input_files ))
[2605]1915    do
1916       (( i = i + 1 ))
[2669]1917       if [[ "${actionin[$i]}" = tr ]]
[2605]1918       then
1919          eval inputfile=${pathin[$i]}/${frelin[$i]}
1920          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
1921       fi
1922    done
1923    if (( i > 0 ))
1924    then
[3025]1925       printf "\n\n  *** input files have been copied to the remote host\n"
[2605]1926    fi
1927 fi
1928 
1929
[2380]1930    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
1931    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
1932 if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
1933 then
1934
1935       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
1936    if [[ $running_in_batch_mode = false ]]
1937    then
1938          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
1939          # FOLDER
[2566]1940       mkdir -p  $tempdir
1941       chmod  go+rx  $tempdir
1942       cd  $tempdir
1943       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $tempdir
1944       printf "\n  *** changed to temporary directory: $tempdir"
[2380]1945
1946    else
1947
1948          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]1949       printf "\n  *** running in temporary directory: $tempdir"
[2380]1950
1951    fi
1952
1953
1954       # PROVIDE THE INPUT FILES
1955       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]1956    optional_files_missing=false
[2380]1957    (( i = 0 ))
[2610]1958    while (( i < nr_of_input_files ))
[2380]1959    do
1960       (( i = i + 1 ))
1961       if (( i == 1 ))
1962       then
1963          printf "\n\n  *** providing INPUT-files:\n$dashes"
1964       fi
1965
1966
1967          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]1968       if [[ "${actionin[$i]}" = unavailable ]]
[2380]1969       then
[2669]1970          optional_files_missing=true
[2380]1971          continue
1972       fi
1973
1974          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
1975       files_for_cores=false; filetype=file
1976       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
1977       then
1978          files_for_cores=true; filetype=files
1979          actionin[$i]=""
1980       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
1981       then
1982          actionin[$i]=""
1983       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
1984       then
1985          files_for_cores=true; filetype=files
1986          actionin[$i]="ln"
1987       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
1988       then
1989          actionin[$i]="ln"
1990       fi
1991
1992       if [[ $files_for_cores = true ]]
1993       then
1994          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
1995       else
1996          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
1997       fi
1998
1999          # INPUT-FILES TO BE LINKED
2000       if [[ "${actionin[$i]}" = ln ]]
2001       then
2002
2003          printf "\n      $filetype will be linked"
2004          if [[ $files_for_cores = false ]]
2005          then
2006             if [[ -f "${absnamein[$i]}" ]]
2007             then
2008                ln  ${absnamein[$i]}  ${localin[$i]}
2009                got_tmp[$i]=true
2010             fi
2011          else
2012             if [[ -d "${absnamein[$i]}" ]]
2013             then
[2396]2014                mkdir -p ${localin[$i]}
[2380]2015                cd ${absnamein[$i]}
2016                for file in $(ls *)
2017                do
[2566]2018                   ln $file $tempdir/${localin[$i]}
[2380]2019                done >|/dev/null 2>&1
[2566]2020                cd $tempdir
[2380]2021             fi
2022
2023                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
2024             if [[ ! -f "${localin[$i]}/_000000" ]]
2025             then
2026                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2027                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
2028             fi
2029
2030             got_tmp[$i]=true
2031          fi
2032       fi
2033
2034          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]2035       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "tr"  ||  "${actionin[$i]}" = "npe" ]]
[2380]2036       then
2037
2038          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
2039          then
2040
2041                # FILE COPIES ARE PROVIDED FOR ALL CORES
2042                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
2043             printf "\n      file will be provided for $cores processors"
[2396]2044             mkdir -p ${localin[$i]}
[2380]2045             ival=$cores
2046             (( ii = 0 ))
2047             while (( ii <= ival-1 ))
2048             do
2049                if (( ii < 10 ))
2050                then
2051                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
2052                elif (( ii < 100 ))
2053                then
2054                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
2055                elif (( ii < 1000 ))
2056                then
2057                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
2058                else
2059                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
2060                fi
2061                (( ii = ii + 1 ))
2062             done
2063
2064          else
2065
2066             if [[ $files_for_cores = true ]]
2067             then
2068
2069                   # PROVIDE FILES FOR EACH CORE
2070                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
2071                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
2072                printf "\n      providing $cores files for the respective cores"
[2396]2073                mkdir -p ${localin[$i]}
[2380]2074                        if [[ $link_local_input = true ]]
2075                              then
2076                                 printf "      files will be linked\n"
2077                                 cd ${absnamein[$i]}
2078                                 for file in $(ls *)
2079                                 do
2080                                    ln -f $file  ${localin[$i]}
2081                                 done
[2566]2082                                 cd $tempdir
[2380]2083                              fi
2084
2085                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
2086                              if [[ ! -f "${localin[$i]}/_000000" ]]
2087                              then
2088                                 if [[ $link_local_input = true ]]
2089                                        then
2090                                        printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2091                                 fi
2092                                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
2093                              fi
2094
2095             else
2096
2097                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
2098                        if [[ $link_local_input = true ]]
2099                        then
2100                                 printf "      file will be linked\n"
2101                                 ln -f  ${absnamein[$i]}  ${localin[$i]}
2102                        fi
[2605]2103                                # If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]2104                        if [[ ! -f "${localin[$i]}" ]]
2105                then
2106                                 if [[ $link_local_input = true ]]
2107                          then
2108                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
2109                                 fi
[2669]2110                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
[2605]2111                   then
2112                      mv  ${absnamein[$i]}  ${localin[$i]}
2113                   else
2114                                 cp  ${absnamein[$i]}  ${localin[$i]}
2115                   fi
[2380]2116                fi
2117             fi
2118          fi
2119       fi
2120
2121    done
2122    if (( i != 0 ))
2123    then
[2669]2124       if [[ $optional_files_missing = true ]]
2125       then
2126          printf "\n  *** INFORMATIVE: some optional INPUT-files are not present"
2127       fi
[2380]2128       printf "\n$dashes\n  *** all INPUT-files provided \n"
2129    fi
2130
2131
2132       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2133    (( i = 0 ))
2134    while (( i < iic ))
2135    do
2136       (( i = i + 1 ))
2137       if (( i == 1 ))
2138       then
2139          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
2140       fi
2141       printf "\n  >>> ${in_command[$i]}"
2142       eval  ${in_command[$i]}
2143       if (( i == iic ))
2144       then
2145          printf "\n$dashes\n"
2146       fi
2147    done
2148
2149
[3313]2150    # CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
2151    if [[ $running_in_batch_mode = true  ||  $running_in_test_mode = true ]]
2152    then
2153       progress_bar_disabled=true
2154    else
2155       progress_bar_disabled=false
2156    fi
2157
2158
[2380]2159       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
2160       # (FILE ENVPAR WILL BE READ BY PALM)
2161    cat  >  ENVPAR  <<  EOF
[3236]2162 &envpar  run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]2163          write_svf = .${write_svf}., write_binary = .${write_binary}.,
2164          read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]2165          maximum_parallel_io_streams = $maximum_parallel_io_streams,
2166          maximum_cpu_time_allowed = ${cpumax}.,
2167          revision = '$global_revision',
[3313]2168          progress_bar_disabled = .${progress_bar_disabled}. /
[2380]2169
2170EOF
2171
2172
2173       # STARTING THE EXECUTABLE
2174    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
[2566]2175    PATH=$PATH:$tempdir
[2380]2176
2177
2178       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]2179    line=`echo  "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//g'`
2180    line2=`echo  "${execute_command}" | sed 's/{{mpi_tasks}}/1/g' | sed 's/{{tasks_per_node}}/1/g' | sed 's/palm/combine_plot_fields.x/g'`
[2380]2181    eval line=\"$line\"
2182    execute_command="$line"
2183
2184
2185       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]2186    if [[ "$execute_command_for_combine" = "" ]]
2187    then
2188       eval line2=\"$line2\"
2189       execute_command_for_combine="$line2"
2190    fi
2191   
[2380]2192
2193
2194       # PROVIDE A HOSTFILE, IF REQUIRED
2195    if [[ "$hostfile" != "" ]]
2196    then
2197
2198       if [[ $hostfile = auto ]]
2199       then
2200             # CREATE A NEW HOSTFILE
2201          (( ii = 1 ))
2202          while (( ii <= cores / threads_per_task ))
2203          do
2204             echo  $(hostname)  >>  hostfile
2205             (( ii = ii + 1 ))
2206          done
2207          if (( cores / threads_per_task == 0 ))
2208          then
2209             echo  $(hostname)  >>  hostfile
2210          fi
2211       
2212       else
2213          cp  $hostfile  hostfile
2214       fi
2215       eval line=\"`head -n $ii  hostfile`\"
2216       printf "\n  *** running on: $line"
2217    fi
2218
2219
2220
2221       # SET THE NUMBER OF OPENMP-THREADS
2222    if [[ $use_openmp = true ]]
2223    then
2224       export OMP_NUM_THREADS=$threads_per_task
2225       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
2226    else
2227       export OMP_NUM_THREADS=1
2228    fi
2229
2230
[2610]2231       # PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]2232    if [[ $run_coupled_model = false ]]
2233    then
2234       if [[ "$ocean_file_appendix" = true ]]
2235       then
2236          echo "precursor_ocean"  >  coupling_steering
2237       else
2238          echo "precursor_atmos"  >  coupling_steering
2239      fi
2240    else
2241       (( iia = $cores_atmos / $threads_per_task ))
2242       (( iio = $cores_ocean / $threads_per_task ))
2243       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
2244       printf "\n\n"
2245       echo "coupled_run $iia $iio"  >  coupling_steering
2246    fi
2247
2248    printf "\n  *** execute command:"
2249    printf "\n      \"$execute_command\" \n\n"
2250
2251
[3393]2252    if [[ $progress_bar_disabled = true ]]
[2380]2253    then
[3402]2254       $execute_command  <  coupling_steering  &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]2255       exit_code=${PIPESTATUS[0]}
2256    else
2257       $execute_command  <  coupling_steering  &> >(tee STDOUT)
2258       exit_code=${PIPESTATUS[0]}
2259    fi
[2380]2260
[3393]2261    if [[ ${exit_code} != 0 ]]
2262    then
2263
[2380]2264           # ABORT IN CASE OF RUNTIME ERRORS
2265       printf "\n  +++ runtime error occured"
2266       locat=execution
2267       exit
2268
2269    else
2270
2271       printf "\n$dashes\n  *** execution finished \n"
2272
2273    fi
2274
2275
2276       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
2277       # BY EACH CORE INTO ONE FILE
2278   if [[ ! -f combine_plot_fields.x ]]
2279   then
2280
2281      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
2282      printf "\n      2d- and/or 3d-data may be incomplete!"
2283      printf "\n      Your previous palmbuild may have failed. Please check.\n"
2284
2285   elif [[ "$combine_plot_fields" == true ]]
2286   then
2287
2288      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
2289      $execute_command_for_combine
2290
2291   else
2292
2293         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]2294         # DATA OUTPUT
[2380]2295      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
2296   fi
2297
2298
2299
2300       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
2301    (( i = 0 ))
2302    while (( i < ioc ))
2303    do
2304       (( i = i + 1 ))
2305       if (( i == 1 ))
2306       then
2307          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
2308       fi
[2799]2309
2310          # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
2311       out_command[$i]=`echo  "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
2312
[2380]2313       printf "\n  >>> ${out_command[$i]}"
2314       eval  ${out_command[$i]}
2315       if (( i == ioc ))
2316       then
2317          printf "\n$dashes\n"
2318       fi
2319    done
2320
2321
[2610]2322       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
2323       # WILDCARDS
[2380]2324    (( i = 0 ))
[2610]2325    (( nr_of_output_files = 0 ))
2326
[2380]2327    while (( i < iout ))
2328    do
[2610]2329
[2380]2330       (( i = i + 1 ))
[2610]2331
2332          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
2333          # CREATE A LIST FOR THE DETECTED ENDINGS
2334       if [[ "${multout[$i]}" = true ]]
2335       then
2336             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
2337          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
2338          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null
2339
2340          endings="DEFAULT"
2341          while  read line
2342          do
2343                 # remove the local name from the beginning
2344              localnamestring="${localout_pre[$i]}"
2345              length_localname=${#localnamestring}
2346              ending=${line:${length_localname}}
2347
2348              if [[ "$ending" != "" ]]
2349              then
2350                 endings="$endings $ending"
2351              fi
2352 
2353          done <filelist
2354
2355          rm filelist
2356
2357       else
2358
2359             # SINGLE NAME
2360          endings=DEFAULT
2361
2362       fi
2363
2364          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
2365       for  ending  in  $endings
2366       do
2367
2368             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
2369          if [[ $ending = DEFAULT ]]
2370          then
2371             ending=""
2372          fi
2373
2374             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
2375          (( nr_of_output_files = nr_of_output_files + 1 ))
2376          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
2377          transout[$nr_of_output_files]="${transout_pre[$i]}"
2378          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
2379          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
2380          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
2381          extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]2382          warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]2383
2384       done
2385
2386    done
2387
2388
2389
2390
2391       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
2392    (( i = 0 ))
2393    while (( i < nr_of_output_files ))
2394    do
2395       (( i = i + 1 ))
[2380]2396       if (( i == 1 ))
2397       then
2398          printf "\n\n  *** saving OUTPUT-files:"
2399
2400             # GET RUN NUMBER ASSIGNED BY PALM
2401          if [[ -f RUN_NUMBER ]]
2402          then
2403              read  run_number  <  RUN_NUMBER
2404              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
2405              usecycle_option="-U $run_number"
2406          else
2407              run_number=0
2408              usecycle_option=""
2409          fi
2410          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
2411          then
[2404]2412             printf "\n  *** in case of SCP transfers to local host"
2413             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
[2380]2414          fi
2415          printf "\n$dashes"
2416       fi
2417
2418       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
2419       then
2420
[3236]2421          eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]2422
2423             # DETERMINE THE CYCLE NUMBER
2424          ls -1 -d $filename    >   filelist  2>/dev/null
2425          ls -1 -d $filename.*  >>  filelist  2>/dev/null
2426          while  read line
2427          do
2428   
2429                # filename without path (i.e. after the last "/")
2430             basefilename=$(basename ${line})
2431   
2432                # check if there is an extension
2433             extension=${basefilename##*.}
2434             if [[ "$extension" = "${extout[$i]}" ]]
2435             then
2436                basefilename=${basefilename%.*}
2437             fi
2438   
2439                # check for an existing cycle number
2440             cycle=${basefilename##*.}
2441             if [[ $cycle =~ ^-?[0-9]+$ ]]
2442             then
[2669]2443                   # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
2444                   # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
2445                (( icycle = $((10#$cycle)) + 1 ))
[2610]2446             else
2447                (( icycle = 1 ))
2448             fi
2449   
2450             if (( icycle > maxcycle ))
2451             then
2452                (( maxcycle = icycle ))
2453             fi
2454   
2455          done <filelist
2456          rm filelist
2457
2458   
2459             # SET THE CYCLE NUMBER
2460             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
2461          if [[ "${actionout[$i]}" = a ]]
2462          then
2463             (( maxcycle = maxcycle - 1 ))
2464          fi
2465         
2466          (( cycnum[$i] = maxcycle ))
2467          pathout[$i]=$filename
2468
2469
2470             # ADD CYCLE NUMBER TO FILENAME
2471             # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]2472          if [[ "${actionout[$i]}" != "a" ]]
2473          then
2474                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
2475                # WITH AN EXISTING CYCLE NUMBER
2476             if (( run_number >= cycnum[$i] ))
2477             then
2478                (( cycnum[$i] = run_number ))
2479             else
2480                if (( run_number > 0 ))
2481                then
2482                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
2483                fi
2484             fi
2485          fi
2486          if (( cycnum[$i] > 0 ))
2487          then
[2600]2488             cyclestring=`printf "%03d" ${cycnum[$i]}`
2489             pathout[$i]=${pathout[$i]}.$cyclestring
[2380]2490          fi
2491       fi           
2492
2493          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
2494       files_for_cores=false; filetype=file
2495       link_local_output=false
2496       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
2497       then
2498          files_for_cores=true; filetype=directory
2499          actionout[$i]=""
2500       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
2501       then
2502          actionout[$i]=""
2503       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
2504       then
2505          files_for_cores=true; filetype=directory
2506          link_local_output=true
2507          actionout[$i]=""
2508       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
2509       then
2510          link_local_output
2511          actionout[$i]=""
2512       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
2513       then
2514          files_for_cores=true; filetype=directory
2515          actionout[$i]="tr"
2516       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
2517       then
2518          actionout[$i]="tr"
2519       fi
2520
2521       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
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       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
2528       then
[2669]2529          if [[ ${warnout[$i]} = true ]]
2530          then
2531             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
2532          fi
[2380]2533       else
2534
2535
2536             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
2537             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
2538          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
2539          then
2540             if [[ $running_on_remote = true ]]
2541             then
2542
2543                   # SET OPTIONS FOR TRANSFER
2544                if [[ "${actionout[$i]}" = tr ]]
2545                then
2546                   if [[ $files_for_cores = false ]]
2547                   then
2548                      catalog_option=""
2549                      catalog_string=""
2550                   else
2551                      catalog_option="-c"
2552                      catalog_string="/"
2553                   fi
2554                   append_option=""
2555                   append_string=""
2556                else
2557                   append_option="-A"
2558                   append_string="append"
2559                fi
2560
2561                transfer_failed=false
2562                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
[3236]2563                printf "\n              ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]2564
2565                   # TRANSFER VIA SCP
2566                if [[ "$remote_loginnode" != "" ]]
2567                then
[3236]2568                   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]2569                else
[3236]2570                   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]2571                fi
[3312]2572                [[ ${PIPESTATUS[0]} != 0 ]]  &&  transfer_failed=true
[2380]2573
2574
2575                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
2576                if [[ $transfer_failed = true ]]
2577                then
2578                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]2579                   printf "      ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]2580
2581                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
2582                   eval  local_catalog=${pathout[$i]}
2583                   if [[ ! -d $local_catalog ]]
2584                   then
2585                      printf "  *** local directory does not exist. Trying to create:\n"
2586                      printf "      $local_catalog \n"
2587                      mkdir -p  $local_catalog
2588                   fi
[3236]2589                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]2590                   transfer_problems=true
2591                fi
2592
2593             else
2594
2595                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
2596                   # BE COPIED OR APPENDED ON THIS MACHINE
2597                if [[ "${actionout[$i]}" = tr ]]
2598                then
2599                   actionout[$i]=""
2600                else
2601                   actionout[$i]="a"
2602                fi
2603             fi
2604          fi
2605
2606
2607             # APPEND ON THIS MACHINE
2608          if [[ "${actionout[$i]}" = "a" ]]
2609          then
2610             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2611             then
2612                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2613                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2614                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
2615             else
2616                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
2617                printf "\n              ${pathout[$i]}\n"
2618                cat  ${localout[$i]}  >>  ${pathout[$i]}
2619             fi
2620          fi
2621
2622             # COPY ON THIS MACHINE
2623             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
2624             # ON DIFFERENT FILE-SYSTEMS
2625          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
2626          then
2627
2628                # COPY IN CASE OF RUNS ON SINGLE CORES
2629             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
2630             then
2631                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2632                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
2633                              if [[ $link_local_output = true ]]
2634                              then
2635                                 printf "      file will be linked\n"
2636                                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2637                              fi
2638                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2639                              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
2640                then
2641                                 if [[ $link_local_output = true ]]
2642                          then
2643                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2644                                 fi
2645                                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
2646                              else
2647                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
2648                fi
2649             else
2650                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
2651                printf "\n              ${pathout[$i]}\n"
2652                              if [[ $link_local_output = true ]]
2653                              then
2654                                 printf "      file will be linked\n"
2655                                 ln -f  ${localout[$i]}  ${pathout[$i]}
2656                              fi
2657                                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
2658                        if [[ ! -f "${pathout[$i]}" ]]
2659                then
2660                                 if [[ $link_local_output = true ]]
2661                          then
2662                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2663                                 fi
2664                                 cp  ${localout[$i]}  ${pathout[$i]}
2665                              else
2666                                 printf "+++ no copy because file ${pathout[$i]} exists\n"
2667                fi
2668             fi
2669
2670          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
2671          then
2672
2673                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
2674                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
2675             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
2676             printf "\n              ${pathout[$i]}\n"
2677                    if [[ $link_local_output = true ]]
2678                    then
2679                              printf "      files will be linked\n"
[2396]2680                              mkdir -p ${pathout[$i]}
[2380]2681                              cd ${localout[$i]}
2682                              for file in $(ls *)
2683                              do
2684                                 ln -f $file  ${pathout[$i]}
2685                              done >|/dev/null 2>&1
[2566]2686                              cd $tempdir
[2380]2687                    fi
2688
2689                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
2690                    if [[ ! -f "${pathout[$i]}/_000000" ]]
2691             then
2692                              if [[ $link_local_output = true ]]
2693                              then
2694                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
2695                              fi
[3025]2696                              [[ ! -d "${pathout[$i]}" ]]  &&  mkdir  ${pathout[$i]}
[2380]2697                              cp -r  ${localout[$i]}/*  ${pathout[$i]}
2698             fi
2699
2700          fi
2701       fi
2702    done
2703
2704    if (( i != 0 ))
2705    then
2706       if [[ $transfer_problems = true ]]
2707       then
2708          printf "\n$dashes\n  *** OUTPUT-files saved"
2709          printf "\n  +++ WARNING: some data transfers failed! \n"
2710       else
2711          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
2712       fi
2713    fi
2714
2715
2716       # IF REQUIRED, START A RESTART-JOB
2717       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
2718    if [[ -f CONTINUE_RUN ]]
2719    then
2720
2721          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
2722          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
2723          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
2724          # -b START A BATCH JOB
2725       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
2726       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
2727       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
2728
[2957]2729          # REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2730          # SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
2731       if [[ $(echo $prc | grep -c "svfout") != 0 ]]
2732       then
2733          prc=`echo $prc | sed 's/svfout/svfin/g'`
2734       fi
[2380]2735
2736          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
2737          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
2738       if [[ $(echo $prc | grep -c "#") != 0 ]]
2739       then
[2381]2740          prc=`echo $prc | sed 's/#/r/g'`
[2380]2741       fi
2742
2743
2744          # START THE RESTART-JOB
2745       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
2746       echo "      $prc"
2747       printf "\n$dashes\n"
2748       if [[ $running_on_remote = true ]]
2749       then
2750
2751          echo "*** ssh will be used to initiate restart-runs!"
2752          echo "    return_address=\"$return_address\" "
2753          echo "    return_username=\"$local_username\" "
2754
2755          if [[ "$remote_loginnode" != "" ]]
2756          then
[3132]2757             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]2758          else
[3132]2759             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  |  tee palmrun_restart.log
[2380]2760          fi
2761
2762             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
2763          sleep 30
2764
2765       else
2766
2767             # START THE RESTART JOB ON THE LOCAL HOST
[3132]2768          eval  $prc  |  tee palmrun_restart.log              # THE ' MUST BE EVALUATED
[2380]2769          cd -  > /dev/null
2770
2771       fi
2772
[3132]2773          # CHECK, IF RESTART JOB HAS BEEN STARTED
2774       if [[ $( grep -c "+++ palmrun killed"  palmrun_restart.log ) != 0 ]]
2775       then
2776          printf "\n$dashes\n  +++ creating restart run failed \n"
2777          locat=create_restart
[3455]2778          rm  palmrun_restart.log
[3132]2779          exit
2780       else
2781          printf "\n$dashes\n  *** restart run initiated \n"
2782          rm  palmrun_restart.log
2783       fi
[2380]2784
[3132]2785
[2380]2786          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
2787          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
2788          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
2789          # MAY BE VERY HUGE)
2790       (( i = 0 ))
[2610]2791       while (( i < nr_of_input_files ))
[2380]2792       do
2793          (( i = i + 1 ))
2794          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
2795          then
2796             rm -r  ${absnamein[$i]}
2797          fi
2798       done
2799
2800    fi
2801
2802
2803       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
2804    cd  $HOME
[2566]2805    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $tempdir
[2380]2806
2807
2808 else
2809
2810
2811       # PREPARING ACTIONS,
2812       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
2813
2814       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]2815    palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]2816    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
2817    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
2818    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
2819    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
2820    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
2821    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]2822    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]2823    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
2824    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
2825    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
2826    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
2827    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]2828    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
[2380]2829    if [[ $create_remote_batch_job = true ]]
2830    then
2831       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]2832       if [[ $do_trace = true ]]
2833       then
2834          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
2835       fi
[2380]2836    elif [[ $create_batch_job = true ]]
2837    then
2838       palmrun_com=${palmrun_com}" -j"
[2420]2839       if [[ $do_trace = true ]]
2840       then
2841          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
2842       fi
[2380]2843    fi
2844
2845
2846       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
2847       # REMOTE HOST
[3236]2848    job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]2849    job_protocol_file=$job_protocol_file_local
2850    if [[ $create_remote_batch_job = true ]]
2851    then
[3236]2852       job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]2853       job_protocol_file=$job_protocol_file_remote
2854       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]2855       scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]2856    fi
2857
2858
2859       # BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]2860    jobfile=jobfile.$run_id_number
[2380]2861
2862
2863       # FIRST CREATE THE BATCH DIRECTIVES
2864    (( i = 0 ))
2865    while (( i < ibd ))
2866    do
2867       (( i = i + 1 ))
[2693]2868       line=`echo  "${batch_directive[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
[2380]2869       eval line=\"$line\"
2870       echo  "$line"                               >>  $jobfile
2871    done
2872    echo " "                                       >>  $jobfile
2873
2874
2875       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
2876       # PROTOCOL
2877    if [[ $create_remote_batch_job = true ]]
2878    then
[3236]2879       echo "set +vx"                                   >>  $jobfile
2880       echo "trap '"                                    >>  $jobfile
2881       echo "set +vx"                                   >>  $jobfile
2882       echo "cd ${remote_jobcatalog}"                   >>  $jobfile
2883       echo "cat >  scpjob.$run_id_number << %%END%%"   >>  $jobfile
[2380]2884
2885          # ADD THE BATCH DIRECTIVES
2886       (( i = 0 ))
2887       while (( i < ibdt ))
2888       do
2889          (( i = i + 1 ))
[2693]2890          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`
[2380]2891          eval line=\"$line\"
2892          echo  "$line"                            >>  $jobfile
2893       done
2894       echo " "                                    >>  $jobfile
2895
2896       echo "set -x"                               >>  $jobfile
[3236]2897       echo "${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]2898       echo "%%END%%"                              >>  $jobfile
2899       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
2900       echo "$submit_command  $scpjob_file"        >>  $jobfile
2901       echo "rm $scpjob_file"                      >>  $jobfile
[2404]2902       echo "rm -rf $job_transfer_protocol_file"   >>  $jobfile
[2380]2903       echo "set -x"                               >>  $jobfile
2904       echo "     ' exit"                          >>  $jobfile
2905    fi
2906
2907
2908       # ACTIVATE ERROR-TRACEBACK
2909    if [[ $do_trace = true ]]
2910    then
2911       echo  "set -x"                                    >>  $jobfile
2912    else
2913       echo  "set +vx"                                   >>  $jobfile
2914    fi
2915
2916
2917       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
2918    if [[ "$login_init_cmd" != "" ]]
2919    then
2920       echo  "$login_init_cmd"        >>  $jobfile
2921    fi
2922    if [[ "$module_commands" != "" ]]
2923    then
2924       echo  "$module_commands"     >>  $jobfile
2925    fi
2926
2927
2928       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]2929    if [[ $create_remote_batch_job = true ]]
2930    then
2931       echo  "mkdir  $tempdir"           >>  $jobfile
2932       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
2933    else
2934          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
2935          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
2936          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
2937       mkdir  $tempdir
2938       chmod  go+rx  $tempdir
2939    fi
2940    echo  "cd  $tempdir"                 >>  $jobfile
2941    echo  "export tempdir=$tempdir"      >>  $jobfile
[2506]2942    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
[2380]2943    echo  "export PATH=.:\$PATH"         >>  $jobfile
2944    echo  "export execute_palmrun=true"  >>  $jobfile
2945
2946
2947       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
2948       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
2949       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
2950    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
2951    echo  "export LOCAL_PWD"                            >>  $jobfile
2952
2953
2954       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]2955    echo  "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS"   >>  $jobfile
[2380]2956    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
2957
2958
2959       # CALL PALMRUN WITHIN THE JOB
2960       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
2961    echo  "set -x"                                              >>  $jobfile
2962    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
2963
2964
2965       # TRANSFER JOBFILE TO THE TARGET HOST
2966    if [[ $create_jobfile_only = false ]]
2967    then
2968
2969       if [[ $create_remote_batch_job = true ]]
2970       then
2971
[2420]2972          echo " "
[2566]2973          echo " *** transfer of job to remote host via scp"
[2420]2974          if [[ $do_trace = true ]]
2975          then
[3236]2976             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]2977          fi
[3236]2978          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}  >  /dev/null
[2380]2979
[2566]2980          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]2981          if [[ $do_trace = true ]]
2982          then
[3236]2983             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]2984          fi
[3236]2985          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]2986
2987       elif [[ $create_batch_job = true ]]
2988       then
2989
[2385]2990          eval  local_jobcatalog=$local_jobcatalog
[3236]2991          cp  $jobfile  ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]2992          cd $local_jobcatalog
[2380]2993          echo " "
[2420]2994          echo " *** submit the job"
2995          if [[ $do_trace = true ]]
2996          then
[3236]2997             echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]2998          fi
[3236]2999          $submit_command ${configuration_identifier}_${run_id}
3000          rm ${configuration_identifier}_${run_id}
[2380]3001          cd -  > /dev/null
3002
3003       fi
3004
3005       rm -rf  $jobfile
3006
3007    else
3008
3009       printf "\n *** jobfile created under name \"$jobfile\" "
3010       printf "\n     no batch-job has been sent!"
3011
3012    fi
3013
3014 fi  # END OF REMOTE-PART
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